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Nichols SL, Haller C, Borodavka A, Esstman SM. Rotavirus NSP2: A Master Orchestrator of Early Viral Particle Assembly. Viruses 2024; 16:814. [PMID: 38932107 PMCID: PMC11209291 DOI: 10.3390/v16060814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024] Open
Abstract
Rotaviruses (RVs) are 11-segmented, double-stranded (ds) RNA viruses and important causes of acute gastroenteritis in humans and other animal species. Early RV particle assembly is a multi-step process that includes the assortment, packaging and replication of the 11 genome segments in close connection with capsid morphogenesis. This process occurs inside virally induced, cytosolic, membrane-less organelles called viroplasms. While many viral and cellular proteins play roles during early RV assembly, the octameric nonstructural protein 2 (NSP2) has emerged as a master orchestrator of this key stage of the viral replication cycle. NSP2 is critical for viroplasm biogenesis as well as for the selective RNA-RNA interactions that underpin the assortment of 11 viral genome segments. Moreover, NSP2's associated enzymatic activities might serve to maintain nucleotide pools for use during viral genome replication, a process that is concurrent with early particle assembly. The goal of this review article is to summarize the available data about the structures, functions and interactions of RV NSP2 while also drawing attention to important unanswered questions in the field.
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Affiliation(s)
- Sarah L. Nichols
- Department of Biology, Wake Forest University, Wake Downtown, 455 Vine Street, Winston-Salem, NC 27106, USA;
| | - Cyril Haller
- Department of Chemical Engineering and Biotechnology, Cambridge University, Philippa Fawcett Drive, Cambridge CB3 0AS, UK;
| | - Alexander Borodavka
- Department of Chemical Engineering and Biotechnology, Cambridge University, Philippa Fawcett Drive, Cambridge CB3 0AS, UK;
| | - Sarah M. Esstman
- Department of Biology, Wake Forest University, Wake Downtown, 455 Vine Street, Winston-Salem, NC 27106, USA;
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2
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Pinheiro MS, Dias JBL, Petrucci MP, Travassos CEPF, Mendes GS, Santos N. Molecular Characterization of Avian Rotaviruses F and G Detected in Brazilian Poultry Flocks. Viruses 2023; 15:v15051089. [PMID: 37243175 DOI: 10.3390/v15051089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Avian rotaviruses (RVs) are important etiologic agents of gastroenteritis in birds. In general, avian RVs are understudied; consequently, there is a paucity of information regarding these viruses. Therefore, the characterization of these viral species is highly relevant because more robust information on genetic, epidemiologic, and evolutionary characteristics can clarify the importance of these infections, and inform efficient prevention and control measures. In this study, we describe partial genome characterizations of two avian RV species, RVF and RVG, detected in asymptomatic poultry flocks in Brazil. Complete or partial sequences of at least one of the genomic segments encoding VP1, VP2, VP4, VP6, VP7, NSP1, NSP4, NSP4, or NSP5 of 23 RVF and 3 RVG strains were obtained, and demonstrated that multiple variants of both RVF and RVG circulate among Brazilian poultry. In this study, new and important information regarding the genomic characteristics of RVF and RVG is described. In addition, the circulation of these viruses in the study region and the genetic variability of the strains detected are demonstrated. Thus, the data generated in this work should help in understanding the genetics and ecology of these viruses. Nonetheless, the availability of a greater number of sequences is necessary to advance the understanding of the evolution and zoonotic potential of these viruses.
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Affiliation(s)
- Mariana S Pinheiro
- Instituto de Microbiologia Paulo de Góes, Departamento de Virologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21947-902, Brazil
| | - Juliana B L Dias
- Instituto de Microbiologia Paulo de Góes, Departamento de Virologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21947-902, Brazil
| | - Melissa P Petrucci
- Centro de Ciências e Tecnologias Agropecuárias, Laboratório de Sanidade Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes 28013-602, Brazil
| | - Carlos E P F Travassos
- Centro de Ciências e Tecnologias Agropecuárias, Laboratório de Sanidade Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes 28013-602, Brazil
| | - Gabriella S Mendes
- Instituto de Microbiologia Paulo de Góes, Departamento de Virologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21947-902, Brazil
| | - Norma Santos
- Instituto de Microbiologia Paulo de Góes, Departamento de Virologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21947-902, Brazil
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3
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Wu S, Zhao Y, Wang D, Chen Z. Mode of Action of Heat Shock Protein (HSP) Inhibitors against Viruses through Host HSP and Virus Interactions. Genes (Basel) 2023; 14:genes14040792. [PMID: 37107550 PMCID: PMC10138296 DOI: 10.3390/genes14040792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023] Open
Abstract
Misfolded proteins after stress-induced denaturation can regain their functions through correct re-folding with the aid of molecular chaperones. As a molecular chaperone, heat shock proteins (HSPs) can help client proteins fold correctly. During viral infection, HSPs are involved with replication, movement, assembly, disassembly, subcellular localization, and transport of the virus via the formation of macromolecular protein complexes, such as the viral replicase complex. Recent studies have indicated that HSP inhibitors can inhibit viral replication by interfering with the interaction of the virus with the HSP. In this review, we describe the function and classification of HSPs, the transcriptional mechanism of HSPs promoted by heat shock factors (HSFs), discuss the interaction between HSPs and viruses, and the mode of action of HSP inhibitors at two aspects of inhibiting the expression of HSPs and targeting the HSPs, and elaborate their potential use as antiviral agents.
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4
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Velikzhanina EI, Sashina TA, Morozova OV, Epifanova NV, Novikova NA. [Variability of genes encoding nonstructural proteins of rotavirus А (Reoviridae: Rotavirus: Rotavirus A) genotype G9P[8] during the period of dominance in the territory of Nizhny Novgorod (central part of Russia) (2011-2020)]. Vopr Virusol 2023; 67:475-486. [PMID: 37264837 DOI: 10.36233/0507-4088-143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Indexed: 06/03/2023]
Abstract
INTRODUCTION In Russia, rotavirus A is the main cause of severe viral gastroenteritis in young children. The molecular features that allow a rotavirus of a particular genotype to gain an evolutionary advantage remain unclear, therefore, the study of the genetic diversity of rotaviruses based on genes encoding nonstructural proteins (NSPs) responsible for the reproduction of the virus in the cell is an urgent task. OBJECTIVE To study the genetic diversity of rotaviruses of genotype G9P[8], which dominated Nizhny Novgorod in 20112020, based on genes encoding nonstructural proteins. MATERIALS AND METHODS Rotavirus-positive samples were subjected to PCR-genotyping and sequencing of NSP1 NSP5 genes. Phylogenetic analysis was carried out in the MEGA X program. RESULTS In the period 20112020, G9P[8] rotaviruses with four variants of the NSP2 gene were co-circulating in Nizhny Novgorod. New alleles were noted in 2012 (N1-a-III), 2016 (N1-a-IV) and in 2019 (N1-a-II). The appearance of new variants of other genes occurred in 2014 (E1-3, NSP4), 2018 (T1-a3-III, NSP3) and in 2019 (A1-b-II, NSP1). NSP2 gene had the most variable amino acid sequence (16 substitutions), 2 to 7 substitutions were observed in NSP1, NSP3 and NSP4, NSP5 was conservative. DISCUSSION The results obtained are consistent with the literature data and indicate the participation of NSP genes in maintaining the heterogeneity of the rotavirus population. CONCLUSION Until 2018, the genetic diversity of rotaviruses in Nizhny Novgorod was determined by the circulation of strains carrying several alleles of the NSP2 gene and conservative genes NSP1, NSP3NSP5. By the end of the study period, new variants of the genotype G9P[8] were formed in the population, carrying previously unknown combinations of alleles of nonstructural genes.
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Affiliation(s)
- E I Velikzhanina
- «Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology»
| | - T A Sashina
- «Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology»
| | - O V Morozova
- «Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology»
| | - N V Epifanova
- «Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology»
| | - N A Novikova
- «Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology»
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5
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Single-molecule visualization of mRNA circularization during translation. Exp Mol Med 2023; 55:283-289. [PMID: 36720916 PMCID: PMC9981743 DOI: 10.1038/s12276-023-00933-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/04/2022] [Accepted: 12/04/2022] [Indexed: 02/02/2023] Open
Abstract
Translation is mediated by precisely orchestrated sequential interactions among translation initiation components, mRNA, and ribosomes. Biochemical, structural, and genetic techniques have revealed the fundamental mechanism that determines what occurs and when, where and in what order. Most mRNAs are circularized via the eIF4E-eIF4G-PABP interaction, which stabilizes mRNAs and enhances translation by recycling ribosomes. However, studies using single-molecule fluorescence imaging have allowed for the visualization of complex data that opposes the traditional "functional circularization" theory. Here, we briefly introduce single-molecule techniques applied to studies on mRNA circularization and describe the results of in vitro and live-cell imaging. Finally, we discuss relevant insights and questions gained from single-molecule research related to translation.
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6
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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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7
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Ding P, Summers MF. Sequestering the 5′‐cap for viral RNA packaging. Bioessays 2022; 44:e2200104. [PMID: 36101513 DOI: 10.1002/bies.202200104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 11/11/2022]
Abstract
Many viruses evolved mechanisms for capping the 5'-ends of their plus-strand RNAs as a means of hijacking the eukaryotic messenger RNA (mRNA) splicing/translation machinery. Although capping is critical for replication, the RNAs of these viruses have other essential functions including their requirement to be packaged as either genomes or pre-genomes into progeny viruses. Recent studies indicate that human immunodeficiency virus type-1 (HIV-1) RNAs are segregated between splicing/translation and packaging functions by a mechanism that involves structural sequestration of the 5'-cap. Here, we examined studies reported for other viruses and retrotransposons that require both selective packaging of their RNAs and 5'-RNA capping for host-mediated translation. Our findings suggest that viruses and retrotransposons have evolved multiple mechanisms to control 5'-cap accessibility, consistent with the hypothesis that removal or sequestration of the 5' cap enables packageable RNAs to avoid capture by the cellular RNA processing and translation machinery.
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Affiliation(s)
- Pengfei Ding
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute University of Maryland Baltimore County Baltimore Maryland USA
| | - Michael F. Summers
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute University of Maryland Baltimore County Baltimore Maryland USA
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8
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Condé L, Allatif O, Ohlmann T, de Breyne S. Translation of SARS-CoV-2 gRNA Is Extremely Efficient and Competitive despite a High Degree of Secondary Structures and the Presence of an uORF. Viruses 2022; 14:1505. [PMID: 35891485 PMCID: PMC9322171 DOI: 10.3390/v14071505] [Citation(s) in RCA: 9] [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: 06/03/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 infection generates up to nine different sub-genomic mRNAs (sgRNAs), in addition to the genomic RNA (gRNA). The 5'UTR of each viral mRNA shares the first 75 nucleotides (nt.) at their 5'end, called the leader, but differentiates by a variable sequence (0 to 190 nt. long) that follows the leader. As a result, each viral mRNA has its own specific 5'UTR in term of length, RNA structure, uORF and Kozak context; each one of these characteristics could affect mRNA expression. In this study, we have measured and compared translational efficiency of each of the ten viral transcripts. Our data show that most of them are very efficiently translated in all translational systems tested. Surprisingly, the gRNA 5'UTR, which is the longest and the most structured, was also the most efficient to initiate translation. This property is conserved in the 5'UTR of SARS-CoV-1 but not in MERS-CoV strain, mainly due to the regulation imposed by the uORF. Interestingly, the translation initiation mechanism on the SARS-CoV-2 gRNA 5'UTR requires the cap structure and the components of the eIF4F complex but showed no dependence in the presence of the poly(A) tail in vitro. Our data strongly suggest that translation initiation on SARS-CoV-2 mRNAs occurs via an unusual cap-dependent mechanism.
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Affiliation(s)
| | | | - Théophile Ohlmann
- CIRI, Centre International de Recherche en Infectiologie, (Team Ohlmann), Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007 Lyon, France; (L.C.); (O.A.)
| | - Sylvain de Breyne
- CIRI, Centre International de Recherche en Infectiologie, (Team Ohlmann), Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007 Lyon, France; (L.C.); (O.A.)
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9
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Abstract
Rotaviruses represent one of the most successful pathogens in the world, with high infectivity and efficient transmission between the young of many animal species, including humans. To overcome host defenses, rotaviruses have evolved a plethora of strategies to effectively evade the innate immune response, establish initial infection in the small intestine, produce progeny, and shed into the environment. Previously, studying the roles and relative contributions of specific rotaviral factors in innate immune evasion had been challenging without a plasmid-only reverse genetics system. Although still in its infancy, current reverse genetics technology will help address important research questions regarding rotavirus innate immune evasion, host range restriction, and viral pathogenesis. In this review, we summarize the current knowledge about the antiviral host innate immune defense mechanisms, countermeasures of rotavirus-encoded factors, and strategies to better understand these interactions using the rotavirus reverse genetics system.
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10
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Biziaev NS, Egorova TV, Alkalaeva EZ. Dynamics of Eukaryotic mRNA Structure during Translation. Mol Biol 2022. [DOI: 10.1134/s0026893322030037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Johne R, Schilling-Loeffler K, Ulrich RG, Tausch SH. Whole Genome Sequence Analysis of a Prototype Strain of the Novel Putative Rotavirus Species L. Viruses 2022; 14:v14030462. [PMID: 35336869 PMCID: PMC8954357 DOI: 10.3390/v14030462] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/05/2023] Open
Abstract
Rotaviruses infect humans and animals and are a main cause of diarrhea. They are non-enveloped viruses with a genome of 11 double-stranded RNA segments. Based on genome analysis and amino acid sequence identities of the capsid protein VP6, the rotavirus species A to J (RVA-RVJ) have been defined so far. In addition, rotaviruses putatively assigned to the novel rotavirus species K (RVK) and L (RVL) have been recently identified in common shrews (Sorex araneus), based on partial genome sequences. Here, the complete genome sequence of strain KS14/0241, a prototype strain of RVL, is presented. The deduced amino acid sequence for VP6 of this strain shows only up to 47% identity to that of RVA to RVJ reference strains. Phylogenetic analyses indicate a clustering separated from the established rotavirus species for all 11 genome segments of RVL, with the closest relationship to RVH and RVJ within the phylogenetic RVB-like clade. The non-coding genome segment termini of RVL showed conserved sequences at the 5′-end (positive-sense RNA strand), which are common to all rotaviruses, and those conserved among the RVB-like clade at the 3′-end. The results are consistent with a classification of the virus into a novel rotavirus species L.
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Affiliation(s)
- Reimar Johne
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (K.S.-L.); (S.H.T.)
- Correspondence:
| | - Katja Schilling-Loeffler
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (K.S.-L.); (S.H.T.)
| | - Rainer G. Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany;
- German Centre for Infection Research (DZIF), 17493 Greifswald-Insel Riems, Germany
| | - Simon H. Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (K.S.-L.); (S.H.T.)
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12
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Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression. Nat Rev Mol Cell Biol 2022; 23:93-106. [PMID: 34594027 PMCID: PMC7614307 DOI: 10.1038/s41580-021-00417-y] [Citation(s) in RCA: 187] [Impact Index Per Article: 93.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 02/06/2023]
Abstract
In eukaryotes, poly(A) tails are present on almost every mRNA. Early experiments led to the hypothesis that poly(A) tails and the cytoplasmic polyadenylate-binding protein (PABPC) promote translation and prevent mRNA degradation, but the details remained unclear. More recent data suggest that the role of poly(A) tails is much more complex: poly(A)-binding protein can stimulate poly(A) tail removal (deadenylation) and the poly(A) tails of stable, highly translated mRNAs at steady state are much shorter than expected. Furthermore, the rate of translation elongation affects deadenylation. Consequently, the interplay between poly(A) tails, PABPC, translation and mRNA decay has a major role in gene regulation. In this Review, we discuss recent work that is revolutionizing our understanding of the roles of poly(A) tails in the cytoplasm. Specifically, we discuss the roles of poly(A) tails in translation and control of mRNA stability and how poly(A) tails are removed by exonucleases (deadenylases), including CCR4-NOT and PAN2-PAN3. We also discuss how deadenylation rate is determined, the integration of deadenylation with other cellular processes and the function of PABPC. We conclude with an outlook for the future of research in this field.
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13
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Hashizume M, Takashima A, Iwasaki M. A small stem-loop-forming region within the 3'-UTR of a non-polyadenylated LCMV mRNA promotes translation. J Biol Chem 2022; 298:101576. [PMID: 35026225 PMCID: PMC8888456 DOI: 10.1016/j.jbc.2022.101576] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/30/2022] Open
Abstract
Mammalian arenavirus (mammarenavirus) mRNAs are characterized by 5′-capped and 3′-nonpolyadenylated untranslated regions (UTRs). We previously reported that the nonpolyadenylated 3′-UTR of viral mRNA (vmRNA), which is derived from the noncoding intergenic region (IGR), regulates viral protein levels at the posttranscriptional level. This finding provided the basis for the development of novel live-attenuated vaccines (LAVs) against human pathogenic mammarenaviruses. Detailed information about the roles of specific vmRNA 3′-UTR sequences in controlling translation efficiency will help in understanding the mechanism underlying attenuation by IGR manipulations. Here, we characterize the roles of cis-acting mRNA regulatory sequences of a prototypic mammarenavirus, lymphocytic choriomeningitis virus (LCMV), in modulating translational efficiency. Using in vitro transcribed RNA mimics encoding a reporter gene, we demonstrate that the 3′-UTR of nucleoprotein (NP) mRNA without a poly(A) tail promotes translation in a poly(A)-binding protein-independent manner. Comparison with the 3′-UTR of glycoprotein precursor mRNA, which is translated less efficiently, revealed that a 10-nucleotide sequence proximal to the NP open reading frame is essential for promoting translation. Modification of this 10-nucleotide sequence also impacted reporter gene expression in recombinant LCMV. Our findings will enable rational design of the 10-nucleotide sequence to further improve our mammarenavirus LAV candidates and to develop a novel LCMV vector capable of controlling foreign gene expression.
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Affiliation(s)
- Mei Hashizume
- Laboratory of Emerging Viral Diseases, International Research Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ayako Takashima
- Laboratory of Emerging Viral Diseases, International Research Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masaharu Iwasaki
- Laboratory of Emerging Viral Diseases, International Research Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan.
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14
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Patra U, Mukhopadhyay U, Mukherjee A, Dutta S, Chawla-Sarkar M. Treading a HOSTile path: Mapping the dynamic landscape of host cell-rotavirus interactions to explore novel host-directed curative dimensions. Virulence 2021; 12:1022-1062. [PMID: 33818275 PMCID: PMC8023246 DOI: 10.1080/21505594.2021.1903198] [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: 09/21/2020] [Revised: 01/20/2021] [Accepted: 03/10/2021] [Indexed: 12/27/2022] Open
Abstract
Viruses are intracellular pathogens and are dependent on host cellular resources to carry out their cycles of perpetuation. Obtaining an integrative view of host-virus interaction is of utmost importance to understand the complex and dynamic interplay between viral components and host machineries. Besides its obvious scholarly significance, a comprehensive host-virus interaction profile also provides a platform where from host determinants of pro-viral and antiviral importance can be identified and further be subjected to therapeutic intervention. Therefore, adjunct to conventional methods of prophylactic vaccination and virus-directed antivirals, this host-targeted antiviral approach holds promising therapeutic potential. In this review, we present a comprehensive landscape of host cellular reprogramming in response to infection with rotavirus (RV) which causes profuse watery diarrhea in neonates and infants. In addition, an emphasis is given on how host determinants are either usurped or subverted by RV in course of infection and how therapeutic manipulation of specific host factors can effectively modulate the RV life cycle.
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Affiliation(s)
- Upayan Patra
- Division of Virology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - Urbi Mukhopadhyay
- Division of Virology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - Arpita Mukherjee
- Division of Virology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
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15
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Kanai Y, Kobayashi T. FAST Proteins: Development and Use of Reverse Genetics Systems for Reoviridae Viruses. Annu Rev Virol 2021; 8:515-536. [PMID: 34586868 DOI: 10.1146/annurev-virology-091919-070225] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Reverse genetics systems for viruses, the technology used to generate gene-engineered recombinant viruses from artificial genes, enable the study of the roles of the individual nucleotides and amino acids of viral genes and proteins in infectivity, replication, and pathogenicity. The successful development of a reverse genetics system for poliovirus in 1981 accelerated the establishment of protocols for other RNA viruses important for human health. Despite multiple efforts, rotavirus (RV), which causes severe gastroenteritis in infants, was refractory to reverse genetics analysis, and the first complete reverse genetics system for RV was established in 2017. This novel technique involves use of the fusogenic protein FAST (fusion-associated small transmembrane) derived from the bat-borne Nelson Bay orthoreovirus, which induces massive syncytium formation. Co-transfection of a FAST-expressing plasmid with complementary DNAs encoding RV genes enables rescue of recombinant RV. This review focuses on methodological insights into the reverse genetics system for RV and discusses applications and potential improvements to this system.
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Affiliation(s)
- Yuta Kanai
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; ,
| | - Takeshi Kobayashi
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; ,
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16
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Vera-Otarola J, Castillo-Vargas E, Angulo J, Barriga FM, Batlle E, Lopez-Lastra M. The viral nucleocapsid protein and the human RNA-binding protein Mex3A promote translation of the Andes orthohantavirus small mRNA. PLoS Pathog 2021; 17:e1009931. [PMID: 34547046 PMCID: PMC8454973 DOI: 10.1371/journal.ppat.1009931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/30/2021] [Indexed: 11/30/2022] Open
Abstract
The capped Small segment mRNA (SmRNA) of the Andes orthohantavirus (ANDV) lacks a poly(A) tail. In this study, we characterize the mechanism driving ANDV-SmRNA translation. Results show that the ANDV-nucleocapsid protein (ANDV-N) promotes in vitro translation from capped mRNAs without replacing eukaryotic initiation factor (eIF) 4G. Using an RNA affinity chromatography approach followed by mass spectrometry, we identify the human RNA chaperone Mex3A (hMex3A) as a SmRNA-3’UTR binding protein. Results show that hMex3A enhances SmRNA translation in a 3’UTR dependent manner, either alone or when co-expressed with the ANDV-N. The ANDV-N and hMex3A proteins do not interact in cells, but both proteins interact with eIF4G. The hMex3A–eIF4G interaction showed to be independent of ANDV-infection or ANDV-N expression. Together, our observations suggest that translation of the ANDV SmRNA is enhanced by a 5’-3’ end interaction, mediated by both viral and cellular proteins. Andes orthohantavirus (ANDV) is endemic in Argentina and Chile and is the primary etiological agent of hantavirus cardiopulmonary syndrome (HCPS) in South America. ANDV is unique among other members of the Hantaviridae family of viruses because of its ability to spread from person to person. The molecular mechanisms driving ANDV protein synthesis remain poorly understood. A previous report showed that translation of the Small segment mRNA (SmRNA) of ANDV relied on both the 5’cap and the 3’untranslated region (UTR) of the SmRNA. In this new study, we further characterize the mechanism by which the 5’ and 3’end of the SmRNA interact to assure viral protein synthesis. We establish that the viral nucleocapsid protein N and the cellular protein hMex3A participate in the process. These observations indicated that both viral and cellular proteins regulate viral gene expression during ANDV infection by enabling the viral mRNA to establish a non-covalent 5’-3’end interaction.
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Affiliation(s)
- Jorge Vera-Otarola
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Centro de Investigaciones Médicas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Unidad de Virología Aplicada, Dirección de Investigación y Doctorados de la Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Estefania Castillo-Vargas
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Centro de Investigaciones Médicas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Facultad de Odontología, Universidad Finis Terrae, Santiago, Chile
| | - Jenniffer Angulo
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Centro de Investigaciones Médicas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Francisco M. Barriga
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Barcelona, Spain
- ICREA, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Marcelo Lopez-Lastra
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Centro de Investigaciones Médicas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- * E-mail:
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17
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Sorokin II, Vassilenko KS, Terenin IM, Kalinina NO, Agol VI, Dmitriev SE. Non-Canonical Translation Initiation Mechanisms Employed by Eukaryotic Viral mRNAs. BIOCHEMISTRY. BIOKHIMIIA 2021; 86:1060-1094. [PMID: 34565312 PMCID: PMC8436584 DOI: 10.1134/s0006297921090042] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022]
Abstract
Viruses exploit the translation machinery of an infected cell to synthesize their proteins. Therefore, viral mRNAs have to compete for ribosomes and translation factors with cellular mRNAs. To succeed, eukaryotic viruses adopt multiple strategies. One is to circumvent the need for m7G-cap through alternative instruments for ribosome recruitment. These include internal ribosome entry sites (IRESs), which make translation independent of the free 5' end, or cap-independent translational enhancers (CITEs), which promote initiation at the uncapped 5' end, even if located in 3' untranslated regions (3' UTRs). Even if a virus uses the canonical cap-dependent ribosome recruitment, it can still perturb conventional ribosomal scanning and start codon selection. The pressure for genome compression often gives rise to internal and overlapping open reading frames. Their translation is initiated through specific mechanisms, such as leaky scanning, 43S sliding, shunting, or coupled termination-reinitiation. Deviations from the canonical initiation reduce the dependence of viral mRNAs on translation initiation factors, thereby providing resistance to antiviral mechanisms and cellular stress responses. Moreover, viruses can gain advantage in a competition for the translational machinery by inactivating individual translational factors and/or replacing them with viral counterparts. Certain viruses even create specialized intracellular "translation factories", which spatially isolate the sites of their protein synthesis from cellular antiviral systems, and increase availability of translational components. However, these virus-specific mechanisms may become the Achilles' heel of a viral life cycle. Thus, better understanding of the unconventional mechanisms of viral mRNA translation initiation provides valuable insight for developing new approaches to antiviral therapy.
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Affiliation(s)
- Ivan I Sorokin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Konstantin S Vassilenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Ilya M Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Natalia O Kalinina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Vadim I Agol
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Institute of Poliomyelitis, Chumakov Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, Moscow, 108819, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
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Hoxie I, Dennehy JJ. Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns. Viruses 2021; 13:v13081460. [PMID: 34452326 PMCID: PMC8402926 DOI: 10.3390/v13081460] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/29/2022] Open
Abstract
Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable tree spaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the weakest association with host species. Bayesian Skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to different host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.
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Affiliation(s)
- Irene Hoxie
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
- Correspondence:
| | - John J. Dennehy
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
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19
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Recent advances in rotavirus reverse genetics and its utilization in basic research and vaccine development. Arch Virol 2021; 166:2369-2386. [PMID: 34216267 PMCID: PMC8254061 DOI: 10.1007/s00705-021-05142-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/27/2021] [Indexed: 11/29/2022]
Abstract
Rotaviruses are segmented double-stranded RNA viruses with a high frequency of gene reassortment, and they are a leading cause of global diarrheal deaths in children less than 5 years old. Two-thirds of rotavirus-associated deaths occur in low-income countries. Currently, the available vaccines in developing countries have lower efficacy in children than those in developed countries. Due to added safety concerns and the high cost of current vaccines, there is a need to develop cost-effective next-generation vaccines with improved safety and efficacy. The reverse genetics system (RGS) is a powerful tool for investigating viral protein functions and developing novel vaccines. Recently, an entirely plasmid-based RGS has been developed for several rotaviruses, and this technological advancement has significantly facilitated novel rotavirus research. Here, we review the recently developed RGS platform and discuss its application in studying infection biology, gene reassortment, and development of vaccines against rotavirus disease.
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20
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López-Labrador FX, Brown JR, Fischer N, Harvala H, Van Boheemen S, Cinek O, Sayiner A, Madsen TV, Auvinen E, Kufner V, Huber M, Rodriguez C, Jonges M, Hönemann M, Susi P, Sousa H, Klapper PE, Pérez-Cataluňa A, Hernandez M, Molenkamp R, der Hoek LV, Schuurman R, Couto N, Leuzinger K, Simmonds P, Beer M, Höper D, Kamminga S, Feltkamp MCW, Rodríguez-Díaz J, Keyaerts E, Nielsen XC, Puchhammer-Stöckl E, Kroes ACM, Buesa J, Breuer J, Claas ECJ, de Vries JJC. Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure. J Clin Virol 2020; 134:104691. [PMID: 33278791 DOI: 10.1016/j.jcv.2020.104691] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/16/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023]
Abstract
Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for implementation of mHTS for virus diagnostics and to give recommendations for development and validation of laboratory methods, including mHTS quality assurance, control and quality assessment protocols.
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Affiliation(s)
- F Xavier López-Labrador
- Virology Laboratory, Genomics and Health Area, Centre for Public Health Research (FISABIO-Public Health), Valencia, Spain; CIBERESP, Instituto de Salud Carlos III, Madrid, Spain.
| | - Julianne R Brown
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, United Kingdom.
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Heli Harvala
- Microbiology Services, NHS Blood and Transplant, London, United Kingdom.
| | - Sander Van Boheemen
- ErasmusMC, Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.
| | - Ondrej Cinek
- Department of Paediatrics and Medical Microbiology, 2nd Faculty of Medicine, Charles University Prague, Czech Republic.
| | - Arzu Sayiner
- Dokuz Eylul University, Faculty of Medicine, Department of Medical Microbiology, Division of Medical Virology. Izmir, Turkey.
| | - Tina Vasehus Madsen
- Department of Clinical Microbiology, University Hospital of Region Zealand, Slagelse, Denmark.
| | - Eeva Auvinen
- Department of Virology, Helsinki University Hospital Laboratory and University of Helsinki, Helsinki, Finland.
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Christophe Rodriguez
- Microbiology Department and NGS Platform, University Hospital Henri Mondor (APHP), Créteil, France.
| | - Marcel Jonges
- Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands; Laboratory of Experimental Virology, Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands.
| | - Mario Hönemann
- Institute of Virology, Leipzig University, Leipzig, Germany.
| | - Petri Susi
- Institute of Biomedicine, University of Turku, Finland.
| | - Hugo Sousa
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal; Virology Service, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal; Molecular Oncology and Viral Pathology Group, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.
| | - Paul E Klapper
- Faculty of Biology, Medicine, and Health, Division of Infection, Immunity, and Respiratory Medicine, University of Manchester, Manchester, United Kingdom.
| | - Alba Pérez-Cataluňa
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Paterna, Valencia, Spain.
| | - Marta Hernandez
- Laboratory of Molecular Biology and Microbiology, Instituto Tecnologico Agrario de Castilla y Leon, Valladolid, Spain.
| | - Richard Molenkamp
- ErasmusMC, Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.
| | - Lia van der Hoek
- Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands; Laboratory of Experimental Virology, Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands.
| | - Rob Schuurman
- Department of Virology, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands; Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.
| | - Karoline Leuzinger
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland; Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland.
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany.
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany.
| | - Sergio Kamminga
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Mariet C W Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Jesús Rodríguez-Díaz
- Department of Microbiology and Ecology, Faculty of Medicine, University of Valencia, Valencia, Spain.
| | - Els Keyaerts
- Laboratorium Klinische en Epidemiologische Virologie (Rega Instituut), Leuven, Belgium.
| | - Xiaohui Chen Nielsen
- Department of Clinical Microbiology, University Hospital of Region Zealand, Slagelse, Denmark.
| | | | - Aloys C M Kroes
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Javier Buesa
- Department of Microbiology and Ecology, Faculty of Medicine, University of Valencia, Valencia, Spain.
| | - Judy Breuer
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, United Kingdom.
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Jutte J C de Vries
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
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21
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Prats AC, David F, Diallo LH, Roussel E, Tatin F, Garmy-Susini B, Lacazette E. Circular RNA, the Key for Translation. Int J Mol Sci 2020; 21:E8591. [PMID: 33202605 PMCID: PMC7697609 DOI: 10.3390/ijms21228591] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
It was thought until the 1990s that the eukaryotic translation machinery was unable to translate a circular RNA. However internal ribosome entry sites (IRESs) and m6A-induced ribosome engagement sites (MIRESs) were discovered, promoting 5' end-independent translation initiation. Today a new family of so-called "noncoding" circular RNAs (circRNAs) has emerged, revealing the pivotal role of 5' end-independent translation. CircRNAs have a strong impact on translational control via their sponge function, and form a new mRNA family as they are translated into proteins with pathophysiological roles. While there is no more doubt about translation of covalently closed circRNA, the linearity of canonical mRNA is only theoretical: it has been shown for more than thirty years that polysomes exhibit a circular form and mRNA functional circularization has been demonstrated in the 1990s by the interaction of initiation factor eIF4G with poly(A) binding protein. More recently, additional mechanisms of 3'-5' interaction have been reported, including m6A modification. Functional circularization enhances translation via ribosome recycling and acceleration of the translation initiation rate. This update of covalently and noncovalently closed circular mRNA translation landscape shows that RNA with circular shape might be the rule for translation with an important impact on disease development and biotechnological applications.
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Affiliation(s)
- Anne-Catherine Prats
- Institut des Maladies Métaboliques et Cardiovasculaires, UMR 1048, Inserm, Université de Toulouse UT3, 1, Avenue Jean Poulhes, BP 84225, 31432 Toulouse CEDEX 4, France; (F.D.); (L.H.D.); (E.R.); (F.T.); (B.G.-S.); (E.L.)
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22
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Chávez-Maya F, García-Espinosa G, López-Arellano ME, Padilla-Noriega L. Mutations in the VP2 gene of rotavirus associated with benzimidazole sensitivity. Virus Res 2020; 291:198189. [PMID: 33049307 DOI: 10.1016/j.virusres.2020.198189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/23/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022]
Abstract
Rotavirus species A (RVA) is the etiological agent of acute gastroenteritis in young individuals of various animal species, including humans. Vaccination has helped to reduce the impact of these viruses on humans and some species of domestic mammals, but they do not confer complete immunity, so antirotavirus agents are another important control option. In this study, millimolar concentrations of benzimidazole inhibited the replication of the Rhesus rotavirus (RRV) strain of RVA. Two mutants partially resistant to the inhibitory effect of benzimidazole were independently selected, and their genomes and those of their parental strains were fully sequenced. Most (7/11) mutations occurred in the gene that encodes the VP2 protein, and similarly most of the missense mutations (5/9), including the only one shared by the two mutants (G2,414 → R[G/A], D800 N), occurred in the VP2 gene. Our results identify the VP2 gene as the primary target affected by benzimidazole.
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Affiliation(s)
- Fernando Chávez-Maya
- Departamento de Medicina y Zootecnia de Aves, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Coyoacán 04510, Ciudad de México, Mexico.
| | - Gary García-Espinosa
- Departamento de Medicina y Zootecnia de Aves, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Coyoacán 04510, Ciudad de México, Mexico.
| | - María Eugenia López-Arellano
- Departamento de Helmintología, Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, INIFAP-México, Jiutepec 62550, Morelos, Mexico.
| | - Luis Padilla-Noriega
- Departamento de Microbiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, edificio A, primer piso, Coyoacán 04510, Ciudad de México, Mexico.
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23
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Reyna-Rosas E, Contreras-Treviño HI, León-Rodríguez R, Rocha-Zavaleta L, Dinkova TD, Padilla-Noriega L. The accumulation of rotavirus NSP3 dimers does not correlate with the extent of host cell translation inhibition. Future Virol 2020. [DOI: 10.2217/fvl-2020-0259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: We aimed to determine the functionality of rotavirus NSP3 dimers. Materials & methods: We expressed rhesus rotavirus NSP3 and determined the kinetics of host cell translation inhibition and the levels of accumulated dimerization intermediates and dimers. Results: We observed a linear kinetics of host cell translation inhibition, which correlated well with the sum of the dimerization intermediates and dimers. Treatment with 17-dimethylaminoethylamino-17-demethoxygeldanamycin reduced the accumulation of NSP3 dimers and potentiated host cell translation inhibition. Conclusion: Our results show that NSP3 dimer formation does not correlate with host cell translation inhibition and suggest that both NSP3 dimers and dimerization intermediates are functional and inhibit host cell translation.
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Affiliation(s)
- Edgar Reyna-Rosas
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Hugo I Contreras-Treviño
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Renato León-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Leticia Rocha-Zavaleta
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Tzvetanka D Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis Padilla-Noriega
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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24
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Alekhina OM, Terenin IM, Dmitriev SE, Vassilenko KS. Functional Cyclization of Eukaryotic mRNAs. Int J Mol Sci 2020; 21:ijms21051677. [PMID: 32121426 PMCID: PMC7084953 DOI: 10.3390/ijms21051677] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 02/24/2020] [Accepted: 02/27/2020] [Indexed: 11/16/2022] Open
Abstract
The closed-loop model of eukaryotic translation states that mRNA is circularized by a chain of the cap-eIF4E-eIF4G-poly(A)-binding protein (PABP)-poly(A) interactions that brings 5' and 3' ends together. This circularization is thought to promote the engagement of terminating ribosomes to a new round of translation at the same mRNA molecule, thus enhancing protein synthesis. Despite the general acceptance and the elegance of the hypothesis, it has never been proved experimentally. Using continuous in situ monitoring of luciferase synthesis in a mammalian in vitro system, we show here that the rate of translation initiation at capped and polyadenylated reporter mRNAs increases after the time required for the first ribosomes to complete mRNA translation. Such acceleration strictly requires the presence of a poly(A)-tail and is abrogated by the addition of poly(A) RNA fragments or m7GpppG cap analog to the translation reaction. The optimal functional interaction of mRNA termini requires 5' untranslated region (UTR) and 3' UTR of moderate lengths and provides stronger acceleration, thus a longer poly(A)-tail. Besides, we revealed that the inhibitory effect of the dominant negative R362Q mutant of initiation factor eIF4A diminishes in the course of translation reaction, suggesting a relaxed requirement for ATP. Taken together, our results imply that, upon the functional looping of an mRNA, the recycled ribosomes can be recruited to the start codon of the same mRNA molecule in an eIF4A-independent fashion. This non-canonical closed-loop assisted reinitiation (CLAR) mode provides efficient translation of the functionally circularized mRNAs.
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Affiliation(s)
- Olga M. Alekhina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia;
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Ilya M. Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, 119991 Moscow, Russia
| | - Sergey E. Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Correspondence: (S.E.D.); (K.S.V.); Tel.: +7-903-2220066 (S.E.D.); +7-496-7318232 (K.S.V.)
| | - Konstantin S. Vassilenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia;
- Correspondence: (S.E.D.); (K.S.V.); Tel.: +7-903-2220066 (S.E.D.); +7-496-7318232 (K.S.V.)
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Communication Is Key: 5'-3' Interactions that Regulate mRNA Translation and Turnover. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:149-164. [PMID: 31811634 DOI: 10.1007/978-3-030-31434-7_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Most eukaryotic mRNAs maintain a 5' cap structure and 3' poly(A) tail, cis-acting elements that are often separated by thousands of nucleotides. Nevertheless, multiple paradigms exist where mRNA 5' and 3' termini interact with each other in order to regulate mRNA translation and turnover. mRNAs recruit translation initiation factors to their termini, which in turn physically interact with each other. This physical bridging of the mRNA termini is known as the "closed loop" model, with years of genetic and biochemical evidence supporting the functional synergy between the 5' cap and 3' poly(A) tail to enhance mRNA translation initiation. However, a number of examples exist of "non-canonical" 5'-3' communication for cellular and viral RNAs that lack 5' cap structures and/or poly(A) tails. Moreover, in several contexts, mRNA 5'-3' communication can function to repress translation. Overall, we detail how various mRNA 5'-3' interactions play important roles in posttranscriptional regulation, wherein depending on the protein factors involved can result in translational stimulation or repression.
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Chen S, Feng C, Fang Y, Zhou X, Xu L, Wang W, Kong X, P Peppelenbosch M, Pan Q, Yin Y. The Eukaryotic Translation Initiation Factor 4F Complex Restricts Rotavirus Infection via Regulating the Expression of IRF1 and IRF7. Int J Mol Sci 2019; 20:ijms20071580. [PMID: 30934842 PMCID: PMC6480131 DOI: 10.3390/ijms20071580] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 03/21/2019] [Accepted: 03/26/2019] [Indexed: 12/13/2022] Open
Abstract
The eIF4F complex is a translation initiation factor that closely regulates translation in response to a multitude of environmental conditions including viral infection. How translation initiation factors regulate rotavirus infection remains poorly understood. In this study, the knockdown of the components of the eIF4F complex using shRNA and CRISPR/Cas9 were performed, respectively. We have demonstrated that loss-of-function of the three components of eIF4F, including eIF4A, eIF4E and eIF4G, remarkably promotes the levels of rotavirus genomic RNA and viral protein VP4. Consistently, knockdown of the negative regulator of eIF4F and programmed cell death protein 4 (PDCD4) inhibits the expression of viral mRNA and the VP4 protein. Mechanically, we confirmed that the silence of the eIF4F complex suppressed the protein level of IRF1 and IRF7 that exert potent antiviral effects against rotavirus infection. Thus, these results demonstrate that the eIF4F complex is an essential host factor restricting rotavirus replication, revealing new targets for the development of new antiviral strategies against rotavirus infection.
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Affiliation(s)
- Sunrui Chen
- Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China.
- Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands.
| | - Cui Feng
- Department of Materials Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Yan Fang
- College of Basic Medicine, Shannxi University of Chinese Medicine, Xianyang 712046, China.
| | - Xinying Zhou
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China.
| | - Lei Xu
- College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Wenshi Wang
- Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands.
| | - Xiangdong Kong
- Department of Materials Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | | | - Qiuwei Pan
- Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China.
- Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands.
| | - Yuebang Yin
- Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands.
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Rotavirus Infection Alters Splicing of the Stress-Related Transcription Factor XBP1. J Virol 2019; 93:JVI.01739-18. [PMID: 30541862 DOI: 10.1128/jvi.01739-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/05/2018] [Indexed: 11/20/2022] Open
Abstract
XBP1 is a stress-regulated transcription factor also involved in mammalian host defenses and innate immune response. Our investigation of XBP1 RNA splicing during rotavirus infection revealed that an additional XBP1 RNA (XBP1es) that corresponded to exon skipping in the XBP1 pre-RNA is induced depending on the rotavirus strain used. We show that the translation product of XBP1es (XBP1es) has trans-activation properties similar to those of XBP1 on ER stress response element (ERSE) containing promoters. Using monoreassortant between ES+ ("skipping") and ES- ("nonskipping") strains of rotavirus, we show that gene 7 encoding the viral translation enhancer NSP3 is involved in this phenomenon and that exon skipping parallels the nuclear relocalization of cytoplasmic PABP. We further show, using recombinant rotaviruses carrying chimeric gene 7, that the ES+ phenotype is linked to the eIF4G-binding domain of NSP3. Because the XBP1 transcription factor is involved in stress and immunological responses, our results suggest an alternative way to activate XBP1 upon viral infection or nuclear localization of PABP.IMPORTANCE Rotavirus is one of the most important pathogens causing severe gastroenteritis in young children worldwide. Here we show that infection with several rotavirus strains induces an alternative splicing of the RNA encoding the stressed-induced transcription factor XBP1. The genetic determinant of XBP1 splicing is the viral RNA translation enhancer NSP3. Since XBP1 is involved in cellular stress and immune responses and since the XBP1 protein made from the alternatively spliced RNA is an active transcription factor, our observations raise the question of whether alternative splicing is a cellular response to rotavirus infection.
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Chen F, Knutson TP, Porter RE, Ciarlet M, Mor SK, Marthaler DG. Genome characterization of Turkey Rotavirus G strains from the United States identifies potential recombination events with human Rotavirus B strains. J Gen Virol 2017; 98:2931-2936. [PMID: 29168675 PMCID: PMC5845698 DOI: 10.1099/jgv.0.000963] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Rotavirus G (RVG) strains have been detected in a variety of avian species, but RVG genomes have been published from only a single pigeon and two chicken strains. Two turkey RVG strains were identified and characterized, one in a hatchery with no reported health issues and the other in a hatchery with high embryo/poult mortality. The two turkey RVG strains shared only an 85.3 % nucleotide sequence identity in the VP7 gene while the other genes possessed high nucleotide identity among them (96.3–99.9 %). Low nucleotide percentage identities (31.6–87.3 %) occurred among the pigeon and chicken RVG strains. Interestingly, potential recombination events were detected between our RVG strains and a human RVB strain, in the VP6 and NSP3 segments. The epidemiology of RVG in avian flocks and the pathogenicity of the two different RVG strains should be further investigated to understand the ecology and impact of RVG in commercial poultry flocks.
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Affiliation(s)
- Fangzhou Chen
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Todd P Knutson
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Robert E Porter
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Max Ciarlet
- Vaccines Clinical Research and Development, GlaxoSmithKline Vaccines, Cambridge, MA 02139, USA
| | - Sunil Kumar Mor
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Douglas G Marthaler
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Manhattan, KS 66506, USA.,Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA
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29
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Du Z, Alekhina OM, Vassilenko KS, Simon AE. Concerted action of two 3' cap-independent translation enhancers increases the competitive strength of translated viral genomes. Nucleic Acids Res 2017; 45:9558-9572. [PMID: 28934492 PMCID: PMC5766195 DOI: 10.1093/nar/gkx643] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/14/2017] [Indexed: 11/13/2022] Open
Abstract
Several families of plant viruses evolved cap-independent translation enhancers (3'CITE) in the 3' untranslated regions of their genomic (g)RNAs to compete with ongoing cap-dependent translation of cellular mRNAs. Umbravirus Pea enation mosaic virus (PEMV)2 is the only example where three 3'CITEs enhance translation: the eIF4E-binding Panicum mosaic virus-like translational enhancer (PTE) and ribosome-binding 3' T-shaped structure (TSS) have been found in viruses of different genera, while the ribosome-binding kl-TSS that provides a long-distance interaction with the 5' end is unique. We report that the PTE is the key translation promoting element, but inhibits translation in cis and in trans in the absence of the kl-TSS by sequestering initiation factor eIF4G. PEMV2 strongly outcompeted a cellular mRNA mimic for translation, indicating that the combination of kl-TSS and PTE is highly efficient. Transferring the 3'-5' interaction from the kl-TSS to the PTE (to fulfill its functionality as found in other viruses) supported translationin vitro, but gRNA did not accumulate to detectable levels in protoplasts in the absence of the kl-TSS. It was shown that the PTE in conjunction with the kl-TSS did not markedly affect the translation initiation rate but rather increased the number of gRNAs available for translation. A model is proposed to explain how 3'CITE-based regulation of ribosome recruitment enhances virus fitness.
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Affiliation(s)
- Zhiyou Du
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Olga M Alekhina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Konstantin S Vassilenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Anne E Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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Contreras-Treviño HI, Reyna-Rosas E, León-Rodríguez R, Ruiz-Ordaz BH, Dinkova TD, Cevallos AM, Padilla-Noriega L. Species A rotavirus NSP3 acquires its translation inhibitory function prior to stable dimer formation. PLoS One 2017; 12:e0181871. [PMID: 28738064 PMCID: PMC5524322 DOI: 10.1371/journal.pone.0181871] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/07/2017] [Indexed: 11/18/2022] Open
Abstract
Species A rotavirus non-structural protein 3 (NSP3) is a translational regulator that inhibits or, under some conditions, enhances host cell translation. NSP3 binds to the translation initiation factor eIF4G1 and evicts poly-(A) binding protein (PABP) from eIF4G1, thus inhibiting translation of polyadenylated mRNAs, presumably by disrupting the effect of PABP bound to their 3’-ends. NSP3 has a long coiled-coil region involved in dimerization that includes a chaperone Hsp90-binding domain (HS90BD). We aimed to study the role in NSP3 dimerization of a segment of the coiled-coil region adjoining the HS90BD. We used a vaccinia virus system to express NSP3 with point mutations in conserved amino acids in the coiled-coil region and determined the effects of these mutations on translation by metabolic labeling of proteins as well as on accumulation of stable NSP3 dimers by non-dissociating Western blot, a method that separates stable NSP3 dimers from the monomer/dimerization intermediate forms of the protein. Four of five mutations reduced the total yield of NSP3 and the formation of stable dimers (W170A, K171E, R173E and R187E:K191E), whereas one mutation had the opposite effects (Y192A). Treatment with the proteasome inhibitor MG132 revealed that stable NSP3 dimers and monomers/dimerization intermediates are susceptible to proteasome degradation. Surprisingly, mutants severely impaired in the formation of stable dimers were still able to inhibit host cell translation, suggesting that NSP3 dimerization intermediates are functional. Our results demonstrate that rotavirus NSP3 acquires its function prior to stable dimer formation and remain as a proteasome target throughout dimerization.
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Affiliation(s)
- Hugo I. Contreras-Treviño
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Edgar Reyna-Rosas
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Renato León-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Blanca H. Ruiz-Ordaz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Tzvetanka D. Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ana M. Cevallos
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis Padilla-Noriega
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- * E-mail:
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Abstract
In infected cells rotavirus (RV) replicates in viroplasms, cytosolic structures that require a stabilized microtubule (MT) network for their assembly, maintenance of the structure and perinuclear localization. Therefore, we hypothesized that RV could interfere with the MT-breakdown that takes place in mitosis during cell division. Using synchronized RV-permissive cells, we show that RV infection arrests the cell cycle in S/G2 phase, thus favoring replication by improving viroplasms formation, viral protein translation, and viral assembly. The arrest in S/G2 phase is independent of the host or viral strain and relies on active RV replication. RV infection causes cyclin B1 down-regulation, consistent with blocking entry into mitosis. With the aid of chemical inhibitors, the cytoskeleton network was linked to specific signaling pathways of the RV-induced cell cycle arrest. We found that upon RV infection Eg5 kinesin was delocalized from the pericentriolar region to the viroplasms. We used a MA104-Fucci system to identify three RV proteins (NSP3, NSP5, and VP2) involved in cell cycle arrest in the S-phase. Our data indicate that there is a strong correlation between the cell cycle arrest and RV replication.
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Viral and cellular mRNA-specific activators harness PABP and eIF4G to promote translation initiation downstream of cap binding. Proc Natl Acad Sci U S A 2017; 114:6310-6315. [PMID: 28559344 DOI: 10.1073/pnas.1610417114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Regulation of mRNA translation is a major control point for gene expression and is critical for life. Of central importance is the complex between cap-bound eukaryotic initiation factor 4E (eIF4E), eIF4G, and poly(A) tail-binding protein (PABP) that circularizes mRNAs, promoting translation and stability. This complex is often targeted to regulate overall translation rates, and also by mRNA-specific translational repressors. However, the mechanisms of mRNA-specific translational activation by RNA-binding proteins remain poorly understood. Here, we address this deficit, focusing on a herpes simplex virus-1 protein, ICP27. We reveal a direct interaction with PABP that is sufficient to promote PABP recruitment and necessary for ICP27-mediated activation. PABP binds several translation factors but is primarily considered to activate translation initiation as part of the PABP-eIF4G-eIF4E complex that stimulates the initial cap-binding step. Importantly, we find that ICP27-PABP forms a complex with, and requires the activity of, eIF4G. Surprisingly, ICP27-PABP-eIF4G complexes act independently of the effects of PABP-eIF4G on cap binding to promote small ribosomal subunit recruitment. Moreover, we find that a cellular mRNA-specific regulator, Deleted in Azoospermia-like (Dazl), also employs the PABP-eIF4G interaction in a similar manner. We propose a mechanism whereby diverse RNA-binding proteins directly recruit PABP, in a non-poly(A) tail-dependent manner, to stimulate the small subunit recruitment step. This strategy may be particularly relevant to biological conditions associated with hypoadenylated mRNAs (e.g., germ cells/neurons) and/or limiting cytoplasmic PABP (e.g., viral infection, cell stress). This mechanism adds significant insight into our knowledge of mRNA-specific translational activation and the function of the PABP-eIF4G complex in translation initiation.
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Amroun A, Priet S, de Lamballerie X, Quérat G. Bunyaviridae RdRps: structure, motifs, and RNA synthesis machinery. Crit Rev Microbiol 2017; 43:753-778. [PMID: 28418734 DOI: 10.1080/1040841x.2017.1307805] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Bunyaviridae family is the largest and most diverse family of RNA viruses. It has more than 350 members divided into five genera: Orthobunyavirus, Phlebovirus, Nairovirus, Hantavirus, and Tospovirus. They are present in the five continents, causing recurrent epidemics, epizootics, and considerable agricultural loss. The genome of bunyaviruses is divided into three segments of negative single-stranded RNA according to their relative size: L (Large), M (Medium) and S (Small) segment. Bunyaviridae RNA-dependent RNA polymerase (RdRp) is encoded by the L segment, and is in charge of the replication and transcription of the viral RNA in the cytoplasm of the infected cell. Viral RdRps share a characteristic right hand-like structure with three subdomains: finger, palm, and thumb subdomains that define the formation of the catalytic cavity. In addition to the N-terminal endonuclease domain, eight conserved motifs (A-H) have been identified in the RdRp of Bunyaviridae. In this review, we have summarized the recent insights from the structural and functional studies of RdRp to understand the roles of different motifs shared by RdRps, the mechanism of viral RNA replication, genome segment packaging by the nucleoprotein, cap-snatching, mRNA transcription, and other RNA mechanisms of bunyaviruses.
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Affiliation(s)
- Abdennour Amroun
- a Faculté de Médecine , UMR "Emergence des Pathologies Virales" (Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP), Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille , Marseille , France
| | - Stéphane Priet
- a Faculté de Médecine , UMR "Emergence des Pathologies Virales" (Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP), Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille , Marseille , France
| | - Xavier de Lamballerie
- a Faculté de Médecine , UMR "Emergence des Pathologies Virales" (Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP), Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille , Marseille , France
| | - Gilles Quérat
- a Faculté de Médecine , UMR "Emergence des Pathologies Virales" (Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP), Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille , Marseille , France
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Hayashi-Miyamoto M, Murakami T, Minami-Fukuda F, Tsuchiaka S, Kishimoto M, Sano K, Naoi Y, Asano K, Ichimaru T, Haga K, Omatsu T, Katayama Y, Oba M, Aoki H, Shirai J, Ishida M, Katayama K, Mizutani T, Nagai M. Diversity in VP3, NSP3, and NSP4 of rotavirus B detected from Japanese cattle. INFECTION GENETICS AND EVOLUTION 2017; 49:97-103. [PMID: 28063924 DOI: 10.1016/j.meegid.2017.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/12/2016] [Accepted: 01/02/2017] [Indexed: 01/24/2023]
Abstract
Bovine rotavirus B (RVB) is an etiological agent of diarrhea mostly in adult cattle. Currently, a few sequences of viral protein (VP)1, 2, 4, 6, and 7 and nonstructural protein (NSP)1, 2, and 5 of bovine RVB are available in the DDBJ/EMBL/GenBank databases, and none have been reported for VP3, NSP3, and NSP4. In order to fill this gap in the genetic characterization of bovine RVB strains, we used a metagenomics approach and sequenced and analyzed the complete coding sequences (CDS) of VP3, NSP3, and NSP4 genes, as well as the partial or complete CDS of other genes of RVBs detected from Japanese cattle. VP3, NSP3, and NSP4 of bovine RVBs shared low nucleotide sequence identities (63.3-64.9% for VP3, 65.9-68.2% for NSP3, and 52.6-56.2% for NSP4) with those of murine, human, and porcine RVBs, suggesting that bovine RVBs belong to a novel genotype. Furthermore, significantly low amino acid sequence identities were observed for NSP4 (36.1-39.3%) between bovine RVBs and the RVBs of other species. In contrast, hydrophobic plot analysis of NSP4 revealed profiles similar to those of RVBs of other species and rotavirus A (RVA) strains. Phylogenetic analyses of all gene segments revealed that bovine RVB strains formed a cluster that branched distantly from other RVBs. These results suggest that bovine RVBs have evolved independently from other RVBs but in a similar manner to other rotaviruses. These findings provide insights into the evolution and diversity of RVB strains.
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Affiliation(s)
| | - Toshiaki Murakami
- Ishikawa Hokubu Livestock Hygiene Service Center, Nanao, Ishikawa 929-2126, Japan
| | - Fujiko Minami-Fukuda
- Ishikawa Hokubu Livestock Hygiene Service Center, Nanao, Ishikawa 929-2126, Japan
| | - Shinobu Tsuchiaka
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Mai Kishimoto
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Kaori Sano
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Yuki Naoi
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Keigo Asano
- Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Toru Ichimaru
- Department of Health and Medical Sciences, Ishikawa Prefectural Nursing University, Kahoku, Ishikawa 929-1210, Japan
| | - Kei Haga
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan; Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Minato, Tokyo 108-8641, Japan
| | - Tsutomu Omatsu
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Mami Oba
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Hiroshi Aoki
- Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
| | - Junsuke Shirai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan; Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Motohiko Ishida
- Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan; Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Minato, Tokyo 108-8641, Japan
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Makoto Nagai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan; Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan.
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35
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Chattopadhyay S, Mukherjee A, Patra U, Bhowmick R, Basak T, Sengupta S, Chawla-Sarkar M. Tyrosine phosphorylation modulates mitochondrial chaperonin Hsp60 and delays rotavirus NSP4-mediated apoptotic signaling in host cells. Cell Microbiol 2016; 19. [PMID: 27665089 DOI: 10.1111/cmi.12670] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 12/29/2022]
Abstract
Phosphoproteomics-based platforms have been widely used to identify post translational dynamics of cellular proteins in response to viral infection. The present study was undertaken to assess differential tyrosine phosphorylation during early hours of rotavirus (RV) SA11 infection. Heat shock proteins (Hsp60) were found to be enriched in the data set of RV-SA11 induced differentially tyrosine-phosphorylated proteins at 2 hr post infection (hpi). Hsp60 was further found to be phosphorylated by an activated form of Src kinase on 227th tyrosine residue, and tyrosine phosphorylation of mitochondrial chaperonin Hsp60 correlated with its proteasomal degradation at 2-2.5hpi. Interestingly, mitochondrial Hsp60 positively influenced translocation of the rotaviral nonstructural protein 4 to mitochondria during RV infections. Phosphorylation and subsequent transient degradation of mitochondrial Hsp60 during early hours of RV-SA11 infection resulted in inhibition of premature import of nonstructural protein 4 into mitochondria, thereby delaying early apoptosis. Overall, the study highlighted one of the many strategies rotavirus undertakes to prevent early apoptosis and subsequent reduced viral progeny yield.
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Affiliation(s)
- Shiladitya Chattopadhyay
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road SchemeP- XM, Beliaghata, Kolkata, 700010, India
| | - Arpita Mukherjee
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road SchemeP- XM, Beliaghata, Kolkata, 700010, India
| | - Upayan Patra
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road SchemeP- XM, Beliaghata, Kolkata, 700010, India
| | - Rahul Bhowmick
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road SchemeP- XM, Beliaghata, Kolkata, 700010, India
| | - Trayambak Basak
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110020, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB campus, New Delhi, India
| | - Shantanu Sengupta
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110020, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB campus, New Delhi, India
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road SchemeP- XM, Beliaghata, Kolkata, 700010, India
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Filbin ME, Kieft JS. Linking Α to Ω: diverse and dynamic RNA-based mechanisms to regulate gene expression by 5'-to-3' communication. F1000Res 2016; 5. [PMID: 27610229 PMCID: PMC4995689 DOI: 10.12688/f1000research.7913.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/16/2016] [Indexed: 12/18/2022] Open
Abstract
Communication between the 5′ and 3′ ends of a eukaryotic messenger RNA (mRNA) or viral genomic RNA is a ubiquitous and important strategy used to regulate gene expression. Although the canonical interaction between initiation factor proteins at the 5′ end of an mRNA and proteins bound to the polyadenylate tail at the 3′ end is well known, in fact there are many other strategies used in diverse ways. These strategies can involve “non-canonical” proteins, RNA structures, and direct RNA-RNA base-pairing between distal elements to achieve 5′-to-3′ communication. Likewise, the communication induced by these interactions influences a variety of processes linked to the use and fate of the RNA that contains them. Recent studies are revealing how dynamic these interactions are, possibly changing in response to cellular conditions or to link various phases of the mRNA’s life, from translation to decay. Thus, 5′-to-3′ communication is about more than just making a closed circle; the RNA elements and associated proteins are key players in controlling gene expression at the post-transcriptional level.
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Affiliation(s)
- Megan E Filbin
- Department of Chemistry, Metropolitan State University of Denver, Denver, Colorado, 80217, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, 80045, USA
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Abstract
Rotavirus, a member of the family Reoviridae, was identified as the leading etiological agent of severe gastroenteritis in infants and young children in 1973. The rotavirus genome is composed of 11 gene segments of double-stranded (ds)RNA. During the last 40 years, a large amount of basic research on rotavirus structure, genome, antigen, replication, pathogenesis, epidemiology, immune responses, and evolution has been accumulated. This article reviews the fundamental aspects of rotavirology including recent important achievements in research.
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Abstract
"Rotaviruses represent the most important etiological agents of acute, severe gastroenteritis in the young of many animal species, including humans." This statement, variations of which are a common beginning in articles about rotaviruses, reflects the fact that these viruses have evolved efficient strategies for evading the innate immune response of the host and for successfully replicating in the population. In this review, we summarize what is known about the defense mechanisms that host cells employ to prevent rotavirus invasion and the countermeasures that these viruses have successfully developed to surpass cellular defenses. Rotaviruses use at least two viral multifunctional proteins to directly interact with, and prevent the activation of, the interferon system, and they use at least one other protein to halt the protein synthesis machinery and prevent the expression of most of the transcriptional antiviral program of the cell. Characterization of the confrontation between rotaviruses and their host cells has allowed us to learn about the virus-host coevolution that prevents the damaging effects of the innate immune response.
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Affiliation(s)
- Susana López
- Departamento de Génetica del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México;
| | - Liliana Sánchez-Tacuba
- Departamento de Génetica del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México;
| | - Joaquin Moreno
- Departamento de Génetica del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México;
| | - Carlos F Arias
- Departamento de Génetica del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México;
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Rissland OS. The organization and regulation of mRNA-protein complexes. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27324829 PMCID: PMC5213448 DOI: 10.1002/wrna.1369] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 12/21/2022]
Abstract
In a eukaryotic cell, each messenger RNA (mRNA) is bound to a variety of proteins to form an mRNA-protein complex (mRNP). Together, these proteins impact nearly every step in the life cycle of an mRNA and are critical for the proper control of gene expression. In the cytoplasm, for instance, mRNPs affect mRNA translatability and stability and provide regulation of specific transcripts as well as global, transcriptome-wide control. mRNPs are complex, diverse, and dynamic, and so they have been a challenge to understand. But the advent of high-throughput sequencing technology has heralded a new era in the study of mRNPs. Here, I will discuss general principles of cytoplasmic mRNP organization and regulation. Using microRNA-mediated repression as a case study, I will focus on common themes in mRNPs and highlight the interplay between mRNP composition and posttranscriptional regulation. mRNPs are an important control point in regulating gene expression, and while the study of these fascinating complexes presents remaining challenges, recent advances provide a critical lens for deciphering gene regulation. WIREs RNA 2017, 8:e1369. doi: 10.1002/wrna.1369 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Olivia S Rissland
- Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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40
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Stress Response and Translation Control in Rotavirus Infection. Viruses 2016; 8:v8060162. [PMID: 27338442 PMCID: PMC4926182 DOI: 10.3390/v8060162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/26/2016] [Accepted: 05/31/2016] [Indexed: 12/30/2022] Open
Abstract
The general stress and innate immune responses are closely linked and overlap at many levels. The outcomes of these responses serve to reprogram host expression patterns to prevent viral invasions. In turn, viruses counter attack these cell responses to ensure their replication. The mechanisms by which viruses attempt to control host cell responses are as varied as the number of different virus families. One of the most recurrent strategies used by viruses to control the antiviral response of the cell is to hijack the translation machinery of the host, such that viral proteins are preferentially synthesized, while the expression of the stress and antiviral responses of the cell are blocked at the translation level. Here, we will review how rotaviruses, an important agent of acute severe gastroenteritis in children, overcome the stress responses of the cell to establish a productive infectious cycle.
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Gratia M, Vende P, Charpilienne A, Baron HC, Laroche C, Sarot E, Pyronnet S, Duarte M, Poncet D. Challenging the Roles of NSP3 and Untranslated Regions in Rotavirus mRNA Translation. PLoS One 2016; 11:e0145998. [PMID: 26727111 PMCID: PMC4699793 DOI: 10.1371/journal.pone.0145998] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/01/2015] [Indexed: 12/20/2022] Open
Abstract
Rotavirus NSP3 is a translational surrogate of the PABP-poly(A) complex for rotavirus mRNAs. To further explore the effects of NSP3 and untranslated regions (UTRs) on rotavirus mRNAs translation, we used a quantitative in vivo assay with simultaneous cytoplasmic NSP3 expression (wild-type or deletion mutant) and electroporated rotavirus-like and standard synthetic mRNAs. This assay shows that the last four GACC nucleotides of viral mRNA are essential for efficient translation and that both the NSP3 eIF4G- and RNA-binding domains are required. We also show efficient translation of rotavirus-like mRNAs even with a 5’UTR as short as 5 nucleotides, while more than eleven nucleotides are required for the 3’UTR. Despite the weak requirement for a long 5’UTR, a good AUG environment remains a requirement for rotavirus mRNAs translation.
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Affiliation(s)
- Matthieu Gratia
- Institut de Biologie Integrative de la Cellule (I2BC), UMR 9198, Département de Virologie, USC INRA 1358, Gif sur Yvette, France
| | - Patrice Vende
- Institut de Biologie Integrative de la Cellule (I2BC), UMR 9198, Département de Virologie, USC INRA 1358, Gif sur Yvette, France
| | - Annie Charpilienne
- Institut de Biologie Integrative de la Cellule (I2BC), UMR 9198, Département de Virologie, USC INRA 1358, Gif sur Yvette, France
| | - Hilma Carolina Baron
- Institut de Biologie Integrative de la Cellule (I2BC), UMR 9198, Département de Virologie, USC INRA 1358, Gif sur Yvette, France
| | - Cécile Laroche
- Institut de Biologie Integrative de la Cellule (I2BC), UMR 9198, Département de Virologie, USC INRA 1358, Gif sur Yvette, France
| | - Emeline Sarot
- INSERM UMR-1037 - Université de Toulouse III-Paul Sabatier, Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Equipe labellisée Ligue Contre le Cancer Toulouse, France
| | - Stéphane Pyronnet
- INSERM UMR-1037 - Université de Toulouse III-Paul Sabatier, Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Equipe labellisée Ligue Contre le Cancer Toulouse, France
| | - Mariela Duarte
- Institut de Biologie Integrative de la Cellule (I2BC), UMR 9198, Département de Virologie, USC INRA 1358, Gif sur Yvette, France
- Université d’Evry Val d’Essonne, Département de Biologie, Evry, France
| | - Didier Poncet
- Institut de Biologie Integrative de la Cellule (I2BC), UMR 9198, Département de Virologie, USC INRA 1358, Gif sur Yvette, France
- * E-mail:
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42
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Bhowmick R, Mukherjee A, Patra U, Chawla-Sarkar M. Rotavirus disrupts cytoplasmic P bodies during infection. Virus Res 2015; 210:344-54. [PMID: 26386333 DOI: 10.1016/j.virusres.2015.09.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/02/2015] [Accepted: 09/03/2015] [Indexed: 12/17/2022]
Abstract
Cytoplasmic Processing bodies (P bodies), the RNA-protein aggregation foci of translationally stalled and potentially decaying mRNA, have been reported to be differentially modulated by viruses. Rotavirus, the causative agent of acute infantile gastroenteritis is a double stranded RNA virus which completes its entire life-cycle exclusively in host cell cytoplasm. In this study, the fate of P bodies was investigated upon rotavirus infection. It was found that P bodies get disrupted during rotavirus infection. The disruption occurred by more than one different mechanism where deadenylating P body component Pan3 was degraded by rotavirus NSP1 and exonuclease XRN1 along with the decapping enzyme hDCP1a were relocalized from cytoplasm to nucleus. Overall the study highlights decay and subcellular relocalization of P body components as novel mechanisms by which rotavirus subverts cellular antiviral responses.
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Affiliation(s)
- Rahul Bhowmick
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Arpita Mukherjee
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Upayan Patra
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata 700010, West Bengal, India.
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43
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Rotavirus NSP3 Is a Translational Surrogate of the Poly(A) Binding Protein-Poly(A) Complex. J Virol 2015; 89:8773-82. [PMID: 26063427 DOI: 10.1128/jvi.01402-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 06/04/2015] [Indexed: 12/26/2022] Open
Abstract
UNLABELLED Through its interaction with the 5' translation initiation factor eIF4G, poly(A) binding protein (PABP) facilitates the translation of 5'-capped and 3'-poly(A)-tailed mRNAs. Rotavirus mRNAs are capped but not polyadenylated, instead terminating in a 3' GACC motif that is recognized by the viral protein NSP3, which competes with PABP for eIF4G binding. Upon rotavirus infection, viral, GACC-tailed mRNAs are efficiently translated, while host poly(A)-tailed mRNA translation is, in contrast, severely impaired. To explore the roles of NSP3 in these two opposing events, the translational capabilities of three capped mRNAs, distinguished by either a GACC, a poly(A), or a non-GACC and nonpoly(A) 3' end, have been monitored after electroporation of cells expressing all rotavirus proteins (infected cells) or only NSP3 (stably or transiently transfected cells). In infected cells, we found that the magnitudes of translation induction (GACC-tailed mRNA) and translation reduction [poly(A)-tailed mRNA] both depended on the rotavirus strain used but that translation reduction not genetically linked to NSP3. In transfected cells, even a small amount of NSP3 was sufficient to dramatically enhance GACC-tailed mRNA translation and, surprisingly, to slightly favor the translation of both poly(A)- and nonpoly(A)-tailed mRNAs, likely by stabilizing the eIF4E-eIF4G interaction. These data suggest that NSP3 is a translational surrogate of the PABP-poly(A) complex; therefore, it cannot by itself be responsible for inhibiting the translation of host poly(A)-tailed mRNAs upon rotavirus infection. IMPORTANCE To control host cell physiology and to circumvent innate immunity, many viruses have evolved powerful mechanisms aimed at inhibiting host mRNA translation while stimulating translation of their own mRNAs. How rotavirus tackles this challenge is still a matter of debate. Using rotavirus-infected cells, we show that the magnitude of cellular poly(A) mRNA translation differs with respect to rotavirus strains but is not genetically linked to NSP3. Using cells expressing rotavirus NSP3, we show that NSP3 alone not only dramatically enhances rotavirus-like mRNA translation but also enhances poly(A) mRNA translation rather than inhibiting it, likely by stabilizing the eIF4E-eIF4G complex. Thus, the inhibition of cellular polyadenylated mRNA translation during rotavirus infection cannot be attributed solely to NSP3 and is more likely the result of global competition between viral and host mRNAs for the cellular translation machinery.
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44
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Gamil AAA, Mutoloki S, Evensen Ø. A piscine birnavirus induces inhibition of protein synthesis in CHSE-214 cells primarily through the induction of eIF2α phosphorylation. Viruses 2015; 7:1987-2005. [PMID: 25885006 PMCID: PMC4411686 DOI: 10.3390/v7041987] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/01/2015] [Accepted: 04/10/2015] [Indexed: 01/19/2023] Open
Abstract
Inhibition of protein synthesis represents one of the antiviral mechanisms employed by cells and it is also used by viruses for their own propagation. To what extent members of the Birnaviridae family employ such strategies is not well understood. Here we use a type-strain of the Aquabirnavirus, infectious pancreatic necrosis virus (IPNV), to investigate this phenomenon in vitro. CHSE-214 cells were infected with IPNV and at 3, 12, 24, and 48 hours post infection (hpi) before the cells were harvested and labeled with S35 methionine to assess protein synthesis. eIF2α phosphorylation was examined by Western blot while RT-qPCR was used to assess virus replication and the expression levels of IFN-α, Mx1 and PKR. Cellular responses to IPNV infection were assessed by DNA laddering, Caspase-3 assays and flow cytometry. The results show that the onset and kinetics of eIF2α phosphorylation was similar to that of protein synthesis inhibition as shown by metabolic labeling. Increased virus replication and virus protein formation was observed by 12 hpi, peaking at 24 hpi. Apoptosis was induced in a small fraction (1−2%) of IPNV-infected CHSE cells from 24 hpi while necrotic/late apoptotic cells increased from 10% by 24 hpi to 59% at 48 hpi, as shown by flow cytometry. These results were in accordance with a small decline in cell viability by 24hpi, dropping below 50% by 48 hpi. IPNV induced IFN-α mRNA upregulation by 24 hpi while no change was observed in the expression of Mx1 and PKR mRNA. Collectively, these findings show that IPNV induces inhibition of protein synthesis in CHSE cells through phosphorylation of eIF2α with minimal involvement of apoptosis. The anticipation is that protein inhibition is used by the virus to evade the host innate antiviral responses.
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Affiliation(s)
- Amr A A Gamil
- Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, P.O. Box 8146 Dep., 0033 Oslo, Norway.
| | - Stephen Mutoloki
- Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, P.O. Box 8146 Dep., 0033 Oslo, Norway.
| | - Øystein Evensen
- Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, P.O. Box 8146 Dep., 0033 Oslo, Norway
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45
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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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46
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Souii A, Ben M'hadheb-Gharbi M, Gharbi J. Role of RNA structure motifs in IRES-dependent translation initiation of the coxsackievirus B3: new insights for developing live-attenuated strains for vaccines and gene therapy. Mol Biotechnol 2014; 55:179-202. [PMID: 23881360 DOI: 10.1007/s12033-013-9674-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Internal ribosome entry site (IRES) elements are highly structured RNA sequences that function to recruit ribosomes for the initiation of translation. In contrast to the canonical cap-binding, the mechanism of IRES-mediated translation initiation is still poorly understood. Translation initiation of the coxsackievirus B3 (CVB3), a causative agent of viral myocarditis, has been shown to be mediated by a highly ordered structure of the 5' untranslated region (5'UTR), which harbors an IRES. Taking into account that efficient initiation of mRNA translation depends on temporally and spatially orchestrated sequence of RNA-protein and RNA-RNA interactions, and that, at present, little is known about these interactions, we aimed to describe recent advances in our understanding of molecular structures and biochemical functions of the translation initiation process. Thus, this review will explore the IRES elements as important RNA structures and the significance of these structures in providing an alternative mechanism of translation initiation of the CVB3 RNA. Since translation initiation is the first intracellular step during the CVB3 infection cycle, the IRES region provides an ideal target for antiviral therapies. Interestingly, the 5' and 3'UTRs represent promising candidates for the study of CVB3 cardiovirulence and provide new insights for developing live-attenuated vaccines.
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Affiliation(s)
- Amira Souii
- Institut Supérieur de Biotechnologie de Monastir-Université de Monastir, Avenue Tahar Hadded, BP 74, 5000, Monastir, Tunisia
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47
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Park R, El-Guindy A, Heston L, Lin SF, Yu KP, Nagy M, Borah S, Delecluse HJ, Steitz J, Miller G. Nuclear translocation and regulation of intranuclear distribution of cytoplasmic poly(A)-binding protein are distinct processes mediated by two Epstein Barr virus proteins. PLoS One 2014; 9:e92593. [PMID: 24705134 PMCID: PMC3976295 DOI: 10.1371/journal.pone.0092593] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 02/25/2014] [Indexed: 01/22/2023] Open
Abstract
Many viruses target cytoplasmic polyA binding protein (PABPC) to effect widespread inhibition of host gene expression, a process termed viral host-shutoff (vhs). During lytic replication of Epstein Barr Virus (EBV) we observed that PABPC was efficiently translocated from the cytoplasm to the nucleus. Translocated PABPC was diffusely distributed but was excluded from viral replication compartments. Vhs during EBV infection is regulated by the viral alkaline nuclease, BGLF5. Transfection of BGLF5 alone into BGLF5-KO cells or uninfected 293 cells promoted translocation of PAPBC that was distributed in clumps in the nucleus. ZEBRA, a viral bZIP protein, performs essential functions in the lytic program of EBV, including activation or repression of downstream viral genes. ZEBRA is also an essential replication protein that binds to viral oriLyt and interacts with other viral replication proteins. We report that ZEBRA also functions as a regulator of vhs. ZEBRA translocated PABPC to the nucleus, controlled the intranuclear distribution of PABPC, and caused global shutoff of host gene expression. Transfection of ZEBRA alone into 293 cells caused nuclear translocation of PABPC in the majority of cells in which ZEBRA was expressed. Co-transfection of ZEBRA with BGLF5 into BGLF5-KO cells or uninfected 293 cells rescued the diffuse intranuclear pattern of PABPC seen during lytic replication. ZEBRA mutants defective for DNA-binding were capable of regulating the intranuclear distribution of PABPC, and caused PABPC to co-localize with ZEBRA. One ZEBRA mutant, Z(S186E), was deficient in translocation yet was capable of altering the intranuclear distribution of PABPC. Therefore ZEBRA-mediated nuclear translocation of PABPC and regulation of intranuclear PABPC distribution are distinct events. Using a click chemistry-based assay for new protein synthesis, we show that ZEBRA and BGLF5 each function as viral host shutoff factors.
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Affiliation(s)
- Richard Park
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Ayman El-Guindy
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Lee Heston
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Su-Fang Lin
- Institute of Cancer Research, National Health Research Institutes, Zhunan Town, Taiwan
| | - Kuan-Ping Yu
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Mate Nagy
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Sumit Borah
- Department of Biochemistry, Howard Hughes Medical Institute, University of Colorado Biofrontiers Institute, Boulder, Colorado, United States of America
| | | | - Joan Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - George Miller
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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48
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Sagar V, Murray KE. The mammalian orthoreovirus bicistronic M3 mRNA initiates translation using a 5' end-dependent, scanning mechanism that does not require interaction of 5'-3' untranslated regions. Virus Res 2014; 183:30-40. [PMID: 24486484 DOI: 10.1016/j.virusres.2014.01.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/15/2014] [Accepted: 01/16/2014] [Indexed: 12/12/2022]
Abstract
Mammalian orthoreovirus mRNAs possess short 5' UTR, lack 3' poly(A) tails, and may lack 5' cap structures at late times post-infection. As such, the mechanisms by which these viral mRNAs recruit ribosomes remain completely unknown. Toward addressing this question, we used bicistronic MRV M3 mRNA to analyze the role of 5' and 3' UTRs during MRV protein synthesis. The 5' UTR was found to be dispensable for translation initiation; however, reducing its length promoted increased downstream initiation. Modifying start site Kozak context altered the ratio of upstream to downstream initiation, whereas mutations in the 3' UTR did not. Moreover, an M3 mRNA lacking a 3' UTR was able to rescue MRV infection to WT levels in an siRNA trans-complementation assay. Together, these data allow us to propose a model in which the MRV M3 mRNA initiates translation using a 5' end-dependent, scanning mechanism that does not require the viral mRNA 3' UTR or 5'-3' UTRs interaction.
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Affiliation(s)
- Vidya Sagar
- Department of Biological Sciences, Florida International University, Miami, FL 33199, United States.
| | - Kenneth E Murray
- Department of Biological Sciences, Florida International University, Miami, FL 33199, United States
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Abstract
Members of the genus Orthoreovirus in the family Reoviridae are nonenveloped, icosahedral viruses. Their genomes contain 10 segments of double-stranded RNA (dsRNA). The orthoreoviruses are divided into two subgroups, the fusogenic and nonfusogenic reoviruses, based on the ability of the virus to induce cell-to-cell fusion. The fusogenic subgroup consists of the avian reovirus, baboon reovirus, pteropine reovirus, and reptilian reovirus, whereas the nonfusogenic subgroup consists of the prototypical mammalian reovirus (MRV) species. MRVs are highly tractable experimental models for studies of segmented dsRNA virus replication and pathogenesis. Moreover, MRVs can selectively kill tumor cells and have been evaluated as oncolytic agents in clinical trials. This review provides a brief overview of current knowledge on the virological features of MRVs.
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Affiliation(s)
- Takeshi Kobayashi
- International Research Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University
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The molecular biology of Bluetongue virus replication. Virus Res 2013; 182:5-20. [PMID: 24370866 DOI: 10.1016/j.virusres.2013.12.017] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/10/2013] [Accepted: 12/11/2013] [Indexed: 01/17/2023]
Abstract
The members of Orbivirus genus within the Reoviridae family are arthropod-borne viruses which are responsible for high morbidity and mortality in ruminants. Bluetongue virus (BTV) which causes disease in livestock (sheep, goat, cattle) has been in the forefront of molecular studies for the last three decades and now represents the best understood orbivirus at a molecular and structural level. The complex nature of the virion structure has been well characterised at high resolution along with the definition of the virus encoded enzymes required for RNA replication; the ordered assembly of the capsid shell as well as the protein and genome sequestration required for it; and the role of host proteins in virus entry and virus release. More recent developments of Reverse Genetics and Cell-Free Assembly systems have allowed integration of the accumulated structural and molecular knowledge to be tested at meticulous level, yielding higher insight into basic molecular virology, from which the rational design of safe efficacious vaccines has been possible. This article is centred on the molecular dissection of BTV with a view to understanding the role of each protein in the virus replication cycle. These areas are important in themselves for BTV replication but they also indicate the pathways that related viruses, which includes viruses that are pathogenic to man and animals, might also use providing an informed starting point for intervention or prevention.
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