大肠杆菌中pheV-tRNA整合基因组岛的进化。

IF 4 2区 生物学 Q1 GENETICS & HEREDITY
PLoS Genetics Pub Date : 2024-10-24 eCollection Date: 2024-10-01 DOI:10.1371/journal.pgen.1011459
Nguyen Thi Khanh Nhu, Brian M Forde, Nouri L Ben Zakour, Minh-Duy Phan, Leah W Roberts, Scott A Beatson, Mark A Schembri
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引用次数: 0

摘要

大肠杆菌在基因组水平上表现出广泛的遗传多样性,尤其是在其附属基因组中。tRNA 整合基因组岛(GIs)是大肠杆菌附属基因组的一部分,在致病性方面发挥着重要作用。然而,由于 GIs 体型庞大、基因含量差异巨大且在基因组草案中组装零散,因此研究 GIs 的进化一直具有挑战性。在这里,我们研究了整合在pheV-tRNA(GI-pheV)上的GI的进化,主要关注尿路致病性大肠杆菌(UPEC)和全球传播的耐多药ST131克隆。我们发现,GI-pheV 的基因内容高度多样化,并以模块化配置排列,其中 P4 整合酶编码基因 intP4 是唯一的保守基因。尽管存在这种多样性,GI-pheV 的基因内容在同一病原型的菌株中仍显示出保守的特征。在 ST131 中,与参考菌株 EC958(EC958_GI-pheV)相对应的 GI-pheV 存在于约 90% 的菌株中。系统发育分析表明,ST131 中的 GI-pheV 与核心基因组一起进化,特定模块(或整个 GI)的丢失/增加与特定菌株事件有关。总之,我们发现 GI-pheV 呈现出一种动态的进化途径,其中的模块和基因是通过插入、缺失和重组等多种事件进化而来的。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Evolution of the pheV-tRNA integrated genomic island in Escherichia coli.

Escherichia coli exhibit extensive genetic diversity at the genome level, particularly within their accessory genome. The tRNA integrated genomic islands (GIs), a part of the E. coli accessory genome, play an important role in pathogenicity. However, studies examining the evolution of GIs have been challenging due to their large size, considerable gene content variation and fragmented assembly in draft genomes. Here we examined the evolution of the GI integrated at pheV-tRNA (GI-pheV), with a primary focus on uropathogenic E. coli (UPEC) and the globally disseminated multidrug resistant ST131 clone. We show the gene content of GI-pheV is highly diverse and arranged in a modular configuration, with the P4 integrase encoding gene intP4 the only conserved gene. Despite this diversity, the GI-pheV gene content displayed conserved features among strains from the same pathotype. In ST131, GI-pheV corresponding to the reference strain EC958 (EC958_GI-pheV) was found in ~90% of strains. Phylogenetic analyses suggested that GI-pheV in ST131 has evolved together with the core genome, with the loss/gain of specific modules (or the entire GI) linked to strain specific events. Overall, we show GI-pheV exhibits a dynamic evolutionary pathway, in which modules and genes have evolved through multiple events including insertions, deletions and recombination.

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来源期刊
PLoS Genetics
PLoS Genetics GENETICS & HEREDITY-
自引率
2.20%
发文量
438
期刊介绍: PLOS Genetics is run by an international Editorial Board, headed by the Editors-in-Chief, Greg Barsh (HudsonAlpha Institute of Biotechnology, and Stanford University School of Medicine) and Greg Copenhaver (The University of North Carolina at Chapel Hill). Articles published in PLOS Genetics are archived in PubMed Central and cited in PubMed.
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