An additional NF-κB site allows HIV-1 subtype C to evade restriction by nuclear PYHIN proteins

Abstract

SUMMARY Subtype C is the most prevalent clade of human immunodeficiency virus type 1 (HIV-1) worldwide. The reasons for this are poorly understood. Here, we demonstrate that a characteristic additional third nuclear factor κB (NF-κB) binding site in the long terminal repeat (LTR) promoter allows subtype C HIV-1 strains to evade restriction by nuclear PYHIN proteins, which sequester the transcription factor Sp1. Further, other LTR alterations are responsible for rare PYHIN resistance of subtype B viruses. Resistance-conferring mutations generally reduce the dependency of HIV-1 on Sp1 for virus production and render LTR transcription highly responsive to stimulation by NF-κB/p65. A third NF-κB binding site increases infectious virus yield in primary CD4 + T cells in an γ-interferon-inducible protein 16 (IFI16)-dependent manner. Comprehensive sequence analyses suggest that the frequency of circulating PYHIN-resistant HIV-1 strains is increasing. Our finding that an additional NF-κB binding site in the LTR confers resistance to nuclear PYHIN proteins helps to explain the dominance of clade C HIV-1 strains.

Traitor-virus-guided discovery of novel antiviral factors

“…IFI16 has been reported to inhibit viral pathogens including HIV-1 by a variety of mechanisms and has also been reported to play roles in innate sensing of viral pathogens [55][56][57] . Our finding that the inhibitory activity of IFI16 is not only evaded by an additional NF-B binding site in the LTR of currently dominating clade C viruses 44 but also counteracted by Nef further supports an important role of this antiviral factors. Our results obtained using otherwise isogenic TV constructs differing in nef are proof-of-concept that genetically closely related pairs HIV-1 strains differing in IFN sensitivity and/or accessory gene function will pinpoint factors involved in virus transmission and/or counteracted by Vif, Vpr, Vpu or Nef.…”

“…6f-h). This came as surprise since we have previously shown that IFI16 inhibits most subtypes of HIV-1 by sequestering the transcription factors Sp1 and that clade C viruses evade this restriction by acquisition of an additional NF-kB binding site 44,45 . Analysis of five pairs of WT and nef -defective HIV-1 strains including two primary subtype B and two clade C IMCs confirmed that the latter are less sensitive to the inhibitory effects of IFI16 (Fig.…”

Replication competent HIV-guided CRISPR screen identifies antiviral factors including targets of the accessory protein Nef

“…6f–h ). This came as surprise since we have previously shown that IFI16 inhibits most subtypes of HIV-1 by sequestering the transcription factor Sp1 and that clade C viruses evade this restriction by acquisition of an additional NF-kB binding site 52 , 53 . Analysis of five pairs of WT and nef -defective HIV-1 strains including two primary subtype B and two clade C IMCs confirmed that the latter are less sensitive to the inhibitory effects of IFI16 (Fig.…”

Single-cell transcriptomics identifies prothymosin α restriction of HIV-1 in vivo

“…It is expected that not all pandemic HIV-1 strains are similarly susceptible to PTMA because they counteract or evade essentially all restriction factors (27). It has recently been shown that an additional nuclear factor κB (NF-κB) site allows HIV-1 subtype C to evade restriction by nuclear Pyrin and hematopoietic IFN-inducible nuclear (HIN) domain-containing (PYHIN) proteins (28), and it will be interesting to determine whether subtype C viruses have also evolved mechanisms to avoid restriction by PTMA. Together, the strength of the inhibitory effect of PTMA was similar to those observed in overexpression assays of tetherin, zinc-finger antiviral protein (ZAP), and guanylate binding protein 5 (GBP5) (29)(30)(31).…”