Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases

Garside, E.L.; Schellenberg, M.J.; Gesner, Emily M.; Bonanno, J.B.; Sauder, J.M.; Burley, S.K.; Almo, Steven C.; Mehta, Garima; MacMillan, Andrew M.

doi:10.1261/rna.033100.112

Cited by 82 publications

(82 citation statements)

References 36 publications

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“…The N-terminal RRM-like domain contains the putative endoribonuclease site, which is centered at a histidine residue. 18,31 Pyrococcus furiosus (Pf ) Cas6 (PDB ID: 3UFC) has an N-terminal RRM-like domain that packs against a twisted β-sheet domain. 21 This RRM-like domain contains an endoribonuclease site that is also centered at a histidine residue, although the exact position differs from that of Bh Cas5d.…”

Section: Structural Comparison Of Csm3 With the Cas Proteins Of The Rmentioning

confidence: 99%

“…11,17 In recent years, structural information on Cas proteins has started to provide insights into the molecular mechanisms of crRNA binding and target recognition. The combination of X-ray crystallography 8,[18][19][20][21][22] and electron microscopic studies of the type I Cascade [23][24][25] and of the Type III-B Cmr-complex [26][27][28] has shown how some of the Cas proteins interact and bind crRNA.…”

Section: Introductionmentioning

confidence: 99%

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Structure and RNA-binding properties of the Type III-A CRISPR-associated protein Csm3

Hrle

Ebert

et al. 2013

RNA Biology

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The prokaryotic adaptive immune system is based on the incorporation of genome fragments of invading viral genetic elements into clusters of regulatory interspaced short palindromic repeats (CRISPRs). The CRISPR loci are transcribed and processed into crRNAs, which are then used to target the invading nucleic acid for degradation. The large family of CRISPR-associated (Cas) proteins mediates this interference response. We have characterized Methanopyrus kandleri Csm3, a protein of the type III-A CRISPR-Cas complex. The 2.4 angstrom resolution crystal structure shows an elaborate four-domain fold organized around a core RRM-like domain. The overall architecture highlights the structural homology to Cas7, the Cas protein that forms the backbone of type I interference complexes. Csm3 binds unstructured RNAs in a sequence non-specific manner, suggesting that it interacts with the variable spacer sequence of the crRNA. The structural and biochemical data provide insights into the similarities and differences in this group of Cas proteins

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Section: Structural Comparison Of Csm3 With the Cas Proteins Of The Rmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Structure and RNA-binding properties of the Type III-A CRISPR-associated protein Csm3

Hrle

Ebert

et al. 2013

RNA Biology

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“…In some types, the 3' handles form hairpin structures (Carte et al, 2010; Carte et al, 2008;Niewoehner et al, 2014;Wang et al, 2011). In type I-C systems, initial processing is performed by Cas5 rather than Cas6 (Garside et al, 2012;Nam et al, 2012b), whereas in other CRISPR-Cas types, Cas5 is catalytically inactive and is thought to interact with the 5' handle of the crRNA . In most type I and type III systems, after initial processing, the crRNA is transferred to CRISPR ribonucleoprotein (crRNP) complexes for secondary processing (Hatoum-Aslan et al, 2011).…”

Section: Transcript Processingmentioning

confidence: 99%

CRISPR-Cas Systems in Prokaryotes

Burmistrz

Pyrć

2015

Pol J Microbiol

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A b s t r a c tProkaryotic organisms possess numerous strategies that enable survival in hostile conditions. Among others, these conditions include the invasion of foreign nucleic acids such as bacteriophages and plasmids. The clustered regularly interspaced palindromic repeats-CRISPRassociated proteins (CRISPR-Cas) system provides the majority of bacteria and archaea with adaptive and hereditary immunity against this threat. This mechanism of immunity is based on short fragments of foreign DNA incorporated within the hosts genome. After transcription, these fragments guide protein complexes that target foreign nucleic acids and promote their degradation. The aim of this review is to summarize the current status of CRISPR-Cas research, including the mechanisms of action, the classification of different types and subtypes of these systems, and the development of new CRISPR-Cas-based molecular biology tools. K e y w o r d s: CRISPR-Cas, prokaryotesBurmistrz M. and Pyrć K. 3 194 spacer sequences can be of either foreign or self-origin (Stern et al., 2010;Vercoe et al., 2013). The proteomic component is responsible for the incorporation of new template sequences, processing them into a form that enables base pairing with target nucleic acids, as well as for scanning and cleavage of target DNA or RNA. Of note, not all CRISPR-Cas systems discovered to date are active (Haft et al., 2005;van der Ploeg, 2009). Structure of the CRISPR-Cas systemThe genomic component of the CRISPR-Cas system is formed by a series of variable spacers, which in some cases share sequence similarity with viruses, plasmids, or bacteria. These regions are interspaced with repeat sequences that are identical or almost identical within a single CRISPR cassette. The length of the repeat sequences varies between 25 and 40 nt, whereas the length of the spacer sequences varies between 21 and 72 nt. As mentioned above, some spacers show high homology with foreign nucleic acids, but the origin of a significant percentage of spacers remains unknown. The sequence homology between the spacer and the target is the major determinant of nucleic acid degradation of the target. Some bacterial species contain more than one CRISPR locus within their genome (Louwen et al., 2014). Depending on the specific bacterial species or strain, a CRISPR locus may contain from a few to several hundred repeat spacer units; however, most commonly, a single CRISPR locus contains approximately 50 units. The CRISPR repeat sequences play an important role during both the acquisition of new spacers and the transcription and maturation of CRISPR RNA (crRNA). Based on the sequence similarity, the CRISPR repeats are assigned into groups (Kunin et al., 2007). These groups were taken into account in the current classification of CRISPR-Cas systems (Makarova et al., 2011). Although most CRISPR arrays are located on chromosomal DNA, there are examples of CRISPRs located on plasmids (Godde and Bickerton, 2006). In general, CRISPR loci are flanked by A/T rich leader sequences containing...

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“…However, both approaches were trained based on a small number of cases with experimental evidence. For example, although more than a thousand repeat consensus sequences (including 442 repeats in the REPEATSLange set, 419 repeats in the REPEATSKunin and 478 in the REPEATShah) were used to train and test CRISPRstrand (Alkhnbashi et al 2014), only the repeats in the REPEATSLange were based on 10 systems (associated with nine species) that had experimental evidence supporting the crRNA processing (Brouns et al 2008;Haurwitz et al 2010;Hatoum-Aslan et al 2011;Garside et al 2012;Juranek et al 2012;Nam et al 2012;Richter et al 2012;Sternberg et al 2012;Nickel et al 2013;Scholz et al 2013). It suggests that there is a demand for having more experimentally supported transcription for development and evaluation of such tools.…”

Section: Introductionmentioning

confidence: 99%

Characterization of CRISPR RNA transcription by exploiting stranded metatranscriptomic data

Zhang

2016

RNA

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CRISPR-Cas systems are bacterial adaptive immune systems, each typically composed of a locus of cas genes and a CRISPR array of spacers flanked by repeats. Processed transcripts of CRISPR arrays (crRNAs) play important roles in the interference process mediated by these systems, guiding targeted immunity. Here we developed computational approaches that allow us to characterize the expression of many CRISPRs in their natural environments, using community RNA-seq (metatranscriptomic) data. By exploiting public human gut metatranscriptomic data sets, we studied the expression of 56 repeat-sequence types of CRISPRs, revealing that most CRISPRs are transcribed in one direction (producing crRNAs). In rarer cases, including a type II system associated with Bacteroides fragilis, CRISPRs are transcribed in both directions. Type III CRISPR-Cas systems were found in the microbiomes, but metatranscriptomic reads were barely found for their CRISPRs. We observed individual-level variation of the crRNA transcription, and an even greater transcription of a CRISPR from the antisense strand than the crRNA strand in one sample. The orientations of CRISPR expression implicated by metatranscriptomic data are largely in agreement with prior predictions for CRISPRs, with exceptions. Our study shows the promise of exploiting community RNA-seq data for investigating the transcription of CRISPR-Cas systems.

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Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases

Cited by 82 publications

References 36 publications

Structure and RNA-binding properties of the Type III-A CRISPR-associated protein Csm3

Structure and RNA-binding properties of the Type III-A CRISPR-associated protein Csm3

CRISPR-Cas Systems in Prokaryotes

Characterization of CRISPR RNA transcription by exploiting stranded metatranscriptomic data

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