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Paulke NJ, Fleischhacker C, Wegener JB, Riedemann GC, Cretu C, Mushtaq M, Zaremba N, Möbius W, Zühlke Y, Wedemeyer J, Liebmann L, Gorshkova AA, Kownatzki-Danger D, Wagner E, Kohl T, Wichmann C, Jahn O, Urlaub H, Toischer K, Hasenfuß G, Moser T, Preobraschenski J, Lenz C, Rog-Zielinska EA, Lehnart SE, Brandenburg S. Dysferlin Enables Tubular Membrane Proliferation in Cardiac Hypertrophy. Circ Res 2024; 135:554-574. [PMID: 39011635 DOI: 10.1161/circresaha.124.324588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 07/17/2024]
Abstract
BACKGROUND Cardiac hypertrophy compensates for increased biomechanical stress of the heart induced by prevalent cardiovascular pathologies but can result in heart failure if left untreated. Here, we hypothesized that the membrane fusion and repair protein dysferlin is critical for the integrity of the transverse-axial tubule (TAT) network inside cardiomyocytes and contributes to the proliferation of TAT endomembranes during pressure overload-induced cardiac hypertrophy. METHODS Stimulated emission depletion and electron microscopy were used to localize dysferlin in mouse and human cardiomyocytes. Data-independent acquisition mass spectrometry revealed the cardiac dysferlin interactome and proteomic changes of the heart in dysferlin-knockout mice. After transverse aortic constriction, we compared the hypertrophic response of wild-type versus dysferlin-knockout hearts and studied TAT network remodeling mechanisms inside cardiomyocytes by live-cell membrane imaging. RESULTS We localized dysferlin in a vesicular compartment in nanometric proximity to contact sites of the TAT network with the sarcoplasmic reticulum, a.k.a. junctional complexes for Ca2+-induced Ca2+ release. Interactome analyses demonstrated a novel protein interaction of dysferlin with the membrane-tethering sarcoplasmic reticulum protein juncophilin-2, a putative interactor of L-type Ca2+ channels and ryanodine receptor Ca2+ release channels in junctional complexes. Although the dysferlin-knockout caused a mild progressive phenotype of dilated cardiomyopathy, global proteome analysis revealed changes preceding systolic failure. Following transverse aortic constriction, dysferlin protein expression was significantly increased in hypertrophied wild-type myocardium, while dysferlin-knockout animals presented markedly reduced left-ventricular hypertrophy. Live-cell membrane imaging showed a profound reorganization of the TAT network in wild-type left-ventricular myocytes after transverse aortic constriction with robust proliferation of axial tubules, which critically depended on the increased expression of dysferlin within newly emerging tubule components. CONCLUSIONS Dysferlin represents a new molecular target in cardiac disease that protects the integrity of tubule-sarcoplasmic reticulum junctional complexes for regulated excitation-contraction coupling and controls TAT network reorganization and tubular membrane proliferation in cardiomyocyte hypertrophy induced by pressure overload.
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Affiliation(s)
- Nora Josefine Paulke
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Carolin Fleischhacker
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Justus B Wegener
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Gabriel C Riedemann
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Constantin Cretu
- Biochemistry of Membrane Dynamics Group, Institute for Auditory Neuroscience and InnerEarLab (C.C., J.P.), University Medical Center Göttingen, Germany
| | - Mufassra Mushtaq
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Nina Zaremba
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Wiebke Möbius
- Department of Neurogenetics, Electron Microscopy, City Campus (W.M.)
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
| | - Yannik Zühlke
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Jasper Wedemeyer
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Lorenz Liebmann
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Anastasiia A Gorshkova
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Daniel Kownatzki-Danger
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Now with Institute of Transfusion Medicine, University Hospital Schleswig-Holstein; Kiel, Germany (D.K.-D)
| | - Eva Wagner
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Tobias Kohl
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Carolin Wichmann
- Molecular Architecture of Synapses Group, Institute for Auditory Neuroscience and InnerEarLab and Center for Biostructural Imaging of Neurodegeneration (C.W.), University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
| | - Olaf Jahn
- Translational Neuroproteomics Group, Department of Psychiatry and Psychotherapy (O.J.), University Medical Center Göttingen, Germany
- Neuroproteomics Group, Department of Molecular Neurobiology (O.J.)
| | - Henning Urlaub
- Department of Clinical Chemistry (H.U., C.L.), University Medical Center Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany (H.U., C.L.)
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
| | - Karl Toischer
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, Germany (K.T., G.H., S.E.L.)
| | - Gerd Hasenfuß
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, Germany (K.T., G.H., S.E.L.)
| | - Tobias Moser
- Institute for Auditory Neuroscience and InnerEarLab (T.M.), University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
| | - Julia Preobraschenski
- Biochemistry of Membrane Dynamics Group, Institute for Auditory Neuroscience and InnerEarLab (C.C., J.P.), University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
| | - Christof Lenz
- Department of Clinical Chemistry (H.U., C.L.), University Medical Center Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany (H.U., C.L.)
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
| | - Eva A Rog-Zielinska
- Institute for Experimental Cardiovascular Medicine, University Heart Center and Faculty of Medicine, University of Freiburg, Germany (E.A.R.-Z.)
| | - Stephan E Lehnart
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, Germany (K.T., G.H., S.E.L.)
| | - Sören Brandenburg
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
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Tarău D, Grünberger F, Pilsl M, Reichelt R, Heiß F, König S, Urlaub H, Hausner W, Engel C, Grohmann D. Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment. Nucleic Acids Res 2024; 52:6017-6035. [PMID: 38709902 PMCID: PMC11162788 DOI: 10.1093/nar/gkae282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 05/08/2024] Open
Abstract
Archaeal transcription is carried out by a multi-subunit RNA polymerase (RNAP) that is highly homologous in structure and function to eukaryotic RNAP II. Among the set of basal transcription factors, only Spt5 is found in all domains of life, but Spt5 has been shaped during evolution, which is also reflected in the heterodimerization of Spt5 with Spt4 in Archaea and Eukaryotes. To unravel the mechanistic basis of Spt4/5 function in Archaea, we performed structure-function analyses using the archaeal transcriptional machinery of Pyrococcus furiosus (Pfu). We report single-particle cryo-electron microscopy reconstructions of apo RNAP and the archaeal elongation complex (EC) in the absence and presence of Spt4/5. Surprisingly, Pfu Spt4/5 also binds the RNAP in the absence of nucleic acids in a distinct super-contracted conformation. We show that the RNAP clamp/stalk module exhibits conformational flexibility in the apo state of RNAP and that the enzyme contracts upon EC formation or Spt4/5 engagement. We furthermore identified a contact of the Spt5-NGN domain with the DNA duplex that stabilizes the upstream boundary of the transcription bubble and impacts Spt4/5 activity in vitro. This study, therefore, provides the structural basis for Spt4/5 function in archaeal transcription and reveals a potential role beyond the well-described support of elongation.
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Affiliation(s)
- Daniela Tarău
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Felix Grünberger
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Michael Pilsl
- Regensburg Center for Biochemistry (RCB), Structural Biochemistry Group, University of Regensburg, Regensburg, Germany
| | - Robert Reichelt
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Florian Heiß
- Regensburg Center for Biochemistry (RCB), Structural Biochemistry Group, University of Regensburg, Regensburg, Germany
| | - Sabine König
- Bioanalytic Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytic Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Winfried Hausner
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry (RCB), Structural Biochemistry Group, University of Regensburg, Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
- Regensburg Center for Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
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Dreyer A, Masanta WO, Lugert R, Bohne W, Groß U, Leha A, Dakna M, Lenz C, Zautner AE. Proteome profiling of Campylobacter jejuni 81-176 at 37 °C and 42 °C by label-free mass spectrometry. BMC Microbiol 2024; 24:191. [PMID: 38822261 PMCID: PMC11140963 DOI: 10.1186/s12866-024-03348-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 05/22/2024] [Indexed: 06/02/2024] Open
Abstract
BACKGROUND The main natural reservoir for Campylobacter jejuni is the avian intestinal tract. There, C. jejuni multiplies optimally at 42 °C - the avian body temperature. After infecting humans through oral intake, the bacterium encounters the lower temperature of 37 °C in the human intestinal tract. Proteome profiling by label-free mass spectrometry (DIA-MS) was performed to examine the processes which enable C. jejuni 81-176 to thrive at 37 °C in comparison to 42 °C. In total, four states were compared with each other: incubation for 12 h at 37 °C, for 24 h at 37 °C, for 12 h at 42 °C and 24 h at 42 °C. RESULTS It was shown that the proteomic changes not only according to the different incubation temperature but also to the length of the incubation period were evident when comparing 37 °C and 42 °C as well as 12 h and 24 h of incubation. Altogether, the expression of 957 proteins was quantifiable. 37.1 - 47.3% of the proteins analyzed showed significant differential regulation, with at least a 1.5-fold change in either direction (i.e. log2 FC ≥ 0.585 or log2 FC ≤ -0.585) and an FDR-adjusted p-value of less than 0.05. The significantly differentially expressed proteins could be arranged in 4 different clusters and 16 functional categories. CONCLUSIONS The C. jejuni proteome at 42 °C is better adapted to high replication rates than that at 37 °C, which was in particular indicated by the up-regulation of proteins belonging to the functional categories "replication" (e.g. Obg, ParABS, and NapL), "DNA synthesis and repair factors" (e.g. DNA-polymerase III, DnaB, and DnaE), "lipid and carbohydrate biosynthesis" (e.g. capsular biosynthesis sugar kinase, PrsA, AccA, and AccP) and "vitamin synthesis, metabolism, cofactor biosynthesis" (e.g. MobB, BioA, and ThiE). The relative up-regulation of proteins with chaperone function (GroL, DnaK, ClpB, HslU, GroS, DnaJ, DnaJ-1, and NapD) at 37 °C in comparison to 42 °C after 12 h incubation indicates a temporary lower-temperature proteomic response. Additionally the up-regulation of factors for DNA uptake (ComEA and RecA) at 37 °C compared to 42 °C indicate a higher competence for the acquisition of extraneous DNA at human body temperature.
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Affiliation(s)
- Annika Dreyer
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Wycliffe O Masanta
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, 37075, Göttingen, Germany
- Department of Medical Microbiology, Maseno University Medical School, Private Bag, Maseno, 40105, Kenya
| | - Raimond Lugert
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Wolfgang Bohne
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Uwe Groß
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Andreas Leha
- Department of Medical Statistics, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Mohammed Dakna
- Department of Medical Statistics, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
- Institute of Clinical Chemistry, Bioanalytics, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Andreas E Zautner
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, 37075, Göttingen, Germany.
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-von-Guericke-University Magdeburg, Leipziger Straße 44, 39120, Magdeburg, Germany.
- CHaMP, Center for Health and Medical Prevention, Otto-von-Guericke-University Magdeburg, 39120, Magdeburg, Germany.
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Carmona A, Carboni E, Gomes LC, Roudeau S, Maass F, Lenz C, Ortega R, Lingor P. Metal dyshomeostasis in the substantia nigra of patients with Parkinson's disease or multiple sclerosis. J Neurochem 2024; 168:128-141. [PMID: 38178798 DOI: 10.1111/jnc.16040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/12/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024]
Abstract
Abnormal metal distribution in vulnerable brain regions is involved in the pathogenesis of most neurodegenerative diseases, suggesting common molecular mechanisms of metal dyshomeostasis. This study aimed to compare the intra- and extra-neuronal metal content and the expression of proteins related to metal homeostasis in the substantia nigra (SN) from patients with Parkinson's disease (PD), multiple sclerosis (MS), and control subjects. Metal quantification was performed via ion-beam micro-analysis in neuromelanin-positive neurons and the surrounding tissue. For proteomic analysis, SN tissue lysates were analyzed on a nanoflow chromatography system hyphenated to a hybrid triple-quadrupole time-of-flight mass spectrometer. We found increased amounts of iron in neuromelanin-positive neurons and surrounding tissue in patients with PD and MS compared to controls (4- to 5-fold higher) that, however, also showed large inter-individual variations. Copper content was systematically lower (-2.4-fold) in neuromelanin-positive neurons of PD patients compared with controls, whereas it remained unchanged in MS. Protein-protein interaction (PPI) network analyses revealed clusters related to Fe and Cu homeostasis among PD-deregulated proteins. An enrichment for the term "metal homeostasis" was observed for MS-deregulated proteins. Important deregulated hub proteins included hemopexin and transferrin in PD, and calreticulin and ferredoxin reductase in MS. Our findings show that PD and MS share commonalities in terms of iron accumulation in the SN. Concomitant proteomics experiments revealed PPI networks related to metal homeostasis, substantiating the results of metal quantification.
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Affiliation(s)
| | - Eleonora Carboni
- Department of Neurology, University Medical Center Göttingen, Göttingen, Lower-Saxony, Germany
| | - Lucas Caldi Gomes
- School of Medicine, Klinikum rechts der Isar, Department of Neurology, Technical University of Munich, München, Bavaria, Germany
| | | | - Fabian Maass
- Department of Neurology, University Medical Center Göttingen, Göttingen, Lower-Saxony, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | | | - Paul Lingor
- School of Medicine, Klinikum rechts der Isar, Department of Neurology, Technical University of Munich, München, Bavaria, Germany
- DZNE, German Center for Neurodegenerative Diseases, Research Site Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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Cepeda AP, Ninov M, Neef J, Parfentev I, Kusch K, Reisinger E, Jahn R, Moser T, Urlaub H. Proteomic Analysis Reveals the Composition of Glutamatergic Organelles of Auditory Inner Hair Cells. Mol Cell Proteomics 2024; 23:100704. [PMID: 38128648 PMCID: PMC10832297 DOI: 10.1016/j.mcpro.2023.100704] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/08/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023] Open
Abstract
In the ear, inner hair cells (IHCs) employ sophisticated glutamatergic ribbon synapses with afferent neurons to transmit auditory information to the brain. The presynaptic machinery responsible for neurotransmitter release in IHC synapses includes proteins such as the multi-C2-domain protein otoferlin and the vesicular glutamate transporter 3 (VGluT3). Yet, much of this likely unique molecular machinery remains to be deciphered. The scarcity of material has so far hampered biochemical studies which require large amounts of purified samples. We developed a subcellular fractionation workflow combined with immunoisolation of VGluT3-containing membrane vesicles, allowing for the enrichment of glutamatergic organelles that are likely dominated by synaptic vesicles (SVs) of IHCs. We have characterized their protein composition in mice before and after hearing onset using mass spectrometry and confocal imaging and provide a fully annotated proteome with hitherto unidentified proteins. Despite the prevalence of IHC marker proteins across IHC maturation, the profiles of trafficking proteins differed markedly before and after hearing onset. Among the proteins enriched after hearing onset were VAMP-7, syntaxin-7, syntaxin-8, syntaxin-12/13, SCAMP1, V-ATPase, SV2, and PKCα. Our study provides an inventory of the machinery associated with synaptic vesicle-mediated trafficking and presynaptic activity at IHC ribbon synapses and serves as a foundation for future functional studies.
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Affiliation(s)
- Andreia P Cepeda
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Momchil Ninov
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Jakob Neef
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany; Auditory Neuroscience & Synaptic Nanophysiology Group Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Iwan Parfentev
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Kathrin Kusch
- Functional Auditory Genomics Group, Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Ellen Reisinger
- Gene Therapy for Hearing Impairment and Deafness, Department for Otolaryngology, Head & Neck Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Reinhard Jahn
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
| | - Tobias Moser
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany; Auditory Neuroscience & Synaptic Nanophysiology Group Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
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6
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Grünberger F, Schmid G, El Ahmad Z, Fenk M, Vogl K, Reichelt R, Hausner W, Urlaub H, Lenz C, Grohmann D. Uncovering the temporal dynamics and regulatory networks of thermal stress response in a hyperthermophile using transcriptomics and proteomics. mBio 2023; 14:e0217423. [PMID: 37843364 PMCID: PMC10746257 DOI: 10.1128/mbio.02174-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE Extreme environments provide unique challenges for life, and the study of extremophiles can shed light on the mechanisms of adaptation to such conditions. Pyrococcus furiosus, a hyperthermophilic archaeon, is a model organism for studying thermal stress response mechanisms. In this study, we used an integrated analysis of RNA-sequencing and mass spectrometry data to investigate the transcriptomic and proteomic responses of P. furiosus to heat and cold shock stress and recovery. Our results reveal the rapid and dynamic changes in gene and protein expression patterns associated with these stress responses, as well as the coordinated regulation of different gene sets in response to different stressors. These findings provide valuable insights into the molecular adaptations that facilitate life in extreme environments and advance our understanding of stress response mechanisms in hyperthermophilic archaea.
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Affiliation(s)
- Felix Grünberger
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Georg Schmid
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Zubeir El Ahmad
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Martin Fenk
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Katharina Vogl
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Robert Reichelt
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Winfried Hausner
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Dina Grohmann
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
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7
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Dai Y, Ignatyeva N, Xu H, Wali R, Toischer K, Brandenburg S, Lenz C, Pronto J, Fakuade FE, Sossalla S, Zeisberg EM, Janshoff A, Kutschka I, Voigt N, Urlaub H, Rasmussen TB, Mogensen J, Lehnart SE, Hasenfuss G, Ebert A. An Alternative Mechanism of Subcellular Iron Uptake Deficiency in Cardiomyocytes. Circ Res 2023; 133:e19-e46. [PMID: 37313752 DOI: 10.1161/circresaha.122.321157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 05/26/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND Systemic defects in intestinal iron absorption, circulation, and retention cause iron deficiency in 50% of patients with heart failure. Defective subcellular iron uptake mechanisms that are independent of systemic absorption are incompletely understood. The main intracellular route for iron uptake in cardiomyocytes is clathrin-mediated endocytosis. METHODS We investigated subcellular iron uptake mechanisms in patient-derived and CRISPR/Cas-edited induced pluripotent stem cell-derived cardiomyocytes as well as patient-derived heart tissue. We used an integrated platform of DIA-MA (mass spectrometry data-independent acquisition)-based proteomics and signaling pathway interrogation. We employed a genetic induced pluripotent stem cell model of 2 inherited mutations (TnT [troponin T]-R141W and TPM1 [tropomyosin 1]-L185F) that lead to dilated cardiomyopathy (DCM), a frequent cause of heart failure, to study the underlying molecular dysfunctions of DCM mutations. RESULTS We identified a druggable molecular pathomechanism of impaired subcellular iron deficiency that is independent of systemic iron metabolism. Clathrin-mediated endocytosis defects as well as impaired endosome distribution and cargo transfer were identified as a basis for subcellular iron deficiency in DCM-induced pluripotent stem cell-derived cardiomyocytes. The clathrin-mediated endocytosis defects were also confirmed in the hearts of patients with DCM with end-stage heart failure. Correction of the TPM1-L185F mutation in DCM patient-derived induced pluripotent stem cells, treatment with a peptide, Rho activator II, or iron supplementation rescued the molecular disease pathway and recovered contractility. Phenocopying the effects of the TPM1-L185F mutation into WT induced pluripotent stem cell-derived cardiomyocytes could be ameliorated by iron supplementation. CONCLUSIONS Our findings suggest that impaired endocytosis and cargo transport resulting in subcellular iron deficiency could be a relevant pathomechanism for patients with DCM carrying inherited mutations. Insight into this molecular mechanism may contribute to the development of treatment strategies and risk management in heart failure.
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Affiliation(s)
- Yuanyuan Dai
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
| | - Nadezda Ignatyeva
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
| | - Hang Xu
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
| | - Ruheen Wali
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
| | - Karl Toischer
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Heart Center, Clinic for Cardiology and Pneumology, University Medical Center Goettingen (K.T., S.B., S.S., G.H.), University of Goettingen, Germany
| | - Sören Brandenburg
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Heart Center, Clinic for Cardiology and Pneumology, University Medical Center Goettingen (K.T., S.B., S.S., G.H.), University of Goettingen, Germany
| | - Christof Lenz
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Department of Clinical Chemistry, University Medical Center Goettingen, (C.L., H.U.), University of Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC; C.L., F.E.F., N.V., S.E.L.), University of Goettingen, Germany
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Goettingen (C.L., H.U.)
| | - Julius Pronto
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, (J.P., F.E.F., N.V.), University of Goettingen, Germany
| | - Funsho E Fakuade
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, (J.P., F.E.F., N.V.), University of Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC; C.L., F.E.F., N.V., S.E.L.), University of Goettingen, Germany
| | - Samuel Sossalla
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- Heart Center, Clinic for Cardiology and Pneumology, University Medical Center Goettingen (K.T., S.B., S.S., G.H.), University of Goettingen, Germany
- Department for Internal Medicine II, University Medical Center Regensburg (S.S.)
| | - Elisabeth M Zeisberg
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
| | - Andreas Janshoff
- Institute for Physical Chemistry (A.J.), University of Goettingen, Germany
| | - Ingo Kutschka
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Department of Thoracic and Cardiovascular Surgery, University Medical Center Göttingen (I.K.)
| | - Niels Voigt
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, (J.P., F.E.F., N.V.), University of Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC; C.L., F.E.F., N.V., S.E.L.), University of Goettingen, Germany
| | - Henning Urlaub
- Department of Clinical Chemistry, University Medical Center Goettingen, (C.L., H.U.), University of Goettingen, Germany
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Goettingen (C.L., H.U.)
| | | | - Jens Mogensen
- Department of Cardiology, Aalborg University Hospital, Denmark (J.M.)
| | - Stephan E Lehnart
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC; C.L., F.E.F., N.V., S.E.L.), University of Goettingen, Germany
| | - Gerd Hasenfuss
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Heart Center, Clinic for Cardiology and Pneumology, University Medical Center Goettingen (K.T., S.B., S.S., G.H.), University of Goettingen, Germany
| | - Antje Ebert
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
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8
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Khan A, Zahid S, Hasan B, Asif AR, Ahmed N. Mass Spectrometry based identification of site-specific proteomic alterations and potential pathways underlying the pathophysiology of schizophrenia. Mol Biol Rep 2023; 50:4931-4943. [PMID: 37076706 DOI: 10.1007/s11033-023-08431-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/04/2023] [Indexed: 04/21/2023]
Abstract
BACKGROUND Schizophrenia (SZ) is a complex multifactorial disorder that affects 1% of the population worldwide with no available effective treatment. Although proteomic alterations are reported in SZ however proteomic expression aberrations among different brain regions are not fully determined. Therefore, the present study aimed spatial differential protein expression profiling of three distinct regions of SZ brain and identification of associated affected biological pathways in SZ progression. METHODS AND RESULTS Comparative protein expression profiling of three distinct autopsied human brain regions (i.e., substantia nigra, hippocampus and prefrontal cortex) of SZ was performed with respective healthy controls. Using two-dimensional electrophoresis (2DE)-based nano liquid chromatography tandem mass spectrometry (Nano-LC MS /MS) analysis, 1443 proteins were identified out of which 58 connote to be significantly dysregulated, representing 26 of substantia nigra,14 of hippocampus and 18 of prefrontal cortex. The 58 differentially expressed proteins were further analyzed using Ingenuity pathway analysis (IPA). The IPA analysis provided protein-protein interaction networks of several proteins including nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kb), extracellular signal regulated kinases 1/2 (ERK1/2), alpha serine / Threonine-protein kinase (AKT1), cellular tumor antigen p53 (TP53) and amyloid precursor protein (APP), holding prime positions in networks and interacts with most of the identified proteins and their closely interacting partners. CONCLUSION These findings provide conceptual insights of novel SZ related pathways and the cross talk of co and contra regulated proteins. This spatial proteomic analysis will further broaden the conceptual framework for schizophrenia research in future.
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Affiliation(s)
- Ayesha Khan
- Neurochemistry Research Laboratory, Department of Biochemistry, University of Karachi, Karachi, 75270, Pakistan
| | - Saadia Zahid
- Neurochemistry Research Laboratory, Department of Biochemistry, University of Karachi, Karachi, 75270, Pakistan
- Neurobiology Research Laboratory, Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Beena Hasan
- Neurochemistry Research Laboratory, Department of Biochemistry, University of Karachi, Karachi, 75270, Pakistan
| | - Abdul R Asif
- Institute of Clinical Chemistry, University Medical Center, Robert-Koch-Str. 40, 37075, Göttingen, Göttingen, Germany
| | - Nikhat Ahmed
- Neurochemistry Research Laboratory, Department of Biochemistry, University of Karachi, Karachi, 75270, Pakistan.
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9
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Schoger E, Bleckwedel F, Germena G, Rocha C, Tucholla P, Sobitov I, Möbius W, Sitte M, Lenz C, Samak M, Hinkel R, Varga ZV, Giricz Z, Salinas G, Gross JC, Zelarayán LC. Single-cell transcriptomics reveal extracellular vesicles secretion with a cardiomyocyte proteostasis signature during pathological remodeling. Commun Biol 2023; 6:79. [PMID: 36681760 PMCID: PMC9867722 DOI: 10.1038/s42003-022-04402-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/23/2022] [Indexed: 01/22/2023] Open
Abstract
Aberrant Wnt activation has been reported in failing cardiomyocytes. Here we present single cell transcriptome profiling of hearts with inducible cardiomyocyte-specific Wnt activation (β-catΔex3) as well as with compensatory and failing hypertrophic remodeling. We show that functional enrichment analysis points to an involvement of extracellular vesicles (EVs) related processes in hearts of β-catΔex3 mice. A proteomic analysis of in vivo cardiac derived EVs from β-catΔex3 hearts has identified differentially enriched proteins involving 20 S proteasome constitutes, protein quality control (PQC), chaperones and associated cardiac proteins including α-Crystallin B (CRYAB) and sarcomeric components. The hypertrophic model confirms that cardiomyocytes reacted with an acute early transcriptional upregulation of exosome biogenesis processes and chaperones transcripts including CRYAB, which is ameliorated in advanced remodeling. Finally, human induced pluripotent stem cells (iPSC)-derived cardiomyocytes subjected to pharmacological Wnt activation recapitulated the increased expression of exosomal markers, CRYAB accumulation and increased PQC signaling. These findings reveal that secretion of EVs with a proteostasis signature contributes to early patho-physiological adaptation of cardiomyocytes, which may serve as a read-out of disease progression and can be used for monitoring cellular remodeling in vivo with a possible diagnostic and prognostic role in the future.
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Affiliation(s)
- Eric Schoger
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen (UMG), 37075, Göttingen, Germany
- German Center for Cardiovascular Research (DZHK) partner site Göttingen, 37075, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075, Göttingen, Germany
| | - Federico Bleckwedel
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen (UMG), 37075, Göttingen, Germany
- German Center for Cardiovascular Research (DZHK) partner site Göttingen, 37075, Göttingen, Germany
| | - Giulia Germena
- German Center for Cardiovascular Research (DZHK) partner site Göttingen, 37075, Göttingen, Germany
- Laboratory Animal Science Unit, Leibnitz-Institut für Primatenforschung, Deutsches Primatenzentrum GmbH, 37075, Göttingen, Germany
| | - Cheila Rocha
- Laboratory Animal Science Unit, Leibnitz-Institut für Primatenforschung, Deutsches Primatenzentrum GmbH, 37075, Göttingen, Germany
| | - Petra Tucholla
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen (UMG), 37075, Göttingen, Germany
- German Center for Cardiovascular Research (DZHK) partner site Göttingen, 37075, Göttingen, Germany
| | - Izzatullo Sobitov
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen (UMG), 37075, Göttingen, Germany
- German Center for Cardiovascular Research (DZHK) partner site Göttingen, 37075, Göttingen, Germany
| | - Wiebke Möbius
- Max-Planck-Institute for Multidisciplinary Sciences, 37075, Göttingen, Germany
| | - Maren Sitte
- NGS Integrative Genomics Core Unit (NIG), University Medical Center Göttingen (UMG), 37075, Göttingen, Germany
| | - Christof Lenz
- Department of Clinical Chemistry, University Medical Center Göttingen (UMG), 37075, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37075, Göttingen, Germany
| | - Mostafa Samak
- German Center for Cardiovascular Research (DZHK) partner site Göttingen, 37075, Göttingen, Germany
- Laboratory Animal Science Unit, Leibnitz-Institut für Primatenforschung, Deutsches Primatenzentrum GmbH, 37075, Göttingen, Germany
| | - Rabea Hinkel
- German Center for Cardiovascular Research (DZHK) partner site Göttingen, 37075, Göttingen, Germany
- Laboratory Animal Science Unit, Leibnitz-Institut für Primatenforschung, Deutsches Primatenzentrum GmbH, 37075, Göttingen, Germany
- Institute for Animal Hygiene, Animal Welfare and Farm Animal Behaviour (ITTN), Stiftung Tierärztliche Hochschule Hannover, University of Veterinary Medicine, 30173, Hannover, Germany
| | - Zoltán V Varga
- HCEMM-SU Cardiometabolic Immunology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, H-1085, Budapest, Hungary
- Pharmahungary Group, H-1085, Budapest, Hungary
| | - Zoltán Giricz
- HCEMM-SU Cardiometabolic Immunology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, H-1085, Budapest, Hungary
- Pharmahungary Group, H-1085, Budapest, Hungary
| | - Gabriela Salinas
- NGS Integrative Genomics Core Unit (NIG), University Medical Center Göttingen (UMG), 37075, Göttingen, Germany
| | - Julia C Gross
- Health and Medical University, D-14471, Potsdam, Germany
| | - Laura C Zelarayán
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen (UMG), 37075, Göttingen, Germany.
- German Center for Cardiovascular Research (DZHK) partner site Göttingen, 37075, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075, Göttingen, Germany.
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10
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Influence of Shear Stress, Inflammation and BRD4 Inhibition on Human Endothelial Cells: A Holistic Proteomic Approach. Cells 2022; 11:cells11193086. [PMID: 36231049 PMCID: PMC9563250 DOI: 10.3390/cells11193086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Atherosclerosis is an important risk factor in the development of cardiovascular diseases. In addition to increased plasma lipid concentrations, irregular/oscillatory shear stress and inflammatory processes trigger atherosclerosis. Inhibitors of the transcription modulatory bromo- and extra-terminal domain (BET) protein family (BETi) could offer a possible therapeutic approach due to their epigenetic mechanism and anti-inflammatory properties. In this study, the influence of laminar shear stress, inflammation and BETi treatment on human endothelial cells was investigated using global protein expression profiling by ion mobility separation-enhanced data independent acquisition mass spectrometry (IMS-DIA-MS). For this purpose, primary human umbilical cord derived vascular endothelial cells were treated with TNFα to mimic inflammation and exposed to laminar shear stress in the presence or absence of the BRD4 inhibitor JQ1. IMS-DIA-MS detected over 4037 proteins expressed in endothelial cells. Inflammation, shear stress and BETi led to pronounced changes in protein expression patterns with JQ1 having the greatest effect. To our knowledge, this is the first proteomics study on primary endothelial cells, which provides an extensive database for the effects of shear stress, inflammation and BETi on the endothelial proteome.
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11
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Stejerean‐Todoran I, Zimmermann K, Gibhardt CS, Vultur A, Ickes C, Shannan B, Bonilla del Rio Z, Wölling A, Cappello S, Sung H, Shumanska M, Zhang X, Nanadikar M, Latif MU, Wittek A, Lange F, Waters A, Brafford P, Wilting J, Urlaub H, Katschinski DM, Rehling P, Lenz C, Jakobs S, Ellenrieder V, Roesch A, Schön MP, Herlyn M, Stanisz H, Bogeski I. MCU
controls melanoma progression through a redox‐controlled phenotype switch. EMBO Rep 2022; 23:e54746. [PMID: 36156348 PMCID: PMC9638851 DOI: 10.15252/embr.202254746] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 01/16/2023] Open
Abstract
Melanoma is the deadliest of skin cancers and has a high tendency to metastasize to distant organs. Calcium and metabolic signals contribute to melanoma invasiveness; however, the underlying molecular details are elusive. The MCU complex is a major route for calcium into the mitochondrial matrix but whether MCU affects melanoma pathobiology was not understood. Here, we show that MCUA expression correlates with melanoma patient survival and is decreased in BRAF kinase inhibitor‐resistant melanomas. Knockdown (KD) of MCUA suppresses melanoma cell growth and stimulates migration and invasion. In melanoma xenografts, MCUA_KD reduces tumor volumes but promotes lung metastases. Proteomic analyses and protein microarrays identify pathways that link MCUA and melanoma cell phenotype and suggest a major role for redox regulation. Antioxidants enhance melanoma cell migration, while prooxidants diminish the MCUA_KD‐induced invasive phenotype. Furthermore, MCUA_KD increases melanoma cell resistance to immunotherapies and ferroptosis. Collectively, we demonstrate that MCUA controls melanoma aggressive behavior and therapeutic sensitivity. Manipulations of mitochondrial calcium and redox homeostasis, in combination with current therapies, should be considered in treating advanced melanoma.
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Affiliation(s)
- Ioana Stejerean‐Todoran
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
| | | | - Christine S Gibhardt
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Adina Vultur
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
- The Wistar Institute Melanoma Research Center Philadelphia PA USA
| | - Christian Ickes
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Batool Shannan
- The Wistar Institute Melanoma Research Center Philadelphia PA USA
- Department of Dermatology, University Hospital Essen, West German Cancer Center University Duisburg‐Essen and the German Cancer Consortium (DKTK)
| | - Zuriñe Bonilla del Rio
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Anna Wölling
- Department of Dermatology, Venereology and Allergology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Sabrina Cappello
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Hsu‐Min Sung
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Magdalena Shumanska
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Xin Zhang
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Maithily Nanadikar
- Department of Cardiovascular Physiology, University Medical Center Göttingen Georg‐August‐University Göttingen Germany
| | - Muhammad U Latif
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology University Medical Center Göttingen Gottingen Germany
| | - Anna Wittek
- Department of NanoBiophotonics Max Planck Institute for Multidisciplinary Sciences Göttingen Germany
- Clinic of Neurology University Medical Center Göttingen Göttingen Germany
| | - Felix Lange
- Department of NanoBiophotonics Max Planck Institute for Multidisciplinary Sciences Göttingen Germany
- Clinic of Neurology University Medical Center Göttingen Göttingen Germany
| | - Andrea Waters
- The Wistar Institute Melanoma Research Center Philadelphia PA USA
| | | | - Jörg Wilting
- Department of Anatomy and Cell Biology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group Max Planck Institute for Multidisciplinary Sciences Göttingen Germany
- Bioanalytics, Institute of Clinical Chemistry University Medical Center Göttingen Germany
| | - Dörthe M Katschinski
- Department of Cardiovascular Physiology, University Medical Center Göttingen Georg‐August‐University Göttingen Germany
| | - Peter Rehling
- Department of Cellular Biochemistry University Medical Center Göttingen, GZMB Göttingen Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group Max Planck Institute for Multidisciplinary Sciences Göttingen Germany
- Bioanalytics, Institute of Clinical Chemistry University Medical Center Göttingen Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics Max Planck Institute for Multidisciplinary Sciences Göttingen Germany
- Clinic of Neurology University Medical Center Göttingen Göttingen Germany
| | - Volker Ellenrieder
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology University Medical Center Göttingen Gottingen Germany
| | - Alexander Roesch
- Department of Dermatology, University Hospital Essen, West German Cancer Center University Duisburg‐Essen and the German Cancer Consortium (DKTK)
| | - Michael P Schön
- Department of Dermatology, Venereology and Allergology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Meenhard Herlyn
- The Wistar Institute Melanoma Research Center Philadelphia PA USA
| | - Hedwig Stanisz
- Department of Dermatology, Venereology and Allergology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Ivan Bogeski
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
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12
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Linnemannstöns K, Karuna M P, Witte L, Choezom D, Honemann‐Capito M, Lagurin AS, Schmidt CV, Shrikhande S, Steinmetz L, Wiebke M, Lenz C, Gross JC. Microscopic and biochemical monitoring of endosomal trafficking and extracellular vesicle secretion in an endogenous in vivo model. J Extracell Vesicles 2022; 11:e12263. [PMID: 36103151 PMCID: PMC9473323 DOI: 10.1002/jev2.12263] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/17/2022] [Accepted: 05/22/2022] [Indexed: 11/10/2022] Open
Abstract
Extracellular vesicle (EV) secretion enables cell-cell communication in multicellular organisms. During development, EV secretion and the specific loading of signalling factors in EVs contributes to organ development and tissue differentiation. Here, we present an in vivo model to study EV secretion using the fat body and the haemolymph of the fruit fly, Drosophila melanogaster. The system makes use of tissue-specific EV labelling and is amenable to genetic modification by RNAi. This allows the unique combination of microscopic visualisation of EVs in different organs and quantitative biochemical purification to study how EVs are generated within the cells and which factors regulate their secretion in vivo. Characterisation of the system revealed that secretion of EVs from the fat body is mainly regulated by Rab11 and Rab35, highlighting the importance of recycling Rab GTPase family members for EV secretion. We furthermore discovered a so far unknown function of Rab14 along with the kinesin Klp98A in EV biogenesis and secretion.
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Affiliation(s)
- Karen Linnemannstöns
- Developmental BiochemistryUniversity Medical Center GoettingenGoettingenGermany
- Hematology and OncologyUniversity Medical Center GoettingenGoettingenGermany
- Molecular OncologyUniversity Medical Center GoettingenGoettingenGermany
| | - Pradhipa Karuna M
- Developmental BiochemistryUniversity Medical Center GoettingenGoettingenGermany
| | - Leonie Witte
- Developmental BiochemistryUniversity Medical Center GoettingenGoettingenGermany
| | - Dolma Choezom
- Developmental BiochemistryUniversity Medical Center GoettingenGoettingenGermany
| | | | - Alex Simon Lagurin
- Developmental BiochemistryUniversity Medical Center GoettingenGoettingenGermany
| | | | - Shreya Shrikhande
- Developmental BiochemistryUniversity Medical Center GoettingenGoettingenGermany
| | | | - Möbius Wiebke
- Electron Microscopy Core Unit, Department of NeurogeneticsMax Planck Institute of Experimental MedicineGöttingenGermany
| | - Christof Lenz
- Institute of Clinical ChemistryUniversity Medical Center GöttingenGöttingenGermany
- Bioanalytical Mass Spectrometry GroupMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Julia Christina Gross
- Developmental BiochemistryUniversity Medical Center GoettingenGoettingenGermany
- Hematology and OncologyUniversity Medical Center GoettingenGoettingenGermany
- Department of MedicineHealth and Medical UniversityPotsdamGermany
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13
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James C, Lenz C, Urlaub H, Kehlenbach RH. Sequestosome 1 Is Part of the Interaction Network of VAPB. Int J Mol Sci 2021; 22:ijms222413271. [PMID: 34948065 PMCID: PMC8707790 DOI: 10.3390/ijms222413271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 12/14/2022] Open
Abstract
VAPB (Vesicle-Associated-membrane Protein-associated protein B) is a tail-anchored membrane protein of the endoplasmic reticulum that can also be detected at the inner nuclear membrane. As a component of many contact sites between the endoplasmic reticulum and other organelles, VAPB is engaged in multiple protein interactions with a plethora of binding partners. A mutant version of VAPB, P56S-VAPB, which results from a single point mutation, is involved in a familial form of amyotrophic lateral sclerosis (ALS8). We performed RAPIDS (rapamycin- and APEX-dependent identification of proteins by SILAC) to identify proteins that interact with or are in close proximity to P56S-VAPB. The mutation abrogates the interaction of VAPB with many known binding partners. Here, we identify Sequestosome 1 (SQSTM1), a well-known autophagic adapter protein, as a major interaction/proximity partner of P56S-VAPB. Remarkably, not only the mutant protein, but also wild-type VAPB interacts with SQSTM1, as shown by proximity ligation assays and co-immunoprecipiation experiments.
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Affiliation(s)
- Christina James
- Department of Molecular Biology, Faculty of Medicine, GZMB (Göttinger Zentrum für Molekulare Biowissenschaften), Georg-August-University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Correspondence: (C.J.); (R.H.K.)
| | - Christof Lenz
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075 Göttingen, Germany; (C.L.); (H.U.)
| | - Henning Urlaub
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075 Göttingen, Germany; (C.L.); (H.U.)
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ralph H. Kehlenbach
- Department of Molecular Biology, Faculty of Medicine, GZMB (Göttinger Zentrum für Molekulare Biowissenschaften), Georg-August-University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Correspondence: (C.J.); (R.H.K.)
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14
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Hasan B, Khan A, Lenz C, Asif AR, Ahmed N. Characterization of functional protein complexes from Alzheimer's disease and healthy brain by mass spectrometry-based proteome analysis. Sci Rep 2021; 11:13891. [PMID: 34230543 PMCID: PMC8260596 DOI: 10.1038/s41598-021-93356-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 06/08/2021] [Indexed: 11/09/2022] Open
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disorder with impaired protein activities. Proteins in the form of complexes have a ubiquitous role in diverse range of cellular functions. The key challenge is to identify novel disease associated protein complexes and their potential role in the progression of AD pathology. Protein complexes were obtained from AD brain prefrontal cortex and age matched controls by Blue Native-Polyacrylamide Gel Electrophoresis. A proteomic analysis was performed using second dimension SDS-PAGE followed by nano LC-MS/MS. Differentially expressed proteins were mapped to existing biological networks by Ingenuity Pathway Analysis (IPA). A total of 13 protein complexes with their interacting proteins were resolved on SDS-PAGE. We identified 34 protein spots and found significant abundance difference between the two experimental samples. IPA analysis revealed degeneration of neurons and cell death as a major consequence of protein dysregulation. Furthermore, focused network analysis suggested an integrated regulation of the identified proteins through APP and MAPT dependent mechanisms. The interacting differentially expressed proteins in AD were found to be part of concomitant signaling cascades terminating in neuronal cell death. The identified protein networks and pathways warrant further research to study their actual contribution to AD pathology.
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Affiliation(s)
- Beena Hasan
- Neurochemistry Research Laboratory, Department of Biochemistry, University of Karachi, Karachi, 75270, Pakistan
| | - Ayesha Khan
- Neurochemistry Research Laboratory, Department of Biochemistry, University of Karachi, Karachi, 75270, Pakistan
| | - Christof Lenz
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, 37075, Germany
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry Group, Göttingen, 37077, Germany
| | - Abdul R Asif
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, 37075, Germany
| | - Nikhat Ahmed
- Neurochemistry Research Laboratory, Department of Biochemistry, University of Karachi, Karachi, 75270, Pakistan.
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15
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Peper J, Kownatzki-Danger D, Weninger G, Seibertz F, Pronto JRD, Sutanto H, Pacheu-Grau D, Hindmarsh R, Brandenburg S, Kohl T, Hasenfuss G, Gotthardt M, Rog-Zielinska EA, Wollnik B, Rehling P, Urlaub H, Wegener J, Heijman J, Voigt N, Cyganek L, Lenz C, Lehnart SE. Caveolin3 Stabilizes McT1-Mediated Lactate/Proton Transport in Cardiomyocytes. Circ Res 2021; 128:e102-e120. [PMID: 33486968 DOI: 10.1161/circresaha.119.316547] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Jonas Peper
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen (J.P., D.K.-D., G.W., S.B., T.K., G.H., J.W., S.E.L.), University Medical Center Göttingen.,Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen
| | - Daniel Kownatzki-Danger
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen (J.P., D.K.-D., G.W., S.B., T.K., G.H., J.W., S.E.L.), University Medical Center Göttingen.,Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen
| | - Gunnar Weninger
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen (J.P., D.K.-D., G.W., S.B., T.K., G.H., J.W., S.E.L.), University Medical Center Göttingen.,Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen
| | - Fitzwilliam Seibertz
- Institute of Pharmacology and Toxicology (F.S., J.R.D.P., N.V.), University Medical Center Göttingen.,DZHK (German Centre for Cardiovascular Research), partner site Göttingen (F.S., S.B., T.K., G.H., J.W., N.V., L.C., S.E.L.)
| | - Julius Ryan D Pronto
- Institute of Pharmacology and Toxicology (F.S., J.R.D.P., N.V.), University Medical Center Göttingen
| | - Henry Sutanto
- Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University (H.S., J.H.)
| | - David Pacheu-Grau
- Cellular Biochemistry, University Medical Center, Georg-August-University (D.P.G., P.R.)
| | - Robin Hindmarsh
- Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen
| | - Sören Brandenburg
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen (J.P., D.K.-D., G.W., S.B., T.K., G.H., J.W., S.E.L.), University Medical Center Göttingen.,Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen.,DZHK (German Centre for Cardiovascular Research), partner site Göttingen (F.S., S.B., T.K., G.H., J.W., N.V., L.C., S.E.L.)
| | - Tobias Kohl
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen (J.P., D.K.-D., G.W., S.B., T.K., G.H., J.W., S.E.L.), University Medical Center Göttingen.,Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen.,DZHK (German Centre for Cardiovascular Research), partner site Göttingen (F.S., S.B., T.K., G.H., J.W., N.V., L.C., S.E.L.)
| | - Gerd Hasenfuss
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen (J.P., D.K.-D., G.W., S.B., T.K., G.H., J.W., S.E.L.), University Medical Center Göttingen.,Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen.,DZHK (German Centre for Cardiovascular Research), partner site Göttingen (F.S., S.B., T.K., G.H., J.W., N.V., L.C., S.E.L.).,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen (G.H., B.W., P.R., N.V., S.E.L.)
| | - Michael Gotthardt
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin (M.G.).,Cardiology, Virchow Klinikum, Charité-University Medicine, Berlin (M.G.).,DZHK (German Center for Cardiovascular Research), partner site Berlin (M.G.)
| | - Eva A Rog-Zielinska
- University Heart Center, Faculty of Medicine, University of Freiburg (E.A.R.-Z.)
| | - Bernd Wollnik
- Institute of Human Genetics (B.W.), University Medical Center Göttingen.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen (G.H., B.W., P.R., N.V., S.E.L.)
| | - Peter Rehling
- Cellular Biochemistry, University Medical Center, Georg-August-University (D.P.G., P.R.).,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen (G.H., B.W., P.R., N.V., S.E.L.)
| | - Henning Urlaub
- Bioanalytics, Institute of Clinical Chemistry (H.U., C.L.), University Medical Center Göttingen.,Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen (H.U., C.L.)
| | - Jörg Wegener
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen (J.P., D.K.-D., G.W., S.B., T.K., G.H., J.W., S.E.L.), University Medical Center Göttingen.,Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen.,DZHK (German Centre for Cardiovascular Research), partner site Göttingen (F.S., S.B., T.K., G.H., J.W., N.V., L.C., S.E.L.)
| | - Jordi Heijman
- Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University (H.S., J.H.)
| | - Niels Voigt
- Institute of Pharmacology and Toxicology (F.S., J.R.D.P., N.V.), University Medical Center Göttingen.,DZHK (German Centre for Cardiovascular Research), partner site Göttingen (F.S., S.B., T.K., G.H., J.W., N.V., L.C., S.E.L.).,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen (G.H., B.W., P.R., N.V., S.E.L.)
| | - Lukas Cyganek
- DZHK (German Centre for Cardiovascular Research), partner site Göttingen (F.S., S.B., T.K., G.H., J.W., N.V., L.C., S.E.L.)
| | - Christof Lenz
- Bioanalytics, Institute of Clinical Chemistry (H.U., C.L.), University Medical Center Göttingen.,Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen (H.U., C.L.)
| | - Stephan E Lehnart
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen (J.P., D.K.-D., G.W., S.B., T.K., G.H., J.W., S.E.L.), University Medical Center Göttingen.,Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen.,DZHK (German Centre for Cardiovascular Research), partner site Göttingen (F.S., S.B., T.K., G.H., J.W., N.V., L.C., S.E.L.).,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen (G.H., B.W., P.R., N.V., S.E.L.).,BioMET, Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore (S.E.L.)
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16
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Karuna M P, Witte L, Linnemannstoens K, Choezom D, Danieli-Mackay A, Honemann-Capito M, Gross JC. Phosphorylation of Ykt6 SNARE Domain Regulates Its Membrane Recruitment and Activity. Biomolecules 2020; 10:biom10111560. [PMID: 33207719 PMCID: PMC7696345 DOI: 10.3390/biom10111560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/17/2022] Open
Abstract
Sensitive factor attachment protein receptors (SNARE) proteins are important mediators of protein trafficking that regulate the membrane fusion of specific vesicle populations and their target organelles. The SNARE protein Ykt6 lacks a transmembrane domain and attaches to different organelle membranes. Mechanistically, Ykt6 activity is thought to be regulated by a conformational change from a closed cytosolic form to an open membrane-bound form, yet the mechanism that regulates this transition is unknown. We identified phosphorylation sites in the SNARE domain of Ykt6 that mediate Ykt6 membrane recruitment and are essential for cellular growth. Using proximity-dependent labeling and membrane fractionation, we found that phosphorylation regulates Ykt6 conversion from a closed to an open conformation. This conformational switch recruits Ykt6 to several organelle membranes, where it functionally regulates the trafficking of Wnt proteins and extracellular vesicle secretion in a concentration-dependent manner. We propose that phosphorylation of its SNARE domain leads to a conformational switch from a cytosolic, auto-inhibited Ykt6 to an active SNARE at different membranes.
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Affiliation(s)
- Pradhipa Karuna M
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Leonie Witte
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Karen Linnemannstoens
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Dolma Choezom
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Adi Danieli-Mackay
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Mona Honemann-Capito
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Julia Christina Gross
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
- HMU Health and Medical University Potsdam, 14471 Potsdam, Germany
- Correspondence:
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17
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Menzel J, Kownatzki-Danger D, Tokar S, Ballone A, Unthan-Fechner K, Kilisch M, Lenz C, Urlaub H, Mori M, Ottmann C, Shattock MJ, Lehnart SE, Schwappach B. 14-3-3 binding creates a memory of kinase action by stabilizing the modified state of phospholamban. Sci Signal 2020; 13:13/647/eaaz1436. [DOI: 10.1126/scisignal.aaz1436] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The cardiac membrane protein phospholamban (PLN) is targeted by protein kinase A (PKA) at Ser16and by Ca2+/calmodulin-dependent protein kinase II (CaMKII) at Thr17. β-Adrenergic stimulation and PKA-dependent phosphorylation of Ser16acutely stimulate the sarcoplasmic reticulum calcium pump (SERCA) by relieving its inhibition by PLN. CaMKII-dependent phosphorylation may lead to longer-lasting SERCA stimulation and may sustain maladaptive Ca2+handling. Here, we demonstrated that phosphorylation at either Ser16or Thr17converted PLN into a target for the phosphoadaptor protein 14-3-3 with different affinities. 14-3-3 proteins were localized within nanometers of PLN and endogenous 14-3-3 coimmunoprecipitated with pentameric PLN from cardiac membranes. Molecular dynamics simulations predicted different molecular contacts for peptides phosphorylated at Ser16or Thr17with the binding groove of 14-3-3, resulting in varied binding affinities. 14-3-3 binding protected either PLN phosphosite from dephosphorylation. β-Adrenergic stimulation of isolated adult cardiomyocytes resulted in the membrane recruitment of endogenous 14-3-3. The exogenous addition of 14-3-3 to β-adrenergic–stimulated cardiomyocytes led to prolonged SERCA activation, presumably because 14-3-3 protected PLN pentamers from dephosphorylation. Phosphorylation of Ser16was disrupted by the cardiomyopathy-associated ∆Arg14mutation, implying that phosphorylation of Thr17by CaMKII may become crucial for 14-3-3 recruitment to ∆Arg14PLN. Consistent with PLN acting as a dynamic hub in the control of Ca2+handling, our results identify 14-3-3 binding to PLN as a contractility-augmenting mechanism.
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Affiliation(s)
- Julia Menzel
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Daniel Kownatzki-Danger
- Heart Research Center Göttingen, Department of Cardiology & Pneumology, Universitätsmedizin Göttingen, Robert-Koch-Straße 42a, 37075 Göttingen, Germany
| | - Sergiy Tokar
- School of Cardiovascular Medicine and Sciences, King’s College London, Westminster Bridge Road, London SE17H, UK
| | - Alice Ballone
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P. O. Box 513, 5600MB Eindhoven, Netherlands
| | - Kirsten Unthan-Fechner
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Markus Kilisch
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Christof Lenz
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075 Göttingen, Germany
- Max-Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075 Göttingen, Germany
- Max-Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P. O. Box 513, 5600MB Eindhoven, Netherlands
| | - Michael J. Shattock
- School of Cardiovascular Medicine and Sciences, King’s College London, Westminster Bridge Road, London SE17H, UK
| | - Stephan E. Lehnart
- Heart Research Center Göttingen, Department of Cardiology & Pneumology, Universitätsmedizin Göttingen, Robert-Koch-Straße 42a, 37075 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells” (MBExC), University of Goettingen, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Blanche Schwappach
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Max-Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells” (MBExC), University of Goettingen, Robert-Koch-Straße 40, 37075 Göttingen, Germany
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18
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Linnemannstöns K, Witte L, Karuna M P, Kittel JC, Danieli A, Müller D, Nitsch L, Honemann-Capito M, Grawe F, Wodarz A, Gross JC. Ykt6-dependent endosomal recycling is required for Wnt secretion in the Drosophila wing epithelium. Development 2020; 147:dev.185421. [PMID: 32611603 PMCID: PMC7438013 DOI: 10.1242/dev.185421] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 06/08/2020] [Indexed: 01/09/2023]
Abstract
Morphogens are important signalling molecules for tissue development and their secretion requires tight regulation. In the wing imaginal disc of flies, the morphogen Wnt/Wingless is apically presented by the secreting cell and re-internalized before final long-range secretion. Why Wnt molecules undergo these trafficking steps and the nature of the regulatory control within the endosomal compartment remain unclear. Here, we have investigated how Wnts are sorted at the level of endosomes by the versatile v-SNARE Ykt6. Using in vivo genetics, proximity-dependent proteomics and in vitro biochemical analyses, we show that most Ykt6 is present in the cytosol, but can be recruited to de-acidified compartments and recycle Wnts to the plasma membrane via Rab4-positive recycling endosomes. Thus, we propose a molecular mechanism by which producing cells integrate and leverage endocytosis and recycling via Ykt6 to coordinate extracellular Wnt levels.
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Affiliation(s)
- Karen Linnemannstöns
- Hematology and Oncology, University Medical Centre Goettingen, Goettingen 37075, Germany.,Developmental Biochemistry, University Medical Centre Goettingen, Goettingen 37077, Germany
| | - Leonie Witte
- Hematology and Oncology, University Medical Centre Goettingen, Goettingen 37075, Germany.,Developmental Biochemistry, University Medical Centre Goettingen, Goettingen 37077, Germany
| | - Pradhipa Karuna M
- Hematology and Oncology, University Medical Centre Goettingen, Goettingen 37075, Germany.,Developmental Biochemistry, University Medical Centre Goettingen, Goettingen 37077, Germany
| | - Jeanette Clarissa Kittel
- Hematology and Oncology, University Medical Centre Goettingen, Goettingen 37075, Germany.,Developmental Biochemistry, University Medical Centre Goettingen, Goettingen 37077, Germany
| | - Adi Danieli
- Hematology and Oncology, University Medical Centre Goettingen, Goettingen 37075, Germany.,Developmental Biochemistry, University Medical Centre Goettingen, Goettingen 37077, Germany
| | - Denise Müller
- Hematology and Oncology, University Medical Centre Goettingen, Goettingen 37075, Germany.,Developmental Biochemistry, University Medical Centre Goettingen, Goettingen 37077, Germany
| | - Lena Nitsch
- Hematology and Oncology, University Medical Centre Goettingen, Goettingen 37075, Germany.,Developmental Biochemistry, University Medical Centre Goettingen, Goettingen 37077, Germany
| | - Mona Honemann-Capito
- Hematology and Oncology, University Medical Centre Goettingen, Goettingen 37075, Germany.,Developmental Biochemistry, University Medical Centre Goettingen, Goettingen 37077, Germany
| | - Ferdinand Grawe
- Molecular Cell Biology, Institute I for Anatomy, University of Cologne Medical School, Cologne 50931, Germany.,Cluster of Excellence-Cellular Stress Response in Aging-Associated Diseases (CECAD), Cologne 50931, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
| | - Andreas Wodarz
- Molecular Cell Biology, Institute I for Anatomy, University of Cologne Medical School, Cologne 50931, Germany.,Cluster of Excellence-Cellular Stress Response in Aging-Associated Diseases (CECAD), Cologne 50931, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
| | - Julia Christina Gross
- Hematology and Oncology, University Medical Centre Goettingen, Goettingen 37075, Germany .,Developmental Biochemistry, University Medical Centre Goettingen, Goettingen 37077, Germany
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19
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Characterization of the protein and peptide of excipient zein by the multi-enzyme digestion coupled with nano-LC-MS/MS. Food Chem 2020; 321:126712. [DOI: 10.1016/j.foodchem.2020.126712] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/11/2020] [Accepted: 03/29/2020] [Indexed: 12/24/2022]
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20
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Extracellular Vesicles Derived from Neural Progenitor Cells--a Preclinical Evaluation for Stroke Treatment in Mice. Transl Stroke Res 2020; 12:185-203. [PMID: 32361827 PMCID: PMC7803677 DOI: 10.1007/s12975-020-00814-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/30/2020] [Accepted: 04/06/2020] [Indexed: 12/16/2022]
Abstract
Stem cells such as mesenchymal stem cells (MSCs) enhance neurological recovery in preclinical stroke models by secreting extracellular vesicles (EVs). Since previous reports have focused on the application of MSC-EVs only, the role of the most suitable host cell for EV enrichment and preclinical stroke treatment remains elusive. The present study aimed to evaluate the therapeutic potential of EVs derived from neural progenitor cells (NPCs) following experimental stroke. Using the PEG technique, EVs were enriched and characterized by electron microscopy, proteomics, rt-PCR, nanosight tracking analysis, and Western blotting. Different dosages of NPC-EVs displaying a characteristic profile in size, shape, cargo protein, and non-coding RNA contents were incubated in the presence of cerebral organoids exposed to oxygen-glucose deprivation (OGD), significantly reducing cell injury when compared with control organoids. Systemic administration of NPC-EVs in male C57BL6 mice following experimental ischemia enhanced neurological recovery and neuroregeneration for as long as 3 months. Interestingly, the therapeutic impact of such NPC-EVs was found to be not inferior to MSC-EVs. Flow cytometric analyses of blood and brain samples 7 days post-stroke demonstrated increased blood concentrations of B and T lymphocytes after NPC-EV delivery, without affecting cerebral cell counts. Likewise, a biodistribution analysis after systemic delivery of NPC-EVs revealed the majority of NPC-EVs to be found in extracranial organs such as the liver and the lung. This proof-of-concept study supports the idea of EVs being a general concept of stem cell–induced neuroprotection under stroke conditions, where EVs contribute to reverting the peripheral post-stroke immunosuppression.
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21
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Vahsen BF, Ribas VT, Sundermeyer J, Boecker A, Dambeck V, Lenz C, Shomroni O, Caldi Gomes L, Tatenhorst L, Barski E, Roser AE, Michel U, Urlaub H, Salinas G, Bähr M, Koch JC, Lingor P. Inhibition of the autophagic protein ULK1 attenuates axonal degeneration in vitro and in vivo, enhances translation, and modulates splicing. Cell Death Differ 2020; 27:2810-2827. [PMID: 32341448 PMCID: PMC7493890 DOI: 10.1038/s41418-020-0543-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 12/13/2022] Open
Abstract
Axonal degeneration is a key and early pathological feature in traumatic and neurodegenerative disorders of the CNS. Following a focal lesion to axons, extended axonal disintegration by acute axonal degeneration (AAD) occurs within several hours. During AAD, the accumulation of autophagic proteins including Unc-51 like autophagy activating kinase 1 (ULK1) has been demonstrated, but its role is incompletely understood. Here, we study the effect of ULK1 inhibition in different models of lesion-induced axonal degeneration in vitro and in vivo. Overexpression of a dominant negative of ULK1 (ULK1.DN) in primary rat cortical neurons attenuates axotomy-induced AAD in vitro. Both ULK1.DN and the ULK1 inhibitor SBI-0206965 protect against AAD after rat optic nerve crush in vivo. ULK1.DN additionally attenuates long-term axonal degeneration after rat spinal cord injury in vivo. Mechanistically, ULK1.DN decreases autophagy and leads to an mTOR-mediated increase in translational proteins. Consistently, treatment with SBI-0206965 results in enhanced mTOR activation. ULK1.DN additionally modulates the differential splicing of the degeneration-associated genes Kif1b and Ddit3. These findings uncover ULK1 as an important mediator of axonal degeneration in vitro and in vivo, and elucidate its function in splicing, defining it as a putative therapeutic target.
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Affiliation(s)
- Björn Friedhelm Vahsen
- Department of Neurology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Vinicius Toledo Ribas
- Department of Morphology, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | - Jonas Sundermeyer
- Department of Neurology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Alexander Boecker
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, 630 Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA, 19104, USA
| | - Vivian Dambeck
- Department of Neurology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.,Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Von-Siebold-Str. 3a, 37075, Göttingen, Germany.,DFG Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Christof Lenz
- Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.,Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Orr Shomroni
- NGS-Integrative Genomics Core Unit (NIG), Institute of Human Genetics, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Lucas Caldi Gomes
- Department of Neurology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Lars Tatenhorst
- Department of Neurology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.,Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Von-Siebold-Str. 3a, 37075, Göttingen, Germany.,DFG Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Elisabeth Barski
- Department of Neurology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Anna-Elisa Roser
- Department of Neurology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.,DFG Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Uwe Michel
- Department of Neurology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Henning Urlaub
- Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.,Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Gabriela Salinas
- NGS-Integrative Genomics Core Unit (NIG), Institute of Human Genetics, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Mathias Bähr
- Department of Neurology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.,DFG Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Jan Christoph Koch
- Department of Neurology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.,DFG Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Paul Lingor
- Department of Neurology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany. .,Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Von-Siebold-Str. 3a, 37075, Göttingen, Germany. .,DFG Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany. .,Department of Neurology, Rechts der Isar Hospital, Technical University Munich, Ismaninger Str. 22, 81675, Munich, Germany.
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22
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Probing the Environment of Emerin by Enhanced Ascorbate Peroxidase 2 (APEX2)-Mediated Proximity Labeling. Cells 2020; 9:cells9030605. [PMID: 32138363 PMCID: PMC7140434 DOI: 10.3390/cells9030605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 12/19/2022] Open
Abstract
Emerin is one of the best characterized proteins of the inner nuclear membrane, but can also occur at the level of the endoplasmic reticulum. We now use enhanced ascorbate peroxidase 2 (APEX2) to probe the environment of emerin. APEX2 can be used as a genetic tag that produces short-lived yet highly reactive biotin species, allowing the modification of proteins that interact with or are in very close proximity to the tagged protein. Biotinylated proteins can be isolated using immobilized streptavidin and analyzed by mass spectrometry. As an alternative to the standard approach with a genetic fusion of APEX2 to emerin, we also used RAPIDS (rapamycin- and APEX-dependent identification of proteins by SILAC), a method with improved specificity, where the peroxidase interacts with the protein of interest (i.e., emerin) only upon addition of rapamycin to the cells. We compare these different approaches, which, together, identify well-known interaction partners of emerin like lamin A and the lamina associated polypeptide 1 (LAP1), as well as novel proximity partners.
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23
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Völkel S, Hein S, Benker N, Pfeifer F, Lenz C, Losensky G. How to Cope With Heavy Metal Ions: Cellular and Proteome-Level Stress Response to Divalent Copper and Nickel in Halobacterium salinarum R1 Planktonic and Biofilm Cells. Front Microbiol 2020; 10:3056. [PMID: 32010107 PMCID: PMC6978704 DOI: 10.3389/fmicb.2019.03056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/18/2019] [Indexed: 11/13/2022] Open
Abstract
Halobacterium salinarum R1 is an extremely halophilic archaeon capable of adhesion and forming biofilms, allowing it to adjust to a range of growth conditions. We have recently shown that living in biofilms facilitates its survival under Cu2+ and Ni2+ stress, with specific rearrangements of the biofilm architecture observed following exposition. In this study, quantitative analyses were performed by SWATH mass spectrometry to determine the respective proteomes of planktonic and biofilm cells after exposition to Cu2+ and Ni2+.Quantitative data for 1180 proteins were obtained, corresponding to 46% of the predicted proteome. In planktonic cells, 234 of 1180 proteins showed significant abundance changes after metal ion treatment, of which 47% occurred in Cu2+ and Ni2+ treated samples. In biofilms, significant changes were detected for 52 proteins. Only three proteins changed under both conditions, suggesting metal-specific stress responses in biofilms. Deletion strains were generated to assess the potential role of selected target genes. Strongest effects were observed for ΔOE5245F and ΔOE2816F strains which exhibited increased and decreased biofilm mass after Ni2+ exposure, respectively. Moreover, EPS obviously plays a crucial role in H. salinarum metal ion resistance. Further efforts are required to elucidate the molecular basis and interplay of additional resistance mechanisms.
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Affiliation(s)
- Sabrina Völkel
- Microbiology and Archaea, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Sascha Hein
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Nathalie Benker
- Atmospheric Aerosol, Institute of Applied Geosciences, Technische Universität Darmstadt, Darmstadt, Germany
| | - Felicitas Pfeifer
- Microbiology and Archaea, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Gerald Losensky
- Microbiology and Archaea, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
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24
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Ramos Y, González A, Sosa‐Acosta P, Perez‐Riverol Y, García Y, Castellanos‐Serra L, Gil J, Sánchez A, González LJ, Besada V. Sodium dodecyl sulfate free gel electrophoresis/electroelution sorting for peptide fractionation. J Sep Sci 2019; 42:3712-3717. [DOI: 10.1002/jssc.201900495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Yassel Ramos
- Department of ProteomicsCenter for Genetic Engineering and Biotechnology La Habana Cuba
| | - Annia González
- Department of ProteomicsCenter for Genetic Engineering and Biotechnology La Habana Cuba
| | - Patricia Sosa‐Acosta
- Department of ProteomicsCenter for Genetic Engineering and Biotechnology La Habana Cuba
| | - Yasset Perez‐Riverol
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)Wellcome Trust Genome Campus Hinxton Cambridge United Kingdom
| | - Yairet García
- Department of ProteomicsCenter for Genetic Engineering and Biotechnology La Habana Cuba
| | | | - Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical CentreDepartment of Biomedical EngineeringLund University, Lund Lund Sweden
| | - Aniel Sánchez
- Section for Clinical ChemistryDepartment of Translational MedicineLund UniversitySkåne University Hospital Malmö Malmö Sweden
| | - Luis J. González
- Department of ProteomicsCenter for Genetic Engineering and Biotechnology La Habana Cuba
| | - Vladimir Besada
- Department of ProteomicsCenter for Genetic Engineering and Biotechnology La Habana Cuba
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25
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Erdmann J, Thöming JG, Pohl S, Pich A, Lenz C, Häussler S. The Core Proteome of Biofilm-Grown Clinical Pseudomonas aeruginosa Isolates. Cells 2019; 8:E1129. [PMID: 31547513 PMCID: PMC6829490 DOI: 10.3390/cells8101129] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/13/2022] Open
Abstract
Comparative genomics has greatly facilitated the identification of shared as well as unique features among individual cells or tissues, and thus offers the potential to find disease markers. While proteomics is recognized for its potential to generate quantitative maps of protein expression, comparative proteomics in bacteria has been largely restricted to the comparison of single cell lines or mutant strains. In this study, we used a data independent acquisition (DIA) technique, which enables global protein quantification of large sample cohorts, to record the proteome profiles of overall 27 whole genome sequenced and transcriptionally profiled clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. Analysis of the proteome profiles across the 27 clinical isolates grown under planktonic and biofilm growth conditions led to the identification of a core biofilm-associated protein profile. Furthermore, we found that protein-to-mRNA ratios between different P. aeruginosa strains are well correlated, indicating conserved patterns of post-transcriptional regulation. Uncovering core regulatory pathways, which drive biofilm formation and associated antibiotic tolerance in bacterial pathogens, promise to give clues to interactions between bacterial species and their environment and could provide useful targets for new clinical interventions to combat biofilm-associated infections.
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Affiliation(s)
- Jelena Erdmann
- Institute for Molecular Bacteriology, TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover 30625, Germany.
- Research Core Unit Proteomics and Institute of Toxicology, Hannover Medical School, Hannover 30625, Germany.
| | - Janne G Thöming
- Institute for Molecular Bacteriology, TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover 30625, Germany.
| | - Sarah Pohl
- Institute for Molecular Bacteriology, TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover 30625, Germany.
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig 38124, Germany.
| | - Andreas Pich
- Research Core Unit Proteomics and Institute of Toxicology, Hannover Medical School, Hannover 30625, Germany.
| | - Christof Lenz
- Institute of Clinical Chemistry, Bioanalytics, University Medical Center Göttingen, Göttingen 37075, Germany.
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, Göttingen 37077, Germany.
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover 30625, Germany.
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig 38124, Germany.
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26
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James C, Müller M, Goldberg MW, Lenz C, Urlaub H, Kehlenbach RH. Proteomic mapping by rapamycin-dependent targeting of APEX2 identifies binding partners of VAPB at the inner nuclear membrane. J Biol Chem 2019; 294:16241-16254. [PMID: 31519755 DOI: 10.1074/jbc.ra118.007283] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 08/05/2019] [Indexed: 11/06/2022] Open
Abstract
Vesicle-associated membrane protein-associated protein B (VAPB) is a tail-anchored protein that is present at several contact sites of the endoplasmic reticulum (ER). We now show by immunoelectron microscopy that VAPB also localizes to the inner nuclear membrane (INM). Using a modified enhanced ascorbate peroxidase 2 (APEX2) approach with rapamycin-dependent targeting of the peroxidase to a protein of interest, we searched for proteins that are in close proximity to VAPB, particularly at the INM. In combination with stable isotope labeling with amino acids in cell culture (SILAC), we confirmed many well-known interaction partners at the level of the ER with a clear distinction between specific and nonspecific hits. Furthermore, we identified emerin, TMEM43, and ELYS as potential interaction partners of VAPB at the INM and the nuclear pore complex, respectively.
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Affiliation(s)
- Christina James
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center for Molecular Biosciences (GZMB), Georg August University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Marret Müller
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center for Molecular Biosciences (GZMB), Georg August University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Martin W Goldberg
- School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Christof Lenz
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ralph H Kehlenbach
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center for Molecular Biosciences (GZMB), Georg August University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
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27
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Coy-Vergara J, Rivera-Monroy J, Urlaub H, Lenz C, Schwappach B. A trap mutant reveals the physiological client spectrum of TRC40. J Cell Sci 2019; 132:jcs.230094. [PMID: 31182645 PMCID: PMC6633398 DOI: 10.1242/jcs.230094] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/31/2019] [Indexed: 12/13/2022] Open
Abstract
The transmembrane recognition complex (TRC) pathway targets tail-anchored (TA) proteins to the membrane of the endoplasmic reticulum (ER). While many TA proteins are known to be able to use this pathway, it is essential for the targeting of only a few. Here, we uncover a large number of TA proteins that engage with TRC40 when other targeting machineries are fully operational. We use a dominant-negative ATPase-impaired mutant of TRC40 in which aspartate 74 was replaced by a glutamate residue to trap TA proteins in the cytoplasm. Manipulation of the hydrophobic TA-binding groove in TRC40 (also known as ASNA1) reduces interaction with most, but not all, substrates suggesting that co-purification may also reflect interactions unrelated to precursor protein targeting. We confirm known TRC40 substrates and identify many additional TA proteins interacting with TRC40. By using the trap approach in combination with quantitative mass spectrometry, we show that Golgi-resident TA proteins such as the golgins golgin-84, CASP and giantin as well as the vesicle-associated membrane-protein-associated proteins VAPA and VAPB interact with TRC40. Thus, our results provide new avenues to assess the essential role of TRC40 in metazoan organisms. This article has an associated First Person interview with the first author of the paper. Summary: A strategy to decipher which tail-anchored proteins do (as opposed to can or must) use the TRC pathway in intact cells generates a comprehensive list of human TRC40 clients.
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Affiliation(s)
- Javier Coy-Vergara
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen 37073, Germany
| | - Jhon Rivera-Monroy
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen 37073, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany.,Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen 37077, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany.,Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen 37077, Germany
| | - Blanche Schwappach
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen 37073, Germany .,Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
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28
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Cytosolic Trapping of a Mitochondrial Heat Shock Protein Is an Early Pathological Event in Synucleinopathies. Cell Rep 2019; 28:65-77.e6. [DOI: 10.1016/j.celrep.2019.06.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 04/19/2019] [Accepted: 06/03/2019] [Indexed: 11/20/2022] Open
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29
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Callegari S, Müller T, Schulz C, Lenz C, Jans DC, Wissel M, Opazo F, Rizzoli SO, Jakobs S, Urlaub H, Rehling P, Deckers M. A MICOS-TIM22 Association Promotes Carrier Import into Human Mitochondria. J Mol Biol 2019; 431:2835-2851. [PMID: 31103774 DOI: 10.1016/j.jmb.2019.05.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/10/2019] [Accepted: 05/10/2019] [Indexed: 01/05/2023]
Abstract
Mitochondrial membrane proteins with internal targeting signals are inserted into the inner membrane by the carrier translocase (TIM22 complex). For this, precursors have to be initially directed from the TOM complex in the outer mitochondrial membrane across the intermembrane space toward the TIM22 complex. How these two translocation processes are topologically coordinated is still unresolved. Using proteomic approaches, we find that the human TIM22 complex associates with the mitochondrial contact site and cristae organizing system (MICOS) complex. This association does not appear to be conserved in yeast, whereby the yeast MICOS complex instead interacts with the presequence translocase. Using a yeast mic10Δ strain and a HEK293T MIC10 knockout cell line, we characterize the role of MICOS for protein import into the mitochondrial inner membrane and matrix. We find that a physiological cristae organization promotes efficient import via the presequence pathway in yeast, while in human mitochondria, the MICOS complex is dispensable for protein import along the presequence pathway. However, in human mitochondria, the MICOS complex is required for the efficient import of carrier proteins into the mitochondrial inner membrane. Our analyses suggest that in human mitochondria, positioning of the carrier translocase at the crista junction, and potentially in vicinity to the TOM complex, is required for efficient transport into the inner membrane.
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Affiliation(s)
- Sylvie Callegari
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Tobias Müller
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Christian Schulz
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Department of Clinical Chemistry, Bioanalytics, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Daniel C Jans
- Department of NanoBiophotonics, Mitochondrial Structure and Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg, 11 37077 Göttingen, Germany; Clinic for Neurology, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Mirjam Wissel
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Felipe Opazo
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, von-Siebold-Strasse 3a, 37075 Göttingen, Germany; Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Silvio O Rizzoli
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, von-Siebold-Strasse 3a, 37075 Göttingen, Germany; Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Mitochondrial Structure and Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg, 11 37077 Göttingen, Germany; Clinic for Neurology, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Department of Clinical Chemistry, Bioanalytics, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany; Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Markus Deckers
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
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30
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Kretschmer J, Rao H, Hackert P, Sloan KE, Höbartner C, Bohnsack MT. The m 6A reader protein YTHDC2 interacts with the small ribosomal subunit and the 5'-3' exoribonuclease XRN1. RNA (NEW YORK, N.Y.) 2018; 24:1339-1350. [PMID: 29970596 PMCID: PMC6140455 DOI: 10.1261/rna.064238.117] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 06/26/2018] [Indexed: 05/20/2023]
Abstract
N6-methyladenosine (m6A) modifications in RNAs play important roles in regulating many different aspects of gene expression. While m6As can have direct effects on the structure, maturation, or translation of mRNAs, such modifications can also influence the fate of RNAs via proteins termed "readers" that specifically recognize and bind modified nucleotides. Several YTH domain-containing proteins have been identified as m6A readers that regulate the splicing, translation, or stability of specific mRNAs. In contrast to the other YTH domain-containing proteins, YTHDC2 has several defined domains and here, we have analyzed the contribution of these domains to the RNA and protein interactions of YTHDC2. The YTH domain of YTHDC2 preferentially binds m6A-containing RNAs via a conserved hydrophobic pocket, whereas the ankyrin repeats mediate an RNA-independent interaction with the 5'-3' exoribonuclease XRN1. We show that the YTH and R3H domains contribute to the binding of YTHDC2 to cellular RNAs, and using crosslinking and analysis of cDNA (CRAC), we reveal that YTHDC2 interacts with the small ribosomal subunit in close proximity to the mRNA entry/exit sites. YTHDC2 was recently found to promote a "fast-track" expression program for specific mRNAs, and our data suggest that YTHDC2 accomplishes this by recruitment of the RNA degradation machinery to regulate the stability of m6A-containing mRNAs and by utilizing its distinct RNA-binding domains to bridge interactions between m6A-containing mRNAs and the ribosomes to facilitate their efficient translation.
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Affiliation(s)
- Jens Kretschmer
- Department of Molecular Biology, University Medical Centre Göttingen, 37073 Göttingen, Germany
| | - Harita Rao
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, 37077 Göttingen, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Centre Göttingen, 37073 Göttingen, Germany
| | - Katherine E Sloan
- Department of Molecular Biology, University Medical Centre Göttingen, 37073 Göttingen, Germany
| | - Claudia Höbartner
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, 37077 Göttingen, Germany
- Institute for Organic Chemistry, University Würzburg, 97074 Würzburg, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, 37073 Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg-August-University, 37073 Göttingen, Germany
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31
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Cyganek L, Tiburcy M, Sekeres K, Gerstenberg K, Bohnenberger H, Lenz C, Henze S, Stauske M, Salinas G, Zimmermann WH, Hasenfuss G, Guan K. Deep phenotyping of human induced pluripotent stem cell-derived atrial and ventricular cardiomyocytes. JCI Insight 2018; 3:99941. [PMID: 29925689 DOI: 10.1172/jci.insight.99941] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/17/2018] [Indexed: 12/20/2022] Open
Abstract
Generation of homogeneous populations of subtype-specific cardiomyocytes (CMs) derived from human induced pluripotent stem cells (iPSCs) and their comprehensive phenotyping is crucial for a better understanding of the subtype-related disease mechanisms and as tools for the development of chamber-specific drugs. The goals of this study were to apply a simple and efficient method for differentiation of iPSCs into defined functional CM subtypes in feeder-free conditions and to obtain a comprehensive understanding of the molecular, cell biological, and functional properties of atrial and ventricular iPSC-CMs on both the single-cell and engineered heart muscle (EHM) level. By a stage-specific activation of retinoic acid signaling in monolayer-based and well-defined culture, we showed that cardiac progenitors can be directed towards a highly homogeneous population of atrial CMs. By combining the transcriptome and proteome profiling of the iPSC-CM subtypes with functional characterizations via optical action potential and calcium imaging, and with contractile analyses in EHM, we demonstrated that atrial and ventricular iPSC-CMs and -EHM highly correspond to the atrial and ventricular heart muscle, respectively. This study provides a comprehensive understanding of the molecular and functional identities characteristic of atrial and ventricular iPSC-CMs and -EHM and supports their suitability in disease modeling and chamber-specific drug screening.
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Affiliation(s)
- Lukas Cyganek
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen (UMG), Göttingen, Germany.,DZHK (German Center for Cardiovascular Research), partner site Göttingen, Germany
| | - Malte Tiburcy
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, Germany.,Institute of Pharmacology and Toxicology, UMG, Göttingen, Germany
| | - Karolina Sekeres
- Institute of Pharmacology and Toxicology, Technische Universität Dresden, Dresden, Germany
| | - Kathleen Gerstenberg
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen (UMG), Göttingen, Germany
| | | | - Christof Lenz
- Institute for Clinical Chemistry, UMG, Göttingen, Germany.,Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sarah Henze
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Michael Stauske
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen (UMG), Göttingen, Germany.,DZHK (German Center for Cardiovascular Research), partner site Göttingen, Germany
| | - Gabriela Salinas
- Transcriptome and Genome Analysis Laboratory Core Unit, UMG, Göttingen, Germany
| | - Wolfram-Hubertus Zimmermann
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, Germany.,Institute of Pharmacology and Toxicology, UMG, Göttingen, Germany
| | - Gerd Hasenfuss
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen (UMG), Göttingen, Germany.,DZHK (German Center for Cardiovascular Research), partner site Göttingen, Germany
| | - Kaomei Guan
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen (UMG), Göttingen, Germany.,DZHK (German Center for Cardiovascular Research), partner site Göttingen, Germany.,Institute of Pharmacology and Toxicology, Technische Universität Dresden, Dresden, Germany
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32
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Zaman U, Urlaub H, Abbasi A. Protein Profiling of Non-model Plant Cuminum cyminum by Gel-Based Proteomic Approach. PHYTOCHEMICAL ANALYSIS : PCA 2018; 29:242-249. [PMID: 29148164 DOI: 10.1002/pca.2738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 09/22/2017] [Accepted: 10/14/2017] [Indexed: 06/07/2023]
Abstract
INTRODUCTION Cumin (Cuminum cyminum), a popular spice has been widely used in traditional medicine to cure various ailments. Despite the existence of scientific literature about its pharmacological properties, no successful proteome profiling has yet been attempted. OBJECTIVE To optimise extraction of cumin proteins and analyse its profile by shotgun proteomics, using one-dimensional electrophoresis coupled with nano-ESI-LC-MS/MS. METHODOLOGY As a first step, we have compared three extraction protocols for total proteins extraction from cumin. Extracted proteins were separated on one-dimensional gel and analysed by state-of-the-art linear ion trap (LTQ)-Orbitrap Velose and Q Exactive HF mass spectrometer. RESULTS Evaluation of extraction method revealed significant differences in protein yield and proteome composition between the three extracts. LC-MS/MS allowed identification of several proteins with functional significance in various biological processes. CONCLUSION This study provides identification of a large number of proteins and offers a molecular basis for future research on potential pharmacologically active cumin proteins. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Uzma Zaman
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077, Göttingen, Germany
- Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Centre, Robert-Koch-Strasse 40, D-37075, Göttingen, Germany
- Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences, Gulzar-e-Hijri, Suparco Road, KDA Scheme -33, Karachi, Pakistan
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077, Göttingen, Germany
- Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Centre, Robert-Koch-Strasse 40, D-37075, Göttingen, Germany
| | - Atiya Abbasi
- International Centre for Chemical and Biochemical Sciences (ICCBS), HEJ Research Institute of Chemistry, University of Karachi, Karachi, -75270, Pakistan
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33
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Warda AS, Kretschmer J, Hackert P, Lenz C, Urlaub H, Höbartner C, Sloan KE, Bohnsack MT. Human METTL16 is a N6-methyladenosine (m 6A) methyltransferase that targets pre-mRNAs and various non-coding RNAs. EMBO Rep 2017; 18:2004-2014. [PMID: 29051200 DOI: 10.15252/embr.201744940] [Citation(s) in RCA: 460] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/17/2017] [Accepted: 09/28/2017] [Indexed: 01/05/2023] Open
Abstract
N6-methyladenosine (m6A) is a highly dynamic RNA modification that has recently emerged as a key regulator of gene expression. While many m6A modifications are installed by the METTL3-METTL14 complex, others appear to be introduced independently, implying that additional human m6A methyltransferases remain to be identified. Using crosslinking and analysis of cDNA (CRAC), we reveal that the putative human m6A "writer" protein METTL16 binds to the U6 snRNA and other ncRNAs as well as numerous lncRNAs and pre-mRNAs. We demonstrate that METTL16 is responsible for N6-methylation of A43 of the U6 snRNA and identify the early U6 biogenesis factors La, LARP7 and the methylphosphate capping enzyme MEPCE as METTL16 interaction partners. Interestingly, A43 lies within an essential ACAGAGA box of U6 that base pairs with 5' splice sites of pre-mRNAs during splicing, suggesting that METTL16-mediated modification of this site plays an important role in splicing regulation. The identification of METTL16 as an active m6A methyltransferase in human cells expands our understanding of the mechanisms by which the m6A landscape is installed on cellular RNAs.
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Affiliation(s)
- Ahmed S Warda
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Jens Kretschmer
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Claudia Höbartner
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August-University, Göttingen, Germany
| | - Katherine E Sloan
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany .,Göttingen Center for Molecular Biosciences, Georg-August-University, Göttingen, Germany
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34
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IEF peptide fractionation method combined to shotgun proteomics enhances the exploration of rice milk proteome. Anal Biochem 2017; 537:72-77. [PMID: 28864145 DOI: 10.1016/j.ab.2017.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/27/2017] [Indexed: 01/03/2023]
Abstract
We conducted a proteomics study in order to detect the proteomic method which provides the most complete characterization of the proteins of rice milk. In particular, we compared the results obtained from LC-MS/MS after protein precipitation with acetone or TCA, as well as the results obtained from LC-MS/MS after protein prefractionation based on SDS-PAGE (GeLC-MS/MS) or ProteoMiner™ technology (ProteoMiner-LC-MS/MS), and after peptide prefractionation based on IEF (pIEF-LC-MS/MS). A total of 158 protein species have been detect in rice milk. The physical-chemical analysis and classification of the identified proteins were also reported. In particular, we showed that pIEF-LC-MS/MS method led to a significant increase in the proteome coverage, allowing the identification of a total of 96 proteins of milk rice. This study demonstrates the utility of a prefractionation step based on pIEF before the shotgun proteomic analysis and offers an in-depth insight into the rice milk proteome.
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35
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Grochalová M, Konečná H, Stejskal K, Potěšil D, Fridrichová D, Srbová E, Ornerová K, Zdráhal Z. Deep coverage of the beer proteome. J Proteomics 2017; 162:119-124. [DOI: 10.1016/j.jprot.2017.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/12/2017] [Accepted: 05/01/2017] [Indexed: 11/25/2022]
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36
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Ashwin NMR, Barnabas L, Ramesh Sundar A, Malathi P, Viswanathan R, Masi A, Agrawal GK, Rakwal R. Advances in proteomic technologies and their scope of application in understanding plant–pathogen interactions. JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY 2017. [DOI: 10.1007/s13562-017-0402-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Loss of the histone methyltransferase EZH2 induces resistance to multiple drugs in acute myeloid leukemia. Nat Med 2016; 23:69-78. [PMID: 27941792 DOI: 10.1038/nm.4247] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/27/2016] [Indexed: 12/13/2022]
Abstract
In acute myeloid leukemia (AML), therapy resistance frequently occurs, leading to high mortality among patients. However, the mechanisms that render leukemic cells drug resistant remain largely undefined. Here, we identified loss of the histone methyltransferase EZH2 and subsequent reduction of histone H3K27 trimethylation as a novel pathway of acquired resistance to tyrosine kinase inhibitors (TKIs) and cytotoxic drugs in AML. Low EZH2 protein levels correlated with poor prognosis in AML patients. Suppression of EZH2 protein expression induced chemoresistance of AML cell lines and primary cells in vitro and in vivo. Low EZH2 levels resulted in derepression of HOX genes, and knockdown of HOXB7 and HOXA9 in the resistant cells was sufficient to improve sensitivity to TKIs and cytotoxic drugs. The endogenous loss of EZH2 expression in resistant cells and primary blasts from a subset of relapsed AML patients resulted from enhanced CDK1-dependent phosphorylation of EZH2 at Thr487. This interaction was stabilized by heat shock protein 90 (HSP90) and followed by proteasomal degradation of EZH2 in drug-resistant cells. Accordingly, inhibitors of HSP90, CDK1 and the proteasome prevented EZH2 degradation, decreased HOX gene expression and restored drug sensitivity. Finally, patients with reduced EZH2 levels at progression to standard therapy responded to the combination of bortezomib and cytarabine, concomitant with the re-establishment of EZH2 expression and blast clearance. These data suggest restoration of EZH2 protein as a viable approach to overcome treatment resistance in this AML patient population.
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Zhang JN, Michel U, Lenz C, Friedel CC, Köster S, d’Hedouville Z, Tönges L, Urlaub H, Bähr M, Lingor P, Koch JC. Calpain-mediated cleavage of collapsin response mediator protein-2 drives acute axonal degeneration. Sci Rep 2016; 6:37050. [PMID: 27845394 PMCID: PMC5109185 DOI: 10.1038/srep37050] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/24/2016] [Indexed: 01/25/2023] Open
Abstract
Axonal degeneration is a key initiating event in many neurological diseases. Focal lesions to axons result in a rapid disintegration of the perilesional axon by acute axonal degeneration (AAD) within several hours. However, the underlying molecular mechanisms of AAD are only incompletely understood. Here, we studied AAD in vivo through live-imaging of the rat optic nerve and in vitro in primary rat cortical neurons in microfluidic chambers. We found that calpain is activated early during AAD of the optic nerve and that calpain inhibition completely inhibits axonal fragmentation on the proximal side of the crush while it attenuates AAD on the distal side. A screening of calpain targets revealed that collapsin response mediator protein-2 (CRMP2) is a main downstream target of calpain activation in AAD. CRMP2-overexpression delayed bulb formation and rescued impairment of axonal mitochondrial transport after axotomy in vitro. In vivo, CRMP2-overexpression effectively protected the proximal axon from fragmentation within 6 hours after crush. Finally, a proteomic analysis of the optic nerve was performed at 6 hours after crush, which identified further proteins regulated during AAD, including several interactors of CRMP2. These findings reveal CRMP2 as an important mediator of AAD and define it as a putative therapeutic target.
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Affiliation(s)
- Jian-Nan Zhang
- Department of Neurology, University Medicine Göttingen, 37075 Göttingen, Germany
| | - Uwe Michel
- Department of Neurology, University Medicine Göttingen, 37075 Göttingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- Institute of Clinical Chemistry, University Medicine Göttingen, 37075 Göttingen, Germany
| | | | - Sarah Köster
- Institute for X-Ray Physics, Georg-August-University Göttingen, 37077 Göttingen, Germany
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37075 Göttingen, Germany
| | - Zara d’Hedouville
- Department of Neurology, University Medicine Göttingen, 37075 Göttingen, Germany
| | - Lars Tönges
- Department of Neurology, University Medicine Göttingen, 37075 Göttingen, Germany
- Department of Neurology, Ruhr-University Bochum, St. Josef-Hospital, 44791 Bochum, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- Institute of Clinical Chemistry, University Medicine Göttingen, 37075 Göttingen, Germany
| | - Mathias Bähr
- Department of Neurology, University Medicine Göttingen, 37075 Göttingen, Germany
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37075 Göttingen, Germany
| | - Paul Lingor
- Department of Neurology, University Medicine Göttingen, 37075 Göttingen, Germany
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37075 Göttingen, Germany
| | - Jan C. Koch
- Department of Neurology, University Medicine Göttingen, 37075 Göttingen, Germany
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37075 Göttingen, Germany
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Kilambi HV, Manda K, Sanivarapu H, Maurya VK, Sharma R, Sreelakshmi Y. Shotgun Proteomics of Tomato Fruits: Evaluation, Optimization and Validation of Sample Preparation Methods and Mass Spectrometric Parameters. FRONTIERS IN PLANT SCIENCE 2016; 7:969. [PMID: 27446192 PMCID: PMC4925719 DOI: 10.3389/fpls.2016.00969] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/17/2016] [Indexed: 05/29/2023]
Abstract
An optimized protocol was developed for shotgun proteomics of tomato fruit, which is a recalcitrant tissue due to a high percentage of sugars and secondary metabolites. A number of protein extraction and fractionation techniques were examined for optimal protein extraction from tomato fruits followed by peptide separation on nanoLCMS. Of all evaluated extraction agents, buffer saturated phenol was the most efficient. In-gel digestion [SDS-PAGE followed by separation on LCMS (GeLCMS)] of phenol-extracted sample yielded a maximal number of proteins. For in-solution digested samples, fractionation by strong anion exchange chromatography (SAX) also gave similar high proteome coverage. For shotgun proteomic profiling, optimization of mass spectrometry parameters such as automatic gain control targets (5E+05 for MS, 1E+04 for MS/MS); ion injection times (500 ms for MS, 100 ms for MS/MS); resolution of 30,000; signal threshold of 500; top N-value of 20 and fragmentation by collision-induced dissociation yielded the highest number of proteins. Validation of the above protocol in two tomato cultivars demonstrated its reproducibility, consistency, and robustness with a CV of < 10%. The protocol facilitated the detection of five-fold higher number of proteins compared to published reports in tomato fruits. The protocol outlined would be useful for high-throughput proteome analysis from tomato fruits and can be applied to other recalcitrant tissues.
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Bundy JL, Inouye BD, Mercer RS, Nowakowski RS. Fractionation-dependent improvements in proteome resolution in the mouse hippocampus by IEF LC-MS/MS. Electrophoresis 2016; 37:2054-62. [DOI: 10.1002/elps.201600076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 04/03/2016] [Accepted: 04/20/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Joseph L. Bundy
- Department of Biomedical Sciences, College of Medicine; Florida State University; Tallahassee FL USA
| | - Brian D. Inouye
- Department of Biological Science; Florida State University; Tallahassee FL USA
| | - Roger S. Mercer
- Translational Science Laboratory; College of Medicine Florida State University; Tallahassee FL USA
| | - Richard S. Nowakowski
- Department of Biomedical Sciences, College of Medicine; Florida State University; Tallahassee FL USA
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Abstract
So-called 'in-depth proteomics' and its applied separation methodology to improve the proteome coverage depth has become an important issue in mass spectrometric-based proteomics and system-wide cell biology studies. Employing a bottom-up approach and a variety of separation techniques, it allows for identification of proteins with low copy numbers and enables researchers to correlate the number of expressed genes in a cell with the proteome. Here we describe recent advances in this field with emphasis on peptide and protein separation technologies. The discussion is focused both on single injection analyses employing long reversed phase liquid chromatography separations of peptides ('single shot proteomics') and on the combination of orthogonal protein and peptide separation methods to achieve maximum protein coverage. Owing to these improvements, in-depth proteomics has now fully entered the field and is being implemented in an increasing number of laboratories.
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Affiliation(s)
- Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Frantzi M, Bhat A, Latosinska A. Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development. Clin Transl Med 2014; 3:7. [PMID: 24679154 PMCID: PMC3994249 DOI: 10.1186/2001-1326-3-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/06/2014] [Indexed: 12/11/2022] Open
Abstract
Biomarker research is continuously expanding in the field of clinical proteomics. A combination of different proteomic-based methodologies can be applied depending on the specific clinical context of use. Moreover, current advancements in proteomic analytical platforms are leading to an expansion of biomarker candidates that can be identified. Specifically, mass spectrometric techniques could provide highly valuable tools for biomarker research. Ideally, these advances could provide with biomarkers that are clinically applicable for disease diagnosis and/ or prognosis. Unfortunately, in general the biomarker candidates fail to be implemented in clinical decision making. To improve on this current situation, a well-defined study design has to be established driven by a clear clinical need, while several checkpoints between the different phases of discovery, verification and validation have to be passed in order to increase the probability of establishing valid biomarkers. In this review, we summarize the technical proteomic platforms that are available along the different stages in the biomarker discovery pipeline, exemplified by clinical applications in the field of bladder cancer biomarker research.
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Affiliation(s)
- Maria Frantzi
- Mosaiques Diagnostics GmbH, Mellendorfer Strasse 7-9, D-30625 Hannover, Germany
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, Greece
| | - Akshay Bhat
- Mosaiques Diagnostics GmbH, Mellendorfer Strasse 7-9, D-30625 Hannover, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Agnieszka Latosinska
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, Greece
- Charité-Universitätsmedizin Berlin, Berlin, Germany
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Paleoproteomics explained to youngsters: how did the wedding of two-dimensional electrophoresis and protein sequencing spark proteomics on: let there be light. J Proteomics 2014; 107:5-12. [PMID: 24657497 DOI: 10.1016/j.jprot.2014.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 11/22/2022]
Abstract
UNLABELLED Taking the opportunity of the 20th anniversary of the word "proteomics", this young adult age is a good time to remember how proteomics came from enormous progress in protein separation and protein microanalysis techniques, and from the conjugation of these advances into a high performance and streamlined working setup. However, in the history of the almost three decades that encompass the first attempts to perform large scale analysis of proteins to the current high throughput proteomics that we can enjoy now, it is also interesting to underline and to recall how difficult the first decade was. Indeed when the word was cast, the battle was already won. This recollection is mostly devoted to the almost forgotten period where proteomics was being conceived and put to birth, as this collective scientific work will never appear when searched through the keyword "proteomics". BIOLOGICAL SIGNIFICANCE The significance of this manuscript is to recall and review the two decades that separated the first attempts of performing large scale analysis of proteins from the solid technical corpus that existed when the word "proteomics" was coined twenty years ago. This recollection is made within the scientific historical context of this decade, which also saw the blossoming of DNA cloning and sequencing. This article is part of a Special Issue entitled: 20 years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini , Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.
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Mayr M, Rabilloud T. Multidimensional separation prior to mass spectrometry: Getting closer to the bottom of the iceberg. Proteomics 2013; 13:2942-3. [DOI: 10.1002/pmic.201300400] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 09/12/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Manuel Mayr
- King's British Heart Foundation Centre; King's College London; London UK
| | - Thierry Rabilloud
- UMR CNRS 5249; Laboratoire de Chimie et Biologie des Métaux; UMR CNRS-CEA-UJF, Grenoble France
- Laboratoire de Chimie et Biologie des Métaux; UMR CNRS-CEA-UJF; Université Joseph Fourier; Grenoble France
- Laboratoire de Chimie et Biologie des Métaux; CEA Grenoble; iRTSV/LCBM; UMR CNRS-CEA-UJF; Grenoble France
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