Role of the DIS hairpin in replication of human immunodeficiency virus type 1

Journal of Virology

Volumn 70, Issue 10, 1996, Pages 6723-6732

  Berkhout, Ben ^a   Van Wamel, Jeroen L B ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; PALINDROMIC DNA;

ARTICLE; BASE PAIRING; DIMERIZATION; GENETIC TRANSFECTION; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; RNA PROCESSING; RNA STRUCTURE; SIMIAN IMMUNODEFICIENCY VIRUS; THERMOSTABILITY; VIRION; VIRUS GENOME; VIRUS REPLICATION;

EID: 0029796006     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.70.10.6723-6732.1996     Document Type: Article

References (55)

1. Aiyar, A., D. Cobrinik, Z. Ge, H. J. Kung, and J. Leis. 1992. Interaction between retroviral US RNA and the TYC loop of the tRNA(Trp) primer is required for efficient initiation of reverse transcription. J. Virol. 66:2464-2472.
2. Awang, G., and D. Sen. 1993. Mode of dimerization of HIV-1 genomic RNA. Biochem. 32:11453-11457.
3. Back, N. K. T., M. Nijnuis, W. Keulen, C. A. B. Boucher, B. B. Oude Essink, A. B. P. van Kuilenburg, A. H. Van Gennip, and B. Berkhout. 1996. Reduced replication of 3TC-resistant HIV-1 variants in primary cells due to a processivity defect of the reverse transcriptase enzyme. EMBO J. 15:4040-4049.
4. Berkhout, B. 1996. Structure and function of the human immunodeficiency virus leader RNA. Progress Nucleic Acid Res. Mol. Biol. 54:1-34.
5. Berkhout, B., B. Klaver, and A. T. Das. 1995. A conserved hairpin structure predicted for the poly(A) signal of human and simian immunodeficiency viruses. Virology 207:276-281.
6. Berkhout, B., B. B. Oude Essink, and I. Schoneveld. 1993. In vitro dimerization of HIV-2 leader RNA in the absence of PuGGAPuA motifs. FASEB J. 7:181-187.
7. Berkhout, B., and I. Schoneveld. 1993. Secondary structure of the HIV-2 leader RNA comprising the tRNA-primer binding site. Nucleic Acids Res. 21:1171-1178.
8. Berkhout, B., and J. L. B. van Wamel. 1996. Accurate scanning of the BssHII endonuclease in search for its DNA cleavage site. J. Biol. Chem. 271:1837-1840.
9. Berkowitz, R. D., and S. P. Goff. 1994. Analysis of binding elements in the human immunodeficiency virus type 1 genomic RNA and nucleocapsid protein. Virology 202:233-246.
10. Bieth, E., C. Gabus, and J.-L. Darlix. 1990. A study of the dimer formation of Rous sarcoma virus RNA and its effect on viral protein synthesis in vitro. Nucleic Acids Res. 18:119-127.
11. Buchschacher, G. L., and A. T. Panganiban. 1992. Human immunodeficiency virus vectors for inducible expression of foreign genes. J. Virol. 66:2731-2739.
12. Clever, J., C. Sassetti, and T. G. Parslow. 1995. RNA secondary structure and binding sites for gag gene products in the 5′ packaging signal of human immunodeficiency virus type 1. J. Virol. 69:2101-2109.
13. Darlix, J.-L., C. Gabus, M. T. Nugeyre, F. Clavel, and F. Barre-Sinoussi. 1990. Cis elements and trans-acting factors involved in the RNA dimerization of the human immunodeficiency virus HIV-1. J. Mol. Biol. 216:689-699.
14. 3Lys J. Virol. 69:3090-3097.
15. De Rocquigny, H., C. Gabus, A. Vincent, M.-C. Fournie-Zaluski, B. Raques, and J.-L. Darlix. 1992. Viral RNA annealing activities of human immunodeficiency virus type 1 nucleocapsid protein require only peptide domains outside the zinc fingers. Proc. Natl. Acad. Sci. USA 89:6472-6476.
16. Devereux, J., P. Haeberli, and O. Smithies. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12:387-395.
17. Freier, S. M., R. Kierzek, J. A. Jaeger, N. Sugimoto, M. H. Caruthers, T. Neilson, and D. H. Turner. 1986. Improved free-energy parameters for predictions of RNA duplex stability. Proc. Nail. Acad. Sci. USA 83:9373-9377.
18. 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. 58:5013-5018.
19. Fu, W., and A. Rein. 1993. Maturation of dimeric viral RNA of Moloney murine leukemia virus. J. Virol. 67:5443-5449.
20. Geigenmuller, U., and M. L. Linial. 1996. Specific binding of human immunodeficiency virus type 1 (HIV-I) Gag-derived proteins to a 5′ HIV-1 genomic RNA sequence. J. Virol. 70:667-671.
21. 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.
22. Hu, W.-S., and H. M. Temin. 1990. Retroviral recombination and reverse transcription. Science 250:1277-1233.
23. Hu, W.-S., and H. M. Temin. 1990. Genetic consequences of packaging two RNA genomes in one retroviral particle: pseudodiploidy and high rate of genetic recombination. Proc. Natl. Acad. Sci. USA 87:1556-1560.
24. Isel, C., C. Ehresmann, G. Keith, B. Ehresmann, and R Marquet. 1995. Initiation of reverse transcription of HIV-1: secondary structure of the HIV-1 RNA/tRNA(3Lys) (template/primer). J. Mol. Biol. 247:236-250.
25. Isel, C., R. Marquet, G. Keith, C. Ehresmann, and B. Ehresmann. 1993. Modified nucleotides of tRNA(3Lys) modulate primer/template loop-loop interaction in the initiation complex of HIV-1 reverse transcription. J. Biol. Chem. 268:25269-25272.
26. 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.
27. Klaver, B., and B. Berkhout. 1994. Evolution of a disrupted TAR RNA hairpin structure in the HIV-1 virus. EMBO J. 13:2650-2659.
28. Koken, S. E. C., J. L. B. van Wamel, J. L. M. C. Geelen, and B. Berkhout. 1994. Functional analysis of the ACTGCTGA sequence motif in the human immunodeficiency virus type 1 long terminal repeat promoter. J. Biomed. Sci. 1:83-92.
29. Laughrea, M., and L. Jette. 1994. A 19-nucleotide sequence upstream of the 5′ major splice donor is part of the dimerization domain of human immunodeficiency virus 1 genomic RNA. Biochemistry 33:13464-13474.
30. Luban, J., and S. P. Goff. 1994. Mutational analysis of cis-acting packaging signals in human immunodeficiency type 1 RNA. J. Virol. 68:3784-3793.
31. Mangel, W. F., H. Delius, and P. H. Duesberg. 1974. 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.
32. Marquet, R., F. Baudin, C. Gabus, J. L. Darlix, M. Mougel, C. Ehresmann, and B. Ehresmann, 1991. Dimerization of human immunodeficiency virus (type 1) RNA: stimulation by cations and possible mechanism. Nucleic Acids Res. 19:2349-2357.
33. Marquet, R., J. C. Paillart, E. Skripkin, C. Ehresmann, and B. Ehresmann. 1994. Dimerization of human immunodeficiency virus type 1 RNA involves sequences located upstream of the splice donor site. Nucleic Acids Res. 22:145-151.
34. McKeating, J. A., A. McKnight, and J. P. Moore. 1991. Differential loss of envelope glycoprotein gp120 from virions of human immunodeficiency virus type 1 isolates: effects on infectivity and neutralization. J. Virol. 65:852-860.
35. Meric, C., and S. P. Goff. 1989. Characterization of Moloney murine leukemia virus mutants with single-amino-acid substitutions in the Cys-His box of the nuclcocapsid protein. J. Virol. 63:1558-1568.
36. Muriaux, D., P.-M. Girard, B. Bonnet-Mathoniere, and J. Paoletti. 1995. Dimerization of HIV-1 LAI RNA at low ionic strength. J. Biol. Chem. 270:8209-8216.
37. Myers, G., S. Wain-Hobson, L. E. Henderson, B. Korber, K. T. Jeang, and G. N. Pavlakis. 1994. Human retroviruses and AIDS 1994. A compilation and analysis of nucleic acid and amino acid sequences. Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, N. Mex.
38. 37a.Oude Essink, B. B., et al. Unpublished results.
39. Paillart, J. C., R. Marquet, E, Skripkin, B. Ehresmann, and C. Ehresmann. 1994. Mutational analysis of the bipartite dinier linkage structure of human immunodeficiency virus type 1 genomic RNA. J. Biol. Chem. 269:27486-27493.
40. Panganiban, A. T., and D. Fiore. 1988. Ordered interstrand and intrastrand DNA transfer during reverse transcription. Science 241:1064-1069.
41. Parolin, C., T. Dorfman, G. Palu, H. Gottlinger, and J. Sodroski. 1994. Analysis in human immunodeficiency virus type 1 vectors of cis-acting sequences that affect gene transfer into human lymphocytes. J. Virol. 68:3888-3895.
42. ELF Virology 185:661-672.
43. Pulsinelli, G. A., and H. M. Temin. 1991. Characterization of large deletions occurring during a single round of retrovirus replication: novel deletion mechanism involving errors in strand transfer. J. Virol. 65:4786-4797.
44. 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 human immunodeficiency virus type 1 nucleocapsid protein. Proc. Nail. Acad. Sci. USA 90:5219-5223.
45. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press. Cold Spring Harbor, N.Y.
46. Skripkin, E., J. C. Paillart, K. Marquet, B. Ehresmann, and C. Ehresmann. 1994. Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro. Proc. Natl. Acad. Sci. USA 91:4945-4949.
47. Stuhlmann, H., and P. Berg. 1992. Homologous recombination of copackaged retrovirus RNAs during reverse transcription. J. Virol. 66:2378-2388.
48. Sundquist, W. I., and S. Heaphy. 1993. Evidence for interstrand quadruplex formation in the dimerization of human immunodeficiency virus 1 genomic RNA. Proc. Natl. Acad. Sci. USA 90:3393-3397.
49. Tchenio, T., and T. Heidmann. 1995. The dimerization/packaging signal is dispensable for both the formation of high-molecular-weight RNA complexes within retroviral particles and the synthesis of proviruses of normal structure. J. Virol. 69:1079-1084.
50. Tsuchihashi, Z., and P. O. Brown. 1994. DNA strand exchange and selective DNA annealing promoted by the human immunodeficiency virus type 1 nucleocapsid protein. J. Virol. 68:5863-5870.
51. Varmus, H., and R. Swanstrom. 1991. Replication of retroviruses, p. 369-512. In R. Weiss, N. Teich, H. Varmus, and J. Coffin (ed.), RNA tumor viruses. Molecular biology of tumor viruses. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
52. Vicenzi, E., D. S. Dimilrov, A. Engelman, T.-S. Migone, D. F. J. Purcell, J. Leonard, G. Englund, and M. A, Martin. 1994. An integration-defective U5 deletion mutant of human immunodeficiency virus type 1 reverts by eliminating additional long terminal repeat sequences. J. Virol. 68:7879-7890.
53. His. J. Virol. 70:966-975.
54. Willey, R. L., D. H. Smith, L. A. Lasky, T. S. Theodore, P. L. Earl, B. Moss, D. J. Capon, and M. A. Martin. 1988. In vitro mutagenesis identifies a region within the envelope gene of the human immunodeficiency virus that is critical for infectivity. J. Virol. 62:139-147.
55. Zuker, M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244:48-52.