tsRNAs及其对植物响应非生物胁迫时基因表达的调控

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

转运RNA(tRNA)衍生的小RNA(tRNA-derived small RNAs,tsRNAs)是一类新兴的保守非编码RNA,通常由在胁迫条件下发生的核酸内切酶切割t RNA前体或成熟t RNA而产生.tsRNAs主要有两种类型,即tRNA衍生的胁迫诱导RNA(tRNA-derived stress-induced RNAs,tiRNAs,也称为tRNA半分子(tRNA halves,tRHs))和t RNA衍生的片段(tRNA-derived fragments,tRFs),两者在成熟t RNA或tRNA前体的切割位点不同.tsRNAs在原核生物和真核生物中都广泛存在,呈现时空特异性表达模式以发挥其功能,它们的失调会引发内稳态失衡(homeostatic imbalance).越来越多的证据表明,tsRNAs主要通过调控基因表达的转录、转录后和翻译水平在各种生物学过程中发挥重要作用.因此,研究tsRNAs的生物学功能及其作用分子机制已成为小分子非编码RNA领域的一个新研究热点.本文主要综述了tsRNAs的分类、生物发生、特征和生物学功能方面的进展,重点介绍了tsRNAs对植物响应非生物胁迫时基因表达的调控作用和植物tsRNAs的研究方法,并讨论了tsRNAs生物学的未来方向,特别是植物tsRNAs的研究方向,将促进对植物小分子非编码RNA的理解.

Transfer RNA(tRNA)-derived small RNAs(tsRNAs)are an emerging class of conserved non-coding RNAs that are usually produced from precursor t RNAs(pre-tRNAs)or mature t RNAs cleavage by endonuclease which occurs under stress conditions.There are mainly two types of ts RNAs:Namely t RNA-derived stress-induced RNAs(ti RNAs),also known as t RNA halves(tRHs),and t RNA-derived fragments(t RFs),which differ in the cleavage sites of mature t RNAs or pre-t RNAs.ti RNAs(including 5’and 3’-ti RNAs)with 30–40 nt in length are generated by ribonuclease A(RNase A)or ribonuclease T2 cleavage in the anticodon-loop of mature t RNA through a Dicer-independent pathway.t RFs(including 5-t RFs,3-t RFs,1-t RFs,2-t RFs,and i-t RFs)are derived from pre-t RNAs or mature t RNAs through both Dicer-dependent and Dicer-independent pathways.5-t RFs are generated through the endonucleolytic cleavage in the D-loop or in the region between D-loop and anticodon-loop of mature t RNAs by Dicer or RNase T2.3-t RFs are produced from the cleavage in the T-loop by Dicer or RNase A.1-t RFs with a 3’poly-U are generated by RNase Z cleavage in the 3’trailer of pre-t RNA during t RNA maturation.2-t RFs generated by unknown ribonuclease contain the complete anticodon-loop and anticodon stem.i-t RFs produced by unknown ribonuclease are derived from the internal region of mature t RNA,including the anticodon-loop and part of D/T-loop.Based on the origins and types of ts RNAs,ts RNAs are named according to a naming convention in the form of X-ts RNAAA-NNN(ts RNA represents the species of ti RNAs and t RFs;X represents ts RNAs subtypes of 1,2,3,and 5;AA represents the abbreviation of amino acid carried by the mapped t RNAs;NNN represents the anticodon of the mapped t RNAs).ts RNAs 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 ts RNAs 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 ts RNAs 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 ts RNAs,with a focus on the regulating roles of ts RNAs in gene expression of plants in response to abiotic stress.Different types of ts RNAs induced by abiotic stresses,such as oxidative stress,phosphate starvation,drought,UV-radiation,salt stress,heat and coldstress,were summarized in various plants.New sequencing technologies,including t RNA-seq(also known as ARM-seq),c P-RNA-seq(2’,3’-cyclic phosphate RNA sequencing beneficial for t RNA halves),YAMAT-seq(an efficient and convenient method for high-throughput sequencing of mature t RNAs),PANDORA-seq(uncovering small RNAs with different termini and nucleoside methylation),and Rtc B s RNA-seq(an Rtc B ligation-based small RNA sequencing method to profile 3’-c P-terminated and 3’-OH-terminated 5’-ti RNAs and 5-t RFs),have been developed to characterize plant ts RNAs more efficiently.Simultaneously,a variety of bioinformatics tools and Web databases have been developed for analyzing plant ts RNAs,such as t Rex(an online repository of Arabidopsis ts RNAs),Pt RFdb(a collection of over 5000 unique ts RNAs from 10 plant species),t RFanalyzer(for spatiotemporally analyzing the expression of t RNAs and ts RNAs in Arabidopsis and rice),and ts RBase(a comprehensive database of over 120000 sequences,expression features and function of ts RNAs from 20 species including five plant species,Arabidopsis thaliana,Oryza sativa,Zea mays,Glycine max and Vitis vinifera).The improvement of next-generation sequencing(NGS)technologies has accelerated the quantification of ts RNA populations in plants,contributing greatly for further functional studies of plant ts RNAs.