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1.  The Human Herpesvirus-7 (HHV-7) U21 Immunoevasin Subverts NK-Mediated Cytoxicity through Modulation of MICA and MICB 
PLoS Pathogens  2011;7(11):e1002362.
Herpesviruses have evolved numerous immune evasion strategies to facilitate establishment of lifelong persistent infections. Many herpesviruses encode gene products devoted to preventing viral antigen presentation as a means of escaping detection by cytotoxic T lymphocytes. The human herpesvirus-7 (HHV-7) U21 gene product, for example, is an immunoevasin that binds to class I major histocompatibility complex molecules and redirects them to the lysosomal compartment. Virus infection can also induce the upregulation of surface ligands that activate NK cells. Accordingly, the herpesviruses have evolved a diverse array of mechanisms to prevent NK cell engagement of NK-activating ligands on virus-infected cells. Here we demonstrate that the HHV-7 U21 gene product interferes with NK recognition. U21 can bind to the NK activating ligand ULBP1 and reroute it to the lysosomal compartment. In addition, U21 downregulates the surface expression of the NK activating ligands MICA and MICB, resulting in a reduction in NK-mediated cytotoxicity. These results suggest that this single viral protein may interfere both with CTL-mediated recognition through the downregulation of class I MHC molecules as well as NK-mediated recognition through downregulation of NK activating ligands.
Author Summary
The long coevolution of herpesviruses with their hosts has resulted in the development of a diverse array of viral immune evasion strategies and host counter-strategies. The identification of viral proteins that impair the function of cellular immune-recognition receptors has proven fertile ground for the discovery of fundamental concepts in immunology and cell biology. While the cytomegaloviruses have demonstrated an extraordinary array of immunoevasive tactics, little is known about the immunoevasive strategies of the closely-related human herpesvirus-7 (HHV-7). We have previously demonstrated that the U21 gene product from HHV-7 likely interferes with viral antigen presentation to cytotoxic T cells by rerouting class I major histocompatibility molecules to lysosomes for degradation. In addition to the host's cytotoxic T cell response, virus infection also induces the expression of Natural-Killer (NK) activating ligands, alerting cytotoxic NK cells to identify and kill virus-infected cells. Here we describe a novel function for the same viral protein - U21 - in interfering with NK cell recognition. Our findings provide the first indication that HHV-7, too, may have found it necessary to strategize mechanisms of NK escape.
doi:10.1371/journal.ppat.1002362
PMCID: PMC3213103  PMID: 22102813
2.  The p36 Isoform of Murine Cytomegalovirus m152 Protein Suffices for Mediating Innate and Adaptive Immune Evasion 
Viruses  2013;5(12):3171-3191.
The MHC-class I (MHC-I)-like viral (MHC-Iv) m152 gene product of murine cytomegalovirus (mCMV) was the first immune evasion molecule described for a member of the β-subfamily of herpesviruses as a paradigm for analogous functions of human cytomegalovirus proteins. Notably, by interacting with classical MHC-I molecules and with MHC-I-like RAE1 family ligands of the activatory natural killer (NK) cell receptor NKG2D, it inhibits presentation of antigenic peptides to CD8 T cells and the NKG2D-dependent activation of NK cells, respectively, thus simultaneously interfering with adaptive and innate immune recognition of infected cells. Although the m152 gene product exists in differentially glycosylated isoforms whose individual contributions to immune evasion are unknown, it has entered the scientific literature as m152/gp40, based on the quantitatively most prominent isoform but with no functional justification. By construction of a recombinant mCMV in which all three N-glycosylation sites are mutated (N61Q, N208Q, and N241Q), we show here that N-linked glycosylation is not essential for functional interaction of the m152 immune evasion protein with either MHC-I or RAE1. These data add an important functional detail to recent structural analysis of the m152/RAE1γ complex that has revealed N-glycosylations at positions Asn61 and Asn208 of m152 distant from the m152/RAE1γ interface.
doi:10.3390/v5123171
PMCID: PMC3967166  PMID: 24351798
antigen presentation; BAC mutagenesis; CD8 T cells; cytomegalovirus; viral immune evasion; natural killer (NK) cells; N-linked glycosylation
3.  The Viral KSHV Chemokine vMIP-II Inhibits the Migration of Naive and Activated Human NK Cells by Antagonizing Two Distinct Chemokine Receptors 
PLoS Pathogens  2013;9(8):e1003568.
Natural killer (NK) cells are innate immune cells able to rapidly kill virus-infected and tumor cells. Two NK cell populations are found in the blood; the majority (90%) expresses the CD16 receptor and also express the CD56 protein in intermediate levels (CD56Dim CD16Pos) while the remaining 10% are CD16 negative and express CD56 in high levels (CD56Bright CD16Neg). NK cells also reside in some tissues and traffic to various infected organs through the usage of different chemokines and chemokine receptors. Kaposi's sarcoma-associated herpesvirus (KSHV) is a human virus that has developed numerous sophisticated and versatile strategies to escape the attack of immune cells such as NK cells. Here, we investigate whether the KSHV derived cytokine (vIL-6) and chemokines (vMIP-I, vMIP-II, vMIP-III) affect NK cell activity. Using transwell migration assays, KSHV infected cells, as well as fusion and recombinant proteins, we show that out of the four cytokine/chemokines encoded by KSHV, vMIP-II is the only one that binds to the majority of NK cells, affecting their migration. We demonstrate that vMIP-II binds to two different receptors, CX3CR1 and CCR5, expressed by naïve CD56Dim CD16Pos NK cells and activated NK cells, respectively. Furthermore, we show that the binding of vMIP-II to CX3CR1 and CCR5 blocks the binding of the natural ligands of these receptors, Fractalkine (Fck) and RANTES, respectively. Finally, we show that vMIP-II inhibits the migration of naïve and activated NK cells towards Fck and RANTES. Thus, we present here a novel mechanism in which KSHV uses a unique protein that antagonizes the activity of two distinct chemokine receptors to inhibit the migration of naïve and activated NK cells.
Author Summary
NK cells belong to the innate immune system, able to rapidly kill tumors and various pathogens. They reside in the blood and in various tissues and traffic to different infected organs through the usage of different chemokines and chemokine receptors. KSHV is a master of immune evasion, and around a quarter of the KSHV encoded genes are dedicated to interfere with immune cell recognition. Here, we investigate the role played by the KSHV derived cytokine and chemokines (vIL-6, vMIP-I, vMIP-II, vMIP-III) in modulating NK cell activity. We show that vMIP-II binds and inhibits the activity of two different receptors, CX3CR1 and CCR5, expressed by naïve NK cells and by activated NK cells, respectively. Thus, we demonstrate here a novel mechanism in which KSHV uses a unique protein that antagonizes the activity of two distinct chemokine receptors to inhibit the migration of naïve and activated NK cells.
doi:10.1371/journal.ppat.1003568
PMCID: PMC3744409  PMID: 23966863
4.  Escape of HIV-1-Infected Dendritic Cells from TRAIL-Mediated NK Cell Cytotoxicity during NK-DC Cross-Talk—A Pivotal Role of HMGB1 
PLoS Pathogens  2010;6(4):e1000862.
Early stages of Human Immunodeficiency Virus-1 (HIV-1) infection are associated with local recruitment and activation of important effectors of innate immunity, i.e. natural killer (NK) cells and dendritic cells (DCs). Immature DCs (iDCs) capture HIV-1 through specific receptors and can disseminate the infection to lymphoid tissues following their migration, which is associated to a maturation process. This process is dependent on NK cells, whose role is to keep in check the quality and the quantity of DCs undergoing maturation. If DC maturation is inappropriate, NK cells will kill them (“editing process”) at sites of tissue inflammation, thus optimizing the adaptive immunity. In the context of a viral infection, NK-dependent killing of infected-DCs is a crucial event required for early elimination of infected target cells. Here, we report that NK-mediated editing of iDCs is impaired if DCs are infected with HIV-1. We first addressed the question of the mechanisms involved in iDC editing, and we show that cognate NK-iDC interaction triggers apoptosis via the TNF-related apoptosis-inducing ligand (TRAIL)-Death Receptor 4 (DR4) pathway and not via the perforin pathway. Nevertheless, once infected with HIV-1, DCHIV become resistant to NK-induced TRAIL-mediated apoptosis. This resistance occurs despite normal amounts of TRAIL released by NK cells and comparable DR4 expression on DCHIV. The escape of DCHIV from NK killing is due to the upregulation of two anti-apoptotic molecules, the cellular-Flice like inhibitory protein (c-FLIP) and the cellular inhibitor of apoptosis 2 (c-IAP2), induced by NK-DCHIV cognate interaction. High-mobility group box 1 (HMGB1), an alarmin and a key mediator of NK-DC cross-talk, was found to play a pivotal role in NK-dependent upregulation of c-FLIP and c-IAP2 in DCHIV. Finally, we demonstrate that restoration of DCHIV susceptibility to NK-induced TRAIL killing can be obtained either by silencing c-FLIP and c-IAP2 by specific siRNA, or by inhibiting HMGB1 with blocking antibodies or glycyrrhizin, arguing for a key role of HMGB1 in TRAIL resistance and DCHIV survival. These findings provide evidence for a new strategy developed by HIV to escape immune attack, they challenge the question of the involvement of HMGB1 in the establishment of viral reservoirs in DCs, and they identify potential therapeutic targets to eliminate infected DCs.
Author Summary
Dendritic cells (DCs), the professional antigen presenting cells, are critical for host immunity by inducing specific immune responses against a broad variety of pathogens. Human Immunodeficiency Virus-1 (HIV-1) has evolved ways to exploit DCs, thereby facilitating viral dissemination and allowing evasion of antiviral immunity. In particular, infected DCs may function as cellular reservoirs for HIV-1, thus contributing to viral persistence in lymphoid tissues. The mechanisms involved in the constitution of HIV reservoirs in DCs are poorly understood. In this study, we reveal that DCs infected with HIV-1 (DCHIV) become resistant to killing by natural killer (NK) cells, early effectors of innate immunity involved in the destruction of virus infected cells or cancer cells. This protection of DCHIV from NK cytotoxicity is induced through a cross-talk between NK cells and DCHIV, which induces the upregulation in DCHIV of two inhibitors of cell death, i.e. cellular-Flice like inhibitory protein (c-FLIP) and cellular inhibitor of apoptosis 2 (c-IAP2). The molecule responsible for the induction of these inhibitors is High-mobility group box 1 (HMGB1), an alarmin involved in the functional maturation of DCs. Blocking HMGB1 restores DCHIV susceptibility to NK cell killing, arguing for a key role of HMGB1 in the persistence of DCHIV. These findings provide evidence of the crucial role of NK-DC cross-talk in promoting viral persistence, and they identify potential therapeutic targets to eliminate infected DCs.
doi:10.1371/journal.ppat.1000862
PMCID: PMC2855334  PMID: 20419158
5.  Epstein-Barr Virus Evades CD4+ T Cell Responses in Lytic Cycle through BZLF1-mediated Downregulation of CD74 and the Cooperation of vBcl-2 
PLoS Pathogens  2011;7(12):e1002455.
Evasion of immune T cell responses is crucial for viruses to establish persistence in the infected host. Immune evasion mechanisms of Epstein-Barr virus (EBV) in the context of MHC-I antigen presentation have been well studied. In contrast, viral interference with MHC-II antigen presentation is less well understood, not only for EBV but also for other persistent viruses. Here we show that the EBV encoded BZLF1 can interfere with recognition by immune CD4+ effector T cells. This impaired T cell recognition occurred in the absence of a reduction in the expression of surface MHC-II, but correlated with a marked downregulation of surface CD74 on the target cells. Furthermore, impaired CD4+ T cell recognition was also observed with target cells where CD74 expression was downregulated by shRNA-mediated inhibition. BZLF1 downregulated surface CD74 via a post-transcriptional mechanism distinct from its previously reported effect on the CIITA promoter. In addition to being a chaperone for MHC-II αβ dimers, CD74 also functions as a surface receptor for macrophage Migration Inhibitory Factor and enhances cell survival through transcriptional upregulation of Bcl-2 family members. The immune-evasion function of BZLF1 therefore comes at a cost of induced toxicity. However, during EBV lytic cycle induced by BZLF1 expression, this toxicity can be overcome by expression of the vBcl-2, BHRF1, at an early stage of lytic infection. We conclude that by inhibiting apoptosis, the vBcl-2 not only maintains cell viability to allow sufficient time for synthesis and accumulation of infectious virus progeny, but also enables BZLF1 to effect its immune evasion function.
Author Summary
Epstein-Barr virus (EBV) is a herpesvirus and an important human pathogen that can cause diseases ranging from non-malignant proliferative disease to fully malignant cancers of lymphocytes and epithelial cells. The persistence of EBV in healthy individuals relies on the balance between host immune responses and viral immune evasion. As CD4+ immune T cell responses include both helper and cytotoxic functions, viral mechanisms for interfering with MHC class II antigen presentation to CD4+ T cells have the potential to greatly influence the outcome of viral infections. Our work on Epstein-Barr virus provides a new paradigm for viral immune evasion of MHC-II presented antigen by targeting CD74. CD74 is a dual function protein; it serves as a surviving receptor as well as a chaperone for MHC-II antigen presentation. Therefore, downregulation of CD74 as a T cell evasion strategy comes at the cost of potentially inducing cell death. However, EBV also encodes a vBcl-2 to attenuate the toxicity associated with reduced CD74, thus enabling the immune-impairment function to be effected. We expect that future studies will identify other viruses utilizing a similar strategy to evade CD4+ immune T cell responses.
doi:10.1371/journal.ppat.1002455
PMCID: PMC3245307  PMID: 22216005
6.  The EBV Immunoevasins vIL-10 and BNLF2a Protect Newly Infected B Cells from Immune Recognition and Elimination 
PLoS Pathogens  2012;8(5):e1002704.
Lifelong persistence of Epstein-Barr virus (EBV) in infected hosts is mainly owed to the virus' pronounced abilities to evade immune responses of its human host. Active immune evasion mechanisms reduce the immunogenicity of infected cells and are known to be of major importance during lytic infection. The EBV genes BCRF1 and BNLF2a encode the viral homologue of IL-10 (vIL-10) and an inhibitor of the transporter associated with antigen processing (TAP), respectively. Both are known immunoevasins in EBV's lytic phase. Here we describe that BCRF1 and BNLF2a are functionally expressed instantly upon infection of primary B cells. Using EBV mutants deficient in BCRF1 and BNLF2a, we show that both factors contribute to evading EBV-specific immune responses during the earliest phase of infection. vIL-10 impairs NK cell mediated killing of infected B cells, interferes with CD4+ T-cell activity, and modulates cytokine responses, while BNLF2a reduces antigen presentation and recognition of newly infected cells by EBV-specific CD8+ T cells. Together, both factors significantly diminish the immunogenicity of EBV-infected cells during the initial, pre-latent phase of infection and may improve the establishment of a latent EBV infection in vivo.
Author Summary
Despite strong cellular and humoral immune responses, herpesviruses persist in their hosts for a lifetime. Epstein-Barr virus (EBV) is a herpesvirus that infects human B cells. This results in a latent infection where only a minimal set of viral proteins is expressed and infected cells cannot be eradicated by immune cells. When the virus reactivates in order to produce progeny, many viral proteins are expressed that are potential targets of immunity, but the virus coexpresses viral “immunoevasins” that blunt immune responses. Similarly, in the very first phase of B cell infection by EBV, called the pre-latent phase, a rather wide spectrum of antigens is expressed. However, it has been unknown whether viral immunoevasion occurs in this phase. Here we show that two viral immunoevasins are active in the pre-latent phase and prevent immune recognition by a variety of mechanisms: they reduce the presentation of EBV antigens to CD8+ killer T cells, prevent an attack by natural killer cells, and reduce the function of CD4+ helper T cells. Thus, it seems to be important for the virus to shield itself from attack by immune cells during the pre-latent stage.
doi:10.1371/journal.ppat.1002704
PMCID: PMC3355093  PMID: 22615564
7.  Varicellovirus UL49.5 Proteins Differentially Affect the Function of the Transporter Associated with Antigen Processing, TAP 
PLoS Pathogens  2008;4(5):e1000080.
Cytotoxic T-lymphocytes play an important role in the protection against viral infections, which they detect through the recognition of virus-derived peptides, presented in the context of MHC class I molecules at the surface of the infected cell. The transporter associated with antigen processing (TAP) plays an essential role in MHC class I–restricted antigen presentation, as TAP imports peptides into the ER, where peptide loading of MHC class I molecules takes place. In this study, the UL49.5 proteins of the varicelloviruses bovine herpesvirus 1 (BHV-1), pseudorabies virus (PRV), and equine herpesvirus 1 and 4 (EHV-1 and EHV-4) are characterized as members of a novel class of viral immune evasion proteins. These UL49.5 proteins interfere with MHC class I antigen presentation by blocking the supply of antigenic peptides through inhibition of TAP. BHV-1, PRV, and EHV-1 recombinant viruses lacking UL49.5 no longer interfere with peptide transport. Combined with the observation that the individually expressed UL49.5 proteins block TAP as well, these data indicate that UL49.5 is the viral factor that is both necessary and sufficient to abolish TAP function during productive infection by these viruses. The mechanisms through which the UL49.5 proteins of BHV-1, PRV, EHV-1, and EHV-4 block TAP exhibit surprising diversity. BHV-1 UL49.5 targets TAP for proteasomal degradation, whereas EHV-1 and EHV-4 UL49.5 interfere with the binding of ATP to TAP. In contrast, TAP stability and ATP recruitment are not affected by PRV UL49.5, although it has the capacity to arrest the peptide transporter in a translocation-incompetent state, a property shared with the BHV-1 and EHV-1 UL49.5. Taken together, these results classify the UL49.5 gene products of BHV-1, PRV, EHV-1, and EHV-4 as members of a novel family of viral immune evasion proteins, inhibiting TAP through a variety of mechanisms.
Author Summary
Herpesviruses have the conspicuous property that they persist for life in the infected host. This is also the case for varicelloviruses, a large subfamily of herpesviruses with representatives in humans (varicella zoster virus or VZV), cattle (bovine herpesvirus 1 or BHV-1), pigs (pseudorabies virus or PRV), and horses (equine herpesvirus or EHV type 1 and 4), among many others. Cytotoxic T-lymphocytes play an important role in the protection against viral infections, which they detect through the recognition of virus-derived peptides, presented in the context of MHC class I molecules at the surface of the infected cell. The transporter associated with antigen processing (TAP) plays an essential role in this process, as TAP imports peptides into the compartment where peptide loading of the MHC class I molecules takes place. In this study, we show that the UL49.5 proteins of BHV-1, PRV, EHV-1, and EHV-4 all block the supply of peptides through the inhibition of TAP, but that the mechanisms employed by these proteins to inhibit TAP function exhibit surprising diversity. VZV UL49.5, on the other hand, binds to TAP, but does not interfere with peptide transport. Our study classifies the UL49.5 proteins of BHV-1, PRV, EHV-1, and EHV-4 as members of a novel family of viral immune evasion proteins, inhibiting TAP through a variety of mechanisms.
doi:10.1371/journal.ppat.1000080
PMCID: PMC2386557  PMID: 18516302
8.  A Role for Host Activation-Induced Cytidine Deaminase in Innate Immune Defense against KSHV 
PLoS Pathogens  2013;9(11):e1003748.
Activation-induced cytidine deaminase (AID) is specifically induced in germinal center B cells to carry out somatic hypermutation and class-switch recombination, two processes responsible for antibody diversification. Because of its mutagenic potential, AID expression and activity are tightly regulated to minimize unwanted DNA damage. Surprisingly, AID expression has been observed ectopically during pathogenic infections. However, the function of AID outside of the germinal centers remains largely uncharacterized. In this study, we demonstrate that infection of human primary naïve B cells with Kaposi's sarcoma-associated herpesvirus (KSHV) rapidly induces AID expression in a cell intrinsic manner. We find that infected cells are marked for elimination by Natural Killer cells through upregulation of NKG2D ligands via the DNA damage pathway, a pathway triggered by AID. Moreover, without having a measurable effect on KSHV latency, AID impinges directly on the viral fitness by inhibiting lytic reactivation and reducing infectivity of KSHV virions. Importantly, we uncover two KSHV-encoded microRNAs that directly regulate AID abundance, further reinforcing the role for AID in the antiviral response. Together our findings reveal additional functions for AID in innate immune defense against KSHV with implications for a broader involvement in innate immunity to other pathogens.
Author Summary
Immune responses to pathogens rely heavily on the ability of B cells to generate a unique set of antibodies that can bind and eliminate the pathogen. Activation-induced cytidine deaminase (AID) is the enzyme specifically upregulated in activated B cells to diversify the antibody repertoire by introducing mutations within the antibody coding genes. Curiously, AID expression has been observed outside of activated B cells upon infection with a number of viral and bacterial pathogens. However, in such cases AID function is poorly characterized and often deemed inappropriate since its mutagenic activity can put the cell at risk for oncogenic transformation. In this study, we investigate the expression of AID in response to infection with an oncogenic human pathogen Kaposi's sarcoma-associated herpesvirus (KSHV) and the antibody-independent immune defense it exerts. We show that AID marks infected cells for elimination by natural killer (NK) cells and directly impinges on viral fitness. Furthermore, we uncover novel viral immune evasion strategies employed by KSHV to counteract AID. Together, our findings demonstrate a protective role for AID in the response to infection with an oncogenic virus such as KSHV and suggest that AID may actually limit transformation rather than serve as its culprit.
doi:10.1371/journal.ppat.1003748
PMCID: PMC3820765  PMID: 24244169
9.  Human Cytomegalovirus UL18 Utilizes US6 for Evading the NK and T-Cell Responses 
PLoS Pathogens  2008;4(8):e1000123.
Human cytomegalovirus (HCMV) US6 glycoprotein inhibits TAP function, resulting in down-regulation of MHC class I molecules at the cell surface. Cells lacking MHC class I molecules are susceptible to NK cell lysis. HCMV expresses UL18, a MHC class I homolog that functions as a surrogate to prevent host cell lysis. Despite a high level of sequence and structural homology between UL18 and MHC class I molecules, surface expression of MHC class I, but not UL18, is down regulated by US6. Here, we describe a mechanism of action by which HCMV UL18 avoids attack by the self-derived TAP inhibitor US6. UL18 abrogates US6 inhibition of ATP binding by TAP and, thereby, restores TAP-mediated peptide translocation. In addition, UL18 together with US6 interferes with the physical association between MHC class I molecules and TAP that is required for optimal peptide loading. Thus, regardless of the recovery of TAP function, surface expression of MHC class I molecules remains decreased. UL18 represents a unique immune evasion protein that has evolved to evade both the NK and the T cell immune responses.
Author Summary
HCMV establishes a lifelong latent infection and causes serious disease in immunocompromised individuals. Cytotoxic T lymphocytes (CTL) and natural killer (NK) cells are the primary effectors for the immune defense against HCMV. However, HCMV has evolved to evade both the innate and adaptive cellular immunity to viral infection. HCMV US6 glycoprotein inhibits TAP function, resulting in down-regulation of MHC class I, while HCMV UL18 is an MHC class I homolog that functions as a surrogate to prevent host cell lysis. Despite significant sequence and structural homology between UL18 and MHC class I molecules, US6 down regulates surface expression of MHC class I, but not UL18. Here, we describe a mechanism by which UL18 circumvents the self-derived TAP inhibitor, US6. UL18 abrogates US6 inhibition of TAP-ATP binding and restores TAP-mediated peptide translocation, thereby making peptides available for the assembly and subsequent surface expression of UL18. Together UL18 and US6 inhibit binding of MHC class I to TAP, thus down regulating surface expression of MHC class I molecules. UL18 represents a unique immune evasion protein resistant to both the NK and T cell immune responses. Our data provide a molecular basis for persistent HCMV infection and will aid in the development of a therapeutic vaccine.
doi:10.1371/journal.ppat.1000123
PMCID: PMC2483941  PMID: 18688275
10.  Two Novel Human Cytomegalovirus NK Cell Evasion Functions Target MICA for Lysosomal Degradation 
PLoS Pathogens  2014;10(5):e1004058.
NKG2D plays a major role in controlling immune responses through the regulation of natural killer (NK) cells, αβ and γδ T-cell function. This activating receptor recognizes eight distinct ligands (the MHC Class I polypeptide-related sequences (MIC) A andB, and UL16-binding proteins (ULBP)1–6) induced by cellular stress to promote recognition cells perturbed by malignant transformation or microbial infection. Studies into human cytomegalovirus (HCMV) have aided both the identification and characterization of NKG2D ligands (NKG2DLs). HCMV immediate early (IE) gene up regulates NKGDLs, and we now describe the differential activation of ULBP2 and MICA/B by IE1 and IE2 respectively. Despite activation by IE functions, HCMV effectively suppressed cell surface expression of NKGDLs through both the early and late phases of infection. The immune evasion functions UL16, UL142, and microRNA(miR)-UL112 are known to target NKG2DLs. While infection with a UL16 deletion mutant caused the expected increase in MICB and ULBP2 cell surface expression, deletion of UL142 did not have a similar impact on its target, MICA. We therefore performed a systematic screen of the viral genome to search of addition functions that targeted MICA. US18 and US20 were identified as novel NK cell evasion functions capable of acting independently to promote MICA degradation by lysosomal degradation. The most dramatic effect on MICA expression was achieved when US18 and US20 acted in concert. US18 and US20 are the first members of the US12 gene family to have been assigned a function. The US12 family has 10 members encoded sequentially through US12–US21; a genetic arrangement, which is suggestive of an ‘accordion’ expansion of an ancestral gene in response to a selective pressure. This expansion must have be an ancient event as the whole family is conserved across simian cytomegaloviruses from old world monkeys. The evolutionary benefit bestowed by the combinatorial effect of US18 and US20 on MICA may have contributed to sustaining the US12 gene family.
Author Summary
Human cytomegalovirus (HCMV) is a herpesvirus that infects most people in the world, usually without producing symptoms. However, infection is life-long and must be kept in check by the immune system. When the immune system is weakened, the outcome of HCMV infection can be very serious. Thus, HCMV is the major cause of birth defects resulting from infection of the fetus during pregnancy, and it can cause severe disease in people with a weakened immune system, especially transplant recipients and HIV/AIDS patients. One type of immune cell, the natural killer (NK) cell, is crucial in controlling cells in the body that are abnormal. They do this by recognizing cells, which have special stress proteins on their surface, and killing them. When cells are infected with HCMV, they start to make these stress proteins. However, the virus has evolved ways to stop NK cells from killing infected cells by quickly stopping the stress proteins from reaching the surface. We have now identified two HCMV genes that target a major stress protein (called MICA) and cause its rapid destruction. Removing these two genes from HCMV renders infected cells very susceptible to killing by NK cells. This discovery might help the development of new ways to fight HCMV.
doi:10.1371/journal.ppat.1004058
PMCID: PMC4006889  PMID: 24787765
11.  The Switch from Latent to Productive Infection in Epstein-Barr Virus-Infected B Cells Is Associated with Sensitization to NK Cell Killing▿  
Journal of Virology  2006;81(2):474-482.
Following activation of Epstein-Barr virus (EBV)-infected B cells from latent to productive (lytic) infection, there is a concomitant reduction in the level of cell surface major histocompatibility complex (MHC) class I molecules and an impaired antigen-presenting function that may facilitate evasion from EBV-specific CD8+ cytotoxic T cells. In some other herpesviruses studied, most notably human cytomegalovirus (HCMV), evasion of virus-specific CD8+ effector responses via downregulation of surface MHC class I molecules is supplemented with specific mechanisms for evading NK cells. We now report that EBV differs from HCMV in this respect. While latently infected EBV-positive B cells were resistant to lysis by two NK lines and by primary polyclonal NK cells from peripheral blood, these effectors efficiently killed cells activated into the lytic cycle. Susceptibility to NK lysis coincided not only with downregulation of HLA-A, -B, and -C molecules that bind to the KIR family of inhibitory receptors on NK cells but also with downregulation of HLA-E molecules binding the CD94/NKG2A inhibitory receptors. Conversely, ULBP-1 and CD112, ligands for the NK cell-activating receptors NKG2D and DNAM-1, respectively, were elevated. Susceptibility of the virus-producing target cells to NK cell lysis was partially reversed by blocking ULBP-1 or CD112 with specific antibodies. These results highlight a fundamental difference between EBV and HCMV with regards to evasion of innate immunity.
doi:10.1128/JVI.01777-06
PMCID: PMC1797427  PMID: 17079298
12.  Tim-3: An Activation Marker and Activation Limiter of Innate Immune Cells 
Tim-3 was initially identified on activated Th1, Th17, and Tc1 cells and induces T cell death or exhaustion after binding to its ligand, Gal-9. The observed relationship between dysregulated Tim-3 expression on T cells and the progression of many clinical diseases has identified this molecule as an important target for intervention in adaptive immunity. Recent data have shown that it also plays critical roles in regulating the activities of macrophages, monocytes, dendritic cells, mast cells, natural killer cells, and endothelial cells. Although the underlying mechanisms remain unclear, dysregulation of Tim-3 expression on these innate immune cells leads to an excessive or inhibited inflammatory response and subsequent autoimmune damage or viral or tumor evasion. In this review, we focus on the expression and function of Tim-3 on innate immune cells and discuss (1) how Tim-3 is expressed and regulated on different innate immune cells; (2) how it affects the activity of different innate immune cells; and (3) how dysregulated Tim-3 expression on innate immune cells affects adaptive immunity and disease progression. Tim-3 is involved in the optimal activation of innate immune cells through its varied expression. A better understanding of the physiopathological role of the Tim-3 pathway in innate immunity will shed new light on the pathogenesis of clinical diseases, such as autoimmune diseases, chronic viral infections, and cancer, and suggest new approaches to intervention.
doi:10.3389/fimmu.2013.00449
PMCID: PMC3857553  PMID: 24339828
TIM-3; innate immunity; negative regulation; tolerance; homeostasis
13.  Quantitative Membrane Proteomics Reveals New Cellular Targets of Viral Immune Modulators 
PLoS Pathogens  2006;2(10):e107.
Immunomodulators of pathogens frequently affect multiple cellular targets, thus preventing recognition by different immune cells. For instance, the K5 modulator of immune recognition (MIR2) from Kaposi sarcoma–associated herpesvirus prevents activation of cytotoxic T cells, natural killer cells, and natural killer T cells by downregulating major histocompatibility complex (MHC) class I molecules, the MHC-like molecule CD1, the cell adhesion molecules ICAM-1 and PECAM, and the co-stimulatory molecule B7.2. K5 belongs to a family of viral- and cellular-membrane-spanning RING ubiquitin ligases. While a limited number of transmembrane proteins have been shown to be targeted for degradation by this family, it is unknown whether additional targets exist. We now describe a quantitative proteomics approach to identify novel targets of this protein family. Using stable isotope labeling by amino acids, we compared the proteome of plasma, Golgi, and endoplasmic reticulum membranes in the presence and absence of K5. Mass spectrometric protein identification revealed four proteins that were consistently underrepresented in the plasma membrane of K5 expression cells: MHC I (as expected), bone marrow stromal antigen 2 (BST-2, CD316), activated leukocyte cell adhesion molecule (ALCAM, CD166) and Syntaxin-4. Downregulation of each of these proteins was independently confirmed by immunoblotting with specific antibodies. We further demonstrate that ALCAM is a bona fide target of both K5 and the myxomavirus homolog M153R. Upon exiting the endoplasmic reticulum, ALCAM is ubiquitinated in the presence of wild-type, but not RING-deficient or acidic motif–deficient, K5, and is targeted for lysosomal degradation via the multivesicular body pathway. Since ALCAM is the ligand for CD6, a member of the immunological synapse of T cells, its removal by viral immune modulators implies a role for CD6 in the recognition of pathogens by T cells. The unbiased global proteome analysis therefore revealed novel immunomodulatory functions of pathogen proteins.
Synopsis
Viral immune modulators often target multiple cellular proteins for destruction. Presumably, this strategy enables viral pathogens to optimize evasion of multiple immune responses. To systematically identify such host cell targets in an unbiased fashion, Bartee et al. applied recently developed quantitative proteomics methods to identify novel targets for K5. K5 belongs to a family of viral ubiquitin ligases found in gamma-herpesviruses and poxviruses that target multiple cellular transmembrane proteins for destruction. Using stable isotope labeling combined with tandem mass spectrometry, the authors compared the abundance of proteins in membrane preparations from cells that expressed K5 to that in cells without K5. In their experiments, three novel membrane proteins (BST-2, Syntaxin-4, and ALCAM) were consistently found in lower abundance in K5-expressing cells. Importantly, the authors were able to confirm the K5-dependent downregulation of all of these proteins in independent experiments and by independent methods. ALCAM was chosen for a more in-depth analysis to firmly demonstrate that this protein is downregulated by K5 in a manner similar to other known targets. This proof-of-principle study demonstrates that novel targets of viral immune modulators can be identified with quantitative proteomics.
doi:10.1371/journal.ppat.0020107
PMCID: PMC1626102  PMID: 17238276
14.  Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction 
Cell  2014;157(6):1460-1472.
Summary
A systematic quantitative analysis of temporal changes in host and viral proteins throughout the course of a productive infection could provide dynamic insights into virus-host interaction. We developed a proteomic technique called “quantitative temporal viromics” (QTV), which employs multiplexed tandem-mass-tag-based mass spectrometry. Human cytomegalovirus (HCMV) is not only an important pathogen but a paradigm of viral immune evasion. QTV detailed how HCMV orchestrates the expression of >8,000 cellular proteins, including 1,200 cell-surface proteins to manipulate signaling pathways and counterintrinsic, innate, and adaptive immune defenses. QTV predicted natural killer and T cell ligands, as well as 29 viral proteins present at the cell surface, potential therapeutic targets. Temporal profiles of >80% of HCMV canonical genes and 14 noncanonical HCMV open reading frames were defined. QTV is a powerful method that can yield important insights into viral infection and is applicable to any virus with a robust in vitro model.
PaperClip
Graphical Abstract
Highlights
•>8,000 proteins quantified over eight time points, including 1,200 cell-surface proteins•Temporal profiles of 139/171 canonical HCMV proteins and 14 noncanonical HCMV ORFs•Multiple families of cell-surface receptors selectively modulated by HCMV•Multiple signaling pathways modulated during HCMV infection
The application of multiplexed tandem-mass-tag-based mass spectrometry to analyze temporal changes in the expression of host and viral proteins during infection reveals insights into viral pathogenesis and host immune responses.
doi:10.1016/j.cell.2014.04.028
PMCID: PMC4048463  PMID: 24906157
15.  Pseudomonas Evades Immune Recognition of Flagellin in Both Mammals and Plants 
PLoS Pathogens  2011;7(8):e1002206.
The building blocks of bacterial flagella, flagellin monomers, are potent stimulators of host innate immune systems. Recognition of flagellin monomers occurs by flagellin-specific pattern-recognition receptors, such as Toll-like receptor 5 (TLR5) in mammals and flagellin-sensitive 2 (FLS2) in plants. Activation of these immune systems via flagellin leads eventually to elimination of the bacterium from the host. In order to prevent immune activation and thus favor survival in the host, bacteria secrete many proteins that hamper such recognition. In our search for Toll like receptor (TLR) antagonists, we screened bacterial supernatants and identified alkaline protease (AprA) of Pseudomonas aeruginosa as a TLR5 signaling inhibitor as evidenced by a marked reduction in IL-8 production and NF-κB activation. AprA effectively degrades the TLR5 ligand monomeric flagellin, while polymeric flagellin (involved in bacterial motility) and TLR5 itself resist degradation. The natural occurring alkaline protease inhibitor AprI of P. aeruginosa blocked flagellin degradation by AprA. P. aeruginosa aprA mutants induced an over 100-fold enhanced activation of TLR5 signaling, because they fail to degrade excess monomeric flagellin in their environment. Interestingly, AprA also prevents flagellin-mediated immune responses (such as growth inhibition and callose deposition) in Arabidopsis thaliana plants. This was due to decreased activation of the receptor FLS2 and clearly demonstrated by delayed stomatal closure with live bacteria in plants. Thus, by degrading the ligand for TLR5 and FLS2, P. aeruginosa escapes recognition by the innate immune systems of both mammals and plants.
Author Summary
Pseudomonas aeruginosa is a common environmental bacterium that can infect and cause disease in a wide variety of hosts, ranging from humans to plants. In healthy individuals, the innate immune system can counteract this microorganism effectively; however immunocompromised patients and cystic fibrosis patients suffer from severe infections with this bacterium. P. aeruginosa can propel itself through tissue by rotation of its long tail, called the flagellum, which is essential to establish colonization and infection of the host. The building blocks of the bacterial flagellum are over a thousand copies of the highly conserved protein flagellin. Mammals and plants have developed recognition systems to detect many different bacteria by sensing flagellin via Toll-like receptor 5 and Flagellin-sensitive 2, respectively. Bacteria actively try to interfere with this recognition (immune evasion). In this study, we describe a novel mechanism of P. aeruginosa to escape flagellin recognition. The secreted protein alkaline protease of P. aeruginosa, degrades immunity activating free flagellin. Bacterial motility is maintained, because flagellin present as building block of flagella is not degraded. In this way, the bacterium impairs recognition and hides itself from destruction by the immune system. Understanding these immune evasion strategies is of extreme importance for the development of new therapeutic approaches.
doi:10.1371/journal.ppat.1002206
PMCID: PMC3161968  PMID: 21901099
16.  Viral Infection: An Evolving Insight into the Signal Transduction Pathways Responsible for the Innate Immune Response 
Advances in Virology  2012;2012:131457.
The innate immune response is initiated by the interaction of stereotypical pathogen components with genetically conserved receptors for extracytosolic pathogen-associated molecular patterns (PAMPs) or intracytosolic nucleic acids. In multicellular organisms, this interaction typically clusters signal transduction molecules and leads to their activations, thereby initiating signals that activate innate immune effector mechanisms to protect the host. In some cases programmed cell death—a fundamental form of innate immunity—is initiated in response to genotoxic or biochemical stress that is associated with viral infection. In this paper we will summarize innate immune mechanisms that are relevant to viral pathogenesis and outline the continuing evolution of viral mechanisms that suppress the innate immunity in mammalian hosts. These mechanisms of viral innate immune evasion provide significant insight into the pathways of the antiviral innate immune response of many organisms. Examples of relevant mammalian innate immune defenses host defenses include signaling to interferon and cytokine response pathways as well as signaling to the inflammasome. Understanding which viral innate immune evasion mechanisms are linked to pathogenesis may translate into therapies and vaccines that are truly effective in eliminating the morbidity and mortality associated with viral infections in individuals.
doi:10.1155/2012/131457
PMCID: PMC3446651  PMID: 22997518
17.  Effect of NKG2D ligand expression on host immune responses 
Immunological reviews  2010;235(1):267-285.
Summary
NKG2D (natural-killer group 2, member D) is an activating receptor present on the surface of natural killer (NK) cells, some NKT cells, CD8+ cytotoxic T cells, γδ T cells, and under certain conditions CD4+ T cells. Present in both humans and mice, this highly conserved receptor binds to a surprisingly diverse family of ligands that are distant relatives of MHC-class-I molecules. There is increasing evidence that ligand expression can result in both immune activation (tumor clearance, viral immunity, autoimmunity, and transplantation) and immune silencing (tumor evasion). In this review, we describe this family of NKG2D ligands and the various mechanisms that control their expression in stressed and normal cells. We also discuss the host response to both membrane-bound and secreted NKG2D ligands and summarize the models proposed to explain the consequences of this differential expression.
doi:10.1111/j.0105-2896.2010.00893.x
PMCID: PMC2885032  PMID: 20536569
natural killer cell; NKG2D; NK cells; MIC; cytotoxicity; cancer; soluble ligands
18.  Natural history of murine gamma-herpesvirus infection. 
Murine gamma-herpesvirus 68 (MHV-68) is a natural pathogen of small rodents and insectivores (mice, voles and shrews). The primary infection is characterized by virus replication in lung epithelial cells and the establishment of a latent infection in B lymphocytes. The virus is also observed to persist in lung epithelial cells, dendritic cells and macrophages. Splenomegaly is observed two weeks after infection, in which there is a CD4+ T-cell-mediated expansion of B and T cells in the spleen. At three weeks post-infection an infectious mononucleosis-like syndrome is observed involving a major expansion of Vbeta4+CD8+ T cells. Later in the course of persistent infection, ca. 10% of mice develop lymphoproliferative disease characterized as lymphomas of B-cell origin. The genome from MHV-68 strain g2.4 has been sequenced and contains ca. 73 genes, the majority of which are collinear and homologous to other gamma-herpesviruses. The genome includes cellular homologues for a complement-regulatory protein, Bcl-2, cyclin D and interleukin-8 receptor and a set of novel genes M1 to M4. The function of these genes in the context of latent infections, evasion of immune responses and virus-mediated pathologies is discussed. Both innate and adaptive immune responses play an active role in limiting virus infection. The absence of type I interferon (IFN) results in a lethal MHV-68 infection, emphasizing the central role of these cytokines at the initial stages of infection. In contrast, type II IFN is not essential for the recovery from infection in the lung, but a failure of type II IFN receptor signalling results in the atrophy of lymphoid tissue associated with virus persistence. Splenic atrophy appears to be the result of immunopathology, since in the absence of CD8+ T cells no pathology occurs. CD8+ T cells play a major role in recovery from the primary infection, and also in regulating latently infected cells expressing the M2 gene product. CD4+ T cells have a key role in surveillance against virus recurrences in the lung, in part mediated through 'help' in the genesis of neutralizing antibodies. In the absence of CD4+ T cells, virus-specific CD8+ T cells are able to control the primary infection in the respiratory tract, yet surprisingly the memory CD8+ T cells generated are unable to inhibit virus recurrences in the lung. This could be explained in part by the observations that this virus can downregulate major histocompatibility complex class I expression and also restrict inflammatory cell responses by producing a chemokine-binding protein (M3 gene product). MHV-68 provides an excellent model to explore methods for controlling gamma-herpesvirus infection through vaccination and chemotherapy. Vaccination with gp150 (a homologue of gp350 of Epstein-Barr virus) results in a reduction in splenomegaly and virus latency but does not block replication in the lung, nor the establishment of a latent infection. Even when lung virus infection is greatly reduced following the action of CD8+ T cells, induced via a prime-boost vaccination strategy, a latent infection is established. Potent antiviral compounds such as the nucleoside analogue 2'deoxy-5-ethyl-beta-4'-thiouridine, which disrupts virus replication in vivo, cannot inhibit the establishment of a latent infection. Clearly, devising strategies to interrupt the establishment of latent virus infections may well prove impossible with existing methods.
doi:10.1098/rstb.2000.0779
PMCID: PMC1088445  PMID: 11313012
19.  Stage-Specific Inhibition of MHC Class I Presentation by the Epstein-Barr Virus BNLF2a Protein during Virus Lytic Cycle 
PLoS Pathogens  2009;5(6):e1000490.
The gamma-herpesvirus Epstein-Barr virus (EBV) persists for life in infected individuals despite the presence of a strong immune response. During the lytic cycle of EBV many viral proteins are expressed, potentially allowing virally infected cells to be recognized and eliminated by CD8+ T cells. We have recently identified an immune evasion protein encoded by EBV, BNLF2a, which is expressed in early phase lytic replication and inhibits peptide- and ATP-binding functions of the transporter associated with antigen processing. Ectopic expression of BNLF2a causes decreased surface MHC class I expression and inhibits the presentation of indicator antigens to CD8+ T cells. Here we sought to examine the influence of BNLF2a when expressed naturally during EBV lytic replication. We generated a BNLF2a-deleted recombinant EBV (ΔBNLF2a) and compared the ability of ΔBNLF2a and wild-type EBV-transformed B cell lines to be recognized by CD8+ T cell clones specific for EBV-encoded immediate early, early and late lytic antigens. Epitopes derived from immediate early and early expressed proteins were better recognized when presented by ΔBNLF2a transformed cells compared to wild-type virus transformants. However, recognition of late antigens by CD8+ T cells remained equally poor when presented by both wild-type and ΔBNLF2a cell targets. Analysis of BNLF2a and target protein expression kinetics showed that although BNLF2a is expressed during early phase replication, it is expressed at a time when there is an upregulation of immediate early proteins and initiation of early protein synthesis. Interestingly, BNLF2a protein expression was found to be lost by late lytic cycle yet ΔBNLF2a-transformed cells in late stage replication downregulated surface MHC class I to a similar extent as wild-type EBV-transformed cells. These data show that BNLF2a-mediated expression is stage-specific, affecting presentation of immediate early and early proteins, and that other evasion mechanisms operate later in the lytic cycle.
Author Summary
Epstein-Barr virus (EBV) is carried by approximately 90% of the world's population, where it persists and is chronically shed despite a vigorous specific immune response, a key component of which are CD8+ T cells that recognize and kill infected cells. The mechanisms the virus uses to evade these responses are not clear. Recently we identified a gene encoded by EBV, BNLF2a, that when expressed ectopically in cells inhibited their recognition by CD8+ T cells. To determine the contribution of BNLF2a to evasion of EBV-specific CD8+ T cell recognition and whether EBV encoded additional immune evasion mechanisms, a recombinant EBV was constructed in which BNLF2a was deleted. We found that cells infected with the recombinant virus were better recognized by CD8+ T cells specific for targets expressed co-incidently with BNLF2a, compared to cells infected with a non-recombinant virus. However, proteins expressed at late stages of the viral infection cycle were poorly recognised by CD8+ T cells, suggesting EBV encodes additional immune evasion genes to prevent effective CD8+ T cell recognition. This study highlights the stage-specific nature of viral immune evasion mechanisms.
doi:10.1371/journal.ppat.1000490
PMCID: PMC2695766  PMID: 19557156
20.  Staphylococcus epidermidis Strategies to Avoid Killing by Human Neutrophils 
PLoS Pathogens  2010;6(10):e1001133.
Staphylococcus epidermidis is a leading nosocomial pathogen. In contrast to its more aggressive relative S. aureus, it causes chronic rather than acute infections. In highly virulent S. aureus, phenol-soluble modulins (PSMs) contribute significantly to immune evasion and aggressive virulence by their strong ability to lyse human neutrophils. Members of the PSM family are also produced by S. epidermidis, but their role in immune evasion is not known. Notably, strong cytolytic capacity of S. epidermidis PSMs would be at odds with the notion that S. epidermidis is a less aggressive pathogen than S. aureus, prompting us to examine the biological activities of S. epidermidis PSMs. Surprisingly, we found that S. epidermidis has the capacity to produce PSMδ, a potent leukocyte toxin, representing the first potent cytolysin to be identified in that pathogen. However, production of strongly cytolytic PSMs was low in S. epidermidis, explaining its low cytolytic potency. Interestingly, the different approaches of S. epidermidis and S. aureus to causing human disease are thus reflected by the adaptation of biological activities within one family of virulence determinants, the PSMs. Nevertheless, S. epidermidis has the capacity to evade neutrophil killing, a phenomenon we found is partly mediated by resistance mechanisms to antimicrobial peptides (AMPs), including the protease SepA, which degrades AMPs, and the AMP sensor/resistance regulator, Aps (GraRS). These findings establish a significant function of SepA and Aps in S. epidermidis immune evasion and explain in part why S. epidermidis may evade elimination by innate host defense despite the lack of cytolytic toxin expression. Our study shows that the strategy of S. epidermidis to evade elimination by human neutrophils is characterized by a passive defense approach and provides molecular evidence to support the notion that S. epidermidis is a less aggressive pathogen than S. aureus.
Author Summary
Staphylococcus epidermidis frequently causes chronic infections, indicating pronounced capacity to evade host defenses. However, S. epidermidis is in general much less aggressive than its close relative, S. aureus. Here we identify molecular underpinnings of that discrepancy by showing that S. epidermidis immune evasion mechanisms are limited to those involving molecules that protect against or eliminate antimicrobial agents secreted by white blood cells, while immune evasion mechanisms of virulent S. aureus include the production of destructive toxins. This is especially noteworthy, because we demonstrate here for the first time that S. epidermidis has the capacity to produce a toxin with great potential to destroy white blood cells, but keeps its production at a very limited level. Thus, our study shows that two closely related human pathogens have adapted specific molecular mechanisms to evade host defenses, reflecting the unique approach used by each to cause human disease.
doi:10.1371/journal.ppat.1001133
PMCID: PMC2951371  PMID: 20949069
21.  Enterovirus 71 Protease 2Apro Targets MAVS to Inhibit Anti-Viral Type I Interferon Responses 
PLoS Pathogens  2013;9(3):e1003231.
Enterovirus 71 (EV71) is the major causative pathogen of hand, foot, and mouth disease (HFMD). Its pathogenicity is not fully understood, but innate immune evasion is likely a key factor. Strategies to circumvent the initiation and effector phases of anti-viral innate immunity are well known; less well known is whether EV71 evades the signal transduction phase regulated by a sophisticated interplay of cellular and viral proteins. Here, we show that EV71 inhibits anti-viral type I interferon (IFN) responses by targeting the mitochondrial anti-viral signaling (MAVS) protein—a unique adaptor molecule activated upon retinoic acid induced gene-I (RIG-I) and melanoma differentiation associated gene (MDA-5) viral recognition receptor signaling—upstream of type I interferon production. MAVS was cleaved and released from mitochondria during EV71 infection. An in vitro cleavage assay demonstrated that the viral 2A protease (2Apro), but not the mutant 2Apro (2Apro-110) containing an inactivated catalytic site, cleaved MAVS. The Protease-Glo assay revealed that MAVS was cleaved at 3 residues between the proline-rich and transmembrane domains, and the resulting fragmentation effectively inactivated downstream signaling. In addition to MAVS cleavage, we found that EV71 infection also induced morphologic and functional changes to the mitochondria. The EV71 structural protein VP1 was detected on purified mitochondria, suggesting not only a novel role for mitochondria in the EV71 replication cycle but also an explanation of how EV71-derived 2Apro could approach MAVS. Taken together, our findings reveal a novel strategy employed by EV71 to escape host anti-viral innate immunity that complements the known EV71-mediated immune-evasion mechanisms.
Author Summary
Enterovirus 71 (EV71) is the causative pathogen of hand, foot, and mouth disease (HFMD). Since the 2008 outbreak of HFMD in Fuyang, Anhui province, China, HFMD has been a severe public health concern affecting children. The major obstacle hindering HFMD prevention and control efforts is the lack of targeted anti-viral treatments and preventive vaccines due to the poorly understood pathogenic mechanisms underlying EV71. Viral evasion of host innate immunity is thought to be a key factor in viral pathogenicity, and many viruses have evolved diverse antagonistic mechanisms during virus-host co-evolution. Here, we show that EV71 has evolved an effective mechanism to inhibit the signal transduction pathway leading to the production of type I interferon, which plays a central role in anti-viral innate immunity. This inhibition is carried out by an EV71-encoded 2A protease (2Apro) that cleaves MAVS—an adaptor molecule critical in the signaling pathway activated by the viral recognition receptors RIG-I and MDA-5—to escape host innate immunity. These findings provide new insights to understand EV71 pathogenesis.
doi:10.1371/journal.ppat.1003231
PMCID: PMC3605153  PMID: 23555247
22.  Misdirection of membrane trafficking by HIV-1 Vpu and Nef 
Cellular Logistics  2011;1(3):90-102.
The HIV-1 accessory protein Nef is well known for its manipulation of host cell endosomal trafficking. By linking transmembrane proteins to endosomal coats, Nef removes them from the surface of infected cells. Modulation of MHC proteins leads to viral evasion of cellular adaptive immunity, whereas modulation of receptors for the HIV envelope glycoprotein, including CD4, enhances viral infectivity. The other HIV-1 accessory proteins, Vif, Vpr and Vpu, share a mechanism of action distinct from Nef in that each interacts with a multi-subunit ubiquitin ligase complex to target cellular proteins for proteosomal degradation. However, newly uncovered functions and mechanistic aspects of Vpu likely involve endosomal trafficking: these include counteraction of the innate antiviral activity of the cellular transmembrane protein BST-2 (tetherin), as well as the removal of the lipid-antigen presenting protein CD1d and the natural killer cell ligand NTB-A from the cell surface. This review focuses on how Nef and Vpu interfere with normal intracellular membrane trafficking to facilitate the spread and virulence of HIV-1.
doi:10.4161/cl.1.3.16708
PMCID: PMC3173656  PMID: 21922073
HIV-1 accessory proteins; Vpu; Nef; host cell trafficking; modulation of surface expression of host cell receptors
23.  Identification of DNA-Damage DNA-Binding Protein 1 as a Conditional Essential Factor for Cytomegalovirus Replication in Interferon-γ-Stimulated Cells 
PLoS Pathogens  2011;7(6):e1002069.
The mouse cytomegaloviral (MCMV) protein pM27 represents an indispensable factor for viral fitness in vivo selectively, antagonizing signal transducer and activator of transcription 2 (STAT2)-mediated interferon signal transduction. We wished to explore by which molecular mechanism pM27 accomplishes this effect. We demonstrate that pM27 is essential and sufficient to curtail the protein half-life of STAT2 molecules. Pharmacologic inhibition of the proteasome restored STAT2 amounts, leading to poly-ubiquitin-conjugated STAT2 forms. PM27 was found in complexes with an essential host ubiquitin ligase complex adaptor protein, DNA-damage DNA-binding protein (DDB) 1. Truncation mutants of pM27 showed a strict correlation between DDB1 interaction and their ability to degrade STAT2. SiRNA-mediated knock-down of DDB1 restored STAT2 in the presence of pM27 and strongly impaired viral replication in interferon conditioned cells, thus phenocopying the growth attenuation of M27-deficient virus. In a constructive process, pM27 recruits DDB1 to exploit ubiquitin ligase complexes catalyzing the obstruction of the STAT2-dependent antiviral state of cells to permit viral replication.
Author Summary
Cytomegaloviruses are strictly species-specific. Mouse cytomegalovirus (MCMV) is a prototypical β-herpesvirus, infecting Mus musculus as natural host and is closely related to the human pathogenic cytomegalovirus (HCMV, HHV-5) which both establish lifelong infection. Thus, MCMV infection constitutes an important model for HCMV pathogenesis. Cytomegaloviral evasion from innate immunity has been observed in many respects, but the molecular mechanisms of most viral factors are still elusive. We recently identified the MCMV-encoded protein pM27 to be required for efficient viral replication in the presence of interferons in vitro and to be essential in vivo. We identified STAT2, a mediator of interferon signalling, as target of pM27. Here we identify the cellular machinery exploited by pM27 to reduce the STAT2 protein half-life. PM27 was sufficient to induce poly-ubiquitination of STAT2, tagging it for proteasomal degradation. Since pM27 lacks domains found within ubiquitin-ligases, we conducted a search for cellular co-factors. We found DDB1, an essential cellular ubiquitin-ligase complex adaptor protein, to associate with pM27. Ablation of DDB1 increased viral susceptibility towards interferon, phenocopying the attenuation of ΔM27-MCMV. This defines DDB1 as conditional essential host factor of CMV replication. Our findings exemplify how cytomegaloviruses exploit an essential host protein to circumvent innate immunity.
doi:10.1371/journal.ppat.1002069
PMCID: PMC3116810  PMID: 21698215
24.  A Systematic Analysis of Host Factors Reveals a Med23-Interferon-λ Regulatory Axis against Herpes Simplex Virus Type 1 Replication 
PLoS Pathogens  2013;9(8):e1003514.
Herpes simplex virus type 1 (HSV-1) is a neurotropic virus causing vesicular oral or genital skin lesions, meningitis and other diseases particularly harmful in immunocompromised individuals. To comprehensively investigate the complex interaction between HSV-1 and its host we combined two genome-scale screens for host factors (HFs) involved in virus replication. A yeast two-hybrid screen for protein interactions and a RNA interference (RNAi) screen with a druggable genome small interfering RNA (siRNA) library confirmed existing and identified novel HFs which functionally influence HSV-1 infection. Bioinformatic analyses found the 358 HFs were enriched for several pathways and multi-protein complexes. Of particular interest was the identification of Med23 as a strongly anti-viral component of the largely pro-viral Mediator complex, which links specific transcription factors to RNA polymerase II. The anti-viral effect of Med23 on HSV-1 replication was confirmed in gain-of-function gene overexpression experiments, and this inhibitory effect was specific to HSV-1, as a range of other viruses including Vaccinia virus and Semliki Forest virus were unaffected by Med23 depletion. We found Med23 significantly upregulated expression of the type III interferon family (IFN-λ) at the mRNA and protein level by directly interacting with the transcription factor IRF7. The synergistic effect of Med23 and IRF7 on IFN-λ induction suggests this is the major transcription factor for IFN-λ expression. Genotypic analysis of patients suffering recurrent orofacial HSV-1 outbreaks, previously shown to be deficient in IFN-λ secretion, found a significant correlation with a single nucleotide polymorphism in the IFN-λ3 (IL28b) promoter strongly linked to Hepatitis C disease and treatment outcome. This paper describes a link between Med23 and IFN-λ, provides evidence for the crucial role of IFN-λ in HSV-1 immune control, and highlights the power of integrative genome-scale approaches to identify HFs critical for disease progression and outcome.
Author Summary
Herpes simplex virus type 1 (HSV-1) infects the vast majority of the global population. Whilst most people experience the relatively mild symptoms of cold sores, some individuals suffer more serious diseases like viral meningitis and encephalitis. HSV-1 is also becoming more common as a cause of genital herpes, traditionally associated with HSV-2 infection. Co-infection with HSV-2 is a major contributor to HIV transmission, so a better understanding of HSV-1/HSV-2 disease has wide implications for global healthcare. After initial infection, all herpesviruses have the ability to remain dormant, and can awaken to cause a symptomatic infection at any stage. Whether the virus remains dormant or active is the result of a finely tuned balance between our immune system and evasion techniques developed by the virus. In this study we have found a new method by which the replication of the virus is counteracted. The cellular protein Med23 was found to actively induce an innate anti-viral immune response in the form of the Type III interferons (IFN-lambda), by binding IRF7, a key regulator of interferons, and modulating its activity. Interferon lambda is well known to be important in the control of Hepatitis C infection, and a genetic mutation correlating to an increase in interferon lambda levels is strongly linked to clearance of infection. Here we find the same association between this genetic mutation and the clinical severity of recurrent cases of HSV-1 infection (coldsores). These data identify a Med23-interferon lambda regulatory axis of innate immunity, show that interferon lambda plays a significant role in HSV-1 infection, and contribute to the expanding evidence for interferon lambda in disease control.
doi:10.1371/journal.ppat.1003514
PMCID: PMC3738494  PMID: 23950709
25.  Natural Killer Cells Promote Early CD8 T Cell Responses against Cytomegalovirus 
PLoS Pathogens  2007;3(8):e123.
Understanding the mechanisms that help promote protective immune responses to pathogens is a major challenge in biomedical research and an important goal for the design of innovative therapeutic or vaccination strategies. While natural killer (NK) cells can directly contribute to the control of viral replication, whether, and how, they may help orchestrate global antiviral defense is largely unknown. To address this question, we took advantage of the well-defined molecular interactions involved in the recognition of mouse cytomegalovirus (MCMV) by NK cells. By using congenic or mutant mice and wild-type versus genetically engineered viruses, we examined the consequences on antiviral CD8 T cell responses of specific defects in the ability of the NK cells to control MCMV. This system allowed us to demonstrate, to our knowledge for the first time, that NK cells accelerate CD8 T cell responses against a viral infection in vivo. Moreover, we identify the underlying mechanism as the ability of NK cells to limit IFN-α/β production to levels not immunosuppressive to the host. This is achieved through the early control of cytomegalovirus, which dramatically reduces the activation of plasmacytoid dendritic cells (pDCs) for cytokine production, preserves the conventional dendritic cell (cDC) compartment, and accelerates antiviral CD8 T cell responses. Conversely, exogenous IFN-α administration in resistant animals ablates cDCs and delays CD8 T cell activation in the face of NK cell control of viral replication. Collectively, our data demonstrate that the ability of NK cells to respond very early to cytomegalovirus infection critically contributes to balance the intensity of other innate immune responses, which dampens early immunopathology and promotes optimal initiation of antiviral CD8 T cell responses. Thus, the extent to which NK cell responses benefit the host goes beyond their direct antiviral effects and extends to the prevention of innate cytokine shock and to the promotion of adaptive immunity.
Author Summary
To fight viral infections, vertebrates have developed a battery of innate and adaptive immune responses aimed at inhibiting viral replication or at killing infected cells. These responses include the early production of innate antiviral cytokines, especially interferons α and β (IFN-α/β), and the activation of cytotoxic lymphocytes such as the innate natural killer (NK) cells and the adaptive CD8 T cells. While critical for antiviral defense, cytokine or CD8 T cell responses can be detrimental or even fatal to the host when deregulated. Therefore, we need to better understand how the different arms of antiviral immunity are regulated. In particular, NK cells are proposed to play a protective role in a variety of viral infection in humans, but the underlying mechanisms remain poorly understood. Here, in a mouse model of cytomegalovirus infection, we demonstrate that NK cells prevent an excessive production of IFN-α/β and promote more efficient antiviral CD8 T cell responses. We thus show that NK cells can help promote health over disease during viral infections by regulating both innate and adaptive immune responses. It will be important to examine in humans whether NK cells control innate cytokine production to prevent immunopathology and to promote adaptive immunity against herpesviruses, HIV-1, influenza, or SARS.
doi:10.1371/journal.ppat.0030123
PMCID: PMC1950948  PMID: 17722980

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