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A tRNA-derived fragment competes with mRNA for ribosome binding and regulates translation during stress

Gebetsberger, Jennifer, Wyss, Leander, Mleczko, Anna M., Reuther, Julia, Polacek, Norbert·2017·RNA Biology
DOI 10.1080/15476286.2016.1257470PMC PMC5711459
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  • Through their interactions with ribosomes and mRNA, small noncoding molecules shape the dynamic molecular spectrum of tissues.

    “Through their interactions with ribosomes and mRNA, these small noncoding molecules shape the dynamic molecular spectrum of tissues (4, 17).”

    From A mouse tissue atlas of small noncoding RNA (2020) · cites this paper as [4]

    The Introduction (page unavailable) says a stress-produced tRNA fragment binds ribosomes and competes with mRNA, reducing protein synthesis. It also describes small RNAs as regulators of cellular RNomes, but the paper does not establish that these interactions shape the molecular spectrum of tissues. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

  • Small ncRNAs are involved in nearly all developmental and pathological processes in mammals.

    “today small ncRNAs are believed to be involved in nearly all developmental and pathological processes in mammals (2–4)”

    From A mouse tissue atlas of small noncoding RNA (2020) · cites this paper as [4]

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Research works printed but not linked: 46

  1. [1]Huttenhofer A, Schattner P, Polacek N Non-coding RNAs: hope or hype? Trends Genet 2005; 21: 289- 97; PMID:15851066; https://doi.org/ 10.1016/j.tig.2005.03.007 15851066 · DOI
  2. [2]Morris KV, Mattick JS The rise of regulatory RNA. Nature Rev 2014; 15: 423- 37; PMID:24776770; https://doi.org/19026782 10.1038/nrg3722 PMC4314111 24776770 · DOI
  3. [3]Mattick JS, Makunin IV Non-coding RNA. Human Mol Genet 2006; 15: R17- 29; PMID:16651366; https://doi.org/19026782 10.1093/hmg/ddl046 16651366 · DOI
  4. [4]Ender C, Krek A, Friedlander MR, Beitzinger M, Weinmann L, Chen W, Pfeffer S, Rajewsky N, Meister G A human snoRNA with microRNA-like functions. Mol Cell 2008; 32: 519- 28; PMID:19026782; https://doi.org/ 10.1016/j.molcel.2008.10.017 19026782 · DOI
  5. [5]Persson H, Kvist A, Vallon-Christersson J, Medstrand P, Borg A, Rovira C The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs. Nat Cell Biol 2009; 11: 1268- 71; PMID:19749744; https://doi.org/ 10.1038/ncb1972 19749744 · DOI
  6. [6]Tuck AC, Tollervey D RNA in pieces. Trends Genet 2011; 27: 422- 32; PMID:21741109; https://doi.org/ 10.1016/j.tig.2011.06.001 21741109 · DOI
  7. [7]Pircher A, Bakowska-Zywicka K, Schneider L, Zywicki M, Polacek N An mRNA-derived noncoding RNA targets and regulates the ribosome. Mol Cell 2014; 54: 147- 55; PMID:24685157; https://doi.org/ 10.1016/j.molcel.2014.02.024 24685157 PMC3988847 · DOI
  8. [8]Luidalepp H, Berger S, Joss O, Tenson T, Polacek N Ribosome shut-down by 16S rRNA fragmentation in stationary-phase Escherichia coli. J Mol Biol 2016; 428: 2237- 47; PMID:27067112; https://doi.org/ 10.1016/j.jmb.2016.01.033 27067112 · DOI
  9. [9]Vesper O, Amitai S, Belitsky M, Byrgazov K, Kaberdina AC, Engelberg-Kulka H, Moll I Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli. Cell 2011; 147: 147- 57; PMID:21944167; https://doi.org/ 10.1016/j.cell.2011.07.047 21944167 PMC4894548 · DOI
  10. [10]Li Z, Ender C, Meister G, Moore PS, Chang Y, John B Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. Nucleic Acids Res 2012; 40: 6787- 99; PMID:22492706; https://doi.org/ 10.1093/nar/gks307 22492706 PMC3413118 · DOI
  11. [11]Gebetsberger J, Polacek N Slicing tRNAs to boost functional ncRNA diversity. RNA Biol 2013; 10: 1798- 806; PMID:24351723; https://doi.org/ 10.4161/rna.27177 24351723 PMC3917982 · DOI
  12. [12]Kirchner S, Ignatova Z Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. Nature Rev 2015; 16: 98- 112; PMID:5534324; https://doi.org/25599528 10.1038/nrg3861 25534324 · DOI
  13. [13]Megel C, Morelle G, Lalande S, Duchene AM, Small I, Marechal-Drouard L Surveillance and cleavage of eukaryotic tRNAs. Int J Mol Sci 2015; 16: 1873- 93; PMID:25599528; https://doi.org/ 10.3390/ijms16011873 25599528 PMC4307339 · DOI
  14. [14]Anderson P, Ivanov P tRNA fragments in human health and disease. FEBS Lett 2014; 588: 4297- 304; PMID:25220675; https://doi.org/ 10.1016/j.febslet.2014.09.001 25220675 PMC4339185 · DOI · Paper page
  15. [15]Keam SP, Hutvagner G tRNA-Derived Fragments (tRFs): Emerging new roles for an ancient RNA in the regulation of gene expression. Life 2015; 5: 1638- 51; PMID:26703738; https://doi.org/ 10.3390/life5041638 26703738 PMC4695841 · DOI
  16. [16]Borek E, Baliga BS, Gehrke CW, Kuo CW, Belman S, Troll W, Waalkes TP High turnover rate of transfer RNA in tumor tissue. Cancer Res 1977; 37: 3362- 6; PMID:884680 884680
  17. [17]Levitz R, Chapman D, Amitsur M, Green R, Snyder L,Kaufmann G The optional E. coli prr locus encodes a latent form of phage T4-induced anticodon nuclease. EMBO J 1990; 9: 1383- 9; PMID:1691706 1691706 PMC551823
  18. [18]Durdevic Z, Schaefer M tRNA modifications: necessary for correct tRNA-derived fragments during the recovery from stress? BioEssays 2013; 35: 323- 7; PMID:23315679; https://doi.org/ 10.1002/bies.201200158 23315679 · DOI
  19. [19]Goodarzi H, Liu X, Nguyen HC, Zhang S, Fish L, Tavazoie SF Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement. Cell 2015; 161: 790- 802; PMID:25957686; https://doi.org/ 10.1016/j.cell.2015.02.053 25957686 PMC4457382 · DOI · Paper page
  20. [20]Honda S, Loher P, Shigematsu M, Palazzo JP, Suzuki R, Imoto I, Rigoutsos I, Kirino Y Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers. Proc Natl Acad Sci USA 2015; 112: E3816- 3825; PMID:26124144; https://doi.org/ 10.1073/pnas.1510077112 26124144 PMC4517238 · DOI
  21. [21]Chen Q, Yan M, Cao Z, Li X, Zhang Y, Shi J, Feng GH, Peng H, Zhang X, Qian J, et al. Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder. Science 2016; 351: 397- 400; PMID:26721680; https://doi.org/ 10.1126/science.aad7977 26721680 · DOI · Paper page
  22. [22]Ivanov P, Emara MM, Villen J, Gygi SP, Anderson P Angiogenin-induced tRNA fragments inhibit translation initiation. Mol Cell 2011; 43: 613- 23; PMID:21855800; https://doi.org/ 10.1016/j.molcel.2011.06.022 21855800 PMC3160621 · DOI
  23. [23]Bakowska-Zywicka K, Kasprzyk M, Twardowski T tRNA-derived short RNAs bind to Saccharomyces cerevisiae ribosomes in a stress-dependent manner and inhibit protein synthesis in vitro. FEMS Yeast Res 2016; 16; PMID:27609601; https://doi.org/ 10.1093/femsyr/fow077 27609601 PMC5049586 · DOI
  24. [24]Gebetsberger J, Zywicki M, Kunzi A, Polacek N tRNA-derived fragments target the ribosome and function as regulatory non-coding RNA in Haloferax volcanii. Archaea 2012; 2012: 260909; PMID:23326205; https://doi.org/ 10.1155/2012/260909 23326205 PMC3544259 · DOI
  25. [25]Pircher A, Gebetsberger J, Polacek N Ribosome-associated ncRNAs: an emerging class of translation regulators. RNA Biol 2014; 11: 1335- 9; PMID:25692232; https://doi.org/ 10.1080/15476286.2014.996459 25692232 PMC4615380 · DOI
  26. [26]Cline SW, Lam WL, Charlebois RL, Schalkwyk LC, Doolittle WF Transformation methods for halophilic archaebacteria. Canadian J Microbiol 1989; 35: 148- 52; PMID:2497937; https://doi.org/1656383 10.1139/m89-022 2497937 · DOI
  27. [27]Russell PJ, Hambidge SJ, Kirkegaard K Direct introduction and transient expression of capped and non-capped RNA in Saccharomyces cerevisiae. Nucleic Acids Res 1991; 19: 4949- 53; PMID:1656383; https://doi.org/ 10.1093/nar/19.18.4949 1656383 PMC328795 · DOI
  28. [28]Gebauer F, Hentze MW Molecular mechanisms of translational control. Nat Rev Mol Cell Biol 2004; 5: 827- 35; PMID:15459663; https://doi.org/ 10.1038/nrm1488 15459663 PMC7097087 · DOI · Paper page
  29. [29]Gualerzi CO, Pon CL Initiation of mRNA translation in prokaryotes. Biochem 1990; 29: 5881- 9; PMID:2200518; https://doi.org/17110332 10.1021/bi00477a001 2200518 · DOI
  30. [30]Qin Y, Polacek N, Vesper O, Staub E, Einfeldt E, Wilson DN, Nierhaus KH The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome. Cell 2006; 127: 721- 33; PMID:17110332; https://doi.org/ 10.1016/j.cell.2006.09.037 17110332 · DOI
  31. [31]Rheinberger HJ, Sternbach H, Nierhaus KH Three tRNA binding sites on Escherichia coli ribosomes. Proc Natl Acad Sci USA 1981; 78: 5310- 4; PMID:7029532; https://doi.org/ 10.1073/pnas.78.9.5310 7029532 PMC348734 · DOI
  32. [32]Desnoyers G, Bouchard MP, Masse E New insights into small RNA-dependent translational regulation in prokaryotes. Trends Genet 2013; 29: 92- 8; PMID:23141721; https://doi.org/ 10.1016/j.tig.2012.10.004 23141721 · DOI
  33. [33]Kramer P, Gabel K, Pfeiffer F, Soppa J Haloferax volcanii, a prokaryotic species that does not use the Shine Dalgarno mechanism for translation initiation at 5′-UTRs. PloS One 2014; 9: e94979; PMID:24733188; https://doi.org/ 10.1371/journal.pone.0094979 24733188 PMC3986360 · DOI
  34. [34]Wilson DN Ribosome-targeting antibiotics and mechanisms of bacterial resistance. Nat Rev Microbiol 2014; 12: 35- 48; PMID:24336183; https://doi.org/ 10.1038/nrmicro3155 24336183 · DOI · Paper page
  35. [35]Lee YS, Shibata Y, Malhotra A, Dutta A A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev 2009; 23: 2639- 49; PMID:19933153; https://doi.org/ 10.1101/gad.1837609 19933153 PMC2779758 · DOI · Paper page
  36. [36]Saikia M, Krokowski D, Guan BJ, Ivanov P, Parisien M, Hu GF, Anderson P, Pan T, Hatzoglou M Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress. J Biol Chem 2012; 287: 42708- 25; PMID:23086926; https://doi.org/ 10.1074/jbc.M112.371799 23086926 PMC3522271 · DOI · Paper page
  37. [37]Thompson DM, Lu C, Green PJ, Parker R tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA 2008; 14: 2095- 103; PMID:18719243; https://doi.org/ 10.1261/rna.1232808 18719243 PMC2553748 · DOI
  38. [38]Sobala A, Hutvagner G Small RNAs derived from the 5′ end of tRNA can inhibit protein translation in human cells. RNA Biol 2013; 10: 553- 63; PMID:23563448; https://doi.org/ 10.4161/rna.24285 23563448 PMC3710361 · DOI · Paper page
  39. [39]Svensson SL, Sharma CM Small RNAs in bacterial virulence and communication. Microbiol Spect 2016; 4; PMID:27337442; https://doi.org/19553343 10.1128/microbiolspec.VMBF-0028-2015 27337442 · DOI
  40. [40]Buck MA, Cooperman BS Single protein omission reconstitution studies of tetracycline binding to the 30S subunit of Escherichia coli ribosomes. Biochem 1990; 29: 5374- 9; PMID:2200507; https://doi.org/19553343 10.1021/bi00474a024 2200507 · DOI · Paper page
  41. [41]Llano-Sotelo B, Hickerson RP, Lancaster L, Noller HF, Mankin AS Fluorescently labeled ribosomes as a tool for analyzing antibiotic binding. RNA 2009; 15: 1597- 604; PMID:19553343; https://doi.org/ 10.1261/rna.1681609 19553343 PMC2714759 · DOI
  42. [42]Allers T, Ngo HP, Mevarech M, Lloyd RG Development of additional selectable markers for the halophilic archaeon Haloferax volcanii based on the leuB and trpA genes. Applied Environ Microbiol 2004; 70: 943- 53; PMID:14766575; https://doi.org/20375101 10.1128/AEM.70.2.943-953.2004 PMC348920 14766575 · DOI
  43. [43]Erlacher MD, Chirkova A, Voegele P, Polacek N Generation of chemically engineered ribosomes for atomic mutagenesis studies on protein biosynthesis. Nature Prot 2011; 6: 580- 92; PMID:21527916; https://doi.org/20375101 10.1038/nprot.2011.306 21527916 · DOI
  44. [44]Chirkova A, Erlacher MD, Clementi N, Zywicki M, Aigner M, Polacek N The role of the universally conserved A2450-C2063 base pair in the ribosomal peptidyl transferase center. Nucleic Acids Res 2010; 38: 4844- 55; PMID:20375101; https://doi.org/ 10.1093/nar/gkq213 20375101 PMC2919715 · DOI
  45. [45]Polacek N, Barta A Metal ion probing of rRNAs: evidence for evolutionarily conserved divalent cation binding pockets. RNA 1998; 4: 1282- 94; PMID:9769102; https://doi.org/ 10.1017/S1355838298980347 9769102 PMC1369700 · DOI
  46. [46]Selmer M, Dunham CM, Murphy FVt, Weixlbaumer A, Petry S, Kelley AC, Weir JR, Ramakrishnan V Structure of the 70S ribosome complexed with mRNA and tRNA. Science 2006; 313: 1935- 42; PMID:16959973PMID:; https://doi.org/ 10.1126/science.1131127 16959973 · DOI

Cited by

Sorted by citations

Authors
Gebetsberger, J., Wyss, L., Mleczko, A. M., Reuther, J., & Polacek, N.
Affiliations
Department of Chemistry and Biochemistry, University of Bern, Freiestrasse, Bern, Switzerland
Venue
RNA Biology
Publisher
Informa UK Limited
Published
2017-03-24
Volume
14
Issue
10
Pages
1364-1373
ISSN
  • 1547-6286
  • 1555-8584
DOI
10.1080/15476286.2016.1257470
PMC
PMC5711459
Cited by
200
References
0
Language
en
Licence
creativecommons.org/licenses/by-nc-nd/4.0/ (vor)

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