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http://dx.doi.org/10.14348/molcells.2019.0214

Transfer RNA-Derived Small Non-Coding RNA: Dual Regulator of Protein Synthesis  

Kim, Hak Kyun (Department of Life Sciences, Chung-Ang University)
Publication Information
Molecules and Cells / v.42, no.10, 2019 , pp. 687-692 More about this Journal
Abstract
Transfer RNA-derived small RNAs (tsRNAs) play a role in various cellular processes. Accumulating evidence has revealed that tsRNAs are deeply implicated in human diseases, such as various cancers and neurological disorders, suggesting that tsRNAs should be investigated to develop novel therapeutic intervention. tsRNAs provide more complexity to the physiological role of transfer RNAs by repressing or activating protein synthesis with distinct mechanisms. Here, we highlight the detailed mechanism of tsRNA-mediated dual regulation in protein synthesis and discuss the necessity of novel sequencing technology to learn more about tsRNAs.
Keywords
tRF; tRNA; tsRNA; translation;
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1 Anderson, P. and Kedersha, N. (2008). Stress granules: the Tao of RNA triage. Trends Biochem. Sci. 33, 141-150.   DOI
2 Cozen, A.E., Quartley, E., Holmes, A.D., Hrabeta-Robinson, E., Phizicky, E.M., and Lowe, T.M. (2015). ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments. Nat. Methods 12, 879-884.   DOI
3 Dang, Y., Kedersha, N., Low, W.K., Romo, D., Gorospe, M., Kaufman, R., Anderson, P., and Liu, J.O. (2006). Eukaryotic initiation factor 2alpha-independent pathway of stress granule induction by the natural product pateamine A. J. Biol. Chem. 281, 32870-32878.   DOI
4 Guzzi, N., Ciesla, M., Ngoc, P.C.T., Lang, S., Arora, S., Dimitriou, M., Pimkova, K., Sommarin, M.N.E., Munita, R., Lubas, M., et al. (2018). Pseudouridylation of tRNA-derived fragments steers translational control in stem cells. Cell 173, 1204-1216.   DOI
5 Haiser, H.J., Karginov, F.V., Hannon, G.J., and Elliot, M.A. (2008). Developmentally regulated cleavage of tRNAs in the bacterium Streptomyces coelicolor. Nucleic Acids Res. 36, 732-741.   DOI
6 Haussecker, D., Huang, Y., Lau, A., Parameswaran, P., Fire, A.Z., and Kay, M.A. (2010). Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA 16, 673-695.   DOI
7 Ivanov, P., Emara, M.M., Villen, J., Gygi, S.P., and Anderson, P. (2011). Angiogenin-induced tRNA fragments inhibit translation initiation. Mol. Cell 43, 613-623.   DOI
8 Ivanov, P., O'Day, E., Emara, M.M., Wagner, G., Lieberman, J., and Anderson, P. (2014). G-quadruplex structures contribute to the neuroprotective effects of angiogenin-induced tRNA fragments. Proc. Natl. Acad. Sci. U. S. A. 111, 18201-18206.   DOI
9 Jochl, C., Rederstorff, M., Hertel, J., Stadler, P.F., Hofacker, I.L., Schrettl, M., Haas, H., and Huttenhofer, A. (2008). Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis. Nucleic Acids Res. 36, 2677-2689.   DOI
10 Elkordy, A., Mishima, E., Niizuma, K., Akiyama, Y., Fujimura, M., Tominaga, T., and Abe, T. (2018). Stress-induced tRNA cleavage and tiRNA generation in rat neuronal PC12 cells. J. Neurochem. 146, 560-569.   DOI
11 Keam, S.P., Sobala, A., Ten Have, S., and Hutvagner, G. (2017). tRNA-derived RNA fragments associate with human multisynthetase complex (MSC) and modulate ribosomal protein translation. J. Proteome Res. 16, 413-420.   DOI
12 Kim, H.K., Fuchs, G., Wang, S., Wei, W., Zhang, Y., Park, H., Roy-Chaudhuri, B., Li, P., Xu, J., Chu, K., et al. (2017). A transfer-RNA-derived small RNA regulates ribosome biogenesis. Nature 552, 57-62.   DOI
13 Kumar, P., Anaya, J., Mudunuri, S.B., and Dutta, A. (2014a). 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. 12, 78.   DOI
14 Kumar, P., Kuscu, C., and Dutta, A. (2016). Biogenesis and function of transfer RNA-related fragments (tRFs). Trends Biochem. Sci. 41, 679-689.   DOI
15 Kumar, P., Mudunuri, S.B., Anaya, J., and Dutta, A. (2014b). tRFdb: a database for transfer RNA fragments. Nucleic Acids Res. 43, D141-D145.   DOI
16 Lee, S.R. and Collins, K. (2005). Starvation-induced cleavage of the tRNA anticodon loop in Tetrahymena thermophila. J. Biol. Chem. 280, 42744-42749.   DOI
17 Lee, Y.S., Shibata, Y., Malhotra, A., and Dutta, A. (2009). A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev. 23, 2639-2649.   DOI
18 Lyons, S.M., Achorn, C., Kedersha, N.L., Anderson, P.J., and Ivanov, P. (2016). YB-1 regulates tiRNA-induced Stress Granule formation but not translational repression. Nucleic Acids Res. 44, 6949-6960.   DOI
19 Levitz, R., Chapman, D., Amitsur, M., Green, R., Snyder, L., and Kaufmann, G. (1990). The optional E. coli prr locus encodes a latent form of phage T4-induced anticodon nuclease. EMBO J. 9, 1383-1389.   DOI
20 Luo, S., He, F., Luo, J., Dou, S., Wang, Y., Guo, A., and Lu, J. (2018). Drosophila tsRNAs preferentially suppress general translation machinery via antisense pairing and participate in cellular starvation response. Nucleic Acids Res. 46, 5250-5268.   DOI
21 Lyons, S.M., Gudanis, D., Coyne, S.M., Gdaniec, Z., and Ivanov, P. (2017). Identification of functional tetramolecular RNA G-quadruplexes derived from transfer RNAs. Nat. Commun. 8, 1127.   DOI
22 Mleczko, A.M., Celichowski, P., and Bakowska-Zywicka, K. (2018). Transfer RNA-derived fragments target and regulate ribosome-associated aminoacyl-transfer RNA synthetases. Biochim. Biophys. Acta Gene Regul. Mech. 1861, 647-656.   DOI
23 Nekrasov, M.P., Ivshina, M.P., Chernov, K.G., Kovrigina, E.A., Evdokimova, V.M., Thomas, A.A.M., Hershey, J.W.B., and Ovchinnikov, L.P. (2003). The mRNA-binding protein YB-1 (p50) prevents association of the eukaryotic initiation factor eIF4G with mRNA and inhibits protein synthesis at the initiation stage. J. Biol. Chem. 278, 13936-13943.   DOI
24 Panas, M.D., Ivanov, P., and Anderson, P. (2016). Mechanistic insights into mammalian stress granule dynamics. J. Cell Biol. 215, 313-323.   DOI
25 Phizicky, E.M. and Hopper, A.K. (2010). tRNA biology charges to the front. Genes Dev. 24, 1832-1860.   DOI
26 Fricker, R., Brogli, R., Luidalepp, H., Wyss, L., Fasnacht, M., Joss, O., Zywicki, M., Helm, M., Schneider, A., Cristodero, M., et al. (2019). A tRNA half modulates translation as stress response in Trypanosoma brucei. Nat. Commun. 10, 118.   DOI
27 Emara, M.M., Ivanov, P., Hickman, T., Dawra, N., Tisdale, S., Kedersha, N., Hu, G.F., and Anderson, P. (2010). Angiogenin-induced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly. J. Biol. Chem. 285, 10959-10968.   DOI
28 Evdokimova, V., Ruzanov, P., Imataka, H., Raught, B., Svitkin, Y., Ovchinnikov, L.P., and Sonenberg, N. (2001). The major mRNA-associated protein YB-1 is a potent 5' cap-dependent mRNA stabilizer. EMBO J. 20, 5491-5502.   DOI
29 Farny, N.G., Kedersha, N.L., and Silver, P.A. (2009). Metazoan stress granule assembly is mediated by P-eIF2alpha-dependent and -independent mechanisms. RNA 15, 1814-1821.   DOI
30 Fu, H., Feng, J., Liu, Q., Sun, F., Tie, Y., Zhu, J., Xing, R., Sun, Z., and Zheng, X. (2009). Stress induces tRNA cleavage by angiogenin in mammalian cells. FEBS Lett. 583, 437-442.   DOI
31 Gebetsberger, J., Wyss, L., Mleczko, A.M., Reuther, J., and Polacek, N. (2017). A tRNA-derived fragment competes with mRNA for ribosome binding and regulates translation during stress. RNA Biol. 14, 1364-1373.   DOI
32 Gebetsberger, J., Zywicki, M., Kunzi, A., and Polacek, N. (2012). tRNAderived fragments target the ribosome and function as regulatory non-coding RNA in haloferax volcanii. Archaea 2012, 260909.
33 Telonis, A.G., Loher, P., Honda, S., Jing, Y., Palazzo, J., Kirino, Y., and Rigoutsos, I. (2015). Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget 6, 24797-24822.   DOI
34 Pliatsika, V., Loher, P., Magee, R., Telonis, A.G., Londin, E., Shigematsu, M., Kirino, Y., and Rigoutsos, I. (2018). MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects. Nucleic Acids Res. 46, D152-D159.   DOI
35 Robledo, S., Idol, R.A., Crimmins, D.L., Ladenson, J.H., Mason, P.J., and Bessler, M. (2008). The role of human ribosomal proteins in the maturation of rRNA and ribosome production. RNA 14, 1918-1929.   DOI
36 Schimmel, P. (2017). The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis. Nat. Rev. Mol. Cell Biol. 19, 45-58.   DOI
37 Yamasaki, S., Ivanov, P., Hu, G.F., and Anderson, P. (2009). Angiogenin cleaves tRNA and promotes stress-induced translational repression. J. Cell Biol. 185, 35-42.   DOI
38 Goodarzi, H., Liu, X., Nguyen, H.C.B., Zhang, S., Fish, L., and Tavazoie, S.F. (2015). Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement. Cell 161, 790-802.   DOI
39 Gupta, N., Singh, A., Zahra, S., and Kumar, S. (2018). PtRFdb: a database for plant transfer RNA-derived fragments. Database (Oxford) 2018, 1-8.   DOI
40 Thompson, D.M., Lu, C., Green, P.J., and Parker, R. (2008). tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA 14, 2095-2103.   DOI
41 Zhang, S., Sun, L., and Kragler, F. (2009). The phloem-delivered RNA pool contains small noncoding RNAs and interferes with translation. Plant Physiol. 150, 378-387.   DOI
42 Zheng, G., Qin, Y., Clark, W.C., Dai, Q., Yi, C., He, C., Lambowitz, A.M., and Pan, T. (2015). Efficient and quantitative high-throughput tRNA sequencing. Nat. Methods 12, 835-837.   DOI
43 Zheng, L.L., Xu, W.L., Liu, S., Sun, W.J., Li, J.H., Wu, J., Yang, J.H., and Qu, L.H. (2016). tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers. Nucleic Acids Res. 44, W185-W193.   DOI