1
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Goodarzi MM, Jalalirad R, Doroud D, Hozouri H, Aghasadeghi M, Paryan M. Determining buffer conditions for downstream processing of VLP-based recombinant hepatitis B surface antigen using multimodal resins in bind-elute and flow-through purification modes. Sci Rep 2023; 13:10745. [PMID: 37400485 DOI: 10.1038/s41598-023-37614-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/24/2023] [Indexed: 07/05/2023] Open
Abstract
The difficulties in purification of VLP-based recombinant hepatitis B surface antigen (rHBsAg) are mainly emerged from inefficient semi-purification step plus proteins physicochemical properties and these issues make the downstream processing (DSP) very lengthy and expensive. In this study, optimization of rHBsAg (recombinantly-expressed in Pichia pastoris) DSP was performed using selection of buffering conditions in the semi-purification step. In the semi-purification optimization step, up to 73% of the protein impurities were eliminated and the utmost increase in rHBsAg purity (ca. 3.6-fold) was achieved using 20 mM sodium acetate, pH 4.5. By using rHBsAg binding and nonbinding situations obtained from the response surface plot in design of experiments (DOE), additional bind-elute and flow-through purification mode experiments were conducted and rHBsAg with high purity (near 100%) and recovery (> 83%) was achieved. Following assessment of critical quality attributes (i.e., purity, particle size distribution, host cell DNA, host cell protein, secondary structures, specific activity and relative potency), it was indicated that the characteristics of rHBsAg purified by the new DSP were similar or superior to the ones obtained from conventional DSP. The purification performance of the resin was constantly retained (97-100%) and no significant resin damage took place after 10 adsorption-elution-cleaning cycles. The new DSP developed for production of rHBsAg in this study can substitute the conventional one with granting satisfactory target protein quality, long-lasting resin efficacy, shorter and less expensive process. This process may be also employable for purification of both non-VLP- and VLP- based target proteins expressed in the yeast.
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Affiliation(s)
- Maryam Moazami Goodarzi
- Department of Research and Development, Production and Research Complex, Pasteur Institute of Iran, Karaj, 3159915111, Iran
| | - Reza Jalalirad
- Department of Research and Development, Production and Research Complex, Pasteur Institute of Iran, Karaj, 3159915111, Iran.
| | - Delaram Doroud
- Department of Research and Development, Production and Research Complex, Pasteur Institute of Iran, Karaj, 3159915111, Iran.
| | - Hamidreza Hozouri
- Department of Quality Management, Production and Research Complex, Pasteur Institute of Iran, Karaj, 3159915111, Iran
| | - Mohammadreza Aghasadeghi
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, 1316943551, Iran
- Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, 1316943551, Iran
| | - Mahdi Paryan
- Department of Research and Development, Production and Research Complex, Pasteur Institute of Iran, Karaj, 3159915111, Iran
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2
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Shi Y, Jin X, Wu S, Liu J, Zhang H, Cai X, Yang Y, Zhang X, Wei J, Luo M, Zhou H, Zhou H, Huang A, Wang D. Release of hepatitis B virions is positively regulated by glucose-regulated protein 78 through direct interaction with preS1. J Med Virol 2023; 95:e28271. [PMID: 36321566 PMCID: PMC10107996 DOI: 10.1002/jmv.28271] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/19/2022] [Accepted: 08/27/2022] [Indexed: 12/04/2022]
Abstract
In this study, we investigated the mechanism of hepatitis B virus (HBV)-enveloped particle release. Specifically, we used preS1 as a bait protein to screen host proteins using mass spectroscopy, with the results of immunofluorescence, western blot, co-immunoprecipitation, isothermal titration calorimetry, and pull-down assays identifying glucose-regulated protein (GRP)78 as a specific target for preS1 binding. We employed transcriptome sequencing, enzyme-linked immunosorbent assays, and particle gel assays to investigate the mechanism of GRP78-mediated positive regulation of HBV-enveloped particle release. Additionally, we performed phage-display, surface plasmon resonance, and molecular-docking assays to assess peptides inhibiting enveloped-particle release. We found that HBV upregulated GRP78 expression in liver cell lines and the serum of patients with chronic hepatitis B. Furthermore, GRP78 promoted the release of HBV-enveloped particles in vitro and in vivo within an HBV transgenic mouse model. Moreover, we identified interactions of preS1 peptides with GRP78 via hydrogen bonding and hydrophobic interactions, which effectively inhibited its interaction with HBV-enveloped particles and their subsequent release. These findings provide novel insights regarding HBV virion release, and demonstrated that GRP78 interacted with preS1 to positively regulate the release of HBV-enveloped particles, suggesting GRP78 as a potential therapeutic target for inhibiting HBV infection.
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Affiliation(s)
- Yueyuan Shi
- Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Yuzhong, Chongqing, China.,College of Laboratory Medicine, Chongqing Medical University, Yuzhong, Chongqing, China.,Department of Clinical Laboratory, The People's Hospital of Yubei District of Chongqing City, Yubei, Chongqing, China
| | - Xin Jin
- College of Laboratory Medicine, Chongqing Medical University, Yuzhong, Chongqing, China.,Department of Clinical Laboratory, The Second Hospital of Harbin, Harbin City, Heilongjiang Province, China
| | - Shuang Wu
- Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Yuzhong, Chongqing, China.,Department of Clinical Laboratory, The Affiliated Children Hospital of Xi'an Jiaotong University, Xi'an City, Shanxi Province, China
| | - Junye Liu
- Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Yuzhong, Chongqing, China.,Department of Clinical Laboratory, Honghui Hospital, Xi'an Jiaotong University, Xi'an City, Shanxi Province, China
| | - Hongpeng Zhang
- Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Yuzhong, Chongqing, China.,Department of Blood Transfusion, Women and Children's Hospital of Chongqing Medical University, Yubei, Chongqing, China
| | - Xuefei Cai
- Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Yuzhong, Chongqing, China
| | - Yuan Yang
- Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Yuzhong, Chongqing, China
| | - Xiang Zhang
- College of Laboratory Medicine, Chongqing Medical University, Yuzhong, Chongqing, China
| | - Jie Wei
- College of Laboratory Medicine, Chongqing Medical University, Yuzhong, Chongqing, China
| | - Miao Luo
- Department of Clinical Laboratory, The People's Hospital of Yubei District of Chongqing City, Yubei, Chongqing, China
| | - Hua Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing, China
| | - Huihao Zhou
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ailong Huang
- Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Yuzhong, Chongqing, China
| | - Deqiang Wang
- Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Yuzhong, Chongqing, China.,College of Laboratory Medicine, Chongqing Medical University, Yuzhong, Chongqing, China
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3
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Prange R. Hepatitis B virus movement through the hepatocyte: An update. Biol Cell 2022; 114:325-348. [PMID: 35984727 DOI: 10.1111/boc.202200060] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/26/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022]
Abstract
Viruses are obligate intracellular pathogens that utilize cellular machinery for many aspects of their propagation and effective egress of virus particles from host cells is one important determinant of virus infectivity. Hijacking host cell processes applies in particular to the hepatitis B virus (HBV), as its DNA genome with about 3 kb in size is one of the smallest viral genomes known. HBV is a leading cause of liver disease and still displays one of the most successful pathogens in human populations worldwide. The extremely successful spread of this virus is explained by its efficient transmission strategies and its versatile particle types, including virions, empty envelopes, naked capsids and others. HBV exploits distinct host trafficking machineries to assemble and release its particle types including nucleocytoplasmic shuttling transport, secretory and exocytic pathways, the Endosomal Sorting Complexes Required for Transport pathway, and the autophagy pathway. Understanding how HBV uses and subverts host membrane trafficking systems offers the chance of obtaining new mechanistic insights into the regulation and function of this essential cellular processes. It can also help to identify potential targets for antiviral interventions. Here, I will provide an overview of HBV maturation, assembly, and budding, with a focus on recent advances, and will point out areas where questions remain that can benefit from future studies. Unless otherwise indicated, almost all presented knowledge was gained from cell culture-based, HBV in vitro -replication and in vitro -infection systems. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Reinhild Prange
- Department of Virology, University Medical Center of the Johannes Gutenberg University Mainz, Augustusplatz, Mainz, D-55131, Germany
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4
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Bazinet M, Anderson M, Pântea V, Placinta G, Moscalu I, Cebotarescu V, Cojuhari L, Jimbei P, Iarovoi L, Smesnoi V, Musteata T, Jucov A, Dittmer U, Gersch J, Holzmayer V, Kuhns M, Cloherty G, Vaillant A. HBsAg isoform dynamics during NAP-based therapy of HBeAg-negative chronic HBV and HBV/HDV infection. Hepatol Commun 2022; 6:1870-1880. [PMID: 35368148 PMCID: PMC9315123 DOI: 10.1002/hep4.1951] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/15/2022] [Accepted: 03/03/2022] [Indexed: 12/11/2022] Open
Abstract
Nucleic acid polymers block the assembly of hepatitis B virus (HBV) subviral particles, effectively preventing hepatitis B surface antigen (HBsAg) replenishment in the circulation. Nucleic acid polymer (NAP)-based combination therapy of HBV infection or HBV/hepatitis D virus (HDV) co-infection is accompanied by HBsAg clearance and seroconversion, HDV-RNA clearance in co-infection, and persistent functional cure of HBV (HBsAg < 0.05 IU/ml, HBV-DNA target not dected, normal alanine aminotransferase) and persistent clearance of HDV RNA. An analysis of HBsAg isoform changes during quantitative HBsAg declines (qHBsAg), and subsequent treatment-free follow-up in the REP 301/REP 301-LTF (HBV/HDV) and REP 401 (HBV) studies was conducted. HBsAg isoforms were analyzed from frozen serum samples using Abbott Research Use Only assays for HBsAg isoforms (large [L], medium [M], and total [T]). The relative change over time in small HBsAg relative to the other isoforms was inferred by the change in the ratio over time of T-HBsAg to M-HBsAg. HBsAg isoform declines followed qHBsAg declines in all participants. No HBsAg isoforms were detectable in any participants with functional cure. HBsAg declines > 2 log10 IU/ml from baseline were correlated with selective clearance of S-HBsAg in 39 of 42 participants. Selective S-HBsAg decline was absent in 9 of 10 participants with HBsAg decline < 2 log10 IU/ml from baseline. Mild qHBsAg rebound during follow-up <10 IU/ml consisted mostly of S-HBsAg and M-HBsAg and not accompanied by significant covalently closed circular DNA activity. Conclusion: The faster observed declines in S-HBsAg indicate the selective clearance of subviral particles from the circulation, consistent with previous mechanistic studies on NAPs. Trace HBsAg rebound in the absence of HBV DNA may reflect HBsAg derived from integrated HBV DNA and not rebound of viral infection.
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Affiliation(s)
| | | | - Victor Pântea
- Department of Infectious DiseasesNicolae Testemiţanu State University of Medicine and PharmacyChișinăuRepublic of Moldova
| | - Gheorghe Placinta
- Department of Infectious DiseasesNicolae Testemiţanu State University of Medicine and PharmacyChișinăuRepublic of Moldova
| | - Iurie Moscalu
- ARENSIA Exploratory MedicineRepublican Clinical HospitalChișinăuRepublic of Moldova
| | - Valentin Cebotarescu
- Department of Infectious DiseasesNicolae Testemiţanu State University of Medicine and PharmacyChișinăuRepublic of Moldova
| | - Lilia Cojuhari
- Department of Infectious DiseasesNicolae Testemiţanu State University of Medicine and PharmacyChișinăuRepublic of Moldova
| | - Pavlina Jimbei
- Toma Ciorbǎ Infectious Clinical HospitalChișinăuRepublic of Moldova
| | - Liviu Iarovoi
- Department of Infectious DiseasesNicolae Testemiţanu State University of Medicine and PharmacyChișinăuRepublic of Moldova
| | | | - Tatina Musteata
- Toma Ciorbǎ Infectious Clinical HospitalChișinăuRepublic of Moldova
| | - Alina Jucov
- Department of Infectious DiseasesNicolae Testemiţanu State University of Medicine and PharmacyChișinăuRepublic of Moldova.,ARENSIA Exploratory MedicineRepublican Clinical HospitalChișinăuRepublic of Moldova
| | - Ulf Dittmer
- Institute for VirologyUniversity of Duisburg-EssenEssenGermany
| | | | | | - Mary Kuhns
- Abbott DiagnosticsAbbott ParkIllinoisUSA
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5
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He W, Li X, Xue H, Yang Y, Mencius J, Bai L, Zhang J, Xu J, Wu B, Xue Y, Quan S. Insights into the client protein release mechanism of the ATP-independent chaperone Spy. Nat Commun 2022; 13:2818. [PMID: 35595811 PMCID: PMC9122904 DOI: 10.1038/s41467-022-30499-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/22/2022] [Indexed: 11/09/2022] Open
Abstract
Molecular chaperones play a central role in regulating protein homeostasis, and their active forms often contain intrinsically disordered regions (IDRs). However, how IDRs impact chaperone action remains poorly understood. Here, we discover that the disordered N terminus of the prototype chaperone Spy facilitates client release. With NMR spectroscopy and molecular dynamics simulations, we find that the N terminus can bind transiently to the client-binding cavity of Spy primarily through electrostatic interactions mediated by the N-terminal D26 residue. This intramolecular interaction results in a dynamic competition of the N terminus with the client for binding to Spy, which promotes client discharge. Our results reveal the mechanism by which Spy releases clients independent of energy input, thus enriching the current knowledge on how ATP-independent chaperones release their clients and highlighting the importance of synergy between IDRs and structural domains in regulating protein function.
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Affiliation(s)
- Wei He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Xinming Li
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, 100084, Beijing, China
| | - Hongjuan Xue
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Yuanyuan Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Jun Mencius
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Ling Bai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Jiayin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Jianhe Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Bin Wu
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.
| | - Yi Xue
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, 100084, Beijing, China.
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China. .,Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China.
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6
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Garg A, Dabburu GR, Singhal N, Kumar M. Investigating the disordered regions (MoRFs, SLiMs and LCRs) and functions of mimicry proteins/peptides in silico. PLoS One 2022; 17:e0265657. [PMID: 35421114 PMCID: PMC9009644 DOI: 10.1371/journal.pone.0265657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/04/2022] [Indexed: 11/24/2022] Open
Abstract
Microbial mimicry of the host proteins/peptides can elicit host auto-reactive T- or B-cells resulting in autoimmune disease(s). Since intrinsically disordered protein regions (IDPRs) are involved in several host cell signaling and PPI networks, molecular mimicry of the IDPRs can help the pathogens in substituting their own proteins in the host cell-signaling and PPI networks and, ultimately hijacking the host cellular machinery. Thus, the present study was conducted to discern the structural disorder and intrinsically disordered protein regions (IDPRs) like, molecular recognition features (MoRFs), short linear motifs (SLiMs), and low complexity regions (LCRs) in the experimentally verified mimicry proteins and peptides (mimitopes) of bacteria, viruses and host. Also, functional characteristics of the mimicry proteins were studied in silico. Our results indicated that 78% of the bacterial host mimicry proteins and 45% of the bacterial host mimitopes were moderately/highly disordered while, 73% of the viral host mimicry proteins and 31% of the viral host mimitopes were moderately/highly disordered. Among the pathogens, 27% of the bacterial mimicry proteins and 13% of the bacterial mimitopes were moderately/highly disordered while, 53% of the viral mimicry proteins and 21% of the viral mimitopes were moderately/highly disordered. Though IDPR were frequent in host, bacterial and viral mimicry proteins, only a few mimitopes overlapped with the IDPRs like, MoRFs, SLiMs and LCRs. This suggests that most of the microbes cannot use molecular mimicry to modulate the host PPIs and hijack the host cell machinery. Functional analyses indicated that most of the pathogens exhibited mimicry with the host proteins involved in ion binding and signaling pathways. This is the first report on the disordered regions and functional aspects of experimentally proven host and microbial mimicry proteins.
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Affiliation(s)
- Anjali Garg
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Govinda Rao Dabburu
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Neelja Singhal
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
- * E-mail: (MK); (NS)
| | - Manish Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
- * E-mail: (MK); (NS)
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7
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The Role of Exosome and the ESCRT Pathway on Enveloped Virus Infection. Int J Mol Sci 2021; 22:ijms22169060. [PMID: 34445766 PMCID: PMC8396519 DOI: 10.3390/ijms22169060] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 02/06/2023] Open
Abstract
The endosomal sorting complex required for transport (ESCRT) system consists of peripheral membrane protein complexes ESCRT-0, -I, -II, -III VPS4-VTA1, and ALIX homodimer. This system plays an important role in the degradation of non-essential or dangerous plasma membrane proteins, the biogenesis of lysosomes and yeast vacuoles, the budding of most enveloped viruses, and promoting membrane shedding of cytokinesis. Recent results show that exosomes and the ESCRT pathway play important roles in virus infection. This review mainly focuses on the roles of exosomes and the ESCRT pathway in virus assembly, budding, and infection of enveloped viruses. The elaboration of the mechanism of exosomes and the ESCRT pathway in some enveloped viruses provides important implications for the further study of the infection mechanism of other enveloped viruses.
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8
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Vaillant A. HBsAg, Subviral Particles, and Their Clearance in Establishing a Functional Cure of Chronic Hepatitis B Virus Infection. ACS Infect Dis 2021; 7:1351-1368. [PMID: 33302622 DOI: 10.1021/acsinfecdis.0c00638] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In diverse viral infections, the production of excess viral particles containing only viral glycoproteins (subviral particles or SVP) is commonly observed and is a commonly evolved mechanism for immune evasion. In hepatitis B virus (HBV) infection, spherical particles contain the hepatitis B surface antigen, outnumber infectious virus 10 000-100 000 to 1, and have diverse inhibitory effects on the innate and adaptive immune response, playing a major role in the chronic nature of HBV infection. The current goal of therapies in development for HBV infection is a clinical outcome called functional cure, which signals a persistent and effective immune control of the infection. Although removal of spherical SVP (and the HBsAg they carry) is an important milestone in achieving functional cure, this outcome is rarely achieved with current therapies due to distinct mechanisms for assembly, secretion, and persistence of SVP, which are poorly targeted by direct acting antivirals or immunotherapies. In this Review, the current understanding of the distinct mechanisms involved in the production and persistence of spherical SVP in chronic HBV infection and their immunoinhibitory activity will be reviewed as well as current therapies in development with the goal of clearing spherical SVP and achieving functional cure.
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Affiliation(s)
- Andrew Vaillant
- Replicor Inc., 6100 Royalmount Avenue, Montreal, Quebec H8Y 3E6, Canada
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9
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Singh SK, Gui M, Koh F, Yip MC, Brown A. Structure and activation mechanism of the BBSome membrane protein trafficking complex. eLife 2020; 9:53322. [PMID: 31939736 PMCID: PMC7018513 DOI: 10.7554/elife.53322] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/06/2020] [Indexed: 12/19/2022] Open
Abstract
Bardet-Biedl syndrome (BBS) is a currently incurable ciliopathy caused by the failure to correctly establish or maintain cilia-dependent signaling pathways. Eight proteins associated with BBS assemble into the BBSome, a key regulator of the ciliary membrane proteome. We report the electron cryomicroscopy (cryo-EM) structures of the native bovine BBSome in inactive and active states at 3.1 and 3.5 Å resolution, respectively. In the active state, the BBSome is bound to an Arf-family GTPase (ARL6/BBS3) that recruits the BBSome to ciliary membranes. ARL6 recognizes a composite binding site formed by BBS1 and BBS7 that is occluded in the inactive state. Activation requires an unexpected swiveling of the β-propeller domain of BBS1, the subunit most frequently implicated in substrate recognition, which widens a central cavity of the BBSome. Structural mapping of disease-causing mutations suggests that pathogenesis results from folding defects and the disruption of autoinhibition and activation.
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Affiliation(s)
- Sandeep K Singh
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, United States
| | - Miao Gui
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, United States
| | - Fujiet Koh
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, United States
| | - Matthew Cj Yip
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, United States
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, United States
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10
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David G, Fogeron ML, Montserret R, Lecoq L, Page A, Delolme F, Nassal M, Böckmann A. Phosphorylation and Alternative Translation on Wheat Germ Cell-Free Protein Synthesis of the DHBV Large Envelope Protein. Front Mol Biosci 2019; 6:138. [PMID: 31850370 PMCID: PMC6902406 DOI: 10.3389/fmolb.2019.00138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/18/2019] [Indexed: 12/13/2022] Open
Abstract
Wheat-germ cell-free protein synthesis (WG-CFPS) is a potent platform for the high-yield production of proteins. It is especially of interest for difficult-to-express eukaryotic proteins, such as toxic and transmembrane proteins, and presents an important tool in high-throughput protein screening. Until recently, an assumed drawback of WG-CFPS was a reduced capacity for post-translational modifications. Meanwhile, phosphorylation has been observed in WG-CFPS; yet, authenticity of the respective phosphorylation sites remained unclear. Here we show that a viral membrane protein, the duck hepatitis B virus (DHBV) large envelope protein (DHBs L), produced by WG-CFPS, is phosphorylated upon translation at the same sites as DHBs L produced during DHBV infection of primary hepatocytes. Furthermore, we show that alternative translation initiation of the L protein, previously identified in virus-producing hepatic cells, occurs on WG-CFPS as well. Together, these findings further strengthen the high potential of WG-CFPS to include the reproduction of specific modifications proteins experience in vivo.
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Affiliation(s)
- Guillaume David
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Marie-Laure Fogeron
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Roland Montserret
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Lauriane Lecoq
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Adeline Page
- Protein Science Facility, SFR BioSciences CNRS UMS3444, Inserm US8, UCBL, ENS de Lyon, Lyon, France
| | - Frédéric Delolme
- Protein Science Facility, SFR BioSciences CNRS UMS3444, Inserm US8, UCBL, ENS de Lyon, Lyon, France
| | - Michael Nassal
- Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
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11
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Zeyen L, Prange R. Host Cell Rab GTPases in Hepatitis B Virus Infection. Front Cell Dev Biol 2018; 6:154. [PMID: 30510928 PMCID: PMC6252318 DOI: 10.3389/fcell.2018.00154] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/31/2018] [Indexed: 12/15/2022] Open
Abstract
Hepatitis B virus (HBV) is a leading cause of liver disease and is presently estimated to infect more than 250 million humans. The extremely successful spread of this virus among the human population is explained by its effective transmission strategies and its manifold particle types, including virions, empty envelopes and naked capsids. Due to its tiny genome, HBV depends on cellular machineries to thrive in infected hepatocytes. To enter, traverse and exit the cell, HBV exploits host membrane trafficking pathways, including intracellular highways directed by Rab GTPases. Here, we review recent discoveries focused on how HBV co-opts and perturbs host Rab GTPase functions with an emphasis on Rab7A- and Rab33B-mediated trafficking pathways. Rab7A plays bidirectional roles in the viral life cycle, as it promotes the endocytic uptake of HBV in early stages, but restricts exocytic virion release in late stages. In intermediate stages of HBV propagation, Rab33B is needed to guide the assembly of replicative progeny nucleocapsids. Rab33B acts together with its Atg5-12/16L1 effector, a protein complex required for autophagosome formation, suggesting the concept that HBV exploits this Rab/effector complex as an assembly scaffold and machine. We also discuss whether Rab-directed trafficking pathways engaged by HBV may be applicable to other virus families. Identification of overlapping Rab functions may offer new chances to develop broad-spectrum host-targeted antiviral strategies.
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Affiliation(s)
- Lisa Zeyen
- Department of Virology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Reinhild Prange
- Department of Virology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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12
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Atkinson SC, Audsley MD, Lieu KG, Marsh GA, Thomas DR, Heaton SM, Paxman JJ, Wagstaff KM, Buckle AM, Moseley GW, Jans DA, Borg NA. Recognition by host nuclear transport proteins drives disorder-to-order transition in Hendra virus V. Sci Rep 2018; 8:358. [PMID: 29321677 PMCID: PMC5762688 DOI: 10.1038/s41598-017-18742-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/15/2017] [Indexed: 01/04/2023] Open
Abstract
Hendra virus (HeV) is a paramyxovirus that causes lethal disease in humans, for which no vaccine or antiviral agent is available. HeV V protein is central to pathogenesis through its ability to interact with cytoplasmic host proteins, playing key antiviral roles. Here we use immunoprecipitation, siRNA knockdown and confocal laser scanning microscopy to show that HeV V shuttles to and from the nucleus through specific host nuclear transporters. Spectroscopic and small angle X-ray scattering studies reveal HeV V undergoes a disorder-to-order transition upon binding to either importin α/β1 or exportin-1/Ran-GTP, dependent on the V N-terminus. Importantly, we show that specific inhibitors of nuclear transport prevent interaction with host transporters, and reduce HeV infection. These findings emphasize the critical role of host-virus interactions in HeV infection, and potential use of compounds targeting nuclear transport, such as the FDA-approved agent ivermectin, as anti-HeV agents.
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Affiliation(s)
- Sarah C Atkinson
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Michelle D Audsley
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Kim G Lieu
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Glenn A Marsh
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Victoria, Australia
| | - David R Thomas
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Steven M Heaton
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Jason J Paxman
- La Trobe Institute for Molecular Sciences and Department of Biochemistry and Genetics, La Trobe University, Melbourne, Victoria, Australia
| | - Kylie M Wagstaff
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Ashley M Buckle
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Gregory W Moseley
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - David A Jans
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.
| | - Natalie A Borg
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.
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13
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Structure-based rational design of peptide inhibitors to disrupt the recognition and interaction between hepatitis B virus large envelope protein and human hepatocyte receptor γ2-adaptin. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1981-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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14
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Computational design of peptide ligands to target the intermolecular interaction between viral envelope protein and pediatric receptor. Comput Biol Chem 2017; 69:120-125. [PMID: 28666141 DOI: 10.1016/j.compbiolchem.2017.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/18/2017] [Accepted: 06/12/2017] [Indexed: 01/06/2023]
Abstract
The recognition and binding of viral envelope protein to pediatric receptor subverts the membrane-trafficking apparatus to mediate virion export in young children. Here, we described a successful computational design of peptide ligands to target the intermolecular interaction between the virus large envelope protein (LHB) and adaptin receptor (ADT). Based on the crystal structure of ADT in complex with an oligopeptide segment corresponding to the core binding site of LHB, a sequence-specific amino acid preference profile was determined systematically for the ADT-binding peptides using structural bioinformatics approach. With the information harvested from the profile, a genetic evolution procedure was run to improve the biological potency of a peptide population generated randomly from the LHB. A number of potential hits were obtained from the evolution, and four were measured to interact with ADT at micromolar level. A high-affinity hit peptide was then optimized according to computational structural analysis. It is revealed that a potent peptide can be divided into three regions, i.e. a negatively charged region at N-terminus, a hydrophobic core region in middle, and a small, polar region at C-terminal tail. In addition, the two termini of peptide are partially out of the active pocket of ADT, thus contributing moderately to the peptide binding.
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15
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γ2 and γ1AP-1 complexes: Different essential functions and regulatory mechanisms in clathrin-dependent protein sorting. Eur J Cell Biol 2017; 96:356-368. [PMID: 28372831 DOI: 10.1016/j.ejcb.2017.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/24/2017] [Accepted: 03/24/2017] [Indexed: 11/20/2022] Open
Abstract
γ2 adaptin is homologous to γ1, but is only expressed in vertebrates while γ1 is found in all eukaryotes. We know little about γ2 functions and their relation to γ1. γ1 is an adaptin of the heterotetrameric AP-1 complexes, which sort proteins in and do form clathrin-coated transport vesicles and they also regulate maturation of early endosomes. γ1 knockout mice develop only to blastocysts and thus γ2 does not compensate γ1-deficiency in development. γ2 has not been classified as a clathrin-coated vesicle adaptor protein in proteome analyses and functions for monomeric γ2 in endosomal protein sorting have been proposed, but adaptin interaction studies suggested formation of heterotetrameric AP-1/γ2 complexes. We detected γ2 at the trans-Golgi network, on peripheral vesicles and identified γ2 clathrin-coated vesicles in mice. Ubiquitous σ1A and tissue-specific σ1B adaptins bind γ2 and γ1. σ1B knockout in mice does not effect γ1/σ1A AP-1 levels, but γ2/σ1A AP-1 levels are increased in brain and adipocytes. Also γ2 is essential in development. In zebrafish AP-1/γ2 and AP-1/γ1 fulfill different, essential functions in brain and the vascular system.
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16
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Yao WL, Ikeda S, Tsukamoto Y, Shindo K, Otakaki Y, Qin M, Iwasawa Y, Takeuchi F, Kaname Y, Chou YC, Chang C, Watashi K, Wakita T, Noda T, Kato H, Fujita T. Establishment of a human hepatocellular cell line capable of maintaining long-term replication of hepatitis B virus. Int Immunol 2017; 29:109-120. [PMID: 28338936 DOI: 10.1093/intimm/dxx012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/10/2017] [Indexed: 12/12/2022] Open
Abstract
Hepatitis B virus (HBV) is a virus whose replication cycle cannot be completely reproduced using cultured cell lines. Here, we report an engineered cell line capable of supporting the complete HBV life cycle. We generated HepG2 cells over-expressing the HBV entry receptor human NTCP (sodium taurocholate cotransporting polypeptide), and defective in RIG-I (retinoic acid-inducible gene-I)-like receptor signaling, by knocking down the IPS-1 (IFNβ-promoter stimulator-1) adaptor molecule. The resultant NtG20.i7 cells were susceptible to HBV, and its replication was detectable at 14 days post-infection and persisted for at least 35 days with a gradual increase of HBV core expression. The cells produced infectious HBV in the culture supernatant, and the addition of preS1 peptide myr47-WT, which blocks HBV entry, impaired the persistence of the infection. These findings suggest that the persistence of the infection was maintained by continuous release of infectious HBV virions and their re-infection. This system is useful for expanding our basic understanding of the HBV replication cycle and for screening of anti-HBV chemicals.
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Affiliation(s)
- Wan-Ling Yao
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Biostudies, Yoshida-Konoecho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sotaro Ikeda
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Biostudies, Yoshida-Konoecho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuta Tsukamoto
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Keiko Shindo
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yukie Otakaki
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Biostudies, Yoshida-Konoecho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mian Qin
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Biostudies, Yoshida-Konoecho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshikazu Iwasawa
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Biostudies, Yoshida-Konoecho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Fumihiko Takeuchi
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Biostudies, Yoshida-Konoecho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuki Kaname
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yu-Chi Chou
- Institute of Microbiology and Immunology, National Yang-Ming University, No.155, Sec.2, Linong Street, Taipei 112, Taiwan
| | - Chungming Chang
- Institute of Microbiology and Immunology, National Yang-Ming University, No.155, Sec.2, Linong Street, Taipei 112, Taiwan
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo 162-8640, Japan
- Department of Applied Biological Science, Tokyo University of Science, 1-3, Kagurazaka Shinjuku-ku, Tokyo 162-8601, Japan
- CREST, JST, Saitama 332-0012, Japan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- Laboratory Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, Yoshida-Konoecho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroki Kato
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Biostudies, Yoshida-Konoecho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takashi Fujita
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Biostudies, Yoshida-Konoecho, Sakyo-ku, Kyoto 606-8501, Japan
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17
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Mattera R, Guardia CM, Sidhu SS, Bonifacino JS. Bivalent Motif-Ear Interactions Mediate the Association of the Accessory Protein Tepsin with the AP-4 Adaptor Complex. J Biol Chem 2015; 290:30736-49. [PMID: 26542808 DOI: 10.1074/jbc.m115.683409] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Indexed: 01/11/2023] Open
Abstract
The heterotetrameric (ϵ-β4-μ4-σ4) complex adaptor protein 4 (AP-4) is a component of a non-clathrin coat involved in protein sorting at the trans-Golgi network (TGN). Considerable interest in this complex has arisen from the recent discovery that mutations in each of its four subunits are the cause of a congenital intellectual disability and movement disorder in humans. Despite its physiological importance, the structure and function of this coat remain poorly understood. To investigate the assembly of the AP-4 coat, we dissected the determinants of interaction of AP-4 with its only known accessory protein, the ENTH/VHS-domain-containing protein tepsin. Using a variety of protein interaction assays, we found that tepsin comprises two phylogenetically conserved peptide motifs, [GS]LFXG[ML]X[LV] and S[AV]F[SA]FLN, within its C-terminal unstructured region, which interact with the C-terminal ear (or appendage) domains of the β4 and ϵ subunits of AP-4, respectively. Structure-based mutational analyses mapped the binding site for the [GS]LFXG[ML]X[LV] motif to a conserved, hydrophobic surface on the β4-ear platform fold. Both peptide-ear interactions are required for efficient association of tepsin with AP-4, and for recruitment of tepsin to the TGN. The bivalency of the interactions increases the avidity of tepsin for AP-4 and may enable cross-linking of multiple AP-4 heterotetramers, thus contributing to the assembly of the AP-4 coat. In addition to revealing critical aspects of this coat, our findings extend the paradigm of peptide-ear interactions, previously established for clathrin-AP-1/AP-2 coats, to a non-clathrin coat.
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Affiliation(s)
- Rafael Mattera
- From the Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 and
| | - Carlos M Guardia
- From the Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 and
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Juan S Bonifacino
- From the Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 and
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18
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Tompa P, Schad E, Tantos A, Kalmar L. Intrinsically disordered proteins: emerging interaction specialists. Curr Opin Struct Biol 2015; 35:49-59. [PMID: 26402567 DOI: 10.1016/j.sbi.2015.08.009] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/23/2015] [Accepted: 08/28/2015] [Indexed: 12/22/2022]
Abstract
Intrinsically disordered proteins or regions of proteins (IDPs/IDRs) most often function through protein-protein interactions, when they permanently or transiently bind partner molecules with diverse functional consequences. There is a rapid advance in our understanding of the ensuing functional modes, obtained from describing atomic details of individual complexes, proteome-wide studies of interactomes and characterizing loosely assembled hydrogels and tightly packed amyloids. Here we briefly survey the most important recent methodological developments and structural-functional observations, with the aim of increasing the general appreciation of IDPs/IDRs as 'interaction specialists'.
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Affiliation(s)
- Peter Tompa
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium; Vrije Universiteit Brussel, Brussels, Belgium; Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Lajos Kalmar
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
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19
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Escape of pathogens from the host immune response by mutations and mimicry. Possible means to improve vaccine performance. Med Hypotheses 2015; 85:664-9. [PMID: 26341417 DOI: 10.1016/j.mehy.2015.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 08/13/2015] [Indexed: 11/21/2022]
Abstract
The ability of certain pathogens, such as human immunodeficiency, hepatitis C, herpes simplex, influenza viruses, Plasmodium falciparum, etc., to escape from host immune response is generally ascribed to high mutation rate of their genome. We challenge this assumption and propose that molecular mimicry of host antigens by these pathogens could also participate to this resistance. Several studies show that there is no correlation between the mutation rate value of a pathogen and the possibility to develop an effective vaccine. On the other hand, pathogens which do not respond to vaccine are usually reported to display host protein mimicry. We propose to suppress in the thymus the epitopes of the self which are in common with the pathogen. This could be achieved by intrathymic injection of antibodies against this microorganism. These antibodies would be obtained by vaccination of a foreign animal species. It is expected that the negative selection of the CD4(+) and CD8(+) T lymphocytes specific for these epitopes would be prevented, that the number of epitopes recognized as foreign to the host would be increased and that the immune response diversity would be enhanced.
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20
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Fuzzy complexes: Specific binding without complete folding. FEBS Lett 2015; 589:2533-42. [PMID: 26226339 DOI: 10.1016/j.febslet.2015.07.022] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/20/2015] [Accepted: 07/21/2015] [Indexed: 12/17/2022]
Abstract
Specific molecular recognition is assumed to require a well-defined set of contacts and devoid of conformational and interaction ambiguities. Growing experimental evidence demonstrates however, that structural multiplicity or dynamic disorder can be retained in protein complexes, termed as fuzziness. Fuzzy regions establish alternative contacts between specific partners usually via transient interactions. Nature often tailors the dynamic properties of these segments via post-translational modifications or alternative splicing to fine-tune affinity. Most experimentally characterized fuzzy complexes are involved in regulation of gene-expression, signal transduction and cell-cycle regulation. Fuzziness is also characteristic to viral protein complexes, cytoskeleton structure, and surprisingly in a few metabolic enzymes. A plausible role of fuzzy complexes in increasing half-life of intrinsically disordered proteins is also discussed.
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21
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Duro N, Miskei M, Fuxreiter M. Fuzziness endows viral motif-mimicry. MOLECULAR BIOSYSTEMS 2015; 11:2821-9. [DOI: 10.1039/c5mb00301f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The local dynamics of host and viral peptide motifs suggests a different scenario for partner recognition. Host peptide motifs serve as molecular recognition elements, while viral motifs preserve the structural heterogeneity and remain fuzzy when bound to the host.
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Affiliation(s)
- Norbert Duro
- MTA-DE Momentum
- Laboratory of Protein Dynamics
- Department of Biochemistry and Molecular Biology
- University of Debrecen
- Hungary
| | - Marton Miskei
- MTA-DE Momentum
- Laboratory of Protein Dynamics
- Department of Biochemistry and Molecular Biology
- University of Debrecen
- Hungary
| | - Monika Fuxreiter
- MTA-DE Momentum
- Laboratory of Protein Dynamics
- Department of Biochemistry and Molecular Biology
- University of Debrecen
- Hungary
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22
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van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones D, Kim PM, Kriwacki R, Oldfield CJ, Pappu RV, Tompa P, Uversky VN, Wright P, Babu MM. Classification of intrinsically disordered regions and proteins. Chem Rev 2014; 114:6589-631. [PMID: 24773235 PMCID: PMC4095912 DOI: 10.1021/cr400525m] [Citation(s) in RCA: 1401] [Impact Index Per Article: 140.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Robin van der Lee
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
- Centre
for Molecular and Biomolecular Informatics, Radboud University Medical Centre, 6500 HB Nijmegen, The
Netherlands
| | - Marija Buljan
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Benjamin Lang
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Robert J. Weatheritt
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Gary W. Daughdrill
- Department
of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 3720 Spectrum Boulevard, Suite 321, Tampa, Florida 33612, United States
| | - A. Keith Dunker
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Monika Fuxreiter
- MTA-DE
Momentum Laboratory of Protein Dynamics, Department of Biochemistry
and Molecular Biology, University of Debrecen, H-4032 Debrecen, Nagyerdei krt 98, Hungary
| | - Julian Gough
- Department
of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, United Kingdom
| | - Joerg Gsponer
- Department
of Biochemistry and Molecular Biology, Centre for High-Throughput
Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - David
T. Jones
- Bioinformatics
Group, Department of Computer Science, University
College London, London, WC1E 6BT, United Kingdom
| | - Philip M. Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular
Genetics, and Department of Computer Science, University
of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Richard
W. Kriwacki
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
| | - Christopher J. Oldfield
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Rohit V. Pappu
- Department
of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Peter Tompa
- VIB Department
of Structural Biology, Vrije Universiteit
Brussel, Brussels, Belgium
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Vladimir N. Uversky
- Department
of Molecular Medicine and USF Health Byrd Alzheimer’s Research
Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Institute for Biological Instrumentation,
Russian Academy of Sciences, Pushchino,
Moscow Region, Russia
| | - Peter
E. Wright
- Department
of Integrative Structural and Computational Biology and Skaggs Institute
of Chemical Biology, The Scripps Research
Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - M. Madan Babu
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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23
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Reddy KD, DeForte S, Uversky VN. Digested disorder: Quarterly intrinsic disorder digest (July-August-September, 2013). INTRINSICALLY DISORDERED PROTEINS 2014; 2:e27833. [PMID: 28232877 PMCID: PMC5314876 DOI: 10.4161/idp.27833] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 01/13/2014] [Indexed: 12/26/2022]
Abstract
The current literature on intrinsically disordered proteins grows fast. To keep interested readers up to speed with this literature, we continue a "Digested Disorder" project and represent a new issue of reader's digest of the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the third quarter of 2013; i.e., during the period of June, July, and September of 2013. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.
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Affiliation(s)
- Krishna D Reddy
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
| | - Shelly DeForte
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA; Department of Biological Sciences; Faculty of Science; King Abdulaziz University; Jeddah, Saudi Arabia; Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
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Stieler JT, Prange R. Involvement of ESCRT-II in hepatitis B virus morphogenesis. PLoS One 2014; 9:e91279. [PMID: 24614091 PMCID: PMC3948859 DOI: 10.1371/journal.pone.0091279] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 02/10/2014] [Indexed: 01/20/2023] Open
Abstract
The hepatitis B virus (HBV) is an enveloped DNA virus that replicates via reverse transcription of its pregenomic RNA (pgRNA). Budding of HBV is supposed to occur at intracellular membranes and requires scission functions of the endosomal sorting complex required for transport (ESCRT) provided by ESCRT-III and VPS4. Here, we have investigated the impact of the upstream-acting ESCRT-I and ESCRT-II complexes in HBV morphogenesis. RNA interference knockdown of the ESCRT-I subunits TSG101 and VPS28 did not block, but rather stimulate virus release. In contrast, RNAi-mediated depletion of the ESCRT-II components EAP20, EAP30 and EAP45 greatly reduced virus egress. By analyzing different steps of the HBV maturation pathway, we find that the knockdown of ESCRT-II not only inhibited the production and/or release of enveloped virions, but also impaired intracellular nucleocapsid formation. Transcription/translation studies revealed that the depletion of ESCRT-II neither affected the synthesis and nuclear export of HBV-specific RNAs nor the expression of the viral core and envelope proteins. Moreover, the absence of ESCRT-II had no effects on the assembly capability and integrity of HBV core/capsids. However, the level of encapsidated pgRNA was significantly reduced in ESCRT-II-depleted cells, implicating that ESCRT-II directs steps accompanying the formation of replication-competent nucleocapsids, like e.g. assisting in RNA trafficking and encapsidation. In support of this, the capsid protein was found to interact and colocalize with ESCRT-II subunits in virus-producing cells. Together, these results indicate an essential role for ESCRT-II in the HBV life cycle and suggest that ESCRT-II functions prior to the final HBV budding reaction.
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Affiliation(s)
- Jens T. Stieler
- Department of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Reinhild Prange
- Department of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- * E-mail:
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Large-scale production and structural and biophysical characterizations of the human hepatitis B virus polymerase. J Virol 2013; 88:2584-99. [PMID: 24352439 DOI: 10.1128/jvi.02575-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
UNLABELLED Hepatitis B virus (HBV) is a major human pathogen that causes serious liver disease and 600,000 deaths annually. Approved therapies for treating chronic HBV infections usually target the multifunctional viral polymerase (hPOL). Unfortunately, these therapies--broad-spectrum antivirals--are not general cures, have side effects, and cause viral resistance. While hPOL remains an attractive therapeutic target, it is notoriously difficult to express and purify in a soluble form at yields appropriate for structural studies. Thus, no empirical structural data exist for hPOL, and this impedes medicinal chemistry and rational lead discovery efforts targeting HBV. Here, we present an efficient strategy to overexpress recombinant hPOL domains in Escherichia coli, purifying them at high yield and solving their known aggregation tendencies. This allowed us to perform the first structural and biophysical characterizations of hPOL domains. Apo-hPOL domains adopt mainly α-helical structures with small amounts of β-sheet structures. Our recombinant material exhibited metal-dependent, reverse transcriptase activity in vitro, with metal binding modulating the hPOL structure. Calcomine orange 2RS, a small molecule that inhibits duck HBV POL activity, also inhibited the in vitro priming activity of recombinant hPOL. Our work paves the way for structural and biophysical characterizations of hPOL and should facilitate high-throughput lead discovery for HBV. IMPORTANCE The viral polymerase from human hepatitis B virus (hPOL) is a well-validated therapeutic target. However, recombinant hPOL has a well-deserved reputation for being extremely difficult to express in a soluble, active form in yields appropriate to the structural studies that usually play an important role in drug discovery programs. This has hindered the development of much-needed new antivirals for HBV. However, we have solved this problem and report here procedures for expressing recombinant hPOL domains in Escherichia coli and also methods for purifying them in soluble forms that have activity in vitro. We also present the first structural and biophysical characterizations of hPOL. Our work paves the way for new insights into hPOL structure and function, which should assist the discovery of novel antivirals for HBV.
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