Structure of a membrane anti-sigma-ECF sigma protein complex yields molecular details into how a bacterium tightly controls expression of a CBASS-CRISPR-Cas defense island that forms part of its antiviral arsenal.

Antiviral adaptive immune CRISPR-Cas systems and innate immune CBASS (cyclic oligonucleotide–based antiphage signaling systems) are widespread in bacteria. How the two systems are controlled and coordinately deployed against an invading virus remains poorly understood. Previously, we described a novel mechanism directed by a transmembrane anti-σ (DdvA) and its cognate extracytoplasmic function (ECF) sigma factor (DdvS) to control a genomic defense island comprising two CBASS and a type III-B CRISPR-Cas system in the soil bacterium Myxococcus xanthus. We have now determined the structure of the DdvA-DdvS complex, the first of a full-length transmembrane anti-sigma bound to its ECF sigma partner and the first of an anti-sigma with a large TPR-CHAT (caspase HetF–associated with TPR) periplasmic domain, using cryo-electron microscopy and nuclear magnetic resonance spectroscopy. This structural study, combined with various other techniques in vivo and in vitro, yields structural and mechanistic insights into how a transmembrane protein complex orchestrates the concerted regulation of a CBASS and CRISPR-Cas defense island in antiviral defense. This study is a fruitful collaboration led by Professors S. Padmanabhan/Padhu (Institute of Physical Chemistry Blas Cabrera; IQF-CSIC), Montserrat Elías Arnanz (University of Murcia/UMU; IQF-CSIC Associated Unit), Iban Ubarretxena-Belandia and Dr. Igor Tascón (Instituto Biofisika/UPV/EHU-CSIC and Ikerbasque) with team members Drs. Diego Bernal Bernal (UMU and Instituto Biofisika), David Pantoja Uceda (IQF-CSIC), Jorge Pedro López Alonso (Instituto Biofisika), Borja Ochoa-Lizarralde (Instituto Biofisika) and Marisa Galbis Martínez (UMU), and doctoral students Alfonso López Rojo (UMU) and José Antonio López Ruiz (UMU). It is published in Science Advances, 25 Oct 2024, Vol 10, Issue 43, DOI: 10.1126/sciadv.adp1053