Fine-Tuning of Gene Expression by tRNA-Derived Fragments during Abiotic Stress Signal Transduction

Abstract

When plants are subjected to unfavorable environmental conditions, overall gene expression in stressed cells is altered from a programmed pattern for normal development to an adaptive pattern for survival. Rapid changes in plant gene expression include production of stress responsive proteins for protection as well as reduction of irrelevant proteins to minimize energy consumption during growth. In addition to the many established mechanisms known to modulate gene expression in eukaryotes, a novel strategy involving tRNA-derived fragments (tRFs) was recently reported to control gene expression. In animals, tRFs are shown to play a certain role in infected or cancer cells. However, tRFs are expected to function in the regulation of gene expression against abiotic stress conditions in plants. Moreover, the underlying mechanism linking up-regulation of tRFs under stress conditions with the stress tolerant response remains unknown. In this review, the biogenesis and putative function of diverse tRFs in abiotic stress signaling are discussed with a focus on tRFs as a transcriptional/post-transcriptional/translational regulator.

Keywords: abiotic stress; abscisic acid; plant; post-transcriptional gene silencing; tRNA derived fragment.

Figure 1

Multiple tRNA genes in Arabidopsis. Numbers of tRNA genes are presented for different amino acids and anticodons. Each graph with different colors indicates a different amino acid. Various isoacceptors (tRNA acceptors that accept the same amino acids) exist for each amino acid. Existence of isodecoders (tRNA genes with the same anticodon but different sequences elsewhere in the tRNA body) for each isoacceptor expand the source of tRNAs for generation of diverse tRFs.

Figure 2

Several types of tRFs are classified by size and sequence location in the tRNA structure. tRFs are generated during pre-tRNA processing or from mature tRNAs. tRF-1 is generated by RNaseZ, which cleaves 3′ trailer sequences from pre-tRNA. Half-sized tRFs are grouped by whether their source sequences are from 5′ or 3′ fragments. Longer tRFs than tRNA halves are termed sitRNAs. In the case of short-length tRFs, subtypes are determined by size and location of the source. See the following references for detailed classification [8,11,18,23,26,28].

Figure 3

A proposed model on the diverse function of tRFs in gene expression during stress responses. Whereas mature tRNAs methylated by Dnmt2 (DNA methyltransferase 2) and Nsun2 (NOP2/Sun RNA methyltransferase family member 2) (yellow mark) participate in translation, unmethylated mature tRNAs or pre-tRNAs are processed into various types of tRFs [9,11,24,43]. Production of tRFs is promoted by abiotic stress conditions to eventually control gene expression by transcriptional, post-transcriptional, and translational regulation.