FERONIA-Dependent Translational Buffering of Ribosome-Associated Genes in Salt-Stressed Tomato Roots

Abstract

Salt stress limits tomato productivity, yet how translational regulation contributes to root salt adaptation remains poorly understood. We integrated RNA-seq and ribosome profiling in wild-type (WT) and fer tomato roots under control and 150 mM NaCl conditions. In WT roots, the salt response was predominantly transcript-driven, but a 29-gene ribosome-associated module showed reduced RNA abundance alongside increased translational efficiency (TE), indicating selective translational buffering. FER deficiency disrupted this balance: it constitutively elevated ribosome occupancy of ribosome-associated genes while reducing basal expression of stress- and ion-transport-related genes. Under salt treatment, fer further showed stronger ion-transport transcriptional responses but weaker ribosome-associated TE responses, consistent with impaired translational selectivity. WT salt stress also shifted ribosome allocation away from the 5'UTR toward the CDS, an effect attenuated in fer; upstream open reading frame (uORF) and coding sequence (CDS) translational efficiency were also positively coupled during salt treatment. Feature modelling confirmed established features associated with uORF translation and further identified weaker local RNA folding around the uORF start codon, proline and charged amino acid enrichment, and TAG or TGA stop codon identity as positive predictors. Together, these results reveal FER-dependent changes in ribosome-associated translational buffering during tomato root salt responses.