This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Clever, J. L.
Right arrow Articles by Parslow, T. G.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Clever, J. L.
Right arrow Articles by Parslow, T. G.

 Previous Article  |  Next Article 

Journal of Virology, January 1999, p. 101-109, Vol. 73, No. 1
0022-538X/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

Genetic Dissociation of the Encapsidation and Reverse Transcription Functions in the 5' R Region of Human Immunodeficiency Virus Type 1

Jared L. Clever, Daniel A. Eckstein, and Tristram G. Parslow*

Departments of Pathology and of Microbiology and Immunology, University of California, San Francisco, California 94143

Received 1 July 1998/Accepted 7 September 1998

The efficient packaging of genomic RNA into virions of human immunodeficiency virus type 1 (HIV-1) is directed by cis-acting encapsidation signals, which have been mapped to particular RNA stem-loop structures near the 5' end of the genome. Earlier studies have shown that three such stem-loops, located adjacent to the major 5' splice donor, are required for optimal packaging; more recent reports further suggest a requirement for the TAR and poly(A) hairpins of the 5' R region. In the present study, we have compared the phenotypes that result from mutating these latter elements in the HIV-1 provirus. Using a single-round infectivity assay, we find that mutations which disrupt base pairing in either the TAR or poly(A) stems cause profound defects in both packaging and viral replication. Decreased genomic packaging in a given mutant was always accompanied by increased packaging of spliced viral RNAs. Compensatory mutations that restored base pairing also restored encapsidation, indicating that the secondary structures of the TAR and poly(A) stems, rather than their primary sequences, are important for packaging activity. Despite having normal RNA contents, however, viruses with compensatory mutations at the base of the TAR stem were severely replication defective, owing to a defect in proviral DNA synthesis. Our findings thus confirm that the HIV-1 TAR stem-loop is required for at least three essential viral functions (transcriptional activation, RNA packaging, and reverse transcription) and reveal that its packaging and reverse transcription activities can be dissociated genetically by mutations at the base of the TAR stem.


* Corresponding author. Mailing address: Dept. of Pathology, Box 0506, University of California, San Francisco, CA 94143. Phone: (415) 476-1015. Fax: (415) 476-9672. E-mail: parslow{at}cgl.ucsf.edu.


Journal of Virology, January 1999, p. 101-109, Vol. 73, No. 1
0022-538X/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.



This article has been cited by other articles:

  • Baig, T. T., Lanchy, J.-M., Lodmell, J. S. (2009). Randomization and In Vivo Selection Reveal a GGRG Motif Essential for Packaging Human Immunodeficiency Virus Type 2 RNA. J. Virol. 83: 802-810 [Abstract] [Full Text]  
  • Ogg, M. M., Patterson, J. L. (2007). RNA Binding Domain of Jamestown Canyon Virus S Segment RNAs. J. Virol. 81: 13754-13760 [Abstract] [Full Text]  
  • Brandt, S., Grunwald, T., Lucke, S., Stang, A., Uberla, K. (2006). Functional replacement of the R region of simian immunodeficiency virus-based vectors by heterologous elements.. J. Gen. Virol. 87: 2297-2307 [Abstract] [Full Text]  
  • Paillart, J.-C., Dettenhofer, M., Yu, X.-f., Ehresmann, C., Ehresmann, B., Marquet, R. (2004). First Snapshots of the HIV-1 RNA Structure in Infected Cells and in Virions. J. Biol. Chem. 279: 48397-48403 [Abstract] [Full Text]  
  • Ooms, M., Huthoff, H., Russell, R., Liang, C., Berkhout, B. (2004). A Riboswitch Regulates RNA Dimerization and Packaging in Human Immunodeficiency Virus Type 1 Virions. J. Virol. 78: 10814-10819 [Abstract] [Full Text]  
  • Kanevsky, I., Vasilenko, N., Dumay-Odelot, H., Fosse, P. (2003). In vitro characterization of a base pairing interaction between the primer binding site and the minimal packaging signal of avian leukosis virus genomic RNA. Nucleic Acids Res 31: 7070-7082 [Abstract] [Full Text]  
  • Gallego, J., Greatorex, J., Zhang, H., Yang, B., Arunachalam, S., Fang, J., Seamons, J., Lea, S., Pomerantz, R. J., Lever, A. M. L. (2003). Rev Binds Specifically to a Purine Loop in the SL1 Region of the HIV-1 Leader RNA. J. Biol. Chem. 278: 40385-40391 [Abstract] [Full Text]  
  • Patel, J., Wang, S.-W., Izmailova, E., Aldovini, A. (2003). The Simian Immunodeficiency Virus 5' Untranslated Leader Sequence Plays a Role in Intracellular Viral Protein Accumulation and in RNA Packaging. J. Virol. 77: 6284-6292 [Abstract] [Full Text]  
  • Clever, J. L., Miranda, D. Jr., 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 [Abstract] [Full Text]  
  • Izmailova, E., Aldovini, A. (2002). Functional Analysis of the Murine Sarcoma Virus RNA Packaging Sequence. J. Virol. 76: 4643-4648 [Abstract] [Full Text]  
  • Paillart, J.-C., Skripkin, E., Ehresmann, B., Ehresmann, C., Marquet, R. (2002). In Vitro Evidence for a Long Range Pseudoknot in the 5'-Untranslated and Matrix Coding Regions of HIV-1 Genomic RNA. J. Biol. Chem. 277: 5995-6004 [Abstract] [Full Text]  
  • Guan, Y., Diallo, K., Whitney, J. B., Liang, C., Wainberg, M. A. (2001). An Intact U5-Leader Stem Is Important for Efficient Replication of Simian Immunodeficiency Virus. J. Virol. 75: 11924-11929 [Abstract] [Full Text]  
  • Huthoff, H., 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 [Abstract] [Full Text]  
  • Hooker, C. W., Lott, W. B., Harrich, D. (2001). Inhibitors of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Target Distinct Phases of Early Reverse Transcription. J. Virol. 75: 3095-3104 [Abstract] [Full Text]  
  • Guan, Y., Whitney, J. B., Diallo, K., Wainberg, M. A. (2000). Leader Sequences Downstream of the Primer Binding Site Are Important for Efficient Replication of Simian Immunodeficiency Virus. J. Virol. 74: 8854-8860 [Abstract] [Full Text]  
  • Ohi, Y., Clever, J. L. (2000). Sequences in the 5' and 3' R Elements of Human Immunodeficiency Virus Type 1 Critical for Efficient Reverse Transcription. J. Virol. 74: 8324-8334 [Abstract] [Full Text]  
  • Harrich, D., Hooker, C. W., 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 [Abstract] [Full Text]  
  • Clever, J. L., Taplitz, R. A., Lochrie, M. A., Polisky, B., Parslow, T. G. (2000). A Heterologous, High-Affinity RNA Ligand for Human Immunodeficiency Virus Gag Protein Has RNA Packaging Activity. J. Virol. 74: 541-546 [Abstract] [Full Text]  
  • Cui, Y., Iwakuma, T., Chang, L.-J. (1999). Contributions of Viral Splice Sites and cis-Regulatory Elements to Lentivirus Vector Function. J. Virol. 73: 6171-6176 [Abstract] [Full Text]