PMID:23818864
| Citation |
Myers, KS, Yan, H, Ong, IM, Chung, D, Liang, K, Tran, F, Keleş, S, Landick, R and Kiley, PJ (2013) Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding. PLoS Genet. 9:e1003565 |
|---|---|
| Abstract |
FNR is a well-studied global regulator of anaerobiosis, which is widely conserved across bacteria. Despite the importance of FNR and anaerobiosis in microbial lifestyles, the factors that influence its function on a genome-wide scale are poorly understood. Here, we report a functional genomic analysis of FNR action. We find that FNR occupancy at many target sites is strongly influenced by nucleoid-associated proteins (NAPs) that restrict access to many FNR binding sites. At a genome-wide level, only a subset of predicted FNR binding sites were bound under anaerobic fermentative conditions and many appeared to be masked by the NAPs H-NS, IHF and Fis. Similar assays in cells lacking H-NS and its paralog StpA showed increased FNR occupancy at sites bound by H-NS in WT strains, indicating that large regions of the genome are not readily accessible for FNR binding. Genome accessibility may also explain our finding that genome-wide FNR occupancy did not correlate with the match to consensus at binding sites, suggesting that significant variation in ChIP signal was attributable to cross-linking or immunoprecipitation efficiency rather than differences in binding affinities for FNR sites. Correlation of FNR ChIP-seq peaks with transcriptomic data showed that less than half of the FNR-regulated operons could be attributed to direct FNR binding. Conversely, FNR bound some promoters without regulating expression presumably requiring changes in activity of condition-specific transcription factors. Such combinatorial regulation may allow Escherichia coli to respond rapidly to environmental changes and confer an ecological advantage in the anaerobic but nutrient-fluctuating environment of the mammalian gut. |
| Links |
PubMed PMC3688515 Online version:10.1371/journal.pgen.1003565 |
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Annotations
<annotationlinks/>
Data
<protect>
| Strain/Organism | Assay | Analyte | Variable Conditions | Notes | Links |
|---|---|---|---|---|---|
|
MG1655 |
ChIP-chip |
FNR |
negative control (fnr deletion) and titration of Ptac-fnr |
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|
MG1655 |
ChIP-seq |
FNR |
Anaerobic |
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|
MG1655 |
ChIP-chip |
FNR |
negative control (fnr deletion) vs anaerobic vs hns stp double mutant |
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|
MG1655 |
ChIP-chip |
H-NS |
aerobic vs anaerobic |
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|
MG1655 |
ChIP-chip |
IHF |
Anaerobic |
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|
MG1655 |
ChIP-chip |
RpoD RNAP sigma70 |
aerobic vs anaerobic |
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|
MG1655 |
ChIP-chip |
RpoB RNAP beta |
aerobic vs anaerobic |
||
| edit table |
</protect>
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