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

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.

FNR Regulates Expression of Important Virulence Factors Contributing to Pathogenicity of Uropathogenic Escherichia coli

“…Our evidence also showed that FNR directly regulates the expression of the two-component signal transduction system KguS/KguR, thus likely indirectly regulating other pathogenicity island genes, such as c5038, through KguS/ KguR. It has been well-known that the global regulator FNR in E. coli K-12 controls 122 operons, which are organized into seven regulatory categories (41). To the best of our knowledge, this is the first report showing that FNR controls the expression of a metabolism island in pathogenic E. coli and contributes to bacterial fitness in vivo.…”

Acid Evolution of Escherichia coli K-12 Eliminates Amino Acid Decarboxylases and Reregulates Catabolism

“…(Table S1). The most prominent anaerobic regulator of E. coli, Fnr normally activates genes under low-oxygen conditions (25)(26)(27)(28)(29).…”

Saccharomyces cerevisiae Sen1 Helicase Domain Exhibits 5′- to 3′-Helicase Activity with a Preference for Translocation on DNA Rather than RNA

“…The cDNA was coupled to 4.5 l of Cy3 mono-reactive dye (GE Healthcare) according to the manufacturer's protocol and purified with a MERmaid kit. The cDNA was hybridized to a custom E. coli K12 MG1655 tiled genome microarray (Roche NimbleGen) and scanned as described previously (23).…”

“…To determine the sequence of these small RNAs, we used them as template for synthesis of firststrand Cy3-labeled cDNA and hybridized the cDNA to a tiled microarray of the E. coli genome (23). After manual filtering of spurious signals, we used MEME to search for common sequence patterns (31).…”