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Agbemabiese CA, Philip AA, Patton JT. Recovery of Recombinant Rotaviruses by Reverse Genetics. Methods Mol Biol 2024; 2733:249-263. [PMID: 38064037 DOI: 10.1007/978-1-0716-3533-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Rotaviruses are the primary cause of severe gastroenteritis in infants and young children throughout the world. To combat rotavirus illness, several live oral vaccines have been developed, or are under development, that are formulated from attenuated human or human-animal reassortant strains of rotavirus. While the effectiveness of these vaccines is generally high in developed countries, the same vaccines are significantly less effective in many developing countries, where the need for rotavirus vaccines is greatest. Recently, reverse genetics systems have been developed that allow modification of the segmented double-stranded (ds)RNA genome of rotavirus, including reprogramming the genome to allow expression of additional proteins that may stimulate expanded neutralizing antibody responses in vaccinated children. The use of reverse genetics systems may not only lead to the development of more potent classes of vaccines but can be used to better explore the intricacies of rotavirus molecular biology and pathogenesis. In this article, we share protocols that can be used to generate recombinant rotaviruses, including modified strains that express foreign proteins.
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Affiliation(s)
- Chantal A Agbemabiese
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Asha A Philip
- Department of Biology, Indiana University, Bloomington, IN, USA
- CSL Seqirus, Waltham, MA, USA
| | - John T Patton
- Department of Biology, Indiana University, Bloomington, IN, USA.
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Hao P, Qu Q, Pang Z, Li L, Du S, Shang L, Jin C, Xu W, Ha Z, Jiang Y, Chen J, Gao Z, Jin N, Wang J, Li C. Interaction of species A rotavirus VP4 with the cellular proteins vimentin and actin related protein 2 discovered by a proximity interactome assay. J Virol 2023; 97:e0137623. [PMID: 37991368 PMCID: PMC10734455 DOI: 10.1128/jvi.01376-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 09/09/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE Rotavirus (RV) is an important zoonosis virus, which can cause severe diarrhea and extra-intestinal infection. To date, some proteins or carbohydrates have been shown to participate in the attachment or internalization of RV, including HGBAs, Hsc70, and integrins. This study attempted to indicate whether there were other proteins that would participate in the entry of RV; thus, the RV VP4-interacting proteins were identified by proximity labeling. After analysis and verification, it was found that VIM and ACTR2 could significantly promote the proliferation of RV in intestinal cells. Through further viral binding assays after knockdown, antibody blocking, and recombinant protein overexpression, it was revealed that both VIM and ACTR2 could promote RV replication.
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Affiliation(s)
- Pengfei Hao
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Qiaoqiao Qu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Zhaoxia Pang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Letian Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Shouwen Du
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Limin Shang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Chaozhi Jin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Wang Xu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Zhuo Ha
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yuhang Jiang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jing Chen
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Zihan Gao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Ningyi Jin
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jian Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Chang Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
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Chaung K, Baharav TZ, Henderson G, Zheludev IN, Wang PL, Salzman J. SPLASH: A statistical, reference-free genomic algorithm unifies biological discovery. Cell 2023; 186:5440-5456.e26. [PMID: 38065078 PMCID: PMC10861363 DOI: 10.1016/j.cell.2023.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/31/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023]
Abstract
Today's genomics workflows typically require alignment to a reference sequence, which limits discovery. We introduce a unifying paradigm, SPLASH (Statistically Primary aLignment Agnostic Sequence Homing), which directly analyzes raw sequencing data, using a statistical test to detect a signature of regulation: sample-specific sequence variation. SPLASH detects many types of variation and can be efficiently run at scale. We show that SPLASH identifies complex mutation patterns in SARS-CoV-2, discovers regulated RNA isoforms at the single-cell level, detects the vast sequence diversity of adaptive immune receptors, and uncovers biology in non-model organisms undocumented in their reference genomes: geographic and seasonal variation and diatom association in eelgrass, an oceanic plant impacted by climate change, and tissue-specific transcripts in octopus. SPLASH is a unifying approach to genomic analysis that enables expansive discovery without metadata or references.
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Affiliation(s)
- Kaitlin Chaung
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Tavor Z Baharav
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - George Henderson
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Ivan N Zheludev
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Peter L Wang
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Julia Salzman
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; Department of Statistics (by courtesy), Stanford University, Stanford, CA 94305, USA; Department of Biology (by courtesy), Stanford University, Stanford, CA 94305, USA.
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Dai J, Agbemabiese CA, Griffin AN, Patton JT. Rotavirus capping enzyme VP3 inhibits interferon expression by inducing MAVS degradation during viral replication. mBio 2023; 14:e0225523. [PMID: 37905816 PMCID: PMC10746195 DOI: 10.1128/mbio.02255-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/22/2023] [Indexed: 11/02/2023] Open
Abstract
The binding of viral RNA to RIG-I-like receptors triggers the formation of mitochondrial antiviral signaling (MAVS) protein aggregates critical for interferon (IFN) expression. Several rotavirus strains have been shown to suppress IFN expression by inducing MAVS degradation. Relying on transient expression assays, previous studies reached different conclusions regarding the identity of the rotavirus protein responsible for MAVS degradation, suggesting it was an activity of the rotavirus capping enzyme VP3 or the interferon antagonist NSP1. Here, we have used recombinant SA11 rotaviruses to identify the endogenous viral protein responsible for MAVS degradation and to analyze how the attack on MAVS impacts IFN expression. The recombinant viruses included those expressing modified VP3 or NSP1 proteins deficient in the ability to induce the degradation of MAVS or interferon regulatory factor-3 (IRF3), or both. With these viruses, we determined that VP3 directs the proteasomal degradation of MAVS but plays no role in IRF3 degradation. Moreover, NSP1 was determined to induce IRF3 degradation but to have no impact on MAVS degradation. Analysis of rotavirus-infected cells indicated that IRF3 degradation was more efficient than MAVS degradation and that NSP1 was primarily responsible for suppressing IFN expression in infected cells. However, VP3-mediated MAVS degradation contributed to IFN suppression in cells that failed to produce functional NSP1, pointing to a subsidiary role for VP3 in the IFN antagonist activity of NSP1. Thus, VP3 is a multifunctional protein with several activities that counter anti-rotavirus innate immune responses, including capping of viral (+)RNAs, hydrolysis of the RNase L 2-5A (2'-5' oligoadenylate) signaling molecule, and proteasomal degradation of MAVS. IMPORTANCE Rotavirus is an enteric RNA virus that causes severe dehydrating gastroenteritis in infants and young children through infection of enterocytes in the small intestine. Timely clearance of the virus demands a robust innate immune response by cells associated with the small intestine, including the expression of interferon (IFN). Previous studies have shown that some rotavirus strains suppress the production of interferon, by inducing the degradation of mitochondrial antiviral signaling (MAVS) protein and interferon regulatory factor-3 (IRF3). In this study, we have used reverse genetics to generate recombinant rotaviruses expressing compromised forms of VP3 or NSP1, or both, to explore the function of these viral proteins in the degradation of MAVS and IRF3. Our results demonstrate that VP3 is responsible for MAVS depletion in rotavirus-infected cells, and through this activity, helps to suppress IFN production. Thus, VP3 functions to support the activity of rotavirus NSP1, the major interferon antagonist of the virus.
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Affiliation(s)
- Jin Dai
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - Ashley N. Griffin
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - John T. Patton
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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Chaung K, Baharav TZ, Henderson G, Zheludev IN, Wang PL, Salzman J. [WITHDRAWN] SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549408. [PMID: 37503014 PMCID: PMC10370119 DOI: 10.1101/2023.07.17.549408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The authors have withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2022/497555. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The correct preprint can be found at doi: https://doi.org/10.1101/2022.06.24.497555.
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Abstract
Alphaviruses contain many human and animal pathogens, such as CHIKV, SINV, and VEEV. Accumulating evidence indicates that innate immunity plays an important role in response to alphaviruses infection. In parallel, alphaviruses have evolved many strategies to evade host antiviral innate immunity. In the current review, we focus on the underlying mechanisms employed by alphaviruses to evade cGAS-STING, IFN, transcriptional host shutoff, translational host shutoff, and RNAi. Dissecting the detailed antiviral immune evasion mechanisms by alphaviruses will enhance our understanding of the pathogenesis of alphaviruses and may provide more effective strategies to control alphaviruses infection.
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Affiliation(s)
- Yihan Liu
- Department of Infectious Diseases, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yupei Yuan
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Leiliang Zhang
- Department of Infectious Diseases, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- *Correspondence: Leiliang Zhang,
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