CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

By E. Deltcheva, K. Chylinski, C. Sharma, Karine Gonzales, Y. Chao, Z. A. Pirzada, M. Eckert, Jörg Vogel, E. Charpentier. Nature, 2011

2,457 citations recorded by the source corpus.

CRISPR/Cas systems constitute a widespread class of immunity systems that protect bacteria and archaea against phages and plasmids, and commonly use repeat/spacer-derived short crRNAs to silence foreign nucleic acids in a sequence-specific manner. Although the maturation of crRNAs represents a key event in CRISPR activation, the responsible endoribonucleases (CasE, Cas6, Csy4) are missing in many CRISPR/Cas subtypes. Here, differential RNA sequencing of the human pathogen Streptococcus pyogenes uncovered tracrRNA, a trans-encoded small RNA with 24-nucleotide complementarity to the repeat regions of crRNA precursor transcripts. We show that tracrRNA directs the maturation of crRNAs by the activities of the widely conserved endogenous RNase III and the CRISPR-associated Csn1 protein; all these components are essential to protect S. pyogenes against prophage-derived DNA. Our study reveals a novel pathway of small guide RNA maturation and the first example of a host factor (RNase III) required for bacterial RNA-mediated immunity against invaders.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/76830f6079c5e7a18cad744dd1fd905233836477

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Citations in the corpus

Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. (2015, background): “Unlike Cas9 systems, Cpf1-containing CRISPR systems have three features: First, Cpf1-associated CRISPR arrays are processed into mature crRNAs without the requirement of an additional trans-activating crRNA (tracrRNA) (Deltcheva et al., 2011; Chylinski et al., 2013).”
Discovery and functional characterization of diverse Class 2 CRISPR-Cas systems (2015, background): “The tracrRNA is partially complementary to repeat portions of the respective CRISPR array transcript (pre-crRNA) and is essential for its processing into crRNA, which is catalyzed by RNase III recognizing the repeat-antirepeat duplex (Deltcheva et al., 2011; Chylinski et al., 2013, 2014).”
Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity (2013, background): “Cas9 targeting is facilitated by base-pairing between the 20-nt guide sequence within the sgRNA and the target DNA (Deltcheva et al., 2011; Deveau et al., 2010; Gasiunas et al., 2012; Jinek et al., 2012).”
Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA (2014, positive): “In contrast, the Type II CRISPR system recognizes and cleaves the target DNA (Garneau et al., 2010) via the RNA-guided endonuclease Cas9 (Sapranauskas et al., 2011) along with two non-coding RNAs, the crRNA and the trans-activating crRNA (tracrRNA) (Deltcheva et al., 2011).”
CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity (2014, background): “Several studies of model CRISPR-Cas systems have also shown adaptive spacer uptake in E. coli type I-E systems (Datsenko et al., 2012; Swarts et al., 2012; Yosef et al., 2012) from plasmid exposure, as well as in a type III system from Sulfolobus solfataricus (Erdmann and Garrett, 2012).”
Transcriptome engineering with RNA-targeting Type VI-D CRISPR effectors (2018, positive): “To assess if the Cas13d repeat array is transcribed and processed into mature CRISPR guide RNAs (gRNA) as predicted (Deltcheva et al., 2011), we cloned the Cas13d CRISPR locus from an uncultured Ruminococcus sp. sample (Ur) into a bacterial expression plasmid.”
WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system (2015, neutral): “CRISPR-encoded RNAs have been shown to serve as guides for the Cas protein complex to defend against viral infection or other types of horizontal gene transfer by cleaving foreign DNA [2-4].”
Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. (2013, methodology): “Maturation of crRNA requires tracrRNA and RNase III (Deltcheva et al., 2011).”
High Efficiency, Homology-Directed Genome Editing in Caenorhabditis elegans Using CRISPR-Cas9 Ribonucleoprotein Complexes (2015, background): “Cas9 is a nuclease that functions with two small RNAs: CRISPR RNA (crRNA), which guides Cas9 to complementary target sequences, and trans-activating crRNA (tracrRNA), which binds to the crRNA and to Cas9 to form the ribonucleoprotein (RNP) complex (Deltcheva et al. 2011).”
CRISPR/Cas9 in Genome Editing and Beyond. (2016, background): “In type II CRISPR systems, the presence of a noncoding trans-activating CRISPR RNA (tracrRNA) that hybridizes with the crRNA repeat sequence is critical for crRNA processing, Cas9 binding, and Cas9-mediated target cleavage (3, 14).”