Abstract
The CRISPR (clusters of regularly interspaced short palindromic repeats)–Cas adaptive immune system is an important defense system in bacteria, providing targeted defense against invasions of foreign nucleic acids. CRISPR–Cas systems consist of CRISPR loci and cas (CRISPR-associated) genes: sequence segments of invaders are incorporated into host genomes at CRISPR loci to generate specificity, while adjacent cas genes encode proteins that mediate the defense process. We pursued an integrated approach to identifying putative cas genes from genomes and metagenomes, combining similarity searches with genomic neighborhood analysis. Application of our approach to bacterial genomes and human microbiome datasets allowed us to significantly expand the collection of cas genes: the sequence space of the Cas9 family, the key player in the recently engineered RNA-guided platforms for genome editing in eukaryotes, is expanded by at least two-fold with metagenomic datasets. We found genes in cas loci encoding other functions, for example, toxins and antitoxins, confirming the recently discovered potential of coupling between adaptive immunity and the dormancy/suicide systems. We further identified 24 novel Cas families; one novel family contains 20 proteins, all identified from the human microbiome datasets, illustrating the importance of metagenomics projects in expanding the diversity of cas genes.
Highlights
Clustered regularly interspaced short palindromic repeats (CRISPR) associated (Cas) protein systems are RNAguided adaptive immunity system that provides bacteria with sequence-directed defense against invading DNAs or RNAs [1,2,3,4,5,6,7]
In total we identified 13 182 known cas genes from complete genomes, 18 318 from draft genomes, and 131 117 from the human microbiome project (HMP) assemblies
We classified the cas loci we identified into different types/subtypes of CRISPR–Cas systems, based on the presence of type-specific Cas families
Summary
Clustered regularly interspaced short palindromic repeats (CRISPR) associated (Cas) protein systems are RNAguided adaptive immunity system that provides bacteria with sequence-directed defense against invading DNAs or RNAs [1,2,3,4,5,6,7]. CRISPR spacer-repeat arrays consist of 24- to 47-bp direct repeats flanking unique spacers acquired from foreign DNAs that have invaded the host and been stored in CRISPR arrays as a consequence. To affect interference, these arrays are transcribed as precursor RNAs, and subsequently truncated to short CRISPR RNAs by Cas proteins, and used to guide attacks on the matching protospacers in invading genomes, using other Cas activities [8,9]. It is generally understood that there are three stages in the silencing of foreign nucleic acids by the CRISPR–Cas systems: adaptation, expression and interference [12]. The later two stages (expression and interference) are referred to as the ‘executive’ subsystem, and involve proteins that are highly variable among different cas loci [12]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
