Nucleic Acids Research Advance Access first published online on June 27, 2008
This version published online on July 4, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn364
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Destabilization of the TAR hairpin affects the structure and function of the HIV-1 leader RNA
Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
*To whom correspondence should be addressed. Tel: +31 205 664 822; Fax: +31 206 916 531; Email: b.berkhout{at}amc.uva.nl
Received May 8, 2008. Accepted May 25, 2008.
The TAR hairpin of the human immunodeficiency virus type 1 (HIV-1) RNA genome is essential for virus replication. TAR forms the binding site for the transcriptional trans-activator protein Tat and multiple additional TAR functions have been proposed. We previously constructed an HIV-1 variant in which the TAR-Tat transcription control mechanism is replaced by the components of the Tet-ON regulatory system. In this context, the surprising finding was that TAR can be truncated or even deleted, but partial TAR deletions that destabilize the stem structure cause a severe replication defect. In this study, we demonstrate that the HIV-1 RNA genome requires a stable hairpin at its 5'-end because unpaired TAR sequences affect the proper folding of the untranslated leader RNA. Consequently, multiple leader-encoded functions are affected by partial TAR deletions. Upon evolution of such mutant viruses, the replication capacity was repaired through the acquisition of additional TAR mutations that restore the local RNA folding, thus preventing the detrimental effect on the leader conformation.