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Cis-element absolutely required for HIV-I pathogenesis and purification of its trans-acting factor RBF-2

University of British Columbia

HIVs are classified into types 1 or 2, groups, subtypes, and specific isolates. They infect CD4+ T-lymphocytes and monocyte/ macrophages. Infection and destruction of CD4+ T-lymphocytes occurs at the pace of billions per day. This massive HIV and CD4+ T-lymphocyte turnover, combined with mutation rate, results in extensive HIV sequence polymorphism. After an average of 11 years, CD4 decline from unbalanced turnover, leads to AIDS and inexorably death. In this thesis I first determined that HIV-1 in Vancouver are of envelope and LTR group M, subtype B. I then extensively investigated the LTR. The LTR contains sequences responsible for RNA pol II recognition and transcription of the HIV-1 genes. I first derived 476 LTR sequences from patients at all stages of HIV-1 infection. I found a surprising number of point and length polymorphisms, predicted to impair binding to targets for dogmatically entrenched transcription factors deemed essential to HIV-1. Some are novel, others have previously been described. I further investigated the function for some LTR variants. I found a wide range of transcription activities, and correlate some to specific sequence polymorphisms. I found no obvious correlation with disease stage for any polymorphism. A -121 position polymorphism, that I termed the Most Frequent Naturally occurring Length Polymorphism (MFNLP), was further investigated. MFNLPs occurred in 38% of patients I sampled. I found no phenotype for MFNLP bearing LTRs. Importantly, I first propose and then prove that MFNLPs all harbor binding sites for the recently characterized transcription factor RBF-2, known to bind the HIV-1 LTR. Thus the MFNLP duplicates an RBF-2 site. Although none of the postulated transcription factor binding sites of the HIV-1 LTR escapes mutation in vivo, only an RBF-2 site is invariably compensated by co-occurrence of it's duplication. Because of MFNLPs, I found an RBF-2 target to be the most conserved site of naturally occurring HIV-1 LTRs. Using MFNLP deleted isogenic mutants, I found a repressive phenotype for the MFNLPs, but only in cells with detectable levels of RBF-2. I further describe the biochemical purification of RBF-2. Analysis of oligo-affinity purified RBF-2 suggests it is a novel complex. All LTRs I have examined, that are derived from patients that progress towards AIDS, have the ability to bind RBF-2. Assuming the current view that viral turnover is itself pathogenic, then by extension, I conclude that the RBF-2 cis-acting element, encompassed in MFNLPs, is required for HIV-1 pathogenesis in vivo. [Scientific formulae used in this abstract could not be reproduced.]

Thesis/Dissertation

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2009-05-29

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http://hdl.handle.net/2429/8484

Pathology

University of British Columbia

UBCV

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