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Sule R, Rivera G, Gomes AV. Western blotting (immunoblotting): history, theory, uses, protocol and problems. Biotechniques 2023; 75:99-114. [PMID: 36971113 DOI: 10.2144/btn-2022-0034] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Western blotting (immunoblotting) is a powerful and commonly used technique that is capable of detecting or semiquantifying an individual protein from complex mixtures of proteins extracted from cells or tissues. The history surrounding the origin of western blotting, the theory behind the western blotting technique, a comprehensive protocol and the uses of western blotting are presented. Lesser known and significant problems in the western blotting field and troubleshooting of common problems are highlighted and discussed. This work is a comprehensive primer and guide for new western blotting researchers and those interested in a better understanding of the technique or getting better results.
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Affiliation(s)
- Rasheed Sule
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
| | - Gabriela Rivera
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
| | - Aldrin V Gomes
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
- Department of Physiology & Membrane Biology, University of California, Davis, Davis, CA 95616, USA
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2
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Liu S, Majeed W, Grigaitis P, Betts MJ, Climer LK, Starkuviene V, Storrie B. Epistatic Analysis of the Contribution of Rabs and Kifs to CATCHR Family Dependent Golgi Organization. Front Cell Dev Biol 2019; 7:126. [PMID: 31428608 PMCID: PMC6687757 DOI: 10.3389/fcell.2019.00126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/26/2019] [Indexed: 01/05/2023] Open
Abstract
Multisubunit members of the CATCHR family: COG and NRZ complexes, mediate intra-Golgi and Golgi to ER vesicle tethering, respectively. We systematically addressed the genetic and functional interrelationships between Rabs, Kifs, and the retrograde CATCHR family proteins: COG3 and ZW10, which are necessary to maintain the organization of the Golgi complex. We scored the ability of siRNAs targeting 19 Golgi-associated Rab proteins and all 44 human Kifs, microtubule-dependent motor proteins, to suppress CATCHR-dependent Golgi fragmentation in an epistatic fluorescent microscopy-based assay. We found that co-depletion of Rab6A, Rab6A’, Rab27A, Rab39A and two minus-end Kifs, namely KIFC3 and KIF25, suppressed both COG3- and ZW10-depletion-induced Golgi fragmentation. ZW10-dependent Golgi fragmentation was suppressed selectively by a separate set of Rabs: Rab11A, Rab33B and the little characterized Rab29. 10 Kifs were identified as hits in ZW10-depletion-induced Golgi fragmentation, and, in contrast to the double suppressive Kifs, these were predominantly plus-end motors. No Rabs or Kifs selectively suppressed COG3-depletion-induced Golgi fragmentation. Protein-protein interaction network analysis indicated putative direct and indirect links between suppressive Rabs and tether function. Validation of the suppressive hits by EM confirmed a restored organization of the Golgi cisternal stack. Based on these outcomes, we propose a three-way competitive model of Golgi organization in which Rabs, Kifs and tethers modulate sequentially the balance between Golgi-derived vesicle formation, consumption, and off-Golgi transport.
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Affiliation(s)
- Shijie Liu
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Waqar Majeed
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Pranas Grigaitis
- Centre for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Heidelberg, Germany
| | - Matthew J Betts
- Centre for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Heidelberg, Germany
| | - Leslie K Climer
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Vytaute Starkuviene
- Centre for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Heidelberg, Germany.,Institute of Pharmacology and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany.,Institute of Biosciences, Vilnius University Life Sciences Centre, Vilnius, Lithuania
| | - Brian Storrie
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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3
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Chuang CF, King CE, Ho BW, Chien KY, Chang YC. Unbiased Proteomic Study of the Axons of Cultured Rat Cortical Neurons. J Proteome Res 2018; 17:1953-1966. [DOI: 10.1021/acs.jproteome.8b00069] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | | | | | - Kun-Yi Chien
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan
- Clinical Proteomics Core Laboratory, Linkou Chang Gung Memorial Hospital, Taoyuan City 33305, Taiwan
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4
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Wasik AA, Schiller HB. Functional proteomics of cellular mechanosensing mechanisms. Semin Cell Dev Biol 2017; 71:118-128. [DOI: 10.1016/j.semcdb.2017.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/23/2017] [Accepted: 06/25/2017] [Indexed: 10/19/2022]
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5
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Lin CH, Chik JHL, Packer NH, Molloy MP. Multidimensional Fractionation Is a Requirement for Quantitation of Golgi-Resident Glycosylation Enzymes from Cultured Human Cells. J Proteome Res 2014; 14:747-55. [DOI: 10.1021/pr500785f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Chi-Hung Lin
- Department
of Chemistry and Biomolecular Sciences, Faculty of Science, and ‡Australian Proteome
Analysis Facility, Macquarie University, Sydney, Australia
| | - Jenny H. L. Chik
- Department
of Chemistry and Biomolecular Sciences, Faculty of Science, and ‡Australian Proteome
Analysis Facility, Macquarie University, Sydney, Australia
| | - Nicolle H. Packer
- Department
of Chemistry and Biomolecular Sciences, Faculty of Science, and ‡Australian Proteome
Analysis Facility, Macquarie University, Sydney, Australia
| | - Mark P. Molloy
- Department
of Chemistry and Biomolecular Sciences, Faculty of Science, and ‡Australian Proteome
Analysis Facility, Macquarie University, Sydney, Australia
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6
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Yang Y, Luo Y, Li X, Yi Y. Differential expression analysis of Golgi apparatus proteomes in hepatocellular carcinomas and the surrounding liver tissues. Hepatol Res 2014; 44:542-50. [PMID: 23621634 DOI: 10.1111/hepr.12151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 04/18/2013] [Accepted: 04/23/2013] [Indexed: 02/08/2023]
Abstract
AIM Hepatocellular carcinoma (HCC) is the sixth most common malignancy worldwide. Liver is the largest human digestive gland with abundant Golgi apparatus involved in cell division, migration and apoptosis and others. METHODS In the present study, Golgi apparatus of HCC and the surrounding liver tissues were isolated by sucrose density gradient centrifugation and identified by electron microscopy and enzymology methods. Using 2-D gel electrophoresis and mass spectrometry, 17 differentially expressed protein of Golgi apparatus in HCC and the surrounding liver tissue were screened and identified in the Mascot database. RESULTS Of those differentially expressed proteins, six were upregulated and 11 were downregulated, some of them were related to the biological processes such as protein sorting, glycosylation, cell cycle regulation, transcription regulation and Golgi integrity. One protein, annexin A5, was verified to be upregulated in HCC by western blot. CONCLUSION The differentially expressed proteins may provide new insight into HCC biology and potential diagnostic and therapeutic biomarkers.
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Affiliation(s)
- Yaying Yang
- Department of Pathology, Molecular Medicine and Tumor Center, China
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7
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Wu L, Han DK. Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics. Expert Rev Proteomics 2014; 3:611-9. [PMID: 17181475 DOI: 10.1586/14789450.3.6.611] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Protein profiling using mass spectrometry technology has emerged as a powerful method for analyzing large-scale protein-expression patterns in cells and tissues. However, a number of challenges are present in proteomics research, one of the greatest being the high degree of protein complexity and huge dynamic range of proteins expressed in the complex biological mixtures, which exceeds six orders of magnitude in cells and ten orders of magnitude in body fluids. Since many important signaling proteins have low expression levels, methods to detect the low-abundance proteins in a complex sample are required. This review will focus on the fundamental fractionation and mass spectrometry techniques currently used for large-scale shotgun proteomics research.
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Affiliation(s)
- Linfeng Wu
- University of Connecticut, School of Medicine, Department of Cell Biology, Farmington, Connecticut, CT 06030, USA.
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8
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Drissi R, Dubois ML, Boisvert FM. Proteomics methods for subcellular proteome analysis. FEBS J 2013; 280:5626-34. [PMID: 24034475 DOI: 10.1111/febs.12502] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 08/14/2013] [Accepted: 08/22/2013] [Indexed: 01/29/2023]
Abstract
The elucidation of the subcellular distribution of proteins under different conditions is a major challenge in cell biology. This challenge is further complicated by the multicompartmental and dynamic nature of protein localization. To address this issue, quantitative proteomics workflows have been developed to reliably identify the protein complement of whole organelles, as well as for protein assignment to subcellular location and relative protein quantification based on different cell culture conditions. Here, we review quantitative MS-based approaches that combine cellular fractionation with proteomic analysis. The application of these methods to the characterization of organellar composition and to the determination of the dynamic nature of protein complexes is improving our understanding of protein functions and dynamics.
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Affiliation(s)
- Romain Drissi
- Department of Anatomy and Cell Biology, Université de Sherbrooke, Québec, Canada
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9
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Hotz A, Hellenbroich Y, Sperner J, Linder-Lucht M, Tacke U, Walter C, Caliebe A, Nagel I, Saunders DE, Wolff G, Martin P, Morris-Rosendahl DJ. Microdeletion 5q14.3 and anomalies of brain development. Am J Med Genet A 2013; 161A:2124-33. [DOI: 10.1002/ajmg.a.36020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 03/31/2013] [Indexed: 02/02/2023]
Affiliation(s)
- Alrun Hotz
- Institute of Human Genetics; Albert-Ludwigs University Medical Centre Freiburg; Freiburg Germany
| | | | | | - Michaela Linder-Lucht
- Zentrum für Kinder- und Jugendmedizin; Albert-Ludwigs-Universitätsklinikum Freiburg; Freiburg Germany
| | - Uta Tacke
- Zentrum für Kinder- und Jugendmedizin; Albert-Ludwigs-Universitätsklinikum Freiburg; Freiburg Germany
| | - Caren Walter
- Institute of Human Genetics; Albert-Ludwigs University Medical Centre Freiburg; Freiburg Germany
| | - Almuth Caliebe
- Institut für Humangenetik; Christian-Albrechts-Universität Kiel; Kiel Germany
| | - Inga Nagel
- Institut für Humangenetik; Christian-Albrechts-Universität Kiel; Kiel Germany
| | - Dawn E. Saunders
- Department of Radiology; Great Ormond Street Hospital; London United Kingdom
| | - Gerhard Wolff
- Institute of Human Genetics; Albert-Ludwigs University Medical Centre Freiburg; Freiburg Germany
| | - Peter Martin
- Séguin Klinik; Epilepsiezentrum Kehl-Kork; Kork Germany
| | - Deborah J. Morris-Rosendahl
- Institute of Human Genetics; Albert-Ludwigs University Medical Centre Freiburg; Freiburg Germany
- National Heart and Lung Institute; Imperial College, London; London United Kingdom
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10
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Dietrich JB. The MEF2 family and the brain: from molecules to memory. Cell Tissue Res 2013; 352:179-90. [DOI: 10.1007/s00441-013-1565-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 01/10/2013] [Indexed: 12/31/2022]
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Metabolism and transportation pathways of GDP-fucose that are required for the O-fucosylation of Notch. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 727:37-46. [PMID: 22399337 DOI: 10.1007/978-1-4614-0899-4_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Notch is a single-pass transmembrane receptor that mediates the local cell-cell interactions necessary for many cell-fate decisions. The extra cellular domain of Notch contains a tandem array of epidermal growth factor-like (EGF-like) repeats. Some of these EGF-like repeats are O-fucosylated by protein O-fucosyltransferase 1 (O-fut1), which is essential for Notch signaling in Drosophila and mouse. This O-fucose is further modified by Fringe, a GlcNAc transferase and other glycosyltransferases (O-fut1 in Drosophila and Pofut1 in mouse), to form an O-linked tetrasaccharide, which modulates Notch's selective binding to its ligands.
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12
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Characterization of the deleted in autism 1 protein family: implications for studying cognitive disorders. PLoS One 2011; 6:e14547. [PMID: 21283809 PMCID: PMC3023760 DOI: 10.1371/journal.pone.0014547] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 12/21/2010] [Indexed: 12/21/2022] Open
Abstract
Autism spectrum disorders (ASDs) are a group of commonly occurring, highly-heritable developmental disabilities. Human genes c3orf58 or Deleted In Autism-1 (DIA1) and cXorf36 or Deleted in Autism-1 Related (DIA1R) are implicated in ASD and mental retardation. Both gene products encode signal peptides for targeting to the secretory pathway. As evolutionary medicine has emerged as a key tool for understanding increasing numbers of human diseases, we have used an evolutionary approach to study DIA1 and DIA1R. We found DIA1 conserved from cnidarians to humans, indicating DIA1 evolution coincided with the development of the first primitive synapses. Nematodes lack a DIA1 homologue, indicating Caenorhabditis elegans is not suitable for studying all aspects of ASD etiology, while zebrafish encode two DIA1 paralogues. By contrast to DIA1, DIA1R was found exclusively in vertebrates, with an origin coinciding with the whole-genome duplication events occurring early in the vertebrate lineage, and the evolution of the more complex vertebrate nervous system. Strikingly, DIA1R was present in schooling fish but absent in fish that have adopted a more solitary lifestyle. An additional DIA1-related gene we named DIA1-Like (DIA1L), lacks a signal peptide and is restricted to the genomes of the echinoderm Strongylocentrotus purpuratus and cephalochordate Branchiostoma floridae. Evidence for remarkable DIA1L gene expansion was found in B. floridae. Amino acid alignments of DIA1 family gene products revealed a potential Golgi-retention motif and a number of conserved motifs with unknown function. Furthermore, a glycine and three cysteine residues were absolutely conserved in all DIA1-family proteins, indicating a critical role in protein structure and/or function. We have therefore identified a new metazoan protein family, the DIA1-family, and understanding the biological roles of DIA1-family members will have implications for our understanding of autism and mental retardation.
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13
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Aziz A, Harrop SP, Bishop NE. DIA1R is an X-linked gene related to Deleted In Autism-1. PLoS One 2011; 6:e14534. [PMID: 21264219 PMCID: PMC3022024 DOI: 10.1371/journal.pone.0014534] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 12/21/2010] [Indexed: 01/28/2023] Open
Abstract
Background Autism spectrum disorders (ASDs) are frequently occurring disorders diagnosed by deficits in three core functional areas: social skills, communication, and behaviours and/or interests. Mental retardation frequently accompanies the most severe forms of ASDs, while overall ASDs are more commonly diagnosed in males. Most ASDs have a genetic origin and one gene recently implicated in the etiology of autism is the Deleted-In-Autism-1 (DIA1) gene. Methodology/Principal Findings Using a bioinformatics-based approach, we have identified a human gene closely related to DIA1, we term DIA1R (DIA1-Related). While DIA1 is autosomal (chromosome 3, position 3q24), DIA1R localizes to the X chromosome at position Xp11.3 and is known to escape X-inactivation. The gene products are of similar size, with DIA1 encoding 430, and DIA1R 433, residues. At the amino acid level, DIA1 and DIA1R are 62% similar overall (28% identical), and both encode signal peptides for targeting to the secretory pathway. Both genes are ubiquitously expressed, including in fetal and adult brain tissue. Conclusions/Significance Examination of published literature revealed point mutations in DIA1R are associated with X-linked mental retardation (XLMR) and DIA1R deletion is associated with syndromes with ASD-like traits and/or XLMR. Together, these results support a model where the DIA1 and DIA1R gene products regulate molecular traffic through the cellular secretory pathway or affect the function of secreted factors, and functional deficits cause disorders with ASD-like symptoms and/or mental retardation.
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Affiliation(s)
- Azhari Aziz
- Department of Microbiology, La Trobe University, Bundoora, Victoria, Australia
| | - Sean P. Harrop
- Department of Microbiology, La Trobe University, Bundoora, Victoria, Australia
| | - Naomi E. Bishop
- Department of Microbiology, La Trobe University, Bundoora, Victoria, Australia
- * E-mail:
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14
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Vogels MW, van Balkom BWM, Kaloyanova DV, Batenburg JJ, Heck AJ, Helms JB, Rottier PJM, de Haan CAM. Identification of host factors involved in coronavirus replication by quantitative proteomics analysis. Proteomics 2010; 11:64-80. [PMID: 21182195 PMCID: PMC7167679 DOI: 10.1002/pmic.201000309] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 09/15/2010] [Accepted: 09/27/2010] [Indexed: 12/24/2022]
Abstract
In this study, we applied a quantitative proteomic approach, based on SILAC, to investigate the interactions of coronaviruses with the secretory pathway of the host cell, with the aim to identify host factors involved in coronavirus replication. Comparison of the protein profiles of Golgi‐enriched fractions of cells that were either mock infected or infected with mouse hepatitis virus revealed the significant depletion or enrichment of 116 proteins. Although ribosomal/nucleic acid binding proteins were enriched in the Golgi‐fractions of mouse hepatitis virus‐infected cells, proteins annotated to localize to several organelles of the secretory pathway were overrepresented among the proteins that were depleted from these fractions upon infection. We hypothesized that proteins, of which the abundance or distribution is affected by infection, are likely to be involved in the virus life cycle. Indeed, depletion of a small subset of the affected proteins by using small interfering RNAs identified several host factors involved in coronavirus infection. Transfection of small interfering RNAs targeting either C11orf59 or Golgi apparatus glycoprotein 1 resulted in increased virus replication, whereas depletion of vesicle‐trafficking protein vesicle‐trafficking protein sec22b enhanced the release of infectious progeny virus. Overexpression of these proteins, on the other hand, had a negative effect on virus replication. Overall, our study shows that the SILAC approach is a suitable tool to study host–pathogen interactions and to identify host proteins involved in virus replication.
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Affiliation(s)
- Mijke W Vogels
- Department of Biochemistry and Cell Biology, Biochemistry Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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15
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Lee YH, Tan HT, Chung MCM. Subcellular fractionation methods and strategies for proteomics. Proteomics 2010; 10:3935-56. [DOI: 10.1002/pmic.201000289] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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16
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Falcón-Pérez JM, Lu SC, Mato JM. Sub-proteome approach to the knowledge of liver. Proteomics Clin Appl 2010; 4:407-15. [PMID: 21137060 DOI: 10.1002/prca.200900123] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Accepted: 08/12/2009] [Indexed: 11/08/2022]
Abstract
In the recent years, global proteomics approaches have been widely used to characterize a number of tissue proteomes including plasma and liver; however, the elevated complexity of these samples in combination with the high abundance of some specific proteins make the study of the lowest abundant proteins difficult. This review is focused on different strategies that have been developed to extend the proteome focused on these two tissues, as, for example, the analysis of sub-cellular proteomes. In this regard, two special kind of extracellular vesicles--exosomes and membrane plasma shedding vesicles--are emerging as excellent biological source both to extend the liver and plasma proteomes and to be applied in the discovery of non-invasive liver-specific disease biomarkers.
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Affiliation(s)
- Juan M Falcón-Pérez
- Metabolomics Unit, CICbioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Bizkaia, Spain.
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Abstract
Exploiting the potential of omics for clinical diagnosis, prognosis, and therapeutic purposes has currently been receiving a lot of attention. In recent years, most of the effort has been put into demonstrating the possible clinical applications of the various omics fields. The cost-effectiveness analysis has been, so far, rather neglected. The cost of omics-derived applications is still very high, but future technological improvements are likely to overcome this problem. In this chapter, we will give a general background of the main omics fields and try to provide some examples of the most successful applications of omics that might be used in clinical diagnosis and in a therapeutic context.
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Affiliation(s)
- Ewa Gubb
- Bioinformatics, Parque Technológico de Bizkaia, Derio, Spain
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18
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Simpson RJ, Lim JW, Moritz RL, Mathivanan S. Exosomes: proteomic insights and diagnostic potential. Expert Rev Proteomics 2009; 6:267-83. [PMID: 19489699 DOI: 10.1586/epr.09.17] [Citation(s) in RCA: 788] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Exosomes are 40-100-nm diameter membrane vesicles of endocytic origin that are released by most cell types upon fusion of multivesicular bodies with the plasma membrane, presumably as a vehicle for cell-free intercellular communication. While early studies focused on their secretion from diverse cell types in vitro, exosomes have now been identified in body fluids such as urine, amniotic fluid, malignant ascites, bronchoalveolar lavage fluid, synovial fluid, breast milk, saliva and blood. Exosomes have pleiotropic biological functions, including immune response, antigen presentation, intracellular communication and the transfer of RNA and proteins. While they have also been implicated in the transport and propagation of infectious cargo, such as prions, and retroviruses, including HIV, suggesting a role in pathological situations, recent studies suggest that the presence of such infectious cargo may be artefacts of exosome-purification strategies. Improvements in mass spectrometry-based proteomic tools, both hardware and software, coupled with improved purification schemes for exosomes, has allowed more in-depth proteome analyses, contributing immensely to our understanding of the molecular composition of exosomes. Proteomic cataloguing of exosomes from diverse cell types has revealed a common set of membrane and cytosolic proteins, suggesting the evolutionary importance of these membrane particles. Additionally, exosomes express an array of proteins that reflect the originating host cell. Recent findings that exosomes contain inactive forms of both mRNA and microRNA that can be transferred to another cell and be functional in that new environment, have initiated many microRNA profiling studies of exosomes circulating in blood. These studies highlight the potential of exosomal microRNA profiles for use as diagnostic biomarkers of disease through a noninvasive blood test. The exacerbated release of exosomes in tumor cells, as evidenced by their increased levels in blood during the late stage of a disease and their overexpression of certain tumor cell biomarkers, suggests an important role of exosomes in diagnosis and biomarker studies. The aim of this article is to provide a brief overview of exosomes, including methods used to isolate and characterize exosomes. New advances in proteomic methods, and both mass spectrometry hardware and informatics tools will be covered briefly.
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Affiliation(s)
- Richard J Simpson
- Ludwig Institute for Cancer Research, PO Box 2008, Royal Melbourne Hospital, Parkville, Victoria 3050, Australia.
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Takatalo MS, Tummers M, Thesleff I, Rönnholm R. Novel Golgi protein, GoPro49, is a specific dental follicle marker. J Dent Res 2009; 88:534-8. [PMID: 19587158 DOI: 10.1177/0022034509338452] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED GoPro49 is a recently identified, novel Golgi protein that is expressed in embryonic mesenchymal tissues, including dental follicle. In the present study, we have tested the hypothesis that the gene is a specific marker for the dental follicle, and examined its expression during the development of mouse incisors and molars. In situ hybridization showed that GoPro49 is expressed in dental follicles from bud to post-eruption stages. The expression is intense throughout the dental follicle during crown development, and persists in the root follicle during root development. In the forming periodontal ligament, GoPro49 expression is down-regulated upon differentiation of the follicle cells to cementoblasts and osteoblasts marked by Bsp1. In cultured dental follicle cells, the GoPro49 protein co-localizes with beta-COP, suggesting that GoPro49 may function in the secretory pathway. We conclude that GoPro49 is a novel, specific marker for the dental follicle and can be used to identify this tissue. ABBREVIATIONS Bsp1, bone sialoprotein 1; GoPro49, Golgi protein 49 kDa; E16, embryonic day 16; HERS, Hertwig's epithelial root sheath; PDL, periodontal ligament; dpn, day post-natal.
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Affiliation(s)
- M S Takatalo
- University of Helsinki, Department of Biological and Environmental Sciences, Division of Biochemistry, P.O. Box 56 (Viikinkaari 5D), University of Helsinki FIN-00014, Finland
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Gauthier DJ, Sobota JA, Ferraro F, Mains RE, Lazure C. Flow cytometry-assisted purification and proteomic analysis of the corticotropes dense-core secretory granules. Proteomics 2008; 8:3848-61. [PMID: 18704904 DOI: 10.1002/pmic.200700969] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The field of organellar proteomics has emerged as an attempt to minimize the complexity of the proteomics data obtained from whole cell and tissue extracts while maximizing the resolution on the protein composition of a single subcellular compartment. Standard methods involve lengthy density-based gradient and/or immunoaffinity purification steps followed by extraction, 1-DE or 2-DE, gel staining, in-gel tryptic digestion, and protein identification by MS. In this paper, we present an alternate approach to purify subcellular organelles containing a fluorescent reporter molecule. The gel-free procedure involves fluorescence-assisted sorting of the secretory granules followed by gentle extraction in a buffer compatible with tryptic digestion and MS. Once the subcellular organelle labeled, this procedure can be done in a single day, requires no major modification to any instrumentation and can be readily adapted to the study of other organelles. When applied to corticotrope secretory granules, it led to a much enriched granular fraction from which numerous proteins could be identified through MS.
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Affiliation(s)
- Daniel J Gauthier
- Neuropeptides Structure and Metabolism Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada
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Sadowski PG, Groen AJ, Dupree P, Lilley KS. Sub-cellular localization of membrane proteins. Proteomics 2008; 8:3991-4011. [DOI: 10.1002/pmic.200800217] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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22
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Expression of the novel Golgi protein GoPro49 is developmentally regulated during mesenchymal differentiation. Dev Dyn 2008; 237:2243-55. [DOI: 10.1002/dvdy.21646] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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23
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Morrow EM, Yoo SY, Flavell SW, Kim TK, Lin Y, Hill RS, Mukaddes NM, Balkhy S, Gascon G, Hashmi A, Al-Saad S, Ware J, Joseph RM, Greenblatt R, Gleason D, Ertelt JA, Apse KA, Bodell A, Partlow JN, Barry B, Yao H, Markianos K, Ferland RJ, Greenberg ME, Walsh CA. Identifying autism loci and genes by tracing recent shared ancestry. Science 2008; 321:218-23. [PMID: 18621663 PMCID: PMC2586171 DOI: 10.1126/science.1157657] [Citation(s) in RCA: 530] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To find inherited causes of autism-spectrum disorders, we studied families in which parents share ancestors, enhancing the role of inherited factors. We mapped several loci, some containing large, inherited, homozygous deletions that are likely mutations. The largest deletions implicated genes, including PCDH10 (protocadherin 10) and DIA1 (deleted in autism1, or c3orf58), whose level of expression changes in response to neuronal activity, a marker of genes involved in synaptic changes that underlie learning. A subset of genes, including NHE9 (Na+/H+ exchanger 9), showed additional potential mutations in patients with unrelated parents. Our findings highlight the utility of "homozygosity mapping" in heterogeneous disorders like autism but also suggest that defective regulation of gene expression after neural activity may be a mechanism common to seemingly diverse autism mutations.
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Affiliation(s)
- Eric M. Morrow
- Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology and Howard Hughes Medical Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- Autism Consortium, 10 Shattuck Street, Boston, MA 02115, USA
| | - Seung-Yun Yoo
- Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology and Howard Hughes Medical Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- Autism Consortium, 10 Shattuck Street, Boston, MA 02115, USA
| | - Steven W. Flavell
- Autism Consortium, 10 Shattuck Street, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Children’s Hospital Boston, and Departments of Neurology and Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Tae-Kyung Kim
- Autism Consortium, 10 Shattuck Street, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Children’s Hospital Boston, and Departments of Neurology and Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Yingxi Lin
- Autism Consortium, 10 Shattuck Street, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Children’s Hospital Boston, and Departments of Neurology and Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert Sean Hill
- Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology and Howard Hughes Medical Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- Autism Consortium, 10 Shattuck Street, Boston, MA 02115, USA
| | - Nahit M. Mukaddes
- Department of Child Psychiatry, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Soher Balkhy
- Department of Neurosciences and Pediatrics, King Faisal Specialist Hospital and Research Centre, Jeddah, Kingdom of Saudi Arabia
| | - Generoso Gascon
- Department of Neurosciences and Pediatrics, King Faisal Specialist Hospital and Research Centre, Jeddah, Kingdom of Saudi Arabia
- Clinical Neurosciences and Pediatrics, Brown University School of Medicine, Providence, Rhode Island 02912, USA
| | - Asif Hashmi
- Department of Neurology, Combined Military Hospital, Lahore, Pakistan
| | | | - Janice Ware
- Autism Consortium, 10 Shattuck Street, Boston, MA 02115, USA
- Developmental Medicine Center, Children’s Hospital Boston, Boston, MA 02115, USA
| | - Robert M. Joseph
- Autism Consortium, 10 Shattuck Street, Boston, MA 02115, USA
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Rachel Greenblatt
- Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology and Howard Hughes Medical Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Danielle Gleason
- Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology and Howard Hughes Medical Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Julia A. Ertelt
- Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology and Howard Hughes Medical Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Kira A. Apse
- Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology and Howard Hughes Medical Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Autism Consortium, 10 Shattuck Street, Boston, MA 02115, USA
| | - Adria Bodell
- Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology and Howard Hughes Medical Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Jennifer N. Partlow
- Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology and Howard Hughes Medical Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Brenda Barry
- Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology and Howard Hughes Medical Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Hui Yao
- Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
| | - Kyriacos Markianos
- Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
| | - Russell J. Ferland
- Department of Biology, Rensselaer Polytechnic Institute, Troy, NY 12180–3590, USA
| | - Michael E. Greenberg
- Autism Consortium, 10 Shattuck Street, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Children’s Hospital Boston, and Departments of Neurology and Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher A. Walsh
- Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology and Howard Hughes Medical Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- Autism Consortium, 10 Shattuck Street, Boston, MA 02115, USA
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Lin CH, Lin CW, Khoo KH. Proteomic identification of specific glycosyltransferases functionally implicated for the biosynthesis of a targeted glyco-epitope. Proteomics 2008; 8:475-83. [DOI: 10.1002/pmic.200700710] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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25
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Cao R, He Q, Zhou J, He Q, Liu Z, Wang X, Chen P, Xie J, Liang S. High-throughput analysis of rat liver plasma membrane proteome by a nonelectrophoretic in-gel tryptic digestion coupled with mass spectrometry identification. J Proteome Res 2008; 7:535-45. [PMID: 18166008 DOI: 10.1021/pr070411f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In-gel digestion is commonly used after proteins are resolved by polyacrylamide gel electrophoresis (SDS-PAGE, 2-DE). It can also be used on its own in conjunction with tandem mass spectrometry (MS/MS) for the direct analysis of complex proteins. Here, we describe a strategy combining isolation of purified plasma membrane, efficient digestion of plasma membrane proteins in polyacrylamide gel, and high-sensitivity analysis by advanced mass spectrometry to create a new rapid and high-throughput method. The plasma membrane protein mixture is directly incorporated into a polyacrylamide gel matrix, After formation of the gel, proteins in the gel section are digested with trypsin, and the resulting peptides are subjected to reversed-phase, high-performance liquid chromatography followed by electrospray ion-trap tandem mass analysis. Using this optimized strategy, we have identified 883 rat liver membrane proteins, of which 490 had a gene ontology (GO) annotation indicating a cellular component, and 294 (60%) of the latter were known integral membrane proteins or membrane proteins. In total, 333 proteins are predicted by the TMHMM 2.0 algorithm to have transmembrane domains (TMDs) and 52% (175 of 333) proteins to contain 2-16 TMDs. The identified membrane proteins provide a broad representation of the rat plasma membrane proteome with little bias evident due to protein p I and molecular weight (MW). Also, membrane proteins with a high GRAVY score (grand average hydrophobicity score) were identified, and basic and acidic membrane proteins were evenly represented. This study not only offered an efficient and powerful method in shotgun proteomics for the identification of proteins of complex plasma membrane samples but also allowed in-depth study of liver membrane proteomes, such as of rat models of liver-related disease. This work represents one of the most comprehensive proteomic analyses of the membrane subproteome of rat liver plasma membrane in general.
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Affiliation(s)
- Rui Cao
- College of Life Sciences, Hunan Normal University, Changsha, P.R. China
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Haynes PA, Roberts TH. Subcellular shotgun proteomics in plants: looking beyond the usual suspects. Proteomics 2007; 7:2963-75. [PMID: 17703495 DOI: 10.1002/pmic.200700216] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this review we examine the current state of analytical methods used for shotgun proteomics experiments in plants. The rapid advances in this field in recent years are discussed, and contrasted with experiments performed using current widely used procedures. We also examine the use of subcellular fractionation approaches as they apply to plant proteomics, and discuss how appropriate sample preparation can produce a great increase in proteome coverage in subsequent analysis. We conclude that the conjunction of these two techniques represents a significant advance in plant proteomics, and the future of plant biology research will continue to be enriched by the ongoing development of proteomic analytical technology.
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Affiliation(s)
- Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
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Brunner Y, Couté Y, Iezzi M, Foti M, Fukuda M, Hochstrasser DF, Wollheim CB, Sanchez JC. Proteomics analysis of insulin secretory granules. Mol Cell Proteomics 2007; 6:1007-17. [PMID: 17317658 DOI: 10.1074/mcp.m600443-mcp200] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Insulin secretory granules (ISGs) are cytoplasmic organelles of pancreatic beta-cells. They are responsible for the storage and secretion of insulin. To date, only about 30 different proteins have been clearly described to be associated with these organelles. However, data from two-dimensional gel electrophoresis analyses suggested that almost 150 different polypeptides might be present within ISGs. The elucidation of the identity and function of the ISG proteins by proteomics strategies would be of considerable help to further understand some of the underlying mechanisms implicated in ISG biogenesis and trafficking. Furthermore it should give the bases to the comprehension of impaired insulin secretion observed during diabetes. A proteomics analysis of an enriched insulin granule fraction from the rat insulin-secreting cell line INS-1E was performed. The efficacy of the fractionation procedure was assessed by Western blot and electron microscopy. Proteins of the ISG fraction were separated by SDS-PAGE, excised from consecutive gel slices, and tryptically digested. Peptides were analyzed by nano-LC-ESI-MS/MS. This strategy identified 130 different proteins that were classified into four structural groups including intravesicular proteins, membrane proteins, novel proteins, and other proteins. Confocal microscopy analysis demonstrated the association of Rab37 and VAMP8 with ISGs in INS-1E cells. In conclusion, the present study identified 130 proteins from which 110 are new proteins associated with ISGs. The elucidation of their role will further help in the understanding of the mechanisms governing impaired insulin secretion during diabetes.
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Affiliation(s)
- Yannick Brunner
- Biomedical Proteomics Research Group, University Medical Center, 1211 Geneva 4, Switzerland
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Devasahayam G, Ritz D, Helliwell SB, Burke DJ, Sturgill TW. Pmr1, a Golgi Ca2+/Mn2+-ATPase, is a regulator of the target of rapamycin (TOR) signaling pathway in yeast. Proc Natl Acad Sci U S A 2006; 103:17840-5. [PMID: 17095607 PMCID: PMC1693834 DOI: 10.1073/pnas.0604303103] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Indexed: 11/18/2022] Open
Abstract
The rapamycin.FKBP12 complex inhibits target of rapamycin (TOR) kinase in TORC1. We screened the yeast nonessential gene deletion collection to identify mutants that conferred rapamycin resistance, and we identified PMR1, encoding the Golgi Ca2+/Mn2+ -ATPase. Deleting PMR1 in two genetic backgrounds confers rapamycin resistance. Epistasis analyses show that Pmr1 functions upstream from Npr1 and Gln-3 in opposition to Lst8, a regulator of TOR. Npr1 kinase is largely cytoplasmic, and a portion localizes to the Golgi where amino acid permeases are modified and sorted. Nuclear translocation of Gln-3 and Gln-3 reporter activity in pmr1 cells are impaired, but expression of functional Gap1 in the plasma membrane of a pmr1 strain in response to nitrogen limitation is enhanced. These two phenotypes suggest up-regulation of Npr1 function in the absence of Pmr1. Together, our results establish that Pmr1-dependent Ca2+ and/or Mn2+ ion homeostasis is necessary for TOR signaling.
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Affiliation(s)
| | - Danilo Ritz
- Division of Biochemistry, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Stephen B. Helliwell
- Division of Biochemistry, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Daniel J. Burke
- Biochemistry and Molecular Genetics, University of Virginia Health Sciences Center, 1300 Jefferson Park Avenue, Charlottesville, VA 22908; and
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