Abiotic Stress-Mediated Modulation of the tncRNome: Unraveling tRNA-Derived RNA Networks in Plant Adaptive Responses

Abstract

Transfer RNA-derived non-coding RNAs (tncRNAs) are potential regulators of gene expression in plants, and its crucial to understand their diversity and functional roles in modulating plant stress responses. Here, we have investigated abiotic stress-responsive tncRNAs in two important crops, rice and chickpea, under drought and salt stress conditions. Small RNA sequencing revealed that 70.2% of tncRNAs in rice and 45% in chickpea were commonly expressed across multiple stress conditions. qRT-PCR validation showed that most tRF-5s were upregulated in both rice and chickpea under drought and salt stress. In rice, 3'tRHs were specifically induced by drought, whereas 5'tRHs responded predominantly to salt stress. In chickpea, tRF-3s were upregulated during drought but downregulated under salt stress. Furthermore, we confirmed the mRNA targets of these stress-associated tRNA fragments using RLM-RACE, thereby verifying the cleavage of specific target mRNAs in both species. Expression profiling of target genes revealed a negative association with their corresponding tRFs in both species. Subcellular localization demonstrated that OsGEM and OsPPR were primarily localized in the nucleus, while CaMIZ1 and CaSKP1 were detected at the plasma membrane. Overall, we identified abiotic stress-responsive tncRNAs from rice and chickpea that suggest their potential contribution to plant resilience under changing environmental conditions.