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Ozavize SF, Qiu CW, Wu F. Astaxanthin induces plant tolerance against cadmium by reducing cadmium uptake and enhancing carotenoid metabolism for antioxidant defense in wheat (Triticum aestivum L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108622. [PMID: 38677187 DOI: 10.1016/j.plaphy.2024.108622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 03/26/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024]
Abstract
Soil cadmium (Cd) contamination poses a significant threat to global food security and the environment. Astaxanthin (AX), a potent biological antioxidant belonging to the carotenoid group, has been demonstrated to confer tolerance against diverse abiotic stresses in plants. This study investigated the potential of AX in mitigating Cd-induced damage in wheat seedlings. Morpho-physiological, ultrastructural, and biochemical analyses were conducted to evaluate the impact of AX on Cd-exposed wheat seedlings. Illumina-based gene expression profiling was employed to uncover the molecular mechanisms underlying the protective effects of AX. The addition of 100 μM AX alleviated Cd toxicity by enhancing various parameters: growth, photosynthesis, carotenoid content, and total antioxidant capacity (T-AOC), while reducing Cd accumulation, malondialdehyde (MDA), and hydrogen peroxide (H2O2) levels. RNA sequencing analysis revealed differentially expressed genes associated with Cd uptake and carotenoid metabolism, such as zinc/iron permease (ZIP), heavy metal-associated protein (HMA), 3-beta hydroxysteroid dehydrogenase/isomerase (3-beta-HSD), and thiolase. These findings suggest that AX enhances Cd tolerance in wheat seedlings by promoting the expression of detoxification and photosynthesis-related genes. This research offers valuable insights into the potential use of AX to address Cd contamination in agricultural systems, highlighting the significance of antioxidant supplementation in plant stress management.
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Affiliation(s)
- Suleiman Fatimoh Ozavize
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, PR China
| | - Cheng-Wei Qiu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, PR China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, PR China.
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, PR China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, PR China.
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Sharma Y, Thakral V, Raturi G, Dutta Dubey K, Sonah H, Pareek A, Sharma TR, Deshmukh R. Structural assessment of OsNIP2;1 highlighted critical residues defining solute specificity and functionality of NIP class aquaporins. J Adv Res 2024; 58:1-11. [PMID: 37164213 PMCID: PMC10982858 DOI: 10.1016/j.jare.2023.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 04/30/2023] [Accepted: 04/30/2023] [Indexed: 05/12/2023] Open
Abstract
INTRODUCTION Nodulin-26-like intrinsic proteins (NIPs) are integral membrane proteins belonging to the aquaporin family, that facilitate the transport of neutral solutes across the bilayer. The OsNIP2;1 a member of NIP-III class of aquaporins is permeable to beneficial elements like silicon and hazardous arsenic. However, the atomistic cross-talk of these molecules traversing the OsNIP2;1 channel is not well understood. OBJECTIVE Due to the lack of genomic variation but the availability of high confidence crystal structure, this study aims to highlight structural determinants of metalloid permeation through OsNIP2;1. METHODS The molecular simulations, combined with site-directed mutagenesis were used to probe the role of specific residues in the metalloid transport activity of OsNIP2;1. RESULTS We drew energetic landscape of OsNIP2;1, for silicic and arsenous acid transport. Potential Mean Force (PMF) construction illuminate three prominent energetic barriers for metalloid passage through the pore. One corresponds to the extracellular molecular entry in the channel, the second located on ar/R filter, and the third size constriction in the cytoplasmic half. Comparative PMF for silicic acid and arsenous acid elucidate a higher barrier for silicic acid at the cytoplasmic constrict resulting in longer residence time for silicon. Furthermore, our simulation studies explained the importance of conserved residues in loop-C and loop-D with a direct effect on pore dynamics and metalloid transport. Next we assessed contribution of predicted key residues for arsenic uptake, by functional complementation in yeast. With the aim of reducing arsenic uptake while maintaining beneficial elements uptake, we identified novel OsNIP2;1 mutants with substantial reduction in arsenic uptake in yeast. CONCLUSION We provide a comprehensive assessment of pore lining residues of OsNIP2;1 with respect to metalloid uptake. The findings will expand mechanistic understanding of aquaporin's metalloid selectivity and facilitate variant interpretation to develop novel alleles with preference for beneficial metalloid species and reducing hazardous ones.
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Affiliation(s)
- Yogesh Sharma
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India; Regional Centre for Biotechnology, Faridabad, Haryana (NCR Delhi), India
| | - Vandana Thakral
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India; Department of Biotechnology, Panjab University, Chandigarh, India
| | - Gaurav Raturi
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India; Department of Biotechnology, Panjab University, Chandigarh, India
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institute of Eminence, Gautam Buddha Nagar, Uttar Pradesh, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India; Department of Biotechnology, Central University of Haryana, Mahendragarh, Haryana, India
| | - Ashwani Pareek
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India; Indian Council of Agricultural Research, Division of Crop Science, Krishi Bhavan, New Delhi, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India; Plaksha University, Mohali, Punjab, India; Department of Biotechnology, Central University of Haryana, Mahendragarh, Haryana, India.
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Shahzad Z, Tournaire-Roux C, Canut M, Adamo M, Roeder J, Verdoucq L, Martinière A, Amtmann A, Santoni V, Grill E, Loudet O, Maurel C. Protein kinase SnRK2.4 is a key regulator of aquaporins and root hydraulics in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:264-279. [PMID: 37844131 DOI: 10.1111/tpj.16494] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/06/2023] [Accepted: 09/14/2023] [Indexed: 10/18/2023]
Abstract
Soil water uptake by roots is a key component of plant water homeostasis contributing to plant growth and survival under ever-changing environmental conditions. The water transport capacity of roots (root hydraulic conductivity; Lpr ) is mostly contributed by finely regulated Plasma membrane Intrinsic Protein (PIP) aquaporins. In this study, we used natural variation of Arabidopsis for the identification of quantitative trait loci (QTLs) contributing to Lpr . Using recombinant lines from a biparental cross (Cvi-0 x Col-0), we show that the gene encoding class 2 Sucrose-Non-Fermenting Protein kinase 2.4 (SnRK2.4) in Col-0 contributes to >30% of Lpr by enhancing aquaporin-dependent water transport. At variance with the inactive and possibly unstable Cvi-0 SnRK2.4 form, the Col-0 form interacts with and phosphorylates the prototypal PIP2;1 aquaporin at Ser121 and stimulates its water transport activity upon coexpression in Xenopus oocytes and yeast cells. Activation of PIP2;1 by Col-0 SnRK2.4 in yeast also requires its protein kinase activity and can be counteracted by clade A Protein Phosphatases 2C. SnRK2.4 shows all hallmarks to be part of core abscisic acid (ABA) signaling modules. Yet, long-term (>3 h) inhibition of Lpr by ABA possibly involves a SnRK2.4-independent inhibition of PIP2;1. SnRK2.4 also promotes stomatal aperture and ABA-induced inhibition of primary root growth. The study identifies a key component of Lpr and sheds new light on the functional overlap and specificity of SnRK2.4 with respect to other ABA-dependent or independent SnRK2s.
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Affiliation(s)
- Zaigham Shahzad
- Institute for Plant Sciences of Montpellier, University Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Colette Tournaire-Roux
- Institute for Plant Sciences of Montpellier, University Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Matthieu Canut
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Mattia Adamo
- Institute for Plant Sciences of Montpellier, University Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Jan Roeder
- School of Life Sciences, Technical University Munich, 85354, Freising-Weihenstephan, Germany
| | - Lionel Verdoucq
- Institute for Plant Sciences of Montpellier, University Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Alexandre Martinière
- Institute for Plant Sciences of Montpellier, University Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Anna Amtmann
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK
| | - Véronique Santoni
- Institute for Plant Sciences of Montpellier, University Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Erwin Grill
- School of Life Sciences, Technical University Munich, 85354, Freising-Weihenstephan, Germany
| | - Olivier Loudet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Christophe Maurel
- Institute for Plant Sciences of Montpellier, University Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
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Pade LR, Stepler KE, Portero EP, DeLaney K, Nemes P. Biological mass spectrometry enables spatiotemporal 'omics: From tissues to cells to organelles. MASS SPECTROMETRY REVIEWS 2024; 43:106-138. [PMID: 36647247 PMCID: PMC10668589 DOI: 10.1002/mas.21824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 06/17/2023]
Abstract
Biological processes unfold across broad spatial and temporal dimensions, and measurement of the underlying molecular world is essential to their understanding. Interdisciplinary efforts advanced mass spectrometry (MS) into a tour de force for assessing virtually all levels of the molecular architecture, some in exquisite detection sensitivity and scalability in space-time. In this review, we offer vignettes of milestones in technology innovations that ushered sample collection and processing, chemical separation, ionization, and 'omics analyses to progressively finer resolutions in the realms of tissue biopsies and limited cell populations, single cells, and subcellular organelles. Also highlighted are methodologies that empowered the acquisition and analysis of multidimensional MS data sets to reveal proteomes, peptidomes, and metabolomes in ever-deepening coverage in these limited and dynamic specimens. In pursuit of richer knowledge of biological processes, we discuss efforts pioneering the integration of orthogonal approaches from molecular and functional studies, both within and beyond MS. With established and emerging community-wide efforts ensuring scientific rigor and reproducibility, spatiotemporal MS emerged as an exciting and powerful resource to study biological systems in space-time.
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Affiliation(s)
- Leena R. Pade
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kaitlyn E. Stepler
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Erika P. Portero
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kellen DeLaney
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
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Ueda M, Kato N, Kurata Y, Imai M, Yang G, Taniguchi K. Host-Selective Phytotoxins Incorporating the Epoxy-Triene-Decacarboxylate Moiety Function through the Hijacking of the Plant-Microbe Interaction System. ACS Chem Biol 2023; 18:12-17. [PMID: 36547375 DOI: 10.1021/acschembio.2c00777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Host selective toxins (HSTs) are small molecule phytotoxins that control the pathogenicity of microbes in the host plant, but the mechanistic basis for their selectivity is unknown. We developed AcIle-EDA (Aclle-(+)-9,10-epoxy-8-hydroxy-9-methyldeca-trienoic acid) as a molecular probe of an HST, examined its mode of action in genetically modified Oryza sativa, and found it to trigger ROS production through NADPH-oxidase OsRBOHB, causing the emergence of pathogenic traits. This result strongly suggests that AcIle-EDA functions through the hijacking of the plant-microbe interaction system.
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Affiliation(s)
- Minoru Ueda
- Graduate School of Science, Tohoku University, 6-3, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8578, Japan
| | - Nobuki Kato
- Graduate School of Science, Tohoku University, 6-3, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8578, Japan
| | - Yoshinori Kurata
- Graduate School of Science, Tohoku University, 6-3, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8578, Japan
| | - Masaki Imai
- Graduate School of Science, Tohoku University, 6-3, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8578, Japan
| | - Gangqiang Yang
- School of Pharmacy, Yantai University, 30, Qingquan RD, Laishan District, Yantai 264005, China
| | - Keigo Taniguchi
- Graduate School of Science, Tohoku University, 6-3, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8578, Japan
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Arefian M, Bhagya N, Prasad TSK. Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops. Biol Rev Camb Philos Soc 2021; 96:2164-2191. [PMID: 34047006 DOI: 10.1111/brv.12748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.
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Affiliation(s)
- Mohammad Arefian
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - N Bhagya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
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Bobrovskikh A, Zubairova U, Kolodkin A, Doroshkov A. Subcellular compartmentalization of the plant antioxidant system: an integrated overview. PeerJ 2020; 8:e9451. [PMID: 32742779 PMCID: PMC7369019 DOI: 10.7717/peerj.9451] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/09/2020] [Indexed: 01/22/2023] Open
Abstract
The antioxidant system (AOS) maintains the optimal concentration of reactive oxygen species (ROS) in a cell and protects it against oxidative stress. In plants, the AOS consists of seven main classes of antioxidant enzymes, low-molecular antioxidants (e.g., ascorbate, glutathione, and their oxidized forms) and thioredoxin/glutaredoxin systems which can serve as reducing agents for antioxidant enzymes. The number of genes encoding AOS enzymes varies between classes, and same class enzymes encoded by different gene copies may have different subcellular localizations, functional loads and modes of evolution. These facts hereafter reinforce the complex nature of AOS regulation and functioning. Further studies can describe new trends in the behavior and functioning of systems components, and provide new fundamental knowledge about systems regulation. The system is revealed to have a lot of interactions and interplay pathways between its components at the subcellular level (antioxidants, enzymes, ROS level, and hormonal and transcriptional regulation). These facts should be taken into account in further studies during the AOS modeling by describing the main pathways of generating and utilizing ROS, as well as the associated signaling processes and regulation of the system on cellular and organelle levels, which is a complicated and ambitious task. Another objective for studying the phenomenon of the AOS is related to the influence of cell dynamics and circadian rhythms on it. Therefore, the AOS requires an integrated and multi-level approach to study. We focused this review on the existing scientific background and experimental data used for the systems biology research of the plant AOS.
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Affiliation(s)
- Aleksandr Bobrovskikh
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Ulyana Zubairova
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
| | - Alexey Kolodkin
- University of Amsterdam, Amsterdam, Netherlands
- The University of Luxembourg, Luxembourg Centre for Systems Biomedicine, Luxembourg, Luxembourg
| | - Alexey Doroshkov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
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8
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Comparative phosphoproteomic analysis of BR-defective mutant reveals a key role of GhSK13 in regulating cotton fiber development. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1905-1917. [PMID: 32632733 DOI: 10.1007/s11427-020-1728-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023]
Abstract
Brassinosteroid (BR), a steroid phytohormone, whose signaling transduction pathways include a series of phosphorylation and dephosphorylation events, and GSK3s are the main negative regulator kinases. BRs have been shown to play vital roles in cotton fiber elongation. However, the underlying mechanism is still elusive. In this study, fibers of a BR-defective mutant Pagoda 1 (pag1), and its corresponding wild-type (ZM24) were selected for a comparative global phosphoproteome analysis at critical developmental time points: fast-growing stage (10 days after pollination (DPA)) and secondary cell wall synthesis stage (20 DPA). Based on the substrate characteristics of GSK3, 900 potential substrates were identified. Their GO and KEGG annotation results suggest that BR functions in fiber development by regulating GhSKs (GSK3s of Gossypium hirsutum L.) involved microtubule cytoskeleton organization, and pathways of glucose, sucrose and lipid metabolism. Further experimental results revealed that among the GhSK members identified, GhSK13 not only plays a role in BR signaling pathway, but also functions in developing fiber by respectively interacting with an AP2-like ethylene-responsive factor GhAP2L, a nuclear transcription factor Gh_DNF_YB19, and a homeodomain zipper member GhHDZ5. Overall, our phosphoproteomic research advances the understanding of fiber development controlled by BR signal pathways especially through GhSKs, and also offers numbers of target proteins for improving cotton fiber quality.
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Tang RJ, Luan M, Wang C, Lhamo D, Yang Y, Zhao FG, Lan WZ, Fu AG, Luan S. Plant Membrane Transport Research in the Post-genomic Era. PLANT COMMUNICATIONS 2020; 1:100013. [PMID: 33404541 PMCID: PMC7747983 DOI: 10.1016/j.xplc.2019.100013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/14/2019] [Accepted: 12/06/2019] [Indexed: 05/17/2023]
Abstract
Membrane transport processes are indispensable for many aspects of plant physiology including mineral nutrition, solute storage, cell metabolism, cell signaling, osmoregulation, cell growth, and stress responses. Completion of genome sequencing in diverse plant species and the development of multiple genomic tools have marked a new era in understanding plant membrane transport at the mechanistic level. Genes coding for a galaxy of pumps, channels, and carriers that facilitate various membrane transport processes have been identified while multiple approaches are developed to dissect the physiological roles as well as to define the transport capacities of these transport systems. Furthermore, signaling networks dictating the membrane transport processes are established to fully understand the regulatory mechanisms. Here, we review recent research progress in the discovery and characterization of the components in plant membrane transport that take advantage of plant genomic resources and other experimental tools. We also provide our perspectives for future studies in the field.
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Affiliation(s)
- Ren-Jie Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Mingda Luan
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Chao Wang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Dhondup Lhamo
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Yang Yang
- Nanjing University–Nanjing Forestry University Joint Institute for Plant Molecular Biology, College of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Fu-Geng Zhao
- Nanjing University–Nanjing Forestry University Joint Institute for Plant Molecular Biology, College of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Wen-Zhi Lan
- Nanjing University–Nanjing Forestry University Joint Institute for Plant Molecular Biology, College of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Ai-Gen Fu
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Corresponding author
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Yang J, Xie MY, Yang XL, Liu BH, Lin HH. Phosphoproteomic Profiling Reveals the Importance of CK2, MAPKs and CDPKs in Response to Phosphate Starvation in Rice. PLANT & CELL PHYSIOLOGY 2019; 60:2785-2796. [PMID: 31424513 DOI: 10.1093/pcp/pcz167] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 08/14/2019] [Indexed: 05/21/2023]
Abstract
Phosphorus is one of the most important macronutrients required for plant growth and development. The importance of phosphorylation modification in regulating phosphate (Pi) homeostasis in plants is emerging. We performed phosphoproteomic profiling to characterize proteins whose degree of phosphorylation is altered in response to Pi starvation in rice root. A subset of 554 proteins, including 546 down-phosphorylated and eight up-phosphorylated proteins, exhibited differential phosphorylation in response to Pi starvation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis with the differentially phosphorylated proteins indicated that RNA processing, transport, splicing and translation and carbon metabolism played critical roles in response to Pi starvation in rice. Levels of phosphorylation of four mitogen-activated protein kinases (MAPKs), including OsMAPK6, five calcium-dependent protein kinases (CDPKs) and OsCK2β3 decreased in response to Pi starvation. The decreased phosphorylation level of OsMAPK6 was confirmed by Western blotting. Mutation of OsMAPK6 led to Pi accumulation under Pi-sufficient conditions. Motif analysis indicated that the putative MAPK, casein kinase 2 (CK2) and CDPK substrates represented about 54.4%, 21.5% and 4.7%, respectively, of the proteins exhibiting differential phosphorylation. Based on the motif analysis, 191, 151 and 46 candidate substrates for MAPK, CK2 and CDPK were identified. These results indicate that modification of phosphorylation profiles provides complementary information on Pi-starvation-induced processes, with CK2, MAPK and CDPK protein kinase families playing key roles in these processes in rice.
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Affiliation(s)
- Jian Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan, Chengdu 610065, China
| | - Meng-Yang Xie
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan, Chengdu 610065, China
| | - Xiao-Li Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan, Chengdu 610065, China
| | - Bao-Hui Liu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Hong-Hui Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan, Chengdu 610065, China
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Cutolo E, Parvin N, Ruge H, Pirayesh N, Roustan V, Weckwerth W, Teige M, Grieco M, Larosa V, Vothknecht UC. The High Light Response in Arabidopsis Requires the Calcium Sensor Protein CAS, a Target of STN7- and STN8-Mediated Phosphorylation. FRONTIERS IN PLANT SCIENCE 2019; 10:974. [PMID: 31417591 PMCID: PMC6682602 DOI: 10.3389/fpls.2019.00974] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/11/2019] [Indexed: 05/18/2023]
Abstract
Reversible phosphorylation of thylakoid proteins contributes to photoacclimation responses in photosynthetic organisms, enabling the fine-tuning of light harvesting under changing light conditions and promoting the onset of photoprotective processes. However, the precise functional role of many of the described phosphorylation events on thylakoid proteins remains elusive. The calcium sensor receptor protein (CAS) has previously been indicated as one of the targets of the state transition kinase 8 (STN8). Here we show that in Arabidopsis thaliana, CAS is also phosphorylated by the state transition kinase 7 (STN7), as well as by another, so-far unknown, Ca2+-dependent kinase. Phosphoproteomics analysis and in vitro phosphorylation assays on CAS variants identified the phylogenetically conserved residues Thr-376, Ser-378, and Thr-380 as the major phosphorylation sites of the STN kinases. Spectroscopic analyses of chlorophyll fluorescence emission at 77K further showed that, while the cas mutant is not affected in state transition, it displays a persistent strong excitation of PSI under high light exposure, similar to the phenotype previously observed in other mutants defective in photoacclimation mechanisms. Together with the observation of a strong concomitant phosphorylation of light harvesting complex II (LHCII) and photosynthetic core proteins under high irradiance in the cas mutant this suggests a role for CAS in the STN7/STN8/TAP38 network of phosphorylation-mediated photoacclimation processes in Arabidopsis.
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Affiliation(s)
- Edoardo Cutolo
- Plant Cell Biology, Institut für Zelluläre und Molekulare Botanik, University of Bonn, Bonn, Germany
| | - Nargis Parvin
- Department of Plant Nutrition, Institut für Nutzpflanzenwissenschaften und Ressourcenschutz, University of Bonn, Bonn, Germany
| | - Henning Ruge
- Department of Biology I, Ludwig Maximilian University of Munich, Munich, Germany
| | - Niloufar Pirayesh
- Plant Cell Biology, Institut für Zelluläre und Molekulare Botanik, University of Bonn, Bonn, Germany
| | - Valentin Roustan
- Department of Molecular Systems Biology, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Molecular Systems Biology, University of Vienna, Vienna, Austria
| | - Markus Teige
- Department of Molecular Systems Biology, University of Vienna, Vienna, Austria
| | - Michele Grieco
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Veronique Larosa
- Laboratory of Genetics and Physiology of Microalgae, InBios, University of Liège, Liège, Belgium
| | - Ute C. Vothknecht
- Plant Cell Biology, Institut für Zelluläre und Molekulare Botanik, University of Bonn, Bonn, Germany
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12
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Wang X, Yang G, Shi M, Hao D, Wei Q, Wang Z, Fu S, Su Y, Xia J. Disruption of an amino acid transporter LHT1 leads to growth inhibition and low yields in rice. BMC PLANT BIOLOGY 2019; 19:268. [PMID: 31221084 PMCID: PMC6584995 DOI: 10.1186/s12870-019-1885-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 06/13/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Research on plant amino acid transporters was mainly performed in Arabidopsis, while our understanding of them is generally scant in rice. OsLHT1 (Lysine/Histidine transporter) has been previously reported as a histidine transporter in yeast, but its substrate profile and function in planta are unclear. The aims of this study are to analyze the substrate selectivity of OsLHT1 and influence of its disruption on rice growth and fecundity. RESULTS Substrate selectivity of OsLHT1 was analyzed in Xenopus oocytes using the two-electrode voltage clamp technique. The results showed that OsLHT1 could transport a broad spectrum of amino acids, including basic, neutral and acidic amino acids, and exhibited a preference for neutral and acidic amino acids. Two oslht1 mutants were generated using CRISPR/Cas9 genome-editing technology, and the loss-of-function of OsLHT1 inhibited rice root and shoot growth, thereby markedly reducing grain yields. QRT-PCR analysis indicated that OsLHT1 was expressed in various rice organs, including root, stem, flag leaf, flag leaf sheath and young panicle. Transient expression in rice protoplast suggested OsLHT1 was localized to the plasma membrane, which is consistent with its function as an amino acid transporter. CONCLUSIONS Our results indicated that OsLHT1 is an amino acid transporter with wide substrate specificity and with preference for neutral and acidic amino acids, and disruption of OsLHT1 function markedly inhibited rice growth and fecundity.
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Affiliation(s)
- Xiaohu Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530005 China
| | - Guangzhe Yang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530005 China
| | - Mingxing Shi
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530005 China
| | - Dongli Hao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71, East Beijing Road, Nanjing, 210008 China
| | - Qiuxing Wei
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530005 China
| | - Zhigang Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530005 China
| | - Shan Fu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530005 China
| | - Yanhua Su
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71, East Beijing Road, Nanjing, 210008 China
| | - Jixing Xia
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530005 China
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13
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Molecular insights into the plasma membrane intrinsic proteins roles for abiotic stress and metalloids tolerance and transport in plants. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s40502-018-0425-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Merlaen B, De Keyser E, Van Labeke MC. Identification and substrate prediction of new Fragaria x ananassa aquaporins and expression in different tissues and during strawberry fruit development. HORTICULTURE RESEARCH 2018; 5:20. [PMID: 29619231 PMCID: PMC5880810 DOI: 10.1038/s41438-018-0019-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 12/15/2017] [Accepted: 01/11/2018] [Indexed: 05/07/2023]
Abstract
The newly identified aquaporin coding sequences presented here pave the way for further insights into the plant-water relations in the commercial strawberry (Fragaria x ananassa). Aquaporins are water channel proteins that allow water to cross (intra)cellular membranes. In Fragaria x ananassa, few of them have been identified hitherto, hampering the exploration of the water transport regulation at cellular level. Here, we present new aquaporin coding sequences belonging to different subclasses: plasma membrane intrinsic proteins subtype 1 and subtype 2 (PIP1 and PIP2) and tonoplast intrinsic proteins (TIP). The classification is based on phylogenetic analysis and is confirmed by the presence of conserved residues. Substrate-specific signature sequences (SSSSs) and specificity-determining positions (SDPs) predict the substrate specificity of each new aquaporin. Expression profiling in leaves, petioles and developing fruits reveals distinct patterns, even within the same (sub)class. Expression profiles range from leaf-specific expression over constitutive expression to fruit-specific expression. Both upregulation and downregulation during fruit ripening occur. Substrate specificity and expression profiles suggest that functional specialization exists among aquaporins belonging to a different but also to the same (sub)class.
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Affiliation(s)
- Britt Merlaen
- Plant Production, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Ellen De Keyser
- Flanders Research Institute for Agriculture Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090 Melle, Belgium
| | - Marie-Christine Van Labeke
- Plant Production, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Gent, Belgium
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15
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Wu XN, Xi L, Pertl-Obermeyer H, Li Z, Chu LC, Schulze WX. Highly Efficient Single-Step Enrichment of Low Abundance Phosphopeptides from Plant Membrane Preparations. FRONTIERS IN PLANT SCIENCE 2017; 8:1673. [PMID: 29042862 PMCID: PMC5632542 DOI: 10.3389/fpls.2017.01673] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 09/12/2017] [Indexed: 05/30/2023]
Abstract
Mass spectrometry (MS)-based large scale phosphoproteomics has facilitated the investigation of plant phosphorylation dynamics on a system-wide scale. However, generating large scale data sets for membrane phosphoproteins usually requires fractionation of samples and extended hands-on laboratory time. To overcome these limitations, we developed "ShortPhos," an efficient and simple phosphoproteomics protocol optimized for research on plant membrane proteins. The optimized workflow allows fast and efficient identification and quantification of phosphopeptides, even from small amounts of starting plant materials. "ShortPhos" can produce label-free datasets with a high quantitative reproducibility. In addition, the "ShortPhos" protocol recovered more phosphorylation sites from membrane proteins, especially plasma membrane and vacuolar proteins, when compared to our previous workflow and other membrane-based data in the PhosPhAt 4.0 database. We applied "ShortPhos" to study kinase-substrate relationships within a nitrate-induction experiment on Arabidopsis roots. The "ShortPhos" identified significantly more known kinase-substrate relationships compared to previous phosphoproteomics workflows, producing new insights into nitrate-induced signaling pathways.
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16
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Almadanim MC, Alexandre BM, Rosa MTG, Sapeta H, Leitão AE, Ramalho JC, Lam TT, Negrão S, Abreu IA, Oliveira MM. Rice calcium-dependent protein kinase OsCPK17 targets plasma membrane intrinsic protein and sucrose-phosphate synthase and is required for a proper cold stress response. PLANT, CELL & ENVIRONMENT 2017; 40:1197-1213. [PMID: 28102545 DOI: 10.1111/pce.12916] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/10/2017] [Accepted: 01/15/2017] [Indexed: 05/20/2023]
Abstract
Calcium-dependent protein kinases (CDPKs) are involved in plant tolerance mechanisms to abiotic stresses. Although CDPKs are recognized as key messengers in signal transduction, the specific role of most members of this family remains unknown. Here, we test the hypothesis that OsCPK17 plays a role in rice cold stress response by analysing OsCPK17 knockout, silencing and overexpressing rice lines under low temperature. Altered OsCPK17 gene expression compromises cold tolerance performance, without affecting the expression of key cold stress-inducible genes. A comparative phosphoproteomic approach led to the identification of six potential in vivo OsCPK17 targets, which are associated with sugar and nitrogen metabolism, and with osmotic regulation. To test direct interaction, in vitro kinase assays were performed, showing that the sucrose-phosphate synthase OsSPS4 and the aquaporin OsPIP2;1/OsPIP2;6 are phosphorylated by OsCPK17 in a calcium-dependent manner. Altogether, our data indicates that OsCPK17 is required for a proper cold stress response in rice, likely affecting the activity of membrane channels and sugar metabolism.
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Affiliation(s)
- M Cecília Almadanim
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Bruno M Alexandre
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Margarida T G Rosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Helena Sapeta
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - António E Leitão
- Plant Stress and Biodiversity, Linking Landscape, Environment, Agriculture and Food (LEAF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia, Universidade de Lisboa, 2784-505, Oeiras, Portugal
| | - José C Ramalho
- Plant Stress and Biodiversity, Linking Landscape, Environment, Agriculture and Food (LEAF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia, Universidade de Lisboa, 2784-505, Oeiras, Portugal
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520-8024, USA
- MS and Proteomics Resource, WM Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT, 06520-8024, USA
| | - Sónia Negrão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Isabel A Abreu
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
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17
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Almeida DM, Oliveira MM, Saibo NJM. Regulation of Na+ and K+ homeostasis in plants: towards improved salt stress tolerance in crop plants. Genet Mol Biol 2017; 40:326-345. [PMID: 28350038 PMCID: PMC5452131 DOI: 10.1590/1678-4685-gmb-2016-0106] [Citation(s) in RCA: 226] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/18/2016] [Indexed: 01/17/2023] Open
Abstract
Soil salinity is a major abiotic stress that results in considerable crop yield losses worldwide. However, some plant genotypes show a high tolerance to soil salinity, as they manage to maintain a high K+/Na+ ratio in the cytosol, in contrast to salt stress susceptible genotypes. Although, different plant genotypes show different salt tolerance mechanisms, they all rely on the regulation and function of K+ and Na+ transporters and H+ pumps, which generate the driving force for K+ and Na+ transport. In this review we will introduce salt stress responses in plants and summarize the current knowledge about the most important ion transporters that facilitate intra- and intercellular K+ and Na+ homeostasis in these organisms. We will describe and discuss the regulation and function of the H+-ATPases, H+-PPases, SOS1, HKTs, and NHXs, including the specific tissues where they work and their response to salt stress.
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Affiliation(s)
- Diego M Almeida
- Genomics of Plant Stress Unit, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa and Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - M Margarida Oliveira
- Genomics of Plant Stress Unit, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa and Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Nelson J M Saibo
- Genomics of Plant Stress Unit, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa and Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
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18
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19
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Loop B serine of a plasma membrane aquaporin type PIP2 but not PIP1 plays a key role in pH sensing. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2778-2787. [DOI: 10.1016/j.bbamem.2016.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 07/08/2016] [Accepted: 08/07/2016] [Indexed: 11/17/2022]
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20
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Toda Y, Wang Y, Takahashi A, Kawai Y, Tada Y, Yamaji N, Feng Ma J, Ashikari M, Kinoshita T. Oryza sativa H+-ATPase (OSA) is Involved in the Regulation of Dumbbell-Shaped Guard Cells of Rice. PLANT & CELL PHYSIOLOGY 2016; 57:1220-30. [PMID: 27048369 PMCID: PMC4904443 DOI: 10.1093/pcp/pcw070] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 03/30/2016] [Indexed: 05/24/2023]
Abstract
The stomatal apparatus consists of a pair of guard cells and regulates gas exchange between the leaf and atmosphere. In guard cells, blue light (BL) activates H(+)-ATPase in the plasma membrane through the phosphorylation of its penultimate threonine, mediating stomatal opening. Although this regulation is thought to be widely adopted among kidney-shaped guard cells in dicots, the molecular basis underlying that of dumbbell-shaped guard cells in monocots remains unclear. Here, we show that H(+)-ATPases are involved in the regulation of dumbbell-shaped guard cells. Stomatal opening of rice was promoted by the H(+)-ATPase activator fusicoccin and by BL, and the latter was suppressed by the H(+)-ATPase inhibitor vanadate. Using H(+)-ATPase antibodies, we showed the presence of phosphoregulation of the penultimate threonine in Oryza sativa H(+)-ATPases (OSAs) and localization of OSAs in the plasma membrane of guard cells. Interestingly, we identified one H(+)-ATPase isoform, OSA7, that is preferentially expressed among the OSA genes in guard cells, and found that loss of function of OSA7 resulted in partial insensitivity to BL. We conclude that H(+)-ATPase is involved in BL-induced stomatal opening of dumbbell-shaped guard cells in monocotyledon species.
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Affiliation(s)
- Yosuke Toda
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602 Japan
| | - Yin Wang
- Institute for Advanced Research, Nagoya University, Chikusa, Nagoya, 464-8602 Japan
| | - Akira Takahashi
- Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, Tsukuba, 305-8602 Japan
| | - Yuya Kawai
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602 Japan
| | - Yasuomi Tada
- Center of Gene Research, Nagoya University, Chikusa, Nagoya, 464-8602 Japan
| | - Naoki Yamaji
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, 710-0046 Japan
| | - Jian Feng Ma
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, 710-0046 Japan
| | - Motoyuki Ashikari
- Bioscience Center, Nagoya University, Chikusa, Nagoya, 464-8601 Japan
| | - Toshinori Kinoshita
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602 Japan Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602 Japan
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21
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Gel-based and gel-free search for plasma membrane proteins in chickpea (Cicer arietinum L.) augments the comprehensive data sets of membrane protein repertoire. J Proteomics 2016; 143:199-208. [PMID: 27109347 DOI: 10.1016/j.jprot.2016.04.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/14/2016] [Accepted: 04/18/2016] [Indexed: 12/20/2022]
Abstract
UNLABELLED Plasma membrane (PM) encompasses total cellular contents, serving as semi-porous barrier to cell exterior. This living barrier regulates all cellular exchanges in a spatio-temporal fashion. Most of the essential tasks of PMs including molecular transport, cell-cell interaction and signal transduction are carried out by their proteinaceous components, which make the PM protein repertoire to be diverse and dynamic. Here, we report the systematic analysis of PM proteome of a food legume, chickpea and develop a PM proteome reference map. Proteins were extracted from highly enriched PM fraction of four-week-old seedlings using aqueous two-phase partitioning. To address a population of PM proteins that is as comprehensive as possible, both gel-based and gel-free approaches were employed, which led to the identification of a set of 2732 non-redundant proteins. These included both integral proteins having bilayer spanning domains as well as peripheral proteins associated with PMs through posttranslational modifications or protein-protein interactions. Further, the proteins were subjected to various in-silico analyses and functionally classified based on their gene ontology. Finally an inventory of the complete set of PM proteins, identified in several monocot and dicot species, was created for comparative study with the generated PM protein dataset of chickpea. BIOLOGICAL SIGNIFICANCE Chickpea, a rich source of dietary proteins, is the second most cultivated legume, which is grown over 10 million hectares of land worldwide. The annual global production of chickpea hovers around 8.5 million metric tons. Recent chickpea genome sequencing effort has provided a broad genetic basis for highlighting the important traits that may fortify other crop legumes. Improvement in chickpea varieties can further strengthen the world food security, which includes food availability, access and utilization. It is known that the phenotypic trait of a cultivar is the manifestation of the orchestrated functions of its proteins. Study of the PM proteome offers insights into the mechanism of communication between the cell and its environment by identification of receptors, signalling proteins and membrane transporters. Knowledge of the PM protein repertoire of a relatively dehydration tolerant chickpea variety, JG-62, can contribute in development of strategies for metabolic reprograming of crop species and breeding applications.
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22
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Grondin A, Mauleon R, Vadez V, Henry A. Root aquaporins contribute to whole plant water fluxes under drought stress in rice (Oryza sativa L.). PLANT, CELL & ENVIRONMENT 2016; 39:347-65. [PMID: 26226878 DOI: 10.1111/pce.12616] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/26/2015] [Indexed: 05/20/2023]
Abstract
Aquaporin activity and root anatomy may affect root hydraulic properties under drought stress. To better understand the function of aquaporins in rice root water fluxes under drought, we studied the root hydraulic conductivity (Lpr) and root sap exudation rate (Sr) in the presence or absence of an aquaporin inhibitor (azide) under well-watered conditions and following drought stress in six diverse rice varieties. Varieties varied in Lpr and Sr under both conditions. The contribution of aquaporins to Lpr was generally high (up to 79% under well-watered conditions and 85% under drought stress) and differentially regulated under drought. Aquaporin contribution to Sr increased in most varieties after drought, suggesting a crucial role for aquaporins in osmotic water fluxes during drought and recovery. Furthermore, root plasma membrane aquaporin (PIP) expression and root anatomical properties were correlated with hydraulic traits. Three chromosome regions highly correlated with hydraulic traits of the OryzaSNP panel were identified, but did not co-locate with known aquaporins. These results therefore highlight the importance of aquaporins in the rice root radial water pathway, but emphasize the complex range of additional mechanisms related to root water fluxes and drought response.
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Affiliation(s)
- Alexandre Grondin
- International Rice Research Institute, Crop Environmental Sciences Division, DAPO Box 7777, Metro Manila, Philippines
- University of Nebraska-Lincoln, Department of Agronomy and Horticulture, Lincoln, NE, 68583, USA
| | - Ramil Mauleon
- International Rice Research Institute, Crop Environmental Sciences Division, DAPO Box 7777, Metro Manila, Philippines
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502 324, Andhra Pradesh, India
| | - Amelia Henry
- International Rice Research Institute, Crop Environmental Sciences Division, DAPO Box 7777, Metro Manila, Philippines
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23
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Krishnamurthy P, Tan XF, Lim TK, Lim TM, Kumar PP, Loh CS, Lin Q. Proteomic analysis of plasma membrane and tonoplast from the leaves of mangrove plant Avicennia officinalis. Proteomics 2015; 14:2545-57. [PMID: 25236605 DOI: 10.1002/pmic.201300527] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 07/15/2014] [Accepted: 09/15/2014] [Indexed: 12/29/2022]
Abstract
In order to understand the salt tolerance and secretion in mangrove plant species, gel electrophoresis coupled with LC-MS-based proteomics was used to identify key transport proteins in the plasma membrane (PM) and tonoplast fractions of Avicennia officinalis leaves. PM and tonoplast proteins were purified using two-aqueous-phase partitioning and density gradient centrifugation, respectively. Forty of the 254 PM proteins and 31 of the 165 tonoplast proteins identified were predicted to have transmembrane domains. About 95% of the identified proteins could be classified based on their functions. The major classes of proteins were predicted to be involved in transport, metabolic processes, defense/stress response, and signal transduction, while a few of the proteins were predicted to be involved in other functions such as membrane trafficking. The main classes of transporter proteins identified included H(+) -ATPases, ATP-binding cassette transporters, and aquaporins, all of which could play a role in salt secretion. These data will serve as the baseline membrane proteomic dataset for Avicennia species. Further, this information can contribute to future studies on understanding the mechanism of salt tolerance in halophytes in addition to salt secretion in mangroves. All MS data have been deposited in the ProteomeXchange with identifier PXD000837 (http://proteomecentral.proteomexchange.org/dataset/PXD000837).
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Affiliation(s)
- Pannaga Krishnamurthy
- Department of Biological Sciences, National University of Singapore, Singapore; NUS Environmental Research Institute (NERI), National University of Singapore, Singapore
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Hedrich R, Sauer N, Neuhaus HE. Sugar transport across the plant vacuolar membrane: nature and regulation of carrier proteins. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:63-70. [PMID: 26000864 DOI: 10.1016/j.pbi.2015.04.008] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 04/16/2015] [Accepted: 04/30/2015] [Indexed: 05/06/2023]
Abstract
The ability of higher plants to store sugars is of crucial importance for plant development, adaption to endogenous or environmental cues and for the economic value of crop species. Sugar storage and accumulation, and its homeostasis in plant cells are managed by the vacuole. Although transport of sugars across the vacuolar membrane has been monitored for about four decades, the molecular entities of the transporters involved have been identified in the last 10 years only. Thus, it is just recently that our pictures of the transporters that channel the sugar load across the tonoplast have gained real shape. Here we describe the molecular nature and regulation of an important group of tonoplast sugar transporter (TST) allowing accumulation of sugars against large concentration gradients. In addition, we report on proton-driven tonoplast sugar exporters and on facilitators, which are also involved in balancing cytosolic and vacuolar sugar levels.
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Affiliation(s)
- Rainer Hedrich
- Molecular Plant Physiology and Biophysics, University of Würzburg, Germany
| | - Norbert Sauer
- Molecular Plant Physiology, University of Erlangen-Nuremberg, Germany
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25
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Wu F, Sheng P, Tan J, Chen X, Lu G, Ma W, Heng Y, Lin Q, Zhu S, Wang J, Wang J, Guo X, Zhang X, Lei C, Wan J. Plasma membrane receptor-like kinase leaf panicle 2 acts downstream of the DROUGHT AND SALT TOLERANCE transcription factor to regulate drought sensitivity in rice. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:271-81. [PMID: 25385766 PMCID: PMC4265162 DOI: 10.1093/jxb/eru417] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Drought is a recurring climatic hazard that reduces the crop yields. To avoid the negative effects of drought on crop production, extensive efforts have been devoted to investigating the complex mechanisms of gene expression and signal transduction during drought stress. Receptor-like kinases (RLKs) play important roles in perceiving extracellular stimuli and activating downstream signalling responses. The rice genome contains >1100 RLK genes, of which only two are reported to function in drought stress. A leucine-rich repeat (LRR)-RLK gene named Leaf Panicle 2 (LP2) was previously found to be strongly expressed in leaves and other photosynthetic tissues, but its function remains unclear. In the present study, it was shown that the expression of LP2 was down-regulated by drought and abscisic acid (ABA). Transgenic plants overexpressing LP2 accumulated less H₂O₂, had more open stomata in leaves, and showed hypersensitivity to drought stress. Further investigation revealed that transcription of LP2 was directly regulated by the zinc finger transcription factor DROUGHT AND SALT TOLERANCE (DST). In addition, LP2 was identified as a functional kinase localized to the plasma membrane and interacted with the drought-responsive aquaporin proteins OsPIP1; 1, OsPIP1; 3, and OsPIP2; 3. Thus, the findings provided evidence that the LRR-RLK LP2, transcriptionally regulated by the drought-related transcription factor DST, served as a negative regulator in drought response.
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Affiliation(s)
- Fuqing Wu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Peike Sheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Junjie Tan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiuling Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Guangwen Lu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Weiwei Ma
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Yueqin Heng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Qibing Lin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Jiulin Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Jie Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Jianmin Wan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, PR China
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Abstract
Cereals are the most important crop plant supplying staple food throughout the world. The economic importance and continued breeding of crop plants such as rice, maize, wheat, or barley require a detailed scientific understanding of adaptive and developmental processes. Protein phosphorylation is one of the most important regulatory posttranslational modifications and its analysis allows deriving functional and regulatory principles in plants. This minireview summarizes the current knowledge of phosphoproteomic studies in cereals.
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Affiliation(s)
- Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuchang Moshan, Wuhan, 430074, China,
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Verdoucq L, Rodrigues O, Martinière A, Luu DT, Maurel C. Plant aquaporins on the move: reversible phosphorylation, lateral motion and cycling. CURRENT OPINION IN PLANT BIOLOGY 2014; 22:101-107. [PMID: 25299641 DOI: 10.1016/j.pbi.2014.09.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/22/2014] [Accepted: 09/22/2014] [Indexed: 05/21/2023]
Abstract
Aquaporins are channel proteins present in the plasma membrane and most of intracellular compartments of plant cells. This review focuses on recent insights into the cellular function of plant aquaporins, with an emphasis on the subfamily of Plasma membrane Intrinsic Proteins (PIPs). Whereas PIPs mostly serve as water channels, novel functions associated with their ability to transport carbon dioxide and hydrogen peroxide are emerging. Phosphorylation of PIPs was found to play a central role in the mechanisms that determine their gating and subcellular dynamics. Dynamic tracking of single aquaporin molecules in native plant membranes and the search for cell signaling intermediates acting upstream of aquaporins are now used to dissect their cellular regulation by hormonal and environmental stimuli.
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Affiliation(s)
- Lionel Verdoucq
- Biochimie et Physiologie Moléculaire des Plantes, Unité Mixte de Recherche 5004, CNRS/INRA/Montpellier SupAgro/Université Montpellier II, F-34060 Montpellier, Cedex 2, France
| | - Olivier Rodrigues
- Biochimie et Physiologie Moléculaire des Plantes, Unité Mixte de Recherche 5004, CNRS/INRA/Montpellier SupAgro/Université Montpellier II, F-34060 Montpellier, Cedex 2, France
| | - Alexandre Martinière
- Biochimie et Physiologie Moléculaire des Plantes, Unité Mixte de Recherche 5004, CNRS/INRA/Montpellier SupAgro/Université Montpellier II, F-34060 Montpellier, Cedex 2, France
| | - Doan Trung Luu
- Biochimie et Physiologie Moléculaire des Plantes, Unité Mixte de Recherche 5004, CNRS/INRA/Montpellier SupAgro/Université Montpellier II, F-34060 Montpellier, Cedex 2, France
| | - Christophe Maurel
- Biochimie et Physiologie Moléculaire des Plantes, Unité Mixte de Recherche 5004, CNRS/INRA/Montpellier SupAgro/Université Montpellier II, F-34060 Montpellier, Cedex 2, France.
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28
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Neuhaus HE, Trentmann O. Regulation of transport processes across the tonoplast. FRONTIERS IN PLANT SCIENCE 2014; 5:460. [PMID: 25309559 PMCID: PMC4160088 DOI: 10.3389/fpls.2014.00460] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 08/26/2014] [Indexed: 05/24/2023]
Abstract
In plants, the vacuole builds up the cellular turgor and represents an important component in cellular responses to diverse stress stimuli. Rapid volume changes of cells, particularly of motor cells, like guard cells, are caused by variation of osmolytes and consequently of the water contents in the vacuole. Moreover, directed solute uptake into or release out of the large central vacuole allows adaptation of cytosolic metabolite levels according to the current physiological requirements and specific cellular demands. Therefore, solute passage across the vacuolar membrane, the tonoplast, has to be tightly regulated. Important principles in vacuolar transport regulation are changes of tonoplast transport protein abundances by differential expression of genes or changes of their activities, e.g., due to post-translational modification or by interacting proteins. Because vacuolar transport is in most cases driven by an electro-chemical gradient altered activities of tonoplast proton pumps significantly influence vacuolar transport capacities. Intense studies on individual tonoplast proteins but also unbiased system biological approaches have provided important insights into the regulation of vacuolar transport. This short review refers to selected examples of tonoplast proteins and their regulation, with special focus on protein phosphorylation.
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Affiliation(s)
| | - Oliver Trentmann
- *Correspondence: Oliver Trentmann, Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Postfach 3049, Kaiserslautern D-67653, Germany e-mail:
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29
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Ma Q, Wu M, Pei W, Li H, Li X, Zhang J, Yu J, Yu S. Quantitative phosphoproteomic profiling of fiber differentiation and initiation in a fiberless mutant of cotton. BMC Genomics 2014; 15:466. [PMID: 24923550 PMCID: PMC4070576 DOI: 10.1186/1471-2164-15-466] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 06/06/2014] [Indexed: 12/21/2022] Open
Abstract
Background The cotton (Gossypium spp.) fiber cell is an important unicellular model for studying cell differentiation. There is evidence suggesting that phosphorylation is a critical post-translational modification involved in regulation of a wide range of cell activities. Nevertheless, the sites of phosphorylation in G. hirsutum and their regulatory roles in fiber cell initiation are largely unknown. In this study, we employed a mass spectrometry-based phosphoproteomics to conduct a global and site-specific phosphoproteome profiling between ovules of a fuzzless-lintless (fl) Upland cotton (G. hirsutum) mutant and its isogenic parental wild type (WT) at -3 and 0 days post-anthesis (DPA). Results A total of 830 phosphopeptides and 1,592 phosphorylation sites from 619 phosphoproteins were identified by iTRAQ (isobaric tags for relative and absolute quantitation). Of these, 76 phosphoproteins and 1,100 phosphorylation sites were identified for the first time after searching the P3DB public database using the BLAST program. Among the detected phosphopeptides, 69 were differentially expressed between the fl mutant and its WT in ovules at -3 and 0 DPA. An analysis using the Motif-X program uncovered 19 phosphorylation motifs, 8 of which were unique to cotton. A further metabolic pathway analysis revealed that the differentially phosphorylated proteins were involved in signal transduction, protein modification, carbohydrate metabolic processes, and cell cycle and cell proliferation. Conclusions Our phosphoproteomics-based research provides the first global overview of phosphorylation during cotton fiber initiation, and also offers a helpful dataset for elucidation of signaling networks in fiber development of G. hirsutum. Electronic supplementary material The online version of this article (doi: 10.1186/1471-2164-15-466) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Jiwen Yu
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
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30
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Ahmad I, Maathuis FJM. Cellular and tissue distribution of potassium: physiological relevance, mechanisms and regulation. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:708-14. [PMID: 24810768 DOI: 10.1016/j.jplph.2013.10.016] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 10/27/2013] [Accepted: 10/28/2013] [Indexed: 05/25/2023]
Abstract
Potassium (K(+)) is the most important cationic nutrient for all living organisms. Its cellular levels are significant (typically around 100mM) and are highly regulated. In plants K(+) affects multiple aspects such as growth, tolerance to biotic and abiotic stress and movement of plant organs. These processes occur at the cell, organ and whole plant level and not surprisingly, plants have evolved sophisticated mechanisms for the uptake, efflux and distribution of K(+) both within cells and between organs. Great progress has been made in the last decades regarding the molecular mechanisms of K(+) uptake and efflux, particularly at the cellular level. For long distance K(+) transport our knowledge is less complete but the principles behind the overall processes are largely understood. In this chapter we will discuss how both long distance transport between different organs and intracellular transport between organelles works in general and in particular for K(+). Where possible, we will provide examples of specific genes and proteins that are responsible for these phenomena.
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Affiliation(s)
- Izhar Ahmad
- Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Frans J M Maathuis
- Department of Biology, University of York, York YO10 5DD, United Kingdom.
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31
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Nuclear phosphoproteome of developing chickpea seedlings (Cicer arietinum L.) and protein-kinase interaction network. J Proteomics 2014; 105:58-73. [PMID: 24747304 DOI: 10.1016/j.jprot.2014.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 03/31/2014] [Accepted: 04/02/2014] [Indexed: 11/21/2022]
Abstract
UNLABELLED Nucleus, the control centre of eukaryotic cell, houses most of the genetic machineries required for gene expression and their regulation. Post translational modifications of proteins, particularly phosphorylation control a wide variety of cellular processes but its functional connectivity, in plants, is still elusive. This study profiled the nuclear phosphoproteome of a grain legume, chickpea, to gain better understanding of such event. Intact nuclei were isolated from 3-week-old seedlings using two independent methods, and nuclear proteins were resolved by 2-DE. In a separate set of experiments, phosphoproteins were enriched using IMAC method and resolved by 1-DE. The separated proteins were stained with phosphospecific Pro-Q Diamond stain. Proteomic analyses led to the identification of 107 putative phosphoproteins, of which 86 were non-redundant. Multiple sites of phosphorylation were predicted on several key elements, which included both regulatory and functional proteins. The analysis revealed an array of phosphoproteins, presumably involved in a variety of cellular functions, viz., protein folding (24%), signalling and gene regulation (22%), DNA replication, repair and modification (16%), and metabolism (13%), among others. These results represent the first nucleus-specific phosphoproteome map of a non-model legume, which would provide insights into the possible function of protein phosphorylation in plants. BIOLOGICAL SIGNIFICANCE Chickpea is grown over 10 million hectares of land worldwide, and global production hovers around 8.5 million metric tons annually. Despite its nutritional merits, it is often referred to as 'orphan' legume and has remained outside the realm of large-scale functional genomics studies. While current chickpea genome initiative has primarily focused on sequence information and functional annotation, proteomics analyses are limited. It is thus important to study the proteome of the cell organelle particularly the nucleus, which harbors most of the genetic information and gene expression machinery. Phosphorylation-dependent modulation of gene expression plays a vital role but the complex networks of phosphorylation are poorly understood. This inventory of nuclear phosphoproteins would provide valuable insights into the dynamic regulation of cellular phenotype through phosphorylation. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Fan S, Meng Y, Song M, Pang C, Wei H, Liu J, Zhan X, Lan J, Feng C, Zhang S, Yu S. Quantitative phosphoproteomics analysis of nitric oxide-responsive phosphoproteins in cotton leaf. PLoS One 2014; 9:e94261. [PMID: 24714030 PMCID: PMC3979775 DOI: 10.1371/journal.pone.0094261] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 03/14/2014] [Indexed: 11/24/2022] Open
Abstract
Knowledge of phosphorylation events and their regulation is crucial to understanding the functional biology of plant proteins, but very little is currently known about nitric oxide-responsive phosphorylation in plants. Here, we report the first large-scale, quantitative phosphoproteome analysis of cotton (Gossypium hirsutum) treated with sodium nitroprusside (nitric oxide donor) by utilizing the isobaric tag for relative and absolute quantitation (iTRAQ) method. A total of 1315 unique phosphopeptides, spanning 1528 non-redundant phosphorylation sites, were detected from 1020 cotton phosphoproteins. Among them, 183 phosphopeptides corresponding to 167 phosphoproteins were found to be differentially phosphorylated in response to sodium nitroprusside. Several of the phosphorylation sites that we identified, including RQxS, DSxE, TxxxxSP and SPxT, have not, to our knowledge, been reported to be protein kinase sites in other species. The phosphoproteins identified are involved in a wide range of cellular processes, including signal transduction, RNA metabolism, intracellular transport and so on. This study reveals unique features of the cotton phosphoproteome and provides new insight into the biochemical pathways that are regulated by nitric oxide.
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Affiliation(s)
- Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan Province, China
| | - Yanyan Meng
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjing River, Institute of Economic Crop, Hubei Academy of Agricultural Science, Wuhan, Hubei Province, China
| | - Meizhen Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan Province, China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan Province, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan Province, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan Province, China
- College of Agronomy, Northwest A & F University, Yangling, Shaanxi Province, China
| | - Xianjin Zhan
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjing River, Institute of Economic Crop, Hubei Academy of Agricultural Science, Wuhan, Hubei Province, China
| | - Jiayang Lan
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjing River, Institute of Economic Crop, Hubei Academy of Agricultural Science, Wuhan, Hubei Province, China
| | - Changhui Feng
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjing River, Institute of Economic Crop, Hubei Academy of Agricultural Science, Wuhan, Hubei Province, China
| | - Shengxi Zhang
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjing River, Institute of Economic Crop, Hubei Academy of Agricultural Science, Wuhan, Hubei Province, China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan Province, China
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Zeng Y, Pan Z, Wang L, Ding Y, Xu Q, Xiao S, Deng X. Phosphoproteomic analysis of chromoplasts from sweet orange during fruit ripening. PHYSIOLOGIA PLANTARUM 2014; 150:252-70. [PMID: 23786612 DOI: 10.1111/ppl.12080] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/18/2013] [Accepted: 05/27/2013] [Indexed: 05/18/2023]
Abstract
Like other types of plastids, chromoplasts have essential biosynthetic and metabolic activities which may be regulated via post-translational modifications, such as phosphorylation, of their resident proteins. We here report a proteome-wide mapping of in vivo phosphorylation sites in chromoplast-enriched samples prepared from sweet orange [Citrus sinensis (L.) Osbeck] at different ripening stages by titanium dioxide-based affinity chromatography for phosphoprotein enrichment with LC-MS/MS. A total of 109 plastid-localized phosphoprotein candidates were identified that correspond to 179 unique phosphorylation sites in 135 phosphopeptides. On the basis of Motif-X analysis, two distinct types of phosphorylation sites, one as proline-directed phosphorylation motif and the other as casein kinase II motif, can be generalized from these identified phosphopeptides. While most identified phosphoproteins show high homology to those already identified in plastids, approximately 22% of them are novel based on BLAST search using the public databases PhosPhAt and P(3) DB. A close comparative analysis showed that approximately 50% of the phosphoproteins identified in citrus chromoplasts find obvious counterparts in the chloroplast phosphoproteome, suggesting a rather high-level of conservation in basic metabolic activities in these two types of plastids. Not surprisingly, the phosphoproteome of citrus chromoplasts is also characterized by the lack of phosphoproteins involved in photosynthesis and by the presence of more phosphoproteins implicated in stress/redox responses. This study presents the first comprehensive phosphoproteomic analysis of chromoplasts and may help to understand how phosphorylation regulates differentiation of citrus chromoplasts during fruit ripening.
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Affiliation(s)
- Yunliu Zeng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, PR China
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34
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Abstract
Class III peroxidases are heme-containing proteins of the secretory pathway with an extremely high number of isoenzymes, indicating the tremendous and important functions of this protein family. This chapter describes fractionation of the cell in subproteomes, their separation by polyacrylamide gel electrophoresis (PAGE) and visualization of peroxidase isoenzymes by heme and specific in-gel staining procedures. Soluble and membrane-bound peroxidases were separated by differential centrifugation. Aqueous polymer two-phase partitioning and discontinuous sucrose density gradient were applied to resolve peroxidase profiles of plasma membranes and tonoplast. Peroxidase isoenzymes of subproteomes were further separated by PAGE techniques such as native isoelectric focussing (IEF), high resolution clear native electrophoresis (hrCNE), and modified sodium dodecyl sulfate (modSDS)-PAGE. These techniques were used as stand-alone method or in combination for two-dimensional PAGE.
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Affiliation(s)
- Sabine Lüthje
- Biocentre Klein Flottbek, University of Hamburg, Hamburg, Germany
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35
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Reuscher S, Akiyama M, Mori C, Aoki K, Shibata D, Shiratake K. Genome-wide identification and expression analysis of aquaporins in tomato. PLoS One 2013; 8:e79052. [PMID: 24260152 PMCID: PMC3834038 DOI: 10.1371/journal.pone.0079052] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 09/20/2013] [Indexed: 11/30/2022] Open
Abstract
The family of aquaporins, also called water channels or major intrinsic proteins, is characterized by six transmembrane domains that together facilitate the transport of water and a variety of low molecular weight solutes. They are found in all domains of life, but show their highest diversity in plants. Numerous studies identified aquaporins as important targets for improving plant performance under drought stress. The phylogeny of aquaporins is well established based on model species like Arabidopsis thaliana, which can be used as a template to investigate aquaporins in other species. In this study we comprehensively identified aquaporin encoding genes in tomato (Solanum lycopersicum), which is an important vegetable crop and also serves as a model for fleshy fruit development. We found 47 aquaporin genes in the tomato genome and analyzed their structural features. Based on a phylogenetic analysis of the deduced amino acid sequences the aquaporin genes were assigned to five subfamilies (PIPs, TIPs, NIPs, SIPs and XIPs) and their substrate specificity was assessed on the basis of key amino acid residues. As ESTs were available for 32 genes, expression of these genes was analyzed in 13 different tissues and developmental stages of tomato. We detected tissue-specific and development-specific expression of tomato aquaporin genes, which is a first step towards revealing the contribution of aquaporins to water and solute transport in leaves and during fruit development.
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Affiliation(s)
- Stefan Reuscher
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan
| | - Masahito Akiyama
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan
| | - Chiharu Mori
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan
| | - Koh Aoki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Gakuen-cho, Sakai, Japan
| | - Daisuke Shibata
- Kazusa DNA Research Institute, Kazusa-kamatari, Kisarazu, Japan
| | - Katsuhiro Shiratake
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan
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Dadacz-Narloch B, Kimura S, Kurusu T, Farmer EE, Becker D, Kuchitsu K, Hedrich R. On the cellular site of two-pore channel TPC1 action in the Poaceae. THE NEW PHYTOLOGIST 2013; 200:663-674. [PMID: 23845012 DOI: 10.1111/nph.12402] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 06/02/2013] [Indexed: 06/02/2023]
Abstract
The slow vacuolar (SV) channel has been characterized in different dicots by patch-clamp recordings. This channel represents the major cation conductance of the largest organelle in most plant cells. Studies with the tpc1-2 mutant of the model dicot plant Arabidopsis thaliana identified the SV channel as the product of the TPC1 gene. By contrast, research on rice and wheat TPC1 suggested that the monocot gene encodes a plasma membrane calcium-permeable channel. To explore the site of action of grass TPC1 channels, we expressed OsTPC1 from rice (Oryza sativa) and TaTPC1 from wheat (Triticum aestivum) in the background of the Arabidopsis tpc1-2 mutant. Cross-species tpc1 complementation and patch-clamping of vacuoles using Arabidopsis and rice tpc1 null mutants documented that both monocot TPC1 genes were capable of rescuing the SV channel deficit. Vacuoles from wild-type rice but not the tpc1 loss-of-function mutant harbor SV channels exhibiting the hallmark properties of dicot TPC1/SV channels. When expressed in human embryonic kidney (HEK293) cells OsTPC1 was targeted to Lysotracker-Red-positive organelles. The finding that the rice TPC1, just like those from the model plant Arabidopsis and even animal cells, is localized and active in lyso-vacuolar membranes associates this cation channel species with endomembrane function.
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Affiliation(s)
- Beata Dadacz-Narloch
- Institute for Molecular Plant Physiology and Biophysics, University of Wuerzburg, D-97082, Wuerzburg, Germany
| | - Sachie Kimura
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, 278-8510, Japan
| | - Takamitsu Kurusu
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, 278-8510, Japan
- School of Bioscience and Biotechnology, Tokyo University of Technology, Hachioji, Tokyo, 192-0982, Japan
| | - Edward E Farmer
- Department of Plant Molecular Biology, University of Lausanne, Biophore, 1015, Lausanne, Switzerland
| | - Dirk Becker
- Institute for Molecular Plant Physiology and Biophysics, University of Wuerzburg, D-97082, Wuerzburg, Germany
| | - Kazuyuki Kuchitsu
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, 278-8510, Japan
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Wuerzburg, D-97082, Wuerzburg, Germany
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Bernfur K, Larsson O, Larsson C, Gustavsson N. Relative abundance of integral plasma membrane proteins in Arabidopsis leaf and root tissue determined by metabolic labeling and mass spectrometry. PLoS One 2013; 8:e71206. [PMID: 23990937 PMCID: PMC3747180 DOI: 10.1371/journal.pone.0071206] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 07/03/2013] [Indexed: 12/21/2022] Open
Abstract
Metabolic labeling of proteins with a stable isotope (15N) in intact Arabidopsis plants was used for accurate determination by mass spectrometry of differences in protein abundance between plasma membranes isolated from leaves and roots. In total, 703 proteins were identified, of which 188 were predicted to be integral membrane proteins. Major classes were transporters, receptors, proteins involved in membrane trafficking and cell wall-related proteins. Forty-one of the integral proteins, including nine of the 13 isoforms of the PIP (plasma membrane intrinsic protein) aquaporin subfamily, could be identified by peptides unique to these proteins, which made it possible to determine their relative abundance in leaf and root tissue. In addition, peptides shared between isoforms gave information on the proportions of these isoforms. A comparison between our data for protein levels and corresponding data for mRNA levels in the widely used database Genevestigator showed an agreement for only about two thirds of the proteins. By contrast, localization data available in the literature for 21 of the 41 proteins show a much better agreement with our data, in particular data based on immunostaining of proteins and GUS-staining of promoter activity. Thus, although mRNA levels may provide a useful approximation for protein levels, detection and quantification of isoform-specific peptides by proteomics should generate the most reliable data for the proteome.
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Affiliation(s)
- Katja Bernfur
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden
- * E-mail:
| | - Olaf Larsson
- Mutation Analysis Facility, Clinical Research Centre, Novum, Huddinge University Hospital, Stockholm, Sweden
| | - Christer Larsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden
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Keunen E, Peshev D, Vangronsveld J, Van Den Ende W, Cuypers A. Plant sugars are crucial players in the oxidative challenge during abiotic stress: extending the traditional concept. PLANT, CELL & ENVIRONMENT 2013; 36:1242-55. [PMID: 23305614 DOI: 10.1111/pce.12061] [Citation(s) in RCA: 355] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 12/20/2012] [Accepted: 12/26/2012] [Indexed: 05/18/2023]
Abstract
Plants suffering from abiotic stress are commonly facing an enhanced accumulation of reactive oxygen species (ROS) with damaging as well as signalling effects at organellar and cellular levels. The outcome of an environmental challenge highly depends on the delicate balance between ROS production and scavenging by both enzymatic and metabolic antioxidants. However, this traditional classification is in need of renewal and reform, as it is becoming increasingly clear that soluble sugars such as disaccharides, raffinose family oligosaccharides and fructans--next to their associated metabolic enzymes--are strongly related to stress-induced ROS accumulation in plants. Therefore, this review aims at extending the current concept of antioxidants functioning during abiotic stress, with special focus on the emanate role of sugars as true ROS scavengers. Examples are given based on their cellular location, as different organelles seem to exploit distinct mechanisms. Moreover, the vacuole comes into the picture as important player in the ROS signalling network of plants. Elucidating the interplay between the mechanisms controlling ROS signalling during abiotic stress will facilitate the development of strategies to enhance crop tolerance to stressful environmental conditions.
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Affiliation(s)
- Els Keunen
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, B-3590, Diepenbeek, Belgium
| | - Darin Peshev
- Laboratory of Molecular Plant Biology and Leuven Food Science and Nutrition Research Centre (LFoRCe), KULeuven, Kasteelpark Arenberg 31, B-3001, Leuven, Belgium
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, B-3590, Diepenbeek, Belgium
| | - Wim Van Den Ende
- Laboratory of Molecular Plant Biology and Leuven Food Science and Nutrition Research Centre (LFoRCe), KULeuven, Kasteelpark Arenberg 31, B-3001, Leuven, Belgium
| | - Ann Cuypers
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, B-3590, Diepenbeek, Belgium
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Itai RN, Ogo Y, Kobayashi T, Nakanishi H, Nishizawa NK. Rice genes involved in phytosiderophore biosynthesis are synchronously regulated during the early stages of iron deficiency in roots. RICE (NEW YORK, N.Y.) 2013; 6:16. [PMID: 24280375 PMCID: PMC4883707 DOI: 10.1186/1939-8433-6-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 06/14/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND The rice transcription factors IDEF1, IDEF2, and OsIRO2 have been identified as key regulators of the genes that control iron (Fe) uptake, including the biosynthesis of mugineic acid-family phytosiderophores (MAs). To clarify the onset of Fe deficiency, changes in gene expression were examined by microarray analysis using rice roots at 3, 6, 9, 12, 24, and 36 h after the onset of Fe-deficiency treatment. RESULTS More than 1000 genes were found to be upregulated over a time course of 36 h. Expression of MAs-biosynthetic genes, OsIRO2, and the Fe3+-MAs complex transporter OsYSL15 was upregulated at the 24 h and 36 h time points. Moreover, these genes showed very similar patterns of expression changes, but their expression patterns were completely different from those of a metallothionein gene (OsIDS1) and the Fe2+-transporter genes OsIRT1 and OsIRT2. OsIDS1 expression was upregulated by the 6 h time point. The early induction of OsIDS1 expression was distinct from the other Fe-deficiency-inducible genes investigated and suggested a functional relationship with heavy-metal homeostasis during the early stages of Fe deficiency. CONCLUSIONS We showed that many genes related to MAs biosynthesis and transports were regulated by a distinct mechanism in roots. Furthermore, differences in expression changes and timing in response to Fe deficiency implied that different combinations of gene regulation mechanisms control the initial responses to Fe deficiency.
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Affiliation(s)
- Reiko Nakanishi Itai
- />Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Yuko Ogo
- />Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Takanori Kobayashi
- />Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
- />Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921–8836 Japan
| | - Hiromi Nakanishi
- />Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Naoko K Nishizawa
- />Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
- />Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921–8836 Japan
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Prado K, Boursiac Y, Tournaire-Roux C, Monneuse JM, Postaire O, Da Ines O, Schäffner AR, Hem S, Santoni V, Maurel C. Regulation of Arabidopsis leaf hydraulics involves light-dependent phosphorylation of aquaporins in veins. THE PLANT CELL 2013; 25:1029-39. [PMID: 23532070 PMCID: PMC3634675 DOI: 10.1105/tpc.112.108456] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/11/2013] [Accepted: 03/04/2013] [Indexed: 05/18/2023]
Abstract
The water status of plant leaves depends on the efficiency of the water supply, from the vasculature to inner tissues. This process is under hormonal and environmental regulation and involves aquaporin water channels. In Arabidopsis thaliana, the rosette hydraulic conductivity (Kros) is higher in darkness than it is during the day. Knockout plants showed that three plasma membrane intrinsic proteins (PIPs) sharing expression in veins (PIP1;2, PIP2;1, and PIP2;6) contribute to rosette water transport, and PIP2;1 can fully account for Kros responsiveness to darkness. Directed expression of PIP2;1 in veins of a pip2;1 mutant was sufficient to restore Kros. In addition, a positive correlation, in both wild-type and PIP2;1-overexpressing plants, was found between Kros and the osmotic water permeability of protoplasts from the veins but not from the mesophyll. Thus, living cells in veins form a major hydraulic resistance in leaves. Quantitative proteomic analyses showed that light-dependent regulation of Kros is linked to diphosphorylation of PIP2;1 at Ser-280 and Ser-283. Expression in pip2;1 of phosphomimetic and phosphorylation-deficient forms of PIP2;1 demonstrated that phosphorylation at these two sites is necessary for Kros enhancement under darkness. These findings establish how regulation of a single aquaporin isoform in leaf veins critically determines leaf hydraulics.
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Affiliation(s)
- Karine Prado
- Biochimie et Physiologie Moléculaire des Plantes, Unité Mixte de Recherche 5004, Centre National de la Recherche Scientifique/Unité Mixte de Recherche 0386, Institut National de la Recherche Agronomique/Montpellier SupAgro/Université Montpellier II, F-34060 Montpellier, cedex 2, France
| | - Yann Boursiac
- Biochimie et Physiologie Moléculaire des Plantes, Unité Mixte de Recherche 5004, Centre National de la Recherche Scientifique/Unité Mixte de Recherche 0386, Institut National de la Recherche Agronomique/Montpellier SupAgro/Université Montpellier II, F-34060 Montpellier, cedex 2, France
| | - Colette Tournaire-Roux
- Biochimie et Physiologie Moléculaire des Plantes, Unité Mixte de Recherche 5004, Centre National de la Recherche Scientifique/Unité Mixte de Recherche 0386, Institut National de la Recherche Agronomique/Montpellier SupAgro/Université Montpellier II, F-34060 Montpellier, cedex 2, France
| | - Jean-Marc Monneuse
- Laboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique Unité de Recherche 1199, F-34060 Montpellier cedex 2, France
| | - Olivier Postaire
- Biochimie et Physiologie Moléculaire des Plantes, Unité Mixte de Recherche 5004, Centre National de la Recherche Scientifique/Unité Mixte de Recherche 0386, Institut National de la Recherche Agronomique/Montpellier SupAgro/Université Montpellier II, F-34060 Montpellier, cedex 2, France
| | - Olivier Da Ines
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Anton R. Schäffner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Sonia Hem
- Laboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique Unité de Recherche 1199, F-34060 Montpellier cedex 2, France
| | - Véronique Santoni
- Biochimie et Physiologie Moléculaire des Plantes, Unité Mixte de Recherche 5004, Centre National de la Recherche Scientifique/Unité Mixte de Recherche 0386, Institut National de la Recherche Agronomique/Montpellier SupAgro/Université Montpellier II, F-34060 Montpellier, cedex 2, France
| | - Christophe Maurel
- Biochimie et Physiologie Moléculaire des Plantes, Unité Mixte de Recherche 5004, Centre National de la Recherche Scientifique/Unité Mixte de Recherche 0386, Institut National de la Recherche Agronomique/Montpellier SupAgro/Université Montpellier II, F-34060 Montpellier, cedex 2, France
- Address correspondence to
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Peshev D, Vergauwen R, Moglia A, Hideg É, Van den Ende W. Towards understanding vacuolar antioxidant mechanisms: a role for fructans? JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:1025-38. [PMID: 23349141 PMCID: PMC3580814 DOI: 10.1093/jxb/ers377] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Recent in vitro, in vivo, and theoretical experiments strongly suggest that sugar-(like) molecules counteract oxidative stress by acting as genuine reactive oxygen species (ROS) scavengers. A concept was proposed to include the vacuole as a part of the cellular antioxidant network. According to this view, sugars and sugar-like vacuolar compounds work in concert with vacuolar phenolic compounds and the 'classic' cytosolic antioxidant mechanisms. Among the biologically relevant ROS (H(2)O(2), O(2)·(-), and ·OH), hydroxyl radicals are the most reactive and dangerous species since there are no enzymatic systems known to neutralize them in any living beings. Therefore, it is important to study in more detail the radical reactions between ·OH and different biomolecules, including sugars. Here, Fenton reactions were used to compare the ·OH-scavenging capacities of a range of natural vacuolar compounds to establish relationships between antioxidant capacity and chemical structure and to unravel the mechanisms of ·OH-carbohydrate reactions. The in vitro work on the ·OH-scavenging capacity of sugars and phenolic compounds revealed a correlation between structure and ·OH-scavenging capacity. The number and position of the C=C type of linkages in phenolic compounds greatly influence antioxidant properties. Importantly, the splitting of disaccharides and oligosaccharides emerged as a predominant outcome of the ·OH-carbohydrate interaction. Moreover, non-enzymatic synthesis of new fructan oligosaccharides was found starting from 1-kestotriose. Based on these and previous findings, a working model is proposed describing the putative radical reactions involving fructans and secondary metabolites at the inner side of the tonoplast and in the vacuolar lumen.
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Affiliation(s)
- Darin Peshev
- KU Leuven, Laboratory of Molecular Plant Biology, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Rudy Vergauwen
- KU Leuven, Laboratory of Molecular Plant Biology, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Andrea Moglia
- University of Turin, DISAFA-Plant Genetics and Breeding, Via Leonardo da Vinci, 44, 10095 Grugliasco (TO), Italy
| | - Éva Hideg
- University of Pécs, Faculty of Science, Institute of Biology, Ifjusag u. 6. H-7624 Pecs, Hungary
| | - Wim Van den Ende
- KU Leuven, Laboratory of Molecular Plant Biology, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
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Shitan N, Yazaki K. New insights into the transport mechanisms in plant vacuoles. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 305:383-433. [PMID: 23890387 DOI: 10.1016/b978-0-12-407695-2.00009-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The vacuole is the largest compartment in plant cells, often occupying more than 80% of the total cell volume. This organelle accumulates a large variety of endogenous ions, metabolites, and xenobiotics. The compartmentation of divergent substances is relevant for a wide range of biological processes, such as the regulation of stomata movement, defense mechanisms against herbivores, flower coloration, etc. Progress in molecular and cellular biology has revealed that a large number of transporters and channels exist at the tonoplast. In recent years, various biochemical and physiological functions of these proteins have been characterized in detail. Some are involved in maintaining the homeostasis of ions and metabolites, whereas others are related to defense mechanisms against biotic and abiotic stresses. In this review, we provide an updated inventory of vacuolar transport mechanisms and a comprehensive summary of their physiological functions.
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Affiliation(s)
- Nobukazu Shitan
- Laboratory of Natural Medicinal Chemistry, Kobe Pharmaceutical University, Kobe, Japan.
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43
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Irving HR, Gehring C. Molecular methods for the study of signal transduction in plants. Methods Mol Biol 2013; 1016:1-11. [PMID: 23681568 DOI: 10.1007/978-1-62703-441-8_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Novel and improved analytical methods have led to a rapid increase in our understanding of the molecular mechanism underlying plant signal transduction. Progress has been made both at the level of single-component analysis and in vivo imaging as well as at the systems level where transcriptomics and particularly phosphoproteomics afford a window into complex biological responses. Here we review the role of the cyclic nucleotides cAMP and cGMP in plant signal transduction as well as the discovery and biochemical and biological characterization of an increasing number of complex multi-domain nucleotide cyclases that catalyze the synthesis of cAMP and cGMP from ATP and GTP, respectively.
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Affiliation(s)
- Helen R Irving
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
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Trentmann O, Haferkamp I. Current progress in tonoplast proteomics reveals insights into the function of the large central vacuole. FRONTIERS IN PLANT SCIENCE 2013; 4:34. [PMID: 23459586 PMCID: PMC3584717 DOI: 10.3389/fpls.2013.00034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Accepted: 02/11/2013] [Indexed: 05/20/2023]
Abstract
Vacuoles of plants fulfill various biologically important functions, like turgor generation and maintenance, detoxification, solute sequestration, or protein storage. Different types of plant vacuoles (lytic versus protein storage) are characterized by different functional properties apparently caused by a different composition/abundance and regulation of transport proteins in the surrounding membrane, the tonoplast. Proteome analyses allow the identification of vacuolar proteins and provide an informative basis for assigning observed transport processes to specific carriers or channels. This review summarizes techniques required for vacuolar proteome analyses, like e.g., isolation of the large central vacuole or tonoplast membrane purification. Moreover, an overview about diverse published vacuolar proteome studies is provided. It becomes evident that qualitative proteomes from different plant species represent just the tip of the iceberg. During the past few years, mass spectrometry achieved immense improvement concerning its accuracy, sensitivity, and application. As a consequence, modern tonoplast proteome approaches are suited for detecting alterations in membrane protein abundance in response to changing environmental/physiological conditions and help to clarify the regulation of tonoplast transport processes.
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Affiliation(s)
- Oliver Trentmann
- Pflanzenphysiologie, Technische Universität KaiserslauternKaiserslautern, Germany
- *Correspondence: Oliver Trentmann, Pflanzenphysiologie, Technische Universität Kaiserslautern, Postfach 3049, D-67653 Kaiserslautern, Germany. e-mail:
| | - Ilka Haferkamp
- Pflanzenphysiologie, Technische Universität KaiserslauternKaiserslautern, Germany
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45
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Kusakina J, Dodd AN. Phosphorylation in the plant circadian system. TRENDS IN PLANT SCIENCE 2012; 17:575-83. [PMID: 22784827 DOI: 10.1016/j.tplants.2012.06.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 06/13/2012] [Accepted: 06/14/2012] [Indexed: 05/17/2023]
Abstract
Circadian regulation is essential for optimum plant performance. In addition to loops and cascades of transcription and translation, the plant circadian clock and its associated signal transduction networks incorporate many post-translational mechanisms. Phosphorylation is a common feature of signal transduction and gene regulation. In this opinion article, we illustrate how phosphorylation events are positioned within the entrainment, functioning, and regulation of the circadian timing system. Phosphorylation regulates protein stability, protein-protein interactions and protein-DNA interactions within the core oscillator. We suggest that phosphorylation provides a potential mechanism for the distribution of circadian timing information within the cell and for the integration of circadian timing information with other signaling pathways.
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Affiliation(s)
- Jelena Kusakina
- Department of Biology, University of York, York YO10 5DD, UK
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46
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Bassil E, Coku A, Blumwald E. Cellular ion homeostasis: emerging roles of intracellular NHX Na+/H+ antiporters in plant growth and development. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:5727-40. [PMID: 22991159 DOI: 10.1093/jxb/ers250] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Recent evidence highlights novel roles for intracellular Na(+)/H(+) antiporters (NHXs) in plants. The availability of knockouts and overexpressors of specific NHX isoforms has provided compelling genetic evidence to support earlier physiological and biochemical data which suggested the involvement of NHX antiporters in ion and pH regulation. Most plants sequenced to date contain multiple NHX members and, based on their sequence identity and localization, can be grouped into three distinct functional classes: plasma membrane, vacuolar, and endosomal associated. Orthologues of each functional class are represented in all sequenced plant genomes, suggesting conserved and fundamental roles across taxa. In this review we seek to highlight recent findings which demonstrate that intracellular NHX antiporters (i.e. vacuolar and endosomal isoforms) play roles in growth and development, including cell expansion, cell volume regulation, ion homeostasis, osmotic adjustment, pH regulation, vesicular trafficking, protein processing, cellular stress responses, as well as flowering. A significant new discovery demonstrated that in addition to the better known vacuolar NHX isoforms, plants also contain endosomal NHX isoforms that regulate protein processing and trafficking of cellular cargo. We draw parallels from close orthologues in yeast and mammals and discuss distinctive NHX functions in plants.
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Affiliation(s)
- Elias Bassil
- Department of Plant Sciences, University of California, One Shields Ave, Davis, CA 95616, USA
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Chang IF, Hsu JL, Hsu PH, Sheng WA, Lai SJ, Lee C, Chen CW, Hsu JC, Wang SY, Wang LY, Chen CC. Comparative phosphoproteomic analysis of microsomal fractions of Arabidopsis thaliana and Oryza sativa subjected to high salinity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 185-186:131-42. [PMID: 22325874 DOI: 10.1016/j.plantsci.2011.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Revised: 09/26/2011] [Accepted: 09/28/2011] [Indexed: 05/20/2023]
Abstract
Plants respond to salt stress by initiating phosphorylation cascades in their cells. Many key phosphorylation events take place at membranes. Microsomal fractions from 400 mM salt-treated Arabidopsis suspension plants were isolated, followed by trypsin shaving, enrichment using Zirconium ion-charged or TiO(2) magnetic beads, and tandem mass spectrometry analyses for site mapping. A total of 27 phosphorylation sites from 20 Arabidopsis proteins including photosystem II reaction center protein H PsbH were identified. In addition to Arabidopsis, microsomal fractions from shoots of 200 mM salt-treated rice was carried out, followed by trypsin digestion using shaving or tube-gel, and enrichment using Zirconium ion-charged or TiO(2) magnetic beads. This yielded identification of 13 phosphorylation sites from 8 proteins including photosystem II reaction center protein H PsbH. Label-free quantitative analysis suggests that the phosphorylation sites of PsbH were regulated by salt stress in Arabidopsis and rice. Sequence alignment of PsbH phosphorylation sites indicates that Thr-2 and Thr-4 are evolutionarily conserved in plants. Four conserved phosphorylation motifs were predicted, and these suggest that a specific unknown kinase or phosphatase is involved in high-salt stress responses in plants.
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Affiliation(s)
- Ing-Feng Chang
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan.
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Schulze WX, Schneider T, Starck S, Martinoia E, Trentmann O. Cold acclimation induces changes in Arabidopsis tonoplast protein abundance and activity and alters phosphorylation of tonoplast monosaccharide transporters. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:529-41. [PMID: 21988472 DOI: 10.1111/j.1365-313x.2011.04812.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Because they are immotile organisms, higher plants have developed efficient strategies for adaptation to temperature changes. During cold acclimation, plants accumulate specific types of solutes to enhance freezing tolerance. The vacuole is a major solute storage organelle, but until now the role of tonoplast proteins in cold acclimation has not been investigated. In a comparative tonoplast proteome analysis, we identified several membrane proteins with altered abundance upon cold acclimation. We found an increased protein abundance of the tonoplast pyrophosphatase and subunits of the vacuolar V-ATPase and a significantly increased V-ATPase activity. This was accompanied by increased vacuolar concentrations of dicarbonic acids and soluble sugars. Consistently, the abundance of the tonoplast dicarbonic acid transporter was also higher in cold-acclimatized plants. However, no change in the protein abundance of tonoplast monosaccharide transporters was detectable. However, a generally higher cold-induced phosphorylation of members of this sugar transporter sub-group was observed. Our results indicate that cold-induced solute accumulation in the vacuole is mediated by increased acidification of this organelle. Thus solute transport activity is either modulated by increased protein amounts or by modification of proteins via phosphorylation.
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Affiliation(s)
- Waltraud X Schulze
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Golm, Germany
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Liu CC, Liu CF, Wang HX, Shen ZY, Yang CP, Wei ZG. Identification and analysis of phosphorylation status of proteins in dormant terminal buds of poplar. BMC PLANT BIOLOGY 2011; 11:158. [PMID: 22074553 PMCID: PMC3234192 DOI: 10.1186/1471-2229-11-158] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 11/11/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND Although there has been considerable progress made towards understanding the molecular mechanisms of bud dormancy, the roles of protein phosphorylation in the process of dormancy regulation in woody plants remain unclear. RESULTS We used mass spectrometry combined with TiO₂ phosphopeptide-enrichment strategies to investigate the phosphoproteome of dormant terminal buds (DTBs) in poplar (Populus simonii × P. nigra). There were 161 unique phosphorylated sites in 161 phosphopeptides from 151 proteins; 141 proteins have orthologs in Arabidopsis, and 10 proteins are unique to poplar. Only 34 sites in proteins in poplar did not match well with the equivalent phosphorylation sites of their orthologs in Arabidopsis, indicating that regulatory mechanisms are well conserved between poplar and Arabidopsis. Further functional classifications showed that most of these phosphoproteins were involved in binding and catalytic activity. Extraction of the phosphorylation motif using Motif-X indicated that proline-directed kinases are a major kinase group involved in protein phosphorylation in dormant poplar tissues. CONCLUSIONS This study provides evidence about the significance of protein phosphorylation during dormancy, and will be useful for similar studies on other woody plants.
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Affiliation(s)
- Chang-Cai Liu
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), 26 Hexing Road, Harbin 150040, China
- Laboratory for Chemical Defence and Microscale Analysis, P.O. Box 3, Zhijiang 443200, China
| | - Chang-Fu Liu
- Shenyang Agricultural University, Dongling Road 120, Shenyang, Liaoning 110866, China
| | - Hong-Xia Wang
- Institute of Basic Medical Sciences, National Center for Biomedical Analysis, 27 Taiping Road, Beijing 100850, China
| | - Zhi-Ying Shen
- Daqing Branch, Harbin Medical University, Daqing 163319, China
| | - Chuan-Ping Yang
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), 26 Hexing Road, Harbin 150040, China
| | - Zhi-Gang Wei
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), 26 Hexing Road, Harbin 150040, China
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50
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Agrawal GK, Bourguignon J, Rolland N, Ephritikhine G, Ferro M, Jaquinod M, Alexiou KG, Chardot T, Chakraborty N, Jolivet P, Doonan JH, Rakwal R. Plant organelle proteomics: collaborating for optimal cell function. MASS SPECTROMETRY REVIEWS 2011; 30:772-853. [PMID: 21038434 DOI: 10.1002/mas.20301] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 02/02/2010] [Accepted: 02/02/2010] [Indexed: 05/10/2023]
Abstract
Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), P.O. Box 13265, Sanepa, Kathmandu, Nepal.
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