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. 2009 Aug 7;75(19):6110–6123. doi: 10.1128/AEM.00914-09

TABLE 5.

Differentially regulated genes in E. coli strains Sakai and TW14359 under chlorine or hydrogen peroxide treatment

Genea Gene/protein annotation Fold change (increase) after treatment withb:
Chlorine
H2O2
Sakai TW14359 Sakai TW14359
Stress regulators
    frmB Putative S-formylglutathione hydrolase 2.34 1.52 1.01 0.88
    frmA Formaldehyde dehydrogenase, glutathione dependent 4.96 2.9 0.97 0.95
    frmR Repressor of frmRAB 5 3.92 0.94 1.05
    marR Multiple antibiotic resistance protein; repressor of mar operon 5.86 5 1.07 0.94
    marA Multiple antibiotic resistance; transcriptional activator of defense systems 4.61 4.44 1.13 1.26
    marB Multiple antibiotic resistance protein 4.4 7.37 1.34 1.85
    b3913 Periplasmic repressor of cpx regulon by interaction with CpxA 3.95 3.97 1.25 1.33
    b3914 Periplasmic repressor of cpx regulon by interaction with CpxA 3.66 3.78 1.18 1.33
    spy Periplasmic protein related to spheroblast formation 2.14 2.32 1.01 1.08
    uspA Universal stress protein; broad regulatory function 1.75 1.46 0.8 0.81
    ydaA Hypothetical protein; also called uspE, paralog of uspA 1.33 1.41 1.08 0.96
    yedW Putative two-component transcriptional regulator 2.1 1.84 1.04 0.93
    yedV Putative two-component sensor protein 1.39 1.33 1.08 0.98
    dps Global regulator, starvation conditions 1.71 1.36 1.58 1.21
    rprA Positive regulatory RNA for rpoS translation 1.46 1.23 1.18 0.87
    rpoS RNA polymerase, sigma S (σ38) factor; synthesis of many growth phase-related proteins 1.55 1.35 1.21 1.28
    phoP Transcriptional regulatory protein 1.4 1.55 1.04 1
    phoU Negative regulator for the Pho regulon and putative enzyme in phosphate metabolism 2.86 2.22 0.9 0.88
    pstB ATP-binding component of high-affinity phosphate-specific transport system 2.1 2.01 0.84 1
    pstA High-affinity phosphate-specific transport system 1.33 1.23 0.84 0.89
    pstC Phosphate transport system permease protein pstC 1.24 1.12 0.84 0.86
    pstS High-affinity phosphate-specific transport system; periplasmic phosphate-binding protein 2.02 1.91 0.89 0.92
    phoB Positive response regulator for the Pho regulon, sensor is PhoR (or CreC) 2.03 1.43 0.94 0.85
    phoR Positive and negative sensor protein for the Pho regulon 1.45 1.4 1.01 1.13
    phoA Alkaline phosphatase 1.51 1.29 1.03 0.99
Genes related to oxidative stress
    ykgC Putative oxidoreductase 7.06 5.46 1.03 0.92
    ykgB Hypothetical protein; inner membrane protein 6.37 5.57 1.04 0.95
    ykgI Hypothetical protein 9.54 8.12 0.97 0.92
    yeeE Putative transport system permease protein; inner membrane protein 5.75 4.56 2.13 2.68
    yeeD Conserved protein 4.61 3.72 1.72 2.14
    yqhD Putative oxidoreductase 4.45 4.32 1.05 0.96
    yedX Hypothetical protein 1.18 2.22 1.37 1.88
    yedY Putative oxidoreductase 4.93 4.95 0.89 0.94
    yedZ Hypothetical protein 4.62 4.29 0.89 0.91
    yjgH Predicted mRNA endoribonuclease; rarD; predicted chloramphenicol resistance permease 2.89 2.42 0.97 0.93
    yjgI Putative oxidoreductase 3.57 3.09 0.95 0.92
    yciW Putative oxidoreductase 4.24 3.71 1.41 1.83
    inaA pH-inducible protein involved in stress response 2.67 2.61 1.17 1.29
    ahpF Alkyl hydroperoxide reductase subunit F 2.53 1.97 1.85 2.16
    nrdH Glutaredoxin-like protein; hydrogen donor 2.09 2.08 2.96 4.81
    nrdI Hypothetical protein; stimulate ribonucleotide reduction 1.94 1.78 2.94 4.55
    nrdE Ribonucleoside-diphosphate reductase 2, alpha subunit 1.62 1.31 2.6 3.45
    nrdF Ribonucleoside-diphosphate reductase 2, beta subunit 1.16 1.33 1.51 2.36
    gst GST 1.45 1.34 1.16 1.27
    yfcF Hypothetical protein 1.18 1.22 1.1 1.29
    yfcG Putative S-transferase 1.18 1.3 1.06 1
    proP Low-affinity transport system; proline permease II 2.16 1.33 1.77 1.81
    soxS Regulation of superoxide response regulon 1.12 0.87 2.61 3.47
    soxR Redox-sensing activator of soxS 1.22 0.93 1.03 0.9
    sodA Superoxide dismutase, manganese 1.21 1.34 1.84 3.19
    sodB Superoxide dismutase, iron 1.32 1.24 0.92 0.73
    sodC Superoxide dismutase precursor (Cu-Zn) 1.36 2.41 0.95 0.91
    ahpC Alkyl hydroperoxide reductase, C22 subunit; detoxification of hydroperoxides; protect against the action of lipid radicals 1.65 1.13 1.51 1.36
    msrA Peptide methionine sulfoxide reductase 1.69 1.75 0.95 1.03
    recN Protein used in recombination and DNA repair 1.68 1.1 2.79 3.25
    nfo Endonuclease IV; role in the repair of oxidative damage 1.29 1.29 2.03 2.07
    katE Catalase; hydroperoxidase HPII(III); responds to H2O2 and oxidative stress 1.28 1.38 1.06 1.08
    katG Catalase; hydroperoxidase HPI(I); responds to H2O2 and oxidative stress 0.91 0.78 1.36 1.33
Fe-S system and thiol-redox system
    c4868 Sulfate-binding protein precursor; periplasmic sulfate-binding protein 3.14 2.61 0.94 0.94
    iscS Cysteine desulfurase, cysteine desulfurase (tRNA sulfurtransferase), PLP dependent 2.87 2.95 1.76 2.46
    iscR Fe-S cluster-containing transcription factor, transcriptional repressor of iscRSUA operon 4.93 5.12 2.42 3.85
    iscU Scaffold protein; putative regulator 1.84 2.07 1.4 1.84
    iscA NifU-like protein; involved in Fe-S synthesis 2.79 2.74 1.69 2.25
    fdx (2Fe-2S) ferredoxin, electron carrier protein 1.97 2.11 1.47 2.08
    hscA DnaK-homologue chaperone Hsc66 2.36 1.79 2.05 2.34
    hscB DnaJ-like chaperon specific for iscU 2.06 1.95 1.74 2.35
    sbp Periplasmic sulfate-binding protein 2.88 2.89 0.93 1.01
    sufE Sulfur acceptor protein 1.39 1.13 2.67 2.83
    sufS Selenocysteine lyase, PLP dependent 1.22 1.21 2.72 3.47
    sufD Component of sufBCD complex 1.38 1.37 2.87 3.78
    sufC Component of sufBCD complex; putative ATP-binding component of a transport system 1.33 1.38 2.77 3.65
    sufB Component of sufBCD complex 1.22 1.49 2.25 3.27
    sufA Fe-S cluster assembly protein 1.33 1.75 3.24 4.05
    yfhJ Hypothetical protein 1.58 1.74 1.38 1.81
    grxA Glutaredoxin 1 redox coenzyme for glutathione-dependent ribonucleotide reductase 1.22 0.77 1.31 1.07
    gshA Gamma-glutamate-cysteine ligase 1.34 1.21 1.09 1.08
    gshB Glutathione synthetase 1.75 1.55 1.07 1.09
Genes encoding Cys synthesis/transport proteins
    cbl Transcriptional regulator cys regulon; accessory regulatory circuit affecting cysM 4.38 3.77 1.14 1.24
    cysC Adenosine 5-phosphosulfate kinase 4.86 4.54 1.68 2.79
    cysN ATP-sulfurylase (ATP:sulfate adenylyltransferase), subunit 1, probably a GTPase 3.73 4.61 2.24 3.95
    cysD ATP:sulfurylase (ATP:sulfate adenylyltransferase), subunit 2 1.36 3.07 1.66 4.68
    cysH 3-Phosphoadenosine 5-phosphosulfate reductase 5.58 5.41 1.77 2.41
    cysI Sulfite reductase, alpha subunit 6.49 7.07 2.46 3.31
    cysJ Sulfite reductase (NADPH), flavoprotein beta subunit 6.31 5.56 2.07 3.39
    cysM Cysteine synthase B, O-acetylserine sulfhydrolase B 3.38 2.63 1.96 2.7
    cysA ATP-binding component of sulfate permease A protein; chromate resistance 7.06 5.45 2.81 3.69
    cysW Sulfate transport system permease W protein 3.54 3.03 1.6 2.44
    cysP Thiosulfate binding protein 4.01 4.1 1.73 2.97
    cysK Cysteine synthase A, O-acetylserine sulfhydrolase A 4.09 3.92 1.99 2.94
    fliY Putative periplasmic binding transport protein; cys transporter unit 4.56 4.01 1.48 1.93
    pepB Peptidase B; a cysteinylglycinase 2.85 3.03 1.78 2.58
Genes related to biofilm formation
    ycfR Hypothetical protein; biofilm formation regulation; change cell surface hydrophobility 10.55 9.21 1.98 1.85
    ycfS Hypothetical protein 2.68 2.89 1.03 1.26
    ycfQ Hypothetical protein 2.86 2.54 1.15 1.18
    ybiM Hypothetical protein; biofilm formation inhibition 5.21 6.15 1.05 1.08
Genes encoding heat-shock proteins
    htpX Heat shock protein, integral membrane protein 2.54 2.99 1.24 1.35
    dnaK Chaperone Hsp70; DNA biosynthesis; autoregulated heat shock proteins 2.02 2.04 1.09 1.24
    dnaJ Chaperone with DnaK; heat shock protein 2.21 1.79 1.06 1.06
    htpG Chaperone Hsp90, heat shock protein C 62.5 2.31 1.99 1.02 1.06
    clpB Heat shock protein 2.26 2.29 0.99 0.98
    b0161 Periplasmic serine protease Do; heat shock protein HtrA 2.01 2.79 1.02 1.24
    b4142 GroES; 10-kDa chaperone binds to Hsp60 in pre-steady-state Mg-ATP, suppressing its ATPase activity 1.51 1.38 1.02 1.05
    hslV Heat shock protein HslVU, proteasome-related peptidase subunit 1.75 1.58 0.98 0.98
    hslU Heat shock protein HslVU, ATPase subunit, homologous to chaperones 1.45 1.29 0.9 0.93
    clpP ATP-dependent proteolytic subunit of clpA-clpP serine protease, heat shock protein F21.5 1.49 1.42 1.01 0.97
    b4143 GroEL, chaperone Hsp60, peptide-dependent ATPase, heat shock protein 1.41 1.38 0.97 1.04
    pspA Phage shock protein, inner membrane protein 1.43 1.38 0.99 1.12
    hslO Heat shock protein, hsp33; chaperone 1.29 1.23 0.92 1.03
Transporters
    yccA Putative carrier/transport protein 3.47 3.87 1.18 1.39
    kefC K+ efflux antiporter, glutathione regulated 1.36 1.17 0.97 1.01
    yecC Putative ATP-binding component of a transport system 1.34 1.51 1.05 1.08
Osmotically inducible genes
    chaA Sodium-calcium proton antiporter; regulated by osmolarity and pH 4.76 4.44 1.39 1.38
    osmB Osmotically inducible lipoprotein 2.46 3.41 1.1 1.08
    osmE Activator of ntrL gene 1.85 2.34 1.12 1.04
    osmC Osmotically inducible protein; stress-inducible peroxidase C 1.78 1.87 1.09 1.08
    osmY Hyperosmotically inducible periplasmic protein 1.34 1.79 1.17 1.82
    otsA Trehalose-6-phosphate synthase; responds to heat and osmotic stress 1.33 1.51 1.09 0.94
    otsB Trehalose-6-phosphate phosphatase, biosynthetic; responds to heat and osmotic stress 1.39 1.66 0.99 1.1
Putative genes and others
    b1971 Putative reductase 4.93 4.95 0.89 0.94
    b1972 Hypothetical protein 4.62 4.29 0.89 0.91
    yhhW Hypothetical protein 3.41 2.42 0.97 0.89
    ybjC Hypothetical protein 3.58 2.99 1.93 2.17
    gadB Glutamate decarboxylase isozyme 4.35 2.56 1.01 0.75
    cynT Carbonic anhydrase 4.85 5.33 0.94 1.04
    cynS Cyanate aminohydrolase, cyanase 5.71 5.48 0.98 0.89
    cynX Cyanate transport 2.34 2.68 0.89 0.96
    add Adenosine deaminase 3.89 3.86 1.16 1.49
    yebE Hypothetical protein 2.78 3.03 1.18 0.99
    ndh Respiratory NADH dehydrogenase; near ycf genes 3.32 2.88 1.37 1.84
    yqhG Hypothetical protein 2.73 2.76 1.01 1.22
    lysA Diaminopimelate decarboxylase 3.27 2.69 0.98 0.98
    yfbE Putative enzyme 2.99 2.69 1.04 0.96
    z1052 Hypothetical protein; putative l-asparaginase 2.83 2.36 1.19 1.19
a

Genes are listed in functional groups based on annotation.

b

The fold change is the ratio of the gene expression level with chlorine or H2O2 treatment relative to that without chlorine or H2O2 treatment.