Functional Incompatibility between the Generic NF-κB Motif and a Subtype-Specific Sp1III Element Drives the Formation of the HIV-1 Subtype C Viral Promoter

Abstract

Of the various genetic subtypes of human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2) and simian immunodeficiency virus (SIV), only in subtype C of HIV-1 is a genetically variant NF-B binding site found at the core of the viral promoter in association with a subtype-specific Sp1III motif. How the subtype-associated variations in the core transcription factor binding sites (TFBS) influence gene expression from the viral promoter has not been examined previously. Using panels of infectious viral molecular clones, we demonstrate that subtype-specific NF-B and Sp1III motifs have evolved for optimal gene expression, and neither of the motifs can be replaced by a corresponding TFBS variant. The variant NF-B motif binds NF-B with an affinity 2-fold higher than that of the generic NF-B site. Importantly, in the context of an infectious virus, the subtype-specific Based on genetic variation, human immunodeficiency virus type 1 (HIV-1) is classified into four distinct groups (M, N, O, and P), and group M is subclassified into nine molecular subtypes (A, B, C, D, F, G, H, J, and K) and numerous circulating recombinant forms, including A/E (1). The global distribution of HIV-1 subtypes is uneven, with C, A, and B being the most widespread subtypes. Subtype C is predominant in southern and eastern African countries, India, and Nepal and in recombinant forms in China, and it is currently emerging in southern Brazil. Subtype C is responsible for approximately half of the global HIV-1 infections and more than 95% of the infections in India (2). The factors that contribute to the widespread expansion of subtype C are not well understood. Diverse viral subtypes differ from one another up to 30 to 35% in certain gene segments, such as the envelope (3). A genetic variation to this large an extent is expected to have a significant impact on the biological properties of the subtypes influencing their relative fitness properties. Subtype-specific genetic variations in elements such as the viral promoter (enhancer and other regulatory elements), regulatory proteins, and structural proteins may underlie the biological differences, although drawing such a correlation between these factors may not always be possible.The individual components of the viral promoter, including the modulator region, the enhancer, and the core promoter, are characterized by several subtype-specific molecular variations. Such differences have been mapped to many transcription factor binding sites (TFBS), including USF, c-Myb, NF-AT, Ap-1, NF-B, and Sp1, and regulatory elements such as the TATA box and

A stronger transcription regulatory circuit of HIV-1C drives the rapid establishment of latency with implications for the direct involvement of Tat

“…A similar examination at the C-LTR has not been performed. A previous report from our laboratory demonstrated that NFAT1, 2, and 5 proteins could be recruited to the C-B motif, the variant NF-κB motif unique for HIV-1C, with an affinity superior to that of the canonical H-B site (Verma A et al, 2016). We attempted to compare the identity of the transcription factors and other host factors binding to the viral promoter between the active and suppressed states under identical experimental conditions.…”

“…Of the various TFBS present in the viral promoter, those of NF-κB and Sp-1, both represented by multiple and tandem binding sites in the LTR, play a crucial role in regulating gene expression and latency (Baeuerle PA and Baltimore D, 1989;Doetzlhofer A et al, 1999;Suzuki T et al, 1998;Williams SA et al, 2006). The most striking feature in the HIV-1C LTR is the copy-number difference of NF-κB motifs, the sequence variation of the additional κB motifs (Bachu M et al, 2012b), and the associated sequence variation of the Sp1III site (Verma A et al, 2016). We demonstrated previously that NF-κB site duplication is unique for HIV-1C not recapitulated by any other HIV-1 genetic family.…”

“…We demonstrated previously that NF-κB site duplication is unique for HIV-1C not recapitulated by any other HIV-1 genetic family. Importantly, in HIV-1C, a unique NF-κB motif (the C-κB element, GGGGCGTTCC) and a genetically distinct and subtype-specific Sp1III site are located at the core of the promoter replacing the canonical H-κB motif (GGGACTTTCC) present in all the other HIV-1 subtypes at this location, in association with a Sp1III motif that shows subtype-specific variations (Verma A et al, 2016).…”

HIV‐1 inhibits haematopoiesis via microRNA secreted by virus‐infected CD4+ T cells

“…We have produced the recombinant HIV‐1 viruses by transfecting into HEK293T cells plasmids encoding the CCR5‐tropic pIndie‐C and CXCR4‐tropic pNL4‐3 viral DNAs …”

“…We have produced the recombinant HIV-1 viruses by transfecting into HEK293T cells plasmids encoding the CCR5-tropic pIndie-C and CXCR4-tropic pNL4-3 viral DNAs. 15,16 HEK293Ts were routinely maintained in Dulbecco's modified minimum essential medium (DMEM) + 10% FBS (both GIBCO).…”