Homologous recombination as a mechanism for genome rearrangements: environmental and genetic effects

The highly leukotoxic JP2 clone of Actinobacillus actinomycetemcomitans is strongly associated with aggressive periodontitis in adolescents of African descent. DNA fingerprinting using the frequently cutting restriction enzyme MspI and multilocus sequence typing (MLST) showed that five strains of this clone were genetically virtually identical, although ribotyping of the six rrn genes and EcoRI RFLP analysis of the seven IS150-like elements revealed differences. PCR analyses demonstrated that these multi-copy sequences are subject to intragenomic homologous recombination, resulting in translocations or large inversions. The genome rearrangements were reflected in differences among 25 strains representing the JP2 clone in DNA fingerprinting using the rare-cutting restriction enzyme XhoI and resolved by PFGE. XhoI DNA fingerprinting provides a tool for studying local epidemiology, including transmission of this particularly pathogenic clone of A. actinomycetemcomitans.

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Paths from DNA damage and signaling to genome rearrangements via homologous recombination

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis ◽

10.1016/j.mrfmmm.2017.07.008 ◽

2017 ◽

Vol 806 ◽

pp. 64-74 ◽

Cited By ~ 12

Author(s):

Jac A. Nickoloff

Keyword(s):

Dna Damage ◽

Homologous Recombination ◽

Genome Rearrangements

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Homologous Recombination Restarts Blocked Replication Forks at the Expense of Genome Rearrangements by Template Exchange

Molecular Cell ◽

10.1016/j.molcel.2010.07.015 ◽

2010 ◽

Vol 39 (3) ◽

pp. 346-359 ◽

Cited By ~ 118

Author(s):

Sarah Lambert ◽

Ken'ichi Mizuno ◽

Joël Blaisonneau ◽

Sylvain Martineau ◽

Roland Chanet ◽

...

Keyword(s):

Homologous Recombination ◽

Genome Rearrangements ◽

Replication Forks

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Cre-loxP Recombination System for Large Genome Rearrangements in Lactococcus lactis

Applied and Environmental Microbiology ◽

10.1128/aem.68.5.2359-2367.2002 ◽

2002 ◽

Vol 68 (5) ◽

pp. 2359-2367 ◽

Cited By ~ 32

Author(s):

Nathalie Campo ◽

Marie-Line Daveran-Mingot ◽

Kees Leenhouts ◽

Paul Ritzenthaler ◽

Pascal Le Bourgeois

Keyword(s):

Homologous Recombination ◽

Fixed Points ◽

Lactococcus Lactis ◽

Genome Organization ◽

Chromosomal Rearrangements ◽

Cre Recombinase ◽

Genome Rearrangements ◽

Large Genome ◽

Gram Positive Bacteria ◽

Recombination System

ABSTRACT We have used a new genetic strategy based on the Cre-loxP recombination system to generate large chromosomal rearrangements in Lactococcus lactis. Two loxP sites were sequentially integrated in inverse order into the chromosome either at random locations by transposition or at fixed points by homologous recombination. The recombination between the two chromosomal loxP sites was highly efficient (approximately 1 × 10−1/cell) when the Cre recombinase was provided in trans, and parental- or inverted-type chromosomal structures were isolated after removal of the Cre recombinase. The usefulness of this approach was demonstrated by creating three large inversions of 500, 1,115, and 1,160 kb in size that modified the lactococcal genome organization to different extents. The Cre-loxP recombination system described can potentially be used for other gram-positive bacteria without further modification.

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High Rates of Genome Rearrangements and Pathogenicity of Shigella spp.

Frontiers in Microbiology ◽

10.3389/fmicb.2021.628622 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zaira Seferbekova ◽

Alexey Zabelkin ◽

Yulia Yakovleva ◽

Robert Afasizhev ◽

Natalia O. Dranenko ◽

...

Keyword(s):

Homologous Recombination ◽

Synteny Block ◽

Genome Rearrangements ◽

Genomic Islands ◽

E Coli ◽

Coding Regions ◽

Shigella Spp ◽

High Level ◽

Protein Ligases

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.

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