Table 4. Irradiation-response patterns of genes involved in replication, repair, and recombination functions in DEIRA. Pathway

Transcription

1 Supporting information for Liu et al. (2003) Proc. Natl. Acad. Sci. USA, /pnas Table 4. Irradiation-response patterns of genes involved in replication, repair, and recombination functions in DEIRA Gene Ogt/Yb DR0248 az Patway O-6-metylguanine DNA metyltransferase DR MutT DR oxo-dGTPase DR AlkA MutY DR2074 DR2584 DR metyladenine DNA glycosylase II 8-oxoguanine DNA glycosylase and AP-lyase, A-G mismatc DNA glycosylase DR, BER BER, MMY Nt-2 DR2438 Endonuclease III and BER Nt-1 DR0289 tymine DR0928 glycol DNA glycosylase YF MutM/ Fpg Nfi (Yjaf) DR0643 DR0493 N6-adenine-specific metylase Formamidopyrimidine and 8-oxoguanine DNA glycosylase BER BER DR2162 Endonuclease V BER PolA DR1707 DNA polymerase I BER Ung DR0689 Uracil DNA glycosylase BER DR

2 Mug DR0715 G/T mismatc-specific tymine DNA glycosylase Patway BER DR1751 BER Uracil DNA glycosylase DR XtA DR0354 Exodeoxyribonuclease III BER RadA Mfd DR1105 DR1532 Predicted ATP-dependent protease Transcription-repair coupling facr; elicase NER, BER NER UvrA-1 DR1771 ATPase, excinuclease NER UvrA-2 DRA UvrB UvrC UvrD MutL MutS XseA/ Nec7 SbcC SbcD DR2275 DR1354 DR1775 DR1669 DR1976 DR0186 DR1922 DR1921 Helicase, excinuclease Nuclease, excinuclease Helicase II, excinuclease ; initiates unwinding from a nick ATPase ATPase NER NER NER, mmm, SOS mmm, VSP mmm, VSP Exonuclease VII, large MM ATPase, SbcCD exonuclease Exonuclease, SbcCD RER RER

3 RecA RecD RecF DR2340 DR1902 DR1089 Recombinase; ssdnadependent ATPase; activar of LexA auproteolysis DNA-dependent ATPase or elicase; in oter bacteria, regulary of te RecBCD recombinase (elicasenuclease); RecB and RecC are missing in DEIRA. Patway RER, SOS RER ATPase; required for daugter-strand gap repair RER RecG DR1916 Holliday junction-specific DNA elicase; branc RER migration inducer RecJ DR1126 Nuclease RER RecN DR1477 ATPase RER RecO DR0819 Biocemical activity unknown; required for daugter-strand gap repair RER RecQ DR2444 DR1289 Helicase; suppressor of illegitimate recombination RER Inactivated Toprim- RecR DR0198 domain protein; required RER for daugter-strand gap

4 Patway repair RuvA DR1274 Holliday-junction-binding of te RuvABC RER resolvasome RuvB DR0596 Helicase of te RuvABC resolvasome RER RuvB DR0440 Endonuclease of te RuvABC resolvasome RER DnaC DR0507 Polymerase of te DNA polymerase III MP oloenzyme DnaQ DR0856 3'-5' exonuclease of te DNA polymerase MP III oloenzyme DnlJ DR2069 NAD-dependnet DNA ligase MP Ssb DR0099 Single-strand binding protein; D. radiodurans R1 as tree incomplete ORFs corresponding different fragments of Ssb; it remains unclear weter D. radiodurans as a functional Ssb. MP Transcriptional regular, LexA DRA0344 repressor of te SOS SOS 1.08 DRA0074 regulon, auprotease YcjD DR0221 Predicted very sort patc VSP?

5 Patway repair DR2566 nuclease HAM1/ DR0179 YggV Uve1/B DR1819 S_Ywj d Yej/R ad25 Rsr DRA0131 DR0690 Xansine tripospate pyropospatase, prevents 6-N-ydroxylaminopurin mutagenesis UV-endonuclease Helicase of superfamily II, predicted nuclease; DRA0131 as an additional McrA nuclease domain Topoisomerase IB, probably of eukaryotic origin DR NER NER ? DR1721 3'->5' nuclease? DR1262 RNA-binding protein Ro; ribonucleoproteins complexed wit several small RNA molecules. Involved in UV-resistance in Deinococcus? Mrr DR1877? Mrr-1 DR0508 Nuclease Mrr-2 DR XerC DRA0155 RER

6 Patway XerD DRB0104 Integrase/recombinase XerC/D DRC GyrA DR1913 DNA gyrase, A general GyrB DR0906 DNA gyrase, B general DnaE DR0601 DNA primase general TopA DR1374 DNA poisomerase general DnaN DR0001 DR2332 DR2410 DNA polymerase III, beta DNA polymerase III gamma and tau, inactivated AAA superfamily ATPase DNA polymerase III, gamma and tau, AAA superfamily ATPase Red, up-regulated; blue, down-regulated; pink, no canges. general general general *Te gene names are from E. coli, wenever an E. coli ortolog exists, or from B. subtilis (wit te prefix BS_). Abbreviations of DNA repair patways: DR, direct damage reversal; BER, base excision repair; NER, nucleotide excision repair; mmm, metylation-dependent mismatc repair; MMY, MutY, dependent mismatc repair; VSP, very sort patc mismatc repair; RER, recombinational repair; SOS, SOS repair; MP, multiple patways. Potential new repair patways are indicated by a question mark; general, genes tat are also involved in replication;?, unknown. Te ratio of te fluorescent intensity of a particular gene te average intensity of all arrayed genes wen nonirradiated sample is used as a labeled probe. Te maximum, minimum, or average ratio of te irradiated sample(s) arvested at te response te nonirradiated control. Tere is no SD and coefficient of variation (CV) for an average ratio of several time points.