A structured RNA motif is involved in correct placement of the tRNA3/(Lys) primer onto the human immunodeficiency virus genome

Journal of Virology

Volumn 74, Issue 5, 2000, Pages 2227-2238

  Beerens, Nancy ^a   Klaver, Bep ^a   Berkhout, Ben ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSFER RNA; VIRUS RNA;

ARTICLE; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; MUTATION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA ANALYSIS; RNA STRUCTURE; THERMODYNAMICS; VIRUS GENOME; VIRUS MUTANT; VIRUS REPLICATION;

5' UNTRANSLATED REGIONS; BASE SEQUENCE; BINDING SITES; CELL LINE; DNA PRIMERS; GENOME, VIRAL; HELA CELLS; HIV-1; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; RNA, TRANSFER, LYS; RNA, VIRAL; STRUCTURE-ACTIVITY RELATIONSHIP; TRANSFECTION; VIRUS REPLICATION;

EID: 0033954179     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.74.5.2227-2238.2000     Document Type: Article

References (56)

1. Trp primer is required for efficient initiation of reverse transcription. J. Virol. 66:2464-2472.
2. Aiyar, A., Z. Ge, and J. Leis. 1994. A specific orientation of RNA secondary structures is required for initiation of reverse transcription. J. Virol. 68:611-618.
3. Baudin, F., R. Marquet, C. Isel, J. L. Darlix, B. Ehresmann, and C. Ehresmann. 1993. Functional sites in the 5′ region of human immunodeficiency virus type 1 RNA from defined structural domains. J. Mol. Biol. 229:382-397.
4. Berkhout, B. 1996. Structure and function of the human immunodeficiency virus leader RNA. Prog. Nucleic Acid Res. Mol. Biol. 54:1-34.
5. Berkhout, B. 1997. The primer-binding site on the RNA genome of human and simian immunodeficiency viruses is flanked by an upstream hairpin structure. Nucleic Acids Res. 25:4013-4017.
6. Berkhout, B., B. Klaver, and A. T. Das. 1997. Forced evolution of a regulatory RNA helix in the HIV-1 genome. Nucleic Acids Res. 25:940-947.
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., R. H. Silverman, and K. T. Jeang. 1989. Tat trans-activates the human immunodeficiency virus through a nascent RNA target. Cell 59:273-282.
9. 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.
10. Berkhout, B., and J. L. B. van Wamel. The leader of the RNA genome forms a compactly folded tertiary structure. RNA, in press.
11. Brown, P. O. 1997. Integration, p. 161-204. In J. M. Coffin, S. H. Hughes, and H. E. Varmus (ed.), Retroviruses. Cold Spring Harbor Laboratory Press, New York, N.Y.
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. 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.
14. Cobrinik, D., A. Aiyar, Z. Ge, M. Katzman, H. Huang, and J. Leis. 1991. Overlapping retrovirus U5 sequence elements are required for efficient integration and initiation of reverse transcription. J. Virol. 65:3864-3872.
15. Damgaard, C. K., H. Dyhr-Mikkełsen, and J. Kjems. 1998. Mapping the RNA binding sites for human immunodeficiency virus type-1 Gag and NC proteins within the complete HIV-1 and -2 untranslated leader regions. Nucleic Acids Res. 26:3667-3676.
16. 3. J. Virol. 69:3090-3097.
17. Das, A. T., B. Klaver, and B. Berkhout. 1999. A hairpin structure in the R region of the human immunodeficiency virus type 1 RNA genome is instrumental in polyadenylation site selection. J. Virol. 73:81-91.
18. Das, A. T., B. Klaver, B. I. F. Klasens, J. L. B. van Wamel, and B. Berkhout. 1997. A conserved hairpin motif in the R-U5 region of the human immunodeficiency virus type 1 RNA genome is essential for replication. J. Virol. 71:2346-2356.
19. Esposito, D., and R. Craigie. 1998. Sequence specificity of viral end DNA binding by HIV-1 integrase reveals critical regions for protein-DNA interaction. EMBO J. 17:5832-5843.
20. Fu, W., B. A. Ortiz-Conde, R. J. Gorelick, S. H. Hughes, and A. Rein. 1997. Placement of tRNA primer on the primer-binding site requires pol gene expression in avian but not murine retroviruses. J. Virol. 71:6940-6946.
21. Harrich, D., G. Mavankal, A. Mette-Snider, and R. B. Gaynor. 1995. Human immunodeficiency virus type 1 TAR element revenant viruses define RNA structures required for efficient viral gene expression and replication. J. Virol. 69:4906-4913.
22. Harrison, G. P., and A. M. L. Lever. 1992. The human immunodeficiency virus type 1 packaging signal and major splice donor region have a conserved stable secondary structure. J. Virol. 66:4144-4153.
23. Hoglund, S., A. Ohagen, J. Goncalves, A. T. Panganiban, and D. Gabuzda. 1997. Ultrastructure of HIV-1 genomic RNA. Virology 233:271-279.
24. Lys incorporation into human immunodeficiency virus type 1. J. Virol. 71:4378-4384.
25. 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.
26. Isel, C., G. Keith, B. Ehresmann, C. Ehresmann, and R. Marquet. 1998. Mutational analysis of the tRNA3Lys/HIV-1 RNA (primer/template) complex. Nucleic Acids Res. 26:1198-1204.
27. Isel, C., E. Westhof, S. F. Le Grice, B. Ehresmann, C. Ehresmann, and R. Marquet. 1999. Structural basis for the specificity of the initiation of HIV-1 reverse transcription. EMBO J. 18:1038-1048.
28. Kang, S.-M., J. K. Wakefield, and C. D. Morrow. 1996. Mutations in both the U5 region and the primer-binding site influence the selection of the tRNA used for the initiation of HIV-1 reverse transcription. Virology 222:401-414.
29. Met. J. Virol. 71:207-217.
30. Klasens, B. I. F., M. Thiesen, A. Virtanen, and B. Berkhout. 1999. The ability of the HIV-1 AAUAAA signal to bind polyadenylation factors is controlled by local RNA structure. Nucleic Acids Res. 27:446-454.
31. Klaver, B., and B. Berkhout. 1994. Comparison of 5′ and 3′ long terminal repeat promoter function in human immunodeficiency virus. J. Virol. 68: 3830-3840.
32. Klaver, B., and B. Berkhout. 1994. Evolution of a disrupted TAR RNA hairpin structure in the HIV-1 virus. EMBO J. 13:2650-2659.
33. Leis, J., A. Aiyar, and D. Cobrinik. 1993. Regulation of initiation of reverse transcription of retroviruses, p. 33-48. In A. M. Skalka and S. P. Goff (ed.), Reverse transcriptase. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
34. Li, X., J. Mak, E. J. Arts, Z. Gu, L. Kleiman, M. A. Wainberg, and M. A. Parniak. 1994. Effects of alterations of primer-binding site sequences on human immunodeficiency virus type 1 replication. J. Virol. 68:6198-6206.
35. His. J. Virol. 71:6315-6322.
36. Liang, C., X. Li, L. Rong, P. Inouye, Y. Quan, L. Kleiman, and M. A. Wainberg. 1997. The importance of the A-rich loop in human immunodeficiency virus type 1 reverse transcription and infectivity. J. Virol. 71:5750-5757.
37. Marquet, R., C. Isel, C. Ehresmann, and B. Ehresmann. 1995. tRNAs as primer of reverse transcriptases. Biochimie 77:113-124.
38. Masuda, T., M. J. Kuroda, and S. Harada. 1998. Specific and independent recognition of U3 and U5 att sites by human immunodeficiency virus type 1 integrase in vivo. J. Virol. 72:8396-8402.
39. 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.
40. Trp primer annealing J. Virol. 73:6307-6318.
41. 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 human immunodeficiency virus type 1 in genomic RNA packaging and proviral DNA synthesis. J. Virol. 70:8348-8354.
42. Prats, A. C., L. Sarih, C. Gabus, S. Litvak, G. Keith, and J. L. Darlix. 1988. Small finger protein of avian and murine retroviruses has nucleic acid annealing activity and positions the replication primer IRNA onto genomic RNA. EMBO J. 7:1777-1783.
43. Puglisi, E. V., and J. D. Puglisi. 1998. HIV-1 A-rich RNA loop mimics the tRNA anticodon structure. Nat. Med. 5:1033-1036
44. Skripkin, E., C. Isel, B. Marquet, B. Ehresmann, and C. Ehresmann. 1996. Psoralen crosslinking between human immunodeficiency virus type 1 RNA and primer tRNAlys3. Nucleic Acids Res. 24:509-514.
45. Telesnitsky, A., and S. P. Goff. 1997. Reverse transcriptase and the generation of retroviral DNA. p. 121-160. In J. M. Coffin, S. H. Hughes, and H. E. Varmus (ed.), Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
46. Van Lint, C., C. A. Amella, S. Emiliani, M. John, T. Jie, and E. Verdin. 1997. Transcription factor binding sites downstream of the human immunodeficiency virus type 1 transcription start site are important for virus infectivity. J. Virol. 71:6113-6127.
47. Verhoef, K., M. Koper, and B. Berkhout. 1997. Determination of the minimal amount of Tat activity required for human immunodeficiency virus type 1 replication. Virology 237:228-236.
48. Vicenzi, E., D. S. Dimitrov, 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.
49. His. J. Virol. 70:966-975.
50. Wakefield, J. K., H. Rhim, and C. D. Morrow. 1994. Minimal sequence requirements of a functional human immunodeficiency virus type 1 primer binding site. J. Virol. 68:1605-1614.
51. Whitcomb, J. M., B. A. Ortiz Conde, and S. H. Hughes. 1995. Replication of avian leukosis viruses with mutations at the primer binding site: use of alternative tRNAs as primer. J. Virol. 69:6228-6238.
52. 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.
53. Wu, M., and I. Tinoco. 1999. RNA folding causes secondary structure rearrangement. Proc. Natl. Acad. Sci. USA 95:11555-11560.
54. His. Virology 226:306-317.
55. Zhang, Z., S.-M. Kang, Y. Li, and C. D. Morrow. 1998. Genetic analysis of the U5-PBS of a novel HIV-1 reveals multiple interactions between the tRNA and RNA genome required for initiation of reverse transcription. RNA 4:394-406.
56. Zuker, M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244:48-52.