Research

Human Immunodeficiency Virus-Type 1 LTR DNA contains an intrinsic gene producing antisense RNA and protein products

Linda B Ludwig^1,4 , Julian L Ambrus Jr¹ , Kristie A Krawczyk¹ , Sanjay Sharma² , Stephen Brooks² , Chiu-Bin Hsiao³ and Stanley A Schwartz¹

¹Division of Allergy, Immunology and Rheumatology, Department of Medicine, School of Biomedical Science and Medicine, State University of New York at Buffalo, Buffalo, New York 14203, USA

²Department of Surgery, School of Biomedical Science and Medicine, State University of New York at Buffalo, Buffalo, New York 14203, USA

³Division of Infectious Disease, Department of Medicine, School of Biomedical Science and Medicine, State University of New York at Buffalo, Buffalo, New York 14203, USA

⁴Present address: 2519 145th Circle, Vancouver, Washington 98686, USA

author email corresponding author email

Retrovirology 2006, 3:80doi:10.1186/1742-4690-3-80

Published:	8 November 2006

Abstract

Background

While viruses have long been shown to capitalize on their limited genomic size by utilizing both strands of DNA or complementary DNA/RNA intermediates to code for viral proteins, it has been assumed that human retroviruses have all their major proteins translated only from the plus or sense strand of RNA, despite their requirement for a dsDNA proviral intermediate. Several studies, however, have suggested the presence of antisense transcription for both HIV-1 and HTLV-1. More recently an antisense transcript responsible for the HTLV-1 bZIP factor (HBZ) protein has been described. In this study we investigated the possibility of an antisense gene contained within the human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR).

Results

Inspection of published sequences revealed a potential transcription initiator element (INR) situated downstream of, and in reverse orientation to, the usual HIV-1 promoter and transcription start site. This antisense initiator (HIVaINR) suggested the possibility of an antisense gene responsible for RNA and protein production. We show that antisense transcripts are generated, in vitro and in vivo, originating from the TAR DNA of the HIV-1 LTR. To test the possibility that protein(s) could be translated from this novel HIV-1 antisense RNA, recombinant HIV antisense gene-FLAG vectors were designed. Recombinant protein(s) were produced and isolated utilizing carboxy-terminal FLAG epitope (DYKDDDDK) sequences. In addition, affinity-purified antisera to an internal peptide derived from the HIV antisense protein (HAP) sequences identified HAPs from HIV+ human peripheral blood lymphocytes.

Conclusion

HIV-1 contains an antisense gene in the U3-R regions of the LTR responsible for both an antisense RNA transcript and proteins. This antisense transcript has tremendous potential for intrinsic RNA regulation because of its overlap with the beginning of all HIV-1 sense RNA transcripts by 25 nucleotides. The novel HAPs are encoded in a region of the LTR that has already been shown to be deleted in some HIV-infected long-term survivors and represent new potential targets for vaccine development.