Appendix 2: Genetic Interactions Surrounding ARV1, BTS1, HMG1, HMG2 and OPI3

Home , Chaperone DnaJ, Polyprenol reductase

Appendix 2: Genetic interactions surrounding ARV1, BTS1, HMG1, HMG2 and OPI3

The tables in this Appendix are the genes which show genetic interactions with ARV1, BTS1, HMG1, HMG2 or OPI3 in S288C, SK1, Y55 or YPS606. The genes depicted in bold also showed a genetic interaction in a second mini array SGA.

Table 1 ARV1-S288C genetic interactions ...... 2

Table 2 ARV1-Y55 genetic interactions ...... 11

Table 3 ARV1-SK1 genetic interactions ...... 25

Table 4 ARV1 - YPS606 genetic interactions ...... 38

Table 5 BTS1 – S288C genetic interactions ...... 50

Table 6 BTS1 Y55 genetic interactions ...... 64

Table 7 BTS1 - SK1 genetic interactions ...... 74

Table 8 BTS1 - YPS606 genetic interactions ...... 93

Table 9 HMG1 - S288C genetic interactions ...... 110

Table 10 HMG1 - Y55 genetic interactions ...... 118

Table 11 HMG1 - SK1 genetic interactions ...... 130

Table 12 HMG2 - S288C genetic interactions ...... 151

Table 13 HMG2 - Y55 genetic interactions ...... 157

Table 14 HMG2 - SK1 genetic interactions ...... 166

Table 15 OPI3 - S288C genetic interactions ...... 177

Table 16 OPI3 - Y55 genetic interactions ...... 190

Table 17 OPI3 - YPS606 genetic interactions ...... 202

Table 1 ARV1-S288C genetic interactions

ORF Gene Desciption

YDL203C ACK1 Protein that functions in the cell wall integrity pathway YCL025C AGP1 Low-affinity amino acid permease with broad substrate range YML022W APT1 Adenine phosphoribosyltransferase YCR048W ARE1 Acyl-CoA:sterol acyltransferase YBR164C ARL1 Soluble GTPase with a role in regulation of membrane traffic YLR085C ARP6 Actin-related protein that binds nucleosomes YOR058C ASE1 Mitotic spindle midzone-localized microtubule bundling protein YGR097W ASK10 Regulator of the Fps1p glycerol channel YNL242W ATG2 Peripheral membrane protein required for autophagic vesicle formation YNL259C ATX1 Cytosolic copper metallochaperone YPR122W AXL1 Haploid specific endoprotease of a-factor mating pheromone YJL095W BCK1 MAPKKK acting in the protein kinase C signaling pathway YER155C BEM2 Rho GTPase activating protein (RhoGAP) YOR304C- BIL1 Protein that binds Bud6p and has a role in actin cable A assembly YFL007W BLM10 Proteasome activator YLR231C BNA5 Kynureninase YLR267W BOP2 Protein of unknown function YNL275W BOR1 Boron efflux transporter of the plasma membrane YDL074C BRE1 E3 ubiquitin ligase YGL007W BRP1 Dubious ORF located in the upstream region of PMA1

YJL188C BUD19 Dubious open reading frame YNL278W CAF120 Part of the CCR4-NOT transcriptional regulatory complex YLR418C CDC73 Component of the Paf1p complex YER061C CEM1 Mitochondrial beta-keto-acyl synthase YGL029W CGR1 Protein involved in nucleolar integrity and processing of pre-rRNA YGR157W CHO2 Phosphatidylethanolamine methyltransferase (PEMT) YBR023C CHS3 Chitin synthase III YLR330W CHS5 Component of the exomer complex YHR142W CHS7 Protein of unknown function YGL019W CKB1 Beta regulatory subunit of casein kinase 2 (CK2) YOR039W CKB2 Beta' regulatory subunit of casein kinase 2 (CK2) YKL190W CNB1 Calcineurin B YNL051W COG5 Component of the conserved oligomeric Golgi complex YGL005C COG7 Component of the conserved oligomeric Golgi complex YML071C COG8 Component of the conserved oligomeric Golgi complex YLR290C COQ11 Putative oxidoreductase, subunit of Coenzyme Q biosynthetic complexes YJR109C CPA2 Large subunit of carbamoyl phosphate synthetase YBR036C CSG2 Endoplasmic reticulum membrane protein YKL139W CTK1 Catalytic (alpha) subunit of C-terminal domain kinase I (CTDK-I) YGL027C CWH41 Processing alpha glucosidase I YIR023W DAL81 Positive regulator of genes in multiple nitrogen degradation pathways YGR092W DBF2 Ser/Thr kinase involved in transcription and stress response YDR093W DNF2 Aminophospholipid translocase (flippase) YDR440W DOT1 Nucleosomal histone H3-Lys79 methylase

YKL204W EAP1 eIF4E-associated protein, competes with eIF4G for binding to eIF4E YLR228C ECM22 Sterol regulatory element binding protein YLR233C EST1 TLC1 RNA-associated factor involved in telomere length regulation YJL157C FAR1 CDK inhibitor and nuclear anchor YLL043W FPS1 Aquaglyceroporin, plasma membrane channel YBL016W FUS3 Mitogen-activated serine/threonine protein kinase involved in mating YGR196C FYV8 Protein of unknown function YML051W GAL80 Transcriptional regulator involved in the repression of GAL genes YMR307W GAS1 Beta-1,3-glucanosyltransferase YGL020C GET1 Subunit of the GET complex YER083C GET2 Subunit of the GET complex YDL100C GET3 Guanine nucleotide exchange factor for Gpa1p YHL031C GOS1 v-SNARE protein involved in Golgi transport YLR258W GSY2 Glycogen synthase YFL031W HAC1 Basic leucine zipper (bZIP) transcription factor (ATF/CREB1 homolog) YBR009C HHF1 Histone H4 YLR450W HMG2 HMG-CoA reductase YJR075W HOC1 Alpha-1,6-mannosyltransferase YGL194C HOS2 Histone deacetylase and subunit of Set3 and Rpd3L complexes YKL101W HSL1 Nim1p-related protein kinase YOL012C HTZ1 Histone variant H2AZ YGL168W HUR1 Protein of unknown function

YIL090W ICE2 Integral ER membrane protein with type-III transmembrane domains YER092W IES5 Non-essential INO80 chromatin remodeling complex subunit YDR123C INO2 Transcription factor YOL108C INO4 Transcription factor involved in phospholipid synthesis YDR072C IPT1 Inositolphosphotransferase YHR079C IRE1 Serine-threonine kinase and endoribonuclease YGL016W KAP122 Karyopherin beta YJR054W KCH1 Potassium transporter that mediates K+ influx YGR040W KSS1 Mitogen-activated protein kinase (MAPK) YJL062W LAS21 Integral plasma membrane protein YNL323W LEM3 Membrane protein of the plasma membrane and ER YKL176C LST4 Protein possibly involved in a post-Golgi secretory pathway YBR115C LYS2 Alpha aminoadipate reductase YEL053C MAK10 Non-catalytic subunit of N-terminal acetyltransferase of the NatC type YLR253W MCP2 Mitochondrial protein of unknown function involved in lipid homeostas YNL291C MID1 N-glycosylated integral membrane protein of the ER and plasma membrane YLR332W MID2 O-glycosylated plasma membrane protein YOR231W MKK1 MAPKK involved in the protein kinase C signaling pathway YDR245W MNN10 Subunit of a Golgi mannosyltransferase complex YGL136C MRM2 Mitochondrial 2' O-ribose methyltransferase YKL074C MUD2 Protein involved in early pre-mRNA splicing

YDR162C NBP2 Protein involved in the HOG (high osmolarity glycerol) pathway YLR254C NDL1 Homolog of nuclear distribution factor NudE YLR265C NEJ1 Protein involved in regulation of nonhomologous end joining YDL002C NHP10 Non-essential INO80 chromatin remodeling complex subunit YJR073C OPI3 Methylene-fatty-acyl-phospholipid synthase YDL096C OPI6 Dubious open reading frame YPR194C OPT2 Oligopeptide transporter YML019W OST6 Subunit of the oligosaccharyltransferase complex of the ER lumen YLR266C PDR8 Transcription factor YER149C PEA2 Coiled-coil 12S polarisome subunit YJL053W PEP8 Vacuolar protein component of the retromer YNL003C PET8 S-adenosylmethionine transporter of the mitochondrial inner membrane YLR273C PIG1 Putative targeting subunit for type-1 protein phosphatase Glc7p YDR276C PMP3 Small plasma membrane protein YGL167C PMR1 High affinity Ca2+/Mn2+ P-type ATPase YKR093W PTR2 Integral membrane peptide transporter YER162C RAD4 Protein that recognizes and binds damaged DNA (with Rad23p) during NER YJL204C RCY1 F-box protein involved in recycling endocytosed proteins YBR260C RGD1 GTPase-activating protein (RhoGAP) for Rho3p and Rho4p YOR275C RIM20 Protein involved in proteolytic activation of Rim101p YNL294C RIM21 pH sensor molecule, component of the RIM101 pathway

YGL045W RIM8 Protein involved in proteolytic activation of Rim101p YPL089C RLM1 MADS-box transcription factor YLR371W ROM2 GDP/GTP exchange factor (GEF) for Rho1p and Rho2p YOR312C RPL20B Ribosomal 60S subunit protein L20B YGL147C RPL9A Ribosomal 60S subunit protein L9A YOR293W RPS10A Protein component of the small (40S) ribosomal subunit YLR264W RPS28B Protein component of the small (40S) ribosomal subunit YLR221C RSA3 Protein with a likely role in ribosomal maturation YNL254C RTC4 Protein of unknown function YGL244W RTF1 Subunit of RNAPII-associated chromatin remodeling Paf1 complex YOR216C RUD3 Golgi matrix protein YDR388W RVS167 Actin-associated protein with roles in endocytosis and exocytosis YKL212W SAC1 Phosphatidylinositol phosphate (PtdInsP) phosphatase YDR159W SAC3 mRNA export factor YKR028W SAP190 Protein that forms a complex with the Sit4p protein phosphatase YDR469W SDC1 Subunit of the COMPASS (Set1C) complex YLR268W SEC22 R-SNARE protein YIL076W SEC28 Epsilon-COP subunit of the coatomer YBL031W SHE1 Mitotic spindle protein YOR035C SHE4 Protein containing a UCS (UNC-45/CRO1/SHE4) domain YBR103W SIF2 WD40 repeat-containing subunit of Set3C histone deacetylase complex YNL257C SIP3 Putative sterol transfer protein YBL061C SKT5 Activator of Chs3p (chitin synthase III) during vegetative growth

YOR008C SLG1 Sensor-transducer of the stress-activated PKC1-MPK1 kinase pathway YHR030C SLT2 Serine/threonine MAP kinase YHL025W SNF6 Subunit of the SWI/SNF chromatin remodeling complex YCR033W SNT1 Subunit of the Set3C deacetylase complex YGL127C SOH1 Subunit of the RNA polymerase II mediator complex YKL184W SPE1 Ornithine decarboxylase YEL031W SPF1 P-type ATPase, ion transporter of the ER membrane YHR041C SRB2 Subunit of the RNA polymerase II mediator complex YCL037C SRO9 Cytoplasmic RNA-binding protein YDR293C SSD1 Translational repressor with a role in polar growth and wall integrity YHR178W STB5 Transcription factor YCL032W STE50 Adaptor protein for various signaling pathways YBR231C SWC5 Component of the SWR1 complex YBR175W SWD3 Essential subunit of the COMPASS (Set1C) complex YJL187C SWE1 Protein kinase that regulates the G2/M transition YJL004C SYS1 Integral membrane protein of the Golgi YPR095C SYT1 Guanine nucleotide exchange factor (GEF) for Arf proteins YEL048C TCA17 Component of transport protein particle (TRAPP) complex II YIL039W TED1 GPI-glycan remodelase YHR025W THR1 Homoserine kinase YLR234W TOP3 DNA Topoisomerase III YDL122W UBP1 Ubiquitin-specific protease YFR010W UBP6 Ubiquitin-specific protease YLR224W UCC1 F-box protein and component of SCF ubiquitin ligase complexes

YDL190C UFD2 Ubiquitin chain assembly factor (E4) YDR207C UME6 Rpd3L histone deacetylase complex subunit YEL040W UTR2 Chitin transglycosylase YOR106W VAM3 Syntaxin-like vacuolar t-SNARE YDL077C VAM6 Guanine nucleotide exchange factor for the GTPase Gtr1p YGL212W VAM7 Vacuolar SNARE protein YHR012W VPS29 Subunit of the membrane-associated retromer complex YDR080W VPS41 Subunit of the HOPS endocytic tethering complex YKR020W VPS51 Component of the GARP (Golgi-associated retrograde protein) complex YLR261C VPS63 Putative protein of unknown function YML097C VPS9 Guanine nucleotide exchange factor (GEF) YOR083W WHI5 Repressor of G1 transcription YNL283C WSC2 Sensor-transducer of the stress-activated PKC1-MPK1 signaling pathway YBL062W YBL062W Dubious open reading frame YCL074W YCL074W Pseudogene: encodes fragment of Ty Pol protein YCR050C YCR050C Non-essential protein of unknown function YDL062W YDL062W Dubious open reading frame YDR455C YDR455C Dubious open reading frame YEL067C YEL067C Putative protein of unknown function YER084W YER084W Protein of unknown function YER119C-A YER119C-A Dubious open reading frame YFL032W YFL032W Dubious open reading frame YGL046W YGL046W Merged open reading frame YGL214W YGL214W Dubious open reading frame YIL012W YIL012W Dubious open reading frame YJL169W YJL169W Dubious open reading frame

YJL175W YJL175W Dubious open reading frame unlikely to encode a functional protein YLR200W YKE2 Subunit of the heterohexameric Gim/prefoldin protein complex YLR217W YLR217W Dubious open reading frame YLR232W YLR232W Dubious open reading frame YLR255C YLR255C Dubious open reading frame YLR257W YLR257W Protein of unknown function YLR271W YLR271W Putative protein of unknown function YLR281C YLR281C Putative protein of unknown function YLR346C YLR346C Putative protein of unknown function found in mitochondria YLR402W YLR402W Dubious open reading frame YLR428C YLR428C Dubious open reading frame YMR031W YMR031W Dubious open reading frame -A -A YMR295C YMR295C Protein of unknown function that associates with ribosomes YNL234W YNL234W Protein of unknown function with similarity to globins YNL296W YNL296W Dubious open reading frame unlikely to encode a functional protein YOL046C YOL046C Dubious open reading frame YPR050C YPR050C Dubious open reading frame YPR126C YPR126C Dubious open reading frame YLR262C YPT6 Rab family GTPase YKL214C YRA2 Member of the REF (RNA and export factor binding proteins) family YFL052W ZNF1 Zinc cluster transcription factor that regulates respiratory growth

YNL241C ZWF1 Glucose-6-phosphate dehydrogenase (G6PD)

Table 2 ARV1-Y55 genetic interactions

ORF Gene Desciption YDL243C AAD4 Putative aryl-alcohol dehydrogenase YCR088W ABP1 Actin-binding protein of the cortical actin cytoskeleton YBL015W ACH1 Protein with CoA transferase activity YDL203C ACK1 Protein that functions in the cell wall integrity pathway YAL054C ACS1 Acetyl-coA synthetase isoform YOR128C ADE2 Phosphoribosylaminoimidazole carboxylase YDR408C ADE8 Phosphoribosyl-glycinamide transformylase YCR105W ADH7 NADPH-dependent medium chain alcohol dehydrogenase YEL052W AFG1 Protein that may act as a chaperone for cytochrome c oxidase subunits YIL087C AIM19 Putative protein of unknown function YJL046W AIM22 Putative lipoate-protein ligase

YMR003W AIM34 Protein of unknown function YCL050C APA1 AP4A phosphorylase YDR441C APT2 Potential adenine phosphoribosyltransferase YDR421W ARO80 Zinc finger transcriptional activator of the Zn2Cys6 family YLR085C ARP6 Actin-related protein that binds nucleosomes YGR097W ASK10 Regulator of the Fps1p glycerol channel YLR189C ATG26 UDP-glucose:sterol glucosyltransferase YLR211C ATG38 Homodimeric subunit of autophagy-specific PtdIns-3- kinase complex I YBL078C ATG8 Component of autophagosomes and Cvt vesicles YDR046C BAP3 Amino acid permease YIL015W BAR1 Aspartyl protease YBR270C BIT2 Subunit of TORC2 membrane-associated complex YLR231C BNA5 Kynureninase YDR428C BNA7 Formylkynurenine formamidase YDL074C BRE1 E3 ubiquitin ligase YPR171W BSP1 Adapter that links synaptojanins to the cortical actin cytoskeleton YPL069C BTS1 Geranylgeranyl diphosphate synthase (GGPS) YOR026W BUB3 Kinetochore checkpoint WD40 repeat protein YJL188C BUD19 Dubious open reading frame YLR220W CCC1 Vacuolar Fe2+/Mn2+ transporter YLR418C CDC73 Component of the Paf1p complex YBR023C CHS3 Chitin synthase III YHR142W CHS7 Protein of unknown function YPR120C CLB5 B-type cyclin involved in DNA replication during S phase YAL058W CNE1 Calnexin YLR218C COA4 Twin Cx(9)C protein involved in cytochrome c oxidase organization

YKL179C COY1 Golgi membrane protein with similarity to mammalian CASP YLR216C CPR6 Peptidyl-prolyl cis-trans isomerase (cyclophilin) YBR036C CSG2 Endoplasmic reticulum membrane protein YMR180C CTL1 RNA 5'-triphosphatase, localizes to both the nucleus and cytoplasm YMR173W DDR48 DNA damage-responsive protein YFL001W DEG1 tRNA:pseudouridine synthase YDR051C DET1 Acid phosphatase YDR093W DNF2 Aminophospholipid translocase (flippase) YBR007C DSF2 Deletion suppressor of mpt5 mutation YNL136W EAF7 Subunit of the NuA4 histone acetyltransferase complex YMR171C EAR1 Specificity factor required for Rsp5p-dependent ubiquitination YDR446W ECM11 Meiosis-specific protein YBL001C ECM15 Non-essential protein of unknown function YLR228C ECM22 Sterol regulatory element binding protein YGL222C EDC1 RNA-binding protein that activates mRNA decapping directly YKL160W ELF1 Transcription elongation factor with a conserved zinc finger domain YDR414C ERD1 Predicted membrane protein required for lumenal ER protein retention YCR075C ERS1 Protein with similarity to human cystinosin YLR233C EST1 TLC1 RNA-associated factor involved in telomere length regulation YBR026C ETR1 2-enoyl thioester reductase YBR041W FAT1 Very long chain fatty acyl-CoA synthetase and fatty acid transporter

YKL187C FAT3 Protein required for fatty acid uptake YGR131W FHN1 Protein of unknown function YCR089W FIG2 Cell wall adhesin, expressed specifically during mating YER032W FIR1 Protein involved in 3' mRNA processing YAL053W FLC2 Putative calcium channel involved in calcium release under hypotonic YLR454W FMP27 Putative protein of unknown function YNR047W FPK1 Ser/Thr protein kinase YLR214W FRE1 Ferric reductase and cupric reductase YCL026C-A FRM2 Type II nitroreductase, using NADH as reductant YCR076C FUB1 Proteasome-binding protein YBR020W GAL1 Galactokinase YBR018C GAL7 Galactose-1-phosphate uridyl transferase YML051W GAL80 Transcriptional regulator involved in the repression of GAL genes YDL215C GDH2 NAD(+)-dependent glutamate dehydrogenase YER083C GET2 Subunit of the GET complex YCL036W GFD2 Protein of unknown function YML094W GIM5 Subunit of the heterohexameric cochaperone prefoldin complex YBR045C GIP1 Meiosis-specific regulatory subunit of the Glc7p protein phosphatase YAL031C GIP4 Cytoplasmic protein that regulates protein phosphatase 1 Glc7p YKR058W GLG1 Glycogenin glucosyltransferase YLR258W GSY2 Glycogen synthase YFL031W HAC1 Basic leucine zipper (bZIP) transcription factor (ATF/CREB1 homolog) YBL008W HIR1 Subunit of the HIR complex

YDR420W HKR1 Mucin family member that functions as an osmosensor in the HOG pathway YML075C HMG1 HMG-CoA reductase YJR147W HMS2 Protein with similarity to heat shock transcription factors YGL077C HNM1 Plasma membrane transporter for choline, ethanolamine, and carnitine YER052C HOM3 Aspartate kinase (L-aspartate 4-P-transferase) YLR207W HRD3 ER membrane protein that plays a central role in ERAD YLL026W HSP104 Disaggregase YER039C HVG1 Protein of unknown function YBR157C ICS2 Protein of unknown function YFL013C IES1 Subunit of the INO80 chromatin remodeling complex YJL106W IME2 Serine/threonine protein kinase involved in activation of meiosis YMR044W IOC4 Member of a complex (Isw1b) with Isw1p and Ioc2p YJL051W IRC8 Bud tip localized protein of unknown function YHR079C IRE1 Serine-threonine kinase and endoribonuclease YOR155C ISN1 Inosine 5'-monophosphate (IMP)-specific 5'-nucleotidase YPR106W ISR1 Predicted protein kinase YDR497C ITR1 Myo-inositol transporter YDR492W IZH1 Membrane protein involved in zinc ion homeostasis YDR475C JIP4 Protein of unknown function YMR065W KAR5 Protein required for nuclear membrane fusion during karyogamy YBL063W KIP1 Kinesin-related motor protein YJL062W LAS21 Integral plasma membrane protein YAL018C LDS1 Protein Involved in spore wall assembly YNL323W LEM3 Membrane protein of the plasma membrane and ER YOR123C LEO1 Component of the Paf1 complex

YDR439W LRS4 Nucleolar protein that forms a complex with Csm1p YFR024C-A LSB3 Protein containing a C-terminal SH3 domain YEL053C MAK10 Non-catalytic subunit of N-terminal acetyltransferase of the NatC type YDL078C MDH3 Peroxisomal malate dehydrogenase YML104C MDM1 PtdIns-3-P binding protein that tethers the ER to vacuoles at NVJs YOL111C MDY2 Protein involved in inserting tail-anchored proteins into ER membranes YKR016W MIC60 Component of the MICOS complex YLR332W MID2 O-glycosylated plasma membrane protein YGL257C MNT2 Mannosyltransferase YDR033W MRH1 Protein that localizes primarily to the plasma membrane YBR122C MRPL36 Mitochondrial ribosomal protein of the large subunit YMR225C MRPL44 Mitochondrial ribosomal protein of the large subunit YBL095W MRX3 Protein that associates with mitochondrial ribosome YOL112W MSB4 GTPase-activating protein of the Ras superfamily YDR205W MSC2 Endoplasmic reticulum zinc transporter YLR219W MSC3 Protein of unknown function YBR119W MUD1 U1 snRNP A protein YKL074C MUD2 Protein involved in early pre-mRNA splicing YDR162C NBP2 Protein involved in the HOG (high osmolarity glycerol) pathway YNR009W NRM1 Transcriptional co-repressor of MBF-regulated gene expression YAL015C NTG1 DNA N-glycosylase and apurinic/apyrimidinic (AP) lyase YOL043C NTG2 DNA N-glycosylase and apurinic/apyrimidinic (AP) lyase YDR001C NTH1 Neutral trehalase, degrades trehalose

YML103C NUP188 Subunit of the inner ring of the nuclear pore complex (NPC) YDL089W NUR1 Protein involved in regulation of mitotic exit YAL051W OAF1 Oleate-activated transcription factor YMR148W OSW5 Protein of unknown function with possible role in spore wall assembly YPL171C OYE3 Conserved NADPH oxidoreductase containing flavin mononucleotide (FMN) YEL049W PAU2 Member of the seripauperin multigene family YBR233W PBP2 RNA binding protein YDL127W PCL2 Cyclin, interacts with cyclin-dependent kinase Pho85p YER178W PDA1 E1 alpha subunit of the pyruvate dehydrogenase (PDH) complex YDR406W PDR15 Plasma membrane ATP binding cassette (ABC) transporter YLR266C PDR8 Transcription factor YOR158W PET123 Mitochondrial ribosomal protein of the small subunit YDR479C PEX29 Peroxisomal integral membrane peroxin YDR459C PFA5 Palmitoyltransferase with autoacylation activity YBR092C PHO3 Constitutively expressed acid phosphatase similar to Pho5p YDR481C PHO8 Repressible vacuolar alkaline phosphatase YML123C PHO84 High-affinity inorganic phosphate (Pi) transporter YMR006C PLB2 Phospholipase B (lysophospholipase) involved in lipid metabolism YDR501W PLM2 Putative transcription factor, contains Forkhead Associated domain YDR276C PMP3 Small plasma membrane protein YDL095W PMT1 Protein O-mannosyltransferase of the ER membrane

YDR307W PMT7 Putative protein mannosyltransferase similar to Pmt1p YDR435C PPM1 Carboxyl methyltransferase YDR452W PPN1 Dual endo- and exopolyphosphatase with a role in phosphate metabolism YCL057W PRD1 Zinc metalloendopeptidase YKL116C PRR1 Serine/threonine protein kinase YBL064C PRX1 Mitochondrial peroxiredoxin with thioredoxin peroxidase activity YAL017W PSK1 PAS domain-containing serine/threonine protein kinase YKR093W PTR2 Integral membrane peptide transporter YLL013C PUF3 Protein of the mitochondrial outer surface YBR005W RCR1 Protein of the ER membrane involved in cell wall chitin deposition YCR106W RDS1 Putative zinc cluster transcription factor YMR133W REC114 Protein involved in early stages of meiotic recombination YLR263W RED1 Protein component of the synaptonemal complex axial elements YMR063W RIM9 Plasma membrane protein of unknown function YBR030W RKM3 Ribosomal lysine methyltransferase YGR044C RME1 Zinc finger protein involved in control of meiosis YBR229C ROT2 Glucosidase II catalytic subunit YER056C- RPL34A Ribosomal 60S subunit protein L34A A YBL072C RPS8A Protein component of the small (40S) ribosomal subunit YNL254C RTC4 Protein of unknown function YER139C RTR1 CTD phosphatase YDR389W SAC7 GTPase activating protein (GAP) for Rho1p YDR502C SAM2 S-adenosylmethionine synthetase YPL274W SAM3 High-affinity S-adenosylmethionine permease

YMR060C SAM37 Component of the Sorting and Assembly Machinery (SAM) complex YKR028W SAP190 Protein that forms a complex with the Sit4p protein phosphatase YBL052C SAS3 Histone acetyltransferase catalytic subunit of NuA3 complex YMR272C SCS7 Sphingolipid alpha-hydroxylase YBR214W SDS24 Protein involved in cell separation during budding YLR292C SEC72 Non-essential subunit of Sec63 complex YKR029C SET3 Defining member of the SET3 histone deacetylase complex YBR103W SIF2 WD40 repeat-containing subunit of Set3C histone deacetylase complex YDR422C SIP1 Alternate beta-subunit of the Snf1p kinase complex YBL061C SKT5 Activator of Chs3p (chitin synthase III) during vegetative growth YBR156C SLI15 Subunit of the conserved chromosomal passenger complex (CPC) YHR030C SLT2 Serine/threonine MAP kinase YAL030W SNC1 Vesicle membrane receptor protein (v-SNARE) YDR011W SNQ2 Plasma membrane ATP-binding cassette (ABC) transporter YDR425W SNX41 Sorting nexin YHR008C SOD2 Mitochondrial manganese superoxide dismutase YEL031W SPF1 P-type ATPase, ion transporter of the ER membrane YIL073C SPO22 Meiosis-specific protein essential for chromosome synapsis YBR250W SPO23 Protein of unknown function YBR169C SSE2 Member of the heat shock protein 70 (HSP70) family

YMR019W STB4 Putative transcription factor YDR463W STP1 Transcription factor YHR006W STP2 Transcription factor YJL187C SWE1 Protein kinase that regulates the G2/M transition YNL081C SWS2 Putative mitochondrial ribosomal protein of the small subunit YAL014C SYN8 Endosomal SNARE related to mammalian syntaxin 8 YEL048C TCA17 Component of transport protein particle (TRAPP) complex II YBR044C TCM62 Protein involved in assembly of the succinate dehydrogenase complex YPL180W TCO89 Subunit of TORC1 (Tor1p or Tor2p-Kog1p-Lst8p-Tco89p) YIL039W TED1 GPI-glycan remodelase YPR121W THI22 Protein with similarity to hydroxymethylpyrimidine phosphate kinases YDR438W THI74 Mitochondrial transporter repressible by thiamine YGL049C TIF4632 Translation initiation factor eIF4G YDL110C TMA17 ATPase dedicated chaperone that adapts proteasome assembly to stress YER175C TMT1 Trans-aconitate methyltransferase YER184C TOG1 Transcriptional activator of oleate genes YLR234W TOP3 DNA Topoisomerase III YGL096W TOS8 Homeodomain-containing protein and putative transcription factor YBR126C TPS1 Synthase subunit of trehalose-6-P synthase/phosphatase complex YMR259C TRM732 Protein involved in 2'-O-methylation of C32 of substrate tRNAs YKL211C TRP3 Indole-3-glycerol-phosphate synthase

YDR108W TRS85 Component of transport protein particle (TRAPP) complex III YBR058C UBP14 Ubiquitin-specific protease YER144C UBP5 Putative ubiquitin-specific protease YKL010C UFD4 Ubiquitin-protein ligase (E3) YBR006W UGA2 Succinate semialdehyde dehydrogenase YLR193C UPS1 Phosphatidic acid transfer protein YDR520C URC2 Putative Zn(II)2Cys6 motif containing transcription factor YBR235W VHC1 Vacuolar membrane cation-chloride cotransporter (CCC) YER064C VHR2 Non-essential nuclear protein YBR105C VID24 GID Complex regulatory subunit YDR485C VPS72 Htz1p-binding component of the SWR1 complex YDR372C VPS74 Golgi phosphatidylinositol-4-kinase effector and PtdIns4P sensor YAL002W VPS8 Membrane-binding component of the CORVET complex YNL107W YAF9 Subunit of NuA4 histone H4 acetyltransferase and SWR1 complexes YAL056C-A YAL056C-A Dubious open reading frame YAR028W YAR028W Putative integral membrane protein YAR043C YAR043C Deleted ORF YBL029W YBL029W Non-essential protein of unknown function YBL062W YBL062W Dubious open reading frame YBL081W YBL081W Non-essential protein of unknown function YBL096C YBL096C Non-essential protein of unknown function YBR016W YBR016W Tail-anchored plasma membrane protein with a conserved CYSTM module YBR027C YBR027C Dubious open reading frame YBR071W YBR071W Protein of unknown function found in the cytoplasm and bud neck

YBR090C YBR090C Putative protein of unknown function YBR139W YBR139W Putative serine type carboxypeptidase YCL026C YCL026C Deleted ORF YCL049C YCL049C Protein of unknown function YCR025C YCR025C Dubious open reading frame YCR043C YCR043C Putative protein of unknown function YCR061W YCR061W Protein of unknown function YCR062W YCR062W Merged open reading frame YCR102W- YCR102W- Dubious open reading frame A A YNL064C YDJ1 Type I HSP40 co-chaperone YDL109C YDL109C Putative lipase YDL124W YDL124W NADPH-dependent alpha-keto amide reductase YDR018C YDR018C Probable membrane protein with three predicted transmembrane domains YDR248C YDR248C Putative gluconokinase YDR271C YDR271C Dubious open reading frame YDR290W YDR290W Dubious open reading frame YDR444W YDR444W Putative hydrolase acting on ester bonds YDR445C YDR445C Dubious open reading frame YDR455C YDR455C Dubious open reading frame YDR474C YDR474C Merged open reading frame YER079W YER079W Putative protein of unknown function YFL032W YFL032W Dubious open reading frame YGR012W YGR012W Putative cysteine synthase YGR111W YGR111W Putative protein of unknown function YGR122C- YGR122C- Dubious open reading frame A A YGR234W YHB1 Nitric oxide oxidoreductase

YHR029C YHI9 Protein of unknown function YDR451C YHP1 Homeobox transcriptional repressor YIL060W YIL060W Mitochondrial protein of unknown function YIL141W YIL141W Dubious open reading frame YIR035C YIR035C Putative cytoplasmic short-chain dehydrogenase/reductase YJL169W YJL169W Dubious open reading frame YJL171C YJL171C GPI-anchored cell wall protein of unknown function YJL211C YJL211C Dubious open reading frame YKR051W YKR051W Putative protein of unknown function YLR217W YLR217W Dubious open reading frame YLR235C YLR235C Dubious open reading frame YLR255C YLR255C Dubious open reading frame YLR257W YLR257W Protein of unknown function YLR279W YLR279W Dubious open reading frame YLR280C YLR280C Dubious open reading frame YLR281C YLR281C Putative protein of unknown function YLR428C YLR428C Dubious open reading frame YBR104W YMC2 Putative mitochondrial inner membrane transporter YML020W YML020W Putative protein of unknown function YMR147W YMR147W Putative protein of unknown function YMR158C- YMR158C- Putative protein of unknown function A A YMR158W YMR158W Dubious open reading frame -B -B YMR262W YMR262W Protein of unknown function YMR317W YMR317W Putative protein of unknown function YNL296W YNL296W Dubious open reading frame unlikely to encode a functional protein

YOL150C YOL150C Dubious open reading frame YBR183W YPC1 Alkaline ceramidase YMR104C YPK2 Protein kinase similar to serine/threonine protein kinase Ypk1p YBR028C YPK3 AGC kinase YPL067C YPL067C Putative protein of unknown function YOL092W YPQ1 Putative vacuolar membrane transporter for cationic amino acids YPR059C YPR059C Dubious open reading frame YPR097W YPR097W Protein that contains a PX domain and binds phosphoinositides YLR262C YPT6 Rab family GTPase YJR099W YUH1 Ubiquitin C-terminal hydrolase YMR273C ZDS1 Protein with a role in regulating Swe1p-dependent polarized growth YBR046C ZTA1 NADPH-dependent quinone reductase

Table 3 ARV1-SK1 genetic interactions

ORF Gene Desciption YDL243C AAD4 Putative aryl-alcohol dehydrogenase YGR037C ACB1 Acyl-CoA-binding protein YCL025C AGP1 Low-affinity amino acid permease with broad substrate range YFL055W AGP3 Low-affinity amino acid permease YIL079C AIR1 Zinc knuckle protein YFL050C ALR2 Probable Mg(2+) transporter YDL192W ARF1 ADP-ribosylation factor YNL020C ARK1 Serine/threonine protein kinase YDR421W ARO80 Zinc finger transcriptional activator of the Zn2Cys6 family YLR085C ARP6 Actin-related protein that binds nucleosomes

YPR200C ARR2 Arsenate reductase required for arsenate resistance YJL095W BCK1 MAPKKK acting in the protein kinase C signaling pathway YDR375C BCS1 Protein translocase and chaperone required for Complex III assembly YGR286C BIO2 Biotin synthase YFR047C BNA6 Quinolinate phosphoribosyl transferase YNL275W BOR1 Boron efflux transporter of the plasma membrane YDL074C BRE1 E3 ubiquitin ligase YDL231C BRE4 Zinc finger protein containing five transmembrane domains YGL007W BRP1 Dubious ORF located in the upstream region of PMA1 YFL025C BST1 GPI inositol deacylase of the endoplasmic reticulum (ER) YGR142W BTN2 v-SNARE binding protein YPL069C BTS1 Geranylgeranyl diphosphate synthase (GGPS) YGR188C BUB1 Protein kinase involved in the cell cycle checkpoint into anaphase YDR241W BUD26 Dubious open reading frame YLR220W CCC1 Vacuolar Fe2+/Mn2+ transporter YLR418C CDC73 Component of the Paf1p complex YER061C CEM1 Mitochondrial beta-keto-acyl synthase YBR023C CHS3 Chitin synthase III YHR142W CHS7 Protein of unknown function YGL019W CKB1 Beta regulatory subunit of casein kinase 2 (CK2) YGL215W CLG1 Cyclin-like protein that interacts with Pho85p YKL190W CNB1 Calcineurin B YFR046C CNN1 Kinetochore protein YMR256C COX7 Subunit VII of cytochrome c oxidase (Complex IV)

YLR216C CPR6 Peptidyl-prolyl cis-trans isomerase (cyclophilin) YNL130C CPT1 Cholinephosphotransferase YLR213C CRR1 Putative glycoside hydrolase of the spore wall envelope YDR179C CSN9 Subunit of the Cop9 signalosome YGL027C CWH41 Processing alpha glucosidase I YNL116W DMA2 Ubiquitin-protein ligase (E3) YDR068W DOS2 Protein of unknown function YGR093W DRN1 Splicing factor that modulates turnover of branched RNAs by Dbr1p YMR299C DYN3 Dynein light intermediate chain (LIC) YLR228C ECM22 Sterol regulatory element binding protein YHL030W ECM29 Scaffold protein YER176W ECM32 DNA dependent ATPase/DNA helicase YER035W EDC2 RNA-binding protein that directly activates mRNA decapping YEL015W EDC3 Non-essential conserved protein with a role in mRNA decapping YBR271W EFM2 S-adenosylmethionine-dependent methyltransferase YMR312W ELP6 Subunit of hexameric RecA-like ATPase Elp456 Elongator subcomplex YDL018C ERP3 Protein with similarity to Emp24p and Erv25p YNL125C ESBP6 Protein with similarity to monocarboxylate permeases YLR233C EST1 TLC1 RNA-associated factor involved in telomere length regulation YFL041W FET5 Multicopper oxidase YGR131W FHN1 Protein of unknown function YER032W FIR1 Protein involved in 3' mRNA processing YNL068C FKH2 Forkhead family transcription factor YDR070C FMP16 Protein of unknown function

YNL168C FMP41 Putative protein of unknown function YGR052W FMP48 Putative protein of unknown function YLR214W FRE1 Ferric reductase and cupric reductase YCR076C FUB1 Proteasome-binding protein YDR009W GAL3 Transcriptional regulator YFR009W GCN20 Positive regulator of the Gcn2p kinase activity YDL215C GDH2 NAD(+)-dependent glutamate dehydrogenase YGL020C GET1 Subunit of the GET complex YDL100C GET3 Guanine nucleotide exchange factor for Gpa1p YMR255W GFD1 Coiled-coiled protein of unknown function YDR152W GIR2 Highly-acidic RWD domain-containing protein of unknown function YNL255C GIS2 Translational activator for mRNAs with internal ribosome entry sites YMR311C GLC8 Regulatory subunit of protein phosphatase 1 (Glc7p) YNL274C GOR1 Glyoxylate reductase YLR258W GSY2 Glycogen synthase YGL084C GUP1 Plasma membrane protein involved in remodeling GPI anchors YFL027C GYP8 GTPase-activating protein for yeast Rab family members YPR008W HAA1 Transcriptional activator involved in adaptation to weak acid stress YOL089C HAL9 Putative transcription factor containing a zinc finger YKL109W HAP4 Transcription factor YML075C HMG1 HMG-CoA reductase YJR075W HOC1 Alpha-1,6-mannosyltransferase YLR207W HRD3 ER membrane protein that plays a central role in ERAD YBR272C HSM3 Proteasome-interacting protein

YLL026W HSP104 Disaggregase YFL011W HXT10 Putative hexose transporter YNL318C HXT14 Protein with similarity to hexose transporter family members YNL037C IDH1 Subunit of mitochondrial NAD(+)-dependent isocitrate dehydrogenase YDL066W IDP1 Mitochondrial NADP-specific isocitrate dehydrogenase YDR072C IPT1 Inositolphosphotransferase YHR079C IRE1 Serine-threonine kinase and endoribonuclease YGL203C KEX1 Cell death protease essential for hypochlorite-induced apoptosis YFL042C LAM5 Putative sterol transfer protein YOR123C LEO1 Component of the Paf1 complex YDR439W LRS4 Nucleolar protein that forms a complex with Csm1p YAL024C LTE1 Protein similar to GDP/GTP exchange factors YER106W MAM1 Monopolin YDL054C MCH1 Protein with similarity to mammalian monocarboxylate permeases YLR253W MCP2 Mitochondrial protein of unknown function involved in lipid homeostas YNL328C MDJ2 Constituent of the mitochondrial import motor YOL027C MDM38 Mitochondrial protein YPR070W MED1 Subunit of the RNA polymerase II mediator complex YKR007W MEH1 Component of the EGO and GSE complexes YNL142W MEP2 Ammonium permease involved in regulation of pseudohyphal growth YNL145W MFA2 Mating pheromone a-factor YDR219C MFB1 Mitochondria-associated F-box protein YPL060W MFM1 Mitochondrial inner membrane magnesium transporter

YNL218W MGS1 Protein with DNA-dependent ATPase and ssDNA annealing activities YFR011C MIC19 Component of the MICOS complex YKR016W MIC60 Component of the MICOS complex YNL291C MID1 N-glycosylated integral membrane protein of the ER and plasma membrane YLR332W MID2 O-glycosylated plasma membrane protein YNL117W MLS1 Malate synthase, enzyme of the glyoxylate cycle YJL186W MNN5 Alpha-1,2-mannosyltransferase YER077C MRX1 Protein that associates with mitochondrial ribosome YLR219W MSC3 Protein of unknown function YGR023W MTL1 Putative plasma membrane sensor YKL074C MUD2 Protein involved in early pre-mRNA splicing YNL119W NCS2 Protein required for uridine thiolation of Lys(UUU) and Glu(UUC) tRNAs YLR254C NDL1 Homolog of nuclear distribution factor NudE YLR265C NEJ1 Protein involved in regulation of nonhomologous end joining YMR285C NGL2 Protein involved in 5.8S rRNA processing YDR383C NKP1 Central kinetochore protein and subunit of the Ctf19 complex YLR315W NKP2 Central kinetochore protein and subunit of the Ctf19 complex YDL096C OPI6 Dubious open reading frame YGR038W ORM1 Protein that mediates sphingolipid homeostasis YDL232W OST4 Subunit of the oligosaccharyltransferase complex of the ER lumen YDR071C PAA1 Polyamine acetyltransferase

YGR078C PAC10 Part of the heteromeric co-chaperone GimC/prefoldin complex YDR538W PAD1 Phenylacrylic acid decarboxylase YMR165C PAH1 Mg2+-dependent phosphatidate (PA) phosphatase YNL289W PCL1 Cyclin, interacts with cyclin-dependent kinase Pho85p YFR023W PES4 Poly(A) binding protein, suppressor of DNA polymerase epsilon mutation YOL044W PEX15 Tail-anchored type II integral peroxisomal membrane protein YGR077C PEX8 Intraperoxisomal organizer of the peroxisomal import machinery YNL097C PHO23 Component of the Rpd3L histone deacetylase complex YFR034C PHO4 Basic helix-loop-helix (bHLH) transcription factor of the myc-family YDR313C PIB1 RING-type ubiquitin ligase of the endosomal and vacuolar membranes YGL023C PIB2 Protein of unknown function YGL059W PKP2 Mitochondrial protein kinase YDL095W PMT1 Protein O-mannosyltransferase of the ER membrane YGL037C PNC1 Nicotinamidase that converts nicotinamide to nicotinic acid YLR209C PNP1 Purine nucleoside phosphorylase YDL188C PPH22 Catalytic subunit of protein phosphatase 2A (PP2A) YGR123C PPT1 Protein serine/threonine phosphatase YCL057W PRD1 Zinc metalloendopeptidase YDL214C PRR2 Serine/threonine protein kinase YOL045W PSK2 PAS-domain containing serine/threonine protein kinase YNL201C PSY2 Subunit of protein phosphatase PP4 complex YKL198C PTK1 Putative serine/threonine protein kinase

YDL230W PTP1 Phosphotyrosine-specific protein phosphatase YGL062W PYC1 Pyruvate carboxylase isoform YFR033C QCR6 Subunit 6 of the ubiquinol cytochrome-c reductase complex YGL163C RAD54 DNA-dependent ATPase that stimulates strand exchange YGL058W RAD6 Ubiquitin-conjugating enzyme (E2) YDR003W RCR2 Vacuolar protein YMR283C RIT1 Initiator methionine 2'-O-ribosyl phosphate transferase YPL089C RLM1 MADS-box transcription factor YFR048W RMD8 Cytosolic protein required for sporulation YFR022W ROG3 Alpha-arrestin involved in ubiquitin-dependent endocytosis YNL301C RPL18B Ribosomal 60S subunit protein L18B YFL034C-A RPL22B Ribosomal 60S subunit protein L22B YFL036W RPO41 Mitochondrial RNA polymerase YDR025W RPS11A Protein component of the small (40S) ribosomal subunit YPR132W RPS23B Ribosomal protein 28 (rp28) of the small (40S) ribosomal subunit YLR264W RPS28B Protein component of the small (40S) ribosomal subunit YBL072C RPS8A Protein component of the small (40S) ribosomal subunit YDL216C RRI1 Catalytic subunit of the COP9 signalosome (CSN) complex YLR221C RSA3 Protein with a likely role in ribosomal maturation YNL254C RTC4 Protein of unknown function YGL244W RTF1 Subunit of RNAPII-associated chromatin remodeling Paf1 complex YDL204W RTN2 Reticulon protein YDL076C RXT3 Component of the Rpd3L histone deacetylase complex

YDR143C SAN1 Ubiquitin-protein ligase YKR028W SAP190 Protein that forms a complex with the Sit4p protein phosphatase YGL229C SAP4 Protein required for function of the Sit4p protein phosphatase YER019C-A SBH2 Ssh1p-Sss1p-Sbh2p complex component YGL083W SCY1 Putative kinase YDR178W SDH4 Membrane anchor subunit of succinate dehydrogenase (SDH) YKR029C SET3 Defining member of the SET3 histone deacetylase complex YGL066W SGF73 Subunit of DUBm module of SAGA and SLIK YIR001C SGN1 Cytoplasmic RNA-binding protein YGL228W SHE10 Protein involved in outer spore wall assembly YGR143W SKN1 Protein involved in sphingolipid biosynthesis YNL167C SKO1 Basic leucine zipper transcription factor of the ATF/CREB family YBL061C SKT5 Activator of Chs3p (chitin synthase III) during vegetative growth YGR212W SLI1 N-acetyltransferase YHR030C SLT2 Serine/threonine MAP kinase YDL194W SNF3 Plasma membrane low glucose sensor, regulates glucose transport YGL131C SNT2 Subunit of Snt2C complex, RING finger ubiquitin ligase (E3) YHR008C SOD2 Mitochondrial manganese superoxide dismutase YGL127C SOH1 Subunit of the RNA polymerase II mediator complex YER150W SPI1 GPI-anchored cell wall protein involved in weak acid resistance

YDL130W-A STF1 Protein involved in regulation of the mitochondrial F1F0-ATP synthase YGR008C STF2 Protein involved in resistance to desiccation stress YDR297W SUR2 Sphinganine C4-hydroxylase YGL162W SUT1 Transcription factor of the Zn(II)2Cys6 family YNR004W SWM2 Protein with a role in snRNA and snoRNA cap trimethylation YFL049W SWP82 Member of the SWI/SNF chromatin remodeling complex YNL081C SWS2 Putative mitochondrial ribosomal protein of the small subunit YNL187W SWT21 Protein involved in mRNA splicing YGL243W TAD1 tRNA-specific adenosine deaminase YNL176C TDA7 Cell cycle-regulated gene of unknown function YNL253W TEX1 Protein involved in mRNA export YMR313C TGL3 Bifunctional triacylglycerol lipase and LPE acyltransferase YCR053W THR4 Threonine synthase YLR234W TOP3 DNA Topoisomerase III YDL201W TRM8 Noncatalytic subunit of a tRNA methyltransferase complex YDL122W UBP1 Ubiquitin-specific protease YFR010W UBP6 Ubiquitin-specific protease YDR207C UME6 Rpd3L histone deacetylase complex subunit YMR271C URA10 Minor orotate phosphoribosyltransferase (OPRTase) isozyme YKL041W VPS24 One of four subunits of the ESCRT-III complex YOR069W VPS5 Nexin-1 homolog

YJL029C VPS53 Component of the GARP (Golgi-associated retrograde protein) complex YDR372C VPS74 Golgi phosphatidylinositol-4-kinase effector and PtdIns4P sensor YFL004W VTC2 Subunit of vacuolar transporter chaperone (VTC) complex YOR359W VTS1 Flap-structured DNA-binding and RNA-binding protein YBL062W YBL062W Dubious open reading frame YGL060W YBP2 Central kinetochore associated protein YCL023C YCL023C Dubious open reading frame YDL180W YDL180W Putative protein of unknown function YDL186W YDL186W Putative protein of unknown function YDL206W YDL206W Putative protein of unknown function YDL211C YDL211C Protein of unknown function YDL218W YDL218W Putative protein of unknown function YDR010C YDR010C Dubious open reading frame YDR018C YDR018C Probable membrane protein with three predicted transmembrane domains YDR048C YDR048C Dubious open reading frame YDR102C YDR102C Dubious open reading frame YDR271C YDR271C Dubious open reading frame YDR338C YDR338C Putative protein of unknown function YDR415C YDR415C Putative aminopeptidase YDR541C YDR541C Aldehyde reductase YEL041W YEF1 ATP-NADH kinase YER079W YER079W Putative protein of unknown function YER091C-A YER091C- Dubious open reading frame A YER158C YER158C Protein of unknown function

YFL043C YFL043C Merged open reading frame YFR006W YFR006W Putative X-Pro aminopeptidase YGL081W YGL081W Putative protein of unknown function YGL214W YGL214W Dubious open reading frame YGR022C YGR022C Dubious open reading frame YGR035C YGR035C Putative protein of unknown function, potential Cdc28p substrate YGR050C YGR050C Protein of unknown function YGR051C YGR051C Dubious open reading frame YGR053C YGR053C Putative protein of unknown function YGR111W YGR111W Putative protein of unknown function YGR168C YGR168C Putative protein of unknown function YHL042W YHL042W Putative protein of unknown function YHR033W YHR033W Putative protein of unknown function YHR049C-A YHR049C- Dubious open reading frame A YHR139C-A YHR139C- Dubious open reading frame A YIL077C YIL077C Putative protein of unknown function YGL198W YIP4 Protein that interacts with Rab GTPases YJL218W YJL218W Putative acetyltransferase YLR200W YKE2 Subunit of the heterohexameric Gim/prefoldin protein complex YKR047W YKR047W Dubious open reading frame YMR284W YKU70 Subunit of the telomeric Ku complex (Yku70p-Yku80p) YLR194C YLR194C Structural constituent of the cell wall YLR232W YLR232W Dubious open reading frame YLR252W YLR252W Dubious open reading frame YLR255C YLR255C Dubious open reading frame

YLR428C YLR428C Dubious open reading frame YMR302C YME2 Integral inner mitochondrial membrane protein YMR244W YMR244 Putative protein of unknown function W YMR254C YMR254C Dubious open reading frame YMR326C YMR326C Dubious open reading frame YNL034W YNL034W Putative protein of unknown function YNL035C YNL035C Nuclear protein of unknown function YNL115C YNL115C Putative protein of unknown function YNL143C YNL143C Protein of unknown function YNL146W YNL146W Putative protein of unknown function YNL190W YNL190W Hydrophilin essential in desiccation-rehydration process YGR281W YOR1 Plasma membrane ATP-binding cassette (ABC) transporter YDR057W YOS9 ER quality-control lectin YKL100C YPF1 Intramembrane aspartyl protease of the perinuclear ER membrane YDR368W YPR1 NADPH-dependent aldo-keto reductase YPR153W YPR153W Putative protein of unknown function YPR195C YPR195C Dubious open reading frame YLR262C YPT6 Rab family GTPase YNL339C YRF1-6 Helicase encoded by the Y' element of subtelomeric regions

Table 4 ARV1 - YPS606 genetic interactions

ORF Gene Description YLR131C ACE2 Transcription factor required for septum destruction after cytokinesis YDL203C ACK1 Protein that functions in the cell wall integrity pathway YDR408C ADE8 Phosphoribosyl-glycinamide transformylase YLR227C ADY4 Structural component of the meiotic outer plaque YBR132C AGP2 Plasma membrane regulator of polyamine and carnitine transport YOR023C AHC1 Subunit of the Ada histone acetyltransferase complex YNR074C AIF1 Mitochondrial cell death effector YJL046W AIM22 Putative lipoate-protein ligase YJR100C AIM25 Putative protein of unknown function YBL009W ALK2 Protein kinase YDR530C APA2 Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase II YJL024C APS3 Small subunit of the clathrin-associated adaptor complex AP-3 YDR421W ARO80 Zinc finger transcriptional activator of the Zn2Cys6 family YIL130W ASG1 Zinc cluster protein proposed to be a transcriptional regulator YBL069W AST1 Lipid raft associated protein YGR177C ATF2 Alcohol acetyltransferase YDL113C ATG20 Sorting nexin family member

YIL146C ATG32 Mitochondrial outer membrane protein required to initiate mitophagy YLR211C ATG38 Homodimeric subunit of autophagy-specific PtdIns-3- kinase complex I YBL089W AVT5 Putative transporter YOR113W AZF1 Zinc-finger transcription factor YJL095W BCK1 MAPKKK acting in the protein kinase C signaling pathway YLR231C BNA5 Kynureninase YNL233W BNI4 Targeting subunit for Glc7p protein phosphatase YNL166C BNI5 Linker protein responsible for recruitment of myosin to the bud neck YIL159W BNR1 Formin YLR267W BOP2 Protein of unknown function YDL074C BRE1 E3 ubiquitin ligase YFL025C BST1 GPI inositol deacylase of the endoplasmic reticulum (ER) YGR142W BTN2 v-SNARE binding protein YPL069C BTS1 Geranylgeranyl diphosphate synthase (GGPS) YGL174W BUD13 Subunit of the RES complex YJL188C BUD19 Dubious open reading frame YGR041W BUD9 Protein involved in bud-site selection YLR418C CDC73 Component of the Paf1p complex YBR274W CHK1 Serine/threonine kinase and DNA damage checkpoint effector YBR023C CHS3 Chitin synthase III YHR142W CHS7 Protein of unknown function YGL019W CKB1 Beta regulatory subunit of casein kinase 2 (CK2) YKL190W CNB1 Calcineurin B

YAL058W CNE1 Calnexin YLR218C COA4 Twin Cx(9)C protein involved in cytochrome c oxidase organization YOL008W COQ10 Coenzyme Q (ubiquinone) binding protein YBR036C CSG2 Endoplasmic reticulum membrane protein YOL007C CSI2 Protein of unknown function YGL110C CUE3 Protein of unknown function YLR361C DCR2 Phosphoesterase YOR173W DCS2 m(7)GpppX pyrophosphatase regulator YER143W DDI1 DNA damage-inducible v-SNARE binding protein YDR093W DNF2 Aminophospholipid translocase (flippase) YLR172C DPH5 Methyltransferase required for synthesis of diphthamide YBR007C DSF2 Deletion suppressor of mpt5 mutation YLR401C DUS3 Dihydrouridine synthase YBL043W ECM13 Non-essential protein of unknown function YLR228C ECM22 Sterol regulatory element binding protein YBR033W EDS1 Putative zinc cluster protein, predicted to be a transcription factor YJL196C ELO1 Elongase I, medium-chain acyl elongase YKL207W EMC3 Member of conserved ER transmembrane complex YDR414C ERD1 Predicted membrane protein required for lumenal ER protein retention YML008C ERG6 Delta(24)-sterol C-methyltransferase YAR002C-A ERP1 Member of the p24 family involved in ER to Golgi transport YLR233C EST1 TLC1 RNA-associated factor involved in telomere length regulation

YBR008C FLR1 Plasma membrane transporter of the major facilitator superfamily YAL022C FUN26 High affinity, broad selectivity, nucleoside/nucleobase transporter YBL016W FUS3 Mitogen-activated serine/threonine protein kinase involved in mating YGR196C FYV8 Protein of unknown function YLR343W GAS2 1,3-beta-glucanosyltransferase YOR120W GCY1 Glycerol dehydrogenase YGL020C GET1 Subunit of the GET complex YER083C GET2 Subunit of the GET complex YDL100C GET3 Guanine nucleotide exchange factor for Gpa1p YMR255W GFD1 Coiled-coiled protein of unknown function YHR061C GIC1 Protein involved in initiation of budding and cellular polarization YHL031C GOS1 v-SNARE protein involved in Golgi transport YBR014C GRX7 Cis-golgi localized monothiol glutaredoxin YOL049W GSH2 Glutathione synthetase YLR258W GSY2 Glycogen synthase YGR163W GTR2 Putative GTP binding protein YHL032C GUT1 Glycerol kinase YJR069C HAM1 Nucleoside triphosphate pyrophosphohydrolase YDR458C HEH2 Inner nuclear membrane (INM) protein YMR207C HFA1 Mitochondrial acetyl-coenzyme A carboxylase YML075C HMG1 HMG-CoA reductase YOL095C HMI1 Mitochondrial inner membrane localized ATP- dependent DNA helicase YBR034C HMT1 Nuclear SAM-dependent mono- and asymmetric methyltransferase

YLR205C HMX1 ER localized heme oxygenase YJR075W HOC1 Alpha-1,6-mannosyltransferase YIL112W HOS4 Subunit of the Set3 complex YLR207W HRD3 ER membrane protein that plays a central role in ERAD YKL101W HSL1 Nim1p-related protein kinase YBR072W HSP26 Small heat shock protein (sHSP) with chaperone activity YOL012C HTZ1 Histone variant H2AZ YBR159W IFA38 Microsomal beta-keto-reductase YJL153C INO1 Inositol-3-phosphate synthase YDR072C IPT1 Inositolphosphotransferase YOR135C IRC14 Dubious open reading frame YOR044W IRC23 Putative protein of unknown function YHR079C IRE1 Serine-threonine kinase and endoribonuclease YLR023C IZH3 Membrane protein involved in zinc ion homeostasis YAR018C KIN3 Nonessential serine/threonine protein kinase YHR082C KSP1 Serine/threonine protein kinase YJL062W LAS21 Integral plasma membrane protein YAL018C LDS1 Protein Involved in spore wall assembly YOL047C LDS2 Protein Involved in spore wall assembly YOR123C LEO1 Component of the Paf1 complex YKL073W LHS1 Molecular chaperone of the endoplasmic reticulum lumen YJR070C LIA1 Deoxyhypusine hydroxylase YDR439W LRS4 Nucleolar protein that forms a complex with Csm1p YHR121W LSM12 Protein of unknown function that may function in RNA processing YLR253W MCP2 Mitochondrial protein of unknown function involved in lipid homeostas YDL078C MDH3 Peroxisomal malate dehydrogenase

YOL027C MDM38 Mitochondrial protein YOL111C MDY2 Protein involved in inserting tail-anchored proteins into ER membranes YIL128W MET18 Component of cytosolic iron-sulfur protein assembly (CIA) machinery YLR332W MID2 O-glycosylated plasma membrane protein YNR059W MNT4 Putative alpha-1,3-mannosyltransferase YIR002C MPH1 3'-5' DNA helicase involved in error-free bypass of DNA lesions YKL142W MRP8 Protein of unknown function YMR225C MRPL44 Mitochondrial ribosomal protein of the large subunit YNR022C MRPL50 Mitochondrial ribosomal protein of the large subunit YLR219W MSC3 Protein of unknown function YKL074C MUD2 Protein involved in early pre-mRNA splicing YLR265C NEJ1 Protein involved in regulation of nonhomologous end joining YLR315W NKP2 Central kinetochore protein and subunit of the Ctf19 complex YOL043C NTG2 DNA N-glycosylase and apurinic/apyrimidinic (AP) lyase YGL151W NUT1 Component of the RNA polymerase II mediator complex YOR269W PAC1 Involved in nuclear migration, part of the dynein/dynactin pathway YBR221C PDB1 E1 beta subunit of the pyruvate dehydrogenase (PDH) complex YOR328W PDR10 ATP-binding cassette (ABC) transporter YLR266C PDR8 Transcription factor YOL003C PFA4 Palmitoyltransferase with autoacylation activity YBR074W PFF1 Multi-spanning vacuolar membrane protease YNL316C PHA2 Prephenate dehydratase

YNL097C PHO23 Component of the Rpd3L histone deacetylase complex YIL045W PIG2 Putative type-1 protein phosphatase targeting subunit YOR104W PIN2 Exomer-dependent cargo protein YJL160C PIR5 Putative protein of unknown function YMR006C PLB2 Phospholipase B (lysophospholipase) involved in lipid metabolism YAL023C PMT2 Protein O-mannosyltransferase of the ER membrane YDR436W PPZ2 Serine/threonine protein phosphatase Z, isoform of Ppz1p YAR031W PRM9 Pheromone-regulated protein YOL061W PRS5 5-phospho-ribosyl-1(alpha)-pyrophosphate synthetase YGL158W RCK1 Protein kinase involved in the response to oxidative stress YJL204C RCY1 F-box protein involved in recycling endocytosed proteins YBR260C RGD1 GTPase-activating protein (RhoGAP) for Rho3p and Rho4p YPL089C RLM1 MADS-box transcription factor YJL121C RPE1 D-ribulose-5-phosphate 3-epimerase YDR471W RPL27B Ribosomal 60S subunit protein L27B YBR031W RPL4A Ribosomal 60S subunit protein L4A YJL191W RPS14B Protein component of the small (40S) ribosomal subunit YBL072C RPS8A Protein component of the small (40S) ribosomal subunit YFR032C RRT5 Putative protein of unknown function YOL048C RRT8 Protein involved in spore wall assembly YOR049C RSB1 Suppressor of sphingoid LCB sensitivity of an LCB-lyase mutation YGR152C RSR1 GTP-binding protein of the Ras superfamily

YGL244W RTF1 Subunit of RNAPII-associated chromatin remodeling Paf1 complex YLL002W RTT109 Histone acetyltransferase YOR138C RUP1 Protein that regulates ubiquitination of Rsp5p YCR009C RVS161 Amphiphysin-like lipid raft protein YDR388W RVS167 Actin-associated protein with roles in endocytosis and exocytosis YDR389W SAC7 GTPase activating protein (GAP) for Rho1p YGL229C SAP4 Protein required for function of the Sit4p protein phosphatase YDR469W SDC1 Subunit of the COMPASS (Set1C) complex YIL084C SDS3 Component of the Rpd3L histone deacetylase complex YBL104C SEA4 Subunit of SEACAT, a subcomplex of the SEA complex YLR292C SEC72 Non-essential subunit of Sec63 complex YOR165W SEY1 Dynamin-like GTPase that mediates homotypic ER fusion YOR140W SFL1 Transcriptional repressor and activator YOR021C SFM1 SPOUT methyltransferase YIR001C SGN1 Cytoplasmic RNA-binding protein YOR035C SHE4 Protein containing a UCS (UNC-45/CRO1/SHE4) domain YOL110W SHR5 Palmitoyltransferase subunit YHL006C SHU1 Component of Shu complex (aka PCSS complex) YDR422C SIP1 Alternate beta-subunit of the Snf1p kinase complex YNL167C SKO1 Basic leucine zipper transcription factor of the ATF/CREB family YBL061C SKT5 Activator of Chs3p (chitin synthase III) during vegetative growth YHR030C SLT2 Serine/threonine MAP kinase YOL122C SMF1 Divalent metal ion transporter

YGL127C SOH1 Subunit of the RNA polymerase II mediator complex YJR010C-A SPC1 Subunit of the signal peptidase complex (SPC) YEL031W SPF1 P-type ATPase, ion transporter of the ER membrane YHR014W SPO13 Meiotic regulator YHR041C SRB2 Subunit of the RNA polymerase II mediator complex YHR066W SSF1 Constituent of 66S pre-ribosomal particles YJR117W STE24 Highly conserved zinc metalloprotease YBR231C SWC5 Component of the SWR1 complex YBR175W SWD3 Essential subunit of the COMPASS (Set1C) complex YAR042W SWH1 Protein similar to mammalian oxysterol-binding protein YPR095C SYT1 Guanine nucleotide exchange factor (GEF) for Arf proteins YHR159W TDA11 Putative protein of unknown function YBR083W TEC1 Transcription factor targeting filamentation genes and Ty1 expression YDR438W THI74 Mitochondrial transporter repressible by thiamine YOR010C TIR2 Putative cell wall mannoprotein YLR234W TOP3 DNA Topoisomerase III YKL174C TPO5 Protein involved in excretion of putrescine and spermidine YOL093W TRM10 tRNA methyltransferase YGR209C TRX2 Cytoplasmic thioredoxin isoenzyme YDL122W UBP1 Ubiquitin-specific protease YBL067C UBP13 Ubiquitin-specific protease that cleaves Ub-protein fusions YIL156W UBP7 Ubiquitin-specific protease that cleaves ubiquitin- protein fusions YDR207C UME6 Rpd3L histone deacetylase complex subunit YKL216W URA1 Dihydroorotate dehydrogenase

YIL008W URM1 Ubiquitin-like protein involved in thiolation of cytoplasmic tRNAs YKR060W UTP30 Putative subunit of U3-containing 90S preribosome complex YEL013W VAC8 Phosphorylated and palmitoylated vacuolar membrane protein YOR068C VAM10 Protein involved in vacuole morphogenesis YLR373C VID22 Glycosylated integral membrane protein localized to plasma membrane YIL017C VID28 GID Complex subunit, serves as adaptor for regulatory subunit Vid24p YLR337C VRP1 Verprolin, proline-rich actin-associated protein YOR043W WHI2 Protein required for full activation of the general stress response YAL056C-A YAL056C- Dubious open reading frame A YHR161C YAP1801 Protein of the AP180 family, involved in clathrin cage assembly YOL028C YAP7 Putative basic leucine zipper (bZIP) transcription factor YAR043C YAR043C Deleted ORF YAR047C YAR047C Dubious open reading frame YBL062W YBL062W Dubious open reading frame YBR062C YBR062C Protein of unknown function that interacts with Msb2p YBR134W YBR134W Dubious open reading frame YBR174C YBR174C Dubious open reading frame YDR290W YDR290W Dubious open reading frame YDR444W YDR444W Putative hydrolase acting on ester bonds YDR455C YDR455C Dubious open reading frame YDR541C YDR541C Aldehyde reductase

YER046W-A YER046W- Dubious open reading frame A YGL081W YGL081W Putative protein of unknown function YGL159W YGL159W Putative protein of unknown function YGR022C YGR022C Dubious open reading frame YGR164W YGR164W Dubious open reading frame YGR210C YGR210C Putative protein of unknown function YDR451C YHP1 Homeobox transcriptional repressor YIL006W YIA6 Mitochondrial NAD+ transporter YIL059C YIL059C Dubious open reading frame YIL060W YIL060W Mitochondrial protein of unknown function YIL077C YIL077C Putative protein of unknown function YJL049W YJL049W Putative protein of unknown function YJL132W YJL132W Putative protein of unknown function YJL182C YJL182C Dubious open reading frame YJR087W YJR087W Dubious open reading frame YLR200W YKE2 Subunit of the heterohexameric Gim/prefoldin protein complex YLR149C YLR149C Protein of unknown function YLR173W YLR173W Putative protein of unknown function YLR194C YLR194C Structural constituent of the cell wall YLR225C YLR225C Putative protein of unknown function YLR232W YLR232W Dubious open reading frame YLR235C YLR235C Dubious open reading frame YLR257W YLR257W Protein of unknown function YLR281C YLR281C Putative protein of unknown function YLR282C YLR282C Dubious open reading frame YLR296W YLR296W Dubious open reading frame YLR297W YLR297W Protein of unknown function

YLR346C YLR346C Putative protein of unknown function found in mitochondria YLR402W YLR402W Dubious open reading frame YLR428C YLR428C Dubious open reading frame YMR254C YMR254C Dubious open reading frame YMR315W YMR315 Protein with NADP(H) oxidoreductase activity W YNL035C YNL035C Nuclear protein of unknown function YNR005C YNR005C Dubious open reading frame YNR021W YNR021W Putative protein of unknown function YNR025C YNR025C Dubious open reading frame YNR040W YNR040W Putative protein of unknown function YOL046C YOL046C Dubious open reading frame YOL057W YOL057W Dipeptidyl-peptidase III YOL107W YOL107W Putative protein of unknown function YOR008C-A YOR008C- Putative protein of unknown function A YOR082C YOR082C Dubious open reading frame YOR121C YOR121C Dubious open reading frame YOR139C YOR139C Dubious open reading frame YOR186W YOR186W Putative protein of unknown function YBR028C YPK3 AGC kinase YPL261C YPL261C Dubious open reading frame YHR105W YPT35 Endosomal protein of unknown function YOR162C YRR1 Zn2-Cys6 zinc-finger transcription factor YLR130C ZRT2 Low-affinity zinc transporter of the plasma membrane

Table 5 BTS1 – S288C genetic interactions

ORF Gene Description YCL025C AGP1 Low-affinity amino acid permease with broad substrate range YBR194W AIM4 Protein proposed to be associated with the nuclear pore complex YDR530C APA2 Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase II YML022W APT1 Adenine phosphoribosyltransferase YNR019W ARE2 Acyl-CoA:sterol acyltransferase 50

YDL192W ARF1 ADP-ribosylation factor YBR164C ARL1 Soluble GTPase with a role in regulation of membrane traffic YPL051W ARL3 ARF-like small GTPase of the RAS superfamily YHL040C ARN1 ARN family transporter for siderophore-iron chelates YDR127W ARO1 Pentafunctional arom protein YLR085C ARP6 Actin-related protein that binds nucleosomes YMR116C ASC1 G-protein beta subunit and guanine dissociation inhibitor for Gpa2p YAL020C ATS1 Protein required for modification of wobble nucleosides in tRNA YNL259C ATX1 Cytosolic copper metallochaperone YJL095W BCK1 MAPKKK acting in the protein kinase C signaling pathway YER155C BEM2 Rho GTPase activating protein (RhoGAP) YNL233W BNI4 Targeting subunit for Glc7p protein phosphatase YLR267W BOP2 Protein of unknown function YNL275W BOR1 Boron efflux transporter of the plasma membrane YNR051C BRE5 Ubiquitin protease cofactor YPR057W BRR1 snRNP protein component of spliceosomal snRNPs YGL174W BUD13 Subunit of the RES complex YJL188C BUD19 Dubious open reading frame YCR063W BUD31 Component of the SF3b subcomplex of the U2 snRNP YDL099W BUG1 Cis-golgi localized protein involved in ER to Golgi transport YNL288W CAF40 Component of the CCR4-NOT transcriptional complex YPL048W CAM1 One of two isoforms of the gamma subunit of eEF1B YJR060W CBF1 Basic helix-loop-helix (bHLH) protein YLR418C CDC73 Component of the Paf1p complex

YGL029W CGR1 Protein involved in nucleolar integrity and processing of pre-rRNA YKL190W CNB1 Calcineurin B YNL051W COG5 Component of the conserved oligomeric Golgi complex YGL005C COG7 Component of the conserved oligomeric Golgi complex YML071C COG8 Component of the conserved oligomeric Golgi complex YJR109C CPA2 Large subunit of carbamoyl phosphate synthetase YJR032W CPR7 Peptidyl-prolyl cis-trans isomerase (cyclophilin) YNR010W CSE2 Subunit of the RNA polymerase II mediator complex YBR036C CSG2 Endoplasmic reticulum membrane protein YKL139W CTK1 Catalytic (alpha) subunit of C-terminal domain kinase I (CTDK-I) YNL155W CUZ1 Protein with a role in the ubiquitin-proteasome pathway YIR023W DAL81 Positive regulator of genes in multiple nitrogen degradation pathways YGR092W DBF2 Ser/Thr kinase involved in transcription and stress response YKR024C DBP7 Putative ATP-dependent RNA helicase of the DEAD-box family YLR361C DCR2 Phosphoesterase YDR440W DOT1 Nucleosomal histone H3-Lys79 methylase YAL026C DRS2 Trans-golgi network aminophospholipid translocase (flippase) YPR023C EAF3 Component of the Rpd3S histone deacetylase complex YNL136W EAF7 Subunit of the NuA4 histone acetyltransferase complex YLR228C ECM22 Sterol regulatory element binding protein YPL046C ELC1 Elongin C, conserved among eukaryotes YGR200C ELP2 Subunit of Elongator complex YPL086C ELP3 Subunit of Elongator complex

YPL101W ELP4 Subunit of hexameric RecA-like ATPase Elp456 Elongator subcomplex YMR312W ELP6 Subunit of hexameric RecA-like ATPase Elp456 Elongator subcomplex YJR125C ENT3 Protein containing an N-terminal epsin-like domain YLL038C ENT4 Protein of unknown function YDR153C ENT5 Protein containing an N-terminal epsin-like domain YGL054C ERV14 COPII-coated vesicle protein YBR041W FAT1 Very long chain fatty acyl-CoA synthetase and fatty acid transporter YER056C FCY2 Purine-cytosine permease YIL098C FMC1 Mitochondrial matrix protein YBL016W FUS3 Mitogen-activated serine/threonine protein kinase involved in mating YBR020W GAL1 Galactokinase YER027C GAL83 One of three possible beta-subunits of the Snf1 kinase complex YNL199C GCR2 Transcriptional activator of genes involved in glycolysis YDL226C GCS1 ADP-ribosylation factor GTPase activating protein (ARF GAP) YGL020C GET1 Subunit of the GET complex YER083C GET2 Subunit of the GET complex YDL100C GET3 Guanine nucleotide exchange factor for Gpa1p YHR108W GGA2 Protein that regulates Arf1p, Arf2p to facilitate Golgi trafficking YNL153C GIM3 Subunit of the heterohexameric cochaperone prefoldin complex YHL031C GOS1 v-SNARE protein involved in Golgi transport

YDR517W GRH1 Acetylated cis-Golgi protein, involved in ER to Golgi transport YFL027C GYP8 GTPase-activating protein for yeast Rab family members YJL110C GZF3 GATA zinc finger protein YFL031W HAC1 Basic leucine zipper (bZIP) transcription factor (ATF/CREB1 homolog) YGL237C HAP2 Subunit of the Hap2p/3p/4p/5p CCAAT-binding complex YEL056W HAT2 Subunit of the Hat1p-Hat2p histone acetyltransferase complex YNL281W HCH1 Heat shock protein regulator YML075C HMG1 HMG-CoA reductase YLR450W HMG2 HMG-CoA reductase YIL110W HPM1 AdoMet-dependent methyltransferase YOL012C HTZ1 Histone variant H2AZ YIL090W ICE2 Integral ER membrane protein with type-III transmembrane domains YLR384C IKI3 Subunit of Elongator complex YLR309C IMH1 Protein involved in vesicular transport YJL082W IML2 Protein of unknown function YIL154C IMP2' Transcriptional activator involved in maintenance of ion homeostasis YDR123C INO2 Transcription factor YOL108C INO4 Transcription factor involved in phospholipid synthesis YNL106C INP52 Polyphosphatidylinositol phosphatase YDR072C IPT1 Inositolphosphotransferase YOL081W IRA2 GTPase-activating protein YHR079C IRE1 Serine-threonine kinase and endoribonuclease YKR019C IRS4 EH domain-containing protein YIR005W IST3 Component of the U2 snRNP

YBR245C ISW1 ATPase subunit of imitation-switch (ISWI) class chromatin remodelers YJR050W ISY1 Member of the NineTeen Complex (NTC) YKL032C IXR1 Transcriptional repressor that regulates hypoxic genes during normoxia YNL227C JJJ1 Co-chaperone that stimulates the ATPase activity of Ssa1p YJR054W KCH1 Potassium transporter that mediates K+ influx YKL110C KTI12 Protein that plays a role in modification of tRNA wobble nucleosides YOR099W KTR1 Alpha-1,2-mannosyltransferase YBR204C LDH1 Serine hydrolase YPL054W LEE1 Zinc-finger protein of unknown function YOR123C LEO1 Component of the Paf1 complex YPL055C LGE1 Protein of unknown function YJR070C LIA1 Deoxyhypusine hydroxylase YOR059C LPL1 Phospholipase YHR081W LRP1 Nuclear exosome-associated nucleic acid binding protein YJL124C LSM1 Lsm (Like Sm) protein YNL147W LSM7 Lsm (Like Sm) protein YBR115C LYS2 Alpha aminoadipate reductase YEL053C MAK10 Non-catalytic subunit of N-terminal acetyltransferase of the NatC type YPR051W MAK3 Catalytic subunit of the NatC type N-terminal acetyltransferase YNL307C MCK1 Dual-specificity ser/thr and tyrosine protein kinase YGL219C MDM34 Mitochondrial component of the ERMES complex YPR070W MED1 Subunit of the RNA polymerase II mediator complex YGL035C MIG1 Transcription factor involved in glucose repression

YLR190W MMR1 Phosphorylated protein of the mitochondrial outer membrane YGL136C MRM2 Mitochondrial 2' O-ribose methyltransferase YNL293W MSB3 Rab GTPase-activating protein YML128C MSC1 Protein of unknown function YNR049C MSO1 Probable component of the secretory vesicle docking complex YJL123C MTC1 Protein of unknown function that may interact with ribosomes YGL211W NCS6 Protein required for uridine thiolation of Gln, Lys, and Glu tRNAs YGR089W NNF2 Protein that exhibits physical and genetic interactions with Rpb8p YOL041C NOP12 Nucleolar protein involved in pre-25S rRNA processing YPR031W NTO1 Subunit of the NuA3 histone acetyltransferase complex YDR360W OPI7 Dubious open reading frame YCR077C PAT1 Deadenylation-dependent mRNA-decapping factor YJL053W PEP8 Vacuolar protein component of the retromer YGR077C PEX8 Intraperoxisomal organizer of the peroxisomal import machinery YBR093C PHO5 Repressible acid phosphatase YJL117W PHO86 Endoplasmic reticulum (ER) resident protein YGL059W PKP2 Mitochondrial protein kinase YNL201C PSY2 Subunit of protein phosphatase PP4 complex YHR189W PTH1 One of two mitochondrially-localized peptidyl-tRNA hydrolases YNL016W PUB1 Poly (A)+ RNA-binding protein YPL212C PUS1 tRNA:pseudouridine synthase YNL292W PUS4 Pseudouridine synthase

YMR201C RAD14 Protein that recognizes and binds damaged DNA during NER YER162C RAD4 Protein that recognizes and binds damaged DNA (with Rad23p) during NER YKL159C RCN1 Protein involved in calcineurin regulation during calcium signaling YJL204C RCY1 F-box protein involved in recycling endocytosed proteins YBR267W REI1 Cytoplasmic pre-60S factor YNL294C RIM21 pH sensor molecule, component of the RIM101 pathway YPL089C RLM1 MADS-box transcription factor YLR371W ROM2 GDP/GTP exchange factor (GEF) for Rho1p and Rho2p YGR085C RPL11B Ribosomal 60S subunit protein L11B YKL006W RPL14A Ribosomal 60S subunit protein L14A YJL177W RPL17B Ribosomal 60S subunit protein L17B YBR084C- RPL19A Ribosomal 60S subunit protein L19A A YBL027W RPL19B Ribosomal 60S subunit protein L19B YOR312C RPL20B Ribosomal 60S subunit protein L20B YPL079W RPL21B Ribosomal 60S subunit protein L21B YLR061W RPL22A Ribosomal 60S subunit protein L22A YDR471W RPL27B Ribosomal 60S subunit protein L27B YFR032C-A RPL29 Ribosomal 60S subunit protein L29 YER056C- RPL34A Ribosomal 60S subunit protein L34A A YDL191W RPL35A Ribosomal 60S subunit protein L35A YLR185W RPL37A Ribosomal 60S subunit protein L37A YIL148W RPL40A Ubiquitin-ribosomal 60S subunit protein L40A fusion protein YNL162W RPL42A Ribosomal 60S subunit protein L42A

YLR448W RPL6B Ribosomal 60S subunit protein L6B YHL033C RPL8A Ribosomal 60S subunit protein L8A YGL147C RPL9A Ribosomal 60S subunit protein L9A YNL067W RPL9B Ribosomal 60S subunit protein L9B YDL130W RPP1B Ribosomal protein P1 beta YOR293W RPS10A Protein component of the small (40S) ribosomal subunit YBR048W RPS11B Protein component of the small (40S) ribosomal subunit YNL302C RPS19B Protein component of the small (40S) ribosomal subunit YJL136C RPS21B Protein component of the small (40S) ribosomal subunit YGR027C RPS25A Protein component of the small (40S) ribosomal subunit YHR021C RPS27B Protein component of the small (40S) ribosomal subunit YLR264W RPS28B Protein component of the small (40S) ribosomal subunit YJR145C RPS4A Protein component of the small (40S) ribosomal subunit YPL090C RPS6A Protein component of the small (40S) ribosomal subunit YBL072C RPS8A Protein component of the small (40S) ribosomal subunit YPL081W RPS9A Protein component of the small (40S) ribosomal subunit YOR001W RRP6 Nuclear exosome exonuclease component YDR083W RRP8 Nucleolar S-adenosylmethionine-dependent rRNA methyltransferase YBR246W RRT2 Methylesterase performing penultimate step of diphthamide biosynthesis YOR216C RUD3 Golgi matrix protein YKL212W SAC1 Phosphatidylinositol phosphate (PtdInsP) phosphatase YDR159W SAC3 mRNA export factor YKR028W SAP190 Protein that forms a complex with the Sit4p protein phosphatase YBL052C SAS3 Histone acetyltransferase catalytic subunit of NuA3 complex YMR272C SCS7 Sphingolipid alpha-hydroxylase

YLR268W SEC22 R-SNARE protein YIL076W SEC28 Epsilon-COP subunit of the coatomer YJL168C SET2 Histone methyltransferase with a role in transcriptional elongation YKR029C SET3 Defining member of the SET3 histone deacetylase complex YOR021C SFM1 SPOUT methyltransferase YBL102W SFT2 Tetra-spanning membrane protein found mostly in the late Golgi YBL031W SHE1 Mitotic spindle protein YOR035C SHE4 Protein containing a UCS (UNC-45/CRO1/SHE4) domain YBR103W SIF2 WD40 repeat-containing subunit of Set3C histone deacetylase complex YNL257C SIP3 Putative sterol transfer protein YNL167C SKO1 Basic leucine zipper transcription factor of the ATF/CREB family YHR030C SLT2 Serine/threonine MAP kinase YOR327C SNC2 Vesicle membrane receptor protein (v-SNARE) YGL115W SNF4 Activating gamma subunit of the AMP-activated Snf1p kinase complex YCR033W SNT1 Subunit of the Set3C deacetylase complex YKL184W SPE1 Ornithine decarboxylase YOL052C SPE2 S-adenosylmethionine decarboxylase YPR069C SPE3 Spermidine synthase YEL031W SPF1 P-type ATPase, ion transporter of the ER membrane YKR091W SRL3 GTB motif (G1/S transcription factor binding) containing protein YPR032W SRO7 Effector of Rab GTPase Sec4p YCL037C SRO9 Cytoplasmic RNA-binding protein

YDR293C SSD1 Translational repressor with a role in polar growth and wall integrity YHR178W STB5 Transcription factor YPL057C SUR1 Mannosylinositol phosphorylceramide (MIPC) synthase catalytic subunit YML052W SUR7 Plasma membrane protein, component of eisosomes YDR320C SWA2 Auxilin-like protein involved in vesicular transport YAL011W SWC3 Protein of unknown function YBR231C SWC5 Component of the SWR1 complex YJL187C SWE1 Protein kinase that regulates the G2/M transition YJL176C SWI3 Subunit of the SWI/SNF chromatin remodeling complex YNR004W SWM2 Protein with a role in snRNA and snoRNA cap trimethylation YDR334W SWR1 Swi2/Snf2-related ATPase YAL014C SYN8 Endosomal SNARE related to mammalian syntaxin 8 YJL004C SYS1 Integral membrane protein of the Golgi YEL048C TCA17 Component of transport protein particle (TRAPP) complex II YPL157W TGS1 Trimethyl guanosine synthase, conserved nucleolar methyl transferase YHR025W THR1 Homoserine kinase YCR053W THR4 Threonine synthase YOR010C TIR2 Putative cell wall mannoprotein YOL018C TLG2 Syntaxin-like t-SNARE YKL056C TMA19 Protein that associates with ribosomes YMR269W TMA23 Nucleolar protein implicated in ribosome biogenesis YNL079C TPM1 Major isoform of tropomyosin YBR126C TPS1 Synthase subunit of trehalose-6-P synthase/phosphatase complex

YOR115C TRS33 Core component of transport protein particle (TRAPP) complexes I-III YGR166W TRS65 Component of transport protein particle (TRAPP) complex II YDR108W TRS85 Component of transport protein particle (TRAPP) complex III YLR435W TSR2 Protein with a potential role in pre-rRNA processing YHR111W UBA4 E1-like protein that activates Urm1p before urmylation YER151C UBP3 Ubiquitin-specific protease involved in transport and osmotic response YNL229C URE2 Nitrogen catabolite repression transcriptional regulator YIL008W URM1 Ubiquitin-like protein involved in thiolation of cytoplasmic tRNAs YOR068C VAM10 Protein involved in vacuole morphogenesis YOR054C VHS3 Negative regulatory subunit of protein phosphatase 1 Ppz1p YLR410W VIP1 Inositol hexakisphosphate and inositol heptakisphosphate kinase YOR132W VPS17 Subunit of the membrane-associated retromer complex YOR089C VPS21 Endosomal Rab family GTPase YHR012W VPS29 Subunit of the membrane-associated retromer complex YPL120W VPS30 Subunit of phosphatidylinositol (PtdIns) 3-kinase complexes I and II YJL154C VPS35 Endosomal subunit of membrane-associated retromer complex YLR360W VPS38 Part of a Vps34p phosphatidylinositol 3-kinase complex YOR069W VPS5 Nexin-1 homolog YKR020W VPS51 Component of the GARP (Golgi-associated retrograde protein) complex

YJL029C VPS53 Component of the GARP (Golgi-associated retrograde protein) complex YLR261C VPS63 Putative protein of unknown function YML041C VPS71 Nucleosome-binding component of the SWR1 complex YDR485C VPS72 Htz1p-binding component of the SWR1 complex YNL246W VPS75 NAP family histone chaperone YAL002W VPS8 Membrane-binding component of the CORVET complex YML097C VPS9 Guanine nucleotide exchange factor (GEF) YLR337C VRP1 Verprolin, proline-rich actin-associated protein YOR043W WHI2 Protein required for full activation of the general stress response YGL173C XRN1 Evolutionarily-conserved 5'-3' exonuclease YBR064W YBR064W Dubious open reading frame YHR135C YCK1 Palmitoylated plasma membrane-bound casein kinase I (CK1) isoform YNL154C YCK2 Palmitoylated plasma membrane-bound casein kinase I (CK1) isoform YCR090C YCR090C Putative protein of unknown function YPL087W YDC1 Alkaline dihydroceramidase, involved in sphingolipid metabolism YNL064C YDJ1 Type I HSP40 co-chaperone YDR090C YDR090C Putative protein of unknown function YDR186C YDR186C Putative protein of unknown function YDR290W YDR290W Dubious open reading frame YDR455C YDR455C Dubious open reading frame YEL068C YEL068C Protein of unknown function YFL032W YFL032W Dubious open reading frame YIL012W YIL012W Dubious open reading frame YJL169W YJL169W Dubious open reading frame

YJL206C YJL206C Putative protein of unknown function YJR084W YJR084W Protein that forms a complex with Thp3p YKR023W YKR023W Putative protein of unknown function YLR184W YLR184W Dubious open reading frame YLR255C YLR255C Dubious open reading frame YLR269C YLR269C Dubious open reading frame YLR346C YLR346C Putative protein of unknown function found in mitochondria YPR024W YME1 Catalytic subunit of i-AAA protease complex YMR031W YMR031W Dubious open reading frame -A -A YMR075C- YMR075C- Dubious open reading frame A A YMR087W YMR087W Putative ADP-ribose-1''-monophosphatase YNL198C YNL198C Dubious open reading frame YNL226W YNL226W Dubious open reading frame YNL228W YNL228W Dubious open reading frame YOL013W- YOL013W- Putative protein of unknown function A A YOL013W- YOL013W- Dubious open reading frame B B YOR062C YOR062C Protein of unknown function YPL080C YPL080C Dubious open reading frame YPL088W YPL088W Putative aryl alcohol dehydrogenase YPL102C YPL102C Dubious open reading frame YPL107W YPL107W Putative protein of unknown function YPL182C YPL182C Dubious open reading frame YPR050C YPR050C Dubious open reading frame YPR089W YPR089W Protein of unknown function

YPR090W YPR090W Merged open reading frame YER031C YPT31 Rab family GTPase YLR262C YPT6 Rab family GTPase YGR270W YTA7 Protein that localizes to chromatin YNL241C ZWF1 Glucose-6-phosphate dehydrogenase (G6PD)

Table 6 BTS1 Y55 genetic interactions

ORF Gene Description YDR216W ADR1 Carbon source-responsive zinc-finger transcription factor YIR003W AIM21 Protein of unknown function YJL046W AIM22 Putative lipoate-protein ligase

YJL131C AIM23 Mitochondrial translation initiation factor 3 (IF3, mIF3) YBR194W AIM4 Protein proposed to be associated with the nuclear pore complex YLR089C ALT1 Alanine transaminase (glutamic pyruvic transaminase) YBR249C ARO4 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase YIL130W ASG1 Zinc cluster protein proposed to be a transcriptional regulator YIL146C ATG32 Mitochondrial outer membrane protein required to initiate mitophagy YLR114C AVL9 Conserved protein involved in exocytic transport from the Golgi YJL095W BCK1 MAPKKK acting in the protein kinase C signaling pathway YBR270C BIT2 Subunit of TORC2 membrane-associated complex YFL025C BST1 GPI inositol deacylase of the endoplasmic reticulum (ER) YGL174W BUD13 Subunit of the RES complex YFL023W BUD27 Unconventional prefoldin protein involved in translation initiation YDR423C CAD1 AP-1-like basic leucine zipper (bZIP) transcriptional activator YLR098C CHA4 DNA binding transcriptional activator YLR330W CHS5 Component of the exomer complex YCR005C CIT2 Citrate synthase, peroxisomal isozyme involved in glyoxylate cycle YPR001W CIT3 Dual specificity mitochondrial citrate and methylcitrate synthase YDL155W CLB3 B-type cyclin involved in cell cycle progression YGL215W CLG1 Cyclin-like protein that interacts with Pho85p

YLR218C COA4 Twin Cx(9)C protein involved in cytochrome c oxidase organization YDR304C CPR5 Peptidyl-prolyl cis-trans isomerase (cyclophilin) of the ER YJR032W CPR7 Peptidyl-prolyl cis-trans isomerase (cyclophilin) YDR179C CSN9 Subunit of the Cop9 signalosome YIR032C DAL3 Ureidoglycolate lyase YKR035W- DID2 Class E protein of the vacuolar protein-sorting (Vps) A pathway YDR440W DOT1 Nucleosomal histone H3-Lys79 methylase YBR278W DPB3 Third-largest subunit of DNA polymerase II (DNA polymerase epsilon) YEL030W ECM10 Heat shock protein of the Hsp70 family YJL201W ECM25 Non-essential protein of unknown function YBR271W EFM2 S-adenosylmethionine-dependent methyltransferase YIL064W EFM4 Lysine methyltransferase YJR088C EMC2 Member of conserved ER transmembrane complex YDR512C EMI1 Non-essential protein of unknown function YCR075C ERS1 Protein with similarity to human cystinosin YBR026C ETR1 2-enoyl thioester reductase YJL155C FBP26 Fructose-2,6-bisphosphatase, required for glucose metabolism YCL026C-A FRM2 Type II nitroreductase, using NADH as reductant YBR045C GIP1 Meiosis-specific regulatory subunit of the Glc7p protein phosphatase YAL031C GIP4 Cytoplasmic protein that regulates protein phosphatase 1 Glc7p YDR096W GIS1 Histone demethylase and transcription factor YCL035C GRX1 Glutathione-dependent disulfide oxidoreductase

YDR221W GTB1 Glucosidase II beta subunit, forms a complex with alpha subunit Rot2p YJL110C GZF3 GATA zinc finger protein YDR458C HEH2 Inner nuclear membrane (INM) protein YER057C HMF1 Member of the p14.5 protein family YLR205C HMX1 ER localized heme oxygenase YER052C HOM3 Aspartate kinase (L-aspartate 4-P-transferase) YIL110W HPM1 AdoMet-dependent methyltransferase YJL214W HXT8 Protein of unknown function with similarity to hexose transporters YIL090W ICE2 Integral ER membrane protein with type-III transmembrane domains YLR099C ICT1 Lysophosphatidic acid acyltransferase YJL216C IMA5 Alpha-glucosidase YDR072C IPT1 Inositolphosphotransferase YJL142C IRC9 Dubious open reading frame YBR245C ISW1 ATPase subunit of imitation-switch (ISWI) class chromatin remodelers YJR050W ISY1 Member of the NineTeen Complex (NTC) YJL207C LAA1 AP-1 accessory protein YDL146W LDB17 Protein involved in the regulation of endocytosis YJR070C LIA1 Deoxyhypusine hydroxylase YLR011W LOT6 FMN-dependent NAD(P)H:quinone reductase YDR439W LRS4 Nucleolar protein that forms a complex with Csm1p YBR115C LYS2 Alpha aminoadipate reductase YJL013C MAD3 Subunit of spindle-assembly checkpoint complex YDL056W MBP1 Transcription factor YBR227C MCX1 Non-proteolytic ATPase of the AAA family

YJL112W MDV1 Peripheral protein of cytosolic face of mitochondrial outer membrane YIR033W MGA2 ER membrane protein involved in regulation of OLE1 transcription YJR008W MHO1 Protein of unknown function YBR262C MIC12 Component of the MICOS complex YLR332W MID2 O-glycosylated plasma membrane protein YDR144C MKC7 GPI-anchored aspartyl protease YJL186W MNN5 Alpha-1,2-mannosyltransferase YJR074W MOG1 Conserved nuclear protein that interacts with GTP-Gsp1p YIR002C MPH1 3'-5' DNA helicase involved in error-free bypass of DNA lesions YJL066C MPM1 Mitochondrial intermembrane space protein of unknown function YCL061C MRC1 S-phase checkpoint protein required for DNA replication YBR122C MRPL36 Mitochondrial ribosomal protein of the large subunit YBR255W MTC4 Protein of unknown function YJL205C NCE101 Protein of unknown function YKL068W NUP100 FG-nucleoporin component of central core of the nuclear pore complex YDL089W NUR1 Protein involved in regulation of mitotic exit YDR179W- NVJ3 Protein with a potential role in tethering ER and vacuoles A YBR230C OM14 Mitochondrial outer membrane receptor for cytosolic ribosomes YJR073C OPI3 Methylene-fatty-acyl-phospholipid synthase YJR051W OSM1 Fumarate reductase, catalyzes the reduction of fumarate to succinate

YDL232W OST4 Subunit of the oligosaccharyltransferase complex of the ER lumen YDR488C PAC11 Dynein intermediate chain, microtubule motor protein YIL145C PAN6 Pantothenate synthase YDR459C PFA5 Palmitoyltransferase with autoacylation activity YDR481C PHO8 Repressible vacuolar alkaline phosphatase YCR037C PHO87 Low-affinity inorganic phosphate (Pi) transporter YMR123W PKR1 V-ATPase assembly factor YBR276C PPS1 Protein phosphatase YIL095W PRK1 Protein serine/threonine kinase YJL108C PRM10 Pheromone-regulated protein YAL017W PSK1 PAS domain-containing serine/threonine protein kinase YML032C RAD52 Protein that stimulates strand exchange YJR033C RAV1 Subunit of RAVE complex (Rav1p, Rav2p, Skp1p) YJL204C RCY1 F-box protein involved in recycling endocytosed proteins YDL135C RDI1 Rho GDP dissociation inhibitor YJL217W REE1 Cytoplasmic protein involved in the regulation of enolase (ENO1) YBR260C RGD1 GTPase-activating protein (RhoGAP) for Rho3p and Rho4p YDL138W RGT2 Plasma membrane high glucose sensor that regulates glucose transport YCR027C RHB1 Putative Rheb-related GTPase YMR063W RIM9 Plasma membrane protein of unknown function YBR030W RKM3 Ribosomal lysine methyltransferase YJL121C RPE1 D-ribulose-5-phosphate 3-epimerase YBL087C RPL23A Ribosomal 60S subunit protein L23A YER056C-A RPL34A Ribosomal 60S subunit protein L34A

YIL148W RPL40A Ubiquitin-ribosomal 60S subunit protein L40A fusion protein YJL136C RPS21B Protein component of the small (40S) ribosomal subunit YKL156W RPS27A Protein component of the small (40S) ribosomal subunit YLR264W RPS28B Protein component of the small (40S) ribosomal subunit YLR388W RPS29A Protein component of the small (40S) ribosomal subunit YDL216C RRI1 Catalytic subunit of the COP9 signalosome (CSN) complex YER066W RRT13 Putative protein of unknown function YBR246W RRT2 Methylesterase performing penultimate step of diphthamide biosynthesis YIL093C RSM25 Mitochondrial ribosomal protein of the small subunit YDR233C RTN1 Reticulon protein YDL204W RTN2 Reticulon protein YJL047C RTT101 Cullin subunit of a Roc1p-dependent E3 ubiquitin ligase complex YCR009C RVS161 Amphiphysin-like lipid raft protein YDR388W RVS167 Actin-associated protein with roles in endocytosis and exocytosis YBR269C SDH8 Protein required for assembly of succinate dehydrogenase YIL076W SEC28 Epsilon-COP subunit of the coatomer YIL074C SER33 3-phosphoglycerate dehydrogenase YJL105W SET4 Protein of unknown function, contains a SET domain YBR258C SHG1 Subunit of the COMPASS (Set1C) complex YBR263W SHM1 Mitochondrial serine hydroxymethyltransferase YBR156C SLI15 Subunit of the conserved chromosomal passenger complex (CPC) YEL031W SPF1 P-type ATPase, ion transporter of the ER membrane YBR250W SPO23 Protein of unknown function

YJL092W SRS2 DNA helicase and DNA-dependent ATPase YLL024C SSA2 ATP-binding protein YBR169C SSE2 Member of the heat shock protein 70 (HSP70) family YBR283C SSH1 Subunit of the Ssh1 translocon complex YCL032W STE50 Adaptor protein for various signaling pathways YIL162W SUC2 Invertase YJL187C SWE1 Protein kinase that regulates the G2/M transition YLR251W SYM1 Protein required for ethanol metabolism YJL004C SYS1 Integral membrane protein of the Golgi YDR438W THI74 Mitochondrial transporter repressible by thiamine YER011W TIR1 Cell wall mannoprotein YJR014W TMA22 Protein of unknown function YDR105C TMS1 Vacuolar membrane protein of unknown function YJL093C TOK1 Outward-rectifier potassium channel of the plasma membrane YLR234W TOP3 DNA Topoisomerase III YDR165W TRM82 Catalytic subunit of a tRNA methyltransferase complex YDR354W TRP4 Anthranilate phosphoribosyl transferase YCR083W TRX3 Mitochondrial thioredoxin YBR058C UBP14 Ubiquitin-specific protease YJL048C UBX6 UBX (ubiquitin regulatory X) domain-containing protein YBR293W VBA2 Permease of basic amino acids in the vacuolar membrane YDR119W VBA4 Protein of unknown function YER064C VHR2 Non-essential nuclear protein YLR373C VID22 Glycosylated integral membrane protein localized to plasma membrane YDL185W VMA1 Subunit A of the V1 peripheral membrane domain of V- ATPase

YLR360W VPS38 Part of a Vps34p phosphatidylinositol 3-kinase complex YDR372C VPS74 Golgi phosphatidylinositol-4-kinase effector and PtdIns4P sensor YJL012C VTC4 Vacuolar membrane polyphosphate polymerase YBR138C YBR138C Cytoplasmic protein of unknown function YBR232C YBR232C Dubious open reading frame YCL060C YCL060C Merged open reading frame YCR043C YCR043C Putative protein of unknown function YCR102C YCR102C Putative protein of unknown function YDL129W YDL129W Protein of unknown function YDL177C YDL177C Putative protein of unknown function YDL187C YDL187C Dubious open reading frame YDR018C YDR018C Probable membrane protein with three predicted transmembrane domains YDR215C YDR215C Dubious open reading frame YEL010W YEL010W Dubious open reading frame YEL014C YEL014C Dubious open reading frame YER158C YER158C Protein of unknown function YGR122C-A YGR122C- Dubious open reading frame A YIL060W YIL060W Mitochondrial protein of unknown function YIL108W YIL108W Putative metalloendopeptidase YIR020C YIR020C Protein of unknown function YJL007C YJL007C Dubious open reading frame YJL049W YJL049W Putative protein of unknown function YJL132W YJL132W Putative protein of unknown function YJL144W YJL144W Cytoplasmic hydrophilin essential in desiccation- rehydration process YJL169W YJL169W Dubious open reading frame

YJL213W YJL213W Protein of unknown function that may interact with ribosomes YJL215C YJL215C Dubious open reading frame YJR011C YJR011C Putative protein of unknown function YJR142W YJR142W 8-oxo-dGTP diphosphatase of the Nudix hydrolase family YLR118C YLR118C Acyl-protein thioesterase responsible for depalmitoylation of Gpa1p YLR184W YLR184W Dubious open reading frame YLR217W YLR217W Dubious open reading frame YLR402W YLR402W Dubious open reading frame YLR428C YLR428C Dubious open reading frame YMR147W YMR147 Putative protein of unknown function W YOL150C YOL150C Dubious open reading frame YDR057W YOS9 ER quality-control lectin YBR183W YPC1 Alkaline ceramidase YBR264C YPT10 Rab family GTP-binding protein YHR016C YSC84 Actin-binding protein YMR243C ZRC1 Vacuolar membrane zinc transporter YBR046C ZTA1 NADPH-dependent quinone reductase

Table 7 BTS1 - SK1 genetic interactions

ORF Gene Description YGR037C ACB1 Acyl-CoA-binding protein YDL203C ACK1 Protein that functions in the cell wall integrity pathway YDR161W ACL4 Specific assembly chaperone for ribosomal protein Rpl4p YOR128C ADE2 Phosphoribosylaminoimidazole carboxylase YMR300C ADE4 Phosphoribosylpyrophosphate amidotransferase (PRPPAT) YOL086C ADH1 Alcohol dehydrogenase YMR009W ADI1 Acireductone dioxygenease involved in methionine salvage pathway YDR216W ADR1 Carbon source-responsive zinc-finger transcription factor YDL239C ADY3 Protein required for spore wall formation YCL025C AGP1 Low-affinity amino acid permease with broad substrate range YJR100C AIM25 Putative protein of unknown function YDL237W AIM6 Putative protein of unknown function YOR067C ALG8 Glucosyl transferase YKL103C APE1 Vacuolar aminopeptidase yscI

YPR029C APL4 Gamma-adaptin YPR192W AQY1 Spore-specific water channel YNR019W ARE2 Acyl-CoA:sterol acyltransferase YDL192W ARF1 ADP-ribosylation factor YGL202W ARO8 Aromatic aminotransferase I YLR085C ARP6 Actin-related protein that binds nucleosomes YOR058C ASE1 Mitotic spindle midzone-localized microtubule bundling protein YJL115W ASF1 Nucleosome assembly factor YDL197C ASF2 Anti-silencing protein YFR021W ATG18 Phosphoinositide binding protein YDL113C ATG20 Sorting nexin family member YIL146C ATG32 Mitochondrial outer membrane protein required to initiate mitophagy YJL185C ATG36 Pex3p interacting protein, required for pexophagy YER016W BIM1 Microtubule plus end-tracking protein YKL061W BLI1 Subunit of the BLOC-1 complex involved in endosomal maturation YJR025C BNA1 3-hydroxyanthranilic acid dioxygenase YNL275W BOR1 Boron efflux transporter of the plasma membrane YDL231C BRE4 Zinc finger protein containing five transmembrane domains YNR051C BRE5 Ubiquitin protease cofactor YGL007W BRP1 Dubious ORF located in the upstream region of PMA1 YFL025C BST1 GPI inositol deacylase of the endoplasmic reticulum (ER) YGL174W BUD13 Subunit of the RES complex YGR041W BUD9 Protein involved in bud-site selection YDR423C CAD1 AP-1-like basic leucine zipper (bZIP) transcriptional activator

YKR036C CAF4 WD40 repeat-containing protein associated with the CCR4-NOT complex YIL034C CAP2 Beta subunit of the capping protein heterodimer (Cap1p and Cap2p) YML042W CAT2 Carnitine acetyl-CoA transferase YER061C CEM1 Mitochondrial beta-keto-acyl synthase YGR157W CHO2 Phosphatidylethanolamine methyltransferase (PEMT) YOR349W CIN1 Tubulin folding factor D involved in beta-tubulin (Tub2p) folding YJL158C CIS3 Mannose-containing glycoprotein constituent of the cell wall YOR061W CKA2 Alpha' catalytic subunit of casein kinase 2 (CK2) YPR120C CLB5 B-type cyclin involved in DNA replication during S phase YGL215W CLG1 Cyclin-like protein that interacts with Pho85p YKL137W CMC1 Copper-binding protein of the mitochondrial intermembrane space YPR013C CMR3 Putative zinc finger protein YNR075W COS10 Protein of unknown function YJR032W CPR7 Peptidyl-prolyl cis-trans isomerase (cyclophilin) YDL142C CRD1 Cardiolipin synthase YLR087C CSF1 Protein required for fermentation at low temperature YCR086W CSM1 Nucleolar protein that mediates homolog segregation during meiosis I YMR180C CTL1 RNA 5'-triphosphatase, localizes to both the nucleus and cytoplasm YNL111C CYB5 Cytochrome b5 YHR028C DAP2 Dipeptidyl aminopeptidase YGR092W DBF2 Ser/Thr kinase involved in transcription and stress response

YFR012W DCV1 Protein of unknown function YKR035W- DID2 Class E protein of the vacuolar protein-sorting (Vps) A pathway YGR227W DIE2 Dolichyl-phosphoglucose-dependent alpha-1,2- glucosyltransferase YIR004W DJP1 Cytosolic J-domain-containing protein YHR043C DOG2 2-deoxyglucose-6-phosphate phosphatase YGR093W DRN1 Splicing factor that modulates turnover of branched RNAs by Dbr1p YDL219W DTD1 D-Tyr-tRNA(Tyr) deacylase YKR054C DYN1 Cytoplasmic heavy chain dynein YPR023C EAF3 Component of the Rpd3S histone deacetylase complex YDR446W ECM11 Meiosis-specific protein YEL015W EDC3 Non-essential conserved protein with a role in mRNA decapping YPL095C EEB1 Acyl-coenzymeA:ethanol O-acyltransferase YKL160W ELF1 Transcription elongation factor with a conserved zinc finger domain YJR088C EMC2 Member of conserved ER transmembrane complex YOL158C ENB1 Endosomal ferric enterobactin transporter YGR254W ENO1 Enolase I, a phosphopyruvate hydratase YLR065C ENV10 Protein proposed to be involved in vacuolar functions YDR414C ERD1 Predicted membrane protein required for lumenal ER protein retention YBR239C ERT1 Transcriptional regulator YBR008C FLR1 Plasma membrane transporter of the major facilitator superfamily YIL098C FMC1 Mitochondrial matrix protein YLR454W FMP27 Putative protein of unknown function

YDL222C FMP45 Integral membrane protein localized to mitochondria YKR049C FMP46 Putative redox protein containing a thioredoxin fold YGR052W FMP48 Putative protein of unknown function YLR214W FRE1 Ferric reductase and cupric reductase YOL152W FRE7 Putative ferric reductase with similarity to Fre2p YOR271C FSF1 Putative protein YBR020W GAL1 Galactokinase YKR039W GAP1 General amino acid permease YOL030W GAS5 1,3-beta-glucanosyltransferase YDL226C GCS1 ADP-ribosylation factor GTPase activating protein (ARF GAP) YDL215C GDH2 NAD(+)-dependent glutamate dehydrogenase YJR031C GEA1 Guanine nucleotide exchange factor for ADP ribosylation factors (ARFs) YEL011W GLC3 Glycogen branching enzyme, involved in glycogen accumulation YKR058W GLG1 Glycogenin glucosyltransferase YNL274C GOR1 Glyoxylate reductase YHL031C GOS1 v-SNARE protein involved in Golgi transport YIL053W GPP1 Constitutively expressed DL-glycerol-3-phosphate phosphatase YML048W GSF2 Endoplasmic reticulum (ER) localized integral membrane protein YDL238C GUD1 Guanine deaminase YGL084C GUP1 Plasma membrane protein involved in remodeling GPI anchors YOR070C GYP1 Cis-golgi GTPase-activating protein (GAP) for yeast Rabs YDL234C GYP7 GTPase-activating protein for yeast Rab family members

YJL110C GZF3 GATA zinc finger protein YFL031W HAC1 Basic leucine zipper (bZIP) transcription factor (ATF/CREB1 homolog) YOL089C HAL9 Putative transcription factor containing a zinc finger YDL223C HBT1 Shmoo tip protein, substrate of Hub1p ubiquitin-like protein YCR065W HCM1 Forkhead transcription factor YNL014W HEF3 Translational elongation factor EF-3 YBR010W HHT1 Histone H3 YJR075W HOC1 Alpha-1,6-mannosyltransferase YIL072W HOP1 Meiosis-specific protein required for chromosome synapsis YEL066W HPA3 D-Amino acid N-acetyltransferase that detoxifies D- amino acids YOL155C HPF1 Haze-protective mannoprotein YDR533C HSP31 Methylglyoxalase that converts methylglyoxal to D- lactate YHR067W HTD2 Mitochondrial 3-hydroxyacyl-thioester dehydratase YLR099C ICT1 Lysophosphatidic acid acyltransferase YJR118C ILM1 Protein of unknown function YJL106W IME2 Serine/threonine protein kinase involved in activation of meiosis YJL082W IML2 Protein of unknown function YMR035W IMP2 Catalytic subunit of mitochondrial inner membrane peptidase complex YDR315C IPK1 Inositol 1,3,4,5,6-pentakisphosphate 2-kinase YDR072C IPT1 Inositolphosphotransferase YOL015W IRC10 Putative protein of unknown function YOR235W IRC13 Dubious open reading frame

YEL001C IRC22 Putative protein of unknown function YHR079C IRE1 Serine-threonine kinase and endoribonuclease YOR155C ISN1 Inosine 5'-monophosphate (IMP)-specific 5'- nucleotidase YJR050W ISY1 Member of the NineTeen Complex (NTC) YOL103W ITR2 Myo-inositol transporter YPR141C KAR3 Minus-end-directed microtubule motor YHR158C KEL1 Protein required for proper cell fusion and cell morphology YGL203C KEX1 Cell death protease essential for hypochlorite-induced apoptosis YGL216W KIP3 Kinesin-related antiparallel sliding motor protein YOR099W KTR1 Alpha-1,2-mannosyltransferase YJL207C LAA1 AP-1 accessory protein YKL073W LHS1 Molecular chaperone of the endoplasmic reticulum lumen YOR084W LPX1 Peroxisomal matrix-localized lipase YDL240W LRG1 GTPase-activating protein (GAP) YHR081W LRP1 Nuclear exosome-associated nucleic acid binding protein YJL124C LSM1 Lsm (Like Sm) protein YDR378C LSM6 Lsm (Like Sm) protein YNL147W LSM7 Lsm (Like Sm) protein YBR115C LYS2 Alpha aminoadipate reductase YDL182W LYS20 Homocitrate synthase isozyme and functions in DNA repair YBR299W MAL32 Maltase (alpha-D-glucosidase) YOR197W MCA1 Ca2+-dependent cysteine protease YGL219C MDM34 Mitochondrial component of the ERMES complex

YGL197W MDS3 Putative component of the TOR regulatory pathway YJL112W MDV1 Peripheral protein of cytosolic face of mitochondrial outer membrane YPR070W MED1 Subunit of the RNA polymerase II mediator complex YDR253C MET32 Zinc-finger DNA-binding transcription factor YDL233W MFG1 Regulator of filamentous growth YPL060W MFM1 Mitochondrial inner membrane magnesium transporter YNL218W MGS1 Protein with DNA-dependent ATPase and ssDNA annealing activities YDL200C MGT1 DNA repair methyltransferase (6-O-methylguanine- DNA methylase) YFR011C MIC19 Component of the MICOS complex YBL049W MOH1 Protein of unknown function, essential for stationary phase survival YHR162W MPC2 Highly conserved subunit of the mitochondrial pyruvate carrier YML009C MRPL39 Mitochondrial ribosomal protein of the large subunit YNR022C MRPL50 Mitochondrial ribosomal protein of the large subunit YJL133W MRS3 Iron transporter, mediates Fe2+ transport across inner mito membrane YJL147C MRX5 Protein that associates with mitochondrial ribosome YOR066W MSA1 Activator of G1-specific transcription factors MBF and SBF YOR188W MSB1 Protein of unknown function YNL053W MSG5 Dual-specificity protein phosphatase YKL062W MSN4 Stress-responsive transcriptional activator YDR335W MSN5 Karyopherin YPR134W MSS18 Nuclear encoded protein needed for splicing of mitochondrial intron

YGR023W MTL1 Putative plasma membrane sensor YKL074C MUD2 Protein involved in early pre-mRNA splicing YJL205C NCE101 Protein of unknown function YMR285C NGL2 Protein involved in 5.8S rRNA processing YPL174C NIP100 Large subunit of the dynactin complex YKL171W NNK1 Protein kinase YOL041C NOP12 Nucleolar protein involved in pre-25S rRNA processing YDL213C NOP6 rRNA-binding protein required for 40S ribosomal subunit biogenesis YHL023C NPR3 Subunit of the Iml1p/SEACIT complex YGR043C NQM1 Transaldolase of unknown function YDR043C NRG1 Transcriptional repressor YDR150W NUM1 Protein required for nuclear migration YDR179W- NVJ3 Protein with a potential role in tethering ER and A vacuoles YDR316W OMS1 Protein integral to the mitochondrial membrane YKR035C OPI8 Dubious open reading frame YPR194C OPT2 Oligopeptide transporter YJR051W OSM1 Fumarate reductase, catalyzes the reduction of fumarate to succinate YDL232W OST4 Subunit of the oligosaccharyltransferase complex of the ER lumen YGR078C PAC10 Part of the heteromeric co-chaperone GimC/prefoldin complex YMR165C PAH1 Mg2+-dependent phosphatidate (PA) phosphatase YDL173W PAR32 Putative protein of unknown function YIL071C PCI8 Possible shared subunit of Cop9 signalosome (CSN) and eIF3

YPL058C PDR12 Plasma membrane ATP-binding cassette (ABC) transporter YDR406W PDR15 Plasma membrane ATP binding cassette (ABC) transporter YFR023W PES4 Poly(A) binding protein, suppressor of DNA polymerase epsilon mutation YOR158W PET123 Mitochondrial ribosomal protein of the small subunit YDR265W PEX10 Peroxisomal membrane E3 ubiquitin ligase YOL044W PEX15 Tail-anchored type II integral peroxisomal membrane protein YJL210W PEX2 RING-finger peroxin and E3 ubiquitin ligase YBR168W PEX32 Peroxisomal integral membrane protein YGR077C PEX8 Intraperoxisomal organizer of the peroxisomal import machinery YDR459C PFA5 Palmitoyltransferase with autoacylation activity YDR281C PHM6 Protein of unknown function YDL236W PHO13 Alkaline phosphatase specific for p-nitrophenyl phosphate YCR037C PHO87 Low-affinity inorganic phosphate (Pi) transporter YGL059W PKP2 Mitochondrial protein kinase YMR123W PKR1 V-ATPase assembly factor YMR008C PLB1 Phospholipase B (lysophospholipase) involved in lipid metabolism YDR435C PPM1 Carboxyl methyltransferase YML047C PRM6 Potassium transporter that mediates K+ influx YDL214C PRR2 Serine/threonine protein kinase YNL169C PSD1 Phosphatidylserine decarboxylase of the mitochondrial inner membrane YOL045W PSK2 PAS-domain containing serine/threonine protein kinase

YDL230W PTP1 Phosphotyrosine-specific protein phosphatase YGL063W PUS2 Mitochondrial tRNA:pseudouridine synthase YFR033C QCR6 Subunit 6 of the ubiquinol cytochrome-c reductase complex YGL163C RAD54 DNA-dependent ATPase that stimulates strand exchange YJR033C RAV1 Subunit of RAVE complex (Rav1p, Rav2p, Skp1p) YDR202C RAV2 Subunit of RAVE complex (Rav1p, Rav2p, Skp1p) YLR084C RAX2 N-glycosylated protein YDL189W RBS1 Protein involved in assembly of the RNA polymerase III (Pol III) comp YKL159C RCN1 Protein involved in calcineurin regulation during calcium signaling YJL204C RCY1 F-box protein involved in recycling endocytosed proteins YER067W RGI1 Protein of unknown function YFL033C RIM15 Protein kinase involved in cell proliferation in response to nutrients YDR198C RKM2 Ribosomal protein lysine methyltransferase YBR030W RKM3 Ribosomal lysine methyltransferase YFR048W RMD8 Cytosolic protein required for sporulation YFR022W ROG3 Alpha-arrestin involved in ubiquitin-dependent endocytosis YJL121C RPE1 D-ribulose-5-phosphate 3-epimerase YDL082W RPL13A Ribosomal 60S subunit protein L13A YIL133C RPL16A Ribosomal 60S subunit protein L16A YOR234C RPL33B Ribosomal 60S subunit protein L33B YIL148W RPL40A Ubiquitin-ribosomal 60S subunit protein L40A fusion protein

YDL184C RPL41A Ribosomal 60S subunit protein L41A YDL020C RPN4 Transcription factor that stimulates expression of proteasome genes YDL081C RPP1A Ribosomal stalk protein P1 alpha YCR031C RPS14A Protein component of the small (40S) ribosomal subunit YJL136C RPS21B Protein component of the small (40S) ribosomal subunit YLR388W RPS29A Protein component of the small (40S) ribosomal subunit YDL216C RRI1 Catalytic subunit of the COP9 signalosome (CSN) complex YOR001W RRP6 Nuclear exosome exonuclease component YNL254C RTC4 Protein of unknown function YPL183C RTT10 WD40 domain-containing protein involved in endosomal recycling YGR275W RTT102 Component of both the SWI/SNF and RSC chromatin remodeling complexes YDR388W RVS167 Actin-associated protein with roles in endocytosis and exocytosis YDR159W SAC3 mRNA export factor YBL091C-A SCS22 Protein involved in regulation of phospholipid metabolism YGR279C SCW4 Cell wall protein with similarity to glucanases YOL071W SDH5 Protein required for flavinylation of Sdh1p YIL084C SDS3 Component of the Rpd3L histone deacetylase complex YJL105W SET4 Protein of unknown function, contains a SET domain YIL099W SGA1 Intracellular sporulation-specific glucoamylase YCL010C SGF29 Component of the HAT/Core module of the SAGA, SLIK, and ADA complexes YGL228W SHE10 Protein involved in outer spore wall assembly YGR143W SKN1 Protein involved in sphingolipid biosynthesis

YGR271W SLH1 Putative RNA helicase related to Ski2p YDR073W SNF11 Subunit of the SWI/SNF chromatin remodeling complex YDL194W SNF3 Plasma membrane low glucose sensor, regulates glucose transport YCR033W SNT1 Subunit of the Set3C deacetylase complex YHR008C SOD2 Mitochondrial manganese superoxide dismutase YER150W SPI1 GPI-anchored cell wall protein involved in weak acid resistance YJL092W SRS2 DNA helicase and DNA-dependent ATPase YDL229W SSB1 Cytoplasmic ATPase that is a ribosome-associated molecular chaperone YDR293C SSD1 Translational repressor with a role in polar growth and wall integrity YHR178W STB5 Transcription factor YDR463W STP1 Transcription factor YGL162W SUT1 Transcription factor of the Zn(II)2Cys6 family YOR179C SYC1 Subunit of the APT subcomplex of cleavage and polyadenylation factor YGL243W TAD1 tRNA-specific adenosine deaminase YHR159W TDA11 Putative protein of unknown function YNL253W TEX1 Protein involved in mRNA export YDR058C TGL2 Triacylglycerol lipase that is localized to the mitochondria YMR313C TGL3 Bifunctional triacylglycerol lipase and LPE acyltransferase YPR121W THI22 Protein with similarity to hydroxymethylpyrimidine phosphate kinases YOR192C THI72 Transporter of thiamine or related compound YJL138C TIF2 Translation initiation factor eIF4A

YGL049C TIF4632 Translation initiation factor eIF4G YER011W TIR1 Cell wall mannoprotein YPR074C TKL1 Transketolase YER007C-A TMA20 Protein of unknown function that associates with ribosomes YJR014W TMA22 Protein of unknown function YHR117W TOM71 Mitochondrial outer membrane protein YGL096W TOS8 Homeodomain-containing protein and putative transcription factor YKL166C TPK3 cAMP-dependent protein kinase catalytic subunit YOL093W TRM10 tRNA methyltransferase YBR061C TRM7 2'-O-ribose methyltransferase YDR354W TRP4 Anthranilate phosphoribosyl transferase YPR066W UBA3 Protein that activates Rub1p (NEDD8) before neddylation YBR082C UBC4 Ubiquitin-conjugating enzyme (E2) YMR022W UBC7 Ubiquitin conjugating enzyme YER151C UBP3 Ubiquitin-specific protease involved in transport and osmotic response YDL210W UGA4 GABA (gamma-aminobutyrate) permease YJR103W URA8 Minor CTP synthase isozyme (see also URA7) YDR520C URC2 Putative Zn(II)2Cys6 motif containing transcription factor YPR152C URN1 Putative protein of unknown function containing WW and FF domains YEL013W VAC8 Phosphorylated and palmitoylated vacuolar membrane protein YOR106W VAM3 Syntaxin-like vacuolar t-SNARE

YGL227W VID30 Central component of GID Complex, involved in FBPase degradation YDL185W VMA1 Subunit A of the V1 peripheral membrane domain of V- ATPase YOR069W VPS5 Nexin-1 homolog YKR020W VPS51 Component of the GARP (Golgi-associated retrograde protein) complex YJR126C VPS70 Protein of unknown function involved in vacuolar protein sorting YFL004W VTC2 Subunit of vacuolar transporter chaperone (VTC) complex YDL224C WHI4 Putative RNA binding protein YML007W YAP1 Basic leucine zipper (bZIP) transcription factor YAR028W YAR028W Putative integral membrane protein YBL036C YBL036C Putative non-specific single-domain racemase YBL081W YBL081W Non-essential protein of unknown function YGL060W YBP2 Central kinetochore associated protein YBR225W YBR225W Putative protein of unknown function YCL023C YCL023C Dubious open reading frame YCL049C YCL049C Protein of unknown function YCR061W YCR061W Protein of unknown function YCR062W YCR062W Merged open reading frame YDL086W YDL086W Putative carboxymethylenebutenolidase YDL199C YDL199C Putative transporter YDL206W YDL206W Putative protein of unknown function YDL211C YDL211C Protein of unknown function YDL218W YDL218W Putative protein of unknown function YDL241W YDL241W Putative protein of unknown function YDL242W YDL242W Dubious open reading frame

YDR008C YDR008C Dubious open reading frame YDR018C YDR018C Probable membrane protein with three predicted transmembrane domains YDR090C YDR090C Putative protein of unknown function YDR102C YDR102C Dubious open reading frame YDR131C YDR131C F-box protein subunit of SCF ubiquitin ligase complex YDR149C YDR149C Dubious open reading frame YDR199W YDR199W Dubious open reading frame YDR215C YDR215C Dubious open reading frame YDR426C YDR426C Dubious open reading frame YEL014C YEL014C Dubious open reading frame YFL040W YFL040W Putative transporter YFR006W YFR006W Putative X-Pro aminopeptidase YFR035C YFR035C Putative protein of unknown function YFR054C YFR054C Dubious open reading frame YGL041C YGL041C Dubious open reading frame YGL132W YGL132W Dubious open reading frame YGL176C YGL176C Putative protein of unknown function YGL177W YGL177W Dubious open reading frame YGR039W YGR039W Dubious open reading frame YGR111W YGR111W Putative protein of unknown function YGR122C-A YGR122C-A Dubious open reading frame YGR259C YGR259C Dubious open reading frame YIL067C YIL067C Uncharacterized protein of unknown function YGL198W YIP4 Protein that interacts with Rab GTPases YGL161C YIP5 Protein that interacts with Rab GTPases YJL016W YJL016W Putative protein of unknown function YJL068C YJL068C Esterase that can function as an S-formylglutathione hydrolase

YJL107C YJL107C Putative protein of unknown function YJL119C YJL119C Dubious open reading frame YJL193W YJL193W Putative protein of unknown function YJR037W YJR037W Dubious open reading frame YJR039W YJR039W Putative protein of unknown function YJR098C YJR098C Putative protein of unknown function YLR200W YKE2 Subunit of the heterohexameric Gim/prefoldin protein complex YKL030W YKL030W Dubious open reading frame YKL063C YKL063C Putative protein of unknown function YKL091C YKL091C Putative phosphatidylinositol/phosphatidylcholine transfer protein YKR051W YKR051W Putative protein of unknown function YKR078W YKR078W Cytoplasmic protein of unknown function YLR053C YLR053C Putative protein of unknown function YMR302C YME2 Integral inner mitochondrial membrane protein YML053C YML053C Putative protein of unknown function YML057C- YML057C-A Dubious open reading frame A YMR010W YMR010W Putative protein of unknown function YMR018W YMR018W Putative protein of unknown function with similarity to human PEX5Rp YMR194C- YMR194C- Dubious open reading frame A A YMR209C YMR209C Putative S-adenosylmethionine-dependent methyltransferase YMR244W YMR244W Putative protein of unknown function YNL011C YNL011C Putative protein of unknown function YNL319W YNL319W Dubious open reading frame

YOL029C YOL029C Putative protein of unknown function YOL079W YOL079W Dubious open reading frame YOL107W YOL107W Putative protein of unknown function YOL159C YOL159C Soluble protein of unknown function YPR028W YOP1 Membrane protein that interacts with Yip1p to mediate membrane traffic YOR019W YOR019W Protein of unknown function YOR029W YOR029W Dubious open reading frame YOR055W YOR055W Dubious open reading frame YDR057W YOS9 ER quality-control lectin YKL100C YPF1 Intramembrane aspartyl protease of the perinuclear ER membrane YPL261C YPL261C Dubious open reading frame YPR003C YPR003C Putative sulfate permease YPR092W YPR092W Dubious open reading frame YPR096C YPR096C Protein of unknown function YPR097W YPR097W Protein that contains a PX domain and binds phosphoinositides YPR109W YPR109W Predicted membrane protein YPR114W YPR114W Putative protein of unknown function YPR153W YPR153W Putative protein of unknown function YPR172W YPR172W Putative pyridoxal 5'-phosphate synthase YML001W YPT7 Rab family GTPase YNL339C YRF1-6 Helicase encoded by the Y' element of subtelomeric regions YJR099W YUH1 Ubiquitin C-terminal hydrolase YOR087W YVC1 Vacuolar cation channel YMR243C ZRC1 Vacuolar membrane zinc transporter YKL175W ZRT3 Vacuolar membrane zinc transporter

Table 8 BTS1 - YPS606 genetic interactions

ORF Gene Description YBL015W ACH1 Protein with CoA transferase activity YKL206C ADD66 Protein involved in 20S proteasome assembly YOR128C ADE2 Phosphoribosylaminoimidazole carboxylase YLR040C AFB1 MATalpha-specific a-factor blocker YJL131C AIM23 Mitochondrial translation initiation factor 3 (IF3, mIF3) YDR530C APA2 Diadenosine5',5'''-P1,P4-tetraphosphate phosphorylase II YKL157W APE2 Aminopeptidase yscII YNR019W ARE2 Acyl-CoA:sterol acyltransferase YDL192W ARF1 ADP-ribosylation factor YBR164C ARL1 Soluble GTPase with a role in regulation of membrane traffic YDR101C ARX1 Nuclear export factor for the ribosomal pre-60S subunit YGR177C ATF2 Alcohol acetyltransferase YPR026W ATH1 Acid trehalase required for utilization of extracellular trehalose YML081C-A ATP18 Subunit of the mitochondrial F1F0 ATP synthase YOR079C ATX2 Golgi membrane protein involved in manganese homeostasis YBL089W AVT5 Putative transporter YJL095W BCK1 MAPKKK acting in the protein kinase C signaling pathway

YER177W BMH1 14-3-3 protein, major isoform YJL060W BNA3 Kynurenine aminotransferase YNL166C BNI5 Linker protein responsible for recruitment of myosin to the bud neck YBL085W BOI1 Protein implicated in polar growth YNR051C BRE5 Ubiquitin protease cofactor YGL007W BRP1 Dubious ORF located in the upstream region of PMA1 YBR290W BSD2 Heavy metal ion homeostasis protein YPR171W BSP1 Adapter that links synaptojanins to the cortical actin cytoskeleton YGR188C BUB1 Protein kinase involved in the cell cycle checkpoint into anaphase YOR026W BUB3 Kinetochore checkpoint WD40 repeat protein YGL174W BUD13 Subunit of the RES complex YNL288W CAF40 Component of the CCR4-NOT transcriptional complex YLR220W CCC1 Vacuolar Fe2+/Mn2+ transporter YKR066C CCP1 Mitochondrial cytochrome-c peroxidase YLR418C CDC73 Component of the Paf1p complex YGR157W CHO2 Phosphatidylethanolamine methyltransferase (PEMT) YGL215W CLG1 Cyclin-like protein that interacts with Pho85p YML057W CMP2 Calcineurin A YPR013C CMR3 Putative zinc finger protein YNL051W COG5 Component of the conserved oligomeric Golgi complex YGL005C COG7 Component of the conserved oligomeric Golgi complex YML071C COG8 Component of the conserved oligomeric Golgi complex

YER130C COM2 Transcription factor that binds IME1 Upstream Activation Signal (UAS) YGR255C COQ6 Flavin-dependent monooxygenase involved in ubiquinone biosynthesis YLR038C COX12 Subunit VIb of cytochrome c oxidase YNL052W COX5A Subunit Va of cytochrome c oxidase YKL179C COY1 Golgi membrane protein with similarity to mammalian CASP YLR216C CPR6 Peptidyl-prolyl cis-trans isomerase (cyclophilin) YJR032W CPR7 Peptidyl-prolyl cis-trans isomerase (cyclophilin) YML112W CTK3 Gamma subunit of C-terminal domain kinase I YDR163W CWC15 Non-essential protein involved in pre-mRNA splicing YNL111C CYB5 Cytochrome b5 YPL170W DAP1 Heme-binding protein YKL149C DBR1 RNA lariat debranching enzyme YDR273W DON1 Meiosis-specific component of the spindle pole body YAL026C DRS2 Trans-golgi network aminophospholipid translocase (flippase) YER124C DSE1 Daughter cell-specific protein YHR143W DSE2 Daughter cell-specific secreted protein with similarity to glucanases YPR017C DSS4 Guanine nucleotide dissociation stimulator for Sec4p YMR299C DYN3 Dynein light intermediate chain (LIC) YPR023C EAF3 Component of the Rpd3S histone deacetylase complex YLR284C ECI1 Peroxisomal delta3,delta2-enoyl-CoA isomerase YGR146C ECL1 Protein of unknown function YJL201W ECM25 Non-essential protein of unknown function YKR076W ECM4 Omega class glutathione transferase

YPL095C EEB1 Acyl-coenzymeA:ethanol O-acyltransferase YIL064W EFM4 Lysine methyltransferase YOR133W EFT1 Elongation factor 2 (EF-2), also encoded by EFT2 YGR200C ELP2 Subunit of Elongator complex YPL086C ELP3 Subunit of Elongator complex YMR312W ELP6 Subunit of hexameric RecA-like ATPase Elp456 Elongator subcomplex YLR083C EMP70 Protein with a role in cellular adhesion and filamentous growth YDR153C ENT5 Protein containing an N-terminal epsin-like domain YBR026C ETR1 2-enoyl thioester reductase YDR261C EXG2 Exo-1,3-beta-glucanase YMR246W FAA4 Long chain fatty acyl-CoA synthetase YNL023C FAP1 Protein that binds to Fpr1p YMR052W FAR3 Protein of unknown function YMR029C FAR8 Protein involved in recovery from arrest in response to pheromone YER060W FCY21 Putative purine-cytosine permease YER060W-A FCY22 Putative purine-cytosine permease YMR319C FET4 Low-affinity Fe(II) transporter of the plasma membrane YKR102W FLO10 Member of the FLO family of cell wall flocculation proteins YLR047C FRE8 Protein with sequence similarity to iron/copper reductases YIL097W FYV10 Subunit of GID complex YGR196C FYV8 Protein of unknown function YGL254W FZF1 Transcription factor involved in sulfite metabolism YGL020C GET1 Subunit of the GET complex

YER083C GET2 Subunit of the GET complex YDL100C GET3 Guanine nucleotide exchange factor for Gpa1p YMR255W GFD1 Coiled-coiled protein of unknown function YHR108W GGA2 Protein that regulates Arf1p, Arf2p to facilitate Golgi trafficking YHR061C GIC1 Protein involved in initiation of budding and cellular polarization YMR135C GID8 Subunit of GID Complex, binds strongly to central component Vid30p YNL153C GIM3 Subunit of the heterohexameric cochaperone prefoldin complex YLR094C GIS3 Protein of unknown function YPL091W GLR1 Cytosolic and mitochondrial glutathione oxidoreductase YDL171C GLT1 NAD(+)-dependent glutamate synthase (GOGAT) YKR030W GMH1 Golgi membrane protein of unknown function YNL274C GOR1 Glyoxylate reductase YHL031C GOS1 v-SNARE protein involved in Golgi transport YML048W GSF2 Endoplasmic reticulum (ER) localized integral membrane protein YLL060C GTT2 Glutathione S-transferase capable of homodimerization YIL155C GUT2 Mitochondrial glycerol-3-phosphate dehydrogenase YDL234C GYP7 GTPase-activating protein for yeast Rab family members YFL027C GYP8 GTPase-activating protein for yeast Rab family members YPR005C HAL1 Cytoplasmic protein involved in halotolerance YOL089C HAL9 Putative transcription factor containing a zinc finger

YKR017C HEL1 RING finger ubiquitin ligase (E3) YML075C HMG1 HMG-CoA reductase YOR032C HMS1 bHLH protein with similarity to myc-family transcription factors YJR147W HMS2 Protein with similarity to heat shock transcription factors YGL194C HOS2 Histone deacetylase and subunit of Set3 and Rpd3L complexes YIL112W HOS4 Subunit of the Set3 complex YIL110W HPM1 AdoMet-dependent methyltransferase YDR258C HSP78 Oligomeric mitochondrial matrix chaperone YDR225W HTA1 Histone H2A YHR067W HTD2 Mitochondrial 3-hydroxyacyl-thioester dehydratase YNR032C-A HUB1 Ubiquitin-like protein modifier YLR099C ICT1 Lysophosphatidic acid acyltransferase YOR109W INP53 Polyphosphatidylinositol phosphatase YDR315C IPK1 Inositol 1,3,4,5,6-pentakisphosphate 2-kinase YDR072C IPT1 Inositolphosphotransferase YJL051W IRC8 Bud tip localized protein of unknown function YJR050W ISY1 Member of the NineTeen Complex (NTC) YKL032C IXR1 Transcriptional repressor that regulates hypoxic genes during normoxia YGL216W KIP3 Kinesin-related antiparallel sliding motor protein YKL168C KKQ8 Putative serine/threonine protein kinase with unknown cellular role YHR082C KSP1 Serine/threonine protein kinase YPL053C KTR6 Probable mannosylphosphate transferase YIL085C KTR7 Putative mannosyltransferase involved in protein glycosylation

YPL056C LCL1 Putative protein of unknown function YPL055C LGE1 Protein of unknown function YJR070C LIA1 Deoxyhypusine hydroxylase YGL090W LIF1 Component of the DNA ligase IV complex YHR156C LIN1 Non-essential component of U5 snRNP YDR378C LSM6 Lsm (Like Sm) protein YNL147W LSM7 Lsm (Like Sm) protein YBR115C LYS2 Alpha aminoadipate reductase YKL029C MAE1 Mitochondrial malic enzyme YKL221W MCH2 Protein with similarity to mammalian monocarboxylate permeases YKL150W MCR1 Mitochondrial NADH-cytochrome b5 reductase YGL219C MDM34 Mitochondrial component of the ERMES complex YPR083W MDM36 Mitochondrial protein YOL027C MDM38 Mitochondrial protein YJL112W MDV1 Peripheral protein of cytosolic face of mitochondrial outer membrane YPR070W MED1 Subunit of the RNA polymerase II mediator complex YIL128W MET18 Component of cytosolic iron-sulfur protein assembly (CIA) machinery YDL233W MFG1 Regulator of filamentous growth YKR016W MIC60 Component of the MICOS complex YKL201C MNN4 Putative positive regulator of mannosylphosphate transferase Mnn6p YBR122C MRPL36 Mitochondrial ribosomal protein of the large subunit YLR219W MSC3 Protein of unknown function YDR335W MSN5 Karyopherin YNR049C MSO1 Probable component of the secretory vesicle docking complex

YMR164C MSS11 Transcription factor YDR277C MTH1 Negative regulator of the glucose-sensing signal transduction pathway YMR004W MVP1 Protein required for sorting proteins to the vacuole YHR086W NAM8 RNA binding protein, component of the U1 snRNP protein YGL211W NCS6 Protein required for uridine thiolation of Gln, Lys, and Glu tRNAs YPL226W NEW1 ATP binding cassette protein YLR315W NKP2 Central kinetochore protein and subunit of the Ctf19 complex YGR089W NNF2 Protein that exhibits physical and genetic interactions with Rpb8p YHL023C NPR3 Subunit of the Iml1p/SEACIT complex YML103C NUP188 Subunit of the inner ring of the nuclear pore complex (NPC) YDR179W-A NVJ3 Protein with a potential role in tethering ER and vacuoles YDR316W OMS1 Protein integral to the mitochondrial membrane YPR194C OPT2 Oligopeptide transporter YLR350W ORM2 Protein that mediates sphingolipid homeostasis YKR003W OSH6 Member of an oxysterol-binding protein family YOR085W OST3 Gamma subunit of the oligosaccharyltransferase complex of the ER lumen YLR054C OSW2 Protein of unknown function reputedly involved in spore wall assembly YLR037C PAU23 Cell wall mannoprotein YLR044C PDC1 Major of three pyruvate decarboxylase isozymes

100

YLR455W PDP3 Component of the NuA3b histone acetyltransferase complex YJL053W PEP8 Vacuolar protein component of the retromer YAL055W PEX22 Putative peroxisomal membrane protein YNL316C PHA2 Prephenate dehydratase YNL097C PHO23 Component of the Rpd3L histone deacetylase complex YKL164C PIR1 O-glycosylated protein required for cell wall stability YER132C PMD1 Protein with an N-terminal kelch-like domain YPL096W PNG1 Conserved peptide N-glycanase YJR043C POL32 Third subunit of DNA polymerase delta YNR032W PPG1 Putative serine/threonine protein phosphatase YOL141W PPM2 AdoMet-dependent tRNA methyltransferase YIL095W PRK1 Protein serine/threonine kinase YJL108C PRM10 Pheromone-regulated protein YML047C PRM6 Potassium transporter that mediates K+ influx YKR013W PRY2 Sterol binding protein involved in the export of acetylated sterols YDR505C PSP1 Asn and gln rich protein of unknown function YML017W PSP2 Asn rich cytoplasmic protein that contains RGG motifs YHR189W PTH1 One of two mitochondrially-localized peptidyl-tRNA hydrolases YKL198C PTK1 Putative serine/threonine protein kinase YER075C PTP3 Phosphotyrosine-specific protein phosphatase YKR093W PTR2 Integral membrane peptide transporter YMR201C RAD14 Protein that recognizes and binds damaged DNA during NER YDR217C RAD9 DNA damage-dependent checkpoint protein

101

YOR101W RAS1 GTPase involved in G-protein signaling in adenylate cyclase activation YNL098C RAS2 GTP-binding protein YOR265W RBL2 Protein involved in microtubule morphogenesis YNL022C RCM1 rRNA m5C methyltransferase YBR267W REI1 Cytoplasmic pre-60S factor YDR379W RGA2 GTPase-activating protein for polarity-establishment protein Cdc42p YMR283C RIT1 Initiator methionine 2'-O-ribosyl phosphate transferase YPL089C RLM1 MADS-box transcription factor YKL132C RMA1 Putative dihydrofolate synthetase YLL046C RNP1 Ribonucleoprotein that contains two RNA recognition motifs (RRM) YBL027W RPL19B Ribosomal 60S subunit protein L19B YFR031C-A RPL2A Ribosomal 60S subunit protein L2A YER056C-A RPL34A Ribosomal 60S subunit protein L34A YKR094C RPL40B Ubiquitin-ribosomal 60S subunit protein L40B fusion protein YNL162W RPL42A Ribosomal 60S subunit protein L42A YGL147C RPL9A Ribosomal 60S subunit protein L9A YDL081C RPP1A Ribosomal stalk protein P1 alpha YOR293W RPS10A Protein component of the small (40S) ribosomal subunit YER131W RPS26B Protein component of the small (40S) ribosomal subunit YPL090C RPS6A Protein component of the small (40S) ribosomal subunit

102

YPL081W RPS9A Protein component of the small (40S) ribosomal subunit YIL093C RSM25 Mitochondrial ribosomal protein of the small subunit YNL254C RTC4 Protein of unknown function YER139C RTR1 CTD phosphatase YOR138C RUP1 Protein that regulates ubiquitination of Rsp5p YER129W SAK1 Upstream serine/threonine kinase for the SNF1 complex YPL273W SAM4 S-adenosylmethionine-homocysteine methyltransferase YDR143C SAN1 Ubiquitin-protein ligase YER087C-B SBH1 Beta subunit of Sec61p ER translocation complex (Sec61p-Sss1p-Sbh1p) YER019C-A SBH2 Ssh1p-Sss1p-Sbh2p complex component YMR272C SCS7 Sphingolipid alpha-hydroxylase YIL113W SDP1 Stress-inducible dual-specificity MAP kinase phosphatase YIL084C SDS3 Component of the Rpd3L histone deacetylase complex YLR268W SEC22 R-SNARE protein YIL076W SEC28 Epsilon-COP subunit of the coatomer YLR292C SEC72 Non-essential subunit of Sec63 complex YAL067C SEO1 Putative permease YJL168C SET2 Histone methyltransferase with a role in transcriptional elongation YOR140W SFL1 Transcriptional repressor and activator YOR021C SFM1 SPOUT methyltransferase YOR007C SGT2 Glutamine-rich cytoplasmic cochaperone YGL228W SHE10 Protein involved in outer spore wall assembly

103

YDR393W SHE9 Protein required for normal mitochondrial morphology YER118C SHO1 Transmembrane osmosensor for filamentous growth and HOG pathways YBR103W SIF2 WD40 repeat-containing subunit of Set3C histone deacetylase complex YJL089W SIP4 C6 zinc cluster transcriptional activator YKR101W SIR1 Protein involved in silencing at mating-type loci HML and HMR YNL167C SKO1 Basic leucine zipper transcription factor of the ATF/CREB family YGR271W SLH1 Putative RNA helicase related to Ski2p YHR030C SLT2 Serine/threonine MAP kinase YOR327C SNC2 Vesicle membrane receptor protein (v-SNARE) YCR033W SNT1 Subunit of the Set3C deacetylase complex YGL127C SOH1 Subunit of the RNA polymerase II mediator complex YDR006C SOK1 Protein of unknown function YER115C SPR6 Protein of unknown function YNL202W SPS19 Peroxisomal 2,4-dienoyl-CoA reductase YDR392W SPT3 Subunit of the SAGA and SAGA-like transcriptional regulatory complexes YLR055C SPT8 Subunit of the SAGA transcriptional regulatory complex YKR091W SRL3 GTB motif (G1/S transcription factor binding) containing protein YCL037C SRO9 Cytoplasmic RNA-binding protein YKR092C SRP40 Nucleolar serine-rich protein YDR293C SSD1 Translational repressor with a role in polar growth and wall integrity

104

YMR183C SSO2 Plasma membrane t-SNARE YPL092W SSU1 Plasma membrane sulfite pump involved in sulfite metabolism YHR178W STB5 Transcription factor YKL178C STE3 Receptor for a factor pheromone YDR463W STP1 Transcription factor YPL057C SUR1 Mannosylinositol phosphorylceramide (MIPC) synthase catalytic subunit YDR320C SWA2 Auxilin-like protein involved in vesicular transport YJL176C SWI3 Subunit of the SWI/SNF chromatin remodeling complex YNR004W SWM2 Protein with a role in snRNA and snoRNA cap trimethylation YDR334W SWR1 Swi2/Snf2-related ATPase YEL048C TCA17 Component of transport protein particle (TRAPP) complex II YKR089C TGL4 Multifunctional lipase/hydrolase/phospholipase YPL157W TGS1 Trimethyl guanosine synthase, conserved nucleolar methyl transferase YKR059W TIF1 Translation initiation factor eIF4A YKL056C TMA19 Protein that associates with ribosomes YJR014W TMA22 Protein of unknown function YMR269W TMA23 Nucleolar protein implicated in ribosome biogenesis YDR105C TMS1 Vacuolar membrane protein of unknown function YGL096W TOS8 Homeodomain-containing protein and putative transcription factor YJL164C TPK1 cAMP-dependent protein kinase catalytic subunit YDR165W TRM82 Catalytic subunit of a tRNA methyltransferase complex

105

YOR115C TRS33 Core component of transport protein particle (TRAPP) complexes I-III YGR166W TRS65 Component of transport protein particle (TRAPP) complex II YDR108W TRS85 Component of transport protein particle (TRAPP) complex III YIL156W UBP7 Ubiquitin-specific protease that cleaves ubiquitin- protein fusions YLR024C UBR2 Cytoplasmic ubiquitin-protein ligase (E3) YLR193C UPS1 Phosphatidic acid transfer protein YKL216W URA1 Dihydroorotate dehydrogenase YMR271C URA10 Minor orotate phosphoribosyltransferase (OPRTase) isozyme YDR520C URC2 Putative Zn(II)2Cys6 motif containing transcription factor YIL008W URM1 Ubiquitin-like protein involved in thiolation of cytoplasmic tRNAs YPR152C URN1 Putative protein of unknown function containing WW and FF domains YOR068C VAM10 Protein involved in vacuole morphogenesis YGL212W VAM7 Vacuolar SNARE protein YKR001C VPS1 Dynamin-like GTPase required for vacuolar sorting YOR069W VPS5 Nexin-1 homolog YDR486C VPS60 Protein involved in late endosome to vacuole transport YLR261C VPS63 Putative protein of unknown function YAL002W VPS8 Membrane-binding component of the CORVET complex YML097C VPS9 Guanine nucleotide exchange factor (GEF)

106

YFL004W VTC2 Subunit of vacuolar transporter chaperone (VTC) complex YOR043W WHI2 Protein required for full activation of the general stress response YDR259C YAP6 Basic leucine zipper (bZIP) transcription factor YAR047C YAR047C Dubious open reading frame YBL081W YBL081W Non-essential protein of unknown function YBR238C YBR238C Mitochondrial membrane protein YNL154C YCK2 Palmitoylated plasma membrane-bound casein kinase I (CK1) isoform YDR090C YDR090C Putative protein of unknown function YDR286C YDR286C Putative protein of unknown function YDR290W YDR290W Dubious open reading frame YDR431W YDR431W Dubious open reading frame YLR020C YEH2 Steryl ester hydrolase YER038W-A YER038W- Mitochondrial protein of unknown function A YER067C-A YER067C-A Dubious open reading frame YER087C-A YER087C-A Dubious open reading frame YER097W YER097W Dubious open reading frame YER135C YER135C Dubious open reading frame YER137C YER137C Putative protein of unknown function YER156C YER156C Putative protein of unknown function YFL032W YFL032W Dubious open reading frame YGR283C YGR283C Putative methyltransferase YHR045W YHR045W Putative protein of unknown function YIL060W YIL060W Mitochondrial protein of unknown function YIL077C YIL077C Putative protein of unknown function YIL161W YIL161W Putative protein of unknown function

107

YJL169W YJL169W Dubious open reading frame YJR107W YJR107W Putative lipase YJR120W YJR120W Protein of unknown function YKL123W YKL123W Dubious open reading frame YKL133C YKL133C Putative protein of unknown function YKL200C YKL200C Merged open reading frame YKL222C YKL222C Protein of unknown function YKR005C YKR005C Putative protein of unknown function YKR015C YKR015C Putative protein of unknown function YKR040C YKR040C Dubious open reading frame YKR047W YKR047W Dubious open reading frame YKR051W YKR051W Putative protein of unknown function YMR284W YKU70 Subunit of the telomeric Ku complex (Yku70p-Yku80p) YLR252W YLR252W Dubious open reading frame YLR278C YLR278C Zinc-cluster protein YLR280C YLR280C Dubious open reading frame YLR294C YLR294C Dubious open reading frame YLR311C YLR311C Dubious open reading frame YLR428C YLR428C Dubious open reading frame YMR302C YME2 Integral inner mitochondrial membrane protein YML057C-A YML057C- Dubious open reading frame A YMR010W YMR010W Putative protein of unknown function YMR031W-A YMR031W Dubious open reading frame -A YMR244W YMR244W Putative protein of unknown function YMR315W YMR315W Protein with NADP(H) oxidoreductase activity YNL013C YNL013C Dubious open reading frame YNL057W YNL057W Dubious open reading frame

108

YNL134C YNL134C NADH-dependent aldehyde reductase, involved in detoxification of furf YNL146W YNL146W Putative protein of unknown function YNL198C YNL198C Dubious open reading frame YNL296W YNL296W Dubious open reading frame unlikely to encode a functional protein YNR005C YNR005C Dubious open reading frame YOR097C YOR097C Putative protein of unknown function YOR139C YOR139C Dubious open reading frame YOR376W YOR376W Dubious open reading frame YPL080C YPL080C Dubious open reading frame YPL088W YPL088W Putative aryl alcohol dehydrogenase YPL102C YPL102C Dubious open reading frame YPL107W YPL107W Putative protein of unknown function YPR011C YPR011C Mitochondrial transporter YPR012W YPR012W Dubious open reading frame YPR015C YPR015C Putative zinc finger transcription factor YPR096C YPR096C Protein of unknown function YER031C YPT31 Rab family GTPase YGL210W YPT32 Rab family GTPase involved in the exocytic pathway YHR105W YPT35 Endosomal protein of unknown function YML001W YPT7 Rab family GTPase YGL255W ZRT1 High-affinity zinc transporter of the plasma membrane

109

Table 9 HMG1 - S288C genetic interactions

ORF Gene Description YCL025C AGP1 Low-affinity amino acid permease with broad substrate range YKL114C APN1 Major apurinic/apyrimidinic endonuclease YML022W APT1 Adenine phosphoribosyltransferase YHL040C ARN1 ARN family transporter for siderophore-iron chelates YLR085C ARP6 Actin-related protein that binds nucleosomes YNL259C ATX1 Cytosolic copper metallochaperone YER167W BCK2 Serine/threonine-rich protein involved in PKC1 signaling pathway YFL007W BLM10 Proteasome activator YER177W BMH1 14-3-3 protein, major isoform YNL233W BNI4 Targeting subunit for Glc7p protein phosphatase YNL275W BOR1 Boron efflux transporter of the plasma membrane YDL074C BRE1 E3 ubiquitin ligase YGL029W CGR1 Protein involved in nucleolar integrity and processing of pre-rRNA 110

YER164W CHD1 Chromatin remodeler that regulates various aspects of transcription YLR330W CHS5 Component of the exomer complex YML057W CMP2 Calcineurin A YKL190W CNB1 Calcineurin B YJR109C CPA2 Large subunit of carbamoyl phosphate synthetase YJR032W CPR7 Peptidyl-prolyl cis-trans isomerase (cyclophilin) YBR036C CSG2 Endoplasmic reticulum membrane protein YML054C CYB2 Cytochrome b2 (L-lactate cytochrome-c oxidoreductase) YIR023W DAL81 Positive regulator of genes in multiple nitrogen degradation pathways YGR092W DBF2 Ser/Thr kinase involved in transcription and stress response YER179W DMC1 Meiosis-specific recombinase required for double- strand break repair YGL043W DST1 General transcription elongation factor TFIIS YPL046C ELC1 Elongin C, conserved among eukaryotes YLL038C ENT4 Protein of unknown function YLR065C ENV10 Protein proposed to be involved in vacuolar functions YNL080C EOS1 Protein involved in N-glycosylation YNL280C ERG24 C-14 sterol reductase YML067C ERV41 Protein localized to COPII-coated vesicles YJL157C FAR1 CDK inhibitor and nuclear anchor YER056C FCY2 Purine-cytosine permease YIL065C FIS1 Protein involved in mitochondrial fission and peroxisome abundance YBL016W FUS3 Mitogen-activated serine/threonine protein kinase involved in mating

111

YML051W GAL80 Transcriptional regulator involved in the repression of GAL genes YNL255C GIS2 Translational activator for mRNAs with internal ribosome entry sites YML121W GTR1 Cytoplasmic GTPase YGL237C HAP2 Subunit of the Hap2p/3p/4p/5p CCAAT-binding complex YNL021W HDA1 Putative catalytic subunit of a class II histone deacetylase complex YPR179C HDA3 Subunit of the HDA1 histone deacetylase complex YJR140C HIR3 Subunit of the HIR complex YLR450W HMG2 HMG-CoA reductase YGL194C HOS2 Histone deacetylase and subunit of Set3 and Rpd3L complexes YIL090W ICE2 Integral ER membrane protein with type-III transmembrane domains YFL013C IES1 Subunit of the INO80 chromatin remodeling complex YER092W IES5 Non-essential INO80 chromatin remodeling complex subunit YDR123C INO2 Transcription factor YOR235W IRC13 Dubious open reading frame YJR054W KCH1 Potassium transporter that mediates K+ influx YNL238W KEX2 Kexin, a subtilisin-like protease (proprotein convertase) YHR081W LRP1 Nuclear exosome-associated nucleic acid binding protein YKL176C LST4 Protein possibly involved in a post-Golgi secretory pathway YBR115C LYS2 Alpha aminoadipate reductase

112

YIL070C MAM33 Specific translational activator for the mitochondrial COX1 mRNA YKR007W MEH1 Component of the EGO and GSE complexes YDR245W MNN10 Subunit of a Golgi mannosyltransferase complex YIR002C MPH1 3'-5' DNA helicase involved in error-free bypass of DNA lesions YJL066C MPM1 Mitochondrial intermembrane space protein of unknown function YGL136C MRM2 Mitochondrial 2' O-ribose methyltransferase YNL295W MRX6 Protein that associates with mitochondrial ribosome YDR128W MTC5 Subunit of SEACAT, a subcomplex of the SEA complex YDR162C NBP2 Protein involved in the HOG (high osmolarity glycerol) pathway YKL040C NFU1 Protein involved in iron metabolism in mitochondria YDL002C NHP10 Non-essential INO80 chromatin remodeling complex subunit YML059C NTE1 Serine esterase YML060W OGG1 Nuclear and mitochondrial glycosylase/lyase YJR073C OPI3 Methylene-fatty-acyl-phospholipid synthase YPR194C OPT2 Oligopeptide transporter YGR038W ORM1 Protein that mediates sphingolipid homeostasis YFL044C OTU1 Deubiquitylation enzyme that binds to the chaperone- ATPase Cdc48p YEL049W PAU2 Member of the seripauperin multigene family YNL003C PET8 S-adenosylmethionine transporter of the mitochondrial inner membrane YJL210W PEX2 RING-finger peroxin and E3 ubiquitin ligase YGR077C PEX8 Intraperoxisomal organizer of the peroxisomal import machinery

113

YBR093C PHO5 Repressible acid phosphatase YGL059W PKP2 Mitochondrial protein kinase YML047C PRM6 Potassium transporter that mediates K+ influx YKL116C PRR1 Serine/threonine protein kinase YMR201C RAD14 Protein that recognizes and binds damaged DNA during NER YER162C RAD4 Protein that recognizes and binds damaged DNA (with Rad23p) during NER YER095W RAD51 Strand exchange protein YDR004W RAD57 Protein that stimulates strand exchange YBR005W RCR1 Protein of the ER membrane involved in cell wall chitin deposition YJL204C RCY1 F-box protein involved in recycling endocytosed proteins YBR267W REI1 Cytoplasmic pre-60S factor YOR275C RIM20 Protein involved in proteolytic activation of Rim101p YNL294C RIM21 pH sensor molecule, component of the RIM101 pathway YGL045W RIM8 Protein involved in proteolytic activation of Rim101p YOR312C RPL20B Ribosomal 60S subunit protein L20B YDR471W RPL27B Ribosomal 60S subunit protein L27B YER056C-A RPL34A Ribosomal 60S subunit protein L34A YLR448W RPL6B Ribosomal 60S subunit protein L6B YGL147C RPL9A Ribosomal 60S subunit protein L9A YDL020C RPN4 Transcription factor that stimulates expression of proteasome genes YDL130W RPP1B Ribosomal protein P1 beta YOR293W RPS10A Protein component of the small (40S) ribosomal subunit

114

YML026C RPS18B Protein component of the small (40S) ribosomal subunit YNL302C RPS19B Protein component of the small (40S) ribosomal subunit YML063W RPS1B Ribosomal protein 10 (rp10) of the small (40S) subunit YJL136C RPS21B Protein component of the small (40S) ribosomal subunit YGR027C RPS25A Protein component of the small (40S) ribosomal subunit YLR264W RPS28B Protein component of the small (40S) ribosomal subunit YMR030W RSF1 Protein required for respiratory growth YDR159W SAC3 mRNA export factor YFR040W SAP155 Protein required for function of the Sit4p protein phosphatase YDR181C SAS4 Subunit of the SAS complex (Sas2p, Sas4p, Sas5p) YDR469W SDC1 Subunit of the COMPASS (Set1C) complex YEL057C SDD1 Protein of unknown function YOR184W SER1 3-phosphoserine aminotransferase YNL257C SIP3 Putative sterol transfer protein YKR072C SIS2 Negative regulatory subunit of protein phosphatase 1 (Ppz1p) YDL013W SLX5 Subunit of the Slx5-Slx8 SUMO-targeted ubiquitin ligase (STUbL) compl YML066C SMA2 Meiosis-specific prospore membrane protein YOL052C SPE2 S-adenosylmethionine decarboxylase YPR069C SPE3 Spermidine synthase YEL031W SPF1 P-type ATPase, ion transporter of the ER membrane

115

YER161C SPT2 Protein involved in negative regulation of transcription YCL037C SRO9 Cytoplasmic RNA-binding protein YLR452C SST2 GTPase-activating protein for Gpa1p YHR178W STB5 Transcription factor YCL032W STE50 Adaptor protein for various signaling pathways YML052W SUR7 Plasma membrane protein, component of eisosomes YNR004W SWM2 Protein with a role in snRNA and snoRNA cap trimethylation YKL081W TEF4 Gamma subunit of translational elongation factor eEF1B YCR053W THR4 Threonine synthase YJL138C TIF2 Translation initiation factor eIF4A YER184C TOG1 Transcriptional activator of oleate genes YDR074W TPS2 Phosphatase subunit of the trehalose-6-P synthase/phosphatase complex YNL299W TRF5 Non-canonical poly(A) polymerase YOR006C TSR3 Protein required for 20S pre-rRNA processing YEL012W UBC8 Ubiquitin-conjugating enzyme that regulates gluconeogenesis YER151C UBP3 Ubiquitin-specific protease involved in transport and osmotic response YFR010W UBP6 Ubiquitin-specific protease YOR106W VAM3 Syntaxin-like vacuolar t-SNARE YGL212W VAM7 Vacuolar SNARE protein YMR088C VBA1 Permease of basic amino acids in the vacuolar membrane YHR012W VPS29 Subunit of the membrane-associated retromer complex

116

YDR080W VPS41 Subunit of the HOPS endocytic tethering complex YJL029C VPS53 Component of the GARP (Golgi-associated retrograde protein) complex YJR126C VPS70 Protein of unknown function involved in vacuolar protein sorting YLR337C VRP1 Verprolin, proline-rich actin-associated protein YNL283C WSC2 Sensor-transducer of the stress-activated PKC1-MPK1 signaling pathway YCL074W YCL074W Pseudogene: encodes fragment of Ty Pol protein YDL144C YDL144C Protein of unknown function YDL199C YDL199C Putative transporter YEL041W YEF1 ATP-NADH kinase YEL010W YEL010W Dubious open reading frame YEL067C YEL067C Putative protein of unknown function YER181C YER181C Dubious open reading frame YFL012W-A YFL012W-A Dubious open reading frame YFL013W-A YFL013W-A Dubious open reading frame YGL214W YGL214W Dubious open reading frame YDR451C YHP1 Homeobox transcriptional repressor YIL012W YIL012W Dubious open reading frame YIL067C YIL067C Uncharacterized protein of unknown function YLR200W YKE2 Subunit of the heterohexameric Gim/prefoldin protein complex YKL069W YKL069W Methionine-R-sulfoxide reductase YKR023W YKR023W Putative protein of unknown function YML057C-A YML057C-A Dubious open reading frame YMR031W- YMR031W- Dubious open reading frame A A YNL171C YNL171C Dubious open reading frame

117

YKL214C YRA2 Member of the REF (RNA and export factor binding proteins) family YFL052W ZNF1 Zinc cluster transcription factor that regulates respiratory growth

Table 10 HMG1 - Y55 genetic interactions

ORF Gene Description YLR040C AFB1 MATalpha-specific a-factor blocker YNR044W AGA1 Anchorage subunit of a-agglutinin of a-cells YPR021C AGC1 Mitochondrial amino acid transporter YDR524C AGE1 ADP-ribosylation factor (ARF) GTPase activating protein (GAP) effector YIL044C AGE2 ADP-ribosylation factor (ARF) GTPase activating protein (GAP) effector YIL087C AIM19 Putative protein of unknown function YML050W AIM32 Putative protein of unknown function YPR029C APL4 Gamma-adaptin YHL019C APM2 Protein of unknown function YLR170C APS1 Small subunit of the clathrin-associated adaptor complex AP-1 YDR441C APT2 Potential adenine phosphoribosyltransferase YOL058W ARG1 Arginosuccinate synthetase YLR085C ARP6 Actin-related protein that binds nucleosomes YNR020C ATP23 Putative metalloprotease of the mitochondrial inner membrane YJL020C BBC1 Protein possibly involved in assembly of actin patches YER155C BEM2 Rho GTPase activating protein (RhoGAP)

118

YPL115C BEM3 Rho GTPase activating protein (RhoGAP) YOR304C-A BIL1 Protein that binds Bud6p and has a role in actin cable assembly YLR063W BMT6 Methyltransferase required for m3U2843 methylation of the 25S rRNA YNL275W BOR1 Boron efflux transporter of the plasma membrane YCR032W BPH1 Protein homologous to Chediak-Higashi syndrome and Beige proteins YDL074C BRE1 E3 ubiquitin ligase YML111W BUL2 Component of the Rsp5p E3-ubiquitin ligase complex YML102W CAC2 Subunit of chromatin assembly factor I (CAF-1), with Rlf2p and Msi1p YDR423C CAD1 AP-1-like basic leucine zipper (bZIP) transcriptional activator YFL028C CAF16 Part of evolutionarily-conserved CCR4-NOT regulatory complex YOR112W CEX1 Component of nuclear aminoacylation-dependent tRNA export pathway YML036W CGI121 Component of the EKC/KEOPS complex YML057W CMP2 Calcineurin A YCR069W CPR4 Peptidyl-prolyl cis-trans isomerase (cyclophilin) YDR304C CPR5 Peptidyl-prolyl cis-trans isomerase (cyclophilin) of the ER YOR100C CRC1 Mitochondrial inner membrane carnitine transporter YBR161W CSH1 Mannosylinositol phosphorylceramide (MIPC) synthase catalytic subunit YOL007C CSI2 Protein of unknown function YPR030W CSR2 Nuclear ubiquitin protein ligase binding protein YML112W CTK3 Gamma subunit of C-terminal domain kinase I

119

YML101C CUE4 Protein of unknown function YDR482C CWC21 Protein involved in RNA splicing by the spliceosome YML054C CYB2 Cytochrome b2 (L-lactate cytochrome-c oxidoreductase) YOR311C DGK1 Diacylglycerol kinase YKR035W-A DID2 Class E protein of the vacuolar protein-sorting (Vps) pathway YDR440W DOT1 Nucleosomal histone H3-Lys79 methylase YIL010W DOT5 Nuclear thiol peroxidase YEL030W ECM10 Heat shock protein of the Hsp70 family YER035W EDC2 RNA-binding protein that directly activates mRNA decapping YEL015W EDC3 Non-essential conserved protein with a role in mRNA decapping YDR036C EHD3 3-hydroxyisobutyryl-CoA hydrolase YDR512C EMI1 Non-essential protein of unknown function YHR110W ERP5 Protein with similarity to Emp24p and Erv25p YCR075C ERS1 Protein with similarity to human cystinosin YBR239C ERT1 Transcriptional regulator YPR037C ERV2 Flavin-linked sulfhydryl oxidase localized to the ER lumen YBR041W FAT1 Very long chain fatty acyl-CoA synthetase and fatty acid transporter YER060W FCY21 Putative purine-cytosine permease YER032W FIR1 Protein involved in 3' mRNA processing YDR519W FPR2 Membrane-bound peptidyl-prolyl cis-trans isomerase (PPIase) YAL022C FUN26 High affinity, broad selectivity, nucleoside/nucleobase transporter

120

YOR183W FYV12 Protein of unknown function YGR196C FYV8 Protein of unknown function YDR009W GAL3 Transcriptional regulator YML051W GAL80 Transcriptional regulator involved in the repression of GAL genes YJR040W GEF1 Voltage-gated chloride channel YEL003W GIM4 Subunit of the heterohexameric cochaperone prefoldin complex YOR040W GLO4 Mitochondrial glyoxalase II YAL056W GPB2 Multistep regulator of cAMP-PKA signaling YOL056W GPM3 Homolog of Gpm1p phosphoglycerate mutase YGL084C GUP1 Plasma membrane protein involved in remodeling GPI anchors YFL027C GYP8 GTPase-activating protein for yeast Rab family members YFL031W HAC1 Basic leucine zipper (bZIP) transcription factor (ATF/CREB1 homolog) YEL056W HAT2 Subunit of the Hat1p-Hat2p histone acetyltransferase complex YDR458C HEH2 Inner nuclear membrane (INM) protein YOR038C HIR2 Subunit of HIR nucleosome assembly complex YDR528W HLR1 Protein involved in regulation of cell wall composition and integrity YLR450W HMG2 HMG-CoA reductase YLR113W HOG1 Mitogen-activated protein kinase involved in osmoregulation YER052C HOM3 Aspartate kinase (L-aspartate 4-P-transferase) YEL066W HPA3 D-Amino acid N-acetyltransferase that detoxifies D- amino acids

121

YLR207W HRD3 ER membrane protein that plays a central role in ERAD YDR191W HST4 NAD(+)-dependent protein deacetylase YHR067W HTD2 Mitochondrial 3-hydroxyacyl-thioester dehydratase YOL012C HTZ1 Histone variant H2AZ YJL214W HXT8 Protein of unknown function with similarity to hexose transporters YML056C IMD4 Inosine monophosphate dehydrogenase YDR072C IPT1 Inositolphosphotransferase YDR332W IRC3 Double-stranded DNA-dependent helicase of the DExH/D-box family YHR079C IRE1 Serine-threonine kinase and endoribonuclease YOR304W ISW2 ATP-dependent DNA translocase involved in chromatin remodeling YDR497C ITR1 Myo-inositol transporter YJL162C JJJ2 Protein of unknown function YDR532C KRE28 Subunit of a kinetochore-microtubule binding complex YKL205W LOS1 Nuclear pore protein YOR084W LPX1 Peroxisomal matrix-localized lipase YDL240W LRG1 GTPase-activating protein (GAP) YJL100W LSB6 Type II phosphatidylinositol 4-kinase YNL268W LYP1 Lysine permease YDR034C LYS14 Transcriptional activator involved in regulating lysine biosynthesis YDR234W LYS4 Homoaconitase YJL199C MBB1 Dubious open reading frame YOL126C MDH2 Cytoplasmic malate dehydrogenase YAL010C MDM10 Subunit of both the ERMES and the SAM complex

122

YOL111C MDY2 Protein involved in inserting tail-anchored proteins into ER membranes YNL277W MET2 L-homoserine-O-acetyltransferase YGL257C MNT2 Mannosyltransferase YDL079C MRK1 Glycogen synthase kinase 3 (GSK-3) homolog YKL142W MRP8 Protein of unknown function YNL284C MRPL10 Mitochondrial ribosomal protein of the large subunit YBR122C MRPL36 Mitochondrial ribosomal protein of the large subunit YNR022C MRPL50 Mitochondrial ribosomal protein of the large subunit YDL027C MRX9 Protein that associates with mitochondrial ribosome YDR128W MTC5 Subunit of SEACAT, a subcomplex of the SEA complex YJL205C NCE101 Protein of unknown function YOL104C NDJ1 Protein that regulates meiotic SPB cohesion and telomere clustering YOL041C NOP12 Nucleolar protein involved in pre-25S rRNA processing YDR026C NSI1 RNA polymerase I termination factor YML059C NTE1 Serine esterase YDR001C NTH1 Neutral trehalase, degrades trehalose YDR150W NUM1 Protein required for nuclear migration YKL068W NUP100 FG-nucleoporin component of central core of the nuclear pore complex YML103C NUP188 Subunit of the inner ring of the nuclear pore complex (NPC) YDL089W NUR1 Protein involved in regulation of mitotic exit YHL029C OCA5 Cytoplasmic protein required for replication of Brome mosaic virus YML060W OGG1 Nuclear and mitochondrial glycosylase/lyase YGR038W ORM1 Protein that mediates sphingolipid homeostasis

123

YML019W OST6 Subunit of the oligosaccharyltransferase complex of the ER lumen YDR071C PAA1 Polyamine acetyltransferase YDR488C PAC11 Dynein intermediate chain, microtubule motor protein YDL173W PAR32 Putative protein of unknown function YBR186W PCH2 Hexameric ring ATPase that remodels chromosome axis protein Hop1p YDR406W PDR15 Plasma membrane ATP binding cassette (ABC) transporter YBL017C PEP1 Type I transmembrane sorting receptor for multiple vacuolar hydrolases YJL053W PEP8 Vacuolar protein component of the retromer YCR044C PER1 Protein of the endoplasmic reticulum YDR479C PEX29 Peroxisomal integral membrane peroxin YDR142C PEX7 Peroxisomal signal receptor for peroxisomal matrix proteins YKL043W PHD1 Transcriptional activator that enhances pseudohyphal growth YDR481C PHO8 Repressible vacuolar alkaline phosphatase YPL036W PMA2 Plasma membrane H+-ATPase YCR014C POL4 DNA polymerase IV YDL134C PPH21 Catalytic subunit of protein phosphatase 2A (PP2A) YML047C PRM6 Potassium transporter that mediates K+ influx YDL214C PRR2 Serine/threonine protein kinase YBL056W PTC3 Type 2C protein phosphatase (PP2C) YCR079W PTC6 Mitochondrial type 2C protein phosphatase (PP2C) YHR076W PTC7 Type 2C serine/threonine protein phosphatase (PP2C)

124

YOL114C PTH4 Protein similar to the human peptidyl-tRNA hydrolase gene ICT1 YGL062W PYC1 Pyruvate carboxylase isoform YJR033C RAV1 Subunit of RAVE complex (Rav1p, Rav2p, Skp1p) YDR202C RAV2 Subunit of RAVE complex (Rav1p, Rav2p, Skp1p) YDR003W RCR2 Vacuolar protein YMR182C RGM1 Putative zinc finger DNA binding transcription factor YDR198C RKM2 Ribosomal protein lysine methyltransferase YDR255C RMD5 Component of GID Complex that confers ubiquitin ligase (U3) activity YJL148W RPA34 RNA polymerase I subunit A34.5 YJL121C RPE1 D-ribulose-5-phosphate 3-epimerase YOR312C RPL20B Ribosomal 60S subunit protein L20B YDL083C RPS16B Protein component of the small (40S) ribosomal subunit YML063W RPS1B Ribosomal protein 10 (rp10) of the small (40S) subunit YKL156W RPS27A Protein component of the small (40S) ribosomal subunit YNL254C RTC4 Protein of unknown function YOL067C RTG1 Transcription factor (bHLH) involved in interorganelle communication YDL025C RTK1 Putative protein kinase, potentially phosphorylated by Cdc28p YDR159W SAC3 mRNA export factor YBR171W SEC66 Non-essential subunit of Sec63 complex YDR077W SED1 Major stress-induced structural GPI-cell wall glycoprotein YKR029C SET3 Defining member of the SET3 histone deacetylase complex

125

YOR035C SHE4 Protein containing a UCS (UNC-45/CRO1/SHE4) domain YLR442C SIR3 Silencing protein YEL065W SIT1 Ferrioxamine B transporter YBR228W SLX1 Endonuclease involved in DNA recombination and repair YLR034C SMF3 Putative divalent metal ion transporter involved in iron homeostasis YDL194W SNF3 Plasma membrane low glucose sensor, regulates glucose transport YDR006C SOK1 Protein of unknown function YCR073W-A SOL2 Protein with a possible role in tRNA export YML055W SPC2 Subunit of signal peptidase complex YEL031W SPF1 P-type ATPase, ion transporter of the ER membrane YML034W SRC1 Inner nuclear membrane protein YAL005C SSA1 ATPase involved in protein folding and NLS-directed nuclear transport YNR031C SSK2 MAP kinase kinase kinase of HOG1 mitogen-activated signaling pathway YMR019W STB4 Putative transcription factor YKL178C STE3 Receptor for a factor pheromone YML052W SUR7 Plasma membrane protein, component of eisosomes YJL187C SWE1 Protein kinase that regulates the G2/M transition YLR182W SWI6 Transcription cofactor YDR334W SWR1 Swi2/Snf2-related ATPase YEL048C TCA17 Component of transport protein particle (TRAPP) complex II YOR086C TCB1 Lipid-binding ER protein involved in ER-plasma membrane tethering

126

YMR291W TDA1 Protein kinase of unknown cellular role YOR337W TEA1 Ty1 enhancer activator involved in Ty enhancer- mediated transcription YOR352W TFB6 Subunit of TFIIH complex YKR059W TIF1 Translation initiation factor eIF4A YER011W TIR1 Cell wall mannoprotein YLR327C TMA10 Protein of unknown function that associates with ribosomes YDR117C TMA64 Protein of unknown function that associates with ribosomes YBR162C TOS1 Covalently-bound cell wall protein of unknown function YIL138C TPM2 Minor isoform of tropomyosin YPR156C TPO3 Polyamine transporter of the major facilitator superfamily YDL201W TRM8 Noncatalytic subunit of a tRNA methyltransferase complex YOR115C TRS33 Core component of transport protein particle (TRAPP) complexes I-III YGR166W TRS65 Component of transport protein particle (TRAPP) complex II YML028W TSA1 Thioredoxin peroxidase YML100W TSL1 Large subunit of trehalose 6-phosphate synthase/phosphatase complex YDL091C UBX3 Subunit of the DSC ubiquitin ligase complex YDR207C UME6 Rpd3L histone deacetylase complex subunit YDL185W VMA1 Subunit A of the V1 peripheral membrane domain of V-ATPase

127

YOL105C WSC3 Sensor-transducer of the stress-activated PKC1-MPK1 signaling pathway YPL239W YAR1 Ankyrin-repeat containing, nucleocytoplasmic shuttling chaperone YBL029W YBL029W Non-essential protein of unknown function YBR027C YBR027C Dubious open reading frame YBR138C YBR138C Cytoplasmic protein of unknown function YBR259W YBR259W Protein of unknown function YCL001W-A YCL001W- Putative protein of unknown function A YCL023C YCL023C Dubious open reading frame YCL026C YCL026C Deleted ORF YCR001W YCR001W Dubious open reading frame YCR087C-A YCR087C-A Putative protein of unknown function YDL023C YDL023C Dubious open reading frame YDL118W YDL118W Dubious open reading frame, unlikely to encode a protein YDR029W YDR029W Dubious open reading frame YDR209C YDR209C Dubious open reading frame YDR210W YDR210W Predicted tail-anchored plasma membrane protein YEL004W YEA4 Uridine diphosphate-N-acetylglucosamine (UDP- GlcNAc) transporter YEL067C YEL067C Putative protein of unknown function YEL068C YEL068C Protein of unknown function YER034W YER034W Protein of unknown function YER046W-A YER046W- Dubious open reading frame A YER152C YER152C Protein with 2-aminoadipate transaminase activity YFL032W YFL032W Dubious open reading frame

128

YFL034W YFL034W Putative integral membrane protein that interacts with Rpp0p YGL177W YGL177W Dubious open reading frame YGL230C YGL230C Putative protein of unknown function YGL242C YGL242C Protein of unknown function YGR051C YGR051C Dubious open reading frame YGR122W YGR122W Protein that may be involved in pH regulation YGR130C YGR130C Component of the eisosome with unknown function YIL060W YIL060W Mitochondrial protein of unknown function YIL165C YIL165C Putative protein of unknown function YJL064W YJL064W Dubious open reading frame YJL169W YJL169W Dubious open reading frame YKL177W YKL177W Dubious open reading frame YKR051W YKR051W Putative protein of unknown function YLR031W YLR031W Putative protein of unknown function YLR152C YLR152C Putative protein of unknown function YLR281C YLR281C Putative protein of unknown function YML038C YMD8 Putative nucleotide sugar transporter YML033W YML033W Merged open reading frame YML047W-A YML047W- Dubious open reading frame A YML057C-A YML057C- Dubious open reading frame A YML099W-A YML099W- Dubious open reading frame A YML100W-A YML100W- Putative protein of unknown function A YML101C-A YML101C- Dubious open reading frame A

129

YNR021W YNR021W Putative protein of unknown function YOL153C YOL153C Blocked reading frame, contains two in-frame stops in translation YOR015W YOR015W Dubious open reading frame YOR263C YOR263C Dubious open reading frame YPR053C YPR053C Dubious open reading frame YER031C YPT31 Rab family GTPase YBR111C YSA1 Nudix hydrolase family member with ADP-ribose pyrophosphatase activity YHR016C YSC84 Actin-binding protein YBR046C ZTA1 NADPH-dependent quinone reductase

Table 11 HMG1 - SK1 genetic interactions

ORF Gene Description YOR128C ADE2 Phosphoribosylaminoimidazole carboxylase

130

YMR009W ADI1 Acireductone dioxygenease involved in methionine salvage pathway YDR214W AHA1 Co-chaperone that binds Hsp82p and activates its ATPase activity YCR082W AHC2 Component of the ADA histone acetyltransferase complex YJL046W AIM22 Putative lipoate-protein ligase YMR003W AIM34 Protein of unknown function YBR059C AKL1 Ser-Thr protein kinase YJL122W ALB1 Shuttling pre-60S factor YBL082C ALG3 Dolichol-P-Man dependent alpha(1-3) mannosyltransferase YOR002W ALG6 Alpha 1,3 glucosyltransferase YOR067C ALG8 Glucosyl transferase YJL084C ALY2 Alpha arrestin YKL157W APE2 Aminopeptidase yscII YHL019C APM2 Protein of unknown function YBR288C APM3 Mu3-like subunit of the clathrin associated protein complex (AP-3) YPR192W AQY1 Spore-specific water channel YPR060C ARO7 Chorismate mutase YLR085C ARP6 Actin-related protein that binds nucleosomes YJL115W ASF1 Nucleosome assembly factor YDL088C ASM4 FG-nucleoporin component of central core of nuclear pore complex (NPC) YOR079C ATX2 Golgi membrane protein involved in manganese homeostasis YFL010W-A AUA1 Protein required for the negative regulation by ammonia of Gap1p

131

YOR011W AUS1 Plasma membrane sterol transporter of the ATP- binding cassette family YNL101W AVT4 Vacuolar transporter YKR027W BCH2 Member of the ChAPs (Chs5p-Arf1p-binding proteins) family YJL095W BCK1 MAPKKK acting in the protein kinase C signaling pathway YNL233W BNI4 Targeting subunit for Glc7p protein phosphatase YGL007W BRP1 Dubious ORF located in the upstream region of PMA1 YDR275W BSC2 Protein of unknown function YGR188C BUB1 Protein kinase involved in the cell cycle checkpoint into anaphase YGL174W BUD13 Subunit of the RES complex YKL092C BUD2 GTPase activating factor for Rsr1p/Bud1p YOR078W BUD21 Component of small ribosomal subunit (SSU) processosome YML102W CAC2 Subunit of chromatin assembly factor I (CAF-1), with Rlf2p and Msi1p YDR423C CAD1 AP-1-like basic leucine zipper (bZIP) transcriptional activator YFL028C CAF16 Part of evolutionarily-conserved CCR4-NOT regulatory complex YKL007W CAP1 Alpha subunit of the capping protein heterodimer (Cap1p and Cap2p) YER061C CEM1 Mitochondrial beta-keto-acyl synthase YGR157W CHO2 Phosphatidylethanolamine methyltransferase (PEMT) YJL099W CHS6 Member of the ChAPs (Chs5p-Arf1p-binding proteins) family YGL019W CKB1 Beta regulatory subunit of casein kinase 2 (CK2)

132

YPR119W CLB2 B-type cyclin involved in cell cycle progression YPR120C CLB5 B-type cyclin involved in DNA replication during S phase YPR013C CMR3 Putative zinc finger protein YKL190W CNB1 Calcineurin B YIL157C COA1 Mitochondrial inner membrane protein YNL052W COX5A Subunit Va of cytochrome c oxidase YDR155C CPR1 Cytoplasmic peptidyl-prolyl cis-trans isomerase (cyclophilin) YJR032W CPR7 Peptidyl-prolyl cis-trans isomerase (cyclophilin) YOR031W CRS5 Copper-binding metallothionein YOL007C CSI2 Protein of unknown function YCR086W CSM1 Nucleolar protein that mediates homolog segregation during meiosis I YMR078C CTF18 Subunit of a complex with Ctf8p YPR135W CTF4 Chromatin-associated protein YML112W CTK3 Gamma subunit of C-terminal domain kinase I YML101C CUE4 Protein of unknown function YNL155W CUZ1 Protein with a role in the ubiquitin-proteasome pathway YML054C CYB2 Cytochrome b2 (L-lactate cytochrome-c oxidoreductase) YNL111C CYB5 Cytochrome b5 YOR037W CYC2 Mitochondrial peripheral inner membrane protein YOR030W DFG16 Probable multiple transmembrane protein YKL121W DGR2 Protein of unknown function YKR035W- DID2 Class E protein of the vacuolar protein-sorting (Vps) A pathway YIR004W DJP1 Cytosolic J-domain-containing protein

133

YJL065C DLS1 Subunit of ISW2/yCHRAC chromatin accessibility complex YDR093W DNF2 Aminophospholipid translocase (flippase) YMR162C DNF3 Trans-golgi network aminophospholipid translocase (flippase) YOR005C DNL4 DNA ligase required for nonhomologous end-joining (NHEJ) YDR440W DOT1 Nucleosomal histone H3-Lys79 methylase YIL103W DPH1 Protein required for synthesis of diphthamide YDR370C DXO1 mRNA 5'-end-capping quality-control protein YMR299C DYN3 Dynein light intermediate chain (LIC) YDR206W EBS1 Protein involved in translation inhibition and nonsense-mediated decay YDR446W ECM11 Meiosis-specific protein YHR132C ECM14 Putative metalloprotease with similarity to zinc carboxypeptidases YHL030W ECM29 Scaffold protein YBR078W ECM33 GPI-anchored protein of unknown function YOR133W EFT1 Elongation factor 2 (EF-2), also encoded by EFT2 YOR144C ELG1 Subunit of an alternative replication factor C complex YLL014W EMC6 Member of conserved ER transmembrane complex YML067C ERV41 Protein localized to COPII-coated vesicles YFR019W FAB1 1-phosphatidylinositol-3-phosphate 5-kinase YPR062W FCY1 Cytosine deaminase YBR101C FES1 Hsp70 (Ssa1p) nucleotide exchange factor YAR050W FLO1 Lectin-like protein involved in flocculation YBL013W FMT1 Methionyl-tRNA formyltransferase YOR381W FRE3 Ferric reductase YCR076C FUB1 Proteasome-binding protein

134

YBL016W FUS3 Mitogen-activated serine/threonine protein kinase involved in mating YBR020W GAL1 Galactokinase YBR019C GAL10 UDP-glucose-4-epimerase YBR018C GAL7 Galactose-1-phosphate uridyl transferase YOR355W GDS1 Protein of unknown function YGL020C GET1 Subunit of the GET complex YMR255W GFD1 Coiled-coiled protein of unknown function YBR045C GIP1 Meiosis-specific regulatory subunit of the Glc7p protein phosphatase YAL031C GIP4 Cytoplasmic protein that regulates protein phosphatase 1 Glc7p YNL255C GIS2 Translational activator for mRNAs with internal ribosome entry sites YML006C GIS4 CAAX box containing protein of unknown function YNL274C GOR1 Glyoxylate reductase YHL031C GOS1 v-SNARE protein involved in Golgi transport YBR121C GRS1 Cytoplasmic and mitochondrial glycyl-tRNA synthase YER174C GRX4 Glutathione-dependent oxidoreductase YML048W GSF2 Endoplasmic reticulum (ER) localized integral membrane protein YDL234C GYP7 GTPase-activating protein for yeast Rab family members YJL165C HAL5 Putative protein kinase YOL089C HAL9 Putative transcription factor containing a zinc finger YBL032W HEK2 RNA binding protein involved in asymmetric localization of ASH1 mRNA YMR161W HLJ1 Co-chaperone for Hsp40p YLR450W HMG2 HMG-CoA reductase

135

YDR158W HOM2 Aspartic beta semi-aldehyde dehydrogenase YPR193C HPA2 Tetrameric histone acetyltransferase YBR215W HPC2 Subunit of the HIR complex YLL026W HSP104 Disaggregase YBR072W HSP26 Small heat shock protein (sHSP) with chaperone activity YOL068C HST1 NAD(+)-dependent histone deacetylase YHR067W HTD2 Mitochondrial 3-hydroxyacyl-thioester dehydratase YOL012C HTZ1 Histone variant H2AZ YIL090W ICE2 Integral ER membrane protein with type-III transmembrane domains YBR157C ICS2 Protein of unknown function YML056C IMD4 Inosine monophosphate dehydrogenase YJL106W IME2 Serine/threonine protein kinase involved in activation of meiosis YJL082W IML2 Protein of unknown function YMR035W IMP2 Catalytic subunit of mitochondrial inner membrane peptidase complex YOR109W INP53 Polyphosphatidylinositol phosphatase YDR315C IPK1 Inositol 1,3,4,5,6-pentakisphosphate 2-kinase YOL015W IRC10 Putative protein of unknown function YOR235W IRC13 Dubious open reading frame YHR079C IRE1 Serine-threonine kinase and endoribonuclease YOR155C ISN1 Inosine 5'-monophosphate (IMP)-specific 5'- nucleotidase YJR050W ISY1 Member of the NineTeen Complex (NTC) YPR061C JID1 Probable Hsp40p co-chaperone YDR475C JIP4 Protein of unknown function YJL094C KHA1 Putative K+/H+ antiporter

136

YAR018C KIN3 Nonessential serine/threonine protein kinase YKL168C KKQ8 Putative serine/threonine protein kinase with unknown cellular role YJL207C LAA1 AP-1 accessory protein YNL071W LAT1 Dihydrolipoamide acetyltransferase component (E2) of the PDC YLL049W LDB18 Component of the dynactin complex YKL073W LHS1 Molecular chaperone of the endoplasmic reticulum lumen YFL018C LPD1 Dihydrolipoamide dehydrogenase YHR081W LRP1 Nuclear exosome-associated nucleic acid binding protein YJL100W LSB6 Type II phosphatidylinositol 4-kinase YJL124C LSM1 Lsm (Like Sm) protein YDR378C LSM6 Lsm (Like Sm) protein YNL147W LSM7 Lsm (Like Sm) protein YKL176C LST4 Protein possibly involved in a post-Golgi secretory pathway YAL024C LTE1 Protein similar to GDP/GTP exchange factors YDL131W LYS21 Homocitrate synthase isozyme YBR297W MAL33 MAL-activator protein YJR024C MDE1 5'-methylthioribulose-1-phosphate dehydratase YPL270W MDL2 Mitochondrial inner membrane half-type ABC transporter YGL219C MDM34 Mitochondrial component of the ERMES complex YPR138C MEP3 Ammonium permease of high capacity and low affinity YBR213W MET8 Bifunctional dehydrogenase and ferrochelatase YDL233W MFG1 Regulator of filamentous growth YGL035C MIG1 Transcription factor involved in glucose repression

137

YKR095W MLP1 Myosin-like protein associated with the nuclear envelope YNL117W MLS1 Malate synthase, enzyme of the glyoxylate cycle YMR166C MME1 Transporter of the mitochondrial inner membrane that exports magnesium YDR245W MNN10 Subunit of a Golgi mannosyltransferase complex YJL183W MNN11 Subunit of a Golgi mannosyltransferase complex YIR002C MPH1 3'-5' DNA helicase involved in error-free bypass of DNA lesions YDR033W MRH1 Protein that localizes primarily to the plasma membrane YPL184C MRN1 RNA-binding protein that may be involved in translational regulation YNL284C MRPL10 Mitochondrial ribosomal protein of the large subunit YBR122C MRPL36 Mitochondrial ribosomal protein of the large subunit YMR188C MRPS17 Mitochondrial ribosomal protein of the small subunit YJL133W MRS3 Iron transporter, mediates Fe2+ transport across inner mito membrane YBL095W MRX3 Protein that associates with mitochondrial ribosome YOR066W MSA1 Activator of G1-specific transcription factors MBF and SBF YOL116W MSN1 Transcriptional activator YDR335W MSN5 Karyopherin YPR134W MSS18 Nuclear encoded protein needed for splicing of mitochondrial intron YBR119W MUD1 U1 snRNP A protein YAL029C MYO4 Type V myosin motor involved in actin-based transport of cargos YOR253W NAT5 Subunit of protein N-terminal acetyltransferase NatA

138

YJL116C NCA3 Protein involved in mitochondrion organization YDR383C NKP1 Central kinetochore protein and subunit of the Ctf19 complex YCR026C NPP1 Nucleotide pyrophosphatase/phosphodiesterase YHL023C NPR3 Subunit of the Iml1p/SEACIT complex YDL167C NRP1 Putative RNA binding protein of unknown function YAL015C NTG1 DNA N-glycosylase and apurinic/apyrimidinic (AP) lyase YBR001C NTH2 Putative neutral trehalase, required for thermotolerance YPR031W NTO1 Subunit of the NuA3 histone acetyltransferase complex YDR150W NUM1 Protein required for nuclear migration YDR179W- NVJ3 Protein with a potential role in tethering ER and A vacuoles YNL056W OCA2 Putative protein of unknown function YCR095C OCA4 Cytoplasmic protein required for replication of Brome mosaic virus YDR316W OMS1 Protein integral to the mitochondrial membrane YPR194C OPT2 Oligopeptide transporter YPR075C OPY2 Integral membrane protein that acts as a membrane anchor for Ste50p YDL232W OST4 Subunit of the oligosaccharyltransferase complex of the ER lumen YGL226C-A OST5 Zeta subunit of the oligosaccharyltransferase complex of the ER lumen YHL013C OTU2 Protein of unknown function YKR065C PAM17 Constituent of the TIM23 complex

139

YGL094C PAN2 Catalytic subunit of the Pan2p-Pan3p poly(A)- ribonuclease complex YPL272C PBI1 Putative protein of unknown function YJL128C PBS2 MAP kinase kinase of the HOG signaling pathway YIL071C PCI8 Possible shared subunit of Cop9 signalosome (CSN) and eIF3 YNL289W PCL1 Cyclin, interacts with cyclin-dependent kinase Pho85p YBL017C PEP1 Type I transmembrane sorting receptor for multiple vacuolar hydrolases YJL053W PEP8 Vacuolar protein component of the retromer YOR158W PET123 Mitochondrial ribosomal protein of the small subunit YJL210W PEX2 RING-finger peroxin and E3 ubiquitin ligase YAL055W PEX22 Putative peroxisomal membrane protein YLR324W PEX30 Peroxisomal integral membrane protein YBR168W PEX32 Peroxisomal integral membrane protein YOL003C PFA4 Palmitoyltransferase with autoacylation activity YBR074W PFF1 Multi-spanning vacuolar membrane protease YMR205C PFK2 Beta subunit of heterooctameric phosphofructokinase YNL097C PHO23 Component of the Rpd3L histone deacetylase complex YBL051C PIN4 Protein involved in G2/M phase progression and response to DNA damage YMR123W PKR1 V-ATPase assembly factor YPL036W PMA2 Plasma membrane H+-ATPase YNL082W PMS1 ATP-binding protein required for mismatch repair YGL037C PNC1 Nicotinamidase that converts nicotinamide to nicotinic acid YOR161C PNS1 Protein of unknown function YJR043C POL32 Third subunit of DNA polymerase delta YHR075C PPE1 Protein with carboxyl methyl esterase activity

140

YDL134C PPH21 Catalytic subunit of protein phosphatase 2A (PP2A) YML047C PRM6 Potassium transporter that mediates K+ influx YBL064C PRX1 Mitochondrial peroxiredoxin with thioredoxin peroxidase activity YNL169C PSD1 Phosphatidylserine decarboxylase of the mitochondrial inner membrane YAL017W PSK1 PAS domain-containing serine/threonine protein kinase YML017W PSP2 Asn rich cytoplasmic protein that contains RGG motifs YER089C PTC2 Type 2C protein phosphatase (PP2C) YBL056W PTC3 Type 2C protein phosphatase (PP2C) YBR125C PTC4 Cytoplasmic type 2C protein phosphatase (PP2C) YMR201C RAD14 Protein that recognizes and binds damaged DNA during NER YML032C RAD52 Protein that stimulates strand exchange YGL163C RAD54 DNA-dependent ATPase that stimulates strand exchange YDR217C RAD9 DNA damage-dependent checkpoint protein YNL098C RAS2 GTP-binding protein YJR033C RAV1 Subunit of RAVE complex (Rav1p, Rav2p, Skp1p) YKL159C RCN1 Protein involved in calcineurin regulation during calcium signaling YBR005W RCR1 Protein of the ER membrane involved in cell wall chitin deposition YJL204C RCY1 F-box protein involved in recycling endocytosed proteins YJR021C REC107 Protein involved in early stages of meiotic recombination

141

YJL217W REE1 Cytoplasmic protein involved in the regulation of enolase (ENO1) YDR379W RGA2 GTPase-activating protein for polarity-establishment protein Cdc42p YPR115W RGC1 Putative regulator of the Fps1p glycerol channel YER067W RGI1 Protein of unknown function YNL180C RHO5 Non-essential small GTPase of the Rho/Rac family of Ras-like proteins YFL033C RIM15 Protein kinase involved in cell proliferation in response to nutrients YBR030W RKM3 Ribosomal lysine methyltransferase YDR255C RMD5 Component of GID Complex that confers ubiquitin ligase (U3) activity YPL024W RMI1 Subunit of the RecQ (Sgs1p) - Topo III (Top3p) complex YGL250W RMR1 Protein required for meiotic recombination and gene conversion YDR156W RPA14 RNA polymerase I subunit A14 YJL121C RPE1 D-ribulose-5-phosphate 3-epimerase YNL069C RPL16B Ribosomal 60S subunit protein L16B YJL177W RPL17B Ribosomal 60S subunit protein L17B YNL301C RPL18B Ribosomal 60S subunit protein L18B YMR194W RPL36A Ribosomal 60S subunit protein L36A YIL148W RPL40A Ubiquitin-ribosomal 60S subunit protein L40A fusion protein YLR448W RPL6B Ribosomal 60S subunit protein L6B YGR214W RPS0A Ribosomal 40S subunit protein S0A YNL302C RPS19B Protein component of the small (40S) ribosomal subunit YLR441C RPS1A Ribosomal protein 10 (rp10) of the small (40S) subunit

142

YML063W RPS1B Ribosomal protein 10 (rp10) of the small (40S) subunit YPR132W RPS23B Ribosomal protein 28 (rp28) of the small (40S) ribosomal subunit YHR203C RPS4B Protein component of the small (40S) ribosomal subunit YPL090C RPS6A Protein component of the small (40S) ribosomal subunit YPL152W RRD2 Peptidyl-prolyl cis/trans-isomerase YBL103C RTG3 bHLH/Zip transcription factor for retrograde (RTG) and TOR pathways YDL204W RTN2 Reticulon protein YDR159W SAC3 mRNA export factor YDR389W SAC7 GTPase activating protein (GAP) for Rho1p YNL083W SAL1 ADP/ATP transporter YPL273W SAM4 S-adenosylmethionine-homocysteine methyltransferase YBL052C SAS3 Histone acetyltransferase catalytic subunit of NuA3 complex YDR181C SAS4 Subunit of the SAS complex (Sas2p, Sas4p, Sas5p) YMR074C SDD2 Protein with homology to human PDCD5 YIL167W SDL1 Blocked reading frame otherwise encoding L-serine dehydratase YIL084C SDS3 Component of the Rpd3L histone deacetylase complex YBR171W SEC66 Non-essential subunit of Sec63 complex YBL066C SEF1 Putative transcription factor YAL067C SEO1 Putative permease YIL099W SGA1 Intracellular sporulation-specific glucoamylase YMR190C SGS1 RecQ family nucleolar DNA helicase YBL031W SHE1 Mitotic spindle protein

143

YOR035C SHE4 Protein containing a UCS (UNC-45/CRO1/SHE4) domain YNL236W SIN4 Subunit of the RNA polymerase II mediator complex YOR076C SKI7 GTP-binding protein that couples the Ski complex and exosome YNL167C SKO1 Basic leucine zipper transcription factor of the ATF/CREB family YDL052C SLC1 1-acyl-sn-glycerol-3-phosphate acyltransferase YGR271W SLH1 Putative RNA helicase related to Ski2p YBR156C SLI15 Subunit of the conserved chromosomal passenger complex (CPC) YAL030W SNC1 Vesicle membrane receptor protein (v-SNARE) YNL086W SNN1 Subunit of the BLOC-1 complex involved in endosomal maturation YNR034W SOL1 Protein with a possible role in tRNA export YEL031W SPF1 P-type ATPase, ion transporter of the ER membrane YJL092W SRS2 DNA helicase and DNA-dependent ATPase YBR169C SSE2 Member of the heat shock protein 70 (HSP70) family YMR183C SSO2 Plasma membrane t-SNARE YHR178W STB5 Transcription factor YDR463W STP1 Transcription factor YHR006W STP2 Transcription factor YDR146C SWI5 Transcription factor that recruits Mediator and Swi/Snf complexes YJL083W TAX4 EH domain-containing protein YBR044C TCM62 Protein involved in assembly of the succinate dehydrogenase complex YLR426W TDA5 Putative protein of unknown function YBR223C TDP1 Tyrosyl-DNA phosphodiesterase I

144

YNL128W TEP1 PTEN homolog with no demonstrated inositol lipid phosphatase activity YJL138C TIF2 Translation initiation factor eIF4A YGL049C TIF4632 Translation initiation factor eIF4G YDR107C TMN2 Protein with a role in cellular adhesion and filamentous growth YER113C TMN3 Protein with a role in cellular adhesion and filamentous growth YBL054W TOD6 PAC motif binding protein involved in rRNA and ribosome biogenesis YOL006C TOP1 Topoisomerase I YLR234W TOP3 DNA Topoisomerase III YGL096W TOS8 Homeodomain-containing protein and putative transcription factor YPR156C TPO3 Polyamine transporter of the major facilitator superfamily YKR050W TRK2 Component of the Trk1p-Trk2p potassium transport system YBR061C TRM7 2'-O-ribose methyltransferase YDR007W TRP1 Phosphoribosylanthranilate isomerase YBR082C UBC4 Ubiquitin-conjugating enzyme (E2) YBR058C UBP14 Ubiquitin-specific protease YJL048C UBX6 UBX (ubiquitin regulatory X) domain-containing protein YDL169C UGX2 Protein of unknown function YAR027W UIP3 Putative integral membrane protein of unknown function YDR213W UPC2 Sterol regulatory element binding protein YLR420W URA4 Dihydroorotase

145

YML106W URA5 Major orotate phosphoribosyltransferase (OPRTase) isozyme YJR103W URA8 Minor CTP synthase isozyme (see also URA7) YDR520C URC2 Putative Zn(II)2Cys6 motif containing transcription factor YPR152C URN1 Putative protein of unknown function containing WW and FF domains YML029W USA1 Scaffold subunit of the Hrd1p ubiquitin ligase YKR105C VBA5 Plasma membrane protein of the Major Facilitator Superfamily (MFS) YOR054C VHS3 Negative regulatory subunit of protein phosphatase 1 Ppz1p YOR270C VPH1 Subunit a of vacuolar-ATPase V0 domain YHR012W VPS29 Subunit of the membrane-associated retromer complex YPR173C VPS4 AAA-ATPase involved in multivesicular body (MVB) protein sorting YOR069W VPS5 Nexin-1 homolog YJL029C VPS53 Component of the GARP (Golgi-associated retrograde protein) complex YOL129W VPS68 Vacuolar membrane protein of unknown function YDR372C VPS74 Golgi phosphatidylinositol-4-kinase effector and PtdIns4P sensor YPL019C VTC3 Subunit of vacuolar transporter chaperone (VTC) complex YJL012C VTC4 Vacuolar membrane polyphosphate polymerase YDL224C WHI4 Putative RNA binding protein YFL010C WWM1 WW domain containing protein of unknown function YAL065C YAL065C Putative protein of unknown function

146

YAL066W YAL066W Dubious open reading frame YAR029W YAR029W Member of DUP240 gene family but contains no transmembrane domains YBL053W YBL053W Dubious open reading frame YBL065W YBL065W Dubious open reading frame YBL096C YBL096C Non-essential protein of unknown function YBR027C YBR027C Dubious open reading frame YBR075W YBR075W Merged open reading frame YBR137W YBR137W Protein with a role in ER delivery of tail-anchored membrane proteins YBR138C YBR138C Cytoplasmic protein of unknown function YBR139W YBR139W Putative serine type carboxypeptidase YBR184W YBR184W Putative protein of unknown function YBR259W YBR259W Protein of unknown function YDR048C YDR048C Dubious open reading frame YDR124W YDR124W Putative protein of unknown function YDR274C YDR274C Dubious open reading frame YDR290W YDR290W Dubious open reading frame YDR455C YDR455C Dubious open reading frame YDR474C YDR474C Merged open reading frame YEL014C YEL014C Dubious open reading frame YFL012W YFL012W Putative protein of unknown function YFL012W-A YFL012W-A Dubious open reading frame YFL013W-A YFL013W-A Dubious open reading frame YFL032W YFL032W Dubious open reading frame YFL034W YFL034W Putative integral membrane protein that interacts with Rpp0p YFL063W YFL063W Dubious open reading frame

147

YDR319C YFT2 Protein required for normal ER membrane biosynthesis YGL042C YGL042C Dubious open reading frame YGR122W YGR122W Protein that may be involved in pH regulation YGR291C YGR291C Dubious open reading frame YMR241W YHM2 Citrate and oxoglutarate carrier protein YDR451C YHP1 Homeobox transcriptional repressor YIL055C YIL055C Putative protein of unknown function YIL060W YIL060W Mitochondrial protein of unknown function YJL007C YJL007C Dubious open reading frame YJL016W YJL016W Putative protein of unknown function YJL064W YJL064W Dubious open reading frame YJL068C YJL068C Esterase that can function as an S-formylglutathione hydrolase YJL181W YJL181W Putative protein of unknown function YJL218W YJL218W Putative acetyltransferase YJR015W YJR015W Putative protein of unknown function YLR200W YKE2 Subunit of the heterohexameric Gim/prefoldin protein complex YKL133C YKL133C Putative protein of unknown function YKL158W YKL158W Merged open reading frame YLR036C YLR036C Putative protein predicted to have transmembrane domains YLR171W YLR171W Dubious open reading frame YBR104W YMC2 Putative mitochondrial inner membrane transporter YML101C-A YML101C-A Dubious open reading frame YMR010W YMR010W Putative protein of unknown function YMR135W- YMR135W-A Dubious open reading frame A

148

YMR153C- YMR153C-A Dubious open reading frame A YMR244W YMR244W Putative protein of unknown function YMR245W YMR245W Dubious open reading frame YNL035C YNL035C Nuclear protein of unknown function YNL109W YNL109W Dubious open reading frame YNL146W YNL146W Putative protein of unknown function YNL190W YNL190W Hydrophilin essential in desiccation-rehydration process YNL303W YNL303W Dubious open reading frame YNL319W YNL319W Dubious open reading frame YNR005C YNR005C Dubious open reading frame YOL085C YOL085C Dubious open reading frame YPR028W YOP1 Membrane protein that interacts with Yip1p to mediate membrane traffic YOR019W YOR019W Protein of unknown function YOR170W YOR170W Dubious open reading frame YOR225W YOR225W Dubious open reading frame YBR183W YPC1 Alkaline ceramidase YBR028C YPK3 AGC kinase YPL080C YPL080C Dubious open reading frame YOL092W YPQ1 Putative vacuolar membrane transporter for cationic amino acids YPR012W YPR012W Dubious open reading frame YPR014C YPR014C Dubious open reading frame YPR027C YPR027C Putative protein of unknown function YPR059C YPR059C Dubious open reading frame YPR117W YPR117W Putative protein of unknown function YPR130C YPR130C Dubious open reading frame

149

YPR196W YPR196W Putative maltose-responsive transcription factor YDR349C YPS7 Putative GPI-anchored aspartic protease YER031C YPT31 Rab family GTPase YML001W YPT7 Rab family GTPase YNL339C YRF1-6 Helicase encoded by the Y' element of subtelomeric regions YGL249W ZIP2 Meiosis-specific protein YMR243C ZRC1 Vacuolar membrane zinc transporter YGL255W ZRT1 High-affinity zinc transporter of the plasma membrane

150

Table 12 HMG2 - S288C genetic interactions

ORF Gene Description YNL141W AAH1 Adenine deaminase (adenine aminohydrolase) YCL025C AGP1 Low-affinity amino acid permease with broad substrate range YML022W APT1 Adenine phosphoribosyltransferase YOR058C ASE1 Mitotic spindle midzone-localized microtubule bundling protein YFL007W BLM10 Proteasome activator YDL074C BRE1 E3 ubiquitin ligase YPL048W CAM1 One of two isoforms of the gamma subunit of eEF1B YLR418C CDC73 Component of the Paf1p complex YGL029W CGR1 Protein involved in nucleolar integrity and processing of pre-rRNA YJR109C CPA2 Large subunit of carbamoyl phosphate synthetase YBR036C CSG2 Endoplasmic reticulum membrane protein YPR135W CTF4 Chromatin-associated protein YIR023W DAL81 Positive regulator of genes in multiple nitrogen degradation pathways YGR092W DBF2 Ser/Thr kinase involved in transcription and stress response

151

YLR437C DIF1 Protein that regulates nuclear localization of Rnr2p and Rnr4p YAL026C DRS2 Trans-golgi network aminophospholipid translocase (flippase) YGL043W DST1 General transcription elongation factor TFIIS YLR443W ECM7 Putative integral membrane protein with a role in calcium uptake YPL046C ELC1 Elongin C, conserved among eukaryotes YNL080C EOS1 Protein involved in N-glycosylation YAL042W ERV46 Protein localized to COPII-coated vesicles YBR026C ETR1 2-enoyl thioester reductase YER060W- FCY22 Putative purine-cytosine permease A YIL065C FIS1 Protein involved in mitochondrial fission and peroxisome abundance YAL008W FUN14 Mitochondrial protein of unknown function YBL016W FUS3 Mitogen-activated serine/threonine protein kinase involved in mating YML121W GTR1 Cytoplasmic GTPase YGL237C HAP2 Subunit of the Hap2p/3p/4p/5p CCAAT-binding complex YNL021W HDA1 Putative catalytic subunit of a class II histone deacetylase complex YPR179C HDA3 Subunit of the HDA1 histone deacetylase complex YML075C HMG1 HMG-CoA reductase YDR158W HOM2 Aspartic beta semi-aldehyde dehydrogenase YGL194C HOS2 Histone deacetylase and subunit of Set3 and Rpd3L complexes

152

YIL090W ICE2 Integral ER membrane protein with type-III transmembrane domains YFL013C IES1 Subunit of the INO80 chromatin remodeling complex YER092W IES5 Non-essential INO80 chromatin remodeling complex subunit YLR432W IMD3 Inosine monophosphate dehydrogenase YDR123C INO2 Transcription factor YOL108C INO4 Transcription factor involved in phospholipid synthesis YMR204C INP1 Peripheral membrane protein of peroxisomes YPL269W KAR9 Karyogamy protein YJR054W KCH1 Potassium transporter that mediates K+ influx YKL176C LST4 Protein possibly involved in a post-Golgi secretory pathway YBR115C LYS2 Alpha aminoadipate reductase YDL078C MDH3 Peroxisomal malate dehydrogenase YLL062C MHT1 S-methylmethionine-homocysteine methyltransferase YDR245W MNN10 Subunit of a Golgi mannosyltransferase complex YJL066C MPM1 Mitochondrial intermembrane space protein of unknown function YDL079C MRK1 Glycogen synthase kinase 3 (GSK-3) homolog YGL136C MRM2 Mitochondrial 2' O-ribose methyltransferase YML128C MSC1 Protein of unknown function YDR128W MTC5 Subunit of SEACAT, a subcomplex of the SEA complex YJR073C OPI3 Methylene-fatty-acyl-phospholipid synthase YLR461W PAU4 Member of the seripauperin multigene family YGR077C PEX8 Intraperoxisomal organizer of the peroxisomal import machinery YBR093C PHO5 Repressible acid phosphatase YGL167C PMR1 High affinity Ca2+/Mn2+ P-type ATPase

153

YGL205W POX1 Fatty-acyl coenzyme A oxidase YER089C PTC2 Type 2C protein phosphatase (PP2C) YBL057C PTH2 One of two mitochondrially-localized peptidyl-tRNA hydrolases YMR201C RAD14 Protein that recognizes and binds damaged DNA during NER YER162C RAD4 Protein that recognizes and binds damaged DNA (with Rad23p) during NER YER095W RAD51 Strand exchange protein YJL204C RCY1 F-box protein involved in recycling endocytosed proteins YOR275C RIM20 Protein involved in proteolytic activation of Rim101p YLR371W ROM2 GDP/GTP exchange factor (GEF) for Rho1p and Rho2p YBL027W RPL19B Ribosomal 60S subunit protein L19B YOR312C RPL20B Ribosomal 60S subunit protein L20B YGL147C RPL9A Ribosomal 60S subunit protein L9A YDL020C RPN4 Transcription factor that stimulates expression of proteasome genes YOR293W RPS10A Protein component of the small (40S) ribosomal subunit YLR441C RPS1A Ribosomal protein 10 (rp10) of the small (40S) subunit YGR027C RPS25A Protein component of the small (40S) ribosomal subunit YLR264W RPS28B Protein component of the small (40S) ribosomal subunit YPL090C RPS6A Protein component of the small (40S) ribosomal subunit YBL072C RPS8A Protein component of the small (40S) ribosomal subunit YGL244W RTF1 Subunit of RNAPII-associated chromatin remodeling Paf1 complex YLL002W RTT109 Histone acetyltransferase YPL273W SAM4 S-adenosylmethionine-homocysteine methyltransferase

154

YFR040W SAP155 Protein required for function of the Sit4p protein phosphatase YCR008W SAT4 Ser/Thr protein kinase involved in salt tolerance YBL031W SHE1 Mitotic spindle protein YKL184W SPE1 Ornithine decarboxylase YOL052C SPE2 S-adenosylmethionine decarboxylase YCL037C SRO9 Cytoplasmic RNA-binding protein YHR178W STB5 Transcription factor YCL032W STE50 Adaptor protein for various signaling pathways YBR231C SWC5 Component of the SWR1 complex YBR175W SWD3 Essential subunit of the COMPASS (Set1C) complex YNR004W SWM2 Protein with a role in snRNA and snoRNA cap trimethylation YKL081W TEF4 Gamma subunit of translational elongation factor eEF1B YCR053W THR4 Threonine synthase YKR059W TIF1 Translation initiation factor eIF4A YJL138C TIF2 Translation initiation factor eIF4A YBR162C TOS1 Covalently-bound cell wall protein of unknown function YDR074W TPS2 Phosphatase subunit of the trehalose-6-P synthase/phosphatase complex YLR435W TSR2 Protein with a potential role in pre-rRNA processing YOR006C TSR3 Protein required for 20S pre-rRNA processing YML013W UBX2 Bridging factor involved in ER-associated protein degradation (ERAD) YLR224W UCC1 F-box protein and component of SCF ubiquitin ligase complexes YEL040W UTR2 Chitin transglycosylase YOR106W VAM3 Syntaxin-like vacuolar t-SNARE

155

YDL077C VAM6 Guanine nucleotide exchange factor for the GTPase Gtr1p YGL212W VAM7 Vacuolar SNARE protein YOR270C VPH1 Subunit a of vacuolar-ATPase V0 domain YOR132W VPS17 Subunit of the membrane-associated retromer complex YDR080W VPS41 Subunit of the HOPS endocytic tethering complex YJL029C VPS53 Component of the GARP (Golgi-associated retrograde protein) complex YML097C VPS9 Guanine nucleotide exchange factor (GEF) YLR337C VRP1 Verprolin, proline-rich actin-associated protein YBR032W YBR032W Dubious open reading frame YCL074W YCL074W Pseudogene: encodes fragment of Ty Pol protein YCR061W YCR061W Protein of unknown function YCR062W YCR062W Merged open reading frame YCR090C YCR090C Putative protein of unknown function YDL199C YDL199C Putative transporter YFL012W-A YFL012W- Dubious open reading frame A YFL013W-A YFL013W- Dubious open reading frame A YGL036W YGL036W Putative protein of unknown function YGL214W YGL214W Dubious open reading frame YIL012W YIL012W Dubious open reading frame YLR200W YKE2 Subunit of the heterohexameric Gim/prefoldin protein complex YKR023W YKR023W Putative protein of unknown function YLR278C YLR278C Zinc-cluster protein YLR346C YLR346C Putative protein of unknown function found in mitochondria

156

YLR402W YLR402W Dubious open reading frame YLR428C YLR428C Dubious open reading frame YLR434C YLR434C Dubious open reading frame YLR460C YLR460C Member of the quinone oxidoreductase family YML003W YML003W Putative protein of unknown function YMR031W- YMR031W- Dubious open reading frame A A YMR144W YMR144W Putative protein of unknown function YNL109W YNL109W Dubious open reading frame YNL170W YNL170W Dubious open reading frame YPR126C YPR126C Dubious open reading frame YBR162W- YSY6 Protein of unknown function A YMR243C ZRC1 Vacuolar membrane zinc transporter

Table 13 HMG2 - Y55 genetic interactions

ORF Gene Description YLR040C AFB1 MATalpha-specific a-factor blocker YDR085C AFR1 Protein required for pheromone-induced projection (shmoo) formation YJL046W AIM22 Putative lipoate-protein ligase YKL037W AIM26 Putative protein of unknown function YJR005W APL1 Beta-adaptin YDR421W ARO80 Zinc finger transcriptional activator of the Zn2Cys6 family YLR085C ARP6 Actin-related protein that binds nucleosomes YDL113C ATG20 Sorting nexin family member 157

YLR412W BER1 Protein involved in microtubule-related processes YGR282C BGL2 Endo-beta-1,3-glucanase YCR032W BPH1 Protein homologous to Chediak-Higashi syndrome and Beige proteins YGL007W BRP1 Dubious ORF located in the upstream region of PMA1 YDL099W BUG1 Cis-golgi localized protein involved in ER to Golgi transport YLR438W CAR2 L-ornithine transaminase (OTAse) YER061C CEM1 Mitochondrial beta-keto-acyl synthase YPR001W CIT3 Dual specificity mitochondrial citrate and methylcitrate synthase YLR003C CMS1 Putative subunit of the 90S preribosome processome complex YLR433C CNA1 Calcineurin A YNL041C COG6 Component of the conserved oligomeric Golgi complex YCR069W CPR4 Peptidyl-prolyl cis-trans isomerase (cyclophilin) YLR216C CPR6 Peptidyl-prolyl cis-trans isomerase (cyclophilin) YOR100C CRC1 Mitochondrial inner membrane carnitine transporter YLR429W CRN1 Coronin YLR213C CRR1 Putative glycoside hydrolase of the spore wall envelope YPR030W CSR2 Nuclear ubiquitin protein ligase binding protein YMR180C CTL1 RNA 5'-triphosphatase, localizes to both the nucleus and cytoplasm YLR422W DCK1 Dock family protein (Dedicator Of CytoKinesis), homolog of human DOCK1 YFR012W DCV1 Protein of unknown function YER143W DDI1 DNA damage-inducible v-SNARE binding protein YMR173W DDR48 DNA damage-responsive protein

158

YOR080W DIA2 Origin-binding F-box protein YLR437C DIF1 Protein that regulates nuclear localization of Rnr2p and Rnr4p YDR263C DIN7 Mitochondrial nuclease functioning in DNA repair and replication YDR440W DOT1 Nucleosomal histone H3-Lys79 methylase YDR424C DYN2 Cytoplasmic light chain dynein, microtubule motor protein YLR436C ECM30 Putative protein of unknown function YDR512C EMI1 Non-essential protein of unknown function YMR015C ERG5 C-22 sterol desaturase YCR075C ERS1 Protein with similarity to human cystinosin YBR026C ETR1 2-enoyl thioester reductase YKL187C FAT3 Protein required for fatty acid uptake YNL168C FMP41 Putative protein of unknown function YAL022C FUN26 High affinity, broad selectivity, nucleoside/nucleobase transporter YBL016W FUS3 Mitogen-activated serine/threonine protein kinase involved in mating YOR183W FYV12 Protein of unknown function YER054C GIP2 Putative regulatory subunit of protein phosphatase Glc7p YNL255C GIS2 Translational activator for mRNAs with internal ribosome entry sites YFR015C GSY1 Glycogen synthase YOL089C HAL9 Putative transcription factor containing a zinc finger YML075C HMG1 HMG-CoA reductase YJR147W HMS2 Protein with similarity to heat shock transcription factors

159

YDR158W HOM2 Aspartic beta semi-aldehyde dehydrogenase YER052C HOM3 Aspartate kinase (L-aspartate 4-P-transferase) YLR207W HRD3 ER membrane protein that plays a central role in ERAD YLL026W HSP104 Disaggregase YJL214W HXT8 Protein of unknown function with similarity to hexose transporters YIL090W ICE2 Integral ER membrane protein with type-III transmembrane domains YBR159W IFA38 Microsomal beta-keto-reductase YLR432W IMD3 Inosine monophosphate dehydrogenase YLR413W INA1 Putative protein of unknown function YDL181W INH1 Protein that inhibits ATP hydrolysis by the F1F0-ATP synthase YDR072C IPT1 Inositolphosphotransferase YMR294W JNM1 Component of the yeast dynactin complex YAR018C KIN3 Nonessential serine/threonine protein kinase YGL216W KIP3 Kinesin-related antiparallel sliding motor protein YNL322C KRE1 Cell wall glycoprotein involved in beta-glucan assembly YHR082C KSP1 Serine/threonine protein kinase YGR040W KSS1 Mitogen-activated protein kinase (MAPK) YBR199W KTR4 Glycosyltransferase involved in protein glycosylation YJL207C LAA1 AP-1 accessory protein YKL008C LAC1 Ceramide synthase component YAL018C LDS1 Protein Involved in spore wall assembly YKL205W LOS1 Nuclear pore protein YKL176C LST4 Protein possibly involved in a post-Golgi secretory pathway YNL268W LYP1 Lysine permease YDL078C MDH3 Peroxisomal malate dehydrogenase

160

YJR008W MHO1 Protein of unknown function YGL257C MNT2 Mannosyltransferase YDL079C MRK1 Glycogen synthase kinase 3 (GSK-3) homolog YNL284C MRPL10 Mitochondrial ribosomal protein of the large subunit YDL040C NAT1 Subunit of protein N-terminal acetyltransferase NatA YJL205C NCE101 Protein of unknown function YPL226W NEW1 ATP binding cassette protein YGR010W NMA2 Nicotinic acid mononucleotide adenylyltransferase YCR026C NPP1 Nucleotide pyrophosphatase/phosphodiesterase YDR001C NTH1 Neutral trehalase, degrades trehalose YDR150W NUM1 Protein required for nuclear migration YKL068W NUP100 FG-nucleoporin component of central core of the nuclear pore complex YMR153W NUP53 FG-nucleoporin component of central core of nuclear pore complex (NPC) YDL089W NUR1 Protein involved in regulation of mitotic exit YGR038W ORM1 Protein that mediates sphingolipid homeostasis YMR148W OSW5 Protein of unknown function with possible role in spore wall assembly YCR077C PAT1 Deadenylation-dependent mRNA-decapping factor YLR461W PAU4 Member of the seripauperin multigene family YBR186W PCH2 Hexameric ring ATPase that remodels chromosome axis protein Hop1p YLR134W PDC5 Minor isoform of pyruvate decarboxylase YPR002W PDH1 Putative 2-methylcitrate dehydratase YDR406W PDR15 Plasma membrane ATP binding cassette (ABC) transporter YCR044C PER1 Protein of the endoplasmic reticulum

161

YNR045W PET494 Mitochondrial translational activator specific for the COX3 mRNA YHR160C PEX18 Peroxin YDR481C PHO8 Repressible vacuolar alkaline phosphatase YOR104W PIN2 Exomer-dependent cargo protein YJL160C PIR5 Putative protein of unknown function YGL059W PKP2 Mitochondrial protein kinase YMR008C PLB1 Phospholipase B (lysophospholipase) involved in lipid metabolism YCR014C POL4 DNA polymerase IV YLR414C PUN1 Plasma membrane protein with a role in cell wall integrity YKL159C RCN1 Protein involved in calcineurin regulation during calcium signaling YOR220W RCN2 Protein of unknown function YDR003W RCR2 Vacuolar protein YLR073C RFU1 Protein that inhibits Doa4p deubiquitinating activity YFR048W RMD8 Cytosolic protein required for sporulation YDR156W RPA14 RNA polymerase I subunit A14 YOR312C RPL20B Ribosomal 60S subunit protein L20B YLR325C RPL38 Ribosomal 60S subunit protein L38 YDL083C RPS16B Protein component of the small (40S) ribosomal subunit YLR441C RPS1A Ribosomal protein 10 (rp10) of the small (40S) subunit YDR083W RRP8 Nucleolar S-adenosylmethionine-dependent rRNA methyltransferase YLR221C RSA3 Protein with a likely role in ribosomal maturation YNL254C RTC4 Protein of unknown function

162

YBR280C SAF1 F-Box protein involved in proteasome-dependent degradation of Aah1p YLL041C SDH2 Iron-sulfur protein subunit of succinate dehydrogenase YLR404W SEI1 Seipin involved in lipid droplet morphology, number, and size YPL165C SET6 SET domain protein of unknown function YJL145W SFH5 Non-classical phosphatidylinositol transfer protein (PITP) YBR103W SIF2 WD40 repeat-containing subunit of Set3C histone deacetylase complex YER116C SLX8 Subunit of Slx5-Slx8 SUMO-targeted ubiquitin ligase (STUbL) complex YDL194W SNF3 Plasma membrane low glucose sensor, regulates glucose transport YCR073W-A SOL2 Protein with a possible role in tRNA export YIL073C SPO22 Meiosis-specific protein essential for chromosome synapsis YOR247W SRL1 Mannoprotein that exhibits a tight association with the cell wall YDR334W SWR1 Swi2/Snf2-related ATPase YOR086C TCB1 Lipid-binding ER protein involved in ER-plasma membrane tethering YMR291W TDA1 Protein kinase of unknown cellular role YLR426W TDA5 Putative protein of unknown function YKR059W TIF1 Translation initiation factor eIF4A YER011W TIR1 Cell wall mannoprotein YDR117C TMA64 Protein of unknown function that associates with ribosomes

163

YPR156C TPO3 Polyamine transporter of the major facilitator superfamily YOL124C TRM11 Catalytic subunit of adoMet-dependent tRNA methyltransferase complex YLR435W TSR2 Protein with a potential role in pre-rRNA processing YDR059C UBC5 Ubiquitin-conjugating enzyme YDL091C UBX3 Subunit of the DSC ubiquitin ligase complex YDR207C UME6 Rpd3L histone deacetylase complex subunit YLR420W URA4 Dihydroorotase YNL229C URE2 Nitrogen catabolite repression transcriptional regulator YNL054W VAC7 Integral vacuolar membrane protein YKR105C VBA5 Plasma membrane protein of the Major Facilitator Superfamily (MFS) YOR089C VPS21 Endosomal Rab family GTPase YLR360W VPS38 Part of a Vps34p phosphatidylinositol 3-kinase complex YDR080W VPS41 Subunit of the HOPS endocytic tethering complex YOL028C YAP7 Putative basic leucine zipper (bZIP) transcription factor YBR027C YBR027C Dubious open reading frame YBR071W YBR071W Protein of unknown function found in the cytoplasm and bud neck YBR206W YBR206W Dubious open reading frame YNL154C YCK2 Palmitoylated plasma membrane-bound casein kinase I (CK1) isoform YCL074W YCL074W Pseudogene: encodes fragment of Ty Pol protein YCR023C YCR023C Vacuolar membrane protein of unknown function YDL023C YDL023C Dubious open reading frame YDR157W YDR157W Dubious open reading frame

164

YDR249C YDR249C Putative protein of unknown function YER034W YER034W Protein of unknown function YGL230C YGL230C Putative protein of unknown function YIL060W YIL060W Mitochondrial protein of unknown function YJR015W YJR015W Putative protein of unknown function YKL177W YKL177W Dubious open reading frame YKR051W YKR051W Putative protein of unknown function YLR041W YLR041W Dubious open reading frame YLR126C YLR126C Putative glutamine amidotransferase YLR415C YLR415C Putative protein of unknown function YLR428C YLR428C Dubious open reading frame YLR456W YLR456W Putative pyridoxal 5'-phosphate synthase YLR460C YLR460C Member of the quinone oxidoreductase family YMR147W YMR147 Putative protein of unknown function W YMR172C-A YMR172C- Dubious open reading frame A YOL099C YOL099C Dubious open reading frame YOL150C YOL150C Dubious open reading frame YOL159C YOL159C Soluble protein of unknown function YBR183W YPC1 Alkaline ceramidase YDR349C YPS7 Putative GPI-anchored aspartic protease YNL339C YRF1-6 Helicase encoded by the Y' element of subtelomeric regions

165

Table 14 HMG2 - SK1 genetic interactions

ORF Gene Description YGR037C ACB1 Acyl-CoA-binding protein

166

YBL015W ACH1 Protein with CoA transferase activity YAL054C ACS1 Acetyl-coA synthetase isoform YMR300C ADE4 Phosphoribosylpyrophosphate amidotransferase (PRPPAT) YGL256W ADH4 Alcohol dehydrogenase isoenzyme type IV YDL239C ADY3 Protein required for spore wall formation YGL160W AIM14 NADPH oxidase localized to the perinuclear ER YJL046W AIM22 Putative lipoate-protein ligase YDL175C AIR2 RNA-binding subunit of the TRAMP nuclear RNA surveillance complex YNL219C ALG9 Mannosyltransferase, involved in N-linked glycosylation YGL021W ALK1 Protein kinase YBR158W AMN1 Protein required for daughter cell separation YGL148W ARO2 Bifunctional chorismate synthase and flavin reductase YLR085C ARP6 Actin-related protein that binds nucleosomes YOR058C ASE1 Mitotic spindle midzone-localized microtubule bundling protein YFR021W ATG18 Phosphoinositide binding protein YLR431C ATG23 Peripheral membrane protein required for autophagy and CVT YBL098W BNA4 Kynurenine 3-monooxygenase YGL007W BRP1 Dubious ORF located in the upstream region of PMA1 YGR142W BTN2 v-SNARE binding protein YGL174W BUD13 Subunit of the RES complex YLR438W CAR2 L-ornithine transaminase (OTAse) YGR110W CLD1 Mitochondrial cardiolipin-specific phospholipase YGL215W CLG1 Cyclin-like protein that interacts with Pho85p

167

YMR012W CLU1 Subunit of the eukaryotic translation initiation factor 3 (eIF3) YPR013C CMR3 Putative zinc finger protein YGL005C COG7 Component of the conserved oligomeric Golgi complex YNL130C CPT1 Cholinephosphotransferase YGR088W CTT1 Cytosolic catalase T YGR092W DBF2 Ser/Thr kinase involved in transcription and stress response YLR361C DCR2 Phosphoesterase YDR051C DET1 Acid phosphatase YLR172C DPH5 Methyltransferase required for synthesis of diphthamide YGL043W DST1 General transcription elongation factor TFIIS YMR299C DYN3 Dynein light intermediate chain (LIC) YGR146C ECL1 Protein of unknown function YGR254W ENO1 Enolase I, a phosphopyruvate hydratase YLR065C ENV10 Protein proposed to be involved in vacuolar functions YOR016C ERP4 Member of the p24 family involved in ER to Golgi transport YLR318W EST2 Reverse transcriptase subunit of the telomerase holoenzyme YFR019W FAB1 1-phosphatidylinositol-3-phosphate 5-kinase YGR131W FHN1 Protein of unknown function YAR050W FLO1 Lectin-like protein involved in flocculation YGR052W FMP48 Putative protein of unknown function YBR019C GAL10 UDP-glucose-4-epimerase YBR018C GAL7 Galactose-1-phosphate uridyl transferase YCL036W GFD2 Protein of unknown function

168

YAL031C GIP4 Cytoplasmic protein that regulates protein phosphatase 1 Glc7p YBR121C GRS1 Cytoplasmic and mitochondrial glycyl-tRNA synthase YNL021W HDA1 Putative catalytic subunit of a class II histone deacetylase complex YML075C HMG1 HMG-CoA reductase YLR113W HOG1 Mitogen-activated protein kinase involved in osmoregulation YOL155C HPF1 Haze-protective mannoprotein YOL012C HTZ1 Histone variant H2AZ YNL318C HXT14 Protein with similarity to hexose transporter family members YBR157C ICS2 Protein of unknown function YMR044W IOC4 Member of a complex (Isw1b) with Isw1p and Ioc2p YGL241W KAP114 Karyopherin, responsible for nuclear import of specific proteins YGL216W KIP3 Kinesin-related antiparallel sliding motor protein YHR082C KSP1 Serine/threonine protein kinase YBR199W KTR4 Glycosyltransferase involved in protein glycosylation YGL009C LEU1 Isopropylmalate isomerase YKL073W LHS1 Molecular chaperone of the endoplasmic reticulum lumen YOR084W LPX1 Peroxisomal matrix-localized lipase YCL051W LRE1 Protein involved in control of cell wall structure and stress response YHR081W LRP1 Nuclear exosome-associated nucleic acid binding protein YDR378C LSM6 Lsm (Like Sm) protein

169

YDL182W LYS20 Homocitrate synthase isozyme and functions in DNA repair YPL060W MFM1 Mitochondrial inner membrane magnesium transporter YNL218W MGS1 Protein with DNA-dependent ATPase and ssDNA annealing activities YNL291C MID1 N-glycosylated integral membrane protein of the ER and plasma membrane YGL257C MNT2 Mannosyltransferase YGL080W MPC1 Highly conserved subunit of mitochondrial pyruvate carrier YBR122C MRPL36 Mitochondrial ribosomal protein of the large subunit YBL095W MRX3 Protein that associates with mitochondrial ribosome YGR023W MTL1 Putative plasma membrane sensor YBR119W MUD1 U1 snRNP A protein YBR057C MUM2 Protein essential for meiotic DNA replication and sporulation YLR265C NEJ1 Protein involved in regulation of nonhomologous end joining YMR285C NGL2 Protein involved in 5.8S rRNA processing YGR010W NMA2 Nicotinic acid mononucleotide adenylyltransferase YGR089W NNF2 Protein that exhibits physical and genetic interactions with Rpb8p YHL023C NPR3 Subunit of the Iml1p/SEACIT complex YOR085W OST3 Gamma subunit of the oligosaccharyltransferase complex of the ER lumen YLR461W PAU4 Member of the seripauperin multigene family YIL071C PCI8 Possible shared subunit of Cop9 signalosome (CSN) and eIF3

170

YBR222C PCS60 Oxalyl-CoA synthetase YOL044W PEX15 Tail-anchored type II integral peroxisomal membrane protein YAL055W PEX22 Putative peroxisomal membrane protein YGR132C PHB1 Subunit of the prohibitin complex (Phb1p-Phb2p) YBR092C PHO3 Constitutively expressed acid phosphatase similar to Pho5p YFR034C PHO4 Basic helix-loop-helix (bHLH) transcription factor of the myc-family YNR013C PHO91 Low-affinity vacuolar phosphate transporter YGL023C PIB2 Protein of unknown function YGL006W PMC1 Vacuolar Ca2+ ATPase involved in depleting cytosol of Ca2+ ions YPL156C PRM4 Pheromone-regulated protein proposed to be involved in mating YBL064C PRX1 Mitochondrial peroxiredoxin with thioredoxin peroxidase activity YNL169C PSD1 Phosphatidylserine decarboxylase of the mitochondrial inner membrane YAL017W PSK1 PAS domain-containing serine/threonine protein kinase YBR125C PTC4 Cytoplasmic type 2C protein phosphatase (PP2C) YNL016W PUB1 Poly (A)+ RNA-binding protein YLR414C PUN1 Plasma membrane protein with a role in cell wall integrity YFR033C QCR6 Subunit 6 of the ubiquinol cytochrome-c reductase complex YGL163C RAD54 DNA-dependent ATPase that stimulates strand exchange

171

YBR005W RCR1 Protein of the ER membrane involved in cell wall chitin deposition YJL204C RCY1 F-box protein involved in recycling endocytosed proteins YGL045W RIM8 Protein involved in proteolytic activation of Rim101p YMR063W RIM9 Plasma membrane protein of unknown function YMR283C RIT1 Initiator methionine 2'-O-ribosyl phosphate transferase YFR022W ROG3 Alpha-arrestin involved in ubiquitin-dependent endocytosis YNL330C RPD3 Histone deacetylase, component of both the Rpd3S and Rpd3L complexes YJL121C RPE1 D-ribulose-5-phosphate 3-epimerase YDL082W RPL13A Ribosomal 60S subunit protein L13A YNL301C RPL18B Ribosomal 60S subunit protein L18B YOR312C RPL20B Ribosomal 60S subunit protein L20B YFR032C-A RPL29 Ribosomal 60S subunit protein L29 YOR234C RPL33B Ribosomal 60S subunit protein L33B YLR185W RPL37A Ribosomal 60S subunit protein L37A YCR031C RPS14A Protein component of the small (40S) ribosomal subunit YNL302C RPS19B Protein component of the small (40S) ribosomal subunit YLR264W RPS28B Protein component of the small (40S) ribosomal subunit YLR388W RPS29A Protein component of the small (40S) ribosomal subunit YPL090C RPS6A Protein component of the small (40S) ribosomal subunit

172

YFR032C RRT5 Putative protein of unknown function YGL175C SAE2 Endonuclease required for telomere elongation YBL052C SAS3 Histone acetyltransferase catalytic subunit of NuA3 complex YGR049W SCM4 Mitochondrial outer membrane protein of unknown function YGL083W SCY1 Putative kinase YOL071W SDH5 Protein required for flavinylation of Sdh1p YBR171W SEC66 Non-essential subunit of Sec63 complex YPL047W SGF11 Integral subunit of SAGA histone acetyltransferase complex YBL031W SHE1 Mitotic spindle protein YNL236W SIN4 Subunit of the RNA polymerase II mediator complex YGL213C SKI8 Ski complex component and WD-repeat protein YGR143W SKN1 Protein involved in sphingolipid biosynthesis YBR156C SLI15 Subunit of the conserved chromosomal passenger complex (CPC) YHR008C SOD2 Mitochondrial manganese superoxide dismutase YBR169C SSE2 Member of the heat shock protein 70 (HSP70) family YLR006C SSK1 Cytoplasmic phosphorelay intermediate osmosensor and regulator YNR031C SSK2 MAP kinase kinase kinase of HOG1 mitogen-activated signaling pathway YGR008C STF2 Protein involved in resistance to desiccation stress YGL162W SUT1 Transcription factor of the Zn(II)2Cys6 family YLR385C SWC7 Protein of unknown function YOR179C SYC1 Subunit of the APT subcomplex of cleavage and polyadenylation factor YLR251W SYM1 Protein required for ethanol metabolism

173

YGL243W TAD1 tRNA-specific adenosine deaminase YBR223C TDP1 Tyrosyl-DNA phosphodiesterase I YMR313C TGL3 Bifunctional triacylglycerol lipase and LPE acyltransferase YGR144W THI4 Thiazole synthase YLR004C THI73 Putative plasma membrane permease YGL179C TOS3 Protein kinase YLR435W TSR2 Protein with a potential role in pre-rRNA processing YOR006C TSR3 Protein required for 20S pre-rRNA processing YBR058C UBP14 Ubiquitin-specific protease YAR027W UIP3 Putative integral membrane protein of unknown function YNL054W VAC7 Integral vacuolar membrane protein YGL212W VAM7 Vacuolar SNARE protein YGL258W VEL1 Protein of unknown function YBR235W VHC1 Vacuolar membrane cation-chloride cotransporter (CCC) YLR373C VID22 Glycosylated integral membrane protein localized to plasma membrane YOR270C VPH1 Subunit a of vacuolar-ATPase V0 domain YLR360W VPS38 Part of a Vps34p phosphatidylinositol 3-kinase complex YGL104C VPS73 Mitochondrial protein YGL173C XRN1 Evolutionarily-conserved 5'-3' exonuclease YAL066W YAL066W Dubious open reading frame YAR028W YAR028W Putative integral membrane protein YBL065W YBL065W Dubious open reading frame YBL094C YBL094C Dubious open reading frame YBL096C YBL096C Non-essential protein of unknown function YBR027C YBR027C Dubious open reading frame

174

YBR032W YBR032W Dubious open reading frame YBR071W YBR071W Protein of unknown function found in the cytoplasm and bud neck YBR090C YBR090C Putative protein of unknown function YBR137W YBR137W Protein with a role in ER delivery of tail-anchored membrane proteins YBR138C YBR138C Cytoplasmic protein of unknown function YBR139W YBR139W Putative serine type carboxypeptidase YBR184W YBR184W Putative protein of unknown function YFR020W YFR020W Protein of unknown function YFR035C YFR035C Putative protein of unknown function YGL046W YGL046W Merged open reading frame YGL081W YGL081W Putative protein of unknown function YGL082W YGL082W Putative protein of unknown function YGL108C YGL108C Protein of unknown function, predicted to be palmitoylated YGL109W YGL109W Dubious open reading frame YGL149W YGL149W Dubious open reading frame YGL176C YGL176C Putative protein of unknown function YGL177W YGL177W Dubious open reading frame YGL214W YGL214W Dubious open reading frame YGL217C YGL217C Dubious open reading frame YGL242C YGL242C Protein of unknown function YGR025W YGR025W Dubious open reading frame YGR026W YGR026W Putative protein of unknown function YGR045C YGR045C Dubious open reading frame YGR050C YGR050C Protein of unknown function YGR051C YGR051C Dubious open reading frame YGR054W YGR054W Eukaryotic initiation factor (eIF) 2A

175

YGR111W YGR111W Putative protein of unknown function YGR130C YGR130C Component of the eisosome with unknown function YGL161C YIP5 Protein that interacts with Rab GTPases YMR284W YKU70 Subunit of the telomeric Ku complex (Yku70p-Yku80p) YLR118C YLR118C Acyl-protein thioesterase responsible for depalmitoylation of Gpa1p YLR252W YLR252W Dubious open reading frame YLR428C YLR428C Dubious open reading frame YLR460C YLR460C Member of the quinone oxidoreductase family YBR104W YMC2 Putative mitochondrial inner membrane transporter YMR302C YME2 Integral inner mitochondrial membrane protein YNL034W YNL034W Putative protein of unknown function YNL165W YNL165W Putative protein of unknown function YNL217W YNL217W Putative protein of unknown function YNL235C YNL235C Dubious open reading frame YNL319W YNL319W Dubious open reading frame YNR005C YNR005C Dubious open reading frame YOR029W YOR029 Dubious open reading frame W YOR139C YOR139C Dubious open reading frame YBR183W YPC1 Alkaline ceramidase YBR028C YPK3 AGC kinase YPL162C YPL162C Putative protein of unknown function YNL339C YRF1-6 Helicase encoded by the Y' element of subtelomeric regions YKL175W ZRT3 Vacuolar membrane zinc transporter YBR046C ZTA1 NADPH-dependent quinone reductase

176

Table 15 OPI3 - S288C genetic interactions

ORF Gene Description YDL243C AAD4 Putative aryl-alcohol dehydrogenase YNL141W AAH1 Adenine deaminase (adenine aminohydrolase) YMR003W AIM34 Protein of unknown function

177

YPL227C ALG5 UDP-glucose:dolichyl-phosphate glucosyltransferase YDR525W API2 Dubious open reading frame YBR164C ARL1 Soluble GTPase with a role in regulation of membrane traffic YLR085C ARP6 Actin-related protein that binds nucleosomes YMR116C ASC1 G-protein beta subunit and guanine dissociation inhibitor for Gpa2p YOR058C ASE1 Mitotic spindle midzone-localized microtubule bundling protein YPL100W ATG21 Phosphoinositide binding protein YJL095W BCK1 MAPKKK acting in the protein kinase C signaling pathway YER155C BEM2 Rho GTPase activating protein (RhoGAP) YPL161C BEM4 Protein involved in establishment of cell polarity and bud emergence YOR304C-A BIL1 Protein that binds Bud6p and has a role in actin cable assembly YER016W BIM1 Microtubule plus end-tracking protein YFL007W BLM10 Proteasome activator YNL233W BNI4 Targeting subunit for Glc7p protein phosphatase YDL074C BRE1 E3 ubiquitin ligase YNR051C BRE5 Ubiquitin protease cofactor YGL007W BRP1 Dubious ORF located in the upstream region of PMA1 YFL025C BST1 GPI inositol deacylase of the endoplasmic reticulum (ER) YGR188C BUB1 Protein kinase involved in the cell cycle checkpoint into anaphase YOR078W BUD21 Component of small ribosomal subunit (SSU) processosome

178

YLR418C CDC73 Component of the Paf1p complex YOR112W CEX1 Component of nuclear aminoacylation-dependent tRNA export pathway YGL029W CGR1 Protein involved in nucleolar integrity and processing of pre-rRNA YGR157W CHO2 Phosphatidylethanolamine methyltransferase (PEMT) YLR330W CHS5 Component of the exomer complex YGL019W CKB1 Beta regulatory subunit of casein kinase 2 (CK2) YOR039W CKB2 Beta' regulatory subunit of casein kinase 2 (CK2) YLR133W CKI1 Choline kinase YDL155W CLB3 B-type cyclin involved in cell cycle progression YKL190W CNB1 Calcineurin B YNL051W COG5 Component of the conserved oligomeric Golgi complex YGL005C COG7 Component of the conserved oligomeric Golgi complex YML071C COG8 Component of the conserved oligomeric Golgi complex YJR109C CPA2 Large subunit of carbamoyl phosphate synthetase YJR032W CPR7 Peptidyl-prolyl cis-trans isomerase (cyclophilin) YLR087C CSF1 Protein required for fermentation at low temperature YBR036C CSG2 Endoplasmic reticulum membrane protein YCR086W CSM1 Nucleolar protein that mediates homolog segregation during meiosis I YPR030W CSR2 Nuclear ubiquitin protein ligase binding protein YPR135W CTF4 Chromatin-associated protein YKL139W CTK1 Catalytic (alpha) subunit of C-terminal domain kinase I (CTDK-I) YGL110C CUE3 Protein of unknown function

179

YNL155W CUZ1 Protein with a role in the ubiquitin-proteasome pathway YIR023W DAL81 Positive regulator of genes in multiple nitrogen degradation pathways YGR092W DBF2 Ser/Thr kinase involved in transcription and stress response YOR311C DGK1 Diacylglycerol kinase YDR440W DOT1 Nucleosomal histone H3-Lys79 methylase YLR436C ECM30 Putative protein of unknown function YPL086C ELP3 Subunit of Elongator complex YMR312W ELP6 Subunit of hexameric RecA-like ATPase Elp456 Elongator subcomplex YCL045C EMC1 Member of conserved endoplasmic reticulum membrane complex YKL207W EMC3 Member of conserved ER transmembrane complex YGL231C EMC4 Member of conserved ER transmembrane complex YIL027C EMC5 Member of conserved ER transmembrane complex YLL014W EMC6 Member of conserved ER transmembrane complex YLR065C ENV10 Protein proposed to be involved in vacuolar functions YOR246C ENV9 Protein proposed to be involved in vacuolar functions YNL080C EOS1 Protein involved in N-glycosylation YMR202W ERG2 C-8 sterol isomerase YML008C ERG6 Delta(24)-sterol C-methyltransferase YML067C ERV41 Protein localized to COPII-coated vesicles YAL042W ERV46 Protein localized to COPII-coated vesicles YLR238W FAR10 Protein involved in recovery from arrest in response to pheromone YMR052W FAR3 Protein of unknown function

180

YMR029C FAR8 Protein involved in recovery from arrest in response to pheromone YBR041W FAT1 Very long chain fatty acyl-CoA synthetase and fatty acid transporter YCR089W FIG2 Cell wall adhesin, expressed specifically during mating YBL016W FUS3 Mitogen-activated serine/threonine protein kinase involved in mating YNL199C GCR2 Transcriptional activator of genes involved in glycolysis YOR355W GDS1 Protein of unknown function YGL020C GET1 Subunit of the GET complex YER083C GET2 Subunit of the GET complex YDR508C GNP1 High-affinity glutamine permease YNL274C GOR1 Glyoxylate reductase YBR121C GRS1 Cytoplasmic and mitochondrial glycyl-tRNA synthase YML121W GTR1 Cytoplasmic GTPase YGR163W GTR2 Putative GTP binding protein YGL084C GUP1 Plasma membrane protein involved in remodeling GPI anchors YOR070C GYP1 Cis-golgi GTPase-activating protein (GAP) for yeast Rabs YFL031W HAC1 Basic leucine zipper (bZIP) transcription factor (ATF/CREB1 homolog) YNL021W HDA1 Putative catalytic subunit of a class II histone deacetylase complex YPR179C HDA3 Subunit of the HDA1 histone deacetylase complex YMR161W HLJ1 Co-chaperone for Hsp40p YGL077C HNM1 Plasma membrane transporter for choline, ethanolamine, and carnitine

181

YGL194C HOS2 Histone deacetylase and subunit of Set3 and Rpd3L complexes YOL012C HTZ1 Histone variant H2AZ YGL168W HUR1 Protein of unknown function YPL244C HUT1 Protein with a role in UDP-galactose transport to the Golgi lumen YIL090W ICE2 Integral ER membrane protein with type-III transmembrane domains YER092W IES5 Non-essential INO80 chromatin remodeling complex subunit YDR123C INO2 Transcription factor YOL108C INO4 Transcription factor involved in phospholipid synthesis YDR072C IPT1 Inositolphosphotransferase YHR079C IRE1 Serine-threonine kinase and endoribonuclease YJL062W LAS21 Integral plasma membrane protein YLL049W LDB18 Component of the dynactin complex YKL176C LST4 Protein possibly involved in a post-Golgi secretory pathway YAL024C LTE1 Protein similar to GDP/GTP exchange factors YBR115C LYS2 Alpha aminoadipate reductase YPR070W MED1 Subunit of the RNA polymerase II mediator complex YIR033W MGA2 ER membrane protein involved in regulation of OLE1 transcription YEL007W MIT1 Transcriptional regulator of pseudohyphal growth YDR245W MNN10 Subunit of a Golgi mannosyltransferase complex YNL297C MON2 Protein with a role in endocytosis and vacuole integrity YGL136C MRM2 Mitochondrial 2' O-ribose methyltransferase

182

YBR122C MRPL36 Mitochondrial ribosomal protein of the large subunit YML128C MSC1 Protein of unknown function YDR162C NBP2 Protein involved in the HOG (high osmolarity glycerol) pathway YPL174C NIP100 Large subunit of the dynactin complex YDR150W NUM1 Protein required for nuclear migration YHL020C OPI1 Transcriptional regulator of a variety of genes YDR360W OPI7 Dubious open reading frame YDL232W OST4 Subunit of the oligosaccharyltransferase complex of the ER lumen YGL226C-A OST5 Zeta subunit of the oligosaccharyltransferase complex of the ER lumen YML019W OST6 Subunit of the oligosaccharyltransferase complex of the ER lumen YDR071C PAA1 Polyamine acetyltransferase YMR165C PAH1 Mg2+-dependent phosphatidate (PA) phosphatase YER059W PCL6 Pho85p cyclin of the Pho80p subfamily YGR202C PCT1 Cholinephosphate cytidylyltransferase YER149C PEA2 Coiled-coil 12S polarisome subunit YJL053W PEP8 Vacuolar protein component of the retromer YCR044C PER1 Protein of the endoplasmic reticulum YBR093C PHO5 Repressible acid phosphatase YOL001W PHO80 Cyclin YJL117W PHO86 Endoplasmic reticulum (ER) resident protein YMR123W PKR1 V-ATPase assembly factor YGL167C PMR1 High affinity Ca2+/Mn2+ P-type ATPase YMR129W POM152 Glycoprotein subunit of transmembrane ring of nuclear pore complex YNR032W PPG1 Putative serine/threonine protein phosphatase

183

YPL192C PRM3 Protein required for nuclear envelope fusion during karyogamy YNL169C PSD1 Phosphatidylserine decarboxylase of the mitochondrial inner membrane YBR125C PTC4 Cytoplasmic type 2C protein phosphatase (PP2C) YMR201C RAD14 Protein that recognizes and binds damaged DNA during NER YER162C RAD4 Protein that recognizes and binds damaged DNA (with Rad23p) during NER YJL204C RCY1 F-box protein involved in recycling endocytosed proteins YKL006W RPL14A Ribosomal 60S subunit protein L14A YOR312C RPL20B Ribosomal 60S subunit protein L20B YLR448W RPL6B Ribosomal 60S subunit protein L6B YGL147C RPL9A Ribosomal 60S subunit protein L9A YDL020C RPN4 Transcription factor that stimulates expression of proteasome genes YFL036W RPO41 Mitochondrial RNA polymerase YOR293W RPS10A Protein component of the small (40S) ribosomal subunit YLR264W RPS28B Protein component of the small (40S) ribosomal subunit YJR145C RPS4A Protein component of the small (40S) ribosomal subunit YOR001W RRP6 Nuclear exosome exonuclease component YGL244W RTF1 Subunit of RNAPII-associated chromatin remodeling Paf1 complex YDR233C RTN1 Reticulon protein YLL002W RTT109 Histone acetyltransferase

184

YOR216C RUD3 Golgi matrix protein YDL076C RXT3 Component of the Rpd3L histone deacetylase complex YDR159W SAC3 mRNA export factor YDR389W SAC7 GTPase activating protein (GAP) for Rho1p YMR060C SAM37 Component of the Sorting and Assembly Machinery (SAM) complex YER019C-A SBH2 Ssh1p-Sss1p-Sbh2p complex component YMR272C SCS7 Sphingolipid alpha-hydroxylase YDR469W SDC1 Subunit of the COMPASS (Set1C) complex YIL076W SEC28 Epsilon-COP subunit of the coatomer YBR171W SEC66 Non-essential subunit of Sec63 complex YOR035C SHE4 Protein containing a UCS (UNC-45/CRO1/SHE4) domain YOL004W SIN3 Component of both the Rpd3S and Rpd3L histone deacetylase complexes YNL257C SIP3 Putative sterol transfer protein YHR030C SLT2 Serine/threonine MAP kinase YDL013W SLX5 Subunit of the Slx5-Slx8 SUMO-targeted ubiquitin ligase (STUbL) compl YDR477W SNF1 AMP-activated serine/threonine protein kinase YGL115W SNF4 Activating gamma subunit of the AMP-activated Snf1p kinase complex YKL184W SPE1 Ornithine decarboxylase YOL052C SPE2 S-adenosylmethionine decarboxylase YEL031W SPF1 P-type ATPase, ion transporter of the ER membrane YCL037C SRO9 Cytoplasmic RNA-binding protein YBR283C SSH1 Subunit of the Ssh1 translocon complex

185

YOR242C SSP2 Sporulation specific protein that localizes to the spore wall YJR117W STE24 Highly conserved zinc metalloprotease YCL032W STE50 Adaptor protein for various signaling pathways YDR310C SUM1 Transcriptional repressor that regulates middle- sporulation genes YDR297W SUR2 Sphinganine C4-hydroxylase YBR231C SWC5 Component of the SWR1 complex YER111C SWI4 DNA binding component of the SBF complex (Swi4p- Swi6p) YDR058C TGL2 Triacylglycerol lipase that is localized to the mitochondria YHR025W THR1 Homoserine kinase YCR053W THR4 Threonine synthase YOL018C TLG2 Syntaxin-like t-SNARE YLR234W TOP3 DNA Topoisomerase III YGR166W TRS65 Component of transport protein particle (TRAPP) complex II YDR108W TRS85 Component of transport protein particle (TRAPP) complex III YDL122W UBP1 Ubiquitin-specific protease YMR304W UBP15 Ubiquitin-specific protease involved in protein deubiquitination YER151C UBP3 Ubiquitin-specific protease involved in transport and osmotic response YGR184C UBR1 E3 ubiquitin ligase (N-recognin) YDL190C UFD2 Ubiquitin chain assembly factor (E4) YDR207C UME6 Rpd3L histone deacetylase complex subunit

186

YNL229C URE2 Nitrogen catabolite repression transcriptional regulator YEL013W VAC8 Phosphorylated and palmitoylated vacuolar membrane protein YOR068C VAM10 Protein involved in vacuole morphogenesis YNL212W VID27 Cytoplasmic protein of unknown function YOR270C VPH1 Subunit a of vacuolar-ATPase V0 domain YOR132W VPS17 Subunit of the membrane-associated retromer complex YKL041W VPS24 One of four subunits of the ESCRT-III complex YPR173C VPS4 AAA-ATPase involved in multivesicular body (MVB) protein sorting YOR069W VPS5 Nexin-1 homolog YKR020W VPS51 Component of the GARP (Golgi-associated retrograde protein) complex YJL029C VPS53 Component of the GARP (Golgi-associated retrograde protein) complex YLR261C VPS63 Putative protein of unknown function YDR372C VPS74 Golgi phosphatidylinositol-4-kinase effector and PtdIns4P sensor YNL246W VPS75 NAP family histone chaperone YML097C VPS9 Guanine nucleotide exchange factor (GEF) YLR090W XDJ1 Chaperone with a role in facilitating mitochondrial protein import YDR369C XRS2 Protein required for DNA repair YBL083C YBL083C Dubious open reading frame YBR032W YBR032W Dubious open reading frame YCL046W YCL046W Dubious open reading frame YCR090C YCR090C Putative protein of unknown function

187

YDL062W YDL062W Dubious open reading frame YDR149C YDR149C Dubious open reading frame YDR186C YDR186C Putative protein of unknown function YDR199W YDR199W Dubious open reading frame YDR455C YDR455C Dubious open reading frame YER084W YER084W Protein of unknown function YER119C-A YER119C-A Dubious open reading frame YFL032W YFL032W Dubious open reading frame YGL081W YGL081W Putative protein of unknown function YGL214W YGL214W Dubious open reading frame YIL012W YIL012W Dubious open reading frame YJR087W YJR087W Dubious open reading frame YLR200W YKE2 Subunit of the heterohexameric Gim/prefoldin protein complex YLR346C YLR346C Putative protein of unknown function found in mitochondria YLR402W YLR402W Dubious open reading frame YPR024W YME1 Catalytic subunit of i-AAA protease complex YMR031W-A YMR031W Dubious open reading frame -A YMR052C-A YMR052C- Dubious open reading frame A YMR075C-A YMR075C- Dubious open reading frame A YNL198C YNL198C Dubious open reading frame YNL296W YNL296W Dubious open reading frame unlikely to encode a functional protein YNR021W YNR021W Putative protein of unknown function YNR071C YNR071C Putative aldose 1-epimerase

188

YPL205C YPL205C Hypothetical protein YPL261C YPL261C Dubious open reading frame YPR126C YPR126C Dubious open reading frame YPR153W YPR153W Putative protein of unknown function YLR262C YPT6 Rab family GTPase YBR111C YSA1 Nudix hydrolase family member with ADP-ribose pyrophosphatase activity YNL241C ZWF1 Glucose-6-phosphate dehydrogenase (G6PD)

189

Table 16 OPI3 - Y55 genetic interactions

ORF Gene Description YPL267W ACM1 Pseudosubstrate inhibitor of the APC/C YKL037W AIM26 Putative protein of unknown function YBR108W AIM3 Protein that inhibits barbed-end actin filament elongation YDL237W AIM6 Putative protein of unknown function YLR102C APC9 Subunit of the Anaphase-Promoting Complex/Cyclosome (APC/C) YKL157W APE2 Aminopeptidase yscII YPL259C APM1 Mu1-like medium subunit of the AP-1 complex YJR058C APS2 Small subunit of the clathrin-associated adaptor complex AP-2 YDR441C APT2 Potential adenine phosphoribosyltransferase YLR370C ARC18 Subunit of the ARP2/3 complex YDL192W ARF1 ADP-ribosylation factor YPR200C ARR2 Arsenate reductase required for arsenate resistance YLR392C ART10 Protein of unknown function that contains 2 PY motifs YDR384C ATO3 Plasma membrane protein, putative ammonium transporter

190

YMR237W BCH1 Member of the ChAPs family (Chs5p-Arf1p-binding proteins) YKR027W BCH2 Member of the ChAPs (Chs5p-Arf1p-binding proteins) family YER155C BEM2 Rho GTPase activating protein (RhoGAP) YNR051C BRE5 Ubiquitin protease cofactor YGL007W BRP1 Dubious ORF located in the upstream region of PMA1 YFL025C BST1 GPI inositol deacylase of the endoplasmic reticulum (ER) YJR092W BUD4 Anillin-like protein involved in bud-site selection YFL028C CAF16 Part of evolutionarily-conserved CCR4-NOT regulatory complex YDR270W CCC2 Cu(+2)-transporting P-type ATPase YOR112W CEX1 Component of nuclear aminoacylation-dependent tRNA export pathway YLR133W CKI1 Choline kinase YDL155W CLB3 B-type cyclin involved in cell cycle progression YGR109C CLB6 B-type cyclin involved in DNA replication during S phase YNL051W COG5 Component of the conserved oligomeric Golgi complex YNL041C COG6 Component of the conserved oligomeric Golgi complex YGL005C COG7 Component of the conserved oligomeric Golgi complex YML071C COG8 Component of the conserved oligomeric Golgi complex YBR036C CSG2 Endoplasmic reticulum membrane protein YMR264W CUE1 Ubiquitin-binding protein

191

YGL110C CUE3 Protein of unknown function YDR430C CYM1 Lysine-specific metalloprotease of the pitrilysin family YPL170W DAP1 Heme-binding protein YKR024C DBP7 Putative ATP-dependent RNA helicase of the DEAD- box family YMR173W DDR48 DNA damage-responsive protein YFL001W DEG1 tRNA:pseudouridine synthase YOR311C DGK1 Diacylglycerol kinase YER179W DMC1 Meiosis-specific recombinase required for double- strand break repair YAL026C DRS2 Trans-golgi network aminophospholipid translocase (flippase) YDL219W DTD1 D-Tyr-tRNA(Tyr) deacylase YKR054C DYN1 Cytoplasmic heavy chain dynein YGR146C ECL1 Protein of unknown function YLR436C ECM30 Putative protein of unknown function YCL045C EMC1 Member of conserved endoplasmic reticulum membrane complex YKL207W EMC3 Member of conserved ER transmembrane complex YIL027C EMC5 Member of conserved ER transmembrane complex YLL014W EMC6 Member of conserved ER transmembrane complex YDR512C EMI1 Non-essential protein of unknown function YLR083C EMP70 Protein with a role in cellular adhesion and filamentous growth YLR065C ENV10 Protein proposed to be involved in vacuolar functions YNL080C EOS1 Protein involved in N-glycosylation YHL010C ETP1 Putative protein of unknown function required for growth on ethanol YBR026C ETR1 2-enoyl thioester reductase

192

YMR052W FAR3 Protein of unknown function YJL155C FBP26 Fructose-2,6-bisphosphatase, required for glucose metabolism YPL103C FMP30 Protein with a role in maintaining mitochondrial morphology YER145C FTR1 High affinity iron permease YML051W GAL80 Transcriptional regulator involved in the repression of GAL genes YJR040W GEF1 Voltage-gated chloride channel YGL020C GET1 Subunit of the GET complex YER083C GET2 Subunit of the GET complex YDL100C GET3 Guanine nucleotide exchange factor for Gpa1p YHR108W GGA2 Protein that regulates Arf1p, Arf2p to facilitate Golgi trafficking YLR445W GMC2 Protein involved in meiotic crossing over YHR104W GRE3 Aldose reductase YLR364W GRX8 Glutaredoxin that employs a dithiol mechanism of catalysis YLL060C GTT2 Glutathione S-transferase capable of homodimerization YHL032C GUT1 Glycerol kinase YOR070C GYP1 Cis-golgi GTPase-activating protein (GAP) for yeast Rabs YDL234C GYP7 GTPase-activating protein for yeast Rab family members YFL031W HAC1 Basic leucine zipper (bZIP) transcription factor (ATF/CREB1 homolog) YLR192C HCR1 eIF3j component of translation initiation factor 3 (eIF3)

193

YPR179C HDA3 Subunit of the HDA1 histone deacetylase complex YMR161W HLJ1 Co-chaperone for Hsp40p YGL077C HNM1 Plasma membrane transporter for choline, ethanolamine, and carnitine YDR191W HST4 NAD(+)-dependent protein deacetylase YDR225W HTA1 Histone H2A YOL012C HTZ1 Histone variant H2AZ YJL214W HXT8 Protein of unknown function with similarity to hexose transporters YLR309C IMH1 Protein involved in vesicular transport YHR079C IRE1 Serine-threonine kinase and endoribonuclease YJR050W ISY1 Member of the NineTeen Complex (NTC) YDR492W IZH1 Membrane protein involved in zinc ion homeostasis YDR475C JIP4 Protein of unknown function YJL162C JJJ2 Protein of unknown function YJR091C JSN1 Member of the Puf family of RNA-binding proteins YJR054W KCH1 Potassium transporter that mediates K+ influx YPL056C LCL1 Putative protein of unknown function YDL240W LRG1 GTPase-activating protein (GAP) YNR008W LRO1 Acyltransferase that catalyzes diacylglycerol esterification YEL053C MAK10 Non-catalytic subunit of N-terminal acetyltransferase of the NatC type YMR115W MGR3 Subunit of the mitochondrial (mt) i-AAA protease supercomplex YJL066C MPM1 Mitochondrial intermembrane space protein of unknown function YKL167C MRP49 Mitochondrial ribosomal protein of the large subunit YBR122C MRPL36 Mitochondrial ribosomal protein of the large subunit

194

YLR219W MSC3 Protein of unknown function YMR109W MYO5 One of two type I myosin motors YDR162C NBP2 Protein involved in the HOG (high osmolarity glycerol) pathway YMR145C NDE1 Mitochondrial external NADH dehydrogenase YLR351C NIT3 Nit protein YDR001C NTH1 Neutral trehalase, degrades trehalose YKL068W NUP100 FG-nucleoporin component of central core of the nuclear pore complex YMR153W NUP53 FG-nucleoporin component of central core of nuclear pore complex (NPC) YDR179W-A NVJ3 Protein with a potential role in tethering ER and vacuoles YLR350W ORM2 Protein that mediates sphingolipid homeostasis YMR174C PAI3 Cytoplasmic proteinase A (Pep4p) inhibitor YGR202C PCT1 Cholinephosphate cytidylyltransferase YDR406W PDR15 Plasma membrane ATP binding cassette (ABC) transporter YNR045W PET494 Mitochondrial translational activator specific for the COX3 mRNA YDR479C PEX29 Peroxisomal integral membrane peroxin YDR490C PKH1 Serine/threonine protein kinase YMR123W PKR1 V-ATPase assembly factor YPL036W PMA2 Plasma membrane H+-ATPase YJR043C POL32 Third subunit of DNA polymerase delta YIL095W PRK1 Protein serine/threonine kinase YPL192C PRM3 Protein required for nuclear envelope fusion during karyogamy

195

YNL169C PSD1 Phosphatidylserine decarboxylase of the mitochondrial inner membrane YBR125C PTC4 Cytoplasmic type 2C protein phosphatase (PP2C) YDR496C PUF6 Pumilio-homology domain protein YMR201C RAD14 Protein that recognizes and binds damaged DNA during NER YJR033C RAV1 Subunit of RAVE complex (Rav1p, Rav2p, Skp1p) YKL159C RCN1 Protein involved in calcineurin regulation during calcium signaling YJL204C RCY1 F-box protein involved in recycling endocytosed proteins YLR329W REC102 Protein involved in early stages of meiotic recombination YMR182C RGM1 Putative zinc finger DNA binding transcription factor YPL024W RMI1 Subunit of the RecQ (Sgs1p) - Topo III (Top3p) complex YGL144C ROG1 Lipase with specificity for monoacylglycerol YOR312C RPL20B Ribosomal 60S subunit protein L20B YJR094W-A RPL43B Ribosomal 60S subunit protein L43B YDL020C RPN4 Transcription factor that stimulates expression of proteasome genes YDR025W RPS11A Protein component of the small (40S) ribosomal subunit YLR221C RSA3 Protein with a likely role in ribosomal maturation YDR159W SAC3 mRNA export factor YMR060C SAM37 Component of the Sorting and Assembly Machinery (SAM) complex YER019C-A SBH2 Ssh1p-Sss1p-Sbh2p complex component YMR272C SCS7 Sphingolipid alpha-hydroxylase YGL028C SCW11 Cell wall protein with similarity to glucanases

196

YLR268W SEC22 R-SNARE protein YBR171W SEC66 Non-essential subunit of Sec63 complex YLR404W SEI1 Seipin involved in lipid droplet morphology, number, and size YJR095W SFC1 Mitochondrial succinate-fumarate transporter YJR134C SGM1 Protein of unknown function YDL052C SLC1 1-acyl-sn-glycerol-3-phosphate acyltransferase YDR515W SLF1 RNA binding protein that associates with polysomes YPR054W SMK1 Middle sporulation-specific mitogen-activated protein kinase (MAPK) YDR073W SNF11 Subunit of the SWI/SNF chromatin remodeling complex YGL115W SNF4 Activating gamma subunit of the AMP-activated Snf1p kinase complex YJR010C-A SPC1 Subunit of the signal peptidase complex (SPC) YEL031W SPF1 P-type ATPase, ion transporter of the ER membrane YDR522C SPS2 Protein expressed during sporulation YBR283C SSH1 Subunit of the Ssh1 translocon complex YJR130C STR2 Cystathionine gamma-synthase, converts cysteine into cystathionine YPR151C SUE1 Protein required for degradation of unstable forms of cytochrome c YPL057C SUR1 Mannosylinositol phosphorylceramide (MIPC) synthase catalytic subunit YDR320C SWA2 Auxilin-like protein involved in vesicular transport YAR003W SWD1 Subunit of the COMPASS (Set1C) complex YAR042W SWH1 Protein similar to mammalian oxysterol-binding protein YDR334W SWR1 Swi2/Snf2-related ATPase

197

YJL004C SYS1 Integral membrane protein of the Golgi YDR058C TGL2 Triacylglycerol lipase that is localized to the mitochondria YJR014W TMA22 Protein of unknown function YDR108W TRS85 Component of transport protein particle (TRAPP) complex III YDR059C UBC5 Ubiquitin-conjugating enzyme YDL122W UBP1 Ubiquitin-specific protease YBL067C UBP13 Ubiquitin-specific protease that cleaves Ub-protein fusions YGR184C UBR1 E3 ubiquitin ligase (N-recognin) YDR207C UME6 Rpd3L histone deacetylase complex subunit YLR420W URA4 Dihydroorotase YDR400W URH1 Uridine nucleosidase (uridine-cytidine N- ribohydrolase) YJR049C UTR1 ATP-NADH kinase YNL054W VAC7 Integral vacuolar membrane protein YOR068C VAM10 Protein involved in vacuole morphogenesis YOR270C VPH1 Subunit a of vacuolar-ATPase V0 domain YKL041W VPS24 One of four subunits of the ESCRT-III complex YHR012W VPS29 Subunit of the membrane-associated retromer complex YOR069W VPS5 Nexin-1 homolog YKR020W VPS51 Component of the GARP (Golgi-associated retrograde protein) complex YJL029C VPS53 Component of the GARP (Golgi-associated retrograde protein) complex YDR486C VPS60 Protein involved in late endosome to vacuole transport

198

YDR372C VPS74 Golgi phosphatidylinositol-4-kinase effector and PtdIns4P sensor YJL012C VTC4 Vacuolar membrane polyphosphate polymerase YAR044W YAR044W Merged open reading frame YBR062C YBR062C Protein of unknown function that interacts with Msb2p YLL048C YBT1 Transporter of the ATP-binding cassette (ABC) family YCL046W YCL046W Dubious open reading frame YDR124W YDR124W Putative protein of unknown function YDR250C YDR250C Dubious open reading frame YDR455C YDR455C Dubious open reading frame YLR020C YEH2 Steryl ester hydrolase YER084W YER084W Protein of unknown function YER152C YER152C Protein with 2-aminoadipate transaminase activity YFL032W YFL032W Dubious open reading frame YGL034C YGL034C Dubious open reading frame YGL081W YGL081W Putative protein of unknown function YGL176C YGL176C Putative protein of unknown function YGR026W YGR026W Putative protein of unknown function YGR122C-A YGR122C-A Dubious open reading frame YHR097C YHR097C Putative protein of unknown function YIL077C YIL077C Putative protein of unknown function YJL213W YJL213W Protein of unknown function that may interact with ribosomes YJR015W YJR015W Putative protein of unknown function YJR038C YJR038C Dubious open reading frame YJR039W YJR039W Putative protein of unknown function YJR084W YJR084W Protein that forms a complex with Thp3p YJR087W YJR087W Dubious open reading frame

199

YJR107W YJR107W Putative lipase YJR111C YJR111C Putative protein of unknown function YJR115W YJR115W Putative protein of unknown function YKL066W YKL066W Dubious open reading frame YKL077W YKL077W Putative protein of unknown function YHL014C YLF2 Protein of unknown function YLR152C YLR152C Putative protein of unknown function YLR171W YLR171W Dubious open reading frame YLR287C YLR287C Putative protein of unknown function YLR428C YLR428C Dubious open reading frame YML099W-A YML099W- Dubious open reading frame A YML100W-A YML100W- Putative protein of unknown function A YMR010W YMR010W Putative protein of unknown function YMR052C-A YMR052C- Dubious open reading frame A YMR075C-A YMR075C- Dubious open reading frame A YMR099C YMR099C Glucose-6-phosphate 1-epimerase (hexose-6- phosphate mutarotase) YMR147W YMR147W Putative protein of unknown function YMR153C-A YMR153C- Dubious open reading frame A YMR155W YMR155W Putative protein of unknown function YMR160W YMR160W Protein of unknown function YMR181C YMR181C Protein of unknown function YMR193C-A YMR193C- Dubious open reading frame A

200

YNL043C YNL043C Dubious open reading frame YNL296W YNL296W Dubious open reading frame unlikely to encode a functional protein YNR021W YNR021W Putative protein of unknown function YOR263C YOR263C Dubious open reading frame YMR104C YPK2 Protein kinase similar to serine/threonine protein kinase Ypk1p YPR050C YPR050C Dubious open reading frame YLR121C YPS3 Aspartic protease YLR262C YPT6 Rab family GTPase YML001W YPT7 Rab family GTPase YBR111C YSA1 Nudix hydrolase family member with ADP-ribose pyrophosphatase activity YFL052W ZNF1 Zinc cluster transcription factor that regulates respiratory growth YMR243C ZRC1 Vacuolar membrane zinc transporter YER033C ZRG8 Protein of unknown function YBR046C ZTA1 NADPH-dependent quinone reductase

201

Table 17 OPI3 - YPS606 genetic interactions

ORF Gene Description YDL243C AAD4 Protein similar to GDP/GTP exchange factors YJR108W ABM1 Nudix hydrolase family member with ADP-ribose pyrophosphatase activity YMR318C ADH6 Mitochondrial ribosomal protein of the large subunit YHL021C AIM17 Soluble GTPase with a role in regulation of membrane traffic

202

YJR100C AIM25 Alkaline ceramidase YMR003W AIM34 Component of the SWR1 complex YHR199C AIM46 Subunit of the Ssh1 translocon complex YBL082C ALG3 Cell wall adhesin, expressed specifically during mating YPL227C ALG5 Transcription factor that stimulates expression of proteasome genes YOR002W ALG6 1-acyl-sn-glycerol-3-phosphate acyltransferase YOR067C ALG8 Guanine nucleotide exchange factor for Gpa1p YNL219C ALG9 Ubiquitin-specific protease YKL103C APE1 B-type cyclin involved in cell cycle progression YNL094W APP1 Putative RNA binding protein YJR058C APS2 Subunit of the oligosaccharyltransferase complex of the ER lumen YLR370C ARC18 Putative aryl-alcohol dehydrogenase YNR019W ARE2 Component of transport protein particle (TRAPP) complex III YBR164C ARL1 Protein involved in the HOG (high osmolarity glycerol) pathway YPR060C ARO7 Protein that interacts with CCT (chaperonin containing TCP-1) complex YNL008C ASI3 Rpd3L histone deacetylase complex subunit YML081C- ATP18 Histone H2A A YNR020C ATP23 Translational repressor with a role in polar growth and wall integrity YIL140W AXL2 Karyopherin YJL095W BCK1 Golgi phosphatidylinositol-4-kinase effector and PtdIns4P sensor YER177W BMH1 Lsm (Like Sm) protein

203

YDL074C BRE1 P-type ATPase, ion transporter of the ER membrane YNR051C BRE5 Non-catalytic subunit of N-terminal acetyltransferase of the NatC type YGL007W BRP1 Apyrase with wide substrate specificity YFL025C BST1 Ssh1p-Sss1p-Sbh2p complex component YGR188C BUB1 Protein of unknown function YGL174W BUD13 Subunit of the GET complex YNR027W BUD17 Non-essential INO80 chromatin remodeling complex subunit YJR092W BUD4 GPI inositol deacylase of the endoplasmic reticulum (ER) YLR418C CDC73 1-phosphatidylinositol-3-phosphate 5-kinase YOR112W CEX1 Protein of unknown function YGR157W CHO2 Component of glucose deprivation induced stress granules YDL155W CLB3 Mitochondrial intermembrane space protein YKL190W CNB1 Protein of unknown function YNL051W COG5 Protein involved in resistance to nitrosoguanidine and 6-azauracil YGL005C COG7 Peroxin required for peroxisomal matrix protein targeting YML071C COG8 Transcriptional regulator of a variety of genes YML129C COX14 Putative protein of unknown function YNL052W COX5A Serine/threonine protein kinase YJR109C CPA2 Protein that binds to cruciform DNA structures YJR032W CPR7 Protein required for proper cell fusion and cell morphology YHR146W CRP1 Putative protein of unknown function YLR087C CSF1 Probable polyprenol reductase

204

YMR078C CTF18 Constitutively expressed DL-glycerol-3-phosphate phosphatase YMR180C CTL1 Integral plasma membrane protein YMR264W CUE1 Integral membrane protein of the Golgi YGL110C CUE3 Component of the GARP (Golgi-associated retrograde protein) complex YNL111C CYB5 Integral plasma membrane protein YIL049W DFG10 Translation initiation factor eIF4A YOR311C DGK1 Protein of unknown function with similarity to hexose transporters YGR227W DIE2 Peptidyl-prolyl cis-trans isomerase (cyclophilin) YJL065C DLS1 Voltage-gated chloride channel YNL001W DOM34 Nucleotide excision repair (NER) protein YBR278W DPB3 Serine/threonine protein kinase YGR093W DRN1 Anillin-like protein involved in bud-site selection YHR143W DSE2 Ubiquitin C-terminal hydrolase YLR405W DUS4 Minor CTP synthase isozyme (see also URA7) YMR299C DYN3 Putative protein of unknown function YJR106W ECM27 Protein of unknown function YOR092W ECM3 Protein containing an N-terminal epsin-like domain YLR436C ECM30 ER membrane protein involved in regulation of OLE1 transcription YCL045C EMC1 Stress-responsive transcriptional activator YKL207W EMC3 Nim1p-related protein kinase YGL231C EMC4 Vacuolar aminopeptidase yscI YIL027C EMC5 Component of the EGO and GSE complexes YLL014W EMC6 Component of the GARP (Golgi-associated retrograde protein) complex YLR083C EMP70 Disaggregase

205

YJR125C ENT3 Protein required for fermentation at low temperature YLR065C ENV10 Lysophosphatidic acid acyltransferase YDR414C ERD1 Protein involved in recovery from arrest in response to pheromone YGR284C ERV29 Lipoyl ligase YFR019W FAB1 Subunit of E3 ubiquitin ligase complex involved in replication repair YLR238W FAR10 Protein involved in early stages of meiotic recombination YMR052W FAR3 Subunit of the ARP2/3 complex YBR041W FAT1 Cytoplasmic protein of unknown function YCR089W FIG2 Putative protein of unknown function YLR342W FKS1 Rab family GTPase YIL098C FMC1 Protein that stimulates strand exchange YGR196C FYV8 Potassium transporter that mediates K+ influx YOL132W GAS4 Component of the conserved oligomeric Golgi complex YJR040W GEF1 Subunit of the mitochondrial F1F0 ATP synthase YGL020C GET1 Mitochondrial cytochrome c oxidase (complex IV) assembly factor YER083C GET2 Putative protein of unknown function YDL100C GET3 Component of the Sorting and Assembly Machinery (SAM) complex YHR061C GIC1 UBX domain-containing protein that interacts with Cdc48p YNL153C GIM3 V-ATPase assembly factor YIL053W GPP1 Mg2+-dependent phosphatidate (PA) phosphatase YML048W GSF2 Ubiquitin-binding protein YMR251W GTO3 Sphingolipid alpha-hydroxylase YML121W GTR1 Subunit Va of cytochrome c oxidase

206

YGR163W GTR2 Phosphatidate phosphatase, converts phosphatidate to diacylglycerol YHL032C GUT1 Cytochrome b5 YIL155C GUT2 Ribosomal 60S subunit protein L42A YOR070C GYP1 Nitrogen catabolite repression transcriptional regulator YJL165C HAL5 Prephenate dehydratase YNL031C HHT2 Acyltransferase that catalyzes diacylglycerol esterification YGL077C HNM1 Acyl-CoA:sterol acyltransferase YKL101W HSL1 Ubiquitin protease cofactor YLL026W HSP104 Mitochondrial protein YDR225W HTA1 Nuclear exosome exonuclease component YPL244C HUT1 Alpha 1,3 glucosyltransferase YER039C HVG1 Glucosyl transferase YJL214W HXT8 Cis-golgi GTPase-activating protein (GAP) for yeast Rabs YLR099C ICT1 Vacuolar cation channel YER092W IES5 Protein of unknown function that associates with translating ribosomes YJR094C IME1 Protein component of the small (40S) ribosomal subunit YDR072C IPT1 Plasma membrane H+-ATPase YPL017C IRC15 Subunit of TORC1 (Tor1p or Tor2p-Kog1p-Lst8p-Tco89p) YHR079C IRE1 Protein required for nuclear envelope fusion during karyogamy YOR304W ISW2 Protein with a role in UDP-galactose transport to the Golgi lumen YJR119C JHD2 Chorismate mutase YHR158C KEL1 Putative peroxisomal membrane protein YOR233W KIN4 Dubious open reading frame

207

YHR082C KSP1 Dolichol-P-Man dependent alpha(1-3) mannosyltransferase YJL062W LAS21 Dubious open reading frame YPL056C LCL1 Very long chain fatty acyl-CoA synthetase and fatty acid transporter YLL049W LDB18 Cytoplasmic type 2C protein phosphatase (PP2C) YNL323W LEM3 Dubious open reading frame YLR239C LIP2 Protein of unknown function YNR008W LRO1 Third-largest subunit of DNA polymerase II (DNA polymerase epsilon) YHR121W LSM12 Component of the HAT/Core module of the SAGA, SLIK, and ADA complexes YDR378C LSM6 Member of conserved endoplasmic reticulum membrane complex YAL024C LTE1 Dubious open reading frame YMR021C MAC1 Putative protein of unknown function YER142C MAG1 E3 ubiquitin ligase YLR427W MAG2 Inositolphosphotransferase YEL053C MAK10 Dubious open reading frame YGL219C MDM34 Protein of unknown function thought to be involved in endocytosis YOL027C MDM38 GTPase activating protein (GAP) for Rho1p YJL112W MDV1 Predicted membrane protein required for lumenal ER protein retention YKR007W MEH1 Dubious open reading frame YIL128W MET18 Protein involved in late endosome to vacuole transport YNL145W MFA2 Phosphorylated and palmitoylated vacuolar membrane protein YML062C MFT1 Protein of unknown function

208

YKR016W MIC60 3-methyl-adenine DNA glycosylase YHR015W MIP6 14-3-3 protein, major isoform YLR320W MMS22 Putative protein of unknown function YKL201C MNN4 Putative mitochondrial transport protein YGR243W MPC3 Component of the conserved oligomeric Golgi complex YIR002C MPH1 Dubious ORF located in the upstream region of PMA1 YNR024W MPP6 Subunit of the GET complex YPL184C MRN1 Plasma membrane transporter for choline, ethanolamine, and carnitine YBR122C MRPL36 Putative protein of unknown function YKL062W MSN4 Subunit of the RES complex YDR335W MSN5 Mitochondrial component of the ERMES complex YBR255W MTC4 Member of conserved ER transmembrane complex YKR048C NAP1 Putative protein of unknown function YIL007C NAS2 Subunit of RNAPII-associated chromatin remodeling Paf1 complex YDR162C NBP2 High-affinity zinc transporter of the plasma membrane YNR009W NRM1 Dubious open reading frame YHL020C OPI1 Splicing factor that modulates turnover of branched RNAs by Dbr1p YDL232W OST4 Phosphatidylethanolamine methyltransferase (PEMT) YMR165C PAH1 Putative component of the protein phosphatase type 2A complex YDR348C PAL1 Putative GTP binding protein YGR178C PBP1 Protein kinase involved in the cell cycle checkpoint into anaphase YGR202C PCT1 Cholinephosphate cytidylyltransferase YNR045W PET494 Phosphoserine phosphatase of the phosphoglycerate pathway

209

YHR160C PEX18 Dubious open reading frame YGR239C PEX21 Dolichyl-phosphoglucose-dependent alpha-1,2- glucosyltransferase YAL055W PEX22 Dubious open reading frame YNL316C PHA2 Protein involved in the regulation of cell wall synthesis YMR123W PKR1 Protein of the AP180 family, involved in clathrin cage assembly YDR183W PLP1 Highly conserved subunit of mitochondrial pyruvate carrier YPL036W PMA2 Putative methyltransferase YOR266W PNT1 Protein localized to COPII-coated vesicles YMR129W POM152 Component of Shu complex (aka PCSS complex) YLR018C POM34 Glycerol kinase YNR032W PPG1 Meiotic regulator YPL192C PRM3 Putative RNA-binding protein YML047C PRM6 Serine/threonine MAP kinase YMR137C PSO2 Putative protein of unknown function YBR125C PTC4 Protein involved in initiation of budding and cellular polarization YHR189W PTH1 Constituent of 66S pre-ribosomal particles YJR059W PTK2 Serine-threonine kinase and endoribonuclease YIL120W QDR1 Endosomal protein of unknown function YML032C RAD52 Mitochondrial thioredoxin reductase YJR052W RAD7 Protein of unknown function that may function in RNA processing YOR265W RBL2 Daughter cell-specific secreted protein with similarity to glucanases YML030W RCF1 Peroxin

210

YNR018W RCF2 Integral membrane protein of the early Golgi apparatus and ER YJL204C RCY1 One of two mitochondrially-localized peptidyl-tRNA hydrolases YLR329W REC102 Non-ATPase base subunit of the 19S RP of the 26S proteasome YLR371W ROM2 Putative protein of unknown function YLR185W RPL37A Protein component of the small (40S) ribosomal subunit YNL162W RPL42A Proteasome-interacting protein YHR200W RPN10 GID Complex subunit, serves as adaptor for regulatory subunit Vid24p YDL020C RPN4 Member of conserved ER transmembrane complex YOR293W RPS10A Ubiquitin-protein ligase involved in ER-associated protein degradation YOL121C RPS19A Protein of unknown function found in the ER and vacuole lumen YHR203C RPS4B Mitochondrial matrix protein YOR001W RRP6 Stress-inducible dual-specificity MAP kinase phosphatase YGL244W RTF1 Multidrug transporter of the major facilitator superfamily YGR161C RTS3 Component of cytosolic iron-sulfur protein assembly (CIA) machinery YLL002W RTT109 Dubious open reading frame YDR389W SAC7 Mitochondrial glycerol-3-phosphate dehydrogenase YMR060C SAM37 3'-5' DNA helicase involved in error-free bypass of DNA lesions YER019C-A SBH2 Dubious open reading frame YMR214W SCJ1 Dubious open reading frame

211

YMR272C SCS7 Sorting nexin YIL113W SDP1 Subunit of ISW2/yCHRAC chromatin accessibility complex YLR292C SEC72 MAPKKK acting in the protein kinase C signaling pathway YGR208W SER2 Peripheral protein of cytosolic face of mitochondrial outer membrane YCL010C SGF29 Putative protein kinase YHL006C SHU1 F-box protein involved in recycling endocytosed proteins YPL026C SKS1 Dubious open reading frame YDL052C SLC1 Small subunit of the clathrin-associated adaptor complex AP-2 YHR030C SLT2 Master regulator of meiosis that is active only during meiotic events YGR229C SMI1 Putative protein of unknown function YNR015W SMM1 Putative protein of unknown function YGR197C SNG1 Putative lipase YJL036W SNX4 Large subunit of carbamoyl phosphate synthetase YEL031W SPF1 Putative protein of unknown function YHR014W SPO13 Putative protein of unknown function YKL020C SPT23 JmjC domain family histone demethylase YDR293C SSD1 Protein of unknown function YHR066W SSF1 Putative protein of unknown function YBR283C SSH1 Ubiquitin-protein ligase (E3) YKL124W SSH4 tRNA threonylcarbamoyladenosine dehydratase YIL030C SSM4 Dubious open reading frame YHR181W SVP26 Specificity factor required for Rsp5p-dependent ubiquitination

212

YBR231C SWC5 Vacuolar membrane zinc transporter YNR004W SWM2 Calcineurin B YJL004C SYS1 Putative positive regulator of mannosylphosphate transferase Mnn6p YKL027W TCD2 Dubious open reading frame YPL180W TCO89 Member of conserved ER transmembrane complex YJR116W TDA4 Putative protein of unknown function YLR426W TDA5 Component of the MICOS complex YJL138C TIF2 Histone chaperone YGR181W TIM13 Histone acetyltransferase YMR269W TMA23 Member of conserved ER transmembrane complex YOR091W TMA46 Dubious open reading frame YNL121C TOM70 Component of the dynactin complex YHR106W TRR2 Subunit of the transmembrane ring of the nuclear pore complex (NPC) YDR108W TRS85 Protein proposed to be involved in vacuolar functions YMR022W UBC7 Protein with a role in cellular adhesion and filamentous growth YDL122W UBP1 Multivesicular body (MVB) protein YMR067C UBX4 Ribosomal 60S subunit protein L37A YKL010C UFD4 Rab family GTPase YDR207C UME6 Non-essential subunit of Sec63 complex YJR103W URA8 Dubious open reading frame YNL229C URE2 Catalytic subunit of 1,3-beta-D-glucan synthase YEL013W VAC8 GDP/GTP exchange factor (GEF) for Rho1p and Rho2p YIL017C VID28 Dihydrouridine synthase YKR020W VPS51 Putative protein of unknown function YJL029C VPS53 Component of the Paf1p complex YDR486C VPS60 Putative protein of unknown function

213

YDR372C VPS74 Dubious open reading frame YLR181C VTA1 Cytochrome c oxidase subunit YDL224C WHI4 Endoplasmic reticulum (ER) localized integral membrane protein YGR241C YAP1802 Subunit of the THO complex YAR047C YAR047C Cytoplasmic GTPase YBL083C YBL083C Protein of unknown function YBR226C YBR226C Copper-sensing transcription factor YCL046W YCL046W Ubiquitin conjugating enzyme YCR090C YCR090C Dubious open reading frame YDR199W YDR199W Protein of unknown function YDR455C YDR455C Dubious open reading frame YER084W YER084W Subunit of a complex with Ctf8p YFR035C YFR035C Glycoprotein subunit of transmembrane ring of nuclear pore complex YFR045W YFR045W Nuclease required for DNA single- and double-strand break repair YGL081W YGL081W RNA 5'-triphosphatase, localizes to both the nucleus and cytoplasm YGL235W YGL235W One of several homologs of bacterial chaperone DnaJ YGR051C YGR051C Vacuolar membrane zinc transporter YGR226C YGR226C Omega class glutathione transferase YGR228W YGR228W Nucleolar protein implicated in ribosome biogenesis YGR283C YGR283C Dynein light intermediate chain (LIC) YHR045W YHR045W NADPH-dependent medium chain alcohol dehydrogenase YHR202W YHR202W Protein that facilitates ribosomal subunit dissociation YIL089W YIL089W Subunit of the nuclear inner membrane Asi ubiquitin ligase complex

214

YIL141W YIL141W Histone H3 YIR020W-A YIR020W-A Dubious open reading frame YJL007C YJL007C Component of the conserved oligomeric Golgi complex YJR038C YJR038C Component of the TOM (translocase of outer membrane) complex YJR098C YJR098C Mating pheromone a-factor YJR107W YJR107W Subunit of the heterohexameric cochaperone prefoldin complex YJR111C YJR111C Mannosyltransferase, involved in N-linked glycosylation YJR120W YJR120W Dubious open reading frame unlikely to encode a functional protein YJR124C YJR124C Membrane protein of the plasma membrane and ER YKL066W YKL066W Protein with a role in snRNA and snoRNA cap trimethylation YKL202W YKL202W Transcriptional co-repressor of MBF-regulated gene expression YKR005C YKR005C Putative protein of unknown function YLL020C YLL020C Dihydrouridine synthase YLR311C YLR311C Cytochrome c oxidase subunit YLR415C YLR415C Putative metalloprotease of the mitochondrial inner membrane YLR428C YLR428C Putative protein of unknown function YMR027W YMR027W Nuclear exosome-associated RNA binding protein YMR052C- YMR052C- Putative pyridoxal kinase A A YMR075C- YMR075C- Putative serine/threonine protein phosphatase A A YER005W YND1 Putative protein of unknown function

215

YNL043C YNL043C Mitochondrial translational activator specific for the COX3 mRNA YNL296W YNL296W Dubious open reading frame YNR014W YNR014W Protein component of the small (40S) ribosomal subunit YNR021W YNR021W 1,3-beta-glucanosyltransferase YNR040W YNR040W Soluble protein of unknown function YOL118C YOL118C Putative protein of unknown function YOL159C YOL159C Putative protein of unknown function YOL163W YOL163W Non-essential protein of unknown function YOR012W YOR012W Component of nuclear aminoacylation-dependent tRNA export pathway YOR300W YOR300W Serine/threonine protein kinase YBR183W YPC1 Protein involved in microtubule morphogenesis YPR063C YPR063C Mitochondrial integral inner membrane protein YHR105W YPT35 Dubious open reading frame YLR262C YPT6 ATP-dependent DNA translocase involved in chromatin remodeling YML001W YPT7 Diacylglycerol kinase YBR111C YSA1 Microtubule associated protein YJR099W YUH1 Putative serine/threonine protein kinase YOR087W YVC1 Putative protein of unknown function YMR243C ZRC1 RNA-binding protein that may be involved in translational regulation YGL255W ZRT1 UDP-glucose:dolichyl-phosphate glucosyltransferase YKL175W ZRT3 ER-localized protein of unknown function

216