AcrDB: A database of anti-CRISPR operons in prokaryotes and viruses

Le Huang; Bowen Yang; Haidong Yi; Amina Asif; Jiawei Wang; Trevor Lithgow; Han Zhang; Fayyaz ul Amir Afsar Minhas; Yanbin Yin

doi:10.1093/nar/gkaa857

AcrDB: A database of anti-CRISPR operons in prokaryotes and viruses

Le Huang, Bowen Yang, Haidong Yi, Amina Asif, Jiawei Wang, Trevor Lithgow, Han Zhang, Fayyaz ul Amir Afsar Minhas, Yanbin Yin

Department of Life Sciences

Research output: Contribution to journal › Article › peer-review

36 Citations (SciVal)

Abstract

CRISPR-Cas is an anti-viral mechanism of prokaryotes that has been widely adopted for genome editing. To make CRISPR-Cas genome editing more controllable and safer to use, anti-CRISPR proteins have been recently exploited to prevent excessive/prolonged Cas nuclease cleavage. Anti-CRISPR (Acr) proteins are encoded by (pro)phages/(pro)viruses, and have the ability to inhibit their host's CRISPR-Cas systems. We have built an online database AcrDB (http://bcb.unl.edu/AcrDB) by scanning ∼19 000 genomes of prokaryotes and viruses with AcrFinder, a recently developed Acr-Aca (Acr-associated regulator) operon prediction program. Proteins in Acr-Aca operons were further processed by two machine learning-based programs (AcRanker and PaCRISPR) to obtain numerical scores/ranks. Compared to other anti-CRISPR databases, AcrDB has the following unique features: (i) It is a genome-scale database with the largest collection of data (39 799 Acr-Aca operons containing Aca or Acr homologs); (ii) It offers a user-friendly web interface with various functions for browsing, graphically viewing, searching, and batch downloading Acr-Aca operons; (iii) It focuses on the genomic context of Acr and Aca candidates instead of individual Acr protein family and (iv) It collects data with three independent programs each having a unique data mining algorithm for cross validation. AcrDB will be a valuable resource to the anti-CRISPR research community.

Original language	English
Pages (from-to)	D622-D629
Journal	Nucleic Acids Research
Volume	49
Issue number	D1
Early online date	17 Oct 2020
DOIs	https://doi.org/10.1093/nar/gkaa857 https://doi.org/10.1093/nar/gkaa857
Publication status	Published - 8 Jan 2021

Bibliographical note

Publisher Copyright:
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.

Acknowledgements

This work was partially completed utilizing the Holland Computing Center of the University of Nebraska, which receives support from the Nebraska Research Initiative.

Funding

National Science Foundation (NSF) CAREER award [DBI-1933521], United States Department of Agriculture (USDA) award [58-8042-9-089]; start-up grant of UNL [2019-YIN to Y.Y.]. Funding for open access charge: NSF CAREER award [DBI-1933521]. Conflict of interest statement. None declared.

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkaa857Licence: CC BY-NC
10.1093/nar/gkaa857

Cite this

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title = "AcrDB: A database of anti-CRISPR operons in prokaryotes and viruses",

abstract = "CRISPR-Cas is an anti-viral mechanism of prokaryotes that has been widely adopted for genome editing. To make CRISPR-Cas genome editing more controllable and safer to use, anti-CRISPR proteins have been recently exploited to prevent excessive/prolonged Cas nuclease cleavage. Anti-CRISPR (Acr) proteins are encoded by (pro)phages/(pro)viruses, and have the ability to inhibit their host's CRISPR-Cas systems. We have built an online database AcrDB (http://bcb.unl.edu/AcrDB) by scanning ∼19 000 genomes of prokaryotes and viruses with AcrFinder, a recently developed Acr-Aca (Acr-associated regulator) operon prediction program. Proteins in Acr-Aca operons were further processed by two machine learning-based programs (AcRanker and PaCRISPR) to obtain numerical scores/ranks. Compared to other anti-CRISPR databases, AcrDB has the following unique features: (i) It is a genome-scale database with the largest collection of data (39 799 Acr-Aca operons containing Aca or Acr homologs); (ii) It offers a user-friendly web interface with various functions for browsing, graphically viewing, searching, and batch downloading Acr-Aca operons; (iii) It focuses on the genomic context of Acr and Aca candidates instead of individual Acr protein family and (iv) It collects data with three independent programs each having a unique data mining algorithm for cross validation. AcrDB will be a valuable resource to the anti-CRISPR research community.",

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AU - ul Amir Afsar Minhas, Fayyaz

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AcrDB: A database of anti-CRISPR operons in prokaryotes and viruses

Abstract

Bibliographical note

Acknowledgements

Funding

ASJC Scopus subject areas

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