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This journal is © The Royal Society of Chemistry 2015 Supplementary Table 1. 109 D/E-rich repeats containing proteins in yeast UniProt D/E-rich repeats Protein function Residue pI Start number Length Histone, nucleosome and kinetochore proteins O74515 VQPDADEEEEEEEADEMEEEFDEEGEGDEEEEEEDDGDGDGEGDGDGE ASF1_SCHPO Histone chaperone cia1 262 3.57 170 48 Q759F6 EAEDEYPPEQPGVDDEEVDDEDEDEDEDEEGADEEGADEEGASDG ASF1_ASHGO Histone chaperone ASF1 276 3.62 155 45 RKVQTEDEEDDEAEEIDLEAEEEEDEDEEDEDGDEAEEVDEEEEDDDGEPVGA 206 55 SE Q59MV1 DNEEGADEYPPEQPEDEEEEEEEEEEGEEEEEDEDEEDDDDDEDLNGDAVVDL ASF1_CANAL Histone chaperone ASF1 247 3.62 154 58 EKEEI P32447 EGDLYPPEQPGVDDEEEEDDEEEDDDEDDEDDEDDDQEDGEGEAEEAAEEEEE ASF1_YEAST Histone chaperone ASF1 279 3.73 158 62 EEEKTEDNE Q59RN6 TENNEEGDDDDEDEDDDYEQGKLEDEEEEEDELLEIDES CHZ1_CANAL Histone H2A.Z-specific chaperone CHZ1 167 4.02 73 39 Q5AQ47 SSSSSSDNDQDNDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEESEINGN HST1_CANAL NAD-dependent protein deacetylase HST1 657 4.23 68 57 QISL Q8WZM0 IEDEDFQENGIDDEDEEEEEEEAKDEGDEDDEEKGEDDEEDDEEKEGEDGEGE GCN5_YARLI Histone acetyltransferase GCN5 464 4.67 30 71 EEDEEEDEEKKREEEEKY P34218 KEDEDEDEDFTLDDDIEDEQISEENDEEEDTYEEDSDDDEDG SAS3_YEAST Histone acetyltransferase SAS3 831 6.13 755 42 P53165 DDDNSNDNNNDDDDDDDNDDNEDDDDADDDDD SGF73_YEAST SAGA-associated factor 73 657 9.13 131 32 P32657 MTTIEDDEDEFEDEEGEEDSGEDEDEEDFEEDDDYYGS CHD1_YEAST Chromo domain-containing protein 1 1468 6.15 53 38 P40340 AHDPEEDDESFHEEDVDDDEEEEEADEFEDEYLDEDS TBP7_YEAST Tat-binding homolog 7 1379 4.93 116 37 P25293 AALEFEFEEDEEEADEDEDEEEDDDHGLEDDDGESAEEQDDF NAP1_YEAST Nucleosome assembly protein 417 4.09 363 42 Q9HGN2 TEAMTEEASDEDESVDLEEDEEEEDEEDEEGDEEKQEPPS YO48_SCHPO Putative nucleosome assembly protein 244 4.16 198 40 C36B7.08c Q12386 SVDPRDVADEEDEDEEGEDEDEDEDDNDVDNEDENDNDNANE ARP8_YEAST Actin-like protein ARP8 881 4.54 70 42 P54784 DVSEDMDSGEISADELEEEEDEEEDEDEEEKEA ORC1_YEAST Origin recognition complex subunit 1 914 5.42 267 33 Q6CA87 VEEVEEEEPEEEEGPEEEEAPEEEVEGDDEEEVQ SWR1_YARLI Helicase SWR1 1772 4.68 123 34 LKEEMTAVEEEEEEELVEEEEEEEEEEEQEEDEEQEQQEEEEEEQEEEVTSR 275 52 LDNIKVERAEEEDEEDEENGDDEDEDEEEDDAEIEEETETTTP 718 43 AIEEDEEEDDAFVIKEEEEEVEVEDDEEEEKAD 816 33 P31380 QSEHEDDDYEEEDEDYNDEEEDVEYDDGDDDDDDDDEFVAT FUN30_YEAST ATP-dependent helicase FUN30 1131 5.12 497 41 P53115 SDIINEKDADEDEEDDEDELEDGEEDMEEDEASTG INO80_YEAST Putative DNA helicase INO80 1489 5.47 132 35 DNENENDNDSDNDDEEENGEEDEEEEEIEDLDEEDFAAFEEQDDNDDEDF 240 50 Q74Z27 RELSGAKLEDEGEGEDDDEEEDEDDEDDEDEDEDEDEEEEEEEELEELEDIQL INO80_ASHGO Putative DNA helicase INO80 1414 6.36 178 62 LDDDNDKDF Q6C931 LDLESDDEDQEEEESEFEVSDDEPEDEDEDSEEFA SPT16_YARLI FACT complex subunit SPT16 1003 5.07 931 35 Transcription factors P38915 ENDSKQDLEGNDDGGEDEEDDDDDDEDDDDDEDEREDDDEQEDDDGEDDAARM SPT8_YEAST Transcription factor SPT8 602 4.13 28 56 DKT Q6C9G2 ALYDDEDEDGDGADGFIDEDDEDDEEDDEEGEGNGFIDDEVEVDEEDQDEDGD BFR2_YARLI Protein BFR2 495 4.18 78 75 EDMEDEQDEDESDEELSENEND Q5ACL9 EELDAESAEEEEDEESEDVADDDEDDQESD BFR2_CANAL Protein BFR2 482 4.24 366 43 Q06631 ENEDEEEEEEEEEEKEEDALSFRTDSEDEEVE BFR2_YEAST Protein BFR2 590 4.34 507 51 P36100 KKQAKLNKEEEEEEEEEEDEEEEEEEEMEDVMDDNDETARENA T2EA_YEAST Transcription initiation factor IIE subunit alpha 990 4.81 91 45 Q05021 RSDAETANNVEEEEEEEEEEEEEDEVDEDEEDDEENDEDEDNVHEREHIQE TAF7_YEAST Transcription initiation factor TFIID subunit 7 956 4.88 58 45 O13936 NDKKEDEDNVEENEEEADANEEEEEDEEDDEEDEEDEDESGGGRR SPT5_SCHPO Transcription elongation factor spt5 1063 4.95 134 44 Q5ALX3 EENNEKEQDQEAGQDEEEQDEDEEEEEDDEEEDEEDEVSSRRKRR SPT5_CANAL Transcription elongation factor SPT5 980 5.02 29 47 P27692 KNSDGDTKDEGDNKDEDDDEDDDDDDDDEDDDDEAPTKRRRQER SPT5_YEAST Transcription elongation factor SPT5 720 5.19 606 45 Q6CC84 IKSEEVDKTQDNVEDEDDEEEEEEEEEEEEEDDDEEDVRQRKKPRRE SPT5_YARLI Transcription elongation factor SPT5 683 6.31 526 36 Q59P39 PNTAENDVPGDDEEEEDDDDDDDDDEEEGEQDDEEEEDGSSTSMS EFH1_CANAL Transcriptional regulator EFH1 719 8.00 541 30 P32432 SQNMVEDQDIDDIDDDDDVDDDDDDDDDDDTENGSS SFP1_YEAST Transcription factor SFP1 512 4.46 106 30 Q03213 EDDDDDGDDEGDGRDNEEDSTAEEDEVDDE HOT1_YEAST High-osmolarity-induced transcription protein 1 534 4.53 96 32 P32351 DVDSEEEGEGNDEDDDDGDGDDMDEEESDEEQ IMPX_YEAST Sugar utilization regulatory protein IMP2 346 4.81 95 32 P08638 DEEEEEDEDEEGEEEEEEEELSSKVPENMD LEUR_YEAST Regulatory protein LEU3 886 5.75 678 30 P38114 SNNNDNDNNINDDDDDDDDDDDDDDDDDDDDDNDDDYSNNGADDDEEDDDYDR TBS1_YEAST Uncharacterized transcriptional regulatory 1094 5.12 981 53 protein TBS1 RNA polymerase subunits P38439 NEYEEDDFLVDDDEEEEAAFDDEEDDNEEEEEEEDADEENASR LEO1_YEAST RNA polymerase-associated protein LEO1 464 4.17 382 43 P36070 QNELDELDDDVDDDDLEEVDLEDDDDLDDDSGDDDDENC RRN3_YEAST RNA polymerase I-specific transcription 627 4.44 245 39 initiation factor RRN3 Q5ALX5 SDNEGGEDIEDDDNDYEDEGDDDEEEEGEEEEEEESDEDEISDIGKS SSN2_CANAL Mediator of RNA polymerase II transcription 1665 4.53 679 47 subunit 13 Q05543 YEVGDGDDDDDDGDNDDDDDDDDDDKNYDDRSND RT103_YEAST Regulator of Ty1 transposition protein 103 409 4.63 263 34 P33441 DEKEESDHEYDDQEDEENEEEDDMEVDVED MFT1_YEAST THO complex subunit MFT1 392 4.27 292 30 Ribosomal proteins Q06672 RVVHIEGDDDEDDEDVEDYDDEDEDEEMDEVVPDLVS TSR2_YEAST Pre-rRNA-processing protein TSR2 205 3.97 146 37 P39520 DYQAVTDGEESENEEEESEEEEEDDDEDDDDDDDDGSDSDSDSETSSDDEN IFH1_YEAST Protein IFH1 1085 4.37 114 51 Q12136 LLEDEDEEEVLAMDEDDESIDEREDEEEEEEEELDG SAS10_YEAST Something about silencing protein 10 610 4.45 54 36 Q59VP7 SDDEDEEEEQEQEEQPQEEENNSDDDDDDDDDDDDN ERB1_CANAL Ribosome biogenesis protein ERB1 849 4.46 51 36 SSQKEEDNKESDNEDEDEEEDNDDDDDDDEPETSS 571 35 RNA processing Q751K8 RARGADDGDVDMLDDDDEEEDDDEDEDDEDSDSDVEIIIG FIP1_ASHGO Pre-mRNA polyadenylation factor FIP1 323 4.06 60 40 P38996 TEEEEEEEHQQKGGNDDDDDDNEEEEEEEEDDDDDDDDDDDDEEEEEEEEEEG NAB3_YEAST Nuclear polyadenylated RNA-binding protein 3 802 4.25 86 63 NDNSSVGSDS Q6C233 DGNGQLVDDYDDDEDDDDEDDEIDEEVDDDLIADENAVDV SQS1_YARLI Protein SQS1 812 4.31 207 40 Q5AFT3 LCFLPFEVIEDDEDEEEEEEEDEEDEDEGEENIDDTKEKKDKK CFT1_CANAL Protein CFT1 1420 4.94 149 43 KIEEKEDNKDDDDNDDDDEDDLYKEEEEEETQ 454 32 P38798 PGKHQAKQDESEDEDDEDDDEDDDDDDDDDDDDGEEGDEDDDEDDDDEDDDDE NMD2_YEAST Nonsense-mediated mRNA decay protein 2 1089 4.85 876 73 EEEDSDSDLEYGGDLDADRD Q9P6R9 GEEDDDENEEDEEDSEETSESEEDESVNDEK CWC22_SCHPO Pre-mRNA-splicing factor cwf22 887 8.66 368 31 Q6C8C5 KEILGDSDDEEEDDSEAEEEADDEEEEEGDEEEEAQAST CWC22_YARLI Pre-mRNA-splicing factor CWC22 954 8.94 464 39 P11745 SKFDDLEVDDFEEVDSEDEEGEDEEDEDEDEKLEEIETERLEKE RNA1_YEAST Ran GTPase-activating protein 1 407 4.39 345 44 P53107 GYEAIEEDEEEDEEEDEEEGKDGEERKEEEEEENKLEDKD YRB30_YEAST Ran-specific GTPase-activating protein 30 440 4.55 337 40 Q6CFG6 APKKAKVEEEESDDDEEDEEDDDDDDDSDDDDSDDSGEPQMEIK EFG1P_YARLI rRNA-processing protein EFG1 305 4.44 218 44 O74363 FADLSVLEEDDDDEDEDEELEGEKEEEEEEKEKPEISN YND2_SCHPO G-patch and R3H domain-containing protein 695 4.65 257 38 C30B4.02c Q6CEW9 KGDDEIDEDEDEEEESENKKDDDNEEAEEDEEDPVIED MRD1_YARLI Multiple RNA-binding domain-containing 828 4.98 192 38 protein 1 Q6CAC9 EQELEEDDIEGAGEEEEEVDEEQEEEEDADDAEEDAEDDSETDKYD UTP25_YARLI U3 small nucleolar RNA-associated protein 25 641 5.14 46 46 C4R2K0 KLEEEQEREEEELQEEDEDEDEEDEEINLEDFESDDESHDD UTP25_PICPG U3 small nucleolar RNA-associated protein 25 697 5.56 102 41 Q6CFT1 DFFELAGKTDDGDDEEEDEEDEEEEEEEKE ESF2_YARLI Pre-rRNA-processing protein ESF2 324 5.33 65 30 Q6C2F4 DFENSEEEGEDDEDEAEDDDDEDVEIHEVDEDEDESGDKS NOP14_YARLI Probable nucleolar complex protein 14 832 5.42 360 40 Q6C2Q7 VDPVRDQQEDKMEVEDEEEDEEEDEEDEEEDEEDEEDEEEKEEDDDDDDDEEE NOP12_YARLI Nucleolar protein 12 509 5.47 30 63 IEEPVIKKSK Q59X38 EKEDGEAVEDTDEEEEEVEIEDGDEDQEDEEEEEDEDLKAQKE PESC_CANAL Pescadillo homolog 587 6.13 458 43 Q6C1W9 EGAEGNDEEDDEDDDDEEEEEEESVSAEPEVVE TRM10_YARLI tRNA (guanine(9)-N1)-methyltransferase 371 5.00 318 33 RNA helicase Q59MW2 DEEEEEEETDESEHESSQDEDINEEEPEEEDED DBP6_CANAL ATP-dependent RNA helicase DBP6 606 4.81 39 33 P32892 MNNGDENQSEEEEEEEEKEEEEEEEEEQEEMTLEKGGKDDE DRS1_YEAST ATP-dependent RNA helicase DRS1 752 5.47 161 41 Q59ZH9 DVEDNETPEVEDEKPTEQEEEEEEEEEEEEEEEEEEEEEEFAGFEDDENNQED MAK5_CANAL ATP-dependent RNA helicase MAK5 782 5.75 97 55 AN Translation Q12532 KVKTSGNEDNGDDDEEEEEEEEEEEEEEEEEEEEEEEEKEEEEKEEEQQQDED TAE2_YEAST Translation-associated element 2 1038 5.47 706 59 DSNEVN Protein-protein interaction Q59S52 KDSGYNSQNLDDEDEDDEDDDEDDEDEEEEDEDDYDDHDLGTINEGI MDM12_CANAL Mitochondrial distribution and morphology 428 3.90 97 47 protein 12 Q12500 EEVGNSEDNEDDDTDEDSEDDDDDGGDDDDSEDDDDDDDGEGDENGDDGEGDE AVL9_YEAST Late secretory pathway protein AVL9 764 4.20 596 57 NGDD P38835 TTKDAEDHGEDDGDGDDGEDDDDDDDDDDDDDDDEDDDDDDDDDDDDDDDDDD YHT1_YEAST PH domain-containing protein YHR131C 850 5.02 793 57 GQIT P40021 NDESSENGDGDNDHDDDYDDDDDDDDDDDESE ZRG8_YEAST Zinc-regulated protein 8 1076 4.60 420 32 Q08979 DEDEFEYEDDEEDEDDGEEEQDAGPLEGDEDEESESDDD KEL3_YEAST Kelch repeat-containing protein 3 651 4.88 518 39 Q99299 IFDGVTVRADEEEEEDEDDEDDEEEEEENDDEEDEEDEEDDEDDEEEEEKRKE AIM44_YEAST Altered inheritance of mitochondria protein 44 758 6.31 642 60 GEGRNLA P48362 EEMPSKNAEEEEEEESEEEEDDDEEDEIVE HGH1_YEAST FAM203 family protein HGH1 394 4.48 363 30 Ubiquitin related proteins Q10435 GSESYERDEDVDEEEEEDDDENNDEGDDEDENENDELRSEN YDE1_SCHPO Probable ubiquitin fusion degradation protein 1647 4.82 240 41 C12B10.01c O74201 VRETVENSWNDDDDEEEEEEDEDEAEDEDDDDDDNIDE UBC2_CANAL Ubiquitin-conjugating enzyme E2 2 179 3.92 141 38 P06104 VKETVEKSWEDDMDDMDDDDDDDDDDDDDEA UBC2_YEAST Ubiquitin-conjugating enzyme E2 2 172 4.02 141 31 Q12161
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    NPR REVIEW View Article Online View Journal | View Issue The phosphopantetheinyl transferases: catalysis of a post-translational modification crucial for life† Cite this: Nat. Prod. Rep.,2014,31,61 Joris Beld,‡a Eva C. Sonnenschein,‡§a Christopher R. Vickery,‡ab Joseph P. Noelb and Michael D. Burkart*a Covering: up to 2013 Although holo-acyl carrier protein synthase, AcpS, a phosphopantetheinyl transferase (PPTase), was characterized in the 1960s, it was not until the publication of the landmark paper by Lambalot et al. in 1996 that PPTases garnered wide-spread attention being classified as a distinct enzyme superfamily. In the past two decades an increasing number of papers have been published on PPTases ranging from Received 11th June 2013 identification, characterization, structure determination, mutagenesis, inhibition, and engineering in DOI: 10.1039/c3np70054b synthetic biology. In this review, we comprehensively discuss all current knowledge on this class of www.rsc.org/npr enzymes that post-translationally install a 40-phosphopantetheine arm on various carrier proteins. 1 Introduction 4.2 The other phosphopantetheinylated proteins and their 2 Types of PPTases PPTases 2.1 Family I: holo-acyl carrier protein synthase (AcpS-type 4.3 Carrier protein recognition by PPTases PPTases) 4.4 Peptide mimics of carrier proteins as substrate of PPTases 2.2 Family II: Sfp-type PPTases 4.5 Regulation by 40-phosphopantetheinylation 2.3 Family III: type I integrated PPTases 5 Structures 3 Importance in primary and secondary metabolism 5.1 Structural
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    Variations on a theme: synthesis and modification of plant benzoic acids Mary C Wildermuth Plant benzoic acids (BAs) are critical regulators of a plant’s species of 30 different families and function as pollinator interaction with its environment. In addition, innumerable plant- attractants [3]. In addition, MeSA is involved in tri- derived pharmacological agents contain benzoyl moieties. trophic interactions; MeSA is emitted in response to Despite the prevalence and import of plant BAs, their herbivore damage (e.g. that caused by aphids or mites), biosynthetic pathways are not well-defined. Mounting attracting the predator of the herbivore [3,4]. As shown evidence suggests that BAs are synthesized both directly from in Figure 1, BAs are also incorporated into numerous plant shikimate/chorismate and from phenylalanine in plants; secondary metabolites that have established roles in however, few genes in these pathways have been identified. plant–herbivore or plant–pathogen interactions, such as Exciting progress has been made in elucidating genes that BA glucosinolate esters (e.g. in A. thaliana [5]), salicin (the modify BAs via methylation, glucosylation, or activation with major phenolic glycoside in willow [6]), xanthones (e.g. in Coenzyme A. As these modifications alter the stability, Hypericum androsaemum [7]), cocaine (in Erythroxylum coca solubility, and activity of the BAs, they impact the functional [8]), and taxol (in Taxus cuspidate [9]). Many of these BA roles of these molecules. The combination of multiple BA and benzoyl compounds are also important pharmacolo- biosynthetic routes with a variety of chemical modifications gical agents; for example, salicylate is the active ingre- probably facilitates precise temporal and spatial control over dient in aspirin, taxol is a potent anti-cancer drug, and active forms, as well as the channeling of intermediates to cocaine is a local analgesic.
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  • Evolution-Guided Optimization of Biosynthetic Pathways
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