Selection-Driven Gene Inactivation in Salmonella

• Published in: Genome biology and evolution Vol. 12; no. 3; pp. 18 - 34
• Main Author: Cherry, Joshua L
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.03.2020
• Subjects: Bacterial Proteins - genetics; Codon, Terminator; DNA Methylation; Evolution, Molecular; Genes, Bacterial; Ligases - genetics; Membrane Proteins - genetics; Membrane Transport Proteins - genetics; Mutation; Phosphoric Diester Hydrolases - genetics; Polysaccharides, Bacterial - biosynthesis; Salmonella enterica - genetics; Salmonella enterica - pathogenicity; Selection, Genetic; Sigma Factor - genetics; Transcription Factors - metabolism; Virulence Factors - genetics; positive selection; gene inactivation; pathogen evolution; bacterial evolution; stop codons
• ISSN: 1759-6653; 1759-6653
• DOI: 10.1093/gbe/evaa010

Abstract Bacterial genes are sometimes found to be inactivated by mutation. This inactivation may be observable simply because selection for function is intermittent or too weak to eliminate inactive alleles quickly. Here, I investigate cases in Salmonella enterica where inactivation is instead positively selected. These are identified by a rate of introduction of premature stop codons to a gene that is higher than expected under selective neutrality, as assessed by comparison to the rate of synonymous changes. I identify 84 genes that meet this criterion at a 10% false discovery rate. Many of these genes are involved in virulence, motility and chemotaxis, biofilm formation, and resistance to antibiotics or other toxic substances. It is hypothesized that most of these genes are subject to an ongoing process in which inactivation is favored under rare conditions, but the inactivated allele is deleterious under most other conditions and is subsequently driven to extinction by purifying selection.