TRNA-derived Small RNAs in Plant Response to Biotic and Abiotic Stresses

Overview

Journal Front Plant Sci

Date 2023 Feb 17

PMID 36798699

Authors

Chaojun Wang

Weiqiang Chen

Maimaiti Aili

Lei Zhu

Yan Chen

Affiliations

Soon will be listed here.

Abstract

tRNA-derived small RNAs (tsRNAs) represent a novel category of small non-coding RNAs and serve as a new regulator of gene expression at both transcriptional and post-transcriptional levels. Growing evidence indicates that tsRNAs can be induced by diverse stimuli and regulate stress-responsive target genes, allowing plants to adapt to unfavorable environments. Here, we discuss the latest developments about the biogenesis and classification of tsRNAs and highlight the expression regulation and potential function of tsRNAs in plant biotic and abiotic stress responses. Of note, we also collect useful bioinformatics tools and resources for tsRNAs study in plants. Finally, we propose current limitations and future directions for plant tsRNAs research. These recent discoveries have refined our understanding of whether and how tsRNAs enhance plant stress tolerance.

Citing Articles

The Role of tRNA-Derived Small RNAs (tsRNAs) in Regulating Cell Death of Cardiovascular Diseases.

Guo J, Chen X, Ren J, Wang Y, Wang K, Yang S Biology (Basel). 2025; 14(2).

PMID: 40001986 PMC: 11853139. DOI: 10.3390/biology14020218.

tRNA gene content, structure, and organization in the flowering plant lineage.

Monloy K, Planta J Front Plant Sci. 2025; 15:1486612.

PMID: 39764226 PMC: 11700998. DOI: 10.3389/fpls.2024.1486612.

Vitamin D-mediated tsRNA-07804 triggers mitochondrial dysfunction and suppresses non-small cell lung cancer progression by targeting CRKL.

Liang Y, Zhang X, Peng J, Liu J, Chen H, Guo S J Cancer Res Clin Oncol. 2024; 150(2):51.

PMID: 38289488 PMC: 10827823. DOI: 10.1007/s00432-023-05586-1.

References

Chen Q, Yan M, Cao Z, Li X, Zhang Y, Shi J . Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder. Science. 2016; 351(6271):397-400. DOI: 10.1126/science.aad7977. View

Jones-Rhoades M, Bartel D, Bartel B . MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol. 2006; 57:19-53. DOI: 10.1146/annurev.arplant.57.032905.105218. View

Addo-Quaye C, Eshoo T, Bartel D, Axtell M . Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol. 2008; 18(10):758-762. PMC: 2583427. DOI: 10.1016/j.cub.2008.04.042. View

Hsieh L, Lin S, Shih A, Chen J, Lin W, Tseng C . Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiol. 2009; 151(4):2120-32. PMC: 2785986. DOI: 10.1104/pp.109.147280. View

Hackenberg M, Gustafson P, Langridge P, Shi B . Differential expression of microRNAs and other small RNAs in barley between water and drought conditions. Plant Biotechnol J. 2014; 13(1):2-13. PMC: 4309496. DOI: 10.1111/pbi.12220. View

Goodarzi H, Liu X, Nguyen H, Zhang S, Fish L, Tavazoie S . Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement. Cell. 2015; 161(4):790-802. PMC: 4457382. DOI: 10.1016/j.cell.2015.02.053. View

Fu H, Feng J, Liu Q, Sun F, Tie Y, Zhu J . Stress induces tRNA cleavage by angiogenin in mammalian cells. FEBS Lett. 2008; 583(2):437-42. DOI: 10.1016/j.febslet.2008.12.043. View

Megel C, Hummel G, Lalande S, Ubrig E, Cognat V, Morelle G . Plant RNases T2, but not Dicer-like proteins, are major players of tRNA-derived fragments biogenesis. Nucleic Acids Res. 2018; 47(2):941-952. PMC: 6344867. DOI: 10.1093/nar/gky1156. View

Chen Q, Zhang F, Dong L, Wu H, Xu J, Li H . SIDT1-dependent absorption in the stomach mediates host uptake of dietary and orally administered microRNAs. Cell Res. 2020; 31(3):247-258. PMC: 8026584. DOI: 10.1038/s41422-020-0389-3. View

10.

Zahra S, Bhardwaj R, Sharma S, Singh A, Kumar S . PtncRNAdb: plant transfer RNA-derived non-coding RNAs (tncRNAs) database. 3 Biotech. 2022; 12(5):105. PMC: 8986922. DOI: 10.1007/s13205-022-03174-7. View

11.

Luhtala N, Parker R . T2 Family ribonucleases: ancient enzymes with diverse roles. Trends Biochem Sci. 2010; 35(5):253-9. PMC: 2888479. DOI: 10.1016/j.tibs.2010.02.002. View

12.

Zhang X, He X, Liu C, Liu J, Hu Q, Pan T . IL-4 Inhibits the Biogenesis of an Epigenetically Suppressive PIWI-Interacting RNA To Upregulate CD1a Molecules on Monocytes/Dendritic Cells. J Immunol. 2016; 196(4):1591-603. DOI: 10.4049/jimmunol.1500805. View

13.

Wang H, Huang R, Li L, Zhu J, Li Z, Peng C . CPA-seq reveals small ncRNAs with methylated nucleosides and diverse termini. Cell Discov. 2021; 7(1):25. PMC: 8053708. DOI: 10.1038/s41421-021-00265-2. View

14.

Deshpande R, Shankar V . Ribonucleases from T2 family. Crit Rev Microbiol. 2002; 28(2):79-122. DOI: 10.1080/1040-840291046704. View

15.

Phizicky E, Hopper A . tRNA biology charges to the front. Genes Dev. 2010; 24(17):1832-60. PMC: 2932967. DOI: 10.1101/gad.1956510. View

16.

Kumar P, Anaya J, Mudunuri S, Dutta A . Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC Biol. 2014; 12:78. PMC: 4203973. DOI: 10.1186/s12915-014-0078-0. View

17.

Irie M . Structure-function relationships of acid ribonucleases: lysosomal, vacuolar, and periplasmic enzymes. Pharmacol Ther. 1999; 81(2):77-89. DOI: 10.1016/s0163-7258(98)00035-7. View

18.

Lyons S, Fay M, Ivanov P . The role of RNA modifications in the regulation of tRNA cleavage. FEBS Lett. 2018; 592(17):2828-2844. PMC: 6986807. DOI: 10.1002/1873-3468.13205. View

19.

Keam S, Young P, McCorkindale A, Dang T, Clancy J, Humphreys D . The human Piwi protein Hiwi2 associates with tRNA-derived piRNAs in somatic cells. Nucleic Acids Res. 2014; 42(14):8984-95. PMC: 4132735. DOI: 10.1093/nar/gku620. View

20.

Lalande S, Merret R, Salinas-Giege T, Drouard L . Arabidopsis tRNA-derived fragments as potential modulators of translation. RNA Biol. 2020; 17(8):1137-1148. PMC: 7549631. DOI: 10.1080/15476286.2020.1722514. View