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Cas9 senses CRISPR RNA abundance to regulate CRISPR spacer acquisition

ABSTRACT: Cas9 senses CRISPR RNA abundance to regulate CRISPR spacer acquisition

PROVIDER: PRJNA1288505 | ENA |

REPOSITORIES: ENA

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Cas9 senses CRISPR RNA abundance to regulate CRISPR spacer acquisition

Project description:Cas9 senses CRISPR RNA abundance to regulate CRISPR spacer acquisition

| PRJNA1029893 | ENA

Cas9 senses CRISPR RNA abundance to regulate CRISPR spacer acquisition

Project description:Prokaryotes create adaptive immune memories by acquiring foreign DNA snippets, known as spacers, into the CRISPR array1. In type II CRISPR-Cas systems, the RNA-guided effector Cas9 also assists the acquisition machinery by selecting spacers from protospacer adjacent motif (PAM)-flanked DNA2,3. Here, we uncover the first biological role for Cas9 that is independent of its dual RNA partners. Following depletion of crRNA and/or tracrRNA, Neisseria apoCas9 stimulates spacer acquisition efficiency. Physiologically, Cas9 senses low levels of crRNA in cells with short CRISPR arrays – such as those undergoing array neogenesis or natural array contractions – and dynamically upregulates acquisition to quickly expand the small immune memory banks. As the CRISPR array expands, rising crRNA abundance in turn reduces apoCas9 availability, thereby dampening acquisition to mitigate autoimmunity risks associate with elevated acquisition. While apoCas9’s nuclease lobe alone suffices for stimulating acquisition, only full-length Cas9 responses to crRNA levels to boost acquisition in cells with low immunity depth. Finally, we show that this activity is evolutionarily conserved across multiple type II-C Cas9 orthologs. Altogether, we establish an auto-replenishing feedback mechanism in which apoCas9 safeguards CRISPR immunity depth by acting as both a crRNA sensor and a regulator of spacer acquisition.

2025-08-29 | GSE302092 | GEO

Continuous CRISPR spacer acquisition in STSV2-infected crenarchaeon Sulfolobus islandicus REY15A over a 6-day period

Project description:A whole transcriptome study was performed on Sulfolobus islandicus REY15A actively undergoing CRISPR spacer acquisition from the crenarchaeal monocaudavirus STSV2 in rich (TYS) and basal (SCV) media over a 6 day period. Spacer acquisition preceded strong host growth retardation, and changes in viral transcript abundance and virus copy numbers showed significant differences between the two media. Results showed that rich medium favoured CRISPR-Cas immunity generation.

2015-12-06 | E-MTAB-4027 | biostudies-arrayexpress

Cas9 senses CRISPR RNA abundance to regulate CRISPR spacer acquisition

Project description:Prokaryotes adapt to viral challenges by acquiring CRISPR memories from invaders through a process called adaptation. Previous study showed that this process requires Cas9 complexed with its RNA partners in type II-A system. How Cas9 functions in adaptation in other type II systems is poorly understood. Here using type II-C system of N. meningitidis and meningococcal disease associated filamentous phage MDAΦ as model, we show that RNA free apoCas9 dramatically enhances adaptation efficiency and that tracrRNA and crRNA together repress rather than enhance adaptation through interacting with Cas9. We also discovered that a Cas9 lacking the recognition lobe can no longer be suppressed by its RNA partners. We demonstrate how this interplay between Cas9 and its RNA partners benefit the host bacteria by regulating adaptation during CRISPR neo-genesis and CRISPR array collapse. We further show that this regulation is a conserved process in type II-C systems. Our results uncover a brand-new adaptation regulation mechanism and demonstrate the first biological function of RNA-free apoCas9.

2025-10-29 | GSE245754 | GEO

Type V-A Spacer Acquisition

Project description:Spacer Acquisition Type V-A CRISPR-Cas system Francisella novicida

| PRJEB34159 | ENA

Spacer acquisition by CRISPR-Cas type I-G

Project description:MiSeq analysis of spacer acquisition by a Gsu type I-G CRISPR system

| PRJEB41616 | ENA

Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas

Project description:Key to CRISPR-Cas adaptive immunity is maintaining an ongoing record of invading nucleic acids that are encountered, a process carried out by the Cas1-Cas2 complex that integrates short segments of foreign genetic material (spacers) into the CRISPR locus. It is hypothesized that Cas1 evolved from casposases, a novel class of transposases. We show here that casposase integration in vitro recapitulates several properties of CRISPR-Cas integrases. The X-ray structure of Methanosarcina mazei casposase bound to DNA representing the product of integration reveals a tetramer with target DNA bound snugly between two dimers in which single-stranded casposon end binding resembles that of spacer 3'-overhangs. The differences between transposase and CRISPR-Cas integrase are largely architectural, and it appears that evolutionary change involved changes in protein-protein interactions to favor Cas2 binding over tetramerization and the separation of Cas1 dimers. This, in turn, led to preferred integration of single spacers over two transposon ends.

2020-02-03 | GSE139037 | GEO

Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas

Project description:Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas

| PRJNA578121 | ENA

Continuous CRISPR spacer acquisition in STSV2-infected crenarchaeon Sulfolobus islandicus REY15A over a 6-day period

Project description:Continuous CRISPR spacer acquisition in STSV2-infected crenarchaeon Sulfolobus islandicus REY15A over a 6-day period

| PRJEB11888 | ENA

Legionella pneumophila subsp. pneumophila strain:Toronto-2005

Project description:CRISPR spacer acquisition under priming

| PRJNA360289 | ENA