1
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Zhang TM, Zhu XN, Qin SW, Guo XF, Xing XK, Zhao LF, Tan SK. Potential and application of abortive transcripts as a novel molecular marker of cancers. World J Exp Med 2024; 14:92343. [PMID: 38948416 PMCID: PMC11212745 DOI: 10.5493/wjem.v14.i2.92343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/25/2024] [Accepted: 05/14/2024] [Indexed: 06/19/2024] Open
Abstract
Abortive transcript (AT) is a 2-19 nt long non-coding RNA that is produced in the abortive initiation stage. Abortive initiation was found to be closely related to RNA polymerase through in vitro experiments. Therefore, the distribution of AT length and the scale of abortive initiation are correlated to the promoter, discriminator, and transcription initiation sequence, and can be affected by transcription elongation factors. AT plays an important role in the occurrence and development of various diseases. Here we summarize the discovery of AT, the factors responsible for AT formation, the detection methods and biological functions of AT, to provide new clues for finding potential targets in the early diagnosis and treatment of cancers.
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Affiliation(s)
- Tian-Miao Zhang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin 541199, Guangxi Zhuang Autonomous Region, China
| | - Xiao-Nian Zhu
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin 541199, Guangxi Zhuang Autonomous Region, China
| | - Shao-Wei Qin
- School of Leisure and Health, Guilin Tourism University, Guilin 541006, Guangxi Zhuang Autonomous Region, China
| | - Xue-Feng Guo
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin 541199, Guangxi Zhuang Autonomous Region, China
| | - Xue-Kun Xing
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin 541199, Guangxi Zhuang Autonomous Region, China
| | - Li-Feng Zhao
- School of Leisure and Health, Guilin Tourism University, Guilin 541006, Guangxi Zhuang Autonomous Region, China
| | - Sheng-Kui Tan
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin 541199, Guangxi Zhuang Autonomous Region, China
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2
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Barchet C, Fréchin L, Holvec S, Hazemann I, von Loeffelholz O, Klaholz BP. Focused classifications and refinements in high-resolution single particle cryo-EM analysis. J Struct Biol 2023; 215:108015. [PMID: 37659578 DOI: 10.1016/j.jsb.2023.108015] [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] [Received: 07/22/2022] [Revised: 06/27/2023] [Accepted: 08/17/2023] [Indexed: 09/04/2023]
Abstract
Recent advances in cryo electron microscopy (cryo-EM) and image processing provide new opportunities to analyse drug targets at high resolution. However, structural heterogeneity limits resolution in many practical cases, hence restricting the level at which structural details can be analysed and drug design be performed. As structural disorder is not spread throughout the entire structure of a given macromolecular complex but instead is found in certain regions that move with respect to others and covering molecular scales from domain conformational changes up to the level of side chain conformations in ligand binding pockets, it is possible to focus the attention on those regions and the associated relative movements. Here we show how the usage of focused classifications and refinements provide insights into global conformational arrangements, exemplified on the human ribosome and on the cannabinoid G protein coupled receptor (GPCR), and how they can improve the local map resolution from an essentially disordered region to the 3-4 Å and finally to the 2 Å resolution range. A systematic analysis with variable spherical masks during focused refinement is presented showing that the choice of an optimal mask size helps refining to high resolution. This study covers several practical approaches on 4 examples illustrating how important mask size & shape and including neighbouring structural elements are for a focused analysis of a macromolecular complex. Such methods will be crucial for cryo-EM structure-based drug design of various medical targets and are applicable to single particle cryo-EM and electron tomography data.
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Affiliation(s)
- Charles Barchet
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (Inserm) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Léo Fréchin
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (Inserm) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Samuel Holvec
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (Inserm) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Isabelle Hazemann
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (Inserm) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Ottilie von Loeffelholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (Inserm) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (Inserm) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France.
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3
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Cai L, Liu H, Zhang W, Xiao S, Zeng Q, Dang S. Cryo-EM structure of cyanophage P-SCSP1u offers insights into DNA gating and evolution of T7-like viruses. Nat Commun 2023; 14:6438. [PMID: 37833330 PMCID: PMC10575957 DOI: 10.1038/s41467-023-42258-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Cyanophages, together with their host cyanobacteria, play important roles in marine biogeochemical cycles and control of marine food webs. The recently identified MPP-C (Marine Picocyanobacteria Podovirus clade C) cyanophages, belonging to the T7-like podoviruses, contain the smallest genomes among cyanopodoviruses and exhibit distinct infection kinetics. However, understanding of the MPP-C cyanophage infection process is hindered by the lack of high-resolution structural information. Here, we report the cryo-EM structure of the cyanophage P-SCSP1u, a representative member of the MPP-C phages, in its native form at near-atomic resolution, which reveals the assembly mechanism of the capsid and molecular interaction of the portal-tail complex. Structural comparison of the capsid proteins of P-SCSP1u and other podoviruses with known structures provides insights into the evolution of T7-like viruses. Furthermore, our study provides the near-atomic resolution structure of portal-tail complex for T7-like viruses. On the basis of previously reported structures of phage T7, we identify an additional valve and gate to explain the DNA gating mechanism for the T7-like viruses.
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Affiliation(s)
- Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen, China
| | - Hang Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Wen Zhang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shiwei Xiao
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
- HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen, China.
- Center for Ocean Research in Hong Kong and Macau, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Shangyu Dang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
- HKUST-Shenzhen Research Institute, Nanshan, Shenzhen 518057, China.
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4
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Konevtsova OV, Golushko IY, Podgornik R, Rochal SB. Integration of Cypoviruses into polyhedrin matrix. NANOSCALE ADVANCES 2023; 5:4140-4148. [PMID: 37560430 PMCID: PMC10408579 DOI: 10.1039/d3na00393k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023]
Abstract
Unlike in other viruses, in Cypoviruses the genome is doubly protected since their icosahedral capsids are embedded into a perfect polyhedrin crystal. Current experimental methods cannot resolve the resulting interface structure and we propose a symmetry-based approach to predict it. We reveal a remarkable match between the surfaces of Cypovirus and the outer polyhedrin matrix. The match arises due to the preservation of the common tetragonal symmetry, allowing perfect contacts of polyhedrin trimers with VP1 and VP5 capsid proteins. We highlight a crucial role of the VP5 proteins in embedding the Cypovirus into the polyhedrin matrix and discuss the relationship between the nucleoside triphosphatase activity of the proteins and their role in the superstructure formation. Additionally, we propose an electrostatic mechanism that drives the viral superstructure disassembly occurring in the alkaline environment of the insect intestines. Our study may underpin novel strategies for engineering proteinaceous nanocontainers in diverse biotechnological and chemical applications.
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Affiliation(s)
| | - Ivan Yu Golushko
- Physics Faculty, Southern Federal University Rostov-on-Don Russia
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences Beijing 100049 China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences Beijing 100190 China
- Wenzhou Institute of the University of Chinese Academy of Sciences Wenzhou Zhejiang 325000 China
| | - Sergei B Rochal
- Physics Faculty, Southern Federal University Rostov-on-Don Russia
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5
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Badiee M, Kenet AL, Ganser LR, Paul T, Myong S, Leung AKL. Switch-like compaction of poly(ADP-ribose) upon cation binding. Proc Natl Acad Sci U S A 2023; 120:e2215068120. [PMID: 37126687 PMCID: PMC10175808 DOI: 10.1073/pnas.2215068120] [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: 09/14/2022] [Accepted: 03/23/2023] [Indexed: 05/03/2023] Open
Abstract
Poly(ADP-ribose) (PAR) is a homopolymer of adenosine diphosphate ribose that is added to proteins as a posttranslational modification to regulate numerous cellular processes. PAR also serves as a scaffold for protein binding in macromolecular complexes, including biomolecular condensates. It remains unclear how PAR achieves specific molecular recognition. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) to evaluate PAR flexibility under different cation conditions. We demonstrate that, compared to RNA and DNA, PAR has a longer persistence length and undergoes a sharper transition from extended to compact states in physiologically relevant concentrations of various cations (Na+, Mg2+, Ca2+, and spermine4+). We show that the degree of PAR compaction depends on the concentration and valency of cations. Furthermore, the intrinsically disordered protein FUS also served as a macromolecular cation to compact PAR. Taken together, our study reveals the inherent stiffness of PAR molecules, which undergo switch-like compaction in response to cation binding. This study indicates that a cationic environment may drive recognition specificity of PAR.
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Affiliation(s)
- Mohsen Badiee
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD21205
| | - Adam L. Kenet
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD21205
| | - Laura R. Ganser
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
| | - Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
| | - Anthony K. L. Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD21205
- Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD21205
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD21205
- Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD21205
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6
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Zhang Q, Gao Y, Baker ML, Liu S, Jia X, Xu H, He J, Kaelber JT, Weng S, Jiang W. The structure of a 12-segmented dsRNA reovirus: New insights into capsid stabilization and organization. PLoS Pathog 2023; 19:e1011341. [PMID: 37083840 PMCID: PMC10155992 DOI: 10.1371/journal.ppat.1011341] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/03/2023] [Accepted: 04/02/2023] [Indexed: 04/22/2023] Open
Abstract
Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell and carry out genome replication and transcription inside the virion. Several cryo-electron microscopy (cryo-EM) structures of reoviruses with 9, 10 or 11 segmented dsRNA genomes have revealed insights into genome arrangement and transcription. However, the structure and genome arrangement of 12-segmented Reovirales members remain poorly understood. Using cryo-EM, we determined the structure of mud crab reovirus (MCRV), a 12-segmented dsRNA virus that is a putative member of Reovirales in the non-turreted Sedoreoviridae family, to near-atomic resolutions with icosahedral symmetry (3.1 Å) and without imposing icosahedral symmetry (3.4 Å). These structures revealed the organization of the major capsid proteins in two layers: an outer T = 13 layer consisting of VP12 trimers and unique VP11 clamps, and an inner T = 1 layer consisting of VP3 dimers. Additionally, ten RNA dependent RNA polymerases (RdRp) were well resolved just below the VP3 layer but were offset from the 5-fold axes and arranged with D5 symmetry, which has not previously been seen in other members of Reovirales. The N-termini of VP3 were shown to adopt four unique conformations; two of which anchor the RdRps, while the other two conformations are likely involved in genome organization and capsid stability. Taken together, these structures provide a new level of understanding for capsid stabilization and genome organization of segmented dsRNA viruses.
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Affiliation(s)
- Qinfen Zhang
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanzhu Gao
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at the University of Texas Health Science Center, Houston, Texas, United States of America
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shanshan Liu
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xudong Jia
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Haidong Xu
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianguo He
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jason T Kaelber
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Shaoping Weng
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
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7
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Badiee M, Kenet AL, Ganser LR, Paul T, Myong S, Leung AKL. Switch-like Compaction of Poly(ADP-ribose) Upon Cation Binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.11.531013. [PMID: 36993178 PMCID: PMC10055007 DOI: 10.1101/2023.03.11.531013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Poly(ADP-ribose) (PAR) is a homopolymer of adenosine diphosphate ribose that is added to proteins as a post-translational modification to regulate numerous cellular processes. PAR also serves as a scaffold for protein binding in macromolecular complexes, including biomolecular condensates. It remains unclear how PAR achieves specific molecular recognition. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) to evaluate PAR flexibility under different cation conditions. We demonstrate that, compared to RNA and DNA, PAR has a longer persistence length and undergoes a sharper transition from extended to compact states in physiologically relevant concentrations of various cations (Na + , Mg 2+ , Ca 2+ , and spermine). We show that the degree of PAR compaction depends on the concentration and valency of cations. Furthermore, the intrinsically disordered protein FUS also served as a macromolecular cation to compact PAR. Taken together, our study reveals the inherent stiffness of PAR molecules, which undergo switch-like compaction in response to cation binding. This study indicates that a cationic environment may drive recognition specificity of PAR. Significance Poly(ADP-ribose) (PAR) is an RNA-like homopolymer that regulates DNA repair, RNA metabolism, and biomolecular condensate formation. Dysregulation of PAR results in cancer and neurodegeneration. Although discovered in 1963, fundamental properties of this therapeutically important polymer remain largely unknown. Biophysical and structural analyses of PAR have been exceptionally challenging due to the dynamic and repetitive nature. Here, we present the first single-molecule biophysical characterization of PAR. We show that PAR is stiffer than DNA and RNA per unit length. Unlike DNA and RNA which undergoes gradual compaction, PAR exhibits an abrupt switch-like bending as a function of salt concentration and by protein binding. Our findings points to unique physical properties of PAR that may drive recognition specificity for its function.
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8
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In situ structures of polymerase complex of mammalian reovirus illuminate RdRp activation and transcription regulation. Proc Natl Acad Sci U S A 2022; 119:e2203054119. [PMID: 36469786 PMCID: PMC9897473 DOI: 10.1073/pnas.2203054119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
Mammalian reovirus (reovirus) is a multilayered, turreted member of Reoviridae characterized by transcription of dsRNA genome within the innermost capsid shell. Here, we present high-resolution in situ structures of reovirus transcriptase complex in an intact double-layered virion, and in the uncoated single-layered core particles in the unloaded, reloaded, pre-elongation, and elongation states, respectively, obtained by cryo-electron microscopy and sub-particle reconstructions. At the template entry of RNA-dependent RNA polymerase (RdRp), the RNA-loading region gets flexible after uncoating resulting in the unloading of terminal genomic RNA and inactivity of transcription. However, upon adding transcriptional substrates, the RNA-loading region is recovered leading the RNAs loaded again. The priming loop in RdRp was found to play a critical role in regulating transcription, which hinders the elongation of transcript in virion and triggers the rearrangement of RdRp C-terminal domain (CTD) during elongation, resulting in splitting of template-transcript hybrid and opening of transcript exit. With the integration of these structures, a transcriptional model of reovirus with five states is proposed. Our structures illuminate the RdRp activation and regulation of the multilayered turreted reovirus.
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9
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Procházková M, Füzik T, Grybchuk D, Yurchenko V, Plevka P. Virion structure of Leishmania RNA virus 1. Virology 2022; 577:149-154. [PMID: 36371873 DOI: 10.1016/j.virol.2022.09.014] [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: 06/09/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022]
Abstract
The presence of Leishmania RNA virus 1 (LRV1) enables Leishmania protozoan parasites to cause more severe disease than the virus-free strains. The structure of LRV1 virus-like particles has been determined previously, however, the structure of the LRV1 virion has not been characterized. Here we used cryo-electron microscopy and single-particle reconstruction to determine the structures of the LRV1 virion and empty particle isolated from Leishmania guyanensis to resolutions of 4.0 Å and 3.6 Å, respectively. The capsid of LRV1 is built from sixty dimers of capsid proteins organized with icosahedral symmetry. RNA genomes of totiviruses are replicated inside the virions by RNA polymerases expressed as C-terminal extensions of a sub-population of capsid proteins. Most of the virions probably contain one or two copies of the RNA polymerase, however, the location of the polymerase domains in LRV1 capsid could not be identified, indicating that it varies among particles. Importance. Every year over 200 000 people contract leishmaniasis and more than five hundred people die of the disease. The mucocutaneous form of leishmaniasis produces lesions that can destroy the mucous membranes of the nose, mouth, and throat. Leishmania parasites carrying Leishmania RNA virus 1 (LRV1) are predisposed to cause aggravated symptoms in the mucocutaneous form of leishmaniasis. Here, we present the structure of the LRV1 virion determined using cryo-electron microscopy.
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Affiliation(s)
- Michaela Procházková
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
| | - Tibor Füzik
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
| | - Danyil Grybchuk
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava, 710 00, Czech Republic
| | - Pavel Plevka
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic.
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10
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Zhou K, Si Z, Ge P, Tsao J, Luo M, Zhou ZH. Atomic model of vesicular stomatitis virus and mechanism of assembly. Nat Commun 2022; 13:5980. [PMID: 36216930 PMCID: PMC9549855 DOI: 10.1038/s41467-022-33664-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/27/2022] [Indexed: 11/22/2022] Open
Abstract
Like other negative-strand RNA viruses (NSVs) such as influenza and rabies, vesicular stomatitis virus (VSV) has a three-layered organization: a layer of matrix protein (M) resides between the glycoprotein (G)-studded membrane envelope and the nucleocapsid, which is composed of the nucleocapsid protein (N) and the encapsidated genomic RNA. Lack of in situ atomic structures of these viral components has limited mechanistic understanding of assembling the bullet-shaped virion. Here, by cryoEM and sub-particle reconstruction, we have determined the in situ structures of M and N inside VSV at 3.47 Å resolution. In the virion, N and M sites have a stoichiometry of 1:2. The in situ structures of both N and M differ from their crystal structures in their N-terminal segments and oligomerization loops. N-RNA, N-N, and N-M-M interactions govern the formation of the capsid. A double layer of M contributes to packaging of the helical nucleocapsid: the inner M (IM) joins neighboring turns of the N helix, while the outer M (OM) contacts G and the membrane envelope. The pseudo-crystalline organization of G is further mapped by cryoET. The mechanism of VSV assembly is delineated by the network interactions of these viral components.
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Affiliation(s)
- Kang Zhou
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Zhu Si
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Peng Ge
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA
- Departments of Chemistry and Biochemistry and Biological Chemistry, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Jun Tsao
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Al, 35294, USA
| | - Ming Luo
- The Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA.
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA.
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11
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Ramaswamy K, Rashid M, Ramasamy S, Jayavelu T, Venkataraman S. Revisiting Viral RNA-Dependent RNA Polymerases: Insights from Recent Structural Studies. Viruses 2022; 14:2200. [PMID: 36298755 PMCID: PMC9612308 DOI: 10.3390/v14102200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 11/07/2022] Open
Abstract
RNA-dependent RNA polymerases (RdRPs) represent a distinctive yet versatile class of nucleic acid polymerases encoded by RNA viruses for the replication and transcription of their genome. The structure of the RdRP is comparable to that of a cupped right hand consisting of fingers, palm, and thumb subdomains. Despite the presence of a common structural core, the RdRPs differ significantly in the mechanistic details of RNA binding and polymerization. The present review aims at exploring these incongruities in light of recent structural studies of RdRP complexes with diverse cofactors, RNA moieties, analogs, and inhibitors.
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Affiliation(s)
- Kavitha Ramaswamy
- Department of Biotechnology, Anna University, Sardar Patel Road, Guindy, Chennai 600025, India; (K.R.); (T.J.)
| | - Mariya Rashid
- Taiwan International Graduate Program, Molecular Cell Biology (National Defense Medical Center and Academia Sinica), Taipei 115, Taiwan;
| | - Selvarajan Ramasamy
- National Research Center for Banana, Somarasempettai−Thogaimalai Rd, Podavur, Tamil Nadu 639103, India;
| | - Tamilselvan Jayavelu
- Department of Biotechnology, Anna University, Sardar Patel Road, Guindy, Chennai 600025, India; (K.R.); (T.J.)
| | - Sangita Venkataraman
- Department of Biotechnology, Anna University, Sardar Patel Road, Guindy, Chennai 600025, India; (K.R.); (T.J.)
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12
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Grybchuk D, Procházková M, Füzik T, Konovalovas A, Serva S, Yurchenko V, Plevka P. Structures of L-BC virus and its open particle provide insight into Totivirus capsid assembly. Commun Biol 2022; 5:847. [PMID: 35986212 PMCID: PMC9391438 DOI: 10.1038/s42003-022-03793-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/03/2022] [Indexed: 11/18/2022] Open
Abstract
L-BC virus persists in the budding yeast Saccharomyces cerevisiae, whereas other viruses from the family Totiviridae infect a diverse group of organisms including protists, fungi, arthropods, and vertebrates. The presence of totiviruses alters the fitness of the host organisms, for example, by maintaining the killer system in yeast or increasing the virulence of Leishmania guyanensis. Despite the importance of totiviruses for their host survival, there is limited information about Totivirus structure and assembly. Here we used cryo-electron microscopy to determine the structure of L-BC virus to a resolution of 2.9 Å. The L-BC capsid is organized with icosahedral symmetry, with each asymmetric unit composed of two copies of the capsid protein. Decamers of capsid proteins are stabilized by domain swapping of the C-termini of subunits located around icosahedral fivefold axes. We show that capsids of 9% of particles in a purified L-BC sample were open and lacked one decamer of capsid proteins. The existence of the open particles together with domain swapping within a decamer provides evidence that Totiviridae capsids assemble from the decamers of capsid proteins. Furthermore, the open particles may be assembly intermediates that are prepared for the incorporation of the virus (+) strand RNA. A 2.9 Å resolution structure of the L-BC virus provides insight into the contacts between capsid proteins and the mechanism of capsid assembly.
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13
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Zhang Y, Cui Y, Sun J, Zhou ZH. Multiple conformations of trimeric spikes visualized on a non-enveloped virus. Nat Commun 2022; 13:550. [PMID: 35087065 PMCID: PMC8795420 DOI: 10.1038/s41467-022-28114-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/10/2022] [Indexed: 11/18/2022] Open
Abstract
Many viruses utilize trimeric spikes to gain entry into host cells. However, without in situ structures of these trimeric spikes, a full understanding of this dynamic and essential process of viral infections is not possible. Here we present four in situ and one isolated cryoEM structures of the trimeric spike of the cytoplasmic polyhedrosis virus, a member of the non-enveloped Reoviridae family and a virus historically used as a model in the discoveries of RNA transcription and capping. These structures adopt two drastically different conformations, closed spike and opened spike, which respectively represent the penetration-inactive and penetration-active states. Each spike monomer has four domains: N-terminal, body, claw, and C-terminal. From closed to opened state, the RGD motif-containing C-terminal domain is freed to bind integrins, and the claw domain rotates to expose and project its membrane insertion loops into the cellular membrane. Comparison between turret vertices before and after detachment of the trimeric spike shows that the trimeric spike anchors its N-terminal domain in the iris of the pentameric RNA-capping turret. Sensing of cytosolic S-adenosylmethionine (SAM) and adenosine triphosphate (ATP) by the turret triggers a cascade of events: opening of the iris, detachment of the spike, and initiation of endogenous transcription. Zhang and Cui et al. present in situ cryoEM structures of the trimeric spike of cytoplasmic polyhedrosis virus in both open and close conformations, and demonstrate that spike detachment from the capsid is triggered by the presence of SAM and ATP.
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Affiliation(s)
- Yinong Zhang
- 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.,California Nanosystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA.,Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA
| | - Yanxiang Cui
- California Nanosystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA
| | - Jingchen Sun
- 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. .,Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA.
| | - Z Hong Zhou
- California Nanosystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA. .,Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA.
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14
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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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15
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Analyses of Leishmania-LRV Co-Phylogenetic Patterns and Evolutionary Variability of Viral Proteins. Viruses 2021; 13:v13112305. [PMID: 34835111 PMCID: PMC8624691 DOI: 10.3390/v13112305] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/09/2021] [Indexed: 01/07/2023] Open
Abstract
Leishmania spp. are important pathogens causing a vector-borne disease with a broad range of clinical manifestations from self-healing ulcers to the life-threatening visceral forms. Presence of Leishmania RNA virus (LRV) confers survival advantage to these parasites by suppressing anti-leishmanial immunity in the vertebrate host. The two viral species, LRV1 and LRV2 infect species of the subgenera Viannia and Leishmania, respectively. In this work we investigated co-phylogenetic patterns of leishmaniae and their viruses on a small scale (LRV2 in L. major) and demonstrated their predominant coevolution, occasionally broken by intraspecific host switches. Our analysis of the two viral genes, encoding the capsid and RNA-dependent RNA polymerase (RDRP), revealed them to be under the pressure of purifying selection, which was considerably stronger for the former gene across the whole tree. The selective pressure also differs between the LRV clades and correlates with the frequency of interspecific host switches. In addition, using experimental (capsid) and predicted (RDRP) models we demonstrated that the evolutionary variability across the structure is strikingly different in these two viral proteins.
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16
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Xia X, Wu W, Cui Y, Roy P, Zhou ZH. Bluetongue virus capsid protein VP5 perforates membranes at low endosomal pH during viral entry. Nat Microbiol 2021; 6:1424-1432. [PMID: 34702979 PMCID: PMC9015746 DOI: 10.1038/s41564-021-00988-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 09/22/2021] [Indexed: 01/25/2023]
Abstract
Bluetongue virus (BTV) is a non-enveloped virus and causes substantial morbidity and mortality in ruminants such as sheep. Fashioning a receptor-binding protein (VP2) and a membrane penetration protein (VP5) on the surface, BTV releases its genome-containing core (VP3 and VP7) into the host cell cytosol after perforation of the endosomal membrane. Unlike enveloped ones, the entry mechanisms of non-enveloped viruses into host cells remain poorly understood. Here we applied single-particle cryo-electron microscopy, cryo-electron tomography and structure-guided functional assays to characterize intermediate states of BTV cell entry in endosomes. Four structures of BTV at the resolution range of 3.4-3.9 Å show the different stages of structural rearrangement of capsid proteins on exposure to low pH, including conformational changes of VP5, stepwise detachment of VP2 and a small shift of VP7. In detail, sensing of the low-pH condition by the VP5 anchor domain triggers three major VP5 actions: projecting the hidden dagger domain, converting a surface loop to a protonated β-hairpin that anchors VP5 to the core and stepwise refolding of the unfurling domains into a six-helix stalk. Cryo-electron tomography structures of BTV interacting with liposomes show a length decrease of the VP5 stalk from 19.5 to 15.5 nm after its insertion into the membrane. Our structures, functional assays and structure-guided mutagenesis experiments combined indicate that this stalk, along with dagger domain and the WHXL motif, creates a single pore through the endosomal membrane that enables the viral core to enter the cytosol. Our study unveils the detailed mechanisms of BTV membrane penetration and showcases general methods to study cell entry of other non-enveloped viruses.
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Affiliation(s)
- Xian Xia
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Weining Wu
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Yanxiang Cui
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Polly Roy
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Z Hong Zhou
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA.
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17
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Levanova AA, Vainio EJ, Hantula J, Poranen MM. RNA-Dependent RNA Polymerase from Heterobasidion RNA Virus 6 Is an Active Replicase In Vitro. Viruses 2021; 13:v13091738. [PMID: 34578320 PMCID: PMC8473416 DOI: 10.3390/v13091738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 11/16/2022] Open
Abstract
Heterobasidion RNA virus 6 (HetRV6) is a double-stranded (ds)RNA mycovirus and a member of the recently established genus Orthocurvulavirus within the family Orthocurvulaviridae. The purpose of the study was to determine the biochemical requirements for RNA synthesis catalyzed by HetRV6 RNA-dependent RNA polymerase (RdRp). HetRV6 RdRp was expressed in Escherichia coli and isolated to near homogeneity using liquid chromatography. The enzyme activities were studied in vitro using radiolabeled UTP. The HetRV6 RdRp was able to initiate RNA synthesis in a primer-independent manner using both virus-related and heterologous single-stranded (ss)RNA templates, with a polymerization rate of about 46 nt/min under optimal NTP concentration and temperature. NTPs with 2'-fluoro modifications were also accepted as substrates in the HetRV6 RdRp-catalyzed RNA polymerization reaction. HetRV6 RdRp transcribed viral RNA genome via semi-conservative mechanism. Furthermore, the enzyme demonstrated terminal nucleotidyl transferase (TNTase) activity. Presence of Mn2+ was required for the HetRV6 RdRp catalyzed enzymatic activities. In summary, our study shows that HetRV6 RdRp is an active replicase in vitro that can be potentially used in biotechnological applications, molecular biology, and biomedicine.
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Affiliation(s)
- Alesia A. Levanova
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
- Correspondence: (A.A.L.); (M.M.P.)
| | - Eeva J. Vainio
- Natural Resources Institute Finland, 00790 Helsinki, Finland; (E.J.V.); (J.H.)
| | - Jarkko Hantula
- Natural Resources Institute Finland, 00790 Helsinki, Finland; (E.J.V.); (J.H.)
| | - Minna M. Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
- Correspondence: (A.A.L.); (M.M.P.)
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18
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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: 18] [Impact Index Per Article: 6.0] [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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19
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Abstract
Trichomonas vaginalis viruses (TVVs) are double-stranded RNA (dsRNA) viruses that cohabitate in Trichomonas vaginalis, the causative pathogen of trichomoniasis, the most common nonviral sexually transmitted disease worldwide. Featuring an unsegmented dsRNA genome encoding a single capsid shell protein (CSP), TVVs contrast with multisegmented dsRNA viruses, such as the diarrhea-causing rotavirus, whose larger genome is split into 10 dsRNA segments encoding 5 unique capsid proteins. Trichomonas vaginalis, the causative pathogen for the most common nonviral sexually transmitted infection worldwide, is itself frequently infected with one or more of the four types of small double-stranded RNA (dsRNA) Trichomonas vaginalis viruses (TVV1 to 4, genus Trichomonasvirus, family Totiviridae). Each TVV encloses a nonsegmented genome within a single-layered capsid and replicates entirely intracellularly, like many dsRNA viruses, and unlike those in the Reoviridae family. Here, we have determined the structure of TVV2 by cryo-electron microscopy (cryoEM) at 3.6 Å resolution and derived an atomic model of its capsid. TVV2 has an icosahedral, T = 2*, capsid comprised of 60 copies of the icosahedral asymmetric unit (a dimer of the two capsid shell protein [CSP] conformers, CSP-A and CSP-B), typical of icosahedral dsRNA virus capsids. However, unlike the robust CSP-interlocking interactions such as the use of auxiliary “clamping” proteins among Reoviridae, only lateral CSP interactions are observed in TVV2, consistent with an assembly strategy optimized for TVVs’ intracellular-only replication cycles within their protozoan host. The atomic model reveals both a mostly negatively charged capsid interior, which is conducive to movement of the loosely packed genome, and channels at the 5-fold vertices, which we suggest as routes of mRNA release during transcription. Structural comparison of TVV2 to the Saccharomyces cerevisiae L-A virus reveals a conserved helix-rich fold within the CSP and putative guanylyltransferase domain along the capsid exterior, suggesting conserved mRNA maintenance strategies among Totiviridae. This first atomic structure of a TVV provides a framework to guide future biochemical investigations into the interplay between Trichomonas vaginalis and its viruses.
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20
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Smith SC, Gribble J, Diller JR, Wiebe MA, Thoner TW, Denison MR, Ogden KM. Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage. J Virol 2021; 95:JVI.02181-20. [PMID: 33472930 PMCID: PMC8103698 DOI: 10.1128/jvi.02181-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/14/2021] [Indexed: 12/12/2022] Open
Abstract
For viruses with segmented genomes, genetic diversity is generated by genetic drift, reassortment, and recombination. Recombination produces RNA populations distinct from full-length gene segments and can influence viral population dynamics, persistence, and host immune responses. Viruses in the Reoviridae family, including rotavirus and mammalian orthoreovirus (reovirus), have been reported to package segments containing rearrangements or internal deletions. Rotaviruses with RNA segments containing rearrangements have been isolated from immunocompromised and immunocompetent children and in vitro following serial passage at relatively high multiplicity. Reoviruses that package small, defective RNA segments have established chronic infections in cells and in mice. However, the mechanism and extent of Reoviridae RNA recombination are undefined. Towards filling this gap in knowledge, we determined the titers and RNA segment profiles for reovirus and rotavirus following serial passage in cultured cells. The viruses exhibited occasional titer reductions characteristic of interference. Reovirus strains frequently accumulated segments that retained 5' and 3' terminal sequences and featured large internal deletions, while similarly fragmented segments were rarely detected in rotavirus populations. Using next-generation RNA-sequencing to analyze RNA molecules packaged in purified reovirus particles, we identified distinct recombination sites within individual viral genome segments. Recombination junctions were frequently but not always characterized by short direct sequence repeats upstream and downstream that spanned junction sites. Taken together, these findings suggest that reovirus accumulates defective gene segments featuring internal deletions during passage and undergoes sequence-directed recombination at distinct sites.IMPORTANCE Viruses in the Reoviridae family include important pathogens of humans and other animals and have segmented RNA genomes. Recombination in RNA virus populations can facilitate novel host exploration and increased disease severity. The extent, patterns, and mechanisms of Reoviridae recombination and the functions and effects of recombined RNA products are poorly understood. Here, we provide evidence that mammalian orthoreovirus regularly synthesizes RNA recombination products that retain terminal sequences but contain internal deletions, while rotavirus rarely synthesizes such products. Recombination occurs more frequently at specific sites in the mammalian orthoreovirus genome, and short regions of identical sequence are often detected at junction sites. These findings suggest that mammalian orthoreovirus recombination events are directed in part by RNA sequences. An improved understanding of recombined viral RNA synthesis may enhance our capacity to engineer improved vaccines and virotherapies in the future.
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Affiliation(s)
- Sydni Caet Smith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
| | - Jennifer Gribble
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
| | - Julia R Diller
- Department of Pediatrics, Vanderbilt University Medical Center
| | - Michelle A Wiebe
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
| | - Timothy W Thoner
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
| | - Mark R Denison
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
- Department of Pediatrics, Vanderbilt University Medical Center
| | - Kristen M Ogden
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
- Department of Pediatrics, Vanderbilt University Medical Center
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21
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Tian L, Qiang T, Liang C, Ren X, Jia M, Zhang J, Li J, Wan M, YuWen X, Li H, Cao W, Liu H. RNA-dependent RNA polymerase (RdRp) inhibitors: The current landscape and repurposing for the COVID-19 pandemic. Eur J Med Chem 2021; 213:113201. [PMID: 33524687 PMCID: PMC7826122 DOI: 10.1016/j.ejmech.2021.113201] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/14/2020] [Accepted: 01/12/2021] [Indexed: 02/06/2023]
Abstract
The widespread nature of several viruses is greatly credited to their rapidly altering RNA genomes that enable the infection to persist despite challenges presented by host cells. Within the RNA genome of infections is RNA-dependent RNA polymerase (RdRp), which is an essential enzyme that helps in RNA synthesis by catalysing the RNA template-dependent development of phosphodiester bonds. Therefore, RdRp is an important therapeutic target in RNA virus-caused diseases, including SARS-CoV-2. In this review, we describe the promising RdRp inhibitors that have been launched or are currently in clinical studies for the treatment of RNA virus infections. Structurally, nucleoside inhibitors (NIs) bind to the RdRp protein at the enzyme active site, and nonnucleoside inhibitors (NNIs) bind to the RdRp protein at allosteric sites. By reviewing these inhibitors, more precise guidelines for the development of more promising anti-RNA virus drugs should be set, and due to the current health emergency, they will eventually be used for COVID-19 treatment.
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Affiliation(s)
- Lei Tian
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Taotao Qiang
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Chengyuan Liang
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
| | - Xiaodong Ren
- Medical College, Guizhou University, Guiyang, 550025, PR China.
| | - Minyi Jia
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Jiayun Zhang
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Jingyi Li
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Minge Wan
- School of Medicine and Pharmacy, Shaanxi University of Business & Commerce, Xi'an, 712046, PR China
| | - Xin YuWen
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Han Li
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Wenqiang Cao
- Zhuhai Jinan Selenium Source Nanotechnology Co., Ltd., Hengqin New Area, Zhuhai, 519030, PR China.
| | - Hong Liu
- Zhuhai Jinan Selenium Source Nanotechnology Co., Ltd., Hengqin New Area, Zhuhai, 519030, PR China.
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22
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Structure Unveils Relationships between RNA Virus Polymerases. Viruses 2021; 13:v13020313. [PMID: 33671332 PMCID: PMC7922027 DOI: 10.3390/v13020313] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 12/30/2022] Open
Abstract
RNA viruses are the fastest evolving known biological entities. Consequently, the sequence similarity between homologous viral proteins disappears quickly, limiting the usability of traditional sequence-based phylogenetic methods in the reconstruction of relationships and evolutionary history among RNA viruses. Protein structures, however, typically evolve more slowly than sequences, and structural similarity can still be evident, when no sequence similarity can be detected. Here, we used an automated structural comparison method, homologous structure finder, for comprehensive comparisons of viral RNA-dependent RNA polymerases (RdRps). We identified a common structural core of 231 residues for all the structurally characterized viral RdRps, covering segmented and non-segmented negative-sense, positive-sense, and double-stranded RNA viruses infecting both prokaryotic and eukaryotic hosts. The grouping and branching of the viral RdRps in the structure-based phylogenetic tree follow their functional differentiation. The RdRps using protein primer, RNA primer, or self-priming mechanisms have evolved independently of each other, and the RdRps cluster into two large branches based on the used transcription mechanism. The structure-based distance tree presented here follows the recently established RdRp-based RNA virus classification at genus, subfamily, family, order, class and subphylum ranks. However, the topology of our phylogenetic tree suggests an alternative phylum level organization.
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23
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Lu Q, Ren F, Yan J, Zhang Y, Awais M, He J, Sun J. Alkaline phosphatase can promote the replication of Bombyx mori cypovirus 1 by interaction with its turret protein. Virus Res 2020; 292:198261. [PMID: 33316354 DOI: 10.1016/j.virusres.2020.198261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 11/28/2020] [Accepted: 12/06/2020] [Indexed: 11/25/2022]
Abstract
Bombyx mori cypovirus 1 (BmCPV1) is a member of the Reoviridae family which is characterized by its single-layered capsid. Similar with other turreted viruses in the Reoviridae, transcription of BmCPV1 occurs inside the capsid, and the nascent mRNA is released to the turret which consists of five turret proteins (TPs) and located at the 5-fold axis of the outer capsid, then the capping enzyme TP will guanylate and methylate the nascent viral mRNA to produce a matured mRNA. However, during these processes, how the BmCPV1 draws other cellular proteins to facilitate its replication is still lesser-known. Here we used an ELISA to investigate the interaction between ALP and BmCPV1. A co-immunoprecipitation technique was employed to detect the interaction of ALP with the Methylase domain of TP. We further studied whether ALP affects the replication of BmCPV1 inside the cell, results show that reducing the expression of ALP through RNAi reduced the transcription level of the BmCPV1 VP1 gene, which was increased by overexpression of ALP. In summary, our data demonstrate an interaction between ALP and BmCPV1 and that ALP promoted the replication of BmCPV1, and support our hypothesis of the ALP is an RTPase to facilitate the capping process of BmCPV1.
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Affiliation(s)
- Qiuyuan Lu
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Feifei Ren
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jiming Yan
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yinong Zhang
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Mian Awais
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jian He
- Public Experimental Teaching Center, Sun Yat-sen University, Guangzhou, Guangdong, 510642, China.
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
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24
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Wu X, Cheng X. Intercellular movement of plant RNA viruses: Targeting replication complexes to the plasmodesma for both accuracy and efficiency. Traffic 2020; 21:725-736. [PMID: 33090653 DOI: 10.1111/tra.12768] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/10/2020] [Accepted: 10/10/2020] [Indexed: 02/06/2023]
Abstract
Replication and movement are two critical steps in plant virus infection. Recent advances in the understanding of the architecture and subcellular localization of virus-induced inclusions and the interactions between viral replication complex (VRC) and movement proteins (MPs) allow for the dissection of the intrinsic relationship between replication and movement, which has revealed that recruitment of VRCs to the plasmodesma (PD) via direct or indirect MP-VRC interactions is a common strategy used for cell-to-cell movement by most plant RNA viruses. In this review, we summarize the recent advances in the understanding of virus-induced inclusions and their roles in virus replication and cell-to-cell movement, analyze the advantages of such coreplicational movement from a viral point of view and discuss the possible mechanical force by which MPs drive the movement of virions or viral RNAs through the PD. Finally, we highlight the missing pieces of the puzzle of viral movement that are especially worth investigating in the near future.
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Affiliation(s)
- Xiaoyun Wu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Xiaofei Cheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
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25
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Chandler-Bostock R, Mata CP, Bingham RJ, Dykeman EC, Meng B, Tuthill TJ, Rowlands DJ, Ranson NA, Twarock R, Stockley PG. Assembly of infectious enteroviruses depends on multiple, conserved genomic RNA-coat protein contacts. PLoS Pathog 2020; 16:e1009146. [PMID: 33370422 PMCID: PMC7793301 DOI: 10.1371/journal.ppat.1009146] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 01/08/2021] [Accepted: 11/11/2020] [Indexed: 02/04/2023] Open
Abstract
Picornaviruses are important viral pathogens, but despite extensive study, the assembly process of their infectious virions is still incompletely understood, preventing the development of anti-viral strategies targeting this essential part of the life cycle. We report the identification, via RNA SELEX and bioinformatics, of multiple RNA sites across the genome of a typical enterovirus, enterovirus-E (EV-E), that each have affinity for the cognate viral capsid protein (CP) capsomer. Many of these sites are evolutionarily conserved across known EV-E variants, suggesting they play essential functional roles. Cryo-electron microscopy was used to reconstruct the EV-E particle at ~2.2 Å resolution, revealing extensive density for the genomic RNA. Relaxing the imposed symmetry within the reconstructed particles reveals multiple RNA-CP contacts, a first for any picornavirus. Conservative mutagenesis of the individual RNA-contacting amino acid side chains in EV-E, many of which are conserved across the enterovirus family including poliovirus, is lethal but does not interfere with replication or translation. Anti-EV-E and anti-poliovirus aptamers share sequence similarities with sites distributed across the poliovirus genome. These data are consistent with the hypothesis that these RNA-CP contacts are RNA Packaging Signals (PSs) that play vital roles in assembly and suggest that the RNA PSs are evolutionarily conserved between pathogens within the family, augmenting the current protein-only assembly paradigm for this family of viruses.
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Affiliation(s)
- Rebecca Chandler-Bostock
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Carlos P. Mata
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Richard J. Bingham
- Department of Mathematics, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, United Kingdom
| | - Eric C. Dykeman
- Department of Mathematics, University of York, York, United Kingdom
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, United Kingdom
| | - Bo Meng
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Tobias J. Tuthill
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - David J. Rowlands
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail: (DJR); (NAR); (RT); (PGS)
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail: (DJR); (NAR); (RT); (PGS)
| | - Reidun Twarock
- Department of Mathematics, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, United Kingdom
- * E-mail: (DJR); (NAR); (RT); (PGS)
| | - Peter G. Stockley
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail: (DJR); (NAR); (RT); (PGS)
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26
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Cryo-electron Microscopy Structure, Assembly, and Mechanics Show Morphogenesis and Evolution of Human Picobirnavirus. J Virol 2020; 94:JVI.01542-20. [PMID: 32938763 DOI: 10.1128/jvi.01542-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/08/2020] [Indexed: 12/17/2022] Open
Abstract
Despite their diversity, most double-stranded-RNA (dsRNA) viruses share a specialized T=1 capsid built from dimers of a single protein that provides a platform for genome transcription and replication. This ubiquitous capsid remains structurally undisturbed throughout the viral cycle, isolating the genome to avoid triggering host defense mechanisms. Human picobirnavirus (hPBV) is a dsRNA virus frequently associated with gastroenteritis, although its pathogenicity is yet undefined. Here, we report the cryo-electron microscopy (cryo-EM) structure of hPBV at 2.6-Å resolution. The capsid protein (CP) is arranged in a single-shelled, ∼380-Å-diameter T=1 capsid with a rough outer surface similar to that of dsRNA mycoviruses. The hPBV capsid is built of 60 quasisymmetric CP dimers (A and B) stabilized by domain swapping, and only the CP-A N-terminal basic region interacts with the packaged nucleic acids. hPBV CP has an α-helical domain with a fold similar to that of fungal partitivirus CP, with many domain insertions in its C-terminal half. In contrast to dsRNA mycoviruses, hPBV has an extracellular life cycle phase like complex reoviruses, which indicates that its own CP probably participates in cell entry. Using an in vitro reversible assembly/disassembly system of hPBV, we isolated tetramers as possible assembly intermediates. We used atomic force microscopy to characterize the biophysical properties of hPBV capsids with different cargos (host nucleic acids or proteins) and found that the CP N-terminal segment not only is involved in nucleic acid interaction/packaging but also modulates the mechanical behavior of the capsid in conjunction with the cargo.IMPORTANCE Despite intensive study, human virus sampling is still sparse, especially for viruses that cause mild or asymptomatic disease. Human picobirnavirus (hPBV) is a double-stranded-RNA virus, broadly dispersed in the human population, but its pathogenicity is uncertain. Here, we report the hPBV structure derived from cryo-electron microscopy (cryo-EM) and reconstruction methods using three capsid protein variants (of different lengths and N-terminal amino acid compositions) that assemble as virus-like particles with distinct properties. The hPBV near-atomic structure reveals a quasisymmetric dimer as the structural subunit and tetramers as possible assembly intermediates that coassemble with nucleic acids. Our structural studies and atomic force microscopy analyses indicate that hPBV capsids are potentially excellent nanocages for gene therapy and targeted drug delivery in humans.
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27
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Liu W, Cui Y, Wang C, Li Z, Gong D, Dai X, Bi GQ, Sun R, Zhou ZH. Structures of capsid and capsid-associated tegument complex inside the Epstein-Barr virus. Nat Microbiol 2020; 5:1285-1298. [PMID: 32719506 DOI: 10.1038/s41564-020-0758-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022]
Abstract
As the first discovered human cancer virus, Epstein-Barr virus (EBV) causes Burkitt's lymphoma and nasopharyngeal carcinoma. Isolating virions for determining high-resolution structures has been hindered by latency-a hallmark of EBV infection-and atomic structures are thus available only for recombinantly expressed EBV proteins. In the present study, by symmetry relaxation and subparticle reconstruction, we have determined near-atomic-resolution structures of the EBV capsid with an asymmetrically attached DNA-translocating portal and capsid-associated tegument complexes from cryogenic electron microscopy images of just 2,048 EBV virions obtained by chemical induction. The resulting atomic models reveal structural plasticity among the 20 conformers of the major capsid protein, 2 conformers of the small capsid protein (SCP), 4 conformers of the triplex monomer proteins and 2 conformers of the triplex dimer proteins. Plasticity reaches the greatest level at the capsid-tegument interfaces involving SCP and capsid-associated tegument complexes (CATC): SCPs crown pentons/hexons and mediate tegument protein binding, and CATCs bind and rotate all five periportal triplexes, but notably only about one peri-penton triplex. These results offer insights into the EBV capsid assembly and a mechanism for recruiting cell-regulating factors into the tegument compartment as 'cargoes', and should inform future anti-EBV strategies.
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Affiliation(s)
- Wei Liu
- 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.,Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yanxiang Cui
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Caiyan Wang
- 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.,International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zihang Li
- 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
| | - Danyang Gong
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | - Xinghong Dai
- 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.,Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Guo-Qiang Bi
- Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ren Sun
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - 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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28
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Ahmad M, Dwivedy A, Mariadasse R, Tiwari S, Kar D, Jeyakanthan J, Biswal BK. Prediction of Small Molecule Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus-2 RNA-dependent RNA Polymerase. ACS OMEGA 2020; 5:18356-18366. [PMID: 32743211 PMCID: PMC7391942 DOI: 10.1021/acsomega.0c02096] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/30/2020] [Indexed: 05/08/2023]
Abstract
The current COVID-19 outbreak warrants the design and development of novel anti-COVID therapeutics. Using a combination of bioinformatics and computational tools, we modelled the 3D structure of the RdRp (RNA-dependent RNA polymerase) of SARS-CoV2 (severe acute respiratory syndrome coronavirus-2) and predicted its probable GTP binding pocket in the active site. GTP is crucial for the formation of the initiation complex during RNA replication. This site was computationally targeted using a number of small molecule inhibitors of the hepatitis C RNA polymerase reported previously. Further optimizations suggested a lead molecule that may prove fruitful in the development of potent inhibitors against the RdRp of SARS-CoV2.
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Affiliation(s)
- Mohammed Ahmad
- National
Institute of Immunology, New Delhi 110067, India
| | | | - Richard Mariadasse
- Department
of Bioinformatics, Alagappa University, karaikudi 630004, Tamil Nadu, India
| | - Satish Tiwari
- National
Institute of Immunology, New Delhi 110067, India
| | - Deepsikha Kar
- National
Institute of Immunology, New Delhi 110067, India
| | - Jeyaraman Jeyakanthan
- Department
of Bioinformatics, Alagappa University, karaikudi 630004, Tamil Nadu, India
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29
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Beren C, Cui Y, Chakravarty A, Yang X, Rao ALN, Knobler CM, Zhou ZH, Gelbart WM. Genome organization and interaction with capsid protein in a multipartite RNA virus. Proc Natl Acad Sci U S A 2020; 117:10673-10680. [PMID: 32358197 PMCID: PMC7245085 DOI: 10.1073/pnas.1915078117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We report the asymmetric reconstruction of the single-stranded RNA (ssRNA) content in one of the three otherwise identical virions of a multipartite RNA virus, brome mosaic virus (BMV). We exploit a sample consisting exclusively of particles with the same RNA content-specifically, RNAs 3 and 4-assembled in planta by agrobacterium-mediated transient expression. We find that the interior of the particle is nearly empty, with most of the RNA genome situated at the capsid shell. However, this density is disordered in the sense that the RNA is not associated with any particular structure but rather, with an ensemble of secondary/tertiary structures that interact with the capsid protein. Our results illustrate a fundamental difference between the ssRNA organization in the multipartite BMV viral capsid and the monopartite bacteriophages MS2 and Qβ for which a dominant RNA conformation is found inside the assembled viral capsids, with RNA density conserved even at the center of the particle. This can be understood in the context of the differing demands on their respective lifecycles: BMV must package separately each of several different RNA molecules and has been shown to replicate and package them in isolated, membrane-bound, cytoplasmic complexes, whereas the bacteriophages exploit sequence-specific "packaging signals" throughout the viral RNA to package their monopartite genomes.
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Affiliation(s)
- Christian Beren
- Department of Chemistry & Biochemistry, University of California, Los Angeles, CA 90095
| | - Yanxiang Cui
- California NanoSystems Institute, University of California, Los Angeles, CA 90095
| | - Antara Chakravarty
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521
| | - Xue Yang
- California NanoSystems Institute, University of California, Los Angeles, CA 90095
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095
| | - A L N Rao
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521;
| | - Charles M Knobler
- Department of Chemistry & Biochemistry, University of California, Los Angeles, CA 90095
| | - Z Hong Zhou
- California NanoSystems Institute, University of California, Los Angeles, CA 90095;
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095
| | - William M Gelbart
- Department of Chemistry & Biochemistry, University of California, Los Angeles, CA 90095;
- California NanoSystems Institute, University of California, Los Angeles, CA 90095
- Molecular Biology Institute, University of California, Los Angeles, CA 90095
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30
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Reoviridae transcription is more than an open-and-shut case. Nat Struct Mol Biol 2019; 26:991-993. [PMID: 31695186 DOI: 10.1038/s41594-019-0328-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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