Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28

Smargon, Aaron Andrew; Cox, David Benjamin Turitz; Pyzocha, Neena; Zheng, Kang‐Cheng; Slaymaker, Ian M.; Gootenberg, Jonathan S.; Abudayyeh, Omar; Essletzbichler, Patrick; Shmakov, Sergey; Makarova, Kira S.; Koonin, Eugene V.; Zhang, Feng

doi:10.1016/j.molcel.2016.12.023

Cited by 478 publications

(467 citation statements)

References 40 publications

Supporting

Mentioning

444

Contrasting

Unclassified

Order By: Relevance

“…For the type V effectors, the direct ancestors are difficult to identify, but different subfamilies of TnpB appear to have given rise to different subtypes, as indicated by sequence similarity and phylogenetic analysis (146, 147). The type VI effectors, Cas13, are unrelated to those in other CRISPR-Cas types and contain two HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domains, which cleave RNA targets (1, 3, 149). As with type V effectors, the exact ancestors of these proteins are difficult to pinpoint, but it appears likely that either HEPN domain–containing Cas proteins of class 1 CRISPR-Cas systems, such as Csx6 and Csn1, or a distinct HEPN domain–containing toxin could be implicated (147).…”

Section: Adaptive Immunity: the Crispr-cas Systemmentioning

confidence: 99%

“…The recent comprehensive search for genomic loci that encode large proteins containing putative nuclease domains that could function as class 2 CRISPR-Cas effectors has revealed, arguably, the most direct links between microbial immunity and programmed cell death so far discovered (1, 146, 147, 149). Type VI effector proteins contain two HEPN domains predicted to possess RNase activity (146, 147).…”

Section: Interactions Between Defense Strategies: Coupling Between Immentioning

confidence: 99%

See 1 more Smart Citation

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

Koonin

Makarova²,

Wolf³

2017

Annu. Rev. Microbiol.

Self Cite

283

235

View full text Add to dashboard Cite

Evolution of bacteria and archaea involves an incessant arms race against an enormous diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most bacteria and archaea are dedicated to antiparasite defense. The functions of these defense systems follow several distinct strategies, including innate immunity; adaptive immunity; and dormancy induction, or programmed cell death. Recent comparative genomic studies taking advantage of the expanding database of microbial genomes and metagenomes, combined with direct experiments, resulted in the discovery of several previously unknown defense systems, including innate immunity centered on Argonaute proteins, bacteriophage exclusion, and new types of CRISPR-Cas systems of adaptive immunity. Some general principles of function and evolution of defense systems are starting to crystallize, in particular, extensive gain and loss of defense genes during the evolution of prokaryotes; formation of genomic defense islands; evolutionary connections between mobile genetic elements and defense, whereby genes of mobile elements are repeatedly recruited for defense functions; the partially selfish and addictive behavior of the defense systems; and coupling between immunity and dormancy induction/programmed cell death.

show abstract

Section: Adaptive Immunity: the Crispr-cas Systemmentioning

confidence: 99%

Section: Interactions Between Defense Strategies: Coupling Between Immentioning

confidence: 99%

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

Koonin

Makarova²,

Wolf³

2017

Annu. Rev. Microbiol.

Self Cite

283

235

View full text Add to dashboard Cite

show abstract

“…Three Cas13 protein families have been identified to date: Cas13a (previously known as C2c2), Cas13b, and Cas13c (12, 13). We recently reported that Cas13a enzymes can be adapted as tools for nucleic acid detection (14) as well as mammalian and plant cell RNA knockdown and transcript tracking (15).…”

Section: Introductionmentioning

confidence: 99%

RNA editing with CRISPR-Cas13

Cox

Gootenberg

Abudayyeh

et al. 2017

Science

Self Cite

1,489

1,574

View full text Add to dashboard Cite

Nucleic acid editing holds promise for treating genetic disease, particularly at the RNA level, where disease-relevant sequences can be rescued to yield functional protein products. Type VI CRISPR-Cas systems contain the programmable single-effector RNA-guided RNases Cas13. Here, we profile Type VI systems to engineer a Cas13 ortholog capable of robust knockdown and demonstrate RNA editing by using catalytically-inactive Cas13 (dCas13) to direct adenosine to inosine deaminase activity by ADAR2 to transcripts in mammalian cells. This system, referred to as RNA Editing for Programmable A to I Replacement (REPAIR), has no strict sequence constraints, can be used to edit full-length transcripts containing pathogenic mutations. We further engineer this system to create a high specificity variant, REPAIRv2, that is 919 times more specific than REPAIRv1 as well as minimize the system to ease viral delivery. REPAIR presents a promising RNA editing platform with broad applicability for research, therapeutics, and biotechnology.

show abstract

“…The mature crRNA consists of a unique spacer of 25 to 65 bp in length (depending on the CRISPR-Cas type and subtype) flanked by portions of the adjacent repeats. In the third and final stage, interference, the effector Cas protein complex mediates recognition of the target DNA or RNA via base-pairing between the spacer and cognate protospacer, followed by cleavage of the target by Cas nucleases (19)(20)(21)(22)(23)(24).…”

mentioning

confidence: 99%

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

Shmakov

Sitnik

Makarova

et al. 2017

mBio

Self Cite

202

195

View full text Add to dashboard Cite

Clustered regularly interspaced short palindromic repeats and CRISPRassociated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR "dark matter." We performed a comprehensive analysis of the spacers from all CRISPR-cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average). Among the detected protospacers, the majority, typically 80 to 90%, originated from viral genomes, including proviruses, and among the rest, the most common source was genes that are integrated into microbial chromosomes but are involved in plasmid conjugation or replication. Thus, almost all spacers with identifiable protospacers target mobile genetic elements (MGE). The GC content, as well as dinucleotide and tetranucleotide compositions, of microbial genomes, their spacer complements, and the cognate viral genomes showed a nearly perfect correlation and were almost identical. Given the near absence of self-targeting spacers, these findings are most compatible with the possibility that the spacers, including the dark matter, are derived almost completely from the species-specific microbial mobilomes. IMPORTANCEThe principal function of CRISPR-Cas systems is thought to be protection of bacteria and archaea against viruses and other parasitic genetic elements. The CRISPR defense function is mediated by sequences from parasitic elements, known as spacers, that are inserted into CRISPR arrays and then transcribed and employed as guides to identify and inactivate the cognate parasitic genomes. However, only a small fraction of the CRISPR spacers match any sequences in the current databases, and of these, only a minority correspond to known parasitic elements. We show that nearly all spacers with matches originate from viral or plasmid genomes that are either free or have been integrated into the host genome. We further demonstrate that spacers with no matches have the same properties as those of identifiable origins, strongly suggesting that all spacers originate from mobile elements.KEYWORDS CRISPR-Cas, bacteriophages, mobilome, oligonucleotide composition, spacer acquisition C RISPR-Cas (clustered regularly interspaced palindromic repeats and CRISPRassociated proteins) systems are adaptive (acquired) immune systems of archaea and bacteria that store memory of past encounters with foreign DNA in unique spacer Citation Shmakov SA, Sitnik V, Makarova KS, Wolf YI, Severinov KV, Koonin EV. 2017. The CRISPR spacer space is dominated by sequences from species-specific mobilomes.

show abstract

Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28

Cited by 478 publications

References 40 publications

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

RNA editing with CRISPR-Cas13

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

Contact Info

Product

Resources

About