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Expanding the catalog of cas genes with metagenomes

The CRISPR (clusters of regularly interspaced short palindromic repeats)–Cas adaptive immune system is an important defense system in bacteria, providing targeted defense against invasions of foreign nucleic acids. CRISPR–Cas systems consist of CRISPR loci and cas (CRISPR-associated) genes: sequence...

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Detalles Bibliográficos
Autores principales: Zhang, Quan, Doak, Thomas G., Ye, Yuzhen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3936711/
https://www.ncbi.nlm.nih.gov/pubmed/24319142
http://dx.doi.org/10.1093/nar/gkt1262
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author Zhang, Quan
Doak, Thomas G.
Ye, Yuzhen
author_facet Zhang, Quan
Doak, Thomas G.
Ye, Yuzhen
author_sort Zhang, Quan
collection PubMed
description The CRISPR (clusters of regularly interspaced short palindromic repeats)–Cas adaptive immune system is an important defense system in bacteria, providing targeted defense against invasions of foreign nucleic acids. CRISPR–Cas systems consist of CRISPR loci and cas (CRISPR-associated) genes: sequence segments of invaders are incorporated into host genomes at CRISPR loci to generate specificity, while adjacent cas genes encode proteins that mediate the defense process. We pursued an integrated approach to identifying putative cas genes from genomes and metagenomes, combining similarity searches with genomic neighborhood analysis. Application of our approach to bacterial genomes and human microbiome datasets allowed us to significantly expand the collection of cas genes: the sequence space of the Cas9 family, the key player in the recently engineered RNA-guided platforms for genome editing in eukaryotes, is expanded by at least two-fold with metagenomic datasets. We found genes in cas loci encoding other functions, for example, toxins and antitoxins, confirming the recently discovered potential of coupling between adaptive immunity and the dormancy/suicide systems. We further identified 24 novel Cas families; one novel family contains 20 proteins, all identified from the human microbiome datasets, illustrating the importance of metagenomics projects in expanding the diversity of cas genes.
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spelling pubmed-39367112014-03-04 Expanding the catalog of cas genes with metagenomes Zhang, Quan Doak, Thomas G. Ye, Yuzhen Nucleic Acids Res Genomics The CRISPR (clusters of regularly interspaced short palindromic repeats)–Cas adaptive immune system is an important defense system in bacteria, providing targeted defense against invasions of foreign nucleic acids. CRISPR–Cas systems consist of CRISPR loci and cas (CRISPR-associated) genes: sequence segments of invaders are incorporated into host genomes at CRISPR loci to generate specificity, while adjacent cas genes encode proteins that mediate the defense process. We pursued an integrated approach to identifying putative cas genes from genomes and metagenomes, combining similarity searches with genomic neighborhood analysis. Application of our approach to bacterial genomes and human microbiome datasets allowed us to significantly expand the collection of cas genes: the sequence space of the Cas9 family, the key player in the recently engineered RNA-guided platforms for genome editing in eukaryotes, is expanded by at least two-fold with metagenomic datasets. We found genes in cas loci encoding other functions, for example, toxins and antitoxins, confirming the recently discovered potential of coupling between adaptive immunity and the dormancy/suicide systems. We further identified 24 novel Cas families; one novel family contains 20 proteins, all identified from the human microbiome datasets, illustrating the importance of metagenomics projects in expanding the diversity of cas genes. Oxford University Press 2014-02 2013-12-05 /pmc/articles/PMC3936711/ /pubmed/24319142 http://dx.doi.org/10.1093/nar/gkt1262 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genomics
Zhang, Quan
Doak, Thomas G.
Ye, Yuzhen
Expanding the catalog of cas genes with metagenomes
title Expanding the catalog of cas genes with metagenomes
title_full Expanding the catalog of cas genes with metagenomes
title_fullStr Expanding the catalog of cas genes with metagenomes
title_full_unstemmed Expanding the catalog of cas genes with metagenomes
title_short Expanding the catalog of cas genes with metagenomes
title_sort expanding the catalog of cas genes with metagenomes
topic Genomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3936711/
https://www.ncbi.nlm.nih.gov/pubmed/24319142
http://dx.doi.org/10.1093/nar/gkt1262
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