A Comprehensive Coexpression Network Analysis in Vibrio cholerae

• Published in: mSystems Vol. 5; no. 4
• Main Authors: DuPai, Cory D., Wilke, Claus O., Davies, Bryan W.
• Format: Journal Article
• Language: English
• Published: Washington American Society for Microbiology 01.08.2020
• Subjects: Cholera; Chromatin; computational biology; Datasets; DNA microarrays; Experiments; Gene regulation; Gene transfer; Genes; Genetic engineering; Genomes; Genomics; Gram-negative bacteria; Horizontal transfer; Immunoprecipitation; Insertion; Metabolism; Molecular Biology and Physiology; Next-generation sequencing; Noise; Pathogenicity; Resource Report; Ribonucleic acid; RNA; Transcription; Vibrio cholerae; Virulence
• ISSN: 2379-5077; 2379-5077
• DOI: 10.1128/mSystems.00550-20

Cholera is a devastating illness that kills tens of thousands of people annually. Vibrio cholerae , the causative agent of cholera, is an important model organism to investigate both bacterial pathogenesis and the impact of horizontal gene transfer on the emergence and dissemination of new virulent strains. Despite the importance of this pathogen, roughly one-third of V. cholerae genes are functionally unannotated, leaving large gaps in our understanding of this microbe. Through coexpression network analysis of existing RNA sequencing data, this work develops an approach to uncover novel gene-gene relationships and contextualize genes with no known function, which will advance our understanding of V. cholerae virulence and evolution. ABSTRACT Research into the evolution and pathogenesis of Vibrio cholerae has benefited greatly from the generation of high-throughput sequencing data to drive molecular analyses. The steady accumulation of these data sets now provides a unique opportunity for in silico hypothesis generation via coexpression analysis. Here, we leverage all published V. cholerae RNA sequencing data, in combination with select data from other platforms, to generate a gene coexpression network that validates known gene interactions and identifies novel genetic partners across the entire V. cholerae genome. This network provides direct insights into genes influencing pathogenicity, metabolism, and transcriptional regulation, further clarifies results from previous sequencing experiments in V. cholerae (e.g., transposon insertion sequencing [Tn-seq] and chromatin immunoprecipitation sequencing [ChIP-seq]), and expands upon microarray-based findings in related Gram-negative bacteria. IMPORTANCE Cholera is a devastating illness that kills tens of thousands of people annually. Vibrio cholerae , the causative agent of cholera, is an important model organism to investigate both bacterial pathogenesis and the impact of horizontal gene transfer on the emergence and dissemination of new virulent strains. Despite the importance of this pathogen, roughly one-third of V. cholerae genes are functionally unannotated, leaving large gaps in our understanding of this microbe. Through coexpression network analysis of existing RNA sequencing data, this work develops an approach to uncover novel gene-gene relationships and contextualize genes with no known function, which will advance our understanding of V. cholerae virulence and evolution.