Arabidopsis tRNA-derived fragments as potential modulators of translation

Abstract

Transfer RNA-derived fragments (tRFs) exist in all branches of life. They are involved in RNA degradation, regulation of gene expression, ribosome biogenesis. In archaebacteria, kinetoplastid, yeast and human cells, they were also shown to regulate translation. In Arabidopsis, the tRFs population fluctuates under developmental or environmental conditions but their functions are yet poorly understood. Here, we show that populations of long (30-35 nt) or short (19-25 nt) tRFs produced from Arabidopsis tRNAs can inhibit in vitro translation of a reporter gene. Analyzing a series of oligoribonucleotides mimicking natural tRFs, we demonstrate that only a limited set of tRFs possess the ability to affect protein synthesis. Out of a dozen of tRFs, only two deriving from tRNA Ala (AGC) and tRNA Asn (GUU) strongly attenuate translation in vitro. Contrary to human tRF(Ala), the 4 Gs present at the 5' extremity of Arabidopsis tRF(Ala) are not implicated in this inhibition while the G18 and G19 residues are essential. Protein synthesis inhibition by tRFs does not require complementarity with the translated mRNA but, having the capability to be associated with polyribosomes, tRFs likely act as general modulation factors of the translation process in plants.

Global profile of tRNA-derived small RNAs in gastric cancer patient plasma and identification of tRF-33-P4R8YP9LON4VDP as a new tumor suppressor

“…Circular RNA can also affect many diseases, including cancers 36 - 38 . However, until recent years, researchers have discovered that the sequence and size of tsRNAs have many previously-overlooked biological functions 39 , 40 . For example, tsRNAs can be used as modifiers to influence protein translation and affect the cellular response to stress 39 - 41 .…”

“…However, until recent years, researchers have discovered that the sequence and size of tsRNAs have many previously-overlooked biological functions 39 , 40 . For example, tsRNAs can be used as modifiers to influence protein translation and affect the cellular response to stress 39 - 41 . In addition, tsRNAs can also affect cell migration, proliferation, or invasion, which influences the occurrence and development of diseases such as cancers 42 , 43 .…”

Translational gene regulation in plants: A green new deal

“…These fragments arise via Dicer‐dependent and RNAse T2‐dependent pathways (Alves et al, 2017; Martinez, Choudury, & Slotkin, 2017; Megel et al, 2019). While some tRFs are tRNA halves clipped at the anticodon, others are smaller and appear in AGO‐containing RISCs (Trolet et al, 2019), where they may potentially affect translation (S. Zhang, Sun, & Kragler, 2009), as recently demonstrated in vitro (Lalande et al, 2020). Interestingly, tRFs arise not only from cytosolic but also from plastidic and mitochondrial precursors (Cognat et al, 2017).…”

Action mechanisms and research methods of tRNA-derived small RNAs

“…19 Lalande et al found that tRFs might be potential regulators in plant translation, such as in Arabidopsis, due to their ability to bind to polyribosomes. 20 It has been found that 5′ tiRNA Ala and 5′tiRNA Cys containing a terminal oligo-G motif (TOG motif) inhibits translation by forming an intermolecular RNA Gquadruplexes (RG4), replacing the translational initiation complex eIF4G/eIF4E on the mRNA cap (m 7 GTP) structure (Fig. 2b).…”