Functional analysis of the core human immunodeficiency virus type 1 packaging signal in a permissive cell line

Journal of Virology

Volumn 72, Issue 7, 1998, Pages 5886-5896

  Harrison, Geoffrey P ^a,d   Miele, Gino ^b   Hunter, Eric ^a   Lever, Andrew M L ^c  

^a University of Alabama at Birmingham   (United States)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d Ribotargets Ltd   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; GAG PROTEIN;

ARTICLE; CELL LINE; GENE MUTATION; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; RNA SEQUENCE; RNA STRUCTURE; SIGNAL TRANSDUCTION; STRUCTURE ANALYSIS;

EID: 0031777343     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.72.7.5886-5896.1998     Document Type: Article

References (67)

1. Aldovini, A., and R. A. Young. 1990. Mutations of RNA and protein sequences involved in human immunodeficiency virus type 1 packaging result in production of noninfectious virus. J. Virol. 64:1920-1926.
2. Awang, G., and D. Sen. 1993. Mode of dimerization of HIV-1 genomic RNA. Biochemistry 32:11453-11457.
3. Baudin, F., R. Marquet, C. Isel, J.-L. Darlix, B. Ehresmann, and C. Ehresmann. 1993. Functional sites in the 5′ region of HIV-1 RNA form defined structural domains. J. Mol. Biol. 229:382-397.
4. Bender, W., and N. Davidson. 1976. Mapping of poly(A) sequences in the electron microscope reveals unusual structure of type C type oncornavirus RNA molecules. Cell 7:595-607.
5. Berkhout, B. 1997. Structure and function of the HIV leader RNA. Prog. Nucleic Acid Res. 54:1-34.
6. Berkhout, B., B. B. Essink, and I. Schoneveld. 1993. In vitro dimerisation of HIV-2 leader RNA in the absence of PuGGAPuA motifs. FASEB J. 7:181-187.
7. Berkhout, B., and J. L. B. van Wamel. 1996. Role of the DIS hairpin in replication of human immunodeficiency virus type 1. J. Virol. 70:6723-6732.
8. Berkowitz, R. D., Å. Öhagen, S. Höglund, and S. P. Goff. 1995. Retroviral nucleocapsid domains mediate the specific recognition of genomic viral RNAs by chimeric Gag polyproteins during RNA packaging in vivo. J. Virol. 69:6445-6456.
9. Clavel, F., and J. M. Orenstein. 1990. A mutant of human immunodeficiency virus with reduced RNA packaging and abnormal particle morphology. J. Virol. 64:5230-5234.
10. Clever, J. L., M. L. Wong, and T. G. Parslow. 1996. Requirements for kissing-loop-mediated dimerization of human immunodeficiency virus type 1 RNA. J. Virol. 70:5902-5908.
11. Clever, J. L., and T. G. Parslow. 1997. Mutant human immunodeficiency virus type 1 genomes with defects in RNA dimerization or encapsidation. J. Virol. 71:3407-3414.
12. Darlix, J.-L., C. Gabus, M. T. Nugeyre, F. Clavel, and F. Barré-Sinoussi. 1990. cis-elements and trans-acting factors involved in the RNA dimerisation of HIV-1. J. Mol. Biol. 216:689-699.
13. Fisher, A. G., E. Collati, L. Ratner, R. C. Gallo, and F. Wong-Staal. 1985. A molecular clone of HTLV III with biological activity. Nature (London) 316:262-265.
14. Fu, W., R. J. Gorelick, and A. Rein. 1994. Characterization of human immunodeficiency virus type 1 dimeric RNA from wild-type and protease-defective virions. J. Virol. 68:5013-5018.
15. Gürtler, L. G., P. H. Hauser, J. Eberle, A. von Brunn, S. Knapp, L. Zekeng, J. M. Tsague, and L. Kaptue. 1994. A new subtype of human immunodeficiency virus type 1 (MVP-5180) from Cameroon. J. Virol. 68:1581-1585.
16. Haddrick, M., A. L. Lear, A. J. Cann, and S. Heaphy. 1996. Evidence that a kissing loop structure facilitates genomic RNA dimerisation in HIV-1. J. Mol. Biol. 259:58-68.
17. Haesevelde, M. V., J. L. Decourt, R. J. DeLeys, B. Vanderborght, G. der Groen, H. van Neuverswiyn, and E. Saman. 1994. Genomic cloning and complete sequence analysis of a highly divergent African human immunodeficiency virus isolate. J. Virol. 68:1586-1596.
18. Harrison, G. P., and A. M. L. Lever. 1992. The 5′ packaging signal and major splice donor region of human immunodeficiency virus type 1 have a conserved stable secondary structure. J. Virol. 66:4144-4153.
19. Harrison, G. P., and A. M. L. Lever. Unpublished observations.
20. Harrison, G. P., E. Hunter, and A. M. L. Lever. 1995. Secondary structure of the Mason-Pfizer monkey virus 5′ leader sequence: identification of a structural motif common to a variety of retroviruses. J. Virol. 69:2175-2186.
21. Heaphy, S., J. T. Finch, M. Gait, J. Karn, and M. Singh. 1991. HIV-1 regulator of virion expression, rev, forms nucleoprotein filaments after binding to a purine-rich "bubble" located within the rev-responsive region of viral mRNAs. Proc. Natl. Acad. Sci. USA 88:7366-7370.
22. Hayashi, T., Y. Ueno, and T. Okamoto. 1993. RNA packaging signal of HIV-1. FEBS Lett. 327:213-218.
23. Höglund, S., Å. Öhagen, J. Goncalves, A. T. Panganiban, and D. Gabuzda. 1997. Ultrastructure of HIV-1 genomic RNA. Virology 233:271-279.
24. Huet, T., R. Cheynier, A. Meyerhans, G. Roelants, and S. Wain-Hobson. 1990. Genetic organization of a chimpanzee lentivirus related to HIV-1. Nature (London) 345:356-359.
25. Jaeger, J. A., D. H. Turner, and M. Zucker. 1989. Improved predictions of secondary structures for RNA. Proc. Natl. Acad. Sci. USA 86:7706-7710.
26. Katoh, I., T. Yasunaga, and Y. Yoshinaka. 1993. Bovine leukemia virus RNA sequences involved in dimerization and specific gag protein binding: close relation to the packaging sites of avian, murine, and human retroviruses. J. Virol. 67:1830-1839.
27. Kaye, J. F., J. H. Richardson, and A. M. L. Lever. 1995. cis-acting sequences involved in human immunodeficiency virus type 1 RNA packaging. J. Virol. 69:6588-6592.
28. Kaye, J. F., and A. M. L. Lever. 1996. trans-acting proteins involved in RNA encapsidation and viral assembly in human immunodeficiency virus type 1. J. Virol. 70:880-886.
29. Kim, H.-J., K. Lee, and J. J. O'Rear. 1994. A short sequence upstream of the 5′ major splice site is important for encapsidation of HIV-1 genomic RNA. Virology 198:336-340.
30. Konings, D. A., M. A. Nash, J. V. Maizel, and R. B. Arlinghaus. 1992. Novel GACG-hairpin motif in the 5′ untranslated region of type C retroviruses related to murine leukemia virus. J. Virol. 66:632-640.
31. Kunkel, T. A., J. D. Roberts, and R. A. Zakour. 1987. Rapid and efficient site specific mutagenesis without phenotypic selection. Methods Enzymol. 154: 367-382.
32. Laughrea, M., and L. Jetté. 1994. A 19 nucleotide sequence upstream of the major splice donor is part of the dimerization domain of HIV-1 genomic RNA. Biochemistry 33:13464-13474.
33. Laughrea, M., and L. Jetté. 1996. HIV-1 genomic dimerisation: formation kinetics and thermal stability of dimeric HIV-1 LAI RNAs are not improved by the 1-232 and 292-790 regions flanking the kissing loop domain. Biochemistry 35:9366-9374.
34. Laughrea, M., and L. Jetté. 1996. Kissing-loop model of HIV-1 genome dimerization: HIV-1 RNAs can assume alternative dimeric forms, and all sequences upstream or downstream of hairpin 248-271 are dispensible for dimer formation. Biochemistry 35:1589-1598.
35. Laughrea, M., L. Jetté, J. Mak, L. Kleiman, C. Liang, and M. A. Wainberg. 1997. Mutations in the kissing loop hairpin of human immunodeficiency virus type 1 reduce viral infectivity as well as genomic RNA dimerization. J. Virol. 71:3397-3406.
36. Lever, A. M. L., H. Gottlinger, W. Haseltine, and J. Sodroski. 1989. Identification of a sequence required for efficient packaging of human immunodeficiency virus type 1 RNA into virions. J. Virol. 63:4085-4087.
37. Li, H., and S. A. White. 1997. RNA aptamers for yeast ribosomal protein L32 have a conserved purine-rich internal loop. RNA 3:245-254.
38. Linial, M. L., and A. D. Miller. 1990. Retroviral RNA packaging: sequence requirements and implications, p. 125-152. In R. Swanstrom and P. K. Vogt (ed.), Retroviruses: strategies of replication. Springer-Verlag, Berlin, Germany.
39. Luban, J., and S. P. Goff. 1994. Mutational analysis of cis acting packaging signals in HIV-1 RNA. J. Virol. 68:3784-3793.
40. Mangel, W. F., H. Delius, and P. H. Duesburg. 1994. Structure and molecular weight of the 60-70S RNA and the 30-40S RNA of Rous sarcoma virus. Proc. Natl. Acad. Sci. USA 71:4541-4545.
41. Marquet, R., J.-C. Paillart, E. Skripkin, C. Ehresmann, and B. Ehresmann. 1994. Dimerization of HIV-1 RNA involves sequences located upstream of the splice donor site. Nucleic Acids Res. 22:145-151.
42. McBride, M. S., and A. T. Panganiban. 1996. The human immunodeficiency virus type 1 encapsidation site is a multipartite RNA element composed of functional hairpin structures. J. Virol. 70:2963-2973.
43. McBride, M. S., M. D. Schwartz, and A. T. Panganiban. 1997. Efficient encapsidation of human immunodeficiency virus type 1 vectors and further characterization of cis elements required for encapsidation. J. Virol. 71: 4544-4554.
44. McCann, E., and A. M. L. Lever. 1997. Location of cis-acting signals important for RNA encapsidation in the leader sequence of human immunodeficiency virus type 2. J. Virol. 71:4133-4137.
45. Miele, G., A. Mouland, G. P. Harrison, E. Cohen, and A. M. L. Lever. 1996. The human immunodeficiency virus type 1 5′ packaging signal structure affects translation but does not function as an internal ribosome entry site structure. J. Virol. 70:944-951.
46. Mougel, M., and E. Barklis. 1997. A role for two hairpin structures as a core RNA encapsidation signal in murine leukemia virus virions. J. Virol. 71: 8061-8065.
47. Muriaux, D., P.-M. Girard, B. Bonnet-Mathonière, and J. Paoletti. 1995. Dimerization of HIV-1LAI at low ionic strength. An autocomplementary sequence in the 5′ leader region is evidenced by an antisense oligonucleotide. J. Biol. Chem. 270:8209-8216.
48. Murti, K. G., M. Bondurant, and A. Tereba. 1981. Secondary structural features in the 70S RNAs of Moloney murine leukemia and Rous sarcoma viruses as observed by electron microscopy. J. Virol. 37:411-419.
49. Osterburg, G., and R. Sommer. 1981. Computer support of DNA sequence analysis. Comput. Programs Biomed. 13:101-109.
50. Paillart, J.-C., E. Skripkin, B. Ehresmann, C. Ehresmann, and R. Marquet. 1996. A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA. Proc. Natl. Acad. Sci. USA 93:5572-5577.
51. Paillart, J.-C., L. Berthoux, M. Ottmann, J.-L. Darlix, R. Marquet, B. Ehresmann, and C. Ehresmann. 1996. A dual role of the putative RNA dimerization initiation site of HIV-1 in genomic RNA packaging and proviral synthesis. J. Virol. 70:8348-8354.
52. Paillart, J.-C., E. Westhof, C. Ehresmann, B. Ehresmann, and R. Marquet. 1997. Noncanonical interactions in a kissing loop complex: the dimerisation initiation site of HIV-1 genomic RNA. J. Mol. Biol. 270:36-49.
53. Peterson, R. D., and J. Feigon. 1996. Structural change in rev responsive element RNA of HIV-1 on binding rev peptide. J. Mol. Biol. 264:863-877.
54. Potts, B. J. 1990. Mini RT assay, p. 103-106. In A. Aldovini and B. D. Walker (ed.), Techniques in HIV research. Stockton Press, New York, N.Y.
55. Rizvi, T. A., and A. T. Panganiban. 1993. Simian immunodeficiency virus RNA is efficiently encapsidated by human immunodeficiency virus type 1 particles. J. Virol. 67:2681-2688.
56. Romaniuk, P. J., P. Lowary, H. N. Wu, G. Stormo, and O. C. Uhlenbeck. 1987. RNA binding site of R17 coat protein. Biochemistry 26:1563-1568.
57. Rosen, C. A., A. Terwilliger, J. Dayton, J. G. Sodroski, and W. A. Haseltine. 1988. Intragenic cis-acting ART responsive sequences of HIV-1. Proc. Natl. Acad. Sci. USA 85:2071-2085.
58. Sakaguchi, K., N. Zambrano, E. T. Baldwin, B. A. Shapiro, J. W. Erickson, J. G. Omichinski, G. M. Clore, A. M. Gronenborn, and E. Appella. 1993. Identification of a binding site for the HIV-1 nucleocapsid protein. Proc. Natl. Acad. Sci. USA 90:5219-5223.
59. Schlesinger, S., S. Makino, and M. L. Linial. 1994. cis-acting genomic elements and trans-acting proteins involved in the assembly of RNA viruses. Semin. Virol. 5:39-49.
60. Selden, R. F. 1987. Transfection using DEAE-dextran, p. 9.2.1.-9.2.6. In R. Asubel, R. E. Brent, D. D. Kingston, J. G. Moore, J. A. Seidman, J. A. Smith, and K. Struhl (ed.), Current protocols in molecular biology, vol. 1. Greene Publishing Associates and Wiley Interscience, New York, N.Y.
61. Skripkin, E., J.-C. Paillart, R. Marquet, B. Ehresmann, and C. Ehresmann. 1994. Identification of the primary site of HIV-1 RNA dimerization in vitro. Proc. Natl. Acad. Sci. USA 91:4945-4949.
62. Sundquist, W. I., and S. Heaphy. 1993. Evidence for interstrand quadruplex formation in the dimerization of HIV-1 genomic RNA. Proc. Natl. Acad. Sci. USA 90:3393-3397.
63. Valegard, K., J. B. Murray, P. G. Stockley, N. J. Stonehouse, and L. Lijas. 1994. Crystal structure of an RNA bacteriophage coat protein-operator complex. Nature (London) 371:623-626.
64. White, S. A., H. Li, and M. E. Rauch. 1995. A thermodynamic and mutational analysis of an RNA purine loop as a protein binding site. J. Biomol. Struct. Dyn. 13:285-299.
65. Williamson, J. R., M. K. Raghuraman, and T. R. Cech. 1989. Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell 59: 871-880.
66. Yang, S., and H. M. Temin. 1994. A double hairpin structure is necessary for the encapsidation of spleen necrosis virus retroviral RNA. EMBO J. 13:713-726.
67. Zuker, M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244:48-52.