Annotation and Classification of CRISPR-Cas Systems

By Kira S. Makarova, Eugene V. Koonin. Methods in molecular biology, 2015

359 citations recorded by the source corpus.

The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) is a prokaryotic adaptive immune system that is represented in most archaea and many bacteria. Among the currently known prokaryotic defense systems, the CRISPR-Cas genomic loci show unprecedented complexity and diversity. Classification of CRISPR-Cas variants that would capture their evolutionary relationships to the maximum possible extent is essential for comparative genomic and functional characterization of this theoretically and practically important system of adaptive immunity. To this end, a multipronged approach has been developed that combines phylogenetic analysis of the conserved Cas proteins with comparison of gene repertoires and arrangements in CRISPR-Cas loci. This approach led to the current classification of CRISPR-Cas systems into three distinct types and ten subtypes for each of which signature genes have been identified. Comparative genomic analysis of the CRISPR-Cas systems in new archaeal and bacterial genomes performed over the 3 years elapsed since the development of this classification makes it clear that new types and subtypes of CRISPR-Cas need to be introduced. Moreover, this classification system captures only part of the complexity of CRISPR-Cas organization and evolution, due to the intrinsic modularity and evolutionary mobility of these immunity systems, resulting in numerous recombinant variants. Moreover, most of the cas genes evolve rapidly, complicating the family assignment for many Cas proteins and the use of family profiles for the recognition of CRISPR-Cas subtype signatures. Further progress in the comparative analysis of CRISPR-Cas systems requires integration of the most sensitive sequence comparison tools, protein structure comparison, and refined approaches for comparison of gene neighborhoods.

Subfields: Genetics, Insect Science, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1a26345d2ff04ee56954717255572ea4128af38d

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Citations in the corpus

Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. (2015, neutral): “It has been shown that the nuclease moieties of Cas9 and Cpf1 are homologous to distinct groups of transposon-encoded TnpB proteins, the first one containing both RuvC and HNH nuclease domains and the second one containing the RuvC-like domain only (Makarova and Koonin, 2015).”
Discovery and functional characterization of diverse Class 2 CRISPR-Cas systems (2015, background): “To identify additional Class 2 systems, we focused on unclassified candidate CRISPR-Cas loci containing long proteins (>500 aa) given that the presence of large singlesubunit effector proteins, such as Cas9 and Cpf1, is the diagnostic feature of type II and type V systems, respectively.”
Biology and Applications of CRISPR Systems: Harnessing Nature's Toolbox for Genome Engineering. (2016, neutral): “Type V and VI systems have only begun to be analyzed, and Type IV systems, bearing some familiar cas genes but no identifiable CRISPR locus, have yet to be characterized experimentally and almost certainly rely on mechanisms distinct from those of traditional CRISPR systems (Makarova and Koonin, 201”
CRISPRDetect: A flexible algorithm to define CRISPR arrays (2016, background): “Proposed updates of the classification of CRISPR-Cas systems would be able to be incorporated into CRISPRDetect [48, 54, 55].”