1
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Nikopoulou C, Kleinenkuhnen N, Parekh S, Sandoval T, Ziegenhain C, Schneider F, Giavalisco P, Donahue KF, Vesting AJ, Kirchner M, Bozukova M, Vossen C, Altmüller J, Wunderlich T, Sandberg R, Kondylis V, Tresch A, Tessarz P. Spatial and single-cell profiling of the metabolome, transcriptome and epigenome of the aging mouse liver. Nat Aging 2023; 3:1430-1445. [PMID: 37946043 PMCID: PMC10645594 DOI: 10.1038/s43587-023-00513-y] [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] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/27/2023] [Indexed: 11/12/2023]
Abstract
Tissues within an organism and even cell types within a tissue can age with different velocities. However, it is unclear whether cells of one type experience different aging trajectories within a tissue depending on their spatial location. Here, we used spatial transcriptomics in combination with single-cell ATAC-seq and RNA-seq, lipidomics and functional assays to address how cells in the male murine liver are affected by age-related changes in the microenvironment. Integration of the datasets revealed zonation-specific and age-related changes in metabolic states, the epigenome and transcriptome. The epigenome changed in a zonation-dependent manner and functionally, periportal hepatocytes were characterized by decreased mitochondrial fitness, whereas pericentral hepatocytes accumulated large lipid droplets. Together, we provide evidence that changing microenvironments within a tissue exert strong influences on their resident cells that can shape epigenetic, metabolic and phenotypic outputs.
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Affiliation(s)
- Chrysa Nikopoulou
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany
| | - Niklas Kleinenkuhnen
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Swati Parekh
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma, Biberach, Germany
| | - Tonantzi Sandoval
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Farina Schneider
- Institute for Pathology, University Hospital Cologne, Cologne, Germany
| | - Patrick Giavalisco
- Metabolic Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Kat-Folz Donahue
- FACS and Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Marcel Kirchner
- FACS and Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Mihaela Bozukova
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany; Berlin Institute of Health at Charité, Core Facility Genomics, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Thomas Wunderlich
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany
- Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vangelis Kondylis
- Institute for Pathology, University Hospital Cologne, Cologne, Germany
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty at Heinrich-Heine-University, Duesseldorf, Germany
| | - Achim Tresch
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany.
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany.
| | - Peter Tessarz
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany.
- Department of Human Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.
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2
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Fischbach A, Johns A, Schneider KL, Hao X, Tessarz P, Nyström T. Artificial Hsp104-mediated systems for re-localizing protein aggregates. Nat Commun 2023; 14:2663. [PMID: 37160881 PMCID: PMC10169802 DOI: 10.1038/s41467-023-37706-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 03/28/2023] [Indexed: 05/11/2023] Open
Abstract
Spatial Protein Quality Control (sPQC) sequesters misfolded proteins into specific, organelle-associated inclusions within the cell to control their toxicity. To approach the role of sPQC in cellular fitness, neurodegenerative diseases and aging, we report on the construction of Hsp100-based systems in budding yeast cells, which can artificially target protein aggregates to non-canonical locations. We demonstrate that aggregates of mutant huntingtin (mHtt), the disease-causing agent of Huntington's disease can be artificially targeted to daughter cells as well as to eisosomes and endosomes with this approach. We find that the artificial removal of mHtt inclusions from mother cells protects them from cell death suggesting that even large mHtt inclusions may be cytotoxic, a trait that has been widely debated. In contrast, removing inclusions of endogenous age-associated misfolded proteins does not significantly affect the lifespan of mother cells. We demonstrate also that this approach is able to manipulate mHtt inclusion formation in human cells and has the potential to be useful as an alternative, complementary approach to study the role of sPQC, for example in aging and neurodegenerative disease.
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Affiliation(s)
- Arthur Fischbach
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden.
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany.
| | - Angela Johns
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Kara L Schneider
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Xinxin Hao
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Peter Tessarz
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), Cologne, Germany
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden.
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3
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Conte M, Eletto D, Pannetta M, Petrone AM, Monti MC, Cassiano C, Giurato G, Rizzo F, Tessarz P, Petrella A, Tosco A, Porta A. Effects of Hst3p inhibition in Candida albicans: a genome-wide H3K56 acetylation analysis. Front Cell Infect Microbiol 2022; 12:1031814. [PMID: 36389164 PMCID: PMC9647175 DOI: 10.3389/fcimb.2022.1031814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/10/2022] [Indexed: 11/30/2022] Open
Abstract
Candida spp. represent the third most frequent worldwide cause of infection in Intensive Care Units with a mortality rate of almost 40%. The classes of antifungals currently available include azoles, polyenes, echinocandins, pyrimidine derivatives, and allylamines. However, the therapeutical options for the treatment of candidiasis are drastically reduced by the increasing antifungal resistance. The growing need for a more targeted antifungal therapy is limited by the concern of finding molecules that specifically recognize the microbial cell without damaging the host. Epigenetic writers and erasers have emerged as promising targets in different contexts, including the treatment of fungal infections. In C. albicans, Hst3p, a sirtuin that deacetylates H3K56ac, represents an attractive antifungal target as it is essential for the fungus viability and virulence. Although the relevance of such epigenetic regulator is documented for the development of new antifungal therapies, the molecular mechanism behind Hst3p-mediated epigenetic regulation remains unrevealed. Here, we provide the first genome-wide profiling of H3K56ac in C. albicans resulting in H3K56ac enriched regions associated with Candida sp. pathogenicity. Upon Hst3p inhibition, 447 regions gain H3K56ac. Importantly, these genomic areas contain genes encoding for adhesin proteins, degradative enzymes, and white-opaque switching. Moreover, our RNA-seq analysis revealed 1330 upregulated and 1081 downregulated transcripts upon Hst3p inhibition, and among them, we identified 87 genes whose transcriptional increase well correlates with the enrichment of H3K56 acetylation on their promoters, including some well-known regulators of phenotypic switching and virulence. Based on our evidence, Hst3p is an appealing target for the development of new potential antifungal drugs.
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Affiliation(s)
- Marisa Conte
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
- Ph.D. Program in Drug Discovery and Development, University of Salerno, Fisciano, Salerno, Italy
| | - Daniela Eletto
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Martina Pannetta
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
- Ph.D. Program in Drug Discovery and Development, University of Salerno, Fisciano, Salerno, Italy
| | - Anna M. Petrone
- Ph.D. Program in Drug Discovery and Development, University of Salerno, Fisciano, Salerno, Italy
| | - Maria C. Monti
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Chiara Cassiano
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
- Department of Pharmacy, University of Naples ‘Federico II’, Naples, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Salerno, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Salerno, Italy
| | - Peter Tessarz
- Max Planck Research Group “Chromatin and Ageing”, Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | | | - Alessandra Tosco
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
- *Correspondence: Amalia Porta, ; Alessandra Tosco,
| | - Amalia Porta
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
- *Correspondence: Amalia Porta, ; Alessandra Tosco,
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4
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Pouikli A, Maleszewska M, Parekh S, Yang M, Nikopoulou C, Bonfiglio JJ, Mylonas C, Sandoval T, Schumacher A, Hinze Y, Matic I, Frezza C, Tessarz P. Hypoxia promotes osteogenesis by facilitating acetyl-CoA-mediated mitochondrial-nuclear communication. EMBO J 2022; 41:e111239. [PMID: 36278281 PMCID: PMC9713713 DOI: 10.15252/embj.2022111239] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 09/17/2022] [Accepted: 09/23/2022] [Indexed: 01/15/2023] Open
Abstract
Bone-derived mesenchymal stem cells (MSCs) reside in a hypoxic niche that maintains their differentiation potential. While hypoxia (low oxygen concentration) was reported to critically support stem cell function and osteogenesis, the molecular events triggering changes in stem cell fate decisions in response to normoxia (high oxygen concentration) remain elusive. Here, we study the impact of normoxia on mitochondrial-nuclear communication during stem cell differentiation. We show that normoxia-cultured murine MSCs undergo profound transcriptional alterations which cause irreversible osteogenesis defects. Mechanistically, high oxygen promotes chromatin compaction and histone hypo-acetylation, particularly on promoters and enhancers of osteogenic genes. Although normoxia induces metabolic rewiring resulting in elevated acetyl-CoA levels, histone hypo-acetylation occurs due to the trapping of acetyl-CoA inside mitochondria owing to decreased citrate carrier (CiC) activity. Restoring the cytosolic acetyl-CoA pool remodels the chromatin landscape and rescues the osteogenic defects. Collectively, our results demonstrate that the metabolism-chromatin-osteogenesis axis is perturbed upon exposure to high oxygen levels and identifies CiC as a novel, oxygen-sensitive regulator of the MSC function.
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Affiliation(s)
- Andromachi Pouikli
- Max Planck Research Group “Chromatin and Ageing”Max Planck Institute for Biology of AgeingCologneGermany,Cologne Excellence Cluster on Stress Responses in Ageing‐Associated Diseases (CECAD)CologneGermany
| | - Monika Maleszewska
- Max Planck Research Group “Chromatin and Ageing”Max Planck Institute for Biology of AgeingCologneGermany,Present address:
CareDx, Inc.San FranciscoCAUSA
| | - Swati Parekh
- Max Planck Research Group “Chromatin and Ageing”Max Planck Institute for Biology of AgeingCologneGermany
| | - Ming Yang
- Cologne Excellence Cluster on Stress Responses in Ageing‐Associated Diseases (CECAD)CologneGermany
| | - Chrysa Nikopoulou
- Max Planck Research Group “Chromatin and Ageing”Max Planck Institute for Biology of AgeingCologneGermany
| | - Juan Jose Bonfiglio
- Research Group “Proteomics and ADP‐Ribosylation Signaling”Max Planck Institute for Biology of AgeingCologneGermany,Present address:
Roche Pharma Research and Early DevelopmentMunichGermany
| | - Constantine Mylonas
- Max Planck Research Group “Chromatin and Ageing”Max Planck Institute for Biology of AgeingCologneGermany,Present address:
Novartis Institutes for BioMedical ResearchCambridgeMAUSA
| | - Tonantzi Sandoval
- Max Planck Research Group “Chromatin and Ageing”Max Planck Institute for Biology of AgeingCologneGermany
| | - Anna‐Lena Schumacher
- FACS & Imaging Core FacilityMax Planck Institute for Biology of AgeingCologneGermany
| | - Yvonne Hinze
- Metabolomics Core Facility, Max Planck Institute for Biology of AgeingCologneGermany
| | - Ivan Matic
- Cologne Excellence Cluster on Stress Responses in Ageing‐Associated Diseases (CECAD)CologneGermany,Research Group “Proteomics and ADP‐Ribosylation Signaling”Max Planck Institute for Biology of AgeingCologneGermany
| | - Christian Frezza
- Cologne Excellence Cluster on Stress Responses in Ageing‐Associated Diseases (CECAD)CologneGermany
| | - Peter Tessarz
- Max Planck Research Group “Chromatin and Ageing”Max Planck Institute for Biology of AgeingCologneGermany,Cologne Excellence Cluster on Stress Responses in Ageing‐Associated Diseases (CECAD)CologneGermany
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5
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Bozukova M, Nikopoulou C, Kleinenkuhnen N, Grbavac D, Goetsch K, Tessarz P. Aging is associated with increased chromatin accessibility and reduced polymerase pausing in liver. Mol Syst Biol 2022; 18:e11002. [PMID: 36082605 PMCID: PMC9459415 DOI: 10.15252/msb.202211002] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
Regulation of gene expression is linked to the organization of the genome. With age, chromatin alterations occur on all levels of genome organization, accompanied by changes in the gene expression profile. However, little is known about the changes in the level of transcriptional regulation. Here, we used a multi‐omics approach and integrated ATAC‐, RNA‐ and NET‐seq to identify age‐related changes in the chromatin landscape of murine liver and to investigate how these are linked to transcriptional regulation. We provide the first systematic inventory of the connection between aging, chromatin accessibility, and transcriptional regulation in a whole tissue. Aging in murine liver is characterized by an increase in chromatin accessibility at promoter regions, but not in an increase in transcriptional output. Instead, aging is accompanied by a decrease in promoter‐proximal pausing of RNA polymerase II (Pol II), while initiation of transcription is not decreased as assessed by RNA polymerase mapping using CUT&RUN. Based on the data reported, we propose that these age‐related changes in transcriptional regulation are due to a reduced stability of the pausing complex.
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Affiliation(s)
- Mihaela Bozukova
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Chrysa Nikopoulou
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Niklas Kleinenkuhnen
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany.,Faculty of Medicine, Institute of Medical Statistics and Computational Biology, University of Cologne, Cologne, Germany
| | - Dora Grbavac
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Katrin Goetsch
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Peter Tessarz
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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6
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Gehling K, Parekh S, Schneider F, Kirchner M, Kondylis V, Nikopoulou C, Tessarz P. RNA-sequencing of single cholangiocyte-derived organoids reveals high organoid-to organoid variability. Life Sci Alliance 2022; 5:e202101340. [PMID: 35914813 PMCID: PMC9348635 DOI: 10.26508/lsa.202101340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 12/13/2022] Open
Abstract
Over the last decades, organoids have been established from most of the tissue-resident stem and iPS cells. They hold great promise for our understanding of mammalian organ development, but also for the study of disease or even personalised medicine. In recent years, several reports hinted at intraculture organoid variability, but a systematic analysis of such heterogeneity has not been performed before. Here, we used RNA-seq of individual intrahepatic cholangiocyte organoids to address this question. We find that batch-to-batch variation is very low, whereas passage number has a profound impact on gene expression profiles. On the other hand, there is organoid-to-organoid variability within a culture. Using differential gene expression, we did not identify specific pathways that drive this variability, pointing towards possible effects of the microenvironment within the culture condition. Taken together, our study provides a framework for organoid researchers to properly consider experimental design.
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Affiliation(s)
- Kristin Gehling
- Max Planck Research Group "Chromatin and Ageing," Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany
| | - Swati Parekh
- Max Planck Research Group "Chromatin and Ageing," Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Farina Schneider
- Institute for Pathology, University Hospital Cologne, Cologne, Germany
| | - Marcel Kirchner
- FACS and Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Vangelis Kondylis
- Institute for Pathology, University Hospital Cologne, Cologne, Germany
| | - Chrysa Nikopoulou
- Max Planck Research Group "Chromatin and Ageing," Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Peter Tessarz
- Max Planck Research Group "Chromatin and Ageing," Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany
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7
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Skowronska-Krawczyk D, Narayan P, Tessarz P. Editorial: Molecular Role of Lipids in Aging. Front Aging 2022; 3:946884. [PMID: 35821810 PMCID: PMC9261349 DOI: 10.3389/fragi.2022.946884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022]
Affiliation(s)
- Dorota Skowronska-Krawczyk
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, University of California Irvine, Irvine, CA, United States
- *Correspondence: Dorota Skowronska-Krawczyk,
| | - Priyanka Narayan
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, United States
| | - Peter Tessarz
- Max Planck Institute for Biology of Ageing, Cologne, Germany
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8
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Grossbach J, Gillet L, Clément‐Ziza M, Schmalohr CL, Schubert OT, Schütter M, Mawer JSP, Barnes CA, Bludau I, Weith M, Tessarz P, Graef M, Aebersold R, Beyer A. The impact of genomic variation on protein phosphorylation states and regulatory networks. Mol Syst Biol 2022; 18:e10712. [PMID: 35574625 PMCID: PMC9109056 DOI: 10.15252/msb.202110712] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/11/2022] Open
Abstract
Genomic variation impacts on cellular networks by affecting the abundance (e.g., protein levels) and the functional states (e.g., protein phosphorylation) of their components. Previous work has focused on the former, while in this context, the functional states of proteins have largely remained neglected. Here, we generated high‐quality transcriptome, proteome, and phosphoproteome data for a panel of 112 genomically well‐defined yeast strains. Genetic effects on transcripts were generally transmitted to the protein layer, but specific gene groups, such as ribosomal proteins, showed diverging effects on protein levels compared with RNA levels. Phosphorylation states proved crucial to unravel genetic effects on signaling networks. Correspondingly, genetic variants that cause phosphorylation changes were mostly different from those causing abundance changes in the respective proteins. Underscoring their relevance for cell physiology, phosphorylation traits were more strongly correlated with cell physiological traits such as chemical compound resistance or cell morphology, compared with transcript or protein abundance. This study demonstrates how molecular networks mediate the effects of genomic variants to cellular traits and highlights the particular importance of protein phosphorylation.
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Affiliation(s)
- Jan Grossbach
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
| | - Ludovic Gillet
- Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland
| | - Mathieu Clément‐Ziza
- Center for Molecular Medicine Cologne (CMMC) Medical Faculty, University of Cologne Cologne Germany
- Lesaffre International Marcq‐en‐Barœul France
| | - Corinna L Schmalohr
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
| | - Olga T Schubert
- Department of Human Genetics University of California, Los Angeles Los Angeles CA USA
| | | | | | | | - Isabell Bludau
- Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland
- Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Martinsried Germany
| | - Matthias Weith
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
| | - Peter Tessarz
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
- Max Planck Institute for Biology of Ageing Cologne Germany
| | - Martin Graef
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
- Max Planck Institute for Biology of Ageing Cologne Germany
| | - Ruedi Aebersold
- Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland
- Faculty of Science University of Zurich Zurich Switzerland
| | - Andreas Beyer
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
- Center for Molecular Medicine Cologne (CMMC) Medical Faculty, University of Cologne Cologne Germany
- Institute for Genetics Faculty of Mathematics and Natural Sciences University of Cologne Cologne Germany
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9
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Mawer JSP, Massen J, Reichert C, Grabenhorst N, Mylonas C, Tessarz P. Nhp2 is a reader of H2AQ105me and part of a network integrating metabolism with rRNA synthesis. EMBO Rep 2021; 22:e52435. [PMID: 34409714 PMCID: PMC8490984 DOI: 10.15252/embr.202152435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 01/16/2023] Open
Abstract
Ribosome biogenesis is an essential cellular process that requires integration of extracellular cues, such as metabolic state, with intracellular signalling, transcriptional regulation and chromatin accessibility at the ribosomal DNA. Here, we demonstrate that the recently identified histone modification, methylation of H2AQ105 (H2AQ105me), is an integral part of a dynamic chromatin network at the rDNA locus. Its deposition depends on a functional mTor signalling pathway and acetylation of histone H3 at position K56, thus integrating metabolic and proliferative signals. Furthermore, we identify a first epigenetic reader of this modification, the ribonucleoprotein Nhp2, which specifically recognizes H2AQ105me. Based on functional and proteomic data, we suggest that Nhp2 functions as an adapter to bridge rDNA chromatin with components of the small subunit processome to efficiently coordinate transcription of rRNA with its post‐transcriptional processing. We support this by showing that an H2AQ105A mutant has a mild defect in early processing of rRNA.
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Affiliation(s)
- Julia S P Mawer
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Jennifer Massen
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Christina Reichert
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Niklas Grabenhorst
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Constantine Mylonas
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Peter Tessarz
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Excellence Cluster on Stress Responses in ageing-associated Diseases (CECAD), Cologne, Germany
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10
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Pouikli A, Parekh S, Maleszewska M, Nikopoulou C, Baghdadi M, Tripodi I, Folz-Donahue K, Hinze Y, Mesaros A, Hoey D, Giavalisco P, Dowell R, Partridge L, Tessarz P. Chromatin remodeling due to degradation of citrate carrier impairs osteogenesis of aged mesenchymal stem cells. Nat Aging 2021; 1:810-825. [PMID: 37117628 PMCID: PMC10154229 DOI: 10.1038/s43587-021-00105-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 07/26/2021] [Indexed: 04/30/2023]
Abstract
Aging is accompanied by a general decline in the function of many cellular pathways. However, whether these are causally or functionally interconnected remains elusive. Here, we study the effect of mitochondrial-nuclear communication on stem cell aging. We show that aged mesenchymal stem cells exhibit reduced chromatin accessibility and lower histone acetylation, particularly on promoters and enhancers of osteogenic genes. The reduced histone acetylation is due to impaired export of mitochondrial acetyl-CoA, owing to the lower levels of citrate carrier (CiC). We demonstrate that aged cells showed enhanced lysosomal degradation of CiC, which is mediated via mitochondrial-derived vesicles. Strikingly, restoring cytosolic acetyl-CoA levels either by exogenous CiC expression or via acetate supplementation, remodels the chromatin landscape and rescues the osteogenesis defects of aged mesenchymal stem cells. Collectively, our results establish a tight, age-dependent connection between mitochondrial quality control, chromatin and stem cell fate, which are linked together by CiC.
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Affiliation(s)
- Andromachi Pouikli
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Swati Parekh
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Monika Maleszewska
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Chrysa Nikopoulou
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Maarouf Baghdadi
- Department of Biological Mechanisms of Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Ignacio Tripodi
- Computer Science, University of Colorado, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Kat Folz-Donahue
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Yvonne Hinze
- Metabolomics Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Andrea Mesaros
- Phenotyping Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - David Hoey
- Trinity Centre for Biomedical Engineering, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- Department of Mechanical, Manufacturing and Biomedical Engineering, School of Engineering, Trinity College Dublin, Dublin, Ireland
- Advanced Materials and Bioengineering Research Centre (AMBER), Royal College of Surgeons in Ireland and Trinity College Dublin, Dublin, Ireland
| | - Patrick Giavalisco
- Metabolomics Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Robin Dowell
- Computer Science, University of Colorado, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Linda Partridge
- Department of Biological Mechanisms of Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), Cologne, Germany
| | - Peter Tessarz
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany.
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), Cologne, Germany.
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11
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Theobald SJ, Simonis A, Georgomanolis T, Kreer C, Zehner M, Eisfeld HS, Albert M, Chhen J, Motameny S, Erger F, Fischer J, Malin JJ, Gräb J, Winter S, Pouikli A, David F, Böll B, Koehler P, Vanshylla K, Gruell H, Suárez I, Hallek M, Fätkenheuer G, Jung N, Cornely OA, Lehmann C, Tessarz P, Altmüller J, Nürnberg P, Kashkar H, Klein F, Koch M, Rybniker J. Long-lived macrophage reprogramming drives spike protein-mediated inflammasome activation in COVID-19. EMBO Mol Med 2021; 13:e14150. [PMID: 34133077 PMCID: PMC8350892 DOI: 10.15252/emmm.202114150] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 01/12/2023] Open
Abstract
Innate immunity triggers responsible for viral control or hyperinflammation in COVID-19 are largely unknown. Here we show that the SARS-CoV-2 spike protein (S-protein) primes inflammasome formation and release of mature interleukin-1β (IL-1β) in macrophages derived from COVID-19 patients but not in macrophages from healthy SARS-CoV-2 naïve individuals. Furthermore, longitudinal analyses reveal robust S-protein-driven inflammasome activation in macrophages isolated from convalescent COVID-19 patients, which correlates with distinct epigenetic and gene expression signatures suggesting innate immune memory after recovery from COVID-19. Importantly, we show that S-protein-driven IL-1β secretion from patient-derived macrophages requires non-specific monocyte pre-activation in vivo to trigger NLRP3-inflammasome signaling. Our findings reveal that SARS-CoV-2 infection causes profound and long-lived reprogramming of macrophages resulting in augmented immunogenicity of the SARS-CoV-2 S-protein, a major vaccine antigen and potent driver of adaptive and innate immune signaling.
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Affiliation(s)
- Sebastian J Theobald
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
- Faculty of Medicine and University Hospital of CologneCenter for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Alexander Simonis
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
- Faculty of Medicine and University Hospital of CologneCenter for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Theodoros Georgomanolis
- Faculty of Medicine and University Hospital of CologneCologne Center for Genomics (CCG)University of CologneCologneGermany
| | - Christoph Kreer
- Laboratory of Experimental ImmunologyInstitute of VirologyFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
| | - Matthias Zehner
- Laboratory of Experimental ImmunologyInstitute of VirologyFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
| | - Hannah S Eisfeld
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
- Faculty of Medicine and University Hospital of CologneCenter for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Marie‐Christine Albert
- Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
- Institute for Medical Microbiology, Immunology and Hygiene (IMMIH)University of CologneCologneGermany
| | - Jason Chhen
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
- Faculty of Medicine and University Hospital of CologneCenter for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Susanne Motameny
- Faculty of Medicine and University Hospital of CologneCologne Center for Genomics (CCG)University of CologneCologneGermany
| | - Florian Erger
- Faculty of Medicine and University Hospital of CologneCologne Center for Genomics (CCG)University of CologneCologneGermany
- Faculty of MedicineInstitute of Human GeneticsUniversity Hospital CologneCologneGermany
| | - Julia Fischer
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
- Faculty of Medicine and University Hospital of CologneCenter for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
- German Center for Infection Research (DZIF), Partner Site Bonn‐CologneCologneGermany
| | - Jakob J Malin
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
- Faculty of Medicine and University Hospital of CologneCenter for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Jessica Gräb
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
- Faculty of Medicine and University Hospital of CologneCenter for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Sandra Winter
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
- Faculty of Medicine and University Hospital of CologneCenter for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Andromachi Pouikli
- Max Planck Research Group “Chromatin and Ageing”Max Planck Institute for Biology of AgeingCologneGermany
| | - Friederike David
- Faculty of Medicine and University Hospital of CologneCologne Center for Genomics (CCG)University of CologneCologneGermany
| | - Boris Böll
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
| | - Philipp Koehler
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
- Faculty of Medicine and University Hospital of CologneCenter for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
- Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Kanika Vanshylla
- Laboratory of Experimental ImmunologyInstitute of VirologyFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
| | - Henning Gruell
- Laboratory of Experimental ImmunologyInstitute of VirologyFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
| | - Isabelle Suárez
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
- German Center for Infection Research (DZIF), Partner Site Bonn‐CologneCologneGermany
| | - Michael Hallek
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
| | - Gerd Fätkenheuer
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
- German Center for Infection Research (DZIF), Partner Site Bonn‐CologneCologneGermany
| | - Norma Jung
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
- German Center for Infection Research (DZIF), Partner Site Bonn‐CologneCologneGermany
| | - Oliver A Cornely
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
- Faculty of Medicine and University Hospital of CologneCenter for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
- Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
- German Center for Infection Research (DZIF), Partner Site Bonn‐CologneCologneGermany
| | - Clara Lehmann
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
- Faculty of Medicine and University Hospital of CologneCenter for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
- German Center for Infection Research (DZIF), Partner Site Bonn‐CologneCologneGermany
| | - Peter Tessarz
- Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
- Max Planck Research Group “Chromatin and Ageing”Max Planck Institute for Biology of AgeingCologneGermany
| | - Janine Altmüller
- Faculty of Medicine and University Hospital of CologneCologne Center for Genomics (CCG)University of CologneCologneGermany
| | - Peter Nürnberg
- Faculty of Medicine and University Hospital of CologneCenter for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
- Faculty of Medicine and University Hospital of CologneCologne Center for Genomics (CCG)University of CologneCologneGermany
| | - Hamid Kashkar
- Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
- Institute for Medical Microbiology, Immunology and Hygiene (IMMIH)University of CologneCologneGermany
| | - Florian Klein
- Laboratory of Experimental ImmunologyInstitute of VirologyFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
- German Center for Infection Research (DZIF), Partner Site Bonn‐CologneCologneGermany
| | - Manuel Koch
- Medical FacultyInstitute for Dental Research and Oral Musculoskeletal BiologyUniversity of CologneCologneGermany
- Medical FacultyCenter for BiochemistryUniversity of CologneCologneGermany
| | - Jan Rybniker
- Department I of Internal MedicineFaculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany
- Faculty of Medicine and University Hospital of CologneCenter for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
- German Center for Infection Research (DZIF), Partner Site Bonn‐CologneCologneGermany
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12
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Kochan DZ, Mawer JSP, Massen J, Tishinov K, Parekh S, Graef M, Spang A, Tessarz P. The RNA-binding protein Puf5 contributes to buffering of mRNA upon chromatin-mediated changes in nascent transcription. J Cell Sci 2021; 134:jcs259051. [PMID: 34350963 PMCID: PMC8353526 DOI: 10.1242/jcs.259051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 07/03/2021] [Indexed: 11/23/2022] Open
Abstract
Gene expression involves regulation of chromatin structure and transcription, as well as processing of the transcribed mRNA. While there are feedback mechanisms, it is not clear whether these include crosstalk between chromatin architecture and mRNA decay. To address this, we performed a genome-wide genetic screen using a Saccharomyces cerevisiae strain harbouring the H3K56A mutation, which is known to perturb chromatin structure and nascent transcription. We identified Puf5 (also known as Mpt5) as essential in an H3K56A background. Depletion of Puf5 in this background leads to downregulation of Puf5 targets. We suggest that Puf5 plays a role in post-transcriptional buffering of mRNAs, and support this by transcriptional shutoff experiments in which Puf5 mRNA targets are degraded slower in H3K56A cells compared to wild-type cells. Finally, we show that post-transcriptional buffering of Puf5 targets is widespread and does not occur only in an H3K56A mutant, but also in an H3K4R background, which leads to a global increase in nascent transcription. Our data suggest that Puf5 determines the fate of its mRNA targets in a context-dependent manner acting as an mRNA surveillance hub balancing deregulated nascent transcription to maintain physiological mRNA levels.
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Affiliation(s)
- David Z. Kochan
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Julia S. P. Mawer
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Jennifer Massen
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Kiril Tishinov
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Swati Parekh
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Martin Graef
- Max Planck Research Group ‘Autophagy and Cellular Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Anne Spang
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Peter Tessarz
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
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13
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Allmeroth K, Kim CS, Annibal A, Pouikli A, Koester J, Derisbourg MJ, Andrés Chacón-Martínez C, Latza C, Antebi A, Tessarz P, Wickström SA, Denzel MS. N1-acetylspermidine is a determinant of hair follicle stem cell fate. J Cell Sci 2021; 134:261953. [PMID: 33973637 PMCID: PMC8182411 DOI: 10.1242/jcs.252767] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 03/20/2021] [Indexed: 12/17/2022] Open
Abstract
Stem cell differentiation is accompanied by increased mRNA translation. The rate of protein biosynthesis is influenced by the polyamines putrescine, spermidine and spermine, which are essential for cell growth and stem cell maintenance. However, the role of polyamines as endogenous effectors of stem cell fate and whether they act through translational control remains obscure. Here, we investigate the function of polyamines in stem cell fate decisions using hair follicle stem cell (HFSC) organoids. Compared to progenitor cells, HFSCs showed lower translation rates, correlating with reduced polyamine levels. Surprisingly, overall polyamine depletion decreased translation but did not affect cell fate. In contrast, specific depletion of natural polyamines mediated by spermidine/spermine N1-acetyltransferase (SSAT; also known as SAT1) activation did not reduce translation but enhanced stemness. These results suggest a translation-independent role of polyamines in cell fate regulation. Indeed, we identified N1-acetylspermidine as a determinant of cell fate that acted through increasing self-renewal, and observed elevated N1-acetylspermidine levels upon depilation-mediated HFSC proliferation and differentiation in vivo. Overall, this study delineates the diverse routes of polyamine metabolism-mediated regulation of stem cell fate decisions. This article has an associated First Person interview with the first author of the paper. Summary: Reduced protein synthesis is required for stem cell functions. Here, we delineate a complex interplay of polyamines and mRNA translation that determines hair follicle stem cell fate decisions.
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Affiliation(s)
- Kira Allmeroth
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931 Cologne, Germany
| | - Christine S Kim
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931 Cologne, Germany
| | - Andrea Annibal
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931 Cologne, Germany
| | - Andromachi Pouikli
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931 Cologne, Germany
| | - Janis Koester
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931 Cologne, Germany.,CECAD - Cluster of Excellence, University of Cologne, Joseph-Stelzmann-Str. 26, D-50931 Cologne, Germany
| | - Maxime J Derisbourg
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931 Cologne, Germany
| | | | - Christian Latza
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931 Cologne, Germany
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931 Cologne, Germany.,CECAD - Cluster of Excellence, University of Cologne, Joseph-Stelzmann-Str. 26, D-50931 Cologne, Germany
| | - Peter Tessarz
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931 Cologne, Germany.,CECAD - Cluster of Excellence, University of Cologne, Joseph-Stelzmann-Str. 26, D-50931 Cologne, Germany
| | - Sara A Wickström
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931 Cologne, Germany.,CECAD - Cluster of Excellence, University of Cologne, Joseph-Stelzmann-Str. 26, D-50931 Cologne, Germany.,Helsinki Institute for Life Science, Biomedicum Helsinki, Haartmaninkatu 8, FI-00290 Helsinki, Finland.,Wihuri Research Institute, Biomedicum Helsinki, Haartmaninkatu 8, FI-00290 Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, Biomedicum Helsinki, Haartmaninkatu 8, FI-00290 Helsinki, Finland
| | - Martin S Denzel
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931 Cologne, Germany.,CECAD - Cluster of Excellence, University of Cologne, Joseph-Stelzmann-Str. 26, D-50931 Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 21, D-50931 Cologne, Germany
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14
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Pouikli A, Tessarz P. Epigenetic alterations in stem cell ageing-a promising target for age-reversing interventions? Brief Funct Genomics 2021; 21:35-42. [PMID: 33738480 PMCID: PMC8789308 DOI: 10.1093/bfgp/elab010] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Ageing is accompanied by loss of tissue integrity and organismal homeostasis partly due to decline in stem cell function. The age-associated decrease in stem cell abundance and activity is often referred to as stem cell exhaustion and is considered one major hallmark of ageing. Importantly, stem cell proliferation and differentiation potential are tightly coupled to the cellular epigenetic state. Thus, research during the last years has started to investigate how the epigenome regulates stem cell function upon ageing. Here, we summarize the role of epigenetic regulation in stem cell fate decisions and we review the impact of age-related changes of the epigenome on stem cell activity. Finally, we discuss how targeted interventions on the epigenetic landscape might delay ageing and extend health-span.
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Affiliation(s)
- Andromachi Pouikli
- Max Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Peter Tessarz
- Max Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany.,Cologne Excellence Cluster on Stress Responses in ageing-associated Diseases (CECAD), Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
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15
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Pouikli A, Tessarz P. Metabolism and chromatin: A dynamic duo that regulates development and ageing: Elucidating the metabolism-chromatin axis in bone-marrow mesenchymal stem cell fate decisions. Bioessays 2021; 43:e2000273. [PMID: 33629755 DOI: 10.1002/bies.202000273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/12/2022]
Abstract
Bone-marrow mesenchymal stem cell (BM-MSC) proliferation and lineage commitment are under the coordinated control of metabolism and epigenetics; the MSC niche contains low oxygen, which is an important determinant of the cellular metabolic state. In turn, metabolism drives stem cell fate decisions via alterations of the chromatin landscape. Due to the fundamental role of BM-MSCs in the development of adipose tissue, bones and cartilage, age-associated changes in metabolism and the epigenome perturb the balance between stem cell proliferation and differentiation leading to stem cell depletion, fat accumulation and bone-quality related diseases. Therefore, understanding the dynamics of the metabolism-chromatin interplay is crucial for maintaining the stem cell pool and delaying the development and progression of ageing. This review summarizes the current knowledge on the role of metabolism in stem cell identity and highlights the impact of the metabolic inputs on the epigenome, with regards to stemness and pluripotency.
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Affiliation(s)
- Andromachi Pouikli
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Peter Tessarz
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Excellence Cluster on Stress Responses in ageing-associated Diseases (CECAD), Cologne, Germany
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16
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Iyer-Bierhoff A, Krogh N, Tessarz P, Ruppert T, Nielsen H, Grummt I. SIRT7-Dependent Deacetylation of Fibrillarin Controls Histone H2A Methylation and rRNA Synthesis during the Cell Cycle. Cell Rep 2019; 25:2946-2954.e5. [PMID: 30540930 DOI: 10.1016/j.celrep.2018.11.051] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 09/17/2018] [Accepted: 11/12/2018] [Indexed: 12/31/2022] Open
Abstract
Fibrillarin (FBL) is a dual-function nucleolar protein that catalyzes 2'-O methylation of pre-rRNA and methylation of histone H2A at glutamine 104 (H2AQ104me). The mechanisms that regulate FBL activity are unexplored. Here, we show that FBL is acetylated at several lysine residues by the acetyltransferase CBP and deacetylated by SIRT7. While reversible acetylation does not impact FBL-mediated pre-rRNA methylation, hyperacetylation impairs the interaction of FBL with histone H2A and chromatin, thereby compromising H2AQ104 methylation (H2AQ104me) and rDNA transcription. SIRT7-dependent deacetylation of FBL ensures H2AQ104me and high levels of rRNA synthesis during interphase. At the onset of mitosis, nucleolar disassembly is accompanied by hyperacetylation of FBL, loss of H2AQ104me, and repression of polymerase I (Pol I) transcription. Overexpression of an acetylation-deficient, but not an acetylation-mimicking, FBL mutant restores H2AQ104me and transcriptional activity. The results reveal that SIRT7-dependent deacetylation impacts nucleolar activity by an FBL-driven circuitry that mediates cell-cycle-dependent fluctuation of rDNA transcription.
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Affiliation(s)
- Aishwarya Iyer-Bierhoff
- Molecular Biology of the Cell II, German Cancer Research Centre (DKFZ), DKFZ-Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, 69120 Heidelberg, Germany
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200N Copenhagen, Denmark
| | - Peter Tessarz
- Department of Chromatin and Ageing, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Thomas Ruppert
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200N Copenhagen, Denmark
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Centre (DKFZ), DKFZ-Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, 69120 Heidelberg, Germany.
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17
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Abstract
The advent of quantitative approaches that enable interrogation of transcription at single nucleotide resolution has allowed a novel understanding of transcriptional regulation previously undefined. However, little is known, at such high resolution, how transcription factors directly influence RNA Pol II pausing and directionality. To map the impact of transcription/elongation factors on transcription dynamics genome-wide at base pair resolution, we developed an adapted NET-seq protocol called NET-prism (Native Elongating Transcription by Polymerase-Regulated Immunoprecipitants in the Mammalian genome). Application of NET-prism on elongation factors (Spt6, Ssrp1), splicing factors (Sf1), and components of the pre-initiation complex (PIC) (TFIID, and Mediator) reveals their inherent command on transcription dynamics, with regards to directionality and pausing over promoters, splice sites, and enhancers/super-enhancers. NET-prism will be broadly applicable as it exposes transcription factor/Pol II dependent topographic specificity and thus, a new degree of regulatory complexity during gene expression.
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Affiliation(s)
- Constantine Mylonas
- a Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing , Cologne , Germany
| | - Peter Tessarz
- a Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing , Cologne , Germany.,b Cologne Excellence Cluster on Cellular Stress Responses in Ageing Associated Diseases (CECAD), University of Cologne , Cologne , Germany
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18
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Abstract
Abstract
Cellular heterogeneity is an important contributor to biological function and is employed by cells, tissues and organisms to adapt, compensate, respond, defend and/or regulate specific processes. Research over the last decades has revealed that transcriptional noise is a major driver for cell-to-cell variability. In this review we will discuss sources of transcriptional variability, in particular bursting of gene expression and how it could contribute to cellular states and fate decisions. We will highlight recent developments in single cell sequencing technologies that make it possible to address cellular heterogeneity in unprecedented detail. Finally, we will review recent literature, in which these new technologies are harnessed to address pressing questions in the field of ageing research, such as transcriptional noise and cellular heterogeneity in the course of ageing.
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Affiliation(s)
- Chrysa Nikopoulou
- Max Planck Research Group ‘Chromatin and Ageing’ , Max Planck Institute for Biology of Ageing , Joseph-Stelzmann-Str. 9b , D-50931 Cologne , Germany
| | - Swati Parekh
- Max Planck Research Group ‘Chromatin and Ageing’ , Max Planck Institute for Biology of Ageing , Joseph-Stelzmann-Str. 9b , D-50931 Cologne , Germany
| | - Peter Tessarz
- Max Planck Research Group ‘Chromatin and Ageing’ , Max Planck Institute for Biology of Ageing , Joseph-Stelzmann-Str. 9b , D-50931 Cologne , Germany
- Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD) , University of Cologne , Joseph-Stelzmann-Str. 26 , D-50931 Cologne , Germany
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19
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Mylonas C, Tessarz P. Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cells. Life Sci Alliance 2018; 1:e201800085. [PMID: 30456357 PMCID: PMC6238418 DOI: 10.26508/lsa.201800085] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 12/22/2022] Open
Abstract
Depletion of FACT in murine embryonic stem cells show mild changes on the nucleosomal landscape but widespread changes in the transcriptome, faster proliferation, and neuronal differentiation rates. The conserved and essential histone chaperone, facilitates chromatin transcription (FACT), reorganizes nucleosomes during DNA transcription, replication, and repair and ensures both efficient elongation of RNA Pol II and nucleosome integrity. In mammalian cells, FACT is a heterodimer, consisting of SSRP1 and SUPT16. Here, we show that in contrast to yeast, FACT accumulates at the transcription start site of genes reminiscent of RNA polymerase II profile. Depletion of FACT in mouse embryonic stem cells leads to deregulation of developmental and pro-proliferative genes concomitant with hyper-proliferation of mES cells. Using MNase-seq, Assay for Transposase-Accessible Chromatin sequencing, and nascent elongating transcript sequencing, we show that up-regulation of genes coincides with loss of nucleosomes upstream of the transcription start site and concomitant increase in antisense transcription, indicating that FACT impacts the promoter architecture to regulate the expression of these genes. Finally, we demonstrate a role for FACT in cell fate determination and show that FACT depletion primes embryonic stem cells for the neuronal lineage.
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Affiliation(s)
| | - Peter Tessarz
- Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing Associated Diseases, University of Cologne, Cologne, Germany
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20
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Abstract
Post-translational modifications of histones regulate all DNA-templated processes, including replication, transcription and repair. These modifications function as platforms for the recruitment of specific effector proteins, such as transcriptional regulators or chromatin remodellers. Recent data suggest that histone modifications also have a direct effect on nucleosomal architecture. Acetylation, methylation, phosphorylation and citrullination of the histone core may influence chromatin structure by affecting histone-histone and histone-DNA interactions, as well as the binding of histones to chaperones.
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Affiliation(s)
- Peter Tessarz
- Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge, CB2 1QN, UK; and the Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, 50931 Cologne, Germany
| | - Tony Kouzarides
- Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge, CB2 1QN, UK
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21
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Tessarz P, Santos-Rosa H, Robson SC, Sylvestersen KB, Nelson CJ, Nielsen ML, Kouzarides T. Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification. Nature 2014; 505:564-8. [PMID: 24352239 PMCID: PMC3901671 DOI: 10.1038/nature12819] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 10/29/2013] [Indexed: 12/03/2022]
Abstract
Nucleosomes are decorated with numerous post-translational modifications capable of influencing many DNA processes. Here we describe a new class of histone modification, methylation of glutamine, occurring on yeast histone H2A at position 105 (Q105) and human H2A at Q104. We identify Nop1 as the methyltransferase in yeast and demonstrate that fibrillarin is the orthologue enzyme in human cells. Glutamine methylation of H2A is restricted to the nucleolus. Global analysis in yeast, using an H2AQ105me-specific antibody, shows that this modification is exclusively enriched over the 35S ribosomal DNA transcriptional unit. We show that the Q105 residue is part of the binding site for the histone chaperone FACT (facilitator of chromatin transcription) complex. Methylation of Q105 or its substitution to alanine disrupts binding to FACT in vitro. A yeast strain mutated at Q105 shows reduced histone incorporation and increased transcription at the ribosomal DNA locus. These features are phenocopied by mutations in FACT complex components. Together these data identify glutamine methylation of H2A as the first histone epigenetic mark dedicated to a specific RNA polymerase and define its function as a regulator of FACT interaction with nucleosomes.
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Affiliation(s)
- Peter Tessarz
- Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Helena Santos-Rosa
- Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Sam C. Robson
- Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Kathrine B. Sylvestersen
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Christopher J Nelson
- Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Michael L. Nielsen
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Tony Kouzarides
- Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge CB2 1QN, UK
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22
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Kohl C, Tessarz P, von der Malsburg K, Zahn R, Bukau B, Mogk A. Cooperative and independent activities of Sgt2 and Get5 in the targeting of tail-anchored proteins. Biol Chem 2011; 392:601-8. [DOI: 10.1515/bc.2011.066] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
TPR proteins modulate the activity of molecular chaperones. Here, we describe the S. cerevisiae TPR protein Sgt2 as interaction partner of Ssa1 and Hsp104 and as a component of the GET pathway by interacting with Get5. The GET pathway mediates the sorting of tail-anchored (TA) proteins, harboring a C-terminal trans-membrane segment, to the ER membrane. S. cerevisiae sgt2Δ cells show partial defects in TA protein sorting. Sgt2 activity in vivo relies on its N- and C-terminal domains, whereas the central TPR domain and thus chaperone interactions are dispensable. We show that TA protein sorting defects are more severe in sgt2Δ get5Δ mutants compared to single knockouts. Furthermore, overproduction of Sgt2 becomes toxic to get3Δ but not to get5Δ cells. Together, these findings indicate an additional, Get5-independent role of Sgt2 in TA protein sorting, pointing to parallel pathways of substrate delivery to Get3.
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23
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Bukau B, Winkler J, Tessarz P, Specht S, Mogk A. Cellular quality control of protein aggregates. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.195.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Bernd Bukau
- Center for Molecular Biology (ZMBH)HeidelbergGermany
| | | | | | | | - Axel Mogk
- Center for Molecular Biology, ZMBHHeidelbergGermany
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24
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Tessarz P, Mogk A, Bukau B. Substrate threading through the central pore of the Hsp104 chaperone as a common mechanism for protein disaggregation and prion propagation. Mol Microbiol 2008; 68:87-97. [PMID: 18312264 DOI: 10.1111/j.1365-2958.2008.06135.x] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oligomeric AAA+ chaperone Hsp104 is essential for thermotolerance development and prion propagation in yeast. Thermotolerance relies on the ability of Hsp104 to cooperate with the Hsp70 chaperone system in the reactivation of heat-aggregated proteins. Prion propagation requires the Hsp104-dependent fragmentation of prion fibrils to create infectious seeds. It remained elusive whether both processes rely on common or different activities of Hsp104. Specifically, protein reactivation has been suggested to require a substrate threading activity of Hsp104 whereas fibril fragmentation may be mediated by a crowbar activity. Here we engineered an Hsp104 variant, HAP, which cooperates with the bacterial peptidase ClpP to form a novel proteolytic system. HAP threads aggregated model substrates as well as the yeast prion Sup35 through its central pore into associated ClpP. HAP variants that harbour a reduced threading activity were affected in both protein disaggregation and prion propagation, demonstrating that substrate threading represents the common mechanism for the processing of both substrate classes.
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Affiliation(s)
- Peter Tessarz
- Universität Heidelberg, Zentrum fuer Molekulare Biologie Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
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25
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Abstract
Cell survival under severe thermal stress requires the activity of a bi-chaperone system, consisting of the ring-forming AAA+ chaperone ClpB (Hsp104) and the DnaK (Hsp70) chaperone system, which acts to solubilize and reactivate aggregated proteins. Recent studies have provided novel insight into the mechanism of protein disaggregation, demonstrating that ClpB/Hsp104 extracts unfolded polypeptides from an aggregate by threading them through its central pore. This translocation activity is necessary but not sufficient for aggregate solubilization. In addition, the middle (M) domain of ClpB and the DnaK system have essential roles, possibly by providing an unfolding force, which facilitates the extraction of misfolded proteins from aggregates.
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Affiliation(s)
- Jimena Weibezahn
- Zentrum für Molekulare Biologie Heidelberg, Universität Heidelberg, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
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26
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Weibezahn J, Tessarz P, Schlieker C, Zahn R, Maglica Z, Lee S, Zentgraf H, Weber-Ban EU, Dougan DA, Tsai FTF, Mogk A, Bukau B. Thermotolerance Requires Refolding of Aggregated Proteins by Substrate Translocation through the Central Pore of ClpB. Cell 2004; 119:653-65. [PMID: 15550247 DOI: 10.1016/j.cell.2004.11.027] [Citation(s) in RCA: 341] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2004] [Revised: 08/20/2004] [Accepted: 10/06/2004] [Indexed: 10/26/2022]
Abstract
Cell survival under severe thermal stress requires the activity of the ClpB (Hsp104) AAA+ chaperone that solubilizes and reactivates aggregated proteins in concert with the DnaK (Hsp70) chaperone system. How protein disaggregation is achieved and whether survival is solely dependent on ClpB-mediated elimination of aggregates or also on reactivation of aggregated proteins has been unclear. We engineered a ClpB variant, BAP, which associates with the ClpP peptidase and thereby is converted into a degrading disaggregase. BAP translocates substrates through its central pore directly into ClpP for degradation. ClpB-dependent translocation is demonstrated to be an integral part of the disaggregation mechanism. Protein disaggregation by the BAP/ClpP complex remains dependent on DnaK, defining a role for DnaK at early stages of the disaggregation reaction. The activity switch of BAP to a degrading disaggregase does not support thermotolerance development, demonstrating that cell survival during severe thermal stress requires reactivation of aggregated proteins.
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Affiliation(s)
- Jimena Weibezahn
- Zentrum für Molekulare Biologie der Universität Heidelberg, Universität Heidelberg, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
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27
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Schlieker C, Weibezahn J, Patzelt H, Tessarz P, Strub C, Zeth K, Erbse A, Schneider-Mergener J, Chin JW, Schultz PG, Bukau B, Mogk A. Substrate recognition by the AAA+ chaperone ClpB. Nat Struct Mol Biol 2004; 11:607-15. [PMID: 15208691 DOI: 10.1038/nsmb787] [Citation(s) in RCA: 202] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Accepted: 04/16/2004] [Indexed: 02/07/2023]
Abstract
The AAA+ protein ClpB cooperates with the DnaK chaperone system to solubilize and refold proteins from an aggregated state. The substrate-binding site of ClpB and the mechanism of ClpB-dependent protein disaggregation are largely unknown. Here we identified a substrate-binding site of ClpB that is located at the central pore of the first AAA domain. The conserved Tyr251 residue that lines the central pore contributes to substrate binding and its crucial role was confirmed by mutational analysis and direct crosslinking to substrates. Because the positioning of an aromatic residue at the central pore is conserved in many AAA+ proteins, a central substrate-binding site involving this residue may be a common feature of this protein family. The location of the identified binding site also suggests a possible translocation mechanism as an integral part of the ClpB-dependent disaggregation reaction.
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Affiliation(s)
- Christian Schlieker
- Zentrum für Molekulare Biologie, Universität Heidelberg, Im Neuenheimer Feld 282, Heidelberg 69120, Germany
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28
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Heessen S, Dantuma NP, Tessarz P, Jellne M, Masucci MG. Inhibition of ubiquitin/proteasome-dependent proteolysis inSaccharomyces cerevisiaeby a Gly-Ala repeat. FEBS Lett 2003; 555:397-404. [PMID: 14644450 DOI: 10.1016/s0014-5793(03)01296-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The glycine-alanine (GA) repeat of the Epstein-Barr virus nuclear antigen-1 inhibits in cis ubiquitin-dependent proteolysis in mammalian cells through a yet unknown mechanism. In the present study we demonstrate that the GA repeat targets an evolutionarily conserved step in proteolysis since it can prevent the degradation of proteasomal substrates in the yeast Saccharomyces cerevisiae. Insertion of yeast codon-optimised recombinant GA (rGA) repeats of different length in green fluorescent protein reporters harbouring N-end rule or ubiquitin fusion degradation signals resulted in efficient stabilisation of these substrates. Protection was also achieved in rpn10delta yeast suggesting that this polyubiquitin binding protein is not required for the rGA effect. The conserved effect of the GA repeat in yeast opens the possibility for the use of genetic screens to unravel its mode of action.
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Affiliation(s)
- Stijn Heessen
- Microbiology and Tumor Biology Center, Karolinska Institutet, Box 280, S-171 77 Stockholm, Sweden
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