Skip to main content
. 2010 Jul 22;6(7):e1001027. doi: 10.1371/journal.pgen.1001027

Table 2. Putative FnrL binding sites detected by ChIP–chip analysis or by bioinformatic analysis of the R. sphaeroides genome sequence.

Chr1 FnrL ChIP-chip peak coordinates2 σ70 peak3 Putative FnrL binding sequence4 FnrL target genes5
Begin End Begin Scores Sequences Loci IDs Regulation Annotation
Chr 1 408824 409553 + 409223 2156.75 TTGACgcggATCAA RSP1819-7 + feoABC
Chr 1 417320 418709 + 417975 2501.25 TTGATtcagATCAA RSP1826-9 coxII-X-XI-III
Chr 1 476545 477386 477119 2554.25 TTGATctggATCAA RSP1877-6 coxI
Chr 1 792149 793028 + 792528 2249.50 TTGATacgcATCAA
Chr 1 862277 863397 + 862812 2276.00 TTGATtcagGTCAA RSP2247 + fusA
Chr 1 963978 964891 + 964492 1693.00 ATGACgcagATCAA RSP2337 + ccpA1
Chr 1 1022044 1022949 + 1022541 2368.75 TTGACttagATCAA RSP2395 ccpA2
Chr 1 1152077 1152912 + 1152640 2249.50 TTGACgcagATCAA RSP2507 + ompW
Chr 1 1217112 1218401 + 1217769 2024.25 TTGACgcagGTCAA RSP2573 +
Chr 1 1675600 1676545 + 1676046 2143.50 TTGATccttATCAA RSP2984 + hemA
Chr 1 1679670 1680230 1680004 −996.75 GTGACttagGGCAG
Chr 1 1811885 1812675 + 1812207 1971.25 CTGATgcagATCAA RSP0100-12 + nuoABCDEFGHJKLMN
Chr 1 1881897 1882994 + 1882413 2249.50 TTGACctgcATCAA RSP0166 + dksA
Chr 1 2007383 2008346 + 2007816 2117.00 TTGACatgcATCAA RSP0281-76 + bchEJGP
Chr 1 2046834 2047877 + 2047244 262.00 TTGCGcaggATCAA RSP0317 + hemN
Chr 1 2193245 2193765 2193494 2382.00 TTGATgcggATCAA
Chr 1 2201048 2202201 + 2201632 2342.25 TTGATgtagGTCAA RSP0466-4 +
RSP0467-8 + ubiD
Chr 1 2206264 2207340 + 2206759 1613.50 TTGACttcaGTCAA RSP6116 ?
Chr 1 2439761 2441022 + 2440385 2196.50 ATGATgtcgATCAA RSP0696-3 + ccoNOQP
2440417 2196.50 TTGACatggATCAA RSP0697 + uspA
Chr 1 2441409 2442838 + 2442182 2501.25 TTGATtcagATCAA RSP0698 fnrL
RSP0699 + hemZ
Chr 1 2518226 2519045 + 2518696 1746.00 CTGATctgcGTCAA RSP0775 +
Chr 1 2565774 2566660 + 2566094 2382.00 TTGATgcggATCAA RSP0820 +
Chr 1 3026608 3027564 + 3027028 1679.75 TTGAGcaagATCAA RSP1257-4 + phbCfabI
Chr 2 77569 78562 78069 1812.25 TTGACgtcaATCAA RSP3044 + dorS
P002 22017 26368 + 24255 977.50 TTGACagctGTCAA
P004 1074 2014 1088 −877.50 CAGATcgagATGAA
P004 51099 52291 + 51739 2050.75 CTGATccagATCAA RSP4201-4 +
Additional putative FnrL binding sites identified by sequence analysis
Chr 1 403983 1891.75 TTGACcgaaATCAA
Chr 1 635560 1679.75 ATGATtttcATCAA
Chr 1 659055 1653.25 TTGACccgcATCAA
Chr 1 1185086 16930 CTGATcctcATCAA
Chr 1 1842368 1732.75 ATGATcttcATCAA
Chr 1 2104074 1640.00 ATGATcctcATCAA
Chr 1 2436687 1666.50 TTGACttcgGTCAA RSP0692-89 + rdxBHIS
Chr 1 2760402 1772.50 ATGACccagATCAA
Chr 2 403914 1640.00 TTGATtgcgATCAA RSP3341 +
Chr 2 748494 1640.00 CTGATaaggATCAA RSP3640-3 + exsB

1Chromosomes or plasmids.

2Genomic coordinates of regions of the genome that were significantly enriched by chromatin immuno-precipitation using antibodies against FnrL.

3Indicates if genomic regions bound by FnrL overlap with regions bound by σ70 as determined by chromatin immuno-precipitation using antibodies against σ70.

4Genomic coordinates, scores (log-likelihood ratio), and sequences of putative FnrL binding sites identified using the position-weighted matrix constructed from the conserved DNA target sequence of the FNR-type proteins across α-proteobacteria.

5Locus number and annotations of the FnrL target genes. The signs indicates whether the transcription of the target operons is increased (+) or decreased (−) by FnrL binding.