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来自温泉微生物群落的Cas1基因的全球系统发育基因组新奇性。

Global phylogenomic novelty of the Cas1 gene from hot spring microbial communities.

作者信息

Salgado Oscar, Guajardo-Leiva Sergio, Moya-Beltrán Ana, Barbosa Carla, Ridley Christina, Tamayo-Leiva Javier, Quatrini Raquel, Mojica Francisco J M, Díez Beatriz

机构信息

Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile.

Núcleo de Ciencias Naturales y Exactas, Universidad Adventista de Chile, Chillán, Chile.

出版信息

Front Microbiol. 2022 Dec 2;13:1069452. doi: 10.3389/fmicb.2022.1069452. eCollection 2022.

DOI:10.3389/fmicb.2022.1069452
PMID:36532491
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9755687/
Abstract

The Cas1 protein is essential for the functioning of CRISPR-Cas adaptive systems. However, despite the high prevalence of CRISPR-Cas systems in thermophilic microorganisms, few studies have investigated the occurrence and diversity of Cas1 across hot spring microbial communities. Phylogenomic analysis of 2,150 Cas1 sequences recovered from 48 metagenomes representing hot springs (42-80°C, pH 6-9) from three continents, revealed similar ecological diversity of Cas1 and 16S rRNA associated with geographic location. Furthermore, phylogenetic analysis of the Cas1 sequences exposed a broad taxonomic distribution in thermophilic bacteria, with new clades of Cas1 homologs branching at the root of the tree or at the root of known clades harboring reference Cas1 types. Additionally, a new family of casposases was identified from hot springs, which further completes the evolutionary landscape of the Cas1 superfamily. This ecological study contributes new Cas1 sequences from known and novel locations worldwide, mainly focusing on under-sampled hot spring microbial mat taxa. Results herein show that circumneutral hot springs are environments harboring high diversity and novelty related to adaptive immunity systems.

摘要

Cas1蛋白对于CRISPR-Cas适应性系统的功能至关重要。然而，尽管CRISPR-Cas系统在嗜热微生物中广泛存在，但很少有研究调查温泉微生物群落中Cas1的存在情况和多样性。对从代表来自三大洲温泉（42-80°C，pH 6-9）的48个宏基因组中回收的2150个Cas1序列进行系统发育基因组分析，揭示了与地理位置相关的Cas1和16S rRNA相似的生态多样性。此外，对Cas1序列的系统发育分析表明，嗜热细菌中Cas1具有广泛的分类分布，新的Cas1同源物分支在树的根部或包含参考Cas1类型的已知分支的根部。此外，还从温泉中鉴定出一个新的转座酶家族，这进一步完善了Cas1超家族的进化图景。这项生态学研究贡献了来自全球已知和新地点的新Cas1序列，主要集中在采样不足的温泉微生物席类群。本文结果表明，中性温泉是与适应性免疫系统相关的高多样性和新颖性的环境。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f9b9/9755687/f24f3422f4b5/fmicb-13-1069452-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f9b9/9755687/769be5d61839/fmicb-13-1069452-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f9b9/9755687/b1f5c6b24db2/fmicb-13-1069452-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f9b9/9755687/a2251d994b37/fmicb-13-1069452-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f9b9/9755687/e32b6a080b28/fmicb-13-1069452-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f9b9/9755687/9e193d3073bb/fmicb-13-1069452-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f9b9/9755687/b34eec5b652b/fmicb-13-1069452-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f9b9/9755687/f24f3422f4b5/fmicb-13-1069452-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f9b9/9755687/769be5d61839/fmicb-13-1069452-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f9b9/9755687/b1f5c6b24db2/fmicb-13-1069452-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f9b9/9755687/a2251d994b37/fmicb-13-1069452-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f9b9/9755687/e32b6a080b28/fmicb-13-1069452-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f9b9/9755687/9e193d3073bb/fmicb-13-1069452-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f9b9/9755687/b34eec5b652b/fmicb-13-1069452-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f9b9/9755687/f24f3422f4b5/fmicb-13-1069452-g007.jpg

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Towards the biogeography of prokaryotic genes.朝向原核生物基因的生物地理学。
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Evolution of Type IV CRISPR-Cas Systems: Insights from CRISPR Loci in Integrative Conjugative Elements of .IV 型 CRISPR-Cas 系统的进化：来自. 整合性 conjugative 元素中的 CRISPR 基因座的见解
Unveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics from either short- or long-read sequencing.
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