tRNA-seq of Arabidopsis leaves during pattern-triggered immunity

During pattern-triggered immunity (PTI), the first line of active defense against infection in plants, the translatome undergoes rapid reprogamming. To understand how defense proteins are selectively translated, we conducted a genetic screen for regulators of PTI using a translational reporter. We identified a mutant of RNA helicase 12 (RH12) showing compromised reporter translation and pathogen resistance. RH12 is a homolog of yeast DEAD-box Helicase Homolog 1, which targets mRNAs with low codon optimality for decay. Therefore, we sequenced the Arabidopsis tRNAome to determine codon optimality during PTI. We discovered a PTI-associated reduction in overall codon optimality of the transcriptome, and found that the decay of transcripts with reduced optimality is mediated by interaction with RH12. Our results demonstrate the first example of codon optimality-associated decay as part of an adaptive response in which the dynamics of both the tRNAome and the transcriptome facilitate rapid changes in translational output during PTI. profiling of tRNA from 3 reps of mock and elf18 treated samples