5
Table S-5. Genes indirectly regulated by Fur and not regulated by RyhB.
b-numbera / Operonb / Protein Productc / WT +O2/ WT -O2d / ∆fur/WT +O2e / ∆fur/WT-O2e / WT +O2f / ∆fur +O2f / WT -O2f / ∆fur -O2f / Fur Reg / Chen
et. alg
Operons with a Fur-dependent change in expression under primarily anaerobic conditions with no ChIP-seq peak
b0006 / yaaA / polypeptide / 1.96 / 1.03 / 1.73 / 15.3 / 15.4 / 14.3 / 15.1 / This study
b0034 / caiF / transcriptional activator / 0.36 / 0.69 / 0.56 / 15.6 / 15.1 / 17.1 / 16.3 / (1)
b0336 / codB(A) / cytosine efflux transporter / 0.97 / 0.81 / 0.62 / 17.7 / 17.4 / 17.7 / 17.0 / (2)
b0450 / glnK-(amtB) / nitrogen regulatory protein / 2.71 / 0.71 / 1.54 / 14.3 / 13.8 / 12.9 / 13.5 / (1)
b0464 / acrR / transcriptional repressor / 1.67 / 0.91 / 1.55 / 14.4 / 14.3 / 13.7 / 14.3 / This study
b0572 / cusC(FBA) / copper/silver efflux system / 1.59 / 1.33 / 0.63 / 14.0 / 14.4 / 13.3 / 12.7 / (1)
b0579 / ybdF / unknown / 1.45 / 1.02 / 1.73 / 15.1 / 15.1 / 14.6 / 15.3 / This study
b0598 / cstA / peptide transporter / 3.52 / 1.20 / 2.60 / 15.4 / 15.7 / 13.6 / 15.0 / This study
b0810 / gln(H)P(Q) / glutamine ABC transporter / 1.72 / 0.94 / 1.62 / 17.0 / 16.9 / 16.2 / 16.9 / This study
b0833 / yliE(F) / alters biotin formation / 1.28 / 0.92 / 1.59 / 14.5 / 14.4 / 14.2 / 14.8 / (1)
b0836 / bssR / regulator of biofilm formation / 0.08 / 1.27 / 1.81 / 14.1 / 14.5 / 17.7 / 18.6 / (1)
b0887 / cydDC / glutathione/L-cysteine efflux transporter / 1.51 / 1.00 / 1.60 / 15.1 / 15.1 / 14.5 / 15.2 / This study
b0900 / ycaN / unknown / 1.14 / 0.99 / 1.55 / 13.8 / 13.8 / 13.7 / 14.3 / (2)
b0990 / cspG / cold shock protein / 1.43 / 0.99 / 1.73 / 13.7 / 13.7 / 13.2 / 14.0 / This study
b1040 / csgD(E)FG / transcriptional regulator / 1.01 / 1.28 / 1.73 / 15.4 / 15.8 / 15.4 / 16.2 / This study
b1055 / yceA / unknown / 9.33 / 1.17 / 1.62 / 17.0 / 17.3 / 13.8 / 14.5 / This study
b1056 / yce(J)I / unknown / 9.15 / 1.05 / 2.03 / 16.6 / 16.6 / 13.4 / 14.4 / This study
b1071 / flg(A)M(N) / anti-sigma factor for FliA / 1.49 / 1.26 / 1.88 / 14.5 / 14.9 / 14.0 / 14.9 / This study
b1174 / min(CD)E / cell division / 1.92 / 0.91 / 1.84 / 18.3 / 18.2 / 17.4 / 18.3 / This study
b1183 / umuD(C ) / SOS mutagenesis, error-prone repair / 1.37 / 1.50 / 1.53 / 14.0 / 14.5 / 13.5 / 14.1 / (1)
b1461 / pptA / aromatic compound metabolism / 1.57 / 1.08 / 2.09 / 16.8 / 16.9 / 16.2 / 17.2 / This study
b1467 / nar(Z)Y(WV) / nitrate reductase Z / 0.76 / 0.81 / 0.65 / 13.3 / 13.0 / 13.7 / 13.1 / (2)
b1477 / yddM / unknown / 1.38 / 1.12 / 1.88 / 14.9 / 15.0 / 14.4 / 15.3 / This study
b1520 / yneE / unknown / 1.81 / 1.16 / 1.72 / 14.6 / 14.8 / 13.8 / 14.5 / This study
b1557 / cspB / transcriptional regulator / 1.23 / 1.06 / 1.60 / 13.3 / 13.4 / 13.0 / 13.7 / (2)
b1607 / ydgC / unknown / 3.59 / 0.96 / 1.78 / 15.6 / 15.5 / 13.8 / 14.6 / This study
b1664 / ydhQ / unknown / 0.71 / 0.87 / 0.66 / 16.2 / 16.0 / 16.7 / 16.1 / This study
b1674 / ydhYV(WXUT) / predicted 4Fe-4S ferredoxin-type protein / 0.36 / 0.96 / 0.37 / 12.8 / 12.8 / 14.3 / 12.8 / This study / +
b1715 / pheM / leader peptide, phenylalanyl-tRNA synthetase / 1.03 / 1.07 / 2.01 / 15.9 / 16.0 / 15.8 / 16.8 / This study
b1741 / cho / endonuclease of nucleotide excision repair / 1.37 / 1.15 / 1.67 / 14.4 / 14.6 / 14.0 / 14.7 / (1)
b1887 / (motAB)-che(A)W / purine-binding chemotaxis / 1.16 / 1.28 / 1.60 / 13.3 / 13.7 / 13.1 / 13.8 / This study
b1892 / flhD(C) / transcriptional regulator / 1.24 / 1.25 / 1.64 / 15.6 / 15.9 / 15.3 / 16.0 / (3) / +
b1924 / fliD(ST) / flagellar cap protein / 1.08 / 1.38 / 1.59 / 13.2 / 13.7 / 13.1 / 13.8 / This study
b1932 / yedL / unknown / 1.85 / 0.90 / 1.83 / 14.7 / 14.5 / 13.8 / 14.6 / (1)
b1967 / hchA / glyoxalase II Hsp31 molecular chaperone / 2.17 / 1.05 / 1.59 / 16.5 / 16.5 / 15.3 / 16.0 / (1)
b1974 / yodB / unknown / 1.38 / 0.76 / 0.65 / 14.5 / 14.1 / 14.1 / 13.4 / (1)
b1982 / amn / AMP nucleosidase / 1.64 / 1.09 / 1.54 / 16.8 / 16.9 / 16.1 / 16.7 / This study
b2011 / sbcB / exonuclease / 1.29 / 0.98 / 1.56 / 15.1 / 15.1 / 14.7 / 15.4 / This study
b2063 / yegH / unknown / 0.98 / 1.09 / 1.55 / 14.7 / 14.9 / 14.8 / 15.4 / This study / +
b2105 / rcnR / transcriptional repressor: Ni/Co resistance / 2.62 / 1.05 / 2.42 / 15.4 / 15.5 / 14.0 / 15.3 / This study / +
b2111 / yehD(CBA) / alters biotin formation / 0.63 / 0.98 / 1.55 / 12.8 / 12.8 / 13.5 / 14.1 / This study
b2159 / nfo / endonuclease IV / 1.48 / 1.17 / 1.69 / 15.6 / 15.9 / 15.1 / 15.8 / (1)
b2252 / ais / protein induced by aluminum / 2.05 / 0.78 / 0.31 / 16.5 / 16.2 / 15.5 / 13.8 / This study
b2310 / argT-hisJQMP / lysine/arginine/ornithine ABC transporter, histidine ABC transporter / 11.67 / 0.85 / 1.60 / 16.7 / 16.5 / 13.2 / 13.9 / This study
b2352 / yfd(GH)I / unknown / 1.70 / 0.85 / 0.61 / 15.6 / 15.4 / 14.9 / 14.2 / (1) / +
b2381 / ypd(A)B(C) / cellular response to nutrients / 1.16 / 1.13 / 1.64 / 15.0 / 15.2 / 14.8 / 15.5 / This study
b2421 / cys(PUWA)M / cysteine synthase B / 0.67 / 0.97 / 0.59 / 16.8 / 16.7 / 17.3 / 16.6 / This study
b2498 / upp-(uraA) / uracil phosphoribosyltransferase / 0.62 / 1.05 / 0.54 / 18.1 / 18.2 / 18.8 / 17.9 / (1)
b2531 / iscR / transcriptional regulator / 6.44 / 1.08 / 2.41 / 17.9 / 18.0 / 15.2 / 16.5 / (1)
b2573 / rpoE-(rseABC) / minor sigma factor, heat shock and other stresses on membrane and periplasmic proteins. / 0.51 / 1.15 / 0.66 / 17.1 / 17.4 / 18.1 / 17.5 / (1)
b2587 / kgtP / transporter for α-ketoglutarate / 8.34 / 1.19 / 1.90 / 18.7 / 19.0 / 15.7 / 16.6 / This study
b2601 / aroF-tyrA / biosynthesis of aromatic amino acids / 0.92 / 0.98 / 0.56 / 17.3 / 17.3 / 17.4 / 16.6 / This study
b2603 / yfiRN / swarming and motility / 1.17 / 0.93 / 1.57 / 14.9 / 14.8 / 14.6 / 15.3 / This study
b2670 / ygaW / L-alanine exporter / 0.86 / 1.15 / 1.73 / 12.9 / 13.1 / 13.1 / 13.9 / This study
b2677 / proV(W)X / glycine betaine / proline ABC transporter / 3.47 / 1.09 / 1.86 / 15.7 / 15.8 / 13.9 / 14.8 / (1)
b2695 / serV-(argVYZQ) / serine tRNA / 0.39 / 1.05 / 0.41 / 17.7 / 17.8 / 19.1 / 17.8 / This study
b2786 / barA / two-component signal transduction system: carbon storage / 1.28 / 0.98 / 1.53 / 14.4 / 14.4 / 14.1 / 14.7 / This study
b2896 / ygf(Y)X / toxin-antitoxin system / 0.96 / 0.63 / 0.60 / 15.3 / 14.6 / 15.4 / 14.6 / (1)
b3506 / slp-dctR / starvation lipoprotein, transcriptional regulator: acid resistance / 0.27 / 0.87 / 0.56 / 17.0 / 16.8 / 18.9 / 18.0 / (1) / +
b3508 / (hdeAB)-yhiD / predicted Mg(2+) transport ATPase / 0.16 / 1.03 / 0.58 / 14.5 / 14.5 / 17.2 / 16.4 / (1)
b3512 / gadE / transcription factor: pH homeostasis / 0.14 / 1.16 / 0.58 / 15.8 / 16.0 / 18.7 / 17.9 / This study
b3514 / mdt(E)F / multidrug efflux transport system / 0.17 / 0.98 / 0.65 / 13.9 / 13.9 / 16.5 / 15.9 / This study
b3615 / yibD / UDP-glucuronate:LPS(HepIII) glycosyltransferase / 1.84 / 0.85 / 0.55 / 14.7 / 14.5 / 13.8 / 13.0 / This study / +
b3769 / ilv(LXG_1G_2)M (EDA) / acetohydroxyacid synthase II / 0.89 / 1.12 / 1.88 / 17.4 / 17.6 / 17.6 / 18.5 / (1)
b3776 / yif(N)O / unknown / 1.19 / 0.97 / 1.53 / 14.5 / 14.5 / 14.3 / 14.9 / This study
b3862 / yihG / unknown / 1.47 / 1.00 / 1.55 / 14.3 / 14.3 / 13.8 / 14.4 / This study
b3870 / glnA(LG) / glutamine synthetase / 2.58 / 0.82 / 1.63 / 18.8 / 18.5 / 17.4 / 18.1 / (1)
b3873 / yhiM / unknown / 0.17 / 1.16 / 0.53 / 13.5 / 13.7 / 16.0 / 15.1 / This study / +
b3941 / metF / methionine biosynthesis / 0.66 / 0.81 / 0.59 / 17.5 / 17.2 / 18.1 / 17.4 / This study
b4016 / ace(BA)K / isocitrate dehydrogenase phosphatase / isocitrate dehydrogenase kinase / 5.45 / 0.78 / 2.25 / 17.0 / 16.7 / 14.6 / 15.7 / (1)
b4034 / malE(FG) / maltose ABC transporter / 4.60 / 0.81 / 1.71 / 16.3 / 16.0 / 14.1 / 14.9 / This study
b4107 / yjdN / unknown / 1.49 / 1.30 / 1.77 / 14.5 / 14.8 / 13.9 / 14.7 / (1)
b4108 / yjdM / unknown / 1.03 / 0.87 / 1.96 / 17.3 / 17.1 / 17.3 / 18.2 / This study
b4113 / basRS / transcriptional regulator: responds to Fe3+ levels / 1.62 / 0.76 / 0.44 / 16.5 / 16.1 / 15. 8 / 14.7 / This study / +
b4114 / eptA / phosphoethanolamine transferase / 2.27 / 0.66 / 0.35 / 16.4 / 15.8 / 15.2 / 13.7 / This study
b4116 / adiY / transcriptional activator / 0.23 / 1.22 / 2.31 / 13.0 / 13.3 / 15.2 / 16.4 / This study
b4124 / dcu(S)R / transcriptional activator / 1.43 / 1.02 / 1.67 / 14.8 / 14.9 / 14.3 / 15.0 / This study
b4187 / aidB / transcriptional repressor: response to alkylating agents / 0.47 / 1.00 / 0.56 / 14.5 / 14.5 / 15.6 / 14.7 / This study
b4281 / yjhD / unknown / 1.06 / 0.96 / 1.69 / 13.6 / 13.6 / 13.6 / 14.3 / This study
b4364 / yjjP / unknown / 0.58 / 0.96 / 1.59 / 13.7 / 13.6 / 14.5 / 15.2 / This study / +
b4433 / sdsR / small regulatory RNA / 1.49 / 0.85 / 1.81 / 14.2 / 13.9 / 13.6 / 14.4 / This study
Operons with a Fur-dependent change in expression under both aerobic and anaerobic conditions with no ChIP-seq peak
b0624 / crcB / fluoride efflux / 0.86 / 0.58 / 0.56 / 15.2 / 14.4 / 15.5 / 14.6 / (1)
b0760 / mod(E)F / unknown / 2.68 / 1.52 / 1.86 / 15.9 / 16.5 / 14.5 / 15.4 / (1)
b0803 / ybiI / unknown / 1.15 / 6.65 / 1.50 / 13.8 / 16.6 / 13.6 / 14.2 / (2)
b1072 / flgA(MN) / flagellar biosynthesis / 1.12 / 1.55 / 1.54 / 13.7 / 14.3 / 13.5 / 14.1 / This study
b1256 / ompW / outer membrane protein / 0.95 / 0.63 / 2.08 / 14.4 / 13.8 / 14.5 / 15.6 / (2)
b1743 / spy / ATP independent periplasmic chaperone / 2.18 / 1.67 / 1.97 / 14.7 / 15.5 / 13.6 / 14.6 / (1)
b1944 / fliL(MNOPQR) / flagellar mobility / 1.25 / 1.66 / 1.86 / 13.4 / 14.1 / 13.1 / 14.0 / This study
b2000 / flu / variable biofilm autotransporter / 1.09 / 0.56 / 0.45 / 15.7 / 14.8 / 15.5 / 14.4 / (1)
b2899 / yqfA / unknown / 1.09 / 1.66 / 2.25 / 14.8 / 15.5 / 14.6 / 15.8 / (1)
b3469 / zntA / zinc, cadmium, lead efflux / 1.38 / 1.89 / 2.33 / 14.3 / 15.2 / 13.9 / 15.1 / (1)
b3707 / tnaC(AB) / leader peptide, aromatic amino acid metabolism / 4.09 / 0.58 / 2.50 / 15.8 / 15.0 / 13.8 / 15.1 / This study
Operons with a Fur-dependent change in expression under primarily aerobic conditions with no ChIP-seq peak
b0288 / ykgJ / unknown / 1.55 / 0.50 / 0.73 / 14.8 / 13.8 / 14.2 / 13.7 / This study
b0386 / proC / proline biosynthesis / 1.43 / 0.52 / 0.79 / 16.3 / 15.3 / 15.7 / 15.4 / (1) / +
b0553 / nmpC / outer membrane porin protein / 1.19 / 0.59 / 1.15 / 19.1 / 18.3 / 18.9 / 19.1 / (1)
b0587 / fepE / ferric enterobactin transport / 0.89 / 1.72 / 1.19 / 12.7 / 13.4 / 12.8 / 13.1 / (2) / +
b0781 / moaABCDE / molybdopterin biosynthesis protein / 1.31 / 2.64 / 1.00 / 16.0 / 17.4 / 15.6 / 15.6 / (1)
b0958 / sulA / SOS cell division inhibitor / 1.06 / 2.51 / 1.50 / 15.4 / 16.7 / 15.3 / 15.9 / (1) / +
b1171 / ymg(G)D / unknown / 0.81 / 0.60 / 0.99 / 16.0 / 15.2 / 16.3 / 16.3 / This study
b1298 / puuDR / γ-glutamyl-γ-aminobutyrate hydrolase / 4.72 / 0.51 / 1.08 / 15.6 / 14.6 / 13.4 / 13.5 / (1)
b1453 / ansP / L-asparagine transporter / 1.32 / 0.66 / 0.81 / 13.7 / 13.1 / 13.3 / 13.0 / (2) / +
b1761 / gdhA / glutamate dehydrogenase / 0.88 / 1.73 / 1.17 / 18.5 / 19.2 / 18.6 / 18.9 / (1)
b1777 / yeaC / unknown / 7.27 / 0.44 / 0.97 / 18.4 / 17.2 / 15.5 / 15.5 / (1)
b1959 / yedA / unknown / 0.85 / 1.62 / 0.90 / 13.2 / 13.9 / 13.4 / 13.3 / This study
b2013 / yeeED / unknown / 0.82 / 2.91 / 1.44 / 16.2 / 17.7 / 16.5 / 17.0 / (1)
b2040 / rfb(B)D(ACX) / dTDP-4-dehydrorhamnose reductase, LPS synthesis / 1.29 / 0.66 / 0.93 / 17.4 / 16.8 / 17.1 / 17.0 / (1)
b2093 / gat(YZA)B(CD) / galactitol metabolism / 1.01 / 0.66 / 0.89 / 19.7 / 19.1 / 19.6 / 19.5 / (1)
b2296 / ackA-(pta) / acetate kinase / 0.21 / 1.59 / 1.04 / 16.7 / 17.4 / 18.9 / 19.0 / (1)
b2936 / yggG / membrane metallopeptidase / 2.09 / 0.60 / 1.14 / 15.4 / 14.7 / 14.3 / 14.5 / (1)
b2971 / yghG / unknown / 1.68 / 0.51 / 1.13 / 14.3 / 13.3 / 13.5 / 13.7 / (1)
b2972 / pppA / peptidase / 1.32 / 0.57 / 1.01 / 14.2 / 13.3 / 13.8 / 13.8 / (1)
b3151 / yraQ / unknown / 0.76 / 1.53 / 0.72 / 14.5 / 15.1 / 14.9 / 14.4 / (1)
b3867 / hemN / coproporphyrinogen III dehydrogenase / 1.06 / 0.60 / 0.77 / 15.6 / 14.9 / 15.5 / 15.2 / (1)
b4019 / metH / cobalamin-dependent methionine synthase / 1.21 / 0.66 / 0.80 / 16.2 / 15.6 / 16.0 / 15.6 / (3) / +
b4315 / fim(A)I(CDFGH) / fimbrial protein / 0.42 / 2.09 / 1.25 / 16.1 / 17.2 / 17.4 / 17.7 / This study
b4466 / yghJ / membrane protein, secretion system / 1.34 / 0.57 / 0.87 / 14.2 / 13.4 / 13.7 / 13.6 / (1)
b4484 / cpxP / regulator of the Cpx response / 3.53 / 0.61 / 1.09 / 15.4 / 14.7 / 13.6 / 13.7 / This study
b4617 / tisA / phantom gene / 0.71 / 2.67 / 1.03 / 16.2 / 17.7 / 16.7 / 16.8 / This study
aIdentification number for first gene in operon, obtained from EcoCyc (4).
bGenes within parentheses were not significantly regulated by Fur. All others show a ≥1.5x fold-change in expression between wild-type and Fur- strains under at least one growth condition (p-value < 0.01).
cAnnotation of the protein product of the first gene in the operon was obtained from EcoCyc (4).
dRNA levels were determined from transcriptomic data from either aerobic (O2) or anaerobic (-O2) wild-type cells and the ratio of the change in expression between these two conditions was determined.
eRNA levels were determined from transcriptomic data from wild-type or Fur- strains grown under either aerobic or anaerobic conditions and the ratio of the change in expression between wild-type and Fur- strains was determined.
fExpression values from the transcriptomic data of the indicated strains under the indicated conditions are reported for the first gene in the operon and are given as log2 values.
gFur binding predicted bioinformatically [Chen et. al (5)].
5