Structure-function relationships of the initiation complex of HIV-1 reverse transcription: The case of mutant viruses using tRNAHis as primer

Nucleic Acids Research

Volumn 31, Issue 19, 2003, Pages 5764-5775

  Rigourd, Mickaël ^b,c   Goldschmidt, Valérie ^b   Brulé, Fabienne ^b,d   Morrow, Casey D ^a   Ehresmann, Bernard ^b   Ehresmann, Chantal ^b   Marquet, Roland ^b  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^b INST DE BIOL MOLEC ET CELLULAIRE   (France)

^c UNIVERSITY OF GENEVA   (Switzerland)

^d CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; GUANINE; HISTIDINE TRANSFER RNA; PRIMER RNA; VIRUS RNA; RNA DIRECTED DNA POLYMERASE; VIRUS DNA;

ANIMAL TISSUE; ANTICODON; ARTICLE; CONTROLLED STUDY; DNA SYNTHESIS INHIBITION; GENE FUNCTION; HUMAN IMMUNODEFICIENCY VIRUS 1; IN VITRO STUDY; MOLECULAR EVOLUTION; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL; PROTEIN RNA BINDING; REVERSE TRANSCRIPTION; RNA PROBE; RNA STRUCTURE; RNA TRANSCRIPTION; VIRUS CULTURE; VIRUS MUTANT; WILD TYPE; BIOSYNTHESIS; COMPARATIVE STUDY; DNA TEMPLATE; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; KINETICS; MACROMOLECULE; METABOLISM; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; RNA PROCESSING; SEQUENCE ALIGNMENT; STRUCTURE ACTIVITY RELATION; TRANSCRIPTION INITIATION SITE;

ANIMALIA; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; RNA VIRUSES;

BASE SEQUENCE; DNA, VIRAL; GENE EXPRESSION REGULATION, VIRAL; HIV-1; HIV-1 REVERSE TRANSCRIPTASE; KINETICS; MACROMOLECULAR SUBSTANCES; MOLECULAR SEQUENCE DATA; MUTATION; RNA PROBES; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, TRANSFER, HIS; RNA, VIRAL; SEQUENCE ALIGNMENT; STRUCTURE-ACTIVITY RELATIONSHIP; TEMPLATES, GENETIC; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION, GENETIC;

EID: 0141974912     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg754     Document Type: Article

References (58)

1. Baltimore,D. (1970) Viral RNA-dependent DNA polymerase. Nature, 226, 1209-1211.
2. Temin,H.M. and Mizutani,S. (1970) RNA-dependent DNA polymerase in virions of Rous sarcoma virus. Nature, 226, 1211-1213.
3. Arts,E.J. and Le Grice,S.F.J. (1998) Interaction of retroviral reverse transcriptase with template-primer duplexes during replication. Progr. Nucleic Acids Res. Mol. Biol., 58, 339-393.
4. Mak,J. and Kleiman,L. (1997) Primer tRNAs for reverse transcription. J. Virol., 71, 8087-8095.
5. Marquet,R., Isel,C., Ehresmann,C. and Ehresmann,B. (1995) tRNAs as primer of reverse transcriptase. Biochimie, 77, 113-124.
6. Trp primer is required for efficient initiation of reverse transcription. J. Virol., 66, 2464-2472.
7. Cobrinik,D., Soskey,L. and Leis,J. (1988) A retroviral RNA secondary structure required for efficient initiation of reverse transcription. J. Virol., 62, 3622-3630.
8. Trp primer. J. Virol., 76, 7571-7577.
9. Lys modulate primer/template loop-loop interaction in the initiation complex of HIV-1 reverse transcription. J. Biol. Chem., 268, 25269-25272.
10. Lys (template/primer) complex. J. Mol. Biol., 247, 236-250.
11. Lys-primed (-) strand DNA synthesis to an HIV-1 reverse transcriptase mutant with extended tRNAs. Implications for retroviral replication. J. Biol. Chem., 271, 9054-9061.
12. Lys interactions inhibiting primer utilization by retroviral reverse transcriptases. Proc. Natl Acad. Sci. USA, 93, 10063-10068.
13. Lys. Nucleic Acids Res., 24, 509-514.
14. Lys/HIV-1 RNA (primer/template) complex. Nucleic Acids Res., 26, 1198-1204.
15. Isel,C., Westhof,E., Massire,C., Le Grice,S.F.J., Ehresmann,C., Ehresmann,B. and Marquet,R. (1999) Structural basis for the specificity of the initiation of HIV-1 reverse transcription. EMBO J., 18, 1038-1048.
16. Lanchy,J.M., Isel,C., Keith,G., Le Grice,S.F., Ehresmann,C., Ehresmann,B. and Marquet,R. (2000) Dynamics of the HIV-1 reverse transcription complex during initiation of DNA synthesis. J. Biol. Chem., 275, 12306-12312.
17. Beerens,N., Groot,F. and Berkhout,B. (2001) Initiation of HIV-1 reverse transcription is regulated by a primer activation signal. J. Biol. Chem., 276, 31247-31256.
18. Beerens,N. and Berkhout,B. (2002) The tRNA primer activation signal in the human immunodeficiency virus type 1 genome is important for initiation and processive elongation of reverse transcription. J. Virol., 76, 2329-2339.
19. Goldschmidt,V., Rigourd,M., Ehresmann,C., Le Grice,S.F.J., Ehresmann,B. and Marquet,R. (2002) Direct and indirect contributions of RNA secondary structure elements to the initiation of HIV-1 reverse transcription. J. Biol. Chem., 277, 43233-43242.
20. Iwatani,Y., Rosen,A.E., Guo,J., Musier-Forsyth,K. and Levin,J.G. (2003) Efficient initiation of HIV-1 reverse transcription in vitro: Requirement for RNA sequences downstream of the primer binding site abrogated by nucleocapsid protein-dependent primer-template interactions. J. Biol. Chem., 278, 14185-14195.
21. Boulme,F., Freund,F., Gryaznov,S., Nielsen,P.E., Tarrago-Litvak,L. and Litvak,S. (2000) Study of HIV-2 primer-template initiation complex using antisense oligonucleotides. Eur. J. Biochem., 267, 2803-2811.
22. Lys3 duplex. Nucleic Acids Res., 29, 2757-2765.
23. Lys,3 with the feline immunodeficiency virus RNA genome governs initiation of minus strand DNA synthesis. J. Biol. Chem., 276, 27721-27730.
24. Met primer are required for initiation of reverse transcription in vivo. Mol. Cell. Biol., 18, 799-806.
25. Met and genomic RNA of the yeast Ty1 retrotransposon. Nucleic Acids Res., 24, 441-449.
26. Gabus,C., Ficheux,D., Rau,M., Keith,G., Sandmeyer,S. and Darlix,J.S. (1998) The yeast Ty3 retrotransposon contains a 5′-3′ bipartite primer-binding site and encodes nucleocapsid protein NCp9 functionally homologous to HIV-1 NCp7. EMBO J., 17, 4873-4880.
27. Lys. EMBO J., 15, 917-924.
28. Lys primer annealed by the nucleocapsid protein: Comparison with the heat annealed complex. RNA, 8, 8-15.
29. Lys. J. Virol., 69, 3090-3097.
30. Li,X.G., Mak,J., Arts,E.J., Gu,Z.X, Kleiman,L., Wainberg,M.A. and Parniak,M.A. (1994) Effects of alterations of primer-binding site sequences on human immunodeficiency virus type 1 replication. J. Virol., 68, 6198-6206.
31. Lys. J. Virol., 69, 6021-6029.
32. His. J. Virol., 70, 966-975.
33. His. Virology, 226, 306-317.
34. His. J. Virol., 71, 6315-6322.
35. Zhang,Z.J., Kang,S.M., Li,Y. and Morrow,C.D. (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.
36. Met. J. Virol., 71, 207-217.
37. Kang,S.M. and Morrow,C.D. (1999) Genetic analysis of a unique human immunodeficiency virus type 1 (HIV-1) with a primer binding site complementary to tRNAMet supports a role for U5-PBS stem-loop RNA structures in initiation of HIV-1 reverse transcription. J. Virol., 73, 1818-1827.
38. Lys,3 for initiation of reverse transcription. Virology, 257, 95-105.
39. Lys primer onto the human immunodeficiency virus genome. J. Virol., 74, 2227-2238.
40. Esposito,D. and Craigie,R. (1998) Sequence specificity of viral end DNA binding by HIV-1 integrase reveals critical regions for protein-DNA interaction. EMBO J., 17, 5832-5843.
41. Brown,H.E., Chen,H. and Engelman,A. (1999) Structure-based mutagenesis of the human immunodeficiency virus type 1 DNA attachment site: effects on integration and cDNA synthesis. J. Virol., 73, 9011-9020.
42. Vicenzi,E., Dimitrov,D.S., Engelman,A., Migone,T.S., Purcell,D.F., Leonard,J., Englund,G. and Martin,M.A. (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.
43. Lys anticodon on the initiation of human immunodeficiency virus type 1 reverse transcription. J. Virol., 70, 4700-4706.
44. Lys,3 and U5 facilitating efficient initiation of reverse transcription by human immunodeficiency virus type 1. AIDS Res. Hum. Retroviruses, 14, 979-988.
45. Lys,3 shows a canonical anticodon loop. RNA, 6, 1347-1355.
46. Marquet,R., Baudin,F., Gabus,C., Darlix,J.L., Mougel,M., Ehresmann,C. and Ehresmann,B. (1991) Dimerization of human immunodeficiency virus (type 1) RNA: stimulation by cations and possible mechanism. Nucleic Acids Res., 19, 2349-2357.
47. His2. Biochimie, 65, 661-672.
48. Baudin,F., Marquet,R., Isel,C., Darlix,J.L., Ehresmann,B. and Ehresmann,C. (1993) Functional sites in the 5′ region of human immunodeficiency virus type-1 RNA form defined structural domains. J. Mol. Biol., 229, 382-397.
49. Lanchy,J.M., Ehresmann,C., Le Grice,S.F.J., Ehresmann,B. and Marquet,R. (1996) Binding and kinetic properties of HIV-1 reverse transcriptase markedly differ during initiation and elongation of reverse transcription. EMBO J., 15, 7178-7187.
50. Lanchy,J.M., Keith,G., Le Grice,S.F.J., Ehresmann,B., Ehresmann,C. and Marquet,R. (1998) Contacts between reverse transcriptase and the primer strand govern the transition from initiation to elongation of HIV-1 reverse transcription. J. Biol. Chem., 273, 24425-24432.
51. Lys during the initiation of reverse transcription? Nucleic Acids Res., 31, 850-859.
52. Lys,3 is stabilized by nucleoside modifications. J. Am. Chem. Soc., 124, 14302-14303.
53. Ehresmann,C., Baudin,F., Mougel,M., Romby,P., Ebel,J.P. and Ehresmann,B. (1987) Probing the structure of RNA in solution. Nucleic Acids Res., 15, 9109-9128.
54. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
55. His. Virology, 238, 273-282.
56. Beerens,N. and Berkhout,B. (2002) Switching the in vitro tRNA usage of HIV-1 by simultaneous adaptation of the PBS and PAS. RNA, 8, 357-369.
57. Lys3 expressed in Escherichia coli: identification of posttranscriptional nucleotide modifications required for efficient initiation of HIV-1 reverse transcription. RNA, 6, 1403-1412.
58. Houssier,C. and Grosjean,H. (1985) Temperature jump relaxation studies on the interactions between transfer RNAs with complementary anticodons. The effect of modified bases adjacent to the anticodon triplet. J. Biomol. Struc. Dyn., 3, 387-399.