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.