Review
Human immunodeficiency virus (HIV) type-1, HIV-2 and simian immunodeficiency virus Nef proteins

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Abstract

The genomes of all retroviruses encode the Gag Pol and Env structural proteins. Human and simian lentiviruses have acquired non-structural proteins among which Nef plays a major role in the evolution of viral infection towards an immunodeficiency syndrome. Indeed, in the absence of a functional nef gene, primate lentiviruses are far less pathogenic than their wild type counterparts. The multiple protein–protein interactions in which Nef is involved all contribute to explain the role played by Nef in HIV- and SIV-associated disease progression. This review summarizes common and distinct features among Nef proteins and how they contribute to increasing HIV and SIV fitness towards their respective hosts.

Introduction

Infection by the human immunodeficiency virus (HIV) originates from cross-species transmission of the simian immunodeficiency virus (SIV) from its monkey host to humans in the 20th century. Several transmissions must have occurred over time, without efficient propagation of the virus, before the socio-economical modifications that took place in some parts of Africa and served as a catalyst to the early spread of the epidemic. Phylogenetic studies traced the origin of HIV type-1 (HIV-1) and HIV-2 to different regions of Africa and divergent strains of SIV, thereby establishing a potential correlation between differential adaptation of simian viral strains and differences in the pathogenesis associated with these two viruses (reviewed in Gisselquist, 2003, Heeney et al., 2006). The close relationship between HIV and SIV has naturally established simian models as the most appropriate for in vivo studies of infection by immunodeficiency viruses; however, phenotypic differences between HIV and SIV revealed the limits of such models. Most importantly, SIV does not cause immunodeficiency in its natural host sooty mangabeys (SIVsm), African green monkeys (SIVagm) and chimpanzees (SIVcpz). On the contrary SIVmac which derived from SIVsm infection of Asian macaques is highly pathogenic in macaques and induces an immunodeficiency syndrome similar to that witnessed in humans infected by HIV. Strikingly, SIV natural hosts do harbor high viral titers but keep low levels of immune activation (Kirchhoff et al., 2008).

The differences that exist between the progression to AIDS of infected primates and humans should result from host-specific or virus specific factors or a combination of both. One of the key players that has been incriminated in the respective pathogenic and non-pathogenic consequences of HIV and SIV infection is the non-structural viral protein Nef, a 27–35 kDa myristylated protein than can interact with multiple factors in infected cells. In addition to genes that encode the elements that are essential to the assembly and budding of all infectious retroviral particles (gag, pol and env), the genome of primate lentiviruses encode non-structural proteins that regulate viral spread in hosts (reviewed in Li et al. (2005)). Early studies of the gene located at the 3′ end of HIV-1 genome (named 3′ORF) suggested that the corresponding protein could attenuate viral replication and be involved in the establishment of latency (Luciw et al., 1987). NEgative Factor (Nef) was thus coined in and replaced 3′ORF; however, soon thereafter, results indicating that Nef would to the contrary have a positive impact on the pathogenesis associated to HIV and SIV infection started accumulating (Hammes et al., 1989, Kim et al., 1989). It has thereon been known that Nef has a positive impact on viral replication in vitro and accelerates the progression towards immunodeficiency in both human hosts infected with HIV-1 and monkeys infected with pathogenic strains of SIV. Because HIV-2 prevalence is low and given the higher proportion of HIV-2 infected individuals who do not progress to AIDS as compared with individuals infected with HIV-1 (de Silva et al., 2008), data on HIV-2 Nef are scarce. On the contrary, SIV being the best animal model to study lentiviral infection in primates, SIV Nef has been thoroughly characterized. In this review, we will focus on the many functions of primate lentiviruses Nef proteins.

Section snippets

Impact of Nef on HIV- and SIV-associated pathogenesis

In 1991, Kestler et al. demonstrated that the presence of an intact nef allele was, at least in part, responsible for the maintenance of high viral loads and progression towards immunodeficiency in macaques infected with the pathogenic strain SIVmac239 (Kestler et al., 1991). Insertion of a stop codon in the nef ORF, abolishing Nef expression, resulted in a decrease of virulence and no or slower progression towards immunodeficiency in infected animals. Follow up of these animals revealed that

Nef down-regulates CD4 from the plasma membrane

Receptor down-regulation upon infection is a common mechanism used by many viruses in order to prevent super-infection that is toxic to cells and responsible for a decreased production of progeny virions (Breiner et al., 2001, Delwart and Panganiban, 1989, Schneider-Schaulies et al., 1995). CD4 is the primary receptor of primate lentiviruses (Dalgleish et al., 1984, Klatzmann et al., 1984). HIV and SIV Nef and Vpu, and to a lower extend Env, have the ability to decrease cell-surface expression

Avoiding immune surveillance: down-regulation of MHC molecules

Nef-mediated MHC-I down-regulation was first described by Schwartz et al. (1996). In vitro modulation of MHC-I cell-surface expression correlates with a protection of HIV and SIV infected cells from lysis mediated by cytotoxic T lymphocytes (Munch et al., 2001). While Nef causes a decrease of the cell-surface expression of HLA-A and -B molecules that are involved in the presentation of endogenous antigens to cytotoxic T lymphocytes, Nef does not affect the cell-surface expression of HLA-C and

Nef promotes virus release from infect cells

HIV-1 Nef alters the trafficking of various cell-surface proteins by connecting cargos to the clathrin-dependent or independent endocytic pathway. As discussed above, AP complexes play a major role in these mechanisms. In addition to prevent super-infection, CD4 down-regulation facilitates virion release by preventing HIV-1 Env to interact with cell-surface CD4 (Aiken et al., 1994, Lama et al., 1999). A connection between HIV-1 Nef and the multivesicular body was also shown to affect virions

Activation

The ability of HIV-1/2 and SIV Nef to promote T cell activation is generally admitted. Various models have been put forward to explain this effect of Nef. While some authors suggest that Nef primes T cells for TCR-dependent activation, others suggest that it might negatively interfere with TCR-dependent activation.

Efficient HIV and SIV proliferation in vitro requires mitogenic activation or engagement of the T cell receptor (Stevenson, 2003); however, replication in purified T cells, PBLs or

Increasing virus infectivity

CD4 down-regulation, together with down-regulation of the co-receptors CXCR4 and CCR5, contribute to prevent super-infection of the cells that would be deleterious to the virus (Michel et al., 2005). There also is a correlation between the ability of Nef to down-regulate CD4 and its ability to increase viral replication in vitro and HIV-1 associated pathogenesis in vivo (Glushakova et al., 2001, Lundquist et al., 2002, Stoddart et al., 2003). Viruses produced from cells that express wild type

Effect of Nef on bystander cells: a soluble form of Nef

Nef expression achieved by infecting cells with HIV or SIV, or upon transfection profoundly alters the host cell biology. In addition, evidence have accumulated showing that Nef can be released from Nef-expressing cells, either as vesicles or as a soluble protein, and affect bystander cells (Campbell et al., 2008, Fujii et al., 1996, Guy et al., 1987, Lenassi et al., 2010, Muratori et al., 2009) (Fig. 4). The cell-free pool of Nef was shown to play a role in HIV-1 pathogenesis in a recent

Conclusions

HIV and SIV Nef proteins have the ability to interfere with many cellular pathways with the ultimate consequence of favoring virus persistence in infected individuals and its transmission. Such properties are accomplished by the interaction of Nef with an increasing number of cellular targets through multiple binding motifs on Nef.

Major Nef functions fall into four distinct categories. Nef makes a connection between cellular proteins and the endocytic machinery, thereby altering their basal

References (188)

  • T.I. de Silva et al.

    HIV-2: the forgotten AIDS virus

    Trends Microbiol.

    (2008)
  • A. Engering et al.

    Subset of DC-SIGN(+) dendritic cells in human blood transmits HIV-1 to T lymphocytes

    Blood

    (2002)
  • O.T. Fackler et al.

    Functional characterization of HIV-1 Nef mutants in the context of viral infection

    Virology

    (2006)
  • J.F. Fortin et al.

    Hyper-responsiveness to stimulation of human immunodeficiency virus-infected CD4+ T cells requires Nef and Tat virus gene products and results from higher NFAT, NF-kappaB, and AP-1 induction

    J. Biol. Chem.

    (2004)
  • Y. Fujii et al.

    Soluble Nef antigen of HIV-1 is cytotoxic for human CD4+ T cells

    FEBS Lett.

    (1996)
  • P. Gallay et al.

    HIV-1 infection of nondividing cells: C-terminal tyrosine phosphorylation of the viral matrix protein is a key regulator

    Cell

    (1995)
  • T.B. Geijtenbeek et al.

    DC-SIGN, a dendritic cell-specific HIV-1-binding protein that enhances trans-infection of T cells

    Cell

    (2000)
  • T.B. Geijtenbeek et al.

    Identification of DC-SIGN, a novel dendritic cell-specific ICAM-3 receptor that supports primary immune responses

    Cell

    (2000)
  • C. Goffinet et al.

    HIV-1 antagonism of CD317 is species specific and involves Vpu-mediated proteasomal degradation of the restriction factor

    Cell Host Microbe

    (2009)
  • A. Gohla et al.

    14-3-3 regulates actin dynamics by stabilizing phosphorylated cofilin

    Curr. Biol.

    (2002)
  • C. Haller et al.

    The HIV-1 pathogenicity factor Nef interferes with maturation of stimulatory T-lymphocyte contacts by modulation of N-Wasp activity

    J. Biol. Chem.

    (2006)
  • C.H. Hung et al.

    HIV-1 Nef assembles a Src family kinase-ZAP-70/Syk-PI3K cascade to downregulate cell-surface MHC-I

    Cell Host Microbe

    (2007)
  • K. Janvier et al.

    HIV-1 Nef stabilizes the association of adaptor protein complexes with membranes

    J. Biol. Chem.

    (2003)
  • J. Kelly et al.

    Human macrophages support persistent transcription from unintegrated HIV-1 DNA

    Virology

    (2008)
  • Y.H. Kim et al.

    HIV-1 Nef plays an essential role in two independent processes in CD4 down-regulation: dissociation of the CD4-p56(lck) complex and targeting of CD4 to lysosomes

    Virology

    (1999)
  • S. Kinoshita et al.

    Host control of HIV-1 parasitism in T cells by the nuclear factor of activated T cells

    Cell

    (1998)
  • D.S. Kwon et al.

    DC-SIGN-mediated internalization of HIV is required for trans-enhancement of T cell infection

    Immunity

    (2002)
  • J. Lama et al.

    Cell-surface expression of CD4 reduces HIV-1 infectivity by blocking Env incorporation in a Nef- and Vpu-inhibitable manner

    Curr. Biol.

    (1999)
  • S. Le Gall et al.

    Nef interacts with the mu subunit of clathrin adaptor complexes and reveals a cryptic sorting signal in MHC I molecules

    Immunity

    (1998)
  • C. Aiken

    Pseudotyping human immunodeficiency virus type 1 (HIV-1) by the glycoprotein of vesicular stomatitis virus targets HIV-1 entry to an endocytic pathway and suppresses both the requirement for Nef and the sensitivity to cyclosporin A

    J. Virol.

    (1997)
  • C. Aiken et al.

    Nef stimulates human immunodeficiency virus type 1 proviral DNA synthesis

    J. Virol.

    (1995)
  • N. Arhel et al.

    The inability to disrupt the immunological synapse between infected human T cells and APCs distinguishes HIV-1 from most other primate lentiviruses

    J. Clin. Invest.

    (2009)
  • I. Bell et al.

    Association of simian immunodeficiency virus Nef with the T-cell receptor (TCR) zeta chain leads to TCR down-modulation

    J. Gen. Virol.

    (1998)
  • M. Bentham et al.

    Role of myristoylation and N-terminal basic residues in membrane association of the human immunodeficiency virus type 1 Nef protein

    J. Gen. Virol.

    (2006)
  • J.S. Bonifacino et al.

    Signals for sorting of transmembrane proteins to endosomes and lysosomes

    Annu. Rev. Biochem.

    (2003)
  • K.M. Breiner et al.

    Envelope protein-mediated down-regulation of hepatitis B virus receptor in infected hepatocytes

    J. Virol.

    (2001)
  • P.A. Bresnahan et al.

    A dileucine motif in HIV-1 Nef acts as an internalization signal for CD4 downregulation and binds the AP-1 clathrin adaptor

    Curr. Biol.

    (1998)
  • P.A. Bresnahan et al.

    Cutting edge: SIV Nef protein utilizes both leucine- and tyrosine-based protein sorting pathways for down-regulation of CD4

    J. Immunol.

    (1999)
  • B. Brugger et al.

    Human immunodeficiency virus type 1 Nef protein modulates the lipid composition of virions and host cell membrane microdomains

    Retrovirology

    (2007)
  • A.A. Bukovsky et al.

    Nef association with human immunodeficiency virus type 1 virions and cleavage by the viral protease

    J. Virol.

    (1997)
  • L. Burleigh et al.

    Infection of dendritic cells (DCs), not DC-SIGN-mediated internalization of human immunodeficiency virus, is required for long-term transfer of virus to T cells

    J. Virol.

    (2006)
  • E.M. Campbell et al.

    Disruption of the actin cytoskeleton can complement the ability of Nef to enhance human immunodeficiency virus type 1 infectivity

    J. Virol.

    (2004)
  • T.D. Campbell et al.

    HIV-1 Nef protein is secreted into vesicles that can fuse with target cells and virions

    Ethnic Dis.

    (2008)
  • L.A. Chakrabarti et al.

    A truncated form of Nef selected during pathogenic reversion of simian immunodeficiency virus SIVmac239Deltanef increases viral replication

    J. Virol.

    (2003)
  • R. Chaudhuri et al.

    Downregulation of CD4 by human immunodeficiency virus type 1 Nef is dependent on clathrin and involves direct interaction of Nef with the AP2 clathrin adaptor

    J. Virol.

    (2007)
  • N. Chazal et al.

    Human immunodeficiency virus type 1 particles pseudotyped with envelope proteins that fuse at low pH no longer require Nef for optimal infectivity

    J. Virol.

    (2001)
  • Y.L. Chen et al.

    The proteolytic cleavage of human immunodeficiency virus type 1 Nef does not correlate with its ability to stimulate virion infectivity

    J. Virol.

    (1998)
  • D. Cluet et al.

    Detection of human immunodeficiency virus type 1 Nef and CD4 physical interaction in living human cells by using bioluminescence resonance energy transfer

    J. Virol.

    (2005)
  • S.H. Coleman et al.

    Leucine-specific, functional interactions between human immunodeficiency virus type 1 Nef and adaptor protein complexes

    J. Virol.

    (2005)
  • S.H. Coleman et al.

    Modulation of cellular protein trafficking by human immunodeficiency virus type 1 Nef: role of the acidic residue in the ExxxLL motif

    J. Virol.

    (2006)
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