1

Table S-2. Fur binding regions mapped across the E. coli K12 genome under aerobic or anaerobic growth conditions using ChIP-seq.

Peak Summita / Geneb / Peak Location Relative to Genec / Fur-dependent Regulationd / Seo et. ale / Chen et. alf
Iron-dependent Fur DNA binding regions present in both aerobic and anaerobic cells
110709 / mutT / upstream / -
146545 / panD / inside / - / +
167437 / fhuA / upstream / + / + / +
189629 / map/tff / upstream / + / + / +
289733 / argF / upstream / - / + / +
296270 / intF / upstream / -
344297 / yahM / upstream / -
365460 / lacZ / upstream / -g
398029 / yaiW / inside / -
455989 / clpP / upstream / -
490056 / priC/ybaN / upstream / + / + / +
496400 / adK / upstream / - / +
579850 / ylcI/nohB / upstream / -g / +
611910 / fepA/fes / upstream / + / + / +
621448 / fepD/entS / upstream / + / + / +
624006 / fepB/entC / upstream / + / + / +
674999 / ybeQ / inside / -g / +
786851 / gpmA / upstream / + / + / +
840882 / fiu / upstream / + / + / +
942120 / dmsA / inside / RyhB-regulated / +
1080526 / efeU_1 / upstream / + / + / +
1088797 / pgaB / inside / -g / +
1118343 / yceJ / upstream / - / +
1123762 / mdtH / inside / -g
1160888 / fhuE/hinT / upstream / + / + / +
1244172 / ycgY / upstream / -g / +
1255624 / ycgV / upstream / - / +
1309051 / yciI/tonB / upstream / + / + / +
1333496 / acnA / upstream / RyhB-regulated / + / +
1515294 / yncL/ydcX / upstream / -
1521257 / yncD/yncE / upstream / + / + / +
1551894 / adhP / upstream / + / +
1577348 / yddA / upstream / + / + / +
1619757 / ydeE / inside / -
1634568 / nohA / upstream / -g / +
1672505 / tqsA / inside / - / + / +
1682591 / tus / inside / -
1709604 / nth / upstream / -g / +
1762483 / sufA / upstream / + / + / +
1787614 / ydiE / upstream / + / + / +
1790012 / ydiV / upstream / -g / + / +
1886643 / fadD / inside / -g / +
1897576 / yoaD / inside / -g / +
1902993 / yobD / inside / - / +
1903440 / mntP / upstream / + / +
1914398 / yebR/yebS / upstream / - / + / +
1926781 / ptrB / inside / -g
1985021 / ftnB / upstream / + / +
1986623 / ftnA / upstream / + / +
1994870 / sdiA / upstream / - / + / +
2000925 / fliC / inside / - / + / +
2066584 / yoeA / upstream / + / + / +
2071684 / flu / inside / - / +
2163221 / yegP / upstream / -
2178132 / yegU / upstream / -g
2194511 / molR_1 / upstream / -g
2244995 / cirA / upstream / + / + / +
2306693 / yojI / upstream / + / + / +
2436388 / flk / inside / - / + / +
2454158 / yfcV / upstream / -g / + / +
2510784 / mntH/nupC / upstream / + / + / +
2550301 / ypeA/amiA / upstream / +
2562629 / yffS / upstream / - / +
2585162 / narQ / inside / -
2749854 / recN / upstream / + / + / +
2758006 / yfjI / inside / - / + / +
2762678 / yfjL / inside / -
2798763 / nrdH / upstream / + / + / +
2832021 / norW / upstream / -g / +
3013889 / ygfK / upstream / -g / + / +
3144497 / hybO / upstream / RyhB-regulated / +
3150084 / exbB / upstream / + / + / +
3258142 / tdcF / upstream / -g / +
3346331 / yrbL / upstream / + / +
3465078 / bfd / upstream / + / +
3499407 / frlB / upstream / -g
3538065 / feoA / upstream / + / + / +
3556771 / rtcR / inside / -
3579062 / ryhB/yhhY / upstream / + / + / +
3758650 / selA / inside / -
3809579 / rpmB / inside / -
3821315 / spoT / inside / -
4073667 / yihX / inside / - / +
4098740 / rhaT/sodA / upstream / + / + / +
4156442 / oxyS/oxyR / upstream / -
4463134 / treB / inside / -g / + / +
4514776 / fecA / upstream / + / + / +
4516301 / fecI / upstream / + / + / +
4570209 / yjiT / upstream / - / + / +
4603758 / fhuF/yjjZ / upstream / + / + / +
Iron-dependent Fur DNA binding regions present only in anaerobic cells
99820 / murG / inside / -
104390 / ftsA / inside / -
154688 / htrE / inside / -g
192846 / frr / upstream / -
198039 / bamA / inside / -
219501 / yaeB / inside / -
230477 / yafC / inside / -
233253 / mltD / inside / -
275729 / mmuM / upstream / -
278401 / afuB / upstream / -
295863 / intF / inside / - / +
343573 / yahL / inside / -g / +
345668 / yahN/yahO / upstream / -g
390567 / yaiT / inside / -
403683 / adrA / inside / - / +
431145 / tsx / upstream / RyhB-regulated
486677 / kefA / inside / -
515626 / ybbL / inside / - / +
559584 / sfmD / inside / -g
571412 / ylcH / upstream / -g
579315 / ybcW/ylcI / downstream / -
582646 / appY / upstream / + / +
676547 / djlB / upstream / -g / +
748939 / ybgP / upstream / -g / +
754215 / gltA/sdhC / upstream / RyhB-regulated
764291 / sucD/mngR / downstream / -
789046 / galK / inside / -
816076 / ybhK/moaA / upstream / -
830796 / rhlE / inside / -
848305 / dps / upstream / + / +
859307 / ybiV / upstream / RyhB-regulated
868786 / gsiB / inside / -
890936 / nfsA / upstream / -
925282 / serW / upstream / - / +
933370 / ftsK / inside / -
970905 / ycbJ / upstream / -
971646 / ycbJ / inside / -
979849 / ycbB / upstream / -
1007797 / rlmL / inside / -
1047189 / gfcD / upstream / -g / +
1057796 / torC / inside / -g
1061157 / torD / inside / -
1117061 / yceA/yceI / downstream / -g
1136928 / flgJ / inside / -g
1214697 / ycgF/ycgZ / upstream / -
1216486 / ycgG / upstream / -g
1216810 / ycgG / inside / - / +
1242354 / ldcA/emtA / upstream / -
1262990 / lolB/hemA / upstream / -
1287854 / purU / upstream / -
1298937 / oppA / upstream / - / +
1300950 / oppB / upstream / RyhB-regulated
1317526 / trpC / inside / -
1382108 / ycjW/ycjX / upstream / -g
1425013 / ynaA / inside / -g
1428774 / stfR / inside / -g
1479610 / ynbD / inside / -
1524316 / ansP/yncG / upstream / - / +
1542067 / narU / upstream / -g / +
1566306 / yddW / inside / -g
1589607 / hipA / inside / - / +
1614803 / ydeA / upstream / RyhB-regulated
1650019 / intQ / inside / -
1651905 / rspB / upstream / -g / +
1655498 / ynfC/ynfD / upstream / - / +
1746384 / ydhS / inside / -
1748876 / ydhX / inside / -g
1785052 / ppsA/ppsR / upstream / RyhB-regulated
1827907 / astD / upstream / -g / +
1847774 / sppA / inside / -
1934772 / yebK / inside / -
1935625 / pykA / upstream / -
1960402 / yecT / inside / -g
1984210 / araF / upstream / -g
2011195 / fliE/fliF / upstream / -g
2016090 / fliJ / inside / -g
2018114 / fliM / upstream / -g
2025822 / yedQ / inside / -g
2026183 / yedQ / upstream / -g
2042887 / yeeJ / upstream / - / +
2096565 / ugd / inside / -
2105805 / glf / inside / - / +
2231897 / preT / upstream / + / +
2254233 / yeiM / inside / -g
2282031 / yejK/yejL / upstream / -
2300984 / napA / upstream / -
2367521 / arnA / inside / RyhB-regulated / + / +
2377401 / menD / upstream / -
2441041 / mnmC / inside / -
2447554 / yfcO / inside / - / +
2461640 / yfdF / inside / -g
2468781 / tfaS / upstream / -
2481423 / emrK/evgA / upstream / -
2516719 / yfeC / inside / -g
2559222 / yffM / upstream / -g
2589238 / yffB / upstream / -
2597740 / dapA/gcvR / upstream / -
2610675 / hyfR / inside / -g
2626673 / yfgF / inside / -g / + / +
2647675 / yfhM / inside / -
2648703 / yfhM / inside / -
2651852 / ryfA / upstream / -g / +
2653364 / sseB / upstream / RyhB-regulated
2654469 / pepB / upstream / RyhB-regulated
2663306 / csiE / upstream / -g / +
2673819 / yphC / upstream / -g / +
2735669 / pheA / upstream / -
2764024 / rnlA / inside / -
2781013 / ypjA / upstream / - / +
2792172 / gabP / upstream / -g / +
2795593 / ygaP / upstream / -g
2904507 / ygcG/eno / downstream / -
2926220 / sdaC / upstream / -g
3098706 / ansB / upstream / -g
3122247 / glcG / upstream / -g / +
3152558 / yqhC / inside / -g
3255578 / yhaO / inside / -g
3273051 / garP/garD / upstream / -g / +
3356166 / gltB / inside / RyhB-regulated
3372180 / nanR / inside / - / +
3393073 / yhdP / inside / -
3401859 / yhdH / inside / -
3429385 / rimN / upstream / -g
3431690 / smf/def / upstream / -g
3453711 / gspC / inside / -g / +
3560914 / glpD / inside / -g
3582781 / yrhB / upstream / - / +
3643289 / prlC/yhiR / upstream / -
3652829 / dctR / inside / -
3699064 / yhjV / inside / -
3744012 / yiaO / upstream / -
3870084 / dgoD / inside / -g
3897147 / yieK / inside / -g
3952413 / ilvD / inside / -
3969214 / rffD / upstream / -g
3991035 / cyaA / inside / -
4016713 / ubiE / upstream / -
4126520 / metJ/metB / upstream / -
4148649 / ppc / inside / -
4159723 / yijD / upstream / -g
4183270 / rpoC / upstream / -
4234928 / yjbG / upstream / -g
4296101 / fdhF / inside / RyhB-regulated
4327032 / yjdA / inside / -g
4382384 / yjeM / inside / -g
4393179 / yjeF / inside / -
4426351 / ytfB / inside / -
4443230 / ytfN / inside / -g
4462478 / treC / inside / -g
4470667 / G7878 / inside / -
4493154 / idnK / inside / -g
4532166 / yjhX / upstream / -g
4535017 / nanS / inside / -
4549340 / gntP / upstream / -g
4558787 / yjiH/kptA / upstream / -
4572369 / yjiV / inside / -g
4611442 / yjjV / upstream / -
Iron-independent Fur DNA binding regions present in both aerobic and anaerobic cells
8396* / talB / inside / -
756243 / sdhA / inside / RyhB-regulated / +
2816548* / serV / inside / -
2922392 / csrB / inside / - / +
3731503 / xylG / inside / - / +
3809019 / mutM / inside / - / +
4078884 / fdhE / inside / - / +
4371296 / yjeI/yjeJ / downstream / -

aThelocation of the peak summit of the Fur-dependent ChIP signal is reported using the genome coordinates of MG1655 (version U00096.2).

bThe gene predicted to be associated with the ChIP signal. If the ChIP signal is located upstream of two divergent genes or downstream of two convergent genes, both genes are given and separated by a "/".

cLocation of the ChIP signal relative to the gene as determined by visual inspection.

dFur regulation of RNA levels was determined from transcriptomic data (Table S-3). “+” are operons whose gene expression changed greater than 1.5 fold when comparing Fur- to WT strains grown under either aerobic or anaerobic conditions. “-” are those that did not change and “-g”are those whose expression was generally low under all conditions. Operons whose expression are also regulated by RyhB are also indicated (Table S-4).

eFur bindingobserved under aerobic conditions by ChIP-exo [Seoet. al(1)].

fFur binding predicted bioinformatically [Chenet. al (2)].

*These peakswere only identified in the iron deficient strain, not WT strains under either aerobic or anaerobic growth conditions.

References

1.Seo SW, Kim D, Latif H, O'Brien EJ, Szubin R, Palsson BO. 2014. Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. Nat Commun 5:4910.

2.Chen Z, Lewis KA, Shultzaberger RK, Lyakhov IG, Zheng M, Doan B, Storz G, Schneider TD. 2007. Discovery of Fur binding site clusters in Escherichia coli by information theory models. Nucleic Acids Res 35:6762-6777.