TsRNAs and their regulation of gene expression in plants in response to abiotic stress

Abstract

<p indent="0mm">Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are an emerging class of conserved non-coding RNAs that are usually produced from precursor tRNAs (pre-tRNAs) or mature tRNAs cleavage by endonuclease which occurs under stress conditions.There are mainly two types of tsRNAs: Namely tRNA-derived stress-induced RNAs (tiRNAs), also known as tRNA halves (tRHs), and tRNA-derived fragments (tRFs), which differ in the cleavage sites of mature tRNAs or pre-tRNAs. tiRNAs (including 5′ and 3′-tiRNAs) with <sc>30–40 nt</sc> in length are generated by ribonuclease A (RNase A) or ribonuclease T2 cleavage in the anticodon-loop of mature tRNA through a Dicer-independent pathway. tRFs (including 5-tRFs, 3-tRFs, 1-tRFs, 2-tRFs, and i-tRFs) are derived from pre-tRNAs or mature tRNAs through both Dicer-dependent and Dicer-independent pathways. 5-tRFs are generated through the endonucleolytic cleavage in the D-loop or in the region between D-loop and anticodon-loop of mature tRNAs by Dicer or RNase T2. 3-tRFs are produced from the cleavage in the T-loop by Dicer or RNase A. 1-tRFs with a 3′ poly-U are generated by RNase Z cleavage in the 3′ trailer of pre-tRNA during tRNA maturation. 2-tRFs generated by unknown ribonuclease contain the complete anticodon-loop and anticodon stem. i-tRFs produced by unknown ribonuclease are derived from the internal region of mature tRNA, including the anticodon-loop and part of D/T-loop. Based on the origins and types of tsRNAs, tsRNAs are named according to a naming convention in the form of X-tsRNA^AA-NNN (tsRNA represents the species of tiRNAs and tRFs; X represents tsRNAs subtypes of 1, 2, 3, and 5; AA represents the abbreviation of amino acid carried by the mapped tRNAs; NNN represents the anticodon of the mapped tRNAs). tsRNAs exist widely in prokaryotes and eukaryotes, exhibiting spatiotemporally specific expression pattern to function properly, while their dysregulation triggers homeostatic imbalance. Accumulating evidence has demonstrated that tsRNAs play important roles in various biological processes mainly through the regulation of gene expression at transcriptional, post-transcriptional and translational levels. Therefore, exploring the biological function and molecular mechanism of tsRNAs has become a new research hotspot in the field of non-coding small RNAs. Here, we briefly review the advances in the classification, biogenesis, characteristics, and biological function of tsRNAs, with a focus on the regulating roles of tsRNAs in gene expression of plants in response to abiotic stress. Different types of tsRNAs induced by abiotic stresses, such as oxidative stress, phosphate starvation, drought, UV-radiation, salt stress, heat and cold-stress, were summarized in various plants. New sequencing technologies, including tRNA-seq (also known as ARM-seq), cP-RNA-seq (2′,3′-cyclic phosphate RNA sequencing beneficial for tRNA halves), YAMAT-seq (an efficient and convenient method for high-throughput sequencing of mature tRNAs), PANDORA-seq (uncovering small RNAs with different termini and nucleoside methylation), and RtcB sRNA-seq (an RtcB ligation-based small RNA sequencing method to profile 3′-cP-terminated and 3′-OH-terminated 5′-tiRNAs and 5-tRFs), have been developed to characterize plant tsRNAs more efficiently. Simultaneously, a variety of bioinformatics tools and Web databases have been developed for analyzing plant tsRNAs, such as tRex (an online repository of <italic>Arabidopsis</italic> tsRNAs), PtRFdb (a collection of over 5000 unique tsRNAs from 10 plant species), tRFanalyzer (for spatiotemporally analyzing the expression of tRNAs and tsRNAs in <italic>Arabidopsis</italic> and rice), and tsRBase (a comprehensive database of over 120000 sequences, expression features and function of tsRNAs from 20 species including five plant species, <italic>Arabidopsis thaliana</italic>, <italic>Oryza sativa</italic>, <italic>Zea mays</italic>, <italic>Glycine max </italic>and<italic> Vitis vinifera</italic>). The improvement of next-generation sequencing (NGS) technologies has accelerated the quantification of tsRNA populations in plants, contributing greatly for further functional studies of plant tsRNAs.