1
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Maio N, Heffner AL, Rouault TA. Iron‑sulfur clusters in viral proteins: Exploring their elusive nature, roles and new avenues for targeting infections. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119723. [PMID: 38599324 PMCID: PMC11139609 DOI: 10.1016/j.bbamcr.2024.119723] [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: 01/25/2024] [Revised: 03/13/2024] [Accepted: 04/01/2024] [Indexed: 04/12/2024]
Abstract
Viruses have evolved complex mechanisms to exploit host factors for replication and assembly. In response, host cells have developed strategies to block viruses, engaging in a continuous co-evolutionary battle. This dynamic interaction often revolves around the competition for essential resources necessary for both host cell and virus replication. Notably, iron, required for the biosynthesis of several cofactors, including iron‑sulfur (FeS) clusters, represents a critical element in the ongoing competition for resources between infectious agents and host. Although several recent studies have identified FeS cofactors at the core of virus replication machineries, our understanding of their specific roles and the cellular processes responsible for their incorporation into viral proteins remains limited. This review aims to consolidate our current knowledge of viral components that have been characterized as FeS proteins and elucidate how viruses harness these versatile cofactors to their benefit. Its objective is also to propose that viruses may depend on incorporation of FeS cofactors more extensively than is currently known. This has the potential to revolutionize our understanding of viral replication, thereby carrying significant implications for the development of strategies to target infections.
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Affiliation(s)
- Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA.
| | - Audrey L Heffner
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
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2
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Kumar S, Ansari S, Narayanan S, Ranjith-Kumar CT, Surjit M. Antiviral activity of zinc against hepatitis viruses: current status and future prospects. Front Microbiol 2023; 14:1218654. [PMID: 37908540 PMCID: PMC10613677 DOI: 10.3389/fmicb.2023.1218654] [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: 05/07/2023] [Accepted: 09/28/2023] [Indexed: 11/02/2023] Open
Abstract
Viral hepatitis is a major public health concern globally. World health organization aims at eliminating viral hepatitis as a public health threat by 2030. Among the hepatitis causing viruses, hepatitis B and C are primarily transmitted via contaminated blood. Hepatitis A and E, which gets transmitted primarily via the feco-oral route, are the leading cause of acute viral hepatitis. Although vaccines are available against some of these viruses, new cases continue to be reported. There is an urgent need to devise a potent yet economical antiviral strategy against the hepatitis-causing viruses (denoted as hepatitis viruses) for achieving global elimination of viral hepatitis. Although zinc was known to mankind for a long time (since before Christ era), it was identified as an element in 1746 and its importance for human health was discovered in 1963 by the pioneering work of Dr. Ananda S. Prasad. A series of follow up studies involving zinc supplementation as a therapy demonstrated zinc as an essential element for humans, leading to establishment of a recommended dietary allowance (RDA) of 15 milligram zinc [United States RDA for zinc]. Being an essential component of many cellular enzymes and transcription factors, zinc is vital for growth and homeostasis of most living organisms, including human. Importantly, several studies indicate potent antiviral activity of zinc. Multiple studies have demonstrated antiviral activity of zinc against viruses that cause hepatitis. This article provides a comprehensive overview of the findings on antiviral activity of zinc against hepatitis viruses, discusses the mechanisms underlying the antiviral properties of zinc and summarizes the prospects of harnessing the therapeutic benefit of zinc supplementation therapy in reducing the disease burden due to viral hepatitis.
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Affiliation(s)
- Shiv Kumar
- Virology Laboratory, Centre for Virus Research, Therapeutics and Vaccines, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Shabnam Ansari
- Virology Laboratory, Centre for Virus Research, Therapeutics and Vaccines, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Sriram Narayanan
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - C. T. Ranjith-Kumar
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Milan Surjit
- Virology Laboratory, Centre for Virus Research, Therapeutics and Vaccines, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
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3
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Chen J, Calderone LA, Pan L, Quist T, Pandelia ME. The Fe and Zn cofactor dilemma. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140931. [PMID: 37353133 DOI: 10.1016/j.bbapap.2023.140931] [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: 04/21/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 06/25/2023]
Abstract
Fe and Zn ions are essential enzymatic cofactors across all domains of life. Fe is an electron donor/acceptor in redox enzymes, while Zn is typically a structural element or catalytic component in hydrolases. Interestingly, the presence of Zn in oxidoreductases and Fe in hydrolases challenge this apparent functional dichotomy. In hydrolases, Fe either substitutes for Zn or specifically catalyzes certain reactions. On the other hand, Zn can replace divalent Fe and substitute for more complex Fe assemblies, known as Fe-S clusters. Although many zinc-binding proteins interchangeably harbor Zn and Fe-S clusters, these cofactors are only sometimes functional proxies.
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Affiliation(s)
- Jiahua Chen
- Department of Biochemistry, Brandeis University, Waltham, MA 02453, USA
| | - Logan A Calderone
- Department of Biochemistry, Brandeis University, Waltham, MA 02453, USA
| | - Luying Pan
- Department of Biochemistry, Brandeis University, Waltham, MA 02453, USA
| | - Trent Quist
- Department of Biochemistry, Brandeis University, Waltham, MA 02453, USA
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4
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Liu W, Yao Q, Su X, Deng Y, Yang M, Peng B, Zhao F, Du C, Zhang X, Zhu J, Wang D, Li W, Li H. Molecular insights into Spindlin1-HBx interplay and its impact on HBV transcription from cccDNA minichromosome. Nat Commun 2023; 14:4663. [PMID: 37537164 PMCID: PMC10400593 DOI: 10.1038/s41467-023-40225-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/11/2023] [Indexed: 08/05/2023] Open
Abstract
Molecular interplay between host epigenetic factors and viral proteins constitutes an intriguing mechanism for sustaining hepatitis B virus (HBV) life cycle and its chronic infection. HBV encodes a regulatory protein, HBx, which activates transcription and replication of HBV genome organized as covalently closed circular (ccc) DNA minichromosome. Here we illustrate how HBx accomplishes its task by hijacking Spindlin1, an epigenetic reader comprising three consecutive Tudor domains. Our biochemical and structural studies have revealed that the highly conserved N-terminal 2-21 segment of HBx (HBx2-21) associates intimately with Tudor 3 of Spindlin1, enhancing histone H3 "K4me3-K9me3" readout by Tudors 2 and 1. Functionally, Spindlin1-HBx engagement promotes gene expression from the chromatinized cccDNA, accompanied by an epigenetic switch from an H3K9me3-enriched repressive state to an H3K4me3-marked active state, as well as a conformational switch of HBx that may occur in coordination with other HBx-binding factors, such as DDB1. Despite a proposed transrepression activity of HBx2-21, our study reveals a key role of Spindlin1 in derepressing this conserved motif, thereby promoting HBV transcription from its chromatinized genome.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Qiyan Yao
- National Institute of Biological Sciences, Beijing, 102206, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xiaonan Su
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Yafang Deng
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Mo Yang
- National Center for Nanoscience and Technology, Beijing, 100190, China
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyles Str., Frederick, MD, 21702, USA
| | - Bo Peng
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Fan Zhao
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Chao Du
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Xiulan Zhang
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Jinsong Zhu
- National Center for Nanoscience and Technology, Beijing, 100190, China
- Suzhou Puxin Life Science Technology, Ltd, Suzhou, 215124, China
| | - Daliang Wang
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, 100084, China.
| | - Wenhui Li
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China.
| | - Haitao Li
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
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5
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Relevance of HBx for Hepatitis B Virus-Associated Pathogenesis. Int J Mol Sci 2023; 24:ijms24054964. [PMID: 36902395 PMCID: PMC10003785 DOI: 10.3390/ijms24054964] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/20/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
The hepatitis B virus (HBV) counts as a major global health problem, as it presents a significant causative factor for liver-related morbidity and mortality. The development of hepatocellular carcinomas (HCC) as a characteristic of a persistent, chronic infection could be caused, among others, by the pleiotropic function of the viral regulatory protein HBx. The latter is known to modulate an onset of cellular and viral signaling processes with emerging influence in liver pathogenesis. However, the flexible and multifunctional nature of HBx impedes the fundamental understanding of related mechanisms and the development of associated diseases, and has even led to partial controversial results in the past. Based on the cellular distribution of HBx-nuclear-, cytoplasmic- or mitochondria-associated-this review encompasses the current knowledge and previous investigations of HBx in context of cellular signaling pathways and HBV-associated pathogenesis. In addition, particular focus is set on the clinical relevance and potential novel therapeutic applications in the context of HBx.
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6
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He L, Shen H, Deng H, Zhang X, Xu Y, Shi C, Ouyang Z. Identification of critical residues in the regulatory protein HBx for Smc5/6 interaction and hepatitis B virus production. Antiviral Res 2023; 211:105519. [PMID: 36592669 DOI: 10.1016/j.antiviral.2022.105519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/13/2022] [Accepted: 12/28/2022] [Indexed: 01/01/2023]
Abstract
The host structural maintenance of chromosomes 5/6 complex (Smc5/6) is a restriction factor of hepatitis B virus (HBV) that inhibits the transcription of viral ccDNA. HBV antagonizes this restriction by expressing the regulatory X protein (HBx) which targets Smc5/6 for degradation via DNA damage-binding protein 1 (DDB1) E3 ubiquitin ligase. However, the molecular insights into how Smc5/6 interacts with HBx remain elusive. In this study, we systematically investigated the interaction between Smc5/6 and HBx. Smc5/6 interacts with HBx through multiple sites in the absence of DDB1 in the pull-down assay. HBx C-terminal is sufficient for the interaction. Most importantly, residue Phe132, which is strictly conserved in all HBV subtypes, is critical for interaction with Smc5/6 both in vitro and in vivo. Mutation of this site (F132A) results in defect in Smc5/6 interaction, extrachromosomal reporter transcription, and HBV production both in cells and in mouse model. Collectively, our data identifies a key residue on HBx for Smc5/6 interaction and viral production. These results provide valuable information for both basic research and therapeutic drugs targeting HBx.
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Affiliation(s)
- Lili He
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei province, 430030, China
| | - Huanyu Shen
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei province, 430030, China
| | - Hui Deng
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei province, 430030, China
| | - Xiaoyan Zhang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei province, 430030, China
| | - Yang Xu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei province, 430030, China
| | - Chunwei Shi
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei province, 430030, China
| | - Zhuqing Ouyang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei province, 430030, China.
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7
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Le‐Trilling VTK, Banchenko S, Paydar D, Leipe PM, Binting L, Lauer S, Graziadei A, Klingen R, Gotthold C, Bürger J, Bracht T, Sitek B, Jan Lebbink R, Malyshkina A, Mielke T, Rappsilber J, Spahn CMT, Voigt S, Trilling M, Schwefel D. Structural mechanism of CRL4-instructed STAT2 degradation via a novel cytomegaloviral DCAF receptor. EMBO J 2023; 42:e112351. [PMID: 36762436 PMCID: PMC9975947 DOI: 10.15252/embj.2022112351] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 02/11/2023] Open
Abstract
Human cytomegalovirus (CMV) is a ubiquitously distributed pathogen whose rodent counterparts such as mouse and rat CMV serve as common infection models. Here, we conducted global proteome profiling of rat CMV-infected cells and uncovered a pronounced loss of the transcription factor STAT2, which is crucial for antiviral interferon signalling. Via deletion mutagenesis, we found that the viral protein E27 is required for CMV-induced STAT2 depletion. Cellular and in vitro analyses showed that E27 exploits host-cell Cullin4-RING ubiquitin ligase (CRL4) complexes to induce poly-ubiquitylation and proteasomal degradation of STAT2. Cryo-electron microscopy revealed how E27 mimics molecular surface properties of cellular CRL4 substrate receptors called DCAFs (DDB1- and Cullin4-associated factors), thereby displacing them from the catalytic core of CRL4. Moreover, structural analyses showed that E27 recruits STAT2 through a bipartite binding interface, which partially overlaps with the IRF9 binding site. Structure-based mutations in M27, the murine CMV homologue of E27, impair the interferon-suppressing capacity and virus replication in mouse models, supporting the conserved importance of DCAF mimicry for CMV immune evasion.
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Affiliation(s)
| | - Sofia Banchenko
- Institute of Medical Physics and BiophysicsCharité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Darius Paydar
- Institute for VirologyUniversity Hospital Essen, University of Duisburg‐EssenEssenGermany
- Zentrum für KinderpsychiatrieUniversitätsklinik ZürichZürichSwitzerland
| | - Pia Madeleine Leipe
- Institute for VirologyUniversity Hospital Essen, University of Duisburg‐EssenEssenGermany
| | - Lukas Binting
- Institute of Medical Physics and BiophysicsCharité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Simon Lauer
- Institute of Medical Physics and BiophysicsCharité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Andrea Graziadei
- Bioanalytics Unit, Institute of BiotechnologyTechnische Universität BerlinBerlinGermany
| | - Robin Klingen
- Institute for VirologyUniversity Hospital Essen, University of Duisburg‐EssenEssenGermany
| | - Christine Gotthold
- Institute of Medical Physics and BiophysicsCharité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Jörg Bürger
- Institute of Medical Physics and BiophysicsCharité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- Microscopy and Cryo‐Electron Microscopy Service GroupMax‐Planck‐Institute for Molecular GeneticsBerlinGermany
| | - Thilo Bracht
- Medizinisches Proteom‐CenterRuhr‐University BochumBochumGermany
- Department of Anesthesia, Intensive Care Medicine and Pain TherapyUniversity Hospital Knappschaftskrankenhaus BochumBochumGermany
| | - Barbara Sitek
- Medizinisches Proteom‐CenterRuhr‐University BochumBochumGermany
- Department of Anesthesia, Intensive Care Medicine and Pain TherapyUniversity Hospital Knappschaftskrankenhaus BochumBochumGermany
| | - Robert Jan Lebbink
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Anna Malyshkina
- Institute for VirologyUniversity Hospital Essen, University of Duisburg‐EssenEssenGermany
| | - Thorsten Mielke
- Microscopy and Cryo‐Electron Microscopy Service GroupMax‐Planck‐Institute for Molecular GeneticsBerlinGermany
| | - Juri Rappsilber
- Bioanalytics Unit, Institute of BiotechnologyTechnische Universität BerlinBerlinGermany
- Wellcome Centre for Cell BiologyUniversity of EdinburghEdinburghUK
| | - Christian MT Spahn
- Institute of Medical Physics and BiophysicsCharité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Sebastian Voigt
- Institute for VirologyUniversity Hospital Essen, University of Duisburg‐EssenEssenGermany
| | - Mirko Trilling
- Institute for VirologyUniversity Hospital Essen, University of Duisburg‐EssenEssenGermany
| | - David Schwefel
- Institute of Medical Physics and BiophysicsCharité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
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8
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Pregenomic RNA Launch Hepatitis B Virus Replication System Facilitates the Mechanistic Study of Antiviral Agents and Drug-Resistant Variants on Covalently Closed Circular DNA Synthesis. J Virol 2022; 96:e0115022. [PMID: 36448800 PMCID: PMC9769369 DOI: 10.1128/jvi.01150-22] [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: 12/05/2022] Open
Abstract
Hepatitis B virus (HBV) replicates its genomic DNA by reverse transcription of an RNA intermediate, termed pregenomic RNA (pgRNA), within nucleocapsid. It had been shown that transfection of in vitro-transcribed pgRNA initiated viral replication in human hepatoma cells. We demonstrated here that viral capsids, single-stranded DNA, relaxed circular DNA (rcDNA) and covalently closed circular DNA (cccDNA) became detectable sequentially at 3, 6, 12, and 24 h post-pgRNA transfection into Huh7.5 cells. The levels of viral DNA replication intermediates and cccDNA peaked at 24 and 48 h post-pgRNA transfection, respectively. HBV surface antigen (HBsAg) became detectable in culture medium at day 4 posttransfection. Interestingly, the early robust viral DNA replication and cccDNA synthesis did not depend on the expression of HBV X protein (HBx), whereas HBsAg production was strictly dependent on viral DNA replication and expression of HBx, consistent with the essential role of HBx in the transcriptional activation of cccDNA minichromosomes. While the robust and synchronized HBV replication within 48 h post-pgRNA transfection is particularly suitable for the precise mapping of the HBV replication steps, from capsid assembly to cccDNA formation, targeted by distinct antiviral agents, the treatment of cells starting at 48 h post-pgRNA transfection allows the assessment of antiviral agents on mature nucleocapsid uncoating, cccDNA synthesis, and transcription, as well as viral RNA stability. Moreover, the pgRNA launch system could be used to readily assess the impacts of drug-resistant variants on cccDNA formation and other replication steps in the viral life cycle. IMPORTANCE Hepadnaviral pgRNA not only serves as a template for reverse transcriptional replication of viral DNA but also expresses core protein and DNA polymerase to support viral genome replication and cccDNA synthesis. Not surprisingly, cytoplasmic expression of duck hepatitis B virus pgRNA initiated viral replication leading to infectious virion secretion. However, HBV replication and antiviral mechanism were studied primarily in human hepatoma cells transiently or stably transfected with plasmid-based HBV replicons. The presence of large amounts of transfected HBV DNA or transgenes in cellular chromosomes hampered the robust analyses of HBV replication and cccDNA function. As demonstrated here, the pgRNA launch HBV replication system permits the accurate mapping of antiviral target and investigation of cccDNA biosynthesis and transcription using secreted HBsAg as a convenient quantitative marker. The effect of drug-resistant variants on viral capsid assembly, genome replication, and cccDNA biosynthesis and function can also be assessed using this system.
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Zhang M, Li L, Wu L, Zhang J. Isarubrolone C Promotes Autophagic Degradation of Virus Proteins via Activating ATG10S in HepG2 Cells. JOURNAL OF NATURAL PRODUCTS 2022; 85:1018-1028. [PMID: 35201775 DOI: 10.1021/acs.jnatprod.1c01161] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Isarubrolone C is a bioactive polycyclic tropoloalkaloid from Streptomyces. Our previous study showed that isarubrolone C could trigger autophagy. Here, we report isarubrolone C potential in broad-spectrum antiviral effect and its antiviral mechanism in vitro. Our results show that isarubrolone C activated autophagy and reduced levels of viral proteins in the cells harboring HCV-CORE/NS5B, HBx, ZIKV-NS5, and HIV-RT, respectively. The role of isarubrolone C in suppression of the viral proteins was via an autophagic degradation pathway rather than a proteasome pathway. Co-immunoprecipitation assays revealed that isarubrolone C promoted both autophagy flux opening and the viral proteins being enwrapped in autolysosomes. PCR assays showed that isarubrolone C elevated the transcription levels of ATG10/ATG10S and IL28A. Further, ATG10S high expression could efficiently enhance IL28A expression and the ability of isarubrolone C to degrade the viral proteins by promoting the colocalization of viral proteins with autolysosomes. Additionally, knockdown of endogenous IL28A caused both losses of the isarubrolone C antiviral effect and autolysosome formation. These results indicate that the role of isarubrolone C antiviruses is achieved by triggering the autophagic mechanism, which is mediated by endogenous ATG10S and IL28A activation. This is the first report about isarubrolone C potential of in vitro broad-spectrum antiviruses.
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Affiliation(s)
- Miaoqing Zhang
- Key Laboratory of Biotechnology of Antibiotics, the National Health Commission (NHC), Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Linli Li
- Key Laboratory of Biotechnology of Antibiotics, the National Health Commission (NHC), Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Linzhuan Wu
- Key Laboratory of Biotechnology of Antibiotics, the National Health Commission (NHC), Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jingpu Zhang
- Key Laboratory of Biotechnology of Antibiotics, the National Health Commission (NHC), Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
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10
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Ueda C, Langton M, Chen J, Pandelia ME. The HBx protein from hepatitis B virus coordinates a redox-active Fe-S cluster. J Biol Chem 2022; 298:101698. [PMID: 35148994 PMCID: PMC9010755 DOI: 10.1016/j.jbc.2022.101698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 12/17/2022] Open
Abstract
The viral protein HBx is the key regulatory factor of the hepatitis B virus (HBV) and the main etiology for HBV-associated liver diseases, such as cirrhosis and hepatocellular carcinoma. Historically, HBx has defied biochemical and structural characterization, deterring efforts to understand its molecular mechanisms. Here we show that soluble HBx fused to solubility tags copurifies with either a [2Fe-2S] or a [4Fe-4S] cluster, a feature that is shared among five HBV genotypes. We show that the O2-stable [2Fe-2S] cluster form converts to an O2-sensitive [4Fe-4S] state when reacted with chemical reductants, a transformation that is best described by a reductive coupling mechanism reminiscent of Fe-S cluster scaffold proteins. In addition, the Fe-S cluster conversions are partially reversible in successive reduction-oxidation cycles, with cluster loss mainly occurring during (re)oxidation. The considerably negative reduction potential of the [4Fe-4S]2+/1+ couple (-520 mV) suggests that electron transfer may not be likely in the cell. Collectively, our findings identify HBx as an Fe-S protein with striking similarities to Fe-S scaffold proteins both in cluster type and reductive transformation. An Fe-S cluster in HBx offers new insights into its previously unknown molecular properties and sets the stage for deciphering the roles of HBx-associated iron (mis)regulation and reactive oxygen species in the context of liver tumorigenesis.
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Affiliation(s)
- Chie Ueda
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
| | - Michelle Langton
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
| | - Jiahua Chen
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
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11
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Nečasová I, Stojaspal M, Motyčáková E, Brom T, Janovič T, Hofr C. Transcriptional regulators of human oncoviruses: structural and functional implications for anticancer therapy. NAR Cancer 2022; 4:zcac005. [PMID: 35252867 PMCID: PMC8892037 DOI: 10.1093/narcan/zcac005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 02/04/2022] [Accepted: 02/15/2022] [Indexed: 11/26/2022] Open
Abstract
Transcription is often the first biosynthetic event of viral infection. Viruses produce preferentially viral transcriptional regulators (vTRs) essential for expressing viral genes and regulating essential host cell proteins to enable viral genome replication. As vTRs are unique viral proteins that promote the transcription of viral nucleic acid, vTRs interact with host proteins to suppress detection and immune reactions to viral infection. Thus, vTRs are promising therapeutic targets that are sequentially and structurally distinct from host cell proteins. Here, we review vTRs of three human oncoviruses: HBx of hepatitis B virus, HBZ of human T-lymphotropic virus type 1, and Rta of Epstein–Barr virus. We present three cunningly exciting and dangerous transcription strategies that make viral infections so efficient. We use available structural and functional knowledge to critically examine the potential of vTRs as new antiviral-anticancer therapy targets. For each oncovirus, we describe (i) the strategy of viral genome transcription; (ii) vTRs’ structure and binding partners essential for transcription regulation; and (iii) advantages and challenges of vTR targeting in antiviral therapies. We discuss the implications of vTR regulation for oncogenesis and perspectives on developing novel antiviral and anticancer strategies.
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Affiliation(s)
- Ivona Nečasová
- Institute of Biophysics of the Czech Academy of Sciences, Scientific Incubator, Královopolská 135, Brno 612 65, Czech Republic
| | - Martin Stojaspal
- Institute of Biophysics of the Czech Academy of Sciences, Scientific Incubator, Královopolská 135, Brno 612 65, Czech Republic
| | - Edita Motyčáková
- Institute of Biophysics of the Czech Academy of Sciences, Scientific Incubator, Královopolská 135, Brno 612 65, Czech Republic
| | - Tomáš Brom
- LifeB, Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Tomáš Janovič
- LifeB, Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Ctirad Hofr
- Institute of Biophysics of the Czech Academy of Sciences, Scientific Incubator, Královopolská 135, Brno 612 65, Czech Republic
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12
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Lin Y, Gross ML. Mass Spectrometry-Based Structural Proteomics for Metal Ion/Protein Binding Studies. Biomolecules 2022; 12:135. [PMID: 35053283 PMCID: PMC8773722 DOI: 10.3390/biom12010135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 01/01/2023] Open
Abstract
Metal ions are critical for the biological and physiological functions of many proteins. Mass spectrometry (MS)-based structural proteomics is an ever-growing field that has been adopted to study protein and metal ion interactions. Native MS offers information on metal binding and its stoichiometry. Footprinting approaches coupled with MS, including hydrogen/deuterium exchange (HDX), "fast photochemical oxidation of proteins" (FPOP) and targeted amino-acid labeling, identify binding sites and regions undergoing conformational changes. MS-based titration methods, including "protein-ligand interactions by mass spectrometry, titration and HD exchange" (PLIMSTEX) and "ligand titration, fast photochemical oxidation of proteins and mass spectrometry" (LITPOMS), afford binding stoichiometry, binding affinity, and binding order. These MS-based structural proteomics approaches, their applications to answer questions regarding metal ion protein interactions, their limitations, and recent and potential improvements are discussed here. This review serves as a demonstration of the capabilities of these tools and as an introduction to wider applications to solve other questions.
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Affiliation(s)
- Yanchun Lin
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
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13
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Wagner ND, Liu H, Rohrs HW, Amarasinghe GK, Gross ML, Leung DW. Nipah Virus V Protein Binding Alters MDA5 Helicase Folding Dynamics. ACS Infect Dis 2022; 8:118-128. [PMID: 35026950 PMCID: PMC8762660 DOI: 10.1021/acsinfecdis.1c00403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nipah virus (NiV) is an emerging and deadly zoonotic paramyxovirus that is responsible for periodic epidemics of acute respiratory illness and encephalitis in humans. Previous studies have shown that the NiV V protein antagonizes host antiviral immunity, but the molecular mechanism is incompletely understood. To address this gap, we biochemically characterized NiV V binding to the host pattern recognition receptor MDA5. We find that the C-terminal domain of NiV V (VCTD) is sufficient to bind the MDA5SF2 domain when recombinantly co-expressed in bacteria. Analysis by hydrogen-deuterium exchange mass spectrometry (HDX-MS) studies revealed that NiV VCTD is conformationally dynamic, and binding to MDA5 reduces the dynamics of VCTD. Our results also suggest that the β-sheet region in between the MDA5 Hel1, Hel2, and Hel2i domains exhibits rapid HDX. Upon VCTD binding, these β-sheet and adjacent residues show significant protection. Collectively, our findings suggest that NiV V binding disrupts the helicase fold and dynamics of MDA5 to antagonize host antiviral immunity.
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Affiliation(s)
- Nicole D. Wagner
- Division of Infectious Diseases, John T. Milliken Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Hejun Liu
- Division of Infectious Diseases, John T. Milliken Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Henry W. Rohrs
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Gaya K. Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Daisy W. Leung
- Division of Infectious Diseases, John T. Milliken Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
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14
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Canonical and Divergent N-Terminal HBx Isoform Proteins Unveiled: Characteristics and Roles during HBV Replication. Biomedicines 2021; 9:biomedicines9111701. [PMID: 34829930 PMCID: PMC8616016 DOI: 10.3390/biomedicines9111701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 11/16/2022] Open
Abstract
Hepatitis B virus (HBV) X protein (HBx) is a viral regulatory and multifunctional protein. It is well-known that the canonical HBx reading frame bears two phylogenetically conserved internal in-frame translational initiation codons at Met2 and Met3, thus possibly generating divergent N-terminal smaller isoforms during translation. Here, we demonstrate that the three distinct HBx isoforms are generated from the ectopically expressed HBV HBx gene, named XF (full-length), XM (medium-length), and XS (short-length); they display different subcellular localizations when expressed individually in cultured hepatoma cells. Particularly, the smallest HBx isoform, XS, displayed a predominantly cytoplasmic localization. To study HBx proteins during viral replication, we performed site-directed mutagenesis to target the individual or combinatorial expression of the HBx isoforms within the HBV viral backbone (full viral genome). Our results indicate that of all HBx isoforms, only the smallest HBx isoform, XS, can restore WT levels of HBV replication, and bind to the viral mini chromosome, thereby establishing an active chromatin state, highlighting its crucial activities during HBV replication. Intriguingly, we found that sequences of HBV HBx genotype H are devoid of the conserved Met3 position, and therefore HBV genotype H infection is naturally silent for the expression of the HBx XS isoform. Finally, we found that the HBx XM (medium-length) isoform shares significant sequence similarity with the N-terminus domain of the COMMD8 protein, a member of the copper metabolism MURR1 domain-containing (COMMD) protein family. This novel finding might facilitate studies on the phylogenetic origin of the HBV X protein. The identification and functional characterization of its isoforms will shift the paradigm by changing the concept of HBx from being a unique, canonical, and multifunctional protein toward the occurrence of different HBx isoforms, carrying out different overlapping functions at different subcellular localizations during HBV genome replication. Significantly, our current work unveils new crucial HBV targets to study for potential antiviral research, and human virus pathogenesis.
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15
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Yue L, Li C, Xu M, Wu M, Ding J, Liu J, Zhang X, Yuan Z. Probing the spatiotemporal patterns of HBV multiplication reveals novel features of its subcellular processes. PLoS Pathog 2021; 17:e1009838. [PMID: 34370796 PMCID: PMC8376071 DOI: 10.1371/journal.ppat.1009838] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 08/19/2021] [Accepted: 07/25/2021] [Indexed: 02/06/2023] Open
Abstract
Through evolution, Hepatitis B Virus (HBV) developed highly intricate mechanisms exploiting host resources for its multiplication within a constrained genetic coding capacity. Yet a clear picture of viral hitchhiking of cellular processes with spatial resolution is still largely unsolved. Here, by leveraging bDNA-based fluorescence in situ hybridization (FISH) combined with immunofluorescence, we developed a microscopic approach for multiplex detection of viral nucleic acids and proteins, which enabled us to probe some of the key aspects of HBV life cycle. We confirmed the slow kinetics and revealed the high variability of viral replication at single-cell level. We directly visualized HBV minichromosome in contact with acetylated histone 3 and RNA polymerase II and observed HBV-induced degradation of Smc5/6 complex only in primary hepatocytes. We quantified the frequency of HBV pregenomic RNAs occupied by translating ribosome or capsids. Statistics at molecular level suggested a rapid translation phase followed by a slow encapsidation and maturation phase. Finally, the roles of microtubules (MTs) on nucleocapsid assembly and virion morphogenesis were analyzed. Disruption of MTs resulted in the perinuclear retention of nucleocapsid. Meanwhile, large multivesicular body (MVB) formation was significantly disturbed as evidenced by the increase in number and decrease in volume of CD63+ vesicles, thus inhibiting mature virion secretion. In conclusion, these data provided spatially resolved molecular snapshots in the context of specific subcellular activities. The heterogeneity observed at single-cell level afforded valuable molecular insights which are otherwise unavailable from bulk measurements. HBV is a hepatotropic, enveloped virus with a partially double-stranded relaxed circular DNA genome. Studies on the molecular biology of HBV mainly rely on biochemical extraction and bulk quantification methods. Detailed spatiotemporal information on virus components in subcellular context is still lacking. Here, we re-evaluated the reproduction schemes of HBV by fluorescence in situ hybridization (FISH). We visualized cccDNA minichromosome formation in an epigenetic context, identified pgRNA associated with actively translating ribosomes and capsids. Moreover, the active participation of microtubules in nucleocapsid transport and MVB-mediated virion secretion was identified. These observations have broad implications for understanding the HBV replication cycle and may facilitate the identification of novel antiviral targets.
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Affiliation(s)
- Lei Yue
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- Research Unit, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Chang Li
- Research Unit, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Mingzhu Xu
- Research Unit, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Min Wu
- Research Unit, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jiahui Ding
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiangxia Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaonan Zhang
- Research Unit, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, ACT, Australia
- * E-mail: (XZ); (ZY)
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- Research Unit, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- * E-mail: (XZ); (ZY)
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16
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Wagner ND, Huang Y, Liu T, Gross ML. Post-HDX Deglycosylation of Fc Gamma Receptor IIIa Glycoprotein Enables HDX Characterization of Its Binding Interface with IgG. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1638-1643. [PMID: 33625217 PMCID: PMC8906513 DOI: 10.1021/jasms.1c00003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Protein glycosylation is a common and highly heterogeneous post-translational modification that challenges biophysical characterization technologies. The heterogeneity of glycoproteins makes their structural analysis difficult; in particular, hydrogen-deuterium exchange mass spectrometry (HDX-MS) often suffers from poor sequence coverage near the glycosylation site. A pertinent example is the Fc gamma receptor RIIIa (FcγRIIIa, CD16a), a glycoprotein expressed on the surface of natural killer cells (NK) that binds the Fc domain of IgG antibodies as a trigger for antibody-dependent cell-mediated cytotoxicity (ADCC). Here, we describe an adaptation of a previously reported method using PNGase A for post-HDX deglycosylation to characterize the binding between the highly glycosylated CD16a and IgG1. Upon optimization of the method to improve sequence coverage while minimizing back-exchange, we achieved coverage of four of the five glycosylation sites of CD16a. Despite some back-exchange, trends in HDX are consistent with previously reported CD16a/IgG-Fc complex structures; furthermore, binding of peptides covering the glycosylated asparagine-164 can be interrogated when using this protocol, previously not seen using standard HDX-MS.
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Affiliation(s)
- Nicole D. Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130 United States
| | - Yining Huang
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285 United States
- Corresponding Authors: ,
| | - Tun Liu
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285 United States
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130 United States
- Corresponding Authors: ,
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17
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Hepatitis B virus X protein and its host partners. Cell Mol Immunol 2021; 18:1345-1346. [PMID: 33846566 PMCID: PMC8040755 DOI: 10.1038/s41423-021-00674-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/06/2021] [Indexed: 12/16/2022] Open
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18
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Affiliation(s)
- Tobias
P. Wörner
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Tatiana M. Shamorkina
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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19
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Han N, Yan L, Wang X, Sun X, Huang F, Tang H. An updated literature review: how HBV X protein regulates the propagation of the HBV. Future Virol 2020. [DOI: 10.2217/fvl-2020-0251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chronic HBV infection constitutes a burden on human beings and is closely associated with hepatocellular carcinoma. The propagation of the HBV is determined by many factors, and the HBV X protein (HBx) could have a significant influence on this. HBx is a regulatory protein that can directly or indirectly interact with many cellular proteins to affect both the propagation of the HBV and the activity of the host cells. In this review, we summarized the possible mechanisms by which HBx regulates HBV replication at transcriptional and post-transcriptional levels in various experimental systems.
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Affiliation(s)
- Ning Han
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, PR China
| | - Libo Yan
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, PR China
| | - Xueer Wang
- Department of Forensic Pathology, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan, PR China
| | - Xuehong Sun
- Department of Forensic Pathology, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan, PR China
| | - Feijun Huang
- Department of Forensic Pathology, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan, PR China
| | - Hong Tang
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, PR China
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20
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Tsukuda S, Watashi K. Hepatitis B virus biology and life cycle. Antiviral Res 2020; 182:104925. [PMID: 32866519 DOI: 10.1016/j.antiviral.2020.104925] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/24/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022]
Abstract
Hepatitis B virus (HBV) specifically infects hepatocytes and causes severe liver diseases. The HBV life cycle is unique in that the genomic DNA (relaxed-circular partially double-stranded DNA: rcDNA) is converted to a molecular template DNA (covalently closed circular DNA: cccDNA) to amplify a viral RNA intermediate, which is then reverse-transcribed back to viral DNA. The highly stable characteristics of cccDNA result in chronic infection and a poor rate of cure. This complex life cycle of HBV offers a variety of targets to develop antiviral agents. We provide here an update on the current knowledge of HBV biology and its life cycle, which may help to identify new antiviral targets.
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Affiliation(s)
- Senko Tsukuda
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan; Department of Applied Biological Science, Tokyo University of Science, Noda, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan; MIRAI, JST, Saitama, Japan.
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21
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Wang Z, Wang W, Wang L. Epigenetic regulation of covalently closed circular DNA minichromosome in hepatitis B virus infection. BIOPHYSICS REPORTS 2020. [DOI: 10.1007/s41048-020-00112-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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22
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Langton M, Pandelia ME. Hepatitis B Virus Oncoprotein HBx Is Not an ATPase. ACS OMEGA 2020; 5:16772-16778. [PMID: 32685845 PMCID: PMC7364715 DOI: 10.1021/acsomega.0c01762] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
HBx is the smallest gene product of the Hepatitis B virus (HBV) and an oncogenic stimulus in chronic infections leading to liver disease. HBx interacts and interferes with numerous cellular processes, but its modes of action remain poorly understood. It has been invoked that HBx employs nucleotide hydrolysis to regulate molecular pathways or protein-protein interactions. In the present study, we reinvestigate the (d)NTP hydrolysis of recombinant HBx to explore its potential as a biochemical probe for antiviral studies. For our investigations, we employed existing soluble constructs (i.e., GST-HBx, MBP-HBx) and engineered new fusion proteins (i.e., DsbC-HBx, NusA-HBx), which are shown to serve as better systems for in vitro research. We performed mutational scanning of the computationally predicted NTP-binding domain, which includes residues associated with clinical cases. Steady-state and end-point activity assays, in tandem with mass-spectrometric analyses, reveal that the observed hydrolysis of all alleged HBx substrates, ATP, dATP, and GTP, is contingent on the presence of the GroEL chaperone, which preferentially copurifies as a contaminant with GST-HBx and MBP-HBx. Collectively, our findings provide new technical standards for recombinant HBx studies and reveal that nucleotide hydrolysis is not an operant mechanism by which HBx contributes to viral HBV carcinogenesis.
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23
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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24
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Cheng M, Asuru A, Kiselar J, Mathai G, Chance MR, Gross ML. Fast Protein Footprinting by X-ray Mediated Radical Trifluoromethylation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1019-1024. [PMID: 32255631 PMCID: PMC7486011 DOI: 10.1021/jasms.0c00085] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Synchrotron radiolysis generates hydroxyl radicals (•OH) that are successful footprinting reagents. Here, we describe a new reagent for the synchrotron platform, the trifluoromethyl radical (•CF3). The radical is produced by •OH displacement of •CF3 from sodium triflinate (Langlois reagent). Upon X-ray beam exposure, the reagent labels proteins extensively without any additional chemicals on a millisecond or shorter time scale. The •CF3 is comparably reactive to •OH and produces footprinting information that complements that of •OH alone. This reagent in combination with •OH should enable novel chemistry for protein footprinting on the synchrotron platform.
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Affiliation(s)
- Ming Cheng
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Awuri Asuru
- Center for Proteomics & Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Janna Kiselar
- Center for Proteomics & Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - George Mathai
- Department of Chemistry, Sacred Heart College, Thevara, Kochi, Kerala 682013, India
| | - Mark R. Chance
- Center for Proteomics & Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
- Corresponding Authors: MLG: Tel: (314)935-4814. Fax: (314)935-7484. , MRC: Phone: (216) 368-4406. Fax: (216) 368-3812.
| | - Michael L. Gross
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
- Corresponding Authors: MLG: Tel: (314)935-4814. Fax: (314)935-7484. , MRC: Phone: (216) 368-4406. Fax: (216) 368-3812.
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25
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HBV X protein mutations affect HBV transcription and association of histone-modifying enzymes with covalently closed circular DNA. Sci Rep 2020; 10:802. [PMID: 31964944 PMCID: PMC6972884 DOI: 10.1038/s41598-020-57637-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/24/2019] [Indexed: 12/13/2022] Open
Abstract
The hepatitis B X protein (HBx) plays a role in the epigenetic regulation of hepatitis B virus (HBV) replication. This study investigated the effects of HBx mutations on HBV transcription and the recruitment of HBx, histone acetyl-transferase P300 and histone deacetylase 1 (HDAC1) to circularized HBV DNA (which resembles covalently closed circular DNA [cccDNA]). Compared with wild type, majority of mutants had lower levels of intracellular HBV RNA (44–77% reduction) and secretory HBsAg (25–81% reduction), and 12 mutants had a reduction in intracellular encapsidated HBV DNA (33–64% reduction). Eight mutants with >70% reduction in HBV RNA and/or HBsAg were selected for chromatin immunoprecipitation analysis. Four HBx mutants with mutations in amino acid residues 55–60 and 121–126 had a lower degree of HBx-cccDNA association than wild type HBx (mean % input: 0.02–0.64% vs. 3.08% in wild type). A reduced association between cccDNA and P300 (mean % input: 0.69–1.81% vs. 3.48% in wild type) and an augmented association with HDAC1 (mean % input: 4.01–14.0% vs. 1.53% in wild type) were detected. HBx amino acid residues 55–60 and 121–126 may play an important role in HBV transcription regulation, via their impeded interaction with cccDNA and altered recruitment of histone modifying enzymes to cccDNA.
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Spatiotemporal Analysis of Hepatitis B Virus X Protein in Primary Human Hepatocytes. J Virol 2019; 93:JVI.00248-19. [PMID: 31167911 PMCID: PMC6675897 DOI: 10.1128/jvi.00248-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/28/2019] [Indexed: 12/18/2022] Open
Abstract
Hepatitis B virus X protein (HBx) is a promising drug target since it promotes the degradation of the host structural maintenance of chromosomes 5/6 complex (Smc5/6) that inhibits HBV transcription. To date, it has not been possible to study HBx in physiologically relevant cell culture systems due to the lack of a highly specific and selective HBx antibody. In this study, we developed a novel monoclonal HBx antibody and performed a spatiotemporal analysis of HBx in a natural infection system. This revealed that HBx localizes to the nucleus of infected cells, is expressed shortly after infection, and has a short half-life. In addition, we demonstrated that inhibiting HBx expression or function promotes the reappearance of Smc6 in the nucleus of infected cells. These data provide new insights into HBx and underscore its potential as a novel target for the treatment of chronic HBV infection. The structural maintenance of chromosomes 5/6 complex (Smc5/6) is a host restriction factor that suppresses hepatitis B virus (HBV) transcription. HBV counters this restriction by expressing the X protein (HBx), which redirects the host DNA damage-binding protein 1 (DDB1) E3 ubiquitin ligase to target Smc5/6 for degradation. HBx is an attractive therapeutic target for the treatment of chronic hepatitis B (CHB), but it is challenging to study this important viral protein in the context of natural infection due to the lack of a highly specific and sensitive HBx antibody. In this study, we developed a novel monoclonal antibody that enables detection of HBx protein in HBV-infected primary human hepatocytes (PHH) by Western blotting and immunofluorescence. Confocal imaging studies with this antibody demonstrated that HBx is predominantly located in the nucleus of HBV-infected PHH, where it exhibits a diffuse staining pattern. In contrast, a DDB1-binding-deficient HBx mutant was detected in both the cytoplasm and nucleus, suggesting that the DDB1 interaction plays an important role in the nuclear localization of HBx. Our study also revealed that HBx is expressed early after infection and has a short half-life (∼3 h) in HBV-infected PHH. In addition, we found that treatment with small interfering RNAs (siRNAs) that target DDB1 or HBx mRNA decreased HBx protein levels and led to the reappearance of Smc6 in the nuclei of HBV-infected PHH. Collectively, these studies provide the first spatiotemporal analysis of HBx in a natural infection system and also suggest that HBV transcriptional silencing by Smc5/6 can be restored by therapeutic targeting of HBx. IMPORTANCE Hepatitis B virus X protein (HBx) is a promising drug target since it promotes the degradation of the host structural maintenance of chromosomes 5/6 complex (Smc5/6) that inhibits HBV transcription. To date, it has not been possible to study HBx in physiologically relevant cell culture systems due to the lack of a highly specific and selective HBx antibody. In this study, we developed a novel monoclonal HBx antibody and performed a spatiotemporal analysis of HBx in a natural infection system. This revealed that HBx localizes to the nucleus of infected cells, is expressed shortly after infection, and has a short half-life. In addition, we demonstrated that inhibiting HBx expression or function promotes the reappearance of Smc6 in the nucleus of infected cells. These data provide new insights into HBx and underscore its potential as a novel target for the treatment of chronic HBV infection.
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