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Structure paper

TitleRNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity.
Journal, issue, pagesNature, Vol. 649, Issue 8099, Page 1312-1321, Year 2026
Publish dateJan 7, 2026
AuthorsOleg Dmytrenko / Biao Yuan / Kadin T Crosby / Max Krebel / Xiye Chen / Jakub S Nowak / Andrzej Chramiec-Głąbik / Bamidele Filani / Anne-Sophie Gribling-Burrer / Wiep van der Toorn / Max von Kleist / Tatjana Achmedov / Redmond P Smyth / Sebastian Glatt / Jack P K Bravo / Dirk W Heinz / Ryan N Jackson / Chase L Beisel /
PubMed AbstractIn all domains of life, tRNAs mediate the transfer of genetic information from mRNAs to proteins. As their depletion suppresses translation and, consequently, viral replication, tRNAs represent long- ...In all domains of life, tRNAs mediate the transfer of genetic information from mRNAs to proteins. As their depletion suppresses translation and, consequently, viral replication, tRNAs represent long-standing and increasingly recognized targets of innate immunity. Here we report Cas12a3 effector nucleases from type V CRISPR-Cas adaptive immune systems in bacteria that preferentially cleave tRNAs after recognition of target RNA. Cas12a3 orthologues belong to one of two previously unreported nuclease clades that exhibit RNA-mediated cleavage of non-target RNA, and are distinct from all other known type V systems. Through cell-based and biochemical assays and direct RNA sequencing, we demonstrate that recognition of a complementary target RNA by the CRISPR RNA triggers Cas12a3 to cleave the conserved 5'-CCA-3' tail of diverse tRNAs to drive growth arrest and anti-phage defence. Cryogenic electron microscopy structures further revealed a distinct tRNA-loading domain that positions the tRNA tail in the RuvC active site of the nuclease. By designing synthetic reporters that mimic the tRNA acceptor stem and tail, we expanded the capacity of current CRISPR-based diagnostics for multiplexed RNA detection. Overall, these findings reveal widespread tRNA inactivation as a previously unrecognized CRISPR-based immune strategy that broadens the application space of the existing CRISPR toolbox.
External linksNature / PubMed:41501459 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 4.0 Å
Structure data

52275

9hlx

EMDB-52275, PDB-9hlx:
Structure of Ba1Cas12a3 binary complex
Method: EM (single particle) / Resolution: 3.8 Å

52285

9hm4

EMDB-52285, PDB-9hm4:
Structure of tRNA bound Ba1Cas12a3
Method: EM (single particle) / Resolution: 3.2 Å

52286

9hm5

EMDB-52286, PDB-9hm5:
Structure of cleaved tRNA fragment bound Ba1Cas12a3
Method: EM (single particle) / Resolution: 3.3 Å

52287

9hm6

EMDB-52287, PDB-9hm6:
Structure of Ba1Cas12a3 ternary complex
Method: EM (single particle) / Resolution: 4.0 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • bacteroidetes bacterium hgw-bacteroidetes-12 (bacteria)
  • bacteroidota bacterium (bacteria)
  • synthetic construct (others)
  • escherichia coli (E. coli)
KeywordsRNA BINDING PROTEIN / crispar-cas nuclease / crispar cas nuclease

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