CRISPR-Cas, Anti-CRISPRs, and Antiviral Defense in Archaea

CRISPR-Cas systems are widespread and diverse in archaea, where they constitute important components of antiviral defense. Archaeal genomes frequently encode CRISPR-Cas systems, particularly Type I and Type III systems, and archaeal viruses display distinctive morphologies, genomes, and replication strategies, including those of Sulfolobus spindle-shaped viruses, rudiviruses, and haloarchaeal pleomorphic viruses. These features make archaeal virus–host systems valuable models for investigating the co-evolutionary arms race between adaptive immunity and viral counterdefense. Although anti-CRISPR (Acr) proteins are increasingly recognized as major modulators of CRISPR-Cas immunity, their diversity, mechanisms, distribution, and ecological relevance in archaeal systems remain poorly understood. In particular, the roles of Acrs and other antiviral defense mechanisms in extreme and non-extreme environments, including hypersaline lakes, acidic hot springs, hydrothermal systems, and deep-sea habitats, require further investigation. Recent advances in archaeal genomics, metagenomics, structural biology, and experimental virology are creating new opportunities to identify defense systems and their inhibitors. However, knowledge remains fragmented across individual model organisms and methodological disciplines, limiting broader understanding of archaeal immunity and virus–host co-evolution.This Research Topic aims to advance understanding of CRISPR-Cas immunity, anti-CRISPR mechanisms, and complementary antiviral defenses in archaea. It will examine how archaeal CRISPR-Cas systems acquire and use immune memory, how archaeal viruses and mobile genetic elements evade or inhibit host defenses, and how these interactions shape the evolution, ecology, and diversification of archaeal populations and their viruses. Contributions may address the mechanisms and regulation of CRISPR-Cas interference, adaptation, and crRNA biogenesis; the discovery and characterization of Acr proteins and anti-CRISPR-associated regulators; and interactions between CRISPR-Cas systems and other defense pathways. The Research Topic will also consider whether archaeal systems support distinctive principles of immune regulation and viral counterdefense that extend or challenge current models developed from bacterial systems.To gather further insights into archaeal CRISPR-Cas immunity, anti-CRISPR mechanisms, and antiviral defense across cultured and uncultured archaeal lineages and their viruses, we welcome articles addressing, but not limited to, the following themes:· Diversity, classification, evolution, and distribution of CRISPR-Cas systems in archaea· Structural and biochemical mechanisms of CRISPR-Cas interference, adaptation, and crRNA biogenesis· Discovery and mechanistic characterization of anti-CRISPR proteins and anti-CRISPR-associated regulators· Anti-CRISPRs encoded by archaeal viruses, plasmids, and other mobile genetic elements· Comparative analyses of archaeal and bacterial CRISPR-Cas and Acr systems· Co-evolutionary dynamics and virus–host arms races in archaeal ecosystems· Interactions between CRISPR-Cas and restriction-modification, toxin–antitoxin, Argonaute-based, and other antiviral defense systems· Ecological and environmental dimensions of archaeal immunity in diverse extreme and mainstream habitats· Bioinformatic and metagenomic approaches for identifying CRISPR arrays, spacers, defense systems, and Acr candidates · Identification and characterization of archaeal toxin-antitoxins systems and their role in stress response and immunity· Biotechnological applications of archaeal CRISPR-Cas systems and Acr proteins, including genome engineering and biocontainmentTopic Editors Kira Makarova declares she holds patents on CRISPR-Cas systems, and Ming Li declares he holds patents related to CRISPR-Cas systems as well as gene editing. All other Topic Editors declare no competing interests with regards to the Research Topic subject. Topic editors: Kira Makarova, Ming Li, Jonathan Strecker, Xu Peng Source: https://www.frontiersin.org/research-topics/85171/crispr-cas-anti-crisprs-and-antiviral-defense-in-archaea