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Evolution and classification of the CRISPR–Cas systems
TLDR
An updated analysis of the evolutionary relationships between CRISPR–Cas systems and Cas proteins is provided and a 'polythetic' classification that integrates the phylogenies of the most common cas genes, the sequence and organization of theCRISPR repeats and the architecture of the CRISpr–cas loci is proposed.
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An updated evolutionary classification of CRISPR–Cas systems
TLDR
An approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR–cas loci into distinct classes, types and subtypes is presented.
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Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements
TLDR
It is shown that CRISPR spacers derive from preexisting sequences, either chromosomal or within transmissible genetic elements such as bacteriophages and conjugative plasmids, implying a relationship betweenCRISPR and immunity against targeted DNA.
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Short motif sequences determine the targets of the prokaryotic CRISPR defence system.
TLDR
It is shown that the conservation of proto-spacer adjacent motifs (PAMs) is a common theme for the most diverse CRISPR systems, implying that there is aCRISPR-type-specific (motif-directed) choice of the spacers, which subsequently determines the interference target.
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Short motif sequences determine the targets of the prokaryotic CRISPR defence system.
TLDR
It is shown that the conservation of proto-spacer adjacent motifs (PAMs) is a common theme for the most diverse CRISPR systems, implying that there is aCRISPR-type-specific (motif-directed) choice of the spacers, which subsequently determines the interference target.
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Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants
TLDR
An updated evolutionary classification of CRISPR–Cas systems and cas genes is provided, with an emphasis on the major developments that have occurred since the publication of the latest classification, in 2015, which includes 2 classes, 6 types and 33 subtypes.
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Complete Genome Sequence of Crohn's Disease-Associated Adherent-Invasive E. coli Strain LF82
TLDR
LF82 genome analysis indicated that a number of genes, gene clusters and pathoadaptative mutations which have been acquired may play a role in virulence of AIEC strain LF82.
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Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria
TLDR
The SRSRs are widespread among the various physiological and phylogenetic groups, probably being present in all the Archaea and hyperthermophilic Bacteria, in at least some members of the cyanobacteria and proteobacteria lineages, as well as in the two subgroups of Gram-positive bacteria (the low and high GC content groups).
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Diversity of CRISPR loci in Escherichia coli.
TLDR
The data suggest that the degeneration of one CRISPR/CAS system in E. coli ancestors could have been brought about by self-interference, and substantiate different levels of activity between loci of both CRISpr types, as well as different target preferences andCRISPR relevances for particular groups of strains.
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Protospacer recognition motifs Mixed identities and functional diversity
TLDR
It is proposed to use the terms protospacer associated motif (PAM) for the conserved DNA sequence and to employ spacer acqusition motif (SAM) and target interference motif (TIM), respectively, for acquisition and interference recognition sites.
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