Evolution and classification of the CRISPR-Cas systems
Kira S. Makarova,Daniel H. Haft,Rodolphe Barrangou,Stan J. J. Brouns,Emmanuelle Charpentier,Philippe Horvath,Sylvain Moineau,Francisco J. M. Mojica,Yuri I. Wolf,Alexander F. Yakunin,John van der Oost,Eugene V. Koonin +11 more
TL;DR: In this paper, the evolutionary relationship between CRISPR-Cas and Cas proteins is analyzed and a unified classification of these systems is proposed based on multiple criteria. But, the classification is based on the phylogenies of the most common cas genes, the sequence and organization of the CRISpr repeats and the architecture of the Cas loci.
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Abstract: The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) modules are adaptive immunity systems that are present in many archaea and bacteria. These defence systems are encoded by operons that have an extraordinarily diverse architecture and a high rate of evolution for both the cas genes and the unique spacer content. Here, we provide an updated analysis of the evolutionary relationships between CRISPR-Cas systems and Cas proteins. Three major types of CRISPR-Cas system are delineated, with a further division into several subtypes and a few chimeric variants. Given the complexity of the genomic architectures and the extremely dynamic evolution of the CRISPR-Cas systems, a unified classification of these systems should be based on multiple criteria. Accordingly, we propose a 'polythetic' classification that integrates the phylogenies of the most common cas genes, the sequence and organization of the CRISPR repeats and the architecture of the CRISPR-cas loci.
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Citations
The chemistry of Cas9 and its CRISPR colleagues
Janice S. Chen,Jennifer A. Doudna +1 more
- 04 Oct 2017
TL;DR: The chemistry and molecular mechanisms of interference by single-effector CRISPR–Cas proteins, used for precise genome engineering, are discussed.
131
CRISPR interference: a structural perspective
TL;DR: Recent progress on the structural biology of the CRISPR/Cas system is covered, focusing on the Cas proteins and complexes that catalyse crRNA biogenesis and interference.
CRISPR/Cas9-Mediated Multiplex Genome Editing of the BnWRKY11 and BnWRKY70 Genes in Brassica napus L
TL;DR: The results demonstrated that BnWRKY70 may function as a regulating factor to negatively control the Sclerotinia resistance and CRISPR/Cas9 system could be used to generate germplasm in B. napus with high resistance against Sclerotiorum.
130
To acquire or resist: the complex biological effects of CRISPR–Cas systems
TL;DR: Data pertaining to the potential in vivo costs and benefits of CRISPR-Cas systems, novel functions for these systems, and how they may be inactivated are reviewed.
128
Cleavage of phage DNA by the Streptococcus thermophilus CRISPR3-Cas system.
TL;DR: This work has shown that the S. thermophilus CRISPR3-Cas system acts by cleaving phage dsDNA genomes at the same specific position inside the targeted protospacer as observed with the CRISpr1- Cas system, and determined that overall phage resistance efficiency is correlated to the total number of newly acquired spacers in bothCRISPR loci.
References
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
Stéphane Guindon,Olivier Gascuel +1 more
TL;DR: This work has used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches.
17.5K
CRISPR provides acquired resistance against viruses in prokaryotes
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Origins and Mechanisms of miRNAs and siRNAs
TL;DR: This work has revealed unexpected diversity in their biogenesis pathways and the regulatory mechanisms that they access, which has direct implications for fundamental biology as well as disease etiology and treatment.
5.1K
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TL;DR: A major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes is described and is expected to be a useful platform for functional annotation of newlysequenced genomes, including those of complex eukARYotes, and genome-wide evolutionary studies.
CRISPR RNA maturation by trans -encoded small RNA and host factor RNase III
Elitza Deltcheva,Krzysztof Chylinski,Krzysztof Chylinski,Cynthia M. Sharma,Karine Gonzales,Yanjie Chao,Zaid Ahmed Pirzada,Maria R. Eckert,Jörg Vogel,Emmanuelle Charpentier,Emmanuelle Charpentier +10 more
TL;DR: In this article, tracrRNA, a trans-encoded small RNA with 24-nucleotide complementarity to the repeat regions of crRNA precursor transcripts, is shown to direct the maturation of crRNAs by the activities of the widely conserved endogenous RNase III and the CRISPR-associated Csn1 protein.