Evolutionary plasticity of SH3 domain binding by Nef proteins of the HIV-1/SIVcpz lentiviral lineage.

Zhe Zhao,Kalle Saksela,Kristina Hopfensperger,Perttu Permi,Smitha Srinivasachar Badarinarayan,Rishikesh Lotke,Riku Fagerlund,Frank Kirchhoff,Kei Sato,Helena Tossavainen,Daniel Sauter

doi:10.1371/journal.ppat.1009728

Abstract

The accessory protein Nef of human and simian immunodeficiency viruses (HIV and SIV) is an important pathogenicity factor known to interact with cellular protein kinases and other signaling proteins. A canonical SH3 domain binding motif in Nef is required for most of these interactions. For example, HIV-1 Nef activates the tyrosine kinase Hck by tightly binding to its SH3 domain. An archetypal contact between a negatively charged SH3 residue and a highly conserved arginine in Nef (Arg77) plays a key role here. Combining structural analyses with functional assays, we here show that Nef proteins have also developed a distinct structural strategy-termed the "R-clamp"-that favors the formation of this salt bridge via buttressing Arg77. Comparison of evolutionarily diverse Nef proteins revealed that several distinct R-clamps have evolved that are functionally equivalent but differ in the side chain compositions of Nef residues 83 and 120. Whereas a similar R-clamp design is shared by Nef proteins of HIV-1 groups M, O, and P, as well as SIVgor, the Nef proteins of SIV from the Eastern chimpanzee subspecies (SIVcpzP.t.s.) exclusively utilize another type of R-clamp. By contrast, SIV of Central chimpanzees (SIVcpzP.t.t.) and HIV-1 group N strains show more heterogenous R-clamp design principles, including a non-functional evolutionary intermediate of the aforementioned two classes. These data add to our understanding of the structural basis of SH3 binding and kinase deregulation by Nef, and provide an interesting example of primate lentiviral protein evolution.

Highlights

Primate lentiviruses comprise human immunodeficiency viruses (HIV-1 and HIV-2), as well as more than 40 simian immunodeficiency viruses (SIVs) infecting non-human primate species from sub-Saharan Africa
We have recently shown that Hck activation by Nef leads to Raf/MAPK pathway activation and triggers the secretion of proinflammatory cytokines [19,21]. In agreement with their enhanced affinity for Hck [9,20], we found that only HIV-1/SIVcpz type Nef proteins but not HIV-2/SIVsmm type Nef proteins show this function
We show that different but functionally equivalent R-clamps have emerged in the HIV-1/SIVcpz lineage to coordinate Hck Src Homology 3 (SH3) domain binding by Nef

Summary

Introduction

Primate lentiviruses comprise human immunodeficiency viruses (HIV-1 and HIV-2), as well as more than 40 simian immunodeficiency viruses (SIVs) infecting non-human primate species from sub-Saharan Africa. HIV-1 groups M, N, O, and P originate from four independent transmissions of SIV from Central chimpanzees (SIVcpzP.t.t.) and gorillas (SIVgor) to humans, whereas HIV-2 groups A to I are derived from nine zoonotic transmissions of SIV from sooty mangabeys (SIVsmm) (reviewed in [1]). SIVsmm was transmitted to macaques, giving rise to SIVmac. The viral protein Nef is a multifunctional accessory factor encoded by all primate lentiviruses. While nef-defective HIV and SIV are replication-competent, infections with such viruses are associated with low viral loads and no or delayed pathogenesis in humans or experimentally infected macaques [5]. Nef itself exhibits no enzymatic activity but instead modulates host cell function by interacting with a plethora of other proteins to hijack cellular signaling and membrane trafficking pathways [6,7,8]

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Results

Conclusion