Sequence Insertions in the HIV Type 1 Subtype C Viral Promoter Predominantly Generate an Additional NF-κB Binding Site

Abstract

After screening a large number of clinical samples of HIV-1 subtype C in India, a subset of viral strains containing sequence insertions upstream of the viral enhancer has been identified. The sequence insertions contained binding sites for at least two different transcription factors NF-jB and RBEIII, importantly, in a mutually exclusive fashion. Furthermore, while some of the viral strains contained insertions of jB-like sites, a few others contained dual insertions of the RBEIII and jB sites together but only one of the two was intact. NFjB acquisition appears to be the most common phenotype unique for subtype C with nearly half of the variant strains containing such insertions. Given that subtype C already contains three functional NF-jB sites in the viral enhancer, acquisition of a fourth NF-jB motif in some variant viral strains is intriguing. Further investigation is warranted to examine the significance of the sequence insertions for the replicative fitness of the variant viral strains.

Multiple NF-κB Sites in HIV-1 Subtype C Long Terminal Repeat Confer Superior Magnitude of Transcription and Thereby the Enhanced Viral Predominance

“…Amplification, Cloning, and Bioinformatics Analysis of the LTR Sequences-The amplification and cloning of the LTR sequences from the patient isolates were performed as we described previously (26). Briefly, full-length or the U3 region of the viral LTR was amplified from the proviral DNA or plasma viral RNA, respectively.…”

“…2A). Several of the Indian LTR sequences used for this analysis have been previously reported (26). A 4-B subtype C promoter contains three types of genetically distinct B sites, and for clarity they are labeled accordingly.…”

“…A subsequent sequence analysis of the viral enhancer in 25 of the 34 viruses demonstrated that the sequence insertions in C-LTR acquired at least two different types of TFBS, predominantly NF-B (12 of 25) and in a minority of the strains the RBEIII site (6 of 25) (26). Additionally, a few viral strains (4 of 25) contained sequence insertions that broadly resembled a canonical NF-B motif hence referred to here as the B-like sites.…”

Targeting NF-κB Signaling with Protein Kinase C Agonists As an Emerging Strategy for Combating HIV Latency

“…Therefore, the increased number of NF-jB binding sites in the viral LTR may impact the establishment of viral predominance. [26][27][28][29][30][31] However, it is not known whether an increased number of NF-jB binding sites in the LTR region has any impact on the kinetics of the establishment of HIV latency. High viremia with a prolonged time period has been observed in patients with primary HIV-1 subtype C infection.…”

“…Therefore, it is possible that a large viral reservoir of latently HIV-infected CD4 + T cells may be established in these patients. [26][27][28][29][30][31] Variations in the jB binding sites in subtypes of HIV may be associated with the establishment of the degree of HIV latency.…”