Classification and Nomenclature of CRISPR-Cas Systems: Where from Here?

Overview

Journal CRISPR J

Specialty Molecular Biology

Date 2019 Apr 26

PMID 31021272

Citations 112

Authors

Kira S Makarova

Yuri I Wolf

Eugene V Koonin

Affiliations

Soon will be listed here.

Abstract

As befits an immune mechanism, CRISPR-Cas systems are highly variable with respect to Cas protein sequences, gene composition, and organization of the genomic loci. Optimal classification of CRISPR-Cas systems and rational nomenclature for CRISPR-associated genes are essential for further progress of CRISPR research. These are highly challenging tasks because of the complexity of CRISPR-Cas and their fast evolution, including frequent module shuffling, as well as the lack of universal markers for a consistent evolutionary classification. The complexity and variability of CRISPR-Cas systems necessitate a multipronged approach to classification and nomenclature. We present a brief summary of the current state of the art and discuss further directions in this area.

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References

Roberts R, Belfort M, Bestor T, Bhagwat A, Bickle T, Bitinaite J . A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res. 2003; 31(7):1805-12. PMC: 152790. DOI: 10.1093/nar/gkg274. View

Soding J . Protein homology detection by HMM-HMM comparison. Bioinformatics. 2004; 21(7):951-60. DOI: 10.1093/bioinformatics/bti125. View

Makarova K, Grishin N, Shabalina S, Wolf Y, Koonin E . A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct. 2006; 1:7. PMC: 1462988. DOI: 10.1186/1745-6150-1-7. View

Roberts R, Vincze T, Posfai J, Macelis D . REBASE--enzymes and genes for DNA restriction and modification. Nucleic Acids Res. 2007; 35(Database issue):D269-70. PMC: 1899104. DOI: 10.1093/nar/gkl891. View

Kunin V, Sorek R, Hugenholtz P . Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol. 2007; 8(4):R61. PMC: 1896005. DOI: 10.1186/gb-2007-8-4-r61. View

Price M, Dehal P, Arkin A . FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010; 5(3):e9490. PMC: 2835736. DOI: 10.1371/journal.pone.0009490. View

Stern A, Sorek R . The phage-host arms race: shaping the evolution of microbes. Bioessays. 2010; 33(1):43-51. PMC: 3274958. DOI: 10.1002/bies.201000071. View

Sinkunas T, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V . Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system. EMBO J. 2011; 30(7):1335-42. PMC: 3094125. DOI: 10.1038/emboj.2011.41. View

Makarova K, Aravind L, Wolf Y, Koonin E . Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct. 2011; 6:38. PMC: 3150331. DOI: 10.1186/1745-6150-6-38. View

10.

Beloglazova N, Petit P, Flick R, Brown G, Savchenko A, Yakunin A . Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference. EMBO J. 2011; 30(22):4616-27. PMC: 3243599. DOI: 10.1038/emboj.2011.377. View

11.

Takeuchi N, Wolf Y, Makarova K, Koonin E . Nature and intensity of selection pressure on CRISPR-associated genes. J Bacteriol. 2011; 194(5):1216-25. PMC: 3294813. DOI: 10.1128/JB.06521-11. View

12.

Westra E, van Erp P, Kunne T, Wong S, Staals R, Seegers C . CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol Cell. 2012; 46(5):595-605. PMC: 3372689. DOI: 10.1016/j.molcel.2012.03.018. View

13.

Shah S, Erdmann S, Mojica F, Garrett R . Protospacer recognition motifs: mixed identities and functional diversity. RNA Biol. 2013; 10(5):891-9. PMC: 3737346. DOI: 10.4161/rna.23764. View

14.

Lange S, Alkhnbashi O, Rose D, Will S, Backofen R . CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. Nucleic Acids Res. 2013; 41(17):8034-44. PMC: 3783184. DOI: 10.1093/nar/gkt606. View

15.

Staals R, Agari Y, Maki-Yonekura S, Zhu Y, Taylor D, van Duijn E . Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus. Mol Cell. 2013; 52(1):135-145. PMC: 4006948. DOI: 10.1016/j.molcel.2013.09.013. View

16.

Makarova K, Wolf Y, Koonin E . The basic building blocks and evolution of CRISPR-CAS systems. Biochem Soc Trans. 2013; 41(6):1392-400. PMC: 5898231. DOI: 10.1042/BST20130038. View

17.

Vestergaard G, Garrett R, Shah S . CRISPR adaptive immune systems of Archaea. RNA Biol. 2014; 11(2):156-67. PMC: 3973734. DOI: 10.4161/rna.27990. View

18.

Chylinski K, Makarova K, Charpentier E, Koonin E . Classification and evolution of type II CRISPR-Cas systems. Nucleic Acids Res. 2014; 42(10):6091-105. PMC: 4041416. DOI: 10.1093/nar/gku241. View

19.

Hochstrasser M, Taylor D, Bhat P, Guegler C, Sternberg S, Nogales E . CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference. Proc Natl Acad Sci U S A. 2014; 111(18):6618-23. PMC: 4020112. DOI: 10.1073/pnas.1405079111. View

20.

Makarova K, Anantharaman V, Grishin N, Koonin E, Aravind L . CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems. Front Genet. 2014; 5:102. PMC: 4012209. DOI: 10.3389/fgene.2014.00102. View