Table 2.

Genes coding for replication, repair, and recombination functions in D. radioduransa

Gene namebGene_IDProtein description and commentsPathwaycPhylogenetic patternd
yhdJ DRC0020Adenine-specific DNA methylasemMM? -m-k--vd-e--huj-------
ogt/ybaZ DR0248 O-6-methylguanine DNA methyltransferaseDR amtkyqvd-ebrhuj---lin-
mutT DR02618-oxo-dGTPase;D. radiodurans encodes another 22 paralogs; only some predicted to function in repairDR --t----d-ebrhuj---lin-
alkA DR2074, DR25843-methyladenine DNA glycosylase II; DR2584 is of eukaryotic typeDR, BER -------d--br-----o--nxa-tky--dcebr----------
mutY DR22858-oxoguanine DNA glycosylase and AP-lyase, A-G mismatch DNA glycosylaseBER, MMY --t----d-ebrhuj---lin-
nth DR2438, DR0289, DR0928Endonuclease III and thymine glycol DNA glycosylase; DR0928 and DR2438 are of archaeal type, and DR0289 is close to yeast proteinBER amtkyqvdcebrhuj--olinx
mutM/fpg DR0493Formamidopyrimidine and 8-oxoguanine DNA glycosylaseBER -------dcebrh--gp-----
nfi (yjaF)DR2162Endonuclease VBER a--k-qvd-eb----------
polA DR1707DNA polymerase IBER --t--qvdcebrhujgpolinx
ung DR0689, DR1663Uracil DNA glycosylase; DR0689 is a likely horizontal transfer from a eukaryote or a eukaryotic virusBER ----y--d-ebrhujgpo-inx
mug DR0715G/T mismatch-specific thymine DNA glycosylase, distantly related to DR1751; present as a domain of many multidomain proteins in many eukaryotesBER -------d-e------------
DR1751, DR0022Uracil DNA glycosylaseBER a--k-qvdc-br-----ol--x
xthA DR0354Exodeoxyribonuclease IIIBER a-t-y--dcebrhuj--ol--x
sms DR1105Predicted ATP-dependent proteaseNER, BER -----qvdcebrhuj---linx
mfd DR1532Transcription repair coupling factor; helicaseNER ------vdcebrhuj--olinx
uvrA DR1771, DRA0188ATPase, DNA bindingNER --t--qvdcebrhujgpolinx
uvrB DR2275HelicaseNER --t--qvdcebrhujgpolinx
uvrC DR1354NucleaseNER --t--qvdcebrhujgpolinx
uvrD DR1775, DR1572Helicase II; initiates unwinding from a nick; DR1572 has a frameshiftNER, mMM, SOS --t-yqvdcebrhujgpolinx
mutL DR1696Predicted ATPasemMM, VSP ----yqvdceb-h----olinx--tk-qvdc-b--uj--o----
mutS DR1976, DR1039ATPase; DR1039 has a frameshiftmMM, VSP ----yqvdceb-h----olinx
xseA/nec7 DR0186Exonuclease VII, large subunitMM ------vd-ebrhuj----inx
sbcC DR1922Exonuclease subunit, predicted ATPaseRER amtkyqvdceb------ol---
sbcD DR1921ExonucleaseRER amtkyqvdcebr-----ol---
recA DR2340Recombinase; single-stranded DNA-dependent ATPase, activator of lexAautoproteolysisRER, SOS amtkyqvdcebrhujgpolinx
recD DR1902Helicase/exonuclease; contains three additional N-terminal helix-hairpin-helix DNA-binding modules; closely related to RecD from B. subtilis andChlamydia RER -m--y--d-ebrh----o-in-
recF DR1089Predicted ATPase; required for daughter strand gap repairRER -------dcebrh-----li-x
recG DR1916Holliday junction-specific DNA helicase; branch migration inducerRER -----qvdcebrhuj--ol--x
recJ DR1126NucleaseRER amtk-qvdceb-huj--olinx
recN DR1477Predicted ATPaseRER -----q-dcebrhuj---l--x
recO DR0819Required for daughter strand gap repairRER -------dcebrh-----lin-
recQ DR2444, DR1289Helicase; suppressor of illegitimate recombinationRER ----y--dceb-h-----l---
recR DR0198Required for daughter-strand gap repairRER -----q-dcebrhuj---linx
ruvA DR1274Holliday junction-binding subunit of the RuvABC resolvasomeRER --t--qvdcebrhujgpolinx
ruvB DR0596Helicase subunit of the RuvABC resolvasomeRER ------vdceb-hujgpolinx
ruvC DR0440Endonuclease subunit of the RuvABC resolvasomeRER ------vdce-rhuj---linx
dnaE DR0507Polymerase subunit of the DNA polymerase III holoenzymeMP -----qvdcebrhujgpolinx
dnaQ DR08563′-5′ exonuclease subunit of the DNA polymerase III holoenzymeMP -----qvdcebrhujgpolinx
dnlJ DR2069DNA ligaseMP -----qvdcebrhujgpolinx
ssb DR0099Single-strand-binding protein; D. radiodurans R1 has three incomplete ORFs corresponding to different fragments of the SSBMP -----qvdcebrhujgpolinx
lexA DRA0344, DRA0074Transcriptional regulator, repressor of the SOS regulon, autoproteaseSOS -----vdcebrh---------
ycjD DR0221, DR2566Uncharacterized proteins related to vsr VSP? --t---vd-e-rh---------
BS_dinB 13 homologs (see Fig. 5)Uncharacterized family of presumably metal-dependent enzymes? -------dc-br----------
ham1/yggV DR0179Xanthosine triphosphate pyrophosphatase, prevents 6-N-hydroxylaminopurine mutagenesisDR amtkyqvdcebrh----olin-
uve1/BS_ywjD DR1819UV endonuclease; activity was characterized inNeurospora NER -------d-b-----------
yejH/rad25 DRA0131DNA or RNA helicase of superfamily II; also predicted nuclease; contains an additionalmcrA nuclease domainNER a--ky--d-e-r------l---
DR0690Topoisomerase IB; currently the only bacterial representative of topoisomerase IB? ----y--d--------------
DR17213′→5′ nuclease; related to baculoviral DNA polymerase exonuclease domain? -------d--------------
DR1262Ro RNA binding protein; ribonucleoproteins complexed with several small RNA molecules; involved in UV resistance inDeinococcus ? -------d--------------
DR1757Predicted nuclease and zinc finger domain-containing protein; an ortholog is present in Pseudomonas aeruginosa ? -------d--------------
mrr DR1877, DR0508, DR0587MRR-like nuclease; restrictase of the recB archaeal Holliday junction resolvase superfamily? ------vdc----u--------
tage 3-Methyladenine DNA glycosylase IBER ---------e-rh---------
vsre Strand-specific, site-specific, GT mismatch endonuclease; fixes deamination resulting fromdcm VSP ---------e------------
rusA(ybcP)e Endonuclease/Holliday junction resolvaseRER -------v-eb-----------
xseBe Exonuclease VII, small subunitMM -------v-ebrh--------x
recBe Helicase/exonucleaseRER ---------ebrhuj--olinx
recCe Helicase/exonucleaseRER ---------e-rh----o-in-
adae O-6 alkylguanine, O-4 alkylthymine alkyltransferase; removes alkyl groups of many types; transcription activatorDR amtkyqv--ebrhuj---lin-
alkBe UnknownDR, BER(?) ---------e------------
dute DUTPaseDR ----yq---ebrhuj---linx
dcde dCTP deaminaseDR amtk-q--ce-rhuj----inx
nfoe Endonuclease IVBER -mtkyqv--ebr---gp--in-
phrBe PhotolyaseDR --t-y---ce------------
mutHe EndonucleasemMM ---------e------------
dame GATC-specific N-6 adenine methlytransferase; imparts strand specificity to mismatch repairmMM -m-k----ce--huj---l---
polBe DNA polymerase IISOS amtky----e------------
sbcBe Exodeoxyribonuclease ImMM, RER ---------e--h---------
dcme Site-specific C-5 cytosine methyltransferase; VSP is targeted toward hot spots created bydcm mMM -mtk---dceb-huj-------
dinPe Specific function unknown (predicted nucleotidyltransferase)MM, RER See umuC
recEe Exonuclease VIIIRER ---------e------------
recTe Annealing proteinRER ---------eb-----------
dinGe Predicted helicase; SOS inducerSOS -mtkyq---ebrh---------
umuCe Error–prone DNA polymerase; in conjunction with umuD and recA, catalyzes translesion DNA synthesisSOS ----y---cebr---gp-----
umuDe In conjunction withumuC and recA, facilitates translesion DNA synthesis; autoproteaseSOS See LexA
radCe Predicted acyltransferase; predicted DNA-binding proteinBER -----qv-ceb-h---------
  • a Based largely on reference20, with modifications

  • b The gene names are from E. coli, whenever an E. coli ortholog exists, or from B. subtilis (with the prefix BS_). ham1 anduve1 genes are from Saccharomyces cerevisiae andNeurospora crassa, respectively; where no ortholog was detectable in either E. coli or B. subtilis, no gene is indicated.

  • c Abbrevistion of DNA repair pathways: DR, direct damage reversal; BER, base excision repair; NER, nucleotide excision repair; mMM, methylation-dependent mismatch repair; MMY,mutY-dependent mismatch repair; VSP, very-short-patch mismatch repair; RER, recombinational repair, SOS, SOS repair; MP, multiple pathways; ?, unknown possible repair pathways or uncertain assignments.

  • d Abbreviations in phylogenetic patterns: a,Archaeoglobus fulgidus; m, Methanococcus jannaschii; t, Methanobacterium thermoautotrophicum; k,Pyrococcus horikoshii; y, Saccharomyces cerevisiae; q, Aquifex aeolicus; v, Thermotoga maritima; c, Synechocystis; e, E. coli; b,Bacillus subtilis; r, Mycobacterium tuberculosus; h, Haemophilus influenzae; u, Helicobacter pylori; j, Helicobacter pylori J99; g, Mycoplasma genitalium; p, Mycoplasma pneumoniae; o, Borrelia burgdorferi; l, Treponema pallidum; i, Chlamydia trachomatis; n, Chlamydia pneumoniae, x,Rickettsia prowazekii.

  • e E. coli repair genes with no orthologs in D. radiodurans.