Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitidis

Zhang, Yan; Heidrich, Nadja; Ampattu, Biju Joseph; Gunderson, Carl W.; Seifert, H. Steven; Schoen, Christoph; Vogel, Jörg; Sontheimer, Erik J.

doi:10.1016/j.molcel.2013.05.001

Cited by 257 publications

(299 citation statements)

References 87 publications

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“…jejuni 81116, Helicobacter mustelae 12198 and Neisseria meningitidis Z2491, consistent with two recent studies (Chylinski et al, 2013;Koonin & Makarova, 2013). While our manuscript was in revision, the first functional study of a type II-C system was reported (Zhang et al, 2013). The type II-C system interfered with natural competence in Neisseria spp.…”

Section: Discussionsupporting

confidence: 88%

Novel configurations of type I and II CRISPR–Cas systems in Corynebacterium diphtheriae

2013

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Clustered regularly interspaced short palindromic repeats (CRISPRs) are major barriers to recombination through recognition of invading nucleic acids, such as phage and plasmids, and promoting their degredation through the action of CRISPR associated (Cas) proteins. The genomic comparison of 17 Corynebacterium diphtheriae strains led to the identification of three novel CRISPR-Cas system variants, based on the Type II (Type II-C) or type I-E systems. The type II-C system was the most common (11/17 isolates) but it lacked the csn2 and cas4 genes that are involved in spacer acquisition. We also identified that this variant type II-C CRISPR-Cas system is present in other bacteria, and the first system was recently characterized in Neisseria meningitidis. In the remaining isolates, the type II-C system was replaced by a variant of type I-E (I-E-a), where the repeat arrays are inserted between the cas3 and cse1 genes. Three isolates with the type II-C system also possess an additional variant of type I-E (I-E-b), elsewhere in the genome, that exhibits a novel divergent gene organization within the cas operon. The nucleotide sequences of the palindromic repeats and the cas1 gene were phylogenetically incongruent to the core genome. The G+C content of the systems is lower (46.0-49.5 mol%) than the overall DNA G+C content (53 mol%), and they are flanked by mobile genetic elements, providing evidence that they were acquired in three independent horizontal gene transfer events. The majority of spacers lack identity with known phage or plasmid sequences, indicating that there is an unexplored reservoir of corynebacteriophages and plasmids. These novel CRISPR-Cas systems may represent a unique mechanism for spacer acquisitions and defence against invading DNA.

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Section: Discussionsupporting

confidence: 88%

Novel configurations of type I and II CRISPR–Cas systems in Corynebacterium diphtheriae

2013

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“…coli containing the deltaproteobacteria CasX CRISPR locus was grown to OD 600 =1 at 25°C in SOB media. RNA was extracted by warm phenol extraction, separated on 10% denaturing polyacrylamide gel and blotted as previously described by Zhang et al (2013) 64 .…”

Section: Northern Blotsmentioning

confidence: 99%

New CRISPR–Cas systems from uncultivated microbes

Burstein

Harrington

Strutt

et al. 2016

Nature

478

367

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CRISPR-Cas systems provide microbes with adaptive immunity by employing short sequences, termed spacers, that guide Cas proteins to cleave foreign DNA 1,2 . Class 2 CRISPR-Cas systems are streamlined versions in which a single Cas protein bound to RNA recognizes and cleaves targeted sequences 3,4 . The programmable nature of these minimal systems has enabled their repurposing as a versatile technology that is broadly revolutionizing biological and clinical research 5 . However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving untapped the vast majority of enzymes from organisms that have not been cultured. Metagenomics, the sequencing of DNA extracted from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms 6,7 . Here, using genome-resolved metagenomics, we identified novel CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life. This divergent Cas9 protein was found in littlestudied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two

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“…Additionally, a small RNA referred as tracrRNA (trans-activating CRISPR RNA), which is located upstream of the CRISPR array and complementary to the repeat region of pre-CRISPR RNA plays an important role in crRNA maturation. In addition, it is essential for crRNA mediated DNA recognition and Cas9 mediated targeting in vitro, even for crRNAs that bypass processing (Jinek et al, 2012;Zhang et al, 2013). Cas9 promotes the base pairing between the tracrRNA and the repeat sequence of the pre-crRNA, which then becomes a substrate for double strand specific RNase III (Fig.…”

Section: Type II Crispr Systemmentioning

confidence: 99%

“…However, in case of leaderless CRISPR array as in Neisseria strains (type II-C), the new spacer integration seems to occur et al, 2013). In such CRISPR arrays, transcription may occur from the promoters proximal to CRISPR array (Lillestol et al, 2006; Lillestol et al, 2009;Zhang et al, 2013).The CRISPR-Cas system shows high diversity owing to the dynamic evolution of CRISPR locus, involving numerous rearrangements and horizontal transfer of complete or individual modules and therefore this precludes a simple phylogenetic classification. Recent classification schemes of CRISPR-Cas systems that evolved over the years combine the analysis of signature protein families, features of the architecture of cas loci and the information of the effector modules involved in interference and categorize them into two distinct classes, six types and nineteen subtypes (Haft et al, 2005; Makarova et al, 2006; Makarova et al, 2017a; Makarova et al, 2017b;Shmakov et al, 2017).…”

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confidence: 99%

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Cutting it Right: Plasticity and Strategy of CRISPR RNA Specific Nucleases

Punetha

Yoganand

Nimkar

et al. 2017

Proceedings of the Indian National Science Academy

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The existence of adaptive immunity in prokaryotes came to light with the discovery of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) in association with CRISPR-associated (Cas) proteins. This RNA mediated defence system confers resistance against the invading mobile genetic elements such as phages and plasmids. The CRISPR-Cas system operates by forming a ribonucleoprotein complex that comprises of an invader derived small RNA and Cas protein(s). Herein the small RNA acts as a guide to recognize the nucleic acid target whereas the Cas proteins facilitate target annihilation. Given the cardinal role adopted by this small RNA, its maturation from the pre-CRISPR transcript forms a pivot for successful adaptive immunity. The mandate to generate the guide CRISPR RNA (crRNA) is fulfilled by specific endoribonuclease, which processes the pre-crRNA transcript in between the repeats to liberate the individual interfering units. Intriguingly, while some endoRNases of the CRISPR system are able to process the pre-crRNA independently, others require participation of additional Cas proteins, which form a multi-protein complex for processing the pre-crRNA. Additionally, some CRISPR variants require non-Cas auxiliary factors to process the pre-crRNA. The mode of crRNA maturation further diversifies as the endoRNases in CRISPR variants coevolve with repeat clusters that exhibit high diversity in sequence and folding. Therefore, the maturation of a specific crRNA requires a distinct mechanistic solution for substrate discrimination by these endoRNases, the understanding of which is essential for appreciating the CRISPR biology. This review highlights the vivid modes adopted by the diverse CRISPR-Cas systems to generate the mature crRNA. Keywords: CRISPR RNA; CRISPR-Cas IntroductionIn order to survive, all organisms must overcome their predators. The prokaryotes and their viral predators coexist in natural and man-made environment and therefore the prokaryotes face a constant threat of getting infected by phages. This results in acute pressure on the microbial community to coevolve with their predators causing an evolutionary arms race between prey and predator. Pitted against a hostile environment, prokaryotes have developed multilayered antiviral defense systems, which act at various stages of the infection cycle of the invader. These include various innate defense systems like surface exclusion (receptor downregulation or masking), super infection exclusion (Sie systems), restrictionmodification systems (R-M and R-M like systems), and abortive infection systems (Abi) (Hyman and Abedon, 2010; Labrie et al., 2010;Westra et al., 2012a). These innate defense mechanisms are diffusive in nature and do not rely on the identity of the predator to elicit a response (Fig 1). Added to this repertoire of arsenals, the recently discovered Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) in association with CRISPRassociated (Cas) proteins endows the bacteria and archaea with an adaptive immunity (Ja...

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Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitidis

Cited by 257 publications

References 87 publications

Novel configurations of type I and II CRISPR–Cas systems in Corynebacterium diphtheriae

Novel configurations of type I and II CRISPR–Cas systems in Corynebacterium diphtheriae

New CRISPR–Cas systems from uncultivated microbes

Cutting it Right: Plasticity and Strategy of CRISPR RNA Specific Nucleases

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