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Mejia Diaz LF, Karasinski J, Wrobel K, Corrales Escobosa AR, Yanez Barrientos E, Halicz L, Bulska E, Wrobel K. Fractionation of selenium isotopes during biofortification of Saccharomyces cerevisiae and the influence of metabolic labeling with 15N. J Biol Inorg Chem 2023; 28:655-667. [PMID: 37646892 DOI: 10.1007/s00775-023-02016-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/08/2023] [Indexed: 09/01/2023]
Abstract
Isotope fractionation of metals/metalloids in biological systems is an emerging research area that demands the application of state-of-the-art analytical chemistry tools and provides data of relevance to life sciences. In this work, Se uptake and Se isotope fractionation were measured during the biofortification of baker's yeast (Saccharomyces cerevisiae)-a product widely used in dietary Se supplementation and in cancer prevention. On the other hand, metabolic labeling with 15N is a valuable tool in mass spectrometry-based comparative proteomics. For Se-yeast, such labeling would facilitate the assessment of Se impact on yeast proteome; however, the question arises whether the presence of 15N in the microorganisms affects Se uptake and its isotope fractionation. To address the above-mentioned aspects, extracellularly reduced and cell-incorporated Se fractions were analyzed by hydride generation-multi-collector inductively coupled plasma-mass spectrometry (HG MC ICP-MS). It was found that extracellularly reduced Se was enriched in light isotopes; for cell-incorporated Se, the change was even more pronounced, which provides new evidence of mass fractionation during biological selenite reduction. In the presence of 15N, a weaker preference for light isotopes was observed in both, extracellular and cell-incorporated Se. Furthermore, a significant increase in Se uptake for 15N compared to 14N biomass was found, with good agreement between hydride generation microwave plasma-atomic emission spectrometry (HG MP-AES) and quadrupole ICP-MS results. Biological effects observed for heavy nitrogen suggest 15N-driven alteration at the proteome level, which facilitated Se access to cells with decreased preference for light isotopes.
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Affiliation(s)
| | - Jakub Karasinski
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-093, Warsaw, Poland
| | - Kazimierz Wrobel
- Chemistry Department, University of Guanajuato, L. de Retana 5, 36000, Guanajuato, Mexico
| | | | | | - Ludwik Halicz
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-093, Warsaw, Poland
- Geological Survey of Israel, Y. Leibovitz, 969200, Jerusalem, Israel
| | - Ewa Bulska
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-093, Warsaw, Poland.
| | - Katarzyna Wrobel
- Chemistry Department, University of Guanajuato, L. de Retana 5, 36000, Guanajuato, Mexico.
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-093, Warsaw, Poland.
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2
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Plasma membrane proteome analyses of Arabidopsis thaliana suspension-cultured cells during cold or ABA treatment: Relationship with freezing tolerance and growth phase. J Proteomics 2020; 211:103528. [DOI: 10.1016/j.jprot.2019.103528] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/28/2019] [Accepted: 09/15/2019] [Indexed: 11/22/2022]
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3
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Plasma Membrane Proteomics of Arabidopsis Suspension-Cultured Cells Associated with Growth Phase Using Nano-LC-MS/MS. Methods Mol Biol 2018; 1696:185-194. [PMID: 29086404 DOI: 10.1007/978-1-4939-7411-5_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Arabidopsis thaliana suspension-cultured cells (T87 line) are important model system for studies of responses to biotic and abiotic stresses at the cellular level in vitro since the cells have certain advantages compared with the whole plant system. However, the physiological and morphological characteristics of the cells are influenced by the progress of the growth phase of cells, which may result in different stress tolerance. To obtain comprehensive proteome profiles of the plasma membrane of Arabidopsis thaliana T87 suspension-cultured cells at the lag, log, or stationary growth phase, a shotgun proteomics method using nano-LC-MS/MS is used. The results obtained indicate that proteome profiles of the plasma membrane with the progress of the growth phase of cells dynamically changed, which may be associated with the physiological and morphological characteristics of the plasma membrane of the suspension-cultured cells. The proteomics results are further applied to explain different responsive patterns in the plasma membrane to cold acclimation and ABA treatment, which lead to understanding of different freezing tolerance associated with the growth phase of the cells.
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Aguilar-Hernández V, Loyola-Vargas VM. Advanced Proteomic Approaches to Elucidate Somatic Embryogenesis. FRONTIERS IN PLANT SCIENCE 2018; 9:1658. [PMID: 30524454 PMCID: PMC6262180 DOI: 10.3389/fpls.2018.01658] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/25/2018] [Indexed: 05/06/2023]
Abstract
Somatic embryogenesis (SE) is a cell differentiation process by which a somatic cell changes its genetic program and develops into an embryonic cell. Investigating this process with various explant sources in vitro has allowed us to trace somatic embryo development from germination to plantlets and has led to the generation of new technologies, including genetic transformation, endangered species conservation, and synthetic seed production. A transcriptome data comparison from different stages of the developing somatic embryo has revealed a complex network controlling the somatic cell's fate, suggesting that an interconnected network acts at the protein level. Here, we discuss the current progress on SE using proteomic-based data, focusing on changing patterns of proteins during the establishment of the somatic embryo. Despite the advanced proteomic approaches available so far, deciphering how the somatic embryo is induced is still in its infancy. The new proteomics techniques that lead to the quantification of proteins with different abundances during the induction of SE are opening this area of study for the first time. These quantitative differences can elucidate the different pathways involved in SE induction. We envisage that the application of these proteomic technologies can be pivotal to identifying proteins critical to the process of SE, demonstrating the cellular localization, posttranslational modifications, and turnover protein events required to switch from a somatic cell to a somatic embryo cell and providing new insights into the molecular mechanisms underlying SE. This work will help to develop biotechnological strategies for mass production of quality crop material.
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Affiliation(s)
- Victor Aguilar-Hernández
- Catedrático CONACYT, Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
- *Correspondence: Victor Aguilar-Hernández, orcid.org/0000-0001-8239-4047
| | - Víctor M. Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
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Aranjuelo I, Molero G, Avice JC, Bourguignon J. A novel method for determination of the (15) N isotopic composition of Rubisco in wheat plants exposed to elevated atmospheric carbon dioxide. PHYSIOLOGIA PLANTARUM 2015; 153:195-203. [PMID: 25272325 DOI: 10.1111/ppl.12294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 09/01/2014] [Accepted: 09/16/2014] [Indexed: 06/03/2023]
Abstract
Although ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is mostly known as a key enzyme involved in CO2 assimilation during the Calvin cycle, comparatively little is known about its role as a pool of nitrogen storage in leaves. For this purpose, we developed a protocol to purify Rubisco that enables later analysis of its (15) N isotope composition (δ(15) N) at the natural abundance and (15) N-labeled plants. In order to test the utility of this protocol, durum wheat (Triticum durum var. Sula) exposed to an elevated CO2 concentration (700 vs 400 µmol mol(-1) ) was labeled with K(15) NO3 (enriched at 2 atom %) during the ear development period. The developed protocol proves to be selective, simple, cost effective and reproducible. The study reveals that (15) N labeling was different in total organic matter, total soluble protein and the Rubisco fraction. The obtained data suggest that photosynthetic acclimation in wheat is caused by Rubisco depletion. This depletion may be linked to preferential nitrogen remobilization from Rubisco toward grain filling.
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Affiliation(s)
- Iker Aranjuelo
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of Basque Country (UPV-EHU), Apdo. 644, E-48080 Bilbao, Vizcaya, Spain; CEA, iRTSV, Laboratoire Physiologie Cellulaire Végétale (PCV), F-38054, Grenoble, France; Université Grenoble Alpes, PCV, F-38041, Grenoble, France; CNRS, UMR5168, PCV, F-38054, Grenoble, France; INRA, USC1359, PCV, F-38054, Grenoble, France
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6
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Taylor NL, Millar AH. Plant mitochondrial proteomics. Methods Mol Biol 2015; 1305:83-106. [PMID: 25910728 DOI: 10.1007/978-1-4939-2639-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Mitochondrial proteomics has significantly developed since the first plant mitochondrial proteomes were published in 2001. Many studies have added to our knowledge of the protein components that make up plant mitochondria in a wide range of species. Here we present two common and one emerging quantitative proteomic techniques that can be used to study the abundance of mitochondrial proteins. For this publication, we have described the methods as an approach to determine the amount of contamination in a mitochondrial isolation to contrast historical approaches that involved the use of use of antibodies to specific marker proteins or the measurement of activity of marker enzymes. However, these approaches could easily be adapted to carry out control versus treatment studies.
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Affiliation(s)
- Nicolas L Taylor
- Plant Energy Biology, Australian Research Council Centre of Excellence and Centre for Comparative Analysis of Biomolecular Networks (CABiN), The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
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Dupae J, Bohler S, Noben JP, Carpentier S, Vangronsveld J, Cuypers A. Problems inherent to a meta-analysis of proteomics data: a case study on the plants' response to Cd in different cultivation conditions. J Proteomics 2014; 108:30-54. [PMID: 24821411 DOI: 10.1016/j.jprot.2014.04.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 03/07/2014] [Accepted: 04/15/2014] [Indexed: 01/14/2023]
Abstract
UNLABELLED This meta-analysis focuses on plant-proteome responses to cadmium (Cd) stress. Initially, some general topics related to a proteomics meta-analysis are discussed: (1) obstacles encountered during data analysis, (2) a consensus in proteomic research, (3) validation and good reporting practices for protein identification and (4) guidelines for statistical analysis of differentially abundant proteins. In a second part, the Cd responses in leaves and roots obtained from a proteomics meta-analysis are discussed in (1) a time comparison (short versus long term exposure), and (2) a culture comparison (hydroponics versus soil cultivation). Data of the meta-analysis confirmed the existence of an initial alarm phase upon Cd exposure. Whereas no metabolic equilibrium is established in hydroponically exposed plants, an equilibrium seems to be manifested in roots of plants grown in Cd-contaminated soil after long term exposure. In leaves, the carbohydrate metabolism is primarily affected independent of the exposure time and the cultivation method. In addition, a metabolic shift from CO2-fixation towards respiration is manifested, independent of the cultivation system. Finally, some ideas for the improvement of proteomics setups and for comparisons between studies are discussed. BIOLOGICAL SIGNIFICANCE This meta-analysis focuses on the plant responses to Cd stress in leaves and roots at the proteome level. This meta-analysis points out the encountered obstacles when performing a proteomics meta-analysis related to inherent technologies, but also related to experimental setups. Furthermore, the question is addressed whether an extrapolation of results obtained in hydroponic cultivation towards soil-grown plants is possible.
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Affiliation(s)
- Joke Dupae
- Environmental Biology, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium.
| | - Sacha Bohler
- Environmental Biology, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium.
| | - Jean-Paul Noben
- Biomedical Institute, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium.
| | - Sebastien Carpentier
- Afdeling Plantenbiotechniek, Catholic University Leuven, Willem de Croylaan 42 - bus 2455, 3001 Leuven, Belgium.
| | - Jaco Vangronsveld
- Environmental Biology, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium.
| | - Ann Cuypers
- Environmental Biology, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium.
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8
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Matthes A, Köhl K, Schulze WX. SILAC and alternatives in studying cellular proteomes of plants. Methods Mol Biol 2014; 1188:65-83. [PMID: 25059605 DOI: 10.1007/978-1-4939-1142-4_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Quantitative proteomics by metabolic labeling has a high impact on the growing field of plant systems biology. SILAC has been pioneered and optimized for plant cell culture systems allowing for SILAC-based quantitative experiments in specialized experimental setups. In comparison to other model organisms, the application of SILAC to whole plants is challenging. As autotrophic organisms, plants under their natural growth conditions can hardly be fully labeled with stable isotope-coded amino acids. The metabolic labeling with inorganic nitrogen is therefore the method of choice for most whole-plant physiological questions. Plants can easily metabolize different inorganic nitrogen isotopes. The incorporation of the labeled inorganic nitrogen then results in proteins and metabolites with distinct molecular mass, which can be detected on a mass spectrometer. In comparative quantitative experiments, similarly as in SILAC experiments, treated and untreated samples are differentially labeled by nitrogen isotopes and jointly processed, thereby minimizing sample-to-sample variation. In recent years, heavy nitrogen labeling has become a widely used strategy in quantitative proteomics and novel approaches were developed for metabolite identification. Here we present a typical hydroponics setup, the workflow for processing of samples, mass spectrometry and data analysis for large-scale metabolic labeling experiments of whole plants.
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Affiliation(s)
- Annemarie Matthes
- Max Planck Institut für molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Golm, Germany
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9
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Szymanski WG, Kierszniowska S, Schulze WX. Metabolic labeling and membrane fractionation for comparative proteomic analysis of Arabidopsis thaliana suspension cell cultures. J Vis Exp 2013:e50535. [PMID: 24121251 DOI: 10.3791/50535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Plasma membrane microdomains are features based on the physical properties of the lipid and sterol environment and have particular roles in signaling processes. Extracting sterol-enriched membrane microdomains from plant cells for proteomic analysis is a difficult task mainly due to multiple preparation steps and sources for contaminations from other cellular compartments. The plasma membrane constitutes only about 5-20% of all the membranes in a plant cell, and therefore isolation of highly purified plasma membrane fraction is challenging. A frequently used method involves aqueous two-phase partitioning in polyethylene glycol and dextran, which yields plasma membrane vesicles with a purity of 95% (1). Sterol-rich membrane microdomains within the plasma membrane are insoluble upon treatment with cold nonionic detergents at alkaline pH. This detergent-resistant membrane fraction can be separated from the bulk plasma membrane by ultracentrifugation in a sucrose gradient (2). Subsequently, proteins can be extracted from the low density band of the sucrose gradient by methanol/chloroform precipitation. Extracted protein will then be trypsin digested, desalted and finally analyzed by LC-MS/MS. Our extraction protocol for sterol-rich microdomains is optimized for the preparation of clean detergent-resistant membrane fractions from Arabidopsis thaliana cell cultures. We use full metabolic labeling of Arabidopsis thaliana suspension cell cultures with K(15)NO3 as the only nitrogen source for quantitative comparative proteomic studies following biological treatment of interest (3). By mixing equal ratios of labeled and unlabeled cell cultures for joint protein extraction the influence of preparation steps on final quantitative result is kept at a minimum. Also loss of material during extraction will affect both control and treatment samples in the same way, and therefore the ratio of light and heave peptide will remain constant. In the proposed method either labeled or unlabeled cell culture undergoes a biological treatment, while the other serves as control (4).
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10
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Lewandowska D, ten Have S, Hodge K, Tillemans V, Lamond AI, Brown JWS. Plant SILAC: stable-isotope labelling with amino acids of arabidopsis seedlings for quantitative proteomics. PLoS One 2013; 8:e72207. [PMID: 23977254 PMCID: PMC3748079 DOI: 10.1371/journal.pone.0072207] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 07/07/2013] [Indexed: 12/20/2022] Open
Abstract
Stable Isotope Labelling by Amino acids in Cell culture (SILAC) is a powerful technique for comparative quantitative proteomics, which has recently been applied to a number of different eukaryotic organisms. Inefficient incorporation of labelled amino acids in cell cultures of Arabidopsis thaliana has led to very limited use of SILAC in plant systems. We present a method allowing, for the first time, efficient labelling with stable isotope-containing arginine and lysine of whole Arabidopsis seedlings. To illustrate the utility of this method, we have combined the high labelling efficiency (>95%) with quantitative proteomics analyses of seedlings exposed to increased salt concentration. In plants treated for 7 days with 80 mM NaCl, a relatively mild salt stress, 215 proteins were identified whose expression levels changed significantly compared to untreated seedling controls. The 92 up-regulated proteins included proteins involved in abiotic stress responses and photosynthesis, while the 123 down-regulated proteins were enriched in proteins involved in reduction of oxidative stress and other stress responses, respectively. Efficient labelling of whole Arabidopsis seedlings by this modified SILAC method opens new opportunities to exploit the genetic resources of Arabidopsis and analyse the impact of mutations on quantitative protein dynamics in vivo.
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Affiliation(s)
- Dominika Lewandowska
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- Division of Plant Sciences, College of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
| | - Sara ten Have
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Kelly Hodge
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Vinciane Tillemans
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Angus I. Lamond
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - John W. S. Brown
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- Division of Plant Sciences, College of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
- * E-mail:
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Abreu IA, Farinha AP, Negrão S, Gonçalves N, Fonseca C, Rodrigues M, Batista R, Saibo NJM, Oliveira MM. Coping with abiotic stress: proteome changes for crop improvement. J Proteomics 2013; 93:145-68. [PMID: 23886779 DOI: 10.1016/j.jprot.2013.07.014] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 07/02/2013] [Accepted: 07/08/2013] [Indexed: 12/20/2022]
Abstract
Plant breeders need new and more precise tools to accelerate breeding programs that address the increasing needs for food, feed, energy and raw materials, while facing a changing environment in which high salinity and drought have major impacts on crop losses worldwide. This review covers the achievements and bottlenecks in the identification and validation of proteins with relevance in abiotic stress tolerance, also mentioning the unexpected consequences of the stress in allergen expression. While addressing the key pathways regulating abiotic stress plant adaptation, comprehensive data is presented on the proteins confirmed as relevant to confer tolerance. Promising candidates still to be confirmed are also highlighted, as well as the specific protein families and protein modifications for which detection and characterization is still a challenge. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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Affiliation(s)
- Isabel A Abreu
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Genomics of Plant Stress Laboratory (GPlantS Lab), Av. da República, 2780-157 Oeiras, Portugal; iBET, Apartado 12, 2781-901 Oeiras, Portugal
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12
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Yadeta KA, Elmore JM, Coaker G. Advancements in the analysis of the Arabidopsis plasma membrane proteome. FRONTIERS IN PLANT SCIENCE 2013; 4:86. [PMID: 23596451 PMCID: PMC3622881 DOI: 10.3389/fpls.2013.00086] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 03/22/2013] [Indexed: 05/09/2023]
Abstract
The plasma membrane (PM) regulates diverse processes essential to plant growth, development, and survival in an ever-changing environment. In addition to maintaining normal cellular homeostasis and plant nutrient status, PM proteins perceive and respond to a myriad of environmental cues. Here we review recent advances in the analysis of the plant PM proteome with a focus on the model plant Arabidopsis thaliana. Due to membrane heterogeneity, hydrophobicity, and low relative abundance, analysis of the PM proteome has been a special challenge. Various experimental techniques to enrich PM proteins and different protein and peptide separation strategies have facilitated the identification of thousands of integral and membrane-associated proteins. Numerous classes of proteins are present at the PM with diverse biological functions. PM microdomains have attracted much attention. However, it still remains a challenge to characterize these cell membrane compartments. Dynamic changes in the PM proteome in response to different biotic and abiotic stimuli are highlighted. Future prospects for PM proteomics research are also discussed.
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Affiliation(s)
- Koste A. Yadeta
- Department of Plant Pathology, University of California DavisDavis, CA, USA
| | - J. Mitch Elmore
- Department of Plant Pathology, University of California DavisDavis, CA, USA
| | - Gitta Coaker
- Department of Plant Pathology, University of California DavisDavis, CA, USA
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13
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Zhang C, Liu Y, Andrews PC. Quantification of histone modifications using ¹⁵N metabolic labeling. Methods 2013; 61:236-43. [PMID: 23454290 DOI: 10.1016/j.ymeth.2013.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 02/11/2013] [Accepted: 02/13/2013] [Indexed: 11/27/2022] Open
Abstract
Mass spectrometry has made major contributions to recent discoveries in the field of epigenetics, particularly in the characterization of the myriad post-translational modifications (PTMs) of histones which are technically challenging to analyze. These new developments have further aroused great interest in development of robust, new mass spectrometric methods to quantitatively study the dynamics of histone modifications. This review covers quantitative analysis of histone PTMs and discuss an ¹⁵N metabolic labeling procedure for quantifying histone PTMs applied to the analysis of methyltransferase knockouts in the model organism, Tetrahymena thermophila.
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Affiliation(s)
- Chunchao Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, USA
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14
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Zhang H, Zhou H, Berke L, Heck AJR, Mohammed S, Scheres B, Menke FLH. Quantitative phosphoproteomics after auxin-stimulated lateral root induction identifies an SNX1 protein phosphorylation site required for growth. Mol Cell Proteomics 2013; 12:1158-69. [PMID: 23328941 DOI: 10.1074/mcp.m112.021220] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein phosphorylation is instrumental to early signaling events. Studying system-wide phosphorylation in relation to processes under investigation requires a quantitative proteomics approach. In Arabidopsis, auxin application can induce pericycle cell divisions and lateral root formation. Initiation of lateral root formation requires transcriptional reprogramming following auxin-mediated degradation of transcriptional repressors. The immediate early signaling events prior to this derepression are virtually uncharacterized. To identify the signal molecules responding to auxin application, we used a lateral root-inducible system that was previously developed to trigger synchronous division of pericycle cells. To identify and quantify the early signaling events following this induction, we combined (15)N-based metabolic labeling and phosphopeptide enrichment and applied a mass spectrometry-based approach. In total, 3068 phosphopeptides were identified from auxin-treated root tissue. This root proteome dataset contains largely phosphopeptides not previously reported and represents one of the largest quantitative phosphoprotein datasets from Arabidopsis to date. Key proteins responding to auxin treatment included the multidrug resistance-like and PIN2 auxin carriers, auxin response factor2 (ARF2), suppressor of auxin resistance 3 (SAR3), and sorting nexin1 (SNX1). Mutational analysis of serine 16 of SNX1 showed that overexpression of the mutated forms of SNX1 led to retarded growth and reduction of lateral root formation due to the reduced outgrowth of the primordium, showing proof of principle for our approach.
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Affiliation(s)
- Hongtao Zhang
- Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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Ullmann-Zeunert L, Muck A, Wielsch N, Hufsky F, Stanton MA, Bartram S, Böcker S, Baldwin IT, Groten K, Svatoš A. Determination of ¹⁵N-incorporation into plant proteins and their absolute quantitation: a new tool to study nitrogen flux dynamics and protein pool sizes elicited by plant-herbivore interactions. J Proteome Res 2012; 11:4947-60. [PMID: 22905865 DOI: 10.1021/pr300465n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Herbivory leads to changes in the allocation of nitrogen among different pools and tissues; however, a detailed quantitative analysis of these changes has been lacking. Here, we demonstrate that a mass spectrometric data-independent acquisition approach known as LC-MS(E), combined with a novel algorithm to quantify heavy atom enrichment in peptides, is able to quantify elicited changes in protein amounts and (15)N flux in a high throughput manner. The reliable identification/quantitation of rabbit phosphorylase b protein spiked into leaf protein extract was achieved. The linear dynamic range, reproducibility of technical and biological replicates, and differences between measured and expected (15)N-incorporation into the small (SSU) and large (LSU) subunits of ribulose-1,5-bisphosphate-carboxylase/oxygenase (RuBisCO) and RuBisCO activase 2 (RCA2) of Nicotiana attenuata plants grown in hydroponic culture at different known concentrations of (15)N-labeled nitrate were used to further evaluate the procedure. The utility of the method for whole-plant studies in ecologically realistic contexts was demonstrated by using (15)N-pulse protocols on plants growing in soil under unknown (15)N-incorporation levels. Additionally, we quantified the amounts of lipoxygenase 2 (LOX2) protein, an enzyme important in antiherbivore defense responses, demonstrating that the approach allows for in-depth quantitative proteomics and (15)N flux analyses of the metabolic dynamics elicited during plant-herbivore interactions.
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Filiou MD, Varadarajulu J, Teplytska L, Reckow S, Maccarrone G, Turck CW. The 15N isotope effect in Escherichia coli: a neutron can make the difference. Proteomics 2012; 12:3121-8. [PMID: 22887715 DOI: 10.1002/pmic.201200209] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 06/25/2012] [Accepted: 08/04/2012] [Indexed: 12/22/2022]
Abstract
Several techniques based on stable isotope labeling are used for quantitative MS. These include stable isotope metabolic labeling methods for cells in culture as well as live organisms with the assumption that the stable isotope has no effect on the proteome. Here, we investigate the (15) N isotope effect on Escherichia coli cultures that were grown in either unlabeled ((14) N) or (15) N-labeled media by LC-ESI-MS/MS-based relative protein quantification. Consistent protein expression level differences and altered growth rates were observed between (14) N and (15) N-labeled cultures. Furthermore, targeted metabolite analyses revealed altered metabolite levels between (14) N and (15) N-labeled bacteria. Our data demonstrate for the first time that the introduction of the (15) N isotope affects protein and metabolite levels in E. coli and underline the importance of implementing controls for unbiased protein quantification using stable isotope labeling techniques.
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Affiliation(s)
- Michaela D Filiou
- Max Planck Institute of Psychiatry, Proteomics and Biomarkers, Munich, Germany
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17
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Arsova B, Kierszniowska S, Schulze WX. The use of heavy nitrogen in quantitative proteomics experiments in plants. TRENDS IN PLANT SCIENCE 2012; 17:102-12. [PMID: 22154826 DOI: 10.1016/j.tplants.2011.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 10/28/2011] [Accepted: 11/04/2011] [Indexed: 05/04/2023]
Abstract
In the growing field of plant systems biology, there is an undisputed need for methods allowing accurate quantitation of proteins and metabolites. As autotrophic organisms, plants can easily metabolize different nitrogen isotopes, resulting in proteins and metabolites with distinct molecular mass that can be separated on a mass spectrometer. In comparative quantitative experiments, treated and untreated samples are differentially labeled by nitrogen isotopes and jointly processed, thereby minimizing sample-to-sample variation. In recent years, heavy nitrogen labeling has become a widely used strategy in quantitative proteomics and novel approaches have been developed for metabolite identification. Here, we present an overview of currently used experimental strategies in heavy nitrogen labeling in plants and provide background on the history and function of this quantitation technique.
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Affiliation(s)
- Borjana Arsova
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany
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18
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Filiou MD, Martins-de-Souza D, Guest PC, Bahn S, Turck CW. To label or not to label: Applications of quantitative proteomics in neuroscience research. Proteomics 2012; 12:736-47. [DOI: 10.1002/pmic.201100350] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 10/18/2011] [Accepted: 10/24/2011] [Indexed: 01/09/2023]
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19
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Li L, Nelson CJ, Solheim C, Whelan J, Millar AH. Determining degradation and synthesis rates of arabidopsis proteins using the kinetics of progressive 15N labeling of two-dimensional gel-separated protein spots. Mol Cell Proteomics 2012; 11:M111.010025. [PMID: 22215636 DOI: 10.1074/mcp.m111.010025] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The growth and development of plant tissues is associated with an ordered succession of cellular processes that are reflected in the appearance and disappearance of proteins. The control of the kinetics of protein turnover is central to how plants can rapidly and specifically alter protein abundance and thus molecular function in response to environmental or developmental cues. However, the processes of turnover are largely hidden during periods of apparent steady-state protein abundance, and even when proteins accumulate it is unclear whether enhanced synthesis or decreased degradation is responsible. We have used a (15)N labeling strategy with inorganic nitrogen sources coupled to a two-dimensional fluorescence difference gel electrophoresis and mass spectrometry analysis of two-dimensional IEF/SDS-PAGE gel spots to define the rate of protein synthesis (K(S)) and degradation (K(D)) of Arabidopsis cell culture proteins. Through analysis of MALDI-TOF/TOF mass spectra from 120 protein spots, we were able to quantify K(S) and K(D) for 84 proteins across six functional groups and observe over 65-fold variation in protein degradation rates. K(S) and K(D) correlate with functional roles of the proteins in the cell and the time in the cell culture cycle. This approach is based on progressive (15)N labeling that is innocuous for the plant cells and, because it can be used to target analysis of proteins through the use of specific gel spots, it has broad applicability.
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Affiliation(s)
- Lei Li
- Australian Research Council Centre of Excellence in Plant Energy Biology & Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, Crawley, Western Australia 6009, Australia
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20
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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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21
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Bindschedler LV, Mills DJS, Cramer R. Hydroponic isotope labeling of entire plants and high-performance mass spectrometry for quantitative plant proteomics. Methods Mol Biol 2012; 893:155-173. [PMID: 22665301 DOI: 10.1007/978-1-61779-885-6_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Hydroponic isotope labeling of entire plants (HILEP) combines hydroponic plant cultivation and metabolic labeling with stable isotopes using (15)N-containing inorganic salts to label whole and mature plants. Employing (15)N salts as the sole nitrogen source for HILEP leads to the production of healthy-looking plants which contain (15)N proteins labeled to nearly 100%. Therefore, HILEP is suitable for quantitative plant proteomic analysis, where plants are grown in either (14)N- or (15)N-hydroponic media and pooled when the biological samples are collected for relative proteome quantitation. The pooled (14)N-/(15)N-protein extracts can be fractionated in any suitable way and digested with a protease for shotgun proteomics, using typically reverse phase liquid chromatography nanoelectrospray ionization tandem mass spectrometry (RPLC-nESI-MS/MS). Best results were obtained with a hybrid ion trap/FT-MS mass spectrometer, combining high mass accuracy and sensitivity for the MS data acquisition with speed and high-throughput MS/MS data acquisition, increasing the number of proteins identified and quantified and improving protein quantitation. Peak processing and picking from raw MS data files, protein identification, and quantitation were performed in a highly automated way using integrated MS data analysis software with minimum manual intervention, thus easing the analytical workflow. In this methodology paper, we describe how to grow Arabidopsis plants hydroponically for isotope labeling using (15)N salts and how to quantitate the resulting proteomes using a convenient workflow that does not require extensive bioinformatics skills.
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22
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Martin SF, Munagapati VS, Salvo-Chirnside E, Kerr LE, Le Bihan T. Proteome turnover in the green alga Ostreococcus tauri by time course 15N metabolic labeling mass spectrometry. J Proteome Res 2011; 11:476-86. [PMID: 22077659 DOI: 10.1021/pr2009302] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein synthesis and degradation determine the cellular levels of proteins, and their control hence enables organisms to respond to environmental change. Experimentally, these are little known proteome parameters; however, recently, SILAC-based mass spectrometry studies have begun to quantify turnover in the proteomes of cell lines, yeast, and animals. Here, we present a proteome-scale method to quantify turnover and calculate synthesis and degradation rate constants of individual proteins in autotrophic organisms such as algae and plants. The workflow is based on the automated analysis of partial stable isotope incorporation with (15)N. We applied it in a study of the unicellular pico-alga Ostreococcus tauri and observed high relative turnover in chloroplast-encoded ATPases (0.42-0.58% h(-1)), core photosystem II proteins (0.34-0.51% h(-1)), and RbcL (0.47% h(-1)), while nuclear-encoded RbcS2 is more stable (0.23% h(-1)). Mitochondrial targeted ATPases (0.14-0.16% h(-1)), photosystem antennae (0.09-0.14% h(-1)), and histones (0.07-0.1% h(-1)) were comparatively stable. The calculation of degradation and synthesis rate constants k(deg) and k(syn) confirms RbcL as the bulk contributor to overall protein turnover. This study performed over 144 h of incorporation reveals dynamics of protein complex subunits as well as isoforms targeted to different organelles.
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Affiliation(s)
- Sarah F Martin
- Centre for Systems Biology at Edinburgh, University of Edinburgh, CH Waddington Building, The Kings Buildings, Mayfield Road, EH9 3JD, United Kingdom
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23
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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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24
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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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25
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Nanjo Y, Nouri MZ, Komatsu S. Quantitative proteomic analyses of crop seedlings subjected to stress conditions; a commentary. PHYTOCHEMISTRY 2011; 72:1263-1272. [PMID: 21084103 DOI: 10.1016/j.phytochem.2010.10.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 10/23/2010] [Accepted: 10/26/2010] [Indexed: 05/27/2023]
Abstract
Quantitative proteomics is one of the analytical approaches used to clarify crop responses to stress conditions. Recent remarkable advances in proteomics technologies allow for the identification of a wider range of proteins than was previously possible. Current proteomic methods fall into roughly two categories: gel-based quantification methods, including conventional two-dimensional gel electrophoresis and two-dimensional fluorescence difference gel electrophoresis, and MS-based quantification methods consists of label-based and label-free protein quantification approaches. Although MS-based quantification methods have become mainstream in recent years, gel-based quantification methods are still useful for proteomic analyses. Previous studies examining crop responses to stress conditions reveal that each method has both advantages and disadvantages in regard to protein quantification in comparative proteomic analyses. Furthermore, one proteomics approach cannot be fully substituted by another technique. In this review, we discuss and highlight the basis and applications of quantitative proteomic analysis approaches in crop seedlings in response to flooding and osmotic stress as two environmental stresses.
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Affiliation(s)
- Yohei Nanjo
- National Institute of Crop Science, Tsukuba 305-8518, Japan
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26
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Bindschedler LV, Cramer R. Fully automated software solution for protein quantitation by global metabolic labeling with stable isotopes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:1461-71. [PMID: 21594918 DOI: 10.1002/rcm.4872] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Metabolic stable isotope labeling is increasingly employed for accurate protein (and metabolite) quantitation using mass spectrometry (MS). It provides sample-specific isotopologues that can be used to facilitate comparative analysis of two or more samples. Stable Isotope Labeling by Amino acids in Cell culture (SILAC) has been used for almost a decade in proteomic research and analytical software solutions have been established that provide an easy and integrated workflow for elucidating sample abundance ratios for most MS data formats. While SILAC is a discrete labeling method using specific amino acids, global metabolic stable isotope labeling using isotopes such as (15)N labels the entire element content of the sample, i.e. for (15)N the entire peptide backbone in addition to all nitrogen-containing side chains. Although global metabolic labeling can deliver advantages with regard to isotope incorporation and costs, the requirements for data analysis are more demanding because, for instance for polypeptides, the mass difference introduced by the label depends on the amino acid composition. Consequently, there has been less progress on the automation of the data processing and mining steps for this type of protein quantitation. Here, we present a new integrated software solution for the quantitative analysis of protein expression in differential samples and show the benefits of high-resolution MS data in quantitative proteomic analyses.
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Affiliation(s)
- L V Bindschedler
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
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27
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Villiers F, Ducruix C, Hugouvieux V, Jarno N, Ezan E, Garin J, Junot C, Bourguignon J. Investigating the plant response to cadmium exposure by proteomic and metabolomic approaches. Proteomics 2011; 11:1650-63. [PMID: 21462346 DOI: 10.1002/pmic.201000645] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/25/2011] [Accepted: 02/01/2011] [Indexed: 11/10/2022]
Abstract
Monitoring molecular dynamics of an organism upon stress is probably the best approach to decipher physiological mechanisms involved in the stress response. Quantitative analysis of proteins and metabolites is able to provide accurate information about molecular changes allowing the establishment of a range of more or less specific mechanisms, leading to the identification of major players in the considered pathways. Such tools have been successfully used to analyze the plant response to cadmium (Cd), a major pollutant capable of causing severe health issues as it accumulates in the food chain. We present a summary of proteomics and metabolomics works that contributed to a better understanding of the molecular aspects involved in the plant response to Cd. This work allowed us to provide a finer picture of general signaling, regulatory and metabolic pathways that appeared to be affected upon Cd stress. In particular, we conclude on the advantage of employing different approaches of global proteome- and metabolome-wide techniques, combined with more targeted analysis to answer molecular questions and unravel biological networks. Finally, we propose possible directions and methodologies for future prospectives in this field, as many aspects of the plant-Cd interaction remain to be discovered.
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Affiliation(s)
- Florent Villiers
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire Végétale, Grenoble, France
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28
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Groen AJ, Lilley KS. Proteomics of total membranes and subcellular membranes. Expert Rev Proteomics 2011; 7:867-78. [PMID: 21142888 DOI: 10.1586/epr.10.85] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Membrane proteins are key molecules in the cell and are important targets for drug development. Much effort has, therefore, been directed towards research of this group of proteins, but their hydrophobic nature can make working with them challenging. Here we discuss methodologies used in the study of the membrane proteome, specifically discussing approaches that circumvent technical issues specific to the membrane. In addition, we review several techniques used for visualization, qualification, quantitation and localization of membrane proteins. The combination of the techniques we describe holds great promise to allow full characterization of the membrane proteome and to map the dynamic changes within it essential for cellular function.
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Affiliation(s)
- Arnoud J Groen
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK
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29
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Vertommen A, Panis B, Swennen R, Carpentier SC. Challenges and solutions for the identification of membrane proteins in non-model plants. J Proteomics 2011; 74:1165-81. [PMID: 21354347 DOI: 10.1016/j.jprot.2011.02.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/04/2011] [Accepted: 02/16/2011] [Indexed: 01/27/2023]
Abstract
The workhorse for proteomics in non-model plants is classical two-dimensional electrophoresis, a combination of iso-electric focusing and SDS-PAGE. However, membrane proteins with multiple membrane spanning domains are hardly detected on classical 2-DE gels because of their low abundance and poor solubility in aqueous media. In the current review, solutions that have been proposed to handle these two problems in non-model plants are discussed. An overview of alternative techniques developed for membrane proteomics is provided together with a comparison of their strong and weak points. Subsequently, strengths and weaknesses of the different techniques and methods to evaluate the identification of membrane proteins are discussed. Finally, an overview of recent plant membrane proteome studies is provided with the used separation technique and the number of identified membrane proteins listed.
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Affiliation(s)
- A Vertommen
- Laboratory of Tropical Crop Improvement, Department of Biosystems, K.U. Leuven, Kasteelpark Arenberg 13, B-3001 Heverlee, Belgium
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Skirycz A, Memmi S, De Bodt S, Maleux K, Obata T, Fernie AR, Devreese B, Inzé D. A reciprocal 15N-labeling proteomic analysis of expanding Arabidopsis leaves subjected to osmotic stress indicates importance of mitochondria in preserving plastid functions. J Proteome Res 2011; 10:1018-29. [PMID: 21142212 DOI: 10.1021/pr100785n] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Plants respond to environmental stress by dynamically reprogramming their growth. Whereas stress onset is accompanied by rapid growth inhibition leading to smaller organs, growth will recover and adapt once the stress conditions become stable and do no threaten plant survival. Here, adaptation of growing Arabidopsis thaliana leaves to mild and prolonged osmotic stress was investigated by means of a complete metabolic labeling strategy with the (15)N-stable isotope as a complement to a previously published transcript and metabolite profiling. Global analysis of protein changes revealed that plastidial ATPase, Calvin cycle, and photorespiration were down-regulated, but mitochondrial ATP synthesis was up-regulated, indicating the importance of mitochondria in preserving plastid functions during water stress. Although transcript and protein data correlated well with the stable and prolonged character of the applied stress, numerous proteins were clearly regulated at the post-transcriptional level that could, at least partly, be related to changes in protein synthesis and degradation. In conclusion, proteomics using the (15)N labeling helped understand the mechanisms underlying growth adaptation to osmotic stress and allowed the identification of candidate genes to improve plant growth under limited water.
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31
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Quantitative plant proteomics. Proteomics 2011; 11:756-75. [DOI: 10.1002/pmic.201000426] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 09/10/2010] [Accepted: 10/13/2010] [Indexed: 01/18/2023]
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32
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Filiou MD, Turck CW, Martins-de-Souza D. Quantitative proteomics for investigating psychiatric disorders. Proteomics Clin Appl 2010; 5:38-49. [DOI: 10.1002/prca.201000060] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 09/09/2010] [Accepted: 09/20/2010] [Indexed: 12/21/2022]
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33
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Schmidt H, Böttcher C, Trampczynska A, Clemens S. Use of recombinantly produced 15N3-labelled nicotianamine for fast and sensitive stable isotope dilution ultra-performance liquid chromatography/electrospray ionization time-of-flight mass spectrometry. Anal Bioanal Chem 2010; 399:1355-61. [DOI: 10.1007/s00216-010-4436-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 11/09/2010] [Accepted: 11/10/2010] [Indexed: 10/18/2022]
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34
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Kabała K, Janicka-Russak M, Kłobus G. Different responses of tonoplast proton pumps in cucumber roots to cadmium and copper. JOURNAL OF PLANT PHYSIOLOGY 2010; 167:1328-1335. [PMID: 20696494 DOI: 10.1016/j.jplph.2010.03.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2009] [Revised: 03/29/2010] [Accepted: 03/29/2010] [Indexed: 05/29/2023]
Abstract
Cadmium (Cd) and copper (Cu) effects on the two tonoplast proton pumps were compared in cucumber roots. Different alterations of vacuolar H+ transporting ATPase (V-ATPase) (EC 3.6.3.14) and vacuolar H+ transporting pyrophosphatase (V-PPase) (EC 3.6.1.1) activities under heavy metal stress were investigated. ATP-dependent proton transport and ATP hydrolysis increased after exposure of seedlings to Cu, whereas both decreased in plants stressed with Cd. PP(i) hydrolysis was relatively insensitive to both heavy metals. However, cadmium, but not copper, clearly inhibited PP(i)-driven H+ transport. Changes in enzyme activities were not due to the metal action on the expression of CsVHA-A, CsVHA-c and CsVP genes encoding V-ATPase subunit A and c, and V-PPase, respectively, in cucumber roots. Moreover, immunoblot analysis using specific antibodies against V-ATPase holoenzyme, phosphoserine and phosphothreonine suggested that the phosphorylation at Ser residue in regulatory subunit B of cucumber V-ATPase was not regulated by metals. Oxidative alterations of membrane lipids were measured as malondialdehyde (MDA) content. Cu ions, in contrast to Cd, visibly enhanced the lipid peroxidation in the root tonoplast fractions. Because ATP and PP(i) are absolutely required by V-ATPase and V-PPase, respectively, for proton transport, their contents were determined in the control roots and roots treated with cadmium and copper. Both ATP and pyrophosphate amounts decreased under heavy metal stress.
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Affiliation(s)
- Katarzyna Kabała
- Department of Plant Physiology, Institute of Plant Biology, University of Wrocław, Kanonia 6/8, 50-328 Wrocław, Poland.
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35
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Liu X, Wen F, Yang J, Chen L, Wei YQ. A review of current applications of mass spectrometry for neuroproteomics in epilepsy. MASS SPECTROMETRY REVIEWS 2010; 29:197-246. [PMID: 19598206 DOI: 10.1002/mas.20243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The brain is unquestionably the most fascinating organ, and the hippocampus is crucial in memory storage and retrieval and plays an important role in stress response. In temporal lobe epilepsy (TLE), the seizure origin typically involves the hippocampal formation. Despite tremendous progress, current knowledge falls short of being able to explain its function. An emerging approach toward an improved understanding of the complex molecular mechanisms that underlie functions of the brain and hippocampus is neuroproteomics. Mass spectrometry has been widely used to analyze biological samples, and has evolved into an indispensable tool for proteomics research. In this review, we present a general overview of the application of mass spectrometry in proteomics, summarize neuroproteomics and systems biology-based discovery of protein biomarkers for epilepsy, discuss the methodology needed to explore the epileptic hippocampus proteome, and also focus on applications of ingenuity pathway analysis (IPA) in disease research. This neuroproteomics survey presents a framework for large-scale protein research in epilepsy that can be applied for immediate epileptic biomarker discovery and the far-reaching systems biology understanding of the protein regulatory networks. Ultimately, knowledge attained through neuroproteomics could lead to clinical diagnostics and therapeutics to lessen the burden of epilepsy on society.
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Affiliation(s)
- Xinyu Liu
- National Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
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36
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Abstract
Mass-spectrometry-based proteomics, the large-scale analysis of proteins by mass spectrometry, has emerged as a new technology over the last decade and become routine in many plant biology laboratories. While early work consisted merely of listing proteins identified in a given organ or under different conditions of interest, there is a growing need to apply comparative and quantitative proteomics strategies toward gaining novel insights into functional aspects of plant proteins and their dynamics. However, during the transition from qualitative to quantitative protein analysis, the potential and challenges will be tightly coupled. Several strategies for differential proteomics that involve stable isotopes or label-free comparisons and their statistical assessment are possible, each having specific strengths and limitations. Furthermore, incomplete proteome coverage and restricted dynamic range still impose the strongest limitations to data throughput and precise quantitative analysis. This review gives an overview of the current state of the art in differential proteomics and possible strategies in data processing.
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Gouw JW, Krijgsveld J, Heck AJR. Quantitative proteomics by metabolic labeling of model organisms. Mol Cell Proteomics 2009; 9:11-24. [PMID: 19955089 DOI: 10.1074/mcp.r900001-mcp200] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In the biological sciences, model organisms have been used for many decades and have enabled the gathering of a large proportion of our present day knowledge of basic biological processes and their derailments in disease. Although in many of these studies using model organisms, the focus has primarily been on genetics and genomics approaches, it is important that methods become available to extend this to the relevant protein level. Mass spectrometry-based proteomics is increasingly becoming the standard to comprehensively analyze proteomes. An important transition has been made recently by moving from charting static proteomes to monitoring their dynamics by simultaneously quantifying multiple proteins obtained from differently treated samples. Especially the labeling with stable isotopes has proved an effective means to accurately determine differential expression levels of proteins. Among these, metabolic incorporation of stable isotopes in vivo in whole organisms is one of the favored strategies. In this perspective, we will focus on methodologies to stable isotope label a variety of model organisms in vivo, ranging from relatively simple organisms such as bacteria and yeast to Caenorhabditis elegans, Drosophila, and Arabidopsis up to mammals such as rats and mice. We also summarize how this has opened up ways to investigate biological processes at the protein level in health and disease, revealing conservation and variation across the evolutionary tree of life.
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Affiliation(s)
- Joost W Gouw
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Centre, 3584CH Utrecht, The Netherlands
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Lanquar V, Loqué D, Hörmann F, Yuan L, Bohner A, Engelsberger WR, Lalonde S, Schulze WX, von Wirén N, Frommer WB. Feedback inhibition of ammonium uptake by a phospho-dependent allosteric mechanism in Arabidopsis. THE PLANT CELL 2009; 21:3610-22. [PMID: 19948793 PMCID: PMC2798313 DOI: 10.1105/tpc.109.068593] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 09/23/2009] [Accepted: 11/06/2009] [Indexed: 05/18/2023]
Abstract
The acquisition of nutrients requires tight regulation to ensure optimal supply while preventing accumulation to toxic levels. Ammonium transporter/methylamine permease/rhesus (AMT/Mep/Rh) transporters are responsible for ammonium acquisition in bacteria, fungi, and plants. The ammonium transporter AMT1;1 from Arabidopsis thaliana uses a novel regulatory mechanism requiring the productive interaction between a trimer of subunits for function. Allosteric regulation is mediated by a cytosolic C-terminal trans-activation domain, which carries a conserved Thr (T460) in a critical position in the hinge region of the C terminus. When expressed in yeast, mutation of T460 leads to inactivation of the trimeric complex. This study shows that phosphorylation of T460 is triggered by ammonium in a time- and concentration-dependent manner. Neither Gln nor l-methionine sulfoximine-induced ammonium accumulation were effective in inducing phosphorylation, suggesting that roots use either the ammonium transporter itself or another extracellular sensor to measure ammonium concentrations in the rhizosphere. Phosphorylation of T460 in response to an increase in external ammonium correlates with inhibition of ammonium uptake into Arabidopsis roots. Thus, phosphorylation appears to function in a feedback loop restricting ammonium uptake. This novel autoregulatory mechanism is capable of tuning uptake capacity over a wide range of supply levels using an extracellular sensory system, potentially mediated by a transceptor (i.e., transporter and receptor).
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Affiliation(s)
- Viviane Lanquar
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Dominique Loqué
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Friederike Hörmann
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Lixing Yuan
- Key Lab of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Anne Bohner
- Molecular Plant Nutrition, Leibniz-Institute for Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | | | - Sylvie Lalonde
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | | | - Nicolaus von Wirén
- Molecular Plant Nutrition, Leibniz-Institute for Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Wolf B. Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
- Address correspondence to
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Emadali A, Gallagher-Gambarelli M. La protéomique quantitative par la méthode SILAC. Med Sci (Paris) 2009; 25:835-42. [DOI: 10.1051/medsci/20092510835] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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40
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Stanislas T, Bouyssie D, Rossignol M, Vesa S, Fromentin J, Morel J, Pichereaux C, Monsarrat B, Simon-Plas F. Quantitative proteomics reveals a dynamic association of proteins to detergent-resistant membranes upon elicitor signaling in tobacco. Mol Cell Proteomics 2009; 8:2186-98. [PMID: 19525550 PMCID: PMC2742443 DOI: 10.1074/mcp.m900090-mcp200] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 06/02/2009] [Indexed: 11/06/2022] Open
Abstract
A large body of evidence from the past decade supports the existence, in membrane from animal and yeast cells, of functional microdomains playing important roles in protein sorting, signal transduction, or infection by pathogens. In plants, as previously observed for animal microdomains, detergent-resistant fractions, enriched in sphingolipids and sterols, were isolated from plasma membrane. A characterization of their proteic content revealed their enrichment in proteins involved in signaling and response to biotic and abiotic stress and cell trafficking suggesting that these domains were likely to be involved in such physiological processes. In the present study, we used (14)N/(15)N metabolic labeling to compare, using a global quantitative proteomics approach, the content of tobacco detergent-resistant membranes extracted from cells treated or not with cryptogein, an elicitor of defense reaction. To analyze the data, we developed a software allowing an automatic quantification of the proteins identified. The results obtained indicate that, although the association to detergent-resistant membranes of most proteins remained unchanged upon cryptogein treatment, five proteins had their relative abundance modified. Four proteins related to cell trafficking (four dynamins) were less abundant in the detergent-resistant membrane fraction after cryptogein treatment, whereas one signaling protein (a 14-3-3 protein) was enriched. This analysis indicates that plant microdomains could, like their animal counterpart, play a role in the early signaling process underlying the setup of defense reaction. Furthermore proteins identified as differentially associated to tobacco detergent-resistant membranes after cryptogein challenge are involved in signaling and vesicular trafficking as already observed in similar studies performed in animal cells upon biological stimuli. This suggests that the ways by which the dynamic association of proteins to microdomains could participate in the regulation of the signaling process may be conserved between plant and animals.
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Affiliation(s)
- Thomas Stanislas
- From the ‡Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) Plante Microbe Environnement 1088/CNRS 5184/Université de Bourgogne, 17 Rue Sully, BP 86510 F-21000 Dijon, France
| | - David Bouyssie
- ¶Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, 205 route de Narbonne, F-31077 Toulouse, France
- ‖IPBS, Université Paul Sabatier, Université de Toulouse, F-31077 Toulouse, France, and
| | - Michel Rossignol
- ¶Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, 205 route de Narbonne, F-31077 Toulouse, France
- ‖IPBS, Université Paul Sabatier, Université de Toulouse, F-31077 Toulouse, France, and
- **IPBS, Institut Fédératif de Recherche 40 Plateforme Protéomique, 205 route de Narbonne, F-31077 Toulouse, France
| | - Simona Vesa
- From the ‡Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) Plante Microbe Environnement 1088/CNRS 5184/Université de Bourgogne, 17 Rue Sully, BP 86510 F-21000 Dijon, France
| | - Jérôme Fromentin
- From the ‡Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) Plante Microbe Environnement 1088/CNRS 5184/Université de Bourgogne, 17 Rue Sully, BP 86510 F-21000 Dijon, France
| | - Johanne Morel
- From the ‡Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) Plante Microbe Environnement 1088/CNRS 5184/Université de Bourgogne, 17 Rue Sully, BP 86510 F-21000 Dijon, France
| | - Carole Pichereaux
- ¶Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, 205 route de Narbonne, F-31077 Toulouse, France
- ‖IPBS, Université Paul Sabatier, Université de Toulouse, F-31077 Toulouse, France, and
- **IPBS, Institut Fédératif de Recherche 40 Plateforme Protéomique, 205 route de Narbonne, F-31077 Toulouse, France
| | - Bernard Monsarrat
- ¶Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, 205 route de Narbonne, F-31077 Toulouse, France
- ‖IPBS, Université Paul Sabatier, Université de Toulouse, F-31077 Toulouse, France, and
| | - Françoise Simon-Plas
- From the ‡Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) Plante Microbe Environnement 1088/CNRS 5184/Université de Bourgogne, 17 Rue Sully, BP 86510 F-21000 Dijon, France
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41
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Schneider T, Schellenberg M, Meyer S, Keller F, Gehrig P, Riedel K, Lee Y, Eberl L, Martinoia E. Quantitative detection of changes in the leaf-mesophyll tonoplast proteome in dependency of a cadmium exposure of barley (Hordeum vulgare L.) plants. Proteomics 2009; 9:2668-77. [PMID: 19391183 DOI: 10.1002/pmic.200800806] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Although the vacuole is the most important final store for toxic heavy metals like cadmium (Cd(2+)), our knowledge on how they are transported into the vacuole is still insufficient. It has been suggested that Cd(2+) can be transported as phytochelatin-Cd(2+) by an unknown ABC transporter or in exchange with protons by cation/proton exchanger (CAX) transporters. To unravel the contribution of vacuolar transporters to Cd(2+) detoxification, a quantitative proteomics approach was performed. Highly purified vacuoles were isolated from barley plants grown under minus, low (20 microM), and high (200 microM) Cd(2+ )conditions and protein levels of the obtained tonoplast samples were analyzed using isobaric tag for relative and absolute quantitation (iTRAQ). Although 56 vacuolar transporter proteins were identified, only a few were differentially expressed. Under low-Cd(2+) conditions, an inorganic pyrophosphatase and a gamma-tonoplast intrinsic protein (gamma-TIP) were up-regulated, indicating changes in energization and water fluxes. In addition, the protein ratio of a CAX1a and a natural resistance-associated macrophage protein (NRAMP), responsible for vacuolar Fe(2+) export was increased. CAX1a might play a role in vacuolar Cd(2+) transport. An increase in NRAMP activity leads to a higher cytosolic Fe(2+) concentration, which may prevent the exchange of Fe(2+) by toxic Cd(2+). Additionally, an ABC transporter homolog to AtMRP3 showed up-regulation. Under high Cd(2+) conditions, the plant response was more specific. Only a protein homologous to AtMRP3 that showed already a response under low Cd(2+) conditions, was up-regulated. Interestingly, AtMRP3 is able to partially rescue a Cd(2+)-sensitive yeast mutant. The identified transporters are good candidates for further investigation of their roles in Cd(2+) detoxification.
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Affiliation(s)
- Thomas Schneider
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland.
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42
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Kierszniowska S, Walther D, Schulze WX. Ratio-dependent significance thresholds in reciprocal 15N-labeling experiments as a robust tool in detection of candidate proteins responding to biological treatment. Proteomics 2009; 9:1916-24. [PMID: 19260003 DOI: 10.1002/pmic.200800443] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Metabolic labeling of plant tissues with (15)N has become widely used in plant proteomics. Here, we describe a robust experimental design and data analysis workflow implementing two parallel biological replicate experiments with reciprocal labeling and series of 1:1 control mixtures. Thereby, we are able to unambiguously distinguish (i) inherent biological variation between cultures and (ii) specific responses to a biological treatment. The data analysis workflow is based on first determining the variation between cultures based on (15)N/(14)N ratios in independent 1:1 mixtures before biological treatment is applied. In a second step, ratio-dependent SD is used to define p-values for significant deviation of protein ratios in the biological experiment from the distribution of protein ratios in the 1:1 mixture. This approach allows defining those proteins showing significant biological response superimposed on the biological variation before treatment. The proposed workflow was applied to a series of experiments, in which changes in composition of detergent resistant membrane domains was analyzed in response to sucrose resupply after carbon starvation. Especially in experiments involving cell culture treatment (starvation) prior to the actual biological stimulus of interest (resupply), a clear distinction between culture to culture variations and biological response is of utmost importance.
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43
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Gevaert K, Impens F, Ghesquière B, Van Damme P, Lambrechts A, Vandekerckhove J. Stable isotopic labeling in proteomics. Proteomics 2009; 8:4873-85. [PMID: 19003869 DOI: 10.1002/pmic.200800421] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Labeling of proteins and peptides with stable heavy isotopes (deuterium, carbon-13, nitrogen-15, and oxygen-18) is widely used in quantitative proteomics. These are either incorporated metabolically in cells and small organisms, or postmetabolically in proteins and peptides by chemical or enzymatic reactions. Only upon measurement with mass spectrometers holding sufficient resolution, light, and heavy labeled peptide ions or reporter peptide fragment ions segregate and their intensity values are subsequently used for quantification. Targeted use of these labels or mass tags further leads to specific monitoring of diverse aspects of dynamic proteomes. In this review article, commonly used isotope labeling strategies are described, both for quantitative differential protein profiling and for targeted analysis of protein modifications.
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Affiliation(s)
- Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent University, Ghent, Belgium
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Sussman MR, Huttlin EL, Wohlbach DJ. Democratization and integration of genomic profiling tools. Methods Mol Biol 2009; 553:373-393. [PMID: 19588117 DOI: 10.1007/978-1-60327-563-7_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Systems biology is a comprehensive means of creating a complete understanding of how all components of an organism work together to maintain and procreate life. By quantitatively profiling one at a time, the effect of thousands and millions of genetic and environmental perturbations on the cell, systems biologists are attempting to recreate and measure the effect of the many different states that have been explored during the 3 billion years in which life has evolved. A key aspect of this work is the development of innovative new approaches to quantify changes in the transcriptome, proteome, and metabolome. In this chapter we provide a review and evaluation of several genomic profiling techniques used in plant systems biology as well as make recommendations for future progress in their use and integration.
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Affiliation(s)
- Michael R Sussman
- Department of Biochemistry, UW Biotechnology Center, University of Wisconsin-Madison, Madison, WI, USA
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Schaff JE, Mbeunkui F, Blackburn K, Bird DM, Goshe MB. SILIP: a novel stable isotope labeling method for in planta quantitative proteomic analysis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 56:840-54. [PMID: 18665915 DOI: 10.1111/j.1365-313x.2008.03639.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Due to ease of manipulation, metabolic isotope coding of samples for proteomic analysis is typically performed in cell culture, thus preventing an accurate in vivo quantitative analysis, which is only achievable in intact organisms. To address this issue in plant biology, we developed SILIP (stable isotope labeling in planta) using tomato plants (Solanum lycopersicum cv. Rutgers) as a method that allows soil-grown plants to be efficiently labeled using a 14N/15N isotope coding strategy. After 2 months of growth on 14N- and 15N-enriched nitrogen sources, proteins were extracted from four distinct tomato tissues (roots, stems, leaves and flowers), digested, and analyzed by LC/MS/MS (data-dependent acquisition, DDA) and alternating low- and elevated-energy MS scans (data-independent acquisition, MS(E)). Using a derived relationship to generate a theoretical standard curve, the measured ratio of the M (monoisotopic) and M-1 isotopologues of 70 identified 15N-labeled peptides from 16 different proteins indicated that 15N incorporation was almost 99%, which is in excellent agreement with the 99.3% 15N-enriched nitrate used in the soil-based medium. Values for the various tissues ranged from 98.2 +/- 0.3% 15N incorporation in leaves to 98.8 2 +/- 0.2% in stems, demonstrating uniform labeling throughout the plant. In addition, SILIP is compatible with root-knot nematode (Meloidogyne spp.) development, and thus provides a new quantitative proteomics tool to study both plant and plant-microorganism systems.
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Affiliation(s)
- Jennifer E Schaff
- Department of Plant Pathology, Center for the Biology of Nematode Parasitism, North Carolina State University, Raleigh, NC 27695-7253, USA
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46
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Oeljeklaus S, Meyer HE, Warscheid B. Advancements in plant proteomics using quantitative mass spectrometry. J Proteomics 2008; 72:545-54. [PMID: 19049910 DOI: 10.1016/j.jprot.2008.11.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Revised: 11/10/2008] [Accepted: 11/11/2008] [Indexed: 10/21/2022]
Abstract
Due to innovative advancements in quantitative MS technologies, proteomics has evolved from taking mere "snapshots" of distinct proteomes in a defined state to monitoring, for instance, changes in abundance, location and/or posttranslational modification(s) of proteins under various conditions, thereby facilitating the functional characterization of proteins in large scale experiments. In plant biology, MS-based quantitative proteomics strategies utilizing stable isotope labeling or label-free methods for protein quantification have only recently been started to find increasing application to comparative and functional proteomics analyses. This review summarizes latest trends and applications in MS-based quantitative plant proteomics and provides insight into different technologies available. In addition, the studies presented here illustrate the enormous potential of quantitative MS for the analysis of important functional aspects with the emphasis on organellar and phosphoproteomics as well as dynamics and turnover of proteins in plants.
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Affiliation(s)
- Silke Oeljeklaus
- Medizinisches Proteom-Center, Zentrum fuer klinische Forschung, Ruhr-Universitaet Bochum, Bochum, Germany
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47
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Feng X, Liu X, Luo Q, Liu BF. Mass spectrometry in systems biology: an overview. MASS SPECTROMETRY REVIEWS 2008; 27:635-660. [PMID: 18636545 DOI: 10.1002/mas.20182] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
As an emerging field, systems biology is currently the talk of the town, which challenges our philosophy in comprehending biology. Instead of the reduction approach advocated in molecular biology, systems biology aims at systems-level understanding of correlations among molecular components. Such comprehensive investigation requires massive information from the "omics" cascade demanding high-throughput screening techniques. Being one of the most versatile analytical methods, mass spectrometry has already been playing a significant role at this early stage of systems biology. In this review, we documented the advances in modern mass spectrometry technologies as well as nascent inventions. Recent applications of mass spectrometry-based techniques and methodologies in genomics, proteomics, transcriptomics and metabolomics will be further elaborated individually. Undoubtedly, more applications of mass spectrometry in systems biology can be expected in the near future.
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Affiliation(s)
- Xiaojun Feng
- The Key Laboratory of Biomedical Photonics of MOE, Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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Quantitative proteomics as a new piece of the systems biology puzzle. J Proteomics 2008; 71:357-67. [PMID: 18640294 DOI: 10.1016/j.jprot.2008.07.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Revised: 06/30/2008] [Accepted: 07/02/2008] [Indexed: 12/19/2022]
Abstract
The definition of the role of each gene product in its cellular context is of outstanding importance in the post-genomics era. Recent technological innovations have driven research in proteomics from single protein characterization to global approaches, aiming to achieve a comprehensive qualitative and quantitative description of complex molecular mechanisms. In this review, we discuss the methodology of quantitative proteomics as it applies to the analysis of complex biological model systems. A special attention will be given to model systems that are suitable for functional genomic studies, where the potential of quantitative proteomics can be effectively demonstrated.
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50
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Semidominant mutations in reduced epidermal fluorescence 4 reduce phenylpropanoid content in Arabidopsis. Genetics 2008; 178:2237-51. [PMID: 18430946 DOI: 10.1534/genetics.107.083881] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plants synthesize an array of natural products that play diverse roles in growth, development, and defense. The plant-specific phenylpropanoid metabolic pathway produces as some of its major products flavonoids, monolignols, and hydroxycinnamic- acid conjugates. The reduced epidermal fluorescence 4 (ref4) mutant is partially dwarfed and accumulates reduced quantities of all phenylpropanoid-pathway end products. Further, plants heterozygous for ref4 exhibit intermediate growth and phenylpropanoid-related phenotypes, suggesting that these mutations are semidominant. The REF4 locus (At2g48110) was cloned by a combined map- and sequencing-based approach and was found to encode a large integral membrane protein that is unique to plants. The mutations in all ref4 alleles cause substitutions in conserved amino acids that are located adjacent to predicted transmembrane regions. Expression of the ref4-3 allele in wild-type and null REF4 plants caused reductions in sinapoylmalate content, lignin content, and growth, demonstrating that the mutant alleles are truly semidominant. Further, a suppressor mutant was isolated that abolishes a WW protein-protein interaction domain that may be important for REF4 function.
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