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Satori CP, Henderson MM, Krautkramer EA, Kostal V, Distefano MM, Arriaga EA. Bioanalysis of eukaryotic organelles. Chem Rev 2013; 113:2733-811. [PMID: 23570618 PMCID: PMC3676536 DOI: 10.1021/cr300354g] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Chad P. Satori
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Michelle M. Henderson
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Elyse A. Krautkramer
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Vratislav Kostal
- Tescan, Libusina trida 21, Brno, 623 00, Czech Republic
- Institute of Analytical Chemistry ASCR, Veveri 97, Brno, 602 00, Czech Republic
| | - Mark M. Distefano
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Edgar A. Arriaga
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
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Liu J, Liu X, Baeyens WRG, Delanghe JR, Ouyang J. A Novel Probe Au(III) for Chemiluminescent Image Detection of Protein Blots on Nitrocellulose Membranes. J Proteome Res 2008; 7:1884-90. [DOI: 10.1021/pr700616u] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jia Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Xia Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Willy R. G. Baeyens
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Joris R. Delanghe
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Jin Ouyang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
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Boettner DR, Huston CD, Linford AS, Buss SN, Houpt E, Sherman NE, Petri WA. Entamoeba histolytica phagocytosis of human erythrocytes involves PATMK, a member of the transmembrane kinase family. PLoS Pathog 2008; 4:e8. [PMID: 18208324 PMCID: PMC2211552 DOI: 10.1371/journal.ppat.0040008] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Accepted: 12/10/2007] [Indexed: 11/19/2022] Open
Abstract
Entamoeba histolytica is the cause of amebic colitis and liver abscess. This parasite induces apoptosis in host cells and utilizes exposed ligands such as phosphatidylserine to ingest the apoptotic corpses and invade deeper into host tissue. The purpose of this work was to identify amebic proteins involved in the recognition and ingestion of dead cells. A member of the transmembrane kinase family, phagosome-associated TMK96 (PATMK), was identified in a proteomic screen for early phagosomal proteins. Anti-peptide affinity-purified antibody produced against PATMK demonstrated that it was a type I integral membrane protein that was expressed on the trophozoite surface, and that co-localized with human erythrocytes at the site of contact. The role of PATMK in erythrophagocytosis in vitro was demonstrated by: (i) incubation of ameba with anti-PATMK antibodies; (ii) PATMK mRNA knock-down using a novel shRNA expression system; and (iii) expression of a carboxy-truncation of PATMK (PATMKΔ932). Expression of the carboxy-truncation of PATMKΔ932 also caused a specific reduction in the ability of E. histolytica to establish infection in the intestinal model of amebiasis, however these amebae retained the ability to cause hepatic abscesses when directly injected in the liver. In conclusion, PATMK was identified as a member of the TMK family that participates in erythrophagocytosis and is uniquely required for intestinal infection. There is a highly ordered process by which the parasite Entamoeba histolytica interacts with human cells. Adherence via a parasite lectin is followed in seconds by killing, with only the corpse and not a living cell ingested by the ameba. This process is so central to pathogenesis that clinicians use the presence of ingested erythrocytes to identify E. histolytica and distinguish it from harmless commensal amebae of the gut. We hypothesized that identification of molecules involved in the ingestion of the corpse might provide insight into how amebae cause colitis. We identified a member of the transmembrane kinase family as an early component of the phagosome. Inhibition of this kinase blocked red cell ingestion and prevented amebae from colonizing and invading the gut. There was no impact on dominant-negative parasites to cause liver abscess, suggesting the pathogenesis program differs between anatomic sites. Future studies of the transmembrane kinanse in erythrophagocytosis may provide insight into how amebae colonize and invade the gut, with the ultimate goal of preventing disease.
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Affiliation(s)
- Douglas R Boettner
- Department of Microbiology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Christopher D Huston
- Department of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Department of Microbiology, University of Vermont, Burlington, Vermont, United States of America
| | - Alicia S Linford
- Department of Microbiology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Sarah N Buss
- Department of Microbiology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Eric Houpt
- Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Nicholas E Sherman
- Department of Microbiology, University of Virginia, Charlottesville, Virginia, United States of America
| | - William A Petri
- Department of Microbiology, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Pathology, University of Virginia, Charlottesville, Virginia, United States of America
- * To whom correspondence should be addressed. E-mail:
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Liu J, Ouyang J, Baeyens WRG, Delanghe JR, Wang Z, Liu J, Zhang H. A novel probe for chemiluminescent image detection of proteins in two-dimensional gel electrophoresis. Electrophoresis 2008; 29:716-25. [DOI: 10.1002/elps.200700424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Garin J, Diez R, Kieffer S, Dermine JF, Duclos S, Gagnon E, Sadoul R, Rondeau C, Desjardins M. The phagosome proteome: insight into phagosome functions. J Cell Biol 2001; 152:165-80. [PMID: 11149929 PMCID: PMC2193653 DOI: 10.1083/jcb.152.1.165] [Citation(s) in RCA: 550] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Phagosomes are key organelles for the innate ability of macrophages to participate in tissue remodeling, clear apoptotic cells, and restrict the spread of intracellular pathogens. To understand the functions of phagosomes, we initiated the systematic identification of their proteins. Using a proteomic approach, we identified >140 proteins associated with latex bead-containing phagosomes. Among these were hydrolases, proton pump ATPase subunits, and proteins of the fusion machinery, validating our approach. A series of unexpected proteins not previously described along the endocytic/phagocytic pathways were also identified, including the apoptotic proteins galectin3, Alix, and TRAIL, the anti-apoptotic protein 14-3-3, the lipid raft-enriched flotillin-1, the anti-microbial molecule lactadherin, and the small GTPase rab14. In addition, 24 spots from which the peptide masses could not be matched to entries in any database potentially represent new phagosomal proteins. The elaboration of a two-dimensional gel database of >160 identified spots allowed us to analyze how phagosome composition is modulated during phagolysosome biogenesis. Remarkably, during this process, hydrolases are not delivered in bulk to phagosomes, but are instead acquired sequentially. The systematic characterization of phagosome proteins provided new insights into phagosome functions and the protein or groups of proteins involved in and regulating these functions.
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Affiliation(s)
- Jérome Garin
- Laboratoire de Chimie des protéines, Commissariat a l'Energie Atomique, 38054 Grenoble, France
| | - Roberto Diez
- Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montréal, Quebec, Canada, H3C 3J7
| | - Sylvie Kieffer
- Laboratoire de Chimie des protéines, Commissariat a l'Energie Atomique, 38054 Grenoble, France
| | - Jean-François Dermine
- Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montréal, Quebec, Canada, H3C 3J7
| | - Sophie Duclos
- Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montréal, Quebec, Canada, H3C 3J7
| | - Etienne Gagnon
- Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montréal, Quebec, Canada, H3C 3J7
| | - Remy Sadoul
- Neurodégénérescence et Plasticité, Hopital A. Michallon, Centre Hospitalier Universitaire, 38043 Grenoble, France
| | - Christiane Rondeau
- Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montréal, Quebec, Canada, H3C 3J7
| | - Michel Desjardins
- Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montréal, Quebec, Canada, H3C 3J7
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Wu CC, Yates JR, Neville MC, Howell KE. Proteomic analysis of two functional states of the Golgi complex in mammary epithelial cells. Traffic 2000; 1:769-82. [PMID: 11208067 DOI: 10.1034/j.1600-0854.2000.011004.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Organellar compartments involved in secretion are expanded during the transition from late pregnancy (basal secretory state) to lactation (maximal secretory state) to accommodate for the increased secretory function required for copious milk production in mammary epithelial cells. The Golgi complex is a major organelle of the secretory pathway and functions to sort, package, distribute, and post-translationally modify newly synthesized proteins and membrane lipids. These complex functions of the Golgi are reflected in the protein complement of the organelle. Therefore, using proteomics, the protein complements of Golgi fractions isolated at two functional states (basal and maximal) were compared to identify some of the molecular changes that occur during this transition. This global analysis has revealed that only a subset of the total proteins is upregulated from steady state during the transition. Identification of these proteins by tandem mass spectrometry has revealed several classes of proteins involved in the regulation of membrane fusion and secretion. This first installment of the functional proteomic analysis of the Golgi complex begins to define the molecular basis for the transition from basal to maximal secretion.
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Affiliation(s)
- C C Wu
- Department of Cellular and Structural Biology, University of Colorado Health Sciences Center, 4200 E. 9th Avenue B-III, Denver, CO 80262, USA
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Duclos S, Desjardins M. Subversion of a young phagosome: the survival strategies of intracellular pathogens. Cell Microbiol 2000; 2:365-77. [PMID: 11207592 DOI: 10.1046/j.1462-5822.2000.00066.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- S Duclos
- Département de pathologie et biologie cellulaire, Université de Montréal, QC, Canada
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Wu CC, Howell KE, Neville MC, Yates JR, McManaman JL. Proteomics reveal a link between the endoplasmic reticulum and lipid secretory mechanisms in mammary epithelial cells. Electrophoresis 2000; 21:3470-82. [PMID: 11079566 DOI: 10.1002/1522-2683(20001001)21:16<3470::aid-elps3470>3.0.co;2-g] [Citation(s) in RCA: 167] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The synthesis and secretion of lipids by mammary epithelial cells is a highly ordered process that involves several distinct steps. Triacylglycerols are synthesized in the endoplasmic reticulum and incorporated into microlipid droplets which coalesce into cytoplasmic lipid droplets. These are vectorially transported to the apical plasma membrane where they are secreted into the milk surrounded by a membrane bilayer. The origin of this membrane as well as the mechanism by which cytoplasmic lipid droplets form and become surrounded by membrane is poorly understood. Proteomic analysis of the protein composition of milk fat globules and cytoplasmic lipid droplet has revealed that the endoplasmic reticulum is not only involved in the synthesis of the lipid but also potentially contributes to the membrane component of milk fat globules. The proteins identified suggest possible mechanisms of multiple steps during this process. Completion of the proteome of milk fat globule membranes and cytoplasmic lipid droplets will provide the necessary reporter molecules to follow and dissect the mechanisms of the sorting and ultimate secretion of cytoplasmic lipid droplets.
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Affiliation(s)
- C C Wu
- Department of Cellular and Structural Biology, University of Colorado Health Sciences Center, Denver 80262, USA
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Abstract
Acquisition of large bodies of genomic sequence is facilitating the use of global techniques to assay cellular function. DNA microarrays have enabled the measurement of global mRNA levels and are able to detect changes in gene expression between different cellular states. Since much of the regulation of physiological processes happens post-translationally, measuring only the mRNA levels gives an incomplete picture. Strategies to assay global expression, localization, or interaction of proteins fall into the emerging field of proteomics, with various combinations of techniques being utilized to separate and identify proteins. In this review, we will present a general overview of the currently available proteomic tools and then give examples of how these tools are being utilized to answer questions in cell biology.
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Affiliation(s)
- W H McDonald
- Department of Cell Biology, 10550 N. Torrey Pines Rd. SR11, Scripps Research Institute, La Jolla, CA 92037, USA
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Fialka I, Pasquali C, Kurzbauer R, Lottspeich F, Huber LA. Loss of epithelial polarity is accompanied by differential association of proteins with intracellular membranes. Electrophoresis 1999; 20:331-43. [PMID: 10197440 DOI: 10.1002/(sici)1522-2683(19990201)20:2<331::aid-elps331>3.0.co;2-a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cellular membranes play an important role in the formation and maintenance of epithelial polarity, which is lost early during carcinogenesis. We set out to identify membrane proteins which are altered during loss of cell polarity in mammary epithelium. As a model system we used murine mammary epithelial cells expressing the conditional oncoprotein c-JunER, which induces a reversible loss of polarity upon beta-estradiol-driven activation [1]. When grown either in the absence or presence of hormone, these cells exhibit a polarized or unpolarized phenotype, respectively. Different membrane fractions of polarized or unpolarized cells were analyzed by two-dimensional electrophoresis (2-DE) and differentially expressed membrane proteins were identified. To distinguish between transmembrane orientation and peripheral attachment of these proteins, were performed extractions with carbonate at high pH or with Triton X-114. In addition, cytosolic proteins of both states were analyzed to investigate their differential association with distinct membrane fractions. We found ten protein spots preferentially or exclusively in polarized cells and 17 other proteins as being upregulated during loss of polarity. Some of the peripheral membrane proteins were identified by microsequencing. The resident Golgi protein nucleobindin and fructose-bisphosphate aldolase were preferentially associated with membranes of polarized cells, whereas alphaB crystallin was detected exclusively and in high amounts in unpolarized cells.
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Affiliation(s)
- I Fialka
- Institute of Molecular Pathology, Vienna, Austria
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11
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Santoni V, Rouquié D, Doumas P, Mansion M, Boutry M, Degand H, Dupree P, Packman L, Sherrier J, Prime T, Bauw G, Posada E, Rouzé P, Dehais P, Sahnoun I, Barlier I, Rossignol M. Use of a proteome strategy for tagging proteins present at the plasma membrane. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1998; 16:633-41. [PMID: 10036779 DOI: 10.1046/j.1365-313x.1998.00335.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A plasma membrane (PM) fraction was purified from Arabidopsis thaliana using a standard procedure and analyzed by two-dimensional (2D) gel electrophoresis. The proteins were classified according to their relative abundance in PM or cell membrane supernatant fractions. Eighty-two of the 700 spots detected on the PM 2D gels were microsequenced. More than half showed sequence similarity to proteins of known function. Of these, all the spots in the PM-specific and PM-enriched fractions, together with half of the spots with similar abundance in PM fraction and supernatant, have previously been found at the PM, supporting the validity of this approach. Extrapolation from this analysis indicates that (i) approximately 550 polypeptides found at the PM could be resolved on 2D gels; (ii) that numerous proteins with multiple locations are found at the PM; and (iii) that approximately 80% of PM-specific spots correspond to proteins with unknown function. Among the later, half are represented by ESTs or cDNAs in databases. In this way, several unknown gene products were potentially localized to the PM. These data are discussed with respect to the efficiency of organelle proteome approaches to link systematically genomic data to genome expression. It is concluded that generalized proteomes can constitute a powerful resource, with future completion of Arabidopsis genome sequencing, for genome-wide exploration of plant function.
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Affiliation(s)
- V Santoni
- Biochimie et Physiologie Moléculaire des Plantes, INRA/ENSA-M/CNRS URA 2133, Montpellier, France
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