Dear editors
In the battle between CRISPR-Cas* prokaryotic immune systems and the elements that they target, a diverse array of “anti-CRISPR” proteins have evolved. These proteins appear to have arisen independently multiple times in evolution and function through diverse mechanisms to inhibit CRISPR-Cas immunity. For comprehensive reviews on anti-CRISPRs, we direct readers to recent publications.1,2
Due to the increasing interest in anti-CRISPRs, many new families of these proteins have been discovered in the past year or so. There are now 36 distinct families of anti-CRISPRs described in the literature that block seven subtypes of CRISPR-Cas systems.3–12 In 2015, a naming system for anti-CRISPR genes and proteins was introduced.6,13 To date, this system has been followed in all subsequent publications describing newly discovered anti-CRISPRs. However, as the rate of anti-CRISPR discovery will likely accelerate in the coming years, we feel that it would be advantageous to establish a database for the registration and tracking of anti-CRISPR names.
The primary goal of this database will be to prevent redundant names being used in publications, thus avoiding confusion in the literature. Anti-CRISPR proteins are named according to the subtype they inhibit and the order in which they were discovered—for example, AcrIF1 was the first anti-CRISPR protein identified to inhibit the type I-F system. The database (a Google document) can be found here: https://tinyurl.com/anti-CRISPR
We propose that this document be updated when researchers have had a manuscript accepted for publication in which new anti-CRISPRs are described. We suggest that the authors upload relevant data to the spreadsheet, including the name, CRISPR-Cas subtype inhibited, reference, and amino-acid sequence of the anti-CRISPR (Table 1). This spreadsheet may also be utilized by those preparing a manuscript for submission to ensure that they use anti-CRISPR names that are still available.
Table 1.
A “Screenshot” from the Database, Depicting the Organization of Anti-CRISPR Entries
| Acr name | Type Inhibited | Species of origin | Type of genomic element | Reference (First author, year, journal) | Sequence |
|---|---|---|---|---|---|
| AcrIF1 | I-F | Pseudomonas aeruginosa | Phage | Bondy-Denomy, 2013, Nature | MKFIKYLSTAHLNYMNIAVYENGS |
| AcrIF2 | I-F | Pseudomonas aeruginosa | Phage | Bondy-Denomy, 2013, Nature | MIAQQHKDTVAACEAAEAIAIAKD |
| AcrIF3 | I-F | Pseudomonas aeruginosa | Phage | Bondy-Denomy, 2013, Nature | MSSTISDRIISRSVIEAARFIQSWE |
To avoid the listing of many orthologues, we propose that the database only contain one entry per Acr, which will be considered the “type” Acr for that sequence family. In a case where a paper has investigated proteins that are homologous to an Acr protein, authors should utilize a subscript (e.g., AcrIF6Pae) to denote the species in which the anti-CRISPR is found. When multiple proteins from one species are investigated, we suggest a format of AcrIF6Pae-1, AcrIF6Pae-2, and so on. The established conventions for naming anti-CRISPR proteins and genes will be described as part of the database. We view this as an open repository for the field and as a complementary resource to a previously described anti-CRISPR database.14
Two of us (J.B.-D. and A.R.D.) were inspired to establish this database by the success of the CRISPR-Cas classification scheme in bringing order to the naming of Cas proteins.15,16 This work has been tremendously valuable for advancing the CRISPR-Cas field. We hope that our contribution to the anti-CRISPR field as presented here will provide a similar long-term benefit.
Clustered Regularly Interspaced Short Palindromic Repeats.
References
- 1.Borges AL, Davidson AR, Bondy-Denomy J. The discovery, mechanisms, and evolutionary impact of anti-CRISPRs. Annu Rev Virol 2017;4:37–59. DOI: 10.1146/annurev-virology-10141-041616. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Pawluk A, Davidson AR, Maxwell KL. Anti-CRISPR: discovery, mechanism and function. Nat Rev Micro 2018;16:12–17. DOI: 10.1038/nrmicro.2017.120. [DOI] [PubMed] [Google Scholar]
- 3.Bondy-Denomy J, Pawluk A, Maxwell KL, et al. . Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 2013;493:429–432. DOI: 10.1038/nature11723. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Pawluk A, Bondy-Denomy J, Cheung VHW, et al. . A new group of phage anti-CRISPR genes inhibits the type I-E CRISPR-Cas system of Pseudomonas aeruginosa. mBio 2014;5:e00896-14. DOI: 10.1128/mBio.00896-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Pawluk A, Staals RH, Taylor C, et al. . Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species. Nat Microbiol 2016;1:1608–5.. DOI: 10.1038/nmicrobiol.2016.85. [DOI] [PubMed] [Google Scholar]
- 6.Pawluk A, Amrani N, Zhang Y, et al. . Naturally occurring off-switches for CRISPR-Cas9. Cell 2016;167:1829–1838.e9. DOI: 10.1016/j.cell.2016.11.017. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Rauch BJ, Silvis MR, Hultquist JF, et al. . Inhibition of CRISPR-Cas9 with bacteriophage proteins. Cell 2017;168:150–158.e10. DOI: 10.1016/j.cell.2016.12.009. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Hynes AP, Rousseau GM, Lemay ML, et al. . An anti-CRISPR from a virulent streptococcal phage inhibits Streptococcus pyogenes Cas9. Nat Microbiol 2017;2:1315–1380. DOI: 10.1038/s41564-017-0004-7. [DOI] [PubMed] [Google Scholar]
- 9.He F, Bhoobalan-Chitty Y, Van LB, et al. . Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity. Nat Microbiol 2018;3:461–469. DOI: 10.1038/s41564-018-0120-z. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Hynes AP, Rousseau GM, Agudelo D, et al. . Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins. Nat Commun 2018;9:291–9.. DOI: 10.1038/s41467-018-05092-w. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Marino ND, Zhang JY, Borges AL, et al. . Discovery of widespread type I and type V CRISPR-Cas inhibitors. Science 2018. Sep 6 [Epub ahead of print]; DOI: 10.1126/science.aau5174. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Watters KE, Fellmann C, Bai HB, et al. . Systematic discovery of natural CRISPR-Cas12a inhibitors. Science 2018. Sep 6 [Epub ahead of print]; DOI: 10.1126/science.aau5138. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Bondy-Denomy J, Garcia B, Strum S, et al. . Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins. Nature 2015;526:136–139. DOI: 10.1038/nature15254. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Dong C, Hao GF, Hua HL, et al. . Anti-CRISPRdb: a comprehensive online resource for anti-CRISPR proteins. Nucleic Acids Res 2018;46:D393–D398. DOI: 10.1093/nar/gkx835. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Makarova KS, Haft DH, Barrangou R, et al. . Evolution and classification of the CRISPR-Cas systems. Nat Rev Micro 2011;9:467–477. DOI: 10.1038/nrmicro2577. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16.Makarova KS, Wolf YI, Alkhnbashi OS, et al. . An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Micro 2015;13:722–736. DOI: 10.1038/nrmicro3569. [DOI] [PMC free article] [PubMed] [Google Scholar]