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Versini R, Sritharan S, Aykac Fas B, Tubiana T, Aimeur SZ, Henri J, Erard M, Nüsse O, Andreani J, Baaden M, Fuchs P, Galochkina T, Chatzigoulas A, Cournia Z, Santuz H, Sacquin-Mora S, Taly A. A Perspective on the Prospective Use of AI in Protein Structure Prediction. J Chem Inf Model 2024; 64:26-41. [PMID: 38124369 DOI: 10.1021/acs.jcim.3c01361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
AlphaFold2 (AF2) and RoseTTaFold (RF) have revolutionized structural biology, serving as highly reliable and effective methods for predicting protein structures. This article explores their impact and limitations, focusing on their integration into experimental pipelines and their application in diverse protein classes, including membrane proteins, intrinsically disordered proteins (IDPs), and oligomers. In experimental pipelines, AF2 models help X-ray crystallography in resolving the phase problem, while complementarity with mass spectrometry and NMR data enhances structure determination and protein flexibility prediction. Predicting the structure of membrane proteins remains challenging for both AF2 and RF due to difficulties in capturing conformational ensembles and interactions with the membrane. Improvements in incorporating membrane-specific features and predicting the structural effect of mutations are crucial. For intrinsically disordered proteins, AF2's confidence score (pLDDT) serves as a competitive disorder predictor, but integrative approaches including molecular dynamics (MD) simulations or hydrophobic cluster analyses are advocated for accurate dynamics representation. AF2 and RF show promising results for oligomeric models, outperforming traditional docking methods, with AlphaFold-Multimer showing improved performance. However, some caveats remain in particular for membrane proteins. Real-life examples demonstrate AF2's predictive capabilities in unknown protein structures, but models should be evaluated for their agreement with experimental data. Furthermore, AF2 models can be used complementarily with MD simulations. In this Perspective, we propose a "wish list" for improving deep-learning-based protein folding prediction models, including using experimental data as constraints and modifying models with binding partners or post-translational modifications. Additionally, a meta-tool for ranking and suggesting composite models is suggested, driving future advancements in this rapidly evolving field.
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Affiliation(s)
- Raphaelle Versini
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Sujith Sritharan
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Burcu Aykac Fas
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Thibault Tubiana
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Sana Zineb Aimeur
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Julien Henri
- Sorbonne Université, CNRS, Laboratoire de Biologie, Computationnelle et Quantitative UMR 7238, Institut de Biologie Paris-Seine, 4 Place Jussieu, F-75005 Paris, France
| | - Marie Erard
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Oliver Nüsse
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Jessica Andreani
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Patrick Fuchs
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
- Université de Paris, UFR Sciences du Vivant, 75013 Paris, France
| | - Tatiana Galochkina
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
| | - Alexios Chatzigoulas
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Hubert Santuz
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Antoine Taly
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
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Pierce DM, Buchanan FJT, Macrae FL, Mills JT, Cox A, Abualsaoud KM, Ward JC, Ariëns RAS, Harris M, Stonehouse NJ, Herod MR. Thrombin cleavage of the hepatitis E virus polyprotein at multiple conserved locations is required for genome replication. PLoS Pathog 2023; 19:e1011529. [PMID: 37478143 PMCID: PMC10395923 DOI: 10.1371/journal.ppat.1011529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 07/03/2023] [Indexed: 07/23/2023] Open
Abstract
The genomes of positive-sense RNA viruses encode polyproteins that are essential for mediating viral replication. These viral polyproteins must undergo proteolysis (also termed polyprotein processing) to generate functional protein units. This proteolysis can be performed by virally-encoded proteases as well as host cellular proteases, and is generally believed to be a key step in regulating viral replication. Hepatitis E virus (HEV) is a leading cause of acute viral hepatitis. The positive-sense RNA genome is translated to generate a polyprotein, termed pORF1, which is necessary and sufficient for viral genome replication. However, the mechanism of polyprotein processing in HEV remains to be determined. In this study, we aimed to understand processing of this polyprotein and its role in viral replication using a combination of in vitro translation experiments and HEV sub-genomic replicons. Our data suggest no evidence for a virally-encoded protease or auto-proteolytic activity, as in vitro translation predominantly generates unprocessed viral polyprotein precursors. However, seven cleavage sites within the polyprotein (suggested by bioinformatic analysis) are susceptible to the host cellular protease, thrombin. Using two sub-genomic replicon systems, we demonstrate that mutagenesis of these sites prevents replication, as does pharmacological inhibition of serine proteases including thrombin. Overall, our data supports a model where HEV uses host proteases to support replication and could have evolved to be independent of a virally-encoded protease for polyprotein processing.
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Affiliation(s)
- Danielle M Pierce
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Frazer J T Buchanan
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Fraser L Macrae
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Jake T Mills
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Abigail Cox
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Khadijah M Abualsaoud
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- Department of Laboratory and Blood Bank, Al Mikhwah General Hospital, Al Mikhwah, Saudi Arabia
| | - Joseph C Ward
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Robert A S Ariëns
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Nicola J Stonehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Morgan R Herod
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
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Ju X, Yu Y, Ren W, Dong L, Meng X, Deng H, Nan Y, Ding Q. The PRMT5/WDR77 complex restricts hepatitis E virus replication. PLoS Pathog 2023; 19:e1011434. [PMID: 37276230 PMCID: PMC10270597 DOI: 10.1371/journal.ppat.1011434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 06/15/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023] Open
Abstract
Hepatitis E virus (HEV) is one of the main pathogenic agents of acute hepatitis in the world. The mechanism of HEV replication, especially host factors governing HEV replication is still not clear. Here, using HEV ORF1 trans-complementation cell culture system and HEV replicon system, combining with stable isotope labelling with amino acids in cell culture (SILAC) and mass spectrometry (MS), we aimed to identify the host factors regulating HEV replication. We identified a diversity of host factors associated with HEV ORF1 protein, which were putatively responsible for viral genomic RNA replication, in these two cell culture models. Of note, the protein arginine methyltransferase 5 (PRMT5)/WDR77 complex was identified in both cell culture models as the top hit. Furthermore, we demonstrated that PRMT5 and WDR77 can specifically inhibit HEV replication, but not other viruses such as HCV or SARS-CoV-2, and this inhibition is conserved among different HEV strains and genotypes. Mechanistically, PRMT5/WDR77 can catalyse methylation of ORF1 on its R458, impairing its replicase activity, and virus bearing R458K mutation in ORF1 relieves the restriction of PRMT5/WDR77 accordingly. Taken together, our study promotes more comprehensive understanding of viral infections but also provides therapeutic targets for intervention.
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Affiliation(s)
- Xiaohui Ju
- School of Medicine, Tsinghua University, Beijing, China
| | - Yanying Yu
- School of Medicine, Tsinghua University, Beijing, China
| | - Wenlin Ren
- School of Medicine, Tsinghua University, Beijing, China
| | - Lin Dong
- School of Medicine, Tsinghua University, Beijing, China
| | - Xianbin Meng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Haiteng Deng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuchen Nan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Qiang Ding
- School of Medicine, Tsinghua University, Beijing, China
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LeDesma R, Heller B, Biswas A, Maya S, Gili S, Higgins J, Ploss A. Structural features stabilized by divalent cation coordination within hepatitis E virus ORF1 are critical for viral replication. eLife 2023; 12:e80529. [PMID: 36852909 PMCID: PMC9977285 DOI: 10.7554/elife.80529] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 02/12/2023] [Indexed: 03/01/2023] Open
Abstract
Hepatitis E virus (HEV) is an RNA virus responsible for over 20 million infections annually. HEV's open reading frame (ORF)1 polyprotein is essential for genome replication, though it is unknown how the different subdomains function within a structural context. Our data show that ORF1 operates as a multifunctional protein, which is not subject to proteolytic processing. Supporting this model, scanning mutagenesis performed on the putative papain-like cysteine protease (pPCP) domain revealed six cysteines essential for viral replication. Our data are consistent with their role in divalent metal ion coordination, which governs local and interdomain interactions that are critical for the overall structure of ORF1; furthermore, the 'pPCP' domain can only rescue viral genome replication in trans when expressed in the context of the full-length ORF1 protein but not as an individual subdomain. Taken together, our work provides a comprehensive model of the structure and function of HEV ORF1.
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Affiliation(s)
- Robert LeDesma
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton UniversityPrincetonUnited States
| | - Brigitte Heller
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton UniversityPrincetonUnited States
| | - Abhishek Biswas
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton UniversityPrincetonUnited States
| | - Stephanie Maya
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton UniversityPrincetonUnited States
| | - Stefania Gili
- Department of Geosciences, Princeton UniversityPrincetonUnited States
| | - John Higgins
- Department of Geosciences, Princeton UniversityPrincetonUnited States
| | - Alexander Ploss
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton UniversityPrincetonUnited States
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Fieulaine S, Tubiana T, Bressanelli S. De novo modelling of HEV replication polyprotein: Five-domain breakdown and involvement of flexibility in functional regulation. Virology 2023; 578:128-140. [PMID: 36527931 DOI: 10.1016/j.virol.2022.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022]
Abstract
Hepatitis E virus (HEV), a major cause of acute viral hepatitis, is a single-stranded, positive-sense RNA virus. As such, it encodes a 1700-residue replication polyprotein pORF1 that directs synthesis of new viral RNA in infected cells. Here we report extensive modeling with AlphaFold2 of the full-length pORF1, and its production by in vitro translation. From this, we give a detailed update on the breakdown into domains of HEV pORF1. We also provide evidence that pORF1's N-terminal domain is likely to oligomerize to form a dodecameric pore, homologously to what has been described for Chikungunya virus. Beyond providing accurate folds for its five domains, our work highlights that there is no canonical protease encoded in pORF1 and that flexibility in several functionally important regions rather than proteolytic processing may serve to regulate HEV RNA synthesis.
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Affiliation(s)
- Sonia Fieulaine
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Thibault Tubiana
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Stéphane Bressanelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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Zhou Y, Zhao C, Tian Y, Xu N, Wang Y. Characteristics and Functions of HEV Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1417:15-32. [PMID: 37223856 DOI: 10.1007/978-981-99-1304-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Hepatitis E virus (HEV) is a non-enveloped virus containing a single-stranded, positive-sense RNA genome of 7.2 kb, which consists of a 5' non-coding region, three open reading frames (ORFs), and a 3' non-coding region. ORF1 is diverse between genotypes and encodes the nonstructural proteins, which include the enzymes needed for virus replication. In addition to its role in virus replication, the function of ORF1 is relevant to viral adaption in culture and may also relate to virus infection and HEV pathogenicity. ORF2 protein is the capsid protein, which is about 660 amino acids in length. It not only protects the integrity of the viral genome, but is also involved in many important physiological activities, such as virus assembly, infection, host interaction, and innate immune response. The main immune epitopes, especially neutralizing epitopes, are located on ORF2 protein, which is a candidate antigen for vaccine development. ORF3 protein is a phosphoprotein of 113 or 114 amino acids with a molecular weight of 13 kDa with multiple functions that can also induce strong immune reactivity. A novel ORF4 has been identified only in genotype 1 HEV and its translation promotes viral replication.
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Affiliation(s)
- Yan Zhou
- RegCMC, Great Regulatory Affairs, Sanofi (China) Investment Co., Ltd, Beijing, China
| | - Chenyan Zhao
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Yabin Tian
- Division II of In Vitro Diagnostics for Infectious Diseases, National Institutes for Food and Drug Control, Beijing, China
| | - Nan Xu
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Youchun Wang
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China.
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Shata MTM, Hetta HF, Sharma Y, Sherman KE. Viral hepatitis in pregnancy. J Viral Hepat 2022; 29:844-861. [PMID: 35748741 PMCID: PMC9541692 DOI: 10.1111/jvh.13725] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/17/2021] [Accepted: 06/13/2022] [Indexed: 12/09/2022]
Abstract
Viral hepatitis is caused by a heterogenous group of viral agents representing a wide range of phylogenetic groups. Many viruses can involve the liver and cause liver injury but only a subset are delineated as 'hepatitis viruses' based upon their primary site of replication and tropism for hepatocytes which make up the bulk of the liver cell population. Since their discovery, beginning with the agent that caused serum hepatitis in the 1960s, the alphabetic designations have been utilized. To date, we have five hepatitis viruses, A through E, though it is postulated that others may exist. This chapter will focus on those viruses. Note that hepatitis D is included as a subset of hepatitis B, as it cannot exist without concurrent hepatitis B infection. Pregnancy has the potential to affect all aspects of these viral agents due to the unique immunologic and physiologic changes that occur during and after the gestational period. In this review, we will discuss the most common viral hepatitis and their effects during pregnancy.
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Affiliation(s)
- Mohamed Tarek M. Shata
- Division of Digestive Disease, Department of Internal MedicineUniversity of CincinnatiCincinnatiOhioUSA
| | - Helal F. Hetta
- Division of Digestive Disease, Department of Internal MedicineUniversity of CincinnatiCincinnatiOhioUSA,Department of Medical Microbiology and Immunology, Faculty of MedicineAssiut UniversityAssiutEgypt
| | - Yeshika Sharma
- Division of Digestive Disease, Department of Internal MedicineUniversity of CincinnatiCincinnatiOhioUSA
| | - Kenneth E. Sherman
- Division of Digestive Disease, Department of Internal MedicineUniversity of CincinnatiCincinnatiOhioUSA
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Goulet A, Cambillau C, Roussel A, Imbert I. Structure Prediction and Analysis of Hepatitis E Virus Non-Structural Proteins from the Replication and Transcription Machinery by AlphaFold2. Viruses 2022; 14:1537. [PMID: 35891516 PMCID: PMC9316534 DOI: 10.3390/v14071537] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 02/04/2023] Open
Abstract
Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in humans globally. Considered for a long while a public health issue only in developing countries, the HEV infection is now a global public health concern. Most human infections are caused by the HEV genotypes 1, 2, 3 and 4 (HEV-1 to HEV-4). Although HEV-3 and HEV-4 can evolve to chronicity in immunocompromised patients, HEV-1 and HEV-2 lead to self-limited infections. HEV has a positive-sense single-stranded RNA genome of ~7.2 kb that is translated into a large pORF1 replicative polyprotein, essential for the viral RNA genome replication and transcription. Unfortunately, the composition and structure of these replicases are still unknown. The recent release of the powerful machine-learning protein structure prediction software AlphaFold2 (AF2) allows us to accurately predict the structure of proteins and their complexes. Here, we used AF2 with the replicase encoded by the polyprotein pORF1 of the human-infecting HEV-3. The boundaries and structures reveal five domains or nonstructural proteins (nsPs): the methyltransferase, Zn-binding domain, macro, helicase, and RNA-dependent RNA polymerase, reliably predicted. Their substrate-binding sites are similar to those observed experimentally for other related viral proteins. Precisely knowing enzyme boundaries and structures is highly valuable to recombinantly produce stable and active proteins and perform structural, functional and inhibition studies.
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Affiliation(s)
- Adeline Goulet
- Aix-Marseille Université, Centre National de la Recherche Scientifique, UMR 7255, LISM, 31 Chemin Joseph Aiguier, 13009 Marseille, France; (A.G.); (A.R.)
| | - Christian Cambillau
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland;
- AlphaGraphix, 24 Carrer d’Amont, 66210 Formiguères, France
| | - Alain Roussel
- Aix-Marseille Université, Centre National de la Recherche Scientifique, UMR 7255, LISM, 31 Chemin Joseph Aiguier, 13009 Marseille, France; (A.G.); (A.R.)
| | - Isabelle Imbert
- Aix-Marseille Université, Centre National de la Recherche Scientifique, UMR 7255, LISM, 31 Chemin Joseph Aiguier, 13009 Marseille, France; (A.G.); (A.R.)
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Wang X, Sun J, Zheng Y, Xie F. Dispersion of synonymous codon usage patterns in hepatitis E virus genomes derived from various hosts. J Basic Microbiol 2022; 62:975-983. [PMID: 35778820 DOI: 10.1002/jobm.202200072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/01/2022] [Accepted: 06/11/2022] [Indexed: 11/09/2022]
Abstract
Hepatitis E virus (HEV) is an important zoonotic pathogen infecting a wide range of host species. It has a positive-sense, single-stranded RNA genome encoding three open reading frames (ORFs). Synonymous codon usages of viruses essentially determine their survival and adaptation to susceptible hosts. To better understand the interplay between the ever-expanding host range and synonymous codon usages of HEV, we quantified the dispersion of synonymous codon usages of HEV genomes isolated from different hosts via Vs calculation and information entropy. HEV ORFs show species-specific synonymous codon usage patterns. Ruminant-derived HEV ORFs own the most synonymous codons with stable usage patterns (Vs value <0.1) which leads to the stable overall codon usage patterns (R value being close to zero). Swine-derived HEV ORFs own more concentrated synonymous codons than those from wild boar. Compared with HEV strains isolated from other hosts, the human-derived HEV exhibits a distinct pattern at the overall codon usage (R < 0). Generally, ORF1 contains more synonymous codons with stable usage patterns (Vs < 0.1) than those of ORFs 2 and 3. Moreover, ORF3 contains more synonymous codons with varied patterns (Vs > 1.0) than ORFs 1 and 2. The host factor serving as one of the evolutionary dynamics probably influences synonymous codon usage patterns of the HEV genome. Taken together, synonymous codons with stable usage patterns in ORF1 might help to sustain the infection, while that with varied usage patterns in ORF3 may facilitate cross-species infection and expand the host range.
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Affiliation(s)
- Xin Wang
- School of Stomatology, Lanzhou University, Lanzhou, Gansu, China
| | - Jing Sun
- Department of Endocrine, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yueyan Zheng
- School of Stomatology, Lanzhou University, Lanzhou, Gansu, China
| | - Fuqiang Xie
- Department of Stomatology, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
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Shafat Z, Ahmed A, Parvez MK, Parveen S. Analysis of codon usage patterns in open reading frame 4 of hepatitis E viruses. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2022; 11:65. [PMID: 35573872 PMCID: PMC9086417 DOI: 10.1186/s43088-022-00244-w] [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: 05/17/2021] [Accepted: 04/19/2022] [Indexed: 12/01/2022] Open
Abstract
Background Hepatitis E virus (HEV) is a member of the family Hepeviridae and causes acute HEV infections resulting in thousands of deaths worldwide. The zoonotic nature of HEV in addition to its tendency from human to human transmission has led scientists across the globe to work on its different aspects. HEV also accounts for about 30% mortality rates in case of pregnant women. The genome of HEV is organized into three open reading frames (ORFs): ORF1 ORF2 and ORF3. A reading frame encoded protein ORF4 has recently been discovered which is exclusive to GT 1 isolates of HEV. The ORF4 is suggested to play crucial role in pregnancy-associated pathology and enhanced replication. Though studies have documented the ORF4’s importance, the genetic features of ORF4 protein genes in terms of compositional patterns have not been elucidated. As codon usage performs critical role in establishment of the host–pathogen relationship, therefore, the present study reports the codon usage analysis (based on nucleotide sequences of HEV ORF4 available in the public database) in three hosts along with the factors influencing the codon usage patterns of the protein genes of ORF4 of HEV. Results The nucleotide composition analysis indicated that ORF4 protein genes showed overrepresentation of C nucleotide and while A nucleotide was the least-represented, with random distribution of G and T(U) nucleotides. The relative synonymous codon usage (RSCU) analysis revealed biasness toward C/G-ended codons (over U/A) in all three natural HEV-hosts (human, rat and ferret). It was observed that all the ORF4 genes were richly endowed with GC content. Further, our results showed the occurrence of both coincidence and antagonistic codon usage patterns among HEV-hosts. The findings further emphasized that both mutational and selection forces influenced the codon usage patterns of ORF4 protein genes. Conclusions To the best of our knowledge, this is first bioinformatics study evaluating codon usage patterns in HEV ORF4 protein genes. The findings from this study are expected to increase our understanding toward significant factors involved in evolutionary changes of ORF4. Supplementary Information The online version contains supplementary material available at 10.1186/s43088-022-00244-w.
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Shafat Z, Ahmed A, Parvez MK, Parveen S. Decoding the codon usage patterns in Y-domain region of hepatitis E viruses. J Genet Eng Biotechnol 2022; 20:56. [PMID: 35404024 PMCID: PMC9001762 DOI: 10.1186/s43141-022-00319-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 02/17/2022] [Indexed: 12/17/2022]
Abstract
Background Hepatitis E virus (HEV) is a positive-sense RNA virus belonging to the family Hepeviridae. The genome of HEV is organized into three open-reading frames (ORFs): ORF1, ORF2, and ORF3. The ORF1 non-structural Y-domain region (YDR) has been demonstrated to play an important role in the HEV pathogenesis. The nucleotide composition, synonymous codon usage bias in conjunction with other factors influencing the viral YDR genes of HEV have not been studied. Codon usage represents a significant mechanism in establishing the host-pathogen relationship. The present study for the first time elucidates the detailed codon usage patterns of YDR among HEV and HEV-hosts (Human, Rabbit, Mongoose, Pig, Wild boar, Camel, Monkey). Results The overall nucleotide composition revealed the abundance of C and U nucleotides in YDR genomes. The relative synonymous codon usage (RSCU) analysis indicated biasness towards C and U over A and G ended codons in HEV across all hosts. Codon frequency comparative analyses among HEV-hosts showed both similarities and discrepancies in usage of preferred codons encoding amino acids, which revealed that HEV codon preference neither completely differed nor completely showed similarity with its hosts. Thus, our results clearly indicated that the synonymous codon usage of HEV is a mixture of the two types of codon usage: coincidence and antagonism. Mutation pressure from virus and natural selection from host seems to be accountable for shaping the codon usage patterns in YDR. The study emphasised that the influence of compositional constraints, codon usage biasness, mutational alongside the selective forces were reflected in the occurrence of YDR codon usage patterns. Conclusions Our study is the first in its kind to have reported the analysis of codon usage patterns on a total of seven different natural HEV hosts. Therefore, knowledge of preferred codons obtained from our study will not only augment our understanding towards molecular evolution but is also envisaged to provide insight into the efficient viral expression, viral adaptation, and host effects on the HEV YDR codon usage. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00319-2.
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Affiliation(s)
- Zoya Shafat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anwar Ahmed
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad K Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
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El-Kafrawy SA, El-Daly MM. Hepatitis E virus in Saudi Arabia: more surveillance needed. Future Virol 2022. [DOI: 10.2217/fvl-2021-0320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hepatitis E virus (HEV) is a small quasi-enveloped ssRNA causing acute hepatitis. HEV is the leading cause of intermittent acute hepatitis and fulminant hepatic failure. Risk factors include drinking contaminated water in developing countries and consumption of infected animal products in developed countries. Previous reports on HEV prevalence in Saudi Arabia had small sample sizes. Nationwide systematic seroprevalence studies are needed to investigate risk factors and annual incidence. Camels play a cultural and economic role in the life of Saudi citizens with frequent human contact and potential role in zoonotic transmission. Future research needs to include larger sample-sizes and nationwide studies. Future studies should also focus on raising awareness of HEV infection and the need for wider population testing and screening.
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Affiliation(s)
- Sherif Aly El-Kafrawy
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Mai Mohamed El-Daly
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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13
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Cancela F, Noceti O, Arbiza J, Mirazo S. Structural aspects of hepatitis E virus. Arch Virol 2022; 167:2457-2481. [PMID: 36098802 PMCID: PMC9469829 DOI: 10.1007/s00705-022-05575-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/04/2022] [Indexed: 12/14/2022]
Abstract
Hepatitis E virus (HEV) is a leading cause of acute hepatitis worldwide. Hepatitis E is an enterically transmitted zoonotic disease that causes large waterborne epidemic outbreaks in developing countries and has become an increasing public-health concern in industrialized countries. In this setting, the infection is usually acute and self-limiting in immunocompetent individuals, although chronic cases in immunocompromised patients have been reported, frequently associated with several extrahepatic manifestations. Moreover, extrahepatic manifestations have also been reported in immunocompetent individuals with acute HEV infection. HEV belongs to the alphavirus-like supergroup III of single-stranded positive-sense RNA viruses, and its genome contains three partially overlapping open reading frames (ORFs). ORF1 encodes a nonstructural protein with eight domains, most of which have not been extensively characterized: methyltransferase, Y domain, papain-like cysteine protease, hypervariable region, proline-rich region, X domain, Hel domain, and RNA-dependent RNA polymerase. ORF2 and ORF3 encode the capsid protein and a multifunctional protein believed to be involved in virion release, respectively. The novel ORF4 is only expressed in HEV genotype 1 under endoplasmic reticulum stress conditions, and its exact function has not yet been elucidated. Despite important advances in recent years, the biological and molecular processes underlying HEV replication remain poorly understood, primarily due to a lack of detailed information about the functions of the viral proteins and the mechanisms involved in host-pathogen interactions. This review summarizes the current knowledge concerning HEV proteins and their biological properties, providing updated detailed data describing their function and focusing in detail on their structural characteristics. Furthermore, we review some unclear aspects of the four proteins encoded by the ORFs, highlighting the current key information gaps and discussing potential novel experimental strategies for shedding light on those issues.
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Affiliation(s)
- Florencia Cancela
- grid.11630.350000000121657640Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ofelia Noceti
- grid.414402.70000 0004 0469 0889Programa Nacional de Trasplante Hepático y Unidad Docente Asistencial Centro Nacional de Tratamiento Hepatobiliopancreatico. Hospital Central de las Fuerzas Armadas, Montevideo, Uruguay
| | - Juan Arbiza
- grid.11630.350000000121657640Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Santiago Mirazo
- grid.11630.350000000121657640Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay ,grid.11630.350000000121657640Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay ,Av. Alfredo Navarro 3051, PC 11600 Montevideo, Uruguay
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Shafat Z, Hamza A, Deeba F, Parvez MK, Parveen S. Molecular insights into the Y-domain of hepatitis E virus using computational analyses. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021. [DOI: 10.1186/s43088-021-00154-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract
Background
Hepatitis E virus (HEV) of the family Hepeviridae is a major causative agent of acute hepatitis in developing countries. The Y-domain is derived from multi-domain non-structural polyprotein encoded by open reading frame 1 (ORF1). Previous studies have demonstrated the essentiality of Y-domain sequences in HEV life cycle; however, its function remains completely unexplored. The following study was thus conceptualized to examine the detailed computational investigation for the putative Y-domain to estimate its phylogenetic assessment, physiochemical properties, structural and functional characteristics using in silico analyses.
Results
The phylogenetic assessment of Y-domain with a vast range of hosts indicated that the protein was very well conserved throughout the course of evolution. The Y-domain was found to be unstable, hydrophilic and basic in nature with high thermostability value. Structural analysis of Y-domain revealed mixed α/β structural fold of the protein having higher percentage of alpha-helices. The three-dimensional (3D) protein model generated through homology modelling revealed the presence of clefts, tunnels and pore. Gene ontology analysis predicted Y-domain protein’s involvement in several binding and catalytic activities as well as significant biological processes. Mutations in the conserved amino acids of the Y-domain suggested that it may stabilize or de-stabilize the protein structure that might affect its structure–function relationship.
Conclusions
This theoretical study will facilitate towards deciphering the role of unexplored Y-domain, thereby providing better understanding towards the pathogenesis of HEV infection.
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Shafat Z, Ahmed A, Parvez MK, Parveen S. Role of "dual-personality" fragments in HEV adaptation-analysis of Y-domain region. J Genet Eng Biotechnol 2021; 19:154. [PMID: 34637041 PMCID: PMC8511232 DOI: 10.1186/s43141-021-00238-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/30/2021] [Indexed: 01/06/2023]
Abstract
BACKGROUND Hepatitis E is a liver disease caused by the pathogen hepatitis E virus (HEV). The largest polyprotein open reading frame 1 (ORF1) contains a nonstructural Y-domain region (YDR) whose activity in HEV adaptation remains uncharted. The specific role of disordered regions in several nonstructural proteins has been demonstrated to participate in the multiplication and multiple regulatory functions of the viruses. Thus, intrinsic disorder of YDR including its structural and functional annotation was comprehensively studied by exploiting computational methodologies to delineate its role in viral adaptation. RESULTS Based on our findings, it was evident that YDR contains significantly higher levels of ordered regions with less prevalence of disordered residues. Sequence-based analysis of YDR revealed it as a "dual personality" (DP) protein due to the presence of both structured and unstructured (intrinsically disordered) regions. The evolution of YDR was shaped by pressures that lead towards predominance of both disordered and regularly folded amino acids (Ala, Arg, Gly, Ile, Leu, Phe, Pro, Ser, Tyr, Val). Additionally, the predominance of characteristic DP residues (Thr, Arg, Gly, and Pro) further showed the order as well as disorder characteristic possessed by YDR. The intrinsic disorder propensity analysis of YDR revealed it as a moderately disordered protein. All the YDR sequences consisted of molecular recognition features (MoRFs), i.e., intrinsic disorder-based protein-protein interaction (PPI) sites, in addition to several nucleotide-binding sites. Thus, the presence of molecular recognition (PPI, RNA binding, and DNA binding) signifies the YDR's interaction with specific partners, host membranes leading to further viral infection. The presence of various disordered-based phosphorylation sites further signifies the role of YDR in various biological processes. Furthermore, functional annotation of YDR revealed it as a multifunctional-associated protein, due to its susceptibility in binding to a wide range of ligands and involvement in various catalytic activities. CONCLUSIONS As DP are targets for regulation, thus, YDR contributes to cellular signaling processes through PPIs. As YDR is incompletely understood, therefore, our data on disorder-based function could help in better understanding its associated functions. Collectively, our novel data from this comprehensive investigation is the first attempt to delineate YDR role in the regulation and pathogenesis of HEV.
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Affiliation(s)
- Zoya Shafat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anwar Ahmed
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad K Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
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Shafat Z, Hamza A, Islam A, Al-Dosari MS, Parvez MK, Parveen S. Structural exploration of Y-domain reveals its essentiality in HEV pathogenesis. Protein Expr Purif 2021; 187:105947. [PMID: 34314826 DOI: 10.1016/j.pep.2021.105947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/08/2021] [Accepted: 07/21/2021] [Indexed: 12/19/2022]
Abstract
Hepatitis E virus (HEV) is a major causative agent of hepatitis E infections across the globe. Although the essentiality of HEV nonstructural polyprotein (pORF1) putative Y-domain (Yd) has been established in viral pathogenesis, its structural-functional role remains elusive. The current research discusses the novel exploration on Yd protein expression, purification, biophysical characterization and structure-based docking analysis. The codon optimized synthetic gene and optimized expression parameters i.e., 5 h induction with 0.25 mM IPTG at 37 °C, resulted in efficient production of Yd protein (∼40 kDa) in E. coli BL21(DE3) cells. Majority of the recombinant Yd (rYd) protein expressed as inclusion bodies was solubilized in 0.5% N-lauroylsarcosine and purified using Ni-NTA chromatography. Circular dichroism (CD) and UV visible absorption spectroscopic studies on Yd revealed both secondary and tertiary structure stability in alkaline range (pH 8.0-10.0), suggesting correlation with its physiological activity. Thus, loss in structure at low pH perhaps play crucial role in cytoplasmic-membrane interaction. The biophysical data were in good agreement with in-silico structural analyses, which suggested mixed α/β fold, non-random and basic nature of Yd protein. Furthermore, due to Yd protein essentiality in HEV replication and pathogenesis, it was considered as a template for docking and drug-likeness analyses. The 3D modeling of Yd protein and structure-based screening and drug-likeness of inhibitory compounds, including established antiviral drugs led to the identification of top nine promising candidates. Nonetheless, in vitro studies on the predicted interaction of Yd with intracellular-membrane towards establishing replication-complexes as well as validations of the proposed therapeutic agents are warranted.
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Affiliation(s)
- Zoya Shafat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Abu Hamza
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohammed S Al-Dosari
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad K Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia.
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
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Kumar M, Hooda P, Khanna M, Patel U, Sehgal D. Development of BacMam Induced Hepatitis E Virus Replication Model in Hepatoma Cells to Study the Polyprotein Processing. Front Microbiol 2020; 11:1347. [PMID: 32625196 PMCID: PMC7315041 DOI: 10.3389/fmicb.2020.01347] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/26/2020] [Indexed: 01/10/2023] Open
Abstract
The processing of polyprotein(s) to form structural and non-structural components remains an enigma due to the non-existence of an efficient and robust Hepatitis E Virus (HEV) culture system. We used the BacMam approach to construct an HEV replication model in which the HEV genome was cloned in the BacMam vector under the CMV promoter. The recombinant BacMam was used to infect Huh7 cells to transfer the HEV genome. HEV replication was authenticated by the presence of RNAs of both the polarity (+) and (-) and formation of hybrid RNA, a replication intermediate. The presence of genes for Papain-like Cysteine Protease (PCP), methyltransferase (MeT), RNA dependent RNA polymerase (RdRp), and ORF2 was confirmed by PCR amplification. Further, the infectious nature of the culture system was established as evidenced by the cross-infection of uninfected cells using the cell lysate from the infected cells. The HEV replication model was validated by detection of the ORF1 (Open Reading Frame1) encoded proteins, identified by Western blotting and Immunofluorescence by using epitope-specific antibodies against each protein. Consequently, discrete bands of 18, 35, 37, and 56 kDa corresponding to PCP, MeT, RdRp, and ORF2, respectively, were seen. Besides demonstrating the presence of non-structural enzymes of HEV along with ORF2, activity of a key enzyme, HEV-methyltransferase has also been observed. A 20% decrease in the replicative forms of RNA could be seen in presence of 100 μM Ribavirin after 48 h of treatment. The inhibition gradually increased from 0 to 24 to 48 h post-treatment. Summarily, infectious HEV culture system has been established, which could demonstrate the presence of HEV replicative RNA forms, the structural and non-structural proteins and the methyltransferase in its active form. The system may also be used to study the mechanism of action of Ribavirin in inhibiting HEV replication and develop a therapy.
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Affiliation(s)
- Manjeet Kumar
- Virology Laboratory, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
| | - Preeti Hooda
- Virology Laboratory, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
| | - Madhu Khanna
- Virology Lab, Department of Virology, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi, India
| | - Utkarsh Patel
- Virology Laboratory, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
| | - Deepak Sehgal
- Virology Laboratory, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
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18
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Saraswat S, Chaudhary M, Sehgal D. Hepatitis E Virus Cysteine Protease Has Papain Like Properties Validated by in silico Modeling and Cell-Free Inhibition Assays. Front Cell Infect Microbiol 2020; 9:478. [PMID: 32039053 PMCID: PMC6989534 DOI: 10.3389/fcimb.2019.00478] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/27/2019] [Indexed: 12/11/2022] Open
Abstract
Hepatitis E virus (HEV) has emerged as a global health concern during the last decade. In spite of a high mortality rate in pregnant women with fulminant hepatitis, no antiviral drugs or licensed vaccine is available in India. HEV-protease is a pivotal enzyme responsible for ORF1 polyprotein processing leading to cleavage of the non-structural enzymes involved in virus replication. HEV-protease region encoding 432–592 amino acids of Genotype-1 was amplified, expressed in Sf21 cells and purified in its native form. The recombinant enzyme was biochemically characterized using SDS-PAGE, Western blotting and Immunofluorescence. The enzyme activity and the inhibition studies were conducted using Zymography, FTC-casein based protease assay and ORF1 polyprotein digestion. To conduct ORF1 digestion assay, the polyprotein, natural substrate of HEV-protease, was expressed in E. coli and purified. Cleavage of 186 kDa ORF1 polyprotein by the recombinant HEV-protease lead to appearance of non-structural proteins viz. Methyltransferase, Protease, Helicase and RNA dependent RNA polymerase which were confirmed through immunoblotting using antibodies generated against specific epitopes of the enzymes. FTC-casein substrate was used for kinetic studies to determine Km and Vmax of the enzyme and also the effect of different metal ions and other protease inhibitors. A 95% inhibition was observed with E-64 which was validated through in silico analysis. The correlation coefficient between inhibition and docking score of Inhibitors was found to have a significant value of r2 = 0.75. The predicted 3D model showed two domain architecture structures similar to Papain like cysteine protease though they differed in arrangements of alpha helices and beta sheets. Hence, we propose that HEV-protease has characteristics of “Papain-like cysteine protease,” as determined through structural homology, active site residues and class-specific inhibition. However, conclusive nature of the enzyme remains to be established.
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Affiliation(s)
- Shweta Saraswat
- Virology Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
| | - Meenakshi Chaudhary
- Virology Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
| | - Deepak Sehgal
- Virology Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
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LeDesma R, Nimgaonkar I, Ploss A. Hepatitis E Virus Replication. Viruses 2019; 11:E719. [PMID: 31390784 PMCID: PMC6723718 DOI: 10.3390/v11080719] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 12/19/2022] Open
Abstract
Hepatitis E virus (HEV) is a small quasi-enveloped, (+)-sense, single-stranded RNA virus belonging to the Hepeviridae family. There are at least 20 million HEV infections annually and 60,000 HEV-related deaths worldwide. HEV can cause up to 30% mortality in pregnant women and progress to liver cirrhosis in immunocompromised individuals and is, therefore, a greatly underestimated public health concern. Although a prophylactic vaccine for HEV has been developed, it is only licensed in China, and there is currently no effective, non-teratogenic treatment. HEV encodes three open reading frames (ORFs). ORF1 is the largest viral gene product, encoding the replicative machinery of the virus including a methyltransferase, RNA helicase, and an RNA-dependent RNA polymerase. ORF1 additionally contains a number of poorly understood domains including a hypervariable region, a putative protease, and the so-called 'X' and 'Y' domains. ORF2 is the viral capsid essential for formation of infectious particles and ORF3 is a small protein essential for viral release. In this review, we focus on the domains encoded by ORF1, which collectively mediate the virus' asymmetric genome replication strategy. We summarize what is known, unknown, and hotly debated regarding the coding and non-coding regions of HEV ORF1, and present a model of how HEV replicates its genome.
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Affiliation(s)
- Robert LeDesma
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544, USA
| | - Ila Nimgaonkar
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544, USA
| | - Alexander Ploss
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544, USA.
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20
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First Crystal Structure of a Nonstructural Hepatitis E Viral Protein Identifies a Putative Novel Zinc-Binding Protein. J Virol 2019; 93:JVI.00170-19. [PMID: 31019049 DOI: 10.1128/jvi.00170-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/17/2019] [Indexed: 12/14/2022] Open
Abstract
Hepatitis E virus (HEV) is a 7.2-kb positive-sense, single-stranded RNA virus containing three partially overlapping reading frames, ORF1 to ORF3. All nonstructural proteins required for viral replication are encoded by ORF1 and are transcribed as a single transcript. Computational analysis of the complete ORF1 polyprotein identified a previously uncharacterized region of predicted secondary structure bordered by two disordered regions coinciding partially with a region predicted as a putative cysteine protease. Following successful cloning, expression, and purification of this region, the crystal structure of the identified protein was determined and identified to have considerable structural homology to a fatty acid binding domain. Further analysis of the structure revealed a metal binding site, shown unambiguously to specifically bind zinc via a nonclassical, potentially catalytic zinc-binding motif. Based on the structural homology of the HEV protein with known structures, along with the presence of a catalytic zinc-binding motif, it is possible that the identified protein corresponds to the HEV protease, which could require activation or repression through the binding of a fatty acid. This represents a significant step forward in the characterization and the understanding of the molecular mechanisms of the HEV genome. We present analysis for the first time of this identified nonstructural protein, expanding the knowledge and understanding of the complex mechanisms of HEV biology.IMPORTANCE Hepatitis E virus (HEV) is an emerging virus found predominately in developing countries; it causes an estimated 20 million infections, which result in approximately 57,000 deaths a year. Although it is known that the nonstructural proteins of HEV ORF1 are expressed as a single transcript, there is debate as to whether ORF1 functions as a single polyprotein or if it is processed into separate domains via a viral or endogenous cellular protease. Here we present the first structural and biophysical characterization of an HEV nonstructural protein using a construct that has partially overlapping boundaries with the predicted putative cysteine protease.
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21
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Hepatitis E Virus Assembly and Release. Viruses 2019; 11:v11060539. [PMID: 31181848 PMCID: PMC6631228 DOI: 10.3390/v11060539] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/31/2019] [Accepted: 06/07/2019] [Indexed: 12/12/2022] Open
Abstract
Hepatitis E is an underestimated threat to public health, caused by the hepatitis E virus (HEV). HEV is the most common cause of acute viral hepatitis in the world, with no available direct-acting antiviral treatment. According to a recent WHO report, 20 million people become infected with HEV annually, resulting in 44,000 deaths. However, due to the scarcity of efficient in vitro cell culture systems for HEV, our knowledge of the life cycle of HEV is incomplete. Recently, significant progress has been made towards gaining a more comprehensive view of the HEV life cycle, as several in vitro culturing systems have been developed in recent years. Here, we review current knowledge and recent advances with regard to the HEV life cycle, with a particular focus on the assembly and release of viral particles. We also discuss the knowledge gaps in HEV assembly and release. Meanwhile, we highlight experimental platforms that could potentially be utilized to fill these gaps. Lastly, we offer perspectives on the future of research into HEV virology and its interaction with host cells.
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22
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Hepatitis E Virus Drug Development. Viruses 2019; 11:v11060485. [PMID: 31141919 PMCID: PMC6631701 DOI: 10.3390/v11060485] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/20/2019] [Accepted: 05/24/2019] [Indexed: 02/08/2023] Open
Abstract
Hepatitis E virus (HEV) is an underestimated disease, leading to estimated 20 million infections and up to 70,000 deaths annually. Infections are mostly asymptomatic but can reach mortality rates up to 25% in pregnant women or become chronic in immunocompromised patients. The current therapy options are limited to the unspecific antivirals Ribavirin (RBV) and pegylated Interferon-α (pegIFN-α). RBV leads to viral clearance in only 80% of patients treated, and is, similar to pegIFN-α, contraindicated in the major risk group of pregnant women, emphasizing the importance of new therapy options. In this review, we focus on the urgent need and current efforts in HEV drug development. We provide an overview of the current status of HEV antiviral research. Furthermore, we discuss strategies for drug development and the limitations of the approaches with respect to HEV.
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23
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Dao Thi VL, Wu X, Rice CM. Stem Cell-Derived Culture Models of Hepatitis E Virus Infection. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a031799. [PMID: 29686039 DOI: 10.1101/cshperspect.a031799] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Similar to other hepatotropic viruses, hepatitis E virus (HEV) has been notoriously difficult to propagate in cell culture, limiting studies to unravel its biology. Recently, major advances have been made by passaging primary HEV isolates and selecting variants that replicate efficiently in carcinoma cells. These adaptations, however, can alter HEV biology. We have explored human embryonic or induced pluripotent stem cell (hESC/iPSC)-derived hepatocyte-like cells (HLCs) as an alternative to conventional hepatoma and hepatocyte cell culture systems for HEV studies. HLCs are permissive for nonadapted HEV isolate genotypes (gt)1-4 replication and can be readily genetically manipulated. HLCs, therefore, enable studies of pan-genotype HEV biology and will serve as a platform for testing anti-HEV treatments. Finally, we discuss how hepatocyte polarity is likely an important factor in the maturation and spread of infectious HEV particles.
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Affiliation(s)
- Viet Loan Dao Thi
- Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, New York 10065
| | - Xianfang Wu
- Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, New York 10065
| | - Charles M Rice
- Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, New York 10065
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Meister TL, Bruening J, Todt D, Steinmann E. Cell culture systems for the study of hepatitis E virus. Antiviral Res 2019; 163:34-49. [PMID: 30653997 DOI: 10.1016/j.antiviral.2019.01.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/08/2019] [Accepted: 01/13/2019] [Indexed: 12/26/2022]
Abstract
Hepatitis E virus (HEV) is the causative agent of hepatitis E in humans and is the leading cause of enterically-transmitted viral hepatitis worldwide. Increasing numbers of HEV infections, together with no available specific anti-HEV treatment, contributes to the pathogen's major health burden. A robust cell culture system is required for virologic studies and the development of new antiviral drugs. Unfortunately, like other hepatitis viruses, HEV is difficult to propagate in conventional cell lines. Many different cell culture systems have been tested using various HEV strains, but viral replication usually progresses very slowly, and infection with low virion counts results in non-productive HEV replication. However, recent progress involving generation of cDNA clones and passaging primary patient isolates in distinct cell lines has improved in vitro HEV propagation. This review describes various approaches to cultivate HEV in cellular and animal models and how these systems are used to study HEV infections and evaluate anti-HEV drug candidates.
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Affiliation(s)
- Toni L Meister
- Ruhr-University Bochum, Faculty of Medicine, Department of Molecular and Medical Virology, Bochum, Germany
| | - Janina Bruening
- Ruhr-University Bochum, Faculty of Medicine, Department of Molecular and Medical Virology, Bochum, Germany
| | - Daniel Todt
- Ruhr-University Bochum, Faculty of Medicine, Department of Molecular and Medical Virology, Bochum, Germany.
| | - Eike Steinmann
- Ruhr-University Bochum, Faculty of Medicine, Department of Molecular and Medical Virology, Bochum, Germany.
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Abstract
Hepatitis E virus (HEV) possesses many of the features of other positive-stranded RNA viruses but also adds HEV-specific nuances, making its virus-host interactions unique. Slow virus replication kinetics and fastidious growth conditions, coupled with the historical lack of an efficient cell culture system to propagate the virus, have left many gaps in our understanding of its structure and replication cycle. Recent advances in culturing selected strains of HEV and resolving the 3D structure of the viral capsid are filling in knowledge gaps, but HEV remains an extremely understudied pathogen. Many steps in the HEV life cycle and many aspects of HEV pathogenesis remain unknown, such as the host and viral factors that determine cross-species infection, the HEV-specific receptor(s) on host cells, what determines HEV chronicity and the ability to replicate in extrahepatic sites, and what regulates processing of the open reading frame 1 (ORF1) nonstructural polyprotein.
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Affiliation(s)
- Scott P Kenney
- Food Animal Health Research Program, The Ohio State University, Wooster, Ohio 44691
| | - Xiang-Jin Meng
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
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Bagdassarian E, Doceul V, Pellerin M, Demange A, Meyer L, Jouvenet N, Pavio N. The Amino-Terminal Region of Hepatitis E Virus ORF1 Containing a Methyltransferase (Met) and a Papain-Like Cysteine Protease (PCP) Domain Counteracts Type I Interferon Response. Viruses 2018; 10:v10120726. [PMID: 30567349 PMCID: PMC6315852 DOI: 10.3390/v10120726] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/07/2018] [Accepted: 12/13/2018] [Indexed: 01/09/2023] Open
Abstract
Hepatitis E virus (HEV) is responsible for large waterborne epidemics of hepatitis in endemic countries and is an emerging zoonotic pathogen worldwide. In endemic regions, HEV-1 or HEV-2 genotypes are frequently associated with fulminant hepatitis in pregnant women, while with zoonotic HEV (HEV-3 and HEV-4), chronic cases of hepatitis and severe neurological disorders are reported. Hence, it is important to characterize the interactions between HEV and its host. Here, we investigated the ability of the nonstructural polyprotein encoded by the first open reading frame (ORF1) of HEV to modulate the host early antiviral response and, in particular, the type I interferon (IFN-I) system. We found that the amino-terminal region of HEV-3 ORF1 (MetYPCP), containing a putative methyltransferase (Met) and a papain-like cysteine protease (PCP) functional domain, inhibited IFN-stimulated response element (ISRE) promoter activation and the expression of several IFN-stimulated genes (ISGs) in response to IFN-I. We showed that the MetYPCP domain interfered with the Janus kinase (JAK)/signal transducer and activator of the transcription protein (STAT) signalling pathway by inhibiting STAT1 nuclear translocation and phosphorylation after IFN-I treatment. In contrast, MetYPCP had no effect on STAT2 phosphorylation and a limited impact on the activation of the JAK/STAT pathway after IFN-II stimulation. This inhibitory function seemed to be genotype-dependent, as MetYPCP from HEV-1 had no significant effect on the JAK/STAT pathway. Overall, this study provides evidence that the predicted MetYPCP domain of HEV ORF1 antagonises STAT1 activation to modulate the IFN response.
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Affiliation(s)
- Eugénie Bagdassarian
- Anses, UMR 1161 Virologie, Laboratoire de Santé Animale, 94700 Maisons-Alfort, France.
- INRA, UMR 1161 Virologie, 94700 Maisons-Alfort, France.
- École Nationale Vétérinaire d'Alfort, UMR 1161 Virologie, 94700 Maisons-Alfort, France.
| | - Virginie Doceul
- Anses, UMR 1161 Virologie, Laboratoire de Santé Animale, 94700 Maisons-Alfort, France.
- INRA, UMR 1161 Virologie, 94700 Maisons-Alfort, France.
- École Nationale Vétérinaire d'Alfort, UMR 1161 Virologie, 94700 Maisons-Alfort, France.
| | - Marie Pellerin
- Anses, UMR 1161 Virologie, Laboratoire de Santé Animale, 94700 Maisons-Alfort, France.
- INRA, UMR 1161 Virologie, 94700 Maisons-Alfort, France.
- École Nationale Vétérinaire d'Alfort, UMR 1161 Virologie, 94700 Maisons-Alfort, France.
| | - Antonin Demange
- Anses, UMR 1161 Virologie, Laboratoire de Santé Animale, 94700 Maisons-Alfort, France.
- INRA, UMR 1161 Virologie, 94700 Maisons-Alfort, France.
- École Nationale Vétérinaire d'Alfort, UMR 1161 Virologie, 94700 Maisons-Alfort, France.
| | - Léa Meyer
- Anses, UMR 1161 Virologie, Laboratoire de Santé Animale, 94700 Maisons-Alfort, France.
- INRA, UMR 1161 Virologie, 94700 Maisons-Alfort, France.
- École Nationale Vétérinaire d'Alfort, UMR 1161 Virologie, 94700 Maisons-Alfort, France.
| | - Nolwenn Jouvenet
- CNRS-UMR3569, Unité de Génomique Virale et Vaccination, Institut Pasteur, 75015 Paris, France.
| | - Nicole Pavio
- Anses, UMR 1161 Virologie, Laboratoire de Santé Animale, 94700 Maisons-Alfort, France.
- INRA, UMR 1161 Virologie, 94700 Maisons-Alfort, France.
- École Nationale Vétérinaire d'Alfort, UMR 1161 Virologie, 94700 Maisons-Alfort, France.
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Activities of Thrombin and Factor Xa Are Essential for Replication of Hepatitis E Virus and Are Possibly Implicated in ORF1 Polyprotein Processing. J Virol 2018; 92:JVI.01853-17. [PMID: 29321328 DOI: 10.1128/jvi.01853-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/19/2017] [Indexed: 01/11/2023] Open
Abstract
Hepatitis E virus (HEV) is a clinically important positive-sense RNA virus. The ORF1 of HEV encodes a nonstructural polyprotein of 1,693 amino acids. It is not clear whether the ORF1 polyprotein (pORF1) is processed into distinct enzymatic domains. Many researchers have attempted to understand the mechanisms of pORF1 processing. However, these studies gave various results and could never convincingly establish the mechanism of pORF1 processing. In this study, we demonstrated the possible role of thrombin and factor Xa in pORF1 processing. We observed that the HEV pORF1 polyprotein bears conserved cleavage sites of thrombin and factor Xa. Using a reverse genetics approach, we demonstrated that an HEV replicon having mutations in the cleavage sites of either thrombin or factor Xa could not replicate efficiently in cell culture. Further, we demonstrated in vitro processing when we incubated recombinant pORF1 fragments with thrombin, and we observed the processing of pORF1 polyprotein. The treatment of a liver cell line with a serine protease inhibitor as well as small interfering RNA (siRNA) knockdown of thrombin and factor Xa resulted in significant reduction in the replication of HEV. Thrombin and factor Xa have been well studied for their roles in blood clotting. Both of these proteins are believed to be present in the active form in the blood plasma. Interestingly, in this report, we demonstrated the presence of biologically active thrombin and factor Xa in a liver cell line. The results suggest that factor Xa and thrombin are essential for the replication of HEV and may be involved in pORF1 polyprotein processing of HEV.IMPORTANCE Hepatitis E virus (HEV) causes a liver disorder called hepatitis in humans, which is mostly an acute and self-limiting infection in adults. A high mortality rate of about 30% is observed in HEV-infected pregnant women in developing countries. There is no convincing opinion about HEV ORF1 polyprotein processing owing to the variability of study results obtained so far. HEV pORF1 has cleavage sites for two host cellular serine proteases, thrombin and factor Xa, that are conserved among HEV genotypes. For the first time, this study demonstrated that thrombin and factor Xa cleavage sites on HEV pORF1 are obligatory for HEV replication. Intracellular biochemical activities of the said serine proteases are also essential for efficient HEV replication in cell culture and must be involved in pORF1 processing. This study sheds light on the presence and roles of clotting factors with respect to virus replication in the cells.
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Sharma S, Kumar A, Kar P, Agarwal S, Ramji S, Husain SA, Prasad S, Sharma S. Risk factors for vertical transmission of hepatitis E virus infection. J Viral Hepat 2017; 24:1067-1075. [PMID: 28570034 DOI: 10.1111/jvh.12730] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/24/2017] [Indexed: 01/10/2023]
Abstract
Hepatitis E virus (HEV) infection can be vertically transmitted, but the factors that transmit the disease to foetuses are still unclear. We studied a total of 144 pregnant women with HEV infection. Cord blood and newborn samples were taken for analysis. Nutritional factors were evaluated on the basis of anthropometric parameters and biochemical factors, and HEV viral load was quantified by real-time PCR. Sequencing of HEV-positive samples was performed. Approximately 14.63% (6/41) of pregnant patients with acute liver failure (ALF) died before delivery. Vertical transmission was observed in 46.09% (59/128) of HEV-IgM-positive mothers. Approximately 23.80% (10/42) of newborns in the acute viral hepatitis group and 29.41% (5/17) in the ALF group were positive for HEV-RNA. No significant difference was observed in the occurrence of vertical transmission in HEV groups. Viral load was found to be a significant predictor for vertical transmission of HEV infection adjusted with haemoglobin and folate in derivation cohort group. Incorporating these variables, a new score predicting vertical transmission of HEV was derived. Using these significant predictors, the probability for vertical transmission of HEV was well stratified in the validation group (P>.05). In conclusion, viral load was associated with vertical transmission of HEV infection. A valid prediction score model was generated that was verified in a validation cohort group.
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Affiliation(s)
- S Sharma
- Department of Obstetrics and Gynecology, Maulana Azad Medical College and Associated Lok Nayak Hospital, New Delhi, India
| | - A Kumar
- Department of Obstetrics and Gynecology, Maulana Azad Medical College and Associated Lok Nayak Hospital, New Delhi, India
| | - P Kar
- Department of Medicine, Maulana Azad Medical College and Associated Lok Nayak Hospital, New Delhi, India
| | - S Agarwal
- Department of Biochemistry, Maulana Azad Medical College and Associated Lok Nayak Hospital, New Delhi, India
| | - S Ramji
- Department of Neonatology, Maulana Azad Medical College and Associated Lok Nayak Hospital, New Delhi, India
| | - S A Husain
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - S Prasad
- Department of Obstetrics and Gynecology, Maulana Azad Medical College and Associated Lok Nayak Hospital, New Delhi, India
| | - S Sharma
- National Institute of Cancer Prevention and Research (NICPR), Noida, India
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29
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Abstract
Hepatitis E virus (HEV) is a globally important pathogen of acute and chronic hepatitis in humans. The HEV ORF1 gene encodes a nonstructural polyprotein, essential for RNA replication and virus infectivity. Expression and processing of ORF1 polyprotein are shown in prokaryotic and eukaryotic systems, however, its proteolysis into individual proteins is still debated. While molecular or biochemical characterization of methyltransferase, protease, hypervariable region, helicase and RNA polymerase domains in ORF1 has been achieved, the role of the X and Y domains in the HEV life cycle has only been demonstrated very recently. Clinically, detection of a number of ORF1 mutants in infected patients is implicated in disease severity, mortality and drug nonresponse. Moreover, several artificial lethal mutations in ORF1 offer a potential basis for developing live-attenuated vaccines for HEV. This article intends to present the molecular and clinical updates on the HEV ORF1 polyprotein.
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Affiliation(s)
- Mohammad Khalid Parvez
- Department of Pharmacognosy, King Saud University College of Pharmacy, Riyadh 11451, Saudi Arabia
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30
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Wu Q, An J, She R, Shi R, Hao W, Soomro M, Yuan X, Yang J, Wang J. Detection of Genotype 4 Swine Hepatitis E Virus in Systemic Tissues in Cross-Species Infected Rabbits. PLoS One 2017; 12:e0171277. [PMID: 28129390 PMCID: PMC5271373 DOI: 10.1371/journal.pone.0171277] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 01/17/2017] [Indexed: 12/14/2022] Open
Abstract
Increasing evidence demonstrates that hepatitis E virus (HEV) can be transmitted across species. According to previous reports, swine HEV has two genotypes, genotype 3 and 4, and both can infect humans by the fecal-oral route. Thus, it is crucial for the control of HEV zoonotic transmission to evaluate the dynamics of viral shedding and distribution in different tissues during cross-species infection by HEV. In this study, rabbits were infected with genotype 4 swine HEV by the intraperitoneal route. The results showed that HEV RNA not only shed in the feces but also in the saliva of some rabbits during infection with swine HEV. Viremia appeared late after infection, and anti-HEV IgG was not obvious until the appearance of high viremia levels. After the rabbits were euthanized, a histopathological examination showed that the livers developed overt hepatitis accompanied by an elevation of alanine aminotransferase (ALT) and aspartate transaminase (AST). Furthermore, HEV RNA was detected in various tissues, especially in the salivary glands and tonsils. Subsequently, negative-stranded HEV RNA was practiced in tissues with positive HEV RNA, which demonstrated that HEV replicated in the tissues. Next, we harvested additional tissues from the liver, salivary gland, tonsil, spleen, thymus gland, lymph node and intestine, which are known as replication sites of swine HEV. Additionally, we also observed the HEV antigen distributed in the organs above through immunohistochemical staining. These results demonstrate that rabbits could be used as an animal model for researching cross-species infection of genotype 4 HEV. It is also noteworthy that HEV can shed in the saliva and presents the risk of droplet transmission. These new data provide valuable information for understanding cross-species infection by HEV.
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Affiliation(s)
- Qiaoxing Wu
- Laboratory of veterinary pathology and public health, college of veterinary medicine, China Agricultural University, Beijing, China
| | - Junqing An
- Laboratory of veterinary pathology and public health, college of veterinary medicine, China Agricultural University, Beijing, China
| | - Ruiping She
- Laboratory of veterinary pathology and public health, college of veterinary medicine, China Agricultural University, Beijing, China
| | - Ruihan Shi
- Laboratory of veterinary pathology and public health, college of veterinary medicine, China Agricultural University, Beijing, China
| | - Wenzhuo Hao
- Laboratory of veterinary pathology and public health, college of veterinary medicine, China Agricultural University, Beijing, China
| | - MajidHussain Soomro
- Laboratory of veterinary pathology and public health, college of veterinary medicine, China Agricultural University, Beijing, China
| | - Xuerui Yuan
- Laboratory of veterinary pathology and public health, college of veterinary medicine, China Agricultural University, Beijing, China
| | - Jinling Yang
- Laboratory of veterinary pathology and public health, college of veterinary medicine, China Agricultural University, Beijing, China
| | - Jingyuan Wang
- Laboratory of veterinary pathology and public health, college of veterinary medicine, China Agricultural University, Beijing, China
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Kelly AG, Netzler NE, White PA. Ancient recombination events and the origins of hepatitis E virus. BMC Evol Biol 2016; 16:210. [PMID: 27733122 PMCID: PMC5062859 DOI: 10.1186/s12862-016-0785-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 09/30/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Hepatitis E virus (HEV) is an enteric, single-stranded, positive sense RNA virus and a significant etiological agent of hepatitis, causing sporadic infections and outbreaks globally. Tracing the evolutionary ancestry of HEV has proved difficult since its identification in 1992, it has been reclassified several times, and confusion remains surrounding its origins and ancestry. RESULTS To reveal close protein relatives of the Hepeviridae family, similarity searching of the GenBank database was carried out using a complete Orthohepevirus A, HEV genotype I (GI) ORF1 protein sequence and individual proteins. The closest non-Hepeviridae homologues to the HEV ORF1 encoded polyprotein were found to be those from the lepidopteran-infecting Alphatetraviridae family members. A consistent relationship to this was found using a phylogenetic approach; the Hepeviridae RdRp clustered with those of the Alphatetraviridae and Benyviridae families. This puts the Hepeviridae ORF1 region within the "Alpha-like" super-group of viruses. In marked contrast, the HEV GI capsid was found to be most closely related to the chicken astrovirus capsid, with phylogenetic trees clustering the Hepeviridae capsid together with those from the Astroviridae family, and surprisingly within the "Picorna-like" supergroup. These results indicate an ancient recombination event has occurred at the junction of the non-structural and structure encoding regions, which led to the emergence of the entire Hepeviridae family. The Astroviridae capsid is also closely related to the Tymoviridae family of monopartite, T = 3 icosahedral plant viruses, whilst its non-structural region is related to viruses of the Potyviridae; a large family of plant-infecting viruses with a flexible filamentous rod-shaped virion. Thus, we identified a separate inter-viral family recombination event, again at the non-structural/structural junction, which likely led to the creation of the Astroviridae. CONCLUSIONS In summary, we have shown that new viral families have been created though recombination at the junction of the genome that encodes non-structural and structural proteins, and such recombination events are implicated in the genesis of important human pathogens; HEV, astrovirus and rubella virus.
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Affiliation(s)
- Andrew G Kelly
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Natalie E Netzler
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia.
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Update on hepatitis E virology: Implications for clinical practice. J Hepatol 2016; 65:200-212. [PMID: 26966047 DOI: 10.1016/j.jhep.2016.02.045] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/15/2016] [Accepted: 02/21/2016] [Indexed: 12/18/2022]
Abstract
Hepatitis E virus (HEV) is a positive-strand RNA virus transmitted by the fecal-oral route. The 7.2kb genome encodes three open reading frames (ORF) which are translated into (i) the ORF1 polyprotein, representing the viral replicase, (ii) the ORF2 protein, corresponding to the viral capsid, and (iii) the ORF3 protein, a small protein involved in particle secretion. Although HEV is a non-enveloped virus in bile and feces, it circulates in the bloodstream wrapped in cellular membranes. HEV genotypes 1 and 2 infect only humans and cause mainly waterborne outbreaks. HEV genotypes 3 and 4 are widely represented in the animal kingdom and are transmitted as a zoonosis mainly via contaminated meat. HEV infection is usually self-limited but may persist and cause chronic hepatitis in immunocompromised patients. Reduction of immunosuppressive treatment or antiviral therapy with ribavirin have proven effective in most patients with chronic hepatitis E but therapy failures have been reported. Alternative treatment options are needed, therefore. Infection with HEV may also cause a number of extrahepatic manifestations, especially neurologic complications. Progress in the understanding of the biology of HEV should contribute to improved control and treatment of HEV infection.
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Zhou Y, Zhao C, Tian Y, Xu N, Wang Y. Characteristics and Functions of HEV Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 948:17-38. [PMID: 27738977 DOI: 10.1007/978-94-024-0942-0_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hepatitis E virus (HEV) is a non-enveloped virus containing a single-stranded, positive-sense RNA genome of 7.2 kb, which consists of a 5' noncoding region, three open reading frames (ORFs), and a 3' noncoding region. ORF1 is diverse between genotypes and encodes the nonstructural proteins, which include the enzymes needed for virus replication. In addition to its role in virus replication, the function of ORF1 is relevant to viral adaption in cultured cells and may also relate to virus infection and HEV pathogenicity. ORF2 protein is the capsid protein, which is about 660 amino acids in length. It not only protects the integrity of the viral genome but is also involved in many important physiological activities, such as virus assembly, infection, and host interaction. The main immune epitopes, especially neutralizing epitopes, are located on ORF2 protein, which is a candidate antigen for vaccine development. ORF3 protein is a phosphoprotein of 113 or 114 amino acids with a molecular weight of 13 kDa with multiple functions that can also induce strong immune reactivity.
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Affiliation(s)
- Yan Zhou
- Division of Drug and Cosmetics Inspection, Center for Food and Drug Inspection, China Food and Drug Administration, No.11 Fa Hua Nan Li, Dongcheng District, Beijing, 100061, China
| | - Chenyan Zhao
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control, No. 2 Tiantanxili, Dongcheng District, Beijing, 100050, China
| | - Yabin Tian
- Division of Diagnosis, National Institutes for Food and Drug Control, No. 2 Tiantanxili, Dongcheng District, Beijing, 100050, China
| | - Nan Xu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control, No. 2 Tiantanxili, Dongcheng District, Beijing, 100050, China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control, No. 2 Tiantanxili, Dongcheng District, Beijing, 100050, China.
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35
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Abstract
INTRODUCTION Hepatitis E virus (HEV) is one of the most common causes of acute viral hepatitis in the world with an estimated 20 million infections per year. Although the mortality rate is < 1% among the general population, pregnant women can have a fatality rate of up to 30%. Additionally, chronic hepatitis E has increasingly become a significant clinical problem in immunocompromised individuals. Effective antivirals against HEV are needed. AREAS COVERED This review article addresses the current state of knowledge of HEV infections with regard to animal and cell culture model systems that are important for antiviral discovery and testing, our current understanding of the molecular mechanisms of virus replication, our understanding of how each viral protein functions, and areas that can potentially be exploited as therapeutic targets. EXPERT OPINION Lack of an efficient cell culture system for HEV propagation, the limited knowledge of HEV lifecycle, and the inherent self-limiting infection within the normal populace make the development of new therapeutic agents against HEV challenging. There are many promising therapeutic targets, and the tools for identifying and testing potential antivirals are rapidly evolving. The development of effective therapeutics against HEV in immunocompromised and pregnant patient populations is warranted.
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Affiliation(s)
- Scott P Kenney
- Virginia Polytechnic Institute and State University (Virginia Tech), College of Veterinary Medicine, Center for Molecular Medicine and Infectious Diseases, Department of Biomedical Sciences and Pathobiology , CRC-Integrated Life Sciences Building (0913), 1981 Kraft Drive, Blacksburg, VA 24061-0913 , USA +1 540 231 6912 ; +1 540 231 3414 ;
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36
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Parvez MK. The hepatitis E virus ORF1 'X-domain' residues form a putative macrodomain protein/Appr-1″-pase catalytic-site, critical for viral RNA replication. Gene 2015; 566:47-53. [PMID: 25870943 PMCID: PMC7127128 DOI: 10.1016/j.gene.2015.04.026] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 03/24/2015] [Accepted: 04/09/2015] [Indexed: 12/13/2022]
Abstract
The hepatitis E virus (HEV) ORF1 gene encodes the non-structural polyprotein wherein the ‘X-domain’ still remains poorly defined. Cellular X-domain associated macrodomain protein/ADP-ribose-1″-monophosphatase (Appr-1″-pase) activities are also reported in coronaviruses (CoV), including identification of its homologs in alpha and rubella viruses. The present study investigated the role(s) of X-domain residues in HEV replication cycle. In silico analysis showed a high degree of evolutionary conservation of X-domain (a.a. 785–942) a.a. positions wherein the N-terminus residues ‘Asn806, Asn809, His812, Gly815, Gly816, and Gly817’ formed a potential catalytic-site homolog of CoVAppr-1″-pase. To experimentally test this prediction, X-domain ‘active-site’ residues were subjected to mutational analysis using the HEV-SAR55 replicon (pSK-GFP). FACS analysis of mutant RNA transfected S10-3 cells showed that Gly816Ala and Gly817Ala constructs completely abrogated HEV replication, similar to their Gly816Val and Gly817Val counterparts. However, ‘Gly815Ala’ mutant replicated very poorly in contrast to ‘Gly815Val’ that completely abolished GFP synthesis. Furthermore, while ‘Asn806Ala’ mutant retained RNA replication, the ‘Asn809Ala’ and His812Leu mutants showed non-viability. Notably, in a sequential-nucleotide mutation analysis, the dispensability of X-domain in HEV replication at transcriptional level has already been demonstrated (Parvez, 2013b). Taken together, the present data strongly argue for an essential role of X-domain residues (Asn809, His812, Gly816 and Gly817) at post-translational level, indicating its involvement in viral replication. In conclusion, the speculated regulatory role of ORF1 X-domain in HEV replication cycle critically depends on the ‘Asn, Asn, His, Gly, Gly, Gly’ segment/secondary structure. Nevertheless, further biochemical or biophysical characterizations of HEV X-domain associated Appr-1″-pase activity would only confirm its biological significance in virus or host-pathogenesis. Cellular ‘X-domain’ associated Appr-1″-pase also reported in RNA viruses Appr-1″-pase active-site homolog ‘NNHGGG’ mapped in HEV X-domain Mutational analysis showed criticality of the active-site a.a. in HEV replication. Dispensability of nt. conservation suggested a putative Appr-1″-pase activity.
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Affiliation(s)
- Mohammad Khalid Parvez
- Department of Pharmacognosy, King Saud University College of Pharmacy, PO Box-2457, Riyadh 11451, Saudi Arabia.
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37
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Quantitative proteomics identifies host factors modulated during acute hepatitis E virus infection in the swine model. J Virol 2014; 89:129-43. [PMID: 25320303 DOI: 10.1128/jvi.02208-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED Hepatitis E virus (HEV) causes acute enterically transmitted hepatitis. In industrialized countries, it is a zoonotic disease, with swine being the major reservoir of human HEV contamination. The occurrence and severity of the disease are variable, with clinical symptoms ranging from asymptomatic to self-limiting acute hepatitis, chronic infection, or fulminant hepatitis. In the absence of a robust cell culture system or small-animal models, the HEV life cycle and pathological process remain unclear. To characterize HEV pathogenesis and virulence mechanisms, a quantitative proteomic analysis was carried out to identify cellular factors and pathways modulated during acute infection of swine. Three groups of pigs were inoculated with three different strains of swine HEV to evaluate the possible role of viral determinants in pathogenesis. Liver samples were analyzed by a differential proteomic approach, two-dimensional difference in gel electrophoresis, and 61 modulated proteins were identified by mass spectroscopy. The results obtained show that the three HEV strains replicate similarly in swine and that they modulate several cellular pathways, suggesting that HEV impairs several cellular processes, which can account for the various types of disease expression. Several proteins, such as heterogeneous nuclear ribonucleoprotein K, apolipoprotein E, and prohibitin, known to be involved in other viral life cycles, were upregulated in HEV-infected livers. Some differences were observed between the three strains, suggesting that HEV's genetic variability may induce variations in pathogenesis. This comparative analysis of the liver proteome modulated during infection with three different strains of HEV genotype 3 provides an important basis for further investigations on the factors involved in HEV replication and the mechanism of HEV pathogenesis. IMPORTANCE Hepatitis E virus (HEV) is responsible for acute hepatitis, with clinical symptoms ranging from asymptomatic to self-limiting acute hepatitis, chronic infection, or fulminant hepatitis. In industrialized countries, HEV is considered an emerging zoonotic disease, with swine being the principal reservoir for human contamination. The viral and cellular factors involved in the replication and/or pathogenesis of HEV are still not fully known. Here we report that several cellular pathways involved in cholesterol and lipid metabolism or cell survival were modulated during HEV infection in the swine model. Moreover, we observed a difference between the different swine strains, suggesting that HEV's genetic variability could play a role in pathogenesis. We also identified some proteins known to be involved in other viral cycles. Our study provides insight into the mechanisms modulated during HEV infection and constitutes a useful reference for future work on HEV pathogenesis and virulence.
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Paliwal D, Panda SK, Kapur N, Varma SPK, Durgapal H. Hepatitis E virus (HEV) protease: a chymotrypsin-like enzyme that processes both non-structural (pORF1) and capsid (pORF2) protein. J Gen Virol 2014; 95:1689-1700. [PMID: 24795447 DOI: 10.1099/vir.0.066142-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hepatitis E virus (HEV), a major cause of acute viral hepatitis across the world, is a non-enveloped, plus-strand RNA virus. Its genome codes three proteins, pORF1 (multifunctional polyprotein), pORF2 (capsid protein) and pORF3 (multi-regulatory protein). pORF1 encodes methyltransferase, putative papain-like cysteine protease, helicase and replicase enzymes. Of these, the protease domain has not been characterized. On the basis of sequence analysis, we cloned and expressed a protein covering aa 440-610 of pORF1, expression of which led to cell death in Escherichia coli BL-21 and Huh7 hepatoma cells. Finally, we expressed and purified this protein from E. coli C43 cells (resistant to toxic proteins). The refolded form of this protein showed protease activity in gelatin zymography. Digestion assays showed cleavage of both pORF1 and pORF2 as observed previously. MS revealed digestion of capsid protein at both the N and C termini. N-terminal sequencing of the ~35 kDa methyltransferase, ~35 kDa replicase and ~56 kDa pORF2 proteins released by protease digestion revealed that the cleavage sites were alanine15/isoleucine16, alanine1364/valine1365 in pORF1 and leucine197/valine198 in pORF2. Specificity of these cleavage sites was validated by site-directed mutagenesis. Further characterization of the HEV protease, carried out using twelve inhibitors, showed chymostatin and PMSF to be the most efficient inhibitors, indicating this protein as a chymotrypsin-like protease. The specificity was further confirmed by cleavage of the chymotrypsin-specific fluorogenic peptide N-succinyl-Leu-Leu-Val-Tyr-7-amido-4-methylcoumarin. Mutational analysis of the conserved serine/cysteine/histidine residues suggested that H443 and C472/C481/C483 are possibly the active site residues. To our knowledge, this is the first direct demonstration of HEV protease and its function.
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Affiliation(s)
- Daizy Paliwal
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Subrat Kumar Panda
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Neeraj Kapur
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Satya Pavan Kumar Varma
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Hemlata Durgapal
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
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Mao J, Zhao Y, She R, Cao B, Xiao P, Wu Q, Guo Z, Ma L, Soomro MH. Detection and localization of rabbit hepatitis e virus and antigen in systemic tissues from experimentally intraperitoneally infected rabbits. PLoS One 2014; 9:e88607. [PMID: 24594631 PMCID: PMC3942314 DOI: 10.1371/journal.pone.0088607] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 01/10/2014] [Indexed: 01/10/2023] Open
Abstract
Rabbit hepatitis E virus (HEV) is a novel genotype of HEV, and is considered to pose a risk of zoonotic transmission. Research into the systemic distribution of rabbit HEV in rabbits during different periods of infection has rarely been reported. To better understand this virus, we infected rabbits with second-passage rabbit HEV via an intraperitoneal route. After inoculation, the infection showed two types, temporary and constant infection. The detection of HEV RNA in the feces varied with time, and serum antigen correlated with fecal HEV RNA. Viremia only appeared 72 days after inoculation. The rabbits remained antibody negative throughout the experimental period. When HEV was localized, several organs besides the liver were HEV RNA positive. Tissue antigen was observed immunohistochemically in the different cells of various organs, especially in parts of the small intestine and the characteristic rabbit gut-associated lymphoid tissue. These data provide valuable information for future research into the pathogenesis of HEV.
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Affiliation(s)
- Jingjing Mao
- Department of Veterinary Pathology, Laboratory of Veterinary Pathology and Public Health, College of Veterinary Medicine, China Agricultural University, Key Laboratory of Zoonosis of Ministry of Agriculture, Beijing, China
| | - Yue Zhao
- Department of Veterinary Pathology, Laboratory of Veterinary Pathology and Public Health, College of Veterinary Medicine, China Agricultural University, Key Laboratory of Zoonosis of Ministry of Agriculture, Beijing, China
| | - Ruiping She
- Department of Veterinary Pathology, Laboratory of Veterinary Pathology and Public Health, College of Veterinary Medicine, China Agricultural University, Key Laboratory of Zoonosis of Ministry of Agriculture, Beijing, China
- * E-mail:
| | - Binbin Cao
- Department of Veterinary Pathology, Laboratory of Veterinary Pathology and Public Health, College of Veterinary Medicine, China Agricultural University, Key Laboratory of Zoonosis of Ministry of Agriculture, Beijing, China
| | - Peng Xiao
- Department of Veterinary Pathology, Laboratory of Veterinary Pathology and Public Health, College of Veterinary Medicine, China Agricultural University, Key Laboratory of Zoonosis of Ministry of Agriculture, Beijing, China
| | - Qiaoxing Wu
- Department of Veterinary Pathology, Laboratory of Veterinary Pathology and Public Health, College of Veterinary Medicine, China Agricultural University, Key Laboratory of Zoonosis of Ministry of Agriculture, Beijing, China
| | - Zhaojie Guo
- Department of Veterinary Pathology, Laboratory of Veterinary Pathology and Public Health, College of Veterinary Medicine, China Agricultural University, Key Laboratory of Zoonosis of Ministry of Agriculture, Beijing, China
| | - Longhuan Ma
- Department of Veterinary Pathology, Laboratory of Veterinary Pathology and Public Health, College of Veterinary Medicine, China Agricultural University, Key Laboratory of Zoonosis of Ministry of Agriculture, Beijing, China
| | - Majid Hussain Soomro
- Department of Veterinary Pathology, Laboratory of Veterinary Pathology and Public Health, College of Veterinary Medicine, China Agricultural University, Key Laboratory of Zoonosis of Ministry of Agriculture, Beijing, China
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40
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Debing Y, Neyts J. Antiviral strategies for hepatitis E virus. Antiviral Res 2013; 102:106-18. [PMID: 24374149 PMCID: PMC7113752 DOI: 10.1016/j.antiviral.2013.12.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 12/12/2013] [Accepted: 12/14/2013] [Indexed: 02/08/2023]
Abstract
The hepatitis E virus is a common cause of acute hepatitis. Contrary to hepatitis B and C, hepatitis E is mostly a mild infection, although it has a high mortality in pregnant women and can evolve to chronicity in immunocompromised patients. Ribavirin and pegylated interferon-α are the only available therapies, but both have side effects that are not acceptable for prophylaxis or treatment of mild infections. In addition, these drugs cannot be used for all patient types (e.g. in case of pregnancy, specific organ transplants or co-morbidities) and in resource-poor settings. Hence there is an urgent need for better antiviral treatments that are efficacious and safe, also during pregnancy. In this review, a concise introduction to the virus and disease is provided, followed by a discussion of the available assay systems and potential molecular targets (viral proteins and host factors) for the development of inhibitors of HEV replication. Finally, directions for future research are presented.
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Affiliation(s)
- Yannick Debing
- Rega Institute for Medical Research, Department of Microbiology and Immunology, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Johan Neyts
- Rega Institute for Medical Research, Department of Microbiology and Immunology, Minderbroedersstraat 10, 3000 Leuven, Belgium.
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41
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Parvez MK, Khan AA. Molecular modeling and analysis of hepatitis E virus (HEV) papain-like cysteine protease. Virus Res 2013; 179:220-4. [PMID: 24321124 PMCID: PMC7114377 DOI: 10.1016/j.virusres.2013.11.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 11/18/2013] [Accepted: 11/19/2013] [Indexed: 12/14/2022]
Abstract
The biochemical or biophysical characterization of a papain-like cysteine protease in HEV ORF1-encoded polyprotein still remains elusive. Very recently, we have demonstrated the indispensability of ORF1 protease-domain cysteines and histidines in HEV replication, ex vivo (Parvez, 2013). In this report, the polyprotein partial sequences of HEV strains and genetically-related RNA viruses were analyzed, in silico. Employing the consensus-prediction results of RUBV-p150 protease as structural-template, a 3D model of HEV-protease was deduced. Similar to RUBV-p150, a ‘papain-like β-barrel fold’ structurally confirmed the classification of HEV-protease. Further, we recognized a catalytic ‘Cys434-His443’ dyad homologue of RUBV-p150 (Cys1152-His1273) and FMDV-Lpro (Cys51-His148) in line with our previous mutational analysis that showed essentiality of ‘His443’ but not ‘His590’ in HEV viability. Moreover, a RUBV ‘Zn2+ binding motif’ (Cys1167-Cys1175-Cys1178-Cys1225-Cys1227) equivalent of HEV was identified as ‘Cys457-His458-Cys459 and Cys481-Cys483’ residues within the ‘β-barrel fold’. Notably, unlike RUBV, ‘His458’ also clustered therein, that was in conformity with the consensus cysteine protease ‘Zn2+-binding motif’. By homology, we also proposed an overlapping ‘Ca2+-binding site’ ‘D-X-[DNS]-[ILVFYW]-[DEN]-G-[GP]-XX-DE’ signature, and a ‘proline-rich motif’ interacting ‘tryptophan (W437-W472)’ module in the modeled structure. Our analysis of the predicted model therefore, warrants critical roles of the ‘catalytic dyad’ and ‘divalent metal-binding motifs’ in HEV protease structural-integrity, ORF1 self-processing, and RNA replication. This however, needs further experimental validations.
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Affiliation(s)
- Mohammad Khalid Parvez
- Department of Pharmacognosy, King Saud University College of Pharmacy, Riyadh 11451, Saudi Arabia.
| | - Azmat Ali Khan
- Department of Pharmaceutical Chemistry, King Saud University College of Pharmacy, Riyadh 11451, Saudi Arabia
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42
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Parvez MK. Molecular characterization of hepatitis E virus ORF1 gene supports a papain-like cysteine protease (PCP)-domain activity. Virus Res 2013; 178:553-6. [PMID: 23978667 PMCID: PMC7125709 DOI: 10.1016/j.virusres.2013.07.020] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 07/25/2013] [Accepted: 07/29/2013] [Indexed: 12/24/2022]
Abstract
Hepatitis E Virus (HEV) ORF1 encodes the nonstructural polyprotein wherein a role of PCP-domain in ORF1 proteolysis and/or RNA replication still remains contested. A series of ORF1 mutants of HEV-SAR55 replicon were constructed and tested for viability in S10-3 cells. Six of PCP-'cysteine' (C457A, C459A, C471A, C472A, C481A and C483A) and three 'histidine' (H443L, H497L and H590L) mutants were lethal. Further, a highly conserved 'glycine-triad' (G815-G816-G817) in downstream X-domain, homologous to rubella virus protease-substrate (G1299-G1300-G1301) was identified where two of X-mutants (G816V and G817V) turned lethal. However, all ORF1 sequential nucleotide-mutants conserving the amino acids were viable, which clearly showed post-translational regulation of HEV replication by PCP- and X-domains. Moreover, while vector-expressed ORF1-fusion polyprotein yielded a ~191 kDa band in vitro, it produced ~78 and ~35 kDa fragments ex vivo. Collectively, the indispensability and functional effects of 'PCP-catalytic' and 'X-substrate' residues on HEV replication strongly supported a viral protease.
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Affiliation(s)
- Mohammad Khalid Parvez
- Department of Pharmacognosy, King Saud University College of Pharmacy, PO Box 2457, Riyadh 11451, Saudi Arabia.
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43
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Panda SK, Varma SP. Hepatitis e: molecular virology and pathogenesis. J Clin Exp Hepatol 2013; 3:114-24. [PMID: 25755485 PMCID: PMC3940135 DOI: 10.1016/j.jceh.2013.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 05/01/2013] [Indexed: 12/12/2022] Open
Abstract
Hepatitis E virus is a single, positive-sense, capped and poly A tailed RNA virus classified under the family Hepeviridae. Enteric transmission, acute self-limiting hepatitis, frequent epidemic and sporadic occurrence, high mortality in affected pregnants are hallmarks of hepatitis E infection. Lack of an efficient culture system and resulting reductionist approaches for the study of replication and pathogenesis of HEV made it to be a less understood agent. Early studies on animal models, sub-genomic expression of open reading frames (ORF) and infectious cDNA clones have helped in elucidating the genome organization, important stages in HEV replication and pathogenesis. The genome contains three ORF's and three untranslated regions (UTR). The 5' distal ORF, ORF1 is translated by host ribosomes in a cap dependent manner to form the non-structural polyprotein including the viral replicase. HEV replicates via a negative-sense RNA intermediate which helps in the formation of the positive-sense genomic RNA and a single bi-cistronic sub-genomic RNA. The 3' distal ORF's including the major structural protein pORF2 and the multifunctional host interacting protein pORF3 are translated from the sub-genomic RNA. Pathogenesis in HEV infections is not well articulated, and remains a concern due to the many aspects like host dependent and genotype specific variations. Animal HEV, zoonosis, chronicity in immunosuppressed patients, and rapid decompensation in affected chronic liver diseased patients warrants detailed investigation of the underlying pathogenesis. Recent advances about structure, entry, egress and functional characterization of ORF1 domains has furthered our understanding about HEV. This article is an effort to review our present understanding about molecular biology and pathogenesis of HEV.
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Affiliation(s)
- Subrat K. Panda
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India,Address for correspondence. Subrat K. Panda, JC Bose Fellow, Professor & Head, Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India. Tel.: +91 11 26594924 (off.); fax: +91 11 26588663, +91 11 26588641.
| | - Satya P.K. Varma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
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44
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Perttilä J, Spuul P, Ahola T. Early secretory pathway localization and lack of processing for hepatitis E virus replication protein pORF1. J Gen Virol 2012; 94:807-816. [PMID: 23255617 DOI: 10.1099/vir.0.049577-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Hepatitis E virus (HEV) is a positive-strand RNA virus and a major causative agent of acute sporadic and epidemic hepatitis. HEV replication protein is encoded by ORF1 and contains the predicted domains of methyltransferase (MT), protease, macro domain, helicase (HEL) and polymerase (POL). In this study, the full-length protein pORF1 (1693 aa) and six truncated variants were expressed by in vitro translation and in human HeLa and hepatic Huh-7 cells by using several vector systems. The proteins were visualized by three specific antisera directed against the MT, HEL and POL domains. In vitro translation of full-length pORF1 yielded smaller quantities of two fragments. However, these fragments were not observed after pORF1 expression and pulse-chase studies in human cells, and their production was not dependent on the predicted protease domain in pORF1. The weight of evidence supports the proposition that pORF1 is not subjected to specific proteolytic processing, which is unusual among animal positive-strand RNA viruses but common for plant viruses. pORF1 was membrane associated in cells and localized to a perinuclear region, where it partially overlapped with localization of the endoplasmic reticulum (ER) marker BAP31 and was closely interspersed with staining of the ER-Golgi intermediate compartment marker protein ERGIC-53. Co-localization with BAP31 was enhanced by treatment with brefeldin A. Therefore, HEV may utilize modified early secretory pathway membranes for replication.
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Affiliation(s)
- Julia Perttilä
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Pirjo Spuul
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Tero Ahola
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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45
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Rogée S, Talbot N, Caperna T, Bouquet J, Barnaud E, Pavio N. New models of hepatitis E virus replication in human and porcine hepatocyte cell lines. J Gen Virol 2012; 94:549-558. [PMID: 23175242 DOI: 10.1099/vir.0.049858-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hepatitis E virus (HEV) causes acute, enterically transmitted hepatitis in human. It is associated with large epidemics in tropical and subtropical regions where it is endemic or with sporadic cases in non-endemic regions. Unlike other hepatitis viruses, HEV has several animal reservoirs. Phylogenetic studies on HEV human and animal sequences, and the identification of cases of direct transmission from animal to human strongly suggest that HEV is a zoonotic agent. The lack of efficient cell culture models limits studies on molecular and cellular aspects of HEV infection and species barrier crossing. The present study reports on the development of two new in vitro models of HEV replication using a human hepatoma-derived cell line, HepaRG, and a porcine embryonic stem cell-derived cell line, PICM-19. These two cell lines have morphological and functional properties similar to primary hepatocytes. These in vitro culture systems support HEV replication and release of encapsidated RNA. These new models represent a powerful tool for studying the viral replication cycle, species barrier crossing and virulence factors.
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Affiliation(s)
- Sophie Rogée
- UMR 1161 Virology, Ecole Nationale Vétérinaire d'Alfort, 94706 Maisons-Alfort, France.,UMR 1161 Virology, INRA, 94706 Maisons-Alfort, France.,UMR 1161 Virology, ANSES, Laboratoire de Santé Animale, 94706 Maisons-Alfort, France
| | - Neil Talbot
- USDA, ARS, Animal and Natural Resources Institute, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| | - Thomas Caperna
- USDA, ARS, Animal and Natural Resources Institute, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| | - Jérôme Bouquet
- UMR 1161 Virology, Ecole Nationale Vétérinaire d'Alfort, 94706 Maisons-Alfort, France.,UMR 1161 Virology, INRA, 94706 Maisons-Alfort, France.,UMR 1161 Virology, ANSES, Laboratoire de Santé Animale, 94706 Maisons-Alfort, France
| | - Elodie Barnaud
- UMR 1161 Virology, Ecole Nationale Vétérinaire d'Alfort, 94706 Maisons-Alfort, France.,UMR 1161 Virology, INRA, 94706 Maisons-Alfort, France.,UMR 1161 Virology, ANSES, Laboratoire de Santé Animale, 94706 Maisons-Alfort, France
| | - Nicole Pavio
- UMR 1161 Virology, Ecole Nationale Vétérinaire d'Alfort, 94706 Maisons-Alfort, France.,UMR 1161 Virology, INRA, 94706 Maisons-Alfort, France.,UMR 1161 Virology, ANSES, Laboratoire de Santé Animale, 94706 Maisons-Alfort, France
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Cao D, Meng XJ. Molecular biology and replication of hepatitis E virus. Emerg Microbes Infect 2012; 1:e17. [PMID: 26038426 PMCID: PMC3630916 DOI: 10.1038/emi.2012.7] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 03/21/2012] [Accepted: 04/08/2012] [Indexed: 02/07/2023]
Abstract
Hepatitis E virus (HEV), a single-stranded, positive-sense RNA virus, is responsible for acute hepatitis E epidemics in many developing countries, and the virus is also endemic in some industrialized countries. Hepatitis E is a recognized zoonotic disease, and several animal species, including pigs, are potential reservoirs for HEV. The genome of HEV contains three open reading frames (ORFs). ORF1 encodes the nonstructural proteins, ORF2 encodes the capsid protein, and ORF3 encodes a small multifunctional protein. The ORF2 and ORF3 proteins are translated from a single, bicistronic mRNA. The coding sequences for these two ORFs overlap each other, but neither overlaps with ORF1. Whereas the mechanisms underlying HEV replication are poorly understood, the construction of infectious viral clones, the identification of cell lines that support HEV replication, and the development of small animal models have allowed for more detailed study of the virus. As result of these advances, recently, our understanding of viral entry, genomic replication and viral egress has improved. Furthermore, the determination of the T=1 and T=3 structure of HEV virus-like particles has furthered our understanding of the replication of HEV. This article reviews the latest developments in the molecular biology of HEV with an emphasis on the genomic organization, the expression and function of genes, and the structure and replication of HEV.
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Affiliation(s)
- Dianjun Cao
- Center for Molecular Medicine and Infectious Diseases, Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University (Virginia Tech) , Blacksburg, VA 24061-0913, USA
| | - Xiang-Jin Meng
- Center for Molecular Medicine and Infectious Diseases, Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University (Virginia Tech) , Blacksburg, VA 24061-0913, USA
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Geng J, Fu H, Wang L, Bu Q, Liu P, Wang M, Sui Y, Wang X, Zhu Y, Zhuang H. Phylogenetic analysis of the full genome of rabbit hepatitis E virus (rbHEV) and molecular biologic study on the possibility of cross species transmission of rbHEV. INFECTION GENETICS AND EVOLUTION 2011; 11:2020-5. [PMID: 21945590 DOI: 10.1016/j.meegid.2011.09.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Revised: 08/31/2011] [Accepted: 09/08/2011] [Indexed: 01/04/2023]
Abstract
Rabbit HEV strains were isolated in China from farmed rabbits, which may be a reservoir of a novel genotype of HEV. However, there is little information regarding host range and zoonotic potential of rabbit HEV. A previous study from this group identified 25 specific nucleotide positions as possibly being involved in specifying the host range of HEV and/or in determining the severity of hepatitis E disease, whereas this previous analysis did not extend to the new rabbit HEVs. Consequently the complete genome of the rabbit HEV strain ch-bj-n1 was amplified as overlapping fragments using a combination of reverse-transcription-nested polymerase chain reaction and rapid amplification of cDNA ends. The resulting sequence together with two other rabbit HEVs were compared with 91 other HEV isolates representative of genotypes 1-4. Phylogenetic analysis showed that the novel rabbit HEV strain should be classified into a new HEV genotype which has a closer evolutionary relationship with genotype 3 than genotypes 1, 2 and 4, with 20 of the 25 specific nucleotide positions identified as being present in rabbit HEV genome. Alpha-helix, hydrophilicity, and surface probability plots together with antigenic index analysis of the ORF2 protein were all undertaken to investigate the antigenicity of rabbit HEV. The alpha-helix plot and antigenicity index of the rabbit ORF2 protein was nearly identical to that of genotype 1 HEV isolates from human. Furthermore, 20 possible host range determinants in rabbit HEV were identical to those isolates from zoonotic groups, which may suggest a potential possibility of cross species transmission of rabbit HEV.
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Affiliation(s)
- Jiabao Geng
- Institute of Hepatology, The 81st Hospital of PLA, Nanjing, Jiangsu Province, China
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Karpe YA, Lole KS. Deubiquitination activity associated with hepatitis E virus putative papain-like cysteine protease. J Gen Virol 2011; 92:2088-2092. [DOI: 10.1099/vir.0.033738-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Hepatitis E virus (HEV) ORF1 protein (pORF1) contains methyltransferase (MetT), papain-like cysteine protease (PCP), RNA helicase (Hel) and RNA-dependent RNA polymerase (RdRp) domains. ORF1 sequence analysis showed two consensus LXGG cleavage sites at 664 and 1205. LXGG sequence is recognized by viral and cellular deubiquitinating enzymes. The protein encompassing the predicted MetT-PCP domains of HEV ORF1 was tested for deubiquitinating activity using fluorogenic substrates – ubiquitin-7-amino-4-methylcoumarin (AMC), IFN-stimulated gene 15 (ISG15)-AMC, Nedd8-AMC and SUMO-AMC. MetT-PCP cleaved all four substrates but processing of ISG15-AMC was more robust. There was no processing of the Hel and RdRp domains having the conserved (1205) LXGG site by the protein. MetT-PCP carried out deISGylation of the ISG15-conjugated cellular proteins, suggesting a possible role in combating cellular antiviral pathways.
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Affiliation(s)
- Yogesh A. Karpe
- Hepatitis Division, National Institute of Virology, Microbial Containment Complex, Sus Road, Pashan, Pune 411021, India
| | - Kavita S. Lole
- Hepatitis Division, National Institute of Virology, Microbial Containment Complex, Sus Road, Pashan, Pune 411021, India
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49
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Suppiah S, Zhou Y, Frey TK. Lack of processing of the expressed ORF1 gene product of hepatitis E virus. Virol J 2011; 8:245. [PMID: 21595991 PMCID: PMC3116494 DOI: 10.1186/1743-422x-8-245] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 05/20/2011] [Indexed: 01/25/2023] Open
Abstract
Background Proteolytic processing is a common mechanism among plus strand RNA viruses and the replicases of all plus strand RNA viruses of animals thus far characterized undergo such processing. The replicase proteins of hepatitis E virus (HEV) are encoded by ORF1. A previous report published by our group [1] provided data that processing potentially occurred when ORF1 (Burma strain; genotype 1) was expressed using a vaccinia virus-based expression system. Findings To further test for processing and to rule out artifacts associated with the expression system, ORF1 was re-expressed using a plasmid-based expression vector with the result that the previous processing profile could not be confirmed. When ORF1 from an HEV infectious cDNA clone (US swine strain; genotype 3) was expressed using the plasmid-based system, the only species detected was the 185 kDa precursor of ORF1. A putative papain-like cysteine protease [2] had been predicted within ORF1 using the original HEV genomic sequence. However, analysis of subsequent ORF1 sequences from a large number of HEV isolates reveals that this protease motif is not conserved. Conclusions The expressed HEV ORF1 gene product does not undergo proteolytic processing, indicating that the replicase precursor of HEV is potentially unique in this regard.
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Affiliation(s)
- Suganthi Suppiah
- Department of Biology, Georgia State University, Atlanta, GA, USA
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Ahmad I, Holla RP, Jameel S. Molecular virology of hepatitis E virus. Virus Res 2011; 161:47-58. [PMID: 21345356 PMCID: PMC3130092 DOI: 10.1016/j.virusres.2011.02.011] [Citation(s) in RCA: 181] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 02/13/2011] [Accepted: 02/13/2011] [Indexed: 12/15/2022]
Abstract
This review details the molecular virology of the hepatitis E virus (HEV). While replicons and in vitro infection systems have recently become available, a lot of information on HEV has been generated through comparisons with better-studied positive-strand RNA viruses and through subgenomic expression of viral open reading frames. These models are now being verified with replicon and infection systems. We provide here the current knowledge on the HEV genome and its constituent proteins--ORF1, ORF2 and ORF3. Based on the available information, we also modify the existing model of the HEV life cycle.
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Affiliation(s)
- Imran Ahmad
- Virology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
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