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Mueller SJ, Hoernstein SNW, Reski R. Approaches to Characterize Organelle, Compartment, or Structure Purity. Methods Mol Biol 2017; 1511:13-28. [PMID: 27730599 DOI: 10.1007/978-1-4939-6533-5_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The function of subcellular structures is defined by their specific sets of proteins, making subcellular protein localization one of the most important topics in organelle research. To date, many organelle proteomics workflows involve the (partial) purification of the desired subcellular structure and the subsequent analysis of the proteome using tandem mass spectrometry (MS/MS). This chapter gives an overview of the methods that have been used to assay the purity and enrichment of subcellular structures, with an emphasis on quantitative proteomics using differently enriched subcellular fractions. We introduce large-scale-based criteria for assignment of proteins to subcellular structures and describe in detail the use of 15N metabolic labeling in moss to characterize plastid and mitochondrial proteomes.
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Affiliation(s)
- Stefanie J Mueller
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Sebastian N W Hoernstein
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany.
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
- FRIAS Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg, Germany.
- TIP Trinational Institute for Plant Research, University of Freiburg, Freiburg, Germany.
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Wang L, Liang W, Xing J, Tan F, Chen Y, Huang L, Cheng CL, Chen W. Dynamics of Chloroplast Proteome in Salt-Stressed Mangrove Kandelia candel (L.) Druce. J Proteome Res 2013; 12:5124-36. [DOI: 10.1021/pr4006469] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lingxia Wang
- Key
Laboratory of Ministry of Education for Genetics, Breeding and Multiple
Utilization of Corps, Fujian Agriculture and Forestry University, Shangxiadian Road No. 15, Cangshan District, Fuzhou 350002, P. R. China
- School
of Life Sciences, Fujian Agriculture and Forestry University, Shangxiadian Road No. 15, Cangshan District, Fuzhou 350002, P. R. China
| | - Wenyu Liang
- School
of Life Sciences, Ningxia University, Helanshan Road No. 489, Xixia District, Yinchuan 750021, P. R. China
| | - Jianhong Xing
- Key
Laboratory of Ministry of Education for Genetics, Breeding and Multiple
Utilization of Corps, Fujian Agriculture and Forestry University, Shangxiadian Road No. 15, Cangshan District, Fuzhou 350002, P. R. China
- School
of Life Sciences, Fujian Agriculture and Forestry University, Shangxiadian Road No. 15, Cangshan District, Fuzhou 350002, P. R. China
| | - Fanglin Tan
- Fujian Academy of Forestry, Shangchiqiao Road No. 35, Xindian, Fuzhou 350012, P. R. China
| | - Yiyong Chen
- Key
Laboratory of Ministry of Education for Genetics, Breeding and Multiple
Utilization of Corps, Fujian Agriculture and Forestry University, Shangxiadian Road No. 15, Cangshan District, Fuzhou 350002, P. R. China
- School
of Life Sciences, Fujian Agriculture and Forestry University, Shangxiadian Road No. 15, Cangshan District, Fuzhou 350002, P. R. China
| | - Li Huang
- Fujian Academy of Forestry, Shangchiqiao Road No. 35, Xindian, Fuzhou 350012, P. R. China
| | - Chi-Lien Cheng
- Department
of Biology, The University of Iowa, 210 Biology Building, Iowa City, Iowa 52242, United States
| | - Wei Chen
- Key
Laboratory of Ministry of Education for Genetics, Breeding and Multiple
Utilization of Corps, Fujian Agriculture and Forestry University, Shangxiadian Road No. 15, Cangshan District, Fuzhou 350002, P. R. China
- School
of Life Sciences, Fujian Agriculture and Forestry University, Shangxiadian Road No. 15, Cangshan District, Fuzhou 350002, P. R. China
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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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Lang EGE, Mueller SJ, Hoernstein SNW, Porankiewicz-Asplund J, Vervliet-Scheebaum M, Reski R. Simultaneous isolation of pure and intact chloroplasts and mitochondria from moss as the basis for sub-cellular proteomics. PLANT CELL REPORTS 2011; 30:205-15. [PMID: 20960201 PMCID: PMC3020298 DOI: 10.1007/s00299-010-0935-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 09/16/2010] [Accepted: 09/24/2010] [Indexed: 05/22/2023]
Abstract
The moss Physcomitrella patens is increasingly being used as a model for plant systems biology studies. While genomic and transcriptomic resources are in place, tools and experimental conditions for proteomic studies need to be developed. In the present study we describe a rapid and efficient protocol for the simultaneous isolation of chloroplasts and mitochondria from moss protonema. Routinely, 60-100 μg mitochondrial and 3-5 mg chloroplast proteins, respectively, were obtained from 20 g fresh weight of green moss tissue. Using 14 plant compartment marker antibodies derived from seed plant and algal protein sequences, respectively, the evolutionary conservation of the compartment marker proteins in the moss was demonstrated and purity and intactness of the extracted organelles confirmed. This isolation protocol and these validated compartment markers may serve as basis for sub-cellular proteomics in P. patens and other mosses.
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Affiliation(s)
- Erika G. E. Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
- Freiburg Initiative for Systems Biology (FRISYS), University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Stefanie J. Mueller
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany
| | - Sebastian N. W. Hoernstein
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | | | - Marco Vervliet-Scheebaum
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
- Freiburg Initiative for Systems Biology (FRISYS), University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
- Freiburg Initiative for Systems Biology (FRISYS), University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany
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Schröter Y, Steiner S, Matthäi K, Pfannschmidt T. Analysis of oligomeric protein complexes in the chloroplast sub-proteome of nucleic acid-binding proteins from mustard reveals potential redox regulators of plastid gene expression. Proteomics 2010; 10:2191-204. [DOI: 10.1002/pmic.200900678] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Jorrín-Novo JV, Maldonado AM, Echevarría-Zomeño S, Valledor L, Castillejo MA, Curto M, Valero J, Sghaier B, Donoso G, Redondo I. Plant proteomics update (2007–2008): Second-generation proteomic techniques, an appropriate experimental design, and data analysis to fulfill MIAPE standards, increase plant proteome coverage and expand biological knowledge. J Proteomics 2009; 72:285-314. [DOI: 10.1016/j.jprot.2009.01.026] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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