Translation Reinitiation Relies on the Interaction between eIF3a/TIF32 and Progressively Folded -Acting mRNA Elements Preceding Short uORFs
Reinitiation is a gene-specific translational control mechanism characterized by the ability of some short upstream uORFs to retain post-termination 40S subunits on mRNA. Its efficiency depends on surrounding cis-acting sequences, uORF elongation rates, various initiation factors, and the intercistronic distance. To unravel effects of cis-acting sequences, we investigated previously unconsidered structural properties of one such a cis-enhancer in the mRNA leader of GCN4 using yeast genetics and biochemistry. This leader contains four uORFs but only uORF1, flanked by two transferrable 5′ and 3′ cis-acting sequences, and allows efficient reinitiation. Recently we showed that the 5′ cis-acting sequences stimulate reinitiation by interacting with the N-terminal domain (NTD) of the eIF3a/TIF32 subunit of the initiation factor eIF3 to stabilize post-termination 40S subunits on uORF1 to resume scanning downstream. Here we identify four discernible reinitiation-promoting elements (RPEs) within the 5′ sequences making up the 5′ enhancer. Genetic epistasis experiments revealed that two of these RPEs operate in the eIF3a/TIF32-dependent manner. Likewise, two separate regions in the eIF3a/TIF32-NTD were identified that stimulate reinitiation in concert with the 5′ enhancer. Computational modeling supported by experimental data suggests that, in order to act, the 5′ enhancer must progressively fold into a specific secondary structure while the ribosome scans through it prior uORF1 translation. Finally, we demonstrate that the 5′ enhancer's stimulatory activity is strictly dependent on and thus follows the 3′ enhancer's activity. These findings allow us to propose for the first time a model of events required for efficient post-termination resumption of scanning. Strikingly, structurally similar RPE was predicted and identified also in the 5′ leader of reinitiation-permissive uORF of yeast YAP1. The fact that it likewise operates in the eIF3a/TIF32-dependent manner strongly suggests that at least in yeasts the underlying mechanism of reinitiation on short uORFs is conserved.
Vyšlo v časopise:
Translation Reinitiation Relies on the Interaction between eIF3a/TIF32 and Progressively Folded -Acting mRNA Elements Preceding Short uORFs. PLoS Genet 7(7): e32767. doi:10.1371/journal.pgen.1002137
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1002137
Souhrn
Reinitiation is a gene-specific translational control mechanism characterized by the ability of some short upstream uORFs to retain post-termination 40S subunits on mRNA. Its efficiency depends on surrounding cis-acting sequences, uORF elongation rates, various initiation factors, and the intercistronic distance. To unravel effects of cis-acting sequences, we investigated previously unconsidered structural properties of one such a cis-enhancer in the mRNA leader of GCN4 using yeast genetics and biochemistry. This leader contains four uORFs but only uORF1, flanked by two transferrable 5′ and 3′ cis-acting sequences, and allows efficient reinitiation. Recently we showed that the 5′ cis-acting sequences stimulate reinitiation by interacting with the N-terminal domain (NTD) of the eIF3a/TIF32 subunit of the initiation factor eIF3 to stabilize post-termination 40S subunits on uORF1 to resume scanning downstream. Here we identify four discernible reinitiation-promoting elements (RPEs) within the 5′ sequences making up the 5′ enhancer. Genetic epistasis experiments revealed that two of these RPEs operate in the eIF3a/TIF32-dependent manner. Likewise, two separate regions in the eIF3a/TIF32-NTD were identified that stimulate reinitiation in concert with the 5′ enhancer. Computational modeling supported by experimental data suggests that, in order to act, the 5′ enhancer must progressively fold into a specific secondary structure while the ribosome scans through it prior uORF1 translation. Finally, we demonstrate that the 5′ enhancer's stimulatory activity is strictly dependent on and thus follows the 3′ enhancer's activity. These findings allow us to propose for the first time a model of events required for efficient post-termination resumption of scanning. Strikingly, structurally similar RPE was predicted and identified also in the 5′ leader of reinitiation-permissive uORF of yeast YAP1. The fact that it likewise operates in the eIF3a/TIF32-dependent manner strongly suggests that at least in yeasts the underlying mechanism of reinitiation on short uORFs is conserved.
Zdroje
1. JacksonRJHellenCUTPestovaTV 2010 The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol 11 113 127
2. CalvoSEPagliariniDJMoothaVK 2009 Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. PNAS 106 7507 7512
3. KozakM 1986 Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44 283 292
4. IngoliaNTGhaemmaghamiSNewmanJRSWeissmanJS 2009 Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling. Science 324 218 223
5. IvanovIPLoughranGAtkinsJF 2008 uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs. PNAS 105 10079 10084
6. HoodHMNeafseyDEGalaganJSachsMS 2009 Evolutionary Roles of Upstream Open Reading Frames in Mediating Gene Regulation in Fungi. Annual Review of Microbiology 63 385 409
7. KozakM 2005 Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 361 13 37
8. HinnebuschAG 2005 Translational regulation of GCN4 and the general amino acid control of yeast. Annu Rev Microbiol 59 407 450
9. KozakM 2001 Constraints on reinitiation of translation in mammals. Nucleic Acids Res 29 5226 5232
10. SzameczBRutkaiECuchalovaLMunzarovaVHerrmannovaA 2008 eIF3a cooperates with sequences 5′ of uORF1 to promote resumption of scanning by post-termination ribosomes for reinitiation on GCN4 mRNA. Genes Dev 22 2414 2425
11. DeverTE 2002 Gene-specific regulation by general translation factors. Cell 108 545 556
12. VattemKMWekRC 2004 Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells. Proc Natl Acad Sci U S A 101 11269 11274
13. GrantCMHinnebuschAG 1994 Effect of sequence context at stop codons on efficiency of reinitiation in GCN4 translational control. Mol Cell Biol 14 606 618
14. GrantCMMillerPFHinnebuschAG 1995 Sequences 5′ of the first upstream open reading frame in GCN4 mRNA are required for efficient translational reinitiation. Nuc Acids Res 23 3980 3988
15. ValášekLMathewAShinBSNielsenKHSzameczB 2003 The Yeast eIF3 Subunits TIF32/a and NIP1/c and eIF5 Make Critical Connections with the 40S Ribosome in vivo. Genes Dev 17 786 799
16. RablJLeibundgutMAtaideSFHaagABanN 2011 Crystal Structure of the Eukaryotic 40S Ribosomal Subunit in Complex with Initiation Factor 1. Science in press
17. CuchalováLKoubaTHerrmannováADanyiIChiuW-l 2010 The RNA Recognition Motif of Eukaryotic Translation Initiation Factor 3g (eIF3g) Is Required for Resumption of Scanning of Posttermination Ribosomes for Reinitiation on GCN4 and Together with eIF3i Stimulates Linear Scanning. Mol Cell Biol 30 4671 4686
18. VilelaCLinzBRodrigues-PousadaCMcCarthyJE 1998 The yeast transcription factor genes YAP1 and YAP2 are subject to differential control at the levels of both translation and mRNA stability. Nucleic Acids Res 26 1150 1159
19. MillerPFHinnebuschAG 1989 Sequences that surround the stop codons of upstream open reading frames in GCN4 mRNA determine their distinct functions in translational control. Genes and Development 3 1217 1225
20. Ruiz-EchevarriaMJPeltzSW 2000 The RNA binding protein Pub1 modulates the stability of transcripts containing upstream open reading frames. Cell 101 741 751
21. HofackerILFontanaWStadlerPFBonhoefferLSTackerM 1994 Fast Folding and Comparison of RNA Secondary Structures. MonatshChem 125 167 188
22. ChenYKortemmeTRobertsonTBakerDVaraniG 2004 A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic Acids Research 32 5147 5162
23. PestovaTVKolupaevaVG 2002 The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection. Genes Dev 16 2906 2922
24. WethmarKBegayVSminkJJZaragozaKWiesenthalV 2010 C/EBPbetaDeltauORF mice – a genetic model for uORF-mediated translational control in mammals. Genes & Development 24 15 20
25. WiestnerASchlemperRJvan der MaasAPCSkodaRC 1998 An activating splice donor mutation in the thrombopoietin gene causes hereditary thrombocythaemia. Nat Genet 18 49 52
26. WenYLiuYXuYZhaoYHuaR 2009 Loss-of-function mutations of an inhibitory upstream ORF in the human hairless transcript cause Marie Unna hereditary hypotrichosis. Nat Genet 41 228 233
27. LiuLDilworthDGaoLMonzonJSummersA 1999 Mutation of the CDKN2A 5′ UTR creates an aberrant initiation codon and predisposes to melanoma. Nat Genet 21 128 132
28. GriffinEReAHamelNFuCBushH 2001 A link between diabetes and atherosclerosis: Glucose regulates expression of CD36 at the level of translation. Nat Med 7 840 846
29. ZhouWSongW 2006 Leaky scanning and reinitiation regulate BACE1 gene expression. Mol Cell Biol 26 3353 3364
30. PisarevAVSkabkinMAPisarevaVPSkabkinaOVRakotondrafaraAM 2010 The Role of ABCE1 in Eukaryotic Posttermination Ribosomal Recycling. 37 196 210
31. PisarevAVKolupaevaVGYusupovMMHellenCUTPestovaTV 2008 Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes. EMBO J 27 1609 1621
32. ParkHSHimmelbachABrowningKSHohnTRyabovaLA 2001 A plant viral “reinitiation” factor interacts with the host translational machinery. Cell 106 723 733
33. RoyBVaughnJNKimB-HZhouFGilchristMA 2010 The h subunit of eIF3 promotes reinitiation competence during translation of mRNAs harboring upstream open reading frames. RNA 16 748 761
34. PassmoreLASchmeingTMMaagDApplefieldDJAckerMG 2007 The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome. Mol Cell 26 41 50
35. PöyryTAKaminskiAConnellEJFraserCSJacksonRJ 2007 The mechanism of an exceptional case of reinitiation after translation of a long ORF reveals why such events do not generally occur in mammalian mRNA translation. Genes Dev 21 3149 3162
36. LuttermannCMeyersG 2009 The importance of inter- and intramolecular base pairing for translation reinitiation on a eukaryotic bicistronic mRNA. Genes Dev 23 331 344
37. Kyu YoungSChun SungKCheol KyuHHack SunCPing-YeeL 2010 uAUG-mediated translational initiations are responsible for human mu opioid receptor gene expression. Journal of Cellular and Molecular Medicine 14 1113 1124
38. CalkhovenCRMullerCLeutzA 2000 Translational control of C/EBPa and C/EBPb isoform expression. Genes Dev 14 1920 1932
39. NielsenKHValášekL 2007 In vivo deletion analysis of the architecture of a multi-protein complex of translation initiation factors. Methods Enzymol 431 15 32
40. ValášekLPhanLSchoenfeldLWValáškováVHinnebuschAG 2001 Related eIF3 subunits TIF32 and HCR1 interact with an RNA recoginition motif in PRT1 required for eIF3 integrity and ribosome binding. EMBO J 20 891 904
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2011 Číslo 7
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
Najčítanejšie v tomto čísle
- Genome-Wide Association Study Identifies Novel Restless Legs Syndrome Susceptibility Loci on 2p14 and 16q12.1
- Loss of the BMP Antagonist, SMOC-1, Causes Ophthalmo-Acromelic (Waardenburg Anophthalmia) Syndrome in Humans and Mice
- Gene-Based Tests of Association
- Genome-Wide Association Study Identifies as a Susceptibility Gene for Pediatric Asthma in Asian Populations