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. 2013 Jun 20;9(6):e1003565. doi: 10.1371/journal.pgen.1003565

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]
a

Genomic location within each FNR ChIP-seq peak with the highest read count (the summit of the peak).

b

Operon downstream of the FNR ChIP-seq peak, and operon designation was obtained from EcoCyc [70].

c

Identification number (B-number) for the first gene in each operon, obtained from EcoCyc [70].

d

Functional description of the products of the operons, obtained from EcoCyc [70].

e

Number of predicted FNR motifs identified within the FNR ChIP-seq peak region.

f

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].

g

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).

h

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).

i

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”.

j

Reference for FNR-dependent change in expression of each operon, if previously identified. Those without previous FNR expression data are marked “None”.