Department of Microbiology, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
mSystems. 2024 Sep 17;9(9):e0080124. doi: 10.1128/msystems.00801-24. Epub 2024 Aug 21.
The opportunistic human pathogen is naturally infected by a large class of temperate, transposable, Mu-like phages. We examined the genotypic and phenotypic diversity of PA14 lysogen populations as they resolve clustered regularly interspaced short palindromic repeat CRISPR) autoimmunity, mediated by an imperfect CRISPR match to the Mu-like DMS3 prophage. After 12 days of evolution, we measured a decrease in spontaneous induction in both exponential and stationary phase growth. Co-existing variation in spontaneous induction rates in the exponential phase depended on the way the coexisting strains resolved genetic conflict. Multiple mutational modes to resolve genetic conflict between host and phage resulted in coexistence in evolved populations of single lysogens that maintained CRISPR immunity to other phages and polylysogens that lost immunity completely. This work highlights a new dimension of the role of lysogenic phages in the evolution of their hosts.IMPORTANCEThe chronic opportunistic multi-drug-resistant pathogen is persistently infected by temperate phages. We assess the contribution of temperate phage infection to the evolution of the clinically relevant strain UCBPP-PA14. We found that a low level of clustered regularly interspaced short palindromic repeat (CRISPR)-mediated self-targeting resulted in polylysogeny evolution and large genome rearrangements in lysogens; we also found extensive diversification in CRISPR spacers and genes. These genomic modifications resulted in decreased spontaneous induction in both exponential and stationary phase growth, increasing lysogen fitness. This work shows the importance of considering latent phage infection in characterizing the evolution of bacterial populations.
人体机会性病原体 自然感染一大类温和、可转移、类似于 Mu 的噬菌体。我们研究了 PA14 溶原菌群体的基因型和表型多样性，因为它们解决了簇状规则间隔短回文重复 (CRISPR) 自身免疫，由 Mu 样 DMS3 前噬菌体的不完全 CRISPR 匹配介导。在 12 天的进化过程中，我们测量到在指数期和静止期生长中自发诱导的减少。指数期共存的自发诱导率的变化取决于共存菌株解决遗传冲突的方式。解决宿主和噬菌体之间遗传冲突的多种突变模式导致进化后的单溶原菌群体共存，这些单溶原菌保持对其他噬菌体的 CRISPR 免疫，而多溶原菌则完全失去免疫。这项工作强调了溶原噬菌体在宿主进化中的作用的一个新维度。
慢性机会性病原体 是一种持续性感染温和噬菌体的多药耐药病原体。我们评估了温和噬菌体感染对临床相关菌株 UCBPP-PA14 进化的贡献。我们发现，低水平的簇状规则间隔短回文重复 (CRISPR) 介导的自我靶向导致多溶原进化和溶原菌中的大规模基因组重排；我们还发现 CRISPR 间隔区和 基因广泛多样化。这些基因组修饰导致指数期和静止期生长中的自发诱导减少，增加了溶原菌的适应性。这项工作表明，在描述细菌种群的进化时，考虑潜伏的噬菌体感染是很重要的。
