LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium

Abstract

Summary We report the first investigation of the binding of the Salmonella enterica LeuO LysR‐type transcription regulator to its genomic targets in vivo. Chromatin‐immunoprecipitation‐on‐chip identified 178 LeuO binding sites on the chromosome of S. enterica serovar Typhimurium strain SL1344. These sites were distributed across both the core and the horizontally acquired genome, and included housekeeping genes and genes known to contribute to virulence. Sixty‐eight LeuO targets were co‐bound by the global repressor protein, H‐NS. Thus, while LeuO may function as an H‐NS antagonist, these functions are unlikely to involve displacement of H‐NS. RNA polymerase bound 173 of the 178 LeuO targets, consistent with LeuO being a transcription regulator. Thus, LeuO targets two classes of genes, those that are bound by H‐NS and those that are not bound by H‐NS. LeuO binding site analysis revealed a logo conforming to the TN11A motif common to LysR‐type transcription factors. It differed in some details from a motif that we composed for Escherichia coli LeuO binding sites; 1263 and 1094 LeuO binding site locations were predicted in the S. Typhimurium SL1344 and E. coli MG1655 genomes respectively. Despite differences in motif composition, many LeuO target genes were common to both species. Thus, LeuO is likely to be a more important global regulator than previously suspected.

DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression

“…The positioning of the bridges is determined by the locations of the binding sites for the DNA bridging proteins. LacI and lambda CI have relatively stringent binding site sequence requirements, unlike LeuO, which recognises a much more degenerate DNA sequence (Dillon and Dorman 2012;Shimada et al 2011). Consequently, LeuO has been found to bind to scores of sites around the bacterial chromosome, giving it the potential to participate in the general organisation of the nucleoid.…”

“…3). These very low stringency requirements for binding site matches make LeuO a useful antagonist for the transcription silencer, H-NS, with its preference for binding to A + T-rich DNA (Dillon et al 2012). A predilection for A + T-rich DNA means that proteins like LeuO and other winged helix-turn-helix proteins must dock with DNA, where the minor groove is up to three times narrower than in more G + C-rich sequences (Oguey et al 2010;Rohs et al 2009).…”

“…LeuO also contributes to nucleoid architecture through its ability to influence the DNA-dependent lateral spreading of the H-NS nucleoid-associated protein locally (Fig. 3) and globally (Dillon et al 2012;Shimada et al 2011).…”

Identification of HilD-Regulated Genes in Salmonella enterica Serovar Typhimurium

“…Even for well-studied transcription factors, ChIP-chip and ChIP-seq experiments have repeatedly revealed novel binding sites, including those previously considered to be noncanonical in nature (e.g., within genes and upstream of seemingly unrelated genes) (17)(18)(19). To date, ChIP-seq and other genome-scale approaches have been sparingly applied to study the layered regulation of S. Typhimurium virulence (19)(20)(21)(22)(23)(24)(25).…”

The Salmonella enterica Serovar Typhi LeuO Global Regulator Forms Tetramers: Residues Involved in Oligomerization, DNA Binding, and Transcriptional Regulation

“…3). Therefore, complex structure-function relationships in LeuO may account for its regulatory functions, acting as a repressor, antirepressor, or activator of a wide variety of nonrelated genes, the number of which is increasing (21,22,58).…”