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Smythers AL, Hicks LM. Mapping the plant proteome: tools for surveying coordinating pathways. Emerg Top Life Sci 2021; 5:203-220. [PMID: 33620075 PMCID: PMC8166341 DOI: 10.1042/etls20200270] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/14/2022]
Abstract
Plants rapidly respond to environmental fluctuations through coordinated, multi-scalar regulation, enabling complex reactions despite their inherently sessile nature. In particular, protein post-translational signaling and protein-protein interactions combine to manipulate cellular responses and regulate plant homeostasis with precise temporal and spatial control. Understanding these proteomic networks are essential to addressing ongoing global crises, including those of food security, rising global temperatures, and the need for renewable materials and fuels. Technological advances in mass spectrometry-based proteomics are enabling investigations of unprecedented depth, and are increasingly being optimized for and applied to plant systems. This review highlights recent advances in plant proteomics, with an emphasis on spatially and temporally resolved analysis of post-translational modifications and protein interactions. It also details the necessity for generation of a comprehensive plant cell atlas while highlighting recent accomplishments within the field.
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Affiliation(s)
- Amanda L Smythers
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Leslie M Hicks
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
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2
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Nitrogen Uptake in Plants: The Plasma Membrane Root Transport Systems from a Physiological and Proteomic Perspective. PLANTS 2021; 10:plants10040681. [PMID: 33916130 PMCID: PMC8066207 DOI: 10.3390/plants10040681] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 11/17/2022]
Abstract
Nitrogen nutrition in plants is a key determinant in crop productivity. The availability of nitrogen nutrients in the soil, both inorganic (nitrate and ammonium) and organic (urea and free amino acids), highly differs and influences plant physiology, growth, metabolism, and root morphology. Deciphering this multifaceted scenario is mandatory to improve the agricultural sustainability. In root cells, specific proteins located at the plasma membrane play key roles in the transport and sensing of nitrogen forms. This review outlines the current knowledge regarding the biochemical and physiological aspects behind the uptake of the individual nitrogen forms, their reciprocal interactions, the influences on root system architecture, and the relations with other proteins sustaining fundamental plasma membrane functionalities, such as aquaporins and H+-ATPase. This topic is explored starting from the information achieved in the model plant Arabidopsis and moving to crops in agricultural soils. Moreover, the main contributions provided by proteomics are described in order to highlight the goals and pitfalls of this approach and to get new hints for future studies.
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3
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Lamelas L, García L, Cañal MJ, Meijón M. Subcellular Proteomics in Conifers: Purification of Nuclei and Chloroplast Proteomes. Methods Mol Biol 2021; 2139:69-78. [PMID: 32462578 DOI: 10.1007/978-1-0716-0528-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The complexity of the plant cell proteome, exhibiting thousands of proteins whose abundance varies in several orders of magnitude, makes impossible to cover most of the plant proteins using standard shotgun-based approaches. Despite this general description of plant proteomes, the complexity is not a big issue (current protocols and instrumentation allow for the identification of several thousand proteins per injection), low or medium abundant proteins cannot be detected most of times, being necessary to fraction or perform targeted analyses in order to detect and quantify them. Among fractioning choices, cell fractioning in its different organelles is a good strategy for gaining not only a deeper coverage of the proteome but also the basis for understanding organelle function, protein dynamics, and trafficking within the cell, as nuclear and chloroplast communication. This approach is used routinely in many labs working with model species; however, the available protocols focusing on tree species are scarce. In this chapter, we provide a simple but robust protocol for isolating nuclei and chloroplasts in pine needles that is fully compatible with later mass spectrometry-based proteome analysis.
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Affiliation(s)
- Laura Lamelas
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, Oviedo, Spain.
| | - Lara García
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, Oviedo, Spain
| | - María Jesús Cañal
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, Oviedo, Spain
| | - Mónica Meijón
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, Oviedo, Spain.
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Imai K, Nakai K. Tools for the Recognition of Sorting Signals and the Prediction of Subcellular Localization of Proteins From Their Amino Acid Sequences. Front Genet 2020; 11:607812. [PMID: 33324450 PMCID: PMC7723863 DOI: 10.3389/fgene.2020.607812] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
At the time of translation, nascent proteins are thought to be sorted into their final subcellular localization sites, based on the part of their amino acid sequences (i.e., sorting or targeting signals). Thus, it is interesting to computationally recognize these signals from the amino acid sequences of any given proteins and to predict their final subcellular localization with such information, supplemented with additional information (e.g., k-mer frequency). This field has a long history and many prediction tools have been released. Even in this era of proteomic atlas at the single-cell level, researchers continue to develop new algorithms, aiming at accessing the impact of disease-causing mutations/cell type-specific alternative splicing, for example. In this article, we overview the entire field and discuss its future direction.
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Affiliation(s)
- Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Kenta Nakai
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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5
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Liu Y, Lu S, Liu K, Wang S, Huang L, Guo L. Proteomics: a powerful tool to study plant responses to biotic stress. PLANT METHODS 2019; 15:135. [PMID: 31832077 PMCID: PMC6859632 DOI: 10.1186/s13007-019-0515-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/29/2019] [Indexed: 05/08/2023]
Abstract
In recent years, mass spectrometry-based proteomics has provided scientists with the tremendous capability to study plants more precisely than previously possible. Currently, proteomics has been transformed from an isolated field into a comprehensive tool for biological research that can be used to explain biological functions. Several studies have successfully used the power of proteomics as a discovery tool to uncover plant resistance mechanisms. There is growing evidence that indicates that the spatial proteome and post-translational modifications (PTMs) of proteins directly participate in the plant immune response. Therefore, understanding the subcellular localization and PTMs of proteins is crucial for a comprehensive understanding of plant responses to biotic stress. In this review, we discuss current approaches to plant proteomics that use mass spectrometry, with particular emphasis on the application of spatial proteomics and PTMs. The purpose of this paper is to investigate the current status of the field, discuss recent research challenges, and encourage the application of proteomics techniques to further research.
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Affiliation(s)
- Yahui Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- National Institute of Metrology, Beijing, China
| | - Song Lu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Kefu Liu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Sheng Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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6
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Chloroplast proteins involved in drought stress response in selected cultivars of common bean ( Phaseolus vulgaris L.). 3 Biotech 2019; 9:331. [PMID: 31456908 DOI: 10.1007/s13205-019-1862-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/05/2019] [Indexed: 10/26/2022] Open
Abstract
One of the major cell organelles, whose functions are affected during drought stress are chloroplasts. In this study, chloroplast proteome under drought was studied in two cultivars of common bean (Phaseolus vulgaris L), Tiber and more sensitive to drought, Starozagorski čern, which were subjected to drought for 6 and 13 days. A comparative proteomic analysis with 2D-DIGE was performed on the isolated chloroplast proteins from leaves. Together, 44 proteins with changed abundance between control and stressed plants were identified with LC-MS/MS from both cultivars. The majority of the identified proteins were involved in photosynthetic processes. The results showed a decrease in abundance in different structure components of photosystem I and II, and ATP synthase, which may indicate a suppression of light-dependent reactions by drought stress. Similar proteomic response for both cultivars after 6 and 13 days of drought was observed. Proteins with contrasting abundance patterns between the cultivars or proteins specific for only one cultivar, such as ferredoxin-NADP reductase, photosystem II stability/assembly factor HCF136, curvature thylakoid protein 1B, and plastidial membrane protein porin were pointed out as major identified proteins revealing differential abundance between the cultivars. Taken together, our results provide insight into the molecular response of chloroplasts in common bean under drought stress, whereas conclusions about the tolerance mechanisms require further studies.
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Geladaki A, Kočevar Britovšek N, Breckels LM, Smith TS, Vennard OL, Mulvey CM, Crook OM, Gatto L, Lilley KS. Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics. Nat Commun 2019; 10:331. [PMID: 30659192 PMCID: PMC6338729 DOI: 10.1038/s41467-018-08191-w] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/18/2018] [Indexed: 01/09/2023] Open
Abstract
The study of protein localisation has greatly benefited from high-throughput methods utilising cellular fractionation and proteomic profiling. Hyperplexed Localisation of Organelle Proteins by Isotope Tagging (hyperLOPIT) is a well-established method in this area. It achieves high-resolution separation of organelles and subcellular compartments but is relatively time- and resource-intensive. As a simpler alternative, we here develop Localisation of Organelle Proteins by Isotope Tagging after Differential ultraCentrifugation (LOPIT-DC) and compare this method to the density gradient-based hyperLOPIT approach. We confirm that high-resolution maps can be obtained using differential centrifugation down to the suborganellar and protein complex level. HyperLOPIT and LOPIT-DC yield highly similar results, facilitating the identification of isoform-specific localisations and high-confidence localisation assignment for proteins in suborganellar structures, protein complexes and signalling pathways. By combining both approaches, we present a comprehensive high-resolution dataset of human protein localisations and deliver a flexible set of protocols for subcellular proteomics.
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Affiliation(s)
- Aikaterini Geladaki
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- Department of Genetics, University of Cambridge, 20 Downing Place, Cambridge, CB2 3EJ, UK
| | - Nina Kočevar Britovšek
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Tom S Smith
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Owen L Vennard
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Claire M Mulvey
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Oliver M Crook
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- MRC Biostatistics Unit, Cambridge Institute for Public Health, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK
| | - Laurent Gatto
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- de Duve Institute, UC Louvain, Avenue Hippocrate 75, Brussels, 1200, Belgium
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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Shekari F, Baharvand H, Salekdeh GH. Organellar proteomics of embryonic stem cells. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 95:215-30. [PMID: 24985774 DOI: 10.1016/b978-0-12-800453-1.00007-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Embryonic stem cells (ESCs) are undifferentiated cells with two common remarkable features known as self-renewal and differentiation. Proteomics plays an increasingly important role in understanding molecular mechanisms underlying self-renewal and pluripotency of ESCs and their applications in cell therapy and developmental biology studies. As the function of a protein is strongly associated with its localization in cell, a complete and accurate picture of the proteome of ESCs cannot be achieved without knowing the subcellular locations of proteins. Subcellular fractionation allows enrichment of low abundant proteins and signaling complexes and reduces the complexity of the sample. It also provided insight into tracking proteins that shuttle between different compartments. Despite the substantial interest and efforts in ESC subcellular proteomics area, progress has been relatively limited. In this review, we present an overview on current status of ESCs organelle proteomics research and discuss challenges in subcellular proteomics.
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Affiliation(s)
- Faezeh Shekari
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran
| | - Hossein Baharvand
- Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran; Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.
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9
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Pandey A, Chakraborty S, Chakraborty N. Nuclear Proteome: Isolation of Intact Nuclei, Extraction of Nuclear Proteins, and 2-DE Analysis. Methods Mol Biol 2018; 1696:41-55. [PMID: 29086395 DOI: 10.1007/978-1-4939-7411-5_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Proteome profiling aims to unravel the mystery of biological complexity encoded by the genome. The successful proteome profiling largely depends upon analytical approaches because single-step proteome characterization of eukaryotic cells is difficult due to the large number of proteins expressed and their complex physiochemical properties. Organellar proteomics helps in identifying a refined set of proteins by pinpointing certain activities to specific organelles, thereby increasing our knowledge of cellular processes. The reliability of a plant organelle proteome is intimately dependent on the purity of the organelle preparation. Methodological improvements in sample handling, organelle fractionation, and protein extraction are therefore crucial to plant subcellular proteomics. The nuclear proteins are organized into complex regulatory networks and perform varied cellular functions. Therefore, characterization of the nuclear proteome is an important step toward accumulating knowledge about regulation of gene expression and function. In this chapter, we present methods for the isolation of nuclei, purification of nuclear proteins, and proteome profiling that have been adapted for proteomic characterization of economically important crop species, such as chickpea.
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Affiliation(s)
- Aarti Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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10
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Lao J, Smith-Moritz AM, Mortimer JC, Heazlewood JL. Enrichment of the Plant Cytosolic Fraction. Methods Mol Biol 2017; 1511:213-232. [PMID: 27730614 DOI: 10.1007/978-1-4939-6533-5_17] [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] [Indexed: 06/06/2023]
Abstract
The cytosol is at the core of cellular metabolism and contains many important metabolic pathways, including glycolysis, gluconeogenesis, and the pentose phosphate pathway. Despite the importance of this matrix, few attempts have sought to specifically enrich this compartment from plants. Although a variety of biochemical pathways and signaling cascades pass through the cytosol, much of the focus has usually been targeted at the reactions that occur within membrane-bound organelles of the plant cell. In this chapter, we outline a method for the enrichment of the cytosol from rice suspension cell cultures which includes sample preparation and enrichment as well as validation using immunoblotting and fluorescence-tagged proteins.
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Affiliation(s)
- Jeemeng Lao
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94702, USA
| | - Andreia M Smith-Moritz
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94702, USA
| | - Jennifer C Mortimer
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94702, USA
| | - Joshua L Heazlewood
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94702, USA.
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.
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11
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Fürtauer L, Nägele T. Approximating the stabilization of cellular metabolism by compartmentalization. Theory Biosci 2016; 135:73-87. [PMID: 27048513 PMCID: PMC4870308 DOI: 10.1007/s12064-016-0225-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/21/2016] [Indexed: 01/13/2023]
Abstract
Biochemical regulation in compartmentalized metabolic networks is highly complex and non-intuitive. This is particularly true for cells of higher plants showing one of the most compartmentalized cellular structures across all kingdoms of life. The interpretation and testable hypothesis generation from experimental data on such complex systems is a challenging step in biological research and biotechnological applications. While it is known that subcellular compartments provide defined reaction spaces within a cell allowing for the tight coordination of complex biochemical reaction sequences, its role in the coordination of metabolic signals during metabolic reprogramming due to environmental fluctuations is less clear. In the present study, we numerically analysed the effects of environmental fluctuations in a subcellular metabolic network with regard to the stability of an experimentally observed steady state in the genetic model plant Arabidopsis thaliana. Applying a method for kinetic parameter normalization, several millions of probable enzyme kinetic parameter constellations were simulated and evaluated with regard to the stability information of the metabolic homeostasis. Information about the stability of the metabolic steady state was derived from real parts of eigenvalues of Jacobian matrices. Our results provide evidence for a differential stabilizing contribution of different subcellular compartments. We could identify stabilizing and destabilizing network components which we could classify according to their subcellular localization. The findings prove that a highly dynamic interplay between intracellular compartments is preliminary for an efficient stabilization of a metabolic homeostasis after environmental perturbation. Further, our results provide evidence that feedback-inhibition originating from the cytosol and plastid seem to stabilize the sucrose homeostasis more efficiently than vacuolar control. In summary, our results indicate stabilizing and destabilizing network components in context of their subcellular organization.
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Affiliation(s)
- Lisa Fürtauer
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria
| | - Thomas Nägele
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
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12
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de Michele R, McFarlane HE, Parsons HT, Meents MJ, Lao J, González Fernández-Niño SM, Petzold CJ, Frommer WB, Samuels AL, Heazlewood JL. Free-Flow Electrophoresis of Plasma Membrane Vesicles Enriched by Two-Phase Partitioning Enhances the Quality of the Proteome from Arabidopsis Seedlings. J Proteome Res 2016; 15:900-13. [PMID: 26781341 DOI: 10.1021/acs.jproteome.5b00876] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The plant plasma membrane is the interface between the cell and its environment undertaking a range of important functions related to transport, signaling, cell wall biosynthesis, and secretion. Multiple proteomic studies have attempted to capture the diversity of proteins in the plasma membrane using biochemical fractionation techniques. In this study, two-phase partitioning was combined with free-flow electrophoresis to produce a population of highly purified plasma membrane vesicles that were subsequently characterized by tandem mass spectroscopy. This combined high-quality plasma membrane isolation technique produced a reproducible proteomic library of over 1000 proteins with an extended dynamic range including plasma membrane-associated proteins. The approach enabled the detection of a number of putative plasma membrane proteins not previously identified by other studies, including peripheral membrane proteins. Utilizing multiple data sources, we developed a PM-confidence score to provide a value indicating association to the plasma membrane. This study highlights over 700 proteins that, while seemingly abundant at the plasma membrane, are mostly unstudied. To validate this data set, we selected 14 candidates and transiently localized 13 to the plasma membrane using a fluorescent tag. Given the importance of the plasma membrane, this data set provides a valuable tool to further investigate important proteins. The mass spectrometry data are available via ProteomeXchange, identifier PXD001795.
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Affiliation(s)
- Roberto de Michele
- Department of Plant Biology, Carnegie Institution for Science , Stanford, California 94305, United States.,Institute of Biosciences and Bioresources (CNR-IBBR), National Research Council of Italy , Palermo 90129, Italy
| | - Heather E McFarlane
- Department of Botany, University of British Columbia , Vancouver, BC V6T 1Z4, Canada.,Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany
| | - Harriet T Parsons
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.,Department of Plant and Environmental Sciences, University of Copenhagen , Copenhagen C-1871, Denmark
| | - Miranda J Meents
- Department of Botany, University of British Columbia , Vancouver, BC V6T 1Z4, Canada
| | - Jeemeng Lao
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Susana M González Fernández-Niño
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Christopher J Petzold
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science , Stanford, California 94305, United States
| | - A Lacey Samuels
- Department of Botany, University of British Columbia , Vancouver, BC V6T 1Z4, Canada
| | - Joshua L Heazlewood
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.,ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne , Melbourne, Victoria 3010, Australia
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13
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Fürtauer L, Weckwerth W, Nägele T. A Benchtop Fractionation Procedure for Subcellular Analysis of the Plant Metabolome. FRONTIERS IN PLANT SCIENCE 2016; 7:1912. [PMID: 28066469 PMCID: PMC5177628 DOI: 10.3389/fpls.2016.01912] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/02/2016] [Indexed: 05/06/2023]
Abstract
Although compartmentation is a key feature of eukaryotic cells, biological research is frequently limited by methods allowing for the comprehensive subcellular resolution of the metabolome. It has been widely accepted that such a resolution would be necessary in order to approximate cellular biochemistry and metabolic regulation, yet technical challenges still limit both the reproducible subcellular fractionation and the sample throughput being necessary for a statistically robust analysis. Here, we present a method and a detailed protocol which is based on the non-aqueous fractionation technique enabling the assignment of metabolites to their subcellular localization. The presented benchtop method aims at unraveling subcellular metabolome dynamics in a precise and statistically robust manner using a relatively small amount of tissue material. The method is based on the separation of cellular fractions via density gradients consisting of organic, non-aqueous solvents. By determining the relative distribution of compartment-specific marker enzymes together with metabolite profiles over the density gradient it is possible to estimate compartment-specific metabolite concentrations by correlation. To support this correlation analysis, a spreadsheet is provided executing a calculation algorithm to determine the distribution of metabolites over subcellular compartments. The calculation algorithm performs correlation of marker enzyme activity and metabolite abundance accounting for technical errors, reproducibility and the resulting error propagation. The method was developed, tested and validated in three natural accessions of Arabidopsis thaliana showing different ability to acclimate to low temperature. Particularly, amino acids were strongly shuffled between subcellular compartments in a cold-sensitive accession while a cold-tolerant accession was characterized by a stable subcellular metabolic homeostasis. Finally, we conclude that subcellular metabolome analysis is essential to unambiguously unravel regulatory strategies being involved in plant-environment interactions.
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Affiliation(s)
- Lisa Fürtauer
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
| | - Thomas Nägele
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
- *Correspondence: Thomas Nägele
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14
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Gong F, Hu X, Wang W. Proteomic analysis of crop plants under abiotic stress conditions: where to focus our research? FRONTIERS IN PLANT SCIENCE 2015; 6:418. [PMID: 26097486 PMCID: PMC4456565 DOI: 10.3389/fpls.2015.00418] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 05/24/2015] [Indexed: 05/23/2023]
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15
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Li J, Silva-Sanchez C, Zhang T, Chen S, Li H. Phosphoproteomics technologies and applications in plant biology research. FRONTIERS IN PLANT SCIENCE 2015; 6:430. [PMID: 26136758 PMCID: PMC4468387 DOI: 10.3389/fpls.2015.00430] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/27/2015] [Indexed: 05/20/2023]
Abstract
Protein phosphorylation has long been recognized as an essential mechanism to regulate many important processes of plant life. However, studies on phosphorylation mediated signaling events in plants are challenged with low stoichiometry and dynamic nature of phosphorylated proteins. Significant advances in mass spectrometry based phosphoproteomics have taken place in recent decade, including phosphoprotein/phosphopeptide enrichment, detection and quantification, and phosphorylation site localization. This review describes a variety of separation and enrichment methods for phosphoproteins and phosphopeptides, the applications of technological innovations in plant phosphoproteomics, and highlights significant achievement of phosphoproteomics in the areas of plant signal transduction, growth and development.
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Affiliation(s)
- Jinna Li
- College of Life Sciences, Heilongjiang UniversityHarbin, China
| | - Cecilia Silva-Sanchez
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
| | - Tong Zhang
- Plant Molecular and Cellular Biology Program, Department of Biology, UF Genetics Institute, University of FloridaGainesville, FL, USA
| | - Sixue Chen
- College of Life Sciences, Heilongjiang UniversityHarbin, China
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
- Plant Molecular and Cellular Biology Program, Department of Biology, UF Genetics Institute, University of FloridaGainesville, FL, USA
| | - Haiying Li
- College of Life Sciences, Heilongjiang UniversityHarbin, China
- *Correspondence: Haiying Li, College of Life Sciences, Heilongjiang University, 74 Xuefu Rd, Harbin 150080, China
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Parsons HT, Heazlewood JL. Beyond the Western front: targeted proteomics and organelle abundance profiling. FRONTIERS IN PLANT SCIENCE 2015; 6:301. [PMID: 25999968 PMCID: PMC4419601 DOI: 10.3389/fpls.2015.00301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/15/2015] [Indexed: 05/09/2023]
Abstract
The application of westerns or immunoblotting techniques for assessing the composition, dynamics, and purity of protein extracts from plant material has become common practice. While the approach is reproducible, can be readily applied and is generally considered robust, the field of plant science suffers from a lack of antibody variety against plant proteins. The development of approaches that employ mass spectrometry to enable both relative and absolute quantification of many hundreds of proteins in a single sample from a single analysis provides a mechanism to overcome the expensive impediment in having to develop antibodies in plant science. We consider it an opportune moment to consider and better develop the adoption of multiple reaction monitoring (MRM)-based analyses in plant biochemistry.
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Affiliation(s)
| | - Joshua L. Heazlewood
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- The Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
- *Correspondence: Joshua L. Heazlewood, The Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Swanston Street, Melbourne, VIC 3010, Australia,
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