“Plant transfer RNA‐derived fragments: Biogenesis and Functions”

UNIVERSITY OF AGRICULTURAL SCIENCES, GKVK, BANGALORE

DEPARTMENT OF GENETICS AND PLANT BREEDING

SEMINAR – GPB 681 (0+1)

“Plant transfer RNA‐derived fragments: Biogenesis and Functions”

    In cells, tRNAs are abundant (~15% of total cellular RNAs) and endonuclease cleavage of some mature tRNAs generates complex populations of tRFs. Rather than being mere leftovers from tRNA processing or degradation, tRFs have multiple cellular functions in various organisms, from microorganisms to mammals and plants. They can originate from tRNA precursor molecules, but most of them derive from mature tRNAs. Mature tRNAs generate two main classes of tRFs depending on the cleavage site: long tRFs (l-tRFs, 30–35 nt in size) when cleavage occurs in the anticodon region, and short tRFs (s-tRFs, 19–25 nt) if the cleavage is located in the D or T regions of tRNA molecules. tRFs are involved in functions such as transcription and translation regulation, RNA degradation, ribosome biogenesis, stress response, regulatory signaling in plant nodulation, and genome protection against transposable elements.

    tRF populations are highly heterogeneous and produced by different mechanisms. Cleavage at the 3′ end of a pre-tRNA by RNase Z releases the 3′ pre-tRNA terminus, termed tRF-1s. Simultaneous cleavages at the tRNA D-loop and TΨC loop generate internal tRFs. However, studies have observed comparable levels of tRFs in seedlings of Arabidopsis dcl234 triple mutant and dcl1234 quadruple mutant, indicating that DCL1 does not play a major role in tRF biogenesis. In plants, the RNase T2 family is composed of three clades. In Arabidopsis, RNS1 and RNS3 are crucial for tRF-5 biogenesis.

    Increasing numbers of studies have focused on characterizing the functions of plant tRFs. Evidence is emerging that tRFs regulate or are associated with different developmental processes and stress responses in plants. The abundances of many plastid tRF-5s significantly increased in plants under cold conditions. They examined heat-responsive chloroplast sRNAs in Chinese cabbage (Brassica rapa) and identified a subset of chloroplast tRFs that are affected during heat stress. Plant tRFs also participate in symbiotic interactions. It was recently demonstrated that the rhizobial symbiont Bradyrhizobium japonicum delivers tRFs to soybean (Glycine max) host root cells, inducing nodulation. Using a green fluorescent protein reporter system in Arabidopsis, one experiment showed that a subset of tRNA halves and other tRFs repress translation in vitro.

    Hence, tRFs represent a novel category of small non-coding RNAs and serve as new regulators of gene expression at both transcriptional and post-transcriptional levels, as well as in epigenetic inheritance.

References

1. COGNAT, V., MORELLE, G., MEGEL, C., LALANDE, S., MOLINIER, J., VINCENT, T., SMALL, I., DUCHÊNE, A.M. AND MARÉCHAL-DROUARD, L., 2017. The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic. Nucleic Acids Res., 45(6):3460-3472.

2. LALANDE, S., MERRET, R., SALINAS-GIEGE, T. AND DROUARD, L., 2020. Arabidopsis tRNA-derived fragments as potential modulators of translation. RNA Biol., 17(8):1137-1148.

3. REN, B., WANG, X., DUAN, J. AND MA, J., 2019. Rhizobial tRNA-derived small RNAs are signal molecules regulating plant nodulation. Science, 365(6456):919-922.