Increased expression of tryptophan and tyrosine tRNAs elevates stop codon readthrough of reporter systems in human cell lines
Jazyk angličtina Země Velká Británie, Anglie Médium print
Typ dokumentu časopisecké články, práce podpořená grantem
PubMed
34009360
PubMed Central
PMC8136774
DOI
10.1093/nar/gkab315
PII: 6261788
Knihovny.cz E-zdroje
- MeSH
- buněčné linie MeSH
- lidé MeSH
- mutace MeSH
- nádorový supresorový protein p53 biosyntéza genetika MeSH
- plazmidy genetika MeSH
- promotorové oblasti (genetika) MeSH
- proteiny genetika MeSH
- proteosyntéza * MeSH
- reportérové geny MeSH
- RNA malá jaderná genetika MeSH
- RNA transferová Trp genetika metabolismus MeSH
- RNA transferová Tyr genetika metabolismus MeSH
- terminační kodon * MeSH
- tryptofan-tRNA-ligasa genetika MeSH
- tyrosin-tRNA-ligasa genetika MeSH
- virové proteiny genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- nádorový supresorový protein p53 MeSH
- proteiny MeSH
- RNA malá jaderná MeSH
- RNA transferová Trp MeSH
- RNA transferová Tyr MeSH
- terminační kodon * MeSH
- tryptofan-tRNA-ligasa MeSH
- tyrosin-tRNA-ligasa MeSH
- U6 small nuclear RNA MeSH Prohlížeč
- virové proteiny MeSH
Regulation of translation via stop codon readthrough (SC-RT) expands not only tissue-specific but also viral proteomes in humans and, therefore, represents an important subject of study. Understanding this mechanism and all involved players is critical also from a point of view of prospective medical therapies of hereditary diseases caused by a premature termination codon. tRNAs were considered for a long time to be just passive players delivering amino acid residues according to the genetic code to ribosomes without any active regulatory roles. In contrast, our recent yeast work identified several endogenous tRNAs implicated in the regulation of SC-RT. Swiftly emerging studies of human tRNA-ome also advocate that tRNAs have unprecedented regulatory potential. Here, we developed a universal U6 promotor-based system expressing various human endogenous tRNA iso-decoders to study consequences of their increased dosage on SC-RT employing various reporter systems in vivo. This system combined with siRNA-mediated downregulations of selected aminoacyl-tRNA synthetases demonstrated that changing levels of human tryptophan and tyrosine tRNAs do modulate efficiency of SC-RT. Overall, our results suggest that tissue-to-tissue specific levels of selected near-cognate tRNAs may have a vital potential to fine-tune the final landscape of the human proteome, as well as that of its viral pathogens.
Zobrazit více v PubMed
Roux P.P., Topisirovic I.. Signaling pathways involved in the regulation of mRNA translation. Mol. Cell. Biol. 2018; 38:e00070-18. PubMed PMC
Buszczak M., Signer R.A., Morrison S.J.. Cellular differences in protein synthesis regulate tissue homeostasis. Cell. 2014; 159:242–251. PubMed PMC
Schimmel P. The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis. Nat. Rev. Mol. Cell Biol. 2018; 19:45–58. PubMed
Parisien M., Wang X., Pan T.. Diversity of human tRNA genes from the 1000-genomes project. RNA Biol. 2013; 10:1853–1867. PubMed PMC
Chan P.P., Lowe T.M.. GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucleic Acids Res. 2016; 44:D184–D189. PubMed PMC
Orioli A. tRNA biology in the omics era: stress signalling dynamics and cancer progression. Bioessays. 2017; 39:1600158. PubMed
Kirchner S., Ignatova Z.. Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. Nat. Rev. Genet. 2015; 16:98–112. PubMed
Huang S.Q., Sun B., Xiong Z.P., Shu Y., Zhou H.H., Zhang W., Xiong J., Li Q.. The dysregulation of tRNAs and tRNA derivatives in cancer. J. Exp. Clin. Cancer Res. 2018; 37:101. PubMed PMC
Santos M., Fidalgo A., Varanda A.S., Oliveira C., Santos M.A.S.. tRNA deregulation and its consequences in cancer. Trends Mol. Med. 2019; 25:853–865. PubMed
Gomez-Roman N., Grandori C., Eisenman R.N., White R.J.. Direct activation of RNA polymerase III transcription by c-Myc. Nature. 2003; 421:290–294. PubMed
Felton-Edkins Z.A., Fairley J.A., Graham E.L., Johnston I.M., White R.J., Scott P.H.. The mitogen-activated protein (MAP) kinase ERK induces tRNA synthesis by phosphorylating TFIIIB. EMBO J. 2003; 22:2422–2432. PubMed PMC
Wei Y., Tsang C.K., Zheng X.F.. Mechanisms of regulation of RNA polymerase III-dependent transcription by TORC1. EMBO J. 2009; 28:2220–2230. PubMed PMC
Truitt M.L., Ruggero D.. New frontiers in translational control of the cancer genome. Nat. Rev. Cancer. 2016; 16:288–304. PubMed PMC
Goodenbour J.M., Pan T.. Diversity of tRNA genes in eukaryotes. Nucleic Acids Res. 2006; 34:6137–6146. PubMed PMC
Chan P.P., Lowe T.M.. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 2009; 37:D93–D97. PubMed PMC
Mahlab S., Tuller T., Linial M.. Conservation of the relative tRNA composition in healthy and cancerous tissues. RNA. 2012; 18:640–652. PubMed PMC
Pavon-Eternod M., Gomes S., Geslain R., Dai Q., Rosner M.R., Pan T.. tRNA over-expression in breast cancer and functional consequences. Nucleic Acids Res. 2009; 37:7268–7280. PubMed PMC
Gingold H., Tehler D., Christoffersen N.R., Nielsen M.M., Asmar F., Kooistra S.M., Christophersen N.S., Christensen L.L., Borre M., Sorensen K.D.et al. .. A dual program for translation regulation in cellular proliferation and differentiation. Cell. 2014; 158:1281–1292. PubMed
Goodarzi H., Nguyen H.C.B., Zhang S., Dill B.D., Molina H., Tavazoie S.F.. Modulated expression of specific tRNAs drives gene expression and cancer progression. Cell. 2016; 165:1416–1427. PubMed PMC
Jackson R.J., Hellen C.U., Pestova T.V.. Termination and post-termination events in eukaryotic translation. Adv. Protein Chem. Struct. Biol. 2012; 86:45–93. PubMed
Valasek L.S., Zeman J., Wagner S., Beznoskova P., Pavlikova Z., Mohammad M.P., Hronova V., Herrmannova A., Hashem Y., Gunisova S.. Embraced by eIF3: structural and functional insights into the roles of eIF3 across the translation cycle. Nucleic Acids Res. 2017; 45:10948–10968. PubMed PMC
Dabrowski M., Bukowy-Bieryllo Z., Zietkiewicz E.. Translational readthrough potential of natural termination codons in eucaryotes–The impact of RNA sequence. RNA Biol. 2015; 12:950–958. PubMed PMC
Schueren F., Thoms S.. Functional translational readthrough: a systems biology perspective. PLos Genet. 2016; 12:e1006196. PubMed PMC
Schueren F., Lingner T., George R., Hofhuis J., Dickel C., Gartner J., Thoms S.. Peroxisomal lactate dehydrogenase is generated by translational readthrough in mammals. Elife. 2014; 3:e03640. PubMed PMC
Loughran G., Chou M.Y., Ivanov I.P., Jungreis I., Kellis M., Kiran A.M., Baranov P.V., Atkins J.F.. Evidence of efficient stop codon readthrough in four mammalian genes. Nucleic Acids Res. 2014; 42:8928–8938. PubMed PMC
Nunes A., Ribeiro D.R., Marques M., Santos M.A.S., Ribeiro D., Soares A.R.. Emerging roles of tRNAs in RNA virus infections. Trends Biochem. Sci. 2020; 45:794–805. PubMed
Namy O., Duchateau-Nguyen G., Hatin I., Denmat Hermann-Le, Termier S., Rousset J.P.. Identification of stop codon readthrough genes in Saccharomyces cerevisiae. Nucleic Acids Res. 2003; 31:2289–2296. PubMed PMC
Dunn J.G., Foo C.K., Belletier N.G., Gavis E.R., Weissman J.S.. Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. Elife. 2013; 2:e01179. PubMed PMC
Napthine S., Yek C., Powell M.L., Brown T.D., Brierley I.. Characterization of the stop codon readthrough signal of Colorado tick fever virus segment 9 RNA. RNA. 2012; 18:241–252. PubMed PMC
Firth A.E., Brierley I.. Non-canonical translation in RNA viruses. J. Gen. Virol. 2012; 93:1385–1409. PubMed PMC
Loughran G., Jungreis I., Tzani I., Power M., Dmitriev R.I., Ivanov I.P., Kellis M., Atkins J.F.. Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response. J. Biol. Chem. 2018; 293:4434–4444. PubMed PMC
Yamaguchi Y., Hayashi A., Campagnoni C.W., Kimura A., Inuzuka T., Baba H.. L-MPZ, a novel isoform of myelin P0, is produced by stop codon readthrough. J. Biol. Chem. 2012; 287:17765–17776. PubMed PMC
Zahonova K., Kostygov A.Y., Sevcikova T., Yurchenko V., Elias M.. An unprecedented non-canonical nuclear genetic code with all three termination codons reassigned as sense codons. Curr. Biol. 2016; 26:2364–2369. PubMed
Heaphy S.M., Mariotti M., Gladyshev V.N., Atkins J.F., Baranov P.V.. Novel ciliate genetic code variants including the reassignment of all three stop codons to sense codons in Condylostoma magnum. Mol. Biol. Evol. 2016; 33:2885–2889. PubMed PMC
Kurosaki T., Maquat L.E.. Nonsense-mediated mRNA decay in humans at a glance. J. Cell Sci. 2016; 129:461–467. PubMed PMC
Linde L., Kerem B.. Introducing sense into nonsense in treatments of human genetic diseases. Trends Genet. 2008; 24:552–563. PubMed
Keeling K.M., Xue X., Gunn G., Bedwell D.M.. Therapeutics based on stop codon readthrough. Annu. Rev. Genomics Hum. Genet. 2014; 15:371–394. PubMed PMC
Namy O., Hatin I., Rousset J.P.. Impact of the six nucleotides downstream of the stop codon on translation termination. EMBO Rep. 2001; 2:787–793. PubMed PMC
Skuzeski J.M., Nichols L.M., Gesteland R.F., Atkins J.F.. The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons. J. Mol. Biol. 1991; 218:365–373. PubMed
Harrell L., Melcher U., Atkins J.F.. Predominance of six different hexanucleotide recoding signals 3′ of read-through stop codons. Nucleic Acids Res. 2002; 30:2011–2017. PubMed PMC
Firth A.E., Wills N.M., Gesteland R.F., Atkins J.F.. Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element. Nucleic Acids Res. 2011; 39:6679–6691. PubMed PMC
Beznoskova P., Wagner S., Jansen M.E., Haar T., Valasek L.S.. Translation initiation factor eIF3 promotes programmed stop codon readthrough. Nucleic Acids Res. 2015; 43:5099–5111. PubMed PMC
Bonetti B., Fu L., Moon J., Bedwell D.M.. The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae. J. Mol. Biol. 1995; 251:334–345. PubMed
McCaughan K.K., Brown C.M., Dalphin M.E., Berry M.J., Tate W.P.. Translational termination efficiency in mammals is influenced by the base following the stop codon. Proc. Natl. Acad. Sci. U.S.A. 1995; 92:5431–5435. PubMed PMC
Cassan M., Rousset J.P.. UAG readthrough in mammalian cells: effect of upstream and downstream stop codon contexts reveal different signals. BMC Mol. Biol. 2001; 2:3. PubMed PMC
Floquet C., Hatin I., Rousset J.P., Bidou L.. Statistical analysis of readthrough levels for nonsense mutations in mammalian cells reveals a major determinant of response to gentamicin. PLoS Genet. 2012; 8:e1002608. PubMed PMC
Beznoskova P., Gunisova S., Valasek L.S.. Rules of UGA-N decoding by near-cognate tRNAs and analysis of readthrough on short uORFs in yeast. RNA. 2016; 22:456–466. PubMed PMC
Beznoskova P., Pavlikova Z., Zeman J., Echeverria Aitken C., Valasek L.S.. Yeast applied readthrough inducing system (YARIS): an invivo assay for the comprehensive study of translational readthrough. Nucleic Acids Res. 2019; 47:6339–6350. PubMed PMC
Gunisova S., Beznoskova P., Mohammad M.P., Vlckova V., Valasek L.S.. In-depth analysis of cis-determinants that either promote or inhibit reinitiation on GCN4 mRNA after translation of its four short uORFs. RNA. 2016; 22:542–558. PubMed PMC
Blanchet S., Cornu D., Argentini M., Namy O.. New insights into the incorporation of natural suppressor tRNAs at stop codons in Saccharomyces cerevisiae. Nucleic Acids Res. 2014; 42:10061–10072. PubMed PMC
Blanchet S., Cornu D., Hatin I., Grosjean H., Bertin P., Namy O.. Deciphering the reading of the genetic code by near-cognate tRNA. Proc. Natl. Acad. Sci. U.S.A. 2018; 115:3018–3023. PubMed PMC
Roy B., Leszyk J.D., Mangus D.A., Jacobson A.. Nonsense suppression by near-cognate tRNAs employs alternative base pairing at codon positions 1 and 3. Proc. Natl. Acad. Sci. U.S.A. 2015; 112:3038–3043. PubMed PMC
Lowe T.M., Eddy S.R.. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25:955–964. PubMed PMC
Chiu W.-L., Wagner S., Herrmannová A., Burela L., Zhang F., Saini A.K., Valášek L., Hinnebusch A.G.. The C-terminal region of eukaryotic translation initiation factor 3a (eIF3a) promotes mRNA recruitment, scanning, and, together with eIF3j and the eIF3b RNA recognition motif, selection of AUG start codons. Mol. Cell. Biol. 2010; 30:4415–4434. PubMed PMC
Khoshnevis S., Gunišová S., Vlčková V., Kouba T., Neumann P., Beznosková P., Ficner R., Valášek L.S.. Structural integrity of the PCI domain of eIF3a/TIF32 is required for mRNA recruitment to the 43S pre-initiation complexes. Nucleic Acids Res. 2014; 42:4123–4139. PubMed PMC
Koukuntla R., Ramsey W.J., Young W.B., Link C.J.. U6 promoter-enhanced GlnUAG suppressor tRNA has higher suppression efficacy and can be stably expressed in 293 cells. J. Gene Med. 2013; 15:93–101. PubMed
Grentzmann G., Ingram J.A., Kelly P.J., Gesteland R.F., Atkins J.F.. A dual-luciferase reporter system for studying recoding signals. RNA. 1998; 4:479–486. PubMed PMC
Loughran G., Howard M.T., Firth A.E., Atkins J.F.. Avoidance of reporter assay distortions from fused dual reporters. RNA. 2017; 23:1285–1289. PubMed PMC
Pelham H.R. Leaky UAG termination codon in tobacco mosaic virus RNA. Nature. 1978; 272:469–471. PubMed
Borchert G.M., Lanier W., Davidson B.L.. RNA polymerase III transcribes human microRNAs. Nat. Struct. Mol. Biol. 2006; 13:1097–1101. PubMed
Wang Z., Rao D.D., Senzer N., Nemunaitis J.. RNA interference and cancer therapy. Pharm. Res. 2011; 28:2983–2995. PubMed
Ivanov P., Emara M.M., Villen J., Gygi S.P., Anderson P.. Angiogenin-induced tRNA fragments inhibit translation initiation. Mol. Cell. 2011; 43:613–623. PubMed PMC
De Bellis M., Pisani F., Mola M.G., Rosito S., Simone L., Buccoliero C., Trojano M., Nicchia G.P., Svelto M., Frigeri A.. Translational readthrough generates new astrocyte AQP4 isoforms that modulate supramolecular clustering, glial endfeet localization, and water transport. Glia. 2017; 65:790–803. PubMed
Hofhuis J., Schueren F., Notzel C., Lingner T., Gartner J., Jahn O., Thoms S.. The functional readthrough extension of malate dehydrogenase reveals a modification of the genetic code. Open Biol. 2016; 6:160246. PubMed PMC
Csibra E., Brierley I., Irigoyen N.. Modulation of stop codon read-through efficiency and its effect on the replication of murine leukemia virus. J. Virol. 2014; 88:10364–10376. PubMed PMC
Irigoyen N., Dinan A.M., Brierley I., Firth A.E.. Ribosome profiling of the retrovirus murine leukemia virus. Retrovirology. 2018; 15:10. PubMed PMC
Bidou L., Allamand V., Rousset J.P., Namy O.. Sense from nonsense: therapies for premature stop codon diseases. Trends Mol. Med. 2012; 18:679–688. PubMed
Perri F., Pisconti S., Della Vittoria Scarpati G.. P53 mutations and cancer: a tight linkage. Ann. Transl. Med. 2016; 4:522. PubMed PMC
Ribosomal A-site interactions with near-cognate tRNAs drive stop codon readthrough
Cysteine tRNA acts as a stop codon readthrough-inducing tRNA in the human HEK293T cell line
Stops making sense - For the people?