1
|
Yu M, Li J, Gao W, Li Z, Zhang W. Multiple E3 ligases act as antiviral factors against SARS-CoV-2 via inducing the ubiquitination and degradation of ORF9b. J Virol 2024; 98:e0162423. [PMID: 38709105 DOI: 10.1128/jvi.01624-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 04/07/2024] [Indexed: 05/07/2024] Open
Abstract
Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) open reading frame 9b (ORF9b) antagonizes the antiviral type I and III interferon (IFN) responses and is ubiquitinated and degraded via the ubiquitin-proteasome pathway. However, E3 ubiquitin ligases that mediate the polyubiquitination and degradation of ORF9b remain unknown. In this study, we identified 14 E3 ligases that specifically bind to SARS-CoV-2 ORF9b. Specifically, three E3 ligases, HECT, UBA, and WWE domain-containing E3 ubiquitin protein ligase 1 (HUWE1), ubiquitin protein ligase E3 component n-recognin 4 (UBR4), and UBR5, induced K48-linked polyubiquitination and degradation of ORF9b, thereby attenuating ORF9b-mediated inhibition of the IFN response and SARS-CoV-2 replication. Moreover, each E3 ligase performed this function independent of the other two E3 ligases. Therefore, the three E3 ligases identified in this study as anti-SARS-CoV-2 host factors provide novel molecular insight into the virus-host interaction.IMPORTANCEUbiquitination is an important post-translational modification that regulates multiple biological processes, including viral replication. Identification of E3 ubiquitin ligases that target viral proteins for degradation can provide novel targets for antagonizing viral infections. Here, we identified multiple E3 ligases, including HECT, UBA, and WWE domain-containing E3 ubiquitin protein ligase 1 (HUWE1), ubiquitin protein ligase E3 component n-recognin 4 (UBR4), and UBR5, that ubiquitinated and induced the degradation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) open reading frame 9b (ORF9b), an interferon (IFN) antagonist, thereby enhancing IFN production and attenuating SARS-CoV-2 replication. Our study provides new possibilities for drug development targeting the interaction between E3 ligases and ORF9b.
Collapse
Affiliation(s)
- Miao Yu
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, China
- Department of Geriatrics and Special medical treatment, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Jie Li
- Department of Geriatrics and Special medical treatment, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Wenying Gao
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, China
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhaolong Li
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, China
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Wenyan Zhang
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, China
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| |
Collapse
|
2
|
Hu Y, Delviks-Frankenberry KA, Wu C, Arizaga F, Pathak VK, Xiong Y. Structural insights into PPP2R5A degradation by HIV-1 Vif. Nat Struct Mol Biol 2024:10.1038/s41594-024-01314-6. [PMID: 38789685 DOI: 10.1038/s41594-024-01314-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 04/11/2024] [Indexed: 05/26/2024]
Abstract
HIV-1 Vif recruits host cullin-RING-E3 ubiquitin ligase and CBFβ to degrade the cellular APOBEC3 antiviral proteins through diverse interactions. Recent evidence has shown that Vif also degrades the regulatory subunits PPP2R5(A-E) of cellular protein phosphatase 2A to induce G2/M cell cycle arrest. As PPP2R5 proteins bear no functional or structural resemblance to A3s, it is unclear how Vif can recognize different sets of proteins. Here we report the cryogenic-electron microscopy structure of PPP2R5A in complex with HIV-1 Vif-CBFβ-elongin B-elongin C at 3.58 Å resolution. The structure shows PPP2R5A binds across the Vif molecule, with biochemical and cellular studies confirming a distinct Vif-PPP2R5A interface that partially overlaps with those for A3s. Vif also blocks a canonical PPP2R5A substrate-binding site, indicating that it suppresses the phosphatase activities through both degradation-dependent and degradation-independent mechanisms. Our work identifies critical Vif motifs regulating the recognition of diverse A3 and PPP2R5A substrates, whereby disruption of these host-virus protein interactions could serve as potential targets for HIV-1 therapeutics.
Collapse
Affiliation(s)
- Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Krista A Delviks-Frankenberry
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Chunxiang Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Fidel Arizaga
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA.
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
| |
Collapse
|
3
|
Martin J, Chen X, Jia X, Shao Q, Liu B. The Disassociation of A3G-Related HIV-1 cDNA G-to-A Hypermutation to Viral Infectivity. Viruses 2024; 16:728. [PMID: 38793610 PMCID: PMC11126051 DOI: 10.3390/v16050728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/18/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
APOBEC3G (A3G) restricts HIV-1 replication primarily by reducing viral cDNA and inducing G-to-A hypermutations in viral cDNA. HIV-1 encodes virion infectivity factor (Vif) to counteract A3G primarily by excluding A3G viral encapsidation. Even though the Vif-induced exclusion is robust, studies suggest that A3G is still detectable in the virion. The impact of encapsidated A3G in the HIV-1 replication is unclear. Using a highly sensitive next-generation sequencing (NGS)-based G-to-A hypermutation detecting assay, we found that wild-type HIV-1 produced from A3G-expressing T-cells induced higher G-to-A hypermutation frequency in viral cDNA than HIV-1 from non-A3G-expressing T-cells. Interestingly, although the virus produced from A3G-expressing T-cells induced higher hypermutation frequency, there was no significant difference in viral infectivity, revealing a disassociation of cDNA G-to-A hypermutation to viral infectivity. We also measured G-to-A hypermutation in the viral RNA genome. Surprisingly, our data showed that hypermutation frequency in the viral RNA genome was significantly lower than in the integrated DNA, suggesting a mechanism exists to preferentially select intact genomic RNA for viral packing. This study revealed a new insight into the mechanism of HIV-1 counteracting A3G antiviral function and might lay a foundation for new antiviral strategies.
Collapse
Affiliation(s)
- Joanie Martin
- Center for AIDS Health Disparities Research, Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA; (J.M.); (X.C.); (X.J.); (Q.S.)
- School of Graduate Studies, Meharry Medical College, Nashville, TN 37208, USA
| | - Xin Chen
- Center for AIDS Health Disparities Research, Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA; (J.M.); (X.C.); (X.J.); (Q.S.)
| | - Xiangxu Jia
- Center for AIDS Health Disparities Research, Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA; (J.M.); (X.C.); (X.J.); (Q.S.)
| | - Qiujia Shao
- Center for AIDS Health Disparities Research, Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA; (J.M.); (X.C.); (X.J.); (Q.S.)
| | - Bindong Liu
- Center for AIDS Health Disparities Research, Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA; (J.M.); (X.C.); (X.J.); (Q.S.)
| |
Collapse
|
4
|
Arman MS, Hasan MZ. A computational exploration of global and temporal dynamics of selection pressure on HIV-1 Vif polymorphism. Virus Res 2024; 341:199323. [PMID: 38237808 PMCID: PMC10831783 DOI: 10.1016/j.virusres.2024.199323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
Virion infectivity factor (Vif), an accessory protein of HIV-1 (human immunodeficiency virus type 1), antagonizes host APOBEC3 protein (apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3) or A3 via proteasomal degradation, facilitating viral replication. HLA (Human leukocyte antigens) alleles, host restriction factors, and error-prone reverse transcription contribute to the global polymorphic dynamics of HIV, impacting effective vaccine design. Our computational analysis of over 50,000 HIV-1 M vif sequences from the Los Alamos National Laboratory (LANL) database (1998-2021) revealed positive selection pressure on the vif gene (nonsynonymous to synonymous ratio, dn/ds=1.58) and an average entropy score of 0.372 in protein level. Interestingly, over the years (1998-2021), a decreasing trend of dn/ds (1.68 to 1.47) and an increasing trend of entropy (0.309 to 0.399) was observed. The predicted mutational frequency against Vif consensus sequence decreased over time (slope = -0.00024, p < 0.0001). Sequence conservation was observed in Vif functional motifs F1, F2, F3, G, BC box, and CBF β binding region, while variability was observed mainly in N- and C- terminal and Zinc finger region, which were dominantly under immune pressure by host HLA-I-restricted CD8+ T cell. Computational analysis of ∆∆Gstability through protein stability prediction tools suggested that missense mutation may affect Vif stability, especially in the Vif-A3 binding interface. Notably, mutations R17K and Y44F in F1 and G box were predicted to destabilize the Vif-A3 binding interface by altering bond formations with adjacent amino acids. Therefore, our analysis demonstrates Vif adaptation with host physiology by maintaining sequence conservation, especially in A3 interacting functional motifs, highlighting important therapeutic candidate regions of Vif against HIV-1 infections.
Collapse
Affiliation(s)
- Md Sakil Arman
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Md Zafrul Hasan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
| |
Collapse
|
5
|
Zhang L, Hao P, Chen X, Lv S, Gao W, Li C, Li Z, Zhang W. CRL4B E3 ligase recruited by PRPF19 inhibits SARS-CoV-2 infection by targeting ORF6 for ubiquitin-dependent degradation. mBio 2024; 15:e0307123. [PMID: 38265236 PMCID: PMC10865787 DOI: 10.1128/mbio.03071-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
The accessory protein ORF6 of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key interferon (IFN) antagonist that strongly suppresses the production of primary IFN as well as the expression of IFN-stimulated genes. However, how host cells respond to ORF6 remains largely unknown. Our research of ORF6-binding proteins by pulldown revealed that E3 ligase components such as Cullin 4B (CUL4B), DDB1, and RBX1 are potential ORF6-interacting proteins. Further study found that the substrate recognition receptor PRPF19 interacts with CUL4B, DDB1, and RBX1 to form a CRL4B-based E3 ligase, which catalyzes ORF6 ubiquitination and subsequent degradation. Overexpression of PRPF19 promotes ORF6 degradation, releasing ORF6-mediated IFN inhibition, which inhibits SARS-CoV-2 replication. Moreover, we found that activation of CUL4B by the neddylation inducer etoposide alleviates lung lesions in a SARS-CoV-2 mouse infection model. Therefore, targeting ORF6 for degradation may be an effective therapeutic strategy against SARS-CoV-2 infection.IMPORTANCEThe cellular biological function of the ubiquitin-proteasome pathway as an important modulator for the regulation of many fundamental cellular processes has been greatly appreciated. The critical role of the ubiquitin-proteasome pathway in viral pathogenesis has become increasingly apparent. It is a powerful tool that host cells use to defend against viral infection. Some cellular proteins can function as restriction factors to limit viral infection by ubiquitin-dependent degradation. In this research, we identificated of CUL4B-DDB1-PRPF19 E3 Ubiquitin Ligase Complex can mediate proteasomal degradation of ORF6, leading to inhibition of viral replication. Moreover, the CUL4B activator etoposide alleviates disease development in a mouse infection model, suggesting that this agent or its derivatives may be used to treat infections caused by SARS-CoV-2. We believe that these results will be extremely useful for the scientific and clinic communities in their search for cues and preventive measures to combat the COVID-19 pandemic.
Collapse
Affiliation(s)
- Linran Zhang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Pengfei Hao
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Xiang Chen
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Shuai Lv
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Wenying Gao
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Chang Li
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Zhaolong Li
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Wenyan Zhang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China
| |
Collapse
|
6
|
Amir N, Taube R. Role of long noncoding RNA in regulating HIV infection-a comprehensive review. mBio 2024; 15:e0192523. [PMID: 38179937 PMCID: PMC10865847 DOI: 10.1128/mbio.01925-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
A complete cure against human immunodeficiency virus (HIV) infection remains out of reach, as the virus persists in stable cell reservoirs that are resistant to antiretroviral therapy. The key to eliminating these reservoirs lies in deciphering the processes that govern viral gene expression and latency. However, while we comprehensively understand how host proteins influence HIV gene expression and viral latency, the emerging role of long noncoding RNAs (lncRNAs) in the context of T cell activation, HIV gene expression, and viral latency remain unexplored. This review dives into the evolving significance of lncRNAs and their impact on HIV gene expression and viral latency. We provide an overview of the current knowledge regarding how lncRNAs regulate HIV gene expression, categorizing them as either activators or inhibitors of viral gene expression and infectivity. Furthermore, we offer insights into the potential therapeutic applications of lncRNAs in combatting HIV. A deeper understanding of how lncRNAs modulate HIV gene transcription holds promise for developing novel RNA-based therapies to complement existing treatment strategies to eradicate HIV reservoirs.
Collapse
Affiliation(s)
- Noa Amir
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Negev, Israel
| | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Negev, Israel
| |
Collapse
|
7
|
Kamba K, Wan L, Unzai S, Morishita R, Takaori-Kondo A, Nagata T, Katahira M. Direct inhibition of human APOBEC3 deaminases by HIV-1 Vif independent of the proteolysis pathway. Biophys J 2024; 123:294-306. [PMID: 38115583 PMCID: PMC10870137 DOI: 10.1016/j.bpj.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 12/01/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023] Open
Abstract
HIV-1 Vif is known to counteract the antiviral activity of human apolipoprotein B mRNA-editing catalytic polypeptide-like (A3), a cytidine deaminase, in various ways. However, the precise mechanism behind this interaction has remained elusive. Within infected cells, Vif forms a complex called VβBCC, comprising CBFβ and the components of E3 ubiquitin ligase, Elongin B, Elongin C, and Cullin5. Together with the ubiquitin-conjugating enzyme, VβBCC induces ubiquitination-mediated proteasomal degradation of A3. However, Vif exhibits additional counteractive effects. In this study, we elucidate that VβBCC inhibits deamination by A3G, A3F, and A3B independently of proteasomal degradation. Surprisingly, we discovered that this inhibition for A3G is directly attributed to the interaction between VβBCC and the C-terminal domain of A3G. Previously, it was believed that Vif did not interact with the C-terminal domain. Our findings suggest that inhibiting the interaction between VβBCC and the C-terminal domain, as well as the N-terminal domain known to be targeted for ubiquitination, of A3G may be needed to prevent counteraction by Vif.
Collapse
Affiliation(s)
- Keisuke Kamba
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Li Wan
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan; Graduate School of Energy Science, Kyoto University, Uji, Kyoto, Japan
| | - Satoru Unzai
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
| | - Ryo Morishita
- CellFree Sciences Co., Ltd., Matsuyama, Ehime, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan; Graduate School of Energy Science, Kyoto University, Uji, Kyoto, Japan.
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan; Graduate School of Energy Science, Kyoto University, Uji, Kyoto, Japan.
| |
Collapse
|
8
|
Chen X, Tian L, Zhang L, Gao W, Yu M, Li Z, Zhang W. Deubiquitinase USP39 promotes SARS-CoV-2 replication by deubiquitinating and stabilizing the envelope protein. Antiviral Res 2024; 221:105790. [PMID: 38158131 DOI: 10.1016/j.antiviral.2023.105790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
The SARS-CoV-2 envelope (E) protein is highly conserved among different viral variants and important for viral assembly and production. Our recent study found that the E protein is ubiquitinated and degraded by the E3 ligase RNF5 through the proteasome pathway. However, whether E ubiquitination can be reversed by host deubiquitinase has not yet been determined. Here, we identify by mass spectrum analysis that the deubiquitinases USP14 and USP39 specifically interact with E, while USP39 potently reverses E polyubiquitination. USP39 interacts with E via the arginine-rich motif (AR) and deubiquitinates E polyubiquitination via the inactive ubiquitin-specific protease domain. Therefore, USP39 protects E from RNF5-mediated degradation, resulting in the enhancement of E stability and E-induced cytokine storms. Moreover, loss-and-gain assays demonstrated that USP39 promotes the replication of various SARS-CoV-2 strains by stabilizing protein level of E that can be ubiquitinated but not other viral proteins. Our findings provide useful targets for the development of novel anti-SARS-CoV-2 strategies.
Collapse
Affiliation(s)
- Xiang Chen
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130021, Jilin, China
| | - Li Tian
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130021, Jilin, China
| | - Linran Zhang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130021, Jilin, China
| | - Wenying Gao
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130021, Jilin, China
| | - Miao Yu
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130021, Jilin, China
| | - Zhaolong Li
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, 130021, Jilin, China; Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130021, Jilin, China.
| | - Wenyan Zhang
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, 130021, Jilin, China; Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130021, Jilin, China.
| |
Collapse
|
9
|
Ji N, Huang W, Dang H, Xiao H, Shi Y, Guo J, Chen K, Wang J, Zou J. CBFβ is induced by spring viremia of carp virus and promotes virus replication in zebrafish. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104751. [PMID: 37268261 DOI: 10.1016/j.dci.2023.104751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023]
Abstract
The core binding factor subunit beta (CBFβ) is a transcription factor that forms a complex with virial proteins to promote viral infection. In this study, we identified a CBFβ homolog from zebrafish (zfCBFβ) and characterized the biological activity. The deduced zfCBFβ protein was highly similar to orthologs from other species. The zfcbfβ gene was constitutively expressed in tissues and was induced in immune tissues after infection with spring viremia carp virus (SVCV) and stimulation with poly(I:C). Interestingly, zfcbfβ is not induced by type I interferons. Overexpression of zfcbfβ induced tnfα expression but inhibited isg15 expression. Also, overexpression of zfcbfβ significantly increased SVCV titer in the EPC cells. Co-immunoprecipitation assay revealed that zfCBFβ interacts with SVCV phosphoprotein (SVCVP) and host p53, resulting in the increased stability of zfCBFβ. Our results provide evidence that CBFβ is targeted by virus to suppress host antiviral response.
Collapse
Affiliation(s)
- Ning Ji
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Wenji Huang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Huifeng Dang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Hehe Xiao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yanjie Shi
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jiahong Guo
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Kangyong Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Junya Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jun Zou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China.
| |
Collapse
|
10
|
Oswald J, Constantine M, Adegbuyi A, Omorogbe E, Dellomo AJ, Ehrlich ES. E3 Ubiquitin Ligases in Gammaherpesviruses and HIV: A Review of Virus Adaptation and Exploitation. Viruses 2023; 15:1935. [PMID: 37766341 PMCID: PMC10535929 DOI: 10.3390/v15091935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
For productive infection and replication to occur, viruses must control cellular machinery and counteract restriction factors and antiviral proteins. Viruses can accomplish this, in part, via the regulation of cellular gene expression and post-transcriptional and post-translational control. Many viruses co-opt and counteract cellular processes via modulation of the host post-translational modification machinery and encoding or hijacking kinases, SUMO ligases, deubiquitinases, and ubiquitin ligases, in addition to other modifiers. In this review, we focus on three oncoviruses, Epstein-Barr virus (EBV), Kaposi's sarcoma herpesvirus (KSHV), and human immunodeficiency virus (HIV) and their interactions with the ubiquitin-proteasome system via viral-encoded or cellular E3 ubiquitin ligase activity.
Collapse
Affiliation(s)
| | | | | | | | | | - Elana S. Ehrlich
- Department of Biological Sciences, Towson University, Towson, MD 21252, USA
| |
Collapse
|
11
|
Ikeda T, Shimizu R, Nasser H, Carpenter MA, Cheng AZ, Brown WL, Sauter D, Harris RS. APOBEC3 degradation is the primary function of HIV-1 Vif determining virion infectivity in the myeloid cell line THP-1. mBio 2023; 14:e0078223. [PMID: 37555667 PMCID: PMC10470580 DOI: 10.1128/mbio.00782-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/22/2023] [Indexed: 08/10/2023] Open
Abstract
HIV-1 must overcome multiple innate antiviral mechanisms to replicate in CD4+ T lymphocytes and macrophages. Previous studies have demonstrated that the apolipoprotein B mRNA editing enzyme polypeptide-like 3 (APOBEC3, A3) family of proteins (at least A3D, A3F, A3G, and stable A3H haplotypes) contribute to HIV-1 restriction in CD4+ T lymphocytes. Virus-encoded virion infectivity factor (Vif) counteracts this antiviral activity by degrading A3 enzymes allowing HIV-1 replication in infected cells. In addition to A3 proteins, Vif also targets other cellular proteins in CD4+ T lymphocytes, including PPP2R5 proteins. However, whether Vif primarily degrades only A3 proteins during viral replication is currently unknown. Herein, we describe the development and characterization of A3F-, A3F/A3G-, and A3A-to-A3G-null THP-1 cells. In comparison to Vif-proficient HIV-1, Vif-deficient viruses have substantially reduced infectivity in parental and A3F-null THP-1 cells, and a more modest decrease in infectivity in A3F/A3G-null cells. Remarkably, disruption of A3A-A3G protein expression completely restores the infectivity of Vif-deficient viruses in THP-1 cells. These results indicate that the primary function of Vif during infectious HIV-1 production from THP-1 cells is the targeting and degradation of A3 enzymes. IMPORTANCE HIV-1 Vif neutralizes the HIV-1 restriction activity of A3 proteins. However, it is currently unclear whether Vif has additional essential cellular targets. To address this question, we disrupted A3A to A3G genes in the THP-1 myeloid cell line using CRISPR and compared the infectivity of wild-type HIV-1 and Vif mutants with the selective A3 neutralization activities. Our results demonstrate that the infectivity of Vif-deficient HIV-1 and the other Vif mutants is fully restored by ablating the expression of cellular A3A to A3G proteins. These results indicate that A3 proteins are the only essential target of Vif that is required for fully infectious HIV-1 production from THP-1 cells.
Collapse
Affiliation(s)
- Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Michael A. Carpenter
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Adam Z. Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
| | - William L. Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
| |
Collapse
|
12
|
Ito F, Alvarez-Cabrera AL, Kim K, Zhou ZH, Chen XS. Structural basis of HIV-1 Vif-mediated E3 ligase targeting of host APOBEC3H. Nat Commun 2023; 14:5241. [PMID: 37640699 PMCID: PMC10462622 DOI: 10.1038/s41467-023-40955-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
Human APOBEC3 (A3) cytidine deaminases are antiviral factors that are particularly potent against retroviruses. As a countermeasure, HIV-1 uses a viral infectivity factor (Vif) to target specific human A3s for proteasomal degradation. Vif recruits cellular transcription cofactor CBF-β and Cullin-5 (CUL5) RING E3 ubiquitin ligase to bind different A3s distinctively, but how this is accomplished remains unclear in the absence of the atomic structure of the complex. Here, we present the cryo-EM structures of HIV-1 Vif in complex with human A3H, CBF-β and components of CUL5 ubiquitin ligase (CUL5, ELOB, and ELOC). Vif nucleates the entire complex by directly binding four human proteins, A3H, CBF-β, CUL5, and ELOC. The structures reveal a large interface area between A3H and Vif, primarily mediated by an α-helical side of A3H and a five-stranded β-sheet of Vif. This A3H-Vif interface unveils the basis for sensitivity-modulating polymorphism of both proteins, including a previously reported gain-of-function mutation in Vif isolated from HIV/AIDS patients. Our structural and functional results provide insights into the remarkable interplay between HIV and humans and would inform development efforts for anti-HIV therapeutics.
Collapse
Affiliation(s)
- Fumiaki Ito
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA90095, USA
| | - Ana L Alvarez-Cabrera
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA90095, USA
| | - Kyumin Kim
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA90095, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
- Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA90089, USA.
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA90089, USA.
- Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA90089, USA.
| |
Collapse
|
13
|
Qian G, Zhang Y, Liu Y, Li M, Xin B, Jiang W, Han W, Wang Y, Tang X, Li L, Zhu L, Sun T, Yan B, Zheng Y, Xu J, Ge B, Zhang Z, Yan D. Glutamylation of an HIV-1 protein inhibits the immune response by hijacking STING. Cell Rep 2023; 42:112442. [PMID: 37099423 DOI: 10.1016/j.celrep.2023.112442] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/04/2023] [Accepted: 04/12/2023] [Indexed: 04/27/2023] Open
Abstract
Cyclic GMP-AMP synthase (cGAS) recognizes Y-form cDNA of human immunodeficiency virus type 1 (HIV-1) and initiates antiviral immune response through cGAS-stimulator of interferon genes (STING)-TBK1-IRF3-type I interferon (IFN-I) signalingcascade. Here, we report that the HIV-1 p6 protein suppresses HIV-1-stimulated expression of IFN-I and promotes immune evasion. Mechanistically, the glutamylated p6 at residue Glu6 inhibits the interaction between STING and tripartite motif protein 32 (TRIM32) or autocrine motility factor receptor (AMFR). This subsequently suppresses the K27- and K63-linked polyubiquitination of STING at K337, therefore inhibiting STING activation, whereas mutation of the Glu6 residue partially reverses the inhibitory effect. However, CoCl2, an agonist of cytosolic carboxypeptidases (CCPs), counteracts the glutamylation of p6 at the Glu6 residue and inhibits HIV-1 immune evasion. These findings reveal a mechanism through which an HIV-1 protein mediates immune evasion and provides a therapeutic drug candidate to treat HIV-1 infection.
Collapse
Affiliation(s)
- Gui Qian
- Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
| | - Yihua Zhang
- Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
| | - Yinan Liu
- Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
| | - Manman Li
- Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
| | - Bowen Xin
- Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
| | - Wenyi Jiang
- Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
| | - Wendong Han
- Biosafety Level 3 Laboratory, Fudan University, Shanghai 200032, China
| | - Yu Wang
- National Engineering Research Centre of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Xian Tang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518112, China
| | - Liuyan Li
- Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
| | - Lingyan Zhu
- Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
| | - Tao Sun
- Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
| | - Bo Yan
- Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
| | - Yongtang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Jianqing Xu
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Baoxue Ge
- Shanghai TB Key Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518112, China
| | - Dapeng Yan
- Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China.
| |
Collapse
|
14
|
Bao Q, Zhou J. Various strategies for developing APOBEC3G protectors to circumvent human immunodeficiency virus type 1. Eur J Med Chem 2023; 250:115188. [PMID: 36773550 DOI: 10.1016/j.ejmech.2023.115188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/18/2023] [Accepted: 02/04/2023] [Indexed: 02/09/2023]
Abstract
Host restriction factor APOBEC3G (A3G) efficiently restricts Vif-deficient HIV-1 by being packaged with progeny virions and causing the G to A mutation during HIV-1 viral DNA synthesis as the progeny virus infects new cells. HIV-1 expresses Vif protein to resist the activity of A3G by mediating A3G degradation. This process requires the self-association of Vif in concert with A3G proteins, protein chaperones, and factors of the ubiquitination machinery, which are potential targets to discover novel anti-HIV drugs. This review will describe compounds that have been reported so far to inhibit viral replication of HIV-1 by protecting A3G from Vif-mediated degradation.
Collapse
Affiliation(s)
- Qiqi Bao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China; Drug Development and Innovation Center, College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China; Drug Development and Innovation Center, College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China.
| |
Collapse
|
15
|
Li YL, Langley CA, Azumaya CM, Echeverria I, Chesarino NM, Emerman M, Cheng Y, Gross JD. The structural basis for HIV-1 Vif antagonism of human APOBEC3G. Nature 2023; 615:728-733. [PMID: 36754086 PMCID: PMC10033410 DOI: 10.1038/s41586-023-05779-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 02/02/2023] [Indexed: 02/10/2023]
Abstract
The APOBEC3 (A3) proteins are host antiviral cellular proteins that hypermutate the viral genome of diverse viral families. In retroviruses, this process requires A3 packaging into viral particles1-4. The lentiviruses encode a protein, Vif, that antagonizes A3 family members by targeting them for degradation. Diversification of A3 allows host escape from Vif whereas adaptations in Vif enable cross-species transmission of primate lentiviruses. How this 'molecular arms race' plays out at the structural level is unknown. Here, we report the cryogenic electron microscopy structure of human APOBEC3G (A3G) bound to HIV-1 Vif, and the hijacked cellular proteins that promote ubiquitin-mediated proteolysis. A small surface explains the molecular arms race, including a cross-species transmission event that led to the birth of HIV-1. Unexpectedly, we find that RNA is a molecular glue for the Vif-A3G interaction, enabling Vif to repress A3G by ubiquitin-dependent and -independent mechanisms. Our results suggest a model in which Vif antagonizes A3G by intercepting it in its most dangerous form for the virus-when bound to RNA and on the pathway to packaging-to prevent viral restriction. By engaging essential surfaces required for restriction, Vif exploits a vulnerability in A3G, suggesting a general mechanism by which RNA binding helps to position key residues necessary for viral antagonism of a host antiviral gene.
Collapse
Affiliation(s)
- Yen-Li Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Caroline A Langley
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | - Caleigh M Azumaya
- Fred Hutchinson Cancer Center, Electron Microscopy Shared Resource, Seattle, WA, USA
| | - Ignacia Echeverria
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- Quantitative Bioscience Institute, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Nicholas M Chesarino
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michael Emerman
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Yifan Cheng
- Quantitative Bioscience Institute, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
- Quantitative Bioscience Institute, University of California, San Francisco, CA, USA.
| |
Collapse
|
16
|
HIV-1 Vpr Induces Degradation of Gelsolin, a Myeloid Cell-Specific Host Factor That Reduces Viral Infectivity by Inhibiting the Expression and Packaging of the HIV-1 Env Glycoprotein. mBio 2023; 14:e0297322. [PMID: 36602307 PMCID: PMC9972982 DOI: 10.1128/mbio.02973-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Gelsolin (GSN) is a structural actin-binding protein that is known to affect actin dynamics in the cell. Using mass spectrometry, we identified GSN as a novel Vpr-interacting protein. Endogenous GSN protein was expressed at detectable levels in monocyte-derived macrophages (MDM) and in THP-1 cells, but it was undetectable at the protein level in other cell lines tested. The HIV-1 infection of MDM was associated with a reduction in GSN steady-state levels, presumably due to the Vpr-induced degradation of GSN. Indeed, the coexpression of GSN and Viral protein R (Vpr) in transiently transfected HEK293T cells resulted in the Vpr-dependent proteasomal degradation of GSN. This effect was observed for Vprs from multiple virus isolates. The overexpression of GSN in HEK293T cells had no effect on Gag expression or particle release, but it reduced the expression and packaging of the HIV-1 envelope (Env) glycoprotein and reduced viral infectivity. An analysis of the HIV-1 splicing patterns did not reveal any GSN-dependent differences, suggesting that the effect of GSN on Env expression was regulated at a posttranscriptional level. Indeed, the treatment of transfected cells with lysosomal inhibitors reversed the effect of GSN on Env stability, suggesting that GSN reduced Env expression via enhanced lysosomal degradation. Our data identify GSN as a macrophage-specific host antiviral factor that reduces the expression of HIV-1 Env. IMPORTANCE Despite dramatic progress in drug therapies, HIV-1 infection remains an incurable disease that affects millions of people worldwide. The virus establishes long-lasting reservoirs that are resistant to currently available drug treatments and allow the virus to rebound whenever drug therapy is interrupted. Macrophages are long-lived cells that are relatively insensitive to HIV-1-induced cytopathicity and thus could contribute to the viral reservoir. Here, we identified a novel host factor, gelsolin, that is expressed at high levels in macrophages and inhibits viral infectivity by modulating the expression of the HIV-1 Env glycoprotein, which is critical in the spread of an HIV-1 infection. Importantly, the viral protein Vpr induces the degradation of gelsolin and thus counteracts its antiviral activity. Our study provides significant and novel insights into HIV-1 virus-host interactions and furthers our understanding of the importance of Vpr in HIV-1 infection and pathogenesis.
Collapse
|
17
|
Stability of APOBEC3F in the Presence of the APOBEC3 Antagonist HIV-1 Vif Increases at the Expense of Co-Expressed APOBEC3H Haplotype I. Viruses 2023; 15:v15020463. [PMID: 36851677 PMCID: PMC9960753 DOI: 10.3390/v15020463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
The seven human APOBEC3 enzymes (APOBEC3A through H, excluding E) are host restriction factors. Most of the APOBEC3 enzymes can restrict HIV-1 replication with different efficiencies. The HIV-1 Vif protein combats APOBEC3-mediated restriction by inducing ubiquitination and degradation in the proteasome. APOBEC3F and APOBEC3G can hetero-oligomerize, which increases their restriction capacity and resistance to Vif. Here we determined if APOBEC3C, APOBEC3F, or APOBEC3G could hetero-oligomerize with APOBEC3H haplotype I. APOBEC3H haplotype I has a short half-life in cells due to ubiquitination and degradation by host proteins, but is also resistant to Vif. We hypothesized that hetero-oligomerization with APOBEC3H haplotype I may result in less Vif-mediated degradation of the interacting APOBEC3 and stabilize APOBEC3H haplotype I, resulting in more efficient HIV-1 restriction. Although we found that all three APOBEC3s could interact with APOBEC3H haplotype I, only APOBEC3F affected APOBEC3H haplotype I by surprisingly accelerating its proteasomal degradation. However, this increased APOBEC3F levels in cells and virions in the absence or presence of Vif and enabled APOBEC3F-mediated restriction of HIV-1 in the presence of Vif. Altogether, the data suggest that APOBEC3 enzymes can co-regulate each other at the protein level and that they cooperate to ensure HIV-1 inactivation rather than evolution.
Collapse
|
18
|
Li Z, Hao P, Zhao Z, Gao W, Huan C, Li L, Chen X, Wang H, Jin N, Luo ZQ, Li C, Zhang W. The E3 ligase RNF5 restricts SARS-CoV-2 replication by targeting its envelope protein for degradation. Signal Transduct Target Ther 2023; 8:53. [PMID: 36737599 PMCID: PMC9897159 DOI: 10.1038/s41392-023-01335-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a severe global health crisis; its structural protein envelope (E) is critical for viral entry, budding, production, and induction of pathology which makes it a potential target for therapeutics against COVID-19. Here, we find that the E3 ligase RNF5 interacts with and catalyzes ubiquitination of E on the 63rd lysine, leading to its degradation by the ubiquitin-proteasome system (UPS). Importantly, RNF5-induced degradation of E inhibits SARS-CoV-2 replication and the RNF5 pharmacological activator Analog-1 alleviates disease development in a mouse infection model. We also found that RNF5 is distinctively expressed in different age groups and in patients displaying different disease severity, which may be exploited as a prognostic marker for COVID-19. Furthermore, RNF5 recognized the E protein from various SARS-CoV-2 strains and SARS-CoV, suggesting that targeting RNF5 is a broad-spectrum antiviral strategy. Our findings provide novel insights into the role of UPS in antagonizing SARS-CoV-2 replication, which opens new avenues for therapeutic intervention to combat the COVID-19 pandemic.
Collapse
Affiliation(s)
- Zhaolong Li
- Departement of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Pengfei Hao
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, Jilin, China
| | - Zhilei Zhao
- Departement of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Wenying Gao
- Departement of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Chen Huan
- Departement of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Letian Li
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, Jilin, China
| | - Xiang Chen
- Departement of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Hong Wang
- Departement of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Ningyi Jin
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, Jilin, China
| | - Zhao-Qing Luo
- Departement of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China.
| | - Chang Li
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, Jilin, China.
| | - Wenyan Zhang
- Departement of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China.
| |
Collapse
|
19
|
Ito F, Alvarez-Cabrera AL, Liu S, Yang H, Shiriaeva A, Zhou ZH, Chen XS. Structural basis for HIV-1 antagonism of host APOBEC3G via Cullin E3 ligase. SCIENCE ADVANCES 2023; 9:eade3168. [PMID: 36598981 PMCID: PMC9812381 DOI: 10.1126/sciadv.ade3168] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Human APOBEC3G (A3G) is a virus restriction factor that inhibits HIV-1 replication and triggers lethal hypermutation on viral reverse transcripts. HIV-1 viral infectivity factor (Vif) breaches this host A3G immunity by hijacking a cellular E3 ubiquitin ligase complex to target A3G for ubiquitination and degradation. The molecular mechanism of A3G targeting by Vif-E3 ligase is unknown, limiting the antiviral efforts targeting this host-pathogen interaction crucial for HIV-1 infection. Here, we report the cryo-electron microscopy structures of A3G bound to HIV-1 Vif in complex with T cell transcription cofactor CBF-β and multiple components of the Cullin-5 RING E3 ubiquitin ligase. The structures reveal unexpected RNA-mediated interactions of Vif with A3G primarily through A3G's noncatalytic domain, while A3G's catalytic domain is poised for ubiquitin transfer. These structures elucidate the molecular mechanism by which HIV-1 Vif hijacks the host ubiquitin ligase to specifically target A3G to establish infection and offer structural information for the rational development of antiretroviral therapeutics.
Collapse
Affiliation(s)
- Fumiaki Ito
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ana L. Alvarez-Cabrera
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - Shiheng Liu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - Hanjing Yang
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Anna Shiriaeva
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
| | - Z. Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - Xiaojiang S. Chen
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Genetic, Molecular, and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
- Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
20
|
Zhao S, Zheng B, Wang L, Cui W, Jiang C, Li Z, Gao W, Zhang W. Deubiquitinase ubiquitin-specific protease 3 (USP3) inhibits HIV-1 replication via promoting APOBEC3G (A3G) expression in both enzyme activity-dependent and -independent manners. Chin Med J (Engl) 2022; 135:2706-2717. [PMID: 36574218 PMCID: PMC9945250 DOI: 10.1097/cm9.0000000000002478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Ubiquitination plays an essential role in many biological processes, including viral infection, and can be reversed by deubiquitinating enzymes (DUBs). Although some studies discovered that DUBs inhibit or enhance viral infection by various mechanisms, there is lack of information on the role of DUBs in virus regulation, which needs to be further investigated. METHODS Immunoblotting, real-time polymerase chain reaction, in vivo / in vitro deubiquitination, protein immunoprecipitation, immunofluorescence, and co-localization biological techniques were employed to examine the effect of ubiquitin-specific protease 3 (USP3) on APOBEC3G (A3G) stability and human immunodeficiency virus (HIV) replication. To analyse the relationship between USP3 and HIV disease progression, we recruited 20 HIV-infected patients to detect the levels of USP3 and A3G in peripheral blood and analysed their correlation with CD4 + T-cell counts. Correlation was estimated by Pearson correlation coefficients (for parametric data). RESULTS The results demonstrated that USP3 specifically inhibits HIV-1 replication in an A3G-dependent manner. Further investigation found that USP3 stabilized 90% to 95% of A3G expression by deubiquitinating Vif-mediated polyubiquitination and blocking its degradation in an enzyme-dependent manner. It also enhances the A3G messenger RNA (mRNA) level by binding to A3G mRNA and stabilizing it in an enzyme-independent manner. Moreover, USP3 expression was positively correlated with A3G expression ( r = 0.5110) and CD4 + T-cell counts ( r = 0.5083) in HIV-1-infected patients. CONCLUSIONS USP3 restricts HIV-1 viral infections by increasing the expression of the antiviral factor A3G. Therefore, USP3 may be an important target for drug development and serve as a novel therapeutic strategy against viral infections.
Collapse
Affiliation(s)
- Simin Zhao
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- College of Life Science of Jilin University, Changchun, Jilin 130012, China
| | - Baisong Zheng
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Liuli Wang
- Department of Regenerative Medicine, School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Wenzhe Cui
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetics, The Second Hospital of Jilin University, Changchun, Jilin 130041, China
| | - Chunlai Jiang
- College of Life Science of Jilin University, Changchun, Jilin 130012, China
| | - Zhuo Li
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Wenying Gao
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Wenyan Zhang
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| |
Collapse
|
21
|
Dominant Negative Mutants of Human Immunodeficiency Virus Type 1 Viral Infectivity Factor (Vif) Disrupt Core-Binding Factor Beta-Vif Interaction. J Virol 2022; 96:e0055522. [PMID: 35950859 PMCID: PMC9472641 DOI: 10.1128/jvi.00555-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Apolipoprotein B mRNA-editing catalytic polypeptide-like 3 family members (APOBEC3s) are host restriction factors that inhibit viral replication. Viral infectivity factor (Vif), a human immunodeficiency virus type 1 (HIV-1) accessory protein, mediates the degradation of APOBEC3s by forming the Vif-E3 complex, in which core-binding factor beta (CBFβ) is an essential molecular chaperone. Here, we screened nonfunctional Vif mutants with high affinity for CBFβ to inhibit HIV-1 in a dominant negative manner. We applied the yeast surface display technology to express Vif random mutant libraries, and mutants showing high CBFβ affinity were screened using flow cytometry. Most of the screened Vif mutants containing random mutations of different frequencies were able to rescue APOBEC3G (A3G). In the subsequent screening, three of the mutants restricted HIV-1, recovered G-to-A hypermutation, and rescued APOBEC3s. Among them, Vif-6M showed a cross-protection effect toward APOBEC3C, APOBEC3F, and African green monkey A3G. Stable expression of Vif-6M in T lymphocytes inhibited the viral replication in newly HIV-1-infected cells and the chronically infected cell line H9/HXB2. Furthermore, the expression of Vif-6M provided a survival advantage to T lymphocytes infected with HIV-1. These results suggest that dominant negative Vif mutants acting on the Vif-CBFβ target potently restrict HIV-1. IMPORTANCE Antiviral therapy cannot eliminate HIV and exhibits disadvantages such as drug resistance and toxicity. Therefore, novel strategies for inhibiting viral replication in patients with HIV are urgently needed. APOBEC3s in host cells are able to inhibit viral replication but are antagonized by HIV-1 Vif-mediated degradation. Therefore, we screened nonfunctional Vif mutants with high affinity for CBFβ to compete with the wild-type Vif (wtVif) as a potential strategy to assist with HIV-1 treatment. Most screened mutants rescued the expression of A3G in the presence of wtVif, especially Vif-6M, which could protect various APOBEC3s and improve the incorporation of A3G into HIV-1 particles. Transduction of Vif-6M into T lymphocytes inhibited the replication of the newly infected virus and the chronically infected virus. These data suggest that Vif mutants targeting the Vif-CBFβ interaction may be promising in the development of a new AIDS therapeutic strategy.
Collapse
|
22
|
Abstract
Ubiquitin signaling is essential for immunity to restrict pathogen proliferation. Due to its enormous impact on human health and the global economy, intensive efforts have been invested in studying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its interactions with hosts. However, the role of the ubiquitin network in pathogenicity has not yet been explored. Here, we found that ORF9b of SARS-CoV-2 is ubiquitinated on Lys-4 and Lys-40 by unknown E3 ubiquitin ligases and is degraded by the ubiquitin proteasomal system. Importantly, we identified USP29 as a host factor that prevents ORF9b ubiquitination and subsequent degradation. USP29 interacts with the carboxyl end of ORF9b and removes ubiquitin chains from the protein, thereby inhibiting type I interferon (IFN) induction and NF-κB activation. We also found that ORF9b stabilization by USP29 enhanced the virulence of VSV-eGFP and transcription and replication-competent SARS-CoV-2 virus-like-particles (trVLP). Moreover, we observed that the mRNA level of USP29 in SARS-CoV-2 patients was higher than that in healthy people. Our findings provide important evidence indicating that targeting USP29 may effectively combat SARS-CoV-2 infection.
Collapse
|
23
|
Meissner ME, Talledge N, Mansky LM. Molecular Biology and Diversification of Human Retroviruses. FRONTIERS IN VIROLOGY 2022; 2:872599. [PMID: 35783361 PMCID: PMC9242851 DOI: 10.3389/fviro.2022.872599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Studies of retroviruses have led to many extraordinary discoveries that have advanced our understanding of not only human diseases, but also molecular biology as a whole. The most recognizable human retrovirus, human immunodeficiency virus type 1 (HIV-1), is the causative agent of the global AIDS epidemic and has been extensively studied. Other human retroviruses, such as human immunodeficiency virus type 2 (HIV-2) and human T-cell leukemia virus type 1 (HTLV-1), have received less attention, and many of the assumptions about the replication and biology of these viruses are based on knowledge of HIV-1. Existing comparative studies on human retroviruses, however, have revealed that key differences between these viruses exist that affect evolution, diversification, and potentially pathogenicity. In this review, we examine current insights on disparities in the replication of pathogenic human retroviruses, with a particular focus on the determinants of structural and genetic diversity amongst HIVs and HTLV.
Collapse
Affiliation(s)
- Morgan E. Meissner
- Institute for Molecular Virology, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Molecular, Cellular, Developmental Biology and Genetics Graduate Program, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
| | - Nathaniel Talledge
- Institute for Molecular Virology, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Masonic Cancer Center, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
| | - Louis M. Mansky
- Institute for Molecular Virology, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Molecular, Cellular, Developmental Biology and Genetics Graduate Program, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Masonic Cancer Center, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
| |
Collapse
|
24
|
Myint W, Schiffer CA, Matsuo H. HIV-1 VIF and human APOBEC3G interaction directly observed through molecular specific labeling using a new dual promotor vector. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 339:107230. [PMID: 35550909 PMCID: PMC9149140 DOI: 10.1016/j.jmr.2022.107230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/06/2022] [Accepted: 04/21/2022] [Indexed: 06/03/2023]
Abstract
Over the last few decades, protein NMR isotope labeling methods using E. coli based expression have revolutionized the information accessible from biomolecular NMR experiments. Selective labeling of a protein of interest in a multi-protein complex can significantly reduce the number of cross-peaks and allow for study of large protein complexes. However, limitations still remain since some proteins are not stable independently and cannot be separately labeled in either NMR active isotope enriched or unenriched media and reconstituted into a multimeric complex. To overcome this limitation, the LEGO NMR method was previously developed using protein expression plasmids containing T7 or araBAD promoters to separately express proteins in the same E. coli after changing between labeled and unlabeled media. Building on this, we developed a method to label the Human Immunodeficiency Virus type 1 viral infectivity factor (HIV-1 Vif), a monomerically unstable protein, in complex with CBFβ, it's host binding partner. We designed a dual promoter plasmid containing both T7 and araBAD promoters to independently control the expression of HIV-1 Vif in NMR active isotope enriched media and CBFβ in unenriched media. Using this method, we assigned the backbone resonance and directly observed the binding of HIV-1 Vif with APOBEC3G, a host restriction factor to HIV-1.
Collapse
Affiliation(s)
- Wazo Myint
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Hiroshi Matsuo
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
| |
Collapse
|
25
|
Shah PS, Beesabathuni NS, Fishburn AT, Kenaston MW, Minami SA, Pham OH, Tucker I. Systems Biology of Virus-Host Protein Interactions: From Hypothesis Generation to Mechanisms of Replication and Pathogenesis. Annu Rev Virol 2022; 9:397-415. [PMID: 35576593 PMCID: PMC10150767 DOI: 10.1146/annurev-virology-100520-011851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As obligate intracellular parasites, all viruses must co-opt cellular machinery to facilitate their own replication. Viruses often co-opt these cellular pathways and processes through physical interactions between viral and host proteins. In addition to facilitating fundamental aspects of virus replication cycles, these virus-host protein interactions can also disrupt physiological functions of host proteins, causing disease that can be advantageous to the virus or simply a coincidence. Consequently, unraveling virus-host protein interactions can serve as a window into molecular mechanisms of virus replication and pathogenesis. Identifying virus-host protein interactions using unbiased systems biology approaches provides an avenue for hypothesis generation. This review highlights common systems biology approaches for identification of virus-host protein interactions and the mechanistic insights revealed by these methods. We also review conceptual innovations using comparative and integrative systems biology that can leverage global virus-host protein interaction data sets to more rapidly move from hypothesis generation to mechanism. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Priya S Shah
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA; .,Department of Chemical Engineering, University of California, Davis, California, USA
| | - Nitin S Beesabathuni
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Adam T Fishburn
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA;
| | - Matthew W Kenaston
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA;
| | - Shiaki A Minami
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Oanh H Pham
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA;
| | - Inglis Tucker
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA;
| |
Collapse
|
26
|
Yan J, Zhao Y, Du J, Wang Y, Wang S, Wang Q, Zhao X, Xu W, Zhao K. RNA sensor MDA5 suppresses LINE-1 retrotransposition by regulating the promoter activity of LINE-1 5'-UTR. Mob DNA 2022; 13:10. [PMID: 35414110 PMCID: PMC9003951 DOI: 10.1186/s13100-022-00268-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 03/29/2022] [Indexed: 01/10/2023] Open
Abstract
Background Type 1 long interspersed elements, or LINE-1, are the only retroelements that replicate autonomously in human cells. The retrotransposition process of LINE-1 can trigger the activation of the innate immune system and has been proposed to play a role in the development of several autoimmune diseases, including Aicardi-Goutières syndrome (AGS). In contrast, all known AGS-associated proteins, except MDA5, have been reported to affect LINE-1 activity. Thus, MDA5 is likely to also function as a LINE-1 suppressor. Results MDA5 was found to potently suppress LINE-1 activity in a reporter-based LINE-1 retrotransposition assay. Although MDA5 is an endogenous RNA sensor able to activate the innate immune system, increased interferon (IFN) expression only contributed in part to MDA5-mediated LINE-1 suppression. Instead, MDA5 potently regulated the promoter activity of LINE-1 5′-UTR, as confirmed by transiently expressed myc-tagged MDA5 or knockdown of endogenous MDA5 expression. Consequently, MDA5 effectively reduced the generation of LINE-1 RNA and the subsequent expression of LINE-1 ORF1p and ORF2p. Interestingly, despite MDA5 being a multi-domain protein, the N-terminal 2CARD domain alone is sufficient to interact with LINE-1 5′-UTR and inhibit LINE-1 promoter activity. Conclusion Our data reveal that MDA5 functions as a promoter regulator; it directly binds to the LINE-1 5′-UTR and suppresses its promoter activity. Consequently, MDA5 reduces LINE-1 RNA and protein levels, and ultimately inhibits LINE-1 retrotransposition. In contrast, MDA5-induced IFN expression only plays a mild role in MDA5-mediated LINE-1 suppression. In addition, the N-terminal 2CARD domain was found to be a functional region for MDA5 upon inhibition of LINE-1 replication. Thus, our data suggest that besides being an initiator of the innate immune system, MDA5 is also an effector against LINE-1 activity, potentially forming a feedback loop by suppressing LINE-1-induced innate immune activation. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00268-0.
Collapse
Affiliation(s)
- Jiaxiu Yan
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China.,Department of Neonatology, First Hospital of Jilin University, Changchun, Jilin, China.,Department of Clinical Laboratory, First Hospital of Jilin University, Changchun, Jilin, China
| | - Yifei Zhao
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China
| | - Juan Du
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China.,Center for Pathogen Biology and Infectious Diseases, First Hospital of Jilin University, Changchun, Jilin, China.,Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, First Hospital of Jilin University, Changchun, Jilin, China
| | - Yu Wang
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China
| | - Shaohua Wang
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China
| | - Qing Wang
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China.,Department of Respiratory Medicine, First Hospital of Jilin University, Changchun, Jilin, China
| | - Xu Zhao
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China.,Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Wei Xu
- Department of Clinical Laboratory, First Hospital of Jilin University, Changchun, Jilin, China.
| | - Ke Zhao
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China. .,Center for Pathogen Biology and Infectious Diseases, First Hospital of Jilin University, Changchun, Jilin, China. .,Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, First Hospital of Jilin University, Changchun, Jilin, China.
| |
Collapse
|
27
|
Liu Y, Lan W, Wang C, Cao C. Two different kinds of interaction modes of deaminase APOBEC3A with single-stranded DNA in solution detected by nuclear magnetic resonance. Protein Sci 2022; 31:443-453. [PMID: 34792260 PMCID: PMC8819843 DOI: 10.1002/pro.4242] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023]
Abstract
APOBEC3A (A3A) deaminates deoxycytidine in target motif TC in a single-stranded DNA (we termed it as TC DNA), which mortally mutates viral pathogens and immunoglobulins, and leads to the diversification and lethality of cancers. The crystal structure of A3A-DNA revealed a unique U-shaped recognition mode of target base dC0 . However, when TC DNA was titrated into 15 N-labeled A3A solution, we observed two sets of 1 H-15 N cross-peaks of A3A in HSQC spectra, and two sets of 1 H-1 H cross-peaks of DNA in two-dimensional 13 C,15 N-filtered TOCSY spectra, indicating two different kinds of conformers of either A3A or TC DNA existing in solution. Here, mainly by NMR, we demonstrated that one DNA conformer interacted with one A3A conformer, forming a specific complex A3AS -DNAS in a way almost similar to that observed in the reported crystal A3A-DNA structure, where dC0 inserted into zinc ion binding center. While the other DNA conformer bound with another A3A conformer, but dC0 did not extend into the zinc-binding pocket, forming a nonspecific A3ANS -DNANS complex. The NMR solution structure implied three sites Asn61 , His182 and Arg189 were necessary to DNA recognition. These observations indicate a distinctive way from that reported in X-ray crystal structure, suggesting an unexpected mode of deaminase APOBEC3A to identify target motif TC in DNA in solution.
Collapse
Affiliation(s)
- Yaping Liu
- State Key Laboratory of Bioorganic and Natural Product ChemistryCenter for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of SciencesShanghaiChina,University of Chinese Academy of ScienceBeijingChina
| | - Wenxian Lan
- State Key Laboratory of Bioorganic and Natural Product ChemistryCenter for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of SciencesShanghaiChina
| | - Chunxi Wang
- State Key Laboratory of Bioorganic and Natural Product ChemistryCenter for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of SciencesShanghaiChina
| | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Product ChemistryCenter for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of SciencesShanghaiChina,University of Chinese Academy of ScienceBeijingChina
| |
Collapse
|
28
|
Wang Y, Qian G, Zhu L, Zhao Z, Liu Y, Han W, Zhang X, Zhang Y, Xiong T, Zeng H, Yu X, Yu X, Zhang X, Xu J, Zou Q, Yan D. HIV-1 Vif suppresses antiviral immunity by targeting STING. Cell Mol Immunol 2022; 19:108-121. [PMID: 34811497 PMCID: PMC8752805 DOI: 10.1038/s41423-021-00802-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/25/2021] [Indexed: 01/03/2023] Open
Abstract
HIV-1 infection-induced cGAS-STING-TBK1-IRF3 signaling activates innate immunity to produce type I interferon (IFN). The HIV-1 nonstructural protein viral infectivity factor (Vif) is essential in HIV-1 replication, as it degrades the host restriction factor APOBEC3G. However, whether and how it regulates the host immune response remains to be determined. In this study, we found that Vif inhibited the production of type I IFN to promote immune evasion. HIV-1 infection induced the activation of the host tyrosine kinase FRK, which subsequently phosphorylated the immunoreceptor tyrosine-based inhibitory motif (ITIM) of Vif and enhanced the interaction between Vif and the cellular tyrosine phosphatase SHP-1 to inhibit type I IFN. Mechanistically, the association of Vif with SHP-1 facilitated SHP-1 recruitment to STING and inhibited the K63-linked ubiquitination of STING at Lys337 by dephosphorylating STING at Tyr162. However, the FRK inhibitor D-65495 counteracted the phosphorylation of Vif to block the immune evasion of HIV-1 and antagonize infection. These findings reveal a previously unknown mechanism through which HIV-1 evades antiviral immunity via the ITIM-containing protein to inhibit the posttranslational modification of STING. These results provide a molecular basis for the development of new therapeutic strategies to treat HIV-1 infection.
Collapse
Affiliation(s)
- Yu Wang
- grid.8547.e0000 0001 0125 2443Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032 China ,grid.410570.70000 0004 1760 6682National Engineering Research Centre of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038 China ,grid.410570.70000 0004 1760 6682Department of Basic Courses, NCO School, Army Medical University, Shijiazhuang, 050081 China
| | - Gui Qian
- grid.8547.e0000 0001 0125 2443Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032 China
| | - Lingyan Zhu
- grid.8547.e0000 0001 0125 2443Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032 China
| | - Zhuo Zhao
- grid.410570.70000 0004 1760 6682National Engineering Research Centre of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038 China
| | - Yinan Liu
- grid.8547.e0000 0001 0125 2443Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032 China
| | - Wendong Han
- grid.8547.e0000 0001 0125 2443Biosafety Level 3 Laboratory, Fudan University, Shanghai, 200032 China
| | - Xiaokai Zhang
- grid.410570.70000 0004 1760 6682National Engineering Research Centre of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038 China
| | - Yihua Zhang
- grid.8547.e0000 0001 0125 2443Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032 China
| | - Tingrong Xiong
- grid.410570.70000 0004 1760 6682National Engineering Research Centre of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038 China
| | - Hao Zeng
- grid.410570.70000 0004 1760 6682National Engineering Research Centre of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038 China
| | - Xianghui Yu
- grid.64924.3d0000 0004 1760 5735National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012 China
| | - Xiaofang Yu
- grid.430605.40000 0004 1758 4110Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130061 China
| | - Xiaoyan Zhang
- grid.8547.e0000 0001 0125 2443Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032 China
| | - Jianqing Xu
- grid.8547.e0000 0001 0125 2443Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032 China
| | - Quanming Zou
- grid.410570.70000 0004 1760 6682National Engineering Research Centre of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038 China
| | - Dapeng Yan
- grid.8547.e0000 0001 0125 2443Department of Immunology, School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity & Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032 China
| |
Collapse
|
29
|
Host restriction factor A3G inhibits the replication of Enterovirus D68 through competitively binding 5' UTR with PCBP1. J Virol 2021; 96:e0170821. [PMID: 34730395 DOI: 10.1128/jvi.01708-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The host restriction factor APOBEC3G (A3G) presents extensively inhibition on a variety of viruses, including retroviruses, DNA and RNA viruses. Our recent study showed that A3G inhibits enterovirus 71 (EV71) and coxsackievirus A16 (CA16) via competitively binding 5'UTR with the host protein poly(C)-binding protein 1 (PCBP1) that is required for multiple EVs replication. However, in addition to EV71 and CA16, whether A3G inhibits other EVs has not been investigated. Here, we demonstrate that A3G could inhibit EVD68 replication, which needs PCBP1 for its replication, but not CA6 that PCBP1 is dispensable for CA6 replication. Further investigation revealed that nucleic acid binding activity of A3G is required for EVD68 restriction, which is similar to the mechanism presented in EV71 restriction. Mechanistically, A3G competitively binds to the cloverleaf (1-123) and the stem-loop IV (234-446) domains of EVD68 5'UTR with PCBP1, thereby inhibiting the 5'UTR activity of EVD68, whereas A3G doesn't interact with CA6 5'UTR results in no effect on CA6 replication. Moreover, non-structural protein 2C encoded by EVD68 overcomes A3G suppression through inducing A3G degradation via the autophagy-lysosome pathway. Our finding revealed that A3G might have broad spectrum antiviral activity against multiple EVs through the general mechanism, which might provide important information for the development of anti-EVs strategy. Importance As the two major pathogens causing hand, food, and mouth disease (HFMD), EV71 and CA16 attract more attention for the discovery of pathogenesis, the involvement of cellular proteins and so on. However, other EVs such as CA6 or EVD68 constantly occurred sporadic or might spread widely in recent years worldwide. Therefore, more information related to these EVs needs to be further investigated so as to develop broad-spectrum anti-EVs inhibitor. In this study, we first reveal that PCBP1 involved in PV and EV71 virus replication, also is required for the replication of EVD68 but not CA6. Then we found that the host restriction factor A3G specifically inhibits the replication of EVD68 but not CA6 via competitively binding to the 5'UTR of EVD68 with PCBP1. Our findings broaden the knowledge related to EVs replication and the interplay between EVs and host factors.
Collapse
|
30
|
Regulation of Viral Restriction by Post-Translational Modifications. Viruses 2021; 13:v13112197. [PMID: 34835003 PMCID: PMC8618861 DOI: 10.3390/v13112197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 12/17/2022] Open
Abstract
Intrinsic immunity is orchestrated by a wide range of host cellular proteins called restriction factors. They have the capacity to interfere with viral replication, and most of them are tightly regulated by interferons (IFNs). In addition, their regulation through post-translational modifications (PTMs) constitutes a major mechanism to shape their action positively or negatively. Following viral infection, restriction factor modification can be decisive. Palmitoylation of IFITM3, SUMOylation of MxA, SAMHD1 and TRIM5α or glycosylation of BST2 are some of those PTMs required for their antiviral activity. Nonetheless, for their benefit and by manipulating the PTMs machinery, viruses have evolved sophisticated mechanisms to counteract restriction factors. Indeed, many viral proteins evade restriction activity by inducing their ubiquitination and subsequent degradation. Studies on PTMs and their substrates are essential for the understanding of the antiviral defense mechanisms and provide a global vision of all possible regulations of the immune response at a given time and under specific infection conditions. Our aim was to provide an overview of current knowledge regarding the role of PTMs on restriction factors with an emphasis on their impact on viral replication.
Collapse
|
31
|
Gao W, Rui Y, Li G, Zhai C, Su J, Liu H, Zheng W, Zheng B, Zhang W, Yang Y, Hua S, Yu X. Specific Deubiquitinating Enzymes Promote Host Restriction Factors Against HIV/SIV Viruses. Front Immunol 2021; 12:740713. [PMID: 34630422 PMCID: PMC8492978 DOI: 10.3389/fimmu.2021.740713] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
Hijacking host ubiquitin pathways is essential for the replication of diverse viruses. However, the role of deubiquitinating enzymes (DUBs) in the interplay between viruses and the host is poorly characterized. Here, we demonstrate that specific DUBs are potent inhibitors of viral proteins from HIVs/simian immunodeficiency viruses (SIVs) that are involved in viral evasion of host restriction factors and viral replication. In particular, we discovered that T cell-functioning ubiquitin-specific protease 8 (USP8) is a potent and specific inhibitor of HIV-1 virion infectivity factor (Vif)-mediated apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3)G (A3G) degradation. Ectopic expression of USP8 inhibited Vif-induced A3G degradation and suppressed wild-type HIV-1 infectivity even in the presence of Vif. In addition, specific DUBs repressed Vpr-, Vpu-, and Vpx-triggered host restriction factor degradation. Our study has revealed a previously unrecognized interplay between the host's DUBs and viral replication. Enhancing the antiviral activity of DUBs therefore represents an attractive strategy against HIVs/SIVs.
Collapse
Affiliation(s)
- Wenying Gao
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
| | - Yajuan Rui
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Guangquan Li
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetics, The Second Hospital of Jilin University, Changchun, China
| | - Chenyang Zhai
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
| | - Jiaming Su
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Han Liu
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
| | - Wenwen Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Baisong Zheng
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
| | - Wenyan Zhang
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
| | - Yongjun Yang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Shucheng Hua
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
| | - Xiaofang Yu
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
32
|
Kaake RM, Echeverria I, Kim SJ, Von Dollen J, Chesarino NM, Feng Y, Yu C, Ta H, Chelico L, Huang L, Gross J, Sali A, Krogan NJ. Characterization of an A3G-Vif HIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes. Mol Cell Proteomics 2021; 20:100132. [PMID: 34389466 PMCID: PMC8459920 DOI: 10.1016/j.mcpro.2021.100132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/15/2021] [Accepted: 08/04/2021] [Indexed: 10/24/2022] Open
Abstract
Structural analysis of host-pathogen protein complexes remains challenging, largely due to their structural heterogeneity. Here, we describe a pipeline for the structural characterization of these complexes using integrative structure modeling based on chemical cross-links and residue-protein contacts inferred from mutagenesis studies. We used this approach on the HIV-1 Vif protein bound to restriction factor APOBEC3G (A3G), the Cullin-5 E3 ring ligase (CRL5), and the cellular transcription factor Core Binding Factor Beta (CBFβ) to determine the structure of the (A3G-Vif-CRL5-CBFβ) complex. Using the MS-cleavable DSSO cross-linker to obtain a set of 132 cross-links within this reconstituted complex along with the atomic structures of the subunits and mutagenesis data, we computed an integrative structure model of the heptameric A3G-Vif-CRL5-CBFβ complex. The structure, which was validated using a series of tests, reveals that A3G is bound to Vif mostly through its N-terminal domain. Moreover, the model ensemble quantifies the dynamic heterogeneity of the A3G C-terminal domain and Cul5 positions. Finally, the model was used to rationalize previous structural, mutagenesis and functional data not used for modeling, including information related to the A3G-bound and unbound structures as well as mapping functional mutations to the A3G-Vif interface. The experimental and computational approach described here is generally applicable to other challenging host-pathogen protein complexes.
Collapse
Affiliation(s)
- Robyn M Kaake
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Ignacia Echeverria
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Seung Joong Kim
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - John Von Dollen
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA
| | - Nicholas M Chesarino
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Yuqing Feng
- Department of Biochemistry, Microbiology, Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Clinton Yu
- Department of Physiology & Biophysics, University of California, Irvine, California, USA
| | - Hai Ta
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Linda Chelico
- Department of Biochemistry, Microbiology, Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, California, USA
| | - John Gross
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Andrej Sali
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA.
| |
Collapse
|
33
|
Zhong X, Luo R, Yan G, Ran K, Shan H, Yang J, Liu Y, Yu S, Pu C, Zheng Y, Li R. Lead optimization to improve the antiviral potency of 2-aminobenzamide derivatives targeting HIV-1 Vif-A3G axis. Eur J Med Chem 2021; 224:113680. [PMID: 34245947 DOI: 10.1016/j.ejmech.2021.113680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/27/2021] [Accepted: 06/27/2021] [Indexed: 02/08/2023]
Abstract
The viral infectivity factor (Vif)-apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G (APOBEC3G) axis has been recognized as a valid target for developing novel small-molecule therapies for acquired immune deficiency syndrome (AIDS) or for enhancing innate immunity against viruses. Our previous work reported the novel Vif antagonist 2-amino-N-(2-methoxyphenyl)-6-((4-nitrophenyl)sulfonyl)benzamide (2) with strong antiviral activity. In this work, through optimizations of ring C of 2, we discovered the more potent compound 6m with an EC50 of 0.07 μM in non-permissive H9 cells, reflecting an approximately 5-fold enhancement of antiviral activity compared to that of 2. Western blotting indicated that 6m more strongly suppressed the defensive protein Vif than 2 at the same concentration. Furthermore, 6m suppressed the replication of various clinical drug-resistant HIV strains (FI, NRTI, NNRTI, IN and PI) with relatively high efficacy. These results suggested that compound 6m is a more potent candidate for treating AIDS.
Collapse
Affiliation(s)
- Xinxin Zhong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Ronghua Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology,Chinese Academy of Sciences, Kunming, Yunnan, 650223, PR China
| | - Guoyi Yan
- School of Pharmacy, Henan University, Kaifeng, Henan, 475001, PR China
| | - Kai Ran
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Huifang Shan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Jie Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Yuanyuan Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Su Yu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Chunlan Pu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Yongtang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology,Chinese Academy of Sciences, Kunming, Yunnan, 650223, PR China.
| | - Rui Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China.
| |
Collapse
|
34
|
Deubiquitinating Enzyme USP21 Inhibits HIV-1 Replication by Downregulating Tat Expression. J Virol 2021; 95:e0046021. [PMID: 33827943 DOI: 10.1128/jvi.00460-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Ubiquitination plays an important role in human immunodeficiency virus 1 (HIV-1) infection. HIV proteins such as Vif and Vpx mediate the degradation of the host proteins APOBEC3 and SAMHD1, respectively, through the proteasome pathway. However, whether deubiquitylating enzymes play an essential role in HIV-1 infection is largely unknown. Here, we demonstrate that the deubiquitinase USP21 potently inhibits HIV-1 production by indirectly downregulating the expression of HIV-1 transactivator of transcription (Tat), which is essential for transcriptional elongation in HIV-1. USP21 deubiquitylates Tat via its deubiquitinase activity, but a stronger ability to reduce Tat expression than a dominant-negative ubiquitin mutant (Ub-KO) showed that other mechanisms may contribute to USP21-mediated inhibition of Tat. Further investigation showed that USP21 downregulates cyclin T1 mRNA levels by increasing methylation of histone K9 in the promoter of cyclin T1, a subunit of the positive transcription elongation factor b (P-TEFb) that interacts with Tat and transactivation response element (TAR) and is required for transcription stimulation and Tat stability. Moreover, USP21 had no effect on the function of other HIV-1 accessory proteins, including Vif, Vpr, Vpx, and Vpu, indicating that USP21 was specific to Tat. These findings improve our understanding of USP21-mediated functional suppression of HIV-1 production. IMPORTANCE Ubiquitination plays an essential role in viral infection. Deubiquitinating enzymes (DUBs) reverse ubiquitination by cleaving ubiquitins from target proteins, thereby affecting viral infection. The role of the members of the USP family, which comprises the largest subfamily of DUBs, is largely unknown in HIV-1 infection. Here, we screened a series of USP members and found that USP21 inhibits HIV-1 production by specifically targeting Tat but not the other HIV-1 accessory proteins. Further investigations revealed that USP21 reduces Tat expression in two ways. First, USP21 deubiquitinates polyubiquitinated Tat, causing Tat instability, and second, USP21 reduces the mRNA levels of cyclin T1 (CycT1), an important component of P-TEFb, that leads to Tat downregulation. Thus, in this study, we report a novel role of the deubiquitinase, USP21, in HIV-1 infection. USP21 represents a potentially useful target for the development of novel anti-HIV drugs.
Collapse
|
35
|
SAMHD1 Inhibits Multiple Enteroviruses by Interfering with the Interaction between VP1 and VP2 Proteins. J Virol 2021; 95:e0062021. [PMID: 33883225 DOI: 10.1128/jvi.00620-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Sterile alpha motif and histidine-aspartic acid domain-containing protein 1 (SAMHD1) possesses multiple biological activities such as virus restriction, innate immunity regulation, and autoimmunity. Our previous study demonstrated that SAMHD1 potently inhibits the replication of enterovirus 71 (EV71). In this study, we observed that SAMHD1 also restricts multiple enteroviruses (EVs), including coxsackievirus A16 (CA16) and enterovirus D68 (EVD68), but not coxsackievirus A6 (CA6). Mechanistically, SAMHD1 competitively interacted with the same domain in VP1 that binds to VP2 of EV71 and EVD68, thereby interfering with the interaction between VP1 and VP2 , and therefore viral assembly. Moreover, we showed that the SAMHD1 T592A mutant maintained the EV71 inhibitory effect by attenuating the interaction between VP1 and VP2, whereas the T592D mutant failed to. We also demonstrated that SAMHD1 could not inhibit CA6 because a different binding site is required for the SAMHD1 and VP1 interaction. Our findings reveal the mechanism of SAMHD1 inhibition of multiple EVs, and this could potentially be important for developing drugs against a broad range of EVs. IMPORTANCE Enterovirus causes a wide variety of diseases, such as hand, foot, and mouth disease (HFMD), which is a severe public problem threatening children under 5 years. Therefore, identifying essential genes which restrict EV infection and exploring the underlying mechanisms are necessary to develop an effective strategy to inhibit EV infection. In this study, we report that host restrictive factor SAMHD1 has broad-spectrum antiviral activity against EV71, CA16, and EVD68 independent of its well-known deoxynucleoside triphosphate triphosphohydrolase (dNTPase) or RNase activity. Mechanistically, SAMHD1 restricts EVs by competitively interacting with the same domain in VP1 that binds to VP2 of EVs, thereby interfering with the interaction between VP1 and VP2, and therefore viral assembly. In contrast, we also demonstrated that SAMHD1 could not inhibit CA6 because a different binding site is required for the SAMHD1 and CA6 VP1 interaction. Our study reveals a novel mechanism for the SAMHD1 anti-EV replication activity.
Collapse
|
36
|
Gaba A, Flath B, Chelico L. Examination of the APOBEC3 Barrier to Cross Species Transmission of Primate Lentiviruses. Viruses 2021; 13:1084. [PMID: 34200141 PMCID: PMC8228377 DOI: 10.3390/v13061084] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
The transmission of viruses from animal hosts into humans have led to the emergence of several diseases. Usually these cross-species transmissions are blocked by host restriction factors, which are proteins that can block virus replication at a specific step. In the natural virus host, the restriction factor activity is usually suppressed by a viral antagonist protein, but this is not the case for restriction factors from an unnatural host. However, due to ongoing viral evolution, sometimes the viral antagonist can evolve to suppress restriction factors in a new host, enabling cross-species transmission. Here we examine the classical case of this paradigm by reviewing research on APOBEC3 restriction factors and how they can suppress human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV). APOBEC3 enzymes are single-stranded DNA cytidine deaminases that can induce mutagenesis of proviral DNA by catalyzing the conversion of cytidine to promutagenic uridine on single-stranded viral (-)DNA if they escape the HIV/SIV antagonist protein, Vif. APOBEC3 degradation is induced by Vif through the proteasome pathway. SIV has been transmitted between Old World Monkeys and to hominids. Here we examine the adaptations that enabled such events and the ongoing impact of the APOBEC3-Vif interface on HIV in humans.
Collapse
Affiliation(s)
| | | | - Linda Chelico
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SA S7H 0E5, Canada; (A.G.); (B.F.)
| |
Collapse
|
37
|
Hu Y, Knecht KM, Shen Q, Xiong Y. Multifaceted HIV-1 Vif interactions with human E3 ubiquitin ligase and APOBEC3s. FEBS J 2021; 288:3407-3417. [PMID: 32893454 PMCID: PMC8172064 DOI: 10.1111/febs.15550] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/01/2020] [Indexed: 12/31/2022]
Abstract
APOBEC3 (A3) proteins are a family of host antiviral restriction factors that potently inhibit various retroviral infections, including human immunodeficiency virus (HIV)-1. To overcome this restriction, HIV-1 virion infectivity factor (Vif) recruits the cellular cofactor CBFβ to assist in targeting A3 proteins to a host E3 ligase complex for polyubiquitination and subsequent proteasomal degradation. Intervention of the Vif-A3 interactions could be a promising therapeutic strategy to facilitate A3-mediated suppression of HIV-1 in patients. In this structural snapshot, we review the structural features of the recently determined structure of human A3F in complex with HIV-1 Vif and its cofactor CBFβ, discuss insights into the molecular principles of Vif-A3 interplay during the arms race between the virus and host, and highlight the therapeutic implications.
Collapse
Affiliation(s)
- Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Kirsten M. Knecht
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Qi Shen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| |
Collapse
|
38
|
Degradation-Independent Inhibition of APOBEC3G by the HIV-1 Vif Protein. Viruses 2021; 13:v13040617. [PMID: 33916704 PMCID: PMC8066197 DOI: 10.3390/v13040617] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/20/2022] Open
Abstract
The ubiquitin–proteasome system plays an important role in the cell under normal physiological conditions but also during viral infections. Indeed, many auxiliary proteins from the (HIV-1) divert this system to its own advantage, notably to induce the degradation of cellular restriction factors. For instance, the HIV-1 viral infectivity factor (Vif) has been shown to specifically counteract several cellular deaminases belonging to the apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC3 or A3) family (A3A to A3H) by recruiting an E3-ubiquitin ligase complex and inducing their polyubiquitination and degradation through the proteasome. Although this pathway has been extensively characterized so far, Vif has also been shown to impede A3s through degradation-independent processes, but research on this matter remains limited. In this review, we describe our current knowledge regarding the degradation-independent inhibition of A3s, and A3G in particular, by the HIV-1 Vif protein, the molecular mechanisms involved, and highlight important properties of this small viral protein.
Collapse
|
39
|
Uriu K, Kosugi Y, Ito J, Sato K. The Battle between Retroviruses and APOBEC3 Genes: Its Past and Present. Viruses 2021; 13:124. [PMID: 33477360 PMCID: PMC7830460 DOI: 10.3390/v13010124] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/07/2021] [Accepted: 01/13/2021] [Indexed: 12/17/2022] Open
Abstract
The APOBEC3 family of proteins in mammals consists of cellular cytosine deaminases and well-known restriction factors against retroviruses, including lentiviruses. APOBEC3 genes are highly amplified and diversified in mammals, suggesting that their evolution and diversification have been driven by conflicts with ancient viruses. At present, lentiviruses, including HIV, the causative agent of AIDS, are known to encode a viral protein called Vif to overcome the antiviral effects of the APOBEC3 proteins of their hosts. Recent studies have revealed that the acquisition of an anti-APOBEC3 ability by lentiviruses is a key step in achieving successful cross-species transmission. Here, we summarize the current knowledge of the interplay between mammalian APOBEC3 proteins and viral infections and introduce a scenario of the coevolution of mammalian APOBEC3 genes and viruses.
Collapse
Affiliation(s)
- Keiya Uriu
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; (K.U.); (J.I.)
- Graduate School of Medicine, The University of Tokyo, Tokyo 1130033, Japan
| | - Yusuke Kosugi
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan;
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; (K.U.); (J.I.)
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; (K.U.); (J.I.)
- Graduate School of Medicine, The University of Tokyo, Tokyo 1130033, Japan
| |
Collapse
|
40
|
Salamango DJ, Harris RS. Dual Functionality of HIV-1 Vif in APOBEC3 Counteraction and Cell Cycle Arrest. Front Microbiol 2021; 11:622012. [PMID: 33510734 PMCID: PMC7835321 DOI: 10.3389/fmicb.2020.622012] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/11/2020] [Indexed: 01/02/2023] Open
Abstract
Accessory proteins are a key feature that distinguishes primate immunodeficiency viruses such as human immunodeficiency virus type I (HIV-1) from other retroviruses. A prime example is the virion infectivity factor, Vif, which hijacks a cellular co-transcription factor (CBF-β) to recruit a ubiquitin ligase complex (CRL5) to bind and degrade antiviral APOBEC3 enzymes including APOBEC3D (A3D), APOBEC3F (A3F), APOBEC3G (A3G), and APOBEC3H (A3H). Although APOBEC3 antagonism is essential for viral pathogenesis, and a more than sufficient functional justification for Vif’s evolution, most viral proteins have evolved multiple functions. Indeed, Vif has long been known to trigger cell cycle arrest and recent studies have shed light on the underlying molecular mechanism. Vif accomplishes this function using the same CBF-β/CRL5 ubiquitin ligase complex to degrade a family of PPP2R5 phospho-regulatory proteins. These advances have helped usher in a new era of accessory protein research and fresh opportunities for drug development.
Collapse
Affiliation(s)
- Daniel J Salamango
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, United States
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, United States.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, United States
| |
Collapse
|
41
|
Potential APOBEC-mediated RNA editing of the genomes of SARS-CoV-2 and other coronaviruses and its impact on their longer term evolution. Virology 2021; 556:62-72. [PMID: 33545556 PMCID: PMC7831814 DOI: 10.1016/j.virol.2020.12.018] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022]
Abstract
Members of the APOBEC family of cytidine deaminases show antiviral activities in mammalian cells through lethal editing in the genomes of small DNA viruses, herpesviruses and retroviruses, and potentially those of RNA viruses such as coronaviruses. Consistent with the latter, APOBEC-like directional C→U transitions of genomic plus-strand RNA are greatly overrepresented in SARS-CoV-2 genome sequences of variants emerging during the COVID-19 pandemic. A C→U mutational process may leave evolutionary imprints on coronavirus genomes, including extensive homoplasy from editing and reversion at targeted sites and the occurrence of driven amino acid sequence changes in viral proteins. If sustained over longer periods, this process may account for the previously reported marked global depletion of C and excess of U bases in human seasonal coronavirus genomes. This review synthesizes the current knowledge on APOBEC evolution and function and the evidence of their role in APOBEC-mediated genome editing of SARS-CoV-2 and other coronaviruses. SARS-CoV-2 sequence variants contain an overabundance of C- > U transitions C- > U transitions are the hallmark of the activity of APOBEC cytosine deaminases Further work is needed to determine APOBEC's role in coronavirus evolution
Collapse
|
42
|
Kostrhon S, Prabu JR, Baek K, Horn-Ghetko D, von Gronau S, Klügel M, Basquin J, Alpi AF, Schulman BA. CUL5-ARIH2 E3-E3 ubiquitin ligase structure reveals cullin-specific NEDD8 activation. Nat Chem Biol 2021; 17:1075-1083. [PMID: 34518685 PMCID: PMC8460447 DOI: 10.1038/s41589-021-00858-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 07/06/2021] [Indexed: 02/08/2023]
Abstract
An emerging mechanism of ubiquitylation involves partnering of two distinct E3 ligases. In the best-characterized E3-E3 pathways, ARIH-family RING-between-RING (RBR) E3s ligate ubiquitin to substrates of neddylated cullin-RING E3s. The E3 ARIH2 has been implicated in ubiquitylation of substrates of neddylated CUL5-RBX2-based E3s, including APOBEC3-family substrates of the host E3 hijacked by HIV-1 virion infectivity factor (Vif). However, the structural mechanisms remained elusive. Here structural and biochemical analyses reveal distinctive ARIH2 autoinhibition, and activation on assembly with neddylated CUL5-RBX2. Comparison to structures of E3-E3 assemblies comprising ARIH1 and neddylated CUL1-RBX1-based E3s shows cullin-specific regulation by NEDD8. Whereas CUL1-linked NEDD8 directly recruits ARIH1, CUL5-linked NEDD8 does not bind ARIH2. Instead, the data reveal an allosteric mechanism. NEDD8 uniquely contacts covalently linked CUL5, and elicits structural rearrangements that unveil cryptic ARIH2-binding sites. The data reveal how a ubiquitin-like protein induces protein-protein interactions indirectly, through allostery. Allosteric specificity of ubiquitin-like protein modifications may offer opportunities for therapeutic targeting.
Collapse
Affiliation(s)
- Sebastian Kostrhon
- grid.418615.f0000 0004 0491 845XDepartment of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J. Rajan Prabu
- grid.418615.f0000 0004 0491 845XDepartment of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kheewoong Baek
- grid.418615.f0000 0004 0491 845XDepartment of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Daniel Horn-Ghetko
- grid.418615.f0000 0004 0491 845XDepartment of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Susanne von Gronau
- grid.418615.f0000 0004 0491 845XDepartment of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maren Klügel
- grid.418615.f0000 0004 0491 845XDepartment of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jérôme Basquin
- grid.418615.f0000 0004 0491 845XDepartment of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Arno F. Alpi
- grid.418615.f0000 0004 0491 845XDepartment of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A. Schulman
- grid.418615.f0000 0004 0491 845XDepartment of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| |
Collapse
|
43
|
Knecht KM, Hu Y, Rubene D, Cook M, Ziegler SJ, Jónsson SR, Xiong Y. Maedi-visna virus Vif protein uses motifs distinct from HIV-1 Vif to bind zinc and the cofactor required for A3 degradation. J Biol Chem 2021; 296:100045. [PMID: 33465707 PMCID: PMC7949081 DOI: 10.1074/jbc.ra120.015828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/23/2020] [Accepted: 11/09/2020] [Indexed: 11/06/2022] Open
Abstract
The mammalian apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3 or A3) family of cytidine deaminases restrict viral infections by mutating viral DNA and impeding reverse transcription. To overcome this antiviral activity, most lentiviruses express a viral accessory protein called the virion infectivity factor (Vif), which recruits A3 proteins to cullin-RING E3 ubiquitin ligases such as cullin-5 (Cul5) for ubiquitylation and subsequent proteasomal degradation. Although Vif proteins from primate lentiviruses such as HIV-1 utilize the transcription factor core-binding factor subunit beta as a noncanonical cofactor to stabilize the complex, the maedi-visna virus (MVV) Vif hijacks cyclophilin A (CypA) instead. Because core-binding factor subunit beta and CypA are both highly conserved among mammals, the requirement for two different cellular cofactors suggests that these two A3-targeting Vif proteins have different biochemical and structural properties. To investigate this topic, we used a combination of in vitro biochemical assays and in vivo A3 degradation assays to study motifs required for the MVV Vif to bind zinc ion, Cul5, and the cofactor CypA. Our results demonstrate that although some common motifs between the HIV-1 Vif and MVV Vif are involved in recruiting Cul5, different determinants in the MVV Vif are required for cofactor binding and stabilization of the E3 ligase complex, such as the zinc-binding motif and N- and C-terminal regions of the protein. Results from this study advance our understanding of the mechanism of MVV Vif recruitment of cellular factors and the evolution of lentiviral Vif proteins.
Collapse
Affiliation(s)
- Kirsten M Knecht
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Diana Rubene
- Institute for Experimental Pathology, University of Iceland, Keldur, Iceland
| | - Matthew Cook
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Samantha J Ziegler
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Stefán R Jónsson
- Institute for Experimental Pathology, University of Iceland, Keldur, Iceland
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
| |
Collapse
|
44
|
Hakata Y, Miyazawa M. Deaminase-Independent Mode of Antiretroviral Action in Human and Mouse APOBEC3 Proteins. Microorganisms 2020; 8:microorganisms8121976. [PMID: 33322756 PMCID: PMC7764128 DOI: 10.3390/microorganisms8121976] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023] Open
Abstract
Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3) proteins (APOBEC3s) are deaminases that convert cytosines to uracils predominantly on a single-stranded DNA, and function as intrinsic restriction factors in the innate immune system to suppress replication of viruses (including retroviruses) and movement of retrotransposons. Enzymatic activity is supposed to be essential for the APOBEC3 antiviral function. However, it is not the only way that APOBEC3s exert their biological function. Since the discovery of human APOBEC3G as a restriction factor for HIV-1, the deaminase-independent mode of action has been observed. At present, it is apparent that both the deaminase-dependent and -independent pathways are tightly involved not only in combating viruses but also in human tumorigenesis. Although the deaminase-dependent pathway has been extensively characterized so far, understanding of the deaminase-independent pathway remains immature. Here, we review existing knowledge regarding the deaminase-independent antiretroviral functions of APOBEC3s and their molecular mechanisms. We also discuss the possible unidentified molecular mechanism for the deaminase-independent antiretroviral function mediated by mouse APOBEC3.
Collapse
Affiliation(s)
- Yoshiyuki Hakata
- Department of Immunology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan;
- Correspondence: ; Tel.: +81-72-367-7660
| | - Masaaki Miyazawa
- Department of Immunology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan;
- Kindai University Anti-Aging Center, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| |
Collapse
|
45
|
Retroviral Restriction Factors and Their Viral Targets: Restriction Strategies and Evolutionary Adaptations. Microorganisms 2020; 8:microorganisms8121965. [PMID: 33322320 PMCID: PMC7764263 DOI: 10.3390/microorganisms8121965] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022] Open
Abstract
The evolutionary conflict between retroviruses and their vertebrate hosts over millions of years has led to the emergence of cellular innate immune proteins termed restriction factors as well as their viral antagonists. Evidence accumulated in the last two decades has substantially increased our understanding of the elaborate mechanisms utilized by these restriction factors to inhibit retroviral replication, mechanisms that either directly block viral proteins or interfere with the cellular pathways hijacked by the viruses. Analyses of these complex interactions describe patterns of accelerated evolution for these restriction factors as well as the acquisition and evolution of their virus-encoded antagonists. Evidence is also mounting that many restriction factors identified for their inhibition of specific retroviruses have broader antiviral activity against additional retroviruses as well as against other viruses, and that exposure to these multiple virus challenges has shaped their adaptive evolution. In this review, we provide an overview of the restriction factors that interfere with different steps of the retroviral life cycle, describing their mechanisms of action, adaptive evolution, viral targets and the viral antagonists that evolved to counter these factors.
Collapse
|
46
|
Duan S, Wang S, Song Y, Gao N, Meng L, Gai Y, Zhang Y, Wang S, Wang C, Yu B, Wu J, Yu X. A novel HIV-1 inhibitor that blocks viral replication and rescues APOBEC3s by interrupting vif/CBFβ interaction. J Biol Chem 2020; 295:14592-14605. [PMID: 32817167 PMCID: PMC7586213 DOI: 10.1074/jbc.ra120.013404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/18/2020] [Indexed: 11/06/2022] Open
Abstract
HIV remains a health challenge worldwide, partly because of the continued development of resistance to drugs. Therefore, it is urgent to find new HIV inhibitors and targets. Apolipoprotein B mRNA-editing catalytic polypeptide-like 3 family members (APOBEC3) are important host restriction factors that inhibit HIV-1 replication by their cytidine deaminase activity. HIV-1 viral infectivity factor (Vif) promotes proteasomal degradation of APOBEC3 proteins by recruiting the E3 ubiquitin ligase complex, in which core-binding factor β (CBFβ) is a necessary molecular chaperone. Interrupting the interaction between Vif and CBFβ can release APOBEC3 proteins to inhibit HIV-1 replication and may be useful for developing new drug targets for HIV-1. In this study, we identified a potent small molecule inhibitor CBFβ/Vif-3 (CV-3) of HIV-1 replication by employing structure-based virtual screening using the crystal structure of Vif and CBFβ (PDB: 4N9F) and validated CV-3's antiviral activity. We found that CV-3 specifically inhibited HIV-1 replication (IC50 = 8.16 µm; 50% cytotoxic concentration >100 µm) in nonpermissive lymphocytes. Furthermore, CV-3 treatment rescued APOBEC3 family members (human APOBEC3G (hA3G), hA3C, and hA3F) in the presence of Vif and enabled hA3G packaging into HIV-1 virions, which resulted in Gly-to-Ala hypermutations in viral genomes. Finally, we used FRET to demonstrate that CV-3 inhibited the interaction between Vif and CBFβ by simultaneously forming hydrogen bonds with residues Gln-67, Ile-102, and Arg-131 of CBFβ. These findings demonstrate that CV-3 can effectively inhibit HIV-1 by blocking the interaction between Vif and CBFβ and that this interaction can serve as a new target for developing HIV-1 inhibitors.
Collapse
Affiliation(s)
- Sizhu Duan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Shiqi Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Yanan Song
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Nan Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Lina Meng
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Yanxin Gai
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Ying Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin Province, China
| | - Chu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Bin Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China; Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Jiaxin Wu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China; Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, Jilin Province, China
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, China; Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, Jilin Province, China.
| |
Collapse
|
47
|
Zou T, Zhang J. Diverse and pivotal roles of neddylation in metabolism and immunity. FEBS J 2020; 288:3884-3912. [PMID: 33025631 DOI: 10.1111/febs.15584] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/15/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022]
Abstract
Neddylation is one type of protein post-translational modification by conjugating a ubiquitin-like protein neural precursor cell-expressed developmentally downregulated protein 8 to substrate proteins via a cascade involving E1, E2, and E3 enzymes. The best-characterized substrates of neddylation are cullins, essential components of cullin-RING E3 ubiquitin-ligase complexes. The discovery of noncullin neddylation targets indicates that neddylation may have diverse biological functions. Indeed, neddylation has been implicated in various cellular processes including cell cycle progression, metabolism, immunity, and tumorigenesis. Here, we summarized the reported neddylation substrates and also discuss the functions of neddylation in the immune system and metabolism.
Collapse
Affiliation(s)
- Tao Zou
- Beijing Institute of Brain Sciences, China
| | | |
Collapse
|
48
|
NF-κB-Interacting Long Noncoding RNA Regulates HIV-1 Replication and Latency by Repressing NF-κB Signaling. J Virol 2020; 94:JVI.01057-20. [PMID: 32581100 DOI: 10.1128/jvi.01057-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/16/2020] [Indexed: 12/22/2022] Open
Abstract
NF-κB-interacting long noncoding RNA (NKILA) was recently identified as a negative regulator of NF-κB signaling and plays an important role in the development of various cancers. It is well known that NF-κB-mediated activation of human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR)-driven gene expression is required for HIV-1 transcription and reactivation of latency. However, whether NKILA plays essential roles in HIV-1 replication and latency is unclear. Here, by ectopic expression and silencing experiments, we demonstrate that NKILA potently inhibits HIV-1 replication in an NF-κB-dependent manner by suppressing HIV-1 LTR promoter activity. Moreover, NKILA showed broad-spectrum inhibition on the replication of HIV-1 clones with different coreceptor tropisms as well as on LTR activity of various HIV-1 clinical subtypes. Chromatin immunoprecipitation (ChIP) assays revealed that NKILA expression abolishes the recruitment of p65 to the duplicated κB binding sites in the HIV-1 LTR. NKILA mutants disrupting NF-κB inhibition also lost the ability to inhibit HIV-1 replication. Notably, HIV-1 infection or reactivation significantly downregulated NKILA expression in T cells in order to facilitate viral replication. Downregulated NKILA was mainly due to reduced acetylation of histone K27 on the promoter of NKILA by HIV-1 infection, which blocks NKILA expression. Knockdown of NKILA promoted the reactivation of latent HIV-1 upon phorbol myristate acetate (PMA) stimulation, while ectopic NKILA suppressed the reactivation in a well-established clinical model of withdrawal of azidothymidine (AZT) in vitro These findings improve our understanding of the functional suppression of HIV-1 replication and latency by NKILA through NF-κB signaling.IMPORTANCE The NF-κB pathway plays key roles in HIV-1 replication and reactivation of HIV-1 latency. A regulator inhibiting NF-κB activation may be a promising therapeutic strategy against HIV-1. Recently, NF-κB-interacting long noncoding RNA (NKILA) was identified to suppress the development of different human cancers by inhibiting IκB kinase (IKK)-induced IκB phosphorylation and NF-κB pathway activation, whereas the relationship between NKILA and HIV-1 replication is still unknown. Here, our results show that NKILA inhibits HIV-1 replication and reactivation by suppressing HIV-1 long terminal repeat (LTR)-driven transcription initiation. Moreover, NKILA inhibited the replication of HIV-1 clones with different coreceptor tropisms. This project may reveal a target for the development of novel anti-HIV drugs.
Collapse
|
49
|
Villanova F, Barreiros M, Leal É. Is the tryptophan codon of gene vif the Achilles' heel of HIV-1? PLoS One 2020; 15:e0225563. [PMID: 32570272 PMCID: PMC7308096 DOI: 10.1371/journal.pone.0225563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/05/2020] [Indexed: 12/04/2022] Open
Abstract
To evaluate the impact of hypermutation on the HIV-1 dissemination at the population level we studied 7072 sequences HIV-1 gene vif retrieved from the public databank. From this dataset 854 sequences were selected because they had associated values of CD4+ T lymphocytes counts and viral loads and they were used to assess the correlation between clinical parameters and hypermutation. We found that the frequency of stop codons at sites 5, 11 and 79 ranged from 2.8x10-4 to 4.2x10-4. On the other hand, at codons 21, 38, 70, 89 and 174 the frequency of stop codons ranged from 1.4x10-3 to 2.5x10-3. We also found a correlation between clinical parameters and hypermutation where patients harboring proviruses with one or more stop codons at the tryptophan sites of the gene vif had higher CD4+ T lymphocytes counts and lower viral loads compared to the population. Our findings indicate that A3 activity potentially restrains HIV-1 replication because individuals with hypermutated proviruses tend to have lower numbers of RNA copies. However, owing to the low frequency of hypermutated sequences observed in the databank (44 out of 7072), it is unlikely that A3 has a significant impact to curb HIV-1 dissemination at the population level.
Collapse
Affiliation(s)
- Fabiola Villanova
- Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Marta Barreiros
- Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Élcio Leal
- Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
- * E-mail:
| |
Collapse
|
50
|
Delviks-Frankenberry KA, Desimmie BA, Pathak VK. Structural Insights into APOBEC3-Mediated Lentiviral Restriction. Viruses 2020; 12:E587. [PMID: 32471198 PMCID: PMC7354603 DOI: 10.3390/v12060587] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 01/18/2023] Open
Abstract
Mammals have developed clever adaptive and innate immune defense mechanisms to protect against invading bacterial and viral pathogens. Human innate immunity is continuously evolving to expand the repertoire of restriction factors and one such family of intrinsic restriction factors is the APOBEC3 (A3) family of cytidine deaminases. The coordinated expression of seven members of the A3 family of cytidine deaminases provides intrinsic immunity against numerous foreign infectious agents and protects the host from exogenous retroviruses and endogenous retroelements. Four members of the A3 proteins-A3G, A3F, A3H, and A3D-restrict HIV-1 in the absence of virion infectivity factor (Vif); their incorporation into progeny virions is a prerequisite for cytidine deaminase-dependent and -independent activities that inhibit viral replication in the host target cell. HIV-1 encodes Vif, an accessory protein that antagonizes A3 proteins by targeting them for polyubiquitination and subsequent proteasomal degradation in the virus producing cells. In this review, we summarize our current understanding of the role of human A3 proteins as barriers against HIV-1 infection, how Vif overcomes their antiviral activity, and highlight recent structural and functional insights into A3-mediated restriction of lentiviruses.
Collapse
Affiliation(s)
| | | | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA; (K.A.D.-F.); (B.A.D.)
| |
Collapse
|