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Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis
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Abstract
Significance: The CRISPR-Cas systems that mediate adaptive immunity in bacteria and archaea encompass a small set of core cas genes that are essential in diverse systems belonging to the same subtype, type, or class. However, a much greater number of genes only sporadically co-occur with CRISPR-Cas, and for most of these, involvement in CRISPR-Cas functions has not been demonstrated. We developed a computational strategy that provides for systematic identification of CRISPR-linked proteins and prediction of their functional association with CRISPR-Cas systems, and employed it to identify 79 previously undetected, putative CRISPR-accessory proteins. A large fraction of these proteins are predicted to be membrane-associated, revealing a potentially unknown side of CRISPR biology.
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Proteins associated with the CRISPR system can be assigned to either the adaptive module (Cas1 and Cas2) or the effector module (destruction of mobile genetic elements through recognition and cleavage), with additional and regulatory proteins also associated.
“Proteins associated with this system can be assigned to either the adaptive module (participating in the acquisition of immunity, main representatives – Cas1 and Cas2), or the effector module (directly involved in the destruction of mobile genetic elements through their recognition and cleavage), with some additional and regulatory proteins also found to be associated with the system [24].”
From CRISPR–Cas9: A History of Its Discovery and Ethical Considerations of Its Use in Genome Editing (2022) · cites this paper as [24]
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Metadata
- Authors
- Shmakov, S. A., Makarova, K. S., Wolf, Y. I., Severinov, K. V., & Koonin, E. V.
- Affiliations
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, 143025 Skolkovo, Russia;
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894;
- ORCID
- Koonin, Eugene V.
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2018-05-21
- Volume
- 115
- Issue
- 23
- ISSN
- 0027-8424
- 1091-6490
- Cited by
- 169
- References
- 5
- Language
- en
- Funders
- U.S. Department of Health and Human Services (Intramural funds)
- Ministry of Education and Science of the Russian Federation (RFMEFI60617X0006)
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