Abstract
BackgroundGenes 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.ResultsIn 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.ConclusionsWe 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.
Highlights
Genes of conserved order in bacterial genomes tend to evolve slower than genes whose order is not conserved
Evolutionary rate and GC content are related to genomic neighborhood conservation We compared the proteins predicted to be encoded in the completely sequenced genome of S
Typhimurium [19] against the proteins encoded in the genome of E. coli K12 [20], both obtained from the NCBI Genomes Division ftp://ftp.ncbi.nih.gov/genomes/Bacteria/ using BLASTP [21]
Summary
Genes of conserved order in bacterial genomes tend to evolve slower than genes whose order is not conserved. Proteins encoded by genes of conserved order in bacteria tend to evolve more slowly when compared to proteins encoded by genes without a conserved order [1,2] and genes with similar or related functions tend to occur in adjacent chromosomal positions in yeast [3]. Genes with conserved order were found to evolve at similar rates [4] and, in prokaryotes, proteins encoded by genes with conserved order appear to interact physically [1]. Following a duplication event one of the two (paralog) genes might keep its original function, whereas the other one might be under less selective pressure. It is not always readily apparent which duplicated genes evolve faster. There have been reports that have marginally correlated sequence conservation with genome context [11], but there must be other, yet unknown, functional features that determine the fate of duplicate genes
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