Skip to main content
PMC home page
RNA logoLink to RNA
. 2001 Jan;7(1):143–157. doi: 10.1017/s1355838201001881

Two alternating structures of the HIV-1 leader RNA.

H Huthoff 1, B Berkhout 1
PMCID: PMC1370064  PMID: 11214176

Abstract

In this study we demonstrate that the HIV-1 leader RNA exists in two alternative conformations, a branched structure consisting of several well-known hairpin motifs and a more stable structure that is formed by extensive long-distance base pairing. The latter conformation was first identified as a compactly folded RNA that migrates unusually fast in nondenaturing gels. The minimally required domains for formation of this conformer were determined by mutational analysis. The poly(A) and DIS regions of the leader are the major determinants of this RNA conformation. Further biochemical characterization of this conformer revealed that both hairpins are disrupted to allow extensive long-distance base pairing. As the DIS hairpin is known to be instrumental for formation of the HIV-1 RNA dimer, the interplay between formation of the conformer and dimerization was addressed. Formation of the conformer and the RNA dimer are mutually exclusive. Consequently, the conformer must rearrange into a branched structure that exposes the dimer initiation signal (DIS) hairpin, thus triggering formation of the RNA dimer. This structural rearrangement is facilitated by the viral nucleocapsid protein NC. We propose that this structural polymorphism of the HIV-1 leader RNA acts as a molecular switch in the viral replication cycle.

Full Text

The Full Text of this article is available as a PDF (1.9 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Aboul-ela F., Karn J., Varani G. Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge. Nucleic Acids Res. 1996 Oct 15;24(20):3974–3981. doi: 10.1093/nar/24.20.3974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Amarasinghe G. K., De Guzman R. N., Turner R. B., Summers M. F. NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novel A-U-A base-triple platform. J Mol Biol. 2000 May 26;299(1):145–156. doi: 10.1006/jmbi.2000.3710. [DOI] [PubMed] [Google Scholar]
  3. Baudin F., Marquet R., Isel C., Darlix J. L., Ehresmann B., Ehresmann C. Functional sites in the 5' region of human immunodeficiency virus type 1 RNA form defined structural domains. J Mol Biol. 1993 Jan 20;229(2):382–397. doi: 10.1006/jmbi.1993.1041. [DOI] [PubMed] [Google Scholar]
  4. Bender W., Davidson N. Mapping of poly(A) sequences in the electron microscope reveals unusual structure of type C oncornavirus RNA molecules. Cell. 1976 Apr;7(4):595–607. doi: 10.1016/0092-8674(76)90210-5. [DOI] [PubMed] [Google Scholar]
  5. Berkhout B., Essink B. B., Schoneveld I. In vitro dimerization of HIV-2 leader RNA in the absence of PuGGAPuA motifs. FASEB J. 1993 Jan;7(1):181–187. doi: 10.1096/fasebj.7.1.8422965. [DOI] [PubMed] [Google Scholar]
  6. Berkhout B., Klaver B., Das A. T. A conserved hairpin structure predicted for the poly(A) signal of human and simian immunodeficiency viruses. Virology. 1995 Feb 20;207(1):276–281. doi: 10.1006/viro.1995.1077. [DOI] [PubMed] [Google Scholar]
  7. Berkhout B., Klaver B., Das A. T. Forced evolution of a regulatory RNA helix in the HIV-1 genome. Nucleic Acids Res. 1997 Mar 1;25(5):940–947. doi: 10.1093/nar/25.5.940. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Berkhout B. Multiple biological roles associated with the repeat (R) region of the HIV-1 RNA genome. Adv Pharmacol. 2000;48:29–73. doi: 10.1016/s1054-3589(00)48003-8. [DOI] [PubMed] [Google Scholar]
  9. Berkhout B., Silverman R. H., Jeang K. T. Tat trans-activates the human immunodeficiency virus through a nascent RNA target. Cell. 1989 Oct 20;59(2):273–282. doi: 10.1016/0092-8674(89)90289-4. [DOI] [PubMed] [Google Scholar]
  10. Berkhout B. Structure and function of the human immunodeficiency virus leader RNA. Prog Nucleic Acid Res Mol Biol. 1996;54:1–34. doi: 10.1016/s0079-6603(08)60359-1. [DOI] [PubMed] [Google Scholar]
  11. Berkhout B. The primer binding site on the RNA genome of human and simian immunodeficiency viruses is flanked by an upstream hairpin structure. Nucleic Acids Res. 1997 Oct 15;25(20):4013–4017. doi: 10.1093/nar/25.20.4013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Berkhout B., van Wamel J. L. Role of the DIS hairpin in replication of human immunodeficiency virus type 1. J Virol. 1996 Oct;70(10):6723–6732. doi: 10.1128/jvi.70.10.6723-6732.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Berkhout B., van Wamel J. L. The leader of the HIV-1 RNA genome forms a compactly folded tertiary structure. RNA. 2000 Feb;6(2):282–295. doi: 10.1017/s1355838200991684. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Brion P., Westhof E. Hierarchy and dynamics of RNA folding. Annu Rev Biophys Biomol Struct. 1997;26:113–137. doi: 10.1146/annurev.biophys.26.1.113. [DOI] [PubMed] [Google Scholar]
  15. Clever J. L., Eckstein D. A., Parslow T. G. Genetic dissociation of the encapsidation and reverse transcription functions in the 5' R region of human immunodeficiency virus type 1. J Virol. 1999 Jan;73(1):101–109. doi: 10.1128/jvi.73.1.101-109.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Clever J. L., Parslow T. G. Mutant human immunodeficiency virus type 1 genomes with defects in RNA dimerization or encapsidation. J Virol. 1997 May;71(5):3407–3414. doi: 10.1128/jvi.71.5.3407-3414.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Damgaard C. K., Dyhr-Mikkelsen H., Kjems J. 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. 1998 Aug 15;26(16):3667–3676. doi: 10.1093/nar/26.16.3667. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Darlix J. L., Gabus C., Nugeyre M. T., Clavel F., Barré-Sinoussi F. Cis elements and trans-acting factors involved in the RNA dimerization of the human immunodeficiency virus HIV-1. J Mol Biol. 1990 Dec 5;216(3):689–699. doi: 10.1016/0022-2836(90)90392-Y. [DOI] [PubMed] [Google Scholar]
  19. Das A. T., Klaver B., Berkhout B. A hairpin structure in the R region of the human immunodeficiency virus type 1 RNA genome is instrumental in polyadenylation site selection. J Virol. 1999 Jan;73(1):81–91. doi: 10.1128/jvi.73.1.81-91.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Das A. T., Klaver B., Klasens B. I., van Wamel J. L., Berkhout B. A conserved hairpin motif in the R-U5 region of the human immunodeficiency virus type 1 RNA genome is essential for replication. J Virol. 1997 Mar;71(3):2346–2356. doi: 10.1128/jvi.71.3.2346-2356.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Fisher A. G., Feinberg M. B., Josephs S. F., Harper M. E., Marselle L. M., Reyes G., Gonda M. A., Aldovini A., Debouk C., Gallo R. C. The trans-activator gene of HTLV-III is essential for virus replication. 1986 Mar 27-Apr 2Nature. 320(6060):367–371. doi: 10.1038/320367a0. [DOI] [PubMed] [Google Scholar]
  22. Girard F., Barbault F., Gouyette C., Huynh-Dinh T., Paoletti J., Lancelot G. Dimer initiation sequence of HIV-1Lai genomic RNA: NMR solution structure of the extended duplex. J Biomol Struct Dyn. 1999 Jun;16(6):1145–1157. doi: 10.1080/07391102.1999.10508323. [DOI] [PubMed] [Google Scholar]
  23. Helga-Maria C., Hammarskjöld M. L., Rekosh D. An intact TAR element and cytoplasmic localization are necessary for efficient packaging of human immunodeficiency virus type 1 genomic RNA. J Virol. 1999 May;73(5):4127–4135. doi: 10.1128/jvi.73.5.4127-4135.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Herschlag D., Khosla M., Tsuchihashi Z., Karpel R. L. An RNA chaperone activity of non-specific RNA binding proteins in hammerhead ribozyme catalysis. EMBO J. 1994 Jun 15;13(12):2913–2924. doi: 10.1002/j.1460-2075.1994.tb06586.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Herschlag D. RNA chaperones and the RNA folding problem. J Biol Chem. 1995 Sep 8;270(36):20871–20874. doi: 10.1074/jbc.270.36.20871. [DOI] [PubMed] [Google Scholar]
  26. Isel C., Ehresmann C., Keith G., Ehresmann B., Marquet R. Initiation of reverse transcription of HIV-1: secondary structure of the HIV-1 RNA/tRNA(3Lys) (template/primer). J Mol Biol. 1995 Mar 24;247(2):236–250. doi: 10.1006/jmbi.1994.0136. [DOI] [PubMed] [Google Scholar]
  27. Jossinet F., Paillart J. C., Westhof E., Hermann T., Skripkin E., Lodmell J. S., Ehresmann C., Ehresmann B., Marquet R. Dimerization of HIV-1 genomic RNA of subtypes A and B: RNA loop structure and magnesium binding. RNA. 1999 Sep;5(9):1222–1234. doi: 10.1017/s1355838299990982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Klasens B. I., Das A. T., Berkhout B. Inhibition of polyadenylation by stable RNA secondary structure. Nucleic Acids Res. 1998 Apr 15;26(8):1870–1876. doi: 10.1093/nar/26.8.1870. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Klasens B. I., Huthoff H. T., Das A. T., Jeeninga R. E., Berkhout B. The effect of template RNA structure on elongation by HIV-1 reverse transcriptase. Biochim Biophys Acta. 1999 Mar 19;1444(3):355–370. doi: 10.1016/s0167-4781(99)00011-1. [DOI] [PubMed] [Google Scholar]
  30. Laughrea M., Jetté L. 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. 1994 Nov 15;33(45):13464–13474. doi: 10.1021/bi00249a035. [DOI] [PubMed] [Google Scholar]
  31. LeCuyer K. A., Crothers D. M. The Leptomonas collosoma spliced leader RNA can switch between two alternate structural forms. Biochemistry. 1993 May 25;32(20):5301–5311. doi: 10.1021/bi00071a004. [DOI] [PubMed] [Google Scholar]
  32. Mathews D. H., Sabina J., Zuker M., Turner D. H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol. 1999 May 21;288(5):911–940. doi: 10.1006/jmbi.1999.2700. [DOI] [PubMed] [Google Scholar]
  33. McBride M. S., Panganiban A. T. The human immunodeficiency virus type 1 encapsidation site is a multipartite RNA element composed of functional hairpin structures. J Virol. 1996 May;70(5):2963–2973. doi: 10.1128/jvi.70.5.2963-2973.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Muesing M. A., Smith D. H., Cabradilla C. D., Benton C. V., Lasky L. A., Capon D. J. Nucleic acid structure and expression of the human AIDS/lymphadenopathy retrovirus. Nature. 1985 Feb 7;313(6002):450–458. doi: 10.1038/313450a0. [DOI] [PubMed] [Google Scholar]
  35. Mujeeb A., Clever J. L., Billeci T. M., James T. L., Parslow T. G. Structure of the dimer initiation complex of HIV-1 genomic RNA. Nat Struct Biol. 1998 Jun;5(6):432–436. doi: 10.1038/nsb0698-432. [DOI] [PubMed] [Google Scholar]
  36. Muriaux D., De Rocquigny H., Roques B. P., Paoletti J. NCp7 activates HIV-1Lai RNA dimerization by converting a transient loop-loop complex into a stable dimer. J Biol Chem. 1996 Dec 27;271(52):33686–33692. doi: 10.1074/jbc.271.52.33686. [DOI] [PubMed] [Google Scholar]
  37. Muriaux D., Girard P. M., Bonnet-Mathonière B., Paoletti J. Dimerization of HIV-1Lai RNA at low ionic strength. An autocomplementary sequence in the 5' leader region is evidenced by an antisense oligonucleotide. J Biol Chem. 1995 Apr 7;270(14):8209–8216. doi: 10.1074/jbc.270.14.8209. [DOI] [PubMed] [Google Scholar]
  38. Puglisi J. D., Tinoco I., Jr Absorbance melting curves of RNA. Methods Enzymol. 1989;180:304–325. doi: 10.1016/0076-6879(89)80108-9. [DOI] [PubMed] [Google Scholar]
  39. Rizvi T. A., Panganiban A. T. Simian immunodeficiency virus RNA is efficiently encapsidated by human immunodeficiency virus type 1 particles. J Virol. 1993 May;67(5):2681–2688. doi: 10.1128/jvi.67.5.2681-2688.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Skripkin E., Paillart J. C., Marquet R., Ehresmann B., Ehresmann C. Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro. Proc Natl Acad Sci U S A. 1994 May 24;91(11):4945–4949. doi: 10.1073/pnas.91.11.4945. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Wei P., Garber M. E., Fang S. M., Fischer W. H., Jones K. A. 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. 1998 Feb 20;92(4):451–462. doi: 10.1016/s0092-8674(00)80939-3. [DOI] [PubMed] [Google Scholar]
  42. Zeffman A., Hassard S., Varani G., Lever A. The major HIV-1 packaging signal is an extended bulged stem loop whose structure is altered on interaction with the Gag polyprotein. J Mol Biol. 2000 Apr 7;297(4):877–893. doi: 10.1006/jmbi.2000.3611. [DOI] [PubMed] [Google Scholar]

Articles from RNA are provided here courtesy of The RNA Society

RESOURCES