Distinctive variation in the U3R region of the 5' Long Terminal Repeat from diverse HIV-1 strains

Abstract

Functional mapping of the 5’LTR has shown that the U3 and the R regions (U3R) contain a cluster of regulatory elements involved in the control of HIV-1 transcription and expression. As the HIV-1 genome is characterized by extensive variability, here we aimed to describe mutations in the U3R from various HIV-1 clades and CRFs in order to highlight strain specific differences that may impact the biological properties of diverse HIV-1 strains. To achieve our purpose, the U3R sequence of plasma derived virus belonging to different clades (A1, B, C, D, F2) and recombinants (CRF02_AG, CRF01_AE and CRF22_01A1) was obtained using Illumina technology. Overall, the R region was very well conserved among and across different strains, while in the U3 region the average inter-strains nucleotide dissimilarity was up to 25%. The TAR hairpin displayed a strain-distinctive cluster of mutations affecting the bulge and the loop, but mostly the stem. Like in previous studies we found a motif in U3 promoter region from the majority of HIV-1 strains and a motif in CRF01_AE; but also in LTRs from CRF22_01A1 isolates. Although LTRs from CRF22_01A1 specimens were assigned CRF01_AE, they contained two NF-kB sites instead of the single TFBS described in CRF01_AE. Also, as previously describe in clade C isolates, we found no C/EBP binding site directly upstream of the enhancer region in CRF22_01A1 specimens. In our study, one-third of CRF02_AG LTRs displayed three NF-kB sites which have been mainly described in clade C isolates. Overall, the number, location and binding patterns of potential regulatory elements found along the U3R might be specific to some HIV-1 strains such as clade F2, CRF02_AG, CRF01_AE and CRF22_01A1. These features may be worth consideration as they may be involved in distinctive regulation of HIV-1 transcription and replication by different and diverse infecting strains.

Hypoxic microenvironment shapes HIV-1 replication and latency

“…The HIV-1 5’LTR is ~640 bp in length and the U3 region is located upstream of the transcription start site and is divided into the modulatory (−454, −105), enhancer (−105, −79), and promoter (−78, −1) regions (numbering based on the HXB2 sequence) 49 . The modulator region contains several transcription factor binding sites 50 , the enhancer region contains binding sites for NF-kB family members and the core promoter encodes three binding sites for Sp1 and the TATA box. The HIF binding site is located in a region around the −246 position in the U3 region relative to the start codon, and overlaps with a CCAAT/enhancer binding site (C/EBP binding site US3, HXB2 numbering) 38 , 51 .…”

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

“…Although the fundamental constitution of the HIV-1 promoter is highly conserved among the various genetic subtypes of HIV-1, within this underlying structural theme, there exist many subtype-specific molecular features that may modulate gene expression considerably from the viral promoter. Such differences are evident in the copy-number and nucleotide sequences of different TFBS especially those of USF, c-Myb, LEF-1, Ets1, NF-AT, Ap-1, NF-κB, and Sp1 binding sites, and regulatory elements such as the TATA box and the TAR element (Jeeninga RE et al, 2000;Mbondji-Wonje C et al, 2018;Montano MA et al, 1997). The critical roles that most of these regulatory elements play in positively regulating the basal and inducible levels of viral transcription have been well documented (Garcia JA et al, 1987;Pereira LA et al, 2000).…”

Genetic variability of the U5 and downstream sequence of major HIV-1 subtypes and circulating recombinant forms

“…This study was done with a total of 80 contigs obtained from a previously described methodology 1 . Briefly, RNA was extracted from selected plasma derived viruses belonging to subtypes B, C, D, F2 and G, as well as CRF02_AG, CRF01_AE and CRF22_01A1 (Table 1 ).…”

“…Nucleotide changes generated from these mechanisms affect the entire viral genome, including its highly structured 5′ end region. Indeed, the HIV-1 genome variability was found to be as much as 23% in the 5′LTR-U3 region, about 10% in the gag/pol genes, and more than 30% in the env gene, with overall differences observed primarily between intra and inter-subtype 1 , 2 . Previous studies have revealed that strain differences may influence transmission, replication, and virulence of HIV-1.…”

“…To date, most reports on regulatory elements that bind transcription factors at the 5′ end of the HIV-1 genome have focused on the sequence upstream of the U5 region. Although the nucleotide sequence reverse-transcribed into the 5′ UTR has been considered as the most conserved region of the viral genome 22 , a few studies have reported strain-specific variation in the R and U5-PBS region 1 , 23 – 26 . Yet, detailed strain-specific variability of this region remains poorly documented.…”