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Bernheim A. [Why so rare if so essentiel: the determinants of the sparse distribution of CRISPR-Cas systems in bacterial genomes]. Biol Aujourdhui 2017; 211:255-264. [PMID: 29956652 DOI: 10.1051/jbio/2018005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Indexed: 11/14/2022]
Abstract
CRISPR-Cas (Cluster of Regularly Interspaced Short Palindromic Repeats) systems confer bacteria and archaea an adaptative immunity against phages and other invading genetic elements playing an important role in bacterial evolution. However, despite the protection they generate and high rate of horizontal transfer, less than 50% of bacterial genomes harbor a CRISPR-Cas system. As a comparison, 90% of archaea encode a CRISPR-Cas system and a bacterial genome codes for two restriction modification systems on average. This review describes CRISPR-Cas systems distribution in bacterial genomes and then details the different hypotheses put forward to explain the relative scarcity of CRISPR-Cas systems. More specifically, phage escape mechanisms, ecological factors such as phage diversity and abundance and intrinsic costs, such as maintenance or autoimmunity, are discussed. Overall, a better understanding of the downsides of encoding CRISPR-Cas systems is essential to explain their evolutionary dynamics and their relative success in different environments and clades.
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Affiliation(s)
- Aude Bernheim
- Synthetic Biology Group, Institut Pasteur, 25-28 rue Dr. Roux, 75015 Paris, France - Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr Roux, 75015 Paris, France - AgroParisTech, 75005 Paris, France
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Ge R, Mai G, Wang P, Zhou M, Luo Y, Cai Y, Zhou F. CRISPRdigger: detecting CRISPRs with better direct repeat annotations. Sci Rep 2016; 6:32942. [PMID: 27596864 PMCID: PMC5011713 DOI: 10.1038/srep32942] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/12/2016] [Indexed: 01/14/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) are important genetic elements in many bacterial and archaeal genomes, and play a key role in prokaryote immune systems’ fight against invasive foreign elements. The CRISPR system has also been engineered to facilitate target gene editing in eukaryotic genomes. Using the common features of mis-annotated CRISPRs in prokaryotic genomes, this study proposed an accurate de novo CRISPR annotation program CRISPRdigger, which can take a partially assembled genome as its input. A comprehensive comparison with the three existing programs demonstrated that CRISPRdigger can recover more Direct Repeats (DRs) for CRISPRs and achieve a higher accuracy for a query genome. The program was implemented by Perl and all the parameters had default values, so that a user could annotate CRISPRs in a query genome by supplying only a genome sequence in the FASTA format. All the supplementary data are available at http://www.healthinformaticslab.org/supp/.
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Affiliation(s)
- Ruiquan Ge
- Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China
| | - Guoqin Mai
- Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Pu Wang
- Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China
| | - Manli Zhou
- Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China
| | - Youxi Luo
- School of Science, Hubei University of Technology, Wuhan, Hubei, 430068, China
| | - Yunpeng Cai
- Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Fengfeng Zhou
- College of Computer Science and Technology, Changchun, Jilin, 130012, China.,Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
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