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PMID:23818864

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Contents

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

Keywords


Significance

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Useful Materials and Methods

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Annotations

Gene product Qualifier GO ID GO term name Evidence Code with/from Aspect Notes Status

Data

Strain/Organism Assay Analyte Variable Conditions Notes Links

MG1655

ChIP-chip

FNR

negative control (fnr deletion) and titration of Ptac-fnr

MG1655

ChIP-seq

FNR

Anaerobic

MG1655

ChIP-chip

FNR

negative control (fnr deletion) vs anaerobic vs hns stp double mutant

MG1655

ChIP-chip

H-NS

aerobic vs anaerobic

MG1655

ChIP-chip

IHF

Anaerobic

MG1655

ChIP-chip

RpoD RNAP sigma70

aerobic vs anaerobic

MG1655

ChIP-chip

RpoB RNAP beta

aerobic vs anaerobic

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See also

References

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