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Coria A, Wienecke A, Knight ML, Desirò D, Laederach A, Borodavka A. Rotavirus RNA chaperone mediates global transcriptome-wide increase in RNA backbone flexibility. Nucleic Acids Res 2022; 50:10078-10092. [PMID: 36062555 PMCID: PMC9508848 DOI: 10.1093/nar/gkac738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 08/09/2022] [Accepted: 08/22/2022] [Indexed: 11/12/2022] Open
Abstract
Due to genome segmentation, rotaviruses must co-package eleven distinct genomic RNAs. The packaging is mediated by virus-encoded RNA chaperones, such as the rotavirus NSP2 protein. While the activities of distinct RNA chaperones are well studied on smaller RNAs, little is known about their global effect on the entire viral transcriptome. Here, we used Selective 2'-hydroxyl Acylation Analyzed by Primer Extension and Mutational Profiling (SHAPE-MaP) to examine the secondary structure of the rotavirus transcriptome in the presence of increasing amounts of NSP2. SHAPE-MaP data reveals that despite the well-documented helix-unwinding activity of NSP2 in vitro, its incubation with cognate rotavirus transcripts does not induce a significant change in the SHAPE reactivities. However, a quantitative analysis of mutation rates measured by mutational profiling reveals a global 5-fold rate increase in the presence of NSP2. We demonstrate that the normalization procedure used in deriving SHAPE reactivities from mutation rates can mask an important global effect of an RNA chaperone. Analysis of the mutation rates reveals a larger effect on stems rather than loops. Together, these data provide the first experimentally derived secondary structure model of the rotavirus transcriptome and reveal that NSP2 acts by globally increasing RNA backbone flexibility in a concentration-dependent manner.
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Affiliation(s)
- Aaztli Coria
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Anastacia Wienecke
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael L Knight
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Daniel Desirò
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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2
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Geiger F, Acker J, Papa G, Wang X, Arter WE, Saar KL, Erkamp NA, Qi R, Bravo JPK, Strauss S, Krainer G, Burrone OR, Jungmann R, Knowles TPJ, Engelke H, Borodavka A. Liquid-liquid phase separation underpins the formation of replication factories in rotaviruses. EMBO J 2021; 40:e107711. [PMID: 34524703 PMCID: PMC8561643 DOI: 10.15252/embj.2021107711] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 12/29/2022] Open
Abstract
RNA viruses induce the formation of subcellular organelles that provide microenvironments conducive to their replication. Here we show that replication factories of rotaviruses represent protein-RNA condensates that are formed via liquid-liquid phase separation of the viroplasm-forming proteins NSP5 and rotavirus RNA chaperone NSP2. Upon mixing, these proteins readily form condensates at physiologically relevant low micromolar concentrations achieved in the cytoplasm of virus-infected cells. Early infection stage condensates could be reversibly dissolved by 1,6-hexanediol, as well as propylene glycol that released rotavirus transcripts from these condensates. During the early stages of infection, propylene glycol treatments reduced viral replication and phosphorylation of the condensate-forming protein NSP5. During late infection, these condensates exhibited altered material properties and became resistant to propylene glycol, coinciding with hyperphosphorylation of NSP5. Some aspects of the assembly of cytoplasmic rotavirus replication factories mirror the formation of other ribonucleoprotein granules. Such viral RNA-rich condensates that support replication of multi-segmented genomes represent an attractive target for developing novel therapeutic approaches.
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Affiliation(s)
- Florian Geiger
- Department of ChemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Julia Acker
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Guido Papa
- International Center for Genetic Engineering and BiotechnologyTriesteItaly
- Present address:
Medical Research Council Laboratory of Molecular Biology (MRC LMB)CambridgeUK
| | - Xinyu Wang
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Kadi L Saar
- Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Nadia A Erkamp
- Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Runzhang Qi
- Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Jack PK Bravo
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Present address:
Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | - Sebastian Strauss
- Department of Physics and Center for NanoscienceMax Planck Institute of BiochemistryMunichGermany
| | - Georg Krainer
- Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Oscar R Burrone
- International Center for Genetic Engineering and BiotechnologyTriesteItaly
| | - Ralf Jungmann
- Department of Physics and Center for NanoscienceMax Planck Institute of BiochemistryMunichGermany
| | | | - Hanna Engelke
- Department of ChemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Institute of Pharmaceutical SciencesKarl‐Franzens‐Universität GrazGrazAustria
| | - Alexander Borodavka
- Department of ChemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Department of Physics and Center for NanoscienceMax Planck Institute of BiochemistryMunichGermany
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3
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Human Rotavirus Reverse Genetics Systems to Study Viral Replication and Pathogenesis. Viruses 2021; 13:v13091791. [PMID: 34578372 PMCID: PMC8473093 DOI: 10.3390/v13091791] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/04/2021] [Accepted: 09/05/2021] [Indexed: 11/19/2022] Open
Abstract
Human rotaviruses (HuRVAs) are highly important causes of acute gastroenteritis in infants and young children worldwide. A lack of reliable and reproducible reverse genetics systems for HuRVAs has limited a proper understanding of HuRVA biology and also the rational design of live-attenuated vaccines. Since the development of the first reverse genetics system for RVAs (partially plasmid-based reverse genetics system) in 2006, there have been many efforts with the goal of generating infectious recombinant HuRVAs entirely from cloned cDNAs. However, the establishment of a HuRVA reverse genetics system was very challenging until 2019. This review article provides an overview of the historical background of the recent development of long-awaited HuRVA reverse genetics systems, beginning with the generation of recombinant human-simian reassortant RVAs with the aid of a helper virus in 2006 and the generation of recombinant animal (simian) RVAs in a helper virus-free manner in 2017, and culminating in the generation of recombinant HuRVAs entirely from plasmid cDNAs in 2019. Notably, the original HuRVA reverse genetics system has already been optimized to increase the efficiency of virus generation. Although the application of HuRVA reverse genetics systems has only just been initiated, these technologies will help to answer HuRVA research questions regarding viral replication and pathogenicity that could not be addressed before, and to develop next-generation vaccines and intestine-specific rotaviral vectors.
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4
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Kumar P, Shukla RS, Patel A, Pullagurla SR, Bird C, Ogun O, Kumru OS, Hamidi A, Hoeksema F, Yallop C, Bines JE, Joshi SB, Volkin DB. Formulation development of a live attenuated human rotavirus (RV3-BB) vaccine candidate for use in low- and middle-income countries. Hum Vaccin Immunother 2021; 17:2298-2310. [PMID: 33861183 PMCID: PMC8189091 DOI: 10.1080/21645515.2021.1885279] [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: 10/01/2020] [Accepted: 01/29/2021] [Indexed: 01/05/2023] Open
Abstract
Formulation development was performed with the live, attenuated, human neonatal rotavirus vaccine candidate (RV3-BB) with three main objectives to facilitate use in low- and middle- income countries including (1) a liquid, 2-8°C stable vaccine, (2) no necessity for pre-neutralization of gastric acid prior to oral administration of a small-volume dose, and (3) a low-cost vaccine dosage form. Implementation of a high-throughput RT-qPCR viral infectivity assay for RV3-BB, which correlated well with traditional FFA assays in terms of monitoring RV3-BB stability profiles, enabled more rapid and comprehensive formulation development studies. A wide variety of different classes and types of pharmaceutical excipients were screened for their ability to stabilize RV3-BB during exposure to elevated temperatures, freeze-thaw and agitation stresses. Sucrose (50-60% w/v), PEG-3350, and a solution pH of 7.8 were selected as promising stabilizers. Using a combination of an in vitro gastric digestion model (to mimic oral delivery conditions) and accelerated storage stability studies, several buffering agents (e.g., succinate, adipate and acetate at ~200 to 400 mM) were shown to protect RV3-BB under acidic conditions, and at the same time, minimize virus destabilization during storage. Several optimized RV3-BB candidate formulations were identified based on negligible viral infectivity losses during storage at 2-8°C and -20°C for up to 12 months, as well as by relative stability comparisons at 15°C and 25°C (up to 12 and 3 months, respectively). These RV3-BB stability results are discussed in the context of stability profiles of other rotavirus serotypes as well as future RV3-BB formulation development activities.
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Affiliation(s)
- Prashant Kumar
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Ravi S. Shukla
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Ashaben Patel
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Swathi R. Pullagurla
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Christopher Bird
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Oluwadara Ogun
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Ozan S. Kumru
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Ahd Hamidi
- Batavia Biosciences B.V., Bioscience Park Leiden, Leiden, The Netherlands
| | - Femke Hoeksema
- Batavia Biosciences B.V., Bioscience Park Leiden, Leiden, The Netherlands
| | - Christopher Yallop
- Batavia Biosciences B.V., Bioscience Park Leiden, Leiden, The Netherlands
| | - Julie E. Bines
- Murdoch Children’s Research Institute, Department of Paediatrics, University of Melbourne, Parkville, Australia
- Department of Gastroenterology and Clinical Nutrition, Royal Children’s Hospital, Parkville, Australia
| | - Sangeeta B. Joshi
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - David B. Volkin
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
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5
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Rapid generation of rotavirus single-gene reassortants by means of eleven plasmid-only based reverse genetics. J Gen Virol 2020; 101:806-815. [DOI: 10.1099/jgv.0.001443] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Reassortment is an important mechanism in the evolution of group A rotaviruses (RVAs), yielding viruses with novel genetic and phenotypic traits. The classical methods for generating RVA reassortants with the desired genetic combinations are laborious and time-consuming because of the screening and selection processes required to isolate a desired reassortant. Taking advantage of a recently developed RVA reverse genetics system based on just 11 cloned cDNAs encoding the RVA genome (11 plasmid-only system), we prepared a panel of simian SA11-L2 virus-based single-gene reassortants, each containing 1 segment derived from human KU virus of the G1P[8] genotype. It was shown that there was no gene-specific restriction of the reassortment potential. In addition to these 11 single-gene reassortants, a triple-gene reassortant with KU-derived core-encoding VP1–3 gene segments with the SA11-L2 genetic background, which make up a virion composed of the KU-based core, and SA11-L2-based intermediate and outer layers, could also be prepared with the 11 plasmid-only system. Finally, for possible clinical application of this system, we generated a series of VP7 reassortants representing all the major human RVA G genotypes (G1–4, G9 and G12) efficiently. The preparation of each of these single-gene reassortants was achieved within just 2 weeks. Our results demonstrate that the 11 plasmid-only system allows the rapid and reliable generation of RVA single-gene reassortants, which will be useful for basic research and clinical applications.
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6
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What are the limits of the packaging capacity for genomic RNA in the cores of rotaviruses and of other members of the Reoviridae? Virus Res 2020; 276:197822. [DOI: 10.1016/j.virusres.2019.197822] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/20/2019] [Accepted: 11/20/2019] [Indexed: 12/16/2022]
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7
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Borodavka A, Desselberger U, Patton JT. Genome packaging in multi-segmented dsRNA viruses: distinct mechanisms with similar outcomes. Curr Opin Virol 2018; 33:106-112. [PMID: 30145433 PMCID: PMC6289821 DOI: 10.1016/j.coviro.2018.08.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 12/20/2022]
Abstract
Segmented double-stranded (ds)RNA viruses share remarkable similarities in their replication strategy and capsid structure. During virus replication, positive-sense single-stranded (+)RNAs are packaged into procapsids, where they serve as templates for dsRNA synthesis, forming progeny particles containing a complete equimolar set of genome segments. How the +RNAs are recognized and stoichiometrically packaged remains uncertain. Whereas bacteriophages of the Cystoviridae family rely on specific RNA-protein interactions to select appropriate +RNAs for packaging, viruses of the Reoviridae instead rely on specific inter-molecular interactions between +RNAs that guide multi-segmented genome assembly. While these families use distinct mechanisms to direct +RNA packaging, both yield progeny particles with a complete set of genomic dsRNAs.
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Affiliation(s)
- Alexander Borodavka
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Ulrich Desselberger
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK
| | - John T Patton
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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8
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Jiménez-Zaragoza M, Yubero MP, Martín-Forero E, Castón JR, Reguera D, Luque D, de Pablo PJ, Rodríguez JM. Biophysical properties of single rotavirus particles account for the functions of protein shells in a multilayered virus. eLife 2018; 7:37295. [PMID: 30201094 PMCID: PMC6133545 DOI: 10.7554/elife.37295] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/01/2018] [Indexed: 12/27/2022] Open
Abstract
The functions performed by the concentric shells of multilayered dsRNA viruses require specific protein interactions that can be directly explored through their mechanical properties. We studied the stiffness, breaking force, critical strain and mechanical fatigue of individual Triple, Double and Single layered rotavirus (RV) particles. Our results, in combination with Finite Element simulations, demonstrate that the mechanics of the external layer provides the resistance needed to counteract the stringent conditions of extracellular media. Our experiments, in combination with electrostatic analyses, reveal a strong interaction between the two outer layers and how it is suppressed by the removal of calcium ions, a key step for transcription initiation. The intermediate layer presents weak hydrophobic interactions with the inner layer that allow the assembly and favor the conformational dynamics needed for transcription. Our work shows how the biophysical properties of the three shells are finely tuned to produce an infective RV virion.
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Affiliation(s)
- Manuel Jiménez-Zaragoza
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marina Pl Yubero
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Jose R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
| | - David Reguera
- Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Barcelona, Spain
| | - Daniel Luque
- Centro Nacional de Microbiología/ISCIII, Majadahonda, Spain
| | - Pedro J de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, Madrid, Spain
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9
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Borodavka A, Dykeman EC, Schrimpf W, Lamb DC. Protein-mediated RNA folding governs sequence-specific interactions between rotavirus genome segments. eLife 2017; 6:27453. [PMID: 28922109 PMCID: PMC5621836 DOI: 10.7554/elife.27453] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/03/2017] [Indexed: 01/06/2023] Open
Abstract
Segmented RNA viruses are ubiquitous pathogens, which include influenza viruses and rotaviruses. A major challenge in understanding their assembly is the combinatorial problem of a non-random selection of a full genomic set of distinct RNAs. This process involves complex RNA-RNA and protein-RNA interactions, which are often obscured by non-specific binding at concentrations approaching in vivo assembly conditions. Here, we present direct experimental evidence of sequence-specific inter-segment interactions between rotavirus RNAs, taking place in a complex RNA- and protein-rich milieu. We show that binding of the rotavirus-encoded non-structural protein NSP2 to viral ssRNAs results in the remodeling of RNA, which is conducive to formation of stable inter-segment contacts. To identify the sites of these interactions, we have developed an RNA-RNA SELEX approach for mapping the sequences involved in inter-segment base-pairing. Our findings elucidate the molecular basis underlying inter-segment interactions in rotaviruses, paving the way for delineating similar RNA-RNA interactions that govern assembly of other segmented RNA viruses. Rotavirus is a highly infectious virus that affects children worldwide, causing severe diarrhoea. Despite the introduction of several highly effective vaccines, more than 200,000 children still die from rotavirus each year. There are currently no drugs that can combat this disease once a child has been infected. Viruses carry the instructions that determine their properties and behavior in molecules of DNA or RNA. Unlike many other viruses, which typically have a single molecule of DNA or RNA, rotavirus has 11 distinct “RNA segments”. After invading a cell the virus begins to replicate itself. During replication, the RNA segments (which consist of two strands of RNA paired together) are copied many times. It is not clear how rotaviruses ‘count’ up to 11 so that each new virus acquires a single copy of each segment. Previous biochemical and structural studies of rotavirus replication suggest that selecting 11 distinct RNA segments must involve the RNAs forming complex interactions with proteins and other RNA molecules. Using a highly sensitive fluorescence-based approach, termed fluorescence cross-correlation spectroscopy, Borodavka et al. now present direct experimental evidence of interactions between the RNA segments that occur via single strands of the rotavirus RNA. These RNA-RNA interactions require the binding of a rotavirus protein NSP2 to the RNA strands, which results in the remodeling of the RNA; this remodeling is required to form stable contacts between different RNA segments. Furthermore, a new experimental approach (called RNA-RNA SELEX) developed by Borodavka et al. identified the parts of the RNA segments that may take part in these interactions. The results presented by Borodavka et al. pave the way for identifying the RNA-RNA interactions that govern how other segmented RNA viruses can package their genetic material. Further work to uncover the entire RNA interaction network in rotaviruses would also accelerate the design of new vaccines and may help us to develop antiviral drugs to treat infections.
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Affiliation(s)
- Alexander Borodavka
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom.,Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilian University of Munich, Munich, Germany
| | - Eric C Dykeman
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom.,Department of Mathematics, University of York, York, United Kingdom.,Department of Biology, University of York, York, United Kingdom
| | - Waldemar Schrimpf
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilian University of Munich, Munich, Germany
| | - Don C Lamb
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilian University of Munich, Munich, Germany
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10
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Guerrero CA, Guerrero RA, Silva E, Acosta O, Barreto E. Experimental Adaptation of Rotaviruses to Tumor Cell Lines. PLoS One 2016; 11:e0147666. [PMID: 26828934 PMCID: PMC4734670 DOI: 10.1371/journal.pone.0147666] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/06/2016] [Indexed: 01/06/2023] Open
Abstract
A number of viruses show a naturally extended tropism for tumor cells whereas other viruses have been genetically modified or adapted to infect tumor cells. Oncolytic viruses have become a promising tool for treating some cancers by inducing cell lysis or immune response to tumor cells. In the present work, rotavirus strains TRF-41 (G5) (porcine), RRV (G3) (simian), UK (G6-P5) (bovine), Ym (G11-P9) (porcine), ECwt (murine), Wa (G1-P8), Wi61 (G9) and M69 (G8) (human), and five wild-type human rotavirus isolates were passaged multiple times in different human tumor cell lines and then combined in five different ways before additional multiple passages in tumor cell lines. Cell death caused by the tumor cell-adapted isolates was characterized using Hoechst, propidium iodide, 7-AAD, Annexin V, TUNEL, and anti-poly-(ADP ribose) polymerase (PARP) and -phospho-histone H2A.X antibodies. Multiple passages of the combined rotaviruses in tumor cell lines led to a successful infection of these cells, suggesting a gain-of-function by the acquisition of greater infectious capacity as compared with that of the parental rotaviruses. The electropherotype profiles suggest that unique tumor cell-adapted isolates were derived from reassortment of parental rotaviruses. Infection produced by such rotavirus isolates induced chromatin modifications compatible with apoptotic cell death.
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Affiliation(s)
- Carlos A. Guerrero
- Department of Physiological Sciences, Faculty of Medicine, Universidad Nacional de Colombia, Bogota, D.C., Colombia
| | - Rafael A. Guerrero
- Department of Physiological Sciences, Faculty of Medicine, Universidad Nacional de Colombia, Bogota, D.C., Colombia
| | - Elver Silva
- Department of Physiological Sciences, Faculty of Medicine, Universidad Nacional de Colombia, Bogota, D.C., Colombia
| | - Orlando Acosta
- Department of Physiological Sciences, Faculty of Medicine, Universidad Nacional de Colombia, Bogota, D.C., Colombia
| | - Emiliano Barreto
- Institute of Biotechnology, Universidad Nacional de Colombia, Bogota, D.C., Colombia
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11
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Boudreaux CE, Kelly DF, McDonald SM. Electron microscopic analysis of rotavirus assembly-replication intermediates. Virology 2015; 477:32-41. [PMID: 25635339 PMCID: PMC4359669 DOI: 10.1016/j.virol.2015.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/14/2014] [Accepted: 01/05/2015] [Indexed: 11/24/2022]
Abstract
Rotaviruses (RVs) replicate their segmented, double-stranded RNA genomes in tandem with early virion assembly. In this study, we sought to gain insight into the ultrastructure of RV assembly-replication intermediates (RIs) using transmission electron microscopy (EM). Specifically, we examined a replicase-competent, subcellular fraction that contains all known RV RIs. Three never-before-seen complexes were visualized in this fraction. Using in vitro reconstitution, we showed that ~15-nm doughnut-shaped proteins in strings were nonstructural protein 2 (NSP2) bound to viral RNA transcripts. Moreover, using immunoaffinity-capture EM, we revealed that ~20-nm pebble-shaped complexes contain the viral RNA polymerase (VP1) and RNA capping enzyme (VP3). Finally, using a gel purification method, we demonstrated that ~30–70-nm electron-dense, particle-shaped complexes represent replicase-competent core RIs, containing VP1, VP3, and NSP2 as well as capsid proteins VP2 and VP6. The results of this study raise new questions about the interactions among viral proteins and RNA during the concerted assembly-replicase process.
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Affiliation(s)
- Crystal E Boudreaux
- Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, VA, USA
| | - Deborah F Kelly
- Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, VA, USA
| | - Sarah M McDonald
- Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, VA, USA; Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, USA.
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12
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Desselberger U. Rotaviruses. Virus Res 2014; 190:75-96. [DOI: 10.1016/j.virusres.2014.06.016] [Citation(s) in RCA: 240] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/26/2014] [Accepted: 06/26/2014] [Indexed: 01/12/2023]
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13
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Burkhardt C, Sung PY, Celma CC, Roy P. Structural constraints in the packaging of bluetongue virus genomic segments. J Gen Virol 2014; 95:2240-2250. [PMID: 24980574 PMCID: PMC4165931 DOI: 10.1099/vir.0.066647-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mechanism used by bluetongue virus (BTV) to ensure the sorting and packaging of its 10 genomic segments is still poorly understood. In this study, we investigated the packaging constraints for two BTV genomic segments from two different serotypes. Segment 4 (S4) of BTV serotype 9 was mutated sequentially and packaging of mutant ssRNAs was investigated by two newly developed RNA packaging assay systems, one in vivo and the other in vitro. Modelling of the mutated ssRNA followed by biochemical data analysis suggested that a conformational motif formed by interaction of the 5' and 3' ends of the molecule was necessary and sufficient for packaging. A similar structural signal was also identified in S8 of BTV serotype 1. Furthermore, the same conformational analysis of secondary structures for positive-sense ssRNAs was used to generate a chimeric segment that maintained the putative packaging motif but contained unrelated internal sequences. This chimeric segment was packaged successfully, confirming that the motif identified directs the correct packaging of the segment.
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Affiliation(s)
- Christiane Burkhardt
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Po-Yu Sung
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Cristina C Celma
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Polly Roy
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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