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Yang S, Wen X, Wagner D, Strauss J, Kallmeyer J, Anthony SE, Liebner S. Microbial assemblages in Arctic coastal thermokarst lakes and lagoons. FEMS Microbiol Ecol 2024; 100:fiae014. [PMID: 38308515 PMCID: PMC10883142 DOI: 10.1093/femsec/fiae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/22/2023] [Accepted: 02/01/2024] [Indexed: 02/04/2024] Open
Abstract
Several studies have investigated changes in microbial community composition in thawing permafrost landscapes, but microbial assemblages in the transient ecosystems of the Arctic coastline remain poorly understood. Thermokarst lakes, abrupt permafrost thaw features, are widespread along the pan-Arctic coast and transform into thermokarst lagoons upon coastal erosion and sea-level rise. This study looks at the effect of marine water inundation (imposing a sulfate-rich, saline environment on top of former thermokarst lake sediments) on microbial community composition and the processes potentially driving microbial community assembly. In the uppermost lagoon sediment influenced from marine water inflow, the microbial structures were significantly different from those deeper in the lagoon sediment and from those of the lakes. In addition, they became more similar along depth compared with lake communities. At the same time, the diversity of core microbial consortia community decreased compared with the lake sediments. This work provides initial observational evidence that Arctic thermokarst lake to lagoon transitions do not only substantially alter microbial communities but also that this transition has a larger effect than permafrost thaw and lake formation history.
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Affiliation(s)
- Sizhong Yang
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, Potsdam, Germany
- Cyrosphere Research Station on the Qinghai-Tibet Plateau, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Donggang West Road 320, Lanzhou 730000, China
| | - Xi Wen
- College of Electrical Engineering, Northwest Minzu University, Xibei Xincun 1, Lanzhou 730070, China
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Jens Strauss
- Permafrost Research Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Telegrafenberg, Potsdam, Germany
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, Potsdam, Germany
| | - Sara E Anthony
- Institute of Geology and Mineralogy, University of Cologne, Zülpicher Str. 49a, 50674 Cologne, Germany
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, Potsdam, Germany
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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Alfaro AJ, Dittner C, Becker J, Loft A, Mhamane A, Maida A, Georgiadi A, Tsokanos F, Klepac K, Molocea C, El‐Merahbi R, Motzler K, Geppert J, Karikari RA, Szendrödi J, Feuchtinger A, Hofmann S, Karaca S, Urlaub H, Berriel Diaz M, Melchior F, Herzig S. Fasting-sensitive SUMO-switch on Prox1 controls hepatic cholesterol metabolism. EMBO Rep 2023; 24:e55981. [PMID: 37560809 PMCID: PMC10561358 DOI: 10.15252/embr.202255981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 07/12/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023] Open
Abstract
Accumulation of excess nutrients hampers proper liver function and is linked to nonalcoholic fatty liver disease (NAFLD) in obesity. However, the signals responsible for an impaired adaptation of hepatocytes to obesogenic dietary cues remain still largely unknown. Post-translational modification by the small ubiquitin-like modifier (SUMO) allows for a dynamic regulation of numerous processes including transcriptional reprogramming. We demonstrate that specific SUMOylation of transcription factor Prox1 represents a nutrient-sensitive determinant of hepatic fasting metabolism. Prox1 is highly SUMOylated on lysine 556 in the liver of ad libitum and refed mice, while this modification is abolished upon fasting. In the context of diet-induced obesity, Prox1 SUMOylation becomes less sensitive to fasting cues. The hepatocyte-selective knock-in of a SUMOylation-deficient Prox1 mutant into mice fed a high-fat/high-fructose diet leads to a reduction of systemic cholesterol levels, associated with the induction of liver bile acid detoxifying pathways during fasting. The generation of tools to maintain the nutrient-sensitive SUMO-switch on Prox1 may thus contribute to the development of "fasting-based" approaches for the preservation of metabolic health.
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Affiliation(s)
- Ana Jimena Alfaro
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Claudia Dittner
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)Heidelberg University, DKFZ‐ZMBH AllianceHeidelbergGermany
| | - Janina Becker
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)Heidelberg University, DKFZ‐ZMBH AllianceHeidelbergGermany
| | - Anne Loft
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
- Center for Functional Genomics and Tissue Plasticity (ATLAS), SDUOdenseDenmark
| | - Amit Mhamane
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Adriano Maida
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Anastasia Georgiadi
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Foivos‐Filippos Tsokanos
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Katarina Klepac
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Claudia‐Eveline Molocea
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Rabih El‐Merahbi
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Karsten Motzler
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Julia Geppert
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Rhoda Anane Karikari
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Julia Szendrödi
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | | | - Susanna Hofmann
- Institute of Diabetes and Regeneration ResearchHelmholtz MunichNeuherbergGermany
| | - Samir Karaca
- Bioanalytical Mass Spectrometry GroupMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry GroupMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
- Bioanalytics, Institute of Clinical ChemistryUniversity Medical Center GöttingenGöttingenGermany
| | - Mauricio Berriel Diaz
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Frauke Melchior
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)Heidelberg University, DKFZ‐ZMBH AllianceHeidelbergGermany
| | - Stephan Herzig
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
- Chair Molecular Metabolic ControlTechnical University MunichMunichGermany
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Schwanke H, Gonçalves Magalhães V, Schmelz S, Wyler E, Hennig T, Günther T, Grundhoff A, Dölken L, Landthaler M, van Ham M, Jänsch L, Büssow K, van den Heuvel J, Blankenfeldt W, Friedel CC, Erhard F, Brinkmann MM. The Cytomegalovirus M35 Protein Directly Binds to the Interferon-β Enhancer and Modulates Transcription of Ifnb1 and Other IRF3-Driven Genes. J Virol 2023; 97:e0040023. [PMID: 37289084 PMCID: PMC10308904 DOI: 10.1128/jvi.00400-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/04/2023] [Indexed: 06/09/2023] Open
Abstract
Induction of type I interferon (IFN) gene expression is among the first lines of cellular defense a virus encounters during primary infection. We previously identified the tegument protein M35 of murine cytomegalovirus (MCMV) as an essential antagonist of this antiviral system, showing that M35 interferes with type I IFN induction downstream of pattern-recognition receptor (PRR) activation. Here, we report structural and mechanistic details of M35's function. Determination of M35's crystal structure combined with reverse genetics revealed that homodimerization is a key feature for M35's immunomodulatory activity. In electrophoretic mobility shift assays (EMSAs), purified M35 protein specifically bound to the regulatory DNA element that governs transcription of the first type I IFN gene induced in nonimmune cells, Ifnb1. DNA-binding sites of M35 overlapped with the recognition elements of interferon regulatory factor 3 (IRF3), a key transcription factor activated by PRR signaling. Chromatin immunoprecipitation (ChIP) showed reduced binding of IRF3 to the host Ifnb1 promoter in the presence of M35. We furthermore defined the IRF3-dependent and the type I IFN signaling-responsive genes in murine fibroblasts by RNA sequencing of metabolically labeled transcripts (SLAM-seq) and assessed M35's global effect on gene expression. Stable expression of M35 broadly influenced the transcriptome in untreated cells and specifically downregulated basal expression of IRF3-dependent genes. During MCMV infection, M35 impaired expression of IRF3-responsive genes aside of Ifnb1. Our results suggest that M35-DNA binding directly antagonizes gene induction mediated by IRF3 and impairs the antiviral response more broadly than formerly recognized. IMPORTANCE Replication of the ubiquitous human cytomegalovirus (HCMV) in healthy individuals mostly goes unnoticed but can impair fetal development or cause life-threatening symptoms in immunosuppressed or -deficient patients. Like other herpesviruses, CMV extensively manipulates its hosts and establishes lifelong latent infections. Murine CMV (MCMV) presents an important model system as it allows the study of CMV infection in the host organism. We previously showed that during entry into host cells, MCMV virions release the evolutionary conserved protein M35 protein to immediately dampen the antiviral type I interferon (IFN) response induced by pathogen detection. Here, we show that M35 dimers bind to regulatory DNA elements and interfere with recruitment of interferon regulatory factor 3 (IRF3), a key cellular factor for antiviral gene expression. Thereby, M35 interferes with expression of type I IFNs and other IRF3-dependent genes, reflecting the importance for herpesviruses to avoid IRF3-mediated gene induction.
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Affiliation(s)
- Hella Schwanke
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
- Virology and Innate Immunity Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Stefan Schmelz
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Helmholtz Association, Berlin, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | | | | | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Helmholtz Association, Berlin, Germany
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marco van Ham
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lothar Jänsch
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Konrad Büssow
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Joop van den Heuvel
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Caroline C. Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Melanie M. Brinkmann
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
- Virology and Innate Immunity Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
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