National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland.
Genome Biol Evol. 2020 Mar 1;12(3):18-34. doi: 10.1093/gbe/evaa010.
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.
细菌基因有时会因突变而失活。这种失活可能是因为功能选择是间歇性的，或者太弱，无法快速消除非活性等位基因。在这里，我研究了沙门氏菌中失活被正向选择的情况。这些情况是通过将过早的终止密码子引入一个基因的速率与选择性中性下的预期进行比较来识别的，这是通过比较同义突变的速率来评估的。我以 10%的假发现率确定了 84 个符合这一标准的基因。这些基因中的许多都与毒力、运动性和趋化性、生物膜形成以及对抗生素或其他有毒物质的抗性有关。据推测，这些基因中的大多数都受到一个持续的过程的影响，在这个过程中，失活在罕见的情况下是有利的，但失活的等位基因在大多数其他情况下是有害的，随后会被纯化选择所淘汰。
