tRNA-derived second messengers confer bacterial immunity

Valentin-Alvarado, L. E.; Yoon, P. H.; Lopez, S. C.; Shulgina, Y.; Langeberg, C.; Armbruster, E.; Ur-Rehman, M. M.; Loi, K.; Taveneau, C.; Esain-Garcia, I.; Koka, M.; Zhang, Z. T.; Kashin, D.; Schwede, F.; Burgio, G.; OConnell, M. R.; Doherty, E. E.; Cate, J. H. D.; Knott, G. J.; Doudna, J. A.

doi:10.64898/2026.10.06.756102

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bioRxiv · 10.64898/2026.10.06.756102

tRNA-derived second messengers confer bacterial immunity

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Abstract

Bacterial small-molecule messengers that function in diverse immune signaling pathways have been thought to derive strictly from biosynthesis using nucleotide and cofactor substrates. Here we report a nuclease-driven immune signaling pathway in which tRNA cleavage generates a specific small molecule that triggers cell death in response to RNA-guided transcript recognition in prokaryotes. We identify a class of type VI-B CRISPR systems in which the RNA-guided nuclease Cas13 and its accessory transmembrane protein, 2TM{beta}, are co-encoded in an operon and are jointly required for bacteriophage defense. Upon target RNA recognition, Cas13 activates 2TM{beta} by producing mono- and dinucleotide messengers bearing 2',3'-cyclic uridine phosphate ends by tRNA cleavage. Activated 2TM{beta} destroys infected cells by forming a multimeric complex that disrupts cell membranes to mediate cell death. These findings demonstrate RNA-programmed tRNA cleavage for second-messenger biogenesis, revealing a new logic for prokaryotic immune signaling.

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Valentin-Alvarado, L. E., Yoon, P. H., Lopez, S. C., Shulgina, Y., Langeberg, C., Armbruster, E., Ur-Rehman, M. M., Loi, K., Taveneau, C., Esain-Garcia, I., Koka, M., Zhang, Z. T., Kashin, D., Schwede, F., Burgio, G., OConnell, M. R., Doherty, E. E., Cate, J. H. D., Knott, G. J., Doudna, J. A.. 2026-10-09. tRNA-derived second messengers confer bacterial immunity. https://doi.org/10.64898/2026.10.06.756102

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