Impact of insertion sequences on convergent evolution of Shigella species
Autoři:
Jane Hawkey aff001; Jonathan M. Monk aff002; Helen Billman-Jacobe aff003; Bernhard Palsson aff002; Kathryn E. Holt aff001
Působiště autorů:
Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
aff001; Department of Bioengineering, University of California, San Diego, San Diego, California, United States of America
aff002; Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
aff003; The London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
aff004
Vyšlo v časopise:
Impact of insertion sequences on convergent evolution of Shigella species. PLoS Genet 16(7): e32767. doi:10.1371/journal.pgen.1008931
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1008931
Souhrn
Shigella species are specialised lineages of Escherichia coli that have converged to become human-adapted and cause dysentery by invading human gut epithelial cells. Most studies of Shigella evolution have been restricted to comparisons of single representatives of each species; and population genomic studies of individual Shigella species have focused on genomic variation caused by single nucleotide variants and ignored the contribution of insertion sequences (IS) which are highly prevalent in Shigella genomes. Here, we investigate the distribution and evolutionary dynamics of IS within populations of Shigella dysenteriae Sd1, Shigella sonnei and Shigella flexneri. We find that five IS (IS1, IS2, IS4, IS600 and IS911) have undergone expansion in all Shigella species, creating substantial strain-to-strain variation within each population and contributing to convergent patterns of functional gene loss within and between species. We find that IS expansion and genome degradation are most advanced in S. dysenteriae and least advanced in S. sonnei; and using genome-scale models of metabolism we show that Shigella species display convergent loss of core E. coli metabolic capabilities, with S. sonnei and S. flexneri following a similar trajectory of metabolic streamlining to that of S. dysenteriae. This study highlights the importance of IS to the evolution of Shigella and provides a framework for the investigation of IS dynamics and metabolic reduction in other bacterial species.
Klíčová slova:
Bacterial genomics – Comparative genomics – Convergent evolution – Genome evolution – Phylogenetic analysis – Pseudogenes – Shigella – Shigella flexneri
Zdroje
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