Table 1. Operons with an upstream FNR ChIP-seq peak and a FNR-dependent change in expression under GMM.
Peak Center (nt)a | Operonb | B-number of first genec | Function of Operon Productd | Number of FNR binding sitese | Location top scoring FNR binding sitef | σ70 occupancy -O2 relative to +O2 g | WT -O2 expression relative to WT +O2 expressionh | Previous Experimental Evidence of FNR Bindingi | Previous Evidence of FNR Regulated Expressionj |
Operons directly activated by FNR (Category 1) | |||||||||
1,003,976 | pyrD | b0945 | Dihydroorotate Dehydrogenase | 1 | −38.5 | + | o | [29] | [17] |
1,656,036 | ynfEFGH- dmsD | b1587 | Putative Selenate Reductase (ynfEFGH); DMS Reductase Maturation Protein (dmsD) | 1 | −40.5 | + | + | None | [18], [19] |
1,935,550 | pykA | b1854 | Pyruvate Kinase II | 1 | −40.5 | + | + | [29] | [19] |
3,611,605 | nikABCDE | b3476 | Nickel Transporter | 1 | −40.5 | + | + | None | [126] |
953,741 | focA-pflB | b0904 | Formate Transporter (focA); Pyruvate Formate-Lyase (pflB) | 2 | −40.5 | + | + | [127] | [128] |
2,714,605 | yfiD | b2579 | Stress-Induced Alternative Pyruvate Formate-Lyase | 1 | −40.5 | + | + | [129] | [129] |
940,035 | dmsABC | b0894 | Dimethyl Sulfoxide Reductase | 1 | −41.5 | + | + | [41] | [41] |
1,279,003 | narGHJI | b1224 | Nitrate Reductase | 1 | −41.5 | + | + | [41] | [130] |
1,627,208 | ydfZ | b1541 | Unknown Function | 2 | −41.5 | + | + | [29] | [18], [19] |
1,837,412 | ynjE | b1757 | Molybdopterin Synthase Sulfurtransferase | 1 | −41.5 | + | + | None | [18] |
3,491,947 | nirBDC- cysG | b3365 | Nitrite Reductase (nirBDC); Uroporphyrin III C-Methyltransferase (cysG) | 1 | −41.5 | + | + | [21] | [130] |
4,285,670 | nrfABCDEFG | b4070 | Periplasmic Nitrite Reductase | 1 | −41.5 | + | + | [42] | [42] |
34,059 | caiF | b0034 | Carnitine Transcriptional Activator | 1 | −41.5 | + | o | [29] | [47] |
1,277,082 | narK | b1223 | Nitrate/Nitrite Antiporter | 1 | −41.5 | + | + | [41] | [131] |
877,441 | bssR | b0836 | Regulator of Biofilm Formation | 1 | −41.5 | + | + | None | None |
1,752,688 | ydhYVWXUT | b1674 | Predicted Oxidoreductase System | 1 | −42.5 | + | + | [132] | [18], [19] |
1,407,150 | fnrS | b4699 | Small Regulatory RNA | 1 | −42.5 | + | N/A | [48], [49] | [48], [49] |
4,380,446 | frdABCD | b4154 | Fumarate Reductase | 1 | −45.5 | + | + | [133] | [43] |
3,635,591 | pitA | b3493 | Phosphate Transporter | 1 | −56.5 | + | o | [29] | [18], [19] |
1,831,403 | ydjXYZ- ynjABCD | b1750 | Predicted Proteins (ydjXYZ-ynjAB); Predicted Transporter (ynjCD) | 1 | −60.5 | + | + | [18] | [18], [19] |
913,151 | hcp-hcr | b0873 | Hybrid-Cluster Protein (hcp); NADH Oxidoreductase (hcr) | 1 | −72.5 | No σ70 Peaks (σE Site) | + | [134] | [134] |
2,411,410 | ackA-pta | b2296 | Acetate Kinase/(ackA); Phosphate Acetyltransferase (pta) | 1 | −74.5 | + | + | [29] | [135] |
4,347,259 | dcuB- fumB | b4123 | Dicarboxylate Transporter (dcuB); Fumarase B (fumB) | 1 | −132.5 | + | + | [29] | [136] |
1,665,279 | ynfK | b1593 | Predicted Dethiobiotin Synthetase | 1 | TSS not known | + | + | [29] | [18], [19] |
2,415,052 | yfcC | b2298 | Putative S-transferase | 1 | TSS not known | + | + | [29] | [19] |
3,299,421 | yhbUV | b3158 | Predicted Peptidase | 1 | TSS not known | + | + | [29] | [18], [19] |
3,352,152 | yhcC | b3211 | Predicted Fe-S Oxidoreductase | 1 | TSS not known | + | + | [29] | [19] |
3,654,199 | yhiD | b3508 | Predicted Mg2+ ATP-dependent Transporter | 1 | TSS not in peak region | + | + | None | [18] |
3,463,910 | yjiML | b4335 | Hypothetical Protein | 1 | TSS not in peak region | + | + | None | [17], [18] |
4,615,181 | yjjI | b4380 | Conserved Protein | 1 | TSS not known | + | + | None | [18], [19] |
655,298 | dcuC | b0621 | Dicarboxylate Transporter | 1 | TSS not in peak region | + | + | None | [137] |
4,228,181 | pepE | b4021 | Peptidase E | 1 | TSS not known | + | + | None | [18] |
Operons directly repressed by FNR with an overall decrease in expression under anaerobic growth conditions (Category 2) | |||||||||
1,397,604 | fnr | b1334 | Anaerobic Transcriptional Regulator | 1 | −0.5 | − | o | [138] | [138] |
142,604 | can | b0126 | Carbonic Anhydrase 2 | 2 | −11.5 | − | − | None | [17] |
2,088,088 | hisLGDC | b2018 | Histidine Biosynthesis | 1 | −11.5 | + | o | None | [18] |
1,165,151 | ndh | b1109 | NADH:Ubiquinone Oxidoreductase II | 1 | −50.5 | − | o | [139] | [139] |
2,176,686 | fbaB | b2097 | Fructose Bisphosphate Aldolase Class I | 1 | −59.5 | No σ70 Peaks (σS Site) | o | None | [18] |
1,030,741 | yccA | b0970 | Putative Transport Protein | 1 | −71.5 | − | o | None | None |
3,217,259 | ygjG | b3073 | Putrescine Aminotransferase | 1 | −96.5 | − | − | None | None |
1,014,801 | rmf | b0953 | Ribosome Modulation Factor | 1 | −98.5 | + | o | None | None |
4,231,491 | lysC | b4024 | Aspartate Kinase III | 2 | −115.5 | + | o | None | None |
1,986,025 | yecR | b1904 | Predicted Protein | 1 | +30 | − | o | None | [18],[19] |
400,328 | iraP | b0382 | Anti-Adaptor Protein for σS Stabilization | 2 | TSS not in peak region | − | − | None | [18], [19] |
1,860,717 | msrB | b1778 | Methionine Sulfoxide Reductase B | 1 | TSS not in peak region | + | − | None | [18] |
2,342,585 | nrdAB | b2234 | Ribonucleoside Diphosphate Reductase I | 1 | TSS not in peak region | − | − | None | [18], [19] |
Operons directly repressed by FNR with an overall increase in expression under anaerobic growth conditions (Category 2) | |||||||||
3,656,030 | gadE | b3512 | Transcriptional Activator | 2 | −22.5 | + | + | None | [18] |
3,654,924 | hdeD | b3511 | Acid-Resistance Membrane Protein | 1 | −43.5 | + | + | None | [18] |
121,987 | pdhR-aceEF-lpdA | b0113 | Pyruvate Dehydrogenase | 1 | −50.5 | − | + | [29] | [140] |
770,404 | cydAB | b0733 | Cytochrome bd-1 Terminal Oxidase | 1 | −53.5 | + | + | [50] | [141] |
3,654,924 | hdeAB-yhiD | b3510 | Acid-Resistance Proteins | 1 | −126.5 | + | + | None | [18] |
1,311,935 | ompW | b1256 | Outer Membrane Protein | 1 | −126.5 | + | + | [29] | [19] |
2,310,730 | ompC | b2215 | Outer Membrane Porin C | 1 | TSS not in peak region | + | + | None | [18] |
2,848,688 | hycABCDEFGHI | b2725 | Hydrogenase 3 | 1 | TSS not in peak region | No σ70 Peaks (σN Site) | + | None | [18] |
Genomic location within each FNR ChIP-seq peak with the highest read count (the summit of the peak).
Operon downstream of the FNR ChIP-seq peak, and operon designation was obtained from EcoCyc [70].
Identification number (B-number) for the first gene in each operon, obtained from EcoCyc [70].
Functional description of the products of the operons, obtained from EcoCyc [70].
Number of predicted FNR motifs identified within the FNR ChIP-seq peak region.
Location of FNR PWM (motif with best PatSer score used if more than one motif identified) relative to the transcription start site (if known). Start site locations obtained from EcoCyc [70] and Kim et al [142].
Analysis of σ70 occupancy (as determined using ChIP-seq data) under aerobic compared to anaerobic growth conditions. Increases (+) and decreases (−) in σ70 occupancy were statistically determined using a one-sided, paired t-test and p-values were corrected using the Bonferroni method. Also listed are those sites with no σ70 ChIP-seq peaks (Table S2).
The expression of each operon in WT −O2 cultures was compared to expression in WT +O2 cultures. Each operon was determined to have a significant (>2 fold) increase (+), decrease (−) and no change (o) in WT −O2 relative to WT +O2 (Table S12).
Reference for experimentally determined FNR binding at the location of the FNR ChIP-seq peak, if previously identified. Those operons without experimentally determined FNR binding data are marked “None”.
Reference for FNR-dependent change in expression of each operon, if previously identified. Those without previous FNR expression data are marked “None”.