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Li M, Cao L, Mwimba M, Zhou Y, Li L, Zhou M, Schnable PS, O'Rourke JA, Dong X, Wang W. Comprehensive mapping of abiotic stress inputs into the soybean circadian clock. Proc Natl Acad Sci U S A 2019; 116:23840-23849. [PMID: 31676549 PMCID: PMC6876155 DOI: 10.1073/pnas.1708508116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The plant circadian clock evolved to increase fitness by synchronizing physiological processes with environmental oscillations. Crop fitness was artificially selected through domestication and breeding, and the circadian clock was identified by both natural and artificial selections as a key to improved fitness. Despite progress in Arabidopsis, our understanding of the crop circadian clock is still limited, impeding its rational improvement for enhanced fitness. To unveil the interactions between the crop circadian clock and various environmental cues, we comprehensively mapped abiotic stress inputs to the soybean circadian clock using a 2-module discovery pipeline. Using the "molecular timetable" method, we computationally surveyed publicly available abiotic stress-related soybean transcriptomes to identify stresses that have strong impacts on the global rhythm. These findings were then experimentally confirmed using a multiplexed RNA sequencing technology. Specific clock components modulated by each stress were further identified. This comprehensive mapping uncovered inputs to the plant circadian clock such as alkaline stress. Moreover, short-term iron deficiency targeted different clock components in soybean and Arabidopsis and thus had opposite effects on the clocks of these 2 species. Comparing soybean varieties with different iron uptake efficiencies suggests that phase modulation might be a mechanism to alleviate iron deficiency symptoms in soybean. These unique responses in soybean demonstrate the need to directly study crop circadian clocks. Our discovery pipeline may serve as a broadly applicable tool to facilitate these explorations.
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Affiliation(s)
- Meina Li
- School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011
| | - Lijun Cao
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011
| | - Musoki Mwimba
- Howard Hughes Medical Institute and Gordon and Betty Moore Foundation, Duke University, Durham, NC 27708
- Department of Biology, Duke University, Durham, NC 27708
| | - Yan Zhou
- Department of Agronomy, Iowa State University, Ames, IA 50011
| | - Ling Li
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39762
| | - Mian Zhou
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011
- College of Life Sciences, Capital Normal University, 100048 Beijing, China
| | | | - Jamie A O'Rourke
- Department of Agronomy, Iowa State University, Ames, IA 50011
- Corn Insects and Crop Genetics Research Unit, Agricultural Research Service, US Department of Agriculture, Ames, IA 50011
| | - Xinnian Dong
- Howard Hughes Medical Institute and Gordon and Betty Moore Foundation, Duke University, Durham, NC 27708;
- Department of Biology, Duke University, Durham, NC 27708
| | - Wei Wang
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011;
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871 Beijing, China
- Peking-Tsinghua Center for Life Sciences, 100871 Beijing, China
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Sade H, Meriga B, Surapu V, Gadi J, Sunita MSL, Suravajhala P, Kavi Kishor PB. Toxicity and tolerance of aluminum in plants: tailoring plants to suit to acid soils. Biometals 2016; 29:187-210. [DOI: 10.1007/s10534-016-9910-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 01/14/2016] [Indexed: 10/22/2022]
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Chen Q, Kan Q, Wang P, Yu W, Yu Y, Zhao Y, Yu Y, Li K, Chen L. Phosphorylation and Interaction with the 14-3-3 Protein of the Plasma Membrane H+-ATPase are Involved in the Regulation of Magnesium-Mediated Increases in Aluminum-Induced Citrate Exudation in Broad Bean (Vicia faba. L). PLANT & CELL PHYSIOLOGY 2015; 56:1144-53. [PMID: 25745032 DOI: 10.1093/pcp/pcv038] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 02/25/2015] [Indexed: 05/18/2023]
Abstract
Several studies have shown that external application of micromolar magnesium (Mg) can increase the resistance of legumes to aluminum (Al) stress by enhancing Al-induced citrate exudation. However, the exact mechanism underlying this regulation remains unknown. In this study, the physiological and molecular mechanisms by which Mg enhances Al-induced citrate exudation to alleviate Al toxicity were investigated in broad bean. Micromolar concentrations of Mg that alleviated Al toxicity paralleled the stimulation of Al-induced citrate exudation and increased the activity of the plasma membrane (PM) H(+)-ATPase. Northern blot analysis shows that a putative MATE-like gene (multidrug and toxic compound extrusion) was induced after treatment with Al for 4, 8 and 12 h, whereas the mRNA abundance of the MATE-like gene showed no significant difference between Al plus Mg and Al-only treatments during the entire treatment period. Real-time reverse transcription-PCR (RT-PCR) and Western blot analyses suggest that the transcription and translation of the PM H(+)-ATPase were induced by Al but not by Mg. In contrast, immunoprecipitation suggests that Mg enhanced the phosphorylation levels of VHA2 and its interaction with the vf14-3-3b protein under Al stress. Taken together, our results suggest that micromolar concentrations of Mg can alleviate the Al rhizotoxicity by increasing PM H(+)-ATPase activity and Al-induced citrate exudation in YD roots. This enhancement is likely to be attributable to Al-induced increases in the expression of the MATE-like gene and vha2 and Mg-induced changes in the phosphorylation levels of VHA2, thus changing its interaction with the vf14-3-3b protein.
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Affiliation(s)
- Qi Chen
- Biotechnology Research Centre, Faculty of Life Science and Biotechnology, Chenggong Campus, Kunming University of Science and Technology, Kunming, 650500, China
| | - Qi Kan
- Biotechnology Research Centre, Faculty of Life Science and Biotechnology, Chenggong Campus, Kunming University of Science and Technology, Kunming, 650500, China
| | - Ping Wang
- Biotechnology Research Centre, Faculty of Life Science and Biotechnology, Chenggong Campus, Kunming University of Science and Technology, Kunming, 650500, China
| | - Wenqian Yu
- Biotechnology Research Centre, Faculty of Life Science and Biotechnology, Chenggong Campus, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yuzhen Yu
- Biotechnology Research Centre, Faculty of Life Science and Biotechnology, Chenggong Campus, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yan Zhao
- Biotechnology Research Centre, Faculty of Life Science and Biotechnology, Chenggong Campus, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yongxiong Yu
- College of Zoological Science and Technology, Southwest University, Chongqing, 400715, China
| | - Kunzhi Li
- Biotechnology Research Centre, Faculty of Life Science and Biotechnology, Chenggong Campus, Kunming University of Science and Technology, Kunming, 650500, China
| | - Limei Chen
- Biotechnology Research Centre, Faculty of Life Science and Biotechnology, Chenggong Campus, Kunming University of Science and Technology, Kunming, 650500, China
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Wang ZQ, Xu XY, Gong QQ, Xie C, Fan W, Yang JL, Lin QS, Zheng SJ. Root proteome of rice studied by iTRAQ provides integrated insight into aluminum stress tolerance mechanisms in plants. J Proteomics 2014; 98:189-205. [PMID: 24412201 DOI: 10.1016/j.jprot.2013.12.023] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 12/13/2013] [Accepted: 12/27/2013] [Indexed: 01/06/2023]
Abstract
One of the major limitations to crop growth on acid soils is the prevalence of soluble aluminum ions (Al(3+)). Rice (Oryza sativa L.) has been reported to be highly Al tolerant; however, large-scale proteomic data of rice in response to Al(3+) are still very scanty. Here, we used an iTRAQ-based quantitative proteomics approach for comparative analysis of the expression profiles of proteins in rice roots in response to Al(3+) at an early phase. A total of 700 distinct proteins (homologous proteins grouped together) with >95% confidence were identified. Among them, 106 proteins were differentially expressed upon Al(3+) toxicity in sensitive and tolerant cultivars. Bioinformatics analysis indicated that glycolysis/gluconeogenesis was the most significantly up-regulated biochemical process in response to excess Al(3+). The mRNA levels of eight proteins mapped in the glycolysis/gluconeogenesis were further analyzed by qPCR and the expression levels of all the eight genes were higher in tolerant cultivar than in sensitive cultivar, suggesting that these compounds may promote Al tolerance by modulating the production of available energy. Although the exact roles of these putative tolerance proteins remain to be examined, our data lead to a better understanding of the Al tolerance mechanisms in rice plants through the proteomics approach. BIOLOGICAL SIGNIFICANCE Aluminum (mainly Al(3+)) is one of the major limitations to the agricultural productivity on acid soils and causes heavy yield loss every year. Rice has been reported to be highly Al tolerant; however, the mechanisms of rice Al tolerance are still not fully understood. Here, a combined proteomics, bioinformatics and qPCR analysis revealed that Al(3+) invasion caused complex proteomic changes in rice roots involving energy, stress and defense, protein turnover, metabolism, signal transduction, transport and intracellular traffic, cell structure, cell growth/division, and transcription. Promotion of the glycolytic/gluconeogenetic pathway in roots appeared crucially important for Al tolerance. These results lead to a better understanding of the Al tolerance mechanisms in rice and help to improve plant performance on acid soils, eventually to increase the crop production.
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Affiliation(s)
- Zhan Qi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Xiao Yan Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Qiao Qiao Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Chen Xie
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100101, China.
| | - Wei Fan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jian Li Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Qi Shan Lin
- UAlbany Proteomics Facility, Center for Functional Genomics, University at Albany, Rensselaer, NY 12144, USA.
| | - Shao Jian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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Victoria FDC, Bervald CMP, da Maia LC, de Sousa RO, Panaud O, de Oliveira AC. Phylogenetic relationships and selective pressure on gene families related to iron homeostasis in land plants. Genome 2012; 55:883-900. [PMID: 23231606 DOI: 10.1139/gen-2012-0064] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Iron is involved in many metabolic processes, such as respiration and photosynthesis, and therefore an essential element for plant development. Comparative analysis of gene copies between crops and lower plant groups can shed light on the evolution of genes important to iron homeostasis. A phylogenetic analysis of five metal homeostasis gene families (NAS, NRAMP, YSL, FRO, and IRT) selected in monocots, dicots, gymnosperms, and bryophytes was performed. The homologous genes were found using known iron homeostasis gene sequences of Oryza sativa, Arabidopsis thaliana, and Physcomitrella patens as queries. The phylogeny was constructed using bioinfomatics tools. A total of 243 gene sequences for 30 plant species were found. The evolutionary fingerprint analysis suggested a purifying selective pressure of iron homeostasis genes for most of the plant gene homologues. The NAS and YSL genes appear to accumulate more negative selection sites, suggesting a strong selective pressure on these two gene families. The divergence time analysis indicates IRT as the most ancient gene family and FRO as the most recent. NRAMP and YSL genes appear to share a close relationship in the evolution of iron homeostasis gene families.
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Chen ZC, Yamaji N, Motoyama R, Nagamura Y, Ma JF. Up-regulation of a magnesium transporter gene OsMGT1 is required for conferring aluminum tolerance in rice. PLANT PHYSIOLOGY 2012; 159:1624-33. [PMID: 22732245 PMCID: PMC3425201 DOI: 10.1104/pp.112.199778] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Magnesium (Mg)-mediated alleviation of aluminum (Al) toxicity has been observed in a number of plant species, but the mechanisms underlying the alleviation are still poorly understood. When a putative rice (Oryza sativa) Mg transporter gene, Oryza sativa MAGNESIUM TRANSPORTER1 (OsMGT1), was knocked out, the tolerance to Al, but not to cadmium and lanthanum, was decreased. However, this inhibition could be rescued by addition of 10 μm Mg, but not by the same concentration of barium or strontium. OsMGT1 was expressed in both the roots and shoots in the absence of Al, but the expression only in the roots was rapidly up-regulated by Al. Furthermore, the expression did not respond to low pH and other metals including cadmium and lanthanum, and was regulated by an Al-responsive transcription factor, AL RESISTANCE TRANSCRIPTION FACTOR1. An investigation of subcellular localization showed that OsMGT1 was localized to the plasma membrane. A short-term (30 min) uptake experiment with stable isotope (25)Mg showed that knockout of OsMGT1 resulted in decreased Mg uptake, but that the uptake in the wild type was enhanced by Al. Mg concentration in the cell sap of the root tips was also increased in the wild-type rice, but not in the knockout lines in the presence of Al. A microarray analysis showed that transcripts of genes related to stress were more up- and down-regulated in the knockout lines. Taken together, our results indicate that OsMGT1 is a transporter for Mg uptake in the roots and that up-regulation of this gene is required for conferring Al tolerance in rice by increasing Mg concentration in the cell.
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You J, Zhang H, Liu N, Gao L, Kong L, Yang Z. Transcriptomic responses to aluminum stress in soybean roots. Genome 2011; 54:923-33. [PMID: 22040275 DOI: 10.1139/g11-060] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aluminum (Al) toxicity is the primary limitation to crop production and plant growth in acid soils. Soybean has multiple mechanisms of Al resistance including the complexing and exclusion of Al in root apices by Al-induced citrate secretion. Microarray analysis is available for the identification of genes in soybean. In the present study, Affymetrix soybean genome array was used to identify the Al-induced differentially expressed genes in Al-resistant genotype Jiyu 70. With a cutoff of > 2.0-fold (p < 0.05) between non Al-treated and Al-treated root apices, 561 genes were upregulated and 78 genes were downregulated when roots were exposed to 30 μmol/L AlCl(3) for 4 h. Quantitative real-time PCR was used to test the microarray data. The analysis showed that nearly half of the Al-responsive genes were of unknown biological function. A higher proportion of genes related to transcription regulation and cell wall processes were observed in Al-induced up- and downregulated genes, respectively. Some genes homologous to the citrate transporter MATE family gene or C(2)H(2) family transcription factor gene, STOP1, were detected in our analysis. Some genes related to lignin deposition were upregulated, which might be related to Al-induced root elongation inhibition.
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Affiliation(s)
- Jiangfeng You
- Agriculture Ecology and Environment laboratory, College of Plant Science, Jilin University, Changchun 130062, PR China
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Percy ME, Kruck TPA, Pogue AI, Lukiw WJ. Towards the prevention of potential aluminum toxic effects and an effective treatment for Alzheimer's disease. J Inorg Biochem 2011; 105:1505-12. [PMID: 22099160 PMCID: PMC3714848 DOI: 10.1016/j.jinorgbio.2011.08.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Revised: 07/31/2011] [Accepted: 08/01/2011] [Indexed: 01/19/2023]
Abstract
In 1991, treatment with low dose intramuscular desferrioxamine (DFO), a trivalent chelator that can remove excessive iron and/or aluminum from the body, was reported to slow the progression of Alzheimer's disease (AD) by a factor of two. Twenty years later this promising trial has not been followed up and why this treatment worked still is not clear. In this critical interdisciplinary review, we provide an overview of the complexities of AD and involvement of metal ions, and revisit the neglected DFO trial. We discuss research done by us and others that is helping to explain involvement of metal ion catalyzed production of reactive oxygen species in the pathogenesis of AD, and emerging strategies for inhibition of metal-ion toxicity. Highlighted are insights to be considered in the quests to prevent potentially toxic effects of aluminum toxicity and prevention and intervention in AD.
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Affiliation(s)
- Maire E Percy
- Neurogenetics Laboratory, Surrey Place Centre, Toronto, ON, Canada M5S 2C2.
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Bose J, Babourina O, Rengel Z. Role of magnesium in alleviation of aluminium toxicity in plants. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:2251-64. [PMID: 21273333 DOI: 10.1093/jxb/erq456] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Magnesium is pivotal for activating a large number of enzymes; hence, magnesium plays an important role in numerous physiological and biochemical processes affecting plant growth and development. Magnesium can also ameliorate aluminium phytotoxicity, but literature reports on the dynamics of magnesium homeostasis upon exposure to aluminium are rare. Herein existing knowledge on the magnesium transport mechanisms and homeostasis maintenance in plant cells is critically reviewed. Even though overexpression of magnesium transporters can alleviate aluminium toxicity in plants, the mechanisms governing such alleviation remain obscure. Possible magnesium-dependent mechanisms include (i) better carbon partitioning from shoots to roots; (ii) increased synthesis and exudation of organic acid anions; (iii) enhanced acid phosphatase activity; (iv) maintenance of proton-ATPase activity and cytoplasmic pH regulation; (v) protection against an aluminium-induced cytosolic calcium increase; and (vi) protection against reactive oxygen species. Future research should concentrate on assessing aluminium toxicity and tolerance in plants with overexpressed or antisense magnesium transporters to increase understanding of the aluminium-magnesium interaction.
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Affiliation(s)
- Jayakumar Bose
- School of Earth and Environment, Faculty of Natural and Agricultural Sciences, University of Western Australia, Crawley WA 6009, Australia
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