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Liu Y, Wang K, Gong X, Qu W, Xiao Y, Sun H, Kang J, Sheng J, Wu F, Dai F. Schisandra chinensis inhibits the entry of BoHV-1 by blocking PI3K-Akt pathway and enhances the m6A methylation of gD to inhibit the entry of progeny virus. Front Microbiol 2024; 15:1444414. [PMID: 39104584 PMCID: PMC11298802 DOI: 10.3389/fmicb.2024.1444414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 07/11/2024] [Indexed: 08/07/2024] Open
Abstract
Schisandra chinensis, a traditional Chinese medicine known for its antitussive and sedative effects, has shown promise in preventing various viral infections. Bovine herpesvirus-1 (BoHV-1) is an enveloped DNA virus that causes respiratory disease in cattle, leading to significant economic losses in the industry. Because the lack of previous reports on Schisandra chinensis resisting BoHV-1 infection, this study aimed to investigate the specific mechanisms involved. Results from TCID50, qPCR, IFA, and western blot analyses demonstrated that Schisandra chinensis could inhibit BoHV-1 entry into MDBK cells, primarily through its extract Methylgomisin O (Meth O). The specific mechanism involved Meth O blocking BoHV-1 entry into cells via clathrin- and caveolin-mediated endocytosis by suppressing the activation of PI3K-Akt signaling pathway. Additionally, findings from TCID50, qPCR, co-immunoprecipitation and western blot assays revealed that Schisandra chinensis blocked BoHV-1 gD transcription through enhancing m6A methylation of gD after virus entry, thereby hindering gD protein expression and preventing progeny virus entry into cells and ultimately inhibiting BoHV-1 replication. Overall, these results suggest that Schisandra chinensis can resist BoHV-1 infection by targeting the PI3K-Akt signaling pathway and inhibiting gD transcription.
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Affiliation(s)
- Yang Liu
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Animal Biosafety Risk Prevention and Control of Ministry of Agriculture and Rural Affairs (South), China Animal Health and Epidemiology Center, Qingdao, China
| | - Kang Wang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Animal Biosafety Risk Prevention and Control of Ministry of Agriculture and Rural Affairs (South), China Animal Health and Epidemiology Center, Qingdao, China
| | - Xiao Gong
- Qingdao YeBio Bio-Engineering Co., Ltd., Qingdao, China
| | - Weijie Qu
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Yangyang Xiao
- Key Laboratory of Animal Biosafety Risk Prevention and Control of Ministry of Agriculture and Rural Affairs (South), China Animal Health and Epidemiology Center, Qingdao, China
- College of Animal Science and Technology, Shihezi University, Xinjiang, China
| | - Hongtao Sun
- Key Laboratory of Animal Biosafety Risk Prevention and Control of Ministry of Agriculture and Rural Affairs (South), China Animal Health and Epidemiology Center, Qingdao, China
| | - Jingli Kang
- Key Laboratory of Animal Biosafety Risk Prevention and Control of Ministry of Agriculture and Rural Affairs (South), China Animal Health and Epidemiology Center, Qingdao, China
| | - Jinliang Sheng
- Key Laboratory of Animal Biosafety Risk Prevention and Control of Ministry of Agriculture and Rural Affairs (South), China Animal Health and Epidemiology Center, Qingdao, China
- College of Animal Science and Technology, Shihezi University, Xinjiang, China
| | - Faxing Wu
- Key Laboratory of Animal Biosafety Risk Prevention and Control of Ministry of Agriculture and Rural Affairs (South), China Animal Health and Epidemiology Center, Qingdao, China
| | - Feiyan Dai
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
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Qin R, Huang M, Jiang Y, Jiang D, Chang D, Xie Y, Dou Y, Wu L, Wei L, Wang M, Tian Z, Li C, Wang C. N6-Methyladenosine (m6A) Sequencing Reveals Heterodera glycines-Induced Dynamic Methylation Promoting Soybean Defense. PHYTOPATHOLOGY 2024; 114:1612-1625. [PMID: 38478699 DOI: 10.1094/phyto-12-23-0474-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Unraveling the intricacies of soybean cyst nematode (Heterodera glycines) race 4 resistance and susceptibility in soybean breeding lines-11-452 (highly resistant) and Dongsheng1 (DS1, highly susceptible)-was the focal point of this study. Employing cutting-edge N6-methyladenosine (m6A) and RNA sequencing techniques, we delved into the impact of m6A modification on gene expression and plant defense responses. Through the evaluation of nematode development in both resistant and susceptible roots, a pivotal time point (3 days postinoculation) for m6A methylation sequencing was identified. Our sequencing data exhibited robust statistics, successful soybean genome mapping, and prevalent m6A peak distributions, primarily in the 3' untranslated region and stop codon regions. Analysis of differential methylation peaks and differentially expressed genes revealed distinctive patterns between resistant and susceptible genotypes. In the highly resistant line (11-452), key resistance and defense-associated genes displayed increased expression coupled with inhibited methylation, encompassing crucial players such as R genes, receptor kinases, and transcription factors. Conversely, the highly susceptible DS1 line exhibited heightened expression correlated with decreased methylation in genes linked to susceptibility pathways, including Mildew Locus O-like proteins and regulatory elements affecting defense mechanisms. Genome-wide assessments, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, and differential methylation peak/differentially expressed gene overlap emphasized the intricate interplay of m6A modifications, alternative splicing, microRNA, and gene regulation in plant defense. Protein-protein interaction networks illuminated defense-pivotal genes, delineating divergent mechanisms in resistant and susceptible responses. This study sheds light on the dynamic correlation between methylation, splicing, and gene expression, providing profound insights into plant responses to nematode infection.
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Affiliation(s)
- Ruifeng Qin
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minghui Huang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, China
| | - Ye Jiang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, China
| | - Dan Jiang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Doudou Chang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifan Xie
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuewen Dou
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lili Wu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liuli Wei
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, China
| | - Mingze Wang
- Heilongjiang Academy of Agricultural Sciences, Daqing 163316, Heilongjiang, China
| | - Zhongyan Tian
- Heilongjiang Academy of Agricultural Sciences, Daqing 163316, Heilongjiang, China
| | - Chunjie Li
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, China
| | - Congli Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, China
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3
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Song P, Cai Z, Jia G. Principles, functions, and biological implications of m 6A in plants. RNA (NEW YORK, N.Y.) 2024; 30:491-499. [PMID: 38531642 PMCID: PMC11019739 DOI: 10.1261/rna.079951.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Over the past decade, N 6-methyladenosine (m6A) has emerged as a prevalent and dynamically regulated modification across the transcriptome; it has been reversibly installed, removed, and interpreted by specific binding proteins, and has played crucial roles in molecular and biological processes. Within this scope, we consolidate recent advancements of m6A research in plants regarding gene expression regulation, diverse physiologic and pathogenic processes, as well as crop trial implications, to guide discussions on challenges associated with and leveraging epitranscriptome editing for crop improvement.
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Affiliation(s)
- Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhihe Cai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- PKU-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Center of RNA Biology, Peking University, Beijing 100871, China
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4
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Yue J, Lu Y, Sun Z, Guo Y, San León D, Pasin F, Zhao M. Methyltransferase-like (METTL) homologues participate in Nicotiana benthamiana antiviral responses. PLANT SIGNALING & BEHAVIOR 2023; 18:2214760. [PMID: 37210738 DOI: 10.1080/15592324.2023.2214760] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/23/2023]
Abstract
Methyltransferase (MTase) enzymes catalyze the addition of a methyl group to a variety of biological substrates. MTase-like (METTL) proteins are Class I MTases whose enzymatic activities contribute to the epigenetic and epitranscriptomic regulation of multiple cellular processes. N6-adenosine methylation (m6A) is a common chemical modification of eukaryotic and viral RNA whose abundance is jointly regulated by MTases and METTLs, demethylases, and m6A binding proteins. m6A affects various cellular processes including RNA degradation, post-transcriptional processing, and antiviral immunity. Here, we used Nicotiana benthamiana and plum pox virus (PPV), an RNA virus of the Potyviridae family, to investigated the roles of MTases in plant-virus interaction. RNA sequencing analysis identified MTase transcripts that are differentially expressed during PPV infection; among these, accumulation of a METTL gene was significantly downregulated. Two N. benthamiana METTL transcripts (NbMETTL1 and NbMETTL2) were cloned and further characterized. Sequence and structural analyses of the two encoded proteins identified a conserved S-adenosyl methionine (SAM) binding domain, showing they are SAM-dependent MTases phylogenetically related to human METTL16 and Arabidopsis thaliana FIONA1. Overexpression of NbMETTL1 and NbMETTL2 caused a decrease of PPV accumulation. In sum, our results indicate that METTL homologues participate in plant antiviral responses.
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Affiliation(s)
- Jianying Yue
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yan Lu
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhenqi Sun
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuqing Guo
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - David San León
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Fabio Pasin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València (CSIC-UPV), Valencia, Spain
| | - Mingmin Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
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5
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Tselika M, Belmezos N, Kallemi P, Andronis C, Chiumenti M, Navarro B, Lavigne M, Di Serio F, Kalantidis K, Katsarou K. PSTVd infection in Nicotiana benthamiana plants has a minor yet detectable effect on CG methylation. FRONTIERS IN PLANT SCIENCE 2023; 14:1258023. [PMID: 38023875 PMCID: PMC10645062 DOI: 10.3389/fpls.2023.1258023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Viroids are small circular RNAs infecting a wide range of plants. They do not code for any protein or peptide and therefore rely on their structure for their biological cycle. Observed phenotypes of viroid infected plants are thought to occur through changes at the transcriptional/translational level of the host. A mechanism involved in such changes is RNA-directed DNA methylation (RdDM). Till today, there are contradictory works about viroids interference of RdDM. In this study, we investigated the epigenetic effect of viroid infection in Nicotiana benthamiana plants. Using potato spindle tuber viroid (PSTVd) as the triggering pathogen and via bioinformatic analyses, we identified endogenous gene promoters and transposable elements targeted by 24 nt host siRNAs that differentially accumulated in PSTVd-infected and healthy plants. The methylation status of these targets was evaluated following digestion with methylation-sensitive restriction enzymes coupled with PCR amplification, and bisulfite sequencing. In addition, we used Methylation Sensitive Amplification Polymorphism (MSAP) followed by sequencing (MSAP-seq) to study genomic DNA methylation of 5-methylcytosine (5mC) in CG sites upon viroid infection. In this study we identified a limited number of target loci differentially methylated upon PSTVd infection. These results enhance our understanding of the epigenetic host changes as a result of pospiviroid infection.
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Affiliation(s)
- Martha Tselika
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | | | - Paraskevi Kallemi
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Christos Andronis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Matthieu Lavigne
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Konstantina Katsarou
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
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6
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He M, Li Z, Xie X. The Roles of N6-Methyladenosine Modification in Plant-RNA Virus Interactions. Int J Mol Sci 2023; 24:15608. [PMID: 37958594 PMCID: PMC10649972 DOI: 10.3390/ijms242115608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/06/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
N6-methyladenosine (m6A) is a dynamic post-transcriptional RNA modification. Recently, its role in viruses has led to the study of viral epitranscriptomics. m6A has been observed in viral genomes and alters the transcriptomes of both the host cell and virus during infection. The effects of m6A modifications on host plant mRNA can either increase the likelihood of viral infection or enhance the resistance of the host to the virus. However, to date, the regulatory mechanisms of m6A in viral infection and host immune responses have not been fully elucidated. With the development of sequencing-based biotechnologies, the study of m6A in plant viruses has received increasing attention. In this mini review, we summarize the positive and negative consequences of m6A modification in different RNA viral infections. Given its increasingly important roles in multiple viruses, m6A represents a new potential target for antiviral defense.
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Affiliation(s)
- Min He
- Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, China;
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Xin Xie
- Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, China;
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7
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Dhingra Y, Gupta S, Gupta V, Agarwal M, Katiyar-Agarwal S. The emerging role of epitranscriptome in shaping stress responses in plants. PLANT CELL REPORTS 2023; 42:1531-1555. [PMID: 37481775 DOI: 10.1007/s00299-023-03046-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023]
Abstract
KEY MESSAGE RNA modifications and editing changes constitute 'epitranscriptome' and are crucial in regulating the development and stress response in plants. Exploration of the epitranscriptome and associated machinery would facilitate the engineering of stress tolerance in crops. RNA editing and modifications post-transcriptionally decorate almost all classes of cellular RNAs, including tRNAs, rRNAs, snRNAs, lncRNAs and mRNAs, with more than 170 known modifications, among which m6A, Ψ, m5C, 8-OHG and C-to-U editing are the most abundant. Together, these modifications constitute the "epitranscriptome", and contribute to changes in several RNA attributes, thus providing an additional structural and functional diversification to the "cellular messages" and adding another layer of gene regulation in organisms, including plants. Numerous evidences suggest that RNA modifications have a widespread impact on plant development as well as in regulating the response of plants to abiotic and biotic stresses. High-throughput sequencing studies demonstrate that the landscapes of m6A, m5C, Am, Cm, C-to-U, U-to-G, and A-to-I editing are remarkably dynamic during stress conditions in plants. GO analysis of transcripts enriched in Ψ, m6A and m5C modifications have identified bonafide components of stress regulatory pathways. Furthermore, significant alterations in the expression pattern of genes encoding writers, readers, and erasers of certain modifications have been documented when plants are grown in challenging environments. Notably, manipulating the expression levels of a few components of RNA editing machinery markedly influenced the stress tolerance in plants. We provide updated information on the current understanding on the contribution of RNA modifications in shaping the stress responses in plants. Unraveling of the epitranscriptome has opened new avenues for designing crops with enhanced productivity and stress resilience in view of global climate change.
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Affiliation(s)
- Yashika Dhingra
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Shitij Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, Switzerland
| | - Vaishali Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Manu Agarwal
- Department of Botany, University of Delhi North Campus, Delhi, 110007, India
| | - Surekha Katiyar-Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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Qian W, Zhou J, Duan L, Wang H, Xu S, Cao Y. m 6A methylation: a potential key player in understanding and treating COVID-2019 infection. Cell Death Discov 2023; 9:300. [PMID: 37596265 PMCID: PMC10439140 DOI: 10.1038/s41420-023-01580-1] [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: 03/12/2023] [Revised: 07/18/2023] [Accepted: 07/26/2023] [Indexed: 08/20/2023] Open
Abstract
Since its discovery in 2019, coronavirus disease 2019 (COVID-2019) spans a wide clinical spectrum from the asymptomatic stage, mild infection, to severe pneumonia. In patients with COVID-2019, factors such as advanced age, diabetes, or hypertension are associated with a significantly increased risk of severe diseases and death. Of note, the mechanisms underlying differences in the risk and symptoms of COVID-2019 among different populations are still poorly characterized. Accordingly, it is imperative to elucidate potential pathophysiological mechanisms and develop targeted therapeutic approaches for COVID-2019 infection. N6-methyladenosine (m6A) is one of the most common modifications in mammalian RNA transcripts and is widely found in messenger RNAs and some non-coding RNAs. It has been reported that m6A methylation modifications are present in viral RNA transcripts, which are of great significance for the regulation of the viral life cycle. Furthermore, m6A methylation has recently been found to be strongly associated with COVID-2019 infection. Therefore, this article reviews recent advances in studies related to the role of m6A methylation in COVID-2019 infection.
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Affiliation(s)
- Weiwei Qian
- Department of Emergency Medicine, Laboratory of Emergency Medicine, West China Hospital, and Disaster Medical Center, Sichuan University, Chengdu, 610044, Sichuan, China
- Department of Emergency,Shangjinnanfu Hospital, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Jian Zhou
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518061, Guangdong, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, 518060, China
| | - Ligeng Duan
- Department of Emergency Medicine, Laboratory of Emergency Medicine, West China Hospital, and Disaster Medical Center, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Haoyu Wang
- Department of Emergency Medicine, Laboratory of Emergency Medicine, West China Hospital, and Disaster Medical Center, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Shuyun Xu
- Department of Emergency Medicine, Laboratory of Emergency Medicine, West China Hospital, and Disaster Medical Center, Sichuan University, Chengdu, 610044, Sichuan, China.
| | - Yu Cao
- Department of Emergency Medicine, Laboratory of Emergency Medicine, West China Hospital, and Disaster Medical Center, Sichuan University, Chengdu, 610044, Sichuan, China.
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9
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ALKBH5 Inhibits Cancer Cell Proliferation in Prostate Cancer through KLF4/TERT Signaling. Andrologia 2023. [DOI: 10.1155/2023/8754940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
N6-methyladenosine (m6A), as a reversible chemical modification of RNA, is a new type of posttranscriptional gene regulation, which plays an important role in cell differentiation and tumorigenesis, and is also a research hotspot in epigenetic transcriptomics in recent years. The purpose of this study was to discuss the action mechanism of m6A demethylase ALKBH5 in the occurrence of prostate cancer (PCa). We found that ALKBH5 was lowly expressed in PCa, and the decreased expression of ALKBH5 was responsible for the poor prognosis of prostate carcinomas. Moreover, ALKBH5 downregulated the expression of Krüppel-like factor 4 (KLF4) by reducing its mRNA stability, which reduced the transcriptional activity of KLF4 on the downstream target telomerase reverse transcriptase (TERT) and decreased TERT expression and telomerase activity, eventually inhibiting PCa cell growth. The findings of this study reveal the action mechanism of ALKBH5 in PCa from the perspective of epitranscriptomics, which would provide new ideas for the prevention of PCa.
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Delmiglio C, Waite DW, Lilly ST, Yan J, Elliott CE, Pattemore J, Guy PL, Thompson JR. New Virus Diagnostic Approaches to Ensuring the Ongoing Plant Biosecurity of Aotearoa New Zealand. Viruses 2023; 15:v15020418. [PMID: 36851632 PMCID: PMC9964515 DOI: 10.3390/v15020418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
To protect New Zealand's unique ecosystems and primary industries, imported plant materials must be constantly monitored at the border for high-threat pathogens. Techniques adopted for this purpose must be robust, accurate, rapid, and sufficiently agile to respond to new and emerging threats. Polymerase chain reaction (PCR), especially real-time PCR, remains an essential diagnostic tool but it is now being complemented by high-throughput sequencing using both Oxford Nanopore and Illumina technologies, allowing unbiased screening of whole populations. The demand for and value of Point-of-Use (PoU) technologies, which allow for in situ screening, are also increasing. Isothermal PoU molecular diagnostics based on recombinase polymerase amplification (RPA) and loop-mediated amplification (LAMP) do not require expensive equipment and can reach PCR-comparable levels of sensitivity. Recent advances in PoU technologies offer opportunities for increased specificity, accuracy, and sensitivities which makes them suitable for wider utilization by frontline or border staff. National and international activities and initiatives are adopted to improve both the plant virus biosecurity infrastructure and the integration, development, and harmonization of new virus diagnostic technologies.
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Affiliation(s)
- Catia Delmiglio
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
- Correspondence: (C.D.); (J.R.T.)
| | - David W. Waite
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
| | - Sonia T. Lilly
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
| | - Juncong Yan
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
| | - Candace E. Elliott
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia
| | - Julie Pattemore
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia
| | - Paul L. Guy
- Department of Botany, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Jeremy R. Thompson
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
- Correspondence: (C.D.); (J.R.T.)
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11
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Rudy E, Grabsztunowicz M, Arasimowicz-Jelonek M, Tanwar UK, Maciorowska J, Sobieszczuk-Nowicka E. N 6-methyladenosine (m 6A) RNA modification as a metabolic switch between plant cell survival and death in leaf senescence. FRONTIERS IN PLANT SCIENCE 2023; 13:1064131. [PMID: 36684776 PMCID: PMC9846058 DOI: 10.3389/fpls.2022.1064131] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Crop losses caused by climate change and various (a)biotic stressors negatively affect agriculture and crop production. Therefore, it is vital to develop a proper understanding of the complex response(s) to (a)biotic stresses and delineate them for each crop plant as a means to enable translational research. In plants, the improvement of crop quality by m6A editing is believed to be a promising strategy. As a reaction to environmental changes, m6A modification showed a high degree of sensitivity and complexity. We investigated differences in gene medleys between dark-induced leaf senescence (DILS) and developmental leaf senescence in barley, including inter alia RNA modifications active in DILS. The identified upregulated genes in DILS include RNA methyltransferases of different RNA types, embracing enzymes modifying mRNA, tRNA, and rRNA. We have defined a decisive moment in the DILS model which determines the point of no return, but the mechanism of its control is yet to be uncovered. This indicates the possibility of an unknown additional switch between cell survival and cell death. Discoveries of m6A RNA modification changes in certain RNA species in different stages of leaf senescence may uncover the role of such modifications in metabolic reprogramming. Nonetheless, there is no such data about the process of leaf senescence in plants. In this scope, the prospect of finding connections between the process of senescence and m6A modification of RNA in plants seems to be compelling.
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Affiliation(s)
- Elżbieta Rudy
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, Poland
| | - Magda Grabsztunowicz
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, Poland
| | - Magdalena Arasimowicz-Jelonek
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, Poland
| | - Umesh Kumar Tanwar
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, Poland
| | - Julia Maciorowska
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, Poland
| | - Ewa Sobieszczuk-Nowicka
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, Poland
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12
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A Comparative Study of Morphology, Photosynthetic Physiology, and Proteome between Diploid and Tetraploid Watermelon ( Citrullus lanatus L.). BIOENGINEERING (BASEL, SWITZERLAND) 2022; 9:bioengineering9120746. [PMID: 36550952 PMCID: PMC9774721 DOI: 10.3390/bioengineering9120746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/20/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
Watermelon is an important fruit that is widely distributed around the world. In particular, the production and consumption of watermelon in China ranks first in the world. Watermelon production is severely affected by a variety of biotic and abiotic stresses during cultivation, and polyploidization can promote stress resistance and yield. However, the morphological and physiological characteristics of tetraploid watermelon and the underlying molecular mechanisms are still poorly understood. In this study, we revealed that the leaves, fruits, and seeds of tetraploid watermelon were significantly larger than those of the diploid genotype. Some physiological characteristics, including photosynthetic rate (Pn) and stomatal conductance (Gs), were greater, whereas the intercellular CO2 concentration (Ci) and transpiration rate (Tr) were lower in tetraploid than in diploid watermelon. Two-dimensional gel electrophoresis combined with tandem mass spectrometry (MALDI-TOF/TOF) was performed to compare proteomic changes between tetraploid and diploid watermelon. A total of 21 differentially expressed proteins were identified; excluding the identical proteins, 8 proteins remained. Among them, four proteins were upregulated and four were downregulated in tetraploid versus diploid genotypes. qRT-PCR results showed inconsistencies in gene expression and protein accumulation, indicating a low correlation between gene expression and protein abundance. Generally, this study extends our understanding of the traits and molecular mechanisms of tetraploid watermelon and provides a theoretical basis for watermelon polyploid breeding.
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13
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Zhang T, Shi C, Hu H, Zhang Z, Wang Z, Chen Z, Feng H, Liu P, Guo J, Lu Q, Zhong K, Chen Z, Liu J, Yu J, Chen J, Chen F, Yang J. N6-methyladenosine RNA modification promotes viral genomic RNA stability and infection. Nat Commun 2022; 13:6576. [PMID: 36323720 PMCID: PMC9629889 DOI: 10.1038/s41467-022-34362-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/22/2022] [Indexed: 11/06/2022] Open
Abstract
Molecular manipulation of susceptibility (S) genes that are antipodes to resistance (R) genes has been adopted as an alternative strategy for controlling crop diseases. Here, we show the S gene encoding Triticum aestivum m6A methyltransferase B (TaMTB) is identified by a genome-wide association study and subsequently shown to be a positive regulator for wheat yellow mosaic virus (WYMV) infection. TaMTB is localized in the nucleus, is translocated into the cytoplasmic aggregates by binding to WYMV NIb to upregulate the m6A level of WYMV RNA1 and stabilize the viral RNA, thus promoting viral infection. A natural mutant allele TaMTB-SNP176C is found to confer an enhanced susceptibility to WYMV infection through genetic variation analysis on 243 wheat varieties. Our discovery highlights this allele can be a useful target for the molecular wheat breeding in the future.
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Affiliation(s)
- Tianye Zhang
- grid.203507.30000 0000 8950 5267State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211 China
| | - Chaonan Shi
- grid.108266.b0000 0004 1803 0494National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/Agronomy College, Henan Agricultural University, Zhengzhou, 450000 China
| | - Haichao Hu
- grid.203507.30000 0000 8950 5267State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211 China
| | - Zhuo Zhang
- grid.410598.10000 0004 4911 9766Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, 410000 China
| | - Ziqiong Wang
- grid.203507.30000 0000 8950 5267State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211 China
| | - Zhiqing Chen
- grid.203507.30000 0000 8950 5267State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211 China
| | - Huimin Feng
- grid.203507.30000 0000 8950 5267State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211 China
| | - Peng Liu
- grid.203507.30000 0000 8950 5267State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211 China
| | - Jun Guo
- grid.203507.30000 0000 8950 5267State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211 China
| | - Qisen Lu
- grid.203507.30000 0000 8950 5267State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211 China
| | - Kaili Zhong
- grid.203507.30000 0000 8950 5267State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211 China
| | - ZhiHui Chen
- grid.8241.f0000 0004 0397 2876University of Dundee, School of Life Sciences, Dow Street, Dundee, DD1 5EH UK
| | - Jiaqian Liu
- grid.203507.30000 0000 8950 5267State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211 China
| | - Jiancheng Yu
- grid.203507.30000 0000 8950 5267Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, Ningbo University, Ningbo, 315211 China
| | - Jianping Chen
- grid.203507.30000 0000 8950 5267State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211 China
| | - Feng Chen
- grid.108266.b0000 0004 1803 0494National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/Agronomy College, Henan Agricultural University, Zhengzhou, 450000 China
| | - Jian Yang
- grid.203507.30000 0000 8950 5267State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211 China
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14
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Yue J, Wei Y, Sun Z, Chen Y, Wei X, Wang H, Pasin F, Zhao M. AlkB RNA demethylase homologues and N 6 -methyladenosine are involved in Potyvirus infection. MOLECULAR PLANT PATHOLOGY 2022; 23:1555-1564. [PMID: 35700092 PMCID: PMC9452765 DOI: 10.1111/mpp.13239] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 05/28/2023]
Abstract
Proteins of the alkylation B (AlkB) superfamily show RNA demethylase activity removing methyl adducts from N6 -methyladenosine (m6 A). m6 A is a reversible epigenetic mark of RNA that regulates human virus replication but has unclear roles in plant virus infection. We focused on Potyvirus-the largest genus of plant RNA viruses-and report here the identification of AlkB domains within P1 of endive necrotic mosaic virus (ENMV) and an additional virus of a putative novel species within Potyvirus. We show that Nicotiana benthamiana m6 A levels are reduced by infection of plum pox virus (PPV) and potato virus Y (PVY). The two potyviruses lack AlkB and the results suggest a general involvement of RNA methylation in potyvirus infection and evolution. Methylated RNA immunoprecipitation sequencing of virus-infected samples showed that m6 A peaks are enriched in plant transcript 3' untranslated regions and in discrete internal and 3' terminal regions of PPV and PVY genomes. Down-regulation of N. benthamiana AlkB homologues of the plant-specific ALKBH9 clade caused a significant decrease in PPV and PVY accumulation. In summary, our study provides evolutionary and experimental evidence that supports the m6 A implication and the proviral roles of AlkB homologues in Potyvirus infection.
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Affiliation(s)
- Jianying Yue
- College of Horticulture and Plant ProtectionInner Mongolia Agricultural UniversityHohhotChina
| | - Yao Wei
- College of Horticulture and Plant ProtectionInner Mongolia Agricultural UniversityHohhotChina
| | - Zhenqi Sun
- College of Horticulture and Plant ProtectionInner Mongolia Agricultural UniversityHohhotChina
| | - Yahan Chen
- College of Plant ProtectionGansu Agricultural UniversityLanzhouChina
| | - Xuefeng Wei
- Development of Fine ChemicalsGuizhou UniversityGuizhouChina
| | - Haijuan Wang
- College of Horticulture and Plant ProtectionInner Mongolia Agricultural UniversityHohhotChina
| | - Fabio Pasin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones Científicas—Universitat Politècnica de València (CSIC‐UPV)ValenciaSpain
- School of ScienceUniversity of PaduaPaduaItaly
| | - Mingmin Zhao
- College of Horticulture and Plant ProtectionInner Mongolia Agricultural UniversityHohhotChina
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15
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Huang T, He WJ, Li C, Zhang JB, Liao YC, Song B, Yang P. Transcriptome-wide analyses of RNA m6A methylation in hexaploid wheat reveal its roles in mRNA translation regulation. FRONTIERS IN PLANT SCIENCE 2022; 13:917335. [PMID: 36092414 PMCID: PMC9453602 DOI: 10.3389/fpls.2022.917335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
N6-methyladenosine (m6A) is the most abundant RNA modification in eukaryotic messenger RNAs. m6A was discovered in wheat about 40 years ago; however, its potential roles in wheat remain unknown. In this study, we profiled m6As in spikelets transcriptome at the flowering stage of hexaploid wheat and found that m6As are evenly distributed across the A, B, and D subgenomes but their extents and locations vary across homeologous genes. m6As are enriched in homeologous genes with close expression levels and the m6A methylated genes are more conserved. The extent of m6A methylation is negatively correlated with mRNA expression levels and its presence on mRNAs has profound impacts on mRNA translation in a location-dependent manner. Specifically, m6As within coding sequences and 3'UTRs repress the translation of mRNAs while the m6As within 5'UTRs and start codons could promote it. The m6A-containing mRNAs are significantly enriched in processes and pathways of "translation" and "RNA transport," suggesting the potential role of m6As in regulating the translation of genes involved in translation regulation. Our data also show a stronger translation inhibition by small RNAs (miRNA and phasiRNA) than by m6A methylation, and no synergistical effect between the two was observed. We propose a secondary amplification machinery of translation regulation triggered by the changes in m6A methylation status. Taken together, our results suggest translation regulation as a key role played by m6As in hexaploid wheat.
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Affiliation(s)
- Tao Huang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wei-Jie He
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Cheng Li
- College of Agriculture, Shihezi University, Shihezi, China
| | - Jing-Bo Zhang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yu-Cai Liao
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bo Song
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Peng Yang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Jiangsu Ruihua Agricultural Science and Technology Co., Ltd., Suqian, China
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16
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Impact of the Potential m6A Modification Sites at the 3′UTR of Alfalfa Mosaic Virus RNA3 in the Viral Infection. Viruses 2022; 14:v14081718. [PMID: 36016339 PMCID: PMC9414508 DOI: 10.3390/v14081718] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/02/2022] [Indexed: 12/10/2022] Open
Abstract
We have previously reported the presence of m6A in the AMV (Alfamovirus, Bromoviridae) genome. Interestingly, two of these putative m6A-sites are in hairpin (hp) structures in the 3’UTR of the viral RNA3. One site (2012AAACU2016) is in the loop of hpB, within the coat protein binding site 1 (CPB1), while the other (1900UGACC1904) is in the lower stem of hpE, a loop previously associated with AMV negative-strand RNA synthesis. In this work, we have performed in vivo experiments to assess the role of these two regions, containing the putative m6A-sites in the AMV cycle, by introducing compensatory point mutations to interfere with or abolish the m6A-tag of these sites. Our results suggest that the loop of hpB could be involved in viral replication/accumulation. Meanwhile, in the 1900UGACC1904 motif of the hpE, the maintenance of the adenosine residue and the lower stem hpE structure are necessary for in vivo plus-strand accumulation. These results extend our understanding of the requirements for hpE in the AMV infection cycle, indicating that both the residue identity and the base-pairing capacity in this structure are essential for viral accumulation.
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17
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Alvarado-Marchena L, Martínez-Pérez M, Aparicio F, Pallas V, Maumus F. Recent Acquisition of Functional m6A RNA Demethylase Domain in Orchid Ty3/Gypsy Elements. FRONTIERS IN PLANT SCIENCE 2022; 13:939843. [PMID: 35860540 PMCID: PMC9289625 DOI: 10.3389/fpls.2022.939843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Long terminal repeats (LTR) retrotransposons are transposable elements (TEs) representing major components of most plant genomes. The fixation of additional conserved protein domains in their genomes is considered a rare event in the course of their evolution. Such changes can bring novel functions and increase their fitness by playing a role in the regulation of their replicative cycle or by affecting their integration landscape so that the detection of new domains can in turn reveal important aspects of host-TE interactions. We have mined angiosperm genomes for the presence of additional domains in LTR retrotransposons. We report a lineage of large (25 kbp) Gypsy-type elements in the genomes of Phalaenopsis orchids that contain an additional open reading frame containing a 2-ODD domain with close similarity to those responsible for m6A RNA demethylase activity in AlkB proteins. By performing in vitro assays, we demonstrate the RNA binding capability and the demethylase activity of the Gypsy-encoded AlkB protein, suggesting it could be functional against cognate TE mRNA or any cellular RNA in planta. In line with recent literature, we propose that the fixation of an RNA demethylase in this lineage of LTR retrotransposons may reflect an important role for epitranscriptomic control in host surveillance against TEs.
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Affiliation(s)
- Luis Alvarado-Marchena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Ingeniero Fausto Elio, Spain
| | - Mireya Martínez-Pérez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Ingeniero Fausto Elio, Spain
| | - Frederic Aparicio
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Ingeniero Fausto Elio, Spain
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Ingeniero Fausto Elio, Spain
| | - Florian Maumus
- INRAE, URGI, Université Paris-Saclay, Versailles, France
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18
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Shoaib Y, Usman B, Kang H, Jung KH. Epitranscriptomics: An Additional Regulatory Layer in Plants' Development and Stress Response. PLANTS (BASEL, SWITZERLAND) 2022; 11:1033. [PMID: 35448761 PMCID: PMC9027318 DOI: 10.3390/plants11081033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Epitranscriptomics has added a new layer of regulatory machinery to eukaryotes, and the advancement of sequencing technology has revealed more than 170 post-transcriptional modifications in various types of RNAs, including messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and long non-coding RNA (lncRNA). Among these, N6-methyladenosine (m6A) and N5-methylcytidine (m5C) are the most prevalent internal mRNA modifications. These regulate various aspects of RNA metabolism, mainly mRNA degradation and translation. Recent advances have shown that regulation of RNA fate mediated by these epitranscriptomic marks has pervasive effects on a plant's development and responses to various biotic and abiotic stresses. Recently, it was demonstrated that the removal of human-FTO-mediated m6A from transcripts in transgenic rice and potatoes caused a dramatic increase in their yield, and that the m6A reader protein mediates stress responses in wheat and apple, indicating that regulation of m6A levels could be an efficient strategy for crop improvement. However, changing the overall m6A levels might have unpredictable effects; therefore, the identification of precise m6A levels at a single-base resolution is essential. In this review, we emphasize the roles of epitranscriptomic modifications in modulating molecular, physiological, and stress responses in plants, and provide an outlook on epitranscriptome engineering as a promising tool to ensure food security by editing specific m6A and m5C sites through robust genome-editing technology.
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Affiliation(s)
- Yasira Shoaib
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
| | - Babar Usman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea;
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
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