251
|
Abstract
NMDA (N-methyl-D-aspartate) receptors are a subtype of ionotropic glutamate receptor with an important role in the physiology and pathophysiology of central neurons. Inappropriate levels of Ca(2+) influx through the NMDA receptor can contribute to neuronal loss in acute trauma such as ischaemia and traumatic brain injury, as well as certain neurodegenerative diseases such as Huntington's disease. However, normal physiological patterns of NMDA receptor activity can promote neuroprotection against both apoptotic and excitotoxic insults. As a result, NMDA receptor blockade can promote neuronal death outright or render neurons vulnerable to secondary trauma. Thus responses to NMDA receptor activity follow a classical hormetic dose-response curve: both too much and too little can be harmful. There is a growing knowledge of the molecular mechanisms underlying both the neuroprotective and neurodestructive effects of NMDA receptor activity, as well as the factors that determine whether an episode of NMDA receptor activity is harmful or beneficial. It is becoming apparent that oxidative stress plays a role in promoting neuronal death in response to both hyper- and hypo-activity of the NMDA receptor. Increased understanding in this field is leading to the discovery of new therapeutic targets and strategies for excitotoxic disorders, as well as a growing appreciation of the harmful consequences of NMDA receptor blockade.
Collapse
Affiliation(s)
- Giles E Hardingham
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh EH8 9XD, UK
| |
Collapse
|
252
|
The role of DNA copy number variation in schizophrenia. Biol Psychiatry 2009; 66:1005-12. [PMID: 19748074 DOI: 10.1016/j.biopsych.2009.07.027] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 07/21/2009] [Accepted: 07/21/2009] [Indexed: 11/23/2022]
Abstract
Schizophrenia is a major psychiatric disease with strong evidence of genetic risk factors. Recent studies based on genome-wide study of copy number variations (CNVs) have detected novel recurrent submicroscopic copy number changes, including recurrent deletions at 1q21.11, 15q11.3, 15q13.3, and the recurrent CNV at the 2p16.3 neurexin 1 locus. These schizophrenia susceptibility CNV loci demonstrate that schizophrenia is, at least in part, genetic in origin and provide the basis for further investigation of mutations associated with the disease. The studies combined have also established the role of rare and-in sporadic cases-de novo variants in schizophrenia. Furthermore, neuronal-related genes and genetic pathways are starting to emerge from the CNV loci associated with schizophrenia. Here, we review the major findings in the recent literature, which begin to unravel the genetic and biological architecture of this complex human neuropsychiatric disorder.
Collapse
|
253
|
Han MH, Lin C, Meng S, Wang X. Proteomics analysis reveals overlapping functions of clustered protocadherins. Mol Cell Proteomics 2009; 9:71-83. [PMID: 19843561 DOI: 10.1074/mcp.m900343-mcp200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The three tandem-arrayed protocadherin (Pcdh) gene clusters, namely Pcdh-alpha, Pcdh-beta, and Pcdh-gamma, play important roles in the development of the vertebrate central nervous system. To gain insight into the molecular action of PCDHs, we performed a systematic proteomics analysis of PCDH-gamma-associated protein complexes. We identified a list of 154 non-redundant proteins in the PCDH-gamma complexes. This list includes nearly 30 members of clustered Pcdh-alpha, -beta, and -gamma families as core components of the complexes and additionally over 120 putative PCDH-associated proteins. We validated a selected subset of PCDH-gamma-associated proteins using specific antibodies. Analysis of the identities of PCDH-associated proteins showed that the majority of them overlap with the proteomic profile of postsynaptic density preparations. Further analysis of membrane protein complexes revealed that several validated PCDH-gamma-associated proteins exhibit reduced levels in Pcdh-gamma-deficient brain tissues. Therefore, PCDH-gamma s are required for the integrity of the complexes. However, the size of the overall complexes and the abundance of many other proteins remained unchanged, raising a possibility that PCDH-alphas and PCDH-betas might compensate for PCDH-gamma function in complex formation. As a test of this idea, RNA interference knockdown of both PCDH-alphas and PCDH-gamma s showed that PCDHs have redundant functions in regulating neuronal survival in the chicken spinal cord. Taken together, our data provide evidence that clustered PCDHs coexist in large protein complexes and have overlapping functions during vertebrate neural development.
Collapse
Affiliation(s)
- Meng-Hsuan Han
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois 60208, USA
| | | | | | | |
Collapse
|
254
|
Li X, Xie C, Jin Q, Liu M, He Q, Cao R, Lin Y, Li J, Li Y, Chen P, Liang S. Proteomic screen for multiprotein complexes in synaptic plasma membrane from rat hippocampus by blue native gel electrophoresis and tandem mass spectrometry. J Proteome Res 2009; 8:3475-86. [PMID: 19432478 DOI: 10.1021/pr900101d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Neuronal synapses are specialized sites for information exchange between neurons. Many diseases, such as addiction and mood disorders, likely result from altered expression of synaptic proteins, or altered formation of synaptic complexes involved in neurotransmission or neuroplasticity. A detailed description of native multiprotein complexes in synaptic plasma membranes (PM) is therefore essential for understanding biological mechanisms and disease processes. For the first time in this study, two-dimensional Blue Native/SDS-PAGE electrophoresis, combined with tandem mass spectrometry, was used to screen multiprotein complexes in synaptic plasma membranes from rat hippocampus. As a result, 514 unique proteins were identified, of which 36% were integral membrane proteins. In addition, 19 potentially novel and known heterooligomeric multiprotein complexes were found, such as the SNARE and ATPase complexes. A potentially novel protein complex, involving syntaxin, synapsin I and Na+/K+ ATPase alpha-1, was further confirmed by co-immunoprecipitation and immunofluorescence staining. As demonstrated here, Blue Native-PAGE is a powerful tool for the separation of hydrophobic membrane proteins. The combination of Blue Native-PAGE and mass spectrometry could systematically identify multiprotein complexes.
Collapse
Affiliation(s)
- Xuanwen Li
- Key Laboratory of Protein Chemistry and Developmental Biology of Education Committee, College of Life Sciences, Hunan Normal University, Changsha, 410081, PR China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
255
|
Abstract
Understanding the evolutionary origins of behaviour is a central aim in the study of biology and may lead to insights into human disorders. Synaptic transmission is observed in a wide range of invertebrate and vertebrate organisms and underlies their behaviour. Proteomic studies of the molecular components of the highly complex mammalian postsynaptic machinery point to an ancestral molecular machinery in unicellular organisms--the protosynapse--that existed before the evolution of metazoans and neurons, and hence challenges existing views on the origins of the brain. The phylogeny of the molecular components of the synapse provides a new model for studying synapse diversity and complexity, and their implications for brain evolution.
Collapse
|
256
|
Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation. BMC Genomics 2009; 10:419. [PMID: 19737397 PMCID: PMC2759968 DOI: 10.1186/1471-2164-10-419] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 09/08/2009] [Indexed: 01/19/2023] Open
Abstract
Background Synapse formation and the development of neural networks are known to be controlled by a coordinated program of mRNA synthesis. microRNAs are now recognized to be important regulators of mRNA translation and stability in a wide variety of organisms. While specific microRNAs are known to be involved in neural development, the extent to which global microRNA and mRNA profiles are coordinately regulated in neural development is unknown. Results We examined mouse primary neuronal cultures, analyzing microRNA and mRNA expression. Three main developmental patterns of microRNA expression were observed: steady-state levels, up-regulated and down-regulated. Co-expressed microRNAs were found to have related target recognition sites and to be encoded in distinct genomic locations. A number of 43 differentially expressed miRNAs were located in five genomic clusters. Their predicted mRNA targets show reciprocal levels of expression. We identified a set of reciprocally expressed microRNAs that target mRNAs encoding postsynaptic density proteins and high-level steady-state microRNAs that target non-neuronal low-level expressed mRNAs. Conclusion We characterized hundreds of miRNAs in neuronal culture development and identified three major modes of miRNA expression. We predict these miRNAs to regulate reciprocally expressed protein coding genes, including many genes involved in synaptogenesis. The identification of miRNAs that target mRNAs during synaptogenesis indicates a new level of regulation of the synapse.
Collapse
|
257
|
Neuroproteomics: understanding the molecular organization and complexity of the brain. Nat Rev Neurosci 2009; 10:635-46. [DOI: 10.1038/nrn2701] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
258
|
Nabet B, Tsai A, Tobias JW, Carstens RP. Identification of a putative network of actin-associated cytoskeletal proteins in glomerular podocytes defined by co-purified mRNAs. PLoS One 2009; 4:e6491. [PMID: 19652713 PMCID: PMC2714980 DOI: 10.1371/journal.pone.0006491] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 06/25/2009] [Indexed: 11/30/2022] Open
Abstract
The glomerular podocyte is a highly specialized and polarized kidney cell type that contains major processes and foot processes that extend from the cell body. Foot processes from adjacent podocytes form interdigitations with those of adjacent cells, thereby creating an essential intercellular junctional domain of the renal filtration barrier known as the slit diaphragm. Interesting parallels have been drawn between the slit diaphragm and other sites of cell-cell contact by polarized cells. Notably mutations in several genes encoding proteins localized to the foot processes can lead to proteinuria and kidney failure. Mutations in the Wilm's tumor gene (WT1) can also lead to kidney disease and one isoform of WT1, WT1(+KTS), has been proposed to regulate gene expression post-transcriptionally. We originally sought to identify mRNAs associated with WT1(+KTS) through an RNA immunoprecipitation and microarray approach, hypothesizing that the proteins encoded by these mRNAs might be important for podocyte morphology and function. We identified a subset of mRNAs that were remarkably enriched for transcripts encoding actin-binding proteins and other cytoskeletal proteins including several that are localized at or near the slit diaphragm. Interestingly, these mRNAs included those of α-actinin-4 and non-muscle myosin IIA that are mutated in genetic forms of kidney disease. However, isolation of the mRNAs occurred independently of the expression of WT1, suggesting that the identified mRNAs were serendipitously co-purified on the basis of co-association in a common subcellular fraction. Mass spectroscopy revealed that other components of the actin cytoskeleton co-purified with these mRNAs, namely actin, tubulin, and elongation factor 1α. We propose that these mRNAs encode a number of proteins that comprise a highly specialized protein interactome underlying the slit diaphragm. Collectively, these gene products and their interactions may prove to be important for the structural integrity of the actin cytoskeleton in podocytes as well as other polarized cell types.
Collapse
Affiliation(s)
- Behnam Nabet
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | | | | | | |
Collapse
|
259
|
Winden KD, Oldham MC, Mirnics K, Ebert PJ, Swan CH, Levitt P, Rubenstein JL, Horvath S, Geschwind DH. The organization of the transcriptional network in specific neuronal classes. Mol Syst Biol 2009; 5:291. [PMID: 19638972 PMCID: PMC2724976 DOI: 10.1038/msb.2009.46] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2008] [Accepted: 06/09/2009] [Indexed: 01/10/2023] Open
Abstract
Genome-wide expression profiling has aided the understanding of the molecular basis of neuronal diversity, but achieving broad functional insight remains a considerable challenge. Here, we perform the first systems-level analysis of microarray data from single neuronal populations using weighted gene co-expression network analysis to examine how neuronal transcriptome organization relates to neuronal function and diversity. We systematically validate network predictions using published proteomic and genomic data. Several network modules of co-expressed genes correspond to interneuron development programs, in which the hub genes are known to be critical for interneuron specification. Other co-expression modules relate to fundamental cellular functions, such as energy production, firing rate, trafficking, and synapses, suggesting that fundamental aspects of neuronal diversity are produced by quantitative variation in basic metabolic processes. We identify two transcriptionally distinct mitochondrial modules and demonstrate that one corresponds to mitochondria enriched in neuronal processes and synapses, whereas the other represents a population restricted to the soma. Finally, we show that galectin-1 is a new interneuron marker, and we validate network predictions in vivo using Rgs4 and Dlx1/2 knockout mice. These analyses provide a basis for understanding how specific aspects of neuronal phenotypic diversity are organized at the transcriptional level.
Collapse
Affiliation(s)
- Kellen D Winden
- Interdepartmental Program for Neuroscience, University of California Los Angeles, Los Angeles, CA, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
260
|
Proteomics in human Parkinson's disease research. J Proteomics 2009; 73:10-29. [PMID: 19632367 DOI: 10.1016/j.jprot.2009.07.007] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 06/25/2009] [Accepted: 07/08/2009] [Indexed: 11/20/2022]
Abstract
During the last decades, considerable advances in the understanding of specific mechanisms underlying neurodegeneration in Parkinson's disease have been achieved, yet neither definite etiology nor unifying sequence of molecular events has been formally established. Current unmet needs in Parkinson's disease research include exploring new hypotheses regarding disease susceptibility, occurrence and progression, identifying reliable diagnostic, prognostic and therapeutic biomarkers, and translating basic research into appropriate disease-modifying strategies. The most popular view proposes that Parkinson's disease results from the complex interplay between genetic and environmental factors and mechanisms believed to be at work include oxidative stress, mitochondrial dysfunction, excitotoxicity, iron deposition and inflammation. More recently, a plethora of data has accumulated pinpointing an abnormal processing of the neuronal protein alpha-synuclein as a pivotal mechanism leading to aggregation, inclusions formation and degeneration. This protein-oriented scenario logically opens the door to the application of proteomic strategies to this field of research. We here review the current literature on proteomics applied to Parkinson's disease research, with particular emphasis on pathogenesis of sporadic Parkinson's disease in humans. We propose the view that Parkinson's disease may be an acquired or genetically-determined brain proteinopathy involving an abnormal processing of several, rather than individual neuronal proteins, and discuss some pre-analytical and analytical developments in proteomics that may help in verifying this concept.
Collapse
|
261
|
Liao L, McClatchy DB, Yates JR. Shotgun proteomics in neuroscience. Neuron 2009; 63:12-26. [PMID: 19607789 PMCID: PMC2746002 DOI: 10.1016/j.neuron.2009.06.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 06/10/2009] [Accepted: 06/10/2009] [Indexed: 11/27/2022]
Abstract
Mass spectrometry-based proteomics is increasingly used to address basic and clinical questions in biomedical research through studies of differential protein expression, protein-protein interactions, and posttranslational modifications. The complex structural and functional organization of the human brain warrants the application of high-throughput, systematic approaches to understand the functional alterations under normal physiological conditions and the perturbations of neurological diseases. This primer focuses on shotgun-proteomics-based tandem mass spectrometry for the identification of proteins in a complex mixture. It describes the basic concepts of protein differential expression analysis and posttranslational modification analysis and discusses several strategies to improve the coverage of the proteome.
Collapse
Affiliation(s)
- Lujian Liao
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | |
Collapse
|
262
|
Proteomic studies of a single CNS synapse type: the parallel fiber/purkinje cell synapse. PLoS Biol 2009; 7:e83. [PMID: 19402746 PMCID: PMC2672601 DOI: 10.1371/journal.pbio.1000083] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Accepted: 03/02/2009] [Indexed: 01/04/2023] Open
Abstract
Precise neuronal networks underlie normal brain function and require distinct classes of synaptic connections. Although it has been shown that certain individual proteins can localize to different classes of synapses, the biochemical composition of specific synapse types is not known. Here, we have used a combination of genetically engineered mice, affinity purification, and mass spectrometry to profile proteins at parallel fiber/Purkinje cell synapses. We identify approximately 60 candidate postsynaptic proteins that can be classified into 11 functional categories. Proteins involved in phospholipid metabolism and signaling, such as the protein kinase MRCKgamma, are major unrecognized components of this synapse type. We demonstrate that MRCKgamma can modulate maturation of dendritic spines in cultured cortical neurons, and that it is localized specifically to parallel fiber/Purkinje cell synapses in vivo. Our data identify a novel synapse-specific signaling pathway, and provide an approach for detailed investigations of the biochemical complexity of central nervous system synapse types.
Collapse
|
263
|
Jordan BA, Kreutz MR. Nucleocytoplasmic protein shuttling: the direct route in synapse-to-nucleus signaling. Trends Neurosci 2009; 32:392-401. [PMID: 19524307 DOI: 10.1016/j.tins.2009.04.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2008] [Revised: 04/16/2009] [Accepted: 04/24/2009] [Indexed: 02/06/2023]
Abstract
In neurons multiple signaling pathways converge in the nucleus to regulate the expression of genes associated with long-term structural changes of synapto-dendritic input. Of pivotal importance for this type of transcriptional regulation is synapse-to-nucleus communication. Several studies suggest that the nuclear transport of proteins from synapses is involved in this signaling process, including evidence that synapses contain proteins with nuclear localization sequences and components of the nuclear import machinery. Here, we review the evidence for synapse-to-nucleus signaling by means of retrograde transport of proteins from distal processes. We discuss the mechanisms involved in their translocation and their role in the control of nuclear gene expression. Finally, we summarize the current thinking regarding the functional implications of nuclear signaling and address open questions in this evolving area of neuroscience.
Collapse
Affiliation(s)
- Bryen A Jordan
- Albert Einstein College of Medicine, Dominick P. Purpura Department of Neuroscience, Bronx, NY 10461, USA
| | | |
Collapse
|
264
|
Webber C, Hehir-Kwa JY, Nguyen DQ, de Vries BBA, Veltman JA, Ponting CP. Forging links between human mental retardation-associated CNVs and mouse gene knockout models. PLoS Genet 2009; 5:e1000531. [PMID: 19557186 PMCID: PMC2694283 DOI: 10.1371/journal.pgen.1000531] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 05/22/2009] [Indexed: 12/20/2022] Open
Abstract
Rare copy number variants (CNVs) are frequently associated with common neurological disorders such as mental retardation (MR; learning disability), autism, and schizophrenia. CNV screening in clinical practice is limited because pathological CNVs cannot be distinguished routinely from benign CNVs, and because genes underlying patients' phenotypes remain largely unknown. Here, we present a novel, statistically robust approach that forges links between 148 MR-associated CNVs and phenotypes from approximately 5,000 mouse gene knockout experiments. These CNVs were found to be significantly enriched in two classes of genes, those whose mouse orthologues, when disrupted, result in either abnormal axon or dopaminergic neuron morphologies. Additional enrichments highlighted correspondences between relevant mouse phenotypes and secondary presentations such as brain abnormality, cleft palate, and seizures. The strength of these phenotype enrichments (>100% increases) greatly exceeded molecular annotations (<30% increases) and allowed the identification of 78 genes that may contribute to MR and associated phenotypes. This study is the first to demonstrate how the power of mouse knockout data can be systematically exploited to better understand genetically heterogeneous neurological disorders.
Collapse
Affiliation(s)
- Caleb Webber
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Jayne Y. Hehir-Kwa
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Duc-Quang Nguyen
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Bert B. A. de Vries
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Joris A. Veltman
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Chris P. Ponting
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
265
|
Abul-Husn NS, Bushlin I, Morón JA, Jenkins SL, Dolios G, Wang R, Iyengar R, Ma'ayan A, Devi LA. Systems approach to explore components and interactions in the presynapse. Proteomics 2009; 9:3303-15. [PMID: 19562802 PMCID: PMC2766278 DOI: 10.1002/pmic.200800767] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Accepted: 03/11/2009] [Indexed: 12/18/2022]
Abstract
The application of proteomic techniques to neuroscientific research provides an opportunity for a greater understanding of nervous system structure and function. As increasing amounts of neuroproteomic data become available, it is necessary to formulate methods to integrate these data in a meaningful way to obtain a more comprehensive picture of neuronal subcompartments. Furthermore, computational methods can be used to make biologically relevant predictions from large proteomic data sets. Here, we applied an integrated proteomics and systems biology approach to characterize the presynaptic (PRE) nerve terminal. For this, we carried out proteomic analyses of presynaptically enriched fractions, and generated a PRE literature-based protein-protein interaction network. We combined these with other proteomic analyses to generate a core list of 117 PRE proteins, and used graph theory-inspired algorithms to predict 92 additional components and a PRE complex containing 17 proteins. Some of these predictions were validated experimentally, indicating that the computational analyses can identify novel proteins and complexes in a subcellular compartment. We conclude that the combination of techniques (proteomics, data integration, and computational analyses) used in this study are useful in obtaining a comprehensive understanding of functional components, especially low-abundance entities and/or interactions in the PRE nerve terminal.
Collapse
Affiliation(s)
- Noura S. Abul-Husn
- Department of Pharmacology & Systems Therapeutics, Mount Sinai School of Medicine One Gustave L. Levy Place, New York, NY 10029
| | - Ittai Bushlin
- Department of Pharmacology & Systems Therapeutics, Mount Sinai School of Medicine One Gustave L. Levy Place, New York, NY 10029
| | - José A. Morón
- Department of Pharmacology & Systems Therapeutics, Mount Sinai School of Medicine One Gustave L. Levy Place, New York, NY 10029
| | - Sherry L. Jenkins
- Department of Pharmacology & Systems Therapeutics, Mount Sinai School of Medicine One Gustave L. Levy Place, New York, NY 10029
| | - Georgia Dolios
- Department of Genetics & Genomic Sciences, Mount Sinai School of Medicine One Gustave L. Levy Place, New York, NY 10029
| | - Rong Wang
- Department of Genetics & Genomic Sciences, Mount Sinai School of Medicine One Gustave L. Levy Place, New York, NY 10029
| | - Ravi Iyengar
- Department of Pharmacology & Systems Therapeutics, Mount Sinai School of Medicine One Gustave L. Levy Place, New York, NY 10029
| | - Avi Ma'ayan
- Department of Pharmacology & Systems Therapeutics, Mount Sinai School of Medicine One Gustave L. Levy Place, New York, NY 10029
| | - Lakshmi A. Devi
- Department of Pharmacology & Systems Therapeutics, Mount Sinai School of Medicine One Gustave L. Levy Place, New York, NY 10029
| |
Collapse
|
266
|
Fernández E, Collins MO, Uren RT, Kopanitsa MV, Komiyama NH, Croning MDR, Zografos L, Armstrong JD, Choudhary JS, Grant SGN. Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins. Mol Syst Biol 2009; 5:269. [PMID: 19455133 PMCID: PMC2694677 DOI: 10.1038/msb.2009.27] [Citation(s) in RCA: 201] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Accepted: 04/01/2009] [Indexed: 01/23/2023] Open
Abstract
The molecular complexity of mammalian proteomes demands new methods for mapping the organization of multiprotein complexes. Here, we combine mouse genetics and proteomics to characterize synapse protein complexes and interaction networks. New tandem affinity purification (TAP) tags were fused to the carboxyl terminus of PSD-95 using gene targeting in mice. Homozygous mice showed no detectable abnormalities in PSD-95 expression, subcellular localization or synaptic electrophysiological function. Analysis of multiprotein complexes purified under native conditions by mass spectrometry defined known and new interactors: 118 proteins comprising crucial functional components of synapses, including glutamate receptors, K+ channels, scaffolding and signaling proteins, were recovered. Network clustering of protein interactions generated five connected clusters, with two clusters containing all the major ionotropic glutamate receptors and one cluster with voltage-dependent K+ channels. Annotation of clusters with human disease associations revealed that multiple disorders map to the network, with a significant correlation of schizophrenia within the glutamate receptor clusters. This targeted TAP tagging strategy is generally applicable to mammalian proteomics and systems biology approaches to disease.
Collapse
Affiliation(s)
- Esperanza Fernández
- Genes to Cognition Programme, The Wellcome Trust Sanger Institute, Cambridge, UK
| | | | | | | | | | | | | | | | | | | |
Collapse
|
267
|
Coba MP, Pocklington AJ, Collins MO, Kopanitsa MV, Uren RT, Swamy S, Croning MDR, Choudhary JS, Grant SGN. Neurotransmitters drive combinatorial multistate postsynaptic density networks. Sci Signal 2009; 2:ra19. [PMID: 19401593 PMCID: PMC3280897 DOI: 10.1126/scisignal.2000102] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The mammalian postsynaptic density (PSD) comprises a complex collection of approximately 1100 proteins. Despite extensive knowledge of individual proteins, the overall organization of the PSD is poorly understood. Here, we define maps of molecular circuitry within the PSD based on phosphorylation of postsynaptic proteins. Activation of a single neurotransmitter receptor, the N-methyl-D-aspartate receptor (NMDAR), changed the phosphorylation status of 127 proteins. Stimulation of ionotropic and metabotropic glutamate receptors and dopamine receptors activated overlapping networks with distinct combinatorial phosphorylation signatures. Using peptide array technology, we identified specific phosphorylation motifs and switching mechanisms responsible for the integration of neurotransmitter receptor pathways and their coordination of multiple substrates in these networks. These combinatorial networks confer high information-processing capacity and functional diversity on synapses, and their elucidation may provide new insights into disease mechanisms and new opportunities for drug discovery.
Collapse
Affiliation(s)
- Marcelo P. Coba
- Genes to Cognition, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Andrew J. Pocklington
- Institute for Adaptive and Neural Computation, Division of Informatics, University of Edinburgh, 5 Forrest Hill, Edinburgh EH1 2QL, UK
| | - Mark O. Collins
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Maksym V. Kopanitsa
- Genes to Cognition, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Rachel T. Uren
- Genes to Cognition, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sajani Swamy
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Mike D. R. Croning
- Genes to Cognition, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jyoti S. Choudhary
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Seth G. N. Grant
- Genes to Cognition, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| |
Collapse
|
268
|
Hahn CG, Banerjee A, Macdonald ML, Cho DS, Kamins J, Nie Z, Borgmann-Winter KE, Grosser T, Pizarro A, Ciccimaro E, Arnold SE, Wang HY, Blair IA. The post-synaptic density of human postmortem brain tissues: an experimental study paradigm for neuropsychiatric illnesses. PLoS One 2009; 4:e5251. [PMID: 19370153 PMCID: PMC2666803 DOI: 10.1371/journal.pone.0005251] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Accepted: 02/19/2009] [Indexed: 01/09/2023] Open
Abstract
Recent molecular genetics studies have suggested various trans-synaptic processes for pathophysiologic mechanisms of neuropsychiatric illnesses. Examination of pre- and post-synaptic scaffolds in the brains of patients would greatly aid further investigation, yet such an approach in human postmortem tissue has yet to be tested. We have examined three methods using density gradient based purification of synaptosomes followed by detergent extraction (Method 1) and the pH based differential extraction of synaptic membranes (Methods 2 and 3). All three methods separated fractions from human postmortem brains that were highly enriched in typical PSD proteins, almost to the exclusion of pre-synaptic proteins. We examined these fractions using electron microscopy (EM) and verified the integrity of the synaptic membrane and PSD fractions derived from human postmortem brain tissues. We analyzed protein composition of the PSD fractions using two dimensional liquid chromatography tandem mass spectrometry (2D LC-MS/MS) and observed known PSD proteins by mass spectrometry. Immunoprecipitation and immunoblot studies revealed that expected protein-protein interactions and certain posttranscriptional modulations were maintained in PSD fractions. Our results demonstrate that PSD fractions can be isolated from human postmortem brain tissues with a reasonable degree of integrity. This approach may foster novel postmortem brain research paradigms in which the stoichiometry and protein composition of specific microdomains are examined.
Collapse
Affiliation(s)
- Chang-Gyu Hahn
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
269
|
Paulo JA, Brucker WJ, Hawrot E. Proteomic analysis of an alpha7 nicotinic acetylcholine receptor interactome. J Proteome Res 2009; 8:1849-58. [PMID: 19714875 PMCID: PMC2891571 DOI: 10.1021/pr800731z] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The alpha7 nicotinic acetylcholine receptor (nAChR) is well established as the principal high-affinity alpha-bungarotoxin-binding protein in the mammalian brain. We isolated carbachol-sensitive alpha-bungarotoxin-binding complexes from total mouse brain tissue by affinity immobilization followed by selective elution, and these proteins were fractionated by SDS-PAGE. The proteins in subdivided gel lane segments were tryptically digested, and the resulting peptides were analyzed by standard mass spectrometry. We identified 55 proteins in wild-type samples that were not present in comparable brain samples from alpha7 nAChR knockout mice that had been processed in a parallel fashion. Many of these 55 proteins are novel proteomic candidates for interaction partners of the alpha7 nAChR, and many are associated with multiple signaling pathways that may be implicated in alpha7 function in the central nervous system. The newly identified potential protein interactions, together with the general methodology that we introduce for alpha-bungarotoxin-binding protein complexes, form a new platform for many interesting follow-up studies aimed at elucidating the physiological role of neuronal alpha7 nAChRs.
Collapse
Affiliation(s)
- Joao A. Paulo
- Graduate Program in Molecular Biology, Cell Biology and Biochemistry, Brown University
| | - William J. Brucker
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University
| | - Edward Hawrot
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University
| |
Collapse
|
270
|
Zheng YZ, Foster LJ. Biochemical and proteomic approaches for the study of membrane microdomains. J Proteomics 2009; 72:12-22. [DOI: 10.1016/j.jprot.2008.09.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 08/14/2008] [Accepted: 09/18/2008] [Indexed: 01/08/2023]
|
271
|
Bajaj G, Zhang Y, Schimerlik MI, Hau AM, Yang J, Filtz TM, Kioussi C, Ishmael JE. N-methyl-D-aspartate receptor subunits are non-myosin targets of myosin regulatory light chain. J Biol Chem 2009; 284:1252-66. [PMID: 18945678 PMCID: PMC2613636 DOI: 10.1074/jbc.m801861200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2008] [Revised: 10/07/2008] [Indexed: 12/29/2022] Open
Abstract
Excitatory synapses contain multiple members of the myosin superfamily of molecular motors for which functions have not been assigned. In this study we characterized the molecular determinants of myosin regulatory light chain (RLC) binding to two major subunits of the N-methyl-d-aspartate receptor (NR). Myosin RLC bound to NR subunits in a manner that could be distinguished from the interaction of RLC with the neck region of non-muscle myosin II-B (NMII-B) heavy chain; NR-RLC interactions did not require the addition of magnesium, were maintained in the absence of the fourth EF-hand domain of the light chain, and were sensitive to RLC phosphorylation. Equilibrium fluorescence spectroscopy experiments indicate that the affinity of myosin RLC for NR1 is high (30 nm) in the context of the isolated light chain. Binding was not favored in the context of a recombinant NMII-B subfragment one, indicating that if the RLC is already bound to NMII-B it is unlikely to form a bridge between two binding partners. We report that sequence similarity in the "GXXXR" portion of the incomplete IQ2 motif found in NMII heavy chain isoforms likely contributes to recognition of NR2A as a non-myosin target of the RLC. Using site-directed mutagenesis to disrupt NR2A-RLC binding in intact cells, we find that RLC interactions facilitate trafficking of NR1/NR2A receptors to the cell membrane. We suggest that myosin RLC can adopt target-dependent conformations and that a role for this light chain in protein trafficking may be independent of the myosin II complex.
Collapse
Affiliation(s)
- Gaurav Bajaj
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA
| | | | | | | | | | | | | | | |
Collapse
|
272
|
GRINL1A colocalizes with N-methyl D-aspartate receptor NR1 subunit and reduces N-methyl D-aspartate toxicity. Neuroreport 2008; 19:1721-6. [PMID: 18849881 DOI: 10.1097/wnr.0b013e328317f05f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We hypothesized that proteins from the GRINL1A complex transcription unit called Gcom proteins modulate glutamatergic neurotransmission through interaction with the NR1 subunit of the N-methyl D-aspartate (NMDA) receptor. Cotransfection of hemagglutinin-tagged Gcom1 (GRINL1A combined transcript 1) and NR1 cDNAs into HEK293 cells revealed overlapping fluorescent signals in the plasma membrane. Coimmunoprecipitation studies demonstrated reciprocal coimmunoprecipitation from rat brain protein isolates, suggesting an interaction between GRINL1A proteins and the NMDA receptor. Anti-Gcom1 and anti-NR1 antibodies revealed colocalization of postsynaptic immunoreactivity in rat cortical and hippocampal neurons. Finally, anti-Gcom1 antibodies specifically inhibited NMDA excitotoxicity in rat cortical neurons, suggesting a functional interaction of Gcom and NR1 proteins. Our results are consistent with a facilatory role of GRINL1A proteins in glutamatergic signal transduction through interaction with the NMDA receptor.
Collapse
|
273
|
O'Leary T, Wyllie DJA. The ups and downs of synaptic plasticity: influences on this particular 'market'. J Physiol 2008; 586:5839-40. [PMID: 19074816 DOI: 10.1113/jphysiol.2008.165720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Timothy O'Leary
- Centre for Integrative Physiology, Hugh Robson Building, University of Edinburgh, George Square, Edinburgh EH8 9XD, UK
| | | |
Collapse
|
274
|
Edbauer D, Cheng D, Batterton MN, Wang CF, Duong DM, Yaffe MB, Peng J, Sheng M. Identification and characterization of neuronal mitogen-activated protein kinase substrates using a specific phosphomotif antibody. Mol Cell Proteomics 2008; 8:681-95. [PMID: 19054758 PMCID: PMC2667352 DOI: 10.1074/mcp.m800233-mcp200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mitogen-activated protein kinases (MAPKs) control neuronal synaptic function; however, little is known about the synaptic substrates regulated by MAPKs. A phosphopeptide library incorporating the MAPK consensus motif (PX(pS/pT)P where pS is phosphoserine and pT is phosphothreonine) was used to raise a phosphospecific antibody that detected MAPK-mediated phosphorylation. The antibody (termed “5557”) recognized a variety of phosphoproteins in the brain, many of which were enriched in postsynaptic density fractions. The immunoblot pattern changed rapidly in response to altered synaptic activity and with the inhibition of specific MAPKs and protein phosphatases. By immunoaffinity purification with 5557 antibody followed by mass spectrometry, we identified 449 putative MAPK substrates of which many appeared dynamically regulated in neuron cultures. Several of the novel candidate MAPK substrates were validated by in vitro phosphorylation assays. Additionally 82 specific phosphorylation sites were identified in 34 proteins, including Ser-447 in δ-catenin, a component of the cadherin adhesion complex. We further raised another phosphospecific antibody to confirm that δ-catenin Ser-447 is modified in neurons by the MAPK JNK in a synaptic activity-dependent manner. Ser-447 phosphorylation by JNK appears to be correlated with δ-catenin degradation, and a δ-catenin mutant defective in Ser-447 phosphorylation showed enhanced ability to promote dendrite branching in cultured neurons. Thus, phosphomotif-based affinity purification is a powerful approach to identify novel substrates of MAPKs in vivo and to reveal functionally significant phosphorylation events.
Collapse
Affiliation(s)
- Dieter Edbauer
- The Picower Institute for Learning and Memory, Howard Hughes Medical Institute, RIKEN-MIT Neuroscience Research Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | | | | | | | | | | | |
Collapse
|
275
|
Ma XM, Kiraly DD, Gaier ED, Wang Y, Kim EJ, Levine ES, Eipper BA, Mains RE. Kalirin-7 is required for synaptic structure and function. J Neurosci 2008; 28:12368-82. [PMID: 19020030 PMCID: PMC2586970 DOI: 10.1523/jneurosci.4269-08.2008] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2008] [Revised: 10/05/2008] [Accepted: 10/06/2008] [Indexed: 11/21/2022] Open
Abstract
Rho GTPases activated by GDP/GTP exchange factors (GEFs) play key roles in the developing and adult nervous system. Kalirin-7 (Kal7), the predominant adult splice form of the multifunctional Kalirin RhoGEF, includes a PDZ [postsynaptic density-95 (PSD-95)/Discs large (Dlg)/zona occludens-1 (ZO-1)] binding domain and localizes to the postsynaptic side of excitatory synapses. In vitro studies demonstrated that overexpression of Kal7 increased dendritic spine density, whereas reduced expression of endogenous Kal7 decreased spine density. To evaluate the role of Kal7 in vivo, mice lacking the terminal exon unique to Kal7 were created. Mice lacking both copies of the Kal7 exon (Kal7(KO)) grew and reproduced normally. Golgi impregnation and electron microscopy revealed decreased hippocampal spine density in Kal7(KO) mice. Behaviorally, Kal7(KO) mice showed decreased anxiety-like behavior in the elevated zero maze and impaired acquisition of a passive avoidance task, but normal behavior in open field, object recognition, and radial arm maze tasks. Kal7(KO) mice were deficient in hippocampal long-term potentiation. Western blot analysis confirmed the absence of Kal7 and revealed compensatory increases in larger Kalirin isoforms. PSDs purified from the cortices of Kal7(KO) mice showed a deficit in Cdk5, a kinase known to phosphorylate Kal7 and play an essential role in synaptic function. The early stages of excitatory synaptic development proceeded normally in cortical neurons prepared from Kal7(KO) mice, with decreased excitatory synapses apparent only after 21 d in vitro. Expression of exogenous Kal7 in Kal7(KO) neurons rescued this deficit. Kal7 plays an essential role in synaptic structure and function, affecting a subset of cognitive processes.
Collapse
Affiliation(s)
- Xin-Ming Ma
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut 06030
| | - Drew D. Kiraly
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut 06030
| | - Eric D. Gaier
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut 06030
| | - Yanping Wang
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut 06030
| | - Eun-Ji Kim
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut 06030
| | - Eric S. Levine
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut 06030
| | - Betty A. Eipper
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut 06030
| | - Richard E. Mains
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut 06030
| |
Collapse
|
276
|
Klemmer P, Smit AB, Li KW. Proteomics analysis of immuno-precipitated synaptic protein complexes. J Proteomics 2008; 72:82-90. [PMID: 19022416 DOI: 10.1016/j.jprot.2008.10.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 10/21/2008] [Accepted: 10/23/2008] [Indexed: 11/18/2022]
Abstract
Synapses are key neuronal elements of the brain. They are responsible for transmission, integration, and storage of information between nerve cells. A synapse is considered as the most complex cellular organelle consisting of approximately 1500 of proteins that are interacting in an activity dependent manner. We have initiated a series of immuno-precipitation experiments in conjunction with LC-MS/MS analysis in order to gain better insight into the organization of the synapse. In particular, we focused on proteins that have been implicated previously in the process of neuroplasticity, i.e., the glutamate receptor (GluR2), scaffolding proteins (PSD-95 and CASK), voltage gated potassium (KCNQ2 and Kv4.2) and calcium (CaV beta4) channel subunits, the signalling protein (GIT1) and synaptic vesicle protein (synaptophysin). This study confirms the previous reported protein-protein interactions and furthermore detects novel interactors. In conjunction with the literature reported protein-protein interaction a simple synaptic protein interactome was constructed. This model implicates the potential interaction of distinct protein complexes, and the engagement of single proteins, especially the scaffolding proteins, in multiple protein complexes.
Collapse
Affiliation(s)
- P Klemmer
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam,De Boelelaan 1085, 1081 Amsterdam, The Netherlands
| | | | | |
Collapse
|
277
|
Croning MDR, Marshall MC, McLaren P, Armstrong JD, Grant SGN. G2Cdb: the Genes to Cognition database. Nucleic Acids Res 2008; 37:D846-51. [PMID: 18984621 PMCID: PMC2686544 DOI: 10.1093/nar/gkn700] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Neuroscience databases linking genes, proteins, (patho)physiology, anatomy and behaviour across species will be valuable in a broad range of studies of the nervous system. G2Cdb is such a neuroscience database aiming to present a global view of the role of synapse proteins in physiology and disease. G2Cdb warehouses sets of genes and proteins experimentally elucidated by proteomic mass spectroscopy of signalling complexes and proteins biochemically isolated from mammalian synapse preparations, giving an experimentally validated definition of the constituents of the mammalian synapse. Using automated text-mining and expert (human) curation we have systematically extracted information from published neurobiological studies in the fields of synaptic signalling electrophysiology and behaviour in knockout and other transgenic mice. We have also surveyed the human genetics literature for associations to disease caused by mutations in synaptic genes. The synapse proteome datasets that G2Cdb provides offer a basis for future work in synapse biology and provide useful information on brain diseases. They have been integrated in a such way that investigators can rapidly query whether a gene or protein is found in brain-signalling complex(es), has a phenotype in rodent models or whether mutations are associated with a human disease. G2Cdb can be freely accessed at http://www.genes2cognition.org.
Collapse
Affiliation(s)
- Mike D R Croning
- Genes to Cognition Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | | | | | | |
Collapse
|
278
|
Liebl FLW, Featherstone DE. Identification and investigation of Drosophila postsynaptic density homologs. Bioinform Biol Insights 2008; 2:369-81. [PMID: 19812789 PMCID: PMC2735971 DOI: 10.4137/bbi.s2010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
AMPA receptors are responsible for fast excitatory transmission in the CNS and the trafficking of these receptors has been implicated in LTP and learning and memory. These receptors reside in the postsynaptic density, a network of proteins that links the receptors to downstream signaling components and to the neuronal cytoskeleton. To determine whether the fruit fly, Drosophila melanogaster, possesses a similar array of proteins as are found at the mammalian PSD, we identified Drosophila homologs of 95.8% of mammalian PSD proteins. We investigated, for the first time, the role of one of these PSD proteins, Pod1 in GluR cluster formation at the Drosophila neuromuscular junction and found that mutations in pod1 resulted in a specific loss of A-type receptors at the synapse.
Collapse
Affiliation(s)
- Faith L W Liebl
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL, USA. fl
| | | |
Collapse
|
279
|
Carlisle HJ, Fink AE, Grant SGN, O'Dell TJ. Opposing effects of PSD-93 and PSD-95 on long-term potentiation and spike timing-dependent plasticity. J Physiol 2008; 586:5885-900. [PMID: 18936077 DOI: 10.1113/jphysiol.2008.163469] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The membrane-associated guanylate kinases (MAGUKs) PSD-95, PSD-93 and SAP102 are thought to have crucial roles in both AMPA receptor trafficking and formation of NMDA receptor-associated signalling complexes involved in synaptic plasticity. While PSD-95, PSD-93, and SAP102 appear to have similar roles in AMPA receptor trafficking, it is not known whether these MAGUKs also have functionally similar roles in synaptic plasticity. To explore this issue we examined several properties of basal synaptic transmission in the hippocampal CA1 region of PSD-93 and PSD-95 mutant mice and compared the ability of a number of different synaptic stimulation protocols to induce long-term potentiation (LTP) and long-term depression (LTD) in these mutants. We find that while both AMPA and NMDA receptor-mediated synaptic transmission are normal in PSD-93 mutants, PSD-95 mutant mice exhibit clear deficits in AMPA receptor-mediated transmission. Moreover, in contrast to the facilitation of LTP induction and disruption of LTD observed in PSD-95 mutant mice, PSD-93 mutant mice exhibit deficits in LTP and normal LTD. Our results suggest that PSD-95 has a unique role in AMPA receptor trafficking at excitatory synapses in the hippocampus of adult mice and indicate that PSD-93 and PSD-95 have essentially opposite roles in LTP, perhaps because these MAGUKs form distinct NMDA receptor signalling complexes that differentially regulate the induction of LTP by different patterns of synaptic activity.
Collapse
Affiliation(s)
- Holly J Carlisle
- Department of Physiology, David Geffen School of Medicine at UCLA, 53-231 Center for the Health Sciences, Box 951751, Los Angeles, CA 90095-1751, USA
| | | | | | | |
Collapse
|
280
|
Nonaka H, Takei K, Umikawa M, Oshiro M, Kuninaka K, Bayarjargal M, Asato T, Yamashiro Y, Uechi Y, Endo S, Suzuki T, Kariya KI. MINK is a Rap2 effector for phosphorylation of the postsynaptic scaffold protein TANC1. Biochem Biophys Res Commun 2008; 377:573-578. [PMID: 18930710 DOI: 10.1016/j.bbrc.2008.10.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Accepted: 10/06/2008] [Indexed: 11/18/2022]
Abstract
Rap1 and Rap2 are similar Ras-like G proteins but perform distinct functions. By the affinity chromatography/mass-spectrometry approach and the yeast two-hybrid screening, we identified Misshapen/NIKs-related kinase (MINK) as a novel Rap2-interacting protein that does not interact with Rap1 or Ras. MINK is a member of the STE20 group of mitogen-activated protein kinase kinase kinase kinases. The interaction between MINK and Rap2 was GTP-dependent and required Phe39 within the effector region of Rap2; the corresponding residue in Rap1 and Ras is Ser. MINK was enriched in the brain, and both MINK and its close relative, Traf2- and Nck-interacting kinase (TNIK), interacted with a postsynaptic scaffold protein containing tetratricopeptide repeats, ankyrin repeats and a coiled-coil region (TANC1) and induced its phosphorylation, under control of Rap2 in cultured cells. These are novel actions of MINK and TNIK, and consistent with a role of MINK as a Rap2 effector in the brain.
Collapse
Affiliation(s)
- Hideo Nonaka
- Division of Cell Biology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa 903-0215, Japan
| | - Kimiko Takei
- Division of Cell Biology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa 903-0215, Japan
| | - Masato Umikawa
- Division of Cell Biology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa 903-0215, Japan
| | - Minoru Oshiro
- Division of Cell Biology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa 903-0215, Japan
| | - Kouichi Kuninaka
- Division of Cell Biology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa 903-0215, Japan
| | - Maitsetseg Bayarjargal
- Division of Cell Biology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa 903-0215, Japan
| | - Tsuyoshi Asato
- Division of Cell Biology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa 903-0215, Japan
| | - Yoshito Yamashiro
- Division of Cell Biology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa 903-0215, Japan
| | - Yukiko Uechi
- Division of Cell Biology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa 903-0215, Japan; Unit for Molecular Neurobiology of Learning and Memory, Initial Research Project, Okinawa Institute of Science and Technology, Japan
| | - Shogo Endo
- Unit for Molecular Neurobiology of Learning and Memory, Initial Research Project, Okinawa Institute of Science and Technology, Japan
| | - Tatsuo Suzuki
- Department of Neuroplasticity, Shinshu University Graduate School of Medicine, Japan
| | - Ken-Ichi Kariya
- Division of Cell Biology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa 903-0215, Japan.
| |
Collapse
|
281
|
Li X, Cao J, Jin Q, Xie C, He Q, Cao R, Xiong J, Chen P, Wang X, Liang S. A proteomic study reveals the diversified distribution of plasma membrane-associated proteins in rat hepatocytes. J Cell Biochem 2008; 104:965-84. [PMID: 18247341 DOI: 10.1002/jcb.21680] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
To investigate the heterogeneous protein composition of highly polarized hepatocyte plasma membrane (PM), three PM-associated subfractions were obtained from freshly isolated rat hepatocytes using density gradient centrifugation. The origins of the three subfractions were determined by morphological analysis and western blotting. The proteins were subjected to either one-dimensional (1-D) SDS-PAGE or two-dimensional (2-D) benzyldimethyl-n-hexadecylammonium chloride (BAC)/SDS-PAGE before nano-Liquid Chromatography-Electrospray Ionization--tandem mass spectrometry analysis (LC-ESI-MS/MS). A total of 613 non-redundant proteins were identified, among which 371 (60.5%) proteins were classified as PM or membrane-associated proteins according to GO annotations and the literatures and 32.4% had transmembrane domains. PM proteins from microsomal portion possessed the highest percentage of transmembrane domain, about 46.5% of them containing at least one transmembrane domain. In addition to proteins known to be located at polarized liver PM regions, such as asialoglycoprotein receptor 2, desmoplakin and bile salt export pump, several proteins which had the potential to become novel subfraction-specific proteins were also identified, such as annexin a6, pannexin and radixin. Our analysis also evaluated the application of 1-D SDS-PAGE and 2-D 16-BAC/SDS-PAGE on the separation of integral membrane proteins.
Collapse
Affiliation(s)
- Xuanwen Li
- Key Laboratory of Protein Chemistry and Developmental Biology of Education Committee, College of Life Sciences, Hunan Normal University, Changsha 410081, P.R. China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
282
|
A comparison of the synaptic proteome in human chronic schizophrenia and rat ketamine psychosis suggest that prohibitin is involved in the synaptic pathology of schizophrenia. Mol Psychiatry 2008; 13:878-96. [PMID: 18504422 DOI: 10.1038/mp.2008.60] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Many studies in recent years suggest that schizophrenia is a synaptic disease that crucially involves a hypofunction of N-methyl-D-aspartate receptor-mediated signaling. However, at present it is unclear how these pathological processes are reflected in the protein content of the synapse. We have employed two-dimensional gel electrophoresis in conjunction with mass spectrometry to characterize and compare the synaptic proteomes of the human left dorsolateral prefrontal cortex in chronic schizophrenia and of the cerebral cortex of rats treated subchronically with ketamine. We found consistent changes in the synaptic proteomes of human schizophrenics and in rats with induced ketamine psychosis compared to controls. However, commonly regulated proteins between both groups were very limited and only prohibitin was found upregulated in both chronic schizophrenia and the rat ketamine model. Prohibitin, however, could be a new potential marker for the synaptic pathology of schizophrenia and might be causally involved in the disease process.
Collapse
|
283
|
An allosteric model of calmodulin explains differential activation of PP2B and CaMKII. Proc Natl Acad Sci U S A 2008; 105:10768-73. [PMID: 18669651 DOI: 10.1073/pnas.0804672105] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Calmodulin plays a vital role in mediating bidirectional synaptic plasticity by activating either calcium/calmodulin-dependent protein kinase II (CaMKII) or protein phosphatase 2B (PP2B) at different calcium concentrations. We propose an allosteric model for calmodulin activation, in which binding to calcium facilitates the transition between a low-affinity [tense (T)] and a high-affinity [relaxed (R)] state. The four calcium-binding sites are assumed to be nonidentical. The model is consistent with previously reported experimental data for calcium binding to calmodulin. It also accounts for known properties of calmodulin that have been difficult to model so far, including the activity of nonsaturated forms of calmodulin (we predict the existence of open conformations in the absence of calcium), an increase in calcium affinity once calmodulin is bound to a target, and the differential activation of CaMKII and PP2B depending on calcium concentration.
Collapse
|
284
|
Ikeda M, Hikita T, Taya S, Uraguchi-Asaki J, Toyo-oka K, Wynshaw-Boris A, Ujike H, Inada T, Takao K, Miyakawa T, Ozaki N, Kaibuchi K, Iwata N. Identification of YWHAE, a gene encoding 14-3-3epsilon, as a possible susceptibility gene for schizophrenia. Hum Mol Genet 2008; 17:3212-22. [PMID: 18658164 DOI: 10.1093/hmg/ddn217] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Schizophrenia is a complex mental disorder with a fairly high degree of heritability. Although the causes of schizophrenia remain unclear, it is now widely accepted that it is a neurodevelopmental and neurodegenerative disorder involving disconnectivity and disorder of the synapses. Disrupted-in-schizophrenia 1 (DISC1) is a promising candidate susceptibility gene involved in neurodevelopment, including maturation of the cerebral cortex. To identify other susceptibility genes for schizophrenia, we screened for DISC1-interacting molecules [NudE-like (NUDEL), Lissencephaly-1 (LIS1), 14-3-3epsilon (YWHAE), growth factor receptor bound protein 2 (GRB2) and Kinesin family 5A of Kinesen1 (KIF5A)], assessing a total of 25 tagging single-nucleotide polymorphisms (SNPs) in a Japanese population. We identified a YWHAE SNP (rs28365859) that showed a highly significant difference between case and control samples, with higher minor allele frequencies in controls (P(allele) = 1.01 x 10(-5) and P(genotype) = 4.08 x 10(-5) in 1429 cases and 1728 controls). Both messenger RNA transcription and protein expression of 14-3-3epsilon were also increased in the lymphocytes of healthy control subjects harboring heterozygous and homozygous minor alleles compared with homozygous major allele subjects. To further investigate a potential role for YWHAE in schizophrenia, we studied Ywhae(+/-) mice in which the level of 14-3-3epsilon protein is reduced to 50% of that in wild-type littermates. These mice displayed weak defects in working memory in the eight-arm radial maze and moderately enhanced anxiety-like behavior in the elevated plus-maze. Our results suggest that YWHAE is a possible susceptibility gene that functions protectively in schizophrenia.
Collapse
Affiliation(s)
- Masashi Ikeda
- Department of Psychiatry, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
285
|
Reintsch WE, Mandato CA. Deciphering animal development through proteomics: requirements and prospects. Proteome Sci 2008; 6:21. [PMID: 18652672 PMCID: PMC2516511 DOI: 10.1186/1477-5956-6-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 07/24/2008] [Indexed: 12/28/2022] Open
Abstract
In recent years proteomic techniques have started to become very useful tools in a variety of model systems of developmental biology. Applications cover many different aspects of development, including the characterization of changes in the proteome during early embryonic stages. During early animal development the embryo becomes patterned through the temporally and spatially controlled activation of distinct sets of genes. Patterning information is then translated, from gastrulation onwards, into regional specific morphogenetic cell and tissue movements that give the embryo its characteristic shape. On the molecular level, patterning is the outcome of intercellular communication via signaling molecules and the local activation or repression of transcription factors. Genetic approaches have been used very successfully to elucidate the processes behind these events. Morphogenetic movements, on the other hand, have to be orchestrated through regional changes in the mechanical properties of cells. The molecular mechanisms that govern these changes have remained much more elusive, at least in part due to the fact that they are more under translational/posttranslational control than patterning events. However, recent studies indicate that proteomic approaches can provide the means to finally unravel the mechanisms that link patterning to the generation of embryonic form. To intensify research in this direction will require close collaboration between proteome scientists and developmental researchers. It is with this aim in mind that we first give an outline of the classical questions of patterning and morphogenesis. We then summarize the proteomic approaches that have been applied in developmental model systems and describe the pioneering studies that have been done to study morphogenesis. Finally we discuss current and future strategies that will allow characterizing the changes in the embryonic proteome and ultimately lead to a deeper understanding of the cellular mechanisms that govern the generation of embryonic form.
Collapse
Affiliation(s)
- Wolfgang E Reintsch
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec, H3A 2B2, Canada
| | - Craig A Mandato
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec, H3A 2B2, Canada
| |
Collapse
|
286
|
Abstract
A significant consequence of protein phosphorylation is to alter protein-protein interactions, leading to dynamic regulation of the components of protein complexes that direct many core biological processes. Recent proteomic studies have populated databases with extensive compilations of cellular phosphoproteins and phosphorylation sites and a similarly deep coverage of the subunit compositions and interactions in multiprotein complexes. However, considerably less data are available on the dynamics of phosphorylation, composition of multiprotein complexes or that define their interdependence. We describe a method to identify candidate phosphoprotein complexes by combining phosphoprotein affinity chromatography, separation by size, denaturing gel electrophoresis, protein identification by tandem mass spectrometry, and informatics analysis. Toward developing phosphoproteome profiling, we have isolated native phosphoproteins using a phosphoprotein affinity matrix, Pro-Q Diamond resin (Molecular Probes-Invitrogen). This resin quantitatively retains phosphoproteins and associated proteins from cell extracts. Pro-Q Diamond purification of a yeast whole cell extract followed by 1-D PAGE separation, proteolysis and ESI LC-MS/MS, a method we term PA-GeLC-MS/MS, yielded 108 proteins, a majority of which were known phosphoproteins. To identify proteins that were purified as parts of phosphoprotein complexes, the Pro-Q eluate was separated into two fractions by size, <100 kDa and >100 kDa, before analysis by PAGE and ESI LC-MS/MS and the component proteins queried against databases to identify protein-protein interactions. The <100 kDa fraction was enriched in phosphoproteins indicating the presence of monomeric phosphoproteins. The >100 kDa fraction contained 171 proteins of 20-80 kDa, nearly all of which participate in known protein-protein interactions. Of these 171, few are known phosphoproteins, consistent with their purification by participation in protein complexes. By comparing the results of our phosphoprotein profiling with the informational databases on phosphoproteomics, protein-protein interactions and protein complexes, we have developed an approach to examining the correlation between protein interactions and protein phosphorylation.
Collapse
Affiliation(s)
- Kolbrun Kristjansdottir
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL 60637, USA
| | - Donald Wolfgeher
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL 60637, USA
| | - Nick Lucius
- De Paul University, School of Computer Science, Telecommunications and Information Systems, Chicago, IL 60604, USA.
| | - David Sigfredo Angulo
- De Paul University, School of Computer Science, Telecommunications and Information Systems, Chicago, IL 60604, USA.
| | - Stephen J. Kron
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
287
|
Gutstein HB, Morris JS, Annangudi SP, Sweedler JV. Microproteomics: analysis of protein diversity in small samples. MASS SPECTROMETRY REVIEWS 2008; 27:316-30. [PMID: 18271009 PMCID: PMC2743962 DOI: 10.1002/mas.20161] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Proteomics, the large-scale study of protein expression in organisms, offers the potential to evaluate global changes in protein expression and their post-translational modifications that take place in response to normal or pathological stimuli. One challenge has been the requirement for substantial amounts of tissue in order to perform comprehensive proteomic characterization. In heterogeneous tissues, such as brain, this has limited the application of proteomic methodologies. Efforts to adapt standard methods of tissue sampling, protein extraction, arraying, and identification are reviewed, with an emphasis on those appropriate to smaller samples ranging in size from several microliters down to single cells. The effects of miniaturization on these analyses are highlighted using neuroscience-related examples, as are statistical issues unique to the high-dimensional datasets generated by proteomic experiments.
Collapse
Affiliation(s)
- Howard B Gutstein
- Department of Anesthesiology, University of Texas-MD Anderson Cancer Center, 1515 Holcombe Blvd., Box 110, Houston, TX 77030-4009, USA.
| | | | | | | |
Collapse
|
288
|
Emes RD, Pocklington AJ, Anderson CNG, Bayes A, Collins MO, Vickers CA, Croning MDR, Malik BR, Choudhary JS, Armstrong JD, Grant SGN. Evolutionary expansion and anatomical specialization of synapse proteome complexity. Nat Neurosci 2008; 11:799-806. [PMID: 18536710 PMCID: PMC3624047 DOI: 10.1038/nn.2135] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 05/07/2008] [Indexed: 11/09/2022]
Abstract
Understanding the origins and evolution of synapses may provide insight into species diversity and the organization of the brain. Using comparative proteomics and genomics, we examined the evolution of the postsynaptic density (PSD) and membrane-associated guanylate kinase (MAGUK)-associated signaling complexes (MASCs) that underlie learning and memory. PSD and MASC orthologs found in yeast carry out basic cellular functions to regulate protein synthesis and structural plasticity. We observed marked changes in signaling complexity at the yeast-metazoan and invertebrate-vertebrate boundaries, with an expansion of key synaptic components, notably receptors, adhesion/cytoskeletal proteins and scaffold proteins. A proteomic comparison of Drosophila and mouse MASCs revealed species-specific adaptation with greater signaling complexity in mouse. Although synaptic components were conserved amongst diverse vertebrate species, mapping mRNA and protein expression in the mouse brain showed that vertebrate-specific components preferentially contributed to differences between brain regions. We propose that the evolution of synapse complexity around a core proto-synapse has contributed to invertebrate-vertebrate differences and to brain specialization.
Collapse
Affiliation(s)
- Richard D Emes
- Institute for Science and Technology in Medicine, Keele University, Thornburrow Drive, Hartshill, Stoke-on-Trent ST4 7QB, UK
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
289
|
Rasche A, Al-Hasani H, Herwig R. Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus. BMC Genomics 2008; 9:310. [PMID: 18590522 PMCID: PMC2515154 DOI: 10.1186/1471-2164-9-310] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 06/30/2008] [Indexed: 12/17/2022] Open
Abstract
Background Multiple functional genomics data for complex human diseases have been published and made available by researchers worldwide. The main goal of these studies is the detailed analysis of a particular aspect of the disease. Complementary, meta-analysis approaches try to extract supersets of disease genes and interaction networks by integrating and combining these individual studies using statistical approaches. Results Here we report on a meta-analysis approach that integrates data of heterogeneous origin in the domain of type-2 diabetes mellitus (T2DM). Different data sources such as DNA microarrays and, complementing, qualitative data covering several human and mouse tissues are integrated and analyzed with a Bootstrap scoring approach in order to extract disease relevance of the genes. The purpose of the meta-analysis is two-fold: on the one hand it identifies a group of genes with overall disease relevance indicating common, tissue-independent processes related to the disease; on the other hand it identifies genes showing specific alterations with respect to a single study. Using a random sampling approach we computed a core set of 213 T2DM genes across multiple tissues in human and mouse, including well-known genes such as Pdk4, Adipoq, Scd, Pik3r1, Socs2 that monitor important hallmarks of T2DM, for example the strong relationship between obesity and insulin resistance, as well as a large fraction (128) of yet barely characterized novel candidate genes. Furthermore, we explored functional information and identified cellular networks associated with this core set of genes such as pathway information, protein-protein interactions and gene regulatory networks. Additionally, we set up a web interface in order to allow users to screen T2DM relevance for any – yet non-associated – gene. Conclusion In our paper we have identified a core set of 213 T2DM candidate genes by a meta-analysis of existing data sources. We have explored the relation of these genes to disease relevant information and – using enrichment analysis – we have identified biological networks on different layers of cellular information such as signaling and metabolic pathways, gene regulatory networks and protein-protein interactions. The web interface is accessible via .
Collapse
Affiliation(s)
- Axel Rasche
- Max-Planck-Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestrasse 63-73, D-14195 Berlin, Germany.
| | | | | |
Collapse
|
290
|
Sornarajah L, Vasuta OC, Zhang L, Sutton C, Li B, El-Husseini A, Raymond LA. NMDA receptor desensitization regulated by direct binding to PDZ1-2 domains of PSD-95. J Neurophysiol 2008; 99:3052-62. [PMID: 18400955 PMCID: PMC3013345 DOI: 10.1152/jn.90301.2008] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Regulation of N-methyl-d-aspartate receptor (NMDAR) activity by desensitization is important in physiological and pathological states; NMDAR desensitization contributes in shaping synaptic responses and may be protective by limiting calcium influx during sustained glutamate insults. We previously reported that glycine-independent desensitization decreases during hippocampal neuronal development, correlating with NMDAR synaptic localization and association with postsynaptic density 95 (PSD-95). PSD-95/Discs large/zona occludens (PDZ)-1,2 domains of PSD-95 bind to the C-terminus of NMDAR NR2 subunits. The role of PSD-95 in anchoring signaling proteins near NMDARs is well documented. To determine if PSD-95-induced changes in NMDAR desensitization occur because of direct binding to NR2 or due to recruitment of regulatory proteins, we tested the effects of various PSD-95 constructs on NMDAR currents in human embryonic kidney 293 (HEK293) cells and neurons. In HEK cells, wild-type PSD-95 significantly reduced wild-type NMDAR desensitization without altering currents of NMDARs containing NR2A-S1462A, a mutation that abolishes PSD-95 binding. The PSD-95 N-terminus truncated after the PDZ1-2 domains was sufficient for this effect in neurons with low endogenous PSD-95 levels; in NMDAR-expressing HEK cells, the effect persisted when PSD-95 multimerization was eliminated. Moreover other PSD-95 family members with highly homologous PDZ1-2 domains significantly reduced NMDAR desensitization. In mature neurons, disruption of PSD-95/NMDAR interaction through protein kinase C (PKC) activation increased desensitization to levels found in immature neurons, and this effect was not due to PKC direct regulation of NMDAR activity. We conclude that direct binding of PSD-95 increases stability of NMDAR responses to agonist exposure in neuronal and nonneuronal cells.
Collapse
Affiliation(s)
- Lavan Sornarajah
- Graduate Program in Neuroscience, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, Canada, V6T 1Z3
| | - Oana Cristina Vasuta
- Graduate Program in Neuroscience, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, Canada, V6T 1Z3
| | - Lily Zhang
- Division of Neuroscience, Department of Psychiatry, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, Canada, V6T 1Z3
| | - Christine Sutton
- Division of Neuroscience, Department of Psychiatry, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, Canada, V6T 1Z3
| | - Bo Li
- Graduate Program in Neuroscience, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, Canada, V6T 1Z3
| | - Alaa El-Husseini
- Division of Neuroscience, Department of Psychiatry, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, Canada, V6T 1Z3
- Brain Research Centre, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, Canada, V6T 1Z3
| | - Lynn A. Raymond
- Division of Neuroscience, Department of Psychiatry, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, Canada, V6T 1Z3
- Brain Research Centre, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, Canada, V6T 1Z3
- Division of Neurology, Department of Medicine, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, Canada, V6T 1Z3
| |
Collapse
|
291
|
Fritschy JM, Harvey RJ, Schwarz G. Gephyrin: where do we stand, where do we go? Trends Neurosci 2008; 31:257-64. [PMID: 18403029 DOI: 10.1016/j.tins.2008.02.006] [Citation(s) in RCA: 243] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Revised: 02/17/2008] [Accepted: 02/19/2008] [Indexed: 11/24/2022]
Abstract
Gephyrin is a multifunctional protein responsible for molybdenum cofactor synthesis and the clustering of glycine and GABA(A) receptors at inhibitory synapses. Based on the structure of its two conserved domains, G and E, gephyrin is thought to form a hexagonal lattice serving as a scaffold for accessory proteins at postsynaptic sites. However, important aspects of gephyrin gene expression, protein structure and regulation, as well as the role of gephyrin in synapse formation and plasticity, remain poorly understood. Here we review the current state of knowledge about gephyrin, highlighting new research avenues based on a different structural model and a revised nomenclature for gephyrin splice variants. Unraveling the biology of gephyrin will further our understanding of glycinergic and GABAergic synapses in health and disease.
Collapse
Affiliation(s)
- Jean-Marc Fritschy
- Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | | | | |
Collapse
|
292
|
Yang W, Steen H, Freeman MR. Proteomic approaches to the analysis of multiprotein signaling complexes. Proteomics 2008; 8:832-51. [PMID: 18297654 DOI: 10.1002/pmic.200700650] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Signal transduction is one of the most active fields in modern biomedical research. Increasing evidence has shown that signaling proteins associate with each other in characteristic ways to form large signaling complexes. These diverse structures operate to boost signaling efficiency, ensure specificity and increase sensitivity of the biochemical circuitry. Traditional methods of protein analysis are inadequate to fully characterize and understand these structures, which are intricate, contain many components and are highly dynamic. Instead, proteomics technologies are currently being applied to investigate the nature and composition of multimeric signaling complexes. This review presents commonly used and potential proteomic methods of analyzing diverse protein complexes along with a discussion and a brief evaluation of alternative approaches. Challenges associated with proteomic analysis of signaling complexes are also discussed.
Collapse
Affiliation(s)
- Wei Yang
- The Urological Diseases Research Center, Department of Urology, Children's Hospital Boston, Boston, MA 02115, USA
| | | | | |
Collapse
|
293
|
DeGiorgis JA, Galbraith JA, Dosemeci A, Chen X, Reese TS. Distribution of the scaffolding proteins PSD-95, PSD-93, and SAP97 in isolated PSDs. ACTA ACUST UNITED AC 2008; 35:239-50. [PMID: 18392731 DOI: 10.1007/s11068-007-9017-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 08/14/2007] [Accepted: 08/21/2007] [Indexed: 10/22/2022]
Abstract
We compared the distribution of three scaffolding proteins, all belonging to a family of membrane-associated guanylate kinases, thought to have key roles in the organization of the postsynaptic density (PSD). Isolated PSDs readily adhered to treated glass coverslips where they were labeled with immunogold and rotary shadowed for analysis by EM. The distribution of proteins within individual PSDs were measured by counting and mapping individual immunogold particles. PSD-95, as previously described, is distributed evenly throughout the PSD. We find here that PSD-93 has a nearly identical distribution suggesting that PSD-95 and PSD-93 could perform similar roles. SAP97, in contrast, is concentrated near edges of cleft sides of the PSDs, and in small clumps on their cytoplasmic sides. The homogenous distribution of PSD-95 and PSD-93 throughout the PSD is consistent with their being part of a backbone that stabilizes their various binding partners within the PSD. The distribution of SAP97 confirms that this protein is actually an integral component of the PSD, and suggests that it may have a role in inserting or stabilizing its main binding partner, Glu-R1, at the edge of the PSD.
Collapse
Affiliation(s)
- Joseph A DeGiorgis
- Laboratory of Neurobiology, National Institutes of Health, NINDS, Building 49, Room 3A60, 49 Convent Drive, Bethesda, MD 20892, USA.
| | | | | | | | | |
Collapse
|
294
|
Pharmacological treatment of Parkinson's disease: life beyond dopamine D2/D3 receptors? J Neural Transm (Vienna) 2008; 115:431-41. [PMID: 18250954 DOI: 10.1007/s00702-007-0852-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Accepted: 10/30/2007] [Indexed: 10/22/2022]
Abstract
Parkinson's disease (PD) is a multisystemic disorder in which several neurotransmitters other than dopamine are affected. Drugs acting on non-dopaminergic systems are envisaged as promising agents to treat PD and levodopa-induced dyskinesias (LID). However, compounds targeting glutamate, adenosine, noradrenaline, 5-hydroxytryptamine, cannabinoid, and opioid transmitter systems have been assessed in human studies showing negative, inconsistent or unsatisfactory results. Most of these drugs had been tested previously in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-lesioned monkeys, as well as in the classic 6-hydroxydopamine-lesioned rat model. These failures raise several questions and concerns about the true reliability of animal studies, the adequacy of the working hypotheses and design of clinical trials, the validity of tools in current use to evaluate a particular effect, and the selectivity of the drugs used. More importantly, observed discrepancies between the results in models and patients, could challenge the validity of current ideas about the pathophysiology of parkinsonism and LID.
Collapse
|
295
|
Arrigoni G, Pagano MA, Sarno S, Cesaro L, James P, Pinna LA. Mass spectrometry analysis of a protein kinase CK2beta subunit interactome isolated from mouse brain by affinity chromatography. J Proteome Res 2008; 7:990-1000. [PMID: 18220339 DOI: 10.1021/pr070500s] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
CK2, an acronym derived from the misnomer "casein kinase 2", denotes a ubiquitous and extremely pleiotropic Ser/Thr protein kinase, the holoenzyme of which is composed of two catalytic (alpha and/or alpha') and two noncatalytic beta subunits acting as a docking platform and the multifarious functions of which are still incompletely understood. By combining affinity chromatography and mass spectrometry, we have identified 144 mouse brain proteins that associate with immobilized CK2beta. A large proportion (60%) of the identified proteins had been previously reported to be functionally related to CK2, and a similar proportion have been classified as phosphoproteins with approximately half of these having the features of CK2 targets. A large number of the identified proteins ( approximately 40%) either are nuclear or shuttle between the nucleus and cytoplasm, and the biggest functional classes of CK2beta interactors are committed to protein synthesis and degradation (32 proteins) and RNA/DNA interaction (20 proteins). Also well represented are the categories of cytoskeletal/structural proteins (19), trafficking proteins (17), and signaling proteins (14). The identified proteins are examined in relation to their functions and potential as targets and/or regulators of CK2, disclosing in some cases unanticipated links between this kinase and a variety of biochemical events.
Collapse
Affiliation(s)
- Giorgio Arrigoni
- Department of Biological Chemistry and CNR Institute of Neurosciences, University of Padova, Padova, Italy.
| | | | | | | | | | | |
Collapse
|
296
|
Lasiecka ZM, Yap CC, Vakulenko M, Winckler B. Chapter 7 Compartmentalizing the Neuronal Plasma Membrane. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 272:303-89. [DOI: 10.1016/s1937-6448(08)01607-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
297
|
Reissner KJ, Boyle HD, Ye X, Carew TJ. Aplysia synapse associated protein (APSAP): identification, characterization, and selective interactions with Shaker-type potassium channels. J Neurochem 2007; 105:1006-18. [PMID: 18182049 DOI: 10.1111/j.1471-4159.2007.05202.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The vertebrate post-synaptic density (PSD) is a region of high molecular complexity in which dynamic protein interactions modulate receptor localization and synaptic function. Members of the membrane-associated guanylate kinase (MAGUK) family of proteins represent a major structural and functional component of the vertebrate PSD. In order to investigate the expression and significance of orthologous PSD components associated with the Aplysia sensory neuron-motor neuron synapse, we have cloned an Aplysia Dlg-MAGUK protein, which we identify as Aplysia synapse associated protein (ApSAP). As revealed by western blot, RT-PCR, and immunocytochemical analyses, ApSAP is predominantly expressed in the CNS and is located in both sensory neuron and motor neurons. The overall amino acid sequence of ApSAP is 55-61% identical to Drosophila Dlg and mammalian Dlg-MAGUK proteins, but is more highly conserved within L27, PDZ, SH3, and guanylate kinase domains. Because these conserved domains mediate salient interactions with receptors and other PSD components of the vertebrate synapse, we performed a series of GST pull-down assays using recombinant C-terminal tail proteins from various Aplysia receptors and channels containing C-terminal PDZ binding sequences. We have found that ApSAP selectively binds to an Aplysia Shaker-type channel AKv1.1, but not to (i) NMDA receptor subunit AcNR1-1, (ii) potassium channel AKv5.1, (iii) receptor tyrosine kinase ApTrkl, (iv) glutamate receptor ApGluR1/4, (v) glutamate receptor ApGluR2/3, or (vi) glutamate receptor ApGluR7. These findings provide preliminary information regarding the expression and interactions of Dlg-MAGUK proteins of the Aplysia CNS, and will inform questions aimed at a functional analysis of how interactions in a protein network such as the PSD may regulate synaptic strength.
Collapse
Affiliation(s)
- Kathryn J Reissner
- Department of Neurobiology and Behavior, University of California, Irvine, California, USA
| | | | | | | |
Collapse
|
298
|
Valor LM, Grant SGN. Clustered gene expression changes flank targeted gene loci in knockout mice. PLoS One 2007; 2:e1303. [PMID: 18074027 PMCID: PMC2110885 DOI: 10.1371/journal.pone.0001303] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Accepted: 11/15/2007] [Indexed: 11/18/2022] Open
Abstract
Background Gene expression profiling using microarrays is a powerful technology widely used to study regulatory networks. Profiling of mRNA levels in mutant organisms has the potential to identify genes regulated by the mutated protein. Methodology/Principle Findings Using tissues from multiple lines of knockout mice we have examined genome-wide changes in gene expression. We report that a significant proportion of changed genes were found near the targeted gene. Conclusions/Significance The apparent clustering of these genes was explained by the presence of flanking DNA from the parental ES cell. We provide recommendations for the analysis and reporting of microarray data from knockout mice
Collapse
Affiliation(s)
- Luis M. Valor
- Genes to Cognition Programme, The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Seth G. N. Grant
- Genes to Cognition Programme, The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
299
|
Abstract
The N-methyl-D-aspartate (NMDA) subtype of ionotropic glutamate receptors plays a Jekyll and Hyde role in the mammalian central nervous system. In pathological scenarios such as ischemia, Ca2+ influx through the NMDA receptor is a key mediator of cell death. However, physiological levels of NMDA-receptor activity can promote neuronal survival and resistance to trauma and play important roles in synaptic plasticity and transmission. This dichotomy may explain the poor tolerance and efficacy of NMDA-receptor antagonists in clinical trials for excitotoxic trauma. There is a growing understanding of the signaling events that mediate the opposing effects of NMDA-receptor activity and the factors that determine whether an episode of NMDA-receptor activity will promote survival or death. This knowledge may lead to therapeutic strategies that enable the selective blockade of prodeath signaling cassettes while sparing physiological signaling to survival and plasticity.
Collapse
Affiliation(s)
- Sofia Papadia
- Centre for Neuroscience Research, University of Edinburgh, Hugh Robson Building, Edinburgh EH8 9XD, UK
| | - Giles E. Hardingham
- Centre for Neuroscience Research, University of Edinburgh, Hugh Robson Building, Edinburgh EH8 9XD, UK
| |
Collapse
|
300
|
Miller LC, Sossin WS. The significance of organellar proteomics for the nervous system. Proteomics Clin Appl 2007; 1:1436-45. [PMID: 21136641 DOI: 10.1002/prca.200700366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Indexed: 12/16/2022]
Abstract
Organellar proteomics is a useful tool for gaining biological insights about structures in the cell. Here, we discuss the tools used in organellar proteomics and the impact of this technique in understanding nervous system function. We will review insights gained from the proteomes of nervous system-specific organelles such as synaptic vesicles and the postsynaptic density. Moreover, we will show how comparison of proteomes between organelles isolated from the nervous system and from other tissues highlight nervous system-specific functions using the examples of clathrin-coated vesicles and RNA granules.
Collapse
Affiliation(s)
- Linda C Miller
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | | |
Collapse
|