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. 1996 Feb;70(2):944–951. doi: 10.1128/jvi.70.2.944-951.1996

The human immunodeficiency virus type 1 5' packaging signal structure affects translation but does not function as an internal ribosome entry site structure.

G Miele 1, A Mouland 1, G P Harrison 1, E Cohen 1, A M Lever 1
PMCID: PMC189898  PMID: 8551634

Abstract

The role of the RNA secondary structure in the 5' packaging signal region of human immunodeficiency virus type 1 (HIV-1) in initiating translation of gag mRNA has been investigated both in vitro and in the presence of cellular cofactors in vivo. Heat denaturation of the structure and mutagenic deletion both lead to an increase in levels of translated products, indicating that the structure is a significant inhibitor of translation. The proximity of the gag AUG to the packaging signal structure suggested that it might function as an internal ribosome entry site. However, in both a cell-free system and eukaryotic cells, translation will initiate at a novel upstream initiation codon introduced within the 5' noncoding region. This codon is utilized exclusively, resulting in gag protein products with an extra 11 amino acids at the amino terminus, which, when expressed in T lymphocytes, are confined intracellularly, probably because of the lack of an N-terminal glycine myristoylation signal. Deletion of the secondary structure abolishes gag production even in the presence of tat and rev in trans. Using dicistronic constructs containing the HIV-1 5' leader cloned between two heterologous open reading frames, we were unable to detect any significant expression of the second open reading frame that would have been supportive of an internal ribosome entry site mechanism. Using mutant proviruses either lacking the entire packaging signal structure region or containing the introduced upstream initiation codon in long-term replication studies, we were unable to detect reverse transcriptase activity in culture supernatants. The 5' packaging signal structure of HIV-1 does not serve as an internal ribosome entry site. The translation of gag is consistent with ribosomal scanning. However, the packaging signal structure causes significant translational inhibition.

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Selected References

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  1. Agol V. I. The 5'-untranslated region of picornaviral genomes. Adv Virus Res. 1991;40:103–180. doi: 10.1016/S0065-3527(08)60278-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Ahringer J., Kimble J. Control of the sperm-oocyte switch in Caenorhabditis elegans hermaphrodites by the fem-3 3' untranslated region. Nature. 1991 Jan 24;349(6307):346–348. doi: 10.1038/349346a0. [DOI] [PubMed] [Google Scholar]
  3. Aldovini A., Young R. A. Mutations of RNA and protein sequences involved in human immunodeficiency virus type 1 packaging result in production of noninfectious virus. J Virol. 1990 May;64(5):1920–1926. doi: 10.1128/jvi.64.5.1920-1926.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Baudin F., Marquet R., Isel C., Darlix J. L., Ehresmann B., Ehresmann C. Functional sites in the 5' region of human immunodeficiency virus type 1 RNA form defined structural domains. J Mol Biol. 1993 Jan 20;229(2):382–397. doi: 10.1006/jmbi.1993.1041. [DOI] [PubMed] [Google Scholar]
  5. Berkhout B., Silverman R. H., Jeang K. T. Tat trans-activates the human immunodeficiency virus through a nascent RNA target. Cell. 1989 Oct 20;59(2):273–282. doi: 10.1016/0092-8674(89)90289-4. [DOI] [PubMed] [Google Scholar]
  6. Berlioz C., Darlix J. L. An internal ribosomal entry mechanism promotes translation of murine leukemia virus gag polyprotein precursors. J Virol. 1995 Apr;69(4):2214–2222. doi: 10.1128/jvi.69.4.2214-2222.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Braun R. E. Temporal translational regulation of the protamine 1 gene during mouse spermatogenesis. Enzyme. 1990;44(1-4):120–128. doi: 10.1159/000468752. [DOI] [PubMed] [Google Scholar]
  8. Carrington J. C., Freed D. D. Cap-independent enhancement of translation by a plant potyvirus 5' nontranslated region. J Virol. 1990 Apr;64(4):1590–1597. doi: 10.1128/jvi.64.4.1590-1597.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Ch'ng J. L., Shoemaker D. L., Schimmel P., Holmes E. W. Reversal of creatine kinase translational repression by 3' untranslated sequences. Science. 1990 May 25;248(4958):1003–1006. doi: 10.1126/science.2343304. [DOI] [PubMed] [Google Scholar]
  10. Clavel F., Orenstein J. M. A mutant of human immunodeficiency virus with reduced RNA packaging and abnormal particle morphology. J Virol. 1990 Oct;64(10):5230–5234. doi: 10.1128/jvi.64.10.5230-5234.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Darlix J. L., Gabus C., Nugeyre M. T., Clavel F., Barré-Sinoussi F. Cis elements and trans-acting factors involved in the RNA dimerization of the human immunodeficiency virus HIV-1. J Mol Biol. 1990 Dec 5;216(3):689–699. doi: 10.1016/0022-2836(90)90392-Y. [DOI] [PubMed] [Google Scholar]
  12. Edery I., Petryshyn R., Sonenberg N. Activation of double-stranded RNA-dependent kinase (dsl) by the TAR region of HIV-1 mRNA: a novel translational control mechanism. Cell. 1989 Jan 27;56(2):303–312. doi: 10.1016/0092-8674(89)90904-5. [DOI] [PubMed] [Google Scholar]
  13. Feinberg M. B., Jarrett R. F., Aldovini A., Gallo R. C., Wong-Staal F. HTLV-III expression and production involve complex regulation at the levels of splicing and translation of viral RNA. Cell. 1986 Sep 12;46(6):807–817. doi: 10.1016/0092-8674(86)90062-0. [DOI] [PubMed] [Google Scholar]
  14. Fisher A. G., Collalti E., Ratner L., Gallo R. C., Wong-Staal F. A molecular clone of HTLV-III with biological activity. Nature. 1985 Jul 18;316(6025):262–265. doi: 10.1038/316262a0. [DOI] [PubMed] [Google Scholar]
  15. Fütterer J., Kiss-László Z., Hohn T. Nonlinear ribosome migration on cauliflower mosaic virus 35S RNA. Cell. 1993 May 21;73(4):789–802. doi: 10.1016/0092-8674(93)90257-q. [DOI] [PubMed] [Google Scholar]
  16. Ganoza M. C., Kofoid E. C., Marlière P., Louis B. G. Potential secondary structure at translation-initiation sites. Nucleic Acids Res. 1987 Jan 12;15(1):345–360. doi: 10.1093/nar/15.1.345. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Geballe A. P., Gray M. K. Variable inhibition of cell-free translation by HIV-1 transcript leader sequences. Nucleic Acids Res. 1992 Aug 25;20(16):4291–4297. doi: 10.1093/nar/20.16.4291. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Gold L. Posttranscriptional regulatory mechanisms in Escherichia coli. Annu Rev Biochem. 1988;57:199–233. doi: 10.1146/annurev.bi.57.070188.001215. [DOI] [PubMed] [Google Scholar]
  19. Hall M. N., Gabay J., Débarbouillé M., Schwartz M. A role for mRNA secondary structure in the control of translation initiation. Nature. 1982 Feb 18;295(5850):616–618. doi: 10.1038/295616a0. [DOI] [PubMed] [Google Scholar]
  20. Harrell C. M., McKenzie A. R., Patino M. M., Walden W. E., Theil E. C. Ferritin mRNA: interactions of iron regulatory element with translational regulator protein P-90 and the effect on base-paired flanking regions. Proc Natl Acad Sci U S A. 1991 May 15;88(10):4166–4170. doi: 10.1073/pnas.88.10.4166. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Harrison G. P., Lever A. M. The human immunodeficiency virus type 1 packaging signal and major splice donor region have a conserved stable secondary structure. J Virol. 1992 Jul;66(7):4144–4153. doi: 10.1128/jvi.66.7.4144-4153.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Hayashi T., Ueno Y., Okamoto T. Elucidation of a conserved RNA stem-loop structure in the packaging signal of human immunodeficiency virus type 1. FEBS Lett. 1993 Jul 26;327(2):213–218. doi: 10.1016/0014-5793(93)80172-q. [DOI] [PubMed] [Google Scholar]
  23. Iserentant D., Fiers W. Secondary structure of mRNA and efficiency of translation initiation. Gene. 1980 Apr;9(1-2):1–12. doi: 10.1016/0378-1119(80)90163-8. [DOI] [PubMed] [Google Scholar]
  24. Jackson R. J., Howell M. T., Kaminski A. The novel mechanism of initiation of picornavirus RNA translation. Trends Biochem Sci. 1990 Dec;15(12):477–483. doi: 10.1016/0968-0004(90)90302-r. [DOI] [PubMed] [Google Scholar]
  25. Jackson R. J. mRNA translation. Initiation without an end. Nature. 1991 Sep 5;353(6339):14–15. doi: 10.1038/353014a0. [DOI] [PubMed] [Google Scholar]
  26. Jang S. K., Davies M. V., Kaufman R. J., Wimmer E. Initiation of protein synthesis by internal entry of ribosomes into the 5' nontranslated region of encephalomyocarditis virus RNA in vivo. J Virol. 1989 Apr;63(4):1651–1660. doi: 10.1128/jvi.63.4.1651-1660.1989. [DOI] [PMC free article] [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., 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 Nov;9(11):3753–3759. doi: 10.1002/j.1460-2075.1990.tb07588.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Kim H. J., Lee K., O'Rear J. J. A short sequence upstream of the 5' major splice site is important for encapsidation of HIV-1 genomic RNA. Virology. 1994 Jan;198(1):336–340. doi: 10.1006/viro.1994.1037. [DOI] [PubMed] [Google Scholar]
  30. Kleiman L., Caudry S., Boulerice F., Wainberg M. A., Parniak M. A. Incorporation of tRNA into normal and mutant HIV-1. Biochem Biophys Res Commun. 1991 Feb 14;174(3):1272–1280. doi: 10.1016/0006-291x(91)91559-u. [DOI] [PubMed] [Google Scholar]
  31. Kozak M. Circumstances and mechanisms of inhibition of translation by secondary structure in eucaryotic mRNAs. Mol Cell Biol. 1989 Nov;9(11):5134–5142. doi: 10.1128/mcb.9.11.5134. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Kozak M. Influences of mRNA secondary structure on initiation by eukaryotic ribosomes. Proc Natl Acad Sci U S A. 1986 May;83(9):2850–2854. doi: 10.1073/pnas.83.9.2850. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Kozak M. Leader length and secondary structure modulate mRNA function under conditions of stress. Mol Cell Biol. 1988 Jul;8(7):2737–2744. doi: 10.1128/mcb.8.7.2737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Kozak M. Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell. 1986 Jan 31;44(2):283–292. doi: 10.1016/0092-8674(86)90762-2. [DOI] [PubMed] [Google Scholar]
  35. Kozak M. The scanning model for translation: an update. J Cell Biol. 1989 Feb;108(2):229–241. doi: 10.1083/jcb.108.2.229. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Kruys V., Beutler B., Huez G. Translational control mediated by UA-rich sequences. Enzyme. 1990;44(1-4):193–202. doi: 10.1159/000468757. [DOI] [PubMed] [Google Scholar]
  37. Kunkel T. A., Roberts J. D., Zakour R. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 1987;154:367–382. doi: 10.1016/0076-6879(87)54085-x. [DOI] [PubMed] [Google Scholar]
  38. Lever A., Gottlinger H., Haseltine W., Sodroski J. Identification of a sequence required for efficient packaging of human immunodeficiency virus type 1 RNA into virions. J Virol. 1989 Sep;63(9):4085–4087. doi: 10.1128/jvi.63.9.4085-4087.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Luban J., Goff S. P. Mutational analysis of cis-acting packaging signals in human immunodeficiency virus type 1 RNA. J Virol. 1994 Jun;68(6):3784–3793. doi: 10.1128/jvi.68.6.3784-3793.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Luukkonen B. G., Tan W., Schwartz S. Efficiency of reinitiation of translation on human immunodeficiency virus type 1 mRNAs is determined by the length of the upstream open reading frame and by intercistronic distance. J Virol. 1995 Jul;69(7):4086–4094. doi: 10.1128/jvi.69.7.4086-4094.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. 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]
  42. Manzella J. M., Blackshear P. J. Regulation of rat ornithine decarboxylase mRNA translation by its 5'-untranslated region. J Biol Chem. 1990 Jul 15;265(20):11817–11822. [PubMed] [Google Scholar]
  43. Manzella J. M., Rychlik W., Rhoads R. E., Hershey J. W., Blackshear P. J. Insulin induction of ornithine decarboxylase. Importance of mRNA secondary structure and phosphorylation of eucaryotic initiation factors eIF-4B and eIF-4E. J Biol Chem. 1991 Feb 5;266(4):2383–2389. [PubMed] [Google Scholar]
  44. Mouland A. J., Bevan S., White J. H., Hendy G. N. Human chromogranin A gene. Molecular cloning, structural analysis, and neuroendocrine cell-specific expression. J Biol Chem. 1994 Mar 4;269(9):6918–6926. [PubMed] [Google Scholar]
  45. Muesing M. A., Smith D. H., Capon D. J. Regulation of mRNA accumulation by a human immunodeficiency virus trans-activator protein. Cell. 1987 Feb 27;48(4):691–701. doi: 10.1016/0092-8674(87)90247-9. [DOI] [PubMed] [Google Scholar]
  46. 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]
  47. Parkin N., Darveau A., Nicholson R., Sonenberg N. cis-acting translational effects of the 5' noncoding region of c-myc mRNA. Mol Cell Biol. 1988 Jul;8(7):2875–2883. doi: 10.1128/mcb.8.7.2875. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. 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]
  49. Rhim H., Park J., Morrow C. D. Deletions in the tRNA(Lys) primer-binding site of human immunodeficiency virus type 1 identify essential regions for reverse transcription. J Virol. 1991 Sep;65(9):4555–4564. doi: 10.1128/jvi.65.9.4555-4564.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Richardson J. H., Child L. A., Lever A. M. Packaging of human immunodeficiency virus type 1 RNA requires cis-acting sequences outside the 5' leader region. J Virol. 1993 Jul;67(7):3997–4005. doi: 10.1128/jvi.67.7.3997-4005.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Rosen C. A. Regulation of HIV gene expression by RNA-protein interactions. Trends Genet. 1991 Jan;7(1):9–14. doi: 10.1016/0168-9525(91)90015-i. [DOI] [PubMed] [Google Scholar]
  52. Rosen C. A., Sodroski J. G., Campbell K., Haseltine W. A. Construction of recombinant murine retroviruses that express the human T-cell leukemia virus type II and human T-cell lymphotropic virus type III trans activator genes. J Virol. 1986 Jan;57(1):379–384. doi: 10.1128/jvi.57.1.379-384.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Roy S., Agy M., Hovanessian A. G., Sonenberg N., Katze M. G. The integrity of the stem structure of human immunodeficiency virus type 1 Tat-responsive sequence of RNA is required for interaction with the interferon-induced 68,000-Mr protein kinase. J Virol. 1991 Feb;65(2):632–640. doi: 10.1128/jvi.65.2.632-640.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Sakaguchi K., Zambrano N., Baldwin E. T., Shapiro B. A., Erickson J. W., Omichinski J. G., Clore G. M., Gronenborn A. M., Appella E. Identification of a binding site for the human immunodeficiency virus type 1 nucleocapsid protein. Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5219–5223. doi: 10.1073/pnas.90.11.5219. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Schwartz S., Felber B. K., Fenyö E. M., Pavlakis G. N. Env and Vpu proteins of human immunodeficiency virus type 1 are produced from multiple bicistronic mRNAs. J Virol. 1990 Nov;64(11):5448–5456. doi: 10.1128/jvi.64.11.5448-5456.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Schwartz S., Felber B. K., Pavlakis G. N. Mechanism of translation of monocistronic and multicistronic human immunodeficiency virus type 1 mRNAs. Mol Cell Biol. 1992 Jan;12(1):207–219. doi: 10.1128/mcb.12.1.207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. SenGupta D. N., Berkhout B., Gatignol A., Zhou A. M., Silverman R. H. Direct evidence for translational regulation by leader RNA and Tat protein of human immunodeficiency virus type 1. Proc Natl Acad Sci U S A. 1990 Oct;87(19):7492–7496. doi: 10.1073/pnas.87.19.7492. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Sodroski J., Goh W. C., Rosen C., Tartar A., Portetelle D., Burny A., Haseltine W. Replicative and cytopathic potential of HTLV-III/LAV with sor gene deletions. Science. 1986 Mar 28;231(4745):1549–1553. doi: 10.1126/science.3006244. [DOI] [PubMed] [Google Scholar]
  60. Sonenberg N. Picornavirus RNA translation continues to surprise. Trends Genet. 1991 Apr;7(4):105–106. doi: 10.1016/0168-9525(91)90440-2. [DOI] [PubMed] [Google Scholar]
  61. Standart N., Hunt T. Control of translation of masked mRNAs in clam oocytes. Enzyme. 1990;44(1-4):106–119. doi: 10.1159/000468751. [DOI] [PubMed] [Google Scholar]
  62. Steffy K., Wong-Staal F. Genetic regulation of human immunodeficiency virus. Microbiol Rev. 1991 Jun;55(2):193–205. doi: 10.1128/mr.55.2.193-205.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. Thach R. E. Cap recap: the involvement of eIF-4F in regulating gene expression. Cell. 1992 Jan 24;68(2):177–180. doi: 10.1016/0092-8674(92)90461-k. [DOI] [PubMed] [Google Scholar]
  64. Thomas A. A., ter Haar E., Wellink J., Voorma H. O. Cowpea mosaic virus middle component RNA contains a sequence that allows internal binding of ribosomes and that requires eukaryotic initiation factor 4F for optimal translation. J Virol. 1991 Jun;65(6):2953–2959. doi: 10.1128/jvi.65.6.2953-2959.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. 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]
  66. Wang C., Sarnow P., Siddiqui A. Translation of human hepatitis C virus RNA in cultured cells is mediated by an internal ribosome-binding mechanism. J Virol. 1993 Jun;67(6):3338–3344. doi: 10.1128/jvi.67.6.3338-3344.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. van de Guchte M., van der Lende T., Kok J., Venema G. A possible contribution of mRNA secondary structure to translation initiation efficiency in Lactococcus lactis. FEMS Microbiol Lett. 1991 Jun 15;65(2):201–208. doi: 10.1111/j.1574-6968.1991.tb04746.x. [DOI] [PubMed] [Google Scholar]

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