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Watanabe E, Kondo M, Kamal MM, Uemura M, Takahashi D, Kawamura Y. Plasma membrane proteomic changes of Arabidopsis DRP1E during cold acclimation in association with the enhancement of freezing tolerance. PHYSIOLOGIA PLANTARUM 2022; 174:e13820. [PMID: 36335535 DOI: 10.1111/ppl.13820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/24/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
The freezing tolerance of plants that live in cold regions increases after exposure to low temperature, a process termed cold acclimation (CA). During CA, restructuring of the plasma membrane (PM) is important to enhance freezing tolerance. We have previously shown that the function of DYNAMIN-RELATED PROTEIN 1 E (DRP1E), which regulates endocytosis by pinching vesicles from the PM, is associated with the enhancement of freezing tolerance during CA in Arabidopsis. DRP1E is predicted to play a role in reconstituting the PM composition during CA. In this study, to test the validity of this hypothesis, we studied the changes in PM proteome patterns induced by drp1e mutation. In a detailed physiological analysis, after 3 days of CA, only young leaves showed significantly less increase in freezing tolerance in the mutant than in the wild type (WT). Using nano-liquid chromatography-tandem mass spectrometry, 496 PM proteins were identified. Among these proteins, 81 or 71 proteins were specifically altered in the WT or the mutant, respectively, in response to CA. Principal component analysis showed that the proteomic pattern differed between the WT and the mutant upon cold acclimation (CA), suggesting that DRP1E contributes to reconstruction of the PM during CA. Cluster analysis revealed that proteins that were significantly increased in the mutant after CA were biased toward glycosylphosphatidylinositol-anchored proteins, such as fasciclin-like arabinogalactan proteins. Thus, a primary target of DRP1E-associated PM reconstruction during CA is considered to be glycosylphosphatidylinositol-anchored proteins, which may be removed from the PM by DRP1E in young leaves after 3 days of CA.
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Affiliation(s)
| | - Mariko Kondo
- Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Md Mostafa Kamal
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
| | - Matsuo Uemura
- Faculty of Agriculture, Iwate University, Morioka, Japan
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
| | - Daisuke Takahashi
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Yukio Kawamura
- Faculty of Agriculture, Iwate University, Morioka, Japan
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
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Takahashi D, Willick IR, Kasuga J, Livingston III DP. Responses of the Plant Cell Wall to Sub-Zero Temperatures: A Brief Update. PLANT & CELL PHYSIOLOGY 2021; 62:1858-1866. [PMID: 34240199 PMCID: PMC8711693 DOI: 10.1093/pcp/pcab103] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/29/2021] [Accepted: 07/07/2021] [Indexed: 05/04/2023]
Abstract
Our general understanding of plant responses to sub-zero temperatures focuses on mechanisms that mitigate stress to the plasma membrane. The plant cell wall receives comparatively less attention, and questions surrounding its role in mitigating freezing injury remain unresolved. Despite recent molecular discoveries that provide insight into acclimation responses, the goal of reducing freezing injury in herbaceous and woody crops remains elusive. This is likely due to the complexity associated with adaptations to low temperatures. Understanding how leaf cell walls of herbaceous annuals promote tissue tolerance to ice does not necessarily lead to understanding how meristematic tissues are protected from freezing by tissue-level barriers formed by cell walls in overwintering tree buds. In this mini-review, we provide an overview of biological ice nucleation and explain how plants control the spatiotemporal location of ice formation. We discuss how sugars and pectin side chains alleviate adhesive injury that develops at sub-zero temperatures between the matrix polysaccharides and ice. The importance of site-specific cell-wall elasticity to promote tissue expansion for ice accommodation and control of porosity to impede ice growth and promote supercooling will be presented. How specific cold-induced proteins modify plant cell walls to mitigate freezing injury will also be discussed. The opinions presented in this report emphasize the importance of a plant's developmental physiology when characterizing mechanisms of freezing survival.
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Affiliation(s)
- Daisuke Takahashi
- *Corresponding authors: Daisuke Takahashi, E-mail, ; Ian R. Willick, E-mail,
| | - Ian R Willick
- *Corresponding authors: Daisuke Takahashi, E-mail, ; Ian R. Willick, E-mail,
| | - Jun Kasuga
- Research Center for Global Agro-Medicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
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Mustafa G, Komatsu S. Plant proteomic research for improvement of food crops under stresses: a review. Mol Omics 2021; 17:860-880. [PMID: 34870299 DOI: 10.1039/d1mo00151e] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Crop improvement approaches have been changed due to technological advancements in traditional plant-breeding methods. Abiotic and biotic stresses limit plant growth and development, which ultimately lead to reduced crop yield. Proteins encoded by genomes have a considerable role in the endurance and adaptation of plants to different environmental conditions. Biotechnological applications in plant breeding depend upon the information generated from proteomic studies. Proteomics has a specific advantage to contemplate post-translational modifications, which indicate the functional effects of protein modifications on crop production. Subcellular proteomics helps in exploring the precise cellular responses and investigating the networking among subcellular compartments during plant development and biotic/abiotic stress responses. Large-scale mass spectrometry-based plant proteomic studies with a more comprehensive overview are now possible due to dramatic improvements in mass spectrometry, sample preparation procedures, analytical software, and strengthened availability of genomes for numerous plant species. Development of stress-tolerant or resilient crops is essential to improve crop productivity and growth. Use of high throughput techniques with advanced instrumentation giving efficient results made this possible. In this review, the role of proteomic studies in identifying the stress-response processes in different crops is summarized. Advanced techniques and their possible utilization on plants are discussed in detail. Proteomic studies accelerate marker-assisted genetic augmentation studies on crops for developing high yielding stress-tolerant lines or varieties under stresses.
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Affiliation(s)
- Ghazala Mustafa
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.
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Kamal MM, Ishikawa S, Takahashi F, Suzuki K, Kamo M, Umezawa T, Shinozaki K, Kawamura Y, Uemura M. Large-Scale Phosphoproteomic Study of Arabidopsis Membrane Proteins Reveals Early Signaling Events in Response to Cold. Int J Mol Sci 2020; 21:E8631. [PMID: 33207747 PMCID: PMC7696906 DOI: 10.3390/ijms21228631] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/22/2022] Open
Abstract
Cold stress is one of the major factors limiting global crop production. For survival at low temperatures, plants need to sense temperature changes in the surrounding environment. How plants sense and respond to the earliest drop in temperature is still not clearly understood. The plasma membrane and its adjacent extracellular and cytoplasmic sites are the first checkpoints for sensing temperature changes and the subsequent events, such as signal generation and solute transport. To understand how plants respond to early cold exposure, we used a mass spectrometry-based phosphoproteomic method to study the temporal changes in protein phosphorylation events in Arabidopsis membranes during 5 to 60 min of cold exposure. The results revealed that brief cold exposures led to rapid phosphorylation changes in the proteins involved in cellular ion homeostasis, solute and protein transport, cytoskeleton organization, vesical trafficking, protein modification, and signal transduction processes. The phosphorylation motif and kinase-substrate network analysis also revealed that multiple protein kinases, including RLKs, MAPKs, CDPKs, and their substrates, could be involved in early cold signaling. Taken together, our results provide a first look at the cold-responsive phosphoproteome changes of Arabidopsis membrane proteins that can be a significant resource to understand how plants respond to an early temperature drop.
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Affiliation(s)
- Md Mostafa Kamal
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
| | - Shinnosuke Ishikawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei 184-8588, Japan; (S.I.); (T.U.)
| | - Fuminori Takahashi
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Koyadai, Tsukuba 305-0074, Japan; (F.T.); (K.S.)
| | - Ko Suzuki
- Department of Biochemistry, Iwate Medical University, Yahaba 028-3694, Japan; (K.S.); (M.K.)
| | - Masaharu Kamo
- Department of Biochemistry, Iwate Medical University, Yahaba 028-3694, Japan; (K.S.); (M.K.)
| | - Taishi Umezawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei 184-8588, Japan; (S.I.); (T.U.)
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Koyadai, Tsukuba 305-0074, Japan; (F.T.); (K.S.)
| | - Yukio Kawamura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
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Iwasaki Y, Itoh T, Hagi Y, Matsuta S, Nishiyama A, Chaya G, Kobayashi Y, Miura K, Komatsu S. Proteomics Analysis of Plasma Membrane Fractions of the Root, Leaf, and Flower of Rice. Int J Mol Sci 2020; 21:ijms21196988. [PMID: 32977500 PMCID: PMC7583858 DOI: 10.3390/ijms21196988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 12/03/2022] Open
Abstract
The plasma membrane regulates biological processes such as ion transport, signal transduction, endocytosis, and cell differentiation/proliferation. To understand the functional characteristics and organ specificity of plasma membranes, plasma membrane protein fractions from rice root, etiolated leaf, green leaf, developing leaf sheath, and flower were analyzed by proteomics. Among the proteins identified, 511 were commonly accumulated in the five organs, whereas 270, 132, 359, 146, and 149 proteins were specifically accumulated in the root, etiolated leaf, green leaf, developing leaf sheath, and developing flower, respectively. The principle component analysis revealed that the functions of the plasma membrane in the root was different from those of green and etiolated leaves and that the plasma membrane protein composition of the leaf sheath was similar to that of the flower, but not that of the green leaf. Functional classification revealed that the root plasma membrane has more transport-related proteins than the leaf plasma membrane. Furthermore, the leaf sheath and flower plasma membranes were found to be richer in proteins involved in signaling and cell function than the green leaf plasma membrane. To validate the proteomics data, immunoblot analysis was carried out, focusing on four heterotrimeric G protein subunits, Gα, Gβ, Gγ1, and Gγ2. All subunits could be detected by both methods and, in particular, Gγ1 and Gγ2 required concentration by immunoprecipitation for mass spectrometry detection.
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Affiliation(s)
- Yukimoto Iwasaki
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui 910-1195, Japan; (T.I.); (Y.H.); (S.M.); (A.N.); (G.C.); (Y.K.); (K.M.)
- Correspondence: (Y.I.); (S.K.); Tel.: +81-776-61-6000 (ext. 3514) (Y.I.); +81-776-29-2466 (S.K.)
| | - Takafumi Itoh
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui 910-1195, Japan; (T.I.); (Y.H.); (S.M.); (A.N.); (G.C.); (Y.K.); (K.M.)
| | - Yusuke Hagi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui 910-1195, Japan; (T.I.); (Y.H.); (S.M.); (A.N.); (G.C.); (Y.K.); (K.M.)
| | - Sakura Matsuta
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui 910-1195, Japan; (T.I.); (Y.H.); (S.M.); (A.N.); (G.C.); (Y.K.); (K.M.)
| | - Aki Nishiyama
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui 910-1195, Japan; (T.I.); (Y.H.); (S.M.); (A.N.); (G.C.); (Y.K.); (K.M.)
| | - Genki Chaya
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui 910-1195, Japan; (T.I.); (Y.H.); (S.M.); (A.N.); (G.C.); (Y.K.); (K.M.)
| | - Yuki Kobayashi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui 910-1195, Japan; (T.I.); (Y.H.); (S.M.); (A.N.); (G.C.); (Y.K.); (K.M.)
| | - Kotaro Miura
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui 910-1195, Japan; (T.I.); (Y.H.); (S.M.); (A.N.); (G.C.); (Y.K.); (K.M.)
| | - Setsuko Komatsu
- Department of Environmental and Food Sciences, Fukui University of Technology, Fukui 910-8505, Japan
- Correspondence: (Y.I.); (S.K.); Tel.: +81-776-61-6000 (ext. 3514) (Y.I.); +81-776-29-2466 (S.K.)
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Meng J, Hu B, Yi G, Li X, Chen H, Wang Y, Yuan W, Xing Y, Sheng Q, Su Z, Xu C. Genome-wide analyses of banana fasciclin-like AGP genes and their differential expression under low-temperature stress in chilling sensitive and tolerant cultivars. PLANT CELL REPORTS 2020; 39:693-708. [PMID: 32128627 DOI: 10.1007/s00299-020-02524-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/15/2020] [Indexed: 06/10/2023]
Abstract
Thirty MaFLAs vary in their molecular features. MaFLA14/18/27/29 are likely to be involved in banana chilling tolerance by facilitating the cold signaling pathway and enhancing the cell wall biosynthesis. Although several studies have identified the molecular functions of individual fasciclin-like arabinogalactan protein (FLA) genes in plant growth and development, little information is available on their involvement in plant tolerance to low-temperature (LT) stress, and the related underlying mechanism is far from clear. In this study, the different expression of FLAs of banana (Musa acuminata) (MaFLAs) in the chilling-sensitive (CS) and chilling-tolerant (CT) banana cultivars under natural LT was investigated. Based on the latest banana genome database, a genome-wide identification of this gene family was done and the molecular features were analyzed. Thirty MaFLAs were distributed in 10 out of 11 chromosomes and these clustered into four major phylogenetic groups based on shared gene structure. Twenty-four MaFLAs contained N-terminal signal, 19 possessed predicted glycosylphosphatidylinositol (GPI), while 16 had both. Most MaFLAs were downregulated by LT stress. However, MaFLA14/18/29 were upregulated by LT in both cultivars with higher expression level recorded in the CT cultivar. Interestingly, MaFLA27 was significantly upregulated in the CT cultivar, but the opposite occurred for the CS cultivar. MaFLA27 possessed only N-terminal signal, MaFLA18 contained only GPI anchor, MaFLA29 possessed both, while MaFLA14 had neither. Thus, it was suggested that the accumulation of these FLAs in banana under LT could improve banana chilling tolerance through facilitating cold signal pathway and thereafter enhancing biosynthesis of plant cell wall components. The results provide background information of MaFLAs, suggest their involvement in plant chilling tolerance and their potential as candidate genes to be targeted when breeding CT banana.
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Affiliation(s)
- Jian Meng
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Bei Hu
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Ganjun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xiaoquan Li
- Institute of Biotechnology, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Houbin Chen
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yingying Wang
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Weina Yuan
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yanqing Xing
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Qiming Sheng
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Zuxiang Su
- Institute of Biotechnology, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Chunxiang Xu
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
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Hoffmanová I, Sánchez D, Szczepanková A, Tlaskalová-Hogenová H. The Pros and Cons of Using Oat in a Gluten-Free Diet for Celiac Patients. Nutrients 2019; 11:nu11102345. [PMID: 31581722 PMCID: PMC6835965 DOI: 10.3390/nu11102345] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/12/2019] [Accepted: 09/25/2019] [Indexed: 02/07/2023] Open
Abstract
A therapeutic gluten-free diet often has nutritional limitations. Nutritional qualities such as high protein content, the presence of biologically active and beneficial substances (fiber, beta-glucans, polyunsaturated fatty acids, essential amino acids, antioxidants, vitamins, and minerals), and tolerance by the majority of celiac patients make oat popular for use in gluten-free diet. The health risk of long-time consumption of oat by celiac patients is a matter of debate. The introduction of oat into the diet is only recommended for celiac patients in remission. Furthermore, not every variety of oat is also appropriate for a gluten-free diet. The risk of sensitization and an adverse immunologically mediated reaction is a real threat in some celiac patients. Several unsolved issues still exist which include the following: (1) determination of the susceptibility markers for the subgroup of celiac patients who are at risk because they do not tolerate dietary oat, (2) identification of suitable varieties of oat and estimating the safe dose of oat for the diet, and (3) optimization of methods for detecting the gliadin contamination in raw oat used in a gluten-free diet.
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Affiliation(s)
- Iva Hoffmanová
- 2nd Department of Internal Medicine, University Hospital Královské Vinohrady and Third Faculty of Medicine, Charles University, Ruská 87, 10000 Prague, Czech Republic.
| | - Daniel Sánchez
- Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic.
| | - Adéla Szczepanková
- Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic.
- First Faculty of Medicine, Charles University, Kateřinská 1660/32, 121 08 Prague, Czech Republic.
| | - Helena Tlaskalová-Hogenová
- Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic.
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Millar AH, Heazlewood JL, Giglione C, Holdsworth MJ, Bachmair A, Schulze WX. The Scope, Functions, and Dynamics of Posttranslational Protein Modifications. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:119-151. [PMID: 30786234 DOI: 10.1146/annurev-arplant-050718-100211] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Assessing posttranslational modification (PTM) patterns within protein molecules and reading their functional implications present grand challenges for plant biology. We combine four perspectives on PTMs and their roles by considering five classes of PTMs as examples of the broader context of PTMs. These include modifications of the N terminus, glycosylation, phosphorylation, oxidation, and N-terminal and protein modifiers linked to protein degradation. We consider the spatial distribution of PTMs, the subcellular distribution of modifying enzymes, and their targets throughout the cell, and we outline the complexity of compartmentation in understanding of PTM function. We also consider PTMs temporally in the context of the lifetime of a protein molecule and the need for different PTMs for assembly, localization, function, and degradation. Finally, we consider the combined action of PTMs on the same proteins, their interactions, and the challenge ahead of integrating PTMs into an understanding of protein function in plants.
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Affiliation(s)
- A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia;
| | - Joshua L Heazlewood
- School of BioSciences, University of Melbourne, Melbourne, Victoria 3010, Australia;
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell, CNRS UMR9198, F-91198 Gif-sur-Yvette Cedex, France;
| | - Michael J Holdsworth
- School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom;
| | - Andreas Bachmair
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria;
| | - Waltraud X Schulze
- Systembiologie der Pflanze, Universität Hohenheim, 70599 Stuttgart, Germany;
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Miki Y, Takahashi D, Kawamura Y, Uemura M. Temporal proteomics of Arabidopsis plasma membrane during cold- and de-acclimation. J Proteomics 2018; 197:71-81. [PMID: 30447334 DOI: 10.1016/j.jprot.2018.11.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/27/2018] [Accepted: 11/09/2018] [Indexed: 01/19/2023]
Abstract
Freezing stress is one of the most important limiting factors of plant survival. Plants have developed a freezing adaptation mechanism upon sensing low temperatures (cold acclimation). Compositional changes in the plasma membrane, one of the initial sites of freezing injury, is prerequisite of achieving cold acclimation and have been investigated in several plant species. Conversely, the cold dehardening process at elevated temperatures (de-acclimation) has not yet been fully characterized and few studies have addressed the importance of the plasma membrane in the de-acclimation process. In the present study, we conducted shotgun proteomics with label-free semiquantification on plasma membrane fractions of Arabidopsis leaves during cold acclimation and de-acclimation. We consequently obtained a list of 873 proteins with significantly changed proteins in response to the two processes. Although the cold-acclimation-responsive proteins were globally returned to non-acclimated levels by de-acclimation, several representative cold-acclimation-responsive proteins tended to remain at higher abundance during de-acclimation process. Taken together, our results suggest plants deharden right after cold acclimation to restart growth and development but some cold-acclimation-induced changes of the plasma membrane may be maintained under de-acclimation to cope with the threat of sudden freezing during de-acclimation process. SIGNIFICANCE: Plant freezing tolerance can be enhanced by low temperature treatment (cold acclimation), while elevated temperatures right after cold acclimation can result in the dehardening of freezing tolerance (de-acclimation). However, the de-acclimation process, particularly its relevance to the plasma membrane as the primary site of freezing injury, has not been elucidated. In the present study, a comprehensive proteomic analysis of the plasma membrane during cold acclimation and de-acclimation was carried out as a first step to elucidating how plants respond to rising temperatures. Cold acclimation induced a number of proteomic changes as reported in previous studies, but most proteins, in general, immediately returned to NA levels during de-acclimation treatment for two days. However, the abundances of stress-related proteins (e.g. LTI29, COR78 and TIL) decreased slower than other functional proteins during de-acclimation. Therefore, plants harden during cold acclimation by aborting growth and development and accumulating stress-responsive proteins but seem to deharden quickly under subsequent elevated temperature to resume these processes while guarding against the threat of sudden temperature drops.
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Affiliation(s)
- Yushi Miki
- Department of Plant-bioscience, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan; Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam D-14476, Germany
| | - Yukio Kawamura
- Department of Plant-bioscience, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan; United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Matsuo Uemura
- Department of Plant-bioscience, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan; United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.
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10
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Ceballos-Laita L, Gutierrez-Carbonell E, Imai H, Abadía A, Uemura M, Abadía J, López-Millán AF. Effects of manganese toxicity on the protein profile of tomato ( Solanum lycopersicum ) roots as revealed by two complementary proteomic approaches, two-dimensional electrophoresis and shotgun analysis. J Proteomics 2018; 185:51-63. [DOI: 10.1016/j.jprot.2018.06.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/11/2018] [Accepted: 06/19/2018] [Indexed: 12/31/2022]
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11
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Komatsu S, Hashiguchi A. Subcellular Proteomics: Application to Elucidation of Flooding-Response Mechanisms in Soybean. Proteomes 2018; 6:E13. [PMID: 29495455 PMCID: PMC5874772 DOI: 10.3390/proteomes6010013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/13/2018] [Accepted: 02/23/2018] [Indexed: 02/06/2023] Open
Abstract
Soybean, which is rich in protein and oil, is cultivated in several climatic zones; however, its growth is markedly decreased by flooding. Proteomics is a useful tool for understanding the flooding-response mechanism in soybean. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and during stress. Under flooding, proteins related to signaling, stress and the antioxidative system are increased in the plasma membrane; scavenging enzymes for reactive-oxygen species are suppressed in the cell wall; protein translation is suppressed through inhibition of proteins related to preribosome biogenesis and mRNA processing in the nucleus; levels of proteins involved in the electron transport chain are reduced in the mitochondrion; and levels of proteins related to protein folding are decreased in the endoplasmic reticulum. This review discusses the advantages of a gel-free/label-free proteomic technique and methods of plant subcellular purification. It also summarizes cellular events in soybean under flooding and discusses future prospects for generation of flooding-tolerant soybean.
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Affiliation(s)
- Setsuko Komatsu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
| | - Akiko Hashiguchi
- Faculty of Medicine, University of Tsukuba, Tsukuba 305-8577, Japan.
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12
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Willick IR, Takahashi D, Fowler DB, Uemura M, Tanino KK. Tissue-specific changes in apoplastic proteins and cell wall structure during cold acclimation of winter wheat crowns. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1221-1234. [PMID: 29373702 PMCID: PMC6019019 DOI: 10.1093/jxb/erx450] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/29/2017] [Indexed: 05/04/2023]
Abstract
The wheat (Triticum aestivum L.) crown is the critical organ of low temperature stress survival over winter. In cold-acclimated crowns, ice formation in the apoplast causes severe tissue disruption as it grows at the expense of intracellular water. While previous crown studies have shown the vascular transition zone (VTZ) to have a higher freezing sensitivity than the shoot apical meristem (SAM), the mechanism behind the differential freezing response is not fully understood. Cooling cold-acclimated crowns to -10 °C resulted in an absence of VTZ tetrazolium chloride staining, whereas the temperatures at which 50% of the SAM stained positive and 50% of plants recovered (LT50) were similar after cold acclimation for 21 (-16 °C) and 42 d (-20 °C) at 4 °C. Proteomic analysis of the apoplastic fluids identified dehydrins, vernalization-responsive proteins, and cold shock proteins preferentially accumulated in the SAM. In contrast, modifications to the VTZ centered on increases in pathogenesis-related proteins, anti-freeze proteins, and sugar hydrolyzing enzymes. Fourier transform infrared spectroscopy focal plane array analysis identified the biochemical modification of the cell wall to enhance methyl-esterified cross-linking of glucuronoarabinoxylans in the VTZ. These findings indicate that the SAM and VTZ express two distinct tissue-specific apoplastic responses during cold acclimation.
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Affiliation(s)
- Ian R Willick
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
- Department of Plant-biosciences and Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - D Brian Fowler
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
- Department of Plant-biosciences and Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Karen K Tanino
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
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13
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Takahashi D, Uemura M, Kawamura Y. Freezing Tolerance of Plant Cells: From the Aspect of Plasma Membrane and Microdomain. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1081:61-79. [PMID: 30288704 DOI: 10.1007/978-981-13-1244-1_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Freezing stress is accompanied by a state change from water to ice and has multiple facets causing dehydration; consequently, hyperosmotic and mechanical stresses coupled with unfavorable chilling stress act in a parallel way. Freezing tolerance varies widely among plant species, and, for example, most temperate plants can overcome deleterious effects caused by freezing temperatures in winter. Destabilization and dysfunction of the plasma membrane are tightly linked to freezing injury of plant cells. Plant freezing tolerance increases upon exposure to nonfreezing low temperatures (cold acclimation). Recent studies have unveiled pleiotropic responses of plasma membrane lipids and proteins to cold acclimation. In addition, advanced techniques have given new insights into plasma membrane structural non-homogeneity, namely, microdomains. This chapter describes physiological implications of plasma membrane responses enhancing freezing tolerance during cold acclimation, with a focus on microdomains.
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Affiliation(s)
- Daisuke Takahashi
- Central Infrastructure Group Genomics and Transcript Profiling, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences and Department of Plant-biosciences, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Yukio Kawamura
- Cryobiofrontier Research Center and Department of Plant-biosciences, and United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, Japan.
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14
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Ceballos-Laita L, Gutierrez-Carbonell E, Takahashi D, Abadía A, Uemura M, Abadía J, López-Millán AF. Effects of Fe and Mn deficiencies on the protein profiles of tomato (Solanum lycopersicum) xylem sap as revealed by shotgun analyses. J Proteomics 2017; 170:117-129. [PMID: 28847647 DOI: 10.1016/j.jprot.2017.08.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/19/2017] [Accepted: 08/24/2017] [Indexed: 12/20/2022]
Abstract
The aim of this work was to study the effects of Fe and Mn deficiencies on the xylem sap proteome of tomato using a shotgun proteomic approach, with the final goal of elucidating plant response mechanisms to these stresses. This approach yielded 643 proteins reliably identified and quantified with 70% of them predicted as secretory. Iron and Mn deficiencies caused statistically significant and biologically relevant abundance changes in 119 and 118 xylem sap proteins, respectively. In both deficiencies, metabolic pathways most affected were protein metabolism, stress/oxidoreductases and cell wall modifications. First, results suggest that Fe deficiency elicited more stress responses than Mn deficiency, based on the changes in oxidative and proteolytic enzymes. Second, both nutrient deficiencies affect the secondary cell wall metabolism, with changes in Fe deficiency occurring via peroxidase activity, and in Mn deficiency involving peroxidase, Cu-oxidase and fasciclin-like arabinogalactan proteins. Third, the primary cell wall metabolism was affected by both nutrient deficiencies, with changes following opposite directions as judged from the abundances of several glycoside-hydrolases with endo-glycolytic activities and pectin esterases. Fourth, signaling pathways via xylem involving CLE and/or lipids as well as changes in phosphorylation and N-glycosylation also play a role in the responses to these stresses. Biological significance In spite of being essential for the delivery of nutrients to the shoots, our knowledge of xylem responses to nutrient deficiencies is very limited. The present work applies a shotgun proteomic approach to unravel the effects of Fe and Mn deficiencies on the xylem sap proteome. Overall, Fe deficiency seems to elicit more stress in the xylem sap proteome than Mn deficiency, based on the changes measured in proteolytic and oxido-reductase proteins, whereas both nutrients exert modifications in the composition of the primary and secondary cell wall. Cell wall modifications could affect the mechanical and permeability properties of the xylem sap vessels, and therefore ultimately affect solute transport and distribution to the leaves. Results also suggest that signaling cascades involving lipid and peptides might play a role in nutrient stress signaling and pinpoint interesting candidates for future studies. Finally, both nutrient deficiencies seem to affect phosphorylation and glycosylation processes, again following an opposite pattern.
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Affiliation(s)
- Laura Ceballos-Laita
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Elain Gutierrez-Carbonell
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Anunciación Abadía
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Javier Abadía
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Ana Flor López-Millán
- USDA-ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, 1100 Bates St., Houston, TX 77030, USA.
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15
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Qiao Z, Brechenmacher L, Smith B, Strout GW, Mangin W, Taylor C, Russell SD, Stacey G, Libault M. The GmFWL1 (FW2-2-like) nodulation gene encodes a plasma membrane microdomain-associated protein. PLANT, CELL & ENVIRONMENT 2017; 40:1442-1455. [PMID: 28241097 DOI: 10.1111/pce.12941] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 01/30/2017] [Accepted: 02/13/2017] [Indexed: 05/14/2023]
Abstract
The soybean gene GmFWL1 (FW2-2-like1) belongs to a plant-specific family that includes the tomato FW2-2 and the maize CNR1 genes, two regulators of plant development. In soybean, GmFWL1 is specifically expressed in root hair cells in response to rhizobia and in nodules. Silencing of GmFWL1 expression significantly reduced nodule numbers supporting its role during soybean nodulation. While the biological role of GmFWL1 has been described, its molecular function and, more generally, the molecular function of plant FW2-2-like proteins is unknown. In this study, we characterized the role of GmFWL1 as a membrane microdomain-associated protein. Specifically, using biochemical, molecular and cellular methods, our data show that GmFWL1 interacts with various proteins associated with membrane microdomains such as remorin, prohibitins and flotillins. Additionally, comparative genomics revealed that GmFWL1 interacts with GmFLOT2/4 (FLOTILLIN2/4), the soybean ortholog to Medicago truncatula FLOTILLIN4, a major regulator of the M. truncatula nodulation process. We also observed that, similarly to MtFLOT4 and GmFLOT2/4, GmFWL1 was localized at the tip of the soybean root hair cells in response to rhizobial inoculation supporting the early function of GmFWL1 in the rhizobium infection process.
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Affiliation(s)
- Zhenzhen Qiao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Laurent Brechenmacher
- Division of Biochemistry and Plant Sciences, C.S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Benjamin Smith
- Samuel Roberts Noble Microscopy Laboratory, University of Oklahoma, Norman, OK, 73019, USA
| | - Gregory W Strout
- Samuel Roberts Noble Microscopy Laboratory, University of Oklahoma, Norman, OK, 73019, USA
| | - William Mangin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Christopher Taylor
- Department of Plant Pathology, Ohio Agricultural Research and Development Center (OARDC), The Ohio State University, Wooster, OH, 44691, USA
| | - Scott D Russell
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Samuel Roberts Noble Microscopy Laboratory, University of Oklahoma, Norman, OK, 73019, USA
| | - Gary Stacey
- Division of Biochemistry and Plant Sciences, C.S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Marc Libault
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
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16
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Ferrer A, Altabella T, Arró M, Boronat A. Emerging roles for conjugated sterols in plants. Prog Lipid Res 2017; 67:27-37. [DOI: 10.1016/j.plipres.2017.06.002] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 11/29/2022]
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17
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Hoermiller II, Naegele T, Augustin H, Stutz S, Weckwerth W, Heyer AG. Subcellular reprogramming of metabolism during cold acclimation in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2017; 40:602-610. [PMID: 27642699 DOI: 10.1111/pce.12836] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/10/2016] [Indexed: 05/18/2023]
Abstract
Metabolite changes in plant leaves during exposure to low temperatures involve re-allocation of a large number of metabolites between sub-cellular compartments. Therefore, metabolite determination at the whole cell level may be insufficient for interpretation of the functional significance of cellular compounds. To investigate the cold-induced metabolite dynamics at the level of individual sub-cellular compartments, an integrative platform was developed that combines quantitative metabolite profiling by gas chromatography coupled to mass spectrometry (GC-MS) with the non-aqueous fractionation technique allowing separation of cytosol, vacuole and the plastidial compartment. Two mutants of Arabidopsis thaliana representing antipodes in the diversion of carbohydrate metabolism between sucrose and starch were compared to Col-0 wildtype before and after cold acclimation to investigate interactions of cold acclimation with subcellular re-programming of metabolism. A multivariate analysis of the data set revealed dominant effects of compartmentation on metabolite concentrations that were modulated by environmental condition and genetic determinants. While for both, the starchless mutant of plastidial phospho-gluco mutase (pgm) and a mutant defective in sucrose-phosphate synthase A1, metabolic constraints, especially at low temperature, could be uncovered based on subcellularly resolved metabolite profiles, only pgm had lowered freezing tolerance. Metabolic profiles of pgm point to redox imbalance as a possible reason for reduced cold acclimation capacity.
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Affiliation(s)
- Imke I Hoermiller
- Institute of Biomaterials and Biomolecular Systems, Department of Plant Biotechnology, University of Stuttgart, 70569, Stuttgart, Germany
| | - Thomas Naegele
- 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
| | - Hanna Augustin
- Institute of Biomaterials and Biomolecular Systems, Department of Plant Biotechnology, University of Stuttgart, 70569, Stuttgart, Germany
| | - Simon Stutz
- Institute of Biomaterials and Biomolecular Systems, Department of Plant Biotechnology, University of Stuttgart, 70569, Stuttgart, Germany
| | - Wolfram Weckwerth
- 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
| | - Arnd G Heyer
- Institute of Biomaterials and Biomolecular Systems, Department of Plant Biotechnology, University of Stuttgart, 70569, Stuttgart, Germany
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18
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Minami A, Takahashi D, Kawamura Y, Uemura M. Isolation of Plasma Membrane and Plasma Membrane Microdomains. Methods Mol Biol 2017; 1511:199-212. [PMID: 27730613 DOI: 10.1007/978-1-4939-6533-5_16] [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: 06/06/2023]
Abstract
The plasma membrane surrounds the cytoplasm of a cell and functions as a barrier to separate the intracellular compartment from the extracellular environment. Protein and lipid components distribute nonuniformly and the components form clusters with various functions in the plasma membrane. These clusters are called as "microdomains." In plant cells, microdomains have been studied extensively because they play important roles in biotic/abiotic stress responses, cellular trafficking, and cell wall metabolism. Here we describe a standard protocol for the isolation of the plasma membrane and microdomains from plant cells, Arabidopsis and oat.
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Affiliation(s)
- Anzu Minami
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Daisuke Takahashi
- United Graduate School of Agricultural Sciences and Cryobiofrontier Research Center, Iwate University, 3-18-8 Ueda, Morioka, 020-8550, Japan
| | - Yukio Kawamura
- United Graduate School of Agricultural Sciences and Cryobiofrontier Research Center, Iwate University, 3-18-8 Ueda, Morioka, 020-8550, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences and Cryobiofrontier Research Center, Iwate University, 3-18-8 Ueda, Morioka, 020-8550, Japan.
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19
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Takahashi D, Kawamura Y, Uemura M. Cold acclimation is accompanied by complex responses of glycosylphosphatidylinositol (GPI)-anchored proteins in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5203-15. [PMID: 27471282 PMCID: PMC5014161 DOI: 10.1093/jxb/erw279] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Cold acclimation results in changes of the plasma membrane (PM) composition. The PM is considered to contain specific lipid/protein-enriched microdomains which can be extracted as detergent-resistant plasma membrane (DRM). Previous studies in animal cells have demonstrated that glycosylphosphatidylinositol-anchored proteins (GPI-APs) can be targeted to microdomains and/or the apoplast. However, the functional significance of GPI-APs during cold acclimation in plants is not yet fully understood. In this study, we aimed to investigate the responsiveness of GPI-APs to cold acclimation treatment in Arabidopsis We isolated the PM, DRM, and apoplast fractions separately and, in addition, GPI-AP-enriched fractions were prepared from the PM preparation. Label-free quantitative shotgun proteomics identified a number of GPI-APs (163 proteins). Among them, some GPI-APs such as fasciclin-like arabinogalactan proteins and glycerophosphoryldiester phosphodiesterase-like proteins predominantly increased in PM- and GPI-AP-enriched fractions while the changes of GPI-APs in the DRM and apoplast fractions during cold acclimation were considerably different from those of other fractions. These proteins are thought to be associated with cell wall structure and properties. Therefore, this study demonstrated that each GPI-AP responded to cold acclimation in a different manner, suggesting that these changes during cold acclimation are involved in rearrangement of the extracellular matrix including the cell wall towards acquisition of freezing tolerance.
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Affiliation(s)
- Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan Cryobiofrontier Research Center, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan Max-Planck-Institut für Molekulare Pflanzenphysiologie, D -14476 Potsdam, Germany
| | - Yukio Kawamura
- United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan Cryobiofrontier Research Center, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan Cryobiofrontier Research Center, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
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20
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Gutierrez-Carbonell E, Takahashi D, Lüthje S, González-Reyes JA, Mongrand S, Contreras-Moreira B, Abadía A, Uemura M, Abadía J, López-Millán AF. A Shotgun Proteomic Approach Reveals That Fe Deficiency Causes Marked Changes in the Protein Profiles of Plasma Membrane and Detergent-Resistant Microdomain Preparations from Beta vulgaris Roots. J Proteome Res 2016; 15:2510-24. [PMID: 27321140 DOI: 10.1021/acs.jproteome.6b00026] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the present study we have used label-free shotgun proteomic analysis to examine the effects of Fe deficiency on the protein profiles of highly pure sugar beet root plasma membrane (PM) preparations and detergent-resistant membranes (DRMs), the latter as an approach to study microdomains. Altogether, 545 proteins were detected, with 52 and 68 of them changing significantly with Fe deficiency in PM and DRM, respectively. Functional categorization of these proteins showed that signaling and general and vesicle-related transport accounted for approximately 50% of the differences in both PM and DRM, indicating that from a qualitative point of view changes induced by Fe deficiency are similar in both preparations. Results indicate that Fe deficiency has an impact in phosphorylation processes at the PM level and highlight the involvement of signaling proteins, especially those from the 14-3-3 family. Lipid profiling revealed Fe-deficiency-induced decreases in phosphatidic acid derivatives, which may impair vesicle formation, in agreement with the decreases measured in proteins related to intracellular trafficking and secretion. The modifications induced by Fe deficiency in the relative enrichment of proteins in DRMs revealed the existence of a group of cytoplasmic proteins that appears to be more attached to the PM in conditions of Fe deficiency.
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Affiliation(s)
| | | | - Sabine Lüthje
- University of Hamburg , Biocenter Klein Flottbek, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - José Antonio González-Reyes
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba , Campus de Rabanales, Edificio Severo Ochoa, Córdoba 14014, Spain
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire, UMR 5200 CNRS-Université Bordeaux Segalen, Bâtiment A3, INRA Bordeaux Aquitaine , 71 Rue Edouard Borlaux, CS 20032, F-33140 Villenave d'Ornon, France
| | | | | | | | | | - Ana Flor López-Millán
- USDA-ARS Chindren's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine , 1100 Bates Street, Houston, Texas 77030, United States
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21
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Wang X, Komatsu S. Plant subcellular proteomics: Application for exploring optimal cell function in soybean. J Proteomics 2016; 143:45-56. [PMID: 26808589 DOI: 10.1016/j.jprot.2016.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/06/2016] [Accepted: 01/13/2016] [Indexed: 01/11/2023]
Abstract
UNLABELLED Plants have evolved complicated responses to developmental changes and stressful environmental conditions. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular compartments during plant development and in response to biotic and abiotic stresses. Soybean, which is a valuable legume crop rich in protein and vegetable oil, can grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. To date, numerous proteomic studies have been performed in soybean to examine the specific protein profiles of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum. In this review, methods for the purification and purity assessment of subcellular organelles from soybean are summarized. In addition, the findings from subcellular proteomic analyses of soybean during development and under stresses, particularly flooding stress, are presented and the proteins regulated among subcellular compartments are discussed. Continued advances in subcellular proteomics are expected to greatly contribute to the understanding of the responses and interactions that occur within and among subcellular compartments during development and under stressful environmental conditions. BIOLOGICAL SIGNIFICANCE Subcellular proteomics has the potential to investigate the cellular events and interactions among subcellular compartments in response to development and stresses in plants. Soybean could grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. Numerous proteomics of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum was carried out to investigate the respecting proteins and their functions in soybean during development or under stresses. In this review, methods of subcellular-organelle enrichment and purity assessment are summarized. In addition, previous findings of subcellular proteomics are presented, and functional proteins regulated among different subcellular are discussed. Subcellular proteomics contributes greatly to uncovering responses and interactions among subcellular compartments during development and under stressful environmental conditions in soybean.
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Affiliation(s)
- Xin Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
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22
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Lipid profiles of detergent resistant fractions of the plasma membrane in oat and rye in association with cold acclimation and freezing tolerance. Cryobiology 2016; 72:123-34. [PMID: 26904981 DOI: 10.1016/j.cryobiol.2016.02.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 02/04/2016] [Accepted: 02/17/2016] [Indexed: 01/24/2023]
Abstract
Cold acclimation (CA) results in alteration of the plasma membrane (PM) lipid composition in plants, which plays a crucial role in the acquisition of freezing tolerance via membrane stabilization. Recent studies have indicated that PM structure is consistent with the fluid mosaic model but is laterally non-homogenous and contains microdomains enriched in sterols, sphingolipids and specific proteins. In plant cells, the function of these microdomains in relation to CA and freezing tolerance is not yet fully understood. The present study aimed to investigate the lipid compositions of detergent resistant fractions of the PM (DRM) which are considered to represent microdomains. They were prepared from leaves of low-freezing tolerant oat and high-freezing tolerant rye. The DRMs contained higher proportions of sterols, sphingolipids and saturated phospholipids than the PM. In particular, one of the sterol lipid classes, acylated sterylglycoside, was the predominant sterol in oat DRM while rye DRM contained free sterol as the major sterol. Oat and rye showed different patterns (or changes) of sterols and 2-hydroxy fatty acids of sphingolipids of DRM lipids during CA. Taken together, these results suggest that CA-induced changes of lipid classes and molecular species in DRMs are associated with changes in the thermodynamic properties and physiological functions of microdomains during CA and hence, influence plant freezing tolerance.
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23
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Fukuyama Y, Nakajima C, Izumi S, Tanaka K. Membrane Protein Analyses Using Alkylated Trihydroxyacetophenone (ATHAP) as a MALDI Matrix. Anal Chem 2016; 88:1688-95. [DOI: 10.1021/acs.analchem.5b03700] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuko Fukuyama
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
- Koichi
Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Chihiro Nakajima
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Shunsuke Izumi
- Department
of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Koichi Tanaka
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
- Koichi
Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
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24
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Nagatani A, Mimura T. Editorial: Emerging Technologies for the Study of Plant Environmental Sensing. PLANT & CELL PHYSIOLOGY 2015; 56:1249-51. [PMID: 26163572 PMCID: PMC4498007 DOI: 10.1093/pcp/pcv095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Affiliation(s)
- Akira Nagatani
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Tetsuro Mimura
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
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25
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Chevalier AS, Chaumont F. Trafficking of plant plasma membrane aquaporins: multiple regulation levels and complex sorting signals. PLANT & CELL PHYSIOLOGY 2015; 56:819-29. [PMID: 25520405 PMCID: PMC7107115 DOI: 10.1093/pcp/pcu203] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 12/04/2014] [Indexed: 05/21/2023]
Abstract
Aquaporins are small channel proteins which facilitate the diffusion of water and small neutral molecules across biological membranes. Compared with animals, plant genomes encode numerous aquaporins, which display a large variety of subcellular localization patterns. More specifically, plant aquaporins of the plasma membrane intrinsic protein (PIP) subfamily were first described as plasma membrane (PM)-resident proteins, but recent research has demonstrated that the trafficking and subcellular localization of these proteins are complex and highly regulated. In the past few years, PIPs emerged as new model proteins to study subcellular sorting and membrane dynamics in plant cells. At least two distinct sorting motifs (one cytosolic, the other buried in the membrane) are required to direct PIPs to the PM. Hetero-oligomerization and interaction with SNAREs (soluble N-ethylmaleimide-sensitive factor protein attachment protein receptors) also influence the subcellular trafficking of PIPs. In addition to these constitutive processes, both the progression of PIPs through the secretory pathway and their dynamics at the PM are responsive to changing environmental conditions.
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Affiliation(s)
- Adrien S Chevalier
- Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4, L7.07.14, B-1348 Louvain-la-Neuve, Belgium
| | - François Chaumont
- Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4, L7.07.14, B-1348 Louvain-la-Neuve, Belgium
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Chen J, Han G, Shang C, Li J, Zhang H, Liu F, Wang J, Liu H, Zhang Y. Proteomic analyses reveal differences in cold acclimation mechanisms in freezing-tolerant and freezing-sensitive cultivars of alfalfa. FRONTIERS IN PLANT SCIENCE 2015; 6:105. [PMID: 25774161 PMCID: PMC4343008 DOI: 10.3389/fpls.2015.00105] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/09/2015] [Indexed: 05/11/2023]
Abstract
Cold acclimation in alfalfa (Medicago sativa L.) plays a crucial role in cold tolerance to harsh winters. To examine the cold acclimation mechanisms in freezing-tolerant alfalfa (ZD) and freezing-sensitive alfalfa (W5), holoproteins, and low-abundance proteins (after the removal of RuBisCO) from leaves were extracted to analyze differences at the protein level. A total of 84 spots were selected, and 67 spots were identified. Of these, the abundance of 49 spots and 24 spots in ZD and W5, respectively, were altered during adaptation to chilling stress. Proteomic results revealed that proteins involved in photosynthesis, protein metabolism, energy metabolism, stress and redox and other proteins were mobilized in adaptation to chilling stress. In ZD, a greater number of changes were observed in proteins, and autologous metabolism and biosynthesis were slowed in response to chilling stress, thereby reducing consumption, allowing for homeostasis. The capability for protein folding and protein biosynthesis in W5 was enhanced, which allows protection against chilling stress. The ability to perceive low temperatures was more sensitive in freezing-tolerant alfalfa compared to freezing-sensitive alfalfa. This proteomics study provides new insights into the cold acclimation mechanism in alfalfa.
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Affiliation(s)
- Jing Chen
- College of Life Sciences and Technology, Harbin Normal UniversityHarbin, China
| | - Guiqing Han
- College of Life Sciences and Technology, Harbin Normal UniversityHarbin, China
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Chen Shang
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Jikai Li
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Hailing Zhang
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Fengqi Liu
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Jianli Wang
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Huiying Liu
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Yuexue Zhang
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
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Jung HJ, Dong X, Park JI, Thamilarasan SK, Lee SS, Kim YK, Lim YP, Nou IS, Hur Y. Genome-wide transcriptome analysis of two contrasting Brassica rapa doubled haploid lines under cold-stresses using Br135K oligomeric chip. PLoS One 2014; 9:e106069. [PMID: 25167163 PMCID: PMC4148347 DOI: 10.1371/journal.pone.0106069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/27/2014] [Indexed: 12/02/2022] Open
Abstract
Genome wide transcription analysis in response to stresses is important to provide a basis of effective engineering strategies to improve stress tolerance in crop plants. We assembled a Brassica rapa oligomeric microarray (Br135K microarray) using sequence information from 41,173 unigenes and analyzed the transcription profiles of two contrasting doubled haploid (DH) lines, Chiifu and Kenshin, under cold-treatments. The two DH lines showed great differences in electrolyte leakage below −4°C, but similar patterns from 4°C to −2°C. Cold-treatments induced 885 and 858 genes in Chiifu and Kenshin, respectively. Overall, 134, and 56 genes showed an intrinsic difference in expression in Chiifu and Kenshin, respectively. Among 5,349 genes that showed no hit found (NHF) in public databases, 61 and 24 were specifically expressed in Chiifu and Kenshin, respectively. Many transcription factor genes (TFs) also showed various characteristics of expression. BrMYB12, BrMYBL2, BrbHLHs, BrbHLH038, a C2H2, a WRKY, BrDREB19 and a integrase-type TF were induced in a Chiifu-specific fashion, while a bHLH (Bra001826/AT3G21330), bHLH, cycling Dof factor and two Dof type TFs were Kenshin specific. Similar to previous studies, a large number of genes were differently induced or regulated among the two genotypes, but many genes, including NHFs, were specifically or intrinsically expressed with genotype specificity. Expression patterns of known-cold responsive genes in plants resulted in discrepancy to membrane leakage in the two DH lines, indicating that timing of gene expression is more important to conferring freezing tolerance rather than expression levels. Otherwise, the tolerance will be related to the levels of transcripts before cold-treatment or regulated by other mechanisms. Overall, these results indicate common signaling pathways and various transcriptional regulatory mechanisms are working together during cold-treatment of B. rapa. Our newly developed Br135K oligomeric microarray will be useful for transcriptome profiling, and will deliver valuable insight into cold stresses in B. rapa.
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Affiliation(s)
- Hee-Jeong Jung
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
| | - Xiangshu Dong
- Department of Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
| | | | - Sang Sook Lee
- Department of Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Yeon-Ki Kim
- GreenGene Biotech Inc., Genomics and Genetics Institute, Yongin, Republic of Korea
| | - Yong-Pyo Lim
- Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
- * E-mail: (ISN); (YH)
| | - Yoonkang Hur
- Department of Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
- * E-mail: (ISN); (YH)
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Zhao Q, Fang F, Liang Y, Yuan H, Yang K, Wu Q, Liang Z, Zhang L, Zhang Y. 1-Dodecyl-3-Methylimidazolium Chloride-Assisted Sample Preparation Method for Efficient Integral Membrane Proteome Analysis. Anal Chem 2014; 86:7544-50. [DOI: 10.1021/ac5013267] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Qun Zhao
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Fei Fang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yu Liang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Huiming Yuan
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Kaiguang Yang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Qi Wu
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhen Liang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Yukui Zhang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
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Gutierrez-Carbonell E, Takahashi D, Lattanzio G, Rodríguez-Celma J, Kehr J, Soll J, Philippar K, Uemura M, Abadía J, López-Millán AF. The distinct functional roles of the inner and outer chloroplast envelope of Pea (Pisum sativum) as revealed by proteomic approaches. J Proteome Res 2014; 13:2941-53. [PMID: 24792535 DOI: 10.1021/pr500106s] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein profiles of inner (IE) and outer (OE) chloroplast envelope membrane preparations from pea were studied using shotgun nLC-MS/MS and two-dimensional electrophoresis, and 589 protein species (NCBI entries) were identified. The relative enrichment of each protein in the IE/OE pair of membranes was used to provide an integrated picture of the chloroplast envelope. From the 546 proteins identified with shotgun, 321 showed a significant differential distribution, with 180 being enriched in IE and 141 in OE. To avoid redundancy and facilitate in silico localization, Arabidopsis homologues were used to obtain a nonredundant list of 409 envelope proteins, with many showing significant OE or IE enrichment. Functional classification reveals that IE is a selective barrier for transport of many metabolites and plays a major role in controlling protein homeostasis, whereas proteins in OE are more heterogeneous and participate in a wide range of processes. Data support that metabolic processes previously described to occur in the envelope such as chlorophyll and tocopherol biosynthesis can be ascribed to the IE, whereas others such as carotenoid or lipid biosynthesis occur in both membranes. Furthermore, results allow empirical assignation to the IE and/or OE of many proteins previously assigned to the bulk chloroplast envelope proteome.
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Affiliation(s)
- Elain Gutierrez-Carbonell
- Plant Nutrition Department, Aula Dei Experimental Station, CSIC , P.O. Box 13034, 50080 Zaragoza, Spain
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