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Supporting Information Makarova et al Table S7. Stress response-related genes in D. radiodurans (DR), D. geothermalis (DG) and T. thermophilus (TT) Type of Stress Heat/ general Heat/ general Heat/ general Heat/ general Heat/ general Protein Description and Comments Heat Shock Protein 10, molecular chaperone Heat Shock Protein 20, molecular chaperone Heat Shock Protein 60, molecular chaperone Heat Shock Protein 70, molecular chaperone Hsp70 chaperone co-factor Gene name GroL GrpE GroS DnaK DnaJ Heat/ general Small heat-shock protein IbpA/ IbpB Heat HSLJ General Related to heat shock protein, HSLJ; DR1940 contains 3 repeats of this domain ATPase subunit of Clp protease General ATPase subunit of Clp protease ClpX General ATP-dependent protease with chaperone activity ATP-dependent Lon serine protease ClpP General General ATP-dependent serine protease Do serine protease, with regulatory PDZ domain Sms HtrA General Tail-specific periplasmic serine protease Prc General Membrane-associated Zn-dependent protease I YaeL General Supporting Information Makarova et al ClpA/ ClpB Lon 1 DR gene_ID DR0607 DR0128 DR0606 DR0129 DR0126; DR1424 DR1114 DR1691 DG gene_ID Dgeo_2231 Dgeo_2077 Dgeo_2230 Dgeo_2076 Dgeo_2078 Dgeo_0451 Dgeo_0505 Dgeo_0859 DR2056 DR1940 DR0588 DR1046 DR1117 - TT gene_ID TTC1714 TTC1126 TTC1713 TTC1127 TTC1812 TTC1116 TTC1120 TTC1257 TTC0203 - COG COG0459 COG0576 COG0234 COG0443 COG2214 COG0484 COG0071 COG3187 TTC1123 COG0542 DR1973; DR0202 (+4 paralogs) DR1972 Dgeo_1475 Dgeo_1210 Dgeo_1215 Dgeo_2867 Dgeo_2152 Dgeo_0702 (+2 paralogs) Dgeo_2151 TTC0251 COG1219 COG0563 TTC0250 COG0740 DR1974 DR0349 DR2189 DR1105 DR0327 DR0745 DR1599 DR1756 DR0984 DR0300 DR1308 DR1491 DR1551 DR1507 Dgeo_2153 Dgeo_0427 Dgeo_1487 Dgeo_1212 Dgeo_2185 Dgeo_2025 Dgeo_1495 Dgeo_0676 Dgeo_0552 Dgeo_0103 Dgeo_0277 Dgeo_1216 Dgeo_1479 Dgeo_1043 TTC0418 TTC0746 COG0466 TTC0173 TTC0417 TTC0956 TTC1905 COG2802 COG1066 COG0265 TTC0929 COG0793 TTC0503 COG0750 General ATP-dependent Zn protease FtsH General Predicted Zn-dependent proteases (possible chaperones) Membrane chaperone HtpX Diadenosine tetraphosphate (Ap4A) hydrolase, HIT family, cell cycle regulation Zn-binding (lipo)protein of the ABC type Zn transport system (surface adhesin A) GTPase, protease modulator Hit DR1621 YebL DR2523 HflX Fibronectin-binding protein, function unknown General stress protein, related to thioredoxin Protease I, related to general stress protein 18, ThiJ superfamily protein Universal stress protein, nucleotide-binding BS_yloA BS_ytxJ ThiJ DR0139 DR0646 DR0559 DR1832 DR1199 DR0491 DR2363 DR2132 Dgeo_2006 Dgeo_1825 Dgeo_1423 Dgeo_1464 Dgeo_0863 SpoT DR1838 Dgeo_1308 Unconfirmed Guanosine polyphoshate (ppGpp) pyrophosphohydrolase/synthetase; No RelA counterpart like in Gram+ bacteria Histone-like DNA-binding protein HupA DRA0065 TTC0984 COG0776 Unconfirmed Starvation Haemoglobin-like flavoprotein ppGpp regulated growth inhibitor Hmp MazF - No COG COG2337 Starvation Unconfirmed Starvation Regulatory protein, MazF antagonist Phosphatase of ppGpp Starvation inducible DNA-binding protein MazE Ppx Dps Dgeo_1936 Dgeo_0281 TTC0636 - COG2336 COG0248 COG0783 Osmotic Osmotic Large conductance mechanosensitive channel Membrane protein Mscl Yggb Dgeo_0305 Dgeo_1833 TTC0261 TTC1353 COG1970 COG0668 Osmotic Osmosensitive K+ channel Histidine kinase sensor domain KdpD DRA0243 DR0417 DR0662 DR0416 DRA0185 DR2263 DRB0092 DR2422 DR1995 DR0211 DRB0088 Dgeo_0175 Dgeo_2501 Dgeo_1937 Dgeo_0389 Dgeo_2852 - COG2205 General General General General Unconfirmed General General General Starvation Supporting Information Makarova et al DR0583 DR1020 DRA0290 DR1904 DR0194 DR1004 DR1005 SugE UspA 2 Dgeo_2075 Dgeo_1832 Dgeo_2182 Dgeo_1282 Dgeo_1957 Dgeo_1956 Dgeo_2170 Dgeo_1329 Dgeo_2064 Dgeo_0534 Dgeo_0155 Dgeo_1279 Dgeo_2742 TTC0035 TTC1128 Supporting Information Makarova et al COG0465 TTC0540 TTC0565 COG0501 COG2738 COG2076 TTC1253 COG0537 TTC0227 COG0803 TTC0198 COG2262 TTC0243 COG1293 No COG COG0693 TTC1088 TTC1585 TTC0539 TTC1692 TTC1794 TTC1633 TTC1355 COG0589 COG0317 TTC0810 Supporting Information Makarova et al COG0569 TTC0809 COG0168 - COG1174 - COG1125 Dgeo_0174 - COG1732 DR1473 Dgeo_0996 TTC1616 COG1842 BS_yloU/ BS_yqhY Csp DR2068 DR0389 DR0907 DR2838 TTC0757 TTC1771 TTC1626 TTC1811 TTC1468 COG1302 CinA Dgeo_0697 Dgeo_1721 Dgeo_0638 Dgeo_1006 Dgeo_2136 KatE Dgeo_2728 - COG0753 KatA S.pombe DR1998 DRA0259 DRA0146 - - COG0753 NA DRA0145 - - COG2837 Oxidative Oxidative Peroxidase; Yet present only in plant Polyporaceae sp. Superoxide dismutase Mn or Fe dependent Superoxide dismutase Cu/Zn dependent SodA SodC Dgeo_0830 - TTC0189 - COG0605 COG2032 Unconfirmed Ferric uptake regulation protein Fur DR1279 DR1546 DRA0202 DR0644 DR0865 COG0735 Oxidative Antioxidant type thioredoxin fold protein Bcp TTC0925 TTC1639 TTC1730 TTC0933 TTP0168 TTC1261 COG1764 Osmotic Osmotic Osmotic Osmotic Osmotic Phage Alkaline Cold Unconfirmed Oxidative Oxidative Oxidative Oxidative Supporting Information Makarova et al Potassium uptake system, NAD-binding component Potassium uptake system component Proline/ glycine betaine ABC-type transport, permease subunit Proline/ glycine betaine ABC-type transport, ATPase subunit Proline/ glycine betaine ABC-type transport, periplasmic binding subunit Phage shock protein A, controls membrane integrity Alkaline shock protein, function unknown Cold shock protein, OB fold nucleic acid binding protein Competence damage protein, mitomycininduced, function unknown Catalase; DRA0259 has C-terminal proteinase I-like domain Catalase; Eukaryotic type, presumably acquired from nitrogen–fixing bacteria Protein involved in alkylperoxide and oxidative stress response, osmotically induced protein TrkA DR1666 Dgeo_1584 ProV DR1667 DR1668 DRA0138 DRA0136 DRA0137 Dgeo_1583 Dgeo_0171 Dgeo_0173 Dgeo_0172 YehZ DRA0135 PspA TrkH/ TrkG ProW DR0846 DR1208 DR1209 DR1538 DR1857 OsmC 3 Dgeo_0284 Dgeo_2141 Dgeo_0519 Dgeo_2727 Dgeo_2729 Dgeo_0990 Dgeo_0526 Dgeo_0446 COG1278 COG1058/COG1546 COG1225 Oxidative Oxidative Oxidative/ detoxication Oxidative/ detoxication Oxidative/ detoxication Detoxication Detoxication Protein involved in alkylperoxide and oxidative stress response, osmotically induced protein Peptide methionine sulfoxide reductase PMSR Thiol-alkyl hydroperoxide reductases YhfA DR1177 Dgeo_1268 TTC1007 Supporting Information Makarova et al COG1765 MsrA AhpC DR1849 DR2242 DR1209 TTP0095 - COG0225 COG0450 Thioredoxin reductase/alkyl hydroperoxide reductase Ahpf/ TrxB Dgeo_0843 Dgeo_0122 Dgeo_0990 Dgeo_2729 Dgeo_2772 Dgeo_1013 Dgeo_1576 Dgeo_2331 Dgeo_0975 TTC0003 TTC0096 TTC0853 TTC1555 - COG0492 - COG0695 TTP0059 COG2124 Glutaredoxin GrxA Cytochrome P450 (uses O2) BS_cypA or TerA of Alcalige-nes Function unknown, involved in tellurium resistance response in Alcaligenes Function unknown, membrane protein TerB of Alcalige-nes TerC of Alcalige-nes Toxic anion resistance protein , possibly tellurite resistance Chemical damaging agent resistance; In Bacillus subtilis, it is involved in low temperature and salt stress responses, TerZ/TerD-like BS_yceH Toxins Arsenate oxidoreductase (arsC-like Rodanese protein) ArsC Desiccation Desiccation protectant, LEA14 family NA Detoxication Detoxication Toxins/ general Supporting Information Makarova et al BS_Scp2 DR1982 DR2623 DR0412 DRB0033 DR2085 DRA0072 DR2473 DR2538 DR1723 DRA0186 DRC0041 DRC0001 DR2220 Dgeo_1508 Dgeo_2583 -- - COG3793 DR2226; DR1187 DRB0131 DR1127 Dgeo_0787 Dgeo_2235 COG2899 COG0861 Dgeo_0931 TTC0142 TTC0750 - DR2225 DR2221 DR2224 DR2223 DRA0057 DR2217 DRA0123DR 0136 - - COG2310 Dgeo_0756 Dgeo_2548 Dgeo_2768 Dgeo_2770 Dgeo_0403 Dgeo_1551 TTC1502 TTC0816 COG0394 COG1393 - No COG DR1372 4 COG2072 Dgeo_0944 Dgeo_0143 COG3853 Desiccation Desiccation Desiccation-related protein from Craterostigma plantagineum. To date, found only in plants. LEA76 family desiccation resistance protein NA DRB0118 NA DR0105 DR1172 DRA0345 DR2257 DR0454 Dgeo_0097 TTP0170 - No COG Dgeo_1473 Dgeo_1051 TTC1814 COG1968 DR0455 - - COG3570 DR0066; DRA0194DR 0394; DR0669 DR0842 Dgeo_2256 Dgeo_2397 Dgeo_1662 Dgeo_2485 - - - COG3231 COG3173 COG2334 no COG COG3467 TTC1957 COG1597 TTC0562 COG0486 - No COG TTC0404 COG2367 TTP0137 TTC0024 TTC0596_2 TTC1190 TTC1694 COG1540 COG0346 Drugs Erythromycin esterase BS_ybfO Drugs BacA bacitracin resistance protein, undecaprenol kinase Streptomycin resistance protein, streptomycin phosphotransferase Antibiotic (aminoglycoside); Kinase family protein BacA 5-Nitroimidazole antibiotic resistance protein; distantly related to pyridoxamine phosphate oxidase, PDXH Function unknown, involved in multidrug resistance NimABCD of Bacteroides BS_bmrU DR2234 DR1363 DR1560 Thiophen and furan oxidation, predicted GTPase tunicamycin resistance protein, predicted ATPase Beta-lactamase ThdR DR1016 Dgeo_2009 Dgeo_1118 Dgeo_1293 Dgeo_2853 Dgeo_0478 BS_tmrB DR1419 - BS_penP DRA0241 DR0433 (+DR1985) DRA0284 DR1695 DR2022 DR2104 DR2208 DR0109 DRA0224 DR1341 DR0670 Drugs Drugs Drugs Drugs Drugs Drugs Drugs Drugs Drugs Supporting Information Makarova et al Function unknown, lactam utilization protein Lactoylgluthation lyase, phosphomicin resistance protein StrA of Strepto-myces BS_ycbJ YbgL GloA 5 Supporting Information Makarova et al No COG Dgeo_0316 Dgeo_1291 Dgeo_1803 Dgeo_1712 Dgeo_1790 Dgeo_0360 Dgeo_1981 Dgeo_2419 Dgeo_0941 Dgeo_2415 COG2312 Drugs Induced by Vancomycin in Enterococcus faecalis BS_yoaR Drugs aminoglycosid N3-acetyltransferase. Present in many other bacteria. Function unknown, homologs of microcine C7 resistance protein MccF 2-nitropropane dioxygenase phosphinothricin aminoacetyltransferase BS_yokD Drugs Drugs Drugs Supporting Information Makarova et al COG2720 Dgeo_1593 Dgeo_2332 TTC1933 Dgeo_1202 - COG2746 BS_yocD DR1619 DR0009 DR0025 DR2034 DR0599 DR2000 - - COG1619 BS_yrpB BS_ywnH DR2545 DR1182 Dgeo_1494 TTC1901 - COG2070 COG1247 Genes that are absent in D. radiodurans Starvation General Oxidative Carbon starvation-induced protein, membrane ATPase subunit of clp photolytic system Glutathione peroxidase Oxidative Catalase (peroxidase I) Oxidative Mn-containing catalase Heat/ general Heat/ general Heat/ general Acid Osmotic Heat Shock Protein 90, molecular chaperone DnaK suppressor protein Transcriptional regulator of heat shock genes unknown Trehalose-6-phosphate synthase Osmotic Trehalose-6-phosphatase Supporting Information Makarova et al CstA ClpY (HslU) BtuE/ BS_bsaA KatG - - TTC0264 - COG1966 COG1220 COG0386 - - - COG0376 - - TTC1872 COG3546 HtpG DksA HrcA YajQ OtsA - Dgeo_0059 TTC1948 - COG0326 COG1734 COG1420 COG1666 COG0380 OtsB - Dgeo_0060 - COG1877 6
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