Table 3. Nomenclature for proteins and protein complexes in different organisms Mammals Budding yeast Fission yeast Flies Plants Archaea Bacteria
Prereplication complex assembly H. sapiens S. cerevisiae S. pombe D. melanogaster A. thaliana S. solfataricus E. coli Hs Sc Sp Dm At Sso Eco ORC ORC ORC ORC ORC [Orc1/Cdc6]-1, 2, 3 DnaA Orc1/p97 Orc1/p104 Orc1/Orp1/p81 Orc1/p103 Orc1a, Orc1b Orc2/p82 Orc2/p71 Orc2/Orp2/p61 Orc2/p69 Orc2 Orc3/p66 Orc3/p72 Orc3/Orp3/p80 Orc3/Lat/p82 Orc3 Orc4/p50 Orc4/p61 Orc4/Orp4/p109 Orc4/p52 Orc4 Orc5L/p50 Orc5/p55 Orc5/Orp5/p52 Orc5/p52 Orc5 Orc6/p28 Orc6/p50 Orc6/Orp6/p31 Orc6/p29 Orc6 Cdc6 Cdc6 Cdc18 Cdc6 Cdc6a, Cdc6b [Orc1/Cdc6]-1, 2, 3 DnaC Cdt1/Rlf-B Tah11/Sid2/Cdt1 Cdt1 Dup/Cdt1 Cdt1a, Cdt1b Whip g MCM helicase MCM helicase MCM helicase MCM helicase MCM helicase Mcm DnaB Mcm2 Mcm2 Mcm2/Nda1/Cdc19 Mcm2 Mcm2 Mcm3 Mcm3 Mcm3 Mcm3 Mcm3 Mcm4 Mcm4/Cdc54 Mcm4/Cdc21 Mcm4/Dpa Mcm4 Mcm5 Mcm5/Cdc46/Bob1 Mcm5/Nda4 Mcm5 Mcm5 Mcm6 Mcm6 Mcm6/Mis5 Mcm6 Mcm6 Mcm7 Mcm7/Cdc47 Mcm7 Mcm7 Mcm7/Prolifera Gmnn/Geminin Geminin Mcm9 Mcm9 Hbo1 Chm/Hat1 Ham1 Ham2 DiaA Ihfa Ihfb Fis SeqA
Replication fork assembly Hs Sc Sp Dm At Sso Eco
Mcm8 Rec/Mcm8 Mcm8 Mcm10 Mcm10/Dna43 Mcm10/Cdc23 Mcm10 Mcm10 DDK complex DDK complex DDK complex DDK complex Cdc7 Cdc7 Hsk1 l(1)G0148 Hsk1-like
1 Dbf4/Ask Dbf4 Dfp1/Him1/Rad35 Chif/chiffon Drf1 Continued 2 Replication fork assembly (Continued ) Hs Sc Sp Dm At Sso Eco
CDK complex CDK complex CDK complex CDK complex CDK complex Cdk1 Cdc28/Cdk1 Cdc2/Cdk1 Cdc2 CdkA Cdk2 Cdc2c CcnA1, A2 CycA CycA1, A2, A3 CcnB1, B2, B3 Clb1 to Clb6 Cig2/Cyc17, Cig1, Cdc13 CycB, B3 CycB1, B2, B3 CcnE1, E2 CycE Cdc45 Cdc45 Cdc45/Sna41/Goa1 Cdc45 Cdc45 PP2A PP2A PP2A PP2A PP2A RecQL4 Sld2/Drc1 Drc1 RecQL4 Treslin Sld3 Sld3 Sld3 TopBP1 Dpb11 Rad4/Cut5 Mus101 Topbp1 GINS complex GINS complex GINS complex GINS complex GINS complex Gins4 Sld5/Cdc105 Sld5 Sld5 Sld5 Gins 23 Gins1 Psf1/Cdc101 Psf1 Psf1 Psf1 Gins 15 Gins2 Psf2/Cdc102 Psf2 Psf2 Psf2 Gins3 Psf3/Cdc103 Psf3 Psf3 Psf3a, Psf3b
DNA synthesis at replication forks Hs Sc Sp Dm At Sso Eco
DNA Pol a DNA Pol a DNA Pol a DNA Pol a DNA Pol a DNA Pol B DNA Pol III core PolA/p180 Pol1/Cdc17/Crt5/Lrs9/Hpr3 Pol1 DNA Pol a180 Pola1 enzyme PolA2/p68 Pol12 Spb70/Pol12 DNA Pol a60 Pola2 DNA primase DNA primase DNA primase DNA primase DNA primase DNA primase DnaG Prim1/p48 Pri1 Spp1 DNA Pol a50 Pola3/Pri1 PriS/p38 Prim2a/p58 Pri2 Spp2 DNA Pol a73 Pola4/Pri2 PriL/p36 DNA Pol d DNA Pol d DNA Pol d DNA Pol d DNA Pol d DNA Pol Db DNA Pol III Pold1/p125 Cdc2/Pol3/Hpr6/Tex 1 Cdc6/Pol3/Mis10 DNA Pol d138 Pold1 holoenzyme Pold2/p50 Hys2/Pol31/Hus2/Sdp5 Cdc1/Mis1 DNA Pol d47 Pold2 Pold3/p66 Pol32 Cdc27 Pold3 Pold4/p12 Cdm1 Pold4 DNA Pol 1 DNA Pol 1 DNA Pol 1 DNA Pol 1 DNA Pol 1 DNA Pol B DNA Pol III Pole/p261 Pol2/Dun2 Cdc20/Pol2 DNA Pol 1 Pole1a, Pole1b holoenzyme Pole2/p59 Dpb2 Dpb2 Pole2 Pole3/p17 Dpb3 Dpb3 Pole3 Pole4/p12 Dpb4 Dpb4 Pole4 DNA Pol g DNA Pol g DNA Pol g DNA Pol g Polg/p140 Mip1 Mip1 Tam/Tamas/-g125 Polg2/p55 DNA Pol g35 RPA complex RPA complex RPA complex RPA complex RPA complex SSB SSB Rpa1/p70 Rfa1/Buf2/Fun3/Rpa1 Ssb1/Rad11/Rpa1 Rpa70 Rpa1a, Rpa1b Rpa1c, Rpa1d Rpa2/p32 Rfa2/Buf1/Rpa2 Ssb2 Rpa30 Rpa2a, Rpa2b Rpa3/p14 Rfa3 Ssb3/Rpa3 Rpa8 Rpa3a, Rpa3b PCNA Pol30 Pcn1 Mus209 PCNA1 PCNA1 b-clamp PCNA2 PCNA2 PCNA3 RFC clamp loader RFC clamp loader RFC clamp loader RFC clamp loader RFC clamp loader RFC clamp loader Fork clamp loader RNaseH2 complex RNaseH2 complex Rnaseh2a Rnh201/Rnh35 Rnh201 Rnh 1 RnaseH2 RnaseH2 RNaseH Rnaseh2b Rnh202 Rnaseh2c Rnh203 Dna2 Dna2/Web2 Dna2 CG2990 Dna2 DNA Pol I Fen1 Rad27/Erc11/Rth1 Rad2/Fen1 Fen1 Fen1 Fen1 DNA Pol I Lig1 Cdc9/Mms8 Cdc17 DNA-ligI Lig1a, Lig1b Lig1 Lig Top1/Topo I Top1/Mak1/Mak17 Top1 Top1 Top1a, Top1b Topo I,c Topo III DNA gyrase Top2/Topo II Top2/Tor3/Trf3 Top2/Ptr11 Top2 Top2 DNA gyrasec DNA gyrase Topo VI Topo IV CDK inhibitors Cdkn1a/p21/Cip1 Cdkn1b/p27/Kip1 Sic1/p40/Sdb25a Rum1/p25a Dap/Dacapo/p26 Krp1 to Krp7 Cdkn1c/p57/Kip2
Replication fork progression and stability Hs Sc Sp Dm At Sso Eco
Clspn/Claspin Mrc1 Mrc1/Huc1 Timeless Tof1 Swi1 Tim/Timeless Tim1 Tipin Csm3 Swi3 Elg1-RFC clamp loader Elg1-RFC clamp loader Elg1-RFC clamp loader Brca2/FANCd1 Brca2a, Brca2b Continued 3 4 Replication fork progression and stability (Continued ) Hs Sc Sp Dm At Sso Eco
RecQ-like helicases RecQ-like RecQ Blm Sgs1 Rqh1 Mus309/DmBlm Wrn RecQL4 RecQ4a Top3a Top3 Top3 Top3 Rmi1 Rmi1/Nec4 Rmi1 Rmi1 Rmi2
Replication-dependent chromatin assembly Hs Sc Sp Dm At Sso Eco
CHAF1/CAF1 complex CAF1 complex CAF1 complex CAF1 complex CAF1 complex p150 Rlf2/Cac1 Pcf1 p180 Fas1 p60 Cac2 Pcf2 p105 Fas2 p48 Msi1/Cac3 Pcf3 p55 Msi1 to Msi4 FACT complex FACT complex FACT complex FACT complex FACT complex Supt16h/Spt16 Spt16/Cdc68 Spt16 dre4/spt16 Spt16 Ssrp1 Pob3 Pob3 Ssrp Ssrp1 Nhp6 Nhp6 Asf1a/Cia Asf1 Cia1 Asf1 Asf1a/Sga2 Asf1b/Cia2 Asf1b/Sga1 Nap1L1 to Nap1L5 Nap1 Nap1 Nap1 Nap1 to Nap4 Nrp1 Nrp2 Npm1/nucleoplasmin Nlp/nucleoplasmin Npm2/nucleoplasmin Npm3/nucleoplasmin Nasp Hif1 Sim3 Df31 ACF complex ISW2 complex ACF complex Baz1a/Acf1 Itc1 Acf1 Acf1 Smarca5/Snf2h Isw2 Isw1 RSF complex Hbxap/Rsf1 Smarca5/hSnf2h Chd1 Chd1 Hrp1/Chd1 Chd CHRAC complex CHRAC complex Baz1a/Acf1 Acf1 Smarca5/Snf2h Iswi Chrac1/Chrac15 Top2 Pole3/Chrac17 Chrac-14 Chrac-16 Ihfa, Ihfb H2a (H2afb1, b2, b3, j, v, Hta1, Hta2 Hta1, Hta2 His2A H2a (Hta1, 2, 6, 7, 10, Alba Hua,Hub y, z)e 12, 13) H2afx/H2ax H2ax (Hta3, Hta5) H2afz/H2az Htz1/H2az Htb1 His2Av/H2AZ H2a.z (Hta4, 8, 9, 11) H2b (H2bfm, s, wt) Htb1, Htb2 His2B H2b (Htb1-11) H3 (H3f3a, H3f3c) Hht1, Hht2 Hht1, Hht2 His3 H3.1 (Htr1-3, 9, 11, Cren7 13) H3.3b (H3f3b) Hht3 H3.3 (Htr4-5, 8) H4 (Hist1h4a – Hist1H4l) Hhf1, Hhf2 Hhf1, Hhf2, Hhf3 His4 H4 (Hfo2 – 8) Sul7d H1 (H1fo, nt, oo, x) Hho1 His1 H1 (Hon1, 2, 3) Fis
Sister chromatid cohesion Hs Sc Sp Dm At Sso Eco
Wdhd1/And-1 Ctf4/Pob1/Chl15 Mcl1 Ctf4 Esco1 Eco1/Ctf7 Eso1 Eco1 Ctf18-RFC clamp loader Ctf18-RFC clamp loader Ctf18-RFC clamp loader Cohesin complex Cohesin complex Cohesin complex Cohesin complex Smc1 Smc1 Psm1 Smc1 Smc1/TTN8 Smc3 Smc3 Psm3 Smc3 Smc3/TTN7 Rad21 Scc1/Mcd1 Rad21 Rad21 Rad21.1, Rad21.2, Rad21.3 Stag1, Stag2 Irr1/Scc3 Psc3 Sa CdcA5/Sororin Dmt/Dalmatian Wfdc5/Wap1 Pds5 Pds5 Pds5 Pds5
DNA damage response Hs Sc Sp Dm At Sso Eco
ATM Tel1 Tel1 Tefu/telomere fusion/ATM ATM RecA MRN complex MRX complex MRN complex MRN complex MRN complex MRN complex RecBCD complex
5 Continued DNA damage response (Continued ) 6 Hs Sc Sp Dm At Sso Eco
ATR Mec1/Esr1/Sad3 Rad3 Mei-41/Mus-103 ATR RecA Atrip Lcd1/Ddc2/Pie1 Rad26 Mus304 Atrip Chek1/Chk1 Chk1 Chk1/Rad27 Grp/Grapes/Chk1 Chek2/Chk2 Rad53/Lsd1/Mec2/Spk1 Cds1 Lok/Loki/Chk2 Cdc25 Mih1 Cdc25/Sal2 Stg/String/Cdc25 Cdc25-like Checkpoint clamp Checkpoint clamp Checkpoint clamp Checkpoint clamp Checkpoint clamp Rad9 Ddc1 Rad9 Rad9 Rad9 Rad1 Rad17 Rad1 Rad1 Rad1 Hus1 Mec3 Hus1 Hus1 Hus1 Rad17-RFC clamp loader Rad24-RFC clamp loader Rad17-RFC clamp loader Rad17-RFC clamp loader Rad17-RFC clamp loader Ctf18-RFC clamp loader Ctf18-RFC clamp loader Ctf18-RFC clamp loader Tp53/p53 p53 Tp53bp1 Mdm2 Mdm2-like Msh2 Msh2/Pms5 Msh2 Spel1 Msh2 Msh3 Msh3 Swi4 Msh3 Msh6 Msh6/Pms3 Msh6 Msh6 Msh6 Mlh1 Mlh1/Pms2 Mlh1 Dmlh1 Mlh1 Mlh3 Mlh3 Pms1 Pms1 Pms1 Pms1 Pms2 Pms2 Dclre1c/Artemis Brca1 Rad9 Rhp9/Crb2 Brca1
Homologous recombination at stalled replication forks Hs Sc Sp Dm At Sso Eco
MRN complex MRX complex MRN complex MRN complex MRN complex MRN complex RecBCD complex Mre11 Mre11 Rad32 Mre11 Mre11 Mre11 RecB Rad50 Rad50 Rad50 Rad50 Rad50 Rad50 RecC Nbs1/Nibrin Xrs2 Nbs1 Nbs1 Nbs1 HerA, NurA RecD Uba2 Sae2 Fub2 Uba2 Sae2 Rad51 Rad51 Rhp51 Spn-a Rad51a, b, c, d RadA RecA Rad52 Rad52 Rhp52/Rad22, Rti1 RecFOR complex REcF RecO RecR Rad54b Rad54 Rhp54 Okr/Okra Rad54 Rad51C Rad55 Rhp55 Rad51c Xrcc3 Rad57 Rhp57 Spn-b Xrcc3 Rad59 Rdh54 Exo1 Exo1 Exo1 Tos/Tosca ExoII FANCi FANCd2
Clamp loaders Hs Sc Sp Dm At Sso Eco
RFC clamp loader RFC clamp loader RFC clamp loader RFC clamp loader RFC clamp loader RFC clamp loader Fork clamp loader Rfc1/p140 Rfc1/Cdc44 Rfc1 Rfc140/Gnf1 Rfc1 Rf-CL t1 Rfc2/p40 Rfc2 Rfc2 Rfc40/Rfc2 Rfc2 (Rf-CS)4 t2 Rfc3/p38 Rfc3 Rfc3 Rfc38 Rfc3 t3 Rfc4/p37 Rfc4 Rfc4 Rfc4 Rfc4 d Rfc5/p36 Rfc5 Rfc5 Rfc5 d0 x c Ctf18-RFC clamp loader Ctf18-RFC clamp loader Ctf18-RFC clamp loader Ctf18-RFC clamp loader Ctf18-RFC clamp g-complex loader g1 Chtf18 Ctf18 Ctf18 Cutlet Ctf18 g2 Dcc1 Dcc1 Dcc1 CG11788 g3 Derpc Ctf8 Ctf8 d Rfc2, 3, 4, 5 Rfc2, 3, 4, 5 Rfc2, 3, 4, 5 Rfc3, 4, 38 d0 Rad17-RFC clamp loader Rad24-RFC clamp loader Rad17-RFC clamp loader Rad17-RFC clamp loader Rad17-RFC clamp Rad17 loader Rad17 Rad24 Rad17 Rfc2, 3, 4, 5 Rad17 Rfc2, 3, 4, 5 Rfc2, 3, 4, 5 Rfc2, 3, 4, 5 Rfc2, 3, 4, 5 Elg1-RFC clamp loader Elg1-RFC clamp loader Elg1-RFC clamp loader Atad5 Elg1 Elg1
7 Rfc2, 3, 4, 5 Rfc2, 3, 4, 5 Rfc2, 3, 4, 5 Continued 8 Telomere maintenance Hs Sc Sp Dm At Sso Eco
Tert Est2 Trt1 Het-A Tert Tart Tahre Est1A, B, C Est1 Est1 Est1 Cdc13 Est3 Stn1 Stn1 Ten1 Terf1/Trf1 Taz1 Trfl6, Trfl3, Trb1, Trb2, Trfl10, Trfl5, Trfl4, Trfl8, Trb3d Terf2/Trf2 Trfl3, Trb1, Trb2, Trb3, Trfl5, Trfl6, Trfl8, Trfl7, Trfl4, Trfl10d Pot1 Pot1 Pot1 Tinf2/Tin2 TPP1/Tint1/Ptop/Pip1 Rap1 Rap1 Rap1 Tnk1/Tank1 Tnk2/Tank2 Xrcc6/Ku70 Yku70 Pku70 Irbp Ku70, Ku70-like Xrcc5/Ku80 Yku80 Pku80 Ku80 Ku80 Rif1 Rif1 Rif2 SMC5/6 complex Smc5/6 complex SMC5/6 complex Smc5 Smc5 Smc5 Smc5 Smc5 Smc6 Smc6 Smc6 Smc6a, Smc6b Nse1 Nse1 Nse1 Nse2 Mms21/Nse2 Nse2 Mms21 Nse3 Nse3 Nse3 Nse4 Nse4 Nse4/Rad62 Nse5 Nse5 Nse5 Nse6 Kre29/Nse6 Nse6 Linking DNA replication to cell division Hs Sc Sp Dm At Sso Eco
CDK complex CDK complex CDK complex CDK complex Cdk4 Cdc28/Cdk1 Cdc2/Cdk1 Cdk4 Cdk6 CcnD1,D2,D3 Cln3 Puc1 CycD CycD Cdc25A, B, C Mih1 Cdc25 Stg/String Twe/Twine APC APC APC APC APC Anapc1 Apc1 Cut4/Apc1 Apc1 Anapc2 Apc2 Apc2 Apc2 Cdc27/Apc3 Cdc27/Apc3 Nuc2/Apc3 Cdc27/Apc3 Apc3a/Cdc27a Apc3b/Cdc27b Anapc4 Apc4 Cut20/Lid1/Apc4 Apc4 Apc4 Anapc5 Apc5 Apc5 Ida/Apc5 Apc5 Cdc16/Apc6 Cdc16/Apc6 Cut9/Dre1/Apc6 Cdc16/Apc6 Apc6/Cdc16 Anapc7 Apc7 Apc7 Cdc23/Apc8 Cdc23/Apc8 Cut23/Apc8 Cdc23/Apc8 Apc8/Cdc23 Mnd2 Apc9 Anapc10 Doc1/Apc10 Apc10 Apc10 Apc10 Anapc11 Apc11 Apc11 Lmg/Apc11 Apc11 Cdc26/Apc12 Cdc26 Hcn1 Anapc13 Swm1/Apc13 Apc13 CG33981/Apc13 Apc14 Apc15 Anapc16 Cdc20 Cdc20 Slp1 Fzy Cdc20 Cdh1 Cdh1 Ste9 Fzr Fzr1/Ccs52a2 Ccs52a1
Emi1 Rca1 Emi2 CRL1/SCF2 Ub ligase CRL1/SCF Ub ligase CRL1/SCF Ub ligase CRL1/SCF Ub ligase CRL1/SCF Ub ligase Cul1 Cul1 Cdc53 Pcu1 Lin19 Rbx1 Rbx1 Hrt1/Rbx1/Roc1/ Rbx1 Skp1 Skp1 Skp1 Skp1 SkpA Rub1 Nedd8 Rub1 Ned8 Nedd8 Skp2a, Skp2b Skp2 Skp2 CG9772 9 Fbxw7 Cdc4 Cdc4 Ago/Archipelago Continued 10
Linking DNA replication to cell division (Continued ) Hs Sc Sp Dm At Sso Eco
CRL4 Ub ligase CRL4 Ub ligase CRL4 Ub ligase CRL4 Ub ligase CRL4 Ub ligase Cul4 Rtt101/Cul4 Pcu4 Cul4 Cul4 Rbx1 Hrt1/Rbx1/Roc1/ Rbx1 Rbx1 Ddb1 Mms1/Ddb1 SPBC17D11.08 Pic Ddb1a, Ddb1b Nedd8 Rub1 Ned8 Nedd8 Rub1 Dtl/Cdt2 Cdt2 L2dtl DNA replication proteins in different organisms that are homologs, orthologs, paralogs, or analogs are aligned. Homologs are proteins related by descent from a common ancestral DNA sequence. Orthologs are proteins that evolved from a common ancestral gene and retain the same function in different species. Paralogs are proteins related by duplication within a genome, but that have evolved a new function. Analogs are proteins that have a similar function but unrelated sequences. Style conventions for gene and protein nomenclature vary extensively among organisms (Table 2). Therefore, to facilitate recognition of related proteins among different organisms, the names of proteins are in Title Case and the names of protein complexes are in CAPITALS. However, as some proteins are so familiar in CAPITALS that they are not immediately recognized in Title Case, exceptions were made: PCNA (proliferating cell nuclear antigen), ATM (ataxia telangiectasia mutated), ATR (ataxia telangiectasia and Rad3 related), FANC (Fanconi anemia proteins), and SSB (single-strand DNA binding protein). Multiple names for the same protein are separated by “/” with the first name the one recommended by the standard database (Table 1). A comma separates names of different proteins of the same family. Molecular weights based on amino acid composition are indicated as p(number) [e.g., p27, protein 27 kDa in size]. ACF, ATP-utilizing chromatin assembly and remodeling factor; APC, anaphase promoting complex; CDK, cyclin-dependent protein kinase; CHAF1/CAF1, chromosome assembly factor 1; CHRAC, chromatin accessibility; CRL, Cullin-RING ubiquitin ligase; DDK, Dbf4-dependent protein kinase; FACT, facilitates chromatin transcription; GINS, Go, Ichi, Ni, and San; MCM, minichromosome maintenance; MRN, Mre11, Rad50, and Nbs1; ORC, origin recognition complex; RFC, replication factor C; RPA, replication protein A; RSF, remodeling and spacing factor. aYeast Sic1 and Rum1 share a structurally conserved inhibitory domain with mammalian p27(Kip1), although they do not inhibit Cdk.G1 cyclins in yeast. bAlthough not found in the Crenarchaeon Sulfolobus, Euryarchaeota also contain Pol D DNA polymerases. Pol D contains 30-50 exonuclease activity, uses RNA primers more efficiently, and has a higher intrinsic processivity than Pol B DNA polymerases. cTopo I and Topo II homologs have been detected in some, but not all species of Archaea, forexample, members of the Sulfolobales do not possess gyrase homologs. dThe Arabidopsis homologs to human Terf1 and to Terf2 are listed in decreasing order of similarity. eThe 31 human histones are divided into eight groups: H2A, H2B, H3, and H4 form the nucleosome core. H2AX is phosphorylated in response to double-strand DNA breaks. H2AZ and H3.3 are enriched at transcriptionally active sites. H1 links core particles together. Subgroups are in parentheses.