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. 2004 Apr 7;3(2):295–300. doi: 10.1016/0959-437X(93)90037-P

Gene regulation: translational initiation by internal ribosome binding

Soo-Kyung Oh 1, Peter Sarnow 1
PMCID: PMC7133282  PMID: 8504255

Abstract

During the past year, several examples of cellular mRNAs have been described in which translational initiation occurs by internal ribosome binding, a mechanism hitherto thought to be restricted to picornaviral RNAs. New insights into the molecular mechanism of internal ribosome entry have been provided by the structural and functional analyses of both the internal ribosome entry sites and the protein factors that stimulate translation mediated by these elements.

Abbreviations: Antp, Antennapedia; eIF, eukaryote initiation factor; EMC, encephalomyocarditis; FMD, foot and mouth disease; HCV, hepatitis C virus; IBV, infectious bronchitis virus; IRES, internal ribosome entry site; 5′ NCR, 5′ non-coding region; Tfm, testicular feminization

References

  • 1.Kozak M. The Scanning Model for Translation: An Update. J Cell Biol. 1989;108:229–241. doi: 10.1083/jcb.108.2.229. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Hershey J.W.B. Translational Control in Mammalian Cells. Annu Rev Biochem. 1991;60:717–755. doi: 10.1146/annurev.bi.60.070191.003441. [DOI] [PubMed] [Google Scholar]
  • 3.Merrick W.C. Mechanism and Regulation of Eukaryotic Protein Synthesis. Microbiol Rev. 1992;56:291–315. doi: 10.1128/mr.56.2.291-315.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.Kozak M. An Analysis of Vertebrate mRNA Sequences: Initiation of Translational Control. J Cell Biol. 1991;115:887–903. doi: 10.1083/jcb.115.4.887. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Toyoda H., Kohara M., Kataoka Y., Suganuma T., Omata T., Imura N., Nomoto A. Complete Nucleotides Sequences of all Three Poliovirus Serotype Genomes: Implication for Genetic Relationship Gene Function and Antigenic Determinants. J Mol Biol. 1984;174:561–585. doi: 10.1016/0022-2836(84)90084-6. [DOI] [PubMed] [Google Scholar]
  • 6.Sonenberg N. Poliovirus Translation. Curr Top Microbiol Immunol. 1990;161:23–47. doi: 10.1007/978-3-642-75602-3_2. [DOI] [PubMed] [Google Scholar]
  • 7.Pelletier J., Sonenberg N. Internal Initiation of Translation of Eukaryotec mRNA Directed by a Sequence Derived from Poliovirus RNA. Nature. 1988;334:320–325. doi: 10.1038/334320a0. [DOI] [PubMed] [Google Scholar]
  • 8.Jang S.K., Kräusslich H.G., Nickln M.J.H., Duke G.M., Palnenberg A.C., Wimmer E. A Segment of the 5′ Non-Translated Region of Encephalomyocarditis Virus RNA Directs Internal Entry of Ribosomes During In Vitro Translation. J Virol. 1988;62:2636–2643. doi: 10.1128/jvi.62.8.2636-2643.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.Dever T.E., Feng I., Wek R.C., Hinnebusch A.G. Phosphorylation of Initiation Factor 2α by Protein Kinase GCN2 Mediates Gene-Specific Translational Control of GCN4 in Yeast. Cell. 1992;68:585–596. doi: 10.1016/0092-8674(92)90193-g. of outstanding interest. [DOI] [PubMed] [Google Scholar]; Elegant genetic and biochemical studies demonstrate that the translation of the yeast GCN4 mRNA is controlled by a mechanism of reinitiation. Specifically, the yeast protein kinase GCN2 was shown to phosphorylate the α subunit of eIF2 on Ser51 in response to amino acid starvation. Because eIF2-GTP is limited under such conditions, it takes longer to reload scanning 40S subunits with eIF2-GTP, resulting in the failure to initiate protein synthesis at an AUG codon (located upstream of the fourth open reading frame) located in the 5′ non-coding region of GCN4 mRNA.
  • 10.Macejak D.G., Sarnow P. Internal Initiation of Translation Mediated by the 5′ Leader of a Cellular mRNA. Nature. 1991;353:90–94. doi: 10.1038/353090a0. [DOI] [PubMed] [Google Scholar]
  • 11.Oh S.-K., Scott M.P., Sarnow P. Homeotic Gene Antennapedia mRNA Contain 5′-Noncoding Sequences that Confer Translational Initiation by Internal Ribosome Binding. Genes Dev. 1992;6:1643–1653. doi: 10.1101/gad.6.9.1643. of outstanding interest. [DOI] [PubMed] [Google Scholar]; Identification of an IRES located in the mRNA of a homeotic gene. This finding suggests that internal initiation may possibly be used to regulate gene expression during development in Drosophila.
  • 12.Bandyopadhyay P.K., Wang C., Lipton H.L. Cap-Independent Translation by the 5′ Untranslated Region of Theiler s Murine Encephalomyelitis Virus. J Virol. 1992;66:6249–6256. doi: 10.1128/jvi.66.11.6249-6256.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Pelletier J., Sonenberg N. Internal Binding of Eucaryotic Ribosomes on Poliovirus RNA Translation in HeLa Cell Extracts. J Virol. 1989;63:441–444. doi: 10.1128/jvi.63.1.441-444.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Kozak M. A Consideration of Alternative Models for the Initiation of Translation in Eukaryotes. Crit Rev Biochem Mol Biol. 1992;27:385–402. doi: 10.3109/10409239209082567. [DOI] [PubMed] [Google Scholar]
  • 15.Nicholson R., Pelletier J., Le S.-Y., Sonenberg N. Structural and Functional Analysis of the Ribosome Landing Pad of Poliovirus Type 2: In Vivo Translation Studies. J Virol. 1991;65:5886–5894. doi: 10.1128/jvi.65.11.5886-5894.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Mola A., Jang S.K., Paul A.V., Reuer Q., Wimmer E. Cardioviral Internal Ribosomal Entry Site is Functional in a Genetically Engineered Dicistronic Poliovirus. Nature. 1992;356:255–257. doi: 10.1038/356255a0. of outstanding interest. [DOI] [PubMed] [Google Scholar]; A novel genetic approach is presented to prove that an IRES element can initiate translation independently of the 5′ end of the mRNA The open reading frame of poliovirus was interrupted by insertion of the EMC virus IRES. This mRNA containing two IRESs was packaged into poliovirions, and the recombinant viruses was successfully propagated in cultured cells.
  • 17.Sonenberg N., Meerovitch K. Translation of Poliovirus mRNA. Enzyme. 1990;44:278–291. doi: 10.1159/000468765. [DOI] [PubMed] [Google Scholar]
  • 18.Jang S.K., Pestova T.V., Helen C.U.T., Witherell G.W., Wiminier E. Cap-Independent Translation of Picornavirus RNAs: Structure and Function of the Internal Ribosome Entry Site. Enzyme. 1990;44:292–309. doi: 10.1159/000468766. [DOI] [PubMed] [Google Scholar]
  • 19.Simoes E.A.F., Sarnow P. An RNA Hairpin at the Extreme 5′ End of the Poliovirus RNA Genome Modulates Viral Translation in Human Cells. J Virol. 1991;65:913–921. doi: 10.1128/jvi.65.2.913-921.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Pelletier J., Kaplan G., Racaniello V.R., Sonenberg N. Cap-Independent Translation of Poliovirus mRNA is Conferred by Sequence Elements Within the 5′ Noncoding Region. Mol Cell Biol. 1988;8:1103–1112. doi: 10.1128/mcb.8.3.1103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.Hahn J., Grandi G., Gryczan T.J., Dubnau D. Translational Attenuation of ermC: A Deletion Analysis. Mol Gen Genet. 1982;186:204–216. doi: 10.1007/BF00331851. [DOI] [PubMed] [Google Scholar]
  • 22.Kozak M. Inability of Circular mRNA to Attach to Eukaryotic Ribosomes. Nature. 1979;280:82–85. doi: 10.1038/280082a0. [DOI] [PubMed] [Google Scholar]
  • 23.Konarska M., Filipowicz W., Domdey H., Gross H.J. Binding of Ribosomes to Linear and Circular Forms of the 5′-Terminal Leader Fragment of Tobacco-Mosaic-Virus RNA. Eur J Biochem. 1981;114:221–227. doi: 10.1111/j.1432-1033.1981.tb05139.x. [DOI] [PubMed] [Google Scholar]
  • 24.Moore M.J., Sharp P.A. Site-Specific Modification of Pre-mRNA The 2′-Hydroxyl Groups at the Splice Sites. Science. 1992;256:992–997. doi: 10.1126/science.1589782. of special interest. [DOI] [PubMed] [Google Scholar]; Describes an efficient method for synthesizing site-specifically modified RNA molecules by joining two RNA molecules, held together by a ‘DNA splint’, with T4 DNA ligase. This strategy can be applied to produce large quantities of circular RNAs.
  • 25.Bornian A., Jackson R.J. Initiation of Translation of Human Rhinovirus RNA: Mapping the Internal Ribosome Entry Site. Virology. 1992;188:685–696. doi: 10.1016/0042-6822(92)90523-r. of outstanding interest. [DOI] [PubMed] [Google Scholar]; An IRES was identified and mapped in the rhinovirus 5′ non-coding region. It was found that the [RES was located upstream of the initiator AUG colon, implying that the mechanisms of rhinovirus and poliovirus mRNA translation are very similar.
  • 26.Kühn R., Luz N., Beck E. Functional Analysis of the Internal Translation Initiation Site of Foot-and-Mouth Disease Virus. J Virol. 1990;64:4625–4631. doi: 10.1128/jvi.64.10.4625-4631.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27.Belsham G.J. Dual Initiation Sites of Protein Synthesis on Foot-and-Mouth Disease Virus RNA are Selected Following Internal Entry and Scanning of Ribosomes In Vivo. EMBO J. 1992;11:1105–1110. doi: 10.1002/j.1460-2075.1992.tb05150.x. of special interest. [DOI] [PMC free article] [PubMed] [Google Scholar]; Two initiator AUG colons, separated by 84 nucleotides, are used for the initiation of FMD virus mRNA translation. This study shows that an IRES, located upstream of the 5′ proximal AUG colon, is used to recruit ribosomal subunits on the mRNA Following scanning, protein synthesis can start at either AUG colon.
  • 28.Kaminski A., Howell M.T., Jackson R.J. Initiation of Encephalomyocarditis Virus RNA Translation: The Authentic Initiation Site is Not Selected by a Scanning Mechanism. EMBO J. 1990;9:3753–3759. doi: 10.1002/j.1460-2075.1990.tb07588.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 29.Meerovitch K., Nicholson R., Sonenberg N. In Vitro Mutational Analysis of Cis-Acting RNA Translational Elements Within the Poliovirus Type 2 5′ Untranslated Region. J Virol. 1991;65:5895–5901. doi: 10.1128/jvi.65.11.5895-5901.1991. of outstanding interest. [DOI] [PMC free article] [PubMed] [Google Scholar]; This study showed that an oligopyrimidine motif and an AUG triplet, located 20 nucleotides downstream of the motif, were important features in the poliovirus type 2 IRES.
  • 30.Pestova T.V., Hellen C.U.T., Wimmer E. Translation of Poliovirus RNA: Role of an Essential Cis-Acting Oligopyrimidine Element Within the 5′ Nontranslated Region and Involvement of a Cellular 57-Kilodalton Protein. J Virol. 1991;65:6194–6204. doi: 10.1128/jvi.65.11.6194-6204.1991. of outstanding interest. [DOI] [PMC free article] [PubMed] [Google Scholar]; A p57 protein, which had previously been found to be involved in EMC virus mRNA translation, was detected to bind upstream of the oligopyrimidine tract in the polioviral [RES. That the same p57 proteins bound specifically to different IRES elements indicates that this protein functions in internal initiation.
  • 31.Pilpenko E.V., Gmyyl A.P., Maslova S.V., Svitkin Y.V., Sinyakov A.N., Agol V.I. Prokaryotic-Like Cis Elements in the Cap-Independent Internal Initiation of Translation on Picornavirus RNA. Cell. 1992;68:119–131. doi: 10.1016/0092-8674(92)90211-t. of outstanding interest. [DOI] [PubMed] [Google Scholar]; With the use of mutant polioviruses it was found that the proper spacing between the oligopyrimidine sequence element and a downstream-located AUG triplet is an essential element in the polioviral IRES. A function for the oligopyrimidine sequence analogous to that of the prokaryotic Shine-Dalgarno motif was also suggested.
  • 32.Del Angel R.M., Papavassilou A.G., Fernández-Tomás C., Silverstein S.J., Racaniello V.R. Vol. 86. 1989. Cell Proteins Bind to Multiple Sites Within the 5′ Untranslated Region of Poliovirus RNA; pp. 8299–8303. (Proc Natl Acad Sci USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 33.Dildine S.L., Semler B.L. Conservation of RNA-Protein Inter .actions Among Picornaviruses. J Virol. 1992;66:4364–4376. doi: 10.1128/jvi.66.7.4364-4376.1992. of special interest. [DOI] [PMC free article] [PubMed] [Google Scholar]; The polloviral 5′ non-coding region harbors at least seven RNA hairpin structures. Interactions of proteins with two of these structures were investigated in this work. Interestingly, these RNA-protein interactions are conserved among certain picomaviruses, implying that this conservation has functional significance.
  • 34.Haller A.A., Semler B.L. Linker Scanning Mutagenesis of the Internal Ribosome Entry Site of Poliovirus RNA. J Virol. 1992;66:5075–5086. doi: 10.1128/jvi.66.8.5075-5086.1992. of outstanding interest. [DOI] [PMC free article] [PubMed] [Google Scholar]; In this remarkable study, 14 sequence alterations were introduced into the polioviral IRES by linker scanning mutagenesis. Viral mutants could be obtained with eight viral nucleotides substituted with those of the linker sequences. Analysis of such viral mutants and of selected revertants revealed that proper spacing between RNA hairpins was a prerequisite for RNA-protein interactions that most likely modulated internal ribosome binding.
  • 35.Meerovitch K., Pelletier J., Sonenberg N. A Cellular Protein that Binds to the 5′-noncoding Region of Poliovirus RNA: Implications for Internal Translation Initiation. Genes Des. 1989;3:1026–1034. doi: 10.1101/gad.3.7.1026. [DOI] [PubMed] [Google Scholar]
  • 36.Luz N., Beck E. Interaction of a Cellular 57-Kilodalton Protein with the Internal Translation Initiation Site of Foot and-Mouth Disease Virus. J Virol. 1991;65:6486–6494. doi: 10.1128/jvi.65.12.6486-6494.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 37.Jang S.K., Wimmer E. Cap-Independent Translation of Encephalomyocarditis Virus RNA: Structural Elements of the Internal Ribosomal Entry Site and Involvement of a Cellular 57-kD RNA-Binding Protein. Genes Der. 1990;4:1560–1572. doi: 10.1101/gad.4.9.1560. [DOI] [PubMed] [Google Scholar]
  • 38.Hambidge S., Sarnow P. Vol. 89. 1992. Translational Enhancement of the Poliovirus 5′ Noncoding Region Mediated by Virus-Encoded Polypeptide 2A; pp. 10272–10276. (Proc Natl Acad Sci USA). of outstanding interest. [DOI] [PMC free article] [PubMed] [Google Scholar]; It was found that in infected cells, at a time when cap-dependent translation was not inhibited, mRNAs containing the polioviral IRES were translated at an enhanced rate compared with mRNAs without IRESs . This effect was mediated by the expression of virus-encoded polypeptide 2A. Thus, viral IRES elements can be regulated by trans-acting proteins.
  • 39.Anthony D.D., Merrick W.C. Eucaroytic Initiation Factor (eIF)-4F. Implications for a Role in Internal Initiation of Translation. J Biol Chem. 1991;266:10218–10226. of outstanding interest. [PubMed] [Google Scholar]; The eukaryotic initiation factor eIF-4F was found to stimulate cap-dependent, as well as cap-independent (by internal ribosome binding), translation. Similarly, eIF-4B showed such an effect, albeit to a lesser extent. That the same factors are involved in cap-dependent and internal initiation has important implications for the mechanism of translational initiation in eukaryotes.
  • 40.Scheper G.C., Voorma H.O., Thomas A.D. Eukaryotic Initiation Factors-4E and -4F Stimulate 5′ Cap-Dependent as well as Internal Initiation of Protein Synthesis. J Biol Chem. 1992;267:7269–7274. of special interest. [PubMed] [Google Scholar]; This study shows that, in addition to eIF-4F (see [38••]), factor eIF-4E stimulated cap-dependent as well as internal initiation of translation. This finding is surprising because eIF-4E is the protein in the eIF-4F complex that interacts directly with the cap structure present at the 5′ ends of MRNAs. Both [38•,39•] indicate that eIF-4F (composed of eIF-4A, eIF-4E and p220) is a multifunctional translation factor which is involved in different modes of translational initiation.
  • 41.Etchison D., Milburn S.C., Edery I., Sonenberg N., Hershey J.W.B. Inhibition of HeLa Cell Protein Synthesis Following Poliovirus Infection Correlates with the Proteolysis of a 220,000 Dalton Polypeptide Associated with Eukaryotic Initiation Factor 3 and a Cap Binding Protein Complex. J Biol Chem. 1982;257:14800–14810. [PubMed] [Google Scholar]
  • 42.Buckley B., Ehrenfeld E. The Cap-Binding Protein Complex in Uninfected and Poliovirus-infected HeLa Cells. J Biol Chem. 1987;262:13599–13606. [PubMed] [Google Scholar]
  • 43.Tsukiyuma-Kohara K., Iizuka N., Kohara M, Nomoto A. Internal Ribosome Entry Site Within Hepatitis C Virus RNA. J Virol. 1992;66:1476–1483. doi: 10.1128/jvi.66.3.1476-1483.1992. of special interest. [DOI] [PMC free article] [PubMed] [Google Scholar]; An IRES was detected in the 5′ non-coding region of HCV in in vitro translation studies employing dicistronic mRNAs. This finding is in contrast to data reported in [44•].
  • 44.Yoo B.J., Spaete R.R., Geballe A.P., Selby M., Houghton M., Han J.H. 5′ End-Dependent Translation Initiation of Hepatitis C Viral RNA and the Presence of Putative Positive and Negative Translational Control Elements Within the 5′ Untranslated Region. Virology. 1992;191:889–899. doi: 10.1016/0042-6822(92)90264-p. of special interest. [DOI] [PubMed] [Google Scholar]; This study shows that the mRNA of HCV was translated extremely poorly in vitro and in vivo. Because no IRES element was detected within the 5′ non-coding region, and deletions within this region of the mRNA enhanced translation of the mRNA, it was concluded that subgenomic viral RNAs may be the functional mRNAs in infected cells. This finding is in contrast to data reported in [43].
  • 45.Liu D.X., Ingus S.C. Internal Entry of Ribosomes on a Tri cistronic mRNA Encoded by Infectious Bronchitis Virus. J Vital. 1992;66:6143–6154. doi: 10.1128/jvi.66.10.6143-6154.1992. of Outstanding Interest. [DOI] [PMC free article] [PubMed] [Google Scholar]; Identifies a functionally tricistronic mRNA. The mRNA3 of IBV was translated by a cap-dependent scanning mechanism to produce protein 3a, by a leaky scanning mechanism to synthesize 3b, and by an internal ribosome-binding mechanism to synthesize polypeptide 3c. This is the first identification of an IRES located within a coding region.
  • 46.Trono d'Andino R., Baltimore D. Translation in Mammalian Cells of a Gene Linked to the Poliovirus 5′ Non-Coding Region. Science. 1988;241:445–448. doi: 10.1126/science.2839901. [DOI] [PubMed] [Google Scholar]
  • 47.Hambidge S., Sarnow P. Terminal 7-Methyl-Guanosine Cap Structure on the Normally Uncapped 5′Noncoding Region of Poliovirus mRNA Inhibits its Translation in Mammalian Cells. J Virol. 1991;65:6312–6315. doi: 10.1128/jvi.65.11.6312-6315.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 48.Sarnow P. Vol. 86. 1989. Translation of Glucose-Regulated Protein 78/immunoglobulin Heavy-Chain Binding Protein mRNA is Increased in Poliovirus-Infected Cells at a Time when Cap Dependent Translation of Cellular mRNAs is Inhibited; pp. 5795–5799. (Proc Natl Acad Sci USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 49.Gaspar M.-L., Meo T., Bourgarel P., Guenet J.-I., Tosi M. Vol. 88. 1991. A Single Base Deletion in the Tfm Androgen Receptor Gene Creates a Short-Lived Messenger RNA that Directs Internal Translation Initiation; pp. 8606–8610. (Proc Nall Acad Sci USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 50.Cavener D.R., Cavener B.A. Translation Start Sites and mRNA Leaders. Atlas of Drosophila Genes. 1992 in press. [Google Scholar]
  • 51.Kozak M. An Analysis of 5′-Noncoding Sequences from 699 Vertebrate Messenger RNAs. Nucleic Acids Res. 1987;15:8125–8132. doi: 10.1093/nar/15.20.8125. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 52.Laughon A., Boulet A.M., Bermingham J.R., Laymon R.A., Scott M.P. Structure of Transcripts from the Homeotic Antennapedia Gene of Drosophila Melanogaster. Two Promot ers Control the Major Protein-Coding Region. Mol Cell Biol. 1986;6:4647–4689. doi: 10.1128/mcb.6.12.4676. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 53.Stroeher V.L., Jorgensen E.M., Garber R.L. Multiple Transcripts from the Antennapedia Gene of Drosophila Melanogaster. Mol Cell Biol. 1986;6:4667–4675. doi: 10.1128/mcb.6.12.4667. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 54.Hooper J.E., Pérez-Alonso M., Bermingham J.R., Prout M., Rocklein B.A., Wagenbach M., Edstrom J.-E., De Frutos R., Scott M.P. Comparative Studies of Drosophila Antennapedia Genes. Genetics. 1992;132:453–469. doi: 10.1093/genetics/132.2.453. [DOI] [PMC free article] [PubMed] [Google Scholar]

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