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Acevedo-Garcia J, Walden K, Leissing F, Baumgarten K, Drwiega K, Kwaaitaal M, Reinstädler A, Freh M, Dong X, James GV, Baus LC, Mascher M, Stein N, Schneeberger K, Brocke-Ahmadinejad N, Kollmar M, Schulze-Lefert P, Panstruga R. Barley Ror1 encodes a class XI myosin required for mlo-based broad-spectrum resistance to the fungal powdery mildew pathogen. Plant J 2022; 112:84-103. [PMID: 35916711 DOI: 10.1111/tpj.15930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/17/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Loss-of-function alleles of plant MLO genes confer broad-spectrum resistance to powdery mildews in many eudicot and monocot species. Although barley (Hordeum vulgare) mlo mutants have been used in agriculture for more than 40 years, understanding of the molecular principles underlying this type of disease resistance remains fragmentary. Forward genetic screens in barley have revealed mutations in two Required for mlo resistance (Ror) genes that partially impair immunity conferred by mlo mutants. While Ror2 encodes a soluble N-ethylmaleimide-sensitive factor-attached protein receptor (SNARE), the identity of Ror1, located at the pericentromeric region of barley chromosome 1H, remained elusive. We report the identification of Ror1 based on combined barley genomic sequence information and transcriptomic data from ror1 mutant plants. Ror1 encodes the barley class XI myosin Myo11A (HORVU.MOREX.r3.1HG0046420). Single amino acid substitutions of this myosin, deduced from non-functional ror1 mutant alleles, map to the nucleotide-binding region and the interface between the relay-helix and the converter domain of the motor protein. Ror1 myosin accumulates transiently in the course of powdery mildew infection. Functional fluorophore-labeled Ror1 variants associate with mobile intracellular compartments that partially colocalize with peroxisomes. Single-cell expression of the Ror1 tail region causes a dominant-negative effect that phenocopies ror1 loss-of-function mutants. We define a myosin motor for the establishment of mlo-mediated resistance, suggesting that motor protein-driven intracellular transport processes are critical for extracellular immunity, possibly through the targeted transfer of antifungal and/or cell wall cargoes to pathogen contact sites.
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Affiliation(s)
- Johanna Acevedo-Garcia
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Kim Walden
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Franz Leissing
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Kira Baumgarten
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Katarzyna Drwiega
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Mark Kwaaitaal
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Anja Reinstädler
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Matthias Freh
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Xue Dong
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Geo Velikkakam James
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Lisa C Baus
- Faculty of Biology, LMU Munich, 82152, Planegg-Martinsried, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Seeland, Germany
- Center of integrated Breeding Research (CiBreed), Department of Crop Sciences, Georg-August-University Göttingen, Von Siebold Str. 8, 37075, Göttingen, Germany
| | - Korbinian Schneeberger
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
- Faculty of Biology, LMU Munich, 82152, Planegg-Martinsried, Germany
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Nahal Brocke-Ahmadinejad
- INRES Crop Bioinformatics, University of Bonn, Katzenburgweg 2, 53115, Bonn, Germany
- Institute of Biochemistry and Molecular Biology, University of Bonn, Nussallee 11, D-53115, Bonn, Germany
| | - Martin Kollmar
- Department of NMR-based Structural Biology, Group Systems Biology of Motor Proteins, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Paul Schulze-Lefert
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
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Hoyer DP, Swoboda S, Treckmann JW, Benkö T, Paul A, Brocke-Ahmadinejad N. Transcriptomic profiles of human livers undergoing rewarming machine perfusion before transplantation-first insights. Funct Integr Genomics 2021; 21:367-376. [PMID: 33733319 PMCID: PMC8298250 DOI: 10.1007/s10142-021-00781-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/18/2021] [Accepted: 02/22/2021] [Indexed: 11/10/2022]
Abstract
Machine perfusion by controlled oxygenated rewarming (COR) is feasible and safe in clinical application and result in a promising outcome. This study utilizes next-generation sequencing (NGS) to investigate the transcriptome of human liver tissue undergoing COR before liver transplantation. Cold-stored livers were subjected to machine-assisted slow COR for ~120 min before transplantation. Biopsies were taken before (preCOR) and after COR (postCOR) and 1 h after reperfusion (postRep). The samples were sequenced, using RNA-seq to analyze differential transcriptional changes between the different stages and treatments of the grafts. Comparison of differential gene expression preCOR and postCOR demonstrated 10 upregulated genes. postRep 97 and 178 genes were upregulated and 7 and 13 downregulated compared to preCOR and postCOR, respectively. A shift of gene expressions by machine perfusion to the TGF-beta pathway was observed. The present study demonstrates distinct transcriptome profiles associated with machine perfusion by COR and transplantation of human livers. Such data provide a deeper understanding of the molecular mechanisms of machine perfusion technology in human liver transplantation.
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Affiliation(s)
- Dieter Paul Hoyer
- General, Visceral and Transplantation Surgery, University Hospital Essen, Essen, Germany
| | - Sandra Swoboda
- General, Visceral and Transplantation Surgery, University Hospital Essen, Essen, Germany
| | | | - Tamas Benkö
- General, Visceral and Transplantation Surgery, University Hospital Essen, Essen, Germany
| | - Andreas Paul
- General, Visceral and Transplantation Surgery, University Hospital Essen, Essen, Germany
| | - Nahal Brocke-Ahmadinejad
- Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Khundadze M, Ribaudo F, Hussain A, Stahlberg H, Brocke-Ahmadinejad N, Franzka P, Varga RE, Zarkovic M, Pungsrinont T, Kokal M, Ganley IG, Beetz C, Sylvester M, Hübner CA. Mouse models for hereditary spastic paraplegia uncover a role of PI4K2A in autophagic lysosome reformation. Autophagy 2021; 17:3690-3706. [PMID: 33618608 PMCID: PMC8632344 DOI: 10.1080/15548627.2021.1891848] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Hereditary spastic paraplegia (HSP) denotes genetically heterogeneous disorders characterized by leg spasticity due to degeneration of corticospinal axons. SPG11 and SPG15 have a similar clinical course and together are the most prevalent autosomal recessive HSP entity. The respective proteins play a role for macroautophagy/autophagy and autophagic lysosome reformation (ALR). Here, we report that spg11 and zfyve26 KO mice developed motor impairments within the same course of time. This correlated with enhanced accumulation of autofluorescent material in neurons and progressive neuron loss. In agreement with defective ALR, tubulation events were diminished in starved KO mouse embryonic fibroblasts (MEFs) and lysosomes decreased in neurons of KO brain sections. Confirming that both proteins act in the same molecular pathway, the pathologies were not aggravated upon simultaneous disruption of both. We further show that PI4K2A (phosphatidylinositol 4-kinase type 2 alpha), which phosphorylates phosphatidylinositol to phosphatidylinositol-4-phosphate (PtdIns4P), accumulated in autofluorescent deposits isolated from KO but not WT brains. Elevated PI4K2A abundance was already found at autolysosomes of neurons of presymptomatic KO mice. Immunolabelings further suggested higher levels of PtdIns4P at LAMP1-positive structures in starved KO MEFs. An increased association with LAMP1-positive structures was also observed for clathrin and DNM2/dynamin 2, which are important effectors of ALR recruited by phospholipids. Because PI4K2A overexpression impaired ALR, while its knockdown increased tubulation, we conclude that PI4K2A modulates phosphoinositide levels at autolysosomes and thus the recruitment of downstream effectors of ALR. Therefore, PI4K2A may play an important role in the pathogenesis of SPG11 and SPG15. Abbreviations: ALR: autophagic lysosome reformation; AP-5: adaptor protein complex 5; BFP: blue fluorescent protein; dKO: double knockout; EBSS: Earle’s balanced salt solution; FBA: foot base angle; GFP: green fluorescent protein; HSP: hereditary spastic paraplegia; KO: knockout; LAMP1: lysosomal-associated membrane protein 1; MAP1LC3B/LC3: microtubule-associated protein 1 light chain 3 beta; MEF: mouse embryonic fibroblast; SQSTM1/p62: sequestosome 1; PI4K2A: phosphatidylinositol 4-kinase type 2 alpha; PtdIns3P: phosphatidylinositol-3-phosphate; PtdIns4P: phosphatidylinositol-4-phosphate; RFP: red fluorescent protein; SPG: spastic paraplegia gene; TGN: trans-Golgi network; WT: wild type
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Affiliation(s)
- Mukhran Khundadze
- Institute of Human Genetics, University Hospital Jena, Friedrich-Schiller-University Jena, Jena, Germany
| | - Federico Ribaudo
- Institute of Human Genetics, University Hospital Jena, Friedrich-Schiller-University Jena, Jena, Germany
| | - Adeela Hussain
- Institute of Human Genetics, University Hospital Jena, Friedrich-Schiller-University Jena, Jena, Germany
| | - Henry Stahlberg
- Institute of Human Genetics, University Hospital Jena, Friedrich-Schiller-University Jena, Jena, Germany
| | - Nahal Brocke-Ahmadinejad
- Core Facility Mass Spectrometry, Institute of Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Patricia Franzka
- Institute of Human Genetics, University Hospital Jena, Friedrich-Schiller-University Jena, Jena, Germany
| | - Rita-Eva Varga
- Institute of Human Genetics, University Hospital Jena, Friedrich-Schiller-University Jena, Jena, Germany
| | - Milena Zarkovic
- Institute of Human Genetics, University Hospital Jena, Friedrich-Schiller-University Jena, Jena, Germany
| | - Thanakorn Pungsrinont
- Institute of Human Genetics, University Hospital Jena, Friedrich-Schiller-University Jena, Jena, Germany
| | - Miriam Kokal
- Institute of Human Genetics, University Hospital Jena, Friedrich-Schiller-University Jena, Jena, Germany
| | - Ian G Ganley
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, Scotland
| | - Christian Beetz
- Institute of Clinical Chemistry, University Hospital Jena, Friedrich-Schiller-University Jena, Germany; Current Affiliation: Centogene GmbH, Rostock, Germany
| | - Marc Sylvester
- Core Facility Mass Spectrometry, Institute of Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Christian A Hübner
- Institute of Human Genetics, University Hospital Jena, Friedrich-Schiller-University Jena, Jena, Germany
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Anand R, Kondadi AK, Meisterknecht J, Golombek M, Nortmann O, Riedel J, Peifer-Weiß L, Brocke-Ahmadinejad N, Schlütermann D, Stork B, Eichmann TO, Wittig I, Reichert AS. MIC26 and MIC27 cooperate to regulate cardiolipin levels and the landscape of OXPHOS complexes. Life Sci Alliance 2020; 3:e202000711. [PMID: 32788226 PMCID: PMC7425215 DOI: 10.26508/lsa.202000711] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 12/14/2022] Open
Abstract
Homologous apolipoproteins of MICOS complex, MIC26 and MIC27, show an antagonistic regulation of their protein levels, making it difficult to deduce their individual functions using a single gene deletion. We obtained single and double knockout (DKO) human cells of MIC26 and MIC27 and found that DKO show more concentric onion-like cristae with loss of CJs than any single deletion indicating overlapping roles in formation of CJs. Using a combination of complexome profiling, STED nanoscopy, and blue-native gel electrophoresis, we found that MIC26 and MIC27 are dispensable for the stability and integration of the remaining MICOS subunits into the complex suggesting that they assemble late into the MICOS complex. MIC26 and MIC27 are cooperatively required for the integrity of respiratory chain (super) complexes (RCs/SC) and the F1Fo-ATP synthase complex and integration of F1 subunits into the monomeric F1Fo-ATP synthase. While cardiolipin was reduced in DKO cells, overexpression of cardiolipin synthase in DKO restores the stability of RCs/SC. Overall, we propose that MIC26 and MIC27 are cooperatively required for global integrity and stability of multimeric OXPHOS complexes by modulating cardiolipin levels.
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Affiliation(s)
- Ruchika Anand
- Institute of Biochemistry and Molecular Biology I, Heinrich Heine University Düsseldorf, Medical Faculty, Düsseldorf, Germany
| | - Arun Kumar Kondadi
- Institute of Biochemistry and Molecular Biology I, Heinrich Heine University Düsseldorf, Medical Faculty, Düsseldorf, Germany
| | - Jana Meisterknecht
- Functional Proteomics, Sonderforschungsbereich (SFB) 815 Core Unit, Faculty of Medicine, Goethe-University, Frankfurt am Main, Germany
- Cluster of Excellence "Macromolecular Complexes", Goethe University, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Mathias Golombek
- Institute of Biochemistry and Molecular Biology I, Heinrich Heine University Düsseldorf, Medical Faculty, Düsseldorf, Germany
| | - Oliver Nortmann
- Institute of Biochemistry and Molecular Biology I, Heinrich Heine University Düsseldorf, Medical Faculty, Düsseldorf, Germany
| | - Julia Riedel
- Institute of Biochemistry and Molecular Biology I, Heinrich Heine University Düsseldorf, Medical Faculty, Düsseldorf, Germany
| | - Leon Peifer-Weiß
- Institute of Biochemistry and Molecular Biology I, Heinrich Heine University Düsseldorf, Medical Faculty, Düsseldorf, Germany
| | - Nahal Brocke-Ahmadinejad
- Institute of Biochemistry and Molecular Biology I, Heinrich Heine University Düsseldorf, Medical Faculty, Düsseldorf, Germany
| | - David Schlütermann
- Institute of Molecular Medicine I, Heinrich Heine University Düsseldorf, Medical Faculty, Düsseldorf, Germany
| | - Björn Stork
- Institute of Molecular Medicine I, Heinrich Heine University Düsseldorf, Medical Faculty, Düsseldorf, Germany
| | - Thomas O Eichmann
- Center for Explorative Lipidomics, BioTechMed-Graz, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Ilka Wittig
- Functional Proteomics, Sonderforschungsbereich (SFB) 815 Core Unit, Faculty of Medicine, Goethe-University, Frankfurt am Main, Germany
- Cluster of Excellence "Macromolecular Complexes", Goethe University, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Andreas S Reichert
- Institute of Biochemistry and Molecular Biology I, Heinrich Heine University Düsseldorf, Medical Faculty, Düsseldorf, Germany
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Elashry AM, Habash SS, Vijayapalani P, Brocke-Ahmadinejad N, Blümel R, Seetharam A, Schoof H, Grundler FMW. Transcriptome and Parasitome Analysis of Beet Cyst Nematode Heterodera schachtii. Sci Rep 2020; 10:3315. [PMID: 32094373 PMCID: PMC7039985 DOI: 10.1038/s41598-020-60186-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 12/20/2019] [Indexed: 11/17/2022] Open
Abstract
Beet cyst nematodes depend on a set of secretory proteins (effectors) for the induction and maintenance of their syncytial feeding sites in plant roots. In order to understand the relationship between the beet cyst nematode H. schachtii and its host, identification of H. schachtii effectors is crucial and to this end, we sequenced a whole animal pre-infective J2-stage transcriptome in addition to pre- and post-infective J2 gland cell transcriptome using Next Generation Sequencing (NGS) and identified a subset of sequences representing putative effectors. Comparison between the transcriptome of H. schachtii and previously reported related cyst nematodes and root-knot nematodes revealed a subset of esophageal gland related sequences and putative effectors in common across the tested species. Structural and functional annotation of H. schachtii transcriptome led to the identification of nearly 200 putative effectors. Six putative effector expressions were quantified using qPCR and three of them were functionally analyzed using RNAi. Phenotyping of the RNAi nematodes indicated that all tested genes decrease the level of nematodes pathogenicity and/or the average female size, thereby regulating cyst nematode parasitism. These discoveries contribute to further understanding of the cyst nematode parasitism.
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Affiliation(s)
- Abdelnaser M Elashry
- INRES Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Str. 13, Bonn, 53115, Germany. .,Strube research GmbH & Co. KG, Hauptstrasse 1, 38387, Söllingen, Germany.
| | - Samer S Habash
- INRES Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Str. 13, Bonn, 53115, Germany
| | | | - Nahal Brocke-Ahmadinejad
- INRES Crop Bioinformatics, University of Bonn, Katzenburgweg 2, 53115, Bonn, Germany.,Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - Roman Blümel
- INRES Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Str. 13, Bonn, 53115, Germany.,Bayer Crop Science, Alfred-Nobel-Str. 50, 40789, Monheim, Germany
| | - Arun Seetharam
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA.,Genome Informatics Facility, Office of Biotechnology, 448 Bessey Hall, Iowa State University, Ames, USA
| | - Heiko Schoof
- INRES Crop Bioinformatics, University of Bonn, Katzenburgweg 2, 53115, Bonn, Germany
| | - Florian M W Grundler
- INRES Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Str. 13, Bonn, 53115, Germany
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Wijasa TS, Sylvester M, Brocke-Ahmadinejad N, Schwartz S, Santarelli F, Gieselmann V, Klockgether T, Brosseron F, Heneka MT. Quantitative proteomics of synaptosome S-nitrosylation in Alzheimer's disease. J Neurochem 2019; 152:710-726. [PMID: 31520481 DOI: 10.1111/jnc.14870] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/23/2019] [Accepted: 09/04/2019] [Indexed: 12/20/2022]
Abstract
Increasing evidence suggests that both synaptic loss and neuroinflammation constitute early pathologic hallmarks of Alzheimer's disease. A downstream event during inflammatory activation of microglia and astrocytes is the induction of nitric oxide synthase type 2, resulting in an increased release of nitric oxide and the post-translational S-nitrosylation of protein cysteine residues. Both early events, inflammation and synaptic dysfunction, could be connected if this excess nitrosylation occurs on synaptic proteins. In the long term, such changes could provide new insight into patho-mechanisms as well as biomarker candidates from the early stages of disease progression. This study investigated S-nitrosylation in synaptosomal proteins isolated from APP/PS1 model mice in comparison to wild type and NOS2-/- mice, as well as human control, mild cognitive impairment and Alzheimer's disease brain tissues. Proteomics data were obtained using an established protocol utilizing an isobaric mass tag method, followed by nanocapillary high performance liquid chromatography tandem mass spectrometry. Statistical analysis identified the S-nitrosylation sites most likely derived from an increase in nitric oxide (NO) in dependence of presence of AD pathology, age and the key enzyme NOS2. The resulting list of candidate proteins is discussed considering function, previous findings in the context of neurodegeneration, and the potential for further validation studies.
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Affiliation(s)
| | - Marc Sylvester
- Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | | | - Stephanie Schwartz
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
| | | | - Volkmar Gieselmann
- Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | - Thomas Klockgether
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Neurology, University of Bonn, Bonn, Germany
| | | | - Michael T Heneka
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
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Schoor C, Brocke-Ahmadinejad N, Gieselmann V, Winter D. Investigation of Oligodendrocyte Precursor Cell Differentiation by Quantitative Proteomics. Proteomics 2019; 19:e1900057. [PMID: 31216117 DOI: 10.1002/pmic.201900057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 06/02/2019] [Indexed: 01/20/2023]
Abstract
Oligodendrocytes, the myelinating cells of the central nervous system, are essential for correct brain function. They originate from oligodendrocyte precursor cells through a differentiation process which is only incompletely understood and impaired in a variety of demyelinating diseases. Better knowledge of this differentiation holds the promise to develop novel therapies for these disorders. The differentiation of rat oligodendrocyte precursor cells to oligodendrocytes in vitro is investigated. After confirmation of differentiation by immunohistochemical analysis using cell type-specific marker proteins, a quantitative proteomics study using tandem mass tags (TMT) is conducted. Four time points of differentiation covering early, intermediate, and late stages are investigated. Data analysis by Mascot and MaxQuant identified 5259 protein groups of which 471 are not described in the context of cells of the oligodendroglial lineage before. Quantitative analysis of the dataset revealed distinct regulation patterns for proteins of different functional categories including metabolic processes, regulation of the cell cycle, and transcriptional control of protein expression. The present data confirm a significant number of proteins known to play a role in oligodendrocytes and myelination. Furthermore, novel candidate proteins are identified which may play an important role in this differentiation process providing a valuable resource for oligodendrocyte research.
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Affiliation(s)
- Carmen Schoor
- Institute for Biochemistry and Molecular Biology, University of Bonn, 53115, Bonn, Germany
| | | | - Volkmar Gieselmann
- Institute for Biochemistry and Molecular Biology, University of Bonn, 53115, Bonn, Germany
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, University of Bonn, 53115, Bonn, Germany
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Schoor C, Brocke-Ahmadinejad N, Gieselmann V, Winter D. Front Cover: Investigation of Oligodendrocyte Precursor Cell Differentiation by Quantitative Proteomics. Proteomics 2019. [DOI: 10.1002/pmic.201970121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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9
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Schmidtke C, Tiede S, Thelen M, Käkelä R, Jabs S, Makrypidi G, Sylvester M, Schweizer M, Braren I, Brocke-Ahmadinejad N, Cotman SL, Schulz A, Gieselmann V, Braulke T. Lysosomal proteome analysis reveals that CLN3-defective cells have multiple enzyme deficiencies associated with changes in intracellular trafficking. J Biol Chem 2019; 294:9592-9604. [PMID: 31040178 DOI: 10.1074/jbc.ra119.008852] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 04/21/2019] [Indexed: 12/25/2022] Open
Abstract
Numerous lysosomal enzymes and membrane proteins are essential for the degradation of proteins, lipids, oligosaccharides, and nucleic acids. The CLN3 gene encodes a lysosomal membrane protein of unknown function, and CLN3 mutations cause the fatal neurodegenerative lysosomal storage disorder CLN3 (Batten disease) by mechanisms that are poorly understood. To define components critical for lysosomal homeostasis that are affected by this disease, here we quantified the lysosomal proteome in cerebellar cell lines derived from a CLN3 knock-in mouse model of human Batten disease and control cells. We purified lysosomes from SILAC-labeled, and magnetite-loaded cerebellar cells by magnetic separation and analyzed them by MS. This analysis identified 70 proteins assigned to the lysosomal compartment and 3 lysosomal cargo receptors, of which most exhibited a significant differential abundance between control and CLN3-defective cells. Among these, 28 soluble lysosomal proteins catalyzing the degradation of various macromolecules had reduced levels in CLN3-defective cells. We confirmed these results by immunoblotting and selected protease and glycosidase activities. The reduction of 11 lipid-degrading lysosomal enzymes correlated with reduced capacity for lipid droplet degradation and several alterations in the distribution and composition of membrane lipids. In particular, levels of lactosylceramides and glycosphingolipids were decreased in CLN3-defective cells, which were also impaired in the recycling pathway of the exocytic transferrin receptor. Our findings suggest that CLN3 has a crucial role in regulating lysosome composition and their function, particularly in degrading of sphingolipids, and, as a consequence, in membrane transport along the recycling endosome pathway.
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Affiliation(s)
- Carolin Schmidtke
- From the Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany 20246
| | - Stephan Tiede
- From the Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany 20246
| | - Melanie Thelen
- Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany D-53115
| | - Reijo Käkelä
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland 00014
| | - Sabrina Jabs
- Leibniz-Institut für Molekulare Pharmakologie (FMP) and Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany 13125
| | - Georgia Makrypidi
- From the Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany 20246
| | - Marc Sylvester
- Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany D-53115
| | - Michaela Schweizer
- the Department of Electron Microscopy, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany 20251
| | - Ingke Braren
- Vector Core Unit, University Medical Center Hamburg-Eppendorf, Hamburg, Germany 20251
| | | | - Susan L Cotman
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - Angela Schulz
- From the Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany 20246
| | - Volkmar Gieselmann
- Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany D-53115
| | - Thomas Braulke
- From the Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany 20246,
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10
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Danyukova T, Ariunbat K, Thelen M, Brocke-Ahmadinejad N, Mole SE, Storch S. Loss of CLN7 results in depletion of soluble lysosomal proteins and impaired mTOR reactivation. Hum Mol Genet 2018; 27:1711-1722. [PMID: 29514215 PMCID: PMC5932567 DOI: 10.1093/hmg/ddy076] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/21/2018] [Accepted: 02/22/2018] [Indexed: 12/15/2022] Open
Abstract
Defects in the MFSD8 gene encoding the lysosomal membrane protein CLN7 lead to CLN7 disease, a neurodegenerative lysosomal storage disorder belonging to the group of neuronal ceroid lipofuscinoses. Here, we have performed a SILAC-based quantitative analysis of the lysosomal proteome using Cln7-deficient mouse embryonic fibroblasts (MEFs) from a Cln7 knockout (ko) mouse model. From 3335 different proteins identified, we detected 56 soluble lysosomal proteins and 29 highly abundant lysosomal membrane proteins. Quantification revealed that the amounts of 12 different soluble lysosomal proteins were significantly reduced in Cln7 ko MEFs compared with wild-type controls. One of the most significantly depleted lysosomal proteins was Cln5 protein that underlies another distinct neuronal ceroid lipofuscinosis disorder. Expression analyses showed that the mRNA expression, biosynthesis, intracellular sorting and proteolytic processing of Cln5 were not affected, whereas the depletion of mature Cln5 protein was due to increased proteolytic degradation by cysteine proteases in Cln7 ko lysosomes. Considering the similar phenotypes of CLN5 and CLN7 patients, our data suggest that depletion of CLN5 may play an important part in the pathogenesis of CLN7 disease. In addition, we found a defect in the ability of Cln7 ko MEFs to adapt to starvation conditions as shown by impaired mammalian target of rapamycin complex 1 reactivation, reduced autolysosome tubulation and increased perinuclear accumulation of autolysosomes compared with controls. In summary, depletion of multiple soluble lysosomal proteins suggest a critical role of CLN7 for lysosomal function, which may contribute to the pathogenesis and progression of CLN7 disease.
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Affiliation(s)
- Tatyana Danyukova
- Section Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Khandsuren Ariunbat
- Section Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Melanie Thelen
- Institute of Biochemistry and Molecular Biology, University of Bonn, 53115 Bonn, Germany
| | | | - Sara E Mole
- MRC Laboratory for Molecular Cell Biology, Department of Genetics, Evolution and Environment & UCL GOSH Institute of Child Health, University College London, London WC1E 6BT, UK
| | - Stephan Storch
- Section Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
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11
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Wijasa TS, Sylvester M, Brocke-Ahmadinejad N, Kummer MP, Brosseron F, Gieselmann V, Heneka MT. Proteome profiling of s-nitrosylated synaptosomal proteins by isobaric mass tags. J Neurosci Methods 2017; 291:95-100. [PMID: 28789995 PMCID: PMC5625850 DOI: 10.1016/j.jneumeth.2017.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 08/03/2017] [Indexed: 11/20/2022]
Abstract
Protocol for quantitative proteomics of nitrosylation on synaptosomal proteins. Identification of endogenous nitrosylation independent of induction by NO donors. Use of iodoTMT sixplex mass tags for stable labeling, enrichment, identification, and multiplex quantitation. Applicable on low amounts of sample material of mouse and human brain tissue.
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Affiliation(s)
| | - Marc Sylvester
- Institute of Biochemistry and Molecular Biology, University of Bonn, Germany
| | | | - Markus P Kummer
- Department of Neurodegenerative Diseases & Gerontopsychiatry, University Hospital Bonn, Bonn, Germany
| | | | - Volkmar Gieselmann
- Institute of Biochemistry and Molecular Biology, University of Bonn, Germany
| | - Michael T Heneka
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; Department of Neurodegenerative Diseases & Gerontopsychiatry, University Hospital Bonn, Bonn, Germany.
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12
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Markmann S, Thelen M, Cornils K, Schweizer M, Brocke-Ahmadinejad N, Willnow T, Heeren J, Gieselmann V, Braulke T, Kollmann K. Lrp1/LDL Receptor Play Critical Roles in Mannose 6-Phosphate-Independent Lysosomal Enzyme Targeting. Traffic 2015; 16:743-59. [DOI: 10.1111/tra.12284] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 03/12/2015] [Accepted: 03/13/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Sandra Markmann
- Department for Biochemistry, Children's Hospital; University Medical Center Hamburg-Eppendorf; D-20246 Hamburg Germany
| | - Melanie Thelen
- Institute of Biochemistry and Molecular Biology; University of Bonn; Nussallee 11 D-53115 Bonn Germany
| | - Kerstin Cornils
- Research Department Cell and Gene Therapy, Clinic for Stem Cell Transplantation; University Medical Center Hamburg-Eppendorf; D-20246 Hamburg Germany
| | - Michaela Schweizer
- Center for Molecular Neurobiology Hamburg, ZMNH; University Medical Center Hamburg-Eppendorf; 20246 Hamburg Germany
| | - Nahal Brocke-Ahmadinejad
- Institute of Biochemistry and Molecular Biology; University of Bonn; Nussallee 11 D-53115 Bonn Germany
| | - Thomas Willnow
- Max Delbrück Center for Molecular Medicine; 13125 Berlin-Buch Germany
| | - Joerg Heeren
- Department of Biochemistry and Molecular Cell Biology; University Medical Center Hamburg-Eppendorf; D-20246 Hamburg Germany
| | - Volkmar Gieselmann
- Institute of Biochemistry and Molecular Biology; University of Bonn; Nussallee 11 D-53115 Bonn Germany
| | - Thomas Braulke
- Department for Biochemistry, Children's Hospital; University Medical Center Hamburg-Eppendorf; D-20246 Hamburg Germany
| | - Katrin Kollmann
- Department for Biochemistry, Children's Hospital; University Medical Center Hamburg-Eppendorf; D-20246 Hamburg Germany
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