H-NS gives invading DNA the silent treatment

Gene socialization: gene order, GC content and gene silencing in Salmonella

Background

Genes of conserved order in bacterial genomes tend to evolve slower than genes whose order is not conserved. In addition, genes with a GC content lower than the GC content of the resident genome are known to be selectively silenced by the histone-like nucleoid structuring protein (H-NS) in Salmonella.

Results

In this study, we use a comparative genomics approach to demonstrate that in Salmonella, genes whose order is not conserved (or genes without homologs) in closely related bacteria possess a significantly lower average GC content in comparison to genes that preserve their relative position in the genome. Moreover, these genes are more frequently targeted by H-NS than genes that have conserved their genomic neighborhood. We also observed that duplicated genes that do not preserve their genomic neighborhood are, on average, under less selective pressure.

Conclusions

We establish a strong association between gene order, GC content and gene silencing in a model bacterial species. This analysis suggests that genes that are not under strong selective pressure (evolve faster than others) in Salmonella tend to accumulate more AT-rich mutations and are eventually silenced by H-NS. Our findings may establish new approaches for a better understanding of bacterial genome evolution and function, using information from functional and comparative genomics.

Modulation of horizontally acquired genes by the Hha-YdgT proteins in Salmonella enterica serovar Typhimurium

We describe a transcriptomic study of the effect of hha and ydgT mutations in Salmonella enterica serovar Typhimurium. A large number of genes showing altered expression are located in AT-rich horizontally acquired DNA sequences. Many of these genes have also been reported to be targets for H-NS. As Hha and YdgT interact with H-NS, our findings strongly suggest that Hha and/or YdgT must form complexes with H-NS when they silence these DNA regions.

H-NS, the genome sentinel

Two recent reports have indicated that the H-NS protein in Salmonella enterica serovar Typhimurium has a key role in selectively silencing the transcription of large numbers of horizontally acquired AT-rich genes, including those that make up its major pathogenicity islands. Broadly similar conclusions have emerged from a study of H-NS binding to DNA in Escherichia coli. How do these findings affect our view of H-NS and its ability to influence bacterial evolution?