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van Gelder CAGH, Altelaar M. Neuroproteomics of the Synapse: Subcellular Quantification of Protein Networks and Signaling Dynamics. Mol Cell Proteomics 2021; 20:100087. [PMID: 33933679 PMCID: PMC8167277 DOI: 10.1016/j.mcpro.2021.100087] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 01/21/2023] Open
Abstract
One of the most fascinating features of the brain is its ability to adapt to its surroundings. Synaptic plasticity, the dynamic mechanism of functional and structural alterations in synaptic strength, is essential for brain functioning and underlies a variety of processes such as learning and memory. Although the molecular mechanisms underlying such rapid plasticity are not fully understood, a consensus exists on the important role of proteins. The study of these neuronal proteins using neuroproteomics has increased rapidly in the last decades, and advancements in MS-based proteomics have broadened our understanding of neuroplasticity exponentially. In this review, we discuss the trends in MS-based neuroproteomics for the study of synaptic protein-protein interactions and protein signaling dynamics, with a focus on sample types, different labeling and enrichment approaches, and data analysis and interpretation. We highlight studies from the last 5 years, with a focus on synapse structure, composition, functioning, or signaling and finally discuss some recent developments that could further advance the field of neuroproteomics.
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Affiliation(s)
- Charlotte A G H van Gelder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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Biological and proteomic studies of Schistosoma mansoni with decreased sensitivity to praziquantel. Comp Immunol Microbiol Infect Dis 2019; 66:101341. [DOI: 10.1016/j.cimid.2019.101341] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/12/2019] [Accepted: 07/26/2019] [Indexed: 12/13/2022]
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dos Santos Júnior ADCM, Ricart CAO, Pontes AH, Fontes W, de Souza AR, Castro MS, de Sousa MV, de Lima BD. Proteome analysis of Phytomonas serpens, a phytoparasite of medical interest. PLoS One 2018; 13:e0204818. [PMID: 30303999 PMCID: PMC6179244 DOI: 10.1371/journal.pone.0204818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 09/15/2018] [Indexed: 02/04/2023] Open
Abstract
The protozoan Phytomonas serpens (class Kinetoplastea) is an important phytoparasite that has gained medical importance due to its similarities to Trypanosoma cruzi, the etiological agent of Chagas disease. The present work describes the first proteome analysis of P. serpens. The parasite was separated into cytosolic and high density organelle fractions, which, together with total cell extract, were subjected to LC-MS/MS analyses. Protein identification was conducted using a comprehensive database composed of genome sequences of other related kinetoplastids. A total of 1,540 protein groups were identified among the three sample fractions. Sequences from Phytomonas sp. in the database allowed the highest number of identifications, with T. cruzi and T. brucei the human pathogens providing the greatest contribution to the identifications. Based on the proteomics data obtained, we proposed a central metabolic map of P. serpens, which includes all enzymes of the citric acid cycle. Data also revealed a new range of proteins possibly responsible for immunological cross-reactivity between P. serpens and T. cruzi.
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Affiliation(s)
- Agenor de Castro Moreira dos Santos Júnior
- Laboratory Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
- Laboratory of Gene Biology, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
| | - Carlos André Ornelas Ricart
- Laboratory Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
| | - Arthur Henriques Pontes
- Laboratory Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
| | - Wagner Fontes
- Laboratory Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
| | - Agnelo Rodrigues de Souza
- Laboratory Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
- Laboratory of Gene Biology, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
| | - Mariana Souza Castro
- Laboratory Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
| | - Marcelo Valle de Sousa
- Laboratory Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
| | - Beatriz Dolabela de Lima
- Laboratory of Gene Biology, Department of Cell Biology, University of Brasília, Brasília, Federal District, Brazil
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Mukilan M, Rajathei DM, Jeyaraj E, Kayalvizhi N, Rajan KE. MiR-132 regulated olfactory bulb proteins linked to olfactory learning in greater short-nosed fruit bat Cynopterus sphinx. Gene 2018; 671:10-20. [PMID: 29859284 DOI: 10.1016/j.gene.2018.05.107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/11/2018] [Accepted: 05/29/2018] [Indexed: 12/21/2022]
Abstract
Earlier, we showed that micro RNA-132 (miR-132) regulate the immediate early genes (IEGs) in the olfactory bulb (OB) of fruit bat Cynopterus sphinx during olfactory learning. This study was designed to examine whether the miR-132 regulate other proteins in OB during olfactory learning. To test this, miR-132 anti-sense oligodeoxynucleotide (AS-ODN) was delivered to the OB and then trained to novel odor. The 2-dimensional gel electrophoresis analysis showed that inhibition of miR-132 altered olfactory training induced expression of 321 proteins. Further, liquid chromatography-mass spectrometry (LC-MS/MS) analysis reveals the identity of differently expressed proteins such as phosphoribosyl transferase domain containing protein (PRTFDC 1), Sorting nexin-8 (SNX8), Creatine kinase B-type (CKB) and Annexin A11 (ANX A11). Among them PRTFDC 1 showing 189 matching peptides with highest sequence coverage (67.0%) and protein-protein interaction analysis showed that PRTFDC 1 is a homolog of hypoxanthine phosphoribosyltransferase-1 (HPRT-1). Subsequent immunohistochemical analysis (IHC) showed that inhibition of miR-132 down-regulated HPRT expression in OB of C. sphinx. In addition, western blot analysis depicts that HPRT, serotonin transporter (SERT), N-methyl-d-asparate (NMDA) receptors (2A,B) were down-regulated, but not altered in OB of non-sense oligodeoxynucleotide (NS-ODN) infused groups. These analyses suggest that miR-132 regulates the process of olfactory learning and memory formation through SERT and NMDA receptors signalling, which is possibly associated with the PRTFDC1-HPRT interaction.
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Affiliation(s)
- Murugan Mukilan
- Behavioural Neuroscience Laboratory, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India
| | - David Mary Rajathei
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India
| | - Edwin Jeyaraj
- Behavioural Neuroscience Laboratory, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India
| | | | - Koilmani Emmanuvel Rajan
- Behavioural Neuroscience Laboratory, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India.
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MALDI imaging: beyond classic diagnosis. BOLETIN MEDICO DEL HOSPITAL INFANTIL DE MEXICO 2017; 74:212-218. [PMID: 29382489 DOI: 10.1016/j.bmhimx.2017.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/21/2017] [Accepted: 03/28/2017] [Indexed: 02/04/2023] Open
Abstract
Mass spectrometry has been the focus of technology development and application for imaging for several decades. Imaging mass spectrometry using matrix-assisted laser desorption ionization is a new and effective tool for molecular studies of complex biological samples such as tissue sections. As histological features remain intact throughout the analysis of a section, distribution maps of multiple analytes can be correlated with histological and clinical features. Spatial molecular arrangements can be assessed without the need for target-specific reagents, allowing the discovery of diagnostic and prognostic markers of different cancer types and enabling the determination of effective therapies.
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Baucum AJ. Proteomic Analysis of Postsynaptic Protein Complexes Underlying Neuronal Plasticity. ACS Chem Neurosci 2017; 8:689-701. [PMID: 28211672 DOI: 10.1021/acschemneuro.7b00008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Normal neuronal communication and synaptic plasticity at glutamatergic synapses requires dynamic regulation of postsynaptic molecules. Protein expression and protein post-translational modifications regulate protein interactions that underlie this organization. In this Review, we highlight data obtained over the last 20 years that have used qualitative and quantitative proteomics-based approaches to identify postsynaptic protein complexes. Herein, we describe how these proteomics studies have helped lay the foundation for understanding synaptic physiology and perturbations in synaptic signaling observed in different pathologies. We also describe emerging technologies that can be useful in these analyses. We focus on protein complexes associated with the highly abundant and functionally critical proteins: calcium/calmodulin-dependent protein kinase II, the N-methyl-d-aspartate, and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid glutamate receptors, and postsynaptic density protein of 95 kDa.
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Affiliation(s)
- Anthony J. Baucum
- Department of Biology, Stark Neurosciences
Research Institute, Indiana University-Purdue University Indianapolis, 723 W. Michigan St., Indianapolis, Indiana 46202, United States
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