Expression Level of HIV-1 Vif Can Be Fluctuated by Natural Nucleotide Variations in the vif-Coding and Regulatory SA1D2prox Sequences of the Proviral Genome.

Naoya Doi,Takaaki Koma,Akio Adachi,Masako Nomaguchi

doi:10.3389/fmicb.2019.02758

Naoya Doi, Takaaki Koma + Show 2 more

Open Access

https://doi.org/10.3389/fmicb.2019.02758

Copy DOI

Abstract

Vif is required for HIV-1 replication in natural target cells by counteracting host restriction factors, APOBEC3 (A3) proteins. We recently demonstrated that Vif expression level can be changed by naturally occurring single-nucleotide variations within SA1D2prox of the HIV-1 genome. We also found that levels for vif/vpr mRNAs are inversely correlated. While amino acid sequence per se is critical for functionality, Vif expression level modulated by signal sequences in its coding region is likely to be important as well. There are two splicing sites in the region involved in vpr expression. To reveal possible fluctuations of Vif-expression level, we examined SA1D2prox and vif gene by chimeric approaches using HIV-1 subtypes B and C with distinct anti-A3 activity. In this report, recombinant clones in subtype B backbone carrying chimeric sequences with respect to SA1D2prox/vif and those within the vif-coding region were generated. Of these, clones containing vif-coding sequence of subtype C, especially its 3′ region, expressed vif/Vif at a decreased level but did at an increased level for vpr/Vpr. Clones with reduced vif/Vif level grew similarly or slightly better than a parental clone in weakly A3G-positive cells but more poorly in highly A3G-expressing cells. Three clones with this property were also tested for their A3-degrading activity. One of the clones appeared to have some defect in addition to the poor ability to express vif/Vif. Taken all together, our results show that natural variations in the SA1D2prox and vif-coding region can change the Vif-expression level and affect the HIV-1 replication potential.

Highlights

We previously demonstrated that vif mRNA/Vif protein expression levels are altered by naturally occurring single nucleotide variations, found within the region around SA1/SD2 through investigation of the HIV-1 sequence compendium1
Together with our previous reports (Nomaguchi et al, 2014, 2016, 2017), our results suggest that viral nucleotide sequences of both SA1D2prox and vif coding-region contribute to determining Vif expression level and affecting HIV-1 replication (Figure 2)
Many splicing regulatory elements (SREs) have been identified around SAs/SDs including those within SA1D2prox and vif-coding sequence (Caputi, 2011; Karn and Stoltzfus, 2012; Sertznig et al, 2018)

Summary

INTRODUCTION

HIV-1 Vif antagonize host intrinsic restriction factors, A3 proteins (A3s) (Malim and Emerman, 2008; Harris et al, 2012; Malim and Bieniasz, 2012; Aydin et al, 2014; Desimmie et al, 2014; Feng et al, 2014; Okada and Iwatani, 2016). We investigated, in the context of proviral genome, effects of nucleotide sequence variations in the SA1D2prox and vif regions on the vif/vpr expression levels and on the HIV-1 growth potential. Vif production levels of NLpInV, InpNLV, and InpInV (the first group of chimeric viruses in Figure 1D as described above) were clearly reduced relative to that of NL4-3, indicating that vif level is decreased by Indie SA1D2prox and vif sequences. Another important point to be mentioned here is that, while the vif/Vif levels of InpInV were reduced relative to those of NLpInV (Figures 2A,B), the two clones grew In this regard, we previously found that the vif expression level in a certain range (0.16 to 0.47 relative to NL4-3) is sufficient to maintain wild-type growth ability (Nomaguchi et al, 2016). Vpr has been reported to exert its function mainly in the myeloid cell lineage (Fujita et al, 2010; Guenzel et al, 2014; González, 2017; Nodder and Gummuluru, 2019)

CONCLUDING REMARKS

Findings

DATA AVAILABILITY STATEMENT