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Ferrer-Orta C, Ferrero DS, Verdaguer N. Dual role of the foot-and-mouth disease virus 3B1 protein in the replication complex: As protein primer and as an essential component to recruit 3Dpol to membranes. PLoS Pathog 2023; 19:e1011373. [PMID: 37126532 PMCID: PMC10174528 DOI: 10.1371/journal.ppat.1011373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/11/2023] [Accepted: 04/18/2023] [Indexed: 05/02/2023] Open
Abstract
Picornavirus genome replication takes place in specialized intracellular membrane compartments that concentrate viral RNA and proteins as well as a number of host factors that also participate in the process. The core enzyme in the replication machinery is the viral RNA-dependent RNA polymerase (RdRP) 3Dpol. Replication requires the primer protein 3B (or VPg) attached to two uridine molecules. 3B uridylylation is also catalysed by 3Dpol. Another critical interaction in picornavirus replication is that between 3Dpol and the precursor 3AB, a membrane-binding protein responsible for the localization of 3Dpol to the membranous compartments at which replication occurs. Unlike other picornaviruses, the animal pathogen foot-and-mouth disease virus (FMDV), encodes three non-identical copies of the 3B (3B1, 3B2, and 3B3) that could be specialized in different functions within the replication complex. Here, we have used a combination of biophysics, molecular and structural biology approaches to characterize the functional binding of FMDV 3B1 to the base of the palm of 3Dpol. The 1.7 Å resolution crystal structure of the FMDV 3Dpol -3B1 complex shows that 3B1 simultaneously links two 3Dpol molecules by binding at the bottom of their palm subdomains in an almost symmetric way. The two 3B1 contact surfaces involve a combination of hydrophobic and basic residues at the N- (G5-P6, R9; Region I) and C-terminus (R16, L19-P20; Region II) of this small protein. Enzyme-Linked Immunosorbent Assays (ELISA) show that the two 3B1 binding sites play a role in 3Dpol binding, with region II presenting the highest affinity. ELISA assays show that 3Dpol has higher binding affinity for 3B1 than for 3B2 or 3B3. Membrane-based pull-down assays show that 3B1 region II, and to a lesser extent also region I play essential roles in mediating the interaction of 3AB with the polymerase and its recruitment to intracellular membranes.
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Affiliation(s)
- Cristina Ferrer-Orta
- Instituto de Biología Molecular de Barcelona. Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Barcelona, Spain
| | - Diego S Ferrero
- Instituto de Biología Molecular de Barcelona. Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Barcelona, Spain
| | - Nuria Verdaguer
- Instituto de Biología Molecular de Barcelona. Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Barcelona, Spain
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Revisiting Viral RNA-Dependent RNA Polymerases: Insights from Recent Structural Studies. Viruses 2022; 14:v14102200. [PMID: 36298755 PMCID: PMC9612308 DOI: 10.3390/v14102200] [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: 08/31/2022] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 11/07/2022] Open
Abstract
RNA-dependent RNA polymerases (RdRPs) represent a distinctive yet versatile class of nucleic acid polymerases encoded by RNA viruses for the replication and transcription of their genome. The structure of the RdRP is comparable to that of a cupped right hand consisting of fingers, palm, and thumb subdomains. Despite the presence of a common structural core, the RdRPs differ significantly in the mechanistic details of RNA binding and polymerization. The present review aims at exploring these incongruities in light of recent structural studies of RdRP complexes with diverse cofactors, RNA moieties, analogs, and inhibitors.
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Courtillon C, Briand FX, Allée C, Contrant M, Beven V, Lucas P, Blanchard Y, Mouchel S, Eterradossi N, Delforterie Y, Grasland B, Brown P. Description of the first isolates of guinea fowl corona and picornaviruses obtained from a case of guinea fowl fulminating enteritis. Avian Pathol 2021; 50:507-521. [PMID: 34545751 DOI: 10.1080/03079457.2021.1976725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Guinea fowl fulminating enteritis has been reported in France since the 1970s. In 2014, a coronavirus was identified and appeared as a possible viral pathogen involved in the disease. In the present study, intestinal content from a guinea fowl involved in a new case of the disease in 2017 was analysed by deep sequencing, revealing the presence of a guinea fowl coronavirus (GfCoV) and a picornavirus (GfPic). Serial passage assays into the intra-amniotic cavity of 13-day-old specific pathogen-free chicken eggs and 20-day-old conventional guinea fowl eggs were attempted. In chicken eggs, isolation assays failed, but in guinea fowl eggs, both viruses were successfully obtained. Furthermore, two GfCoV and two GfPic isolates were obtained from the same bird but from different sections of its intestines. This shows that using eggs of the same species, in which the virus has been detected, can be the key for successful isolation. The consensus sequence of the full-length genomes of both GfCoV isolates was highly similar, and correlated to those previously described in terms of genome organization, ORF length and phylogenetic clustering. According to full-length genome analysis and the structure of the Internal Ribosome Entry Site, both GfPic isolates belong to the Anativirus genus and specifically the species Anativirus B. The availability of the first isolates of GfCoV and GfPic will now provide a means of assessing their pathogenicity in guinea fowl in controlled experimental conditions and to assess whether they are primary viral pathogens of the disease "guinea fowl fulminating enteritis".RESEARCH HIGHLIGHTSFirst isolation of guinea fowl coronaviruses and picornaviruses.Eggs homologous to the infected species are key for isolation.Isolates available to precisely evaluate the virus roles in fulminating enteritis.First full-length genome sequences of guinea fowl picornaviruses.
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Affiliation(s)
- Céline Courtillon
- VIPAC Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | - François-Xavier Briand
- VIPAC Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | - Chantal Allée
- VIPAC Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | - Maud Contrant
- GVB Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | - Véronique Beven
- GVB Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | - Pierrick Lucas
- GVB Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | - Yannick Blanchard
- GVB Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | | | - Nicolas Eterradossi
- VIPAC Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | | | - Béatrice Grasland
- VIPAC Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | - Paul Brown
- VIPAC Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
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Watkins CL, Kempf BJ, Beaucourt S, Barton DJ, Peersen OB. Picornaviral polymerase domain exchanges reveal a modular basis for distinct biochemical activities of viral RNA-dependent RNA polymerases. J Biol Chem 2020; 295:10624-10637. [PMID: 32493771 PMCID: PMC7397104 DOI: 10.1074/jbc.ra120.013906] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/28/2020] [Indexed: 01/23/2023] Open
Abstract
Picornaviral RNA-dependent RNA polymerases (RdRPs) have low replication fidelity that is essential for viral fitness and evolution. Their global fold consists of the classical "cupped right hand" structure with palm, fingers, and thumb domains, and these RdRPs also possess a unique contact between the fingers and thumb domains. This interaction restricts movements of the fingers, and RdRPs use a subtle conformational change within the palm domain to close their active sites for catalysis. We have previously shown that this core RdRP structure and mechanism provide a platform for polymerases to fine-tune replication rates and fidelity to optimize virus fitness. Here, we further elucidated the structural basis for differences in replication rates and fidelity among different viruses by generating chimeric RdRPs from poliovirus and coxsackievirus B3. We designed these chimeric polymerases by exchanging the fingers, pinky finger, or thumb domains. The results of biochemical, rapid-quench, and stopped-flow assays revealed that differences in biochemical activity map to individual modular domains of this polymerase. We found that the pinky finger subdomain is a major regulator of initiation and that the palm domain is the major determinant of catalytic rate and nucleotide discrimination. We further noted that thumb domain interactions with product RNA regulate translocation and that the palm and thumb domains coordinately control elongation complex stability. Several RdRP chimeras supported the growth of infectious poliovirus, providing insights into enterovirus species-specific protein-protein interactions required for virus replication.
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Affiliation(s)
- Colleen L Watkins
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Brian J Kempf
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | - David J Barton
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Olve B Peersen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
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