A nuclear tRNA-derived fragment triggers immunity in Arabidopsis.

In Arabidopsis, effector-triggered immunity (ETI) against avirulent Pseudomonas syringae pv. tomato (Pst) correlates with the rapid, Dicer-Like 1 (DCL1)-dependent nuclear accumulation of a 31-nt 5'-tRNA fragment derived from Asp-tRNA (tRF). Several tRFs, including tRF, are induced at early stages of infection and associate with AGO2 in the nucleus. Infiltrating Arabidopsis leaves with synthetic tRF induces over 500 defense-associated genes, conferring immunity against virulent and avirulent Pst as well as aphids, while tRF depletion compromises resistance to avirulent Pst. The biological activity of tRF requires its 5' sequence and predicted stem-loop structure, and its loading into AGO2 or related clade members may contribute to activating defense responses. Chromatin affinity precipitation-sequencing revealed that tRF binds specific sequences in defense genes and the Gypsy superfamily of LTR retrotransposons, particularly at their primer binding sites (PBS). tRF binding appears to modulate transcriptional reprogramming, inducing neighboring tRF-responsive defense genes while suppressing active retrotransposons. Since Gypsy retrotransposon proliferation is primed by tRNA binding at PBS, tRF may exploit a similar mechanism to coordinate defense responses. Together, these findings reveal a role for DCL1 and tRF in regulating plant immunity and transcriptional dynamics at defense-associated loci and retrotransposons.