Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding

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. © 2013 myers et al.