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Killingbeck EE, Wilburn DB, Merrihew GE, MacCoss MJ, Swanson WJ. Proteomics support the threespine stickleback egg coat as a protective oocyte envelope. Mol Reprod Dev 2021; 88:500-515. [PMID: 34148267 PMCID: PMC8362008 DOI: 10.1002/mrd.23517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 05/20/2021] [Accepted: 05/22/2021] [Indexed: 12/20/2022]
Abstract
Ancestrally marine threespine stickleback fish (Gasterosteus aculeatus) have undergone an adaptive radiation into freshwater environments throughout the Northern Hemisphere, creating an excellent model system for studying molecular adaptation and speciation. Ecological and behavioral factors have been suggested to underlie stickleback reproductive isolation and incipient speciation, but reproductive proteins mediating gamete recognition during fertilization have so far remained unexplored. To begin to investigate the contribution of reproductive proteins to stickleback reproductive isolation, we have characterized the stickleback egg coat proteome. We find that stickleback egg coats are comprised of homologs to the zona pellucida (ZP) proteins ZP1 and ZP3, as in other teleost fish. Our molecular evolutionary analyses indicate that across teleosts, ZP3 but not ZP1 has experienced positive Darwinian selection. Mammalian ZP3 is also rapidly evolving, and surprisingly some residues under selection in stickleback and mammalian ZP3 directly align. Despite broad homology, however, we find differences between mammalian and stickleback ZP proteins with respect to glycosylation, disulfide bonding, and sites of synthesis. Taken together, the changes we observe in stickleback ZP protein architecture suggest that the egg coats of stickleback fish, and perhaps fish more generally, have evolved to fulfill a more protective functional role than their mammalian counterparts.
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Affiliation(s)
- Emily E Killingbeck
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Damien B Wilburn
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Gennifer E Merrihew
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Willie J Swanson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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Biomarkers in major depressive disorder: the role of mass spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:545-60. [PMID: 24952202 DOI: 10.1007/978-3-319-06068-2_27] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Major depressive disorder (MDD) is common. Despite numerous available treatments, many individuals fail to improve clinically. MDD continues to be diagnosed exclusively via behavioral rather than biological methods. Biomarkers-which include measurements of genes, proteins, and patterns of brain activity-may provide an important objective tool for the diagnosis of MDD or in the rational selection of treatments. Proteomic analysis and validation of its results as biomarkers is less explored than other areas of biomarker research in MDD. Mass spectrometry (MS) is a comprehensive, unbiased means of proteomic analysis, which can be complemented by directed protein measurements, such as Western Blotting. Prior studies have focused on MS analysis of several human biomaterials in MDD, including human post-mortem brain, cerebrospinal fluid (CSF), blood components, and urine. Further studies utilizing MS and proteomic analysis in MDD may help solidify and establish biomarkers for use in diagnosis, identification of new treatment targets, and understanding of the disorder. The ultimate goal is the validation of a biomarker or a biomarker signature that facilitates a convenient and inexpensive predictive test for depression treatment response and helps clinicians in the rational selection of next-step treatments.
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Ngounou Wetie AG, Sokolowska I, Woods AG, Roy U, Deinhardt K, Darie CC. Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. Cell Mol Life Sci 2014; 71:205-28. [PMID: 23579629 PMCID: PMC11113707 DOI: 10.1007/s00018-013-1333-1] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 03/25/2013] [Accepted: 03/26/2013] [Indexed: 11/28/2022]
Abstract
Following the sequencing of the human genome and many other organisms, research on protein-coding genes and their functions (functional genomics) has intensified. Subsequently, with the observation that proteins are indeed the molecular effectors of most cellular processes, the discipline of proteomics was born. Clearly, proteins do not function as single entities but rather as a dynamic network of team players that have to communicate. Though genetic (yeast two-hybrid Y2H) and biochemical methods (co-immunoprecipitation Co-IP, affinity purification AP) were the methods of choice at the beginning of the study of protein-protein interactions (PPI), in more recent years there has been a shift towards proteomics-based methods and bioinformatics-based approaches. In this review, we first describe in depth PPIs and we make a strong case as to why unraveling the interactome is the next challenge in the field of proteomics. Furthermore, classical methods of investigation of PPIs and structure-based bioinformatics approaches are presented. The greatest emphasis is placed on proteomic methods, especially native techniques that were recently developed and that have been shown to be reliable. Finally, we point out the limitations of these methods and the need to set up a standard for the validation of PPI experiments.
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Affiliation(s)
- Armand G. Ngounou Wetie
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Izabela Sokolowska
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Alisa G. Woods
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Urmi Roy
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Katrin Deinhardt
- Centre for Biological Sciences, University of Southampton, Life Sciences Building 85, Southampton, SO17 1BJ UK
- Institute for Life Sciences, University of Southampton, Life Sciences Building 85, Southampton, SO17 1BJ UK
| | - Costel C. Darie
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
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The potential of biomarkers in psychiatry: focus on proteomics. J Neural Transm (Vienna) 2013; 122 Suppl 1:S9-18. [DOI: 10.1007/s00702-013-1134-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 12/02/2013] [Indexed: 02/06/2023]
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Ngounou Wetie AG, Sokolowska I, Wormwood K, Beglinger K, Michel TM, Thome J, Darie CC, Woods AG. Mass spectrometry for the detection of potential psychiatric biomarkers. J Mol Psychiatry 2013; 1:8. [PMID: 25408901 PMCID: PMC4223884 DOI: 10.1186/2049-9256-1-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 02/12/2013] [Indexed: 12/20/2022] Open
Abstract
The search for molecules that can act as potential biomarkers is increasing in the scientific community, including in the field of psychiatry. The field of proteomics is evolving and its indispensability for identifying biomarkers is clear. Among proteomic tools, mass spectrometry is the core technique for qualitative and quantitative identification of protein markers. While significant progress has been made in the understanding of biomarkers for neurodegenerative diseases such as Alzheimer's disease, multiple sclerosis and Parkinson's disease, psychiatric disorders have not been as extensively investigated. Recent and successful applications of mass spectrometry-based proteomics in fields such as cardiovascular disease, cancer, infectious diseases and neurodegenerative disorders suggest a similar path for psychiatric disorders. In this brief review, we describe mass spectrometry and its use in psychiatric biomarker research and highlight some of the possible challenges of undertaking this type of work. Further, specific examples of candidate biomarkers are highlighted. A short comparison of proteomic with genomic methods for biomarker discovery research is presented. In summary, mass spectrometry-based techniques may greatly facilitate ongoing efforts to understand molecular mechanisms of psychiatric disorders.
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Affiliation(s)
- Armand G Ngounou Wetie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Izabela Sokolowska
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Kelly Wormwood
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Katherine Beglinger
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Tanja Maria Michel
- Department of Psychiatry, University of Rostock, Rostock, Gehlsheimer Straße 20, D-18147 Germany
| | - Johannes Thome
- Department of Psychiatry, University of Rostock, Rostock, Gehlsheimer Straße 20, D-18147 Germany ; College of Medicine, Swansea University, Singleton Park, Swansea, SA2 8PP UK
| | - Costel C Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Alisa G Woods
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA ; Neuropsychology Clinic and Psychoeducation Services, SUNY Plattsburgh, 101 Broad St, Plattsburgh, 12901 NY USA
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Sokolowska I, Ngounou Wetie AG, Woods AG, Darie CC. Automatic determination of disulfide bridges in proteins. ACTA ACUST UNITED AC 2012; 17:408-16. [PMID: 22885790 DOI: 10.1177/2211068212454737] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Precise determination of disulfide linkages between cysteine (Cys) residues in proteins is essential in the determination of protein structure. Therefore, a reliable automated method for the identification of disulfide bridges can serve as an important tool in the analysis of the tertiary structure of proteins of interest. Here, we describe the current and past methods used to identify disulfide bridges in proteins, with a focus on mass spectrometry (MS)-based methods and a particular emphasis on nanoliquid chromatography-tandem mass spectrometry (nanoLC-MS/MS)-based methods. We also show the development of an easy method based on the separation of disulfide-linked proteins by sodium dodecyl sulfate-polyacrylamide gel electrophoresis under denaturing and nonreducing conditions and selective in-gel digestion of proteins using reducing and nonreducing conditions, followed by analysis of the resulting peptide mixture by nanoACQUITY UPLC coupled to a quadrupole time-of-flight (QTOF) Micro mass spectrometer (nanoLC-MS/MS). Data-dependent analysis (DDA) nanoLC-MS/MS and information-dependent analysis (IDA) nanoLC-MS/MS were used for random and targeted identification of disulfide-linked peptides. Finally, an example of electrospray-MS (ESI-MS) and ESI-MS/MS-based determination of disulfide-linked peptides is shown.
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Sokolowska I, Woods AG, Wagner J, Dorler J, Wormwood K, Thome J, Darie CC. Mass Spectrometry for Proteomics-Based Investigation of Oxidative Stress and Heat Shock Proteins. ACS SYMPOSIUM SERIES 2011. [DOI: 10.1021/bk-2011-1083.ch013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Izabela Sokolowska
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810, U.S.A
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany
| | - Alisa G. Woods
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810, U.S.A
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany
| | - Jessica Wagner
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810, U.S.A
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany
| | - Jeannette Dorler
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810, U.S.A
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany
| | - Kelly Wormwood
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810, U.S.A
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany
| | - Johannes Thome
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810, U.S.A
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany
| | - Costel C. Darie
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810, U.S.A
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany
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