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Jiao Y, Nigam D, Barry K, Daum C, Yoshinaga Y, Lipzen A, Khan A, Parasa SP, Wei S, Lu Z, Tello-Ruiz MK, Dhiman P, Burow G, Hayes C, Chen J, Brandizzi F, Mortimer J, Ware D, Xin Z. A large sequenced mutant library - valuable reverse genetic resource that covers 98% of sorghum genes. Plant J 2024; 117:1543-1557. [PMID: 38100514 DOI: 10.1111/tpj.16582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/08/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023]
Abstract
Mutant populations are crucial for functional genomics and discovering novel traits for crop breeding. Sorghum, a drought and heat-tolerant C4 species, requires a vast, large-scale, annotated, and sequenced mutant resource to enhance crop improvement through functional genomics research. Here, we report a sorghum large-scale sequenced mutant population with 9.5 million ethyl methane sulfonate (EMS)-induced mutations that covered 98% of sorghum's annotated genes using inbred line BTx623. Remarkably, a total of 610 320 mutations within the promoter and enhancer regions of 18 000 and 11 790 genes, respectively, can be leveraged for novel research of cis-regulatory elements. A comparison of the distribution of mutations in the large-scale mutant library and sorghum association panel (SAP) provides insights into the influence of selection. EMS-induced mutations appeared to be random across different regions of the genome without significant enrichment in different sections of a gene, including the 5' UTR, gene body, and 3'-UTR. In contrast, there were low variation density in the coding and UTR regions in the SAP. Based on the Ka /Ks value, the mutant library (~1) experienced little selection, unlike the SAP (0.40), which has been strongly selected through breeding. All mutation data are publicly searchable through SorbMutDB (https://www.depts.ttu.edu/igcast/sorbmutdb.php) and SorghumBase (https://sorghumbase.org/). This current large-scale sequence-indexed sorghum mutant population is a crucial resource that enriched the sorghum gene pool with novel diversity and a highly valuable tool for the Poaceae family, that will advance plant biology research and crop breeding.
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Affiliation(s)
- Yinping Jiao
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, 79409, USA
| | - Deepti Nigam
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, 79409, USA
| | - Kerrie Barry
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Chris Daum
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Yuko Yoshinaga
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Anna Lipzen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Adil Khan
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, 79409, USA
| | - Sai-Praneeth Parasa
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, 79409, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | - Zhenyuan Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | | | - Pallavi Dhiman
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, 79409, USA
| | - Gloria Burow
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, Texas, 79424, USA
| | - Chad Hayes
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, Texas, 79424, USA
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, Texas, 79424, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Jenny Mortimer
- Joint BioEnergy Institute, Emeryville, California, 94608, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California, 94720, USA
- School of Agriculture, Food and Wine, Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, South Australia, 5064, Australia
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
- USDA-ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, New York, 14853, USA
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, Texas, 79424, USA
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2
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Kawamura Y, Komoto S, Fukuda S, Kugita M, Tang S, Patel A, Pieknik JR, Nagao S, Taniguchi K, Krause PR, Yoshikawa T. Development of recombinant rotavirus carrying herpes simplex virus 2 glycoprotein D gene based on reverse genetics technology. Microbiol Immunol 2024; 68:56-64. [PMID: 38098134 DOI: 10.1111/1348-0421.13107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/23/2023] [Accepted: 11/30/2023] [Indexed: 02/07/2024]
Abstract
Vaccine development for herpes simplex virus 2 (HSV-2) has been attempted, but no vaccines are yet available. A plasmid-based reverse genetics system for Rotavirus (RV), which can cause gastroenteritis, allows the generation of recombinant RV containing foreign genes. In this study, we sought to develop simian RV (SA11) as a vector to express HSV-2 glycoprotein D (gD2) and evaluated its immunogenicity in mice. We generated the recombinant SA11-gD2 virus (rSA11-gD2) and confirmed its ability to express gD2 in vitro. The virus was orally inoculated into suckling BALB/c mice and into 8-week-old mice. Serum IgG and IgA titers against RV and gD2 were measured by ELISA. In the 8-week-old mice inoculated with rSA11-gD2, significant increases in not only antibodies against RV but also IgG against gD2 were demonstrated. In the suckling mice, antibodies against RV were induced, but gD2 antibody was not detected. Diarrhea observed after the first inoculation of rSA11-gD2 in suckling mice was similar to that induced by the parent virus. A gD2 expressing simian RV recombinant, which was orally inoculated, induced IgG against gD2. This strategy holds possibility for genital herpes vaccine development.
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Affiliation(s)
- Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Department of Pediatrics, Fujita Health University Okazaki Medical Center, Okazaki, Aichi, Japan
| | - Satoshi Komoto
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Center for Infectious Disease Research, Research Promotion Headquarters, Fujita Health University, Toyoake, Aichi, Japan
- Division of One Health, Research Center for GLOBAL and LOCAL Infectious Diseases (RCGLID), Oita University, Yufu, Oita, Japan
| | - Saori Fukuda
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Masanori Kugita
- Advanced Medical Research Center for Animal Models of Human Disease, Fujita Health University, Toyoake, Aichi, Japan
| | - Shuang Tang
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Amita Patel
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Julianna R Pieknik
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Shizuko Nagao
- Advanced Medical Research Center for Animal Models of Human Disease, Fujita Health University, Toyoake, Aichi, Japan
| | - Koki Taniguchi
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Philip R Krause
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
- Independent Consultant, Bethesda, Maryland, USA
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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3
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Liu ZY, Li XF, Qin CF. A Stable Reverse Genetics System of Zika Virus Based on a Self-Splicing Group II Intron. Methods Mol Biol 2024; 2733:207-229. [PMID: 38064035 DOI: 10.1007/978-1-0716-3533-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Zika virus (ZIKV) is a mosquito-borne flavivirus of the Flaviviridae family first isolated from a sentinel monkey in the Zika Forest, Uganda, in 1947. Since 2007, the virus has had a vast geographic expansion that extended to the Americas in 2015, leading to a series of large outbreaks. Although mainly transmitted by the bite of Aedes mosquitoes, human infection of ZIKV can also happen through unconventional routes such as sexual intercourse and, more importantly, vertical transmission. The genome of ZIKV is a single-stranded, positive-sense RNA molecule about 11 kb in length. The genome contains a single opening reading frame (ORF) flanked by highly structured 5' and 3' untranslated regions. To understand the mechanisms about ZIKV replication, transmission, and pathogenesis, reverse genetic tools are of great importance. In this chapter, a novel system is described for the generation and manipulation of a ZIKV infectious clone stabilized by a self-splicing group II intron, a mobile element with ribozyme activity. The intron can be spliced in vitro, and thus full-length vRNA can be prepared allowing virus genome manipulation required for further studies.
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Affiliation(s)
- Zhong-Yu Liu
- School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Xiao-Feng Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Cheng-Feng Qin
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China.
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4
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Olmedo-Velarde A, Larrea-Sarmiento A, Wang X, Hu J, Melzer M. A Breakthrough in Kitavirids: Genetic Variability, Reverse Genetics, Koch's Postulates, and Transmission of Hibiscus Green Spot Virus 2. Phytopathology 2024; 114:282-293. [PMID: 37366568 DOI: 10.1094/phyto-04-23-0110-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Hibiscus green spot virus 2 (HGSV-2), a member of the genus Higrevirus (family Kitaviridae), is a positive-stranded RNA virus associated with leprosis-like symptoms in citrus and green spots on leaves in hibiscus. HGSV-2 has only been reported in Hawaii, and while it is speculated that mites in the genus Brevipalpus might be responsible for its transmission, proper transmission assays have yet to be conducted. This study characterizes additional citrus and hibiscus isolates of HGSV-2 collected from two Hawaiian Islands. We constructed an infectious cDNA clone from a hibiscus isolate of HGSV-2 collected on Oahu and demonstrated its ability to infect several experimental hosts, including Phaseolus vulgaris, Nicotiana tabacum, and N. benthamiana, as well as natural hosts, Citrus reticulata and Hibiscus arnottianus. Bacilliform virions with varied sizes of 33 to 120 nm (length) and 14 to 70 nm (diameter) were observed in partially purified preparations obtained from agroinoculated leaves. Virus progeny from the infectious cDNA clone was found to be infectious after mechanical transmission to N. benthamiana and to cause local lesions. Finally, an isoline colony of the mite Brevipalpus azores had vector competence to transmit a citrus isolate of HGSV-2 collected from Maui to citrus and hibiscus plants, demonstrating the mite-borne nature of HGSV-2. The infectious cDNA clone developed in this study is the first reverse-genetics system for a kitavirid and will be fundamental to better characterize basic biology of HGSV-2 and its interactions with host plants and mite vectors.
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Affiliation(s)
- Alejandro Olmedo-Velarde
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Adriana Larrea-Sarmiento
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Xupeng Wang
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - John Hu
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Michael Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
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5
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Silva Júnior JVJ, da Silva ANMR, da Silva Santos JJ, Gil LHVG. Reverse Genetics of Dengue Virus. Methods Mol Biol 2024; 2733:231-248. [PMID: 38064036 DOI: 10.1007/978-1-0716-3533-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Dengue virus (DENV) is one of the most important and widespread arthropod-borne viruses, causing millions of infections over the years. Considering its epidemiological importance, efforts have been directed towards understanding various aspects of DENV biology, which have been facilitated by the development of different molecular strategies for engineering viral genomes, such as reverse genetics approaches. Reverse genetic systems are a powerful tool for investigating virus-host interaction, for vaccine development, and for high-throughput screening of antiviral compounds. However, stable manipulation of DENV genomes is a major molecular challenge, especially when using conventional cloning systems. To circumvent this issue, we describe a simple and efficient yeast-based reverse genetics system to recover infectious DENV clones.
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Affiliation(s)
- José Valter Joaquim Silva Júnior
- Virology Sector, Department of Preventive Veterinary Medicine, Federal University of Santa Maria, Santa Maria, RS, Brazil
- Virology Sector, Laboratory of Immunopathology Keizo Asami, Federal University of Pernambuco, Recife, PE, Brazil
| | | | | | - Laura Helena Vega Gonzales Gil
- Laboratory of Virology and Experimental Therapy, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE, Brazil.
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6
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Kessler S, García-Sastre A, Schwemmle M, Ciminski K. Reverse Genetics of Bat Influenza A Viruses. Methods Mol Biol 2024; 2733:75-86. [PMID: 38064027 DOI: 10.1007/978-1-0716-3533-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
New World fruit bats were recently found to harbor two distinct and previously unknown influenza A viruses (IAVs) of the subtypes H17N10 and H18N11. Although viral genome sequences were detected in the liver, intestine, lung, and kidney of infected bats and the complete genome sequences have been isolated from their rectal swab samples, all attempts to isolate an infectious virus from bats in nature have failed. The lack of an infectious bat IAV isolate was overcome by reverse genetic approaches that led to the generation of an infectious virus in vitro. Using such synthetic bat IAVs enabled the identification of their unconventional cell entry via major histocompatibility complex II (MCH-II) molecules and their ability to replicate in mice, ferrets, and bats. Importantly, we also showed that these synthetic recombinant bat IAVs are not able to reassort with conventional IAVs, preventing the acquisition of enhanced transmission properties in non-bat species by reassortment with conventional IAVs. As authentic viruses are key for understanding the molecular biology of bat IAVs, in this chapter, we describe our recently established reverse genetics protocol for generating H17N10 and H18N11 in vitro. This step-by-step protocol starts with cloning of cDNA copies of the viral RNA segments into reverse genetics plasmids, followed by the generation of a highly concentrated stock and finally a method to determine viral titers.
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Affiliation(s)
- Susanne Kessler
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Martin Schwemmle
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kevin Ciminski
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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7
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Yogarajah T, Chu JJH. Construction of Infectious Clones for Human Enteroviruses. Methods Mol Biol 2024; 2733:155-174. [PMID: 38064032 DOI: 10.1007/978-1-0716-3533-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
The infectious clone has been constructed for years via various mechanisms using reverse genetics of viral RNA into cDNA. The mechanism of construction has evolved to DNA-launch plasmids which simplify infectious clone manipulation and expression in mammalian cells. Infectious clones have enormously allowed manipulation of the enterovirus genome to discover antivirals, viral replication mechanisms, and functions of essential viral proteins. Here we will be discussing methods for the production of DNA-launch human enterovirus infectious clones and viral genome engineered with a fluorescent reporter gene.
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Affiliation(s)
- Thinesshwary Yogarajah
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Justin Jang Hann Chu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, Singapore, Singapore.
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Córdoba L, Ruiz-Padilla A, Pardo-Medina J, Rodríguez-Romero JL, Ayllón MA. Construction of a Mycoviral Infectious Clone for Reverse Genetics in Botrytis cinerea. Methods Mol Biol 2024; 2751:47-68. [PMID: 38265709 DOI: 10.1007/978-1-0716-3617-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The most important advances in our understanding of the viral life cycle, such as genome replication, packaging, transmission, and host interactions, have been made via the development of viral infectious full-length clones. Here, we describe the detailed protocols for the construction of an infectious clone derived from Botrytis virus F (BVF), a mycoflexivirus infecting the plant pathogenic fungus Botrytis cinerea, the determination of the complete sequence of the cloned mycovirus, the preparation of fungal protoplasts, and the transfection of protoplasts using transcripts derived from the BVF infectious clone.
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Affiliation(s)
- Laura Córdoba
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
| | - Ana Ruiz-Padilla
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
| | - Javier Pardo-Medina
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Julio L Rodríguez-Romero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain.
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9
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Suzuki R, Suzuki T. Reverse Genetics of Hepatitis C Virus Using an RNA Polymerase I-Mediated Transcription. Methods Mol Biol 2024; 2733:175-183. [PMID: 38064033 DOI: 10.1007/978-1-0716-3533-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
The reverse genetics system commonly used for the production of hepatitis C virus (HCV), which is a major causative agent of liver diseases, involves introduction of the viral genomic RNA synthesized in vitro into human hepatoma cells by electroporation. As an alternative methodology, we describe a cell culture system based on transfection with an expression plasmid containing a full-length HCV cDNA clone flanked by RNA polymerase I promoter and terminator sequences to generate infectious virus particles from transfected cells.
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Affiliation(s)
- Ryosuke Suzuki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuro Suzuki
- Department of Microbiology and Immunology, Hamamatsu University School of Medicine, Hamamatsu, Japan.
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10
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Bodmer BS, Hoenen T. Reverse Genetics Systems for Filoviruses. Methods Mol Biol 2024; 2733:1-14. [PMID: 38064023 DOI: 10.1007/978-1-0716-3533-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Filoviruses are causative agents of severe hemorrhagic fevers with high case fatality rates in humans. For studies of virus biology and the subsequent development of countermeasures, reverse genetic systems, and especially those facilitating the generation of recombinant filoviruses, are indispensable. Here, we describe the generation of recombinant filoviruses from cDNA.
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Affiliation(s)
- Bianca S Bodmer
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald, Insel Riems, Germany
| | - Thomas Hoenen
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald, Insel Riems, Germany.
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11
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Tercero B, Makino S. Reverse Genetics System for Rift Valley Fever Virus. Methods Mol Biol 2024; 2733:101-113. [PMID: 38064029 DOI: 10.1007/978-1-0716-3533-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Rift Valley fever virus (RVFV) is an important mosquito-borne virus that can cause severe disease manifestations in humans including ocular damage, vision loss, late-onset encephalitis, and hemorrhagic fever. In ruminants, RVFV can cause high mortality rates in young animals and high rates of abortion in pregnant animals resulting in an enormous negative impact on the economy of affected regions. To date, no licensed vaccines in humans or anti-RVFV therapeutics for animal or human use are available. The development of reverse genetics has facilitated the generation of recombinant infectious viruses that serve as powerful tools for investigating the molecular biology and pathogenesis of RVFV. Infectious recombinant RVFV can be rescued entirely from cDNAs containing predetermined mutations in their genomes to investigate virus-host interactions and mechanisms of pathogenesis and generate live-attenuated vaccines. In this chapter, we will describe the experimental procedures for the implementation of RVFV reverse genetics.
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Affiliation(s)
- Breanna Tercero
- Departments of Microbiology and Immunology, Galveston, TX, USA
| | - Shinji Makino
- Departments of Microbiology and Immunology, Galveston, TX, USA.
- Institute of Human Infection and Immunity, Galveston, TX, USA.
- Center for Biodefense and Emerging Infectious Diseases, Galveston, TX, USA.
- UTMB Center for Tropical Diseases, Galveston, TX, USA.
- The Sealy Institute for Vaccine Sciences, Galveston, TX, USA.
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12
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Cai HL, Huang YW. Reverse genetics systems for SARS-CoV-2: Development and applications. Virol Sin 2023; 38:837-850. [PMID: 37832720 PMCID: PMC10786661 DOI: 10.1016/j.virs.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023] Open
Abstract
The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused serious harm to human health and struck a blow to global economic development. Research on SARS-CoV-2 has greatly benefited from the use of reverse genetics systems, which have been established to artificially manipulate the viral genome, generating recombinant and reporter infectious viruses or biosafety level 2 (BSL-2)-adapted non-infectious replicons with desired modifications. These tools have been instrumental in studying the molecular biological characteristics of the virus, investigating antiviral therapeutics, and facilitating the development of attenuated vaccine candidates. Here, we review the construction strategies, development, and applications of reverse genetics systems for SARS-CoV-2, which may be applied to other CoVs as well.
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Affiliation(s)
- Hou-Li Cai
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Yao-Wei Huang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China; State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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13
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Peng YX, Liu ZY, Lin PX, Su SC, Gao CF, Wu SF. Reverse genetic study reveals the molecular targets of chordotonal organ TRPV channel modulators. Pestic Biochem Physiol 2023; 196:105584. [PMID: 37945222 DOI: 10.1016/j.pestbp.2023.105584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/15/2023] [Accepted: 08/22/2023] [Indexed: 11/12/2023]
Abstract
Insecticides have been widely used for the control of insect pests that have a significant impact on agriculture and human health. A better understanding of insecticide targets is needed for effective insecticide design and resistance management. Pymetrozine, afidopyropen and flonicamid are reported to target on proteins that located on insect chordotonal organs, resulting in the disruption of insect coordination and the inhibition of feeding. In this study, we systematically examined the susceptibility of six Drosophila melanogaster mutants (five transient receptor potential channels and one mechanoreceptor) to three commercially used insecticides, in order to identify the receptor subunits critical to the insect's response to insecticides. Our results showed that iav1, nan36aand wtrw1 mutants exhibited significantly reduced susceptibility to pymetrozine and afidopyropen, but not to flonicamid. The number of eggs produced by the three mutant females were significantly less than that of the w1118 strain. Meanwhile, the longevity of all male mutants and females of nan36a and wtrw1 mutants was significantly shorter than that of the w1118 strain as the control. However, we observed no gravitaxis defects in wtrw1 mutants and the anti-gravitaxis of wtrw1 mutants was abolished by pymetrozine. Behavioral assays using thermogenetic tools further confirmed the bioassay results and supported the idea that Nan as a TRPV subfamily member located in Drosophila chordotonal neurons, acting as a target of pymetrozine, which interferes with Drosophila and causes motor deficits with gravitaxis defects. Taken together, this study elucidates the interactions of pymetrozine and afidopyropen with TRPV channels, Nan and Iav, and TRPA channel, Wtrw. Our research provides another evidence that pymetrozine and afidopyropen might target on nan, iav and wtrw channels and provides insights into the development of sustainable pest management strategies.
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Affiliation(s)
- Yu-Xuan Peng
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Sanya Institute of Nanjing Agricultural University, Sanya 572025, China
| | - Zhao-Yu Liu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Sanya Institute of Nanjing Agricultural University, Sanya 572025, China
| | - Pin-Xuan Lin
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Sanya Institute of Nanjing Agricultural University, Sanya 572025, China
| | - Shao-Cong Su
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Sanya Institute of Nanjing Agricultural University, Sanya 572025, China
| | - Cong-Fen Gao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Sanya Institute of Nanjing Agricultural University, Sanya 572025, China.
| | - Shun-Fan Wu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Sanya Institute of Nanjing Agricultural University, Sanya 572025, China.
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14
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Jain S, Shrivastava-Ranjan P, Flint M, Montgomery JM, Spiropoulou CF, Albariño CG. Development of reverse genetic tools to study Chapare and Machupo viruses. Virology 2023; 588:109888. [PMID: 37774602 DOI: 10.1016/j.virol.2023.109888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023]
Abstract
Arenaviruses are highly pathogenic viruses that pose a serious public health threat. Chapare virus (CHAV) and Machupo virus (MACV), two New World arenaviruses, cause hemorrhagic fevers with case fatality rates of up to 45%. Research on therapeutic drug targets and vaccines for these viruses is limited because biosafety level 4 containment is required for handling them. In this study, we developed reverse genetics systems, including minigenomes and recombinant viruses, that will facilitate the study of these pathogens. The minigenome system is based on the S segment of CHAV or MACV genomes expressing the fluorescent reporter gene ZsGreen (ZsG). We also generated recombinant CHAV and MACV with and without the ZsG reporter gene. As a proof-of-concept study, we used both minigenomes and recombinant viruses to test the inhibitory effects of previously reported antiviral compounds. The new reverse genetics system described here will facilitate future therapeutic studies for these two life-threatening arenaviruses.
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Affiliation(s)
- Shilpi Jain
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Punya Shrivastava-Ranjan
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mike Flint
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joel M Montgomery
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Christina F Spiropoulou
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - César G Albariño
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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Jiang H, Wang T, Kong L, Li B, Peng Q. Reverse Genetics Systems for Emerging and Re-Emerging Swine Coronaviruses and Applications. Viruses 2023; 15:2003. [PMID: 37896780 PMCID: PMC10611186 DOI: 10.3390/v15102003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Emerging and re-emerging swine coronaviruses (CoVs), including porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), and swine acute diarrhea syndrome-CoV (SADS-CoV), cause severe diarrhea in neonatal piglets, and CoV infection is associated with significant economic losses for the swine industry worldwide. Reverse genetics systems realize the manipulation of RNA virus genome and facilitate the development of new vaccines. Thus far, five reverse genetics approaches have been successfully applied to engineer the swine CoV genome: targeted RNA recombination, in vitro ligation, bacterial artificial chromosome-based ligation, vaccinia virus -based recombination, and yeast-based method. This review summarizes the advantages and limitations of these approaches; it also discusses the latest research progress in terms of their use for virus-related pathogenesis elucidation, vaccine candidate development, antiviral drug screening, and virus replication mechanism determination.
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Affiliation(s)
- Hui Jiang
- Nanchang Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang 330045, China; (H.J.); (T.W.)
- Institute of Pathogenic Microorganism, Jiangxi Agricultural University, Nanchang 330045, China
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Ting Wang
- Nanchang Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang 330045, China; (H.J.); (T.W.)
- Institute of Pathogenic Microorganism, Jiangxi Agricultural University, Nanchang 330045, China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Lingbao Kong
- Nanchang Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang 330045, China; (H.J.); (T.W.)
- Institute of Pathogenic Microorganism, Jiangxi Agricultural University, Nanchang 330045, China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
| | - Qi Peng
- Nanchang Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang 330045, China; (H.J.); (T.W.)
- Institute of Pathogenic Microorganism, Jiangxi Agricultural University, Nanchang 330045, China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
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Takahashi T, Ueno S, Sugiura Y, Shimizu K, Kamitani W. Establishment of a new reverse genetics system for respiratory syncytial virus under the control of RNA polymerase II. Microbiol Immunol 2023; 67:413-421. [PMID: 37424190 DOI: 10.1111/1348-0421.13088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/30/2023] [Accepted: 06/20/2023] [Indexed: 07/11/2023]
Abstract
A reverse genetics system for the respiratory syncytial virus (RSV), which causes acute respiratory illness, is an effective tool for understanding the pathogenicity of RSV. To date, a method dependent on T7 RNA polymerase is commonly used for RSV. Although this method is well established and recombinant RSV is well rescued from transfected cells, the requirement for artificial supply of T7 RNA polymerase limits its application. To overcome this, we established a reverse genetics system dependent on RNA polymerase II, which is more convenient for the recovery of recombinant viruses from various cell lines. First, we identified human cell lines with high transfection efficiency in which RSV can replicate effectively. Two human cell lines, Huh-7 and 293T, permitted the propagation of recombinant green fluorescent protein-expressing RSV. Our minigenome system revealed that efficient transcription and replication of RSV occurred in both Huh-7 and 293T cells. We then confirmed that recombinant green fluorescent protein-expressing RSV was rescued in both Huh-7 and 293T cells. Furthermore, the growth capability of viruses rescued from Huh-7 and 293T cells was similar to that of recombinant RSV rescued using the conventional method. Thus, we succeeded in establishing a new reverse genetics system for RSV that is dependent on RNA polymerase II.
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Affiliation(s)
- Tatsuki Takahashi
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Maebashi-shi, Gunma, Japan
| | - Shiori Ueno
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Maebashi-shi, Gunma, Japan
| | - Yoshiro Sugiura
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Maebashi-shi, Gunma, Japan
| | - Kenta Shimizu
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Maebashi-shi, Gunma, Japan
| | - Wataru Kamitani
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Maebashi-shi, Gunma, Japan
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Komorizono R, Fujino K, Kessler S, Runge S, Kanda T, Horie M, Makino A, Rubbenstroth D, Tomonaga K. Reverse genetics of parrot bornavirus 4 reveals a unique splicing of the glycoprotein gene that affects viral propagation. J Virol 2023; 97:e0050923. [PMID: 37578232 PMCID: PMC10506466 DOI: 10.1128/jvi.00509-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/27/2023] [Indexed: 08/15/2023] Open
Abstract
Viruses can utilize host splicing machinery to enable the expression of multiple genes from a limited-sized genome. Orthobornaviruses use alternative splicing to regulate the expression level of viral proteins and achieve efficient viral replication in the nucleus. Although more than 20 orthobornaviruses have been identified belonging to eight different viral species, virus-specific splicing has not been demonstrated. Here, we demonstrate that the glycoprotein (G) transcript of parrot bornavirus 4 (PaBV-4; species Orthobornavirus alphapsittaciforme), a highly virulent virus in psittacines, undergoes mRNA splicing and expresses a soluble isoform termed sGP. Interestingly, the splicing donor for sGP is not conserved in other orthobornaviruses, including those belonging to the same orthobornavirus species, suggesting that this splicing has evolved as a PaBV-4-specific event. We have also shown that exogenous expression of sGP does not affect PaBV-4 replication or de novo virion infectivity. In this study, to investigate the role of sGP in viral replication, we established a reverse genetics system for PaBV-4 by using avian cell lines and generated a recombinant virus lacking the spliced mRNA for sGP. Using the recombinant viruses, we show that the replication of the sGP-deficient virus is significantly slower than that of the wild-type virus and that the exogenous expression of sGP cannot restore its propagation efficiency. These results suggest that autologous or controlled expression of sGP by splicing may be important for PaBV-4 propagation. The reverse genetics system for avian bornaviruses developed here will be a powerful tool for understanding the replication strategies and pathogenesis of avian orthobornaviruses. IMPORTANCE Parrot bornavirus 4 (PaBV-4) is the dominant cause of proventricular dilatation disease, a severe gastrointestinal and central nervous system disease among avian bornaviruses. In this study, we discovered that PaBV-4 expresses a soluble isoform of glycoprotein (G), called sGP, through alternative splicing of the G mRNA, which is unique to this virus. To understand the role of sGP in viral replication, we generated recombinant PaBV-4 lacking the newly identified splicing donor site for sGP using a reverse genetics system and found that its propagation was significantly slower than that of the wild-type virus, suggesting that sGP plays an essential role in PaBV-4 infection. Our results provide important insights not only into the replication strategy but also into the pathogenesis of PaBV-4, which is the most prevalent bornavirus in captive psittacines worldwide.
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Affiliation(s)
- Ryo Komorizono
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan
| | - Kan Fujino
- Laboratory of Microbiology, School of Veterinary Medicine, Azabu University, Kanagawa, Japan
- Institute of Virology, Medical Centre - University of Freiburg, Freiburg, Germany
| | - Susanne Kessler
- Institute of Virology, Medical Centre - University of Freiburg, Freiburg, Germany
| | - Solveig Runge
- Institute of Virology, Medical Centre - University of Freiburg, Freiburg, Germany
| | - Takehiro Kanda
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan
- Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masayuki Horie
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Akiko Makino
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan
- Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Dennis Rubbenstroth
- Institute of Virology, Medical Centre - University of Freiburg, Freiburg, Germany
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Insel, Riems, Germany
| | - Keizo Tomonaga
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan
- Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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18
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Conde JN, Himmler GE, Mladinich MC, Setoh YX, Amarilla AA, Schutt WR, Saladino N, Gorbunova EE, Salamango DJ, Benach J, Kim HK, Mackow ER. Establishment of a CPER reverse genetics system for Powassan virus defines attenuating NS1 glycosylation sites and an infectious NS1-GFP11 reporter virus. mBio 2023; 14:e0138823. [PMID: 37489888 PMCID: PMC10470542 DOI: 10.1128/mbio.01388-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 07/26/2023] Open
Abstract
Powassan virus (POWV) is an emerging tick-borne Flavivirus that causes lethal encephalitis and long-term neurologic damage. Currently, there are no POWV therapeutics, licensed vaccines, or reverse genetics systems for producing infectious POWVs from recombinant DNA. Using a circular polymerase extension reaction (CPER), we generated recombinant LI9 (recLI9) POWVs with attenuating NS1 protein mutations and a recLI9-split-eGFP reporter virus. NS1 proteins are highly conserved glycoproteins that regulate replication, spread, and neurovirulence. POWV NS1 contains three putative N-linked glycosylation sites that we modified individually in infectious recLI9 mutants (N85Q, N208Q, and N224Q). NS1 glycosylation site mutations reduced replication kinetics and were attenuated, with 1-2 log decreases in titer. Severely attenuated recLI9-N224Q exhibited a 2- to 3-day delay in focal cell-to-cell spread and reduced NS1 secretion but was lethal when intracranially inoculated into suckling mice. However, footpad inoculation of recLI9-N224Q resulted in the survival of 80% of mice and demonstrated that NS1-N224Q mutations reduce POWV neuroinvasion in vivo. To monitor NS1 trafficking, we CPER fused a split GFP11-tag to the NS1 C-terminus and generated an infectious reporter virus, recLI9-NS1-GFP11. Cells infected with recLI9-NS1-GFP11 revealed NS1 trafficking in live cells and the novel formation of large NS1-lined intracellular vesicles. An infectious recLI9-NS1-GFP11 reporter virus permits real-time analysis of NS1 functions in POWV replication, assembly, and secretion and provides a platform for evaluating antiviral compounds. Collectively, our robust POWV reverse genetics system permits analysis of viral spread and neurovirulence determinants in vitro and in vivo and enables the rational genetic design of live attenuated POWV vaccines. IMPORTANCE Our findings newly establish a mechanism for genetically modifying Powassan viruses (POWVs), systematically defining pathogenic determinants and rationally designing live attenuated POWV vaccines. This initial study demonstrates that mutating POWV NS1 glycosylation sites attenuates POWV spread and neurovirulence in vitro and in vivo. Our findings validate a robust circular polymerase extension reaction approach as a mechanism for developing, and evaluating, attenuated genetically modified POWVs. We further designed an infectious GFP-tagged reporter POWV that permits us to monitor secretory trafficking of POWV in live cells, which can be applied to screen potential POWV replication inhibitors. This robust system for modifying POWVs provides the ability to define attenuating POWV mutations and create genetically attenuated recPOWV vaccines.
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Affiliation(s)
- Jonas N. Conde
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Grace E. Himmler
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
- Molecular and Cell Biology Program, Stony Brook University, Stony Brook, New York, USA
| | - Megan C. Mladinich
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Yin Xiang Setoh
- Microbiology and Molecular Epidemiology Division, Environmental Health Institute, National Environmental Agency, Singapore, Singapore
| | - Alberto A. Amarilla
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - William R. Schutt
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- Center for Infectious Disease, Stony Brook University, Stony Brook, New York, USA
| | - Nicholas Saladino
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Elena E. Gorbunova
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- Center for Infectious Disease, Stony Brook University, Stony Brook, New York, USA
| | - Daniel J. Salamango
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Jorge Benach
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- Center for Infectious Disease, Stony Brook University, Stony Brook, New York, USA
| | - Hwan Keun Kim
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- Molecular and Cell Biology Program, Stony Brook University, Stony Brook, New York, USA
- Center for Infectious Disease, Stony Brook University, Stony Brook, New York, USA
| | - Erich R. Mackow
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- Molecular and Cell Biology Program, Stony Brook University, Stony Brook, New York, USA
- Center for Infectious Disease, Stony Brook University, Stony Brook, New York, USA
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Liu N, Gu C, Yang Y, Gao Z, Kang N, Liu J, Xie Y. Establishment and characterization of a novel reverse genetic system of BK polyomavirus. J Med Virol 2023; 95:e28995. [PMID: 37522259 DOI: 10.1002/jmv.28995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023]
Abstract
BK polyomavirus (BKV) is a small non-enveloped DNA virus. BKV infection or reactivation may cause BKV-associated nephropathy and hemorrhagic cystitis in immunosuppressed transplant recipients. No effective antivirals or prevention strategies are available against BKV infections. The current BKV reverse system employs the transfection of purified full-length linear viral genomes released by enzyme digestion from BKV genomic plasmids. The method is laborious and often results in variable DNA yield and quality, which can affect the efficiency of transfection and subsequent formation of circular viral genomes in cells. In this study, we report the generation of circular viral genomes by Cre-mediated DNA recombination in cells directly transfected with BKV precursor genomic plasmids. The novel system supported efficient viral expression and replication, and produced a higher level of infectious virions compared with the transfection with linear BKV genomes. Furthermore, we successfully constructed recombinant BKV capable of reporter gene expression. In conclusion, the novel BKV reverse genetic system allows for simpler manipulation of BKV genome with better virus yield, providing a tool for the study of BKV life cycle and antiviral screening.
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Affiliation(s)
- Nannan Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Diseases and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chenjian Gu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Diseases and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yang Yang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Diseases and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zixiang Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Diseases and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ning Kang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Diseases and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jing Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Diseases and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Youhua Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Diseases and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Clinical Laboratory, Children's Hospital, Fudan University, Shanghai, China
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Moroki Y, Komori M, Ogawa Y, Nagumo E, Ohno H, Fukamachi S. An Attempt to Identify the Medaka Receptor for Somatolactin Alpha Using a Reverse Genetics Approach. Genes (Basel) 2023; 14:genes14040796. [PMID: 37107554 PMCID: PMC10137387 DOI: 10.3390/genes14040796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/19/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Somatolactin alpha (SLα) is a fish-specific hormone involved in body color regulation. The growth hormone (GH) is another hormone that is expressed in all vertebrates and promotes growth. These peptide hormones act by binding to receptors (SLα receptor (SLR) and GH receptor (GHR)); however, the relationships between these ligands and their receptors vary among species. Here, we first performed phylogenetic tree reconstruction by collecting the amino-acid sequences classified as SLR, GHR, or GHR-like from bony fish. Second, we impaired SLR or GHR functions in medaka (Oryzias sakaizumii) using CRISPR/Cas9. Lastly, we analyzed SLR and GHR mutants for phenotypes to deduce their functions. Phylogenetic tree reconstruction was performed using a total of 222 amino-acid sequences from 136 species, which revealed that many GHRa and GHRb are vaguely termed as GHR or GHR-like, while showing no orthologous/paralogous relationships. SLR and GHR mutants were successfully established for phenotyping. SLR mutants exhibited premature lethality after hatching, indicating an essential role for SLR in normal growth. GHR mutations did not affect viability, body length, or body color. These results provide no evidence that either SLR or GHR functions as a receptor for SLα; rather, phylogenetically and functionally, they seem to be receptors for GH, although their (subfunctionalized) roles warrant further investigation.
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Choi WS, Oh S, Antigua KJC, Jeong JH, Kim BK, Yun YS, Kang DH, Min SC, Lim BK, Kim WS, Lee JH, Kim EG, Choi YK, Baek YH, Song MS. Development of a Universal Cloning System for Reverse Genetics of Human Enteroviruses. Microbiol Spectr 2023; 11:e0316722. [PMID: 36651758 PMCID: PMC9927166 DOI: 10.1128/spectrum.03167-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/13/2022] [Indexed: 01/19/2023] Open
Abstract
Enteroviruses (EVs) have been associated with several human diseases. Due to their continuous emergence and divergence, EV species have generated more than 100 types and recombinant strains, increasing the public health threat caused by them. Hence, an efficient and universal cloning system for reverse genetics (RG) of highly divergent viruses is needed to understand the molecular mechanisms of viral pathology and evolution. In this study, we generated a versatile human EV whole-genome cDNA template by enhancing the template-switching method and designing universal primers capable of simultaneous cloning and rapid amplification of cDNA ends (RACE)-PCR of EVs. Moreover, by devising strategies to overcome limitations of previous cloning methods, we simplified significant cloning steps to be completed within a day. Of note, we successfully verified our efficient universal cloning system enabling RG of a broad range of human EVs, including EV-A (EV-A71), EV-B (CV-B5, ECHO6, and ECHO30), EV-C (CV-A24), and EV-D (EV-D68), with viral titers and phenotypes comparable to those of their wild types. This rapid and straightforward universal EV cloning strategy will help us elucidate molecular characteristics, pathogenesis, and applications of a broad range of EV serotypes for further development of genetic vaccines and delivery tools using various replication systems. IMPORTANCE Due to the broad spread, incidence, and genetic divergence of enteroviruses (EVs), it has been challenging to deal with this virus that causes severe human diseases, including aseptic meningitis, myocarditis, encephalitis, and poliomyelitis. Therefore, an efficient and universal cloning system for the reverse genetics of highly divergent EVs contributes to an understanding of the viral pathology and molecular mechanisms of evolution. We have simplified the important cloning steps, hereby enhancing the template-switching method and designing universal primers, which enable the important cloning steps to be completed in a day. We have also successfully demonstrated recovery of a broad range of human EVs, including EV-A to -D types, using this advanced universal cloning system. This rapid and robust universal EV cloning strategy will aid in elucidating the molecular characteristics, pathogenesis, and applications of a wide range of EVs for further development of genetic vaccines and antiviral screening using various replication systems.
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Affiliation(s)
- Won-Suk Choi
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
- Microuni Co., Ltd., Cheongju, Chungbuk, Republic of Korea
| | - Sol Oh
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Khristine Joy C. Antigua
- Animal Health and Welfare Division, Bureau of Animal Industry (BAI), Department of Agriculture (DA), Quezon City, Philippines
| | - Ju Hwan Jeong
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Beom Kyu Kim
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Yu Soo Yun
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Da Hyeon Kang
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Seong Cheol Min
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Byung-Kwan Lim
- Department of Biomedical Science, Jungwon University, Goesan-gun, Chungbuk, Republic of Korea
| | - Won Seop Kim
- Department of Pediatrics, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Ji-Hyuk Lee
- Department of Pediatrics, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Eung-Gook Kim
- Department of Biochemistry, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Young Ki Choi
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Yun Hee Baek
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Min-Suk Song
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
- Microuni Co., Ltd., Cheongju, Chungbuk, Republic of Korea
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22
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Cheng J, Tang A, Chen J, Zhang D, Meng C, Li C, Wei H, Liu G. A cDNA-based reverse genetics system for feline calicivirus identifies the 3' untranslated region as an essential element for viral replication. Arch Virol 2023; 168:33. [PMID: 36609724 DOI: 10.1007/s00705-022-05695-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/14/2022] [Indexed: 01/09/2023]
Abstract
Virulent systemic feline calicivirus (VS-FCV) is a newly emerging FCV variant that is associated with a severe acute multisystem disease in cats that is characterized by jaundice, oedema, and high mortality (approximately 70%). VS-FCV has spread throughout the world, but there are no effective vaccines or therapeutic options to combat infection. VS-FCV may therefore pose a serious threat to the health of felines. The genomic characteristics and functions of VS-FCV are still poorly understood, and the reason for its increased pathogenicity is unknown. Reverse genetics systems are powerful tools for studying the molecular biology of RNA viruses, but a reverse genetics system for VS-FCV has not yet been reported. In this study, we developed a plasmid-based reverse genetics system for VS-FCV in which infectious progeny virus is produced in plasmid-transfected CRFK cells. Using this system, we found that the 3' untranslated region (UTR) and poly(A) tail are important for maintaining the infection and replication capacity of VS-FCV and that shortening of the poly(A) tail to less than 28 bases eliminated the ability to rescue infectious progeny virus. Whether these observations are unique to VS-FCV or represent more-general features of FCV remains to be determined. In conclusion, we successfully established a rapid and efficient VS-FCV reverse genetics system, which provides a good platform for future research on the gene functions and pathogenesis of VS-FCV. The effects of the deletion of 3' UTR and poly(A) tail on VS-FCV infectivity and replication also provided new information about the pathogenesis of VS-FCV.
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Affiliation(s)
- Jie Cheng
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Aoxing Tang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Jing Chen
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Da Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Chunchun Meng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Chuanfeng Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Hulai Wei
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China.
| | - Guangqing Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
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23
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Amaya M, Broder CC, Laing ED. Recombinant Cedar Virus: A Henipavirus Reverse Genetics Platform. Methods Mol Biol 2023; 2682:73-86. [PMID: 37610574 DOI: 10.1007/978-1-0716-3283-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The isolation of Cedar virus, a nonpathogenic henipavirus that is closely related to the highly pathogenic Nipah virus and Hendra virus, provides a new platform for henipavirus experimentation and a tool to investigate biological differences among these viruses under less stringent biological containment. Here, we detail a reverse genetics system used to rescue two replication-competent, recombinant Cedar virus variants: a recombinant wild-type Cedar virus and a recombinant Cedar virus that express a green fluorescent protein from an open reading frame inserted between the phosphoprotein and matrix genes. This recombinant Cedar virus platform may be utilized to characterize the determinants of pathogenesis across the henipaviruses, investigate their receptor tropisms, and identify novel pan-henipavirus antivirals safely under biosafety level-2 conditions.
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Affiliation(s)
- Moushimi Amaya
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Eric D Laing
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA.
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24
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Vogt E, Sonderegger L, Chen YY, Segessemann T, Künzler M. Structural and Functional Analysis of Peptides Derived from KEX2-Processed Repeat Proteins in Agaricomycetes Using Reverse Genetics and Peptidomics. Microbiol Spectr 2022; 10:e0202122. [PMID: 36314921 PMCID: PMC9769878 DOI: 10.1128/spectrum.02021-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/06/2022] [Indexed: 12/24/2022] Open
Abstract
Bioactivities of fungal peptides are of interest for basic research and therapeutic drug development. Some of these peptides are derived from "KEX2-processed repeat proteins" (KEPs), a recently defined class of precursor proteins that contain multiple peptide cores flanked by KEX2 protease cleavage sites. Genome mining has revealed that KEPs are widespread in the fungal kingdom. Their functions are largely unknown. Here, we present the first in-depth structural and functional analysis of KEPs in a basidiomycete. We bioinformatically identified KEP-encoding genes in the genome of the model agaricomycete Coprinopsis cinerea and established a detection protocol for the derived peptides by overexpressing the C. cinerea KEPs in the yeast Pichia pastoris. Using this protocol, which includes peptide extraction and mass spectrometry with data analysis using the search engine Mascot, we confirmed the presence of several KEP-derived peptides in C. cinerea, as well as in the edible mushrooms Lentinula edodes, Pleurotus ostreatus, and Pleurotus eryngii. While CRISPR-mediated knockout of C. cinerea kep genes did not result in any detectable phenotype, knockout of kex genes caused defects in mycelial growth and fruiting body formation. These results suggest that KEP-derived peptides may play a role in the interaction of C. cinerea with the biotic environment and that the KEP-processing KEX proteases target a variety of substrates in agaricomycetes, including some important for mycelial growth and differentiation. IMPORTANCE Two recent bioinformatics studies have demonstrated that KEX2-processed repeat proteins are widespread in the fungal kingdom. However, despite the prevalence of KEPs in fungal genomes, only few KEP-derived peptides have been detected and studied so far. Here, we present a protocol for the extraction and structural characterization of KEP-derived peptides from fungal culture supernatants and tissues. The protocol was successfully used to detect several linear and minimally modified KEP-derived peptides in the agaricomycetes C. cinerea, L. edodes, P. ostreatus, and P. eryngii. Our study establishes a new protocol for the targeted search of KEP-derived peptides in fungi, which will hopefully lead to the discovery of more of these interesting fungal peptides and allow a further characterization of KEPs.
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Affiliation(s)
- Eva Vogt
- ETH Zürich, Department of Biology, Institute of Microbiology, Zürich, Switzerland
| | - Lukas Sonderegger
- ETH Zürich, Department of Biology, Institute of Microbiology, Zürich, Switzerland
| | - Ying-Yu Chen
- ETH Zürich, Department of Biology, Institute of Microbiology, Zürich, Switzerland
| | - Tina Segessemann
- ETH Zürich, Department of Biology, Institute of Microbiology, Zürich, Switzerland
| | - Markus Künzler
- ETH Zürich, Department of Biology, Institute of Microbiology, Zürich, Switzerland
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25
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Lisboa RO, Sekula RF, Bezamat M, Deeley K, Santana-da-Silva LC, Vieira AR. Pain perception genes, asthma, and oral health: A reverse genetics study. PLoS One 2022; 17:e0277036. [PMID: 36395102 PMCID: PMC9671307 DOI: 10.1371/journal.pone.0277036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/18/2022] [Indexed: 11/19/2022] Open
Abstract
Pain is an experience of a subjective nature, interpreted in a personal way and according to an extensive palette of factors unique to each individual. Orofacial pain can be acute or chronic and it is usually the main reason for the patient to seek dental care. Pain perception varies widely among individuals. This variability is considered a mosaic of factors, which include biopsychosocial factors and genetic factors. Understanding these differences can be extremely beneficial for pain management in a personalized and more efficient way. We performed association studies to investigate phenotypes associated with genetic markers in pain-related genes in two groups of patients who received more or less anesthesia during dental treatment. The study group was comprised of 1289 individuals participating in the Dental Registry and DNA Repository Project (DRDR) of the University of Pittsburgh, with 900 participants in the group that received the most anesthesia and 389 constituting the comparison group that received less anesthesia. We tested 58 phenotypes and genotypic data of seven SNPs in genes that are associated with pain perception, pain modulation and response to drugs used in pain treatment: COMT (rs4818 and rs6269), GCH1 (rs3783641), DRD2 (rs6276), OPRM1 (rs1799971), SCN9A (rs6746030) and SCN10A (rs6795970). The analysis revealed a protective effect of rs1799971 on asthma in the total sample. rs3783641 was associated with salivary secretion disorders in females who received more anesthesia. rs1799971 was also associated with periodontitis in Whites who received less anesthesia. rs4818 was associated with disease and other tongue conditions in the group composed of Blacks who received less anesthesia. In conclusion, our study implicated variants in pain-related genes in asthma and oral phenotypes.
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Affiliation(s)
- Rosany O. Lisboa
- Laboratory of Inborn Errors of Metabolism, Institute of Biological Sciences, Federal University of Pará, Pará, Brazil
- Departments of Oral and Craniofacial Sciences, Pediatric Dentistry and Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Graduate Program in Oncology and Medical Sciences, Federal University of Pará, Pará, Brazil
| | - Raymond F. Sekula
- Department of Neurological Surgery, Columbia University Vagelos School of Medicine, New York, New York, United States of America
| | - Mariana Bezamat
- Departments of Oral and Craniofacial Sciences, Pediatric Dentistry and Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kathleen Deeley
- Departments of Oral and Craniofacial Sciences, Pediatric Dentistry and Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Luiz Carlos Santana-da-Silva
- Laboratory of Inborn Errors of Metabolism, Institute of Biological Sciences, Federal University of Pará, Pará, Brazil
- Graduate Program in Oncology and Medical Sciences, Federal University of Pará, Pará, Brazil
| | - Alexandre R. Vieira
- Departments of Oral and Craniofacial Sciences, Pediatric Dentistry and Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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26
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Kanda T, Tomonaga K. Reverse Genetics and Artificial Replication Systems of Borna Disease Virus 1. Viruses 2022; 14:v14102236. [PMID: 36298790 PMCID: PMC9612284 DOI: 10.3390/v14102236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/08/2022] [Accepted: 10/09/2022] [Indexed: 11/16/2022] Open
Abstract
Borna disease virus 1 (BoDV-1) is a neurotropic RNA virus belonging to the family Bornaviridae within the order Mononegavirales. Whereas BoDV-1 causes neurological and behavioral disorders, called Borna disease (BD), in a wide range of mammals, its virulence in humans has been debated for several decades. However, a series of case reports in recent years have established the nature of BoDV-1 as a zoonotic pathogen that causes fatal encephalitis in humans. Although many virological properties of BoDV-1 have been revealed to date, the mechanism by which it causes fatal encephalitis in humans remains unclear. In addition, there are no effective vaccines or antiviral drugs that can be used in clinical practice. A reverse genetics approach to generating replication-competent recombinant viruses from full-length cDNA clones is a powerful tool that can be used to not only understand viral properties but also to develop vaccines and antiviral drugs. The rescue of recombinant BoDV-1 (rBoDV-1) was first reported in 2005. However, due to the slow nature of the replication of this virus, the rescue of high-titer rBoDV-1 required several months, limiting the use of this system. This review summarizes the history of the reverse genetics and artificial replication systems for orthobornaviruses and explores the recent progress in efforts to rescue rBoDV-1.
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Affiliation(s)
- Takehiro Kanda
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
- Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Keizo Tomonaga
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
- Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan
- Correspondence:
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27
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Diebold O, Gonzalez V, Venditti L, Sharp C, Blake RA, Tan WS, Stevens J, Caddy S, Digard P, Borodavka A, Gaunt E. Using Species a Rotavirus Reverse Genetics to Engineer Chimeric Viruses Expressing SARS-CoV-2 Spike Epitopes. J Virol 2022; 96:e0048822. [PMID: 35758692 PMCID: PMC9327695 DOI: 10.1128/jvi.00488-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/31/2022] [Indexed: 02/02/2023] Open
Abstract
Species A rotavirus (RVA) vaccines based on live attenuated viruses are used worldwide in humans. The recent establishment of a reverse genetics system for rotoviruses (RVs) has opened the possibility of engineering chimeric viruses expressing heterologous peptides from other viral or microbial species in order to develop polyvalent vaccines. We tested the feasibility of this concept by two approaches. First, we inserted short SARS-CoV-2 spike peptides into the hypervariable region of the simian RV SA11 strain viral protein (VP) 4. Second, we fused the receptor binding domain (RBD) of the SARS-CoV-2 spike protein, or the shorter receptor binding motif (RBM) nested within the RBD, to the C terminus of nonstructural protein (NSP) 3 of the bovine RV RF strain, with or without an intervening Thosea asigna virus 2A (T2A) peptide. Mutating the hypervariable region of SA11 VP4 impeded viral replication, and for these mutants, no cross-reactivity with spike antibodies was detected. To rescue NSP3 mutants, we established a plasmid-based reverse genetics system for the bovine RV RF strain. Except for the RBD mutant that demonstrated a rescue defect, all NSP3 mutants delivered endpoint infectivity titers and exhibited replication kinetics comparable to that of the wild-type virus. In ELISAs, cell lysates of an NSP3 mutant expressing the RBD peptide showed cross-reactivity with a SARS-CoV-2 RBD antibody. 3D bovine gut enteroids were susceptible to infection by all NSP3 mutants, but cross-reactivity with SARS-CoV-2 RBD antibody was only detected for the RBM mutant. The tolerance of large SARS-CoV-2 peptide insertions at the C terminus of NSP3 in the presence of T2A element highlights the potential of this approach for the development of vaccine vectors targeting multiple enteric pathogens simultaneously. IMPORTANCE We explored the use of rotaviruses (RVs) to express heterologous peptides, using SARS-CoV-2 as an example. Small SARS-CoV-2 peptide insertions (<34 amino acids) into the hypervariable region of the viral protein 4 (VP4) of RV SA11 strain resulted in reduced viral titer and replication, demonstrating a limited tolerance for peptide insertions at this site. To test the RV RF strain for its tolerance for peptide insertions, we constructed a reverse genetics system. NSP3 was C-terminally tagged with SARS-CoV-2 spike peptides of up to 193 amino acids in length. With a T2A-separated 193 amino acid tag on NSP3, there was no significant effect on the viral rescue efficiency, endpoint titer, and replication kinetics. Tagged NSP3 elicited cross-reactivity with SARS-CoV-2 spike antibodies in ELISA. We highlight the potential for development of RV vaccine vectors targeting multiple enteric pathogens simultaneously.
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Affiliation(s)
- Ola Diebold
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Victoria Gonzalez
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Luca Venditti
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Colin Sharp
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Rosemary A. Blake
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Wenfang S. Tan
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Joanne Stevens
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Sarah Caddy
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paul Digard
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Alexander Borodavka
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Eleanor Gaunt
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
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28
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Kozhukhar N, Spadafora D, Rodriguez YAR, Alexeyev MF. A Method for In Situ Reverse Genetic Analysis of Proteins Involved mtDNA Replication. Cells 2022; 11:cells11142168. [PMID: 35883613 PMCID: PMC9316749 DOI: 10.3390/cells11142168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/29/2022] [Accepted: 07/10/2022] [Indexed: 02/01/2023] Open
Abstract
The unavailability of tractable reverse genetic analysis approaches represents an obstacle to a better understanding of mitochondrial DNA replication. Here, we used CRISPR-Cas9 mediated gene editing to establish the conditional viability of knockouts in the key proteins involved in mtDNA replication. This observation prompted us to develop a set of tools for reverse genetic analysis in situ, which we called the GeneSwap approach. The technique was validated by identifying 730 amino acid (aa) substitutions in the mature human TFAM that are conditionally permissive for mtDNA replication. We established that HMG domains of TFAM are functionally independent, which opens opportunities for engineering chimeric TFAMs with customized properties for studies on mtDNA replication, mitochondrial transcription, and respiratory chain function. Finally, we present evidence that the HMG2 domain plays the leading role in TFAM species-specificity, thus indicating a potential pathway for TFAM-mtDNA evolutionary co-adaptations.
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29
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Jiang C, Lei M, Guo Y, Gao G, Shi L, Jin Y, Cai Y, Himmelbach A, Zhou S, He Q, Yao X, Kan J, Haberer G, Duan F, Li L, Liu J, Zhang J, Spannagl M, Liu C, Stein N, Feng Z, Mascher M, Yang P. A reference-guided TILLING by amplicon-sequencing platform supports forward and reverse genetics in barley. Plant Commun 2022; 3:100317. [PMID: 35605197 PMCID: PMC9284286 DOI: 10.1016/j.xplc.2022.100317] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/13/2022] [Accepted: 03/11/2022] [Indexed: 05/26/2023]
Abstract
Barley is a diploid species with a genome smaller than those of other members of the Triticeae tribe, making it an attractive model for genetic studies in Triticeae crops. The recent development of barley genomics has created a need for a high-throughput platform to identify genetically uniform mutants for gene function investigations. In this study, we report an ethyl methanesulfonate (EMS)-mutagenized population consisting of 8525 M3 lines in the barley landrace "Hatiexi" (HTX), which we complement with a high-quality de novo assembly of a reference genome for this genotype. The mutation rate within the population ranged from 1.51 to 4.09 mutations per megabase, depending on the treatment dosage of EMS and the mutation discrimination platform used for genotype analysis. We implemented a three-dimensional DNA pooling strategy combined with multiplexed amplicon sequencing to create a highly efficient and cost-effective TILLING (targeting induced locus lesion in genomes) platform in barley. Mutations were successfully identified from 72 mixed amplicons within a DNA pool containing 64 individual mutants and from 56 mixed amplicons within a pool containing 144 individuals. We discovered abundant allelic mutants for dozens of genes, including the barley Green Revolution contributor gene Brassinosteroid insensitive 1 (BRI1). As a proof of concept, we rapidly determined the causal gene responsible for a chlorotic mutant by following the MutMap strategy, demonstrating the value of this resource to support forward and reverse genetic studies in barley.
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Affiliation(s)
- Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Miaomiao Lei
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yu Guo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Guangqi Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijie Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yanlong Jin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Cai
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Shenghui Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuefeng Yao
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jinhong Kan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Georg Haberer
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Fengying Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manuel Spannagl
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Chunming Liu
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Zongyun Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany.
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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30
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Hu X, Chen Z, Wu X, Ding Z, Zeng Q, Wu H. An Improved, Dual-Direction, Promoter-Driven, Reverse Genetics System for the Infectious Bursal Disease Virus (IBDV). Viruses 2022; 14:v14071396. [PMID: 35891377 PMCID: PMC9324645 DOI: 10.3390/v14071396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 12/10/2022] Open
Abstract
The infectious bursal disease virus (IBDV), one member of the Birnaviridae family, causes immunosuppression in young chickens by damaging the mature B cells of the bursa of Fabricius (BF), the central immune system of young chickens. The genome of IBDV is a bisegmented, double-strand RNA (dsRNA). Reverse genetics systems for IBDV allow the generation of genetically manipulated infectious virus via transfected plasmid DNA, encoding the two genomic viral RNA segments as well as major viral proteins. For this purpose, the minus-sense of both segment A and segment B are inserted into vectors between the polymerase I promoter and the corresponding terminator I. These plasmids facilitate the transcription of the viral minus-sense genome but copy the plus-sense genome as well viral protein translation depends on the activity of VP1 and VP3, when transfected into 293T cells. To further improve rescue efficiency, dual-direction promoters were generated based on the polymerase II promoter in the reverse direction in the backbone of the pCDNA3.0 vector. Therefore, the polymerase I promoter transcribes the viral minus-sense genome in the forward direction and the polymerase II promoter transcribes viral mRNA, translated into viral proteins that produce infectious IBDV. We also found that the rescue efficiency of transfecting two plasmids is significantly higher than that of transfecting four plasmids. In addition, this dual-direction promoter rescue system was used to generate R186A mutant IBDV since Arg186 is the arginine monomer-methylation site identified by LC–MS. Our data furtherly showed that the Arg186 monomer methylation mutant was due to a reduction in VP1 polymerase activity as well as virus replication, suggesting that the Arg186 methylation site is essential for IBDV replication.
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Affiliation(s)
- Xifeng Hu
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Zhimin Street, Qingshan Lake, Nanchang 330045, China; (X.H.); (Z.C.); (X.W.); (Z.D.); (Q.Z.)
- Jiangxi Provincial Key Laboratory for Animal Science and Technology, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zheng Chen
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Zhimin Street, Qingshan Lake, Nanchang 330045, China; (X.H.); (Z.C.); (X.W.); (Z.D.); (Q.Z.)
- Jiangxi Provincial Key Laboratory for Animal Science and Technology, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiangdong Wu
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Zhimin Street, Qingshan Lake, Nanchang 330045, China; (X.H.); (Z.C.); (X.W.); (Z.D.); (Q.Z.)
- Jiangxi Provincial Key Laboratory for Animal Science and Technology, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhen Ding
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Zhimin Street, Qingshan Lake, Nanchang 330045, China; (X.H.); (Z.C.); (X.W.); (Z.D.); (Q.Z.)
- Jiangxi Provincial Key Laboratory for Animal Science and Technology, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qinghua Zeng
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Zhimin Street, Qingshan Lake, Nanchang 330045, China; (X.H.); (Z.C.); (X.W.); (Z.D.); (Q.Z.)
- Jiangxi Provincial Key Laboratory for Animal Science and Technology, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Huansheng Wu
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Zhimin Street, Qingshan Lake, Nanchang 330045, China; (X.H.); (Z.C.); (X.W.); (Z.D.); (Q.Z.)
- Jiangxi Provincial Key Laboratory for Animal Science and Technology, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
- Correspondence:
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Bernard MC, Waldock J, Commandeur S, Strauß L, Trombetta CM, Marchi S, Zhou F, van de Witte S, van Amsterdam P, Ho S, Hoschler K, Lugovtsev V, Weir JP, Montomoli E, Cox RJ, Engelhardt OG, Friel D, Wagner R, Ollinger T, Germain S, Sediri-Schön H. Validation of a Harmonized Enzyme-Linked-Lectin-Assay (ELLA-NI) Based Neuraminidase Inhibition Assay Standard Operating Procedure (SOP) for Quantification of N1 Influenza Antibodies and the Use of a Calibrator to Improve the Reproducibility of the ELLA-NI With Reverse Genetics Viral and Recombinant Neuraminidase Antigens: A FLUCOP Collaborative Study. Front Immunol 2022; 13:909297. [PMID: 35784305 PMCID: PMC9248865 DOI: 10.3389/fimmu.2022.909297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/20/2022] [Indexed: 11/21/2022] Open
Abstract
Current vaccination strategies against influenza focus on generating an antibody response against the viral haemagglutination surface protein, however there is increasing interest in neuraminidase (NA) as a target for vaccine development. A critical tool for development of vaccines that target NA or include an NA component is available validated serology assays for quantifying anti-NA antibodies. Additionally serology assays have a critical role in defining correlates of protection in vaccine development and licensure. Standardisation of these assays is important for consistent and accurate results. In this study we first validated a harmonized enzyme-linked lectin assay (ELLA)- Neuraminidase Inhibition (NI) SOP for N1 influenza antigen and demonstrated the assay was precise, linear, specific and robust within classical acceptance criteria for neutralization assays for vaccine testing. Secondly we tested this SOP with NA from influenza B viruses and showed the assay performed consistently with both influenza A and B antigens. Third, we demonstrated that recombinant NA (rNA) could be used as a source of antigen in ELLA-NI. In addition to validating a harmonized SOP we finally demonstrated a clear improvement in inter-laboratory agreement across several studies by using a calibrator. Importantly we showed that the use of a calibrator significantly improved agreement when using different sources of antigen in ELLA-NI, namely reverse genetics viruses and recombinant NA. We provide a freely available and detailed harmonized SOP for ELLA-NI. Our results add to the growing body of evidence in support of developing biological standards for influenza serology.
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Affiliation(s)
| | - Joanna Waldock
- Influenza Resource Centre, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Sylvie Commandeur
- Department of Research and Development, Sanofi Pasteur, Marcy L’Etoile, France
| | - Lea Strauß
- Section viral vaccines, Virology Division, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany
| | | | - Serena Marchi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Fan Zhou
- Influenza Centre, Department of Clinical Sciences, University of Bergen, Bergen, Norway
| | | | | | - Sammy Ho
- UK Health Security Agency, Colindale, United Kingdom
| | | | - Vladimir Lugovtsev
- Laboratory of DNA Viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Jerry P. Weir
- Laboratory of DNA Viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Emanuele Montomoli
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Rebecca J. Cox
- Influenza Centre, Department of Clinical Sciences, University of Bergen, Bergen, Norway
| | - Othmar G. Engelhardt
- Influenza Resource Centre, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | | | - Ralf Wagner
- Section viral vaccines, Virology Division, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany
| | | | | | - Hanna Sediri-Schön
- Section viral vaccines, Virology Division, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany
- *Correspondence: Hanna Sediri-Schön,
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Kumar J, Kumar A, Sen Gupta D, Kumar S, DePauw RM. Reverse genetic approaches for breeding nutrient-rich and climate-resilient cereal and food legume crops. Heredity (Edinb) 2022; 128:473-496. [PMID: 35249099 PMCID: PMC9178024 DOI: 10.1038/s41437-022-00513-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/21/2022] Open
Abstract
In the last decade, advancements in genomics tools and techniques have led to the discovery of many genes. Most of these genes still need to be characterized for their associated function and therefore, such genes remain underutilized for breeding the next generation of improved crop varieties. The recent developments in different reverse genetic approaches have made it possible to identify the function of genes controlling nutritional, biochemical, and metabolic traits imparting drought, heat, cold, salinity tolerance as well as diseases and insect-pests. This article focuses on reviewing the current status and prospects of using reverse genetic approaches to breed nutrient-rich and climate resilient cereal and food legume crops.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sachin Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Ron M DePauw
- Advancing Wheat Technologies, 118 Strathcona Rd SW, Calgary, AB, T3H 1P3, Canada
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Cao Z, Chen J, Li L, Liu J, Tong W, Zhou Y, Tong G, Wang G, Gao F. A rescued NADC30-like virus by reverse genetic manipulation exhibits moderate virulence and a promising application perspective. Virus Res 2022; 316:198801. [PMID: 35550390 DOI: 10.1016/j.virusres.2022.198801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/06/2022] [Accepted: 05/07/2022] [Indexed: 12/15/2022]
Abstract
NADC30-like porcine reproductive and respiratory syndrome virus (PRRSV), which is highly homologous to the NADC30 strain isolated in the United States. The NADC30-like PRRSV was first reported in 2014 in China, where it spread and gradually caused an epidemic. Currently, growing research has shown that NADC30-like strains have greater propensity to recombine with other PRRSV strains, particularly the PPRSV vaccine virus used clinically, making the prevention and control of PRRSV highly complex. To carry out an in-depth molecular biology and virulence analysis, a full-length infectious clone of the NADC30-like strain was successfully constructed and rescued by reverse genetic manipulation. The rescued virus, rZJqz, was indistinguishable from its parental virus, ZJqz21, based on virological characteristics. Further animal experiments demonstrated that rZJqz retained similar pathogenicity and induced the typical clinical symptoms and viral shedding observed in the ZJqz21 challenge model. Together, these results provide a useful tool for further study of the biological characteristics and pathogenicity of NADC30-like strains. Moreover, these findings also provide a solid foundation for studying the recombination of different PRRSVs and developing new and effective universal vaccines in the future.
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Affiliation(s)
- Zhengda Cao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China; Shandong Agricultural University, Shandong, 271018, China
| | - Jinxia Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Liwei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Jiachen Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Yanjun Zhou
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Guihua Wang
- Shandong Agricultural University, Shandong, 271018, China.
| | - Fei Gao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
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Fang X, Qiao J, Zang Y, Gao Q, Xu W, Gao D, Yang Y, Xie L, Wang Y, Wang X. Developing reverse genetics systems of northern cereal mosaic virus to reveal superinfection exclusion of two cytorhabdoviruses in barley plants. Mol Plant Pathol 2022; 23:749-756. [PMID: 35124878 PMCID: PMC8995060 DOI: 10.1111/mpp.13188] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 06/11/2023]
Abstract
Recently, reverse genetics systems of plant negative-stranded RNA (NSR) viruses have been developed to study virus-host interactions. Nonetheless, genetic rescue of plant NSR viruses in both insect vectors and monocot plants is very limited. Northern cereal mosaic virus (NCMV), a plant cytorhabdovirus, causes severe diseases in cereal plants through transmission by the small brown planthopper (SBPH, Laodelphax striatellus) in a propagative manner. In this study, we first developed a minireplicon system of NCMV in Nicotiana benthamiana plants, and then recovered a recombinant NCMV virus (rNCMV-RFP), with a red fluorescent protein (RFP) insertion, in SBPHs and barley plants. We further used rNCMV-RFP and green fluorescent protein (GFP)-tagged barley yellow striate mosaic virus (rBYSMV-GFP), a closely related cytorhabdovirus, to study superinfection exclusion, a widely observed phenomenon in dicot plants rarely studied in monocot plants. Interestingly, cellular superinfection exclusion of rBYSMV-GFP and rNCMV-RFP was observed in barley leaves. Our results demonstrate that two insect-transmitted cytorhabdoviruses are enemies rather than friends at the cellular level during coinfections in plants.
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Affiliation(s)
- Xiao‐Dong Fang
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Ji‐Hui Qiao
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Ying Zang
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Qiang Gao
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
- College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Wen‐Ya Xu
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Dong‐Min Gao
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yi‐Zhou Yang
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Liang Xie
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Ying Wang
- College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Xian‐Bing Wang
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
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Hume AJ, Heiden B, Olejnik J, Suder EL, Ross S, Scoon WA, Bullitt E, Ericsson M, White MR, Turcinovic J, Thao TTN, Hekman RM, Kaserman JE, Huang J, Alysandratos KD, Toth GE, Jakab F, Kotton DN, Wilson AA, Emili A, Thiel V, Connor JH, Kemenesi G, Cifuentes D, Mühlberger E. Recombinant Lloviu virus as a tool to study viral replication and host responses. PLoS Pathog 2022; 18:e1010268. [PMID: 35120176 PMCID: PMC8849519 DOI: 10.1371/journal.ppat.1010268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 02/16/2022] [Accepted: 01/11/2022] [Indexed: 01/06/2023] Open
Abstract
Next generation sequencing has revealed the presence of numerous RNA viruses in animal reservoir hosts, including many closely related to known human pathogens. Despite their zoonotic potential, most of these viruses remain understudied due to not yet being cultured. While reverse genetic systems can facilitate virus rescue, this is often hindered by missing viral genome ends. A prime example is Lloviu virus (LLOV), an uncultured filovirus that is closely related to the highly pathogenic Ebola virus. Using minigenome systems, we complemented the missing LLOV genomic ends and identified cis-acting elements required for LLOV replication that were lacking in the published sequence. We leveraged these data to generate recombinant full-length LLOV clones and rescue infectious virus. Similar to other filoviruses, recombinant LLOV (rLLOV) forms filamentous virions and induces the formation of characteristic inclusions in the cytoplasm of the infected cells, as shown by electron microscopy. Known target cells of Ebola virus, including macrophages and hepatocytes, are permissive to rLLOV infection, suggesting that humans could be potential hosts. However, inflammatory responses in human macrophages, a hallmark of Ebola virus disease, are not induced by rLLOV. Additional tropism testing identified pneumocytes as capable of robust rLLOV and Ebola virus infection. We also used rLLOV to test antivirals targeting multiple facets of the replication cycle. Rescue of uncultured viruses of pathogenic concern represents a valuable tool in our arsenal for pandemic preparedness. Due to increasing utilization of high-throughput sequencing technologies, RNA sequences of many unknown viruses have been discovered in bats and other animal species. Research on the pathogenic potential of these viruses is hampered by incomplete viral genome sequences and difficulties in isolating infectious virus from the animal hosts. One example of these potentially zoonotic pathogens is Lloviu virus (LLOV), a filovirus which is closely related to Ebola virus. Here we applied molecular virological approaches, including minigenome assays, to complement the incomplete LLOV genome ends with sequences from related viruses and identify cis-acting elements required for LLOV replication and transcription that were missing in the published LLOV sequence. The resulting full-length clones were used to generate infectious recombinant LLOV. We used this virus for electron microscopic analyses, infection studies in human cells, host response analysis, and antiviral drug testing. Our results provide new insights into the pathogenic potential of LLOV and delineate a roadmap for studying uncultured viruses.
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Affiliation(s)
- Adam J. Hume
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
- * E-mail: (AJH); (EM)
| | - Baylee Heiden
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Judith Olejnik
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Ellen L. Suder
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Stephen Ross
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
- Department of Biochemistry, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Whitney A. Scoon
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Esther Bullitt
- Department of Physiology & Biophysics, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Maria Ericsson
- Department of Cell Biology, Harvard Medical School; Boston, Massachusetts, United States of America
| | - Mitchell R. White
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
- Program in Bioinformatics, Boston University; Boston, Massachusetts, United States of America
| | - Tran T. N. Thao
- Institute of Virology and Immunology (IVI); Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern; Bern, Switzerland
| | - Ryan M. Hekman
- Department of Biochemistry, Boston University School of Medicine; Boston, Massachusetts, United States of America
- Center for Network Systems Biology, Boston University; Boston, Massachusetts, United States of America
| | - Joseph E. Kaserman
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Gabor E. Toth
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre, University of Pécs; Pécs, Hungary
| | - Ferenc Jakab
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre, University of Pécs; Pécs, Hungary
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston Medical Center; Boston, Massachusetts, United States of America
| | - Andrew A. Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Andrew Emili
- Department of Biochemistry, Boston University School of Medicine; Boston, Massachusetts, United States of America
- Center for Network Systems Biology, Boston University; Boston, Massachusetts, United States of America
- Department of Biology, Boston University; Boston, Massachusetts, United States of America
| | - Volker Thiel
- Institute of Virology and Immunology (IVI); Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern; Bern, Switzerland
| | - John H. Connor
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Gabor Kemenesi
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre, University of Pécs; Pécs, Hungary
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
- * E-mail: (AJH); (EM)
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Liu S, Magne K, Daniel S, Sibout R, Ratet P. Brachypodium distachyon UNICULME4 and LAXATUM-A are redundantly required for development. Plant Physiol 2022; 188:363-381. [PMID: 34662405 PMCID: PMC8774750 DOI: 10.1093/plphys/kiab456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
In cultivated grasses, tillering, leaf, and inflorescence architecture, as well as abscission ability, are major agronomical traits. In barley (Hordeum vulgare), maize (Zea mays), rice (Oryza sativa), and brachypodium (Brachypodium distachyon), NOOT-BOP-COCH-LIKE (NBCL) genes are essential regulators of vegetative and reproductive development. Grass species usually possess 2-4 NBCL copies and until now a single study in O. sativa showed that the disruption of all NBCL genes strongly altered O. sativa leaf development. To improve our understanding of the role of NBCL genes in grasses, we extended the study of the two NBCL paralogs BdUNICULME4 (CUL4) and BdLAXATUM-A (LAXA) in the nondomesticated grass B. distachyon. For this, we applied reversed genetics and generated original B. distachyon single and double nbcl mutants by clustered regularly interspaced short palindromic repeats - CRISPR associated protein 9 (CRISPR-Cas9) approaches and genetic crossing between nbcl targeting induced local lesions in genomes (TILLING) mutants. Through the study of original single laxa CRISPR-Cas9 null alleles, we validated functions previously proposed for LAXA in tillering, leaf patterning, inflorescence, and flower development and also unveiled roles for these genes in seed yield. Furthermore, the characterization of cul4laxa double mutants revealed essential functions for nbcl genes in B. distachyon development, especially in the regulation of tillering, stem cell elongation and secondary cell wall composition as well as for the transition toward the reproductive phase. Our results also highlight recurrent antagonist interactions between NBCLs occurring in multiple aspects of B. distachyon development.
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Affiliation(s)
- Shengbin Liu
- Université Paris-Saclay, INRAE, CNRS, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay 91405, France
| | - Kévin Magne
- Université Paris-Saclay, INRAE, CNRS, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay 91405, France
| | - Sylviane Daniel
- UR1268 BIA (Biopolymères Interactions Assemblages), INRAE, Nantes 44300, France
| | - Richard Sibout
- UR1268 BIA (Biopolymères Interactions Assemblages), INRAE, Nantes 44300, France
| | - Pascal Ratet
- Université Paris-Saclay, INRAE, CNRS, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay 91405, France
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Suzuki T, Saito A. [Advances in the reverse genetics system for RNA viruses]. Nihon Yakurigaku Zasshi 2022; 157:134-138. [PMID: 35228446 DOI: 10.1254/fpj.21072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
RNA viruses are responsible for several infectious diseases, including dengue fever, Zika fever, and COVID-19. Reverse genetics is a powerful tool to elucidate which domain or mutations in RNA viruses determine their pathogenicity and ability to evade antiviral drugs and host immune response. Previous reverse genetics systems for flaviviruses and coronaviruses have been technically challenging and time-consuming, thereby hampering the further understanding of events during viral evolution. A novel reverse genetics system-circular polymerase extension reaction (CPER)-has been developed to overcome this limitation. CPER is based on PCR-mediated assembly of DNA fragments that encode the whole genome of these viruses. CPER requires a relatively short time to introduce specific mutations into the viral genome of flaviviruses and SARS-CoV-2. In this review article, we explain the mode of action of this system and discuss the future direction of reverse genetics for RNA viruses.
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Affiliation(s)
- Tatsuya Suzuki
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University
| | - Akatsuki Saito
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki
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38
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Ghazy NA, Suzuki T. Environmental RNAi-based reverse genetics in the predatory mite Neoseiulus californicus: Towards improved methods of biological control. Pestic Biochem Physiol 2022; 180:104993. [PMID: 34955179 DOI: 10.1016/j.pestbp.2021.104993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/31/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
The predatory mite Neoseiulus californicus (McGregor) (Mesostigmata: Phytoseiidae) has been commercialized by manufacturers in the pest control industry and is used worldwide as a natural enemy of spider mites. However, because its genome has not been sequenced, reverse genetics techniques that could be used to analyze gene function have not been established. Here we partially sequenced the gene that encodes the vacuolar-type H+-ATPase (V-ATPase), an ATP-dependent proton pump, in N. californicus (NcVATPase) and then conducted a functional analysis using environmental RNA interference (eRNAi) by orally administering sequence-specific exogenous dsRNA (dsRNA-NcVATPase) to larvae and adult females. The larvae treated with dsRNA-NcVATPase took longer to develop and had lower survivorship, fecundity, and offspring viability at the adult stage than those treated with a control dsRNA. Adult females treated with dsRNA-NcVATPase showed significant reductions in survival, fecundity, and prey consumption, and their endogenous gene expression level of NcVATPase was reduced by approximately 65% compared with the control. Our findings suggest that the NcVATPase gene, silencing of which inhibits feeding and reproduction, is an excellent biomarker for investigating the eRNAi mechanism in N. californicus. The highly efficient experimental system of eRNAi established in this study paves the way for applied research using eRNAi to enhance the predatory ability of N. californicus.
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Affiliation(s)
- Noureldin Abuelfadl Ghazy
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan; Agriculture Zoology Department, Faculty of Agriculture, Mansoura University, 35516 El-Mansoura, Egypt; Japan Society for the Promotion of Science, Chiyoda, Tokyo 102-0083, Japan.
| | - Takeshi Suzuki
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan; Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8538, Japan.
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Ricardo-Lax I, Luna JM, Thao TTN, Le Pen J, Yu Y, Hoffmann HH, Schneider WM, Razooky BS, Fernandez-Martinez J, Schmidt F, Weisblum Y, Trüeb BS, Berenguer Veiga I, Schmied K, Ebert N, Michailidis E, Peace A, Sánchez-Rivera FJ, Lowe SW, Rout MP, Hatziioannou T, Bieniasz PD, Poirier JT, MacDonald MR, Thiel V, Rice CM. Replication and single-cycle delivery of SARS-CoV-2 replicons. Science 2021; 374:1099-1106. [PMID: 34648371 PMCID: PMC9007107 DOI: 10.1126/science.abj8430] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 10/06/2021] [Indexed: 01/16/2023]
Abstract
Molecular virology tools are critical for basic studies of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and for developing new therapeutics. Experimental systems that do not rely on viruses capable of spread are needed for potential use in lower-containment settings. In this work, we use a yeast-based reverse genetics system to develop spike-deleted SARS-CoV-2 self-replicating RNAs. These noninfectious self-replicating RNAs, or replicons, can be trans-complemented with viral glycoproteins to generate replicon delivery particles for single-cycle delivery into a range of cell types. This SARS-CoV-2 replicon system represents a convenient and versatile platform for antiviral drug screening, neutralization assays, host factor validation, and viral variant characterization.
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Affiliation(s)
- Inna Ricardo-Lax
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Joseph M. Luna
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Tran Thi Nhu Thao
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Jérémie Le Pen
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Yingpu Yu
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - H.-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - William M. Schneider
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Brandon S. Razooky
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | | | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Bettina Salome Trüeb
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Inês Berenguer Veiga
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Kimberly Schmied
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Avery Peace
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | | | - Scott W. Lowe
- Cancer Biology and Genetics, MSKCC, New York, NY 10065, USA
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | | | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - John T. Poirier
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Margaret R. MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
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Muruato A, Vu MN, Johnson BA, Davis-Gardner ME, Vanderheiden A, Lokugamage K, Schindewolf C, Crocquet-Valdes PA, Langsjoen RM, Plante JA, Plante KS, Weaver SC, Debbink K, Routh AL, Walker D, Suthar MS, Shi PY, Xie X, Menachery VD. Mouse-adapted SARS-CoV-2 protects animals from lethal SARS-CoV challenge. PLoS Biol 2021; 19:e3001284. [PMID: 34735434 PMCID: PMC8594810 DOI: 10.1371/journal.pbio.3001284] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/16/2021] [Accepted: 10/17/2021] [Indexed: 01/16/2023] Open
Abstract
The emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has resulted in a pandemic causing significant damage to public health and the economy. Efforts to understand the mechanisms of Coronavirus Disease 2019 (COVID-19) have been hampered by the lack of robust mouse models. To overcome this barrier, we used a reverse genetic system to generate a mouse-adapted strain of SARS-CoV-2. Incorporating key mutations found in SARS-CoV-2 variants, this model recapitulates critical elements of human infection including viral replication in the lung, immune cell infiltration, and significant in vivo disease. Importantly, mouse adaptation of SARS-CoV-2 does not impair replication in human airway cells and maintains antigenicity similar to human SARS-CoV-2 strains. Coupled with the incorporation of mutations found in variants of concern, CMA3p20 offers several advantages over other mouse-adapted SARS-CoV-2 strains. Using this model, we demonstrate that SARS-CoV-2-infected mice are protected from lethal challenge with the original Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), suggesting immunity from heterologous Coronavirus (CoV) strains. Together, the results highlight the use of this mouse model for further study of SARS-CoV-2 infection and disease.
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Affiliation(s)
- Antonio Muruato
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Michelle N. Vu
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Bryan A. Johnson
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Meredith E. Davis-Gardner
- Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Abigail Vanderheiden
- Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Kumari Lokugamage
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Craig Schindewolf
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | | | - Rose M. Langsjoen
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jessica A. Plante
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kenneth S. Plante
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Scott C. Weaver
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kari Debbink
- Department of Natural Science, Bowie State University, Bowie, Maryland, United States of America
| | - Andrew L. Routh
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - David Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Mehul S. Suthar
- Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | - Pei-Yong Shi
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Xuping Xie
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Vineet D. Menachery
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
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Nabi RBS, Rolly NK, Tayade R, Khan M, Shahid M, Yun BW. Enhanced Resistance of atbzip62 against Pseudomonas syringae pv. tomato Suggests Negative Regulation of Plant Basal Defense and Systemic Acquired Resistance by AtbZIP62 Transcription Factor. Int J Mol Sci 2021; 22:ijms222111541. [PMID: 34768971 PMCID: PMC8584143 DOI: 10.3390/ijms222111541] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
The intrinsic defense mechanisms of plants toward pathogenic bacteria have been widely investigated for years and are still at the center of interest in plant biosciences research. This study investigated the role of the AtbZIP62 gene encoding a transcription factor (TF) in the basal defense and systemic acquired resistance in Arabidopsis using the reverse genetics approach. To achieve that, the atbzip62 mutant line (lacking the AtbZIP62 gene) was challenged with Pseudomonas syringae pv. tomato (Pst DC3000) inoculated by infiltration into Arabidopsis leaves at the rosette stage. The results indicated that atbzip62 plants showed an enhanced resistance phenotype toward Pst DC3000 vir over time compared to Col-0 and the susceptible disease controls, atgsnor1-3 and atsid2. In addition, the transcript accumulation of pathogenesis-related genes, AtPR1 and AtPR2, increased significantly in atbzip62 over time (0–72 h post-inoculation, hpi) compared to that of atgsnor1-3 and atsid2 (susceptible lines), with AtPR1 prevailing over AtPR2. When coupled with the recorded pathogen growth (expressed as a colony-forming unit, CFU mL−1), the induction of PR genes, associated with the salicylic acid (SA) defense signaling, in part explained the observed enhanced resistance of atbzip62 mutant plants in response to Pst DC3000 vir. Furthermore, when Pst DC3000 avrB was inoculated, the expression of AtPR1 was upregulated in the systemic leaves of Col-0, while that of AtPR2 remained at a basal level in Col-0. Moreover, the expression of AtAZI (a systemic acquired resistance -related) gene was significantly upregulated at all time points (0–24 h post-inoculation, hpi) in atbzip62 compared to Col-0 and atgsnor1-3 and atsid2. Under the same conditions, AtG3DPH exhibited a high transcript accumulation level 48 hpi in the atbzip62 background. Therefore, all data put together suggest that AtPR1 and AtPR2 coupled with AtAZI and AtG3DPH, with AtAZI prevailing over AtG3DPH, would contribute to the recorded enhanced resistance phenotype of the atbzip62 mutant line against Pst DC3000. Thus, the AtbZIP62 TF is proposed as a negative regulator of basal defense and systemic acquired resistance in plants under Pst DC3000 infection.
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Affiliation(s)
- Rizwana Begum Syed Nabi
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (R.B.S.N.); (N.K.R.); (M.K.); (M.S.)
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Nkulu Kabange Rolly
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (R.B.S.N.); (N.K.R.); (M.K.); (M.S.)
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Korea
- National Laboratory of Seed Testing, National Seed Service, SENASEM, Ministry of Agriculture, Kinshasa 904KIN1, Democratic Republic of the Congo
| | - Rupesh Tayade
- Laboratory of Plant Breeding, School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea;
| | - Murtaza Khan
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (R.B.S.N.); (N.K.R.); (M.K.); (M.S.)
| | - Muhammad Shahid
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (R.B.S.N.); (N.K.R.); (M.K.); (M.S.)
- Agriculture Research Institute Mingora, Swat 19130, Khyber Pakhtunkhwa, Pakistan
| | - Byung-Wook Yun
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (R.B.S.N.); (N.K.R.); (M.K.); (M.S.)
- Correspondence: ; Tel.: +82-53-950-5712
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Ding S, Greenberg HB. Perspectives for the optimization and utility of the rotavirus reverse genetics system. Virus Res 2021; 303:198500. [PMID: 34331991 DOI: 10.1016/j.virusres.2021.198500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 11/21/2022]
Abstract
Following Kobayashi and colleagues' seminal paper in 20171, in the past four years the rotavirus (RV) field has witnessed a burst in research and publications based on the use of a fully plasmid-based RV reverse genetics systems and subsequent modifications2,3. However, in most cases, the rotaviral strain under interrogation has been the prototypic simian RV SA11-L2 strain (G3P[2]). Of note, a variety of other weakly-to-modestly replication-competent animal and human RV strains, bioluminescent and fluorescent reporter viruses, and clinical isolates of human RVs have proved hard or impossible to rescue using the original reverse genetics system2,4, highlighting a critical need to further enhance the recovery efficiency and expand the rescue tool kit. A number of further modifications of the initial reverse genetics system have enabled the rescue of other RV strains such as the human RV KU and CDC-9 strains, and a murine RV D6/2-like strain4,5. Here, we discuss future possible modifications of existing RV reverse genetics systems to further increase efficiency based on past experience with the improvement of influenza A virus recovery. The development of RV to accommodate the insertion and expression of heterologous sequences has substantial potential in the design of next-generation RV vaccine candidates and enteric viral vectors.
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Affiliation(s)
- Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Harry B Greenberg
- Department of Medicine, Division of Gastroenterology and Hepatology, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA; VA Palo Alto Health Care System, Department of Veterans Affairs, Palo Alto, CA, USA.
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Feng M, Li L, Cheng R, Yuan Y, Dong Y, Chen M, Guo R, Yao M, Xu Y, Zhou Y, Wu J, Ding XS, Zhou X, Tao X. Development of a Mini-Replicon-Based Reverse-Genetics System for Rice Stripe Tenuivirus. J Virol 2021; 95:e0058921. [PMID: 33952642 PMCID: PMC8223943 DOI: 10.1128/jvi.00589-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/26/2021] [Indexed: 01/27/2023] Open
Abstract
Negative-stranded RNA (NSR) viruses include both animal- and plant-infecting viruses that often cause serious diseases in humans and livestock and in agronomic crops. Rice stripe tenuivirus (RSV), a plant NSR virus with four negative-stranded/ambisense RNA segments, is one of the most destructive rice pathogens in many Asian countries. Due to the lack of a reliable reverse-genetics technology, molecular studies of RSV gene functions and its interaction with host plants are severely hampered. To overcome this obstacle, we developed a mini-replicon-based reverse-genetics system for RSV gene functional analysis in Nicotiana benthamiana. We first developed a mini-replicon system expressing an RSV genomic RNA3 enhanced green fluorescent protein (eGFP) reporter [MR3(-)eGFP], a nucleocapsid (NP), and a codon usage-optimized RNA-dependent RNA polymerase (RdRpopt). Using this mini-replicon system, we determined that RSV NP and RdRpopt are indispensable for the eGFP expression from MR3(-)eGFP. The expression of eGFP from MR3(-)eGFP can be significantly enhanced in the presence of four viral suppressors of RNA silencing (VSRs), NSs, and P19-HcPro-γb. In addition, NSvc4, the movement protein of RSV, facilitated eGFP trafficking between cells. We also developed an antigenomic RNA3-based replicon in N. benthamiana. However, we found that the RSV NS3 coding sequence acts as a cis element to regulate viral RNA expression. Finally, we made mini-replicons representing all four RSV genomic RNAs. This is the first mini-replicon-based reverse-genetics system for monocot-infecting tenuivirus. We believe that the mini-replicon system described here will allow studies of the RSV replication, transcription, cell-to-cell movement, and host machinery underpinning RSV infection in plants. IMPORTANCE Plant-infecting segmented negative-stranded RNA (NSR) viruses are grouped into three genera: Orthotospovirus, Tenuivirus, and Emaravirus. Reverse-genetics systems have been established for members of the genera Orthotospovirus and Emaravirus. However, there is still no reverse-genetics system available for Tenuivirus. Rice stripe virus (RSV) is a monocot-infecting tenuivirus with four negative-stranded/ambisense RNA segments. It is one of the most destructive rice pathogens and causes significant damage to the rice industry in Asian countries. Due to the lack of a reliable reverse-genetics system, molecular characterizations of RSV gene functions and the host machinery underpinning RSV infection in plants are extremely difficult. To overcome this obstacle, we developed a mini-replicon-based reverse-genetics system for RSV in Nicotiana benthamiana. This is the first mini-replicon-based reverse-genetics system for tenuivirus. We consider that this system will provide researchers a new working platform to elucidate the molecular mechanisms dictating segmented tenuivirus infections in plants.
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Affiliation(s)
- Mingfeng Feng
- Key Laboratory of Plant Immunity, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Luyao Li
- Key Laboratory of Plant Immunity, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Ruixiang Cheng
- Key Laboratory of Plant Immunity, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Yulong Yuan
- Key Laboratory of Plant Immunity, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Yongxin Dong
- Key Laboratory of Plant Immunity, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Minglong Chen
- Key Laboratory of Plant Immunity, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Rong Guo
- Key Laboratory of Plant Immunity, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Min Yao
- Key Laboratory of Plant Immunity, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Yi Xu
- Key Laboratory of Plant Immunity, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Yijun Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, People’s Republic of China
| | - Jianxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People’s Republic of China
| | - Xin Shun Ding
- Key Laboratory of Plant Immunity, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People’s Republic of China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Xiaorong Tao
- Key Laboratory of Plant Immunity, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People’s Republic of China
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Abstract
Several recently developed high-throughput techniques have changed the field of molecular virology. For example, proteomics studies reveal complete interactomes of a viral protein, genome-wide CRISPR knockout and activation screens probe the importance of every single human gene in aiding or fighting a virus, and ChIP-seq experiments reveal genome-wide epigenetic changes in response to infection. Deep mutational scanning is a relatively novel form of protein science which allows the in-depth functional analysis of every nucleotide within a viral gene or genome, revealing regions of importance, flexibility, and mutational potential. In this review, we discuss the application of this technique to RNA viruses including members of the Flaviviridae family, Influenza A Virus and Severe Acute Respiratory Syndrome Coronavirus 2. We also briefly discuss the reverse genetics systems which allow for analysis of viral replication cycles, next-generation sequencing technologies and the bioinformatics tools that facilitate this research.
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Affiliation(s)
| | - Nicholas S. Eyre
- College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia;
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Prell C, Busche T, Rückert C, Nolte L, Brandenbusch C, Wendisch VF. Adaptive laboratory evolution accelerated glutarate production by Corynebacterium glutamicum. Microb Cell Fact 2021; 20:97. [PMID: 33971881 PMCID: PMC8112011 DOI: 10.1186/s12934-021-01586-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/26/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The demand for biobased polymers is increasing steadily worldwide. Microbial hosts for production of their monomeric precursors such as glutarate are developed. To meet the market demand, production hosts have to be improved constantly with respect to product titers and yields, but also shortening bioprocess duration is important. RESULTS In this study, adaptive laboratory evolution was used to improve a C. glutamicum strain engineered for production of the C5-dicarboxylic acid glutarate by flux enforcement. Deletion of the L-glutamic acid dehydrogenase gene gdh coupled growth to glutarate production since two transaminases in the glutarate pathway are crucial for nitrogen assimilation. The hypothesis that strains selected for faster glutarate-coupled growth by adaptive laboratory evolution show improved glutarate production was tested. A serial dilution growth experiment allowed isolating faster growing mutants with growth rates increasing from 0.10 h-1 by the parental strain to 0.17 h-1 by the fastest mutant. Indeed, the fastest growing mutant produced glutarate with a twofold higher volumetric productivity of 0.18 g L-1 h-1 than the parental strain. Genome sequencing of the evolved strain revealed candidate mutations for improved production. Reverse genetic engineering revealed that an amino acid exchange in the large subunit of L-glutamic acid-2-oxoglutarate aminotransferase was causal for accelerated glutarate production and its beneficial effect was dependent on flux enforcement due to deletion of gdh. Performance of the evolved mutant was stable at the 2 L bioreactor-scale operated in batch and fed-batch mode in a mineral salts medium and reached a titer of 22.7 g L-1, a yield of 0.23 g g-1 and a volumetric productivity of 0.35 g L-1 h-1. Reactive extraction of glutarate directly from the fermentation broth was optimized leading to yields of 58% and 99% in the reactive extraction and reactive re-extraction step, respectively. The fermentation medium was adapted according to the downstream processing results. CONCLUSION Flux enforcement to couple growth to operation of a product biosynthesis pathway provides a basis to select strains growing and producing faster by adaptive laboratory evolution. After identifying candidate mutations by genome sequencing causal mutations can be identified by reverse genetics. As exemplified here for glutarate production by C. glutamicum, this approach allowed deducing rational metabolic engineering strategies.
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Affiliation(s)
- Carina Prell
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Tobias Busche
- Technology Platform Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
| | - Christian Rückert
- Technology Platform Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
| | - Lea Nolte
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Christoph Brandenbusch
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Volker F. Wendisch
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
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Busch J, Chey S, Sieg M, Vahlenkamp TW, Liebert UG. Mutated Measles Virus Matrix and Fusion Protein Influence Viral Titer In Vitro and Neuro-Invasion in Lewis Rat Brain Slice Cultures. Viruses 2021; 13:605. [PMID: 33916225 PMCID: PMC8066528 DOI: 10.3390/v13040605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 12/20/2022] Open
Abstract
Measles virus (MV) can cause severe acute diseases as well as long-lasting clinical deteriorations due to viral-induced immunosuppression and neuronal manifestation. How the virus enters the brain and manages to persist in neuronal tissue is not fully understood. Various mutations in the viral genes were found in MV strains isolated from patient brains. In this study, reverse genetics was used to introduce mutations in the fusion, matrix and polymerase genes of MV. The generated virus clones were characterized in cell culture and used to infect rat brain slice cultures. A mutation in the carboxy-terminal domain of the matrix protein (R293Q) promoted the production of progeny virions. This effect was observed in Vero cells irrespective of the expression of the signaling lymphocyte activation molecule (SLAM). Furthermore, a mutation in the fusion protein (I225M) induced syncytia formation on Vero cells in the absence of SLAM and promoted viral spread throughout the rat brain slices. In this study, a solid ex vivo model was established to elucidate the MV mutations contributing to neural manifestation.
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Affiliation(s)
- Johannes Busch
- Institute of Virology, University Hospital Leipzig, Johannisallee 30, 04103 Leipzig, Germany; (S.C.); (U.G.L.)
- Faculty of Veterinary Medicine, Institute of Virology, Leipzig University, An den Tierkliniken 29, 04103 Leipzig, Germany; (M.S.); (T.W.V.)
| | - Soroth Chey
- Institute of Virology, University Hospital Leipzig, Johannisallee 30, 04103 Leipzig, Germany; (S.C.); (U.G.L.)
| | - Michael Sieg
- Faculty of Veterinary Medicine, Institute of Virology, Leipzig University, An den Tierkliniken 29, 04103 Leipzig, Germany; (M.S.); (T.W.V.)
| | - Thomas W. Vahlenkamp
- Faculty of Veterinary Medicine, Institute of Virology, Leipzig University, An den Tierkliniken 29, 04103 Leipzig, Germany; (M.S.); (T.W.V.)
| | - Uwe G. Liebert
- Institute of Virology, University Hospital Leipzig, Johannisallee 30, 04103 Leipzig, Germany; (S.C.); (U.G.L.)
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Alencar ALF, Cuenca A, Olesen NJ, Rasmussen TB. Technical challenges in the development of reverse genetics for a viral haemorrhagic septicaemia virus (VHSV) genotype Ib isolate: Alternative cell lines and general troubleshooting. J Virol Methods 2021; 292:114132. [PMID: 33741408 DOI: 10.1016/j.jviromet.2021.114132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/10/2021] [Accepted: 03/15/2021] [Indexed: 11/19/2022]
Abstract
Several reverse genetics systems for viral haemorrhagic septicaemia virus (VHSV) have been developed over the last decade. These systems have been based on genotype Ia, IVa and IVb isolates and have used the fish cell line EPC, which is less susceptible to some VHSV isolates belonging to genotype I and genotypes II and III. While developing a reverse genetics system in our laboratories for VHSV genotype Ib, we realized that the isolate in interest (SE SVA 1033 9C) did not grow in EPC cells and it was necessary to adapt the reverse genetics protocols to the BF-2 fish cell line. This cell line is very sensitive to high temperatures and is therefore not compatible with the original protocols based on the use of recombinant vaccinia virus (vTF7-3) as a provider of the T7 RNA polymerase (T7-RNAP) to the system, which includes incubation periods at 37 °C. Transfection efficiency was assessed in BF-2 cells using a reporter plasmid and it showed to be highest when using Lipofectamine™ 3000 compared to other transfection reagents. A luciferase assay was performed to determine the optimal activity of T7-RNAP in BF-2 cells with different amounts of vTF7-3. We successfully recovered recombinant VHSV (rVHSV) in BF-2 cells by reducing the incubation time at 37 °C after transfection to both 3 and 6 h. Another strategy we attempted successfully was to transfect mammalian BHK-21 cells, which are routinely used to propagate vTF7-3, and after the 37 °C incubation period, a BF-2 cell suspension was added hypothesizing that the virions formed in the transfected mammalian cells would infect the subsequently added fish cells at 15 °C incubation over the following days. We have successfully recovered rVHSV from both BHK-21 with a BF-2 cells suspension as well as a new protocol for VHSV reverse genetics in BF-2 cells has been established.
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Affiliation(s)
- Anna Luiza Farias Alencar
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark - DTU Aqua, Kemitorvet, Building 202, 2800, Kgs Lyngby, Denmark
| | - Argelia Cuenca
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark - DTU Aqua, Kemitorvet, Building 202, 2800, Kgs Lyngby, Denmark.
| | - Niels Jørgen Olesen
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark - DTU Aqua, Kemitorvet, Building 202, 2800, Kgs Lyngby, Denmark
| | - Thomas Bruun Rasmussen
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark.
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48
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Lin JW, Tang C, Wei HC, Du B, Chen C, Wang M, Zhou Y, Yu MX, Cheng L, Kuivanen S, Ogando NS, Levanov L, Zhao Y, Li CL, Zhou R, Li Z, Zhang Y, Sun K, Wang C, Chen L, Xiao X, Zheng X, Chen SS, Zhou Z, Yang R, Zhang D, Xu M, Song J, Wang D, Li Y, Lei S, Zeng W, Yang Q, He P, Zhang Y, Zhou L, Cao L, Luo F, Liu H, Wang L, Ye F, Zhang M, Li M, Fan W, Li X, Li K, Ke B, Xu J, Yang H, He S, Pan M, Yan Y, Zha Y, Jiang L, Yu C, Liu Y, Xu Z, Li Q, Jiang Y, Sun J, Hong W, Wei H, Lu G, Vapalahti O, Luo Y, Wei Y, Connor T, Tan W, Snijder EJ, Smura T, Li W, Geng J, Ying B, Chen L. Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response. Cell Host Microbe 2021; 29:489-502.e8. [PMID: 33548198 PMCID: PMC7846228 DOI: 10.1016/j.chom.2021.01.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 02/05/2023]
Abstract
The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance. We identified 35 recurrent variants, some of which are associated with clinical phenotypes related to severity. One variant, containing a deletion in the Nsp1-coding region (Δ500-532), was found in more than 20% of our sequenced samples and associates with higher RT-PCR cycle thresholds and lower serum IFN-β levels of infected patients. Deletion variants in this locus were found in 37 countries worldwide, and viruses isolated from clinical samples or engineered by reverse genetics with related deletions in Nsp1 also induce lower IFN-β responses in infected Calu-3 cells. Taken together, our virologic surveillance characterizes recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance, which collectively may aid molecular diagnostics and drug design.
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Affiliation(s)
- Jing-Wen Lin
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China.
| | - Chao Tang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Han-Cheng Wei
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Baowen Du
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Chuan Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Minjin Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Yongzhao Zhou
- Department of Respiratory and Critical Care Medicine, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ming-Xia Yu
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Lu Cheng
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Department of Computer Science, School of Science, Aalto University, Aalto FI-00076, Finland
| | - Suvi Kuivanen
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland
| | - Natacha S Ogando
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lev Levanov
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland
| | - Yuancun Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Chang-Ling Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ran Zhou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Zhidan Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Yiming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ke Sun
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Chengdi Wang
- Department of Respiratory and Critical Care Medicine, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Li Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Xia Xiao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Xiuran Zheng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Sha-Sha Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Zhen Zhou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ruirui Yang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Dan Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Mengying Xu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Junwei Song
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Danrui Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Yupeng Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - ShiKun Lei
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Wanqin Zeng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Qingxin Yang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ping He
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Yaoyao Zhang
- Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Lifang Zhou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ling Cao
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Feng Luo
- Wuhan Chain Medical Labs, Wuhan, Hubei 430011, China
| | - Huayi Liu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Liping Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Fei Ye
- NHC Key Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Mengjiao Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Wei Fan
- Department of Respiratory and Critical Care Medicine, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xinqiong Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Bowen Ke
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Jiannan Xu
- Sichuan Center for Disease Control and Prevention, No. 6 Zhongxue Rd, Chengdu 610041, China
| | - Huiping Yang
- Sichuan Center for Disease Control and Prevention, No. 6 Zhongxue Rd, Chengdu 610041, China
| | - Shusen He
- Sichuan Center for Disease Control and Prevention, No. 6 Zhongxue Rd, Chengdu 610041, China
| | - Ming Pan
- Sichuan Center for Disease Control and Prevention, No. 6 Zhongxue Rd, Chengdu 610041, China
| | - Yichen Yan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Yi Zha
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Lingyu Jiang
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Changxiu Yu
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Yingfen Liu
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Zhiyong Xu
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Qingfeng Li
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Yongmei Jiang
- Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Jiufeng Sun
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong 511430, China
| | - Wei Hong
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangwen Lu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Olli Vapalahti
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland; University of Helsinki and Helsinki University Hospital, Department of Virology, Helsinki, Finland; Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Yunzi Luo
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yuquan Wei
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Thomas Connor
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Wenjie Tan
- NHC Key Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Teemu Smura
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland; University of Helsinki and Helsinki University Hospital, Department of Virology, Helsinki, Finland.
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China.
| | - Binwu Ying
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China.
| | - Lu Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China.
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49
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Li H, Huang L, Yu Y, Ren X, Li B, Zhang J, Liao M, Qi W. Generation of recombinant influenza virus bearing strep tagged PB2 and effective identification of interactional host factors. Vet Microbiol 2021; 254:108985. [PMID: 33550110 DOI: 10.1016/j.vetmic.2021.108985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/07/2021] [Indexed: 11/19/2022]
Abstract
The genome of influenza A virus is negative-sense and segmented RNA, which is transcribed and replicated by the viral RNA-dependent RNA polymerase (RdRp) during the virus life cycle. The viral RdRp is thought to be an important host range and virulence determinant factor, and the 627 site of PB2 subunit is a highly acceptable key site of RdRp function. Besides, the function of RdRp is modulated by several host factors. Identification of the host factors interacting with RdRp is of great interest. Here, we tried to explore an effective method to study virus-host interaction by rescuing replication-competent recombinant influenza viruses carrying Strep tagged PB2. Subsequently, we tested several biological characteristics of recombinant viruses in cells and pathogenicity in mice. Then, we purified of protein complex of Strep tagged PB2 and host factors of interest from 293 T cells infected with recombinant viruses. After purification, we performed mass spectrometry to identify these proteins that interacting with PB2. We identified 57 host factors in total. Through Gene Ontology (GO) and Protein-Protein interaction (PPI) network analysis, we revealed the function and network of these proteins. In summary, we generated replication-competent recombinant influenza viruses by inserting a Strep-Tag into PB2 and purified host factors interacting with viral RdRp bearing a 627 K or 627E PB2. These proteins might function as host range and virulence determinants of influenza virus.
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Affiliation(s)
- Huanan Li
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, 510642, China; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou, 510642, China
| | - Lihong Huang
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Yuandi Yu
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Chongqing Academy of Animal Sciences, Chonqing, 402460, China
| | - Xingxing Ren
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Bo Li
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, 510642, China; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou, 510642, China
| | - Jiahao Zhang
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, 510642, China; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou, 510642, China
| | - Ming Liao
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, 510642, China; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou, 510642, China.
| | - Wenbao Qi
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, 510642, China; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou, 510642, China.
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Elbehairy MA, Khattar SK, Samal SK. Recovery of Recombinant Avian Paramyxovirus Type-3 Strain Wisconsin by Reverse Genetics and Its Evaluation as a Vaccine Vector for Chickens. Viruses 2021; 13:v13020316. [PMID: 33669530 PMCID: PMC7922763 DOI: 10.3390/v13020316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 01/22/2023] Open
Abstract
A reverse genetic system for avian paramyxovirus type-3 (APMV-3) strain Wisconsin was created and the infectious virus was recovered from a plasmid-based viral antigenomic cDNA. Green fluorescent protein (GFP) gene was cloned into the recombinant APMV-3 genome as a foreign gene. Stable expression of GFP by the recovered virus was confirmed for at least 10 consecutive passages. APMV-3 strain Wisconsin was evaluated against APMV-3 strain Netherlands and APMV-1 strain LaSota as a vaccine vector. The three viral vectors expressing GFP as a foreign protein were compared for level of GFP expression level, growth rate in chicken embryo fibroblast (DF-1) cells, and tissue distribution and immunogenicity in specific pathogen-free (SPF) day-old chickens. APMV-3 strain Netherlands showed highest growth rate and GFP expression level among the three APMV vectors in vitro. APMV-3 strain Wisconsin and APMV-1 strain LaSota vectors were mainly confined to the trachea after vaccination of day-old SPF chickens without any observable pathogenicity, whereas APMV-3 strain Netherlands showed wide tissue distribution in different body organs (brain, lungs, trachea, and spleen) with mild observable pathogenicity. In terms of immunogenicity, both APMV-3 strain-vaccinated groups showed HI titers two to three fold higher than that induced by APMV-1 strain LaSota vaccinated group. This study offers a novel paramyxovirus vector (APMV-3 strain Wisconsin) which can be used safely for vaccination of young chickens as an alternative for APMV-1 strain LaSota vector.
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Affiliation(s)
- Mohamed A. Elbehairy
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD 20740, USA; (M.A.E.); (S.K.K.)
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Sunil K. Khattar
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD 20740, USA; (M.A.E.); (S.K.K.)
| | - Siba K. Samal
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD 20740, USA; (M.A.E.); (S.K.K.)
- Correspondence: ; Tel.: +1-(301)314-6813
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