High rates of genome rearrangements and pathogenicity of Shigella spp.

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

A recently isolated human commensal Escherichia coli ST10 clone member mediates enhanced thermotolerance and tetrathionate respiration on a P1 phage- derived IncY plasmid

The ubiquitous human commensal Escherichia coli has been well investigated through its model representative E. coli K- 12. In this work, we initially characterized E. coli Fec10, a recently isolated human commensal strain of phylogroup A/sequence type ST10. Compared to E. coli K- 12, the 4.88 Mbp Fec10 genome is characterized by distinct single- nucleotide polymorphisms and acquisition of genomic islands. In addition, E. coli Fec10 possesses a 155.86 kbp IncY plasmid, a composite element based on phage P1. pFec10 harbours multiple cargo genes such as coding for a tetrathionate reductase and its corresponding regulatory two- component system. Among the cargo genes is also the Transmissible Locus of Protein Quality Control (TLPQC), which mediates tolerance to lethal temperatures in bacteria. The disaggregase ClpGGI of TLPQC constitutes a major determinant of the thermotolerance of E. coli Fec10. We confirmed stand- alone disaggregation activity, but observed distinct biochemical characteristics of ClpGGI- Fec10 compared to the nearly identical Pseudomonas aeruginosa ClpGGI- SG17M. Furthermore, we noted a unique contribution of ClpGGI- Fec10 to the exquisite thermotolerance of E. coli Fec10, suggesting functional differences between both disaggregases in vivo. Detection of thermotolerance in 10% of human commensal E. coli isolates hints to the successful establishment of food- borne heat- resistant strains in the human gut.The ubiquitousness of commensal Escherichia coli in post- industrial humans calls for the investigation of their physiological characteristics. Thermotolerance, unconventional anaerobic respiration, and detoxification cargo genes are encoded on an IncY derived plasmid harbored by a typical member of the common ST10 clone. Thermotolerance is well represented in commensal isolates with the key disaggregase ClpGGI to be exquisitely thermostable. Fire symbol by ya- webdesign.com.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/166341/1/mmi14614.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/166341/2/mmi14614-sup-0001-Supinfo.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/166341/3/mmi14614_am.pd

A recently isolated human commensal Escherichia coli ST10 clone member mediates enhanced thermotolerance and tetrathionate respiration on a P1 phage derived IncY plasmid.

The ubiquitous human commensal Escherichia coli has been well investigated through its model representative E. coli K-12. In this work, we initially characterized E. coli Fec10, a recently isolated human commensal strain of phylogroup A/sequence type ST10. Compared to E. coli K-12, the 4.88 Mbp Fec10 genome is characterized by distinct single nucleotide polymorphisms and acquisition of genomic islands. In addition, E. coli Fec10 possesses a 155.86 kbp IncY plasmid, a composite element based on phage P1. pFec10 codes for a variety of cargo genes such as a tetrathionate reductase and its corresponding regulatory two-component system. Among cargo gene products is also the Transmissible Locus of Protein Quality Control (TLPQC), which mediates tolerance to lethal temperatures in bacteria. The disaggregase ClpGGI of TLPQC constitutes a major determinant of thermotolerance of E. coli Fec10. We confirm stand-alone disaggregation activity, but observe distinct biochemical characteristics of ClpGGI-Fec10 compared to the nearly identical Pseudomonas aeruginosa ClpGGI-SG17M. Furthermore, we observed a unique contribution of ClpGGI-Fec10 to the exquisite thermotolerance of E. coli Fec10 suggesting functional differences between both disaggregases in vivo. Detection of thermotolerance in 10% of human commensal E. coli isolates suggests successful establishment of food-borne heat resistant strains in the human gut