ArticleRNA biology2019
Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families.
Article in RNA biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- Structural mechanism of SAM-AMP and SAM-AMPNature communications · 2026Article
- Extremophile survives the transient pressures associated with impact-induced ejection from Mars.PNAS nexus · 2026Article
- A synthetic system for RNA-responsive pyroptosis based on type III-E CRISPR nuclease-protease.Nature communications · 2026Article
- Structural plasticity enables broad cAn binding and dual activation of CRISPR-associated ribonuclease Cdn1.Nucleic acids research · 2026Article
- Comprehensive analysis of CRISPR array repeat mutations reveals subtype-specific patterns and links to spacer dynamics.microLife · 2026Article
- Diversity and abundance of ring nucleases in type III CRISPR-Cas loci.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.Nucleic acids research · 2025Article
- Adaptive immunity of type VI CRISPR-Cas systems associated with reverse transcriptase-Cas1 fusion proteins.Nucleic acids research · 2024Article
- Design, potential and limitations of conjugation-based antibacterial strategies.Microbial biotechnology · 2024Review
- Bioinformatic analysis of type III CRISPR systems reveals key properties and new effector families.Nucleic acids research · 2024Article
- Regulatory sequence-based discovery of anti-defense genes in archaeal viruses.Nature communications · 2024Article
- CRISPR antiphage defence mediated by the cyclic nucleotide-binding membrane protein Csx23.Nucleic acids research · 2024Article
- Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2.Nucleic acids research · 2024Article
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- Corneal gene therapy: Structural and mechanistic understanding.The ocular surface · 2023Article
- Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering.Microbial biotechnology · 2023Article
- Expanding known viral diversity in the healthy infant gut.Nature microbiology · 2023Article
- Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems.Science advances · 2023Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A study was undertaken to identify conserved proteins that are encoded adjacent to cas gene cassettes of Type III CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats - CRISPR associated) interference modules. Type III modules have been shown to target and degrade dsDNA, ssDNA and ssRNA and are frequently intertwined with cofunctional accessory genes, including genes encoding CRISPR-associated Rossman Fold (CARF) domains. Using a comparative genomics approach, and defining a Type III association score accounting for coevolution and specificity of flanking genes, we identified and classified 39 new Type III associated gene families. Most archaeal and bacterial Type III modules were seen to be flanked by several accessory genes, around half of which did not encode CARF domains and remain of unknown function. Northern blotting and interference assays in Synechocystis confirmed that one particular non-CARF accessory protein family was involved in crRNA maturation. Non-CARF accessory genes were generally diverse, encoding nuclease, helicase, protease, ATPase, transporter and transmembrane domains with some encoding no known domains. We infer that additional families of non-CARF accessory proteins remain to be found. The method employed is scalable for potential application to metagenomic data once automated pipelines for annotation of CRISPR-Cas systems have been developed. All accessory genes found in this study are presented online in a readily accessible and searchable format for researchers to audit their model organism of choice: http://accessory.crispr.dk .
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