Structural basis for regulation of a CBASS-CRISPR-Cas defense island by a transmembrane anti-σ factor and its ECF σ partner

Abstract

17 pags., 8 figs.How CRISPR-Cas and cyclic oligonucleotide-based antiphage signaling systems (CBASS) are coordinately deployed against invaders remains unclear. We show that a locus containing two CBASS and one type III-B CRISPR-Cas system, regulated by the transmembrane anti-σ DdvA and its cognate extracytoplasmic function (ECF) σ DdvS, can defend Myxococcus xanthus against a phage. Cryo-electron microscopy reveals DdvA-DdvS pairs assemble as arrow-shaped transmembrane dimers. Each DdvA periplasmic domain adopts a separase/craspase-type tetratricopeptide repeat (TPR)-caspase HetF-associated with TPR (TPR-CHAT) architecture with an incomplete His-Cys active site, lacking three α-helices conserved among CHAT domains. Each active site faces the dimer interface, raising the possibility that signal-induced caspase-like DdvA autoproteolysis in trans precedes RseP-mediated intramembrane proteolysis and DdvS release. Nuclear magnetic resonance reveals a DdvA cytoplasmic CHCC-type zinc-bound three-helix bundle that binds to DdvS σ2 and σ4 domains, undergoing σ4-induced helix extension to trap DdvS. Altogether, we provide structural-mechanistic insights into membrane anti-σ-ECF σ regulation of an antiviral CBASS-CRISPR-Cas defense island.this work was supported by grants Pid2021- 123336nB- c21 (to M.e.- A.), Pid2021- 123336nB- c22 (to S.P.), Pid2020- 112821GB- i00 (to d.P.- U.), and Pid2019- 104423GB- i00 and Pid2022- 143177nB- i00 (to i.U.- B.) funded by the Ministerio de ciencia e innovación (Mcin)/Agencia estatal de investigación (Aei)- Spain (Mcin/Aei/10.13039/ 501100011033) and the “eRdF A way of making europe”; grant 21939/Pi/22 (to M.e.- A.) funded by Fundación Séneca- Murcia (Spain); Ph.d. fellowships from the Ministerio de Universidades- Spain (to A.l.- R.), and Mcin- Aei to J.A.l.- R. i.t. is an ikerbasque Research Fellow (Basque Foundation for Science- Spain). J.P.l.- A. holds a PtA contract granted by Mcin/Aei. d.B.- B. was supported by the Plan de Recuperación, transformación y Resiliencia (PRtR) funded by the nextGenerationeU (PRtR- c17.i1) program. cryo- eM was performed at the Basque Resource for electron Microscopy located at instituto Biofisika (UPv/ ehU, cSic), supported primarily by the department of education and the innovation Fund of the Basque Government, with additional support from Fundación Biofísica Bizkaia and Mcin with funding from european Union nextGenerationeU (PRtR- c17.i1).Peer reviewe