1
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Ayagama T, Charles PD, Bose SJ, Boland B, Priestman DA, Aston D, Berridge G, Fischer R, Cribbs AP, Song Q, Mirams GR, Amponsah K, Heather L, Galione A, Herring N, Kramer H, Capel RA, Platt FM, Schotten U, Verheule S, Burton RA. Compartmentalization proteomics revealed endolysosomal protein network changes in a goat model of atrial fibrillation. iScience 2024; 27:109609. [PMID: 38827406 PMCID: PMC11141153 DOI: 10.1016/j.isci.2024.109609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/07/2024] [Accepted: 03/25/2024] [Indexed: 06/04/2024] Open
Abstract
Endolysosomes (EL) are known for their role in regulating both intracellular trafficking and proteostasis. EL facilitate the elimination of damaged membranes, protein aggregates, membranous organelles and play an important role in calcium signaling. The specific role of EL in cardiac atrial fibrillation (AF) is not well understood. We isolated atrial EL organelles from AF goat biopsies and conducted a comprehensive integrated omics analysis to study the EL-specific proteins and pathways. We also performed electron tomography, protein and enzyme assays on these biopsies. Our results revealed the upregulation of the AMPK pathway and the expression of EL-specific proteins that were not found in whole tissue lysates, including GAA, DYNLRB1, CLTB, SIRT3, CCT2, and muscle-specific HSPB2. We also observed structural anomalies, such as autophagic-vacuole formation, irregularly shaped mitochondria, and glycogen deposition. Our results provide molecular information suggesting EL play a role in AF disease process over extended time frames.
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Affiliation(s)
- Thamali Ayagama
- Department of Pharmacology, University of Oxford, Oxford, UK
| | | | - Samuel J. Bose
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Barry Boland
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland
| | | | - Daniel Aston
- Department of Anaesthesia and Critical Care, Royal Papworth Hospital NHS Foundation Trust, Papworth Road, Cambridge CB2 0AY, UK
| | | | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - Adam P. Cribbs
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Headington OX3 7LD, UK
| | - Qianqian Song
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Gary R. Mirams
- Centre for Mathematical Medicine & Biology, Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Kwabena Amponsah
- Centre for Mathematical Medicine & Biology, Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Lisa Heather
- Department of Physiology, Anatomy and Genetics, , University of Oxford, South Park Road, Oxford OX1 3PT, UK
| | - Antony Galione
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Neil Herring
- Department of Physiology, Anatomy and Genetics, , University of Oxford, South Park Road, Oxford OX1 3PT, UK
| | - Holger Kramer
- Mass spectrometry Facility, The MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | | | - Ulrich Schotten
- Departments of Physiology and Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, the Netherlands
| | - Sander Verheule
- Departments of Physiology and Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, the Netherlands
| | - Rebecca A.B. Burton
- Department of Pharmacology, University of Oxford, Oxford, UK
- University of Liverpool, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, Liverpool, UK
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2
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Bergeron JJM. Proteomics Impact on Cell Biology to Resolve Cell Structure and Function. Mol Cell Proteomics 2024; 23:100758. [PMID: 38574860 PMCID: PMC11070594 DOI: 10.1016/j.mcpro.2024.100758] [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: 02/07/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
The acceleration of advances in proteomics has enabled integration with imaging at the EM and light microscopy levels, cryo-EM of protein structures, and artificial intelligence with proteins comprehensively and accurately resolved for cell structures at nanometer to subnanometer resolution. Proteomics continues to outpace experimentally based structural imaging, but their ultimate integration is a path toward the goal of a compendium of all proteins to understand mechanistically cell structure and function.
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Affiliation(s)
- John J M Bergeron
- Department of Medicine, McGill University Hospital Research Institute, Montreal, Quebec, Canada.
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3
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Kondethimmanahalli C, Ganta RR. Proteome analysis of Ehrlichia chaffeensis containing phagosome membranes revealed the presence of numerous bacterial and host proteins. Front Cell Infect Microbiol 2022; 12:1070356. [PMID: 36619760 PMCID: PMC9816426 DOI: 10.3389/fcimb.2022.1070356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Tick-transmitted Ehrlichia chaffeensis, the causative agent for human monocytic ehrlichiosis, resides and multiplies within a host cell phagosome. Infection progression of E. chaffeensis includes internalization into a host cell by host cell membrane fusion events following engulfment leading to the formation of E. chaffeensis containing vacuole (ECV). Revealing the molecular composition of ECV is important in understanding the host cellular processes, evasion of host defense pathways and in defining host-pathogen interactions. ECVs purified from infected host cells were analyzed to define both host and bacterial proteomes associated with the phagosome membranes. About 160 bacterial proteins and 2,683 host proteins were identified in the ECV membranes. The host proteins included predominantly known phagosome proteins involved in phagocytic trafficking, fusion of vesicles, protein transport, Ras signaling pathway and pathogenic infection. Many highly expressed proteins were similar to the previously documented proteins of phagosome vacuole membranes containing other obligate pathogenic bacteria. The finding of many bacterial membrane proteins is novel; they included multiple outer membrane proteins, such as the p28-Omps, the 120 kDa protein, preprotein translocases, lipoproteins, metal binding proteins, and chaperonins, although the presence of ankyrin repeat proteins, several Type I and IV secretion system proteins is anticipated. This study demonstrates that ECV membrane is extensively modified by the pathogen. This study represents the first and the most comprehensive description of ECV membrane proteome. The identity of many host and Ehrlichia proteins in the ECV membrane will be a valuable to define pathogenic mechanisms critical for the replication of the pathogen within macrophages.
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Affiliation(s)
| | - Roman R. Ganta
- Center of Excellence for Vector-Borne Diseases, Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
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4
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Ayagama T, Bose SJ, Capel RA, Priestman DA, Berridge G, Fischer R, Galione A, Platt FM, Kramer H, Burton RA. A modified density gradient proteomic-based method to analyze endolysosomal proteins in cardiac tissue. iScience 2021; 24:102949. [PMID: 34466782 PMCID: PMC8384914 DOI: 10.1016/j.isci.2021.102949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/04/2021] [Accepted: 08/02/2021] [Indexed: 11/22/2022] Open
Abstract
The importance of lysosomes in cardiac physiology and pathology is well established, and evidence for roles in calcium signaling is emerging. We describe a label-free proteomics method suitable for small cardiac tissue biopsies based on density-separated fractionation, which allows study of endolysosomal (EL) proteins. Density gradient fractions corresponding to tissue lysate; sarcoplasmic reticulum (SR), mitochondria (Mito) (1.3 g/mL); and EL with negligible contamination from SR or Mito (1.04 g/mL) were analyzed using Western blot, enzyme activity assay, and liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis (adapted discontinuous Percoll and sucrose differential density gradient). Kyoto Encyclopedia of Genes and Genomes, Reactome, Panther, and Gene Ontology pathway analysis showed good coverage of RAB proteins and lysosomal cathepsins (including cardiac-specific cathepsin D) in the purified EL fraction. Significant EL proteins recovered included catalytic activity proteins. We thus present a comprehensive protocol and data set of guinea pig atrial EL organelle proteomics using techniques also applicable for non-cardiac tissue.
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Affiliation(s)
- Thamali Ayagama
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Samuel J. Bose
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Rebecca A. Capel
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | | | - Georgina Berridge
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Antony Galione
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Frances M. Platt
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, W12 0NN UK
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5
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Boutchueng-Djidjou M, Belleau P, Bilodeau N, Fortier S, Bourassa S, Droit A, Elowe S, Faure RL. A type 2 diabetes disease module with a high collective influence for Cdk2 and PTPLAD1 is localized in endosomes. PLoS One 2018; 13:e0205180. [PMID: 30300385 PMCID: PMC6177195 DOI: 10.1371/journal.pone.0205180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/20/2018] [Indexed: 01/19/2023] Open
Abstract
Despite the identification of many susceptibility genes our knowledge of the underlying mechanisms responsible for complex disease remains limited. Here, we identified a type 2 diabetes disease module in endosomes, and validate it for functional relevance on selected nodes. Using hepatic Golgi/endosomes fractions, we established a proteome of insulin receptor-containing endosomes that allowed the study of physical protein interaction networks on a type 2 diabetes background. The resulting collated network is formed by 313 nodes and 1147 edges with a topology organized around a few major hubs with Cdk2 displaying the highest collective influence. Overall, 88% of the nodes are associated with the type 2 diabetes genetic risk, including 101 new candidates. The Type 2 diabetes module is enriched with cytoskeleton and luminal acidification–dependent processes that are shared with secretion-related mechanisms. We identified new signaling pathways driven by Cdk2 and PTPLAD1 whose expression affects the association of the insulin receptor with TUBA, TUBB, the actin component ACTB and the endosomal sorting markers Rab5c and Rab11a. Therefore, the interactome of internalized insulin receptors reveals the presence of a type 2 diabetes disease module enriched in new layers of feedback loops required for insulin signaling, clearance and islet biology.
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Affiliation(s)
- Martial Boutchueng-Djidjou
- Départment of Pediatrics, Faculty of Medicine, Université Laval, Centre de Recherche du CHU de Québec, Québec city, Canada
| | - Pascal Belleau
- Plateforme Protéomique de l’Est du Québec, Université Laval. Université Laval, Québec, QC, Canada
| | - Nicolas Bilodeau
- Départment of Pediatrics, Faculty of Medicine, Université Laval, Centre de Recherche du CHU de Québec, Québec city, Canada
| | - Suzanne Fortier
- Départment of Pediatrics, Faculty of Medicine, Université Laval, Centre de Recherche du CHU de Québec, Québec city, Canada
| | - Sylvie Bourassa
- Plateforme Protéomique de l’Est du Québec, Université Laval. Université Laval, Québec, QC, Canada
| | - Arnaud Droit
- Plateforme Protéomique de l’Est du Québec, Université Laval. Université Laval, Québec, QC, Canada
| | - Sabine Elowe
- Départment of Pediatrics, Faculty of Medicine, Université Laval, Centre de Recherche du CHU de Québec, Québec city, Canada
| | - Robert L. Faure
- Départment of Pediatrics, Faculty of Medicine, Université Laval, Centre de Recherche du CHU de Québec, Québec city, Canada
- * E-mail:
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6
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Shekari F, Baharvand H, Salekdeh GH. Organellar proteomics of embryonic stem cells. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 95:215-30. [PMID: 24985774 DOI: 10.1016/b978-0-12-800453-1.00007-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Embryonic stem cells (ESCs) are undifferentiated cells with two common remarkable features known as self-renewal and differentiation. Proteomics plays an increasingly important role in understanding molecular mechanisms underlying self-renewal and pluripotency of ESCs and their applications in cell therapy and developmental biology studies. As the function of a protein is strongly associated with its localization in cell, a complete and accurate picture of the proteome of ESCs cannot be achieved without knowing the subcellular locations of proteins. Subcellular fractionation allows enrichment of low abundant proteins and signaling complexes and reduces the complexity of the sample. It also provided insight into tracking proteins that shuttle between different compartments. Despite the substantial interest and efforts in ESC subcellular proteomics area, progress has been relatively limited. In this review, we present an overview on current status of ESCs organelle proteomics research and discuss challenges in subcellular proteomics.
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Affiliation(s)
- Faezeh Shekari
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran
| | - Hossein Baharvand
- Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran; Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.
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7
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Tharkeshwar AK, Gevaert K, Annaert W. Organellar Omics-A Reviving Strategy to Untangle the Biomolecular Complexity of the Cell. Proteomics 2017; 18:e1700113. [PMID: 29125683 DOI: 10.1002/pmic.201700113] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/23/2017] [Indexed: 12/18/2022]
Abstract
A eukaryotic cell encompasses many membrane-enclosed organelles, each of these holding several types of biomolecules that exhibit tremendous diversity in terms of their localization and expression. Despite the development of increasingly sensitive analytical tools, the enormous biomolecular complexity that exists within a cell cannot yet be fully resolved as low abundant molecules often remain unrecognized. Moreover, a drawback of whole cell analysis is that it does not provide spatial information and therefore it is not capable of assigning distinct biomolecules to specific compartments or analyzing changes in the composition of these compartments. Reduction of the biomolecular complexity of a sample helps to identify low abundant molecules, but such a reductionist approach requires methods that enable proper isolation and purification of individual cellular organelles. Decades of research have led to the development of a plethora of isolation methods for a broad range of subcellular organelles; yet, in particular, intrinsically dynamic compartments belonging to the endocytic machinery, including the plasma membrane, remain difficult to isolate in a sufficiently pure fraction. In this review, we discuss various methods that are commonly used to isolate subcellular organelles from cells and evaluate their advantages and disadvantages.
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Affiliation(s)
- Arun Kumar Tharkeshwar
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium.,Laboratory for Membrane Trafficking, Department of Neurosciences, KU Leuven, Leuven, Belgium.,Department of Cell Biology, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biochemistry, Ghent University, Belgium
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium.,Laboratory for Membrane Trafficking, Department of Neurosciences, KU Leuven, Leuven, Belgium
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8
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Hinckelmann MV, Virlogeux A, Niehage C, Poujol C, Choquet D, Hoflack B, Zala D, Saudou F. Self-propelling vesicles define glycolysis as the minimal energy machinery for neuronal transport. Nat Commun 2016; 7:13233. [PMID: 27775035 PMCID: PMC5078996 DOI: 10.1038/ncomms13233] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/14/2016] [Indexed: 12/21/2022] Open
Abstract
The glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) facilitates fast axonal transport in neurons. However, given that GAPDH does not produce ATP, it is unclear whether glycolysis per se is sufficient to propel vesicles. Although many proteins regulating transport have been identified, the molecular composition of transported vesicles in neurons has yet to be fully elucidated. Here we selectively enrich motile vesicles and perform quantitative proteomic analysis. In addition to the expected molecular motors and vesicular proteins, we find an enrichment of all the glycolytic enzymes. Using biochemical approaches and super-resolution microscopy, we observe that most glycolytic enzymes are selectively associated with vesicles and facilitate transport of vesicles in neurons. Finally, we provide evidence that mouse brain vesicles produce ATP from ADP and glucose, and display movement in a reconstituted in vitro transport assay of native vesicles. We conclude that transport of vesicles along microtubules can be autonomous. How neurons produce energy to fuel fast axonal transport is only partially understood. Authors here report that most glycolytic enzymes are enriched in motile vesicles, and such glycolytic machinery can produce ATP autonomously to propel vesicle movement along microtubules in a cell-free assay.
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Affiliation(s)
- María-Victoria Hinckelmann
- Institut Curie, F-91405 Orsay, France.,CNRS, UMR3306, F-91405 Orsay, France.,Inserm, U1005, F-91405 Orsay, France.,Faculté de Médecine, Univ. Paris Sud11, F-94276 Le Kremlin-Bicêtre, France
| | - Amandine Virlogeux
- Institut Curie, F-91405 Orsay, France.,CNRS, UMR3306, F-91405 Orsay, France.,Inserm, U1005, F-91405 Orsay, France.,Faculté de Médecine, Univ. Paris Sud11, F-94276 Le Kremlin-Bicêtre, France.,Grenoble Institut des Neurosciences, GIN, Univ. Grenoble Alpes, F-38000 Grenoble, France.,Inserm, U1216, F-38000 Grenoble, France
| | - Christian Niehage
- Biotechnology Center, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Christel Poujol
- CNRS, UMR 5297, F-33000 Bordeaux, France.,Interdisciplinary Institute for Neuroscience, IINS, Univ. Bordeaux, F-33077 Bordeaux, France
| | - Daniel Choquet
- CNRS, UMR 5297, F-33000 Bordeaux, France.,Interdisciplinary Institute for Neuroscience, IINS, Univ. Bordeaux, F-33077 Bordeaux, France
| | - Bernard Hoflack
- Biotechnology Center, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Diana Zala
- Institut Curie, F-91405 Orsay, France.,CNRS, UMR3306, F-91405 Orsay, France.,Inserm, U1005, F-91405 Orsay, France
| | - Frédéric Saudou
- Institut Curie, F-91405 Orsay, France.,CNRS, UMR3306, F-91405 Orsay, France.,Inserm, U1005, F-91405 Orsay, France.,Grenoble Institut des Neurosciences, GIN, Univ. Grenoble Alpes, F-38000 Grenoble, France.,Inserm, U1216, F-38000 Grenoble, France.,CHU Grenoble Alpes, F-38000 Grenoble, France
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9
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Yeu Y, Yoon Y, Park S. Protein localization vector propagation: a method for improving the accuracy of drug repositioning. MOLECULAR BIOSYSTEMS 2016; 11:2096-102. [PMID: 25998487 DOI: 10.1039/c5mb00306g] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Identifying alternative indications for known drugs is important for the pharmaceutical industry. Many computational methods have been proposed for predicting unknown associations between drugs and target proteins associated with diseases. To produce better prediction, researchers should not only develop accurate algorithms but identify good features that reflect intracellular systems. In this paper, we proposed a novel method for exploiting protein localization. We generated localization vectors (LVs) from protein localization and propagated LVs through a protein interaction network to increase the coverage of the localization information. The LVs showed distinct patterns among targets of known drugs as well as independent characteristics compared to existing features. Based on the experimental results, we determined that including LVs improves cross-validation accuracy and, produces better novel predictions with real and independent clinical trial data. Moreover, the propagation of LVs showed a positive result that it can help in increasing the coverage of the prediction results.
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Affiliation(s)
- Yunku Yeu
- Department of Computer Science, Yonsei Univertity, 50 Yonsei-Ro, SeoDaeMun-Gu, Seoul 120-749, Republic of Korea.
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10
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Lee JS, Wu Y, Skallos P, Fang J, Zhang X, Karnovsky A, Woods J, Stemmer PM, Liu M, Zhang K, Chen X. Proteomics analysis of rough endoplasmic reticulum in pancreatic beta cells. Proteomics 2015; 15:1508-11. [PMID: 25546123 PMCID: PMC4489703 DOI: 10.1002/pmic.201400345] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 11/02/2014] [Accepted: 12/18/2014] [Indexed: 12/20/2022]
Abstract
Pancreatic beta cells have well-developed ER to accommodate for the massive production and secretion of insulin. ER homeostasis is vital for normal beta cell function. Perturbation of ER homeostasis contributes to beta cell dysfunction in both type 1 and type 2 diabetes. To systematically identify the molecular machinery responsible for proinsulin biogenesis and maintenance of beta cell ER homeostasis, a widely used mouse pancreatic beta cell line, MIN6 cell was used to purify rough ER. Two different purification schemes were utilized. In each experiment, the ER pellets were solubilized and analyzed by 1D SDS-PAGE coupled with HPLC-MS/MS. A total of 1467 proteins were identified in three experiments with ≥95% confidence, among which 1117 proteins were found in at least two separate experiments and 737 proteins found in all three experiments. GO analysis revealed a comprehensive profile of known and novel players responsible for proinsulin biogenesis and ER homeostasis. Further bioinformatics analysis also identified potential beta cell specific ER proteins as well as ER proteins present in the risk genetic loci of type 2 diabetes. This dataset defines a molecular environment in the ER for proinsulin synthesis, folding and export and laid a solid foundation for further characterizations of altered ER homeostasis under diabetes-causing conditions. All MS data have been deposited in the ProteomeXchange with identifier PXD001081 (http://proteomecentral.proteomexchange.org/dataset/PXD001081).
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Affiliation(s)
- Jin-sook Lee
- Department of Physiology, Wayne State University, Detroit, MI 48201
| | - Yanning Wu
- Department of Physiology, Wayne State University, Detroit, MI 48201
| | - Patracia Skallos
- Department of Physiology, Wayne State University, Detroit, MI 48201
| | - Jingye Fang
- Department of Physiology, Wayne State University, Detroit, MI 48201
| | - Xuebao Zhang
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201
| | - Alla Karnovsky
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109
| | - James Woods
- Department of Physiology, Wayne State University, Detroit, MI 48201
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201
| | - Ming Liu
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Kezhong Zhang
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201
| | - Xuequn Chen
- Department of Physiology, Wayne State University, Detroit, MI 48201
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11
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Kang MG, Byun K, Kim JH, Park NH, Heinsen H, Ravid R, Steinbusch HW, Lee B, Park YM. Proteogenomics of the human hippocampus: The road ahead. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:788-97. [PMID: 25770686 DOI: 10.1016/j.bbapap.2015.02.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 02/10/2015] [Accepted: 02/15/2015] [Indexed: 12/26/2022]
Abstract
The hippocampus is one of the most essential components of the human brain and plays an important role in learning and memory. The hippocampus has drawn great attention from scientists and clinicians due to its clinical importance in diseases such as Alzheimer's disease (AD), non-AD dementia, and epilepsy. Understanding the function of the hippocampus and related disease mechanisms requires comprehensive knowledge of the orchestration of the genome, epigenome, transcriptome, proteome, and post-translational modifications (PTMs) of proteins. The past decade has seen remarkable advances in the high-throughput sequencing techniques that are collectively called next generation sequencing (NGS). NGS enables the precise analysis of gene expression profiles in cells and tissues, allowing powerful and more feasible integration of expression data from the gene level to the protein level, even allowing "-omic" level assessment of PTMs. In addition, improved bioinformatics algorithms coupled with NGS technology are finally opening a new era for scientists to discover previously unidentified and elusive proteins. In the present review, we will focus mainly on the proteomics of the human hippocampus with an emphasis on the integrated analysis of genomics, epigenomics, transcriptomics, and proteomics. Finally, we will discuss our perspectives on the potential and future of proteomics in the field of hippocampal biology. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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Affiliation(s)
- Myoung-Goo Kang
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea; Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | - Kyunghee Byun
- Center for Genomics and Proteomics, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 406-840, Republic of Korea
| | - Jae Ho Kim
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea; Mass Spectrometry Research Center, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea
| | - Nam Hyun Park
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea; Mass Spectrometry Research Center, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Helmut Heinsen
- Morphological Brain Research Unit, Department of Psychiatry, Universität of Würzburg, Würzburg, Germany
| | - Rivka Ravid
- Brain Bank Consultant, Amsterdam, The Netherlands
| | - Harry W Steinbusch
- School for Mental Health and Neuroscience, Department of Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Bonghee Lee
- Mass Spectrometry Research Center, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea.
| | - Young Mok Park
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea; Mass Spectrometry Research Center, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Republic of Korea.
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12
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Tribl F, Meyer HE, Marcus K. Analysis of organelles within the nervous system: impact on brain and organelle functions. Expert Rev Proteomics 2014; 5:333-51. [DOI: 10.1586/14789450.5.2.333] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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13
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Han HM, Bouchet-Marquis C, Huebinger J, Grabenbauer M. Golgi apparatus analyzed by cryo-electron microscopy. Histochem Cell Biol 2013; 140:369-81. [PMID: 23954988 PMCID: PMC3787787 DOI: 10.1007/s00418-013-1136-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2013] [Indexed: 11/28/2022]
Abstract
In 1898, the Golgi apparatus was discovered by light microscopy, and since the 1950s, the ultrastructure composition is known by electron microscopic investigation. The complex three-dimensional morphology fascinated researchers and was sometimes even the driving force to develop novel visualization techniques. However, the highly dynamic membrane systems of Golgi apparatus are delicate and prone to fixation artifacts. Therefore, the understanding of Golgi morphology and its function has been improved significantly with the development of better preparation methods. Nowadays, cryo-fixation is the method of choice to arrest instantly all dynamic and physiological processes inside cells, tissues, and small organisms. Embedded in amorphous ice, such samples can be further processed by freeze substitution or directly analyzed in their fully hydrated state by cryo-electron microscopy and tomography. Even though the overall morphology of vitrified Golgi stacks is comparable to well-prepared and resin-embedded samples, previously unknown structural details can be observed solely based on their native density. At this point, any further improvement of sample preparation would gain novel insights, perhaps not in terms of general morphology, but on fine structural details of this dynamic organelle.
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Affiliation(s)
- Hong-Mei Han
- Department of Systemic Cell Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Cedric Bouchet-Marquis
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO USA
- FEI Company, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124 USA
| | - Jan Huebinger
- Department of Systemic Cell Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Markus Grabenbauer
- Institute of Anatomy and Cell Biology, Heidelberg University, INF 307, 69120 Heidelberg, Germany
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14
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Yang JS, Kim J, Park S, Jeon J, Shin YE, Kim S. Spatial and functional organization of mitochondrial protein network. Sci Rep 2013; 3:1403. [PMID: 23466738 PMCID: PMC3590558 DOI: 10.1038/srep01403] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 02/21/2013] [Indexed: 12/24/2022] Open
Abstract
Characterizing the spatial organization of the human mitochondrial proteome will enhance our understanding of mitochondrial functions at the molecular level and provide key insight into protein-disease associations. However, the sub-organellar location and possible association with mitochondrial diseases are not annotated for most mitochondrial proteins. Here, we characterized the functional and spatial organization of mitochondrial proteins by assessing their position in the Mitochondrial Protein Functional (MPF) network. Network position was assigned to the MPF network and facilitated the determination of sub-organellar location and functional organization of mitochondrial proteins. Moreover, network position successfully identified candidate disease genes of several mitochondrial disorders. Thus, our data support the use of network position as a novel method to explore the molecular function and pathogenesis of mitochondrial proteins.
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Affiliation(s)
- Jae-Seong Yang
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Nam-gu, Pohang, Gyeongbuk, Korea, 790-784
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15
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Wu HF, Gopal J, Abdelhamid HN, Hasan N. Quantum dot applications endowing novelty to analytical proteomics. Proteomics 2013; 12:2949-61. [PMID: 22930415 DOI: 10.1002/pmic.201200295] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This review surveys all the state-of-art applications of quantum dots (QDs) in conventional and modern analytical methods in proteomic studies. A brief introduction of QDs and their properties is initially presented followed by outlining the application of QDs in fluorescence, MS, imaging, and cancer-based proteomics. The in-depth application of QDs in MALDI-MS and surface assisted laser desorption/ionization-MS has been elaborately discussed, summarizing the speculated mechanism behind the protein-QDs interactions during QD matrix applications leading to enhanced detection sensitivity.
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Affiliation(s)
- Hui-Fen Wu
- Department of Chemistry, National Sun Yat Sen University, Kaohsiung, Taiwan.
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16
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Jung S, Smith JJ, von Haller PD, Dilworth DJ, Sitko KA, Miller LR, Saleem RA, Goodlett DR, Aitchison JD. Global analysis of condition-specific subcellular protein distribution and abundance. Mol Cell Proteomics 2013; 12:1421-35. [PMID: 23349476 DOI: 10.1074/mcp.o112.019166] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Cellular control of protein activities by modulation of their abundance or compartmentalization is not easily measured on a large scale. We developed and applied a method to globally interrogate these processes that is widely useful for systems-level analyses of dynamic cellular responses in many cell types. The approach involves subcellular fractionation followed by comprehensive proteomic analysis of the fractions, which is enabled by a data-independent acquisition mass spectrometry approach that samples every available mass to charge channel systematically to maximize sensitivity. Next, various fraction-enrichment ratios are measured for all detected proteins across different environmental conditions and used to group proteins into clusters reflecting changes in compartmentalization and relative conditional abundance. Application of the approach to characterize the response of yeast proteins to fatty acid exposure revealed dynamics of peroxisomes and novel dynamics of MCC/eisosomes, specialized plasma membrane domains comprised of membrane compartment occupied by Can1 (MCC) and eisosome subdomains. It also led to the identification of Fat3, a fatty acid transport protein of the plasma membrane, previously annotated as Ykl187.
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Affiliation(s)
- Sunhee Jung
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA
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17
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Smirle J, Au CE, Jain M, Dejgaard K, Nilsson T, Bergeron J. Cell biology of the endoplasmic reticulum and the Golgi apparatus through proteomics. Cold Spring Harb Perspect Biol 2013; 5:a015073. [PMID: 23284051 DOI: 10.1101/cshperspect.a015073] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Enriched endoplasmic reticulum (ER) and Golgi membranes subjected to mass spectrometry have uncovered over a thousand different proteins assigned to the ER and Golgi apparatus of rat liver. This, in turn, led to the uncovering of several hundred proteins of poorly understood function and, through hierarchical clustering, showed that proteins distributed in patterns suggestive of microdomains in cognate organelles. This has led to new insights with respect to their intracellular localization and function. Another outcome has been the critical testing of the cisternal maturation hypothesis showing overwhelming support for a predominant role of COPI vesicles in the transport of resident proteins of the ER and Golgi apparatus (as opposed to biosynthetic cargo). Here we will discuss new insights gained and also highlight new avenues undertaken to further explore the cell biology of the ER and the Golgi apparatus through tandem mass spectrometry.
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Affiliation(s)
- Jeffrey Smirle
- The Research Institute of the McGill University Health Centre and the Department of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
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18
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Abstract
High-content screening (HCS) as a methodological tool has evolved relatively recently, largely driven by the demand for in depth spatial and temporal information from intact cells exposed to a range of chemical and/or genomic perturbations. The technology is based around automated fluorescence microscopy in combination with advanced imaging processing and analysis tools, which together can provide quantitative information as a first-level description of complex cellular events. HCS and high-content analysis are particularly powerful when combined with perturbation techniques such as RNA interference (RNAi), as this allows large families of genes to be interrogated with respect to a biological pathway or process of interest. In this methodology chapter, we describe an approach by which HCS can be applied to study the morphological state of the Golgi complex in cultured mammalian cells. We provide a detailed protocol for the highly parallel downregulation of gene activity using RNAi in 384-well plates and describe an automated image analysis routine that could be used to quantify Golgi complex in a genome-wide RNAi context.
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Affiliation(s)
- George Galea
- School of Biology and Environmental Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Dublin, Ireland
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19
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Savino R, Paduano S, Preianò M, Terracciano R. The proteomics big challenge for biomarkers and new drug-targets discovery. Int J Mol Sci 2012. [PMID: 23203042 PMCID: PMC3509558 DOI: 10.3390/ijms131113926] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
In the modern process of drug discovery, clinical, functional and chemical proteomics can converge and integrate synergies. Functional proteomics explores and elucidates the components of pathways and their interactions which, when deregulated, lead to a disease condition. This knowledge allows the design of strategies to target multiple pathways with combinations of pathway-specific drugs, which might increase chances of success and reduce the occurrence of drug resistance. Chemical proteomics, by analyzing the drug interactome, strongly contributes to accelerate the process of new druggable targets discovery. In the research area of clinical proteomics, proteome and peptidome mass spectrometry-profiling of human bodily fluid (plasma, serum, urine and so on), as well as of tissue and of cells, represents a promising tool for novel biomarker and eventually new druggable targets discovery. In the present review we provide a survey of current strategies of functional, chemical and clinical proteomics. Major issues will be presented for proteomic technologies used for the discovery of biomarkers for early disease diagnosis and identification of new drug targets.
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Affiliation(s)
- Rocco Savino
- Department of Health Sciences, Laboratory of Mass Spectrometry and Proteomics, University "Magna Græcia", Catanzaro, University Campus, Europa Avenue, 88100 Catanzaro, Italy.
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20
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Lescuyer P, Bianchi L, Hochstrasser D, Bini L, Sanchez JC. Translational proteomics. J Proteomics 2012; 75:4571-2. [DOI: 10.1016/j.jprot.2012.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 06/05/2012] [Indexed: 10/28/2022]
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21
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Sigismund S, Confalonieri S, Ciliberto A, Polo S, Scita G, Di Fiore PP. Endocytosis and signaling: cell logistics shape the eukaryotic cell plan. Physiol Rev 2012; 92:273-366. [PMID: 22298658 DOI: 10.1152/physrev.00005.2011] [Citation(s) in RCA: 236] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Our understanding of endocytosis has evolved remarkably in little more than a decade. This is the result not only of advances in our knowledge of its molecular and biological workings, but also of a true paradigm shift in our understanding of what really constitutes endocytosis and of its role in homeostasis. Although endocytosis was initially discovered and studied as a relatively simple process to transport molecules across the plasma membrane, it was subsequently found to be inextricably linked with almost all aspects of cellular signaling. This led to the notion that endocytosis is actually the master organizer of cellular signaling, providing the cell with understandable messages that have been resolved in space and time. In essence, endocytosis provides the communications and supply routes (the logistics) of the cell. Although this may seem revolutionary, it is still likely to be only a small part of the entire story. A wealth of new evidence is uncovering the surprisingly pervasive nature of endocytosis in essentially all aspects of cellular regulation. In addition, many newly discovered functions of endocytic proteins are not immediately interpretable within the classical view of endocytosis. A possible framework, to rationalize all this new knowledge, requires us to "upgrade" our vision of endocytosis. By combining the analysis of biochemical, biological, and evolutionary evidence, we propose herein that endocytosis constitutes one of the major enabling conditions that in the history of life permitted the development of a higher level of organization, leading to the actuation of the eukaryotic cell plan.
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Affiliation(s)
- Sara Sigismund
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
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22
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Liu X, Fagotto F. A method to separate nuclear, cytosolic, and membrane-associated signaling molecules in cultured cells. Sci Signal 2011; 4:pl2. [PMID: 22169476 DOI: 10.1126/scisignal.2002373] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Direct comparison of protein distribution between the nucleus, the cytoplasm, and the plasma membrane is important for understanding cellular processes and, in particular, signal transduction, where cascades generated at the cell surface regulate functions in other cellular compartments, such as the nucleus. Yet, many commonly used methods fail to effectively separate the plasma membrane and the cytoskeleton from the nucleus, and the cytosol from the nucleosol. This problem has led to confounding results in the study of signaling pathways due to incorrect assignment of cellular localization to signaling molecules and presents challenges in the biochemical study of soluble proteins that shuttle between the cytoplasm and the nucleus. We present a simple method, based on partial membrane permeabilization with detergent followed by density gradient centrifugation, that provides rapid separation of cytosolic, nucleosolic, nuclear insoluble, and membrane components in various mammalian cell lines.
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Affiliation(s)
- Xiaoyong Liu
- Department of Biology, McGill University, 1205 Dr. Penfield Avenue, Montreal, Quebec H3A 1B1, Canada
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23
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Park S, Yang JS, Shin YE, Park J, Jang SK, Kim S. Protein localization as a principal feature of the etiology and comorbidity of genetic diseases. Mol Syst Biol 2011; 7:494. [PMID: 21613983 PMCID: PMC3130560 DOI: 10.1038/msb.2011.29] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 04/19/2011] [Indexed: 01/14/2023] Open
Abstract
Proteins localized within the same subcellular compartment tend to be functionally associated. This study shows that subcellular localization and network distance between disease-associated proteins provide complementary information explaining patterns of disease comorbidity. A positive correlation was found between subcellular localization of disease-associated protein pairs and measures of comorbidity. A higher comorbidity tendency was found for disease-associated protein pairs that are positioned within a shorter distance in the protein interaction network. The integration of subcellular localization information with protein interaction network sheds light onto the potential molecular connections underlying comorbidity patterns and will help to understand the mechanisms of human disease.
It was shown that the emergence of phenotypically similar diseases are triggered as a result of molecular connections between disease-causing genes (Oti and Brunner, 2007; Zaghloul and Katsanis, 2010). From a genetics, perspective diseases are associated with certain genes (Goh et al, 2007; Feldman et al, 2008), whereas from a proteomics perspective phenotypically similar diseases are connected via biological modules such as protein–protein interactions (PPIs) or molecular pathways (Lage et al, 2007; Jiang et al, 2008; Wu et al, 2008; Linghu et al, 2009; Suthram et al, 2010). These molecular connections between diseases were observed on the population level as well: diseases connected through molecular connections such as shared genes, PPIs, and metabolic pathways tend to show elevated comorbidity (Rzhetsky et al, 2007; Lee et al, 2008; Zhernakova et al, 2009; Park et al, 2009a, 2009b). While these findings constitute a step toward improving our understanding of the mechanism of disease progression, there are still many more molecule-level connections between disease pairs that need to be explored in order to establish a firmer comorbidity association. Subcellular localization provides spatial information of proteins in the cell; proteins target subcellular localizations to interact with appropriate partners and form functional complexes in signaling pathways and metabolic processes (Au et al, 2007). Abnormal protein localizations are known to lead to the loss of functional effects in diseases (Luheshi et al, 2008; Laurila and Vihinen, 2009). For example, mis-localizations of nuclear/cytoplasmic transport have been detected in many types of carcinoma cells (Kau et al, 2004). A proper identification of protein subcellular localization can hence be useful in discovering disease-associated proteins (Giallourakis et al, 2005; Calvo and Mootha, 2010). With this understanding, we postulate that disease-associated proteins connected by subcellular localizations could also explain the phenotypic similarities between diseases. Furthermore, such connections may also couple to disease progressions that contribute to multiple disease manifestation, that is, comorbidity. Protein subcellular localization has been extensively studied through various methods to determine a variety of protein functions. To the best of our knowledge, the connection between diseases and subcellular localizations are yet to be studied systematically. To resolve this we constructed, for the first time, a human Disease-associated Protein and subcellular Localization (DPL) matrix (top panel in Box 1). Our DPL matrix provides the ‘cellular localization map of diseases' that represents the spatial index of diseases in the cell. We found that each disease shows unique characteristics of subcellular localization profile in the DPL matrix. We were interested in determining whether subsets of 1284 human diseases exhibit distinct enrichment profiles across subcellular localizations. We calculated pairwise correlations and performed a hierarchical clustering of the enrichments of the 1284 diseases across 10 different subcellular localizations. Our DPL matrix revealed that 778 diseases (∼62%, P=1.40 × 10−3) are enriched in a single localization and 273 diseases (∼21%, P=3.45 × 10−3) are enriched in dual localizations. In the DPL matrix, certain disease-associated proteins are likely to be found in membrane-bounded organelles such as mitochondria, lysosome, and peroxisome, indicating that the mutations of proteins localized to these compartments are connected to the pathophysiological conditions of those organelles. Meanwhile, certain disease-associated proteins in the DPL matrix are enriched in dual localizations, such as extracellular/plasma membrane or endoplasmic reticulum/Golgi. Although these two pairs of subcellular localizations appear to be distinct compartments at first, they are functionally related compartments in close proximity during protein translocation process in the cell, and thus are likely to share interacting protein partners (Gandhi et al, 2006). Comorbidity represents the co-occurrence of multiple diseases in the same individual (Lee et al, 2008; Hidalgo et al, 2009; Park et al, 2009a). Many comorbid disease pairs have been shown to share common genes in the human disease network. For example, Diabetes and Alzheimer's disease share a risk factor in angiotensin I converting enzyme, and frequently occur together in an individual. In such instances, comorbidity can be partially attributed to the disease connections on the molecular level. To explore the impact of protein subcellular localization on comorbidity, we hypothesized that certain disease pairs could also be connected via subcellular localization by the molecular connections between the disease-associated proteins (bottom panel in Box 1). We found a positive correlation between subcellular localization similarity and relative risk (Figure 3B, Pearson's correlation coefficient between relative risk and subcellular localization similarity=0.81, P=2.96 × 10−5). The subcellular localization similarity represents the correlation of subcellular localization profiles between disease pairs. To our surprise, when we compared the relative risk of disease pairs linked via various molecular connections, we found that disease pairs connected by subcellular localization showed a near three-fold higher comorbidity tendency (with link distances equal to 2 or 3) when compared with random pairs (Figure 3E). We then assessed quantitatively the impact of network distances and subcellular localizations on the comorbidity tendency of disease pairs. We expected the proteins associated with comorbid disease pairs to be located closely in the protein interaction network via fewer links compared with random disease pairs. Indeed, a higher comorbidity tendency was found when two disease-associated proteins were positioned within a shorter distance (gray plots in Figure 3F). Moreover, when subcellular localization information was combined with small network distances, the comorbidity tendency increased dramatically (orange plots in Figure 3F). It suggests that subcellular localization and close network distances, two conceptually distinct molecular connections, contributed synergistically to the comorbidity tendency. Disease progression is not restricted to the mutation of disease-causing genes, but also affected by molecular connections in ‘disease modules,' resulting in comorbidity (Fraser, 2006; Lee et al, 2008). In this study, for the first time we applied subcellular localization information to elucidate the molecular connections between comorbid diseases. We believe that, based on our finding, our approach helps to define the boundaries of ‘disease modules.' Taken together, integration of diverse molecular connections should improve the molecular level understanding of hitherto unexplained comorbid disease pairs and help us in expanding the scope of our knowledge of the mechanism of human disease progression. Proteins targeting the same subcellular localization tend to participate in mutual protein–protein interactions (PPIs) and are often functionally associated. Here, we investigated the relationship between disease-associated proteins and their subcellular localizations, based on the assumption that protein pairs associated with phenotypically similar diseases are more likely to be connected via subcellular localization. The spatial constraints from subcellular localization significantly strengthened the disease associations of the proteins connected by subcellular localizations. In particular, certain disease types were more prevalent in specific subcellular localizations. We analyzed the enrichment of disease phenotypes within subcellular localizations, and found that there exists a significant correlation between disease classes and subcellular localizations. Furthermore, we found that two diseases displayed high comorbidity when disease-associated proteins were connected via subcellular localization. We newly explained 7584 disease pairs by using the context of protein subcellular localization, which had not been identified using shared genes or PPIs only. Our result establishes a direct correlation between protein subcellular localization and disease association, and helps to understand the mechanism of human disease progression.
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Affiliation(s)
- Solip Park
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Korea
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24
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Savino R, Casadonte F, Terracciano R. In mesopore protein digestion: a new forthcoming strategy in proteomics. Molecules 2011; 16:5938-62. [PMID: 21765391 PMCID: PMC6264412 DOI: 10.3390/molecules16075938] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 07/07/2011] [Accepted: 07/13/2011] [Indexed: 01/11/2023] Open
Abstract
The conventional protocols for in solution or in gel protein digestion require many steps and long reaction times. The use of trypsin immobilized onto solid supports has recently captured the attention of many research groups, because these systems can speed-up protein digestion significantly. The utilization of new materials such as mesoporous silica as supports, in which enzyme and substrate are dramatically concentrated and confined in the nanospace, offers new opportunities to reduce the complexity of proteomics workflows. An overview of the procedures for in situ proteolysis of single proteins or complex protein mixtures is reported, with a special focus on porous materials used as catalysts. The challenging efforts for designing such systems aimed at mimicking the biochemistry of living cells are reviewed. Potentials, limitations and challenges of this branch of enzyme catalysis, which we indicate as in mesopore digestion, are discussed, in relation to its suitability for high-speed and high-throughput proteomics.
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Affiliation(s)
| | | | - Rosa Terracciano
- Author to whom correspondence should be addressed; ; Tel.: +39-0961-3694085; Fax: +39-0961-3694090
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25
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Organelle proteomics. Methods Mol Biol 2011. [PMID: 21604119 DOI: 10.1007/978-1-61779-148-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Proteomics has significantly contributed to improve our understanding of cell structures and functions in the last decade. The possibility to identify large sets of proteins from minute amount of material, linked with the isolation of cellular organelles using various cell fractionation methods, has provided unique insights into the molecular mechanisms governing cell functions in health and disease. The success of this approach relies on the isolation of highly enriched cell fractions enabling the separation of organelles with minimal contamination by other cellular structures.
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26
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Colucci-D'Amato L, Farina A, Vissers JPC, Chambery A. Quantitative neuroproteomics: classical and novel tools for studying neural differentiation and function. Stem Cell Rev Rep 2011; 7:77-93. [PMID: 20352529 DOI: 10.1007/s12015-010-9136-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mechanisms underlying neural stem cell proliferation, differentiation and maturation play a critical role in the formation and wiring of neuronal connections. This process involves the activation of multiple serial events, which guide the undifferentiated cells to different lineages via distinctive developmental programs, forming neuronal circuits and thus shaping the adult nervous system. Furthermore, alterations within these strictly regulated pathways can lead to severe neurological and psychiatric diseases. In this framework, the investigation of the high dynamic protein expression changes and other factors affecting protein functions, for example post-translational modifications, the alterations of protein interaction networks, is of pivotal importance for the understanding of the molecular mechanisms responsible for cell differentiation. More recently, proteomic studies in neuroscience ("neuroproteomics") are receiving increased interest for the primary understanding of the regulatory networks underlying neuronal differentiation processes. Besides the classical two-dimensional-based proteomic strategies, the emerging platforms for LC-MS shotgun proteomic analysis hold great promise in unraveling the molecular basis of neural stem cell differentiation. In this review, recent advancements in label-free LC-MS quantitative neuroproteomics are highlighted as a new tool for the study of neural differentiation and functions, in comparison to mass spectrometry-based labeling approaches. The more commonly used protein profiling strategies and model systems for the analysis of neural differentiation are also discussed, along with the challenging proteomic approaches aimed to analyze the nervous system-specific organelles, the neural cells secretome and the specific protein interaction networks.
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Affiliation(s)
- Luca Colucci-D'Amato
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
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27
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Abstract
Pseudorabies virus (PRV), a member of the Alphaherpesvirinae, has a complex multilayered extracellular virion that is structurally conserved among other herpesviruses. PRV virions contain a double-stranded DNA genome within a proteinaceous capsid surrounded by the tegument, a layer of viral and cellular proteins. The envelope layer, which encloses the capsid and tegument, contains viral transmembrane proteins anchored in a phospholipid bilayer. The viral and host proteins contained within virions execute important functions during viral spread and pathogenesis, but a detailed understanding of the composition of PRV virions has been lacking. In this report, we present the first comprehensive proteomic characterization of purified PRV virions by mass spectrometry using two complementary approaches. To exclude proteins present in the extracellular medium that may nonspecifically associate with virions, we also analyzed virions treated with proteinase K and samples prepared from mock-infected cells. Overall, we identified 47 viral proteins associated with PRV virions, 40 of which were previously localized to the capsid, tegument, and envelope layers using traditional biochemical approaches. Additionally, we identified seven viral proteins that were previously undetected in virions, including pUL8, pUL20, pUL32, pUL40 (RR2), pUL42, pUL50 (dUTPase), and Rsp40/ICP22. Furthermore, although we did not enrich for posttranslational modifications, we detected phosphorylation of four virion proteins: pUL26, pUL36, pUL46, and pUL48. Finally, we identified 48 host proteins associated with PRV virions, many of which have known functions in important cellular pathways such as intracellular signaling, mRNA translation and processing, cytoskeletal dynamics, and membrane organization. This analysis extends previous work aimed at determining the composition of herpesvirus virions and provides novel insights critical for understanding the mechanisms underlying PRV entry, assembly, egress, spread, and pathogenesis.
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28
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Groen AJ, Lilley KS. Proteomics of total membranes and subcellular membranes. Expert Rev Proteomics 2011; 7:867-78. [PMID: 21142888 DOI: 10.1586/epr.10.85] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Membrane proteins are key molecules in the cell and are important targets for drug development. Much effort has, therefore, been directed towards research of this group of proteins, but their hydrophobic nature can make working with them challenging. Here we discuss methodologies used in the study of the membrane proteome, specifically discussing approaches that circumvent technical issues specific to the membrane. In addition, we review several techniques used for visualization, qualification, quantitation and localization of membrane proteins. The combination of the techniques we describe holds great promise to allow full characterization of the membrane proteome and to map the dynamic changes within it essential for cellular function.
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Affiliation(s)
- Arnoud J Groen
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK
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29
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Li Q, Jagannath C, Rao PK, Singh CR, Lostumbo G. Analysis of phagosomal proteomes: from latex-bead to bacterial phagosomes. Proteomics 2011; 10:4098-116. [PMID: 21080496 DOI: 10.1002/pmic.201000210] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phagosomal proteome characterization has contributed significantly to the understanding of host-pathogen interaction and the mechanism of infectious diseases caused by intracellular bacteria. The latex bead-containing phagosome has been widely used as a model system to study phagosomal proteomes at a global level. In contrast, the study of bacteria-containing phagosomes at a similar level has just begun. A number of intracellular microbial species are studied for their proteomes during the invasion of a host, providing insight into their metabolic adaptation in host cells and interaction with host-cell antimicrobial environments. In this review, we attempt to summarize the most recent advancements in the proteomic study of microbial phagosomes, especially those originating from mouse or human cells. We also briefly describe the proteomics of latex bead-containing phagosomes because they are often used as model phagosomes for study. We provide descriptions on major biological and technological components in phagosomal proteome studies. We also discuss the role of phagosomal proteome study in the broader horizon of systems biology and the technological challenges in phagosomal proteome characterization.
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Affiliation(s)
- Qingbo Li
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, USA.
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Kaur N, Hu J. Defining the plant peroxisomal proteome: from Arabidopsis to rice. FRONTIERS IN PLANT SCIENCE 2011; 2:103. [PMID: 22645559 PMCID: PMC3355810 DOI: 10.3389/fpls.2011.00103] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 12/08/2011] [Indexed: 05/08/2023]
Abstract
Peroxisomes are small subcellular organelles mediating a multitude of processes in plants. Proteomics studies over the last several years have yielded much needed information on the composition of plant peroxisomes. In this review, the status of peroxisome proteomics studies in Arabidopsis and other plant species and the cumulative advances made through these studies are summarized. A reference Arabidopsis peroxisome proteome is generated, and some unique aspects of Arabidopsis peroxisomes that were uncovered through proteomics studies and hint at unanticipated peroxisomal functions are also highlighted. Knowledge gained from Arabidopsis was utilized to compile a tentative list of peroxisome proteins for the model monocot plant, rice. Differences in the peroxisomal proteome between these two model plants were drawn, and novel facets in rice were expounded upon. Finally, we discuss about the current limitations of experimental proteomics in decoding the complete and dynamic makeup of peroxisomes, and complementary and integrated approaches that would be beneficial to defining the peroxisomal metabolic and regulatory roadmaps. The synteny of genomes in the grass family makes rice an ideal model to study peroxisomes in cereal crops, in which these organelles have received much less attention, with the ultimate goal to improve crop yield.
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Affiliation(s)
- Navneet Kaur
- MSU-DOE Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, USA
| | - Jianping Hu
- MSU-DOE Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, USA
- Plant Biology Department, Michigan State UniversityEast Lansing, MI, USA
- *Correspondence: Jianping Hu, MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA. e-mail:
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Gatto L, Vizcaíno JA, Hermjakob H, Huber W, Lilley KS. Organelle proteomics experimental designs and analysis. Proteomics 2010; 10:3957-69. [DOI: 10.1002/pmic.201000244] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Casadonte F, Pasqua L, Savino R, Terracciano R. Smart Trypsin Adsorption into N-(2-Aminoethyl)-3-aminopropyl-Modified Mesoporous Silica for Ultra Fast Protein Digestion. Chemistry 2010; 16:8998-9001. [DOI: 10.1002/chem.201000120] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Bilodeau N, Fiset A, Boulanger MC, Bhardwaj S, Winstall E, Lavoie JN, Faure RL. Proteomic analysis of Src family kinases signaling complexes in Golgi/endosomal fractions using a site-selective anti-phosphotyrosine antibody: identification of LRP1-insulin receptor complexes. J Proteome Res 2010; 9:708-17. [PMID: 19947650 DOI: 10.1021/pr900481b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A role for Src Family Kinases (SFKs) in the dynamics of endocytic and secretory pathways has previously been reported. Identification of low-abundance compartmentalized complexes still remains challenging, highlighting the need for novel tools. Here we describe analysis of SFK-signaling complexes of hepatic Golgi/endosomes (G/E) fractions by sequential affinity enrichment of proteins. Mouse G/E permeabilized membranes were first validated in terms of electron microscopy, 1-D electrophoresis (1-DE), insulin-mediated endocytosis and protein content. With the use of quantitative N-terminal labeling of tryptic peptides (iTRAQ), 1-DE and IEF tryptic peptides separation methods, a total of 666 proteins were identified, including the SFK Lyn. Following insulin injection, a series of proteins were recognized by an anti-phosphotyrosine antibody (alpha P42-2) raised against the residue most frequently phosphorylated by SFK on the adenoviral protein E4orf4 and that cross-reacts with endosomal SFK targets. By using affinity chromatography coupled with mass spectrometry, we identified 16 proteins classified as (1) recycling receptors, (2) vesicular trafficking proteins, (3) actin network proteins, (4) metabolism proteins, or (5) signaling proteins. One of these proteins, low density lipoprotein-related protein 1 (LRP1), which is a known SFK substrate, was found to associate with the internalized insulin receptor (IR), suggesting the presence of a co-internalization process. The identification of these proteomes should, thus, contribute to a better understanding of the molecular mechanisms that regulate trafficking events and insulin clearance.
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Cui Z, Hou J, Chen X, Li J, Xie Z, Xue P, Cai T, Wu P, Xu T, Yang F. The Profile of Mitochondrial Proteins and Their Phosphorylation Signaling Network in INS-1 β Cells. J Proteome Res 2010; 9:2898-908. [DOI: 10.1021/pr100139z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ziyou Cui
- Laborotary of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, Tianjin Key Laboratory for Biomarkers of Occupational and Environmental Hazard, Medical College of CAPF, Tianjin 300162, China, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, and Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junjie Hou
- Laborotary of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, Tianjin Key Laboratory for Biomarkers of Occupational and Environmental Hazard, Medical College of CAPF, Tianjin 300162, China, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, and Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiulan Chen
- Laborotary of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, Tianjin Key Laboratory for Biomarkers of Occupational and Environmental Hazard, Medical College of CAPF, Tianjin 300162, China, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, and Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Li
- Laborotary of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, Tianjin Key Laboratory for Biomarkers of Occupational and Environmental Hazard, Medical College of CAPF, Tianjin 300162, China, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, and Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhensheng Xie
- Laborotary of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, Tianjin Key Laboratory for Biomarkers of Occupational and Environmental Hazard, Medical College of CAPF, Tianjin 300162, China, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, and Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Xue
- Laborotary of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, Tianjin Key Laboratory for Biomarkers of Occupational and Environmental Hazard, Medical College of CAPF, Tianjin 300162, China, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, and Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tanxi Cai
- Laborotary of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, Tianjin Key Laboratory for Biomarkers of Occupational and Environmental Hazard, Medical College of CAPF, Tianjin 300162, China, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, and Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Wu
- Laborotary of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, Tianjin Key Laboratory for Biomarkers of Occupational and Environmental Hazard, Medical College of CAPF, Tianjin 300162, China, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, and Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Xu
- Laborotary of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, Tianjin Key Laboratory for Biomarkers of Occupational and Environmental Hazard, Medical College of CAPF, Tianjin 300162, China, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, and Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuquan Yang
- Laborotary of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, Tianjin Key Laboratory for Biomarkers of Occupational and Environmental Hazard, Medical College of CAPF, Tianjin 300162, China, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, and Graduate University of Chinese Academy of Sciences, Beijing 100049, China
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Qattan AT, Mulvey C, Crawford M, Natale DA, Godovac-Zimmermann J. Quantitative organelle proteomics of MCF-7 breast cancer cells reveals multiple subcellular locations for proteins in cellular functional processes. J Proteome Res 2010; 9:495-508. [PMID: 19911851 PMCID: PMC4261601 DOI: 10.1021/pr9008332] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We have combined sucrose density gradient subcellular fractionation with quantitative, tandem-mass-spectrometry-based shotgun proteomics to investigate spatial distributions of proteins in MCF-7 breast cancer cells. Emphasis was placed on four major organellar compartments: cytosol, plasma membrane, endoplasmic reticulum, and mitochondrion. Two-thousand one-hundred eighty-four proteins were securely identified. Four-hundred eighty-one proteins (22.0% of total proteins identified) were found in unique sucrose gradient fractions, suggesting they may have unique subcellular locations. 454 proteins (20.8%) were found to be ubiquitously distributed. The remaining 1249 proteins (57.2%) were consistent with intermediate distribution over multiple, but not all, subcellular locations. Ninety-four proteins implicated in breast cancer and 478 other proteins which share the same five major cellular biological processes with a majority of the breast cancer proteins were observed in 334 and 1223 subcellular locations, respectively. The data obtained is used to evaluate the possibility of defining more exact sets of subcellular organelles, the completeness of current descriptions of spatial distribution of cellular proteins, the importance of multiple subcellular locations for proteins in functional processes, the subcellular distribution of proteins related to breast cancer, and the possibility of using these methods for dynamic spatio/temporal studies of function/regulation in MCF-7 breast cancer cells.
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Affiliation(s)
- Amal T. Qattan
- Division of Medicine, University College London, 5 University Street, London WC1E 6JF, United Kingdom
| | - Claire Mulvey
- Division of Medicine, University College London, 5 University Street, London WC1E 6JF, United Kingdom
| | - Mark Crawford
- Division of Medicine, University College London, 5 University Street, London WC1E 6JF, United Kingdom
| | - Darren A. Natale
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven Street, NW, Washington, D.C. 20007
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Katoh Y, Ritter B, Gaffry T, Blondeau F, Höning S, McPherson PS. The clavesin family, neuron-specific lipid- and clathrin-binding Sec14 proteins regulating lysosomal morphology. J Biol Chem 2009; 284:27646-54. [PMID: 19651769 PMCID: PMC2785693 DOI: 10.1074/jbc.m109.034884] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 07/20/2009] [Indexed: 11/06/2022] Open
Abstract
Clathrin-coated vesicles (CCVs) originating from the trans-Golgi network (TGN) provide a major transport pathway from the secretory system to endosomes/lysosomes. Herein we describe paralogous Sec14 domain-bearing proteins, clavesin 1/CRALBPL and clavesin 2, identified through a proteomic analysis of CCVs. Clavesins are enriched on CCVs and form a complex with clathrin heavy chain (CHC) and adaptor protein-1, major coat components of TGN-derived CCVs. The proteins co-localize with markers of endosomes and the TGN as well as with CHC and adaptor protein-1. A membrane mimic assay using the Sec14 domain of clavesin 1 reveals phosphatidylinositol 3,5-bisphosphate as a specific lipid partner. Phosphatidylinositol 3,5-bisphosphate is localized to late endosomes/lysosomes, and interestingly, isoform-specific knockdown of clavesins in neurons using lentiviral delivery of interfering RNA leads to enlargement of a lysosome-associated membrane protein 1-positive membrane compartment with no obvious influence on the CCV machinery at the TGN. Since clavesins are expressed exclusively in neurons, this new protein family appears to provide a unique neuron-specific regulation of late endosome/lysosome morphology.
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Affiliation(s)
- Yohei Katoh
- From the Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada and
| | - Brigitte Ritter
- From the Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada and
| | - Thomas Gaffry
- the Institute of Biochemistry I and Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Francois Blondeau
- From the Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada and
| | - Stefan Höning
- the Institute of Biochemistry I and Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Peter S. McPherson
- From the Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada and
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39
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Simpson JC. Screening the secretion machinery: High throughput imaging approaches to elucidate the secretory pathway. Semin Cell Dev Biol 2009; 20:903-9. [DOI: 10.1016/j.semcdb.2009.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 07/08/2009] [Accepted: 07/28/2009] [Indexed: 10/20/2022]
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40
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Towards understanding epithelial–mesenchymal transition: A proteomics perspective. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1325-31. [DOI: 10.1016/j.bbapap.2009.05.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Accepted: 05/05/2009] [Indexed: 11/19/2022]
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41
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Wilkins MR. Hares and tortoises: the high- versus low-throughput proteomic race. Electrophoresis 2009; 30 Suppl 1:S150-5. [PMID: 19441020 DOI: 10.1002/elps.200900175] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The analysis of the proteome can be undertaken with parallel, high-throughput techniques or those that analyze proteins in a serial, one-at-a-time manner. The former include 2-D gels and shotgun MS/MS; the latter includes libraries containing fusion proteins (GST, green fluorescent protein, TAP-tag and others) that are engineered onto each protein in a proteome and then studied one by one. In this review, we explore the progress that these scientifically contrasting paradigms have made in measuring protein abundance, half-life, post-translational modifications, localization in cells and tissues and in protein membership of complexes, pathways and networks. We find that our understanding of the yeast proteome has been furthered more substantially by the slower "tortoise techniques" than the "high-throughput hares". A number of aspects of the human proteome are also likely to be elucidated most accurately with low-throughput approaches. However, the high-throughput techniques are expected to remain crucial for comparative analyses and most studies of proteome dynamics. This review also briefly explores how electrophoretic separations can continue to support the field of proteomics.
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Affiliation(s)
- Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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42
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Mayer U, Küller A, Daiber PC, Neudorf I, Warnken U, Schnölzer M, Frings S, Möhrlen F. The proteome of rat olfactory sensory cilia. Proteomics 2009; 9:322-34. [PMID: 19086097 DOI: 10.1002/pmic.200800149] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Olfactory sensory neurons expose to the inhaled air chemosensory cilia which bind odorants and operate as transduction organelles. Odorant receptors in the ciliary membrane activate a transduction cascade which uses cAMP and Ca(2+) for sensory signaling in the ciliary lumen. Although the canonical transduction pathway is well established, molecular components for more complex aspects of sensory transduction, like adaptation, regulation, and termination of the receptor response have not been systematically identified. Moreover, open questions in olfactory physiology include how the cilia exchange solutes with the surrounding mucus, assemble their highly polarized set of proteins, and cope with noxious substances in the ambient air. A specific ciliary proteome would promote research efforts in all of these fields. We have improved a method to detach cilia from rat olfactory sensory neurons and have isolated a preparation specifically enriched in ciliary membrane proteins. Using LC-ESI-MS/MS analysis, we identified 377 proteins which constitute the olfactory cilia proteome. These proteins represent a comprehensive data set for olfactory research since more than 80% can be attributed to the characteristic functions of olfactory sensory neurons and their cilia: signal processing, protein targeting, neurogenesis, solute transport, and cytoprotection. Organellar proteomics thus yielded decisive information about the diverse physiological functions of a sensory organelle.
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Affiliation(s)
- Ulrich Mayer
- Department of Molecular Physiology, Institute of Zoology, University of Heidelberg, Heidelberg, Germany
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43
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Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S, Nilsson T, Bergeron JJ. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat Methods 2009; 6:423-30. [PMID: 19448641 PMCID: PMC2785450 DOI: 10.1038/nmeth.1333] [Citation(s) in RCA: 256] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Accepted: 04/03/2009] [Indexed: 12/11/2022]
Abstract
We performed a test sample study to try to identify errors leading to irreproducibility, including incompleteness of peptide sampling, in liquid chromatography-mass spectrometry-based proteomics. We distributed an equimolar test sample, comprising 20 highly purified recombinant human proteins, to 27 laboratories. Each protein contained one or more unique tryptic peptides of 1,250 Da to test for ion selection and sampling in the mass spectrometer. Of the 27 labs, members of only 7 labs initially reported all 20 proteins correctly, and members of only 1 lab reported all tryptic peptides of 1,250 Da. Centralized analysis of the raw data, however, revealed that all 20 proteins and most of the 1,250 Da peptides had been detected in all 27 labs. Our centralized analysis determined missed identifications (false negatives), environmental contamination, database matching and curation of protein identifications as sources of problems. Improved search engines and databases are needed for mass spectrometry-based proteomics.
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Affiliation(s)
- Alexander W. Bell
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec, Canada H3A 2B2
| | | | - Catherine E. Au
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec, Canada H3A 2B2
| | - Robert E. Kearney
- Department of Biomedical Engineering, McGill University, Montreal, Canada
| | - Ron Beavis
- Biomedical Research Centre, University of British Columbia, Vancouver, Canada
| | - Salvatore Sechi
- Division Diabetes, Endocrinology, & Metabolic Diseases, NIDDK, National Institutes of Health, 6707 Democracy Blvd., Bethesda, MD 20817
| | - Tommy Nilsson
- The Research Institute of the McGill University Health Centre and the Department of Medicine, McGill University, 687 Pine Avenue West, Montreal, Quebec, Canada H3A 1A1, Canada
| | - John J.M. Bergeron
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec, Canada H3A 2B2
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Gauci S, Veenhoff LM, Heck AJR, Krijgsveld J. Orthogonal Separation Techniques for the Characterization of the Yeast Nuclear Proteome. J Proteome Res 2009; 8:3451-63. [DOI: 10.1021/pr9000948] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sharon Gauci
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Netherlands Proteomics Centre and Centre for Biomedical Genetics, The Netherlands, and Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Liesbeth M. Veenhoff
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Netherlands Proteomics Centre and Centre for Biomedical Genetics, The Netherlands, and Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Netherlands Proteomics Centre and Centre for Biomedical Genetics, The Netherlands, and Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jeroen Krijgsveld
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Netherlands Proteomics Centre and Centre for Biomedical Genetics, The Netherlands, and Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Abstract
Receptors represent an abundant class of integral membrane proteins that transmit information on various types of signals within the cell. Assemblages of receptors and their interacting proteins (receptor complexes) have emerged as important units of signal transduction for various types of receptors including G protein coupled, ligand-gated ion channel, and receptor tyrosine kinase. This review aims to summarize the major approaches and findings of receptor proteomics. Isolation and characterization of receptor complexes from cells has become common using the methods of immunoaffinity-, ligand-, and tag-based chromatography followed by MS for the analysis of enriched receptor preparations. In addition, tools such as stable isotope labeling have contributed to understanding quantitative properties and PTMs to receptors and their interacting proteins. As data from studies on receptor-protein interactions considerably expands, complementary approaches such as bioinformatics and computational biology will undoubtedly play a significant role in defining cellular and network functions for various types of receptor complexes. Findings from receptor proteomics may also shed light on the mechanism of action for pharmacological drugs and can be of value in understanding molecular pathologies of disease states.
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Affiliation(s)
- Nadine Kabbani
- Institut Jacques Monod, CNRS/Universités Paris 6, Paris, France.
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47
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Baginsky S. Plant proteomics: concepts, applications, and novel strategies for data interpretation. MASS SPECTROMETRY REVIEWS 2009; 28:93-120. [PMID: 18618656 DOI: 10.1002/mas.20183] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Proteomics is an essential source of information about biological systems because it generates knowledge about the concentrations, interactions, functions, and catalytic activities of proteins, which are the major structural and functional determinants of cells. In the last few years significant technology development has taken place both at the level of data analysis software and mass spectrometry hardware. Conceptual progress in proteomics has made possible the analysis of entire proteomes at previously unprecedented density and accuracy. New concepts have emerged that comprise quantitative analyses of full proteomes, database-independent protein identification strategies, targeted quantitative proteomics approaches with proteotypic peptides and the systematic analysis of an increasing number of posttranslational modifications at high temporal and spatial resolution. Although plant proteomics is making progress, there are still several analytical challenges that await experimental and conceptual solutions. With this review I will highlight the current status of plant proteomics and put it into the context of the aforementioned conceptual progress in the field, illustrate some of the plant-specific challenges and present my view on the great opportunities for plant systems biology offered by proteomics.
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Affiliation(s)
- Sacha Baginsky
- Institute of Plant Sciences, Swiss Federal Institute of Technology, Universitätsstrasse 2, 8092 Zurich, Switzerland.
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48
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Robinson JM, Vandré DD, Ackerman WE. Placental proteomics: a shortcut to biological insight. Placenta 2008; 30 Suppl A:S83-9. [PMID: 19070895 DOI: 10.1016/j.placenta.2008.10.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 10/27/2008] [Accepted: 10/28/2008] [Indexed: 12/30/2022]
Abstract
Proteomics analysis of biological samples has the potential to identify novel protein expression patterns and/or changes in protein expression patterns in different developmental or disease states. An important component of successful proteomics research, at least in its present form, is to reduce the complexity of the sample if it is derived from cells or tissues. One method to simplify complex tissues is to focus on a specific, highly purified sub-proteome. Using this approach we have developed methods to prepare highly enriched fractions of the apical plasma membrane of the syncytiotrophoblast. Through proteomics analysis of this fraction we have identified over five hundred proteins several of which were previously not known to reside in the syncytiotrophoblast. Herein, we focus on two of these, dysferlin and myoferlin. These proteins, largely known from studies of skeletal muscle, may not have been found in the human placenta were it not for discovery-based proteomics analysis. This new knowledge, acquired through a discovery-driven approach, can now be applied for the generation of hypothesis-based experimentation. Thus discovery-based and hypothesis-based research are complimentary approaches that when coupled together can hasten scientific discoveries.
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Affiliation(s)
- J M Robinson
- Department of Physiology and Cell Biology, Ohio State University, Columbus, OH 43210, USA.
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49
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Gauthier DJ, Lazure C. Complementary methods to assist subcellular fractionation in organellar proteomics. Expert Rev Proteomics 2008; 5:603-17. [PMID: 18761470 DOI: 10.1586/14789450.5.4.603] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Organellar proteomics aims to describe the full complement of proteins of subcellular structures and organelles. When compared with whole-cell or whole-tissue proteomes, the more focused results from subcellular proteomic studies have yielded relatively simpler datasets from which biologically relevant information can be more easily extracted. In every proteomic study, the quality and purity of the biological sample to be investigated is of the utmost importance for a successful analysis. In organellar proteomics, one of the most crucial steps in sample preparation is the initial subcellular fractionation procedure by which the enriched preparation of the sought-after organelle is obtained. In nearly all available organellar proteomic studies, the method of choice relies on one or several rounds of density-based gradient centrifugation. Although this method has been recognized for decades as yielding relatively pure preparations of organelles, recent technological advances in protein separation and identification can now reveal even minute amounts of contamination, which in turn can greatly complicate data interpretation. The scope of this review focuses on recently published innovative complementary or alternative methods to perform subcellular fractionation, which can further refine the way in which sample preparation is accomplished in organellar proteomics.
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Affiliation(s)
- Daniel J Gauthier
- Neuropeptides Structure and Metabolism Research Unit, Institut de Recherches Cliniques de Montréal, University of Montréal, 110 Pine Avenue West, Montréal, Québec, Canada H2W 1R7.
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50
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Primary processes in sensory cells: current advances. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2008; 195:1-19. [PMID: 19011871 DOI: 10.1007/s00359-008-0389-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2008] [Revised: 10/25/2008] [Accepted: 10/25/2008] [Indexed: 12/20/2022]
Abstract
In the course of evolution, the strong and unremitting selective pressure on sensory performance has driven the acuity of sensory organs to its physical limits. As a consequence, the study of primary sensory processes illustrates impressively how far a physiological function can be improved if the survival of a species depends on it. Sensory cells that detect single-photons, single molecules, mechanical motions on a nanometer scale, or incredibly small fluctuations of electromagnetic fields have fascinated physiologists for a long time. It is a great challenge to understand the primary sensory processes on a molecular level. This review points out some important recent developments in the search for primary processes in sensory cells that mediate touch perception, hearing, vision, taste, olfaction, as well as the analysis of light polarization and the orientation in the Earth's magnetic field. The data are screened for common transduction strategies and common transduction molecules, an aspect that may be helpful for researchers in the field.
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