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Gretzmeier C, Eiselein S, Johnson GR, Engelke R, Nowag H, Zarei M, Küttner V, Becker AC, Rigbolt KTG, Høyer-Hansen M, Andersen JS, Münz C, Murphy RF, Dengjel J. Degradation of protein translation machinery by amino acid starvation-induced macroautophagy. Autophagy 2017; 13:1064-1075. [PMID: 28453381 DOI: 10.1080/15548627.2016.1274485] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Macroautophagy is regarded as a nonspecific bulk degradation process of cytoplasmic material within the lysosome. However, the process has mainly been studied by nonspecific bulk degradation assays using radiolabeling. In the present study we monitor protein turnover and degradation by global, unbiased approaches relying on quantitative mass spectrometry-based proteomics. Macroautophagy is induced by rapamycin treatment, and by amino acid and glucose starvation in differentially, metabolically labeled cells. Protein dynamics are linked to image-based models of autophagosome turnover. Depending on the inducing stimulus, protein as well as organelle turnover differ. Amino acid starvation-induced macroautophagy leads to selective degradation of proteins important for protein translation. Thus, protein dynamics reflect cellular conditions in the respective treatment indicating stimulus-specific pathways in stress-induced macroautophagy.
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Affiliation(s)
- Christine Gretzmeier
- a Department of Dermatology , Medical Center - University of Freiburg , Freiburg , Germany.,b Freiburg Institute for Advanced Studies (FRIAS), and ZBSA Center for Biological Systems Analysis, University of Freiburg , Freiburg , Germany
| | - Sven Eiselein
- a Department of Dermatology , Medical Center - University of Freiburg , Freiburg , Germany.,b Freiburg Institute for Advanced Studies (FRIAS), and ZBSA Center for Biological Systems Analysis, University of Freiburg , Freiburg , Germany
| | - Gregory R Johnson
- c Computational Biology Department , Carnegie Mellon University , Pittsburgh , PA , USA
| | - Rudolf Engelke
- b Freiburg Institute for Advanced Studies (FRIAS), and ZBSA Center for Biological Systems Analysis, University of Freiburg , Freiburg , Germany
| | - Heike Nowag
- d Institute of Experimental Immunology, University of Zürich , Zürich , Switzerland
| | - Mostafa Zarei
- a Department of Dermatology , Medical Center - University of Freiburg , Freiburg , Germany.,b Freiburg Institute for Advanced Studies (FRIAS), and ZBSA Center for Biological Systems Analysis, University of Freiburg , Freiburg , Germany
| | - Victoria Küttner
- a Department of Dermatology , Medical Center - University of Freiburg , Freiburg , Germany.,b Freiburg Institute for Advanced Studies (FRIAS), and ZBSA Center for Biological Systems Analysis, University of Freiburg , Freiburg , Germany
| | - Andrea C Becker
- b Freiburg Institute for Advanced Studies (FRIAS), and ZBSA Center for Biological Systems Analysis, University of Freiburg , Freiburg , Germany
| | - Kristoffer T G Rigbolt
- b Freiburg Institute for Advanced Studies (FRIAS), and ZBSA Center for Biological Systems Analysis, University of Freiburg , Freiburg , Germany
| | - Maria Høyer-Hansen
- e Apoptosis Department and Center for Genotoxic Stress Research , Danish Cancer Society , Copenhagen , Denmark
| | - Jens S Andersen
- f Center for Experimental BioInformatics , Department of Biochemistry and Molecular Biology, University of Southern Denmark , Odense , Denmark
| | - Christian Münz
- d Institute of Experimental Immunology, University of Zürich , Zürich , Switzerland
| | - Robert F Murphy
- b Freiburg Institute for Advanced Studies (FRIAS), and ZBSA Center for Biological Systems Analysis, University of Freiburg , Freiburg , Germany.,c Computational Biology Department , Carnegie Mellon University , Pittsburgh , PA , USA
| | - Jörn Dengjel
- a Department of Dermatology , Medical Center - University of Freiburg , Freiburg , Germany.,b Freiburg Institute for Advanced Studies (FRIAS), and ZBSA Center for Biological Systems Analysis, University of Freiburg , Freiburg , Germany.,g Department of Biology , University of Fribourg , Fribourg , Switzerland
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2
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Autophagy and proteasome interconnect to coordinate cross-presentation through MHC class I pathway in B cells. Immunol Cell Biol 2016; 94:964-974. [PMID: 27297581 DOI: 10.1038/icb.2016.59] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 12/31/2022]
Abstract
Cross-presentation of exogenous protein antigens by B cells through the major histocompatibility complex (MHC) class I pathway in lymphoid malignancies, and transplant setting has been recognised as an important mediator of immune pathogenesis and T cell-mediated immune regulation. However, the precise mechanism of cross-presentation of exogenous antigens in B cells has remained unresolved. Here we have delineated a novel pathway for cross-presentation in B cells, which involves synergistic cooperation of the proteasome and autophagy. After endocytosis, protein antigen is processed through an autophagy- and proteasome-dependent pathway and CD8+ T-cell epitopes are loaded onto MHC class I molecules within the autophagolysomal compartment rather than the conventional secretory pathway, which requires transporters associated with antigen processing-dependent transport. Interestingly, this cross-presentation was critically dependent on valosin-containing protein (VCP)/p97 ATPase through its participation in autophagy. Loss of VCP/p97 ATPase was coincident with accumulation of LC3-II and marked reduction in antigen presentation. These observations provide unique insight on how the autophagy and proteasomal degradation systems interconnect to coordinate MHC class I-restricted cross-presentation in B cells.
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Dumit VI, Küttner V, Käppler J, Piera-Velazquez S, Jimenez SA, Bruckner-Tuderman L, Uitto J, Dengjel J. Altered MCM protein levels and autophagic flux in aged and systemic sclerosis dermal fibroblasts. J Invest Dermatol 2014; 134:2321-2330. [PMID: 24496236 PMCID: PMC4121389 DOI: 10.1038/jid.2014.69] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 12/18/2013] [Accepted: 12/20/2013] [Indexed: 01/31/2023]
Abstract
Aging is a common risk factor of many disorders. With age, the level of insoluble extracellular matrix increases leading to increased stiffness of a number of tissues. Matrix accumulation can also be observed in fibrotic disorders, such as systemic sclerosis (SSc). Although the intrinsic aging process in skin is phenotypically distinct from SSc, here we demonstrate similar behavior of aged and SSc skin fibroblasts in culture. We have used quantitative proteomics to characterize the phenotype of dermal fibroblasts from healthy subjects of various ages and from patients with SSc. Our results demonstrate that proteins involved in DNA and RNA processing decrease with age and in SSc, while those involved in mitochondrial and other metabolic processes behave the opposite. Specifically, mini-chromosome maintenance (MCM) helicase proteins are less abundant with age and SSc, and they exhibit an altered subcellular distribution. We observed that lower levels of MCM7 correlate with reduced cell proliferation, lower autophagic capacity and higher intracellular protein expression phenotypes of aged and SSc cells. Additionally, we show that SSc fibroblasts exhibit higher levels of senescence than their healthy counterparts, suggesting further similarities between the fibrotic disorder and the aging process. Hence, at the molecular level, SSc fibroblasts exhibit intrinsic characteristics of fibroblasts from aged skin.
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Affiliation(s)
- Verónica I Dumit
- Freiburg Institute for Advanced Studies (FRIAS), School of Life Science (LifeNet), University of Freiburg, Freiburg, Germany; Center for Biological Systems Analysis (ZBSA), University Medical Center Freiburg, Freiburg, Germany.
| | - Victoria Küttner
- Freiburg Institute for Advanced Studies (FRIAS), School of Life Science (LifeNet), University of Freiburg, Freiburg, Germany; Center for Biological Systems Analysis (ZBSA), University Medical Center Freiburg, Freiburg, Germany; Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Jakob Käppler
- Center for Biological Systems Analysis (ZBSA), University Medical Center Freiburg, Freiburg, Germany
| | - Sonsoles Piera-Velazquez
- Department of Dermatology and Cutaneous Biology, Jefferson Medical College, Philadelphia, Pennsylvania, USA
| | - Sergio A Jimenez
- Department of Dermatology and Cutaneous Biology, Jefferson Medical College, Philadelphia, Pennsylvania, USA
| | - Leena Bruckner-Tuderman
- Freiburg Institute for Advanced Studies (FRIAS), School of Life Science (LifeNet), University of Freiburg, Freiburg, Germany; Center for Biological Systems Analysis (ZBSA), University Medical Center Freiburg, Freiburg, Germany; Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Jouni Uitto
- Freiburg Institute for Advanced Studies (FRIAS), School of Life Science (LifeNet), University of Freiburg, Freiburg, Germany; Department of Dermatology and Cutaneous Biology, Jefferson Medical College, Philadelphia, Pennsylvania, USA
| | - Jörn Dengjel
- Freiburg Institute for Advanced Studies (FRIAS), School of Life Science (LifeNet), University of Freiburg, Freiburg, Germany; Center for Biological Systems Analysis (ZBSA), University Medical Center Freiburg, Freiburg, Germany; Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany.
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Abstract
Autophagy is one of the two major degradation pathways within eukaryotic cells. Nevertheless, little is known about the protein composition of autophagosomes, the vesicles shuttling proteins to lysosomes for degradation. Protein correlation profiling in combination with stable isotope labeling by amino acids in cell culture is a stringent method to investigate the dynamics of the autophagosomal proteome. It enables the discrimination between autophagosomal and co-purifying proteins identifying organellar candidate proteins for further investigation.
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Affiliation(s)
- Andrea C Becker
- Department of Dermatology, Medical Center - University of Freiburg, Hauptstr. 7, 79104, Freiburg, Germany
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Rigbolt KT, Zarei M, Sprenger A, Becker AC, Diedrich B, Huang X, Eiselein S, Kristensen AR, Gretzmeier C, Andersen JS, Zi Z, Dengjel J. Characterization of early autophagy signaling by quantitative phosphoproteomics. Autophagy 2013; 10:356-71. [PMID: 24275748 DOI: 10.4161/auto.26864] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Under conditions of nutrient shortage autophagy is the primary cellular mechanism ensuring availability of substrates for continuous biosynthesis. Subjecting cells to starvation or rapamycin efficiently induces autophagy by inhibiting the MTOR signaling pathway triggering increased autophagic flux. To elucidate the regulation of early signaling events upon autophagy induction, we applied quantitative phosphoproteomics characterizing the temporal phosphorylation dynamics after starvation and rapamycin treatment. We obtained a comprehensive atlas of phosphorylation kinetics within the first 30 min upon induction of autophagy with both treatments affecting widely different cellular processes. The identification of dynamic phosphorylation already after 2 min demonstrates that the earliest events in autophagy signaling occur rapidly after induction. The data was subjected to extensive bioinformatics analysis revealing regulated phosphorylation sites on proteins involved in a wide range of cellular processes and an impact of the treatments on the kinome. To approach the potential function of the identified phosphorylation sites we performed a screen for MAP1LC3-interacting proteins and identified a group of binding partners exhibiting dynamic phosphorylation patterns. The data presented here provide a valuable resource on phosphorylation events underlying early autophagy induction.
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Affiliation(s)
- Kristoffer Tg Rigbolt
- Freiburg Institute for Advanced Studies (FRIAS); School of Life Sciences-LifeNet; Freiburg, Germany; ZBSA Center for Biological Systems Analysis; University of Freiburg; Freiburg, Germany
| | - Mostafa Zarei
- Freiburg Institute for Advanced Studies (FRIAS); School of Life Sciences-LifeNet; Freiburg, Germany; ZBSA Center for Biological Systems Analysis; University of Freiburg; Freiburg, Germany
| | - Adrian Sprenger
- Freiburg Institute for Advanced Studies (FRIAS); School of Life Sciences-LifeNet; Freiburg, Germany; ZBSA Center for Biological Systems Analysis; University of Freiburg; Freiburg, Germany; Department of Dermatology; University Freiburg Medical Center; Freiburg, Germany
| | - Andrea C Becker
- Freiburg Institute for Advanced Studies (FRIAS); School of Life Sciences-LifeNet; Freiburg, Germany; ZBSA Center for Biological Systems Analysis; University of Freiburg; Freiburg, Germany
| | - Britta Diedrich
- Freiburg Institute for Advanced Studies (FRIAS); School of Life Sciences-LifeNet; Freiburg, Germany; ZBSA Center for Biological Systems Analysis; University of Freiburg; Freiburg, Germany
| | - Xun Huang
- BIOSS Centre for Biological Signaling Studies; University of Freiburg; Freiburg, Germany
| | - Sven Eiselein
- Freiburg Institute for Advanced Studies (FRIAS); School of Life Sciences-LifeNet; Freiburg, Germany; ZBSA Center for Biological Systems Analysis; University of Freiburg; Freiburg, Germany; BIOSS Centre for Biological Signaling Studies; University of Freiburg; Freiburg, Germany
| | - Anders R Kristensen
- Centre for High-throughput Biology; Department of Biochemistry and Molecular Biology; University of British Columbia; Vancouver, BC CA
| | - Christine Gretzmeier
- Freiburg Institute for Advanced Studies (FRIAS); School of Life Sciences-LifeNet; Freiburg, Germany; ZBSA Center for Biological Systems Analysis; University of Freiburg; Freiburg, Germany
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense, Denmark
| | - Zhike Zi
- BIOSS Centre for Biological Signaling Studies; University of Freiburg; Freiburg, Germany
| | - Jörn Dengjel
- Freiburg Institute for Advanced Studies (FRIAS); School of Life Sciences-LifeNet; Freiburg, Germany; ZBSA Center for Biological Systems Analysis; University of Freiburg; Freiburg, Germany; Department of Dermatology; University Freiburg Medical Center; Freiburg, Germany; BIOSS Centre for Biological Signaling Studies; University of Freiburg; Freiburg, Germany
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Halbach S, Rigbolt KT, Wöhrle FU, Diedrich B, Gretzmeier C, Brummer T, Dengjel J. Alterations of Gab2 signalling complexes in imatinib and dasatinib treated chronic myeloid leukaemia cells. Cell Commun Signal 2013; 11:30. [PMID: 23607741 PMCID: PMC3640961 DOI: 10.1186/1478-811x-11-30] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 03/25/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The Gab2 docking protein acts as an important signal amplifier downstream of various growth factor receptors and Bcr-Abl, the driver of chronic myeloid leukaemia (CML). Despite the success of Bcr-Abl tyrosine kinase inhibitors (TKI) in the therapy of CML, TKI-resistance remains an unsolved problem in the clinic. We have recently shown that Gab2 signalling counteracts the efficacy of four distinct Bcr-Abl inhibitors. In the course of that project, we noticed that two clinically relevant drugs, imatinib and dasatinib, provoke distinct alterations in the electrophoretic mobility of Gab2, its signalling output and protein interactions. As the signalling potential of the docking protein is highly modulated by its phosphorylation status, we set out to obtain more insights into the impact of TKIs on Gab2 phosphorylation. FINDINGS Using stable isotope labelling by amino acids in cell culture (SILAC)-based quantitative mass spectrometry (MS), we show now that imatinib and dasatinib provoke distinct effects on the phosphorylation status and interactome of Gab2. This study identifies several new phosphorylation sites on Gab2 and confirms many sites previously known from other experimental systems. At equimolar concentrations, dasatinib is more effective in preventing Gab2 tyrosine and serine/threonine phosphorylation than imatinib. It also affects the phosphorylation status of more residues than imatinib. In addition, we also identify novel components of the Gab2 signalling complex, such as casein kinases, stathmins and PIP1 as well as known interaction partners whose association with Gab2 is disrupted by imatinib and/or dasatinib. CONCLUSIONS By using MS-based proteomics, we have identified new and confirmed known phosphorylation sites and interaction partners of Gab2, which may play an important role in the regulation of this docking protein. Given the growing importance of Gab2 in several tumour entities we expect that our results will help to understand the complex regulation of Gab2 and how this docking protein can contribute to malignancy.
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Affiliation(s)
- Sebastian Halbach
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University Freiburg, Stefan-Meier-Str, 17, Freiburg 79104, Germany.
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Global remodelling of cellular microenvironment due to loss of collagen VII. Mol Syst Biol 2013; 9:657. [PMID: 23591773 PMCID: PMC3658272 DOI: 10.1038/msb.2013.17] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 03/13/2013] [Indexed: 01/18/2023] Open
Abstract
Loss of collagen VII causes recessive dystrophic epidermolysis bullosa. Quantitative proteomics analysis of the extracellular matrix and secretome of human fibroblasts derived from pathologically altered skin reveals a global remodelling of the cellular microenvironment. ![]()
A global analysis of the microenvironment of human skin fibroblasts was carried out to reveal disease-related alterations in the extracellular proteome. The loss of collagen VII causes a deregulation of the basement membrane and dermal matrix proteome. Post-translational modifications of secreted proteins were altered in fibroblasts from recessive dystrophic epidermolysis bullosa samples. Metalloproteases displayed reduced activity and turnover in collagen VII-deficient cells.
The mammalian cellular microenvironment is shaped by soluble factors and structural components, the extracellular matrix, providing physical support, regulating adhesion and signalling. A global, quantitative mass spectrometry strategy, combined with bioinformatics data processing, was developed to assess proteome differences in the microenvironment of primary human fibroblasts. We studied secreted proteins of fibroblasts from normal and pathologically altered skin and their post-translational modifications. The influence of collagen VII, an important structural component, which is lost in genetic skin fragility, was used as model. Loss of collagen VII had a global impact on the cellular microenvironment and was associated with proteome alterations highly relevant for disease pathogenesis including decrease in basement membrane components, increase in dermal matrix proteins, TGF-β and metalloproteases, but not higher protease activity. The definition of the proteome of fibroblast microenvironment and its plasticity in health and disease identified novel disease mechanisms and potential targets of intervention.
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Boerries M, Grahammer F, Eiselein S, Buck M, Meyer C, Goedel M, Bechtel W, Zschiedrich S, Pfeifer D, Laloë D, Arrondel C, Gonçalves S, Krüger M, Harvey SJ, Busch H, Dengjel J, Huber TB. Molecular fingerprinting of the podocyte reveals novel gene and protein regulatory networks. Kidney Int 2013; 83:1052-64. [PMID: 23364521 DOI: 10.1038/ki.2012.487] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A thorough characterization of the transcriptome and proteome of endogenous podocytes has been hampered by low cell yields during isolation. Here we describe a double fluorescent reporter mouse model combined with an optimized bead perfusion protocol and efficient single cell dissociation to yield more than 500,000 podocytes per mouse allowing for global, unbiased downstream applications. Combining mRNA and miRNA transcriptional profiling with quantitative proteomic analyses revealed programs of highly specific gene regulation tightly controlling cytoskeleton, cell differentiation, endosomal transport, and peroxisome function in podocytes. Strikingly, the analyses further predict that these podocyte-specific gene regulatory networks are accompanied by alternative splicing of respective genes. Thus, our 'omics' approach will facilitate the discovery and integration of novel gene, protein, and organelle regulatory networks that deepen our systematic understanding of podocyte biology.
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Affiliation(s)
- Melanie Boerries
- Freiburg Institute for Advanced Studies-LifeNet, Albert-Ludwigs-University Freiburg, Freiburg, Germany
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Dumit VI, Dengjel J. Autophagosomal protein dynamics and influenza virus infection. Front Immunol 2012; 3:43. [PMID: 22566925 PMCID: PMC3342335 DOI: 10.3389/fimmu.2012.00043] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 02/23/2012] [Indexed: 01/08/2023] Open
Abstract
Autophagy is a constitutive, catabolic process leading to the lysosomal degradation of cytosolic proteins and organelles. However, it is also induced under stress conditions, remodeling the eukaryotic cell by regulating energy, protein, and lipid homeostasis. It is likely that the autophagosomal/lysosomal pathway evolved primordially to recycle cell components, but further functionally developed as to become part of the immune system to defend against invading pathogens. Likewise, pathogenic, foreign agents developed strategies to fight back and even to employ the autophagy machinery to their own benefit. Hence, the regulation of autophagy has many implications on human health and disease. This review summarizes the molecular dynamics of autophagosome formation, maturation, and target selection. Membrane dynamics, as well as protein–protein and protein–membrane interactions are particularly addressed. In addition, it recapitulates current knowledge of the influences of influenza virus infection on the process.
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Affiliation(s)
- Verónica I Dumit
- School of Life Sciences - LifeNet, Freiburg Institute for Advanced Studies, University of Freiburg Freiburg, Germany
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Dengjel J, Høyer-Hansen M, Nielsen MO, Eisenberg T, Harder LM, Schandorff S, Farkas T, Kirkegaard T, Becker AC, Schroeder S, Vanselow K, Lundberg E, Nielsen MM, Kristensen AR, Akimov V, Bunkenborg J, Madeo F, Jäättelä M, Andersen JS. Identification of autophagosome-associated proteins and regulators by quantitative proteomic analysis and genetic screens. Mol Cell Proteomics 2012; 11:M111.014035. [PMID: 22311637 PMCID: PMC3316729 DOI: 10.1074/mcp.m111.014035] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Autophagy is one of the major intracellular catabolic pathways, but little is known about the composition of autophagosomes. To study the associated proteins, we isolated autophagosomes from human breast cancer cells using two different biochemical methods and three stimulus types: amino acid deprivation or rapamycin or concanamycin A treatment. The autophagosome-associated proteins were dependent on stimulus, but a core set of proteins was stimulus-independent. Remarkably, proteasomal proteins were abundant among the stimulus-independent common autophagosome-associated proteins, and the activation of autophagy significantly decreased the cellular proteasome level and activity supporting interplay between the two degradation pathways. A screen of yeast strains defective in the orthologs of the human genes encoding for a common set of autophagosome-associated proteins revealed several regulators of autophagy, including subunits of the retromer complex. The combined spatiotemporal proteomic and genetic data sets presented here provide a basis for further characterization of autophagosome biogenesis and cargo selection.
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Affiliation(s)
- Jörn Dengjel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.
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