1
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Yao L, Zhang W, Chen X, Yi M, Jia K. Methyltransferase-like 3 suppresses red spotted grouper nervous necrosis virus and viral hemorrhagic septicemia virus infection by enhancing type I interferon responses in sea perch. FISH & SHELLFISH IMMUNOLOGY 2023; 140:108993. [PMID: 37573969 DOI: 10.1016/j.fsi.2023.108993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/01/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
Methylation at the N6 position of adenosine (m6A) is the most abundant internal mRNA modification in eukaryotes, tightly associating with regulation of viral life circles and immune responses. Here, a methyltransferase-like 3 homolog gene from sea perch (Lateolabrax japonicus), designated LjMETTL3, was cloned and characterized, and its negative role in fish virus pathogenesis was uncovered. The cDNA of LjMETTL3 encoded a 601-amino acid protein with a MT-A70 domain, which shared the closest genetic relationship with Echeneis naucrates METTL3. Spatial expression analysis revealed that LjMETTL3 was more abundant in the immune tissues of sea perch post red spotted grouper nervous necrosis virus (RGNNV) or viral hemorrhagic septicemia virus (VHSV) infection. LjMETTL3 expression was significantly upregulated at 12 and 24 h post RGNNV and VHSV infection in vitro. In addition, ectopic expression of LjMETTL3 inhibited RGNNV and VHSV infection in LJB cells at 12 and 24 h post infection, whereas knockdown of LjMETTL3 led to opposite effects. Furthermore, we found that LjMETTL3 may participate in boosting the type I interferon responses by interacting with TANK-binding kinase. Taken together, these results disclosed the antiviral role of fish METTL3 against RGNNV and VHSV and provided evidence for understanding the potential mechanisms of fish METTL3 in antiviral innate immunity.
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Affiliation(s)
- Lan Yao
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, China
| | - Wanwan Zhang
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, China
| | - Xiaoqi Chen
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, China
| | - Meisheng Yi
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, China.
| | - Kuntong Jia
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, China.
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2
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Jesse ST, Ribó-Molina P, Jo WK, Rautenschlein S, Vuong O, Fouchier RAM, Ludlow M, Osterhaus ADME. Molecular characterization of avian metapneumovirus subtype C detected in wild mallards (Anas platyrhynchos) in The Netherlands. Transbound Emerg Dis 2022; 69:3360-3370. [PMID: 36029486 DOI: 10.1111/tbed.14688] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 07/21/2022] [Accepted: 08/10/2022] [Indexed: 02/07/2023]
Abstract
Avian metapneumovirus (AMPV) represents a long-term threat to the poultry industry due to its etiological role in the induction of acute respiratory disease and/or egg drop syndrome in domestic turkeys, chickens, and ducks. Although this disease is commonly referred to as turkey rhinotracheitis, the host range of AMPV encompasses many avian species. We have screened 1323 oropharyngeal- and cloacal swab samples obtained from wild mallards in the Netherlands from 2017 to 2019 by RT-PCR using a degenerate primer pair to detect all members of the Paramyxoviridae and Pneumoviridae or an avian metapneumovirus subtype C (AMPV-C)-specific RT-qPCR assay. We identified a total of seven cases of AMPV-C infections in wild, healthy mallards (Anas platyrhynchos), of which two AMPV-C positive samples were further processed using next-generation sequencing. Phylogenetic analysis of the two complete genomes showed that the newly identified AMPV-C strains share closest sequence identity (97%) with Eurasian lineage AMPV-C strains identified in Muscovy ducks in China that presented with severe respiratory disease and egg production loss in 2011. Further analysis of G protein amino acid sequences showed a high degree of variability between the newly identified AMPV-C variants. PONDR scoring of the G protein has revealed the ectodomain of AMPV-C to be partitioned into a long intrinsically disordered and short ordered region, giving insights into AMPV G protein structural biology. In summary, we provide the first report of full-length AMPV-C genome sequences derived from wild birds in Europe. This emphasizes the need for further surveillance efforts to better characterize the host range, epidemiologic distribution, and pathogenicity of AMPV-C to determine the risk posed by cross-species jumps from wildfowl to domesticated avian species.
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Affiliation(s)
- Sonja T Jesse
- Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany
| | - Pau Ribó-Molina
- Department Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Wendy K Jo
- Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany
| | - Silke Rautenschlein
- Clinic for Poultry, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Oanh Vuong
- Department Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ron A M Fouchier
- Clinic for Poultry, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Martin Ludlow
- Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany
| | - Albert D M E Osterhaus
- Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany
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3
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Dhulipala S, Uversky VN. Looking at the Pathogenesis of the Rabies Lyssavirus Strain Pasteur Vaccins through a Prism of the Disorder-Based Bioinformatics. Biomolecules 2022; 12:1436. [PMID: 36291645 PMCID: PMC9599798 DOI: 10.3390/biom12101436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/28/2022] Open
Abstract
Rabies is a neurological disease that causes between 40,000 and 70,000 deaths every year. Once a rabies patient has become symptomatic, there is no effective treatment for the illness, and in unvaccinated individuals, the case-fatality rate of rabies is close to 100%. French scientists Louis Pasteur and Émile Roux developed the first vaccine for rabies in 1885. If administered before the virus reaches the brain, the modern rabies vaccine imparts long-lasting immunity to the virus and saves more than 250,000 people every year. However, the rabies virus can suppress the host's immune response once it has entered the cells of the brain, making death likely. This study aimed to make use of disorder-based proteomics and bioinformatics to determine the potential impact that intrinsically disordered protein regions (IDPRs) in the proteome of the rabies virus might have on the infectivity and lethality of the disease. This study used the proteome of the Rabies lyssavirus (RABV) strain Pasteur Vaccins (PV), one of the best-understood strains due to its use in the first rabies vaccine, as a model. The data reported in this study are in line with the hypothesis that high levels of intrinsic disorder in the phosphoprotein (P-protein) and nucleoprotein (N-protein) allow them to participate in the creation of Negri bodies and might help this virus to suppress the antiviral immune response in the host cells. Additionally, the study suggests that there could be a link between disorder in the matrix (M) protein and the modulation of viral transcription. The disordered regions in the M-protein might have a possible role in initiating viral budding within the cell. Furthermore, we checked the prevalence of functional disorder in a set of 37 host proteins directly involved in the interaction with the RABV proteins. The hope is that these new insights will aid in the development of treatments for rabies that are effective after infection.
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Affiliation(s)
- Surya Dhulipala
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Moscow Region, Russia
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4
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Redwan EM, Aljadawi AA, Uversky VN. Hepatitis C Virus Infection and Intrinsic Disorder in the Signaling Pathways Induced by Toll-Like Receptors. BIOLOGY 2022; 11:1091. [PMID: 36101469 PMCID: PMC9312352 DOI: 10.3390/biology11071091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022]
Abstract
In this study, we examined the interplay between protein intrinsic disorder, hepatitis C virus (HCV) infection, and signaling pathways induced by Toll-like receptors (TLRs). To this end, 10 HCV proteins, 10 human TLRs, and 41 proteins from the TLR-induced downstream pathways were considered from the prevalence of intrinsic disorder. Mapping of the intrinsic disorder to the HCV-TLR interactome and to the TLR-based pathways of human innate immune response to the HCV infection demonstrates that substantial levels of intrinsic disorder are characteristic for proteins involved in the regulation and execution of these innate immunity pathways and in HCV-TLR interaction. Disordered regions, being commonly enriched in sites of various posttranslational modifications, may play important functional roles by promoting protein-protein interactions and support the binding of the analyzed proteins to other partners such as nucleic acids. It seems that this system represents an important illustration of the role of intrinsic disorder in virus-host warfare.
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Affiliation(s)
- Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
- Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, Alexandria 21934, Egypt
| | - Abdullah A. Aljadawi
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
| | - Vladimir N. Uversky
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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5
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Goh GKM, Dunker AK, Foster JA, Uversky VN. Shell Disorder Models Detect That Omicron Has Harder Shells with Attenuation but Is Not a Descendant of the Wuhan-Hu-1 SARS-CoV-2. Biomolecules 2022; 12:631. [PMID: 35625559 PMCID: PMC9139003 DOI: 10.3390/biom12050631] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/17/2022] [Accepted: 04/20/2022] [Indexed: 02/01/2023] Open
Abstract
Before the SARS-CoV-2 Omicron variant emergence, shell disorder models (SDM) suggested that an attenuated precursor from pangolins may have entered humans in 2017 or earlier. This was based on a shell disorder analysis of SARS-CoV-1/2 and pangolin-Cov-2017. The SDM suggests that Omicron is attenuated with almost identical N (inner shell) disorder as pangolin-CoV-2017 (N-PID (percentage of intrinsic disorder): 44.8% vs. 44.9%-lower than other variants). The outer shell disorder (M-PID) of Omicron is lower than that of other variants and pangolin-CoV-2017 (5.4% vs. 5.9%). COVID-19-related CoVs have the lowest M-PIDs (hardest outer shell) among all CoVs. This is likely to be responsible for the higher contagiousness of SARS-CoV-2 and Omicron, since hard outer shell protects the virion from salivary/mucosal antimicrobial enzymes. Phylogenetic study using M reveals that Omicron branched off from an ancestor of the Wuhan-Hu-1 strain closely related to pangolin-CoVs. M, being evolutionarily conserved in COVID-19, is most ideal for COVID-19 phylogenetic study. Omicron may have been hiding among burrowing animals (e.g., pangolins) that provide optimal evolutionary environments for attenuation and increase shell hardness, which is essential for fecal-oral-respiratory transmission via buried feces. Incoming data support SDM e.g., the presence of fewer infectious particles in the lungs than in the bronchi upon infection.
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Affiliation(s)
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - James A. Foster
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA;
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142290 Moscow Region, Russia
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6
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Cardone C, Caseau CM, Bardiaux B, Thureaux A, Galloux M, Bajorek M, Eléouët JF, Litaudon M, Bontems F, Sizun C. A Structural and Dynamic Analysis of the Partially Disordered Polymerase-Binding Domain in RSV Phosphoprotein. Biomolecules 2021; 11:biom11081225. [PMID: 34439894 PMCID: PMC8392014 DOI: 10.3390/biom11081225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022] Open
Abstract
The phosphoprotein P of Mononegavirales (MNV) is an essential co-factor of the viral RNA polymerase L. Its prime function is to recruit L to the ribonucleocapsid composed of the viral genome encapsidated by the nucleoprotein N. MNV phosphoproteins often contain a high degree of disorder. In Pneumoviridae phosphoproteins, the only domain with well-defined structure is a small oligomerization domain (POD). We previously characterized the differential disorder in respiratory syncytial virus (RSV) phosphoprotein by NMR. We showed that outside of RSV POD, the intrinsically disordered N-and C-terminal regions displayed a structural and dynamic diversity ranging from random coil to high helical propensity. Here we provide additional insight into the dynamic behavior of PCα, a domain that is C-terminal to POD and constitutes the RSV L-binding region together with POD. By using small phosphoprotein fragments centered on or adjacent to POD, we obtained a structural picture of the POD–PCα region in solution, at the single residue level by NMR and at lower resolution by complementary biophysical methods. We probed POD–PCα inter-domain contacts and showed that small molecules were able to modify the dynamics of PCα. These structural properties are fundamental to the peculiar binding mode of RSV phosphoprotein to L, where each of the four protomers binds to L in a different way.
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Affiliation(s)
- Christophe Cardone
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Claire-Marie Caseau
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 78015 Paris, France;
| | | | - Marie Galloux
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Monika Bajorek
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - François Bontems
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
- Correspondence:
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7
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Feng Q, Zhao H, Xu L, Xie Z. N6-Methyladenosine Modification and Its Regulation of Respiratory Viruses. Front Cell Dev Biol 2021; 9:699997. [PMID: 34368152 PMCID: PMC8342946 DOI: 10.3389/fcell.2021.699997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/28/2021] [Indexed: 11/23/2022] Open
Abstract
N6-methyladenosine (m6A) is a ubiquitous RNA modification in eukaryotes. It plays important roles in the translocation, stabilization and translation of mRNA. Many recent studies have shown that the dysregulation of m6A modification is connected with diseases caused by pathogenic viruses, and studies on the role of m6A in virus-host interactions have shown that m6A plays a wide range of regulatory roles in the life cycle of viruses. Respiratory viruses are common pathogens that can impose a large disease burden on young children and elderly people. Here, we review the effects of m6A modification on respiratory virus replication and life cycle and host immunity against viruses.
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Affiliation(s)
- Qianyu Feng
- Beijing Key Laboratory of Paediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, National Key Discipline of Paediatrics (Capital Medical University), Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing Paediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China.,Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Hongwei Zhao
- Beijing Key Laboratory of Paediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, National Key Discipline of Paediatrics (Capital Medical University), Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing Paediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China.,Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Lili Xu
- Beijing Key Laboratory of Paediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, National Key Discipline of Paediatrics (Capital Medical University), Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing Paediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China.,Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhengde Xie
- Beijing Key Laboratory of Paediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, National Key Discipline of Paediatrics (Capital Medical University), Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing Paediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China.,Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
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8
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Cardone C, Caseau CM, Pereira N, Sizun C. Pneumoviral Phosphoprotein, a Multidomain Adaptor-Like Protein of Apparent Low Structural Complexity and High Conformational Versatility. Int J Mol Sci 2021; 22:ijms22041537. [PMID: 33546457 PMCID: PMC7913705 DOI: 10.3390/ijms22041537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 01/16/2023] Open
Abstract
Mononegavirales phosphoproteins (P) are essential co-factors of the viral polymerase by serving as a linchpin between the catalytic subunit and the ribonucleoprotein template. They have highly diverged, but their overall architecture is conserved. They are multidomain proteins, which all possess an oligomerization domain that separates N- and C-terminal domains. Large intrinsically disordered regions constitute their hallmark. Here, we exemplify their structural features and interaction potential, based on the Pneumoviridae P proteins. These P proteins are rather small, and their oligomerization domain is the only part with a defined 3D structure, owing to a quaternary arrangement. All other parts are either flexible or form short-lived secondary structure elements that transiently associate with the rest of the protein. Pneumoviridae P proteins interact with several viral and cellular proteins that are essential for viral transcription and replication. The combination of intrinsic disorder and tetrameric organization enables them to structurally adapt to different partners and to act as adaptor-like platforms to bring the latter close in space. Transient structures are stabilized in complex with protein partners. This class of proteins gives an insight into the structural versatility of non-globular intrinsically disordered protein domains.
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9
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Baillon L, Mérour E, Cabon J, Louboutin L, Vigouroux E, Alencar ALF, Cuenca A, Blanchard Y, Olesen NJ, Panzarin V, Morin T, Brémont M, Biacchesi S. The Viral Hemorrhagic Septicemia Virus (VHSV) Markers of Virulence in Rainbow Trout ( Oncorhynchus mykiss). Front Microbiol 2020; 11:574231. [PMID: 33193184 PMCID: PMC7606196 DOI: 10.3389/fmicb.2020.574231] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022] Open
Abstract
Viral hemorrhagic septicemia virus (VHSV) is a highly contagious virus leading to high mortality in a large panel of freshwater and marine fish species. VHSV isolates originating from marine fish show low pathogenicity in rainbow trout. The analysis of several nearly complete genome sequences from marine and freshwater isolates displaying varying levels of virulence in rainbow trout suggested that only a limited number of amino acid residues might be involved in regulating the level of virulence. Based on a recent analysis of 55 VHSV strains, which were entirely sequenced and phenotyped in vivo in rainbow trout, several amino acid changes putatively involved in virulence were identified. In the present study, these amino acid changes were introduced, alone or in combination, in a highly-virulent VHSV 23–75 genome backbone by reverse genetics. A total of 35 recombinant VHSV variants were recovered and characterized for virulence in trout by bath immersion. Results confirmed the important role of the NV protein (R116S) and highlighted a major contribution of the nucleoprotein N (K46G and A241E) in regulating virulence. Single amino acid changes in these two proteins drastically affect virus pathogenicity in rainbow trout. This is particularly intriguing for the N variant (K46G) which is unable to establish an active infection in the fins of infected trout, the main portal of entry of VHSV in this species, allowing further spread in its host. In addition, salmonid cell lines were selected to assess the kinetics of replication and cytopathic effect of recombinant VHSV and discriminate virulent and avirulent variants. In conclusion, three major virulence markers were identified in the NV and N proteins. These markers explain almost all phenotypes (92.7%) observed in trout for the 55 VHSV strains analyzed in the present study and herein used for the backward validation of virulence markers. The identification of VHSV specific virulence markers in this species is of importance both to predict the in vivo phenotype of viral isolates with targeted diagnostic tests and to improve prophylactic methods such as the development of safer live-attenuated vaccines.
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Affiliation(s)
- Laury Baillon
- Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Université de Versailles Saint-Quentin-en-Yvelines, Jouy-en-Josas, France
| | - Emilie Mérour
- Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Université de Versailles Saint-Quentin-en-Yvelines, Jouy-en-Josas, France
| | - Joëlle Cabon
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Unité Pathologies Virales des Poissons, Plouzané, France
| | - Lénaïg Louboutin
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Unité Pathologies Virales des Poissons, Plouzané, France
| | - Estelle Vigouroux
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Unité Pathologies Virales des Poissons, Plouzané, France
| | - Anna Luiza Farias Alencar
- Unit for Fish and Shellfish Diseases, EURL for Fish and Crustacean Diseases, National Institute of Aquatic Resources, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Argelia Cuenca
- Unit for Fish and Shellfish Diseases, EURL for Fish and Crustacean Diseases, National Institute of Aquatic Resources, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Yannick Blanchard
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Unité Génétique Virale et Biosécurité, Ploufragan, France
| | - Niels Jørgen Olesen
- Unit for Fish and Shellfish Diseases, EURL for Fish and Crustacean Diseases, National Institute of Aquatic Resources, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Valentina Panzarin
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Padua, Italy
| | - Thierry Morin
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Unité Pathologies Virales des Poissons, Plouzané, France
| | - Michel Brémont
- Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Université de Versailles Saint-Quentin-en-Yvelines, Jouy-en-Josas, France
| | - Stéphane Biacchesi
- Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Université de Versailles Saint-Quentin-en-Yvelines, Jouy-en-Josas, France
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10
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Gupta MN, Roy I. Drugs, host proteins and viral proteins: how their promiscuities shape antiviral design. Biol Rev Camb Philos Soc 2020; 96:205-222. [PMID: 32918378 DOI: 10.1111/brv.12652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/24/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022]
Abstract
The reciprocal nature of drug specificity and target specificity implies that the same is true for their respective promiscuities. Protein promiscuity has two broadly different types of footprint in drug design. The first is relaxed specificity of binding sites for substrates, inhibitors, effectors or cofactors. The second involves protein-protein interactions of regulatory processes such as signal transduction and transcription, and here protein intrinsic disorder plays an important role. Both viruses and host cells exploit intrinsic disorder for their survival, as do the design and discovery programs for antivirals. Drug action, strictly speaking, always relies upon promiscuous activity, with drug promiscuity enlarging its scope. Drug repurposing searches for additional promiscuity on the part of both the drug and the target in the host. Understanding the subtle nuances of these promiscuities is critical in the design of novel and more effective antivirals.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab, 160062, India
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11
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Blundell TL, Gupta MN, Hasnain SE. Intrinsic disorder in proteins: Relevance to protein assemblies, drug design and host-pathogen interactions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 156:34-42. [PMID: 32628954 DOI: 10.1016/j.pbiomolbio.2020.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023]
Abstract
Intrinsic disorder in proteins resulting in considerable variation in structure can lead to multiple functions including multi-specificity and diverse pathologies. Protein interfaces can involve disordered regions that assemble through a concerted-fold-and-bind mechanism. The binding involves both enthalpic and entropic gains by exploiting 'hot spots' on the partner and displacing water molecules placed in thermodynamically unfavorable situations. The examples of Rad51-BRCA2 and Artemis-DNA-PKCs/LigIV complexes illustrate this in the context of drug design. This overview tracks the seamless involvement of protein disorder in multi-specificity of biocatalysts, protein assembly formations and host-pathogen interactions, where intrinsic disorder can in Mycobacteria, compensate for genome reduction by carrying out multiple functions and in some RNA viruses facilitate adaption to the host. These present challenging opportunities for designing new drugs and interventions.
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Affiliation(s)
- Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, CB21GA, UK
| | - Munishwar N Gupta
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Seyed E Hasnain
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, India; Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Prof C.R. Rao Road, Hyderabad, India.
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12
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Kumar D, Singh A, Kumar P, Uversky VN, Rao CD, Giri R. Understanding the penetrance of intrinsic protein disorder in rotavirus proteome. Int J Biol Macromol 2020; 144:892-908. [PMID: 31739058 PMCID: PMC7112477 DOI: 10.1016/j.ijbiomac.2019.09.166] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/09/2019] [Accepted: 09/20/2019] [Indexed: 01/03/2023]
Abstract
Rotavirus is a major cause of severe acute gastroenteritis in the infants and young children. The past decade has evidenced the role of intrinsically disordered proteins/regions (IDPs)/(IDPRs) in viral and other diseases. In general, (IDPs)/(IDPRs) are considered as dynamic conformational ensembles that devoid of a specific 3D structure, being associated with various important biological phenomena. Viruses utilize IDPs/IDPRs to survive in harsh environments, to evade the host immune system, and to highjack and manipulate host cellular proteins. The role of IDPs/IDPRs in Rotavirus biology and pathogenicity are not assessed so far, therefore, we have designed this study to deeply look at the penetrance of intrinsic disorder in rotavirus proteome consisting 12 proteins encoded by 11 segments of viral genome. Also, for all human rotaviral proteins, we have deciphered molecular recognition features (MoRFs), which are disorder based binding sites in proteins. Our study shows the wide spread of intrinsic disorder in several rotavirus proteins, primarily the nonstructural proteins NSP3, NSP4, and NSP5 that are involved in viral replication, translation, viroplasm formation and/or maturation. This study may serve as a primer for understanding the role of IDPs/MoRFs in rotavirus biology, design of alternative therapeutic strategies, and development of disorder-based drugs.
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Affiliation(s)
- Deepak Kumar
- Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh 175005, India
| | - Ankur Singh
- Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh 175005, India
| | - Prateek Kumar
- Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh 175005, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - C Durga Rao
- SRM University, AP - Amaravati, Neerukonda, Mangalagiri Mandal Guntur District, Mangalagiri, Andhra Pradesh 522502, India.
| | - Rajanish Giri
- Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh 175005, India; BioX Center, Indian Institute of Technology Mandi, Himachal Pradesh, India.
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13
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Goh GKM, Dunker AK, Foster JA, Uversky VN. Zika and Flavivirus Shell Disorder: Virulence and Fetal Morbidity. Biomolecules 2019; 9:biom9110710. [PMID: 31698857 PMCID: PMC6920988 DOI: 10.3390/biom9110710] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022] Open
Abstract
Zika virus (ZIKV) was first discovered in 1947 in Africa. Since then, sporadic ZIKV infections of humans have been reported in Africa and Asia. For a long time, this virus was mostly unnoticed due to its mild symptoms and low fatality rates. However, during the 2015-2016 epidemic in Central and South America, when millions of people were infected, it was discovered that ZIKV causes microcephaly in the babies of mothers infected during pregnancy. An examination of the M and C proteins of the ZIKV shell using the disorder predictor PONDR VLXT revealed that the M protein contains relatively high disorder levels comparable only to those of the yellow fever virus (YFV). On the other hand, the disorder levels in the C protein are relatively low, which can account for the low case fatality rate (CFR) of this virus in contrast to the more virulent YFV, which is characterized by high disorder in its C protein. A larger variation was found in the percentage of intrinsic disorder (PID) in the C protein of various ZIKV strains. Strains of African lineage are characterized by higher PIDs. Using both in vivo and in vitro experiments, laboratories have also previously shown that strains of African origin have a greater potential to inflict higher fetal morbidity than do strains of Asian lineage, with dengue-2 virus (DENV-2) having the least potential. Strong correlations were found between the potential to inflict fetal morbidity and shell disorder in ZIKV (r2 = 0.9) and DENV-2 (DENV-2 + ZIKV, r2 = 0.8). A strong correlation between CFR and PID was also observed when ZIKV was included in an analysis of sets of shell proteins from a variety of flaviviruses (r2 = 0.8). These observations have potential implications for antiviral vaccine development and for the design of cancer therapeutics in terms of developing therapeutic viruses that penetrate hard-to-reach organs.
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Affiliation(s)
- Gerard Kian-Meng Goh
- Goh’s BioComputing, Singapore 548957, Singapore
- Correspondence: ; Tel.: +65-8648-5440
| | - A. Keith Dunker
- Center for Computational Biology, Indiana and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - James A. Foster
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA;
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
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14
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Lyngdoh D, Shukla H, Sonkar A, Anupam R, Tripathi T. Portrait of the Intrinsically Disordered Side of the HTLV-1 Proteome. ACS OMEGA 2019; 4:10003-10018. [PMID: 31460093 PMCID: PMC6648719 DOI: 10.1021/acsomega.9b01017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 05/28/2019] [Indexed: 05/07/2023]
Abstract
Intrinsically disordered proteins (IDPs) lack an ordered 3D structure. These proteins contain one or more intrinsically disordered protein regions (IDPRs). IDPRs interact promiscuously with other proteins, which leads to their structural transition from a disordered to an ordered state. Such interaction-prone regions of IDPs are known as molecular recognition features. Recent studies suggest that IDPs provide structural plasticity and functional diversity to viral proteins that are involved in rapid replication and immune evasion within the host cells. In the present study, we evaluated the prevalence of IDPs and IDPRs in human T lymphotropic virus type 1 (HTLV-1) proteome. We also investigated the presence of MoRF regions in the structural and nonstructural proteins of HTLV-1. We found abundant IDPRs in HTLV-1 bZIP factor, p30, Rex, and structural nucleocapsid p15 proteins, which are involved in diverse functions such as virus proliferation, mRNA export, and genomic RNA binding. Our study analyzed the HTLV-1 proteome with the perspective of intrinsic disorder identification. We propose that the intrinsic disorder analysis of HTLV-1 proteins may form the basis for the development of protein disorder-based drugs.
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Affiliation(s)
- Denzelle
L. Lyngdoh
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Harish Shukla
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Amit Sonkar
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Rajaneesh Anupam
- Department
of Biotechnology, Dr. Harisingh Gour Central
University, Sagar 470003, India
| | - Timir Tripathi
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
- E-mail: , . Phone: +91-364-2722141. Fax: +91-364-2550108
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15
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Ramamurthy M, Sankar S, Abraham AM, Nandagopal B, Sridharan G. B cell epitopes in the intrinsically disordered regions of neuraminidase and hemagglutinin proteins of H5N1 and H9N2 avian influenza viruses for peptide-based vaccine development. J Cell Biochem 2019; 120:17534-17544. [PMID: 31111560 DOI: 10.1002/jcb.29017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/12/2022]
Abstract
Avian influenza viruses (AIV) are very active in several parts of the globe and are the cause of huge economic loss for the poultry industry and also human fatalities. Three dimensional modeling was carried out for neuraminidase (NA) and hemagglutinin (HA) proteins of AIV. The C-score, estimated TM-Score, and estimated root-mean-square deviation (RMSD) score for NA of H5N1 were -1.18, 0.57 ± 0.15, and 9.8 ± 7.6, respectively. The C-score, estimated TM-Score, and estimated RMSD score for NA of H9N2 were -1.43, 0.54 ± 0.15, and 10.5 ± 4.6, respectively. The C-score, estimated TM-Score, and estimated RMSD score for HA of H5N1 were -0.03, 0.71 ± 0.12, and 7.7 ± 4.3, respectively. The C-score, estimated TM-Score, and estimated RMSD score for HA of H9N2 were -0.57, 0.64 ± 0.13, and 8.9 ± 4.6, respectively. Intrinsically disordered regions were identified for the NA and HA proteins of H5N1 and H9N2 with the use of PONDR program. Linear B cell epitope was predicted using BepiPred 2 program for NA and HA of H5N1 and H9N2 avian influenza strains. Discontinuous epitopes were predicted by Discotope 2 program. The linear epitopes that were considered likely to be immunogenic and within the intrinsically disordered region for the NA of H5N1 was TKSTNSRSGFEMIWDPNGWTGTDSSFSVK, and for H9N2 it was VGDTPRNDDSSSSSNCRDPNNERGAP. In the case of HA of H5N1, it was QRLVPKIATRSKVNGQSG and ATGLRNSPQRERRRKK; for H9N2 it was INRTFKPLIGPRPLVNGLQG and SLKLAVGLRNVPARSSR. The discontinuous epitopes of NA of H5N1 and H9N2 were identified at various regions of the protein structure spanning from amino acid residue positions 90 to 449 and 107 to 469, respectively. Similarly, the discontinuous epitopes of HA of H5N1 and H9N2 were identified in the amino acid residue positions 27 to 517 and 136 to 521, respectively. This study has identified potential and highly immunogenic linear and conformational B-cell epitopes towards developing a vaccine against AIV both for human and poultry use.
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Affiliation(s)
- Mageshbabu Ramamurthy
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Vellore, Tamil Nadu, India
| | - Sathish Sankar
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Vellore, Tamil Nadu, India
| | - Asha Mary Abraham
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Balaji Nandagopal
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Vellore, Tamil Nadu, India
| | - Gopalan Sridharan
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Vellore, Tamil Nadu, India
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16
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Meshram CD, Oomens AGP. Identification of a human respiratory syncytial virus phosphoprotein domain required for virus-like-particle formation. Virology 2019; 532:48-54. [PMID: 31009855 DOI: 10.1016/j.virol.2019.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 10/27/2022]
Abstract
Perceived inefficiency and inadequate knowledge of the human respiratory syncytial virus (hRSV) assembly process present a hurdle for large-scale production of authentic hRSV virus-like particles (VLPs) for vaccine purposes. We previously established that the matrix protein, phosphoprotein (P), and fusion protein carboxy-terminus were sufficient to generate VLPs that resemble filamentous wildtype hRSV. Here, the contribution of P was examined. By co-expressing matrix, fusion, and modified P proteins, a ser/thr-rich P region (residues 39-57) was found to be critical for VLP formation, whereas the oligomerization domain was not. Substitutions throughout region 39-57 inhibited VLP formation and relevant amino acids were identified. Phosphomimetic substitutions of serines and threonines inhibited VLP formation; Phosphoblatant substitutions did not. The data show that P not only co-regulates replication and transcription but also has an important role in assembly, mediated by a separate domain that likely interacts with M and/or F and is highly regulated by phosphorylation.
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Affiliation(s)
- Chetan D Meshram
- Department of Microbiology. University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Antonius G P Oomens
- Center for Veterinary Health Sciences, Oklahoma State University, 250 McElroy Hall, Stillwater, OK, 74078, USA.
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17
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Redwan EM, AlJaddawi AA, Uversky VN. Structural disorder in the proteome and interactome of Alkhurma virus (ALKV). Cell Mol Life Sci 2019; 76:577-608. [PMID: 30443749 PMCID: PMC7079808 DOI: 10.1007/s00018-018-2968-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/30/2018] [Accepted: 11/05/2018] [Indexed: 12/13/2022]
Abstract
Infection by the Alkhurma virus (ALKV) leading to the Alkhurma hemorrhagic fever is a common thread in Saudi Arabia, with no efficient treatment or prevention available as of yet. Although the rational drug design traditionally uses information on known 3D structures of viral proteins, intrinsically disordered proteins (i.e., functional proteins that do not possess unique 3D structures), with their multitude of disorder-dependent functions, are crucial for the biology of viruses. Here, viruses utilize disordered regions in their invasion of the host organisms and in hijacking and repurposing of different host systems. Furthermore, the ability of viruses to efficiently adjust and accommodate to their hostile habitats is also intrinsic disorder-dependent. However, little is currently known on the level of penetrance and functional utilization of intrinsic disorder in the ALKV proteome. To fill this gap, we used here multiple computational tools to evaluate the abundance of intrinsic disorder in the ALKV genome polyprotein. We also analyzed the peculiarities of intrinsic disorder predisposition of the individual viral proteins, as well as human proteins known to be engaged in interaction with the ALKV proteins. Special attention was paid to finding a correlation between protein functionality and structural disorder. To the best of our knowledge, this work represents the first systematic study of the intrinsic disorder status of ALKV proteome and interactome.
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Affiliation(s)
- Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia.
| | - Abdullah A AlJaddawi
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia
| | - Vladimir N Uversky
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia.
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142290, Moscow Region, Russia.
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18
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On the Regularities of the Polar Profiles of Proteins Related to Ebola Virus Infection and their Functional Domains. Cell Biochem Biophys 2018; 76:411-431. [PMID: 29511990 PMCID: PMC7090660 DOI: 10.1007/s12013-018-0839-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 02/16/2018] [Indexed: 11/25/2022]
Abstract
The number of fatalities and economic losses caused by the Ebola virus infection across the planet culminated in the havoc that occurred between August and November 2014. However, little is known about the molecular protein profile of this devastating virus. This work represents a thorough bioinformatics analysis of the regularities of charge distribution (polar profiles) in two groups of proteins and their functional domains associated with Ebola virus disease: Ebola virus proteins and Human proteins interacting with Ebola virus. Our analysis reveals that a fragment exists in each of these proteins—one named the “functional domain”—with the polar profile similar to the polar profile of the protein that contains it. Each protein is formed by a group of short sub-sequences, where each fragment has a different and distinctive polar profile and where the polar profile between adjacent short sub-sequences changes orderly and gradually to coincide with the polar profile of the whole protein. When using the charge distribution as a metric, it was observed that it effectively discriminates the proteins from their functional domains. As a counterexample, the same test was applied to a set of synthetic proteins built for that purpose, revealing that any of the regularities reported here for the Ebola virus proteins and human proteins interacting with Ebola virus were not present in the synthetic proteins. Our results indicate that the polar profile of each protein studied and its corresponding functional domain are similar. Thus, when building each protein from its functional domai—adding one amino acid at a time and plotting each time its polar profile—it was observed that the resulting graphs can be divided into groups with similar polar profiles.
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