Defence systems and horizontal gene transfer in bacteria

IF 4.3 2区 生物学 Q2 MICROBIOLOGY
Roman Kogay, Yuri I. Wolf, Eugene V. Koonin
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Abstract

Horizontal gene transfer (HGT) is a fundamental process in prokaryotic evolution, contributing significantly to diversification and adaptation. HGT is typically facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages, which often impose fitness costs on their hosts. However, a considerable number of bacterial genes are involved in defence mechanisms that limit the propagation of MGEs, suggesting they may actively restrict HGT. In our study, we investigated whether defence systems limit HGT by examining the relationship between the HGT rate and the presence of 73 defence systems across 12 bacterial species. We discovered that only six defence systems, three of which were different CRISPR-Cas subtypes, were associated with a reduced gene gain rate at the species evolution scale. Hosts of these defence systems tend to have a smaller pangenome size and fewer phage-related genes compared to genomes without these systems. This suggests that these defence mechanisms inhibit HGT by limiting prophage integration. We hypothesize that the restriction of HGT by defence systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and the fitness effect of HGT in bacterial populations.

Abstract Image

细菌的防御系统和水平基因转移
横向基因转移(HGT)是原核生物进化的一个基本过程,对生物的多样化和适应性有重大贡献。移动遗传因子(MGEs)通常会促进基因水平转移,如共轭质粒和噬菌体,它们通常会给宿主带来健康成本。然而,相当多的细菌基因参与了限制 MGEs 传播的防御机制,这表明它们可能会主动限制 HGT。在我们的研究中,我们通过检测 12 个细菌物种的 HGT 率与 73 种防御系统之间的关系,研究了防御系统是否限制了 HGT。我们发现,在物种进化尺度上,只有六种防御系统(其中三种是不同的 CRISPR-Cas 亚型)与基因增殖率降低有关。与不使用这些防御系统的基因组相比,使用这些防御系统的宿主往往具有较小的泛基因组规模和较少的噬菌体相关基因。这表明这些防御机制通过限制噬菌体整合来抑制 HGT。我们假设,防御系统对 HGT 的限制具有物种特异性,并取决于各种生态和遗传因素,包括 MGEs 负担和 HGT 在细菌种群中的适应效应。
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来源期刊
Environmental microbiology
Environmental microbiology 环境科学-微生物学
CiteScore
9.90
自引率
3.90%
发文量
427
审稿时长
2.3 months
期刊介绍: Environmental Microbiology provides a high profile vehicle for publication of the most innovative, original and rigorous research in the field. The scope of the Journal encompasses the diversity of current research on microbial processes in the environment, microbial communities, interactions and evolution and includes, but is not limited to, the following: the structure, activities and communal behaviour of microbial communities microbial community genetics and evolutionary processes microbial symbioses, microbial interactions and interactions with plants, animals and abiotic factors microbes in the tree of life, microbial diversification and evolution population biology and clonal structure microbial metabolic and structural diversity microbial physiology, growth and survival microbes and surfaces, adhesion and biofouling responses to environmental signals and stress factors modelling and theory development pollution microbiology extremophiles and life in extreme and unusual little-explored habitats element cycles and biogeochemical processes, primary and secondary production microbes in a changing world, microbially-influenced global changes evolution and diversity of archaeal and bacterial viruses new technological developments in microbial ecology and evolution, in particular for the study of activities of microbial communities, non-culturable microorganisms and emerging pathogens
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