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Title: Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome

Here, the genetic make-up of most bacteria is encoded in a single chromosome while about 10% have more than one chromosome. Among these, Vibrio cholerae, with two chromosomes, has served as a model system to study various aspects of chromosome maintenance, mainly replication, and faithful partitioning of multipartite genomes. Here, we describe the genomic characterization of strains that are an exception to the two chromosome rules: naturally occurring single-chromosome V. cholerae. Whole genome sequence analyses of NSCV1 and NSCV2 (natural single-chromosome vibrio) revealed that the Chr1 and Chr2 fusion junctions contain prophages, IS elements, and direct repeats, in addition to large-scale chromosomal rearrangements such as inversions, insertions, and long tandem repeats elsewhere in the chromosome compared to prototypical two chromosome V. cholerae genomes. Many of the known cholera virulence factors are absent. The two origins of replication and associated genes are generally intact with synonymous mutations in some genes, as arerecAand mismatch repair (MMR) genes dam, mutH, and mutL; MutS function is probably impaired in NSCV2. These strains are ideal tools for studying mechanistic aspects of maintenance of chromosomes with multiple origins and other rearrangements and the biological, functional, and evolutionary significance of multipartite genome architecture in general.
Authors:
ORCiD logo [1] ; ORCiD logo [1] ;  [1] ;  [2] ;  [3] ;  [1] ;  [1] ; ORCiD logo [4]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  2. Morgan State Univ., Baltimore, MD (United States)
  3. Philipps-Univ. Marburg, Marburg (Germany)
  4. Tauri Group, LLC, Alexandria, VA (United States); Defense Biological Product Assurance Office, Frederick, MD (United States)
Publication Date:
Report Number(s):
LA-UR-17-21600
Journal ID: ISSN 2314-436X
Grant/Contract Number:
AC52-06NA25396
Type:
Accepted Manuscript
Journal Name:
International Journal of Genomics
Additional Journal Information:
Journal Volume: 2017; Journal ID: ISSN 2314-436X
Publisher:
Hindawi
Research Org:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org:
Defense Threat Reduction Agency (DTRA); USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Biological Science; V. cholerae; non-O1/non-O139 serogroup; whole genome sequencing; single chromosome; DNA adenine methyl transferase; dam; origin of replication; mismatch repair
OSTI Identifier:
1398918

Xie, Gary, Johnson, Shannon Lyn, Davenport, Karen Walston, Rajavel, Mathumathi, Waldminghaus, Torsten, Detter, John Chris, Chain, Patrick Sam Guy, and Sozhamannan, Shanmuga. Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome. United States: N. p., Web. doi:10.1155/2017/8724304.
Xie, Gary, Johnson, Shannon Lyn, Davenport, Karen Walston, Rajavel, Mathumathi, Waldminghaus, Torsten, Detter, John Chris, Chain, Patrick Sam Guy, & Sozhamannan, Shanmuga. Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome. United States. doi:10.1155/2017/8724304.
Xie, Gary, Johnson, Shannon Lyn, Davenport, Karen Walston, Rajavel, Mathumathi, Waldminghaus, Torsten, Detter, John Chris, Chain, Patrick Sam Guy, and Sozhamannan, Shanmuga. 2017. "Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome". United States. doi:10.1155/2017/8724304. https://www.osti.gov/servlets/purl/1398918.
@article{osti_1398918,
title = {Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome},
author = {Xie, Gary and Johnson, Shannon Lyn and Davenport, Karen Walston and Rajavel, Mathumathi and Waldminghaus, Torsten and Detter, John Chris and Chain, Patrick Sam Guy and Sozhamannan, Shanmuga},
abstractNote = {Here, the genetic make-up of most bacteria is encoded in a single chromosome while about 10% have more than one chromosome. Among these, Vibrio cholerae, with two chromosomes, has served as a model system to study various aspects of chromosome maintenance, mainly replication, and faithful partitioning of multipartite genomes. Here, we describe the genomic characterization of strains that are an exception to the two chromosome rules: naturally occurring single-chromosome V. cholerae. Whole genome sequence analyses of NSCV1 and NSCV2 (natural single-chromosome vibrio) revealed that the Chr1 and Chr2 fusion junctions contain prophages, IS elements, and direct repeats, in addition to large-scale chromosomal rearrangements such as inversions, insertions, and long tandem repeats elsewhere in the chromosome compared to prototypical two chromosome V. cholerae genomes. Many of the known cholera virulence factors are absent. The two origins of replication and associated genes are generally intact with synonymous mutations in some genes, as arerecAand mismatch repair (MMR) genes dam, mutH, and mutL; MutS function is probably impaired in NSCV2. These strains are ideal tools for studying mechanistic aspects of maintenance of chromosomes with multiple origins and other rearrangements and the biological, functional, and evolutionary significance of multipartite genome architecture in general.},
doi = {10.1155/2017/8724304},
journal = {International Journal of Genomics},
number = ,
volume = 2017,
place = {United States},
year = {2017},
month = {8}
}

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