Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1997 Jan 15;25(2):362–369. doi: 10.1093/nar/25.2.362

A common RNA structural motif involved in the internal initiation of translation of cellular mRNAs.

S Y Le 1, J V Maizel Jr 1
PMCID: PMC146446  PMID: 9016566

Abstract

The 5'-non-translated regions (5'NTR) of human immunoglobulin heavy chain binding protein (BiP), Antennapedia (Antp) ofDrosophilaand human fibroblast growth factor 2 (FGF-2) mRNAs are reported to mediate translation initiation by an internal ribosome binding mechanism. In this study, we investigate predicted features of the higher order structures folded in these 5'NTR sequences. Statistical analyses of RNA folding detected a 92 nt unusual folding region (UFR) from 129 to 220, close to the initiator AUG in the BiP mRNA. Details of the structural analyses show that the UFR forms a Y-type stem-loop structure with an additional stem-loop in the 3'-end resembling the common structure core found in the internal ribosome entry site (IRES) elements of picornavirus. The Y-type structural motif is also conserved among a number of divergent BiP mRNAs. We also find two RNA elements in the 5'-leader sequence of human FGF-2. The first RNA element (96 nt) is 2 nt upstream of the first CUG start codon located in the reported IRES element of human FGF-2. The second (107 nt) is immediately upstream of the authentic initiator AUG of the main open reading frame. Intriguingly, the folded RNA structural motif in the two RNA elements is conserved in other members of FGF family and shares the same structural features as that found in the 5'NTR of divergent BiP mRNAs. We suggest that the common RNA structural motif conserved in the diverse BiP and FGF-2 mRNAs has a general function in the internal ribosome binding mechanism of cellular mRNAs.

Full Text

The Full Text of this article is available as a PDF (220.8 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Abraham J. A., Mergia A., Whang J. L., Tumolo A., Friedman J., Hjerrild K. A., Gospodarowicz D., Fiddes J. C. Nucleotide sequence of a bovine clone encoding the angiogenic protein, basic fibroblast growth factor. Science. 1986 Aug 1;233(4763):545–548. doi: 10.1126/science.2425435. [DOI] [PubMed] [Google Scholar]
  2. 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 Nov;66(11):6249–6256. doi: 10.1128/jvi.66.11.6249-6256.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bangs J. D., Uyetake L., Brickman M. J., Balber A. E., Boothroyd J. C. Molecular cloning and cellular localization of a BiP homologue in Trypanosoma brucei. Divergent ER retention signals in a lower eukaryote. J Cell Sci. 1993 Aug;105(Pt 4):1101–1113. doi: 10.1242/jcs.105.4.1101. [DOI] [PubMed] [Google Scholar]
  4. 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 Mar;11(3):1105–1110. doi: 10.1002/j.1460-2075.1992.tb05150.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Borman A., Howell M. T., Patton J. G., Jackson R. J. The involvement of a spliceosome component in internal initiation of human rhinovirus RNA translation. J Gen Virol. 1993 Sep;74(Pt 9):1775–1788. doi: 10.1099/0022-1317-74-9-1775. [DOI] [PubMed] [Google Scholar]
  6. Borman A., Jackson R. J. Initiation of translation of human rhinovirus RNA: mapping the internal ribosome entry site. Virology. 1992 Jun;188(2):685–696. doi: 10.1016/0042-6822(92)90523-r. [DOI] [PubMed] [Google Scholar]
  7. Brookes S., Smith R., Thurlow J., Dickson C., Peters G. The mouse homologue of hst/k-FGF: sequence, genome organization and location relative to int-2. Nucleic Acids Res. 1989 Jun 12;17(11):4037–4045. doi: 10.1093/nar/17.11.4037. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Brown E. A., Day S. P., Jansen R. W., Lemon S. M. The 5' nontranslated region of hepatitis A virus RNA: secondary structure and elements required for translation in vitro. J Virol. 1991 Nov;65(11):5828–5838. doi: 10.1128/jvi.65.11.5828-5838.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Cech T. R. Conserved sequences and structures of group I introns: building an active site for RNA catalysis--a review. Gene. 1988 Dec 20;73(2):259–271. doi: 10.1016/0378-1119(88)90492-1. [DOI] [PubMed] [Google Scholar]
  10. Cech T. R., Tanner N. K., Tinoco I., Jr, Weir B. R., Zuker M., Perlman P. S. Secondary structure of the Tetrahymena ribosomal RNA intervening sequence: structural homology with fungal mitochondrial intervening sequences. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3903–3907. doi: 10.1073/pnas.80.13.3903. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Chang S. C., Wooden S. K., Nakaki T., Kim Y. K., Lin A. Y., Kung L., Attenello J. W., Lee A. S. Rat gene encoding the 78-kDa glucose-regulated protein GRP78: its regulatory sequences and the effect of protein glycosylation on its expression. Proc Natl Acad Sci U S A. 1987 Feb;84(3):680–684. doi: 10.1073/pnas.84.3.680. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Chen J. H., Le S. Y., Shapiro B., Currey K. M., Maizel J. V. A computational procedure for assessing the significance of RNA secondary structure. Comput Appl Biosci. 1990 Jan;6(1):7–18. doi: 10.1093/bioinformatics/6.1.7. [DOI] [PubMed] [Google Scholar]
  13. Delli Bovi P., Curatola A. M., Kern F. G., Greco A., Ittmann M., Basilico C. An oncogene isolated by transfection of Kaposi's sarcoma DNA encodes a growth factor that is a member of the FGF family. Cell. 1987 Aug 28;50(5):729–737. doi: 10.1016/0092-8674(87)90331-x. [DOI] [PubMed] [Google Scholar]
  14. Finch P. W., Rubin J. S., Miki T., Ron D., Aaronson S. A. Human KGF is FGF-related with properties of a paracrine effector of epithelial cell growth. Science. 1989 Aug 18;245(4919):752–755. doi: 10.1126/science.2475908. [DOI] [PubMed] [Google Scholar]
  15. Freier S. M., Kierzek R., Jaeger J. A., Sugimoto N., Caruthers M. H., Neilson T., Turner D. H. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9373–9377. doi: 10.1073/pnas.83.24.9373. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Glass M. J., Summers D. F. Identification of a trans-acting activity from liver that stimulates hepatitis A virus translation in vitro. Virology. 1993 Apr;193(2):1047–1050. doi: 10.1006/viro.1993.1225. [DOI] [PubMed] [Google Scholar]
  17. Gupta R. S., Aitken K., Falah M., Singh B. Cloning of Giardia lamblia heat shock protein HSP70 homologs: implications regarding origin of eukaryotic cells and of endoplasmic reticulum. Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):2895–2899. doi: 10.1073/pnas.91.8.2895. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Gutell R. R., Larsen N., Woese C. R. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev. 1994 Mar;58(1):10–26. doi: 10.1128/mr.58.1.10-26.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Gutell R. R., Weiser B., Woese C. R., Noller H. F. Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol. 1985;32:155–216. doi: 10.1016/s0079-6603(08)60348-7. [DOI] [PubMed] [Google Scholar]
  20. Haub O., Drucker B., Goldfarb M. Expression of the murine fibroblast growth factor 5 gene in the adult central nervous system. Proc Natl Acad Sci U S A. 1990 Oct;87(20):8022–8026. doi: 10.1073/pnas.87.20.8022. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hellen C. U., Witherell G. W., Schmid M., Shin S. H., Pestova T. V., Gil A., Wimmer E. A cytoplasmic 57-kDa protein that is required for translation of picornavirus RNA by internal ribosomal entry is identical to the nuclear pyrimidine tract-binding protein. Proc Natl Acad Sci U S A. 1993 Aug 15;90(16):7642–7646. doi: 10.1073/pnas.90.16.7642. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Heschl M. F., Baillie D. L. Characterization of the hsp70 multigene family of Caenorhabditis elegans. DNA. 1989 May;8(4):233–243. doi: 10.1089/dna.1.1989.8.233. [DOI] [PubMed] [Google Scholar]
  23. 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 Oct;132(2):453–469. doi: 10.1093/genetics/132.2.453. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Iizuka N., Chen C., Yang Q., Johannes G., Sarnow P. Cap-independent translation and internal initiation of translation in eukaryotic cellular mRNA molecules. Curr Top Microbiol Immunol. 1995;203:155–177. doi: 10.1007/978-3-642-79663-0_8. [DOI] [PubMed] [Google Scholar]
  25. Jaeger J. A., Turner D. H., Zuker M. Improved predictions of secondary structures for RNA. Proc Natl Acad Sci U S A. 1989 Oct;86(20):7706–7710. doi: 10.1073/pnas.86.20.7706. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. James B. D., Olsen G. J., Liu J. S., Pace N. R. The secondary structure of ribonuclease P RNA, the catalytic element of a ribonucleoprotein enzyme. Cell. 1988 Jan 15;52(1):19–26. doi: 10.1016/0092-8674(88)90527-2. [DOI] [PubMed] [Google Scholar]
  27. Jang S. K., Kräusslich H. G., Nicklin M. J., Duke G. M., Palmenberg A. C., Wimmer E. A segment of the 5' nontranslated region of encephalomyocarditis virus RNA directs internal entry of ribosomes during in vitro translation. J Virol. 1988 Aug;62(8):2636–2643. doi: 10.1128/jvi.62.8.2636-2643.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Kaminski A., Hunt S. L., Patton J. G., Jackson R. J. Direct evidence that polypyrimidine tract binding protein (PTB) is essential for internal initiation of translation of encephalomyocarditis virus RNA. RNA. 1995 Nov;1(9):924–938. [PMC free article] [PubMed] [Google Scholar]
  29. Kozak M. An analysis of vertebrate mRNA sequences: intimations of translational control. J Cell Biol. 1991 Nov;115(4):887–903. doi: 10.1083/jcb.115.4.887. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Kühn R., Luz N., Beck E. Functional analysis of the internal translation initiation site of foot-and-mouth disease virus. J Virol. 1990 Oct;64(10):4625–4631. doi: 10.1128/jvi.64.10.4625-4631.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Laing L. G., Draper D. E. Thermodynamics of RNA folding in a conserved ribosomal RNA domain. J Mol Biol. 1994 Apr 15;237(5):560–576. doi: 10.1006/jmbi.1994.1255. [DOI] [PubMed] [Google Scholar]
  32. Le S. Y., Chen J. H., Maizel J. V., Jr Prediction of alternative RNA secondary structures based on fluctuating thermodynamic parameters. Nucleic Acids Res. 1993 May 11;21(9):2173–2178. doi: 10.1093/nar/21.9.2173. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Le S. Y., Siddiqui A., Maizel J. V., Jr A common structural core in the internal ribosome entry sites of picornavirus, hepatitis C virus, and pestivirus. Virus Genes. 1996;12(2):135–147. doi: 10.1007/BF00572952. [DOI] [PubMed] [Google Scholar]
  34. Le S. Y., Zhang K., Maizel J. V., Jr A method for predicting common structures of homologous RNAs. Comput Biomed Res. 1995 Feb;28(1):53–66. doi: 10.1006/cbmr.1995.1005. [DOI] [PubMed] [Google Scholar]
  35. Le S. Y., Zuker M. Common structures of the 5' non-coding RNA in enteroviruses and rhinoviruses. Thermodynamical stability and statistical significance. J Mol Biol. 1990 Dec 5;216(3):729–741. doi: 10.1016/0022-2836(90)90395-3. [DOI] [PubMed] [Google Scholar]
  36. MacArthur C. A., Shankar D. B., Shackleford G. M. Fgf-8, activated by proviral insertion, cooperates with the Wnt-1 transgene in murine mammary tumorigenesis. J Virol. 1995 Apr;69(4):2501–2507. doi: 10.1128/jvi.69.4.2501-2507.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Macejak D. G., Sarnow P. Internal initiation of translation mediated by the 5' leader of a cellular mRNA. Nature. 1991 Sep 5;353(6339):90–94. doi: 10.1038/353090a0. [DOI] [PubMed] [Google Scholar]
  38. Meerovitch K., Svitkin Y. V., Lee H. S., Lejbkowicz F., Kenan D. J., Chan E. K., Agol V. I., Keene J. D., Sonenberg N. La autoantigen enhances and corrects aberrant translation of poliovirus RNA in reticulocyte lysate. J Virol. 1993 Jul;67(7):3798–3807. doi: 10.1128/jvi.67.7.3798-3807.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Michel F., Westhof E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol. 1990 Dec 5;216(3):585–610. doi: 10.1016/0022-2836(90)90386-Z. [DOI] [PubMed] [Google Scholar]
  40. Miyamoto M., Naruo K., Seko C., Matsumoto S., Kondo T., Kurokawa T. Molecular cloning of a novel cytokine cDNA encoding the ninth member of the fibroblast growth factor family, which has a unique secretion property. Mol Cell Biol. 1993 Jul;13(7):4251–4259. doi: 10.1128/mcb.13.7.4251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Murphy F. L., Wang Y. H., Griffith J. D., Cech T. R. Coaxially stacked RNA helices in the catalytic center of the Tetrahymena ribozyme. Science. 1994 Sep 16;265(5179):1709–1712. doi: 10.1126/science.8085157. [DOI] [PubMed] [Google Scholar]
  42. Oh S. K., Scott M. P., Sarnow P. Homeotic gene Antennapedia mRNA contains 5'-noncoding sequences that confer translational initiation by internal ribosome binding. Genes Dev. 1992 Sep;6(9):1643–1653. doi: 10.1101/gad.6.9.1643. [DOI] [PubMed] [Google Scholar]
  43. Pelletier J., Sonenberg N. Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA. Nature. 1988 Jul 28;334(6180):320–325. doi: 10.1038/334320a0. [DOI] [PubMed] [Google Scholar]
  44. Pilipenko E. V., Blinov V. M., Chernov B. K., Dmitrieva T. M., Agol V. I. Conservation of the secondary structure elements of the 5'-untranslated region of cardio- and aphthovirus RNAs. Nucleic Acids Res. 1989 Jul 25;17(14):5701–5711. doi: 10.1093/nar/17.14.5701. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Poole T. L., Wang C., Popp R. A., Potgieter L. N., Siddiqui A., Collett M. S. Pestivirus translation initiation occurs by internal ribosome entry. Virology. 1995 Jan 10;206(1):750–754. doi: 10.1016/s0042-6822(95)80003-4. [DOI] [PubMed] [Google Scholar]
  46. Prats A. C., Vagner S., Prats H., Amalric F. cis-acting elements involved in the alternative translation initiation process of human basic fibroblast growth factor mRNA. Mol Cell Biol. 1992 Oct;12(10):4796–4805. doi: 10.1128/mcb.12.10.4796. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Prats H., Kaghad M., Prats A. C., Klagsbrun M., Lélias J. M., Liauzun P., Chalon P., Tauber J. P., Amalric F., Smith J. A. High molecular mass forms of basic fibroblast growth factor are initiated by alternative CUG codons. Proc Natl Acad Sci U S A. 1989 Mar;86(6):1836–1840. doi: 10.1073/pnas.86.6.1836. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Rose M. D., Misra L. M., Vogel J. P. KAR2, a karyogamy gene, is the yeast homolog of the mammalian BiP/GRP78 gene. Cell. 1989 Jun 30;57(7):1211–1221. doi: 10.1016/0092-8674(89)90058-5. [DOI] [PubMed] [Google Scholar]
  49. Shimasaki S., Emoto N., Koba A., Mercado M., Shibata F., Cooksey K., Baird A., Ling N. Complementary DNA cloning and sequencing of rat ovarian basic fibroblast growth factor and tissue distribution study of its mRNA. Biochem Biophys Res Commun. 1988 Nov 30;157(1):256–263. doi: 10.1016/s0006-291x(88)80041-x. [DOI] [PubMed] [Google Scholar]
  50. Ting J., Lee A. S. Human gene encoding the 78,000-dalton glucose-regulated protein and its pseudogene: structure, conservation, and regulation. DNA. 1988 May;7(4):275–286. doi: 10.1089/dna.1988.7.275. [DOI] [PubMed] [Google Scholar]
  51. Ting J., Wooden S. K., Kriz R., Kelleher K., Kaufman R. J., Lee A. S. The nucleotide sequence encoding the hamster 78-kDa glucose-regulated protein (GRP78) and its conservation between hamster and rat. Gene. 1987;55(1):147–152. doi: 10.1016/0378-1119(87)90258-7. [DOI] [PubMed] [Google Scholar]
  52. Tsukiyama-Kohara K., Iizuka N., Kohara M., Nomoto A. Internal ribosome entry site within hepatitis C virus RNA. J Virol. 1992 Mar;66(3):1476–1483. doi: 10.1128/jvi.66.3.1476-1483.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Vagner S., Gensac M. C., Maret A., Bayard F., Amalric F., Prats H., Prats A. C. Alternative translation of human fibroblast growth factor 2 mRNA occurs by internal entry of ribosomes. Mol Cell Biol. 1995 Jan;15(1):35–44. doi: 10.1128/mcb.15.1.35. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Walter A. E., Turner D. H. Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces. Biochemistry. 1994 Oct 25;33(42):12715–12719. doi: 10.1021/bi00208a024. [DOI] [PubMed] [Google Scholar]
  55. Wang C., Le S. Y., Ali N., Siddiqui A. An RNA pseudoknot is an essential structural element of the internal ribosome entry site located within the hepatitis C virus 5' noncoding region. RNA. 1995 Jul;1(5):526–537. [PMC free article] [PubMed] [Google Scholar]
  56. Wang C., Sarnow P., Siddiqui A. A conserved helical element is essential for internal initiation of translation of hepatitis C virus RNA. J Virol. 1994 Nov;68(11):7301–7307. doi: 10.1128/jvi.68.11.7301-7307.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Wilbur W. J., Lipman D. J. Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci U S A. 1983 Feb;80(3):726–730. doi: 10.1073/pnas.80.3.726. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. de Lapeyriere O., Rosnet O., Benharroch D., Raybaud F., Marchetto S., Planche J., Galland F., Mattei M. G., Copeland N. G., Jenkins N. A. Structure, chromosome mapping and expression of the murine Fgf-6 gene. Oncogene. 1990 Jun;5(6):823–831. [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES