1
|
Brand C, Geiss BJ, Bisaillon M. Deciphering the interaction surface between the West Nile virus NS3 and NS5 proteins. Access Microbiol 2024; 6:000675.v3. [PMID: 39045235 PMCID: PMC11261718 DOI: 10.1099/acmi.0.000675.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 04/25/2024] [Indexed: 07/25/2024] Open
Abstract
West Nile virus (WNV) is the most prevalent mosquito-borne virus and the leading cause of viral encephalitis in the continental United States. It belongs to the family Flaviviridae which includes other important human pathogens such as dengue virus (DENV), Japanese encephalitis virus (JEV) and Zika viruses (ZIKV). Despite several decades of research, no specific antiviral drugs are available to treat flavivirus infections. The present study characterizes the interaction between the WNV NS3 and NS5 proteins for the purpose of identifying hotspots in the protein-protein interaction which could be targeted for the development of antiviral therapeutics. We previously developed an interaction model in silico based on data available in the literature. Here, potential interacting residues on NS3 and NS5 were mutated in a WNV replicon, and seven mutations in the NS3 protein were found to drastically reduce viral replication. In addition to being well conserved among mosquito-borne flaviviruses, these residues are located on the protein's surface in two clusters which might be interesting new targets for future drug development.
Collapse
Affiliation(s)
- Carolin Brand
- Département de Biochimie et de Génomique Fonctionnelle, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Brian J. Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA
| | - Martin Bisaillon
- Département de Biochimie et de Génomique Fonctionnelle, Université de Sherbrooke, Sherbrooke, QC, Canada
| |
Collapse
|
2
|
Li H, Zhu Y, Wang X, Feng Y, Qian Y, Ma Q, Li X, Chen Y, Chen K. Joining Forces: The Combined Application of Therapeutic Viruses and Nanomaterials in Cancer Therapy. Molecules 2023; 28:7679. [PMID: 38005401 PMCID: PMC10674375 DOI: 10.3390/molecules28227679] [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: 09/29/2023] [Revised: 11/10/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Cancer, on a global scale, presents a monumental challenge to our healthcare systems, posing a significant threat to human health. Despite the considerable progress we have made in the diagnosis and treatment of cancer, realizing precision cancer therapy, reducing side effects, and enhancing efficacy remain daunting tasks. Fortunately, the emergence of therapeutic viruses and nanomaterials provides new possibilities for tackling these issues. Therapeutic viruses possess the ability to accurately locate and attack tumor cells, while nanomaterials serve as efficient drug carriers, delivering medication precisely to tumor tissues. The synergy of these two elements has led to a novel approach to cancer treatment-the combination of therapeutic viruses and nanomaterials. This advantageous combination has overcome the limitations associated with the side effects of oncolytic viruses and the insufficient tumoricidal capacity of nanomedicines, enabling the oncolytic viruses to more effectively breach the tumor's immune barrier. It focuses on the lesion site and even allows for real-time monitoring of the distribution of therapeutic viruses and drug release, achieving a synergistic effect. This article comprehensively explores the application of therapeutic viruses and nanomaterials in tumor treatment, dissecting their working mechanisms, and integrating the latest scientific advancements to predict future development trends. This approach, which combines viral therapy with the application of nanomaterials, represents an innovative and more effective treatment strategy, offering new perspectives in the field of tumor therapy.
Collapse
Affiliation(s)
- Hongyu Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (Y.Z.); (Y.F.); (Y.Q.); (Q.M.); (X.L.); (Y.C.)
- Ocean College, Beibu Gulf University, Qinzhou 535011, China
| | - Yunhuan Zhu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (Y.Z.); (Y.F.); (Y.Q.); (Q.M.); (X.L.); (Y.C.)
| | - Xin Wang
- Center of Infectious Disease Research, School of Life Science, Westlake University, Hangzhou 310024, China;
| | - Yilu Feng
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (Y.Z.); (Y.F.); (Y.Q.); (Q.M.); (X.L.); (Y.C.)
| | - Yuncheng Qian
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (Y.Z.); (Y.F.); (Y.Q.); (Q.M.); (X.L.); (Y.C.)
| | - Qiman Ma
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (Y.Z.); (Y.F.); (Y.Q.); (Q.M.); (X.L.); (Y.C.)
| | - Xinyuan Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (Y.Z.); (Y.F.); (Y.Q.); (Q.M.); (X.L.); (Y.C.)
| | - Yihan Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (Y.Z.); (Y.F.); (Y.Q.); (Q.M.); (X.L.); (Y.C.)
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China; (Y.Z.); (Y.F.); (Y.Q.); (Q.M.); (X.L.); (Y.C.)
| |
Collapse
|
3
|
Kumar G, Singh AK, Agarwal D. Structural and functional characterization of RNA dependent RNA polymerase of Macrobrachium rosenbergii nodavirus (MnRdRp). J Biomol Struct Dyn 2023; 41:12825-12837. [PMID: 36757137 DOI: 10.1080/07391102.2023.2175384] [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: 07/21/2022] [Accepted: 01/07/2023] [Indexed: 02/10/2023]
Abstract
Macrobrachium rosenbergii is a highly valued farmed freshwater species and its production has been affected globally by white tail disease caused by M. rosenbergii nodavirus (MrNV). MrNV is a single stranded positive sense RNA virus encoding RNA-dependent RNA polymerase (RdRp) for genome replication. Due to its essentiality for pathogenesis, it is an important drug target. The domain prediction of the complete sequence revealed the presence of two enzymatic regions namely methyl transferase and RdRp separated by transmembrane region. The predicted three-dimensional (3D) structure of MnRdRp using AlphaFold 2 shows that the structure is composed of three major sub-domains common for other polymerases namely fingers, palm and thumb. Structural similarity search revealed its similarity with other flaviviridea members especially with BVDV RdRp (BvdvRdRp). The structure of fingers and palm sub-domains is more conserved than the thumb sub-domain. A small α-helix named 'priming helix' having conserve Tyr was identified at position 829-833 with a potential role in de novo initiation. Analysis of electrostatic potential revealed that nucleotide and template channels are electropositive. Metal binding residues were identified as Asp599, Asp704 and Asp705. The α and β phosphates of incoming nucleotide interact with two Mn2+, Arg455 and Arg537. For recognition of 2'-OH of incoming rNTP, Asp604, Ser661 and Asn670 were identified which can form H-bond network with 2'-OH group. Docking study revealed that Dasabuvir can potentially inhibit MnRdRp. The study concluded that the overall structure and function of MnRdRp are similar to Flaviviridae polymerases and their inhibitors can work against this enzyme.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Gulshan Kumar
- College of Fisheries Science Gunla, Birsa Agricultural University, Ranchi, Jharkhand, India
| | - A K Singh
- College of Fisheries Science Gunla, Birsa Agricultural University, Ranchi, Jharkhand, India
| | - Deepak Agarwal
- TNJFU, Institute of Fisheries Post Graduate Studies, OMR, Chennai, Tamil Nadu, India
| |
Collapse
|
4
|
Nodavirus RNA replication crown architecture reveals proto-crown precursor and viral protein A conformational switching. Proc Natl Acad Sci U S A 2023; 120:e2217412120. [PMID: 36693094 PMCID: PMC9945985 DOI: 10.1073/pnas.2217412120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Positive-strand RNA viruses replicate their genomes in virus-induced membrane vesicles, and the resulting RNA replication complexes are a major target for virus control. Nodavirus studies first revealed viral RNA replication proteins forming a 12-fold symmetric "crown" at the vesicle opening to the cytosol, an arrangement recently confirmed to extend to distantly related alphaviruses. Using cryoelectron microscopy (cryo-EM), we show that mature nodavirus crowns comprise two stacked 12-mer rings of multidomain viral RNA replication protein A. Each ring contains an ~19 nm circle of C-proximal polymerase domains, differentiated by strikingly diverged positions of N-proximal RNA capping/membrane binding domains. The lower ring is a "proto-crown" precursor that assembles prior to RNA template recruitment, RNA synthesis, and replication vesicle formation. In this proto-crown, the N-proximal segments interact to form a toroidal central floor, whose 3.1 Å resolution structure reveals many mechanistic details of the RNA capping/membrane binding domains. In the upper ring, cryo-EM fitting indicates that the N-proximal domains extend radially outside the polymerases, forming separated, membrane-binding "legs." The polymerase and N-proximal domains are connected by a long linker accommodating the conformational switch between the two rings and possibly also polymerase movements associated with RNA synthesis and nonsymmetric electron density in the lower center of mature crowns. The results reveal remarkable viral protein multifunctionality, conformational flexibility, and evolutionary plasticity and insights into (+)RNA virus replication and control.
Collapse
|
5
|
den Boon JA, Zhan H, Unchwaniwala N, Horswill M, Slavik K, Pennington J, Navine A, Ahlquist P. Multifunctional Protein A Is the Only Viral Protein Required for Nodavirus RNA Replication Crown Formation. Viruses 2022; 14:v14122711. [PMID: 36560715 PMCID: PMC9788154 DOI: 10.3390/v14122711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
Positive-strand RNA virus RNA genome replication occurs in membrane-associated RNA replication complexes (RCs). Nodavirus RCs are outer mitochondrial membrane invaginations whose necked openings to the cytosol are "crowned" by a 12-fold symmetrical proteinaceous ring that functions as the main engine of RNA replication. Similar protein crowns recently visualized at the openings of alphavirus and coronavirus RCs highlight their broad conservation and functional importance. Using cryo-EM tomography, we earlier showed that the major nodavirus crown constituent is viral protein A, whose polymerase, RNA capping, membrane interaction and multimerization domains drive RC formation and function. Other viral proteins are strong candidates for unassigned EM density in the crown. RNA-binding RNAi inhibitor protein B2 co-immunoprecipitates with protein A and could form crown subdomains that protect nascent viral RNA and dsRNA templates. Capsid protein may interact with the crown since nodavirus virion assembly has spatial and other links to RNA replication. Using cryoelectron tomography and complementary approaches, we show that, even when formed in mammalian cells, nodavirus RC crowns generated without B2 and capsid proteins are functional and structurally indistinguishable from mature crowns in infected Drosophila cells expressing all viral proteins. Thus, the only nodaviral factors essential to form functional RCs and crowns are RNA replication protein A and an RNA template. We also resolve apparent conflicts in prior results on B2 localization in infected cells, revealing at least two distinguishable pools of B2. The results have significant implications for crown structure, assembly, function and control as an antiviral target.
Collapse
Affiliation(s)
- Johan A. den Boon
- John W. and Jeanne M. Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715, USA
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, WI 53706, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI 53705, USA
| | - Hong Zhan
- John W. and Jeanne M. Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715, USA
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Nuruddin Unchwaniwala
- John W. and Jeanne M. Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715, USA
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Mark Horswill
- John W. and Jeanne M. Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715, USA
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, WI 53706, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI 53705, USA
| | - Kailey Slavik
- John W. and Jeanne M. Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715, USA
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Janice Pennington
- John W. and Jeanne M. Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715, USA
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Amanda Navine
- John W. and Jeanne M. Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715, USA
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Paul Ahlquist
- John W. and Jeanne M. Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715, USA
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, WI 53706, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI 53705, USA
- Correspondence:
| |
Collapse
|
6
|
Tan YB, Chmielewski D, Law MCY, Zhang K, He Y, Chen M, Jin J, Luo D. Molecular architecture of the Chikungunya virus replication complex. SCIENCE ADVANCES 2022; 8:eadd2536. [PMID: 36449616 PMCID: PMC9710867 DOI: 10.1126/sciadv.add2536] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
To better understand how positive-strand (+) RNA viruses assemble membrane-associated replication complexes (RCs) to synthesize, process, and transport viral RNA in virus-infected cells, we determined both the high-resolution structure of the core RNA replicase of chikungunya virus and the native RC architecture in its cellular context at subnanometer resolution, using in vitro reconstitution and in situ electron cryotomography, respectively. Within the core RNA replicase, the viral polymerase nsP4, which is in complex with nsP2 helicase-protease, sits in the central pore of the membrane-anchored nsP1 RNA-capping ring. The addition of a large cytoplasmic ring next to the C terminus of nsP1 forms the holo-RNA-RC as observed at the neck of spherules formed in virus-infected cells. These results represent a major conceptual advance in elucidating the molecular mechanisms of RNA virus replication and the principles underlying the molecular architecture of RCs, likely to be shared with many pathogenic (+) RNA viruses.
Collapse
Affiliation(s)
- Yaw Bia Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - David Chmielewski
- Biophysics Graduate Program, Departments of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Michelle Cheok Yien Law
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Kuo Zhang
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Yu He
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Muyuan Chen
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Jing Jin
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
- Vitalant Research Institute, San Francisco, CA 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| |
Collapse
|
7
|
Editorial overview: Virus structure and expression. Curr Opin Virol 2022; 57:101277. [PMID: 36327658 DOI: 10.1016/j.coviro.2022.101277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
8
|
Jiang X, Luan Y, Chai M, Yang Y, Wang Y, Deng W, Li Y, Cheng X, Wu X. The N-Terminal α-Helix of Potato Virus X-Encoded RNA-Dependent RNA Polymerase Is Required for Membrane Association and Multimerization. Viruses 2022; 14:v14091907. [PMID: 36146714 PMCID: PMC9504981 DOI: 10.3390/v14091907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Positive-sense single-stranded RNA viruses replicate in virus-induced membranous organelles for maximum efficiency and immune escaping. The replication of potato virus X (PVX) takes place on the endoplasmic reticulum (ER); however, how PVX-encoded RNA-dependent RNA polymerase (RdRp) is associated with the ER is still unknown. A proline-kinked amphipathic α-helix was recently found in the MET domain of RdRp. In this study, we further illustrate that the first α-helix of the MET domain is also required for ER association. Moreover, we found that the MET domain forms multimers on ER and the first α-helix is essential for multimerization. These results suggest that the RdRp of PVX adopts more than one hydrophobic motif for membrane association and for multimerization.
Collapse
Affiliation(s)
- Xue Jiang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yameng Luan
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Mengzhu Chai
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yingshuai Yang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yuting Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Wenjia Deng
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yonggang Li
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Xiaofei Cheng
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China
- Correspondence: (X.C.); (X.W.)
| | - Xiaoyun Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
- Correspondence: (X.C.); (X.W.)
| |
Collapse
|
9
|
Neufeldt CJ, Cortese M. Membrane architects: how positive-strand RNA viruses restructure the cell. J Gen Virol 2022; 103. [PMID: 35976091 DOI: 10.1099/jgv.0.001773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Virus infection is a process that requires combined contributions from both virus and host factors. For this process to be efficient within the crowded host environment, viruses have evolved ways to manipulate and reorganize host structures to produce cellular microenvironments. Positive-strand RNA virus replication and assembly occurs in association with cytoplasmic membranes, causing a reorganization of these membranes to create microenvironments that support viral processes. Similarities between virus-induced membrane domains and cellular organelles have led to the description of these structures as virus replication organelles (vRO). Electron microscopy analysis of vROs in positive-strand RNA virus infected cells has revealed surprising morphological similarities between genetically diverse virus species. For all positive-strand RNA viruses, vROs can be categorized into two groups: those that make invaginations into the cellular membranes (In-vRO), and those that cause the production of protrusions from cellular membranes (Pr-vRO), most often in the form of double membrane vesicles (DMVs). In this review, we will discuss the current knowledge on the structure and biogenesis of these two different vRO classes as well as comparing morphology and function of vROs between various positive-strand RNA viruses. Finally, we will discuss recent studies describing pharmaceutical intervention in vRO formation as an avenue to control virus infection.
Collapse
Affiliation(s)
- Christopher John Neufeldt
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Mirko Cortese
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| |
Collapse
|
10
|
Nishikiori M, den Boon JA, Unchwaniwala N, Ahlquist P. Crowning Touches in Positive-Strand RNA Virus Genome Replication Complex Structure and Function. Annu Rev Virol 2022; 9:193-212. [PMID: 35610038 DOI: 10.1146/annurev-virology-092920-021307] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Positive-strand RNA viruses, the largest genetic class of eukaryotic viruses, include coronaviruses and many other established and emerging pathogens. A major target for understanding and controlling these viruses is their genome replication, which occurs in virus-induced membrane vesicles that organize replication steps and protect double-stranded RNA intermediates from innate immune recognition. The structure of these complexes has been greatly illuminated by recent cryo-electron microscope tomography studies with several viruses. One key finding in diverse systems is the organization of crucial viral RNA replication factors in multimeric rings or crowns that among other functions serve as exit channels gating release of progeny genomes to the cytosol for translation and encapsidation. Emerging results suggest that these crowns serve additional important purposes in replication complex assembly, function, and interaction with downstream processes such as encapsidation. The findings provide insights into viral function and evolution and new bases for understanding, controlling, and engineering positive-strand RNA viruses. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Masaki Nishikiori
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, USA; .,Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Johan A den Boon
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, USA; .,Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nuruddin Unchwaniwala
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, USA; .,Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Current affiliation: Assembly Biosciences, Inc., South San Francisco, California, USA
| | - Paul Ahlquist
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, USA; .,Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|
11
|
Abstract
Reverse genetics is the prospective analysis of how genotype determines phenotype. In a typical experiment, a researcher alters a viral genome, then observes the phenotypic outcome. Among RNA viruses, this approach was first applied to positive-strand RNA viruses in the mid-1970s and over nearly 50 years has become a powerful and widely used approach for dissecting the mechanisms of viral replication and pathogenesis. During this time the global health importance of two virus groups, flaviviruses (genus Flavivirus, family Flaviviridae) and betacoronaviruses (genus Betacoronavirus, subfamily Orthocoronavirinae, family Coronaviridae), have dramatically increased, yet these viruses have genomes that are technically challenging to manipulate. As a result, several new techniques have been developed to overcome these challenges. Here I briefly review key historical aspects of positive-strand RNA virus reverse genetics, describe some recent reverse genetic innovations, particularly as applied to flaviviruses and coronaviruses, and discuss their benefits and limitations within the larger context of rigorous genetic analysis.
Collapse
|