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Tholey A, Taylor NL, Heazlewood JL, Bendixen E. We Are Not Alone: The iMOP Initiative and Its Roles in a Biology- and Disease-Driven Human Proteome Project. J Proteome Res 2017; 16:4273-4280. [DOI: 10.1021/acs.jproteome.7b00408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Nicolas L. Taylor
- Australian
Research Council Centre of Excellence in Plant Energy Biology, School
of Molecular Sciences and Institute of Agriculture, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Joshua L. Heazlewood
- School
of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Emøke Bendixen
- Department
of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, 8000 Aarhus, Denmark
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Heazlewood JL, Schrimpf SP, Becher D, Riedel K, Tholey A, Bendixen E. Multi-Organism Proteomes (iMOP): Advancing our Understanding of Human Biology. Proteomics 2016; 15:2885-94. [PMID: 26331910 DOI: 10.1002/pmic.201570153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Joshua L Heazlewood
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria, 3010, Australia.,Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94702, USA
| | - Sabine P Schrimpf
- Institute of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland
| | - Dörte Becher
- Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Greifswald, Germany
| | - Katrin Riedel
- Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Greifswald, Germany
| | - Andreas Tholey
- Systematische Proteomforschung & Bioanalytik, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Emøke Bendixen
- Department of Molecular Biology and Genetics, University of Aarhus, Denmark
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Edison AS, Hall RD, Junot C, Karp PD, Kurland IJ, Mistrik R, Reed LK, Saito K, Salek RM, Steinbeck C, Sumner LW, Viant MR. The Time Is Right to Focus on Model Organism Metabolomes. Metabolites 2016; 6:E8. [PMID: 26891337 PMCID: PMC4812337 DOI: 10.3390/metabo6010008] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/30/2016] [Accepted: 02/02/2016] [Indexed: 11/16/2022] Open
Abstract
Model organisms are an essential component of biological and biomedical research that can be used to study specific biological processes. These organisms are in part selected for facile experimental study. However, just as importantly, intensive study of a small number of model organisms yields important synergies as discoveries in one area of science for a given organism shed light on biological processes in other areas, even for other organisms. Furthermore, the extensive knowledge bases compiled for each model organism enable systems-level understandings of these species, which enhance the overall biological and biomedical knowledge for all organisms, including humans. Building upon extensive genomics research, we argue that the time is now right to focus intensively on model organism metabolomes. We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to relate organism metabolic pathways within the context of evolutionary metabolomics, i.e., phylometabolomics. These efforts should focus on a series of established model organisms in microbial, animal and plant research.
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Affiliation(s)
- Arthur S Edison
- Departments of Genetics and Biochemistry, Complex Carbohydrate Research Center and Institute of Bioinformatics, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA.
| | - Robert D Hall
- Wageningen University & Research Centre, PO Box 16, 6700AA Wageningen, The Netherlands.
| | - Christophe Junot
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, CEA Saclay, Building 136, 91191 Gif-sur-Yvette cedex, France.
| | - Peter D Karp
- Bioinformatics Research Group, SRI International, 333 Ravenswood Avenue AE206, Menlo Park, CA 94025, USA.
| | - Irwin J Kurland
- Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA.
| | | | - Laura K Reed
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA.
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045; Chiba University, Chiba 260-8675, Japan.
| | - Reza M Salek
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Christoph Steinbeck
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Lloyd W Sumner
- University of Missouri, Department of Biochemistry, Columbia, MO 65211, USA.
| | - Mark R Viant
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.
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Cassidy L, Tholey A. Model organism proteomics as a tool for the study of host-microbiome interactions. Proteomics Clin Appl 2014; 8:665-76. [DOI: 10.1002/prca.201300083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 10/25/2013] [Accepted: 12/03/2013] [Indexed: 01/05/2023]
Affiliation(s)
- Liam Cassidy
- Institut für Experimentelle Medizin - AG Systematische Proteomforschung; Christian-Albrechts-Universität zu Kiel; Kiel Germany
| | - Andreas Tholey
- Institut für Experimentelle Medizin - AG Systematische Proteomforschung; Christian-Albrechts-Universität zu Kiel; Kiel Germany
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Tholey A, Treitz C, Kussmann M, Bendixen E, Schrimpf SP, Hengartner MO. Model Organisms Proteomics-From Holobionts to Human Nutrition. Proteomics 2013; 13:2537-41. [DOI: 10.1002/pmic.201370144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Andreas Tholey
- Division of Systematic Proteome Research; Institute for Experimental Medicine; Christian-Albrechts-Universität zu Kiel; Kiel; Germany
| | - Christian Treitz
- Division of Systematic Proteome Research; Institute for Experimental Medicine; Christian-Albrechts-Universität zu Kiel; Kiel; Germany
| | | | - Emöke Bendixen
- Department of Molecular Biology and Genetics; Laboratory of Proteomics and Mass spectrometry; Aarhus University; Arhus; Denmark
| | - Sabine P. Schrimpf
- Institute of Molecular Life Sciences; University of Zurich; Zurich; Switzerland
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Becnel LB, McKenna NJ. Minireview: progress and challenges in proteomics data management, sharing, and integration. Mol Endocrinol 2012; 26:1660-74. [PMID: 22902541 DOI: 10.1210/me.2012-1180] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The proteome represents the identity, expression levels, interacting partners, and posttranslational modifications of proteins expressed within any given cell. Proteomic studies aim to census the quantitative and qualitative factors regulating the biological relationships of proteins acting in concert as functional cellular networks. In the field of endocrinology, proteomics has been of considerable value in determining the function and mechanism of action of endocrine signaling molecules in the cell membrane, cytoplasm, and nucleus and for the discovery of proteins as candidates for clinical biomarkers. The volume of data that can be generated by proteomics methodologies, up to gigabytes of data within a few hours, brings with it its own logistical hurdles and presents significant challenges to realizing the full potential of these datasets. In this minireview, we describe selected current proteomics methodologies and their application in basic and translational endocrinology before focusing on mass spectrometry as a model for current progress and challenges in data analysis, management, sharing, and integration.
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Affiliation(s)
- Lauren B Becnel
- Department of Medicine, Hematology and Oncology, Baylor College of Medicine, 1 Baylor Plaza MS-BCM305, Houston, Texas 77030, USA.
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