Table 3.

Stress response-related genes in D. radiodurans

Gene nameGene_IDProtein description and commentsaType of stressPhylogenetic patterna
groL DR0607Hsp10, molecular chaperoneHeat, general amtkyqvdcebrhujgpolinx
grpE DR0128Hsp20, molecular chaperoneHeat, general --t--qvdcebrhujgpolinx
groS DR0606Hsp60, molecular chaperoneHeat, general ----yqvdcebrhujgpolinx
dnaK DR0129Hsp70, molecular chaperoneHeat, general --t-yqvdcebrhujgpolinx
dnaJ DR0126, DR1424Hsp70 chaperone cofactorHeat, general --t-yqvdcebrhujgpolinx
ibpA/ibpB DR1114, DR1691Small heat shock proteinHeat, general amtkyqvdcebr---------x
hslJ DR2056, DR1940Related to heat shock protein, HslJ; DR1940 contains three repeats of this domainHeat -------dce------------
clpA/clpB DR0588, DR1046, DR1117ATPase subunit of Clp proteaseGeneral --t-yqvdcebrhujgpolinx
clpX DR1973, DR0202ATPase subunit of Clp proteaseGeneral ----yqvdcebrhuj--olinx
clpP DR1972ATP-dependent protease with chaperone activityGeneral ----yqvdcebrhuj--olinx
lon DR1974, DR2189, DR0349ATP-dependent Lon serine proteaseGeneral ----yqvd-eb-hujgpolinx
sms DR1105ATP-dependent serine proteaseGeneral -----qvdcebrhuj---linx
htrA DR0327, DR0745, DR1599, DR1756, DR0984, DR0300Do serine protease, with regulatory PDZ domainGeneral --t-yqvdcebrhuj--olinx
prc DR1308, DR1491, DR1551Tail-specific periplasmic serine proteaseGeneral -----qvdceb-huj--olinx
yaeL DR1507Membrane-associated Zn-dependent protease IGeneral amtk-qvdcebrhuj--olinx
ftsH DR0583, DR1020, DRA0290ATP-dependent Zn proteaseGeneral ----yqvdcebrhujgpolinx
htpX DR0190, DR0194Predicted Zn-dependent proteases (possible chaperones)General amtkyq-dcebrhuj-------
sugE DR1004, DR1005Membrane chaperoneGeneral -------d-ebr----------
hit DR1621Diadenosine tetraphosphate (Ap4A) hydrolase, HIT family, cell cycle regulationGeneral amtkyq-dcebrhujgpo-inx
yebL DR2523Zn-binding (lipo)protein of the ABC type Zn transport system (surface adhesin A)General amtk-qvdcebrh-----linx
hflX DR0139, DR0646GTPase, protease modulatorGeneral -m-k-qvdcebrhujgpolinx
BS_yloA DR0559Fibronectin-binding protein, function unknown? amtky-vdc-b--uj--o----
BS_ytxJ DR1832General stress protein, related to thioredoxinGeneral -------d--b-----------
thiJ DR0491, DR1199Protease I, related to general stress protein 18, ThiJ superfamily proteinGeneral am-kyq-dcebrhujgpol---
uspA DR2363, DR2132Universal stress protein, nucleotide-bindingGeneral amtk-q-dcebrh--------x
spoT DR1838Guanosine polyphosphate (ppGpp) pyrophosphohydrolase/synthetase: no RelA counterpart like in gram-positive bacteriaStarvation -------dcebrhujgpo----
hupA DRA0065Histone-like DNA-binding protein? -----qvdcebrhujgpolinx
hmp DRA0243Haemoglobin-like flavoprotein? ----yq-d-eb-----------
mazF DR0417, DR0662ppGpp-regulated growth inhibitorStarvation -------d-ebr----------
mazE DR0416Regulatory protein, MazF antagonistStarvation -------dce------------
ppx DRA0185Phosphatase of ppGpp? ----yqvdce--huj------x
dps DR2263, DRB0092Starvation inducible DNA-binding proteinStarvation -------dceb-huj-ol--x
mscL DR2422Large conductance mechanosensitive channelOsmotic -------dcebrh--------
yggB DR1995, DR0211Membrane proteinOsmotic amtk-qvdcebrhuj-ol--x
kdpD DRB0088Osmosensitive K+ channel histidine kinase sensor domainOsmotic -------dce-r----------
trkA DR1666Potassium uptake system, NAD-binding componentOsmotic amtk-q-dcebrh-gpol---
trkH/trkG DR1667, DR1668Potassium uptake system componentOsmotic amtk-qydceb-h-gpol---
proW DRA0138, DRA0139Proline/glycine betaine ABC-type transport, permease subunitOsmotic a------debr-hj--o----
proV DRA0137Proline/glycine betaine ABC-type transport, ATPase subunitOsmotic a------debr-hj--o----
yehZ DRA0135Proline/glycine betaine ABC-type transport, periplasmic binding subunitOsmotic a------debr-hj-------
pspA DR1473Phage shock protein A, controls membrane integrityPhage -----q-dceb-----------
BS_yloU/BS_yqhY DR2068, DR0389Alkaline shock protein, function unknownAlkaline ------vd--b--------in-
csp DR0907Cold shock protein, OB fold nucleic acid-binding proteinCold -----qvd-ebrh--------x
cinA DR2838Competence damage protein, mitomycin-induced, function unknown? -----qvdcebr-hjgp-----
katE DR1998, DRA0259Catalase; DRA0259 has C-terminal proteinase I-like domainOxidative ----y--d-eb-huj-------
catA(S. pombe)DRA0146Catalase; eukaryotic type, presumably acquired from nitrogen-fixing bacteriaOxidative -------d--------------
NAc DRA0145Peroxidase; Yet present only in plant Polyporaceae spp.Oxidative -------d--------------
sodA DR1279Superoxide dismutase, Mn or Fe dependentOxidative -t--yq-dcebrhuj--o-inx
sodC DR1546, DRA0202Superoxide dismutase, Cu/Zn dependentOxidative ----yq-d-ebr----------
fur DR0865Ferric uptake regulation protein? a----qvdcebrhujgpo----
bcp DR0846, DR1208Antioxidant type thioredoxin fold proteinOxidative ----yqvdcebrhuj-------
osmC DR1538, DR1857Protein involved in alkylperoxide and oxidative stress response, osmotically induced proteinOxidative -------d-eb----gp-----
yhfA DR1177Protein involved in alkylperoxide and oxidative stress response, osmotically induced proteinOxidative ---k-qvd-e------------
msrA DR1849Peptide methionine sulfoxide reductase PMSROxidative -t-y--dcebrhujgp-l---
ahpC DR2242, DR1209Thiol-alkyl hydroperoxide reductasesOxidative/detoxication amtkyqvdcebr-uj---linx
ahpF/trxB DR1982, DR2623, DR0412, DRB0033Thioredoxin reductase/alkyl hydroperoxide reductaseOxidative/detoxication amtkyqvdcebrhujgpolinx
grxA DR2085, DRA0072GlutaredoxinOxidative/detoxication a-tky-vdcebrh-----l-x
BS_cypA or terA ofAlcaligenes DR2473, DR2538, DR1723, DRA0186, DRC0041, DRC0001Cytochrome P450 (uses O2)Detoxication ----y--dc-b-----------
terB of Alcaligenes DR2220Function unknown; involved in tellurium resistance response inAlcaligenes Detoxication -------d--------------
terC of Alcaligenes DR2226, DR1187, DRB0131Function unknown; membrane proteinDetoxication -------dcebrhuj------x
BS_yceH DR1127Toxic anion resistance protein; possibly tellurite resistanceDetoxication --------d-b------------
BS_scp2 DR2225, DR2221, DR2224, DR2223, DRA203Chemical damaging agent resistance; in B. subtilisit is involved in low-temperature and salt stress responseToxins/general -------dc-b------------
arsC DRA0123, DR0136Arsenate oxidoreductase (arsC-like rodanese protein)Toxins -------d-ebh-----------
NADR1372Desiccation protectant, LEA14 familyDesiccation am-k---d--------------
NADRB0118Desiccation-related protein fromCraterostigma plantagineum; found to date only in plantsDesiccation -------d-------------
NADR0105, DR1172LEA76 family desiccation resistance proteinDesiccation -------d--------------
BS_ybfO DRA0345, DR2257Erythromycin esteraseDrugs -------d--br----------
bacA DR0454BacA bacitracin resistance protein, undecaprenol kinaseDrugs -----qvdcebr-----o----
strA ofStreptomyces DR0455Streptomycin resistance protein, streptomycin phosphotransferaseDrugs -------d--------------
BS_ycbJ DR0066, DRA0194, DR0394, DR0669Antibiotic (aminoglycoside) kinase family proteinDrugs -------dc-br----------
nimABCD ofBacteroides DR08425-Nitroimidazole antibiotic resistance protein; distantly related to pyridoxamine phosphate oxidase (PDXH)Drugs -------d--------------
BS_bmrU DR2234, DR1363, DR1560Function unknown; involved in multidrug resistanceDrugs ----y-vdcebr----------
thdR DR1016Thiophen and furan oxidation, predicted GTPaseDrugs ----yqvdceb-hujgpolinx
BS_tmrB DR1419Tunicamycin resistance protein, predicted ATPaseDrugs -------d--b-----------
BS_penP DRA0241, DR0433β-LactamaseDrugs -------dc-br----------
ybgL DRA0284Function unknown, lactam utilization proteinDrugs ---k---d-eb-h----------
gloA DR1695, DR2022, DR2104, DR2208, DR0109, DRA0224Lactoylgluthation lyase, fosphomicin resistance proteinDrugs amtk---dcebrh----------
BS_yoaR DR1619, DR0009, DR0025Induced by vancomycin in Enterococcus faecalis Drugs -------d--b-----------
BS_yokD DR2034, DR0599Aminoglycoside N3-acetyltransferase; present in many other bacteriaDrugs -------d--b-----------
BS_yocD DR2000Function unknown; homologs of microcine C7 resistance protein MccFDrugs -------dceb--------l--x
lytB DR2164Function unknown; penicillin tolerance proteinDrugs -----qvdcebrhuj---lin-
BS_yrpB DR25452-Nitropropane dioxygenaseDrugs a---yqvd--br-uj-------
BS_ywnH DR1182Phosphinothricin aminoacetyltransferaseDrugs -------dceb-----------
cstAb Carbon starvation-induced protein, membraneStarvation -----q---ebrhuj-------
clpYb ATPase subunit of clp proteopltic systemGeneral -----qv--eb-huj---o---x
btuE/BS_bsaAb Glutathione peroxidaseOxidative ----y---ceb-----------
katGb Catalase (peroxidase I)Oxidative a---y---ce-r----------
htpGb HSP90, molecular chaperoneHeat, general ----y---cebrhuj--ol-x
dksAb DnaK suppressor proteinHeat, general -----q---eb-h----olinx
hrcAb Transcriptional regulator of heat shock genesHeat, general ------v-c-br-ujgp--in-
yajQb UnknownAcid ---------ebrh---------
otsAb Trehalose-6-phosphate synthaseOsmotic --t-y----e-r----------
otsBb Trehalose-6-phosphataseOsmotic --t-y---c-r----------
  • a Abbreviations in the phylogenetic patterns and gene descriptions are as in Table 2.

  • b Genes that are absent in D. radiodurans.

  • c NA, not applicable.