Characterization of Eukaryotic Release Factor 3 (eRF3) Translation Termination Factor in Plants Original Paper First Online: 06 December 2018 Abstract
Eukaryotic translation termination is mediated by two conserved interacting release factors, eRF1 and eRF3. eRF1 recognizes the stop codon and promotes the hydrolysis of the polypeptide chain, while eukaryotic eRF3 stimulates eRF1 release activity in the presence of GTP. It is widely believed that translation termination is highly conserved in eukaryotes. However, recent results that eRF1 is present in multiple, partially redundant copies in plants and that eRF1 expression is controlled by a complex, plant-specific autoregulatory circuit suggest that regulation of translation termination might be especially complex in plants. Surprisingly, very little is known about translation termination in plant, for instance, the eRF3 termination factor has not been analyzed in plants yet. Thus, we wanted to identify and characterize the eRF3 translation termination factor in plants. By combining a range of transient and transgenic assay here, we identified plant eRF3 and showed that it directly interacts with eRF1. In contrast to eRF1, plant eRF3 is not autoregulated, while eRF3 and eRF1 expressions are connected. We also demonstrated that eRF3 interacts with the core NMD factor, UPF1, and the expression of eRF3 is NMD regulated in certain plant species suggesting that in addition to the normal translation termination, eRF3 could be connected to plant nonsense-mediated decay (NMD). Finally, it appears that the plant termination factors are present in physiologically different concentrations, while eRF1 concentration limits the efficiency of both translation termination and NMD, eRF3 is present in non-limiting concentration.
Keywords Translation termination complex eRF3 Cross-regulation NMD Abbreviations eRF1
eukaryotic release factor 1
eukaryotic release factor 3
poly (A) binding protein
PABP-interacting motif 2
premature termination codon
open reading frame
upstream open reading frame
dominant-negative version of UPF1 NMD factor
Electronic supplementary material
The online version of this article (
) contains supplementary material, which is available to authorized users. https://doi.org/10.1007/s11105-018-1128-5 Notes Funding Information
This work was supported by the Agricultural Ministry of Hungary, the Hungarian Scientific Research Fund (NKFIH OTKA K109835 and K116963). A. Auber is a graduate student of the ELTE “Classical and Molecular Genetics” PhD program. We are grateful for K. Riha for the
smg7-1 line. Compliance with Ethical Standards Conflict of Interest
The authors declare that they have no conflict of interest.
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Amrani N, Dong S, He F, Ganesan R, Ghosh S, Kervestin S, Li C, Mangus DA, Spatrick P, Jacobson A (2006) Aberrant termination triggers nonsense-mediated mRNA decay. Biochem Soc Trans 34:39–42.
https://doi.org/10.1042/BST20060039 CrossRef PubMed Google Scholar
Atkinson GC, Baldauf SL, Hauryliuk V (2008) Evolution of nonstop, no-go and nonsense-mediated mRNA decay and their termination factor-derived components. BMC Evol Biol 8:1–18.
https://doi.org/10.1186/1471-2148-8-290 CrossRef Google Scholar
Chamieh H, Ballut L, Bonneau F, Le Hir H (2008) NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and stimulate its RNA helicase activity. Nat Struct Mol Biol 15:85–93.
https://doi.org/10.1038/nsmb1330 CrossRef PubMed Google Scholar
Chapman B, Brown C (2004) Translation termination in Arabidopsis thaliana: characterisation of three versions of release factor 1. Gene 341:219–225.
https://doi.org/10.1016/j.gene.2004.06.053 CrossRef PubMed Google Scholar
Chauvin C, Jean-Jean O (2008) Proteasomal degradation of human release factor eRF3a regulates translation termination complex formation. RNA 14:240–245.
https://doi.org/10.1261/rna.728608 CrossRef PubMed PubMedCentral Google Scholar
Firczuk H, Kannambath S, Pahle J, Claydon A, Beynon R, Duncan J, Westerhoff H, Mendes P, McCarthy JE (2013) An in vivo control map for the eukaryotic mRNA translation machinery. Mol Syst Biol 9:635.
https://doi.org/10.1038/msb.2012.73 CrossRef PubMed PubMedCentral Google Scholar
Firth AE, Wills NM, Gesteland RF, Atkins JF (2011) Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element. Nucleic Acids Res 39:6679–6691.
https://doi.org/10.1093/nar/gkr224 CrossRef PubMed PubMedCentral Google Scholar
Goetz AE, Wilkinson M (2017) Stress and the nonsense-mediated RNA decay pathway. Cell Mol Life Sci 74:3509–3531.
https://doi.org/10.1007/s00018-017-2537-6 CrossRef PubMed PubMedCentral Google Scholar
Hashimoto Y, Hosoda N, Datta P, Alnemri ES, Hoshino SI (2012) Translation termination factor eRF3 is targeted for caspase-mediated proteolytic cleavage and degradation during DNA damage-induced apoptosis. Apoptosis 17:1287–1299.
https://doi.org/10.1007/s10495-012-0765-7 CrossRef PubMed Google Scholar
Hellens RP, Brown CM, Chisnall MAW, Waterhouse PM, Macknight RC (2016) The emerging world of small ORFs. Trends Plant Sci 21:317–328.
https://doi.org/10.1016/j.tplants.2015.11.005 CrossRef PubMed Google Scholar
Hogg JR, Goff SP (2010) Upf1 senses 3’UTR length to potentiate mRNA decay. Cell 143:379–389.
https://doi.org/10.1016/j.cell.2010.10.005 CrossRef PubMed PubMedCentral Google Scholar
Hoshino SI (2012) Mechanism of the initiation of mRNA decay: role of eRF3 family G proteins. Wiley Interdiscip Rev RNA 3:743–757.
https://doi.org/10.1002/wrna.1133 CrossRef PubMed Google Scholar
Ivanov A, Mikhailova T, Eliseev B, Yeramala L, Sokolova E, Susorov D, Shuvalov A, Schaffitzel C, Alkalaeva E (2016) PABP enhances release factor recruitment and stop codon recognition during translation termination. Nucleic Acids Res 44:7766–7776.
https://doi.org/10.1093/nar/gkw635 CrossRef PubMed PubMedCentral Google Scholar
Jackson RJ, Hellen CUT, Pestova TV (2012) Termination and post-termination events in eukaryotic translation. Adv Protein Chem Struct Biol 86:45–93.
Keeling K, Lanier J, Du M et al (2004) Leaky termination at premature stop codons antagonizes nonsense-mediated mRNA decay in S. cerevisiae leaky termination at premature stop codons antagonizes nonsense-mediated mRNA decay in S. cerevisiae. Rna 10:691–703.
https://doi.org/10.1261/rna.5147804.facilitates CrossRef PubMed PubMedCentral Google Scholar
Kerényi Z, Mérai Z, Hiripi L, Benkovics A, Gyula P, Lacomme C, Barta E, Nagy F, Silhavy D (2008) Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay. EMBO J 27:1585–1595.
https://doi.org/10.1038/emboj.2008.88 CrossRef PubMed PubMedCentral Google Scholar
Kertész S, Kerényi Z, Mérai Z, Bartos I, Pálfy T, Barta E, Silhavy D (2006) Both introns and long 3′-UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants. Nucleic Acids Res 34:6147–6157.
https://doi.org/10.1093/nar/gkl737 CrossRef PubMed PubMedCentral Google Scholar
Kozlov G, Gehring K (2010) Molecular basis of eRF3 recognition by the MLLE domain of poly(A)-binding protein. PLoS One 5:3–8.
https://doi.org/10.1371/journal.pone.0010169 CrossRef Google Scholar
Lao NT, Maloney AP, Atkins JF, Kavanagh TA (2009) Versatile dual reporter gene systems for investigating stop codon readthrough in plants. PLoS One 4:e7354.
https://doi.org/10.1371/journal.pone.0007354 CrossRef PubMed PubMedCentral Google Scholar
Lejeune F (2017) Nonsense-mediated mRNA decay at the crossroads of many cellular pathways. BMB Rep 50:175–185
CrossRef PubMed PubMedCentral Google Scholar
Merai Z, Kerenyi Z, Molnar A, Barta E, Valoczi A, Bisztray G, Havelda Z, Burgyan J, Silhavy D (2005) Aureusvirus P14 is an efficient RNA silencing suppressor that binds double-stranded RNAs without size specificity. J Virol 79:7217–7226.
https://doi.org/10.1128/JVI.79.11.7217-7226.2005 CrossRef PubMed PubMedCentral Google Scholar
Mérai Z, Benkovics AH, Nyikó T, Debreczeny M, Hiripi L, Kerényi Z, Kondorosi É, Silhavy D (2013) The late steps of plant nonsense-mediated mRNA decay. Plant J 73:50–62.
https://doi.org/10.1111/tpj.12015 CrossRef PubMed Google Scholar
Merkulova TI, Frolova LY, Lazar M, Camonis J, Kisselev LL (1999) C-terminal domains of human translation termination factors eRF1 and eRF3 mediate their in vivo interaction. FEBS Lett 443:41–47
CrossRef PubMed Google Scholar
Miras M, Miller WA, Truniger V, Aranda MA (2017) Non-canonical translation in plant RNA viruses. Front Plant Sci 8:494.
https://doi.org/10.3389/fpls.2017.00494 CrossRef PubMed PubMedCentral Google Scholar
Nagy E, Maquat LE (1998) A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance. Trends Biochem Sci 23:198–199.
https://doi.org/10.1016/S0968-0004(98)01208-0 CrossRef PubMed Google Scholar
Nasif S, Contu L, Mühlemann O (2017) Beyond quality control: the role of nonsense-mediated mRNA decay (NMD) in regulating gene expression. Semin Cell Dev Biol 75:78–87.
https://doi.org/10.1016/j.semcdb.2017.08.053 CrossRef PubMed Google Scholar
Nizhnikov AA, Antonets KS, Inge-Vechtomov SG, Derkatch IL (2014) Modulation of efficiency of translation termination in Saccharomyces cerevisiae. Prion 8:247–260.
https://doi.org/10.4161/pri.29851 CrossRef PubMed PubMedCentral Google Scholar
Nyikó T, Sonkoly B, Mérai Z, Benkovics AH, Silhavy D (2009) Plant upstream ORFs can trigger nonsense-mediated mRNA decay in a size-dependent manner. Plant Mol Biol 71:367–378.
https://doi.org/10.1007/s11103-009-9528-4 CrossRef PubMed Google Scholar
Nyikó T, Kerényi F, Szabadkai L, Benkovics AH, Major P, Sonkoly B, Mérai Z, Barta E, Niemiec E, Kufel J, Silhavy D (2013) Plant nonsense-mediated mRNA decay is controlled by different autoregulatory circuits and can be induced by an EJC-like complex. Nucleic Acids Res 41:6715–6728.
https://doi.org/10.1093/nar/gkt366 CrossRef PubMed PubMedCentral Google Scholar
Nyikó T, Auber A, Szabadkai L, Benkovics A, Auth M, Mérai Z, Kerényi Z, Dinnyés A, Nagy F, Silhavy D (2017) Expression of the eRF1 translation termination factor is controlled by an autoregulatory circuit involving readthrough and nonsense-mediated decay in plants. Nucleic Acids Res 45:4174–4188.
https://doi.org/10.1093/nar/gkw1303 CrossRef PubMed PubMedCentral Google Scholar
Petsch KA, Mylne J, Botella JR (2005) Cosuppression of eukaryotic release factor 1-1 in Arabidopsis affects cell elongation and radial cell division. Plant Physiol 139:115–126.
https://doi.org/10.1104/pp.105.062695 CrossRef PubMed PubMedCentral Google Scholar
Ratcliff FG, Macfarlane SA, Baulcombe DC (1999) Gene silencing without DNA: RNA-mediated cross-protection between viruses. Plant Cell 11:1207–1215.
https://doi.org/10.1105/tpc.11.7.1207 CrossRef PubMed PubMedCentral Google Scholar
Riehs N, Akimcheva S, Puizina J, Bulankova P, Idol RA, Siroky J, Schleiffer A, Schweizer D, Shippen DE, Riha K (2008) Arabidopsis SMG7 protein is required for exit from meiosis. J Cell Sci 121:2208–2216.
https://doi.org/10.1242/jcs.027862 CrossRef PubMed Google Scholar
Roque S, Cerciat M, Gaugué I, Mora L, Floch AG, de Zamaroczy M, Heurgué-Hamard V, Kervestin S (2015) Interaction between the poly(A)-binding protein Pab1 and the eukaryotic release factor eRF3 regulates translation termination but not mRNA decay in Saccharomyces cerevisiae. RNA 21:124–134.
https://doi.org/10.1261/rna.047282.114 CrossRef PubMed PubMedCentral Google Scholar
Schueren F, Thoms S (2016) Functional translational readthrough: a systems biology perspective. PLoS Genet 12:e1006196.
https://doi.org/10.1371/journal.pgen.1006196 CrossRef PubMed PubMedCentral Google Scholar
Silhavy D, Molnár A, Lucioli A, Szittya G, Hornyik C, Tavazza M, Burgyán J (2002) A viral protein suppresses RNA silencing and binds silencing-generated, 21- to 25-nucleotide double-stranded RNAs. EMBO J 21:3070–3080.
https://doi.org/10.1093/emboj/cdf312 CrossRef PubMed PubMedCentral Google Scholar
Skuzeski JM, Nichols LM, Gesteland RF, Atkins JF (1991) The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons. J Mol Biol 218:365–373
CrossRef PubMed Google Scholar
True HL, Bedin I, Lindquist SL (2004) Epigenetic regulation of translation reveals hidden genetic variation to produce complex traits. Nature 431:184–187.
https://doi.org/10.1038/nature02885 CrossRef PubMed Google Scholar
Vexler K, Cymerman MA, Berezin I, Fridman A, Golani L, Lasnoy M, Saul H, Shaul O (2016) The Arabidopsis NMD factor UPF3 is feedback-regulated at multiple levels and plays a role in plant response to salt stress. Front Plant Sci 7:1–11.
https://doi.org/10.3389/fpls.2016.01376 CrossRef Google Scholar
von der Haar T, Tuite MF (2007) Regulated translational bypass of stop codons in yeast. Trends Microbiol 15:78–86.
https://doi.org/10.1016/j.tim.2006.12.002 CrossRef PubMed Google Scholar
Zhang Y, Sachs MS (2015) Control of mRNA stability in fungi by NMD, EJC and CBC factors through 3′UTR introns. Genetics 200:1133–1148.
Zhou X, Cooke P, Li L (2010) Eukaryotic release factor 1-2 affects Arabidopsis responses to glucose and phytohormones during germination and early seedling development. J Exp Bot 61:357–367.
https://doi.org/10.1093/jxb/erp308 CrossRef PubMed Google Scholar
Zhou X, Sun TH, Wang N, Ling HQ, Lu S, Li L (2011) The cauliflower Orange gene enhances petiole elongation by suppressing expression of eukaryotic release factor 1. New Phytol 190:89–100.
https://doi.org/10.1111/j.1469-8137.2010.03578.x CrossRef PubMed Google Scholar Copyright information
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