AUTHOR=Seferbekova Zaira , Zabelkin Alexey , Yakovleva Yulia , Afasizhev Robert , Dranenko Natalia O. , Alexeev Nikita , Gelfand Mikhail S. , Bochkareva Olga O. 

TITLE=High Rates of Genome Rearrangements and Pathogenicity of Shigella spp.

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.628622

DOI=10.3389/fmicb.2021.628622

ISSN=1664-302X

ABSTRACT=<p><italic>Shigella</italic> are pathogens originating within the <italic>Escherichia</italic> lineage but frequently classified as a separate genus. <italic>Shigella</italic> genomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of <italic>E. coli</italic> and <italic>Shigella</italic> strains to assess the contribution of genomic rearrangements to <italic>Shigella</italic> evolution. We found that <italic>Shigella</italic> experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic <italic>E. coli</italic>. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different <italic>Shigella</italic> lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all <italic>Shigella</italic> strains that also showed a high level of sequence conservation in the promoter and further in the 5′-intergenic region. In the only available enteroinvasive <italic>E. coli</italic> (EIEC) strain, which is a pathogenic <italic>E. coli</italic> with a phenotype intermediate between <italic>Shigella</italic> and non-pathogenic <italic>E. coli</italic>, we found a rate of genome rearrangements comparable to those in other <italic>E. coli</italic> and no functional copies of the two <italic>Shigella</italic>-specific E3 ubiquitin ligases. These data indicate that the accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands.</p>