Research output: Contribution to journal › Article › peer-review
High Rates of Genome Rearrangements and Pathogenicity of Shigella spp. / Сефербекова, Заира; Забелкин, Алексей; Яковлева, Юлия Александровна; Афасижев, Роберт; Драненко, Наталия; Алексеев, Никита; Гельфанд, Михаил; Бочкарева, Ольга.
In: Frontiers in Microbiology, Vol. 12, 628622, 2021.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - High Rates of Genome Rearrangements and Pathogenicity of Shigella spp.
AU - Сефербекова, Заира
AU - Забелкин, Алексей
AU - Яковлева, Юлия Александровна
AU - Афасижев, Роберт
AU - Драненко, Наталия
AU - Алексеев, Никита
AU - Гельфанд, Михаил
AU - Бочкарева, Ольга
N1 - Publisher Copyright: © Copyright © 2021 Seferbekova, Zabelkin, Yakovleva, Afasizhev, Dranenko, Alexeev, Gelfand and Bochkareva.
PY - 2021
Y1 - 2021
N2 - Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella 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 E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella 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 E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-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.
AB - Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella 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 E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella 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 E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-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.
KW - E3 ubiquitin-ligases
KW - Escherichia coli
KW - IS
KW - Shigella
KW - pathogens
KW - rearrangements
KW - recombination
KW - SEQUENCES
KW - ESCHERICHIA-COLI
KW - ORIGINS
KW - EVOLUTION
KW - ALIGNMENT
KW - DNA
KW - PROTEINS
KW - TOOL
UR - http://www.scopus.com/inward/record.url?scp=85104987158&partnerID=8YFLogxK
UR - https://www.mendeley.com/catalogue/213298d4-a27e-3002-a4f2-d080daf678b8/
U2 - 10.3389/fmicb.2021.628622
DO - 10.3389/fmicb.2021.628622
M3 - Article
C2 - 33912145
VL - 12
JO - Frontiers in Microbiology
JF - Frontiers in Microbiology
SN - 1664-302X
M1 - 628622
ER -
ID: 75995687