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Munawar N, Olivero G, Jerman E, Doyle B, Streubel G, Wynne K, Bracken A, Cagney G. Native gel analysis of macromolecular protein complexes in cultured mammalian cells. Proteomics 2015. [DOI: https://doi.org/10.1002/pmic.201500045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nayla Munawar
- School of Biomolecular and Biomedical Research; University College Dublin; Belfield Ireland
| | - Giorgio Olivero
- School of Biomolecular and Biomedical Research; University College Dublin; Belfield Ireland
| | - Emilia Jerman
- Smurfit Institute of Genetics; Trinity College; Dublin Ireland
| | - Benjamin Doyle
- School of Biomolecular and Biomedical Research; University College Dublin; Belfield Ireland
| | | | - Kieran Wynne
- School of Biomolecular and Biomedical Research; University College Dublin; Belfield Ireland
| | - Adrian Bracken
- Smurfit Institute of Genetics; Trinity College; Dublin Ireland
| | - Gerard Cagney
- School of Biomolecular and Biomedical Research; University College Dublin; Belfield Ireland
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102
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Wirsing L, Klawonn F, Sassen WA, Lünsdorf H, Probst C, Hust M, Mendel RR, Kruse T, Jänsch L. Linear Discriminant Analysis Identifies Mitochondrially Localized Proteins in Neurospora crassa. J Proteome Res 2015. [PMID: 26215788 DOI: 10.1021/acs.jproteome.5b00329] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Besides their role as powerhouses, mitochondria play a pivotal role in the spatial organization of numerous enzymatic functions. They are connected to the ER, and many pathways are organized through the mitochondrial membranes. Thus, the precise definition of mitochondrial proteomes remains a challenging task. Here, we have established a proteomic strategy to accurately determine the mitochondrial localization of proteins from the fungal model organism Neurospora crassa. This strategy relies on both highly pure mitochondria as well as the quantitative monitoring of mitochondrial components along their consecutive enrichment. Pure intact mitochondria were obtained by a multistep approach combining differential and density Percoll (ultra) centrifugations. When compared with three other intermediate enrichment stages, peptide sequencing and quantitative profiling of pure mitochondrial fractions revealed prototypic regulatory profiles of per se mitochondrial components. These regulatory profiles constitute a distinct cluster defining the mitochondrial compartment and support linear discriminant analyses, which rationalized the annotation process. In total, this approach experimentally validated the mitochondrial localization of 512 proteins including 57 proteins that had not been reported for N. crassa before.
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Affiliation(s)
- Lisette Wirsing
- Cellular Proteomics Research Group, §Central Facility for Microscopy, Helmholtz Centre for Infection Research , 38124 Braunschweig, Germany
| | - Frank Klawonn
- Cellular Proteomics Research Group, §Central Facility for Microscopy, Helmholtz Centre for Infection Research , 38124 Braunschweig, Germany.,Department of Computer Science, Ostfalia University of Applied Sciences , 38302 Wolfenbüttel, Germany
| | | | | | | | | | | | | | - Lothar Jänsch
- Cellular Proteomics Research Group, §Central Facility for Microscopy, Helmholtz Centre for Infection Research , 38124 Braunschweig, Germany
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103
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Larance M, Lamond AI. Multidimensional proteomics for cell biology. Nat Rev Mol Cell Biol 2015; 16:269-80. [DOI: 10.1038/nrm3970] [Citation(s) in RCA: 311] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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104
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Jorrín-Novo JV, Pascual J, Sánchez-Lucas R, Romero-Rodríguez MC, Rodríguez-Ortega MJ, Lenz C, Valledor L. Fourteen years of plant proteomics reflected in Proteomics: moving from model species and 2DE-based approaches to orphan species and gel-free platforms. Proteomics 2015; 15:1089-112. [PMID: 25487722 DOI: 10.1002/pmic.201400349] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 10/23/2014] [Accepted: 12/04/2014] [Indexed: 12/21/2022]
Abstract
In this article, the topic of plant proteomics is reviewed based on related papers published in the journal Proteomics since publication of the first issue in 2001. In total, around 300 original papers and 41 reviews published in Proteomics between 2000 and 2014 have been surveyed. Our main objective for this review is to help bridge the gap between plant biologists and proteomics technologists, two often very separate groups. Over the past years a number of reviews on plant proteomics have been published . To avoid repetition we have focused on more recent literature published after 2010, and have chosen to rather make continuous reference to older publications. The use of the latest proteomics techniques and their integration with other approaches in the "systems biology" direction are discussed more in detail. Finally we comment on the recent history, state of the art, and future directions of plant proteomics, using publications in Proteomics to illustrate the progress in the field. The review is organized into two major blocks, the first devoted to provide an overview of experimental systems (plants, plant organs, biological processes) and the second one to the methodology.
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Affiliation(s)
- Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Cordoba-CeiA3, Cordoba, Spain
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105
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Arango-Argoty GA, Jaramillo-Garzón JA, Castellanos-Domínguez G. Feature extraction by statistical contact potentials and wavelet transform for predicting subcellular localizations in gram negative bacterial proteins. J Theor Biol 2015; 364:121-30. [PMID: 25219623 DOI: 10.1016/j.jtbi.2014.08.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 08/27/2014] [Accepted: 08/28/2014] [Indexed: 11/16/2022]
Abstract
Predicting the localization of a protein has become a useful practice for inferring its function. Most of the reported methods to predict subcellular localizations in Gram-negative bacterial proteins make use of standard protein representations that generally do not take into account the distribution of the amino acids and the structural information of the proteins. Here, we propose a protein representation based on the structural information contained in the pairwise statistical contact potentials. The wavelet transform decodes the information contained in the primary structure of the proteins, allowing the identification of patterns along the proteins, which are used to characterize the subcellular localizations. Then, a support vector machine classifier is trained to categorize them. Cellular compartments like periplasm and extracellular medium are difficult to predict, having a high false negative rate. The wavelet-based method achieves an overall high performance while maintaining a low false negative rate, particularly, on "periplasm" and "extracellular medium". Our results suggest the proposed protein characterization is a useful alternative to representing and predicting protein sequences over the classical and cutting edge protein depictions.
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Affiliation(s)
- G A Arango-Argoty
- Signal Processing and Recognition Group, Universidad Nacional de Colombia, s. Manizales, Campus La Nubia, km 7 via al Magdalena, Manizales, Colombia; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave, Pittsburgh, PA 15260, USA.
| | - J A Jaramillo-Garzón
- Signal Processing and Recognition Group, Universidad Nacional de Colombia, s. Manizales, Campus La Nubia, km 7 via al Magdalena, Manizales, Colombia; Research Center of the Instituto Tecnologico Metropolitano, Calle 73 No 76A-354, Medellín, Colombia
| | - G Castellanos-Domínguez
- Signal Processing and Recognition Group, Universidad Nacional de Colombia, s. Manizales, Campus La Nubia, km 7 via al Magdalena, Manizales, Colombia
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106
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Zargar SM, Fujiwara M, Inaba S, Kobayashi M, Kurata R, Ogata Y, Fukao Y. Correlation analysis of proteins responsive to Zn, Mn, or Fe deficiency in Arabidopsis roots based on iTRAQ analysis. PLANT CELL REPORTS 2015; 34:157-66. [PMID: 25366567 DOI: 10.1007/s00299-014-1696-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/21/2014] [Accepted: 10/07/2014] [Indexed: 05/25/2023]
Abstract
For discovering the functional correlation between the identified and quantified proteins by iTRAQ analysis, here we propose a correlation analysis method with cosine correlation coefficients as a powerful tool. iTRAQ analysis is a quantitative proteomics approach that enables identification and quantification of a large number of proteins. In order to obtain proteins responsive to Zn, Mn, or Fe mineral deficiency, we conducted iTRAQ analysis using a microsomal fraction of protein extractions from Arabidopsis root tissues. We identified and quantified 730 common proteins in three biological replicates with less than 1 % false discovery rate. To determine the role of these proteins in tolerating mineral deficiencies and their relation to each other, we calculated cosine correlation coefficients and represented the outcomes on a correlation map for visual understanding of functional relations among the identified proteins. Functionally similar proteins were gathered into the same clusters. Interestingly, a cluster of proteins (FRO2, IRT1, AHA2, PDR9/ABCG37, and GLP5) highly responsive to Fe deficiency was identified, which included both known and unknown novel proteins involved in tolerating Fe deficiency. We propose that the correlation analysis with the cosine correlation coefficients is a powerful method for finding important proteins of interest to several biological processes through comprehensive data sets.
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Affiliation(s)
- Sajad Majeed Zargar
- Plant Global Education Project Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama, 8916-5, Ikoma, 630-0192, Japan
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Scott NE, Brown LM, Kristensen AR, Foster LJ. Development of a computational framework for the analysis of protein correlation profiling and spatial proteomics experiments. J Proteomics 2014; 118:112-29. [PMID: 25464368 DOI: 10.1016/j.jprot.2014.10.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/18/2014] [Accepted: 10/27/2014] [Indexed: 01/12/2023]
Abstract
UNLABELLED Standard approaches to studying an interactome do not easily allow conditional experiments but in recent years numerous groups have demonstrated the potential for co-fractionation/co-migration based approaches to assess an interactome at a similar sensitivity and specificity yet significantly lower cost and higher speed than traditional approaches. Unfortunately, there is as yet no implementation of the bioinformatics tools required to robustly analyze co-fractionation data in a way that can also integrate the valuable information contained in biological replicates. Here we have developed a freely available, integrated bioinformatics solution for the analysis of protein correlation profiling SILAC data. This modular solution allows the deconvolution of protein chromatograms into individual Gaussian curves enabling the use of these chromatography features to align replicates and assemble a consensus map of features observed across replicates; the chromatograms and individual curves are then used to quantify changes in protein interactions and construct the interactome. We have applied this workflow to the analysis of HeLa cells infected with a Salmonella enterica serovar Typhimurium infection model where we can identify specific interactions that are affected by the infection. These bioinformatics tools simplify the analysis of co-fractionation/co-migration data to the point where there is no specialized knowledge required to measure an interactome in this way. BIOLOGICAL SIGNIFICANCE We describe a set of software tools for the bioinformatics analysis of co-migration/co-fractionation data that integrates the results from multiple replicates to generate an interactome, including the impact on individual interactions of any external perturbation. This article is part of a Special Issue entitled: Protein dynamics in health and disease. Guest Editors: Pierre Thibault and Anne-Claude Gingras.
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Affiliation(s)
- Nichollas E Scott
- Centre for High-throughput Biology, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada.
| | - Lyda M Brown
- Centre for High-throughput Biology, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
| | - Anders R Kristensen
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver V5Z 4S6, British Columbia, Canada
| | - Leonard J Foster
- Centre for High-throughput Biology, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada.
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108
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Borner GHH, Hein MY, Hirst J, Edgar JR, Mann M, Robinson MS. Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein-protein interactions. Mol Biol Cell 2014; 25:3178-94. [PMID: 25165137 PMCID: PMC4196868 DOI: 10.1091/mbc.e14-07-1198] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/06/2014] [Accepted: 08/07/2014] [Indexed: 01/06/2023] Open
Abstract
We developed "fractionation profiling," a method for rapid proteomic analysis of membrane vesicles and protein particles. The approach combines quantitative proteomics with subcellular fractionation to generate signature protein abundance distribution profiles. Functionally associated groups of proteins are revealed through cluster analysis. To validate the method, we first profiled >3500 proteins from HeLa cells and identified known clathrin-coated vesicle proteins with >90% accuracy. We then profiled >2400 proteins from Drosophila S2 cells, and we report the first comprehensive insect clathrin-coated vesicle proteome. Of importance, the cluster analysis extends to all profiled proteins and thus identifies a diverse range of known and novel cytosolic and membrane-associated protein complexes. We show that it also allows the detailed compositional characterization of complexes, including the delineation of subcomplexes and subunit stoichiometry. Our predictions are presented in an interactive database. Fractionation profiling is a universal method for defining the clathrin-coated vesicle proteome and may be adapted for the analysis of other types of vesicles and particles. In addition, it provides a versatile tool for the rapid generation of large-scale protein interaction maps.
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Affiliation(s)
- Georg H H Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Marco Y Hein
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Margaret S Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
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109
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Rennie EA, Ebert B, Miles GP, Cahoon RE, Christiansen KM, Stonebloom S, Khatab H, Twell D, Petzold CJ, Adams PD, Dupree P, Heazlewood JL, Cahoon EB, Scheller HV. Identification of a sphingolipid α-glucuronosyltransferase that is essential for pollen function in Arabidopsis. THE PLANT CELL 2014; 26:3314-25. [PMID: 25122154 PMCID: PMC4371831 DOI: 10.1105/tpc.114.129171] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 06/20/2014] [Accepted: 07/22/2014] [Indexed: 05/20/2023]
Abstract
Glycosyl inositol phosphorylceramide (GIPC) sphingolipids are a major class of lipids in fungi, protozoans, and plants. GIPCs are abundant in the plasma membrane in plants, comprising around a quarter of the total lipids in these membranes. Plant GIPCs contain unique glycan decorations that include a conserved glucuronic acid (GlcA) residue and various additional sugars; however, no proteins responsible for glycosylating GIPCs have been identified to date. Here, we show that the Arabidopsis thaliana protein INOSITOL PHOSPHORYLCERAMIDE GLUCURONOSYLTRANSFERASE1 (IPUT1) transfers GlcA from UDP-GlcA to GIPCs. To demonstrate IPUT1 activity, we introduced the IPUT1 gene together with genes for a UDP-glucose dehydrogenase from Arabidopsis and a human UDP-GlcA transporter into a yeast mutant deficient in the endogenous inositol phosphorylceramide (IPC) mannosyltransferase. In this engineered yeast strain, IPUT1 transferred GlcA to IPC. Overexpression or silencing of IPUT1 in Nicotiana benthamiana resulted in an increase or a decrease, respectively, in IPC glucuronosyltransferase activity in vitro. Plants in which IPUT1 was silenced accumulated IPC, the immediate precursor, as well as ceramides and glucosylceramides. Plants overexpressing IPUT1 showed an increased content of GIPCs. Mutations in IPUT1 are not transmitted through pollen, indicating that these sphingolipids are essential in plants.
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Affiliation(s)
- Emilie A Rennie
- Joint BioEnergy Institute, Emeryville, California 94608 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Berit Ebert
- Joint BioEnergy Institute, Emeryville, California 94608 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Godfrey P Miles
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Rebecca E Cahoon
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - Katy M Christiansen
- Joint BioEnergy Institute, Emeryville, California 94608 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Solomon Stonebloom
- Joint BioEnergy Institute, Emeryville, California 94608 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Hoda Khatab
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - David Twell
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, California 94608 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, California 94608 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 Department of Bioengineering, University of California, Berkeley, California 94720
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Joshua L Heazlewood
- Joint BioEnergy Institute, Emeryville, California 94608 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Edgar B Cahoon
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - Henrik Vibe Scheller
- Joint BioEnergy Institute, Emeryville, California 94608 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
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110
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Burkhart JM, Gambaryan S, Watson SP, Jurk K, Walter U, Sickmann A, Heemskerk JWM, Zahedi RP. What can proteomics tell us about platelets? Circ Res 2014; 114:1204-19. [PMID: 24677239 DOI: 10.1161/circresaha.114.301598] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
More than 130 years ago, it was recognized that platelets are key mediators of hemostasis. Nowadays, it is established that platelets participate in additional physiological processes and contribute to the genesis and progression of cardiovascular diseases. Recent data indicate that the platelet proteome, defined as the complete set of expressed proteins, comprises >5000 proteins and is highly similar between different healthy individuals. Owing to their anucleate nature, platelets have limited protein synthesis. By implication, in patients experiencing platelet disorders, platelet (dys)function is almost completely attributable to alterations in protein expression and dynamic differences in post-translational modifications. Modern platelet proteomics approaches can reveal (1) quantitative changes in the abundance of thousands of proteins, (2) post-translational modifications, (3) protein-protein interactions, and (4) protein localization, while requiring only small blood donations in the range of a few milliliters. Consequently, platelet proteomics will represent an invaluable tool for characterizing the fundamental processes that affect platelet homeostasis and thus determine the roles of platelets in health and disease. In this article we provide a critical overview on the achievements, the current possibilities, and the future perspectives of platelet proteomics to study patients experiencing cardiovascular, inflammatory, and bleeding disorders.
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Affiliation(s)
- Julia M Burkhart
- From the Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany (J.M.B., A.S., R.P.Z); Institut für Klinische Biochemie und Pathobiochemie, Universitätsklinikum Würzburg, Würzburg, Germany (S.G.); Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia (S.G.); Centre for Cardiovascular Sciences, Institute for Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom (S.P.W.); Center for Thrombosis and Hemostasis, Universitätsklinikum der Johannes Gutenberg-Universität Mainz, Mainz, Germany (K.J., U.W.); Medizinisches Proteom Center, Ruhr Universität Bochum, Bochum, Germany (A.S.); Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom (A.S.); and Department of Biochemistry, CARIM, Maastricht University, Maastricht, The Netherlands (J.W.M.H.)
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111
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Arrivault S, Guenther M, Florian A, Encke B, Feil R, Vosloh D, Lunn JE, Sulpice R, Fernie AR, Stitt M, Schulze WX. Dissecting the subcellular compartmentation of proteins and metabolites in arabidopsis leaves using non-aqueous fractionation. Mol Cell Proteomics 2014; 13:2246-59. [PMID: 24866124 DOI: 10.1074/mcp.m114.038190] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Non-aqueous fractionation is a technique for the enrichment of different subcellular compartments derived from lyophilized material. It was developed to study the subcellular distribution of metabolites. Here we analyzed the distribution of about 1,000 proteins and 70 metabolites, including 22 phosphorylated intermediates in wild-type Arabidopsis rosette leaves, using non-aqueous gradients divided into 12 fractions. Good separation of plastidial, cytosolic, and vacuolar metabolites and proteins was achieved, but cytosolic, mitochondrial, and peroxisomal proteins clustered together. There was considerable heterogeneity in the fractional distribution of transcription factors, ribosomal proteins, and subunits of the vacuolar-ATPase, indicating diverse compartmental location. Within the plastid, sub-organellar separation of thylakoids and stromal proteins was observed. Metabolites from the Calvin-Benson cycle, photorespiration, starch and sucrose synthesis, glycolysis, and the tricarboxylic acid cycle grouped with their associated proteins of the respective compartment. Non-aqueous fractionation thus proved to be a powerful method for the study of the organellar, and in some cases sub-organellar, distribution of proteins and their association with metabolites. It remains the technique of choice for the assignment of subcellular location to metabolites in intact plant tissues, and thus the technique of choice for doing combined metabolite-protein analysis on a single tissue sample.
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Affiliation(s)
- Stéphanie Arrivault
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Manuela Guenther
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alexandra Florian
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Beatrice Encke
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Regina Feil
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Daniel Vosloh
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; §Stellenbosch University, Private Bag X1, Matieland 7602, Stellenbosch, South Africa
| | - John E Lunn
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Ronan Sulpice
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; ¶National University of Ireland, University Rd., Galway, Ireland
| | - Alisdair R Fernie
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Mark Stitt
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Waltraud X Schulze
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; ‖Department of Plant Systems Biology, Universität Hohenheim, 70593 Stuttgart, Germany
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112
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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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113
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Kustatscher G, Hégarat N, Wills KLH, Furlan C, Bukowski-Wills JC, Hochegger H, Rappsilber J. Proteomics of a fuzzy organelle: interphase chromatin. EMBO J 2014; 33:648-64. [PMID: 24534090 PMCID: PMC3983682 DOI: 10.1002/embj.201387614] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 01/12/2014] [Accepted: 01/14/2014] [Indexed: 12/30/2022] Open
Abstract
Chromatin proteins mediate replication, regulate expression, and ensure integrity of the genome. So far, a comprehensive inventory of interphase chromatin has not been determined. This is largely due to its heterogeneous and dynamic composition, which makes conclusive biochemical purification difficult, if not impossible. As a fuzzy organelle, it defies classical organellar proteomics and cannot be described by a single and ultimate list of protein components. Instead, we propose a new approach that provides a quantitative assessment of a protein's probability to function in chromatin. We integrate chromatin composition over a range of different biochemical and biological conditions. This resulted in interphase chromatin probabilities for 7635 human proteins, including 1840 previously uncharacterized proteins. We demonstrate the power of our large-scale data-driven annotation during the analysis of cyclin-dependent kinase (CDK) regulation in chromatin. Quantitative protein ontologies may provide a general alternative to list-based investigations of organelles and complement Gene Ontology.
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Affiliation(s)
- Georg Kustatscher
- Wellcome Trust Centre for Cell Biology, University of EdinburghEdinburgh, UK
| | - Nadia Hégarat
- Genome Damage and Stability Centre, University of SussexBrighton, UK
| | - Karen L H Wills
- Wellcome Trust Centre for Cell Biology, University of EdinburghEdinburgh, UK
| | - Cristina Furlan
- Wellcome Trust Centre for Cell Biology, University of EdinburghEdinburgh, UK
| | | | - Helfrid Hochegger
- Genome Damage and Stability Centre, University of SussexBrighton, UK
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, University of EdinburghEdinburgh, UK
- Department of Biotechnology, Technische Universität BerlinBerlin, Germany
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114
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115
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Groen AJ, Sancho-Andrés G, Breckels LM, Gatto L, Aniento F, Lilley KS. Identification of trans-golgi network proteins in Arabidopsis thaliana root tissue. J Proteome Res 2014; 13:763-76. [PMID: 24344820 PMCID: PMC3929368 DOI: 10.1021/pr4008464] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
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Knowledge of protein
subcellular localization assists in the elucidation
of protein function and understanding of different biological mechanisms
that occur at discrete subcellular niches. Organelle-centric proteomics
enables localization of thousands of proteins simultaneously. Although
such techniques have successfully allowed organelle protein catalogues
to be achieved, they rely on the purification or significant enrichment
of the organelle of interest, which is not achievable for many organelles.
Incomplete separation of organelles leads to false discoveries, with
erroneous assignments. Proteomics methods that measure the distribution
patterns of specific organelle markers along density gradients are
able to assign proteins of unknown localization based on comigration
with known organelle markers, without the need for organelle purification.
These methods are greatly enhanced when coupled to sophisticated computational
tools. Here we apply and compare multiple approaches to establish
a high-confidence data set of Arabidopsis root tissue
trans-Golgi network (TGN) proteins. The method employed involves immunoisolations
of the TGN, coupled to probability-based organelle proteomics techniques.
Specifically, the technique known as LOPIT (localization of organelle
protein by isotope tagging), couples density centrifugation with quantitative
mass-spectometry-based proteomics using isobaric labeling and targeted
methods with semisupervised machine learning methods. We demonstrate
that while the immunoisolation method gives rise to a significant
data set, the approach is unable to distinguish cargo proteins and
persistent contaminants from full-time residents of the TGN. The LOPIT
approach, however, returns information about many subcellular niches
simultaneously and the steady-state location of proteins. Importantly,
therefore, it is able to dissect proteins present in more than one
organelle and cargo proteins en route to other cellular destinations
from proteins whose steady-state location favors the TGN. Using this
approach, we present a robust list of Arabidopsis TGN proteins.
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Affiliation(s)
- Arnoud J Groen
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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116
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Pan S, Carter CJ, Raikhel NV. Understanding protein trafficking in plant cells through proteomics. Expert Rev Proteomics 2014; 2:781-92. [PMID: 16209656 DOI: 10.1586/14789450.2.5.781] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The functions of approximately one-third of the proteins encoded by the Arabidopsis thaliana genome are completely unknown. Moreover, many annotations of the remainder of the genome supply tentative functions, at best. Knowing the ultimate localization of these proteins, as well as the pathways used for getting there, may provide clues as to their functions. The putative localization of most proteins currently relies on in silico-based bioinformatics approaches, which, unfortunately, often result in erroneous predictions. Emerging proteomics techniques coupled with other systems biology approaches now provide researchers with a plethora of methods for elucidating the final location of these proteins on a large scale, as well as the ability to dissect protein-sorting pathways in plants.
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Affiliation(s)
- Songqin Pan
- WM Keck Proteomics Laboratory, Center for Plant Cell Biology, Botany & Plant Sciences, University of California, Riverside, CA 92521, USA.
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117
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Tribl F, Meyer HE, Marcus K. Analysis of organelles within the nervous system: impact on brain and organelle functions. Expert Rev Proteomics 2014; 5:333-51. [DOI: 10.1586/14789450.5.2.333] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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118
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Abstract
Autophagy is one of the two major degradation pathways within eukaryotic cells. Nevertheless, little is known about the protein composition of autophagosomes, the vesicles shuttling proteins to lysosomes for degradation. Protein correlation profiling in combination with stable isotope labeling by amino acids in cell culture is a stringent method to investigate the dynamics of the autophagosomal proteome. It enables the discrimination between autophagosomal and co-purifying proteins identifying organellar candidate proteins for further investigation.
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Affiliation(s)
- Andrea C Becker
- Department of Dermatology, Medical Center - University of Freiburg, Hauptstr. 7, 79104, Freiburg, Germany
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119
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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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120
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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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121
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Gronemeyer T, Wiese S, Ofman R, Bunse C, Pawlas M, Hayen H, Eisenacher M, Stephan C, Meyer HE, Waterham HR, Erdmann R, Wanders RJ, Warscheid B. The proteome of human liver peroxisomes: identification of five new peroxisomal constituents by a label-free quantitative proteomics survey. PLoS One 2013; 8:e57395. [PMID: 23460848 PMCID: PMC3583843 DOI: 10.1371/journal.pone.0057395] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 01/24/2013] [Indexed: 01/11/2023] Open
Abstract
The peroxisome is a key organelle of low abundance that fulfils various functions essential for human cell metabolism. Severe genetic diseases in humans are caused by defects in peroxisome biogenesis or deficiencies in the function of single peroxisomal proteins. To improve our knowledge of this important cellular structure, we studied for the first time human liver peroxisomes by quantitative proteomics. Peroxisomes were isolated by differential and Nycodenz density gradient centrifugation. A label-free quantitative study of 314 proteins across the density gradient was accomplished using high resolution mass spectrometry. By pairing statistical data evaluation, cDNA cloning and in vivo colocalization studies, we report the association of five new proteins with human liver peroxisomes. Among these, isochorismatase domain containing 1 protein points to the existence of a new metabolic pathway and hydroxysteroid dehydrogenase like 2 protein is likely involved in the transport or β-oxidation of fatty acids in human peroxisomes. The detection of alcohol dehydrogenase 1A suggests the presence of an alternative alcohol-oxidizing system in hepatic peroxisomes. In addition, lactate dehydrogenase A and malate dehydrogenase 1 partially associate with human liver peroxisomes and enzyme activity profiles support the idea that NAD+ becomes regenerated during fatty acid β-oxidation by alternative shuttling processes in human peroxisomes involving lactate dehydrogenase and/or malate dehydrogenase. Taken together, our data represent a valuable resource for future studies of peroxisome biochemistry that will advance research of human peroxisomes in health and disease.
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Affiliation(s)
- Thomas Gronemeyer
- Department of Molecular Genetics and Cell Biology, Ulm University, Ulm, Germany
| | - Sebastian Wiese
- Institut für Biologie II, Funktionelle Proteomik, Fakultät für Biologie and BIOSS Centre for Biological Signalling Studies, Universität Freiburg, Freiburg, Germany
| | - Rob Ofman
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry and Pediatrics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Christian Bunse
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Magdalena Pawlas
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Heiko Hayen
- Leibniz-Institut für Analytische Wissenschaften - ISAS e.V., Dortmund, Germany
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Christian Stephan
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Helmut E. Meyer
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Hans R. Waterham
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry and Pediatrics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ralf Erdmann
- Abteilung für Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, Bochum, Germany
| | - Ronald J. Wanders
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry and Pediatrics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Bettina Warscheid
- Institut für Biologie II, Funktionelle Proteomik, Fakultät für Biologie and BIOSS Centre for Biological Signalling Studies, Universität Freiburg, Freiburg, Germany
- * E-mail:
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122
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Hemsley PA, Weimar T, Lilley KS, Dupree P, Grierson CS. A proteomic approach identifies many novel palmitoylated proteins in Arabidopsis. THE NEW PHYTOLOGIST 2013; 197:805-814. [PMID: 23252521 DOI: 10.1111/nph.12077] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 10/31/2012] [Indexed: 05/06/2023]
Abstract
S-acylation (palmitoylation) is a poorly understood post-translational modification of proteins involving the addition of acyl lipids to cysteine residues. S-acylation promotes the association of proteins with membranes and influences protein stability, microdomain partitioning, membrane targeting and activation state. No consensus motif for S-acylation exists and it therefore requires empirical identification. Here, we describe a biotin switch isobaric tagging for relative and absolute quantification (iTRAQ)-based method to identify S-acylated proteins from Arabidopsis. We use these data to predict and confirm S-acylation of proteins not in our dataset. We identified c. 600 putative S-acylated proteins affecting diverse cellular processes. These included proteins involved in pathogen perception and response, mitogen-activated protein kinases (MAPKs), leucine-rich repeat receptor-like kinases (LRR-RLKs) and RLK superfamily members, integral membrane transporters, ATPases, soluble N-ethylmaleimide-sensitive factor-activating protein receptors (SNAREs) and heterotrimeric G-proteins. The prediction of S-acylation of related proteins was demonstrated by the identification and confirmation of S-acylation sites within the SNARE and LRR-RLK families. We showed that S-acylation of the LRR-RLK FLS2 is required for a full response to elicitation by the flagellin derived peptide flg22, but is not required for localization to the plasma membrane. Arabidopsis contains many more S-acylated proteins than previously thought. These data can be used to identify S-acylation sites in related proteins. We also demonstrated that S-acylation is required for full LRR-RLK function.
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Affiliation(s)
- Piers A Hemsley
- School of Biological Science, University of Bristol, Woodland Road, Bristol, BS8 1UG, UK
| | - Thilo Weimar
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Claire S Grierson
- School of Biological Science, University of Bristol, Woodland Road, Bristol, BS8 1UG, UK
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123
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Arango-Argoty GA, Jaramillo-Garzón JA, Castellanos-Domínguez CG. Contact potentials via wavelet transform for prediction of subcellular localizations in gram negative bacterial proteins. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2013; 2013:643-646. [PMID: 24109769 DOI: 10.1109/embc.2013.6609582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Predicting the localization of a protein has become a useful practice for inferring its function. Most of the reported methods to predict subcellular localizations in Gram-negative bacterial proteins have shown a low false positive rate. However, some subcellular compartmens like "periplasm" and "extracellular medium" are difficult to predict and remain high false negative rates. In this paper, a method based on representation from statistical contact potentials and wavelet transform is presented. The wavelet-based method achieves an overall high performance holding low false and negative rates particularly on periplasm and extracellular medium. Results suggest the contact potentials as an useful alternative to characterize protein sequences.
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124
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Smirle J, Au CE, Jain M, Dejgaard K, Nilsson T, Bergeron J. Cell biology of the endoplasmic reticulum and the Golgi apparatus through proteomics. Cold Spring Harb Perspect Biol 2013; 5:a015073. [PMID: 23284051 DOI: 10.1101/cshperspect.a015073] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Enriched endoplasmic reticulum (ER) and Golgi membranes subjected to mass spectrometry have uncovered over a thousand different proteins assigned to the ER and Golgi apparatus of rat liver. This, in turn, led to the uncovering of several hundred proteins of poorly understood function and, through hierarchical clustering, showed that proteins distributed in patterns suggestive of microdomains in cognate organelles. This has led to new insights with respect to their intracellular localization and function. Another outcome has been the critical testing of the cisternal maturation hypothesis showing overwhelming support for a predominant role of COPI vesicles in the transport of resident proteins of the ER and Golgi apparatus (as opposed to biosynthetic cargo). Here we will discuss new insights gained and also highlight new avenues undertaken to further explore the cell biology of the ER and the Golgi apparatus through tandem mass spectrometry.
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Affiliation(s)
- Jeffrey Smirle
- The Research Institute of the McGill University Health Centre and the Department of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
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125
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Kristensen AR, Foster LJ. High throughput strategies for probing the different organizational levels of protein interaction networks. MOLECULAR BIOSYSTEMS 2013; 9:2201-12. [DOI: 10.1039/c3mb70135b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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126
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Wang Y, Mortimer JC, Davis J, Dupree P, Keegstra K. Identification of an additional protein involved in mannan biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:105-17. [PMID: 22966747 PMCID: PMC3558879 DOI: 10.1111/tpj.12019] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 08/24/2012] [Accepted: 09/07/2012] [Indexed: 05/18/2023]
Abstract
Galactomannans comprise a β-1,4-mannan backbone substituted with α-1,6-galactosyl residues. Genes encoding the enzymes that are primarily responsible for backbone synthesis and side-chain addition of galactomannans were previously identified and characterized. To identify additional genes involved in galactomannan biosynthesis, we previously performed deep EST profiling of fenugreek (Trigonella foenum-graecum L.) seed endosperm, which accumulates large quantities of galactomannans as a reserve carbohydrate during seed development. One of the candidate genes encodes a protein that is likely to be a glycosyltransferase. Because this protein is involved in mannan biosynthesis, we named it 'mannan synthesis-related' (MSR). Here, we report the characterization of a fenugreek MSR gene (TfMSR) and its two Arabidopsis homologs, AtMSR1 and AtMSR2. TfMSR was highly and specifically expressed in the endosperm. TfMSR, AtMSR1 and AtMSR2 proteins were all determined to be localized to the Golgi by fluorescence confocal microscopy. The level of mannosyl residues in stem glucomannans decreased by approximately 40% for Arabidopsis msr1 single T-DNA insertion mutants and by more than 50% for msr1 msr2 double mutants, but remained unchanged for msr2 single mutants. In addition, in vitro mannan synthase activity from the stems of msr1 single and msr1 msr2 double mutants also decreased. Expression of AtMSR1 or AtMSR2 in the msr1 msr2 double mutant completely or partially restored mannosyl levels. From these results, we conclude that the MSR protein is important for mannan biosynthesis, and offer some ideas about its role.
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Affiliation(s)
- Yan Wang
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Energy Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, 48824, USA
| | | | - Jonathan Davis
- Department of Energy Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Paul Dupree
- Department of Biochemistry, University of CambridgeCambridge, CB2 1QW, UK
| | - Kenneth Keegstra
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Energy Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
- *For correspondence (e-mail )
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127
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Larance M, Ahmad Y, Kirkwood KJ, Ly T, Lamond AI. Global subcellular characterization of protein degradation using quantitative proteomics. Mol Cell Proteomics 2012; 12:638-50. [PMID: 23242552 PMCID: PMC3591657 DOI: 10.1074/mcp.m112.024547] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Protein degradation provides an important regulatory mechanism used to control cell cycle progression and many other cellular pathways. To comprehensively analyze the spatial control of protein degradation in U2OS osteosarcoma cells, we have combined drug treatment and SILAC-based quantitative mass spectrometry with subcellular and protein fractionation. The resulting data set analyzed more than 74,000 peptides, corresponding to ∼5000 proteins, from nuclear, cytosolic, membrane, and cytoskeletal compartments. These data identified rapidly degraded proteasome targets, such as PRR11 and highlighted a feedback mechanism resulting in translation inhibition, induced by blocking the proteasome. We show this is mediated by activation of the unfolded protein response. We observed compartment-specific differences in protein degradation, including proteins that would not have been characterized as rapidly degraded through analysis of whole cell lysates. Bioinformatic analysis of the entire data set is presented in the Encyclopedia of Proteome Dynamics, a web-based resource, with proteins annotated for stability and subcellular distribution.
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Affiliation(s)
- Mark Larance
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom
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128
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Liu X, Wu J, Clark G, Lundy S, Lim M, Arnold D, Chan J, Tang W, Muday GK, Gardner G, Roux SJ. Role for apyrases in polar auxin transport in Arabidopsis. PLANT PHYSIOLOGY 2012; 160:1985-95. [PMID: 23071251 PMCID: PMC3510125 DOI: 10.1104/pp.112.202887] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 10/10/2012] [Indexed: 05/20/2023]
Abstract
Recent evidence indicates that extracellular nucleotides regulate plant growth. Exogenous ATP has been shown to block auxin transport and gravitropic growth in primary roots of Arabidopsis (Arabidopsis thaliana). Cells limit the concentration of extracellular ATP in part through the activity of ectoapyrases (ectonucleoside triphosphate diphosphohydrolases), and two nearly identical Arabidopsis apyrases, APY1 and APY2, appear to share this function. These findings, plus the fact that suppression of APY1 and APY2 blocks growth in Arabidopsis, suggested that the expression of these apyrases could influence auxin transport. This report tests that hypothesis. The polar movement of [(3)H]indole-3-acetic acid in both hypocotyl sections and primary roots of Arabidopsis seedlings was measured. In both tissues, polar auxin transport was significantly reduced in apy2 null mutants when they were induced by estradiol to suppress the expression of APY1 by RNA interference. In the hypocotyl assays, the basal halves of APY-suppressed hypocotyls contained considerably lower free indole-3-acetic acid levels when compared with wild-type plants, and disrupted auxin transport in the APY-suppressed roots was reflected by their significant morphological abnormalities. When a green fluorescent protein fluorescence signal encoded by a DR5:green fluorescent protein construct was measured in primary roots whose apyrase expression was suppressed either genetically or chemically, the roots showed no signal asymmetry following gravistimulation, and both their growth and gravitropic curvature were inhibited. Chemicals that suppress apyrase activity also inhibit gravitropic curvature and, to a lesser extent, growth. Taken together, these results indicate that a critical step connecting apyrase suppression to growth suppression is the inhibition of polar auxin transport.
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129
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Chiu TY, Christiansen K, Moreno I, Lao J, Loqué D, Orellana A, Heazlewood JL, Clark G, Roux SJ. AtAPY1 and AtAPY2 function as Golgi-localized nucleoside diphosphatases in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2012; 53:1913-25. [PMID: 23034877 DOI: 10.1093/pcp/pcs131] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nucleoside triphosphate diphosphohydrolases (NTPDases; apyrases) (EC 3.6.1.5) hydrolyze di- and triphosphate nucleotides, but not monophosphate nucleotides. They are categorized as E-type ATPases, have a broad divalent cation (Mg(2+), Ca(2+)) requirement for activation and are insensitive to inhibitors of F-type, P-type and V-type ATPases. Among the seven NTPDases identified in Arabidopsis, only APYRASE 1 (AtAPY1) and APYRASE 2 (AtAPY2) have been previously characterized. In this work, either AtAPY1 or AtAPY2 tagged with C-terminal green fluorescent protein (GFP) driven by their respective native promoter can rescue the apy1 apy2 double knockout (apy1 apy2 dKO) successfully, and confocal microscopy reveals that these two Arabidopsis apyrases reside in the Golgi apparatus. In Saccharomyces cerevisiae, both AtAPY1 and AtAPY2 can complement the Golgi-localized GDA1 mutant, rescuing its aberrant protein glycosylation phenotype. In Arabidopsis, microsomes of the wild type show higher substrate preferences toward UDP compared with other NDP substrates. Loss-of-function Arabidopsis AtAPY1 mutants exhibit reduced microsomal UDPase activity, and this activity is even more significantly reduced in the loss-of-function AtAPY2 mutant and in the AtAPY1/AtAPY2 RNA interference (RNAi) technology repressor lines. Microsomes from wild-type plants also have detectable GDPase activity, which is significantly reduced in apy2 but not apy1 mutants. The GFP-tagged AtAPY1 or AtAPY2 constructs in the apy1 apy2 dKO plants can restore microsomal UDP/GDPase activity, confirming that they both also have functional competency. The cell walls of apy1, apy2 and the RNAi-silenced lines all have an increased composition of galactose, but the transport efficiency of UDP-galactose across microsomal membranes was not altered. Taken together, these results reveal that AtAPY1 and AtAPY2 are Golgi-localized nucleotide diphosphatases and are likely to have roles in regulating UDP/GDP concentrations in the Golgi lumen.
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Affiliation(s)
- Tsan-Yu Chiu
- Section of Molecular Cell and Developmental Biology, University of Texas, Austin, TX 78712, USA
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130
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Batistic O. Genomics and localization of the Arabidopsis DHHC-cysteine-rich domain S-acyltransferase protein family. PLANT PHYSIOLOGY 2012; 160:1597-612. [PMID: 22968831 PMCID: PMC3490592 DOI: 10.1104/pp.112.203968] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 09/07/2012] [Indexed: 05/18/2023]
Abstract
Protein lipid modification of cysteine residues, referred to as S-palmitoylation or S-acylation, is an important secondary and reversible modification that regulates membrane association, trafficking, and function of target proteins. This enzymatic reaction is mediated by protein S-acyl transferases (PATs). Here, the phylogeny, genomic organization, protein topology, expression, and localization pattern of the 24 PAT family members from Arabidopsis (Arabidopsis thaliana) is described. Most PATs are expressed at ubiquitous levels and tissues throughout the development, while few genes are expressed especially during flower development preferentially in pollen and stamen. The proteins display large sequence and structural variations but exhibit a common protein topology that is preserved in PATs from various organisms. Arabidopsis PAT proteins display a complex targeting pattern and were detected at the endoplasmic reticulum, Golgi, endosomal compartments, and the vacuolar membrane. However, most proteins were targeted to the plasma membrane. This large concentration of plant PAT activity to the plasma membrane suggests that the plant cellular S-acylation machinery is functionally different compared with that of yeast (Saccharomyces cerevisiae) and mammalians.
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Affiliation(s)
- Oliver Batistic
- Institut für Biologie und Biotechnologie der Pflanzen, Universität Münster, 48149 Muenster, Germany.
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131
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Nikolovski N, Rubtsov D, Segura MP, Miles GP, Stevens TJ, Dunkley TP, Munro S, Lilley KS, Dupree P. Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics. PLANT PHYSIOLOGY 2012; 160:1037-51. [PMID: 22923678 PMCID: PMC3461528 DOI: 10.1104/pp.112.204263] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 08/22/2012] [Indexed: 05/18/2023]
Abstract
The Golgi apparatus is the central organelle in the secretory pathway and plays key roles in glycosylation, protein sorting, and secretion in plants. Enzymes involved in the biosynthesis of complex polysaccharides, glycoproteins, and glycolipids are located in this organelle, but the majority of them remain uncharacterized. Here, we studied the Arabidopsis (Arabidopsis thaliana) membrane proteome with a focus on the Golgi apparatus using localization of organelle proteins by isotope tagging. By applying multivariate data analysis to a combined data set of two new and two previously published localization of organelle proteins by isotope tagging experiments, we identified the subcellular localization of 1,110 proteins with high confidence. These include 197 Golgi apparatus proteins, 79 of which have not been localized previously by a high-confidence method, as well as the localization of 304 endoplasmic reticulum and 208 plasma membrane proteins. Comparison of the hydrophobic domains of the localized proteins showed that the single-span transmembrane domains have unique properties in each organelle. Many of the novel Golgi-localized proteins belong to uncharacterized protein families. Structure-based homology analysis identified 12 putative Golgi glycosyltransferase (GT) families that have no functionally characterized members and, therefore, are not yet assigned to a Carbohydrate-Active Enzymes database GT family. The substantial numbers of these putative GTs lead us to estimate that the true number of plant Golgi GTs might be one-third above those currently annotated. Other newly identified proteins are likely to be involved in the transport and interconversion of nucleotide sugar substrates as well as polysaccharide and protein modification.
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132
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Engelke R, Becker AC, Dengjel J. The degradative inventory of the cell: proteomic insights. Antioxid Redox Signal 2012; 17:803-12. [PMID: 22074050 DOI: 10.1089/ars.2011.4393] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
SIGNIFICANCE Protein degradation has been identified as being deregulated in numerous human diseases. Hence, proteins involved in proteasomal as well as lysosomal degradation are regarded as interesting potential drug targets and are thoroughly investigated in clinical studies. RECENT ADVANCES Technical advances in the field of quantitative mass spectrometry (MS)-based proteomics allow for detailed investigations of protein degradation dynamics and identifications of responsible protein-protein interaction networks enabling a systematic analysis of the degradative inventory of the cell and its underlying molecular mechanisms. CRITICAL ISSUES In the current review we outline recent technical advances and their limitations in MS-based proteomics and discuss their use for the analysis of protein dynamics involved in degradation processes. FUTURE DIRECTIONS In the next years the analysis of crosstalk between different posttranslational modifications (PTMs) will be a major focus of MS-based proteomics studies. Increasing evidence highlights the complexity of PTMs with positive and negative feedbacks being discovered. In this regard, the generation of absolute quantitative proteomic data will be essential for theoretical scientists to construct predictive network models that constitute a valuable tool for fast hypothesis testing and for explaining underlying molecular mechanisms.
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Affiliation(s)
- Rudolf Engelke
- Freiburg Institute for Advanced Studies, School of Life Science-LifeNet, University of Freiburg, Germany
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133
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Borner GHH, Antrobus R, Hirst J, Bhumbra GS, Kozik P, Jackson LP, Sahlender DA, Robinson MS. Multivariate proteomic profiling identifies novel accessory proteins of coated vesicles. ACTA ACUST UNITED AC 2012; 197:141-60. [PMID: 22472443 PMCID: PMC3317806 DOI: 10.1083/jcb.201111049] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A multivariate proteomics approach identified numerous new clathrin-coated vesicle proteins as well as the first AP-4 accessory protein, and also revealed how auxilin depletion causes mitotic arrest through sequestration of spindle proteins in clathrin cages. Despite recent advances in mass spectrometry, proteomic characterization of transport vesicles remains challenging. Here, we describe a multivariate proteomics approach to analyzing clathrin-coated vesicles (CCVs) from HeLa cells. siRNA knockdown of coat components and different fractionation protocols were used to obtain modified coated vesicle-enriched fractions, which were compared by stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative mass spectrometry. 10 datasets were combined through principal component analysis into a “profiling” cluster analysis. Overall, 136 CCV-associated proteins were predicted, including 36 new proteins. The method identified >93% of established CCV coat proteins and assigned >91% correctly to intracellular or endocytic CCVs. Furthermore, the profiling analysis extends to less well characterized types of coated vesicles, and we identify and characterize the first AP-4 accessory protein, which we have named tepsin. Finally, our data explain how sequestration of TACC3 in cytosolic clathrin cages causes the severe mitotic defects observed in auxilin-depleted cells. The profiling approach can be adapted to address related cell and systems biological questions.
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Affiliation(s)
- Georg H H Borner
- Cambridge Institute for Medical Research, Wellcome Trust/Medical Research Council Building, University of Cambridge, Cambridge CB2 0XY, England, UK.
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134
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Tan YF, Millar AH, Taylor NL. Components of mitochondrial oxidative phosphorylation vary in abundance following exposure to cold and chemical stresses. J Proteome Res 2012; 11:3860-79. [PMID: 22574745 DOI: 10.1021/pr3003535] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Plant mitochondria are highly responsive organelles that vary their metabolism in response to a wide range of chemical and environmental conditions. Quantitative proteomics studies have begun to allow the analysis of these large-scale protein changes in mitochondria. However studies of the integral membrane proteome of plant mitochondria, arguably the site responsible for the most fundamental mitochondrial processes of oxidative phosphorylation, protein import and metabolite transport, remain a technical challenge. Here we have investigated the changes in protein abundance in response to a number of chemical stresses and cold. In addition to refining the subcellular localization of 66 proteins, we have been able to characterize 596 protein × treatment combinations following a range of stresses. To date it has been assumed that the main mitochondrial response to stress involved the induction of alternative respiratory proteins such as AOX, UCPs, and alternative NAD(P)H dehydrogenases; we now provide evidence for a number of very specific protein abundance changes that have not been highlighted previously by transcript studies. This includes both previously characterized stress responsive proteins as well as major components of oxidative phosphorylation, protein import/export, and metabolite transport.
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Affiliation(s)
- Yew-Foon Tan
- ARC Centre of Excellence in Plant Energy Biology, MCS Building M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Western Australia, Australia
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135
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Parsons HT, Christiansen K, Knierim B, Carroll A, Ito J, Batth TS, Smith-Moritz AM, Morrison S, McInerney P, Hadi MZ, Auer M, Mukhopadhyay A, Petzold CJ, Scheller HV, Loqué D, Heazlewood JL. Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis. PLANT PHYSIOLOGY 2012; 159:12-26. [PMID: 22430844 PMCID: PMC3375956 DOI: 10.1104/pp.111.193151] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/04/2012] [Indexed: 05/17/2023]
Abstract
The plant Golgi plays a pivotal role in the biosynthesis of cell wall matrix polysaccharides, protein glycosylation, and vesicle trafficking. Golgi-localized proteins have become prospective targets for reengineering cell wall biosynthetic pathways for the efficient production of biofuels from plant cell walls. However, proteomic characterization of the Golgi has so far been limited, owing to the technical challenges inherent in Golgi purification. In this study, a combination of density centrifugation and surface charge separation techniques have allowed the reproducible isolation of Golgi membranes from Arabidopsis (Arabidopsis thaliana) at sufficiently high purity levels for in-depth proteomic analysis. Quantitative proteomic analysis, immunoblotting, enzyme activity assays, and electron microscopy all confirm high purity levels. A composition analysis indicated that approximately 19% of proteins were likely derived from contaminating compartments and ribosomes. The localization of 13 newly assigned proteins to the Golgi using transient fluorescent markers further validated the proteome. A collection of 371 proteins consistently identified in all replicates has been proposed to represent the Golgi proteome, marking an appreciable advancement in numbers of Golgi-localized proteins. A significant proportion of proteins likely involved in matrix polysaccharide biosynthesis were identified. The potential within this proteome for advances in understanding Golgi processes has been demonstrated by the identification and functional characterization of the first plant Golgi-resident nucleoside diphosphatase, using a yeast complementation assay. Overall, these data show key proteins involved in primary cell wall synthesis and include a mixture of well-characterized and unknown proteins whose biological roles and importance as targets for future research can now be realized.
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136
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Schvartz D, Brunner Y, Couté Y, Foti M, Wollheim CB, Sanchez JC. Improved characterization of the insulin secretory granule proteomes. J Proteomics 2012; 75:4620-31. [PMID: 22569486 DOI: 10.1016/j.jprot.2012.04.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 02/22/2012] [Accepted: 04/20/2012] [Indexed: 11/15/2022]
Abstract
Insulin secretory granules (ISGs) are pivotal organelles of pancreatic ß-cells and represent a key participant to glucose homeostasis. Indeed, insulin is packed and processed within these vesicles before its release by exocytosis. It is therefore crucial to acquire qualitative and quantitative data on the ISG proteome, in order to increase our knowledge on ISG biogenesis, maturation and exocytosis. Despites efforts made in the past years, the coverage of the ISG proteome is still incomplete and comprises many potential protein contaminants most likely coming from suboptimal sample preparations. We developed here a 3-step gradient purification procedure combined to Stable Isotope Labeling with Amino acids in Cell culture (SILAC) to further characterize the ISG protein content. Our results allowed to build three complementary proteomes containing 1/ proteins which are enriched in mature ISGs, 2/ proteins sharing multiple localizations including ISGs, and finally 3/ proteins sorted out from immature ISGs and/or co-purifying contaminants. As a proof of concept, the ProSAAS, a neuronal protein found in ISGs was further characterized and its granular localization proved. ProSAAS might represent a novel potential target allowing to better understand the defaults in insulin processing and secretion observed during type 2 diabetes progression. This article is part of a special issue entitled: Translational Proteomics.
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Affiliation(s)
- Domitille Schvartz
- Biomedical Proteomics Research Group, Department of Human Protein Sciences, University Medical Center, Geneva, Switzerland
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137
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Wang X, Li F, Song G, Guo S, Liu H, Chen G, Li Z. Broad-spectrum four-dimensional orthogonal electrophoresis: a novel comprehensively feasible system for protein complexomics investigation. Mol Cell Proteomics 2012; 11:786-99. [PMID: 22375076 DOI: 10.1074/mcp.m111.012450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The major challenge of "protein complexomics" is to separate intact protein complexes or interactional proteins without dissociation or denaturation from complex biological samples and to characterize structural subunits of protein complexes. To address these issues, we developed a novel approach termed "broad-spectrum four-dimensional orthogonal electrophoresis (BS4-DE) system," which is composed of a nondenaturing part I and denaturing part II. Here we developed a mild acidic-native-PAGE to constitute part I, together with native-thin-layer-IEF and basic-native-PAGE, widening the range of BS4-DE system application for extremely basic proteins with the range of pI from about 8 to 11 (there are obviously 1000 kinds of proteins in this interval), and also speculated on the mechanism of separating. We first proposed ammonium hydroxide-ultrasonic protein extractive strategy as a seamless connection between part I and part II, and also speculated on the extractive mechanism. More than 4000 protein complexes could be theoretically solved by this system. Using this approach, we focus on blood rich in protein complexes which make it challenging to sera/plasma proteome study. Our results indicated that the BS4-DE system could be applied to blood protein complexomics investigation, providing a comprehensively feasible approach for disease proteomics.
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Affiliation(s)
- Xiaodong Wang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
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138
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Rodríguez-Piñeiro AM, van der Post S, Johansson MEV, Thomsson KA, Nesvizhskii AI, Hansson GC. Proteomic study of the mucin granulae in an intestinal goblet cell model. J Proteome Res 2012; 11:1879-90. [PMID: 22248381 PMCID: PMC3292267 DOI: 10.1021/pr2010988] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Goblet cells specialize in producing and secreting mucus
with its
main component, mucins. An inducible goblet-like cell line was used
for the purification of the mucus vesicles stored in these cells by
density gradient ultracentrifugation, and their proteome was analyzed
by nanoLC-MS and MS/MS. Although the density of these vesicles coincides
with others, it was possible to reveal a number of proteins that after
immunolocalization on colon tissue and functional analyses were likely
to be linked to the MUC2 vesicles. Most of the proteins were associated
with the vesicle membrane or their outer surface. The ATP6AP2, previously
suggested to be associated with vesicular proton pumps, was colocalized
with MUC2 without other V-ATPase proteins and, thus, probably has
roles in mucin vesicle function yet to be discovered. FAM62B, known
to be a calcium-sensitive protein involved in vesicle fusion, also
colocalized with the MUC2 vesicles and is probably involved in unknown
ways in the later events of the MUC2 vesicles and their secretion.
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Affiliation(s)
- Ana M Rodríguez-Piñeiro
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg , Box 440, 40530 Gothenburg, Sweden
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139
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Abdallah C, Dumas-Gaudot E, Renaut J, Sergeant K. Gel-based and gel-free quantitative proteomics approaches at a glance. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2012; 2012:494572. [PMID: 23213324 PMCID: PMC3508552 DOI: 10.1155/2012/494572] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/12/2012] [Indexed: 05/06/2023]
Abstract
Two-dimensional gel electrophoresis (2-DE) is widely applied and remains the method of choice in proteomics; however, pervasive 2-DE-related concerns undermine its prospects as a dominant separation technique in proteome research. Consequently, the state-of-the-art shotgun techniques are slowly taking over and utilising the rapid expansion and advancement of mass spectrometry (MS) to provide a new toolbox of gel-free quantitative techniques. When coupled to MS, the shotgun proteomic pipeline can fuel new routes in sensitive and high-throughput profiling of proteins, leading to a high accuracy in quantification. Although label-based approaches, either chemical or metabolic, gained popularity in quantitative proteomics because of the multiplexing capacity, these approaches are not without drawbacks. The burgeoning label-free methods are tag independent and suitable for all kinds of samples. The challenges in quantitative proteomics are more prominent in plants due to difficulties in protein extraction, some protein abundance in green tissue, and the absence of well-annotated and completed genome sequences. The goal of this perspective assay is to present the balance between the strengths and weaknesses of the available gel-based and -free methods and their application to plants. The latest trends in peptide fractionation amenable to MS analysis are as well discussed.
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Affiliation(s)
- Cosette Abdallah
- Environment and Agro-Biotechnologies Department, Centre de Recherche Public-Gabriel Lippmann, 41 rue du Brill, 4422 Belvaux, Luxembourg
- UMR Agroécologie INRA 1347/Agrosup/Université de Bourgogne, Pôle Interactions Plantes Microorganismes ERL 6300 CNRS, Boite Postal 86510, 21065 Dijon Cedex, France
| | - Eliane Dumas-Gaudot
- UMR Agroécologie INRA 1347/Agrosup/Université de Bourgogne, Pôle Interactions Plantes Microorganismes ERL 6300 CNRS, Boite Postal 86510, 21065 Dijon Cedex, France
| | - Jenny Renaut
- Environment and Agro-Biotechnologies Department, Centre de Recherche Public-Gabriel Lippmann, 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Kjell Sergeant
- Environment and Agro-Biotechnologies Department, Centre de Recherche Public-Gabriel Lippmann, 41 rue du Brill, 4422 Belvaux, Luxembourg
- *Kjell Sergeant:
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140
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Buschow SI, Lasonder E, Szklarczyk R, Oud MM, de Vries IJM, Figdor CG. Unraveling the human dendritic cell phagosome proteome by organellar enrichment ranking. J Proteomics 2011; 75:1547-62. [PMID: 22146474 DOI: 10.1016/j.jprot.2011.11.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 11/18/2011] [Accepted: 11/22/2011] [Indexed: 12/24/2022]
Abstract
Dendritic cells (DC) take up pathogens through phagocytosis and process them into protein and lipid fragments for presentation to T cells. So far, the proteome of the human DC phagosome, a detrimental compartment for antigen processing and presentation as well as for DC activation, remains largely uncharacterized. Here we have analyzed the protein composition of phagosomes from human monocyte-derived DC. For LC-MS/MS analysis we purified phagosomes from DC using latex beads targeted to DC-SIGN, and quantified proteins using a label-free method. We used organellar enrichment ranking (OER) to select proteins with a high potential to be relevant for phagosome function. The method compares phagosome protein abundance with protein abundance in whole DC. Phagosome enrichment indicates specific recruitment to the phagosome rather than co-purification or passive incorporation. Using OER we extracted the most enriched proteins that we further complemented with functionally associated proteins to define a set of 90 phagosomal proteins that included many proteins with established relevance on DC phagosomes as well as high potential novel candidates. We already experimentally confirmed phagosomal recruitment of Galectin-9, which has not been previously associated with phagocytosis, to both bead and pathogen containing phagosomes, suggesting a role for Galectin-9 in DC phagocytosis.
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Affiliation(s)
- Sonja I Buschow
- Department of Tumor Immunology at the Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Postbox 9101, 6500 HB Nijmegen, The Netherlands
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141
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Abstract
Systems biology requires comprehensive data at all molecular levels. Mass spectrometry (MS)-based proteomics has emerged as a powerful and universal method for the global measurement of proteins. In the most widespread format, it uses liquid chromatography (LC) coupled to high-resolution tandem mass spectrometry (MS/MS) to identify and quantify peptides at a large scale. This peptide intensity information is the basic quantitative proteomic data type. It is used to quantify proteins between different proteome states, including the temporal variation of the proteome, to determine the complete primary structure of proteins including posttranslational modifications, to localize proteins to organelles, and to determine protein interactions. Here, we describe the principles of analysis and the areas of biology where proteomics can make unique contributions. The large-scale nature of proteomics data and its high accuracy pose special opportunities as well as challenges in systems biology that have been largely untapped so far.
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Affiliation(s)
- Jürgen Cox
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried D-82152, Germany.
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142
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143
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Agrawal GK, Bourguignon J, Rolland N, Ephritikhine G, Ferro M, Jaquinod M, Alexiou KG, Chardot T, Chakraborty N, Jolivet P, Doonan JH, Rakwal R. Plant organelle proteomics: collaborating for optimal cell function. MASS SPECTROMETRY REVIEWS 2011; 30:772-853. [PMID: 21038434 DOI: 10.1002/mas.20301] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 02/02/2010] [Accepted: 02/02/2010] [Indexed: 05/10/2023]
Abstract
Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), P.O. Box 13265, Sanepa, Kathmandu, Nepal.
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144
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Liu HJ, Tan YR, Li ML, Liu C, Xiang Y, Qin XQ. Cloning of a novel protein interacting with BRS-3 and its effects in wound repair of bronchial epithelial cells. PLoS One 2011; 6:e23072. [PMID: 21857995 PMCID: PMC3153462 DOI: 10.1371/journal.pone.0023072] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2011] [Accepted: 07/05/2011] [Indexed: 11/19/2022] Open
Abstract
Bombesin receptor subtype 3 (BRS-3), the orphan bombesin receptor, may play a role in the regulation of stress responses in lung and airway epithelia. Bombesin receptor activated protein (BRAP )is a novel protein we found in our previous study which interacts with BRS-3. This study was designed to observe the subcellular location and wound repair function of BRAP in human bronchial epithelial cells (HBECs). BRAP ORF was amplified by RT-PCR and ligated to pEGFP-C1 vector, and then the recombinant plasmid pEGFP-C1-BRAP was transfected into Hela cells. The location of BRAP protein was observed by laser confocal microscope, and the expression of it was analyzed by Western-blot. At the same time,we built the recombinant plasmid pcDNA3.1(+)-BRAP, transfected it into HBECs and observed its impact on cell cycle and wound repair of HBECs. The results showed that BRAP locates in membrane and cytoplasm and increases significantly in transfected cells. Flow cytometry results demonstrated that the recombinant plasmid increases S phase plus G2 phase of cell cycle by 25%. Microscopic video analysis system showed that the repair index of wounded HBECs increases by 20% through stable expression of BRAP. The present study demonstrated that BRAP locates in the membrane and cytoplasm, suggesting that this protein is a cytoplasm protein, which promotes cell cycle and wound repair of HBECs.
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Affiliation(s)
- Hui Jun Liu
- Department of Physiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Yu Rong Tan
- Department of Physiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Meng Lan Li
- Department of Physiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Chi Liu
- Department of Physiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Yang Xiang
- Department of Physiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Xiao Qun Qin
- Department of Physiology, Xiangya School of Medicine, Central South University, Changsha, China
- * E-mail:
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145
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Kota U, Goshe MB. Advances in qualitative and quantitative plant membrane proteomics. PHYTOCHEMISTRY 2011; 72:1040-60. [PMID: 21367437 DOI: 10.1016/j.phytochem.2011.01.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 01/13/2011] [Accepted: 01/19/2011] [Indexed: 05/08/2023]
Abstract
The membrane proteome consists of integral and membrane-associated proteins that are involved in various physiological and biochemical functions critical for cellular function. It is also dynamic in nature, where many proteins are only expressed during certain developmental stages or in response to environmental stress. These proteins can undergo post-translational modifications in response to these different conditions, allowing them to transiently associate with the membrane or other membrane proteins. Along with their increased size, hydrophobicity, and the additional organelle and cellular features of plant cells relative to mammalian systems, the characterization of the plant membrane proteome presents unique challenges for effective qualitative and quantitative analysis using mass spectrometry (MS) analysis. Here, we present the latest advancements developed for the isolation and fractionation of plant organelles and their membrane components amenable to MS analysis. Separations of membrane proteins from these enriched preparations that have proven effective are discussed for both gel- and liquid chromatography-based MS analysis. In this context, quantitative membrane proteomic analyses using both isotope-coded and label-free approaches are presented and reveal the potential to establish a wider-biological interpretation of the function of plant membrane proteins that will ultimately lead to a more comprehensive understanding of plant physiology and their response mechanisms.
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Affiliation(s)
- Uma Kota
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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146
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Guo G, Li N. Relative and accurate measurement of protein abundance using 15N stable isotope labeling in Arabidopsis (SILIA). PHYTOCHEMISTRY 2011; 72:1028-39. [PMID: 21315391 DOI: 10.1016/j.phytochem.2011.01.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 01/04/2011] [Accepted: 01/07/2011] [Indexed: 05/04/2023]
Abstract
In the quantitative proteomic studies, numerous in vitro and in vivo peptide labeling strategies have been successfully applied to measure differentially regulated protein and peptide abundance. These approaches have been proven to be versatile and repeatable in biological discoveries. (15)N metabolic labeling is one of these widely adopted and economical methods. However, due to the differential incorporation rates of (15)N or (14)N, the labeling results produce imperfectly matched isotopic envelopes between the heavy and light nitrogen-labeled peptides. In the present study, we have modified the solid Arabidopsis growth medium to standardize the (15)N supply, which led to a uniform incorporation of (15)N into the whole plant protein complement. The incorporation rate (97.43±0.11%) of (15)N into (15)N-coded peptides was determined by correlating the intensities of peptide ions with the labeling efficiencies according to Gaussian distribution. The resulting actual incorporation rate (97.44%) and natural abundance of (15)N/(14)N-coded peptides are used to re-calculate the intensities of isotopic envelopes of differentially labeled peptides, respectively. A modified (15)N/(14)N stable isotope labeling strategy, SILIA, is assessed and the results demonstrate that this approach is able to differentiate the fold change in protein abundance down to 10%. The machine dynamic range limitation and purification step will make the precursor ion ratio deriving from the actual ratio fold change. It is suggested that the differentially mixed (15)N-coded and (14)N-coded plant protein samples that are used to establish the protein abundance standard curve should be prepared following a similar protein isolation protocol used to isolate the proteins to be quantitated.
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Affiliation(s)
- Guangyu Guo
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
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147
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Fagerberg L, Stadler C, Skogs M, Hjelmare M, Jonasson K, Wiking M, Åbergh A, Uhlén M, Lundberg E. Mapping the Subcellular Protein Distribution in Three Human Cell Lines. J Proteome Res 2011; 10:3766-77. [DOI: 10.1021/pr200379a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Linn Fagerberg
- School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), Stockholm, SE-106 91, Sweden
| | - Charlotte Stadler
- Science for Life Laboratory, Royal Institute of Technology (KTH), Stockholm, SE-171 65, Sweden
| | - Marie Skogs
- Science for Life Laboratory, Royal Institute of Technology (KTH), Stockholm, SE-171 65, Sweden
| | - Martin Hjelmare
- Science for Life Laboratory, Royal Institute of Technology (KTH), Stockholm, SE-171 65, Sweden
| | - Kalle Jonasson
- School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), Stockholm, SE-106 91, Sweden
| | - Mikaela Wiking
- Science for Life Laboratory, Royal Institute of Technology (KTH), Stockholm, SE-171 65, Sweden
| | - Annica Åbergh
- Science for Life Laboratory, Royal Institute of Technology (KTH), Stockholm, SE-171 65, Sweden
| | - Mathias Uhlén
- School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), Stockholm, SE-106 91, Sweden
- Science for Life Laboratory, Royal Institute of Technology (KTH), Stockholm, SE-171 65, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, Royal Institute of Technology (KTH), Stockholm, SE-171 65, Sweden
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148
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Brown AP, Kroon JTM, Topping JF, Robson JL, Simon WJ, Slabas AR. Components of Complex Lipid Biosynthetic Pathways in Developing Castor (Ricinus communis) Seeds Identified by MudPIT Analysis of Enriched Endoplasmic Reticulum. J Proteome Res 2011; 10:3565-77. [DOI: 10.1021/pr2002066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Adrian P. Brown
- School of Biological and Biomedical Sciences, University of Durham, South Road, Durham, DH1 3LE, United Kingdom
| | - Johan T. M. Kroon
- School of Biological and Biomedical Sciences, University of Durham, South Road, Durham, DH1 3LE, United Kingdom
| | - Jennifer F. Topping
- School of Biological and Biomedical Sciences, University of Durham, South Road, Durham, DH1 3LE, United Kingdom
| | - Joanne L. Robson
- School of Biological and Biomedical Sciences, University of Durham, South Road, Durham, DH1 3LE, United Kingdom
| | - William J. Simon
- School of Biological and Biomedical Sciences, University of Durham, South Road, Durham, DH1 3LE, United Kingdom
| | - Antoni R. Slabas
- School of Biological and Biomedical Sciences, University of Durham, South Road, Durham, DH1 3LE, United Kingdom
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149
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Reumann S. Toward a definition of the complete proteome of plant peroxisomes: Where experimental proteomics must be complemented by bioinformatics. Proteomics 2011; 11:1764-79. [PMID: 21472859 DOI: 10.1002/pmic.201000681] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 02/06/2011] [Accepted: 02/11/2011] [Indexed: 12/23/2022]
Abstract
In the past few years, proteome analysis of Arabidopsis peroxisomes has been established by the complementary efforts of four research groups and has emerged as the major unbiased approach to identify new peroxisomal proteins on a large scale. Collectively, more than 100 new candidate proteins from plant peroxisomes have been identified, including long-awaited low-abundance proteins. More than 50 proteins have been validated as peroxisome targeted, nearly doubling the number of established plant peroxisomal proteins. Sequence homologies of the new proteins predict unexpected enzyme activities, novel metabolic pathways and unknown non-metabolic peroxisome functions. Despite this remarkable success, proteome analyses of plant peroxisomes remain highly material intensive and require major preparative efforts. Characterization of the membrane proteome or post-translational protein modifications poses major technical challenges. New strategies, including quantitative mass spectrometry methods, need to be applied to allow further identifications of plant peroxisomal proteins, such as of stress-inducible proteins. In the long process of defining the complete proteome of plant peroxisomes, the prediction of peroxisome-targeted proteins from plant genome sequences emerges as an essential complementary approach to identify additional peroxisomal proteins that are, for instance, specific to peroxisome variants from minor tissues and organs or to abiotically stressed model and crop plants.
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Affiliation(s)
- Sigrun Reumann
- Centre for Organelle Research, University of Stavanger, Stavanger, Norway.
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150
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Agrawal GK, Job D, Zivy M, Agrawal VP, Bradshaw RA, Dunn MJ, Haynes PA, van Wijk KJ, Kikuchi S, Renaut J, Weckwerth W, Rakwal R. Time to articulate a vision for the future of plant proteomics - A global perspective: An initiative for establishing the International Plant Proteomics Organization (INPPO). Proteomics 2011; 11:1559-68. [DOI: 10.1002/pmic.201000608] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Revised: 11/23/2010] [Accepted: 12/27/2010] [Indexed: 01/11/2023]
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