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Leseva MN, Buttari B, Saso L, Dimitrova PA. Infection Meets Inflammation: N6-Methyladenosine, an Internal Messenger RNA Modification as a Tool for Pharmacological Regulation of Host-Pathogen Interactions. Biomolecules 2023; 13:1060. [PMID: 37509095 PMCID: PMC10377384 DOI: 10.3390/biom13071060] [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: 05/26/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
The significance of internal mRNA modifications for the modulation of transcript stability, for regulation of nuclear export and translation efficiency, and their role in suppressing innate immunity is well documented. Over the years, the molecular complexes involved in the dynamic regulation of the most prevalent modifications have been characterized-we have a growing understanding of how each modification is set and erased, where it is placed, and in response to what cues. Remarkably, internal mRNA modifications, such as methylation, are emerging as an additional layer of regulation of immune cell homeostasis, differentiation, and function. A fascinating recent development is the investigation into the internal modifications of host/pathogen RNA, specifically N6-methyladenosine (m6A), its abundance and distribution during infection, and its role in disease pathogenesis and in shaping host immune responses. Low molecular weight compounds that target RNA-modifying enzymes have shown promising results in vitro and in animal models of different cancers and are expanding the tool-box in immuno-oncology. Excitingly, such modulators of host mRNA methyltransferase or demethylase activity hold profound implications for the development of new broad-spectrum therapeutic agents for infectious diseases as well. This review describes the newly uncovered role of internal mRNA modification in infection and in shaping the function of the immune system in response to invading pathogens. We will also discuss its potential as a therapeutic target and identify pitfalls that need to be overcome if it is to be effectively leveraged against infectious agents.
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Affiliation(s)
- Milena N Leseva
- Laboratory of Experimental Immunotherapy, Department of Immunology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Brigitta Buttari
- Department of Cardiovascular and Endocrine-Metabolic Diseases and Aging, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", La Sapienza University of Rome, 00185 Rome, Italy
| | - Petya A Dimitrova
- Laboratory of Experimental Immunotherapy, Department of Immunology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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2
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Liu H, Cheng L. Viral Capsid and Polymerase in Reoviridae. Subcell Biochem 2022; 99:525-552. [PMID: 36151388 DOI: 10.1007/978-3-031-00793-4_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The members of the family Reoviridae (reoviruses) consist of 9-12 discrete double-stranded RNA (dsRNA) segments enclosed by single, double, or triple capsid layers. The outer capsid proteins of reoviruses exhibit the highest diversity in both sequence and structural organization. By contrast, the conserved RNA-dependent RNA polymerase (RdRp) structure in the conserved innermost shell in all reoviruses suggests that they share common transcriptional regulatory mechanisms. After reoviruses are delivered into the cytoplasm of a host cell, their inner capsid particles (ICPs) remain intact and serve as a stable nanoscale machine for RNA transcription and capping performed using enzymes in ICPs. Advances in cryo-electron microscopy have enabled the reconstruction at near-atomic resolution of not only the icosahedral capsid, including capping enzymes, but also the nonicosahedrally distributed complexes of RdRps within the capsid at different transcriptional stages. These near-atomic resolution structures allow us to visualize highly coordinated structural changes in the related enzymes, genomic RNA, and capsid protein during reovirus transcription. In addition, reoviruses encode their own enzymes for nascent RNA capping before RNA releasing from their ICPs.
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Affiliation(s)
- Hongrong Liu
- Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha, China.
| | - Lingpeng Cheng
- Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha, China.
- School of Life Sciences, Tsinghua University, Beijing, China.
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3
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Pan M, Alvarez-Cabrera AL, Kang JS, Wang L, Fan C, Zhou ZH. Asymmetric reconstruction of mammalian reovirus reveals interactions among RNA, transcriptional factor µ2 and capsid proteins. Nat Commun 2021; 12:4176. [PMID: 34234134 PMCID: PMC8263624 DOI: 10.1038/s41467-021-24455-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/17/2021] [Indexed: 12/02/2022] Open
Abstract
Mammalian reovirus (MRV) is the prototypical member of genus Orthoreovirus of family Reoviridae. However, lacking high-resolution structures of its RNA polymerase cofactor μ2 and infectious particle, limits understanding of molecular interactions among proteins and RNA, and their contributions to virion assembly and RNA transcription. Here, we report the 3.3 Å-resolution asymmetric reconstruction of transcribing MRV and in situ atomic models of its capsid proteins, the asymmetrically attached RNA-dependent RNA polymerase (RdRp) λ3, and RdRp-bound nucleoside triphosphatase μ2 with a unique RNA-binding domain. We reveal molecular interactions among virion proteins and genomic and messenger RNA. Polymerase complexes in three Spinoreovirinae subfamily members are organized with different pseudo-D3d symmetries to engage their highly diversified genomes. The above interactions and those between symmetry-mismatched receptor-binding σ1 trimers and RNA-capping λ2 pentamers balance competing needs of capsid assembly, external protein removal, and allosteric triggering of endogenous RNA transcription, before, during and after infection, respectively. Mammalian reovirus (MRV) is a double-stranded RNA (dsRNA) virus that affects the gastrointestinal and respiratory tracts. Here, the authors present the 3.3 Å cryo-EM asymmetric reconstruction of transcribing MRV that reveals the organization of the dsRNA genome, RNA interaction with the polymerase complex, and how the polymerase interacts extensively with its co-factor, µ2, to form a transcription enzyme complex, which engages and regulates RNA transcription.
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Affiliation(s)
- Muchen Pan
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.,California NanoSystems Institute, UCLA, Los Angeles, CA, USA.,University of Chinese Academy of Sciences, Beijing, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ana L Alvarez-Cabrera
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.,California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - Joon S Kang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.,California NanoSystems Institute, UCLA, Los Angeles, CA, USA.,Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Lihua Wang
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.,The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA. .,California NanoSystems Institute, UCLA, Los Angeles, CA, USA. .,Molecular Biology Institute, UCLA, Los Angeles, CA, USA.
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4
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Kniert J, Lin QF, Shmulevitz M. Captivating Perplexities of Spinareovirinae 5' RNA Caps. Viruses 2021; 13:v13020294. [PMID: 33668598 PMCID: PMC7918360 DOI: 10.3390/v13020294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 11/16/2022] Open
Abstract
RNAs with methylated cap structures are present throughout multiple domains of life. Given that cap structures play a myriad of important roles beyond translation, such as stability and immune recognition, it is not surprising that viruses have adopted RNA capping processes for their own benefit throughout co-evolution with their hosts. In fact, that RNAs are capped was first discovered in a member of the Spinareovirinae family, Cypovirus, before these findings were translated to other domains of life. This review revisits long-past knowledge and recent studies on RNA capping among members of Spinareovirinae to help elucidate the perplex processes of RNA capping and functions of RNA cap structures during Spinareovirinae infection. The review brings to light the many uncertainties that remain about the precise capping status, enzymes that facilitate specific steps of capping, and the functions of RNA caps during Spinareovirinae replication.
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Cui Y, Zhang Y, Zhou K, Sun J, Zhou ZH. Conservative transcription in three steps visualized in a double-stranded RNA virus. Nat Struct Mol Biol 2019; 26:1023-1034. [PMID: 31695188 DOI: 10.1038/s41594-019-0320-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/19/2019] [Indexed: 01/28/2023]
Abstract
Endogenous RNA transcription characterizes double-stranded RNA (dsRNA) viruses in the Reoviridae, a family that is exemplified by its simple, single-shelled member cytoplasmic polyhedrosis virus (CPV). Because of the lack of in situ structures of the intermediate stages of RNA-dependent RNA polymerase (RdRp) during transcription, it is poorly understood how RdRp detects environmental cues and internal transcriptional states to initiate and coordinate repeated cycles of transcript production inside the capsid. Here, we captured five high-resolution (2.8-3.5 Å) RdRp-RNA in situ structures-representing quiescent, initiation, early elongation, elongation and abortive states-under seven experimental conditions of CPV. We observed the 'Y'-form initial RNA fork in the initiation state and the complete transcription bubble in the elongation state. These structures reveal that de novo RNA transcription involves three major conformational changes during state transitions. Our results support an ouroboros model for endogenous conservative transcription in dsRNA viruses.
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Affiliation(s)
- Yanxiang Cui
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yinong Zhang
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.,Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Kang Zhou
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jingchen Sun
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA. .,Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.
| | - Z Hong Zhou
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA. .,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
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In situ structures of RNA-dependent RNA polymerase inside bluetongue virus before and after uncoating. Proc Natl Acad Sci U S A 2019; 116:16535-16540. [PMID: 31350350 DOI: 10.1073/pnas.1905849116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bluetongue virus (BTV), a major threat to livestock, is a multilayered, nonturreted member of the Reoviridae, a family of segmented dsRNA viruses characterized by endogenous RNA transcription through an RNA-dependent RNA polymerase (RdRp). To date, the structure of BTV RdRp has been unknown, limiting our mechanistic understanding of BTV transcription and hindering rational drug design effort targeting this essential enzyme. Here, we report the in situ structures of BTV RdRp VP1 in both the triple-layered virion and double-layered core, as determined by cryo-electron microscopy (cryoEM) and subparticle reconstruction. BTV RdRp has 2 unique motifs not found in other viral RdRps: a fingernail, attached to the conserved fingers subdomain, and a bundle of 3 helices: 1 from the palm subdomain and 2 from the N-terminal domain. BTV RdRp VP1 is anchored to the inner surface of the capsid shell via 5 asymmetrically arranged N termini of the inner capsid shell protein VP3A around the 5-fold axis. The structural changes of RdRp VP1 and associated capsid shell proteins between BTV virions and cores suggest that the detachment of the outer capsid proteins VP2 and VP5 during viral entry induces both global movements of the inner capsid shell and local conformational changes of the N-terminal latch helix (residues 34 to 51) of 1 inner capsid shell protein VP3A, priming RdRp VP1 within the capsid for transcription. Understanding this mechanism in BTV also provides general insights into RdRp activation and regulation during viral entry of other multilayered, nonturreted dsRNA viruses.
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7
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Li Y, Wu K, Quan W, Yu L, Chen S, Cheng C, Wu Q, Zhao S, Zhang Y, Zhou L. The dynamics of FTO binding and demethylation from the m 6A motifs. RNA Biol 2019; 16:1179-1189. [PMID: 31149892 DOI: 10.1080/15476286.2019.1621120] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
N6-methyladenosine (m6A) is considered as a reversible RNA modification occurring more frequently on the GAC than AAC context in vivo, which regulates post-transcriptional gene expression in mammalian cells. m6A 'writers' METTL3 and METTL14 demonstrate a strong preference for binding AC-containing motifs in living cells. However, this evidence is currently lacking for m6A erasers, leaving the dynamics of the internal m6A modification under debate recently. We analysed three recently published FTO CLIP-seq data sets and two generated in this study, one of the two known m6A 'erasers'. FTO binding peaks from all cell lines contain RRACH motifs. Only those from K562, 3T3-L1and HeLa cells were enriched in AC-containing motifs, while those from HEK293 were not. The exogenously overexpressed FTO effectively binds to m6A motif-containing RNA sites. FTO overexpression specifically removed m6A modification from GGACU and RRACU motifs in a concentration-dependent manner. These findings underline the dynamics of FTO in target selection, which is predicted to contribute to both the m6A dynamics and the FTO plasticity in biological functions and diseases.
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Affiliation(s)
- Yixing Li
- a State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University , Nanning , P.R. China
| | - Kejing Wu
- b Center for Genome Analysis, ABLife Inc ., Wuhan , Hubei , China
| | - Weili Quan
- b Center for Genome Analysis, ABLife Inc ., Wuhan , Hubei , China.,c Laboratory for Genome Regulation and Human Health, ABLife Inc ., Wuhan , Hubei , China
| | - Lin Yu
- a State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University , Nanning , P.R. China
| | - Shuang Chen
- c Laboratory for Genome Regulation and Human Health, ABLife Inc ., Wuhan , Hubei , China
| | - Chao Cheng
- b Center for Genome Analysis, ABLife Inc ., Wuhan , Hubei , China
| | - Qijia Wu
- c Laboratory for Genome Regulation and Human Health, ABLife Inc ., Wuhan , Hubei , China
| | - Shuhong Zhao
- d Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University , Wuhan , P. R. China
| | - Yi Zhang
- b Center for Genome Analysis, ABLife Inc ., Wuhan , Hubei , China.,c Laboratory for Genome Regulation and Human Health, ABLife Inc ., Wuhan , Hubei , China
| | - Lei Zhou
- a State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University , Nanning , P.R. China
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8
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Fry M. Dissolution of hypotheses in biochemistry: three case studies. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2016; 38:17. [PMID: 27813029 DOI: 10.1007/s40656-016-0118-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 10/26/2016] [Indexed: 06/06/2023]
Abstract
The history of biochemistry and molecular biology is replete with examples of erroneous theories that persisted for considerable lengths of time before they were rejected. This paper examines patterns of dissolution of three such erroneous hypotheses: The idea that nucleic acids are tetrads of the four nucleobases ('the tetranucleotide hypothesis'); the notion that proteins are collinear with their encoding genes in all branches of life; and the hypothesis that proteins are synthesized by reverse action of proteolytic enzymes. Analysis of these cases indicates that amassed contradictory empirical findings did not prompt critical experimental testing of the prevailing theories nor did they elicit alternative hypotheses. Rather, the incorrect models collapsed when experiments that were not purposely designed to test their validity exposed new facts.
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Affiliation(s)
- Michael Fry
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, POB 9649, 31096, Haifa, Israel.
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9
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Zhang X, Ding K, Yu X, Chang W, Sun J, Zhou ZH. In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus. Nature 2015; 527:531-534. [PMID: 26503045 PMCID: PMC5086257 DOI: 10.1038/nature15767] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/07/2015] [Indexed: 01/15/2023]
Abstract
Viruses in the Reoviridae, like the triple-shelled human rotavirus and the single-shelled insect cytoplasmic polyhedrosis virus (CPV), all package a genome of segmented double-stranded RNAs (dsRNAs) inside the viral capsid and carry out endogenous messenger RNA synthesis through a transcriptional enzyme complex (TEC). By direct electron-counting cryoelectron microscopy and asymmetric reconstruction, we have determined the organization of the dsRNA genome inside quiescent CPV (q-CPV) and the in situ atomic structures of TEC within CPV in both quiescent and transcribing (t-CPV) states. We show that the ten segmented dsRNAs in CPV are organized with ten TECs in a specific, non-symmetric manner, with each dsRNA segment attached directly to a TEC. The TEC consists of two extensively interacting subunits: an RNA-dependent RNA polymerase (RdRP) and an NTPase VP4. We find that the bracelet domain of RdRP undergoes marked conformational change when q-CPV is converted to t-CPV, leading to formation of the RNA template entry channel and access to the polymerase active site. An amino-terminal helix from each of two subunits of the capsid shell protein (CSP) interacts with VP4 and RdRP. These findings establish the link between sensing of environmental cues by the external proteins and activation of endogenous RNA transcription by the TEC inside the virus.
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MESH Headings
- Capsid Proteins/chemistry
- Capsid Proteins/metabolism
- Capsid Proteins/ultrastructure
- Catalytic Domain
- Cryoelectron Microscopy
- Genome, Viral/genetics
- Models, Molecular
- Multienzyme Complexes/chemistry
- Multienzyme Complexes/metabolism
- Multienzyme Complexes/ultrastructure
- Nucleoside-Triphosphatase/metabolism
- Nucleoside-Triphosphatase/ultrastructure
- Protein Subunits/chemistry
- Protein Subunits/metabolism
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/ultrastructure
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Messenger/ultrastructure
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- RNA, Viral/ultrastructure
- RNA-Dependent RNA Polymerase/chemistry
- RNA-Dependent RNA Polymerase/metabolism
- RNA-Dependent RNA Polymerase/ultrastructure
- Reoviridae/enzymology
- Reoviridae/genetics
- Reoviridae/ultrastructure
- Templates, Genetic
- Transcription, Genetic
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Affiliation(s)
- Xing Zhang
- California Nanosystems Institute, Los Angeles, CA 90095, USA
| | - Ke Ding
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Xuekui Yu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Winston Chang
- California Nanosystems Institute, Los Angeles, CA 90095, USA
| | - Jingchen Sun
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Z. Hong Zhou
- California Nanosystems Institute, Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- Bioengineering, University of California, Los Angeles, CA 90095, USA
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Yu X, Jiang J, Sun J, Zhou ZH. A putative ATPase mediates RNA transcription and capping in a dsRNA virus. eLife 2015; 4:e07901. [PMID: 26240998 PMCID: PMC4522710 DOI: 10.7554/elife.07901] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 06/19/2015] [Indexed: 11/13/2022] Open
Abstract
mRNA transcription in dsRNA viruses is a highly regulated process but the mechanism of this regulation is not known. Here, by nucleoside triphosphatase (NTPase) assay and comparisons of six high-resolution (2.9-3.1 Å) cryo-electron microscopy structures of cytoplasmic polyhedrosis virus with bound ligands, we show that the large sub-domain of the guanylyltransferase (GTase) domain of the turret protein (TP) also has an ATP-binding site and is likely an ATPase. S-adenosyl-L-methionine (SAM) acts as a signal and binds the methylase-2 domain of TP to induce conformational change of the viral capsid, which in turn activates the putative ATPase. ATP binding/hydrolysis leads to an enlarged capsid for efficient mRNA synthesis, an open GTase domain for His217-mediated guanylyl transfer, and an open methylase-1 domain for SAM binding and methyl transfer. Taken together, our data support a role of the putative ATPase in mediating the activation of mRNA transcription and capping within the confines of the virus.
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Affiliation(s)
- Xuekui Yu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Jiansen Jiang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Jingchen Sun
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
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FURUICHI Y. Discovery of m(7)G-cap in eukaryotic mRNAs. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2015; 91:394-409. [PMID: 26460318 PMCID: PMC4729855 DOI: 10.2183/pjab.91.394] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Terminal structure analysis of an insect cytoplasmic polyhedrosis virus (CPV) genome RNA in the early 1970s at the National Institute of Genetics in Japan yielded a 2'-O-methylated nucleotide in the 5' end of double-stranded RNA genome. This finding prompted me to add S-adenosyl-L-methionine, a natural methylation donor, to the in vitro transcription reaction of viruses that contain RNA polymerase. This effort resulted in unprecedented mRNA synthesis that generates a unique blocked and methylated 5' terminal structure (referred later to as "cap" or "m(7)G-cap") in the transcription of silkworm CPV and human reovirus and vaccinia viruses that contain RNA polymerase in virus particles. Initial studies with viruses paved the way to discover the 5'-cap m(7)GpppNm structure present generally in cellular mRNAs of eukaryotes. I participated in those studies and was able to explain the pathway of cap synthesis and the significance of the 5' cap (and capping) in gene expression processes, including transcription and protein synthesis. In this review article I concentrate on the description of these initial studies that eventually led us to a new paradigm of mRNA capping.
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Affiliation(s)
- Yasuhiro FURUICHI
- GeneCare Research Institute Co., Ltd., Kanagawa, Japan
- Correspondence should be addressed: Y. Furuichi, GeneCare Research Institute Co., Ltd., 19-2 Kajiwara, Kamakura, Kanagawa 247-0063, Japan (e-mail: )
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12
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Kuchino Y, Nishimura S, Smith RE, Furuichi Y. Homologous Terminal Sequences in the Double-Stranded RNA Genome Segments of Cytoplasmic Polyhedrosis Virus of the Silkworm Bombyx mori. J Virol 2010; 44:538-43. [PMID: 16789232 PMCID: PMC256297 DOI: 10.1128/jvi.44.2.538-543.1982] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 3'-terminal regions (20 to 32 residues) of the genome double-stranded RNA (dsRNA) segments of cytoplasmic polyhedrosis virus were sequenced. The dsRNAs, which were labeled at their 3' termini by incubation with [5'-(32)P]pCp and T4 RNA ligase, were denatured and resolved into the plus and minus strands by agarose-urea gel electrophoresis. Ten single-stranded RNAs thus obtained from the five dsRNA segments IV, V, VIII, IX, and X were sequenced by postlabeling methods. Common 3'-terminal sequences, -GUUAGCC and -UUACU, were found in the plus and minus strands, respectively, of all five dsRNA segments. However, adjacent sequences diverged and were considerably variable. The homologous sequences found in the 3' end may be important recognition signals for viral RNA polymerases and for assembly of the genome segments.
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Affiliation(s)
- Y Kuchino
- National Cancer Center Research Institute, Tsukiji 5-1-1, Chuo-ku, Tokyo, Japan
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13
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Structural evolution of reoviridae revealed by oryzavirus in acquiring the second capsid shell. J Virol 2008; 82:11344-53. [PMID: 18787002 DOI: 10.1128/jvi.02375-07] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The conservation of the core structure and diversification of the external features among the turreted reoviruses appear to be relevant to structural evolution in facilitating the infection of diverse host species. The structure of Rice ragged stunt virus (RRSV), in the genus Oryzavirus of the family Reoviridae, is determined to show a core composed of capsid shell, clamps, and long turrets. The RRSV core structure is equivalent to the core structure of Orthoreovirus and the virion structure of Cytoplasmic polyhedrosis virus (CPV). In RRSV, five peripheral trimers surround each long turret and sit at the Q trimer position in the T=13l icosahedral symmetry, a structural feature unique to turreted reoviruses. That is, the core of RRSV is partially covered by 60 copies of the peripheral trimer. In contrast, the core of Orthoreovirus is covered by 200 copies of the trimer that sit at the Q, R, S, and T trimer positions. Our results suggest that among the three viruses, RRSV has a structure intermediate between that of Orthoreovirus and the CPV virion. This conclusion coincides with the results of the phylogenetic analysis of amino acid sequences of RNA-dependent RNA polymerases.
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Smith RE, Furuichi Y. Gene mapping of cytoplasmic polyhedrosis virus of silkworm by the full-length mRNA prepared under optimized conditions of transcription in vitro. Virology 2008; 103:279-90. [PMID: 18631652 DOI: 10.1016/0042-6822(80)90187-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/1980] [Indexed: 11/29/2022]
Abstract
Viral mRNA synthesis by the RNA polymerase associated with purified cytoplasmic polyhedrosis virus (CPV) was studied. The formation of full-length mRNA products was facilitated by including in the reaction mixture 100 mM sodium acetate, high concentrations of ribonucleoside triphosphates, and proteinase K. The 10 different species of CPV mRNAS were resolved into 9 discrete RNA bands by agarose gel electrophoresis at pH 3.5 in buffer containing 7 M urea. Each purified viral mRNA hybridized specifically to one of the viral genome segments which were separated by polyacrylamide gel electrophoresis into the 10 species of dsRNA. The relationship between the genome segments and their cognate mRNAs synthesized in vitro is thus established. Under optimal conditions of mRNA synthesis each of the genome segments was transcribed at a similar rate as determined from the yield of individual separated mRNA species. A recycling model of genome-associated RNA polymerase for viral transcription is discussed.
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Affiliation(s)
- R E Smith
- Roche Institute of Molecular Biology, Nutley, New Jersey 07110, USA
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15
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Yazaki K, Miura K. Relation of the structure of cytoplasmic polyhedrosis virus and the synthesis of its messenger RNA. Virology 2008; 105:467-79. [PMID: 18631679 DOI: 10.1016/0042-6822(80)90047-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/1980] [Indexed: 11/29/2022]
Abstract
Cytoplasmic polyhedrosis virus (CPV) was observed under an electron microscope using a combination of staining and shadowing methods. Projections, not only in positions horizontal to the grid but also vertical, were clearly visualized. When the particle was mildly disrupted with EDTA, genome dsRNA was released from a projection. If the particle was previously fixed with glutaraldehyde and then disrupted, dsRNA was released with a protein particle, which seemed to correspond to the base part of the projection. The protein particle was in most cases at the end of the strand, which sometimes takes a supercoiled structure. When CPV was incubated during mRNA synthesis, the protein particles appeared in various positions along the strands, and loop formations of dsRNA appeared. From these observations, we suggest that transcription in this virus particle proceeds as follows: genome dsRNA is transcribed by passing through the base part of the projection, where the enzymes for mRNA synthesis are located. A completed mRNA is released from the virion at the projection.
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Affiliation(s)
- K Yazaki
- Hepatitis Division, Tokyo Metropolitan Institute of Medical Science, Honkomagome, Bunkyo-ku, Tokyo, 113, Japan
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16
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Zhou ZH, Zhang H, Jakana J, Lu XY, Zhang JQ. Cytoplasmic polyhedrosis virus structure at 8 A by electron cryomicroscopy: structural basis of capsid stability and mRNA processing regulation. Structure 2003; 11:651-63. [PMID: 12791254 DOI: 10.1016/s0969-2126(03)00091-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The single-shelled cytoplasmic polyhedrosis virus (CPV) is a unique member of the Reoviridae. Despite lacking protective outer shells, it exhibits striking capsid stability and is capable of endogenous RNA transcription and processing. The 8 A three-dimensional structure of CPV by electron cryomicroscopy reveals secondary structure elements present in the capsid proteins CSP, LPP, and TP, which have alpha+beta folds. The extensive nonequivalent interactions between CSP and LPP, the unique CSP protrusion domain, and the perfect inter-CSP surface complementarities may account for the enhanced capsid stability. The slanted disposition of TP functional domains and the stacking of channel constrictions suggest an iris diaphragm-like mechanism for opening/closing capsid pores and turret channels in regulating the highly coordinated steps of mRNA transcription, processing, and release.
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Affiliation(s)
- Z Hong Zhou
- Department of Pathology and Laboratory Medicine, University of Texas Medical School, Houston, TX 77030, USA.
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17
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Xia Q, Jakana J, Zhang JQ, Zhou ZH. Structural comparisons of empty and full cytoplasmic polyhedrosis virus. Protein-RNA interactions and implications for endogenous RNA transcription mechanism. J Biol Chem 2003; 278:1094-100. [PMID: 12401805 DOI: 10.1074/jbc.m205964200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Viruses in the family Reoviridae are capable of transcription within the intact capsids. As the only single-shelled and thus the simplest member of the Reoviridae, cytoplasmic polyhedrosis virus (CPV) provides an attractive system for studying endogenous transcription. We report the structures of the full and empty CPV determined at 13-A resolution by electron cryomicroscopy. The structure of the empty CPV reveals a density attributed to the transcription enzyme complex, which is attached to the internal surface of the capsid shell below each of the 12 turrets. The full capsid has an identical capsid shell but contains additional internal densities contributed by the genomic double-stranded (ds) RNA. The RNA densities proximal to the capsid shell are organized into layers with a dodecahedral appearance, suggesting a genome organization of dsRNA segments each having a cone shape spooling around a transcription enzyme complex. Our structures also suggest that the capsid shell serves as a scaffold for appropriate positioning of the RNA genome, whereas nascent mRNA release takes place through the constricted central channel of the turret. Based on these observations, a detailed moving template transcription mechanism is proposed that may provide insight into the well coordinated and highly efficient endogenous RNA transcription of dsRNA viruses.
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Affiliation(s)
- Qing Xia
- Department of Pathology and Laboratory Medicine, University of Texas, Houston Medical School, 77030, USA
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18
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Abstract
This chapter focuses on the history of the discovery of cap and an update of research on viral and cellular-messenger RNA (mRNA) capping. Cap structures of the type m7 GpppN(m)pN(m)p are present at the 5′ ends of nearly all eukaryotic cellular and viral mRNAs. A cap is added to cellular mRNA precursors and to the transcripts of viruses that replicate in the nucleus during the initial phases of transcription and before other processing events, including internal N6A methylation, 3′-poly (A) addition, and exon splicing. Despite the variations on the methylation theme, the important biological consequences of a cap structure appear to correlate with the N7-methyl on the 5′-terminal G and the two pyrophosphoryl bonds that connect m7G in a 5′–5′ configuration to the first nucleotide of mRNA. In addition to elucidating the biochemical mechanisms of capping and the downstream effects of this 5′- modification on gene expression, the advent of gene cloning has made available an ever-increasing amount of information on the proteins responsible for producing caps and the functional effects of other cap-related interactions. Genetic approaches have demonstrated the lethal consequences of cap failure in yeasts, and complementation studies have shown the evolutionary functional conservation of capping from unicellular to metazoan organisms.
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Affiliation(s)
- Y Furuichi
- AGENE Research Institute, Kamakura, Japan
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19
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Yuan CS, Liu S, Wnuk SF, Robins MJ, Borchardt RT. Design and synthesis of S-adenosylhomocysteine hydrolase inhibitors as broad-spectrum antiviral agents. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s1075-8593(96)80103-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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20
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Kuribayashi-Ohta K, Tamatsukuri S, Hikata M, Miyamoto C, Furuichi Y. Application of oligo(dT)30-latex for rapid purification of poly(A)+ mRNA and for hybrid subtraction with the in situ reverse transcribed cDNA. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1156:204-12. [PMID: 7678989 DOI: 10.1016/0304-4165(93)90137-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The carboxyl groups on the surface of latex beads were linked to amino moiety of cytidine residue of oligo(dC)10(dT)30. The resultant latex beads-(dC)10(dT)30 showed a very stable suspension and yet is precipitable to a small pellet by centrifugation. These properties merits the oligomer-linked beads to be applied for experiments in which poly(A)+ mRNAs are involved. An efficient (> 95%) hybridization to poly(A)+ mRNA occurred in a short reaction period (10 min), and more than 95% of bound mRNAs were recovered from the beads by heating (65 degrees C, 5 min) followed by centrifugation. Interestingly, the poly(A)+ mRNAs could be transcribed to cDNAs in situ by reverse transcriptase, with the covalently linked oligo(dT)30 as primers. These properties allowed the oligo(dT)30-latex to prepare the cDNA covalently bound to latex which was used for mRNA hybrid subtraction. In a model experiment with the mixture of vaccinia virus and HeLa mRNAs, about 200-fold enrichment of vaccinia mRNA species was obtained after four cycles of hybrid subtraction with HeLa cDNA-latex.
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Affiliation(s)
- K Kuribayashi-Ohta
- Tsukuba Research Laboratory, Japan Synthetic Rubber Co., Ltd., Ibaragi, Japan
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21
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Reddy R, Singh R, Shimba S. Methylated cap structures in eukaryotic RNAs: structure, synthesis and functions. Pharmacol Ther 1992; 54:249-67. [PMID: 1465477 DOI: 10.1016/0163-7258(92)90002-h] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
There are more than twenty capped small nuclear RNAs characterized in eukaryotic cells. All the capped RNAs appear to be involved in the processing of other nuclear premessenger or preribosomal RNAs. These RNAs contain either trimethylguanosine (TMG) cap structure or methylated gamma phosphate (Mppp) cap structure. The TMG capped RNAs are capped with M7G during transcription by RNA polymerase II and trimethylated further post-transcriptionally. The Mppp-capped RNAs are transcribed by RNA polymerase III and also capped post-transcriptionally. The cap structures improve the stability of the RNAs and in some cases TMG cap is required for transport of the ribonucleoproteins from cytoplasm to the nucleus. Where tested, the cap structures were not essential for their function in processing other RNAs.
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Affiliation(s)
- R Reddy
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030
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22
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23
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Boccardo G, Accotto GP. RNA-dependent RNA polymerase activity in two morphologically different white clover cryptic viruses. Virology 1988; 163:413-9. [PMID: 3354201 DOI: 10.1016/0042-6822(88)90282-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
RNA-dependent RNA polymerase activities were detected in purified particles of white clover cryptic viruses 1 and 2. The polymerases of the two viruses had different requirements for optimum activity. Enzyme activity was dependent upon the presence of virus particles, Mg2+, and the four ribonucleoside triphosphates, and was insensitive to actinomycin D, alpha-amanitin, and rifampicin. The labeled reaction products were dsRNAs as indicated by CF 11 column chromatography and by their ionic-strength-dependent sensitivity to hydrolysis by RNase A and resistance to S1 nuclease. The dsRNAs synthesized in vitro had the same electrophoretic mobilities as the corresponding viral templates.
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Affiliation(s)
- G Boccardo
- Istituto di Fitovirologia Applicata del CNR, Torino, Italy
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24
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Abstract
Recent progress in molecular biological techniques revealed that genomes of animal viruses are complex in structure, for example, with respect to the chemical nature (DNA or RNA), strandedness (double or single), genetic sense (positive or negative), circularity (circle or linear), and so on. In agreement with this complexity in the genome structure, the modes of transcription and replication are various among virus families. The purpose of this article is to review and bring up to date the literature on viral RNA polymerases involved in transcription of animal DNA viruses and in both transcription and replication of RNA viruses. This review shows that the viral RNA polymerases are complex in both structure and function, being composed of multiple subunits and carrying multiple functions. The functions exposed seem to be controlled through structural interconversion.
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Affiliation(s)
- A Ishihama
- Department of Molecular Genetics, National Institute of Genetics, Shizuoka, Japan
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25
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26
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Benghiat E, Crooks PA, Goodwin R, Rottman F. Inhibition of vaccinia RNA guanine 7-methyltransferase by compounds designed as multisubstrate adducts. J Pharm Sci 1986; 75:142-5. [PMID: 3958922 DOI: 10.1002/jps.2600750207] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Several potential inhibitors of mRNA guanine 7-methyltransferase, which were designed from mechanism-based considerations, were evaluated against the vaccinia virus capping enzyme complex. Of the compounds tested, 5'-deoxy-5'[6-(2-aminopyrrolo[2,3-d]-pyrimidine-4-one) methylthio]adenosine (9) had good selective inhibitory activity against vaccinia mRNA guanine 7-methyltransferase, exhibiting an IC50 of 9.2 X 10(-5) M. Structure-activity considerations suggest that specific inhibition of RNA methyltransferases by low molecular weight multisubstrate adduct inhibitors may be achievable.
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27
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28
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Mertens PP, Payne CC. The effects of S-adenosyl methionine (AdoMet) and its analogues on the control of transcription and translation in vitro of the mRNA products of two cytoplasmic polyhedrosis viruses. Virology 1983; 131:18-29. [PMID: 6359667 DOI: 10.1016/0042-6822(83)90529-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
S-Adenosyl methionine (AdoMet) and several structurally related compounds were added to in vitro systems for the synthesis of single-stranded RNA by cytoplasmic polyhedrosis virus (CPV) types 1 and 2. The effects of these compounds were examined on the level of transcription and methylation of the RNA products. Of the compounds tested, five increased the polymerase activity in both viruses, the most effective being the D- and L-stereoisomers of S-adenosyl homocysteine (AdoHcy), and the least effective, adenosine. L-AdoHcy, unlike D-AdoHcy, was also a competitive inhibitor of RNA methylation in the presence of [3H]AdoMet. The different response of both viruses to D- and L-AdoHcy suggests that CPV virions contain at least two functionally distinct sites to which AdoMet, or its analogues, bind. One of these is the transcription control site, while the other is the active site(s) for RNA methylation. CPV RNA synthesised in the presence of the methyl donor AdoMet was more efficiently translated in vitro in a wheat-germ translation system than RNA synthesised in the presence of methylation inhibitors. Type 2 CPV-RNA transcripts had a greater degree of methylation than type 1 CPV transcripts and were more effective in stimulating protein synthesis in the translation system. It seems likely that the allosteric control of CPV polymerase by AdoMet and its analogues, and the methylation of the transcripts, ensures the effective transcription and translation of the CPV genome and the stability of the viral messenger RNA.
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29
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Smith RE, Furuichi Y. The double-stranded RNA genome segments of cytoplasmic polyhedrosis virus are independently transcribed. J Virol 1982; 41:326-9. [PMID: 7045390 PMCID: PMC256755 DOI: 10.1128/jvi.41.1.326-329.1982] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The in vitro transcription of the genome segments of insect cytoplasmic polyhedrosis virus was examined for a possible mechanism of coordinate control. Initiation of the first transcription cycle, primed by preincubation in the absence of CTP, was synchronous for all 10 viral genome segments. The time required for the completion of each genome transcript was proportional to the chain length, and all 10 mRNA's were synthesized in molar amounts inversely proportional to their molecular weights. The rate of chain elongation for all mRNA's was approximately 6 nucleotides per s. The combined results indicate that each of the viral genome segments is transcribed independently and suggest that RNA chain elongation, not initiation, is rate limiting for cytoplasmic polyhedrosis virus mRNA synthesis in vitro.
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30
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Smith R, Furuichi Y. A unique class of compound, guanosine-nucleoside tetraphosphate G(5‘)pppp(5‘)N, synthesized during the in vitro transcription of cytoplasmic polyhedrosis virus of Bombyx mori. Structural determination and mechanism of formation. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(19)68390-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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31
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Furuichi Y. Allosteric stimulatory effect of S-adenosylmethionine on the RNA polymerase in cytoplasmic polyhedrosis virus. A model for the positive control of eukaryotic transcription. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)70163-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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32
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Yamamoto T, de Crombrugghe B, Pastan I. Identification of a functional promoter in the long terminal repeat of Rous sarcoma virus. Cell 1980; 22:787-97. [PMID: 6257399 DOI: 10.1016/0092-8674(80)90555-3] [Citation(s) in RCA: 137] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Specific initiation of transcription of Rous sarcoma virus by RNA polymerase II was obtained in a cell-free system using cloned RSV DNA as template. The site of initiation is located in the common "C" region of the long terminal repeat (LTR), 23 bp downstream from the promoter-like sequence TATTTAAG. This finding indicates that the basic information necessary for RSV transcription lies within the viral genome.
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33
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Welsh JD, Leibowitz MJ, Wickner RB. Virion DNA-independent RNA polymerase from Saccharomyces cerevisiae. Nucleic Acids Res 1980; 8:2349-63. [PMID: 7003533 PMCID: PMC324086 DOI: 10.1093/nar/8.11.2349] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The "killer" plasmid and a larger double-stranded RNA plasmid of yeast exist in intracellular virion particles. Purification of these particles from a diploid killer strain of yeast (grown into stationary growth on ethanol) resulted in co-purification of a DNA-independent RNA polymerase activity. This activity incorporates and requires all four ribonucleoside triphosphates and will not act on deoxyribonucleoside triphosphates. The reaction requires magnesium, is inhibited by sulfhydryl-oxidizing reagents and high concentrations of monovalent cation, but is insensitive to DNase, alpha-amanitin, and actinomycin D. Pyrophosphate inhibits the reaction as does ethidium bromide. Exogenous nucleic acids have no effect on the reaction. The product is mostly single-stranded RNA, some of which is released from the enzymatically active virions.
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34
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Wertheimer A, Chen S, Borchardt R, Furuichi Y. S-Adenosylmethionine and its analogs. Structural features correlated with synthesis and methylation of mRNAs of cytoplasmic polyhedrosis virus. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)70719-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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35
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36
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Malinoski F, Stollar V. Inhibition of Sindbis virus replication in Aedes albopictus cells by virazole (ribavirin) and its reversal by actinomycin: a correction. Virology 1980; 102:473-6. [PMID: 7368572 DOI: 10.1016/0042-6822(80)90117-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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37
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Munns TW, Liszewski MK. Antibodies specific for modified nucleosides: an immunochemical approach for the isolation and characterization of nucleic acids. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1980; 24:109-65. [PMID: 7005966 DOI: 10.1016/s0079-6603(08)60673-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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38
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Malygin AG, Shemyakin MF. Adenosine, NAD and FAD can initiate template-dependent RNA synthesis catalyzed by Escherichia coli RNA polymerase. FEBS Lett 1979; 102:51-4. [PMID: 222618 DOI: 10.1016/0014-5793(79)80926-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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39
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40
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41
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Payne CC, Mertens PP, Katagiri K. A comparative study of three closely related cytoplasmic polyhedrosis viruses. J Invertebr Pathol 1978. [DOI: 10.1016/0022-2011(78)90194-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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42
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Terrioux C, Crépin M, Gros F, Robert-Géro M, Lederer E. Effect of 5'-deoxy-5'-S-isobutyl-adenosine (SIBA) on mouse mammary tumour cells and on the expression of mouse mammary tumour virus. Biochem Biophys Res Commun 1978; 83:673-8. [PMID: 81053 DOI: 10.1016/0006-291x(78)91042-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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43
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Germershausen J, Goodman D, Somberg EW. 5' Cap methylation of homologous poly A(+) RNA by a RNA (guanine-7) methyltransferase from Neurospora crassa. Biochem Biophys Res Commun 1978; 82:871-8. [PMID: 151539 DOI: 10.1016/0006-291x(78)90864-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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44
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Furuichi Y. "Pretranscriptional capping" in the biosynthesis of cytoplasmic polyhedrosis virus mRNA. Proc Natl Acad Sci U S A 1978; 75:1086-90. [PMID: 349555 PMCID: PMC411413 DOI: 10.1073/pnas.75.3.1086] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The in vitro synthesis of cytoplasmic polyhedrosis virus (CPV) mRNA was previously shown to be dependent upon the presence of the methyl donor S-adenosylmethionine (AdoMet). We now find that the competitive inhibitor of methylation, S-adenosylhomocysteine (AdoHcy), also stimulates CPV mRNA synthesis efficiently, resulting in the synthesis of viral mRNAs containing 5'-terminal GpppA and ppA, rather than m(7)GpppAm as observed with Adomet. In addition to AdoHcy, other AdoMet analogues, including S-adenosylethionine and adenosine, also stimulate CPV mRNA synthesis but to a smaller extent than does AdoHcy or AdoMet. In order to study the relationship between cap formation and mRNA synthesis, nucleoside triphosphates were replaced in the RNA-synthesizing reaction mixture (containing AdoMet) by the corresponding beta,gamma-imido analogues, which are resistant to nucleotide phosphohydrolase, an enzyme involved in cap formation. Although mRNA synthesis occurred in the presence of UMP-pNHp or GMP-pNHp, none was observed when AMP-pNHp was substituted for ATP. Because the ATP molecule that becomes the 5'-terminal nucleotide of CPV mRNA must be cleaved at the beta-gamma position during cap formation, the results suggest that, in this viral transcription system, cap formation is prerequisite to mRNA synthesis-i.e., a "pretranscriptional" event.
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45
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Abstract
An RNA-dependent RNA polymerase activity has been demonstrated for spring viremia of carp virus (SVCV). The optimal temperature for in vitro synthesis of RNA was 20 to 25 degrees C. The SVCV enzyme activity was stimulated when the methyl donor S-adenosyl-L-methionine was included in the reaction mixture. S-adenosyl-L-methionine was not particularly effective in stimulating the virion RNA polymerase activity of vesicular stomatitis virus or pike fry rhabdovirus. The 5' nucleotide of the SVCV viral RNA is pppAp.
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46
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Molloy G, Puckett L. The metabolism of heterogeneous nuclear RNA and the formation of cytoplasmic messenger RNA in animal cells. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1978; 31:1-38. [PMID: 785543 DOI: 10.1016/0079-6107(78)90003-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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47
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Rao MS, Hirsch F, Wu BC, Spohn WH, Busch H. Comparative studies on the '5'-cap' and in vitro translational activity of cytoplasmic and nuclear poly A(+) RNA1. Mol Cell Biochem 1977; 15:3-13. [PMID: 194141 DOI: 10.1007/bf01731284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The translational activities of cytoplasmic poly A(+)RNA of normal rat liver and Novikoff hepatoma cells in the wheat germ cell free system were found to be approximately 15-20 times greater than tose of the corresponding nuclear poly A(+) RNA. The translationsl activities were 85 and 62 pmoles 3H-leucine incorporated/micron g cytoglasmic poly A(+) RNA for the liver and tumor respectively and 3-4 pmoles 3H-leucine incoporated/micron g nuclear poly A(+)RNA. Inasmuch as intergity of the '5'-cap' of mRNA is essential for its translational activity, quantitative comparisons were made of its content in these RNA fractions. Of the total 32P incorporated into the tumor cytoplasmic poly A(+) RNA, 0.41% was in the '5'-cap'; in nuclear poly A(+) RNA, the '5'-cap' contained 0.11%. After periodate oxidation and labeling with KB3H4, m7 guanosine, the 5'-terminal nucleoside in both liver and Novikoff hepatoma nuclear poly A(+) RNA contained approximately 20% as much isotope as in the cytoplasmic poly A(+) RNA. These results suggest the lower translational activity of nuclear poly A(+) RNA is partly related to its lower content of the '5'-cap'. Molecular selection of poly A(+) RNA for transport out of the nucleus or further cytoplasmic processing may account for the higher percentage of the '5-cap' and the greater translational activity of the cytoplasmic poly A(+) RNA. During these studies, it was also found that the m7 guanosine of the '5'-cap' was not removed during translation of the mRNA in the wheat germ system; this result suggests that the '5'-cap' may associate with allosteric binding sites of initiation factor(s).
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48
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49
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Rhodes DP, Reddy DV, MacLeod R, Black LM, Banerjee AK. In vitro synthesis of RNA containing 5'-terminal structure 7nG(5')ppp(5')Apm... by purified wound tumor virus. Virology 1977; 76:554-9. [PMID: 841848 DOI: 10.1016/0042-6822(77)90237-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Rottman FM, Desrosiers RC, Friderici K. Nucleotide methylation patterns in eukaryotic mRNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1977; 19:21-38. [PMID: 190642 DOI: 10.1016/s0079-6603(08)60906-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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