H-NS Mediates the Silencing of Laterally Acquired Genes in Bacteria

Sacha Lucchini,Douglas Hurd,Martin D Goldberg,Gary Rowley,Jay C D Hinton,Marcus Harrison,Ralph R Isberg

doi:10.1371/journal.ppat.0020081

Abstract

Histone-like nucleoid structuring protein (H-NS) is a modular protein that is associated with the bacterial nucleoid. We used chromatin immunoprecipitation to determine the binding sites of H-NS and RNA polymerase on the Salmonella enterica serovar Typhimurium chromosome. We found that H-NS does not bind to actively transcribed genes and does not co-localize with RNA polymerase. This shows that H-NS principally silences gene expression by restricting the access of RNA polymerase to the DNA. H-NS had previously been shown to preferentially bind to curved DNA in vitro. In fact, at the genomic level we discovered that the level of H-NS binding correlates better with the AT-content of DNA. This is likely to have evolutionary consequences because we show that H-NS binds to many Salmonella genes acquired by lateral gene transfer, and functions as a gene silencer. The removal of H-NS from the cell causes un-controlled expression of several Salmonella pathogenicity islands, and we demonstrate that this has deleterious consequences for bacterial fitness. Our discovery of this novel role for H-NS may have implications for the acquisition of foreign genes by enteric bacteria.

Highlights

Bacteria have an extraordinary capacity to adapt to changes in their external environment
Using chromatin immunoprecipitation on chip (ChIP-on-chip) [18,19], we have addressed the question of where histone-like nucleoid-structuring protein (H-NS) binds to DNA in the macro-molecular context of a living bacterial cell and show how this correlates with the distribution of RNA polymerase on the chromosome
Only 20 (6.1%) of the 330 genes down-regulated in JH4000 were bound by H-NS. These findings demonstrate a role for H-NS as a global gene silencer, and this was confirmed by the observed negative correlation between histone-like nucleoid structuring protein (HNS) binding and gene expression levels (Figure 2C)

Summary

Introduction

Bacteria have an extraordinary capacity to adapt to changes in their external environment. As DNA curvature is most pronounced around the transcriptional start of genes [15] a simple model involving the preferential binding of H-NS to regulatory regions has been considered [16], with resultant effects upon global gene expression. H-NS and RNA polymerase binding sites on the chromosome of live Salmonella enterica serovar Typhimurium (S. typhimurium) LT2 cells were identified by ChIP-on-chip, using a tiled oligonucleotide microarray (Figure 1, outer circles).

Results

Conclusion