TABLE 2

Genes with increased transcript levels following UV-irradiation

Wild type: minutes post irradiationclexA1: minutes post irradiation
GeneWT
(ave)b
lexA1
(ave)
51020406020
(No
UV)
60
(No
UV)
51020406020
(No
UV)
60
(No
UV)
Possible function
Replication and repair
umuCa20.60.9745.2220.5915.5839.3622.741.110.90.950.910.950.971.041.040.94PolV, SOS mutagenesis
recNa20.180.93728.9426.226.729.7623.071.361.310.790.80.850.90.760.990.76Protein used in DNA repair
umuDa17.361.0465.1312.4228.5627.0781.180.690.941.011.111.011.0310.95SOS mutagenesis; forms complex with PolV
recAa10.081.2516.166.289.268.494.570.60.781.090.950.931.041.120.80.84Homologous strand pairing, DNA strand exchange
dinBa7.7491.0983.665.87.085.725.250.711.031.020.810.941.030.880.88PolIV
uvrBa4.1421.4963.164.4245.034.620.941.111.151.111.351.631.680.980.87DNA repair; excision nuclease subunit B
uvrAa3.8461.1671.961.791.681.371.180.390.441.071.010.880.850.830.740.85DNA repair; excision nuclease subunit A
ruvAa3.5521.0434.544.63.073.763.31.061.111.1611.11.071.21.150.97Holliday junction helicase subunit B; branch migration
polBa3.21.0981.461.71.611.652.140.520.550.910.760.730.822.190.911.06DNA polymerase II
ydjQa3.3610.8522.783.352.132.412.270.630.910.870.790.680.690.590.860.84Putative excinuclease subunit
uvrDa2.5051.1271.251.021.221.471.490.470.561.11.031.171.21.331.090.98DNA excision repair; helicase II
recF1.7921.6751.221.10.990.981.310.590.662.011.651.110.980.910.860.73ssDNA and dsDNA binding, ATP binding
dnaN1.6841.591.831.461.091.051.350.810.82.251.751.61.151.081.020.95DNA polymerase III, b-subunit
dnaA1.6271.6332.451.321.591.21.370.841.112.572.071.721.351.271.031.17DNA initiation of chromosome replication
dnaC1.4821.6212.061.521.321.641.281.20.911.681.411.541.881.921.150.93DNA replication initiation and chain elongation
rep1.6221.4331.130.830.81.11.330.570.711.671.531.561.681.911.141.19Rep helicase, chromosome replication
ruvBa1.9310.8893.192.962.662.782.221.421.441.011.011.011.020.861.091.12Holliday junction helicase subunit A; branch migration
ruvC1.3751.4521.010.760.890.810.620.50.691.581.511.551.491.641.160.98Holliday junction nuclease; resolution of structures
Transcription and transcriptional regulation
lexAa4.80.9143.213.073.082.772.510.610.610.840.60.670.60.490.780.62Regulator for SOS(lexA) regulon
dinIa4.4611.022.462.813.242.781.980.490.71.0411.061.10.90.971.03Damage-inducible protein I
deaD1.4792.8191.310.650.850.640.580.50.592.111.351.621.72.10.650.61Inducible ATP-independent RNA helicase
rpoD1.712.1312.331.841.361.430.950.870.982.782.732.412.432.861.281.2RNA polymerase, sigma(70) factor
hepA1.92ND1.841.821.772.161.530.891.01Probable ATP-dependent RNA helicase
fisa2.2941.3663.022.191.942.011.220.830.981.631.431.561.441.521.051.17DNA inversion factor, transcription factor
suhBa2.0811.5551.941.331.351.60.960.690.692.382.072.252.562.711.441.64Enhances synthesis of s32 in mutant
ttka2.1791.4082.672.071.772.561.771.090.91.41.521.581.441.170.94Putative transcriptional regulator
ydeOa2.4121.0091.643.3710.332.981.581.651.131.111.191.231.321.181.19Putative ARAC-type regulatory protein
rph1.751.5951.531.080.821.41.250.690.71.691.661.762.041.821.221.03RNase PH
srmB1.4741.8391.961.421.161.541.290.881.122.782.42.32.492.721.311.45ATP-dependent RNA helicase
soxS1.7281.3452.071.482.10.951.060.851.061.11.231.481.050.930.83Regulation of superoxide response regulon
rnpA1.6961.3292.321.471.241.341.050.810.941.451.281.241.291.450.941.08RNase P component; processes tRNA, 4.5S RNA
Nucleoside metabolism
nrdA2.0515.0462.112.063.158.286.52.371.941.061.664.9111.7420.491.771.39Ribonucleoside reductase 1, α-subunit, B1
grxAa4.5151.2052.1825.259.651.91.21.661.91.070.9111.061.230.950.8Glutaredoxin coenzyme for ribonucleotide reductase
nrdB2.1172.9561.41.262.515.924.471.531.410.811.052.255.237.141.151.08Ribonucleoside reductase 1, β-subunit, B2
upp2.1261.92214.459.437.348.623.323.934.1943.532.262.632.761.531.63Uracil phosphoribosyltransferase
pyrF1.7341.7012.131.971.22.662.11.11.221.961.571.491.761.980.931.13Orotidine-59-phosphate decarboxylase
tsx1.9641.3314.082.341.612.121.240.931.391.721.511.421.261.211.051.09Nucleoside channel; phage T6 receptor and colicinK
guaA1.8331.4472.041.891.082.091.470.910.961.721.891.51.61.611.051.25GMP synthetase (glutamine-hydrolyzing)
speB1.4941.7571.131.060.890.880.970.620.71.681.491.811.751.660.920.99Agmatinase
purF1.7281.5153.132.371.273.242.171.311.512.51.91.611.671.561.141.3PRPP aminotransferase
dfp1.6011.6022.91.951.962.192.651.411.52.061.621.81.781.751.290.96Flavoprotein affecting DNA panthothenate metabolism
pyrH1.6021.562.361.331.131.81.230.851.111.711.531.721.561.011.08Uridylate kinase
ntpA1.4161.7321.541.531.251.761.390.921.191.551.791.81.881.911.06dATP pyrophosphohydrolase
dut1.6411.5041.681.280.951.421.480.840.821.361.431.51.551.641.060.93Deoxyuridinetriphosphatase
gauB1.5091.5322.641.761.532.331.811.231.442.021.981.751.971.511.211.2IMP dehydrogenase
purB1.4791.5263.312.822.393.382.261.492.342.142.21.862.181.921.361.34Adenylosuccinate lyase
gpt1.6661.3192.852.0121.91.031.091.261.671.511.361.481.41.011.24Guanine-hypoxanthine phosphoribosyltransferase
pyrD1.5571.4268.045.092.985.82.732.763.572.021.71.171.291.21.011.06Dihydro-orotate dehydrogenase
purH1.4941.4780.720.930.491.511.730.580.861.651.551.81.681.121.14AICAR formyltransferase; IMP cyclohydrolase
pyrE1.8391.1241.381.060.851.31.250.60.671.131.060.921.020.930.940.86Orotate phosphoribosyltransferase
murB1.4571.4383.182.012.352.682.61.631.891.21.171.251.331.090.870.81UDP-N-acetylenolpyruvoylglucosamine reductase
cmk1.51.371.691.80.992.181.481.240.931.481.461.371.461.391.081.01Cytidylatate kinase
kdsB1.6231.2250.821.110.661.851.320.70.7211.150.811.050.950.850.77CTP:CMP-3deoxy-d-manno-octulosonate transferase
Translation/amino acid metabolism
argS1.7081.6452.512.81.593.362.551.671.331.861.71.461.831.911.131Arginine tRNA synthetase
prfC1.6561.5762.011.491.281.751.790.981.031.981.581.681.921.11.22Peptide chain release factor RF-3
aspS1.6621.542.131.651.271.531.691.010.982.191.822.042.152.041.381.28Aspartate tRNA synthetase
speA1.4851.7151.621.491.11.261.250.870.942.122.241.761.871.71.031.23Biosynthetic arginine decarboxylase
prfB1.5981.5941.971.391.371.732.130.971.181.61.621.591.671.450.961.03Peptide chain release factor RF-2
fabZ1.6981.4923.632.72.712.941.821.641.611.511.461.51.661.591.041.03(3R)-hydroxymyristol acyl carrier dehydratase
tgt1.6821.5072.21.651.641.961.591.071.081.91.841.861.91.691.21.24tRNA-guanine transglycosylase
yjeA1.7591.2981.851.631.141.40.930.950.631.581.391.451.451.431.051.2Putative lysyl-tRNA synthetase
gltX1.671.3753.652.841.883.492.671.951.531.681.671.61.972.051.21.41Glutamate tRNA synthetase, catalytic subunit
queA1.6131.3811.220.840.831.050.90.610.591.81.51.551.581.821.141.25Synthesis of queuine in tRNA
yafTa1.7471.1231.161.151.91.730.960.890.691.161.051.141.341.151.011.07Putative aminopeptidase
Heat shock, transport proteins
ycgHa5.8231.0864.1620.6710.372.071.291.911.131.081.121.171.581.041.2Putative ATP-binding transport system component
glvBa5.7370.9021.653.694.643.843.820.740.491.051.0811.10.911.111.17PTS system, arbutin-like IIB component
yeeF3.0862.8156.085.672.973.51.221.251.274.983.82.872.442.381.171.17Putative amino acid/amine transport protein
ybeWa2.9860.9130.91.768.271.971.080.840.91.031.121.040.961.2Putative dnaK protein
ibpB*2.2161.3352.992.712.593.161.91.281.131.191.241.261.391.561.090.9Heat-shock protein
corA1.8051.631.881.371.152.212.010.980.932.392.042.082.522.381.431.37Mg21 transport, system I
yhfC1.7711.5732.112.011.272.221.511.031.032.271.61.811.791.771.141.21Putative transport
sdaC1.7621.3841.821.850.721.891.431.170.581.71.61.591.541.71.261.09Probable serine transporter
potBa1.8331.2264.543.131.982.772.061.541.621.761.291.041.091.010.971.05Spermidine/putrescine transport system permease
hslU1.5591.4981.641.731.412.072.541.211.21.241.792.12.022.511.411.17Heat-shock protein hslVU, ATPase subunit
potC1.5011.4894.533.661.752.612.051.822.072.442.021.341.261.281.011.23Spermidine/putrescine transport system permease
uraA1.5541.382.852.140.881.650.990.821.372.372.051.151.311.161.061.27Uracil transport
potD1.3831.4982.032.31.991.581.231.241.41.982.692.232.091.721.51.36Spermidine/putrescine periplasmic transport protein
potA1.611.2414.433.361.752.511.471.981.381.741.821.381.191.161.061.29ATP-binding component of spermidine transport
artP1.5031.3053.152.891.432.921.521.751.421.751.581.321.641.541.281.12Third arginine transport system, ATP-binding
Cell Division
sulA*9.5611.10813.7411.713.1711.559.361.051.440.850.920.760.90.890.890.67Suppressor of lon; inhibits cell division
Prophage genes
ymfNa7.571.0340.093.357.120.540.391.11.031.141.10.931.150.9Orf, hypothetical protein
intEa4.2920.9051.051.171.767.9621.111.651.430.910.960.951.011.151.031.17Prophage e14 integrase
ymfJa3.6581.0040.71.021.1713.564.951.171.030.90.940.960.9410.9Orf, hypothetical protein
ymfGa2.5140.9960.751.311.054.56.281.11.110.981.041.031.121.011.051.03Orf, hypothetical protein
ogrKa2.1911.2422.984.76.893.231.591.691.851.121.111.1421.090.941.14Prophage P2 ogr protein
ybcUa1.8541.0049.355.63.685.152.972.613.161.161.051.021.031.011.021.08Bacteriophage l Bor protein homolog
Others
prfB2.159ND1.961.411.241.732.080.78
fabF1.7882.2493.052.232.532.731.81.381.381.81.891.972.242.951.020.913-oxoacyl-[acyl-carrier-protein] synthase II
pphB2.7431.1892.183.188.51.291.241.31.091.111.021.011.071.080.940.84Protein phosphatase 2
yhdG2.0871.7441.831.591.241.660.880.680.72.382.012.131.931.841.181.18Putative dehydrogenase
hlyE1.894ND2.522.974.353.081.571.281.78Hemolysin E
ribH1.8571.7031.140.990.81.11.170.410.711.641.571.481.61.630.930.93Riboflavin synthase, b chain
gidA1.6781.5581.140.870.780.931.020.520.611.391.421.651.461.440.831.06Glucose-inhibited division; chromosome replication?
prmA1.595ND1.291.181.041.311.120.630.86
cvpA1.7911.3683.053.151.774.852.672.031.431.611.311.291.441.190.941.06Membrane protein required for colicin V production
pabC1.555ND1.251.191.251.571.270.840.844-amino-4-deoxychorismate lyase
pta1.661.4441.721.731.142.572.261.261.011.471.731.761.992.111.21.31Phosphotransacetylase
nuoB1.5671.4922.112.461.233.122.481.511.42.171.481.531.481.321.091.05NADH dehydrogenase I chain B
gidB1.6981.3542.081.41.791.71.520.851.151.351.31.391.311.3510.98Glucose-inhibited division; chromosome replication?
fldA1.4911.4745.954.414.55.53.643.293.151.81.511.682.112.221.171.36Flavodoxin 1
plsX1.5941.3632.011.371.11.81.330.990.921.481.321.311.51.411.041.02Glycerolphosphate auxotrophy in plsB background
smpAa1.950.9842.152.052.61.961.6711.141.031.010.940.860.930.941Small membrane protein A
smpBa1.7551.1692.642.331.672.391.811.281.191.231.491.231.281.231.081.13Small protein B
emrB1.6061.2861.281.061.041.151.050.650.741.321.061.161.430.981.050.8Multidrug resistance; putative translocase
ackA1.5411.3423.412.912.973.272.621.922.021.231.341.251.371.520.991.01Actate kinase
fabG1.2651.5762.131.841.862.041.271.31.591.241.441.471.722.010.941.063-oxoacyl-[acyl-carrier-protein] reductase
sbp1.3441.4810.840.811.143.663.361.471.450.61.11.62.212.971.181.11Periplasmic sulfate-binding protein
Unknowns
dinDa10.471.0286.715.956.025.486.190.560.60.770.720.570.710.520.780.5DNA-damage-inducible protein
oraAa9.0021.0874.835.996.28.433.130.670.61.091.051.081.041.040.970.98Regulator, OraA protein
yebGa8.8531.1753.874.515.646.13.340.440.620.950.820.750.840.870.670.77Orf, hypothetical protein
yfaE2.182.6910.861.474.093.481.190.810.770.941.783.614.670.870.88Orf, hypothetical protein
yigFa3.8131.0571.8415.183.022.031.191.221.090.980.971.081.061.020.94Orf, hypothetical protein
yigNa3.9690.8662.112.382.133.134.140.660.740.790.820.860.760.710.890.93Putative a-helix chain
arpBa3.7490.9962.2912.295.322.581.611.231.341.081.010.950.940.80.970.95Orf, hypothetical protein
dinFa3.6211.0292.11.981.261.811.540.580.381.021.060.870.840.840.950.85DNA-damage-inducible protein F
yafOa3.4861.0313.734.973.513.352.830.81.310.980.960.860.961.111.020.87Orf, hypothetical protein
yegQ2.0342.4032.321.850.861.631.020.630.883.663.182.532.352.461.181.18Orf, hypothetical protein
yoaA2.182ND1.431.21.081.431.350.60.59Putative enzyme
yafNa2.7381.09733.713.662.281.051.261.011.080.950.820.920.84Orf, hypothetical protein
yebFa2.9090.8593.244.063.334.672.881.251.051.0110.890.8411.23Orf, hypothetical protein
yafPa2.6221.132.293.293.182.651.830.841.181.0510.970.870.80.830.83Orf, hypothetical protein
ydiYa2.1971.5394.652.391.852.11.371.071.182.861.591.41.281.181.021.14Orf, hypothetical protein
ydjMa2.6291.1041.923.083.032.651.941.030.891.031.010.850.810.840.86Orf, hypothetical protein
yebC1.9441.692.672.142.171.91.280.971.121.511.921.642.332.361.21.11Orf, hypothetical protein
yfgB2.0641.5552.051.291.081.331.060.60.721.561.411.381.441.480.960.91Orf, hypothetical protein
ygjO1.7961.7031.141.10.711.060.930.580.522.111.481.621.591.631.010.97Putative enzyme
yebEa2.3791.0471.561.681.691.491.610.630.720.950.880.710.760.860.880.71Orf, hypothetical protein
ydgN1.9311.4541.951.050.960.991.230.540.741.851.351.311.261.210.950.97Putative membrane protein
yliG1.7741.5442.141.761.32.281.31.010.9721.581.71.951.841.161.19Orf, hypothetical protein
ybiNa2.0721.2222.921.722.82.131.151.081.311.161.11.31.241.020.98Orf, hypothetical protein
dcrB1.7321.4981.981.941.512.42.651.211.211.741.481.712.332.181.141.38Orf, hypothetical protein
ycePa2.0281.1831.792.211.931.441.450.870.8710.921.030.960.940.80.84Orf, hypothetical protein
yciH1.9711.2212.331.961.412.081.630.91.011.631.341.221.251.461.011.25Orf, hypothetical protein
yedM1.8261.3551.863.914.612.731.731.811.441.020.982.111.20.890.950.88Orf, hypothetical protein
ycgW1.582ND1.833.122.993.774.471.972.12Orf, hypothetical protein
yebU1.6411.4764.462.752.533.352.211.971.761.741.331.481.51.441.110.92Putative nucleolar proteins
ycfB1.7571.3581.891.420.961.681.430.990.691.431.21.261.431.370.881.09Orf, hypothetical protein
yjiWa2.2550.8552.4921.81.711.470.70.980.971.020.981.070.811.151.12Orf, hypothetical protein
yifLa2.1850.9071.551.431.631.651.170.680.930.90.710.90.640.870.93Orf, hypothetical protein
ybfE1.6771.3642.462.52.913.422.041.271.911.241.081.141.51.350.860.99Orf, hypothetical protein
yhbC1.2761.7541.780.991.090.770.760.820.871.411.0610.950.930.620.6Orf, hypothetical protein
ydeTa2.0830.963.172.81.912.471.261.21.031.351.081.050.961.011.171.1Putative outer membrane protein
ygcM1.781.252.271.932.222.911.661.331.141.121.21.081.091.260.841Putative 6-pyruvoyl tetrahydrobiopterin synthase
yfjA1.5481.4672.711.481.321.951.4811.311.431.481.571.61.881.091.08Orf, hypothetical protein
ychF1.6131.3942.341.961.532.071.71.11.281.841.771.851.871.871.271.37Putative GTP-binding protein
ygiR1.5131.4941.50.890.770.921.140.550.831.911.441.421.531.321.050.99Orf, hypothetical protein
IS5K1.6961.2921.821.441.521.751.230.930.91.051.181.071.151.040.830.87Orf, hypothetical protein
yfhE1.1571.8280.470.570.470.610.570.420.511.341.81.841.631.660.90.91Orf, hypothetical protein
yeeA1.7531.2292.782.712.632.531.841.471.381.041.141.020.990.850.870.77Orf, hypothetical protein
yaeS1.6791.2211.681.151.111.410.880.631.221.261.221.281.281.060.99Orf, hypothetical protein
yaaH1.7061.1931.530.950.840.90.770.460.711.11.151.080.90.990.930.82Orf, hypothetical protein
ycfQ1.6751.2853.393.333.433.031.981.891.731.481.321.451.531.481.340.92Orf, hypothetical protein
b12281.6241.330.610.860.981.371.010.560.631.231.151.171.271.30.890.95Orf, hypothetical protein
ydjRa1.8841.0551.762.171.581.681.710.851.041.030.840.940.910.920.950.81Orf, hypothetical protein
yrfH1.4811.4531.241.290.931.661.8810.891.181.231.41.61.61.010.92Orf, hypothetical protein
ybjF1.6271.3381.71.311.311.731.270.810.991.681.461.61.51.621.181.17Putative enzyme
yacL1.4961.3852.792.662.312.692.341.721.71.411.411.481.612.021.131.16Orf, hypothetical protein
yfgK1.3951.4991.10.990.981.121.180.740.81.131.331.471.51.690.910.99Putative GTP-binding factor
ydgO1.4491.4151.671.281.141.040.740.740.881.531.171.171.081.030.880.81Orf, hypothetical protein
yleA1.5121.3451.451.191.011.210.960.660.881.181.451.021.131.240.890.9Orf, hypothetical protein
yiaD1.5321.3181.951.31.981.611.470.881.291.211.451.741.651.331.11.14Putative outer membrane protein
ygeQ1.4241.4232.431.571.731.541.241.31.091.181.061.151.091.210.740.86Orf, hypothetical protein
yccFa1.7651.0672.051.71.843.041.341.041.221.40.861.091.181.020.981.1Orf, hypothetical protein
yabO1.6241.2071.191.11.151.10.820.610.711.091.11.011.011.10.870.89Orf, hypothetical protein
yhdJ1.6861.1172.551.711.231.380.760.731.081.551.071.161.031.110.951.17Putative methyltransferase
  • a Induced in a lexA-dependent manner.

  • b Ave represents the average transcript level in irradiated samples compared to that in unirradiated samples as described in materials and methods.

  • c Values represent the fold change in transcript level at the time indicated compared to the beginning of the experiment as described in materials and methods.