The functions of a 5′ tRNA-Ala-derived fragment in gene expression

Abstract

Transfer RNA (tRNA) can produce smaller RNA fragments called tRNA-derived fragments (tRFs). tRFs play critical roles in multiple cellular programs, although the functional mechanisms of tRFs remain largely unknown in plants. In this study, we examined the phenotype associated with 5′ tRF-Ala (tRF-Ala, produced from tRNA-Ala) overexpression and knockdown lines (tDR-Ala-OE and tDR-Ala-kd, respectively) and the mechanisms by which tRF-Ala affects mRNA levels in Arabidopsis (Arabidopsis thaliana). We investigated the candidate proteins associated with tRF-Ala by quantitative proteomics and confirmed the direct interaction between tRF-Ala and the splicing factor SERINE-ARGININE RICH PROTEIN 34 (SR34). A transcriptome sequencing analysis showed that 318 genes among all the genes (786) with substantial alternative splicing (AS) variance in tDR-Ala-OE lines are targets of SR34. tRF-Ala diminished the binding affinity between SR34 and its targets by direct competition for interaction with SR34. These findings reveal the critical roles of tRF-Ala in regulating mRNA levels and splicing.

Transfer RNA and ribosomal RNA fragments – emerging players in plant–microbe interactions

“…A more comprehensive study later revealed that only a subset of the Arabidopsis tRFs can interfere with translation (Lalande et al ., 2020). Based on A. thaliana overexpression and knockdown lines, a recent paper reported that the 5′‐tRF Ala‐TGC associates with a splicing factor (SR34), resulting in a set of genes with altered transcript levels and differentially spliced transcript variants (Li et al ., 2023). The latter work might point at additional, presently understudied roles for tRFs in the context of plant biology.…”

Stress-induced tRNA fragments take action in alternative splicing in Arabidopsis

“…B) Stress-induced tDR-Ala-5D plays roles in regulating mRNA splicing and protein translation. Li et al (2023) show that tDR-Ala-5D interacts with the splicing factor SR34 and interferes with precursor mRNA alternative splicing of crucial genes associated with stress responses. A previous work by Ivanov et al (2011) demonstrated that tDR-Ala-5D also binds to the translation initiation complex eIF4F, which results in attenuated protein synthesis in response to stress.…”

“…Progress in this field has brought exciting changes to the paradigm of RNA world. In this issue of Plant Physiology , Li et al (2023) found new functions of a plant tDR in stress responses via interacting with the mRNA splicing factor SERINE-ARGININE RICH PROTEIN 34 (SR34).…”

“…Small RNAs derived from the 5ʹ fragment of tRNA Ala (tDR-Ala-5D), which show increased accumulation in response to biotic and abiotic stresses, have been extensively studied ( Cognat et al 2017 ; Gu et al 2022 ). Li et al (2023) found that a tDR-Ala-5D (with a standard name of tDR-1:20-Ala-CGC-1-M2 in the consensus nomenclature, hereafter tDR-Ala-5D for short) showed increased accumulation in Arabidopsis in response to toxic arsenite. Overexpression of tDR-Ala-5D resulted in an increased sensitivity to abscisic acid (ABA) and NaCl stresses.…”

“…Thus, the changes in the sensitivity to ABA and NaCl stresses likely resulted from the difference in tDR-Ala-5D abundance. To investigate how tDR-Ala-5D is involved in the regulation of stress resistance, Li et al (2023) identified proteins interacting with tDR-Ala-5D using the RNA interactome capture technology. The biotin-labeled tDR-Ala-5D was incubated with total proteins extracted from Arabidopsis seedlings.…”