ArticleFrontiers in genetics2014
CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems.
Article in Frontiers in genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 131 papers.
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Who cites it
131 citing papers in PubMed, 198 citations in OpenAlex.
- MtvS1 and MtvS2 Interact with RNA polymerase to regulate the Francisella type V-A CRISPR-Cas system.Nature communications · 2026Article
- Transcription activation mechanism of a noncanonical DNA damage response pathway by the WYL-activator, DriD.Science advances · 2026Article
- Structural and functional insights into the adenosine deaminase of the type III-B CRISPR-Cas system.Nucleic acids research · 2026Article
- Functional characterization of a type I-F1 CRISPR-cas system from the clinical isolate Shewanella xiamenensis Sh95 reveals constitutive activity and plasmid-curing capability.Scientific reports · 2026Article
- Expanding the landscape of BREX diversity: uncovering multi-layered functional frameworks and identification of novel BREX-related defense systems.Nucleic acids research · 2026Article
- The twist-and-squeeze activation of CARF-fused adenosine deaminase by cyclic oligoadenylates.The EMBO journal · 2025Article
- Heterogeneity in responses to ribosome-targeting antibiotics mediated by bacterial RNA repair.Nature communications · 2025Article
- YprA family helicases provide the missing link between diverse prokaryotic immune systems.bioRxiv : the preprint server for biology · 2025Article
- Defence systems encoded by core genomic islands of seventh pandemicPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- An activator regulates the DNA damage response and anti-phage defense networks in Moraxellaceae.Nucleic acids research · 2025Article
- Allosteric activation mechanism of DriD, a WYL-domain containing transcription regulator.Communications biology · 2025Article
- Structure-guided insights into TIR-mediated bacterial and eukaryotic immunity.Structure (London, England : 1993) · 2025Review
- A WYL domain transcription factor regulates Lactiplantibacillus plantarum intestinal colonization via perceiving c-di-GMP.Nature communications · 2025Article
- Single-stranded DNA binding to the transcription factor PafBC triggers the mycobacterial DNA damage response.Science advances · 2025Article
- Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems.Nucleic acids research · 2025Article
- The CRISPR-associated adenosine deaminase Cad1 converts ATP to ITP to provide antiviral immunity.Cell · 2024Article
- Bacterial WYL domain transcriptional repressors sense single-stranded DNA to control gene expression.Nucleic acids research · 2024Article
- Article
- The SAVED domain of the type III CRISPR protease CalpL is a ring nuclease.Nucleic acids research · 2024Article
- Bioinformatic analysis of type III CRISPR systems reveals key properties and new effector families.Nucleic acids research · 2024Article
71 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
CRISPR-Cas adaptive immunity systems of bacteria and archaea insert fragments of virus or plasmid DNA as spacer sequences into CRISPR repeat loci. Processed transcripts encompassing these spacers guide the cleavage of the cognate foreign DNA or RNA. Most CRISPR-Cas loci, in addition to recognized cas genes, also include genes that are not directly implicated in spacer acquisition, CRISPR transcript processing or interference. Here we comprehensively analyze sequences, structures and genomic neighborhoods of one of the most widespread groups of such genes that encode proteins containing a predicted nucleotide-binding domain with a Rossmann-like fold, which we denote CARF (CRISPR-associated Rossmann fold). Several CARF protein structures have been determined but functional characterization of these proteins is lacking. The CARF domain is most frequently combined with a C-terminal winged helix-turn-helix DNA-binding domain and "effector" domains most of which are predicted to possess DNase or RNase activity. Divergent CARF domains are also found in RtcR proteins, sigma-54 dependent regulators of the rtc RNA repair operon. CARF genes frequently co-occur with those coding for proteins containing the WYL domain with the Sm-like SH3 β-barrel fold, which is also predicted to bind ligands. CRISPR-Cas and possibly other defense systems are predicted to be transcriptionally regulated by multiple ligand-binding proteins containing WYL and CARF domains which sense modified nucleotides and nucleotide derivatives generated during virus infection. We hypothesize that CARF domains also transmit the signal from the bound ligand to the fused effector domains which attack either alien or self nucleic acids, resulting, respectively, in immunity complementing the CRISPR-Cas action or in dormancy/programmed cell death.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.