1887

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated CRISPR-associated sequence (CAS) proteins constitute a novel antiviral defence system that is widespread in prokaryotes. Repeats are separated by spacers, some of them homologous to sequences in mobile genetic elements. Although the whole process involved remains uncharacterized, it is known that new spacers are incorporated into CRISPR loci of the host during a phage challenge, conferring specific resistance against the virus. Moreover, it has been demonstrated that such interference is based on small RNAs carrying a spacer. These RNAs would guide the defence apparatus to foreign molecules carrying sequences that match the spacers. Despite this essential role, the spacer uptake mechanism has not been addressed. A first step forward came from the detection of motifs associated with spacer precursors (proto-spacers) of , revealing a specific recognition of donor sequences in this species. Here we show that the conservation of proto-spacer adjacent motifs (PAMs) is a common theme for the most diverse CRISPR systems. The PAM sequence depends on the CRISPR-CAS variant, implying that there is a CRISPR-type-specific (motif-directed) choice of the spacers, which subsequently determines the interference target. PAMs also direct the orientation of spacers in the repeat arrays. Remarkably, observations based on such polarity argue against a recognition of the spacer precursors on transcript RNA molecules as a general rule.

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/content/journal/micro/10.1099/mic.0.023960-0
2009-03-01
2019-11-13
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CRISPR arrays analysed for spacer homologues [ PDF] (69 kb) Genetic elements carrying proto-spacers [ PDF] (26 kb) PAM conservation in repeats and leaders for each CRISPR type [ PDF] (14 kb) Distribution of E. coli CRISPR-2 PAMs with respect to the leader and adjoining CRISPR ends [ PDF] (10 kb) Alignments of spacers with proto-spacer regions [ PDF] (533 kb) Proto-spacer region logos built for sequences corresponding to spacers in arrays of the same CRISPR, located in either a genome or in related strains [ PDF] (6233 kb) Schematic illustration of the orientation of spacers in CRISPR arrays of representative genomes [ PDF] (260 kb)

PDF

CRISPR arrays analysed for spacer homologues [ PDF] (69 kb) Genetic elements carrying proto-spacers [ PDF] (26 kb) PAM conservation in repeats and leaders for each CRISPR type [ PDF] (14 kb) Distribution of E. coli CRISPR-2 PAMs with respect to the leader and adjoining CRISPR ends [ PDF] (10 kb) Alignments of spacers with proto-spacer regions [ PDF] (533 kb) Proto-spacer region logos built for sequences corresponding to spacers in arrays of the same CRISPR, located in either a genome or in related strains [ PDF] (6233 kb) Schematic illustration of the orientation of spacers in CRISPR arrays of representative genomes [ PDF] (260 kb)

PDF

CRISPR arrays analysed for spacer homologues [ PDF] (69 kb) Genetic elements carrying proto-spacers [ PDF] (26 kb) PAM conservation in repeats and leaders for each CRISPR type [ PDF] (14 kb) Distribution of E. coli CRISPR-2 PAMs with respect to the leader and adjoining CRISPR ends [ PDF] (10 kb) Alignments of spacers with proto-spacer regions [ PDF] (533 kb) Proto-spacer region logos built for sequences corresponding to spacers in arrays of the same CRISPR, located in either a genome or in related strains [ PDF] (6233 kb) Schematic illustration of the orientation of spacers in CRISPR arrays of representative genomes [ PDF] (260 kb)

PDF

CRISPR arrays analysed for spacer homologues [ PDF] (69 kb) Genetic elements carrying proto-spacers [ PDF] (26 kb) PAM conservation in repeats and leaders for each CRISPR type [ PDF] (14 kb) Distribution of E. coli CRISPR-2 PAMs with respect to the leader and adjoining CRISPR ends [ PDF] (10 kb) Alignments of spacers with proto-spacer regions [ PDF] (533 kb) Proto-spacer region logos built for sequences corresponding to spacers in arrays of the same CRISPR, located in either a genome or in related strains [ PDF] (6233 kb) Schematic illustration of the orientation of spacers in CRISPR arrays of representative genomes [ PDF] (260 kb)

PDF

CRISPR arrays analysed for spacer homologues [ PDF] (69 kb) Genetic elements carrying proto-spacers [ PDF] (26 kb) PAM conservation in repeats and leaders for each CRISPR type [ PDF] (14 kb) Distribution of E. coli CRISPR-2 PAMs with respect to the leader and adjoining CRISPR ends [ PDF] (10 kb) Alignments of spacers with proto-spacer regions [ PDF] (533 kb) Proto-spacer region logos built for sequences corresponding to spacers in arrays of the same CRISPR, located in either a genome or in related strains [ PDF] (6233 kb) Schematic illustration of the orientation of spacers in CRISPR arrays of representative genomes [ PDF] (260 kb)

PDF

CRISPR arrays analysed for spacer homologues [ PDF] (69 kb) Genetic elements carrying proto-spacers [ PDF] (26 kb) PAM conservation in repeats and leaders for each CRISPR type [ PDF] (14 kb) Distribution of E. coli CRISPR-2 PAMs with respect to the leader and adjoining CRISPR ends [ PDF] (10 kb) Alignments of spacers with proto-spacer regions [ PDF] (533 kb) Proto-spacer region logos built for sequences corresponding to spacers in arrays of the same CRISPR, located in either a genome or in related strains [ PDF] (6233 kb) Schematic illustration of the orientation of spacers in CRISPR arrays of representative genomes [ PDF] (260 kb)

PDF

CRISPR arrays analysed for spacer homologues [ PDF] (69 kb) Genetic elements carrying proto-spacers [ PDF] (26 kb) PAM conservation in repeats and leaders for each CRISPR type [ PDF] (14 kb) Distribution of E. coli CRISPR-2 PAMs with respect to the leader and adjoining CRISPR ends [ PDF] (10 kb) Alignments of spacers with proto-spacer regions [ PDF] (533 kb) Proto-spacer region logos built for sequences corresponding to spacers in arrays of the same CRISPR, located in either a genome or in related strains [ PDF] (6233 kb) Schematic illustration of the orientation of spacers in CRISPR arrays of representative genomes [ PDF] (260 kb)

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