ArticlePloS one2011
Gene decay in Shigella as an incipient stage of host-adaptation.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 53 citations in OpenAlex.
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- Radical genome remodelling accompanied the emergence of a novel host-restricted bacterial pathogen.PLoS pathogens · 2021Article
- Comparative genomics of a novel clade shed light on the evolution of the genus Erysipelothrix and characterise an emerging species.Scientific reports · 2021Article
- A One Health Perspective for Defining and DecipheringComparative medicine · 2021Review
- High Rates of Genome Rearrangements and Pathogenicity ofFrontiers in microbiology · 2021Article
- Phylogenetic Relatedness and Genome Structure ofFrontiers in microbiology · 2021Article
- Campylobacter jejuni and Campylobacter coli autotransporter genes exhibit lineage-associated distribution and decay.BMC genomics · 2020Article
- Complete genome sequence and annotation of the laboratory reference strain Shigella flexneri serotype 5a M90T and genome-wide transcriptional start site determination.BMC genomics · 2020Article
- The MFS efflux pump EmrKY contributes to the survival of Shigella within macrophages.Scientific reports · 2019Article
- A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes.Bioinformatics (Oxford, England) · 2016Article
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- Natural Selection in Virulence Genes of Francisella tularensis.Journal of molecular evolution · 2016Article
- The genomic signatures of Shigella evolution, adaptation and geographical spread.Nature reviews. Microbiology · 2016Review
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMany facultative bacterial pathogens have undergone extensive gene decay processes, possibly due to lack of selection pressure during evolutionary conversion from free-living to intracellular lifestyle. Shigella, the causative agents of human shigellosis, have arisen from different E. coli-like ancestors independently by convergent paths. As these bacteria all have lost large numbers of genes by mutation or deletion, they can be used as ideal models for systematically studying the process of gene function loss in different bacteria living under similar selection pressures. METHODOLOGIES/PRINCIPAL
findingsWe compared the sequenced Shigella genomes and re-defined decayed genes (pseudogenes plus deleted genes) in these bacteria. Altogether, 85 genes are commonly decayed in the five analyzed Shigella strains and 1456 genes are decayed in at least one Shigella strain. Genes coding for carbon utilization, cell motility, transporter or membrane proteins are prone to be inactivated. Decayed genes tend to concentrate in certain operons rather than distribute averagely across the whole genome. Genes in the decayed operon accumulated more non-synonymous mutations than the rest genes and meanwhile have lower expression levels.
conclusionsDifferent Shigella lineages underwent convergent gene decay processes, and inactivation of one gene would lead to a lesser selection pressure for the other genes in the same operon. The pool of superfluous genes for Shigella may contain at least two thousand genes and the gene decay processes may still continue in Shigella until a minimum genome harboring only essential genes is reached.
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