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Issa A, Schlotter F, Flayac J, Chen J, Wacheul L, Philippe M, Sardini L, Mostefa L, Vandermoere F, Bertrand E, Verheggen C, Lafontaine DL, Massenet S. The nucleolar phase of signal recognition particle assembly. Life Sci Alliance 2024; 7:e202402614. [PMID: 38858088 PMCID: PMC11165425 DOI: 10.26508/lsa.202402614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024] Open
Abstract
The signal recognition particle is essential for targeting transmembrane and secreted proteins to the endoplasmic reticulum. Remarkably, because they work together in the cytoplasm, the SRP and ribosomes are assembled in the same biomolecular condensate: the nucleolus. How important is the nucleolus for SRP assembly is not known. Using quantitative proteomics, we have investigated the interactomes of SRP components. We reveal that SRP proteins are associated with scores of nucleolar proteins important for ribosome biogenesis and nucleolar structure. Having monitored the subcellular distribution of SRP proteins upon controlled nucleolar disruption, we conclude that an intact organelle is required for their proper localization. Lastly, we have detected two SRP proteins in Cajal bodies, which indicates that previously undocumented steps of SRP assembly may occur in these bodies. This work highlights the importance of a structurally and functionally intact nucleolus for efficient SRP production and suggests that the biogenesis of SRP and ribosomes may be coordinated in the nucleolus by common assembly factors.
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Affiliation(s)
- Amani Issa
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Florence Schlotter
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Justine Flayac
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Jing Chen
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Ludivine Wacheul
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | | | - Lucas Sardini
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Lalia Mostefa
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
| | | | | | | | - Denis Lj Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Séverine Massenet
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
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2
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Horner SM, Reaves JV. Recent insights into N 6-methyladenosine during viral infection. Curr Opin Genet Dev 2024; 87:102213. [PMID: 38901100 DOI: 10.1016/j.gde.2024.102213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/15/2024] [Accepted: 06/03/2024] [Indexed: 06/22/2024]
Abstract
The RNA modification of N6-methyladenosine (m6A) controls many aspects of RNA function that impact biological processes, including viral infection. In this review, we highlight recent work that shapes our current understanding of the diverse mechanisms by which m6A can regulate viral infection by acting on viral or cellular mRNA molecules. We focus on emerging concepts and understanding, including how viral infection alters the localization and function of m6A machinery proteins, how m6A regulates antiviral innate immunity, and the multiple roles of m6A in regulating specific viral infections. We also summarize the recent studies on m6A during SARS-CoV-2 infection, focusing on points of convergence and divergence. Ultimately, this review provides a snapshot of the latest research on m6A during viral infection.
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Affiliation(s)
- Stacy M Horner
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Jordan V Reaves
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA
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3
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Baquero-Pérez B, Bortoletto E, Rosani U, Delgado-Tejedor A, Medina R, Novoa EM, Venier P, Díez J. Elucidation of the Epitranscriptomic RNA Modification Landscape of Chikungunya Virus. Viruses 2024; 16:945. [PMID: 38932237 PMCID: PMC11209572 DOI: 10.3390/v16060945] [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: 05/02/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
The genomes of positive-sense (+) single-stranded RNA (ssRNA) viruses are believed to be subjected to a wide range of RNA modifications. In this study, we focused on the chikungunya virus (CHIKV) as a model (+) ssRNA virus to study the landscape of viral RNA modification in infected human cells. Among the 32 distinct RNA modifications analysed by mass spectrometry, inosine was found enriched in the genomic CHIKV RNA. However, orthogonal validation by Illumina RNA-seq analyses did not identify any inosine modification along the CHIKV RNA genome. Moreover, CHIKV infection did not alter the expression of ADAR1 isoforms, the enzymes that catalyse the adenosine to inosine conversion. Together, this study highlights the importance of a multidisciplinary approach to assess the presence of RNA modifications in viral RNA genomes.
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Affiliation(s)
- Belinda Baquero-Pérez
- Molecular Virology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Enrico Bortoletto
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; (E.B.); (U.R.)
| | - Umberto Rosani
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; (E.B.); (U.R.)
| | - Anna Delgado-Tejedor
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; (A.D.-T.); (R.M.); (E.M.N.)
| | - Rebeca Medina
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; (A.D.-T.); (R.M.); (E.M.N.)
| | - Eva Maria Novoa
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; (A.D.-T.); (R.M.); (E.M.N.)
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Paola Venier
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; (E.B.); (U.R.)
| | - Juana Díez
- Molecular Virology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
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4
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Mansfield KD. RNA Binding by the m6A Methyltransferases METTL16 and METTL3. BIOLOGY 2024; 13:391. [PMID: 38927271 PMCID: PMC11200852 DOI: 10.3390/biology13060391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/10/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024]
Abstract
Methyltransferases are a wide-ranging, yet well-conserved, class of molecules that have been found to modify a wide variety of substrates. Interest in RNA methylation has surged in recent years with the identification of the major eukaryotic mRNA m6A methyltransferase METTL3. METTL16 has also been identified as an RNA m6A methyltransferase; however, much less is known about its targets and actions. Interestingly, in addition to their catalytic activities, both METTL3 and METTL16 also have "methylation-independent" functions, including translational regulation, which have been discovered. However, evidence suggests that METTL16's role as an RNA-binding protein may be more significant than is currently recognized. In this review, we will introduce RNA methylation, specifically m6A, and the enzymes responsible for its deposition. We will discuss the varying roles that these enzymes perform and delve deeper into their RNA targets and possible roles as methylation-independent RNA binding proteins. Finally, we will touch upon the many open questions still remaining.
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Affiliation(s)
- Kyle D Mansfield
- Biochemistry and Molecular Biology Department, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
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5
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Picavet LW, van Vroonhoven ECN, Scholman RC, Smits YTH, Banerjee R, Besteman SB, Viveen MC, van der Vlist MM, Tanenbaum ME, Lebbink RJ, Vastert SJ, van Loosdregt J. m 6A Reader YTHDC1 Impairs Respiratory Syncytial Virus Infection by Downregulating Membrane CX3CR1 Expression. Viruses 2024; 16:778. [PMID: 38793659 PMCID: PMC11125786 DOI: 10.3390/v16050778] [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: 04/03/2024] [Revised: 05/02/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
Respiratory syncytial virus (RSV) is the most prevalent cause of acute lower respiratory infection in young children. Currently, the first RSV vaccines are approved by the FDA. Recently, N6-methyladenosine (m6A) RNA methylation has been implicated in the regulation of the viral life cycle and replication of many viruses, including RSV. m6A methylation of RSV RNA has been demonstrated to promote replication and prevent anti-viral immune responses by the host. Whether m6A is also involved in viral entry and whether m6A can also affect RSV infection via different mechanisms than methylation of viral RNA is poorly understood. Here, we identify m6A reader YTH domain-containing protein 1 (YTHDC1) as a novel negative regulator of RSV infection. We demonstrate that YTHDC1 abrogates RSV infection by reducing the expression of RSV entry receptor CX3C motif chemokine receptor 1 (CX3CR1) on the cell surface of lung epithelial cells. Altogether, these data reveal a novel role for m6A methylation and YTHDC1 in the viral entry of RSV. These findings may contribute to the development of novel treatment options to control RSV infection.
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Affiliation(s)
- Lucas W. Picavet
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (L.W.P.); (E.C.N.v.V.); (R.C.S.); (M.C.V.); (M.M.v.d.V.); (S.J.V.)
| | - Ellen C. N. van Vroonhoven
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (L.W.P.); (E.C.N.v.V.); (R.C.S.); (M.C.V.); (M.M.v.d.V.); (S.J.V.)
| | - Rianne C. Scholman
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (L.W.P.); (E.C.N.v.V.); (R.C.S.); (M.C.V.); (M.M.v.d.V.); (S.J.V.)
| | - Yesper T. H. Smits
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (L.W.P.); (E.C.N.v.V.); (R.C.S.); (M.C.V.); (M.M.v.d.V.); (S.J.V.)
| | - Rupa Banerjee
- Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands (M.E.T.)
- Oncode Institute, 3584 CX Utrecht, The Netherlands
| | - Sjanna B. Besteman
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (L.W.P.); (E.C.N.v.V.); (R.C.S.); (M.C.V.); (M.M.v.d.V.); (S.J.V.)
| | - Mattheus C. Viveen
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (L.W.P.); (E.C.N.v.V.); (R.C.S.); (M.C.V.); (M.M.v.d.V.); (S.J.V.)
| | - Michiel M. van der Vlist
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (L.W.P.); (E.C.N.v.V.); (R.C.S.); (M.C.V.); (M.M.v.d.V.); (S.J.V.)
- Oncode Institute, 3584 CX Utrecht, The Netherlands
| | - Marvin E. Tanenbaum
- Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands (M.E.T.)
- Oncode Institute, 3584 CX Utrecht, The Netherlands
- Department of Bionanoscience, Delft University of Technology, 2600 AA Delft, The Netherlands
| | - Robert J. Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands;
| | - Sebastiaan J. Vastert
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (L.W.P.); (E.C.N.v.V.); (R.C.S.); (M.C.V.); (M.M.v.d.V.); (S.J.V.)
| | - Jorg van Loosdregt
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (L.W.P.); (E.C.N.v.V.); (R.C.S.); (M.C.V.); (M.M.v.d.V.); (S.J.V.)
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6
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Yang M, Zheng X, Fan J, Cheng W, Yan TM, Lai Y, Zhang N, Lu Y, Qi J, Huo Z, Xu Z, Huang J, Jiao Y, Liu B, Pang R, Zhong X, Huang S, Luo GZ, Lee G, Jobin C, Eren AM, Chang EB, Wei H, Pan T, Wang X. Antibiotic-Induced Gut Microbiota Dysbiosis Modulates Host Transcriptome and m 6A Epitranscriptome via Bile Acid Metabolism. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2307981. [PMID: 38713722 DOI: 10.1002/advs.202307981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 04/15/2024] [Indexed: 05/09/2024]
Abstract
Gut microbiota can influence host gene expression and physiology through metabolites. Besides, the presence or absence of gut microbiome can reprogram host transcriptome and epitranscriptome as represented by N6-methyladenosine (m6A), the most abundant mammalian mRNA modification. However, which and how gut microbiota-derived metabolites reprogram host transcriptome and m6A epitranscriptome remain poorly understood. Here, investigation is conducted into how gut microbiota-derived metabolites impact host transcriptome and m6A epitranscriptome using multiple mouse models and multi-omics approaches. Various antibiotics-induced dysbiotic mice are established, followed by fecal microbiota transplantation (FMT) into germ-free mice, and the results show that bile acid metabolism is significantly altered along with the abundance change in bile acid-producing microbiota. Unbalanced gut microbiota and bile acids drastically change the host transcriptome and the m6A epitranscriptome in multiple tissues. Mechanistically, the expression of m6A writer proteins is regulated in animals treated with antibiotics and in cultured cells treated with bile acids, indicating a direct link between bile acid metabolism and m6A biology. Collectively, these results demonstrate that antibiotic-induced gut dysbiosis regulates the landscape of host transcriptome and m6A epitranscriptome via bile acid metabolism pathway. This work provides novel insights into the interplay between microbial metabolites and host gene expression.
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Affiliation(s)
- Meng Yang
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xiaoqi Zheng
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jiajun Fan
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Wei Cheng
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tong-Meng Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau, 999078, China
| | - Yushan Lai
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Nianping Zhang
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yi Lu
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jiali Qi
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Zhengyi Huo
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Zihe Xu
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jia Huang
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yuting Jiao
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Biaodi Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Xiang Zhong
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shi Huang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Guan-Zheng Luo
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Gina Lee
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Irvine, CA, 92697, USA
| | - Christian Jobin
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | - A Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity, 26129, Oldenburg, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129, Oldenburg, Germany
| | - Eugene B Chang
- Department of Medicine, Knapp Center for Biomedical Discovery, The University of Chicago Knapp Center for Biomedical Discovery, Chicago, IL, 60637, USA
| | - Hong Wei
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiaoyun Wang
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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7
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Sinha S, Singh K, Ravi Kumar YS, Roy R, Phadnis S, Meena V, Bhattacharyya S, Verma B. Dengue virus pathogenesis and host molecular machineries. J Biomed Sci 2024; 31:43. [PMID: 38649998 PMCID: PMC11036733 DOI: 10.1186/s12929-024-01030-9] [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: 01/24/2024] [Accepted: 04/14/2024] [Indexed: 04/25/2024] Open
Abstract
Dengue viruses (DENV) are positive-stranded RNA viruses belonging to the Flaviviridae family. DENV is the causative agent of dengue, the most rapidly spreading viral disease transmitted by mosquitoes. Each year, millions of people contract the virus through bites from infected female mosquitoes of the Aedes species. In the majority of individuals, the infection is asymptomatic, and the immune system successfully manages to control virus replication within a few days. Symptomatic individuals may present with a mild fever (Dengue fever or DF) that may or may not progress to a more critical disease termed Dengue hemorrhagic fever (DHF) or the fatal Dengue shock syndrome (DSS). In the absence of a universally accepted prophylactic vaccine or therapeutic drug, treatment is mostly restricted to supportive measures. Similar to many other viruses that induce acute illness, DENV has developed several ways to modulate host metabolism to create an environment conducive to genome replication and the dissemination of viral progeny. To search for new therapeutic options, understanding the underlying host-virus regulatory system involved in various biological processes of the viral life cycle is essential. This review aims to summarize the complex interaction between DENV and the host cellular machinery, comprising regulatory mechanisms at various molecular levels such as epigenetic modulation of the host genome, transcription of host genes, translation of viral and host mRNAs, post-transcriptional regulation of the host transcriptome, post-translational regulation of viral proteins, and pathways involved in protein degradation.
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Affiliation(s)
- Saumya Sinha
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Kinjal Singh
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Y S Ravi Kumar
- Department of Biotechnology, M. S. Ramaiah Institute of Technology, MSR Nagar, Bengaluru, India
| | - Riya Roy
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Sushant Phadnis
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Varsha Meena
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Bhupendra Verma
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
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8
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Horner SM, Thompson MG. Challenges to mapping and defining m 6A function in viral RNA. RNA (NEW YORK, N.Y.) 2024; 30:482-490. [PMID: 38531643 PMCID: PMC11019751 DOI: 10.1261/rna.079959.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Viral RNA molecules contain multiple layers of regulatory information. This includes features beyond the primary sequence, such as RNA structures and RNA modifications, including N6-methyladenosine (m6A). Many recent studies have identified the presence and location of m6A in viral RNA and have found diverse regulatory roles for this modification during viral infection. However, to date, viral m6A mapping strategies have limitations that prevent a complete understanding of the function of m6A on individual viral RNA molecules. While m6A sites have been profiled on bulk RNA from many viruses, the resulting m6A maps of viral RNAs described to date present a composite picture of m6A across viral RNA molecules in the infected cell. Thus, for most viruses, it is unknown if unique viral m6A profiles exist throughout infection, nor if they regulate specific viral life cycle stages. Here, we describe several challenges to defining the function of m6A in viral RNA molecules and provide a framework for future studies to help in the understanding of how m6A regulates viral infection.
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Affiliation(s)
- Stacy M Horner
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Matthew G Thompson
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina 27710, USA
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9
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Karandashov I, Kachanov A, Dukich M, Ponomareva N, Brezgin S, Lukashev A, Pokrovsky VS, Chulanov V, Kostyusheva A, Kostyushev D. m 6A Methylation in Regulation of Antiviral Innate Immunity. Viruses 2024; 16:601. [PMID: 38675942 PMCID: PMC11054785 DOI: 10.3390/v16040601] [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: 03/13/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
The epitranscriptomic modification m6A is a prevalent RNA modification that plays a crucial role in the regulation of various aspects of RNA metabolism. It has been found to be involved in a wide range of physiological processes and disease states. Of particular interest is the role of m6A machinery and modifications in viral infections, serving as an evolutionary marker for distinguishing between self and non-self entities. In this review article, we present a comprehensive overview of the epitranscriptomic modification m6A and its implications for the interplay between viruses and their host, focusing on immune responses and viral replication. We outline future research directions that highlight the role of m6A in viral nucleic acid recognition, initiation of antiviral immune responses, and modulation of antiviral signaling pathways. Additionally, we discuss the potential of m6A as a prognostic biomarker and a target for therapeutic interventions in viral infections.
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Affiliation(s)
- Ivan Karandashov
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia; (I.K.); (A.K.); (M.D.); (N.P.); (S.B.); (A.L.)
| | - Artyom Kachanov
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia; (I.K.); (A.K.); (M.D.); (N.P.); (S.B.); (A.L.)
| | - Maria Dukich
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia; (I.K.); (A.K.); (M.D.); (N.P.); (S.B.); (A.L.)
- Faculty of Virology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Natalia Ponomareva
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia; (I.K.); (A.K.); (M.D.); (N.P.); (S.B.); (A.L.)
- Division of Biotechnology, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Pharmaceutical and Toxicological Chemistry, Sechenov First Moscow State Medical University, 119048 Moscow, Russia
| | - Sergey Brezgin
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia; (I.K.); (A.K.); (M.D.); (N.P.); (S.B.); (A.L.)
- Division of Biotechnology, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Alexander Lukashev
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia; (I.K.); (A.K.); (M.D.); (N.P.); (S.B.); (A.L.)
| | - Vadim S. Pokrovsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia;
- Blokhin National Medical Research Center of Oncology, 117198 Moscow, Russia
- Faculty of Biochemistry, RUDN University, 117198 Moscow, Russia
| | - Vladimir Chulanov
- Department of Infectious Diseases, First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia;
| | - Anastasiya Kostyusheva
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia; (I.K.); (A.K.); (M.D.); (N.P.); (S.B.); (A.L.)
| | - Dmitry Kostyushev
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia; (I.K.); (A.K.); (M.D.); (N.P.); (S.B.); (A.L.)
- Division of Biotechnology, Sirius University of Science and Technology, 354340 Sochi, Russia
- Faculty of Bioengineering and Biotechnologies, Lomonosov Moscow State University, 119234 Moscow, Russia
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10
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Baquero-Pérez B, Yonchev ID, Delgado-Tejedor A, Medina R, Puig-Torrents M, Sudbery I, Begik O, Wilson SA, Novoa EM, Díez J. N 6-methyladenosine modification is not a general trait of viral RNA genomes. Nat Commun 2024; 15:1964. [PMID: 38467633 PMCID: PMC10928186 DOI: 10.1038/s41467-024-46278-9] [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: 09/27/2023] [Accepted: 02/16/2024] [Indexed: 03/13/2024] Open
Abstract
Despite the nuclear localization of the m6A machinery, the genomes of multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively m6A-modified. However, these findings are mostly based on m6A-Seq, an antibody-dependent technique with a high rate of false positives. Here, we address the presence of m6A in CHIKV and DENV RNAs. For this, we combine m6A-Seq and the antibody-independent SELECT and nanopore direct RNA sequencing techniques with functional, molecular, and mutagenesis studies. Following this comprehensive analysis, we find no evidence of m6A modification in CHIKV or DENV transcripts. Furthermore, depletion of key components of the host m6A machinery does not affect CHIKV or DENV infection. Moreover, CHIKV or DENV infection has no effect on the m6A machinery's localization. Our results challenge the prevailing notion that m6A modification is a general feature of cytoplasmic RNA viruses and underscore the importance of validating RNA modifications with orthogonal approaches.
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Affiliation(s)
- Belinda Baquero-Pérez
- Molecular Virology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Ivaylo D Yonchev
- Sheffield Institute for Nucleic Acids (SInFoNiA) and School of Biosciences, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Anna Delgado-Tejedor
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Rebeca Medina
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Mireia Puig-Torrents
- Molecular Virology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Ian Sudbery
- Sheffield Institute for Nucleic Acids (SInFoNiA) and School of Biosciences, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Oguzhan Begik
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Stuart A Wilson
- Sheffield Institute for Nucleic Acids (SInFoNiA) and School of Biosciences, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
| | - Eva Maria Novoa
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
| | - Juana Díez
- Molecular Virology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003, Barcelona, Spain.
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11
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Sun L, Chen X, Zhu S, Wang J, Diao S, Liu J, Xu J, Li X, Sun Y, Huang C, Meng X, Lv X, Li J. Decoding m 6A mRNA methylation by reader proteins in liver diseases. Genes Dis 2024; 11:711-726. [PMID: 37692496 PMCID: PMC10491919 DOI: 10.1016/j.gendis.2023.02.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/22/2023] [Indexed: 09/12/2023] Open
Abstract
N6-methyladenosine (m6A) is a dynamic and reversible epigenetic regulation. As the most prevalent internal post-transcriptional modification in eukaryotic RNA, it participates in the regulation of gene expression through various mechanisms, such as mRNA splicing, nuclear export, localization, translation efficiency, mRNA stability, and structural transformation. The involvement of m6A in the regulation of gene expression depends on the specific recognition of m6A-modified RNA by reader proteins. In the pathogenesis and treatment of liver disease, studies have found that the expression levels of key genes that promote or inhibit the development of liver disease are regulated by m6A modification, in which abnormal expression of reader proteins determines the fate of these gene transcripts. In this review, we introduce m6A readers, summarize the recognition and regulatory mechanisms of m6A readers on mRNA, and focus on the biological functions and mechanisms of m6A readers in liver cancer, viral hepatitis, non-alcoholic fatty liver disease (NAFLD), hepatic fibrosis (HF), acute liver injury (ALI), and other liver diseases. This information is expected to be of high value to researchers deciphering the links between m6A readers and human liver diseases.
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Affiliation(s)
- Lijiao Sun
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
- Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xin Chen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
- Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei, Anhui 230032, China
| | - Sai Zhu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- Department of Nephropathy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Jianan Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
| | - Shaoxi Diao
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
- Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jinyu Liu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
- Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jinjin Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
- Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xiaofeng Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
| | - Yingyin Sun
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, China
| | - Cheng Huang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
- Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xiaoming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
| | - Xiongwen Lv
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
- Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
- The Key Laboratory of Anti-inflammatory and Immune Medicines, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, China
- Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei, Anhui 230032, China
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12
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Moon JS, Lee W, Cho YH, Kim Y, Kim GW. The Significance of N6-Methyladenosine RNA Methylation in Regulating the Hepatitis B Virus Life Cycle. J Microbiol Biotechnol 2024; 34:233-239. [PMID: 37942519 PMCID: PMC10940779 DOI: 10.4014/jmb.2309.09013] [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: 09/08/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023]
Abstract
N6-methyladenosine (m6A) RNA methylation has recently emerged as a significant co-transcriptional modification involved in regulating various RNA functions. It plays a vital function in numerous biological processes. Enzymes referred to as m6A methyltransferases, such as the methyltransferaselike (METTL) 3-METTL14-Wilms tumor 1 (WT1)-associated protein (WTAP) complex, are responsible for adding m6A modifications, while m6A demethylases, including fat mass and obesity-associated protein (FTO) and alkB homolog 5 (ALKBH5), can remove m6A methylation. The functions of m6A-methylated RNA are regulated through the recognition and interaction of m6A reader proteins. Recent research has shown that m6A methylation takes place at multiple sites within hepatitis B virus (HBV) RNAs, and the location of these modifications can differentially impact the HBV infection. The addition of m6A modifications to HBV RNA can influence its stability and translation, thereby affecting viral replication and pathogenesis. Furthermore, HBV infection can also alter the m6A modification pattern of host RNA, indicating the virus's ability to manipulate host cellular processes, including m6A modification. This manipulation aids in establishing chronic infection, promoting liver disease, and contributing to pathogenesis. A comprehensive understanding of the functional roles of m6A modification during HBV infection is crucial for developing innovative approaches to combat HBV-mediated liver disease. In this review, we explore the functions of m6A modification in HBV replication and its impact on the development of liver disease.
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Affiliation(s)
- Jae-Su Moon
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wooseong Lee
- Center for Convergent Research of Emerging virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Yong-Hee Cho
- Data Convergence Drug Research Center, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
- Department of Medical Chemistry and Pharmacology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Yonghyo Kim
- Data Convergence Drug Research Center, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Geon-Woo Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 34134, Republic of Korea
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13
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Zhu M, Wu N, Zhong J, Chen C, Liu W, Ren Y, Wang X, Jin H. N 6-methyladenosine modification of the mRNA for a key gene in purine nucleotide metabolism regulates virus proliferation in an insect vector. Cell Rep 2024; 43:113821. [PMID: 38368611 DOI: 10.1016/j.celrep.2024.113821] [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: 09/11/2023] [Revised: 01/10/2024] [Accepted: 02/02/2024] [Indexed: 02/20/2024] Open
Abstract
The titer of viruses that persist and propagate in their insect vector must be high enough for transmission yet not harm the insect, but the mechanism of this dynamic balance is unclear. Here, expression of inosine monophosphate dehydrogenase (LsIMPDH), a rate-limiting enzyme for guanosine triphosphate (GTP) synthesis, is shown to be downregulated by increased levels of N6-methyladenosine (m6A) on LsIMPDH mRNA in rice stripe virus (RSV)-infected small brown planthoppers (SBPHs; Laodelphax striatellus), the RSV vector, which decreases GTP content, thus limiting viral proliferation. Moreover, planthopper methyltransferase-like protein 3 (LsMETTL3) and m6A reader protein LsYTHDF3 are found to catalyze and recognize the m6A on LsIMPDH mRNA, respectively, and cooperate in destabilizing LsIMPDH transcripts. Co-silencing assays show that negative regulation of viral proliferation by both LsMETTL3 and LsYTHDF3 is partially dependent on LsIMPDH. This distinct mechanism limits virus replication in an insect vector, providing a potential gene target to block viral transmission.
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Affiliation(s)
- Mengjie Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Nan Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiayi Zhong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chen Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yingdang Ren
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Huaibing Jin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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14
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Roy A, Ghosh A. Epigenetic Restriction Factors (eRFs) in Virus Infection. Viruses 2024; 16:183. [PMID: 38399958 PMCID: PMC10892949 DOI: 10.3390/v16020183] [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: 12/09/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The ongoing arms race between viruses and their hosts is constantly evolving. One of the ways in which cells defend themselves against invading viruses is by using restriction factors (RFs), which are cell-intrinsic antiviral mechanisms that block viral replication and transcription. Recent research has identified a specific group of RFs that belong to the cellular epigenetic machinery and are able to restrict the gene expression of certain viruses. These RFs can be referred to as epigenetic restriction factors or eRFs. In this review, eRFs have been classified into two categories. The first category includes eRFs that target viral chromatin. So far, the identified eRFs in this category include the PML-NBs, the KRAB/KAP1 complex, IFI16, and the HUSH complex. The second category includes eRFs that target viral RNA or, more specifically, the viral epitranscriptome. These epitranscriptomic eRFs have been further classified into two types: those that edit RNA bases-adenosine deaminase acting on RNA (ADAR) and pseudouridine synthases (PUS), and those that covalently modify viral RNA-the N6-methyladenosine (m6A) writers, readers, and erasers. We delve into the molecular machinery of eRFs, their role in limiting various viruses, and the mechanisms by which viruses have evolved to counteract them. We also examine the crosstalk between different eRFs, including the common effectors that connect them. Finally, we explore the potential for new discoveries in the realm of epigenetic networks that restrict viral gene expression, as well as the future research directions in this area.
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Affiliation(s)
- Arunava Roy
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
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15
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Dang Y, Li J, Li Y, Wang Y, Zhao Y, Zhao N, Li W, Zhang H, Ye C, Ma H, Zhang L, Liu H, Dong Y, Yao M, Lei Y, Xu Z, Zhang F, Ye W. N-acetyltransferase 10 regulates alphavirus replication via N4-acetylcytidine (ac4C) modification of the lymphocyte antigen six family member E (LY6E) mRNA. J Virol 2024; 98:e0135023. [PMID: 38169284 PMCID: PMC10805074 DOI: 10.1128/jvi.01350-23] [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: 11/19/2023] [Indexed: 01/05/2024] Open
Abstract
Epitranscriptomic RNA modifications can regulate the stability of mRNA and affect cellular and viral RNA functions. The N4-acetylcytidine (ac4C) modification in the RNA viral genome was recently found to promote viral replication; however, the mechanism by which RNA acetylation in the host mRNA regulates viral replication remains unclear. To help elucidate this mechanism, the roles of N-acetyltransferase 10 (NAT10) and ac4C during the infection and replication processes of the alphavirus, Sindbis virus (SINV), were investigated. Cellular NAT10 was upregulated, and ac4C modifications were promoted after alphavirus infection, while the loss of NAT10 or inhibition of its N-acetyltransferase activity reduced alphavirus replication. The NAT10 enhanced alphavirus replication as it helped to maintain the stability of lymphocyte antigen six family member E mRNA, which is a multifunctional interferon-stimulated gene that promotes alphavirus replication. The ac4C modification was thus found to have a non-conventional role in the virus life cycle through regulating host mRNA stability instead of viral mRNA, and its inhibition could be a potential target in the development of new alphavirus antivirals.IMPORTANCEThe role of N4-acetylcytidine (ac4C) modification in host mRNA and virus replication is not yet fully understood. In this study, the role of ac4C in the regulation of Sindbis virus (SINV), a prototype alphavirus infection, was investigated. SINV infection results in increased levels of N-acetyltransferase 10 (NAT10) and increases the ac4C modification level of cellular RNA. The NAT10 was found to positively regulate SINV infection in an N-acetyltransferase activity-dependent manner. Mechanistically, the NAT10 modifies lymphocyte antigen six family member E (LY6E) mRNA-the ac4C modification site within the 3'-untranslated region (UTR) of LY6E mRNA, which is essential for its translation and stability. The findings of this study demonstrate that NAT10 regulated mRNA stability and translation efficiency not only through the 5'-UTR or coding sequence but also via the 3'-UTR region. The ac4C modification of host mRNA stability instead of viral mRNA impacting the viral life cycle was thus identified, indicating that the inhibition of ac4C could be a potential target when developing alphavirus antivirals.
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Affiliation(s)
- Yamei Dang
- Department of Microbiology, Airforce Medical University (Fourth Military Medical University), Xi’an, Shaanxi, China
| | - Jia Li
- Department of Neurology, Xi’an International Medical Center Hospital, Xi’an, Shaanxi, China
| | - Yuchang Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Yuan Wang
- Department of Microbiology, Airforce Medical University (Fourth Military Medical University), Xi’an, Shaanxi, China
| | - Yajing Zhao
- Department of Oral and Maxillofacial Surgery, State Key Laboratory of Military Stomatology, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, School of Stomatology, Airforce Medical University (Fourth Military Medical University), Xi’an, Shaanxi, China
| | - Ningbo Zhao
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Wanying Li
- Department of Microbiology, Airforce Medical University (Fourth Military Medical University), Xi’an, Shaanxi, China
- Department of Pathogenic Biology, School of Preclinical Medicine, Yan’an University, Yan’an, Shaanxi, China
| | - Hui Zhang
- Department of Microbiology, Airforce Medical University (Fourth Military Medical University), Xi’an, Shaanxi, China
| | - Chuantao Ye
- Department of Infectious Diseases, Tangdu Hospital, Airforce Medical University (Fourth Military Medical University), Xi’an, Shaanxi, China
| | - Hongwei Ma
- Department of Microbiology, Airforce Medical University (Fourth Military Medical University), Xi’an, Shaanxi, China
| | - Liang Zhang
- Department of Microbiology, Airforce Medical University (Fourth Military Medical University), Xi’an, Shaanxi, China
| | - He Liu
- Department of Microbiology, Airforce Medical University (Fourth Military Medical University), Xi’an, Shaanxi, China
| | - Yangchao Dong
- Department of Microbiology, Airforce Medical University (Fourth Military Medical University), Xi’an, Shaanxi, China
| | - Min Yao
- Department of Microbiology, Airforce Medical University (Fourth Military Medical University), Xi’an, Shaanxi, China
| | - Yingfeng Lei
- Department of Microbiology, Airforce Medical University (Fourth Military Medical University), Xi’an, Shaanxi, China
| | - Zhikai Xu
- Department of Microbiology, Airforce Medical University (Fourth Military Medical University), Xi’an, Shaanxi, China
| | - Fanglin Zhang
- Department of Microbiology, Airforce Medical University (Fourth Military Medical University), Xi’an, Shaanxi, China
| | - Wei Ye
- Department of Microbiology, Airforce Medical University (Fourth Military Medical University), Xi’an, Shaanxi, China
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16
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Yao M, Cheng Z, Li X, Li Y, Ye W, Zhang H, Liu H, Zhang L, Lei Y, Zhang F, Lv X. N6-methyladenosine modification positively regulate Japanese encephalitis virus replication. Virol J 2024; 21:23. [PMID: 38243270 PMCID: PMC10799421 DOI: 10.1186/s12985-023-02275-w] [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: 10/19/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024] Open
Abstract
N6-methyladenosine (m6A) is present in diverse viral RNA and plays important regulatory roles in virus replication and host antiviral innate immunity. However, the role of m6A in regulating JEV replication has not been investigated. Here, we show that the JEV genome contains m6A modification upon infection of mouse neuroblast cells (neuro2a). JEV infection results in a decrease in the expression of m6A writer METTL3 in mouse brain tissue. METTL3 knockdown by siRNA leads to a substantial decrease in JEV replication and the production of progeny viruses at 48 hpi. Mechanically, JEV triggered a considerable increase in the innate immune response of METTL3 knockdown neuro2a cells compared to the control cells. Our study has revealed the distinctive m6A signatures of both the virus and host in neuro2a cells infected with JEV, illustrating the positive role of m6A modification in JEV infection. Our study further enhances understanding of the role of m6A modification in Flaviviridae viruses.
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Affiliation(s)
- Min Yao
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
| | - Zhirong Cheng
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
- College of Life Science, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Xueyun Li
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
- College of Basic Medicine, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Yuexiang Li
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
| | - Wei Ye
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
| | - Hui Zhang
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
| | - He Liu
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
| | - Liang Zhang
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
| | - Yingfeng Lei
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
| | - Fanglin Zhang
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China.
| | - Xin Lv
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China.
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17
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Tao X, Wang G, Wei W, Su J, Chen X, Shi M, Liao Y, Qin T, Wu Y, Lu B, Liang H, Ye L, Jiang J. A bibliometric analysis of m6A methylation in viral infection from 2000 to 2022. Virol J 2024; 21:20. [PMID: 38238848 PMCID: PMC10797797 DOI: 10.1186/s12985-024-02294-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 01/11/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) methylation has become an active research area in viral infection, while little bibliometric analysis has been performed. In this study, we aim to visualize hotspots and trends using bibliometric analysis to provide a comprehensive and objective overview of the current research dynamics in this field. METHODS The data related to m6A methylation in viral infection were obtained through the Web of Science Core Collection form 2000 to 2022. To reduce bias, the literature search was conducted on December 1, 2022. Bibliometric and visual analyzes were performed using CiteSpace and Bibliometrix package. After screening, 319 qualified records were retrieved. RESULTS These publications mainly came from 28 countries led by China and the United States (the US), with the US ranking highest in terms of total link strength.The most common keywords were m6A, COVID-19, epitranscriptomics, METTL3, hepatitis B virus, innate immunity and human immunodeficiency virus 1. The thematic map showed that METTL3, plant viruses, cancer progression and type I interferon (IFN-I) reflected a good development trend and might become a research hotspot in the future, while post-transcriptional modification, as an emerging or declining theme, might not develop well. CONCLUSIONS In conclusion, m6A methylation in viral infection is an increasingly important topic in articles. METTL3, plant viruses, cancer progression and IFN-I may still be research hotspots and trends in the future.
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Affiliation(s)
- Xing Tao
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Gang Wang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Wudi Wei
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
- Biosafety Level -3 Laboratory, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Jinming Su
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
- Biosafety Level -3 Laboratory, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiu Chen
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Minjuan Shi
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Yinlu Liao
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Tongxue Qin
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Yuting Wu
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Beibei Lu
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China.
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China.
- Biosafety Level -3 Laboratory, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China.
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China.
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China.
| | - Junjun Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China.
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China.
- Biosafety Level -3 Laboratory, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China.
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18
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Zhang L, Huang X, Wang D, Fan C, Jiang H, Xie D. Transcriptomic evaluation of N6-methyladenosine modification can be used to identify differentially gene and immune-related biological processes in TX mice with liver fibrosis. Mol Biol Rep 2024; 51:149. [PMID: 38236359 DOI: 10.1007/s11033-023-09163-0] [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: 08/16/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND N6-methyladenosine (m6A) modification controls the stability, splicing, and translation of mRNA, which is important in the development of illnesses. Wilson's disease (WD) is an autosomal recessive liver copper metabolic disorder that causes liver fibrosis. The role of m6A methylation in WD-induced liver fibrosis development is still unclear. Thus, the goal of this study was to examine the scope of m6A methylation and further explore the potential targets related to WD-induced liver fibrosis. RESULTS A total of 1930 significantly different m6A peaks were found on 1737 mRNAs, of which 993 were hypermethylated and 744 were hypomethylated when comparing normal and WD-induced liver fibrosis mice (n = 3). In parallel, 1261 differentially expressed mRNAs, comprising 557 upregulated and 704 downregulated mRNAs, were found. Overall, 114 mRNAs with significant changes in m6A levels and RNA expression were identified via joint analysis. Then, through PPI network construction and functional enrichment analysis, 12 hub genes were identified, these genes were mainly enriched in the inflammatory response and immunomodulation, and they are associated with immune cell infiltration. CONCLUSIONS The significant difference in the amount of mRNA m6A modifications indicates that m6A modification is involved in the progression of WD-induced liver fibrosis, and theidentified hub genes are involved in inflammation and immune infiltration. These results may provide insights for subsequent studies on potential regulatory mechanisms.
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Affiliation(s)
- Lili Zhang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Xiaofeng Huang
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Dan Wang
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Chang Fan
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Hui Jiang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
| | - Daojun Xie
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
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19
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Ding S, Liu H, Liu L, Ma L, Chen Z, Zhu M, Liu L, Zhang X, Hao H, Zuo L, Yang J, Wu X, Zhou P, Huang F, Zhu F, Guan W. Epigenetic addition of m 5C to HBV transcripts promotes viral replication and evasion of innate antiviral responses. Cell Death Dis 2024; 15:39. [PMID: 38216565 PMCID: PMC10786922 DOI: 10.1038/s41419-023-06412-9] [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: 08/18/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 01/14/2024]
Abstract
Eukaryotic five-methylcytosine (m5C) is an important regulator of viral RNA splicing, stability, and translation. However, its role in HBV replication remains largely unknown. In this study, functional m5C sites are identified in hepatitis B virus (HBV) mRNA. The m5C modification at nt 1291 is not only indispensable for Aly/REF export factor (ALYREF) recognition to promote viral mRNA export and HBx translation but also for the inhibition of RIG-I binding to suppress interferon-β (IFN-β) production. Moreover, NOP2/Sun RNA methyltransferase 2 (NSUN2) catalyzes the addition of m5C to HBV mRNA and is transcriptionally downregulated by the viral protein HBx, which suppresses the binding of EGR1 to the NSUN2 promoter. Additionally, NSUN2 expression correlates with m5C modification of type I IFN mRNA in host cells, thus, positively regulating IFN expression. Hence, the delicate regulation of NSUN2 expression induces m5C modification of HBV mRNA while decreasing the levels of m5C in host IFN mRNA, making it a vital component of the HBV life cycle. These findings provide new molecular insights into the mechanism of HBV-mediated IFN inhibition and may inform the development of new IFN-α based therapies.
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Affiliation(s)
- Shuang Ding
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Haibin Liu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
- Hubei JiangXia Laboratory, Wuhan, Hubei, 430200, China
| | - Lijuan Liu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Li Ma
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Zhen Chen
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Miao Zhu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Lishi Liu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Xueyan Zhang
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Haojie Hao
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Li Zuo
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Jingwen Yang
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Xiulin Wu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Ping Zhou
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Fang Huang
- Hubei JiangXia Laboratory, Wuhan, Hubei, 430200, China
| | - Fan Zhu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China.
- Hubei Province Key Laboratory of Allergy & Immunology, Wuhan University, Wuhan, Hubei, 430071, China.
| | - Wuxiang Guan
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China.
- Hubei JiangXia Laboratory, Wuhan, Hubei, 430200, China.
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20
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Coutts HL, Courtney DG. Identifying Individual Pseudouridine (Ψ) Sites Across Transcripts from HIV-1 Infected Cells. Methods Mol Biol 2024; 2807:229-242. [PMID: 38743232 DOI: 10.1007/978-1-0716-3862-0_16] [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: 05/16/2024]
Abstract
The identification of RNA modifications at single nucleotide resolution has become an emerging area of interest within biology and specifically among virologists seeking to ascertain how this untapped area of RNA regulation may be altered or hijacked upon viral infection. Herein, we describe a straightforward biochemical approach modified from two original published Ψ mapping protocols, BID-seq and PRAISE, to specifically identify pseudouridine modifications on mRNA transcripts from an HIV-1 infected T cell line. This protocol could readily be adapted for other viral infected cell types and additionally for populations of purified virions from infected cells.
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Affiliation(s)
- Hannah L Coutts
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - David G Courtney
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK.
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21
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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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22
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Chen Y, Wang W, Zhang W, He M, Li Y, Qu G, Tong J. Emerging roles of biological m 6A proteins in regulating virus infection: A review. Int J Biol Macromol 2023; 253:126934. [PMID: 37722640 DOI: 10.1016/j.ijbiomac.2023.126934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
N6-methyladenosine (m6A) is the most prevalent chemical modifications of intracellular RNA, which recently emerging as a multifaceted effector of viral genomic RNA. As a dynamic process, three groups of biological proteins control the levels of m6A modification in eukaryocyte, designed as m6A writers, erasers, and readers. The m6A writers comprising of methyltransferases complex initiate the modification process. On the contrary, the m6A erasers ALKBH5 or FTO abolish the modification through three-step demethylation: m6A to N6-hydroxymethyl adenosine (hm6A), then hm6A to N6-methyladenosine (f6A), and finally f6A to adenosine. The known m6A readers include the YTH family and the hnRNP family. As m6A modification regulates RNA nuclear exportation, stability, and translation, m6A proteins commonly participate in virus infection by regulating viral genomic RNA synthesis. Moreover, m6A proteins establish molecular linkages between virus genome/viral encode proteins and host cells proteins via their multifunctional roles in cellular RNA metabolism. The m6A writers and erasers directly impact interferon expression and macrophage innate immune responses, facilitating them to act as anti-/pro-viral factors. The m6A readers enable to alter cell metabolism and stress granules (SGs) production to regulate virus-host interactions. Here, the latest progress of m6A proteins in regulating viral infection is reviewed. Demonstrating the roles of m6A proteins will enhance the understanding of epigenetic regulation of virus infection and stimulate the development of novel antiviral strategies.
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Affiliation(s)
- Yuran Chen
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Wenjing Wang
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Wuchao Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Mei He
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Yuming Li
- School of Public Health, Shandong First Medical University, Shandong Academy of Medical Sciences, Ji'nan 250117, China; Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University, Shandong Academy of Medical Sciences, Tai'an 271000, China.
| | - Guosheng Qu
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China.
| | - Jie Tong
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China.
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23
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He H, Jia M, Liu J, Zhou X, Li F. Roles of RNA m 6A modifications in plant-virus interactions. STRESS BIOLOGY 2023; 3:57. [PMID: 38105385 PMCID: PMC10725857 DOI: 10.1007/s44154-023-00133-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 10/31/2023] [Indexed: 12/19/2023]
Abstract
Viral RNAs have been known to contain N6-methyladenosine (m6A) modifications since the 1970s. The function of these modifications remained unknown until the development of genome-wide methods to map m6A residues. Increasing evidence has recently revealed a strong association between m6A modifications and plant viral infection. This highlight introduces advances in the roles of RNA m6A modifications in plant-virus interactions.
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Affiliation(s)
- Hao He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingxuan Jia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
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24
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Li C, Wu X, Yang Y, Shi J, Wang S, Li J, Tian Y, Liu C, Han H, Xu S, Han X, Ma Y, Zheng L, Li J. METTL14 and FTO mediated m 6A modification regulate PCV2 replication by affecting miR-30a-5p maturity. Virulence 2023; 14:2232910. [PMID: 37418592 PMCID: PMC10332184 DOI: 10.1080/21505594.2023.2232910] [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: 02/15/2023] [Revised: 05/16/2023] [Accepted: 06/26/2023] [Indexed: 07/09/2023] Open
Abstract
The epigenetic modification of the N6-methyladenosine (m6A) methylation plays an important role in virus infection and replication. However, its role in Porcine circovirus type 2 (PCV2) replication has not been well studied. Here, we demonstrated that m6A modifications are increased in PK-15 cells after PCV2 infection. In particular, PCV2 infection could increase the expression of methyltransferase METTL14 and demethylase FTO. Moreover, interfering with METTL14 accumulation reduced the m6A methylation level and virus reproduction, whereas depleting the FTO demethylase enhanced the m6A methylation level and stimulated virus reproduction. Besides, we showed that METTL14 and FTO regulate PCV2 replication by affecting the process of miRNA maturity, especially the miRNA-30a-5p. Taken together, our results demonstrated that the m6A modification positively affects PCV2 replication and the role of m6A modification in the replication mechanism of the PCV2 virus provides a new idea for the prevention and control of the PCV2.
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Affiliation(s)
- Chen Li
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, jinan, P. R. China
| | - Xiaoyan Wu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, jinan, P. R. China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Ying Yang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jianli Shi
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, jinan, P. R. China
| | - Shuo Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Qingdao, China
| | - Jiaxin Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Yao Tian
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Chang Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, jinan, P. R. China
| | - Hong Han
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, jinan, P. R. China
| | - Shaojian Xu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, jinan, P. R. China
| | - Xianjie Han
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Yingru Ma
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Limei Zheng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Jun Li
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, jinan, P. R. China
- College of Life Sciences, Shandong Normal University, Jinan, China
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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25
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Feng J, Xu T, He M, Li J, Yao P, Ma C, Yang S, Xu Z, Yan K, Chen X, Wang H, Liu J, Zeng C, Xia Y, Yan H, Zhou L, Chen Y. NSUN2-mediated m5C modification of HBV RNA positively regulates HBV replication. PLoS Pathog 2023; 19:e1011808. [PMID: 38048324 PMCID: PMC10721180 DOI: 10.1371/journal.ppat.1011808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/14/2023] [Accepted: 11/07/2023] [Indexed: 12/06/2023] Open
Abstract
Chronic hepatitis B virus (HBV) infection is a major cause of liver cirrhosis and liver cancer, despite strong prevention and treatment efforts. The study of the epigenetic modification of HBV has become a research hotspot, including the N6-methyladenosine (m6A) modification of HBV RNA, which plays complex roles in the HBV life cycle. In addition to m6A modification, 5-methylcytosine (m5C) is another major modification of eukaryotic mRNA. In this study, we explored the roles of m5C methyltransferase and demethyltransferase in the HBV life cycle. The results showed that m5C methyltransferase NSUN2 deficiency could negatively regulate the expression of HBV while m5C demethyltransferase TET2 deficiency positively regulates the expression of HBV. Subsequently, we combined both in vitro bisulfite sequencing and high-throughput bisulfite sequencing methods to determine the distribution and stoichiometry of m5C modification in HBV RNA. Two sites: C2017 and C131 with the highest-ranking methylation rates were identified, and mutations at these two sites could lead to the decreased expression and replication of HBV, while the mutation of the "fake" m5C site had no effect. Mechanistically, NSUN2-mediated m5C modification promotes the stability of HBV RNA. In addition, compared with wild-type HepG2-NTCP cells and primary human hepatocytes, the replication level of HBV after NSUN2 knockdown decreased, and the ability of the mutant virus to infect and replicate in wild-type HepG2-NTCP cells and PHHs was substantially impaired. Similar results were found in the experiments using C57BL/6JGpt-Nsun2+/- mice. Interestingly, we also found that HBV expression and core protein promoted the endogenous expression of NSUN2, which implied a positive feedback loop. In summary, our study provides an accurate and high-resolution m5C profile of HBV RNA and reveals that NSUN2-mediated m5C modification of HBV RNA positively regulates HBV replication by maintaining RNA stability.
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Affiliation(s)
- Jiangpeng Feng
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Tianmo Xu
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- Animal Bio-safety Level III Laboratory/Institute for Vaccine Research, Wuhan University School of Medicine, Wuhan, China
| | - Miao He
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jiali Li
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Peipei Yao
- Animal Bio-safety Level III Laboratory/Institute for Vaccine Research, Wuhan University School of Medicine, Wuhan, China
- Wuhan University Taikang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Chengbao Ma
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Shimin Yang
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Zaichao Xu
- Wuhan University Taikang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Kun Yan
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Xianying Chen
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Hongyun Wang
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Jiejie Liu
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Cong Zeng
- School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yuchen Xia
- Wuhan University Taikang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Huan Yan
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Li Zhou
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- Animal Bio-safety Level III Laboratory/Institute for Vaccine Research, Wuhan University School of Medicine, Wuhan, China
- Wuhan University Taikang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Yu Chen
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- Animal Bio-safety Level III Laboratory/Institute for Vaccine Research, Wuhan University School of Medicine, Wuhan, China
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Li XH, Chen J, Ou YD, Zhong X, Hu JH, Sun RC, Lv YJ, Wei JC, Go YY, Zhou B. m 6A modification associated with YTHDF1 is involved in Japanese encephalitis virus infection. Vet Microbiol 2023; 287:109887. [PMID: 37925877 DOI: 10.1016/j.vetmic.2023.109887] [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: 08/04/2023] [Revised: 09/20/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023]
Abstract
N6-methyladenosine (m6A), the most common modification in mammalian mRNA and viral RNA, regulates mRNA structure, stability, translation, and nuclear export. The Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus causing severe neurologic disease in humans. To date, the role of m6A modification in JEV infection remains unclear. Herein, we aimed to determine the impact of m6A methylation modification on JEV replication in vitro and in vivo. Our results demonstrated that the overexpression of the m6A reader protein YTHDF1 in vitro significantly inhibits JEV proliferation. Additionally, YTHDF1 negatively regulates JEV proliferation in YTHDF1 knockdown cells and YTHDF1 knockout mice. MeRIP-seq analysis indicated that YTHDF1 interacts with several interferon-stimulated genes (ISGs), especially in IFIT3. Overall, our data showed that YTHDF1 played a vital role in inhibiting JEV replication. These findings bring novel insights into the specific mechanisms involved in the innate immune response to infection with JEV. They can be used in the development of novel therapeutics for controlling JEV infection.
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Affiliation(s)
- Xiao-Han Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jing Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yu-da Ou
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiang Zhong
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jia-Huan Hu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Rui-Cong Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Ying-Jun Lv
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jian-Chao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yun Young Go
- Department of Infectious Diseases and Public Health, City University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Bin Zhou
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
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Ferrasi AC, Lima SVG, Galvani AF, Delafiori J, Dias-Audibert FL, Catharino RR, Silva GF, Praxedes RR, Santos DB, Almeida DTDM, Lima EO. Metabolomics in chronic hepatitis C: Decoding fibrosis grading and underlying pathways. World J Hepatol 2023; 15:1237-1249. [DOI: 10.4254/wjh.v15.i11.1237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/22/2023] [Accepted: 10/23/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Chronic Hepatitis C (CHC) affects 71 million people globally and leads to liver issues such as fibrosis, cirrhosis, cancer, and death. A better understanding and prognosis of liver involvement are vital to reduce morbidity and mortality. The accurate identification of the fibrosis stage is crucial for making treatment decisions and predicting outcomes. Tests used to grade fibrosis include histological analysis and imaging but have limitations. Blood markers such as molecular biomarkers can offer valuable insights into fibrosis.
AIM To identify potential biomarkers that might stratify these lesions and add information about the molecular mechanisms involved in the disease.
METHODS Plasma samples were collected from 46 patients with hepatitis C and classified into fibrosis grades F1 (n = 13), F2 (n = 12), F3 (n = 6), and F4 (n = 15). To ensure that the identified biomarkers were exclusive to liver lesions (CHC fibrosis), healthy volunteer participants (n = 50) were also included. An untargeted metabolomic technique was used to analyze the plasma metabolites using mass spectrometry and database verification. Statistical analyses were performed to identify differential biomarkers among groups.
RESULTS Six differential metabolites were identified in each grade of fibrosis. This six-metabolite profile was able to establish a clustering tendency in patients with the same grade of fibrosis; thus, they showed greater efficiency in discriminating grades.
CONCLUSION This study suggests that some of the observed biomarkers, once validated, have the potential to be applied as prognostic biomarkers. Furthermore, it suggests that liquid biopsy analyses of plasma metabolites are a good source of molecular biomarkers capable of stratifying patients with CHC according to fibrosis grade.
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Affiliation(s)
| | | | - Aline Faria Galvani
- Department of Internal Medicine, Sao Paulo State University, Botucatu 18618-686, Brazil
| | - Jeany Delafiori
- Innovare Biomarkers Laboratory, University of Campinas, Campinas 13083-877, Brazil
| | | | | | - Giovanni Faria Silva
- Department of Internal Medicine, Sao Paulo State University, Botucatu 18618-686, Brazil
| | | | | | | | - Estela Oliveira Lima
- Department of Internal Medicine, Sao Paulo State University, Botucatu 18618-686, Brazil
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Chan C, Kwan Sze NS, Suzuki Y, Ohira T, Suzuki T, Begley TJ, Dedon PC. Dengue virus exploits the host tRNA epitranscriptome to promote viral replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.05.565734. [PMID: 37986976 PMCID: PMC10659268 DOI: 10.1101/2023.11.05.565734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The 40-50 RNA modifications of the epitranscriptome regulate posttranscriptional gene expression. Here we show that flaviviruses hijack the host tRNA epitranscriptome to promote expression of pro-viral proteins, with tRNA-modifying ALKBH1 acting as a host restriction factor in dengue virus infection. Early in the infection of human Huh-7 cells, ALKBH1 and its tRNA products 5-formylcytidine (f5C) and 2'-O-methyl-5-formylcytidine (f5Cm) were reduced. ALKBH1 knockdown mimicked viral infection, but caused increased viral NS3 protein levels during infection, while ALKBH1 overexpression reduced NS3 levels and viral replication, and increased f5C and f5Cm. Viral NS5, but not host FTSJ1, increased f5Cm levels late in infection. Consistent with reports of impaired decoding of leucine UUA codon by f5Cm-modified tRNALeu(CAA), ALKBH1 knockdown induced translation of UUA-deficient transcripts, most having pro-viral functions. Our findings support a dynamic ALKBH1/f5Cm axis during dengue infection, with virally-induced remodeling of the proteome by tRNA reprogramming and codon-biased translation.
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Affiliation(s)
- Cheryl Chan
- Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore
| | - Newman Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
| | - Yuka Suzuki
- Department of Bioengineering, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takayuki Ohira
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Bioengineering, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Thomas J. Begley
- Department of Biological Sciences and The RNA Institute, College of Arts and Science, University at Albany, SUNY, Albany, NY, 12222, USA
| | - Peter C. Dedon
- Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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Jiang Y, Pan Y, Long T, Qi J, Liu J, Zhang M. Significance of RNA N6-methyladenosine regulators in the diagnosis and subtype classification of coronary heart disease using the Gene Expression Omnibus database. Front Cardiovasc Med 2023; 10:1185873. [PMID: 37928762 PMCID: PMC10621741 DOI: 10.3389/fcvm.2023.1185873] [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: 04/04/2023] [Accepted: 08/21/2023] [Indexed: 11/07/2023] Open
Abstract
Background Many investigations have revealed that alterations in m6A modification levels may be linked to coronary heart disease (CHD). However, the specific link between m6A alteration and CHD warrants further investigation. Methods Gene expression profiles from the Gene Expression Omnibus (GEO) databases. We began by constructing a Random Forest model followed by a Nomogram model, both aimed at enhancing our predictive capabilities on specific m6A markers. We then shifted our focus to identify distinct molecular subtypes based on the key m6A regulators and to discern differentially expressed genes between the unique m6A clusters. Following this molecular exploration, we embarked on an in-depth analysis of the biological characteristics associated with each m6A cluster, revealing profound differences between them. Finally, we delved into the identification and correlation analysis of immune cell infiltration across these clusters, emphasizing the potential interplay between m6A modification and the immune system. Results In this research, 37 important m6Aregulators were identified by comparing non-CHD and CHD patients from the GSE20680, GSE20681, and GSE71226 datasets. To predict the risk of CHD, seven candidate m6A regulators (CBLL1, HNRNPC, YTHDC2, YTHDF1, YTHDF2, YTHDF3, ZC3H13) were screened using the logistic regression model. Based on the seven possible m6A regulators, a nomogram model was constructed. An examination of decision curves revealed that CHD patients could benefit from the nomogram model. On the basis of the selected relevant m6A regulators, patients with CHD were separated into two m6A clusters (cluster1 and cluster2) using the consensus clustering approach. The Single Sample Gene Set Enrichment Analysis (ssGSEA) and CIBERSORT methods were used to estimate the immunological characteristics of two separate m6A Gene Clusters; the results indicated a close association between seven candidate genes and immune cell composition. The drug sensitivity of seven candidate regulators was predicted, and these seven regulators appeared in numerous diseases as pharmacological targets while displaying strong drug sensitivity. Conclusion m6A regulators play crucial roles in the development of CHD. Our research of m6A clusters may facilitate the development of novel molecular therapies and inform future immunotherapeutic methods for CHD.
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Affiliation(s)
- Yu Jiang
- Department of Cardiovascular Surgery, Yan'an Hospital affiliated to Kunming Medical University, Yunnan, China
| | - Yaqiang Pan
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Tao Long
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Junqing Qi
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Jianchao Liu
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Mengya Zhang
- Department of Cardiology, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School of Nanjing Medical University, Suzhou, China
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Mo J, Weng X, Zhou X. Detection, Clinical Application, and Manipulation of RNA Modifications. Acc Chem Res 2023; 56:2788-2800. [PMID: 37769231 DOI: 10.1021/acs.accounts.3c00395] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
ConspectusWith increasing research interest, more than 170 types of chemical modifications of RNA have been characterized. The epigenetic modifications of RNA do not alter the primary sequence of RNA but modulate the gene activity. Increasing numbers of regulatory functions of these RNA modifications, particularly in controlling mRNA fate and gene expression, are being discovered. To gain a deeper understanding of the biological significance and clinical prospects of RNA modifications, the development of innovative labeling and detection methodologies is of great importance. Owing to the dynamic features of RNA modifications and the fact that only a portion of genes are modified, detection methods should accurately reveal the precise distribution and modification level of RNA modifications. In general, detection methodologies identify specific RNA modifications in two ways: (1) enriching modification-containing RNAs; and (2) altering the Watson-Crick base pairing pattern to produce truncation or mutation signatures. Additionally, it is important to develop flexible and accurate manipulation tools that enable the installation or removal of RNA modifications at specific positions to investigate the biological functions of a single site. With the development of detection and manipulation methods, the scientific understanding of the biological functions of RNA modifications has increased, paving the way for applications of RNA modifications in disease diagnosis and treatments.In this Account, we provide a brief summary of recent efforts to develop methodologies for detecting RNA modifications. Through the evolution of these detection techniques, our team has uncovered the potential biological roles of RNA modifications in diseases such as diabetic cardiovascular complications, viral infections, and hematologic malignancies. We mainly summarize the recently developed strategies for manipulating RNA modifications. The advent of these programmable editing tools allows for the precise installation or removal of RNA modifications at specific positions. As a result, the biological functions of RNA modifications at these specific loci could be identified, further advancing our knowledge in this field.With this Account, we anticipate providing chemical and biological researchers with comprehensive strategies to discover the underlying mechanisms of RNA modification-mediated biological processes. Although the field of RNA modifications has undergone rapid progress in recent years, our understanding of most of these RNA modifications remains incomplete. We hope to inspire efforts to expand the toolbox for investigating RNA modifications and promote translational research on epigenetics in clinical diagnosis and treatment.
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Affiliation(s)
- Jing Mo
- College of Chemistry and Molecular Sciences, Department of Clinical Laboratory of Zhongnan Hospital, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Department of Clinical Laboratory of Zhongnan Hospital, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Department of Clinical Laboratory of Zhongnan Hospital, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
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Martínez‐Pérez M, Aparicio F, Arribas‐Hernández L, Tankmar MD, Rennie S, von Bülow S, Lindorff‐Larsen K, Brodersen P, Pallas V. Plant YTHDF proteins are direct effectors of antiviral immunity against an N6-methyladenosine-containing RNA virus. EMBO J 2023; 42:e113378. [PMID: 37431920 PMCID: PMC10505913 DOI: 10.15252/embj.2022113378] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 07/12/2023] Open
Abstract
In virus-host interactions, nucleic acid-directed first lines of defense that allow viral clearance without compromising growth are of paramount importance. Plants use the RNA interference pathway as a basal antiviral immune system, but additional RNA-based mechanisms of defense also exist. The infectivity of a plant positive-strand RNA virus, alfalfa mosaic virus (AMV), relies on the demethylation of viral RNA by the recruitment of the cellular N6-methyladenosine (m6 A) demethylase ALKBH9B, but how demethylation of viral RNA promotes AMV infection remains unknown. Here, we show that inactivation of the Arabidopsis cytoplasmic YT521-B homology domain (YTH)-containing m6 A-binding proteins ECT2, ECT3, and ECT5 is sufficient to restore AMV infectivity in partially resistant alkbh9b mutants. We further show that the antiviral function of ECT2 is distinct from its previously demonstrated function in the promotion of primordial cell proliferation: an ect2 mutant carrying a small deletion in its intrinsically disordered region is partially compromised for antiviral defense but not for developmental functions. These results indicate that the m6 A-YTHDF axis constitutes a novel branch of basal antiviral immunity in plants.
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Affiliation(s)
- Mireya Martínez‐Pérez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValènciaValenciaSpain
| | - Frederic Aparicio
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValènciaValenciaSpain
| | | | | | - Sarah Rennie
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Sören von Bülow
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | | | - Peter Brodersen
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValènciaValenciaSpain
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Zhang X, Meng W, Feng J, Gao X, Qin C, Feng P, Huang Y, Gao SJ. METTL16 controls Kaposi's sarcoma-associated herpesvirus replication by regulating S-adenosylmethionine cycle. Cell Death Dis 2023; 14:591. [PMID: 37673880 PMCID: PMC10482891 DOI: 10.1038/s41419-023-06121-3] [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: 06/19/2023] [Revised: 08/22/2023] [Accepted: 08/29/2023] [Indexed: 09/08/2023]
Abstract
Oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV) consists of latent and lytic replication phases, both of which are important for the development of KSHV-related cancers. As one of the most abundant RNA modifications, N6-methyladenosine (m6A) and its related complexes regulate KSHV life cycle. However, the role of METTL16, a newly discovered RNA methyltransferase, in KSHV life cycle remains unknown. In this study, we have identified a suppressive role of METTL16 in KSHV lytic replication. METTL16 knockdown increased while METTL16 overexpression reduced KSHV lytic replication. METTL16 binding to and writing of m6A on MAT2A transcript are essential for its splicing, maturation and expression. As a rate-limiting enzyme in the methionine-S-adenosylmethionine (SAM) cycle, MAT2A catalyzes the conversion of L-methionine to SAM required for the transmethylation of protein, DNA and RNA, transamination of polyamines, and transsulfuration of cystathionine. Consequently, knockdown or chemical inhibition of MAT2A reduced intracellular SAM level and enhanced KSHV lytic replication. In contrast, SAM treatment was sufficient to inhibit KSHV lytic replication and reverse the effect of the enhanced KSHV lytic program caused by METTL16 or MAT2A knockdown. Mechanistically, METTL16 or MAT2A knockdown increased while SAM treatment decreased the intracellular reactive oxygen species level by altering glutathione level, which is essential for efficient KSHV lytic replication. These findings demonstrate that METTL16 suppresses KSHV lytic replication by modulating the SAM cycle to maintain intracellular SAM level and redox homeostasis, thus illustrating the linkage of KSHV life cycle with specific m6A modifications, and cellular metabolic and oxidative conditions.
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Affiliation(s)
- Xinquan Zhang
- Cancer Virology Program, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Wen Meng
- Cancer Virology Program, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jian Feng
- Cancer Virology Program, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Xinghong Gao
- Cancer Virology Program, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Chao Qin
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Pinghui Feng
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yufei Huang
- Cancer Virology Program, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Electrical and Computer Engineering, Swanson School of Engineering, Pittsburgh, PA, USA
| | - Shou-Jiang Gao
- Cancer Virology Program, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA.
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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Breger K, Kunkler CN, O'Leary NJ, Hulewicz JP, Brown JA. Ghost authors revealed: The structure and function of human N 6 -methyladenosine RNA methyltransferases. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1810. [PMID: 37674370 PMCID: PMC10915109 DOI: 10.1002/wrna.1810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 09/08/2023]
Abstract
Despite the discovery of modified nucleic acids nearly 75 years ago, their biological functions are still being elucidated. N6 -methyladenosine (m6 A) is the most abundant modification in eukaryotic messenger RNA (mRNA) and has also been detected in non-coding RNAs, including long non-coding RNA, ribosomal RNA, and small nuclear RNA. In general, m6 A marks can alter RNA secondary structure and initiate unique RNA-protein interactions that can alter splicing, mRNA turnover, and translation, just to name a few. Although m6 A marks in human RNAs have been known to exist since 1974, the structures and functions of methyltransferases responsible for writing m6 A marks have been established only recently. Thus far, there are four confirmed human methyltransferases that catalyze the transfer of a methyl group from S-adenosylmethionine (SAM) to the N6 position of adenosine, producing m6 A: methyltransferase-like protein (METTL) 3/METTL14 complex, METTL16, METTL5, and zinc-finger CCHC-domain-containing protein 4. Though the methyltransferases have unique RNA targets, all human m6 A RNA methyltransferases contain a Rossmann fold with a conserved SAM-binding pocket, suggesting that they utilize a similar catalytic mechanism for methyl transfer. For each of the human m6 A RNA methyltransferases, we present the biological functions and links to human disease, RNA targets, catalytic and kinetic mechanisms, and macromolecular structures. We also discuss m6 A marks in human viruses and parasites, assigning m6 A marks in the transcriptome to specific methyltransferases, small molecules targeting m6 A methyltransferases, and the enzymes responsible for hypermodified m6 A marks and their biological functions in humans. Understanding m6 A methyltransferases is a critical steppingstone toward establishing the m6 A epitranscriptome and more broadly the RNome. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Kurtis Breger
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Nathan J O'Leary
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jacob P Hulewicz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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Huo FC, Zhu ZM, Du WQ, Pan YJ, Jiang X, Kang MJ, Liu BW, Mou J, Pei DS. HPV E7-drived ALKBH5 promotes cervical cancer progression by modulating m6A modification of PAK5. Pharmacol Res 2023; 195:106863. [PMID: 37480971 DOI: 10.1016/j.phrs.2023.106863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 07/24/2023]
Abstract
Human papillomavirus (HPV) infection is a causative agent of cervical cancer (CC). N6-methyladenosine (m6A) modification is implicated in carcinogenesis and tumor progression. However, the involvement of m6A modification in HPV-involved CC remains unclear. Here we showed that HPV E6/7 oncoproteins affected the global m6A modification and E7 specifically promoted the expression of ALKBH5. We found that ALKBH5 was significantly upregulated in CC and might serve as a valuable prognostic marker. Forced expression of ALKBH5 enhanced the malignant phenotypes of CC cells. Mechanistically, we discovered that E7 increased ALKBH5 expression through E2F1-mediated activation of the H3K27Ac and H3K4Me3 histone modifications, as well as post-translational modification mediated by DDX3. ALKBH5-mediated m6A demethylation enhanced the expression of PAK5. The m6A reader YTHDF2 bound to PAK5 mRNA and regulated its stability in an m6A-dependent manner. Moreover, ALKBH5 promoted tumorigenesis and metastasis of CC by regulating PAK5. Overall, our findings herein demonstrate a significant role of ALKBH5 in CC progression in HPV-positive cells. Thus, we propose that ALKBH5 may serve as a prognostic biomarker and therapeutic target for CC patients.
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Affiliation(s)
- Fu-Chun Huo
- Department of Pathology, Xuzhou Medical University, 209 Tong-shan Road, Xuzhou 221004, Jiangsu, China
| | - Zhi-Man Zhu
- Department of Pathology, Xuzhou Medical University, 209 Tong-shan Road, Xuzhou 221004, Jiangsu, China
| | - Wen-Qi Du
- Department of Pathology, Xuzhou Medical University, 209 Tong-shan Road, Xuzhou 221004, Jiangsu, China
| | - Yao-Jie Pan
- Department of Pathology, Xuzhou Medical University, 209 Tong-shan Road, Xuzhou 221004, Jiangsu, China
| | - Xin Jiang
- Department of Pathology, Xuzhou Medical University, 209 Tong-shan Road, Xuzhou 221004, Jiangsu, China
| | - Meng-Jie Kang
- Department of Pathology, Xuzhou Medical University, 209 Tong-shan Road, Xuzhou 221004, Jiangsu, China
| | - Bo-Wen Liu
- Department of Pathology, Xuzhou Medical University, 209 Tong-shan Road, Xuzhou 221004, Jiangsu, China
| | - Jie Mou
- Jiangsu Key Laboratory of New drug and Clinical Pharmacy, Xuzhou Medical University, 209 Tong-shan Road, Xuzhou 221004, Jiangsu, China.
| | - Dong-Sheng Pei
- Department of Pathology, Xuzhou Medical University, 209 Tong-shan Road, Xuzhou 221004, Jiangsu, China.
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35
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Mhlekude B, Postmus D, Stenzel S, Weiner J, Jansen J, Zapatero-Belinchón FJ, Olmer R, Richter A, Heinze J, Heinemann N, Mühlemann B, Schroeder S, Jones TC, Müller MA, Drosten C, Pich A, Thiel V, Martin U, Niemeyer D, Gerold G, Beule D, Goffinet C. Pharmacological inhibition of bromodomain and extra-terminal proteins induces an NRF-2-mediated antiviral state that is subverted by SARS-CoV-2 infection. PLoS Pathog 2023; 19:e1011657. [PMID: 37747932 PMCID: PMC10629670 DOI: 10.1371/journal.ppat.1011657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/07/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
Inhibitors of bromodomain and extra-terminal proteins (iBETs), including JQ-1, have been suggested as potential prophylactics against SARS-CoV-2 infection. However, molecular mechanisms underlying JQ-1-mediated antiviral activity and its susceptibility to viral subversion remain incompletely understood. Pretreatment of cells with iBETs inhibited infection by SARS-CoV-2 variants and SARS-CoV, but not MERS-CoV. The antiviral activity manifested itself by reduced reporter expression of recombinant viruses, and reduced viral RNA quantities and infectious titers in the culture supernatant. While we confirmed JQ-1-mediated downregulation of expression of angiotensin-converting enzyme 2 (ACE2) and interferon-stimulated genes (ISGs), multi-omics analysis addressing the chromatin accessibility, transcriptome and proteome uncovered induction of an antiviral nuclear factor erythroid 2-related factor 2 (NRF-2)-mediated cytoprotective response as an additional mechanism through which JQ-1 inhibits SARS-CoV-2 replication. Pharmacological inhibition of NRF-2, and knockdown of NRF-2 and its target genes reduced JQ-1-mediated inhibition of SARS-CoV-2 replication. Serial passaging of SARS-CoV-2 in the presence of JQ-1 resulted in predominance of ORF6-deficient variant, which exhibited resistance to JQ-1 and increased sensitivity to exogenously administered type I interferon (IFN-I), suggesting a minimised need for SARS-CoV-2 ORF6-mediated repression of IFN signalling in the presence of JQ-1. Importantly, JQ-1 exhibited a transient antiviral activity when administered prophylactically in human airway bronchial epithelial cells (hBAECs), which was gradually subverted by SARS-CoV-2, and no antiviral activity when administered therapeutically following an established infection. We propose that JQ-1 exerts pleiotropic effects that collectively induce an antiviral state in the host, which is ultimately nullified by SARS-CoV-2 infection, raising questions about the clinical suitability of the iBETs in the context of COVID-19.
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Affiliation(s)
- Baxolele Mhlekude
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
- Virology and Innate Immunity Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Dylan Postmus
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Saskia Stenzel
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - January Weiner
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Jenny Jansen
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Francisco J. Zapatero-Belinchón
- Department of Biochemistry, University of Veterinary Medicine Hannover, Hannover, Germany
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research; a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Clinical Microbiology, Virology & Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Ruth Olmer
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH—Center for Translational Regenerative Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Anja Richter
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Julian Heinze
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicolas Heinemann
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Barbara Mühlemann
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Simon Schroeder
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Terry C. Jones
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Marcel A. Müller
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andreas Pich
- Institute of Toxicology, Hannover Medical School, Core Facility Proteomics, Hannover, Germany
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), University of Bern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH—Center for Translational Regenerative Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Daniela Niemeyer
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gisa Gerold
- Department of Biochemistry, University of Veterinary Medicine Hannover, Hannover, Germany
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research; a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Clinical Microbiology, Virology & Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Dieter Beule
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Christine Goffinet
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool United Kingdom
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Yao L, Zhang W, Chen X, Yi M, Jia K. Methyltransferase-like 3 suppresses red spotted grouper nervous necrosis virus and viral hemorrhagic septicemia virus infection by enhancing type I interferon responses in sea perch. FISH & SHELLFISH IMMUNOLOGY 2023; 140:108993. [PMID: 37573969 DOI: 10.1016/j.fsi.2023.108993] [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: 05/17/2023] [Revised: 08/01/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
Methylation at the N6 position of adenosine (m6A) is the most abundant internal mRNA modification in eukaryotes, tightly associating with regulation of viral life circles and immune responses. Here, a methyltransferase-like 3 homolog gene from sea perch (Lateolabrax japonicus), designated LjMETTL3, was cloned and characterized, and its negative role in fish virus pathogenesis was uncovered. The cDNA of LjMETTL3 encoded a 601-amino acid protein with a MT-A70 domain, which shared the closest genetic relationship with Echeneis naucrates METTL3. Spatial expression analysis revealed that LjMETTL3 was more abundant in the immune tissues of sea perch post red spotted grouper nervous necrosis virus (RGNNV) or viral hemorrhagic septicemia virus (VHSV) infection. LjMETTL3 expression was significantly upregulated at 12 and 24 h post RGNNV and VHSV infection in vitro. In addition, ectopic expression of LjMETTL3 inhibited RGNNV and VHSV infection in LJB cells at 12 and 24 h post infection, whereas knockdown of LjMETTL3 led to opposite effects. Furthermore, we found that LjMETTL3 may participate in boosting the type I interferon responses by interacting with TANK-binding kinase. Taken together, these results disclosed the antiviral role of fish METTL3 against RGNNV and VHSV and provided evidence for understanding the potential mechanisms of fish METTL3 in antiviral innate immunity.
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Affiliation(s)
- Lan Yao
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, China
| | - Wanwan Zhang
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, China
| | - Xiaoqi Chen
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, China
| | - Meisheng Yi
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, China.
| | - Kuntong Jia
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, China.
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Qiu L, Jing Q, Li Y, Han J. RNA modification: mechanisms and therapeutic targets. MOLECULAR BIOMEDICINE 2023; 4:25. [PMID: 37612540 PMCID: PMC10447785 DOI: 10.1186/s43556-023-00139-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023] Open
Abstract
RNA modifications are dynamic and reversible chemical modifications on substrate RNA that are regulated by specific modifying enzymes. They play important roles in the regulation of many biological processes in various diseases, such as the development of cancer and other diseases. With the help of advanced sequencing technologies, the role of RNA modifications has caught increasing attention in human diseases in scientific research. In this review, we briefly summarized the basic mechanisms of several common RNA modifications, including m6A, m5C, m1A, m7G, Ψ, A-to-I editing and ac4C. Importantly, we discussed their potential functions in human diseases, including cancer, neurological disorders, cardiovascular diseases, metabolic diseases, genetic and developmental diseases, as well as immune disorders. Through the "writing-erasing-reading" mechanisms, RNA modifications regulate the stability, translation, and localization of pivotal disease-related mRNAs to manipulate disease development. Moreover, we also highlighted in this review all currently available RNA-modifier-targeting small molecular inhibitors or activators, most of which are designed against m6A-related enzymes, such as METTL3, FTO and ALKBH5. This review provides clues for potential clinical therapy as well as future study directions in the RNA modification field. More in-depth studies on RNA modifications, their roles in human diseases and further development of their inhibitors or activators are needed for a thorough understanding of epitranscriptomics as well as diagnosis, treatment, and prognosis of human diseases.
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Affiliation(s)
- Lei Qiu
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Qian Jing
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Yanbo Li
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Junhong Han
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China.
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Jansens RJ, Olarerin-George A, Verhamme R, Mirza A, Jaffrey S, Favoreel HW. Alphaherpesvirus-mediated remodeling of the cellular transcriptome results in depletion of m6A-containing transcripts. iScience 2023; 26:107310. [PMID: 37575180 PMCID: PMC10415716 DOI: 10.1016/j.isci.2023.107310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/04/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023] Open
Abstract
The mechanisms by which viruses regulate host mRNAs during infection are still poorly understood. Several host transcripts that encode proteins that contribute to the anti-viral response contain the N6-methyladenosine nucleotide (m6A). In this study, we investigated if and how viruses from different (sub) families specifically affect m6A-containing host transcripts. Systematic analysis of host transcriptomes after infection with diverse types of viruses showed that m6A-methylated transcripts are selectively downregulated during infection with Sendai virus, African swine fever virus and the alphaherpesviruses herpes simplex virus 1 (HSV-1) and pseudorabies virus (PRV). Focusing on PRV and HSV-1, we found that downregulation of m6A-methylated transcripts depends on the YTHDF family of m6A-binding proteins, and correlates with localization of these proteins to enlarged P-bodies. Knockdown of YTHDF proteins in primary cells reduced PRV protein expression and increased expression of antiviral interferon-stimulated genes, suggesting that virus-induced depletion of host m6A-containing transcripts constitutes an immune evasion strategy.
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Affiliation(s)
- Robert J.J. Jansens
- Department of Translational Physiology, Infectiology and Public Health
- Department of Pharmacology, Weill Medical College, Cornell University, New York NY 10021, USA
| | - Anthony Olarerin-George
- Department of Pharmacology, Weill Medical College, Cornell University, New York NY 10021, USA
| | - Ruth Verhamme
- Department of Translational Physiology, Infectiology and Public Health
| | - Aashiq Mirza
- Department of Pharmacology, Weill Medical College, Cornell University, New York NY 10021, USA
| | - Samie Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York NY 10021, USA
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39
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Jaguri A, Steinhoff M, Ahmad A. Epigenetic m6A RNA Modification Reader YTHDF1 in Merkel Cell Carcinoma. Cancers (Basel) 2023; 15:4075. [PMID: 37627103 PMCID: PMC10452270 DOI: 10.3390/cancers15164075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Merkel cell carcinoma (MCC) is a rare and aggressive neuroendocrine cutaneous malignancy that commonly affects older individuals with a high mortality rate [...].
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Affiliation(s)
- Aayami Jaguri
- Weill Cornell Medicine-Qatar, Doha 24811, Qatar; (A.J.); (M.S.)
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
| | - Martin Steinhoff
- Weill Cornell Medicine-Qatar, Doha 24811, Qatar; (A.J.); (M.S.)
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
- Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
- Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha 3050, Qatar
- Department of Dermatology, Weill Cornell Medicine, New York, NY 10065, USA
- School of Medicine, Qatar University, Doha 2713, Qatar
- School of Life Sciences, Hamad-Bin-Khalifa University, Doha 34110, Qatar
| | - Aamir Ahmad
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
- Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
- Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha 3050, Qatar
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40
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Crawford JM, Buechlein AM, Moline DA, Rusch DB, Hardy RW. Host Derivation of Sindbis Virus Influences Mammalian Type I Interferon Response to Infection. Viruses 2023; 15:1685. [PMID: 37632027 PMCID: PMC10458878 DOI: 10.3390/v15081685] [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: 04/28/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Arboviruses are defined by their ability to replicate in both mosquito vectors and mammalian hosts. There is good evidence that arboviruses "prime" their progeny for infection of the next host, such as via differential glycosylation of their outer glycoproteins or packaging of host ribosomal subunits. We and others have previously shown that mosquito-derived viruses more efficiently infect mammalian cells than mammalian-derived viruses. These observations are consistent with arboviruses acquiring host-specific adaptations, and we hypothesized that a virus derived from either the mammalian host or mosquito vector elicits different responses when infecting the mammalian host. Here, we perform an RNA-sequencing analysis of the transcriptional response of Human Embryonic Kidney 293 (HEK-293) cells to infection with either mosquito (Aedes albopictus, C7/10)- or mammalian (Baby Hamster Kidney, BHK-21)-derived Sindbis virus (SINV). We show that the C7/10-derived virus infection leads to a more robust transcriptional response in HEK-293s compared to infection with the BHK-derived virus. Surprisingly, despite more efficient infection, we found an increase in interferon-β (IFN-β) and interferon-stimulated gene (ISG) transcripts in response to the C7/10-derived virus infection versus the BHK-derived virus infection. However, translation of interferon-stimulated genes was lower in HEK-293s infected with the C7/10-derived virus, starkly contrasting with the transcriptional response. This inhibition of ISG translation is reflective of a more rapid overall shut-off of host cell translation following infection with the C7/10-derived virus. Finally, we show that the C7/10-derived virus infection of HEK-293 cells leads to elevated levels of phosphorylated eukaryotic translation elongation factor-2 (eEF2), identifying a potential mechanism leading to the more rapid shut-off of host translation. We postulate that the rapid shut-off of host translation in mammalian cells infected with the mosquito-derived virus acts to counter the IFN-β-stimulated transcriptional response.
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Affiliation(s)
- John M. Crawford
- Department of Biology, Indiana University, Bloomington, IN 47405, USA; (J.M.C.); (D.A.M.)
| | - Aaron M. Buechlein
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA; (A.M.B.); (D.B.R.)
| | - Davis A. Moline
- Department of Biology, Indiana University, Bloomington, IN 47405, USA; (J.M.C.); (D.A.M.)
| | - Douglas B. Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA; (A.M.B.); (D.B.R.)
| | - Richard W. Hardy
- Department of Biology, Indiana University, Bloomington, IN 47405, USA; (J.M.C.); (D.A.M.)
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Wang Y, Zhou X. N 6-methyladenosine and Its Implications in Viruses. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:695-706. [PMID: 35835441 PMCID: PMC10787122 DOI: 10.1016/j.gpb.2022.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/21/2022] [Accepted: 04/19/2022] [Indexed: 12/27/2022]
Abstract
N6-methyladenine (m6A) is the most abundant RNA modification in mammalian messenger RNAs (mRNAs), which participates in and regulates many important biological activities, such as tissue development and stem cell differentiation. Due to an improved understanding of m6A, researchers have discovered that the biological function of m6A can be linked to many stages of mRNA metabolism and that m6A can regulate a variety of complex biological processes. In addition to its location on mammalian mRNAs, m6A has been identified on viral transcripts. m6A also plays important roles in the life cycle of many viruses and in viral replication in host cells. In this review, we briefly introduce the detection methods of m6A, the m6A-related proteins, and the functions of m6A. We also summarize the effects of m6A-related proteins on viral replication and infection. We hope that this review provides researchers with some insights for elucidating the complex mechanisms of the epitranscriptome related to viruses, and provides information for further study of the mechanisms of other modified nucleobases acting on processes such as viral replication. We also anticipate that this review can stimulate collaborative research from different fields, such as chemistry, biology, and medicine, and promote the development of antiviral drugs and vaccines.
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Affiliation(s)
- Yafen Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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Ribeiro DR, Nunes A, Ribeiro D, Soares AR. The hidden RNA code: implications of the RNA epitranscriptome in the context of viral infections. Front Genet 2023; 14:1245683. [PMID: 37614818 PMCID: PMC10443596 DOI: 10.3389/fgene.2023.1245683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023] Open
Abstract
Emerging evidence highlights the multifaceted roles of the RNA epitranscriptome during viral infections. By modulating the modification landscape of viral and host RNAs, viruses enhance their propagation and elude host surveillance mechanisms. Here, we discuss how specific RNA modifications, in either host or viral RNA molecules, impact the virus-life cycle and host antiviral responses, highlighting the potential of targeting the RNA epitranscriptome for novel antiviral therapies.
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Leseva MN, Buttari B, Saso L, Dimitrova PA. Infection Meets Inflammation: N6-Methyladenosine, an Internal Messenger RNA Modification as a Tool for Pharmacological Regulation of Host-Pathogen Interactions. Biomolecules 2023; 13:1060. [PMID: 37509095 PMCID: PMC10377384 DOI: 10.3390/biom13071060] [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: 05/26/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
The significance of internal mRNA modifications for the modulation of transcript stability, for regulation of nuclear export and translation efficiency, and their role in suppressing innate immunity is well documented. Over the years, the molecular complexes involved in the dynamic regulation of the most prevalent modifications have been characterized-we have a growing understanding of how each modification is set and erased, where it is placed, and in response to what cues. Remarkably, internal mRNA modifications, such as methylation, are emerging as an additional layer of regulation of immune cell homeostasis, differentiation, and function. A fascinating recent development is the investigation into the internal modifications of host/pathogen RNA, specifically N6-methyladenosine (m6A), its abundance and distribution during infection, and its role in disease pathogenesis and in shaping host immune responses. Low molecular weight compounds that target RNA-modifying enzymes have shown promising results in vitro and in animal models of different cancers and are expanding the tool-box in immuno-oncology. Excitingly, such modulators of host mRNA methyltransferase or demethylase activity hold profound implications for the development of new broad-spectrum therapeutic agents for infectious diseases as well. This review describes the newly uncovered role of internal mRNA modification in infection and in shaping the function of the immune system in response to invading pathogens. We will also discuss its potential as a therapeutic target and identify pitfalls that need to be overcome if it is to be effectively leveraged against infectious agents.
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Affiliation(s)
- Milena N Leseva
- Laboratory of Experimental Immunotherapy, Department of Immunology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Brigitta Buttari
- Department of Cardiovascular and Endocrine-Metabolic Diseases and Aging, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", La Sapienza University of Rome, 00185 Rome, Italy
| | - Petya A Dimitrova
- Laboratory of Experimental Immunotherapy, Department of Immunology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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Glaß M, Hüttelmaier S. IGF2BP1-An Oncofetal RNA-Binding Protein Fuels Tumor Virus Propagation. Viruses 2023; 15:1431. [PMID: 37515119 PMCID: PMC10385356 DOI: 10.3390/v15071431] [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: 05/19/2023] [Revised: 06/13/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
The oncofetal RNA-binding protein IGF2BP1 has been reported to be a driver of tumor progression in a multitude of cancer entities. Its main function is the stabilization of target transcripts by shielding these from miRNA-mediated degradation. However, there is growing evidence that several virus species recruit IGF2BP1 to promote their propagation. In particular, tumor-promoting viruses, such as hepatitis B/C and human papillomaviruses, benefit from IGF2BP1. Moreover, recent evidence suggests that non-oncogenic viruses, such as SARS-CoV-2, also take advantage of IGF2BP1. The only virus inhibited by IGF2BP1 reported to date is HIV-1. This review summarizes the current knowledge about the interactions between IGF2BP1 and different virus species. It further recapitulates several findings by presenting analyses from publicly available high-throughput datasets.
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Affiliation(s)
- Markus Glaß
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
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Manners O, Baquero-Perez B, Mottram TJ, Yonchev ID, Trevelyan CJ, Harper KL, Menezes S, Patterson MR, Macdonald A, Wilson SA, Aspden JL, Whitehouse A. m 6A Regulates the Stability of Cellular Transcripts Required for Efficient KSHV Lytic Replication. Viruses 2023; 15:1381. [PMID: 37376680 DOI: 10.3390/v15061381] [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: 04/12/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The epitranscriptomic modification N6-methyladenosine (m6A) is a ubiquitous feature of the mammalian transcriptome. It modulates mRNA fate and dynamics to exert regulatory control over numerous cellular processes and disease pathways, including viral infection. Kaposi's sarcoma-associated herpesvirus (KSHV) reactivation from the latent phase leads to the redistribution of m6A topology upon both viral and cellular mRNAs within infected cells. Here we investigate the role of m6A in cellular transcripts upregulated during KSHV lytic replication. Our results show that m6A is crucial for the stability of the GPRC5A mRNA, whose expression is induced by the KSHV latent-lytic switch master regulator, the replication and transcription activator (RTA) protein. Moreover, we demonstrate that GPRC5A is essential for efficient KSHV lytic replication by directly regulating NFκB signalling. Overall, this work highlights the central importance of m6A in modulating cellular gene expression to influence viral infection.
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Affiliation(s)
- Oliver Manners
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Belinda Baquero-Perez
- Molecular Virology Unit, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Timothy J Mottram
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Ivaylo D Yonchev
- Sheffield Institute for Nucleic Acids, School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Christopher J Trevelyan
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Katherine L Harper
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sarah Menezes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Molly R Patterson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Andrew Macdonald
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Stuart A Wilson
- Sheffield Institute for Nucleic Acids, School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- LeedsOmics, University of Leeds, Leeds LS2 9JT, UK
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
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46
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Meng H, Li Z, Wang L, Lyu L, Liu S, Wei R, Ni B, Liu F. Cells at early and late stages of infection with Senecavirus A: Comparative analysis of N 6-methyladenosine modification on mRNAs. Virology 2023; 585:186-195. [PMID: 37379620 DOI: 10.1016/j.virol.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 06/30/2023]
Abstract
Infection with Senecavirus A (SVA) causes differential phenotypes in cells. In this study, cells were inoculated with SVA for culture. At 12 and 72 h post infection, cells were independently harvested for high-throughput RNA sequencing, and further methylated RNA immunoprecipitation sequencing. The resultant data were comprehensively analyzed for mapping N6-methyladenosine (m6A)-modified profiles of SVA-infected cells. More importantly, m6A-modified regions were identified in the SVA genome. A dataset of m6A-modified mRNAs was generated for screening out differentially m6A-modified mRNAs, further subjected to a series of in-depth analyses. This study not only showed statistical differentiation of m6A-modified sites between two SVA-infected groups, but also demonstrated that SVA genome, as a positive-sense, single-stranded mRNA, itself could be modified through the m6A pattern. Out of the six samples of SVA mRNAs, only three were identified to be m6A-modified, implying that the epigenetic effect might not be a crucial driving force for SVA evolution.
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Affiliation(s)
- Hailan Meng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ziwei Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China; Surveillance Laboratory of Livestock Diseases, China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Ling Wang
- University Hospital, Qingdao Agricultural University, Qingdao, 266109, China
| | - Liangpeng Lyu
- Qingdao Workstation of Animal Husbandry, Qingdao, 266199, China
| | - Shuqing Liu
- Qingdao Center for Animal Disease Control & Prevention, Qingdao, 266199, China
| | - Rong Wei
- Surveillance Laboratory of Livestock Diseases, China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Bo Ni
- Surveillance Laboratory of Livestock Diseases, China Animal Health and Epidemiology Center, Qingdao, 266032, China.
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China.
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47
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Kong Y, Mead EA, Fang G. Navigating the pitfalls of mapping DNA and RNA modifications. Nat Rev Genet 2023; 24:363-381. [PMID: 36653550 PMCID: PMC10722219 DOI: 10.1038/s41576-022-00559-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2022] [Indexed: 01/19/2023]
Abstract
Chemical modifications to nucleic acids occur across the kingdoms of life and carry important regulatory information. Reliable high-resolution mapping of these modifications is the foundation of functional and mechanistic studies, and recent methodological advances based on next-generation sequencing and long-read sequencing platforms are critical to achieving this aim. However, mapping technologies may have limitations that sometimes lead to inconsistent results. Some of these limitations are technical in nature and specific to certain types of technology. Here, however, we focus on common (yet not always widely recognized) pitfalls that are shared among frequently used mapping technologies and discuss strategies to help technology developers and users mitigate their effects. Although the emphasis is primarily on DNA modifications, RNA modifications are also discussed.
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Affiliation(s)
- Yimeng Kong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edward A Mead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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48
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Yang D, Zhao G, Zhang HM. m 6A reader proteins: the executive factors in modulating viral replication and host immune response. Front Cell Infect Microbiol 2023; 13:1151069. [PMID: 37325513 PMCID: PMC10266107 DOI: 10.3389/fcimb.2023.1151069] [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: 01/25/2023] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
N6-Methyladenosine (m6A) modification is the most abundant covalent modification of RNA. It is a reversible and dynamic process induced by various cellular stresses including viral infection. Many m6A methylations have been discovered, including on the genome of RNA viruses and on RNA transcripts of DNA viruses, and these methylations play a positive or negative role on the viral life cycle depending on the viral species. The m6A machinery, including the writer, eraser, and reader proteins, achieves its gene regulatory role by functioning in an orchestrated manner. Notably, data suggest that the biological effects of m6A on target mRNAs predominantly depend on the recognition and binding of different m6A readers. These readers include, but are not limited to, the YT521-B homology (YTH) domain family, heterogeneous nuclear ribonucleoproteins (HNRNPs), insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs), and many others discovered recently. Indeed, m6A readers have been recognized not only as regulators of RNA metabolism but also as participants in a variety of biological processes, although some of these reported roles are still controversial. Here, we will summarize the recent advances in the discovery, classification, and functional characterization of m6A reader proteins, particularly focusing on their roles and mechanisms of action in RNA metabolism, gene expression, and viral replication. In addition, we also briefly discuss the m6A-associated host immune responses in viral infection.
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Affiliation(s)
- Decheng Yang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
| | - Guangze Zhao
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
| | - Huifang Mary Zhang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
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49
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Lv Z, Ran R, Yang Y, Xiang M, Su H, Huang J. The interplay between N6-methyladenosine and precancerous liver disease: molecular functions and mechanisms. Discov Oncol 2023; 14:78. [PMID: 37227534 DOI: 10.1007/s12672-023-00695-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/19/2023] [Indexed: 05/26/2023] Open
Abstract
N6-methyladenosine(m6A) is one of the most abundant modifications of mammalian cellular RNAs. m6A regulates various biological functions in epitranscriptomic ways, including RNA stability, decay, splicing, translation and nuclear export. Recent studies have indicated the growing importance of m6A modification in precancerous disease, influencing viral replication, immune escape, and carcinogenesis. Here, we review the role of m6A modification in HBV/HCV infection, NAFLD and liver fibrosis, and its function in liver disease pathogenesis. Our review will provide a new sight for the innovative treatment strategy for precancerous liver disease.
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Affiliation(s)
- Zhihua Lv
- Department of Clinical Laboratory, Institute of Translational Medcine, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Ruoxi Ran
- Department of Clinical Laboratory, Institute of Translational Medcine, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Yuting Yang
- Department of General Office, School of Stomatology, Wuhan University, Wuhan, China
| | - Meixian Xiang
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China
| | - Hanwen Su
- Department of Clinical Laboratory, Institute of Translational Medcine, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Jingtao Huang
- Department of Clinical Laboratory, Institute of Translational Medcine, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China.
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50
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Tang J, Chen S, Jia G. Detection, regulation, and functions of RNA N 6-methyladenosine modification in plants. PLANT COMMUNICATIONS 2023; 4:100546. [PMID: 36627844 DOI: 10.1016/j.xplc.2023.100546] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/22/2022] [Accepted: 01/05/2023] [Indexed: 05/11/2023]
Abstract
N6-Methyladenosine (m6A) is the most abundant internal chemical modification in eukaryotic mRNA and plays important roles in gene expression regulation, including transcriptional and post-transcriptional regulation. m6A is a reversible modification that is installed, removed, and recognized by methyltransferases (writers), demethylases (erasers), and m6A-binding proteins (readers), respectively. Recently, the breadth of research on m6A in plants has expanded, and the vital roles of m6A in plant development, biotic and abiotic stress responses, and crop trait improvement have been investigated. In this review, we discuss recent developments in research on m6A and highlight the detection methods, distribution, regulatory proteins, and molecular and biological functions of m6A in plants. We also offer some perspectives on future investigations, providing direction for subsequent research on m6A in plants.
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Affiliation(s)
- Jun Tang
- 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
| | - Shuyan Chen
- 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; Peking-Tsinghua Center for Life Sciences, Beijing 100871, China.
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