Ecological drivers of CRISPR immune systems.

IF 5 2区 生物学 Q1 MICROBIOLOGY
mSystems Pub Date : 2024-11-06 DOI:10.1128/msystems.00568-24
Wei Xiao, J L Weissman, Philip L F Johnson
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引用次数: 0

Abstract

CRISPR-Cas is the only known adaptive immune system of prokaryotes. It is a powerful defense system against mobile genetic elements such as bacteriophages. While CRISPR-Cas systems can be found throughout the prokaryotic tree of life, they are distributed unevenly across taxa and environments. Since adaptive immunity is more useful in environments where pathogens persist or reoccur, the density and/or diversity of the host/pathogen community may drive the uneven distribution of CRISPR systems. We directly tested hypotheses connecting CRISPR incidence with prokaryotic density/diversity by analyzing 16S rRNA and metagenomic data from publicly available environmental sequencing projects. In terms of density, we found that CRISPR systems are significantly favored in lower abundance (less dense) taxa and disfavored in higher abundance taxa, at least in marine environments. When we extended this work to compare taxonomic diversity between samples, we found CRISPR system incidence strongly correlated with diversity in human oral environments. Together, these observations confirm that, at least in certain types of environments, the prokaryotic ecological context indeed plays a key role in selecting for CRISPR immunity.

Importance: Microbes must constantly defend themselves against viral pathogens, and a large proportion of prokaryotes do so using the highly effective CRISPR-Cas adaptive immune system. However, many prokaryotes do not. We investigated the ecological factors behind this uneven distribution of CRISPR-Cas immune systems in natural microbial populations. We found strong patterns linking CRISPR-Cas systems to prokaryotic density within ocean environments and to prokaryotic diversity within human oral environments. Our study validates previous within-lab experimental results that suggested these factors might be important and confirms that local environment and ecological context interact to select for CRISPR immunity.

CRISPR 免疫系统的生态驱动因素。
CRISPR-Cas 是原核生物中唯一已知的适应性免疫系统。它是抵御噬菌体等移动遗传因子的强大防御系统。虽然 CRISPR-Cas 系统遍布整个原核生物生命树,但它们在不同类群和环境中的分布并不均衡。由于适应性免疫在病原体持续存在或再次发生的环境中更有用,宿主/病原体群落的密度和/或多样性可能会驱动CRISPR系统的不均匀分布。我们通过分析来自公开环境测序项目的16S rRNA和元基因组数据,直接测试了将CRISPR发生率与原核生物密度/多样性联系起来的假设。我们发现,至少在海洋环境中,CRISPR系统在丰度较低(密度较低)的类群中明显受到青睐,而在丰度较高的类群中则不受青睐。当我们将这项工作扩展到比较样本间的分类多样性时,我们发现 CRISPR 系统的发生率与人类口腔环境中的多样性密切相关。这些观察结果共同证实,至少在某些类型的环境中,原核生物的生态环境确实在选择CRISPR免疫力方面起着关键作用:微生物必须不断抵御病毒病原体,而很大一部分原核生物是利用高效的CRISPR-Cas适应性免疫系统来做到这一点的。然而,许多原核生物并没有这样做。我们研究了自然微生物种群中 CRISPR-Cas 免疫系统分布不均背后的生态因素。我们发现了 CRISPR-Cas 系统与海洋环境中原核生物密度以及人类口腔环境中原核生物多样性之间的紧密联系。我们的研究验证了之前的实验室内实验结果,这些结果表明这些因素可能很重要,并证实了当地环境和生态环境相互作用,选择了CRISPR免疫系统。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
mSystems
mSystems Biochemistry, Genetics and Molecular Biology-Biochemistry
CiteScore
10.50
自引率
3.10%
发文量
308
审稿时长
13 weeks
期刊介绍: mSystems™ will publish preeminent work that stems from applying technologies for high-throughput analyses to achieve insights into the metabolic and regulatory systems at the scale of both the single cell and microbial communities. The scope of mSystems™ encompasses all important biological and biochemical findings drawn from analyses of large data sets, as well as new computational approaches for deriving these insights. mSystems™ will welcome submissions from researchers who focus on the microbiome, genomics, metagenomics, transcriptomics, metabolomics, proteomics, glycomics, bioinformatics, and computational microbiology. mSystems™ will provide streamlined decisions, while carrying on ASM''s tradition of rigorous peer review.
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