Destabilization of the TAR hairpin affects the structure and function of the HIV-1 leader RNA

Nucleic Acids Research

Volumn 36, Issue 13, 2008, Pages 4352-4363

  Vrolijk, Martine M ^a   Ooms, Marcel ^a   Harwig, Alex ^a   Das, Atze T ^a   Berkhout, Ben ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

TAR HAIRPIN PROTEIN; VIRUS PROTEIN; VIRUS RNA;

AMINO ACID SEQUENCE; ARTICLE; GENE DELETION; GENE FUNCTION; GENETIC CODE; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; RNA STRUCTURE; VIRAL GENETICS; VIRUS GENOME; VIRUS MUTANT; VIRUS REPLICATION;

5' UNTRANSLATED REGIONS; BASE SEQUENCE; DIMERIZATION; HIV LONG TERMINAL REPEAT; HIV-1; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; POLY A; RNA, VIRAL; SEQUENCE DELETION; VIRUS REPLICATION;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 48149098589     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn364     Document Type: Article

References (39)

1. Berkhout,B. (1996) Structure and function of the human immunodeficiency virus leader RNA. Prog. Nucleic Acid Res. Mol. Biol., 54, 1-34.
2. Huthoff,H. and Berkhout,B. (2001) Two alternating structures for the HIV-1 leader RNA. RNA, 7, 143-157.
3. Laughrea,M. and Jette,L. (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.
4. Skripkin,E., Paillart,J.C., Marquet,R., Ehresmann,B. and Ehresmann,C. (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.
5. Laughrea,M. and Jette,L. (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 dispensable for dimer formation. Biochemistry, 35, 1589-1598.
6. Muriaux,D., Fosse,P. and Paoletti,J. (1996) A kissing complex together with a stable dimer is involved in the HIV-1 LAI RNA dimerization process in vitro. Biochemistry, 35, 5075-5082.
7. Bannwarth,S. and Gatignol,A. (2005) HIV-1 TAR RNA: The target of molecular interactions between the virus and its host. Curr. HIV Res. 3, 61-71.
8. Brady,J. and Kashanchi,F. (2005) Tat gets the "green" light on transcription initiation. Retrovirology, 2, 69.
9. Tan,R., Brodsky,A., Williamson,J.R. and Frankel,A.D. (1997) RNA recognition by HIV-1 Tat and Rev. Semin. Virol., 8, 186-193.
10. Richter,S., Ping,Y.H. and Rana,T.M. (2002) TAR RNA loop: A scaffold for the assembly of a regulatory switch in HIV replication. Proc. Natl Acad. Sci. USA, 99, 7928-7933.
11. Wei,P., Garber,M.E., Fang,S.-M., Fisher,W.H. and Jones,K.A. (1998) A novel CDK9-associated C-type cyclin interacts directly with HIV-1 Tat and mediates its high-affinity, loop-specific binding to TAR RNA. Cell, 92, 451-462.
12. Andersen,E.S., Contera,S.A., Knudsen,B., Damgaard,C.K., Besenbacher,F. and Kjems,J. (2004) Role of the trans-activation response element in dimerization of HIV-1 RNA. J. Biol. Chem., 279, 22243-22249.
13. Clever,J.L., Mirandar,D. Jr and Parslow,T.G. (2002) RNA structure and packaging signals in the 5′ leader region of the human immunodeficiency virus type 1 genome. J. Virol., 76, 12381-12387.
14. Helga-Maria,C., Hammarskjold,M.L. and Rekosh,D. (1999) An intact TAR element and cytoplasmic localization are necessary for efficient packaging of human immunodeficiency virus type 1 genomic RNA. J. Virol., 73, 4127-4135.
15. Ooms,M., Huthoff,H., Russell,R., Liang,C. and Berkhout,B. (2004) A riboswitch regulates RNA dimerization and packaging in human immunodeficiency virus type 1 virions. J. Virol., 78, 10814-10819.
16. Russell,R.S., Hu,J., Beriault,V., Mouland,A.J., Laughrea,M., Kleiman,L., Wainberg,M.A. and Liang,C. (2003) Sequences downstream of the 5′ splice donor site are required for both packaging and dimerization of human immunodeficiency virus type 1 RNA. J. Virol., 77, 84-96.
17. Berkhout,B., Vastenhouw,N.L., Klasens,B.I. and Huthoff,H. (2001) Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription. RNA, 7, 1097-1114.
18. Berkhout,B. (2000) Multiple biological roles associated with the repeat (R) region of the HIV-1 RNA genome. Adv. Pharmacol., 48, 29-73.
19. Das,A.T., Klaver,B. and Berkhout,B. (1998) The 5′ and 3′ TAR elements of the human immunodeficiency virus exert effects at several points in the virus life cycle. J. Virol., 72, 9217-9223.
20. Harrich,D., Hooker,C.W. and Parry,E. (2000) The human immunodeficiency virus type 1 TAR RNA upper stem-loop plays distinct roles in reverse transcription and RNA packaging. J. Virol., 74, 5639-5646.
21. Das,A.T., Verhoef,K. and Berkhout,B. (2004) A conditionally replicating virus as a novel approach toward an HIV vaccine. Methods Enzymol., 388, 359-379.
22. Smith,S.M., Markham,R.B. and Jeang,K.-T. (1996) Conditional reduction of human immunodeficiency virus type 1 replication by a gain-of-herpes simplex virus 1 thymidine kinase function. Proc. Natl Acad. Sci. USA 93, 7955-7960.
23. Verhoef,K., Marzio,G., Hillen,W., Bujard,H. and Berkhout,B. (2001) Strict control of human immunodeficiency virus type 1 replication by a genetic switch: Tet for Tat. J. Virol., 75, 979-987.
24. Urlinger,S., Baron,U., Thellmann,M., Hasan,M.T., Bujard,H. and Hillen,W. (2000) Exploring the sequence space for tetracycline dependent transcriptional activators: Novel mutations yield expanded range and sensitivity. Proc. Natl Acad. Sci. USA, 97, 7963-7968.
25. Das,A.T., Harwig,A., Vrolijk,M.M. and Berkhout,B. (2007) The TAR hairpin of human immunodeficiency virus type-1 can be deleted when not required for Tat-mediated activation of transcription. J. Virol., 81, 7742-7748.
26. Berkhout,B., Ooms,M., Beerens,N., Huthoff,H., Southern,E. and Verhoef,K. (2002) In vitro evidence that the untranslated leader of the HIV-1 genome is an RNA checkpoint that regulates multiple functions through conformational changes. J. Biol. Chem., 277, 19967-19975.
27. Abbink,T.E.M., Ooms,M., Haasnoot,P.C.J. and Berkhout,B. (2005) The HIV-1 leader RNA conformational switch regulates RNA dimerization but does not regulate mRNA translation. Biochemistry, 44, 9058-9066.
28. ELI. Virol., 185, 661-672.
29. Das,A.T., Zhou,X., Vink,M., Klaver,B., Verhoef,K., Marzio,G. and Berkhout,B. (2004) Viral evolution as a tool to improve the tetracycline-regulated gene expression system. J. Biol. Chem., 279, 18776-18782.
30. Huthoff,H. and Berkhout,B. (2001) Mutations in the TAR hairpin affect the equilibrium between alternative conformations of the HIV-1 leader RNA. Nucleic Acids Res., 29, 2594-2600.
31. Ooms,M., Cupac,D., Abbink,T.E.M., Huthoff,H. and Berkhout,B. (2007) The availability of the primer activation signal (PAS) affects the efficiency of HIV-1 reverse transcription initiation. Nucleic Acids Res., 35, 1649-1659.
32. Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
33. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
34. Westerhout,E.M., Ooms,M., Vink,M., Das,A.T. and Berkhout,B. (2005) HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome. Nucleic Acids Res., 33, 796-804.
35. Ooms,M., Cupac,D., Abbink,T.E., Huthoff,H. and Berkhout,B. (2007) The availability of the primer activation signal (PAS) affects the efficiency of HIV-1 reverse transcription initiation. Nucleic Acids Res., 35, 1649-1659.
36. Mujeeb,A., Clever,J.L., Billeci,T.M., James,T.L. and Parslow,T.G. (1998) Structure of the dimer initiation complex of HIV-1 genomic RNA. Nat. Struct. Biol., 5, 432-436.
37. Berkhout,B. and Klaver,B. (1995) Revertants and pseudo-revertants of human immunodeficiency virus type 1 viruses mutated in the long terminal repeat promoter region. J. Gen. Virol., 76, 845-853.
38. Klaver,B. and Berkhout,B. (1994) Evolution of a disrupted TAR RNA hairpin structure in the HIV-1 virus. EMBO J., 13, 2650-2659.
39. Abbink,T.E.M. and Berkhout,B. (2003) A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the gag start codon. J. Biol. Chem., 278, 11601-11611.