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Tomar S, Subba A, Chatterjee Y, Singhal NK, Pareek A, Singla-Pareek SL. A cystathionine beta-synthase domain containing protein, OsCBSCBS4, interacts with OsSnRK1A and OsPKG and functions in abiotic stress tolerance in rice. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39073079 DOI: 10.1111/pce.15061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/30/2024]
Abstract
The Cystathionine-β-Synthase (CBS) domain-containing proteins (CDCPs) constitute a functionally diverse protein superfamily, sharing an evolutionary conserved CBS domain either in pair or quad. Rice genome (Oryza sativa subsp. indica) encodes 42 CDCPs; their functions remain largely unexplored. This study examines OsCBSCBS4, a quadruple CBS domain containing protein towards its role in regulating the abiotic stress tolerance in rice. Gene expression analyses revealed upregulation of OsCBSCBS4 in response to diverse abiotic stresses. Further, the cytoplasm-localised OsCBSCBS4 showed interaction with two different kinases, a cytoplasmic localised cGMP-dependant protein kinase (OsPKG) and the nucleo-cytoplasmic catalytic subunit of sucrose-nonfermentation 1-related protein kinase 1 (OsSnRK1A). The interaction with the latter assisted in trafficking of OsCBSCBS4 to the nucleus as well. Overexpression of OsCBSCBS4 in rice resulted in enhanced tolerance to drought and salinity stress, via maintaining better physiological parameters and antioxidant activity. Additionally, OsCBSCBS4-overexpressing rice plants exhibited reduced yield penalty under stress conditions. The in silico docking and in vitro binding analyses of OsCBSCBS4 with ATP suggest its involvement in cellular energy balance. Overall, this study provides novel insight into the unexplored functions of OsCBSCBS4 and demonstrates it as a new promising target for augmenting crop resilience.
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Affiliation(s)
- Surabhi Tomar
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashish Subba
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Yajnaseni Chatterjee
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | | | - Ashwani Pareek
- National Agri-Food Biotechnology Institute, Mohali, India
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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2
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Zhang B, Zhang S, Polovitskaya MM, Yi J, Ye B, Li R, Huang X, Yin J, Neuens S, Balfroid T, Soblet J, Vens D, Aeby A, Li X, Cai J, Song Y, Li Y, Tartaglia M, Li Y, Jentsch TJ, Yang M, Liu Z. Molecular basis of ClC-6 function and its impairment in human disease. SCIENCE ADVANCES 2023; 9:eadg4479. [PMID: 37831762 PMCID: PMC10575590 DOI: 10.1126/sciadv.adg4479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 09/08/2023] [Indexed: 10/15/2023]
Abstract
ClC-6 is a late endosomal voltage-gated chloride-proton exchanger that is predominantly expressed in the nervous system. Mutated forms of ClC-6 are associated with severe neurological disease. However, the mechanistic role of ClC-6 in normal and pathological states remains largely unknown. Here, we present cryo-EM structures of ClC-6 that guided subsequent functional studies. Previously unrecognized ATP binding to cytosolic ClC-6 domains enhanced ion transport activity. Guided by a disease-causing mutation (p.Y553C), we identified an interaction network formed by Y553/F317/T520 as potential hotspot for disease-causing mutations. This was validated by the identification of a patient with a de novo pathogenic variant p.T520A. Extending these findings, we found contacts between intramembrane helices and connecting loops that modulate the voltage dependence of ClC-6 gating and constitute additional candidate regions for disease-associated gain-of-function mutations. Besides providing insights into the structure, function, and regulation of ClC-6, our work correctly predicts hotspots for CLCN6 mutations in neurodegenerative disorders.
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Affiliation(s)
- Bing Zhang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 201204 Shanghai, China
| | - Sensen Zhang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Maya M. Polovitskaya
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), 13125 Berlin, Germany
| | - Jingbo Yi
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Binglu Ye
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 201204 Shanghai, China
| | - Ruochong Li
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Xueying Huang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 201204 Shanghai, China
| | - Jian Yin
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Sebastian Neuens
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Tom Balfroid
- Department of Pediatric Neurology, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Julie Soblet
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Department of Genetics, Hôpital Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Daphné Vens
- Pediatric Intensive Care Unit, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Alec Aeby
- Department of Pediatric Neurology, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Xiaoling Li
- Wuya College of Innovation, Shenyang Pharmaceutical University, 110016 Shenyang, China
| | - Jinjin Cai
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Yingcai Song
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 201204 Shanghai, China
| | - Yuanxi Li
- Institute for Cognitive Neurodynamics, School of Mathematics, East China University of Science and Technology, 200237 Shanghai, China
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Yang Li
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Thomas J. Jentsch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), 13125 Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
- Cryo-EM Facility Center, Southern University of Science & Technology, 518055 Shenzhen, Guangdong, China
| | - Zhiqiang Liu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 201204 Shanghai, China
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3
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Yang Z, Zhang X, Ye S, Zheng J, Huang X, Yu F, Chen Z, Cai S, Zhang P. Molecular mechanism underlying regulation of Arabidopsis CLCa transporter by nucleotides and phospholipids. Nat Commun 2023; 14:4879. [PMID: 37573431 PMCID: PMC10423218 DOI: 10.1038/s41467-023-40624-z] [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: 05/12/2023] [Accepted: 08/03/2023] [Indexed: 08/14/2023] Open
Abstract
Chloride channels (CLCs) transport anion across membrane to regulate ion homeostasis and acidification of intracellular organelles, and are divided into anion channels and anion/proton antiporters. Arabidopsis thaliana CLCa (AtCLCa) transporter localizes to the tonoplast which imports NO3- and to a less extent Cl- from cytoplasm. The activity of AtCLCa and many other CLCs is regulated by nucleotides and phospholipids, however, the molecular mechanism remains unclear. Here we determine the cryo-EM structures of AtCLCa bound with NO3- and Cl-, respectively. Both structures are captured in ATP and PI(4,5)P2 bound conformation. Structural and electrophysiological analyses reveal a previously unidentified N-terminal β-hairpin that is stabilized by ATP binding to block the anion transport pathway, thereby inhibiting the AtCLCa activity. While AMP loses the inhibition capacity due to lack of the β/γ- phosphates required for β-hairpin stabilization. This well explains how AtCLCa senses the ATP/AMP status to regulate the physiological nitrogen-carbon balance. Our data further show that PI(4,5)P2 or PI(3,5)P2 binds to the AtCLCa dimer interface and occupies the proton-exit pathway, which may help to understand the inhibition of AtCLCa by phospholipids to facilitate guard cell vacuole acidification and stomatal closure. In a word, our work suggests the regulatory mechanism of AtCLCa by nucleotides and phospholipids under certain physiological scenarios and provides new insights for future study of CLCs.
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Affiliation(s)
- Zhao Yang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xue Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Shiwei Ye
- University of Chinese Academy of Sciences, Beijing, 100039, China
- Center for Excellence in Brain Sciences and Intelligence Technology, Institute of Neuronscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jingtao Zheng
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xiaowei Huang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Fang Yu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhenguo Chen
- The Fifth People's Hospital of Shanghai, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Shiqing Cai
- Center for Excellence in Brain Sciences and Intelligence Technology, Institute of Neuronscience, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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4
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Cryo-EM structure of the plant nitrate transporter AtCLCa reveals characteristics of the anion-binding site and the ATP-binding pocket. J Biol Chem 2022; 299:102833. [PMID: 36581207 PMCID: PMC9898749 DOI: 10.1016/j.jbc.2022.102833] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/27/2022] Open
Abstract
Nitrate is one of the major nitrogen sources for most plants. Chloride channel (CLC) proteins mediate the transport and vacuole storage of nitrate in plants, but the structural basis of nitrate transport by plant CLC proteins remains unknown. Here, we solved the cryo-EM structure of ATP-bound Arabidopsis thaliana CLCa (AtCLCa) at 2.8 Å resolution. Structural comparison between nitrate-selective AtCLCa and chloride-selective CLC-7 reveals key differences in the central anion-binding site. We observed that the central nitrate is shifted by ∼1.4 Å from chloride, which is likely caused by a weaker interaction between the anion and Pro160; the side chains of aromatic residues around the central binding site are rearranged to accommodate the larger nitrate. Additionally, we identified the ATP-binding pocket of AtCLCa to be located between the cytosolic cystathionine β-synthase domains and the N-terminus. The N-terminus may mediate the ATP inhibition of AtCLCa by interacting with both ATP and the pore-forming transmembrane helix. Together, our studies provide insights into the nitrate selectivity and ATP regulation of plant CLCs.
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5
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Mao P, Run Y, Wang H, Han C, Zhang L, Zhan K, Xu H, Cheng X. Genome-Wide Identification and Functional Characterization of the Chloride Channel TaCLC Gene Family in Wheat (Triticum aestivum L.). Front Genet 2022; 13:846795. [PMID: 35368658 PMCID: PMC8966409 DOI: 10.3389/fgene.2022.846795] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/11/2022] [Indexed: 12/27/2022] Open
Abstract
In plants, chloride channels (CLC) are involved in a series of specific functions, such as regulation of nutrient transport and stress tolerance. Members of the wheat Triticum aestivum L. CLC (TaCLC) gene family have been proposed to encode anion channels/transporters that may be related to nitrogen transportation. To better understand their roles, TaCLC family was screened and 23 TaCLC gene sequences were identified using a Hidden Markov Model in conjunction with wheat genome database. Gene structure, chromosome location, conserved motif, and expression pattern of the resulting family members were then analyzed. Phylogenetic analysis showed that the TaCLC family can be divided into two subclasses (I and II) and seven clusters (-a, -c1, -c2, -e, -f1, -f2, and -g2). Using a wheat RNA-seq database, the expression pattern of TaCLC family members was determined to be an inducible expression type. In addition, seven genes from seven different clusters were selected for quantitative real-time PCR (qRT-PCR) analysis under low nitrogen stress or salt stress conditions, respectively. The results indicated that the gene expression levels of this family were up-regulated under low nitrogen stress and salt stress, except the genes of TaCLC-c2 cluster which were from subfamily -c. The yeast complementary experiments illustrated that TaCLC-a-6AS-1, TaCLC-c1-3AS, and TaCLC-e-3AL all had anion transport functions for NO3− or Cl−, and compensated the hypersensitivity of yeast GEF1 mutant strain YJR040w (Δgef1) in restoring anion-sensitive phenotype. This study establishes a theoretical foundation for further functional characterization of TaCLC genes and provides an initial reference for better understanding nitrate nitrogen transportation in wheat.
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Affiliation(s)
| | | | | | | | | | | | - Haixia Xu
- *Correspondence: Haixia Xu, ; Xiyong Cheng,
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6
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Kashtoh H, Baek KH. Structural and Functional Insights into the Role of Guard Cell Ion Channels in Abiotic Stress-Induced Stomatal Closure. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122774. [PMID: 34961246 PMCID: PMC8707303 DOI: 10.3390/plants10122774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/25/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
A stomatal pore is formed by a pair of specialized guard cells and serves as a major gateway for water transpiration and atmospheric CO2 influx for photosynthesis in plants. These pores must be tightly controlled, as inadequate CO2 intake and excessive water loss are devastating for plants. When the plants are exposed to extreme weather conditions such as high CO2 levels, O3, low air humidity, and drought, the turgor pressure of the guard cells exhibits an appropriate response against these stresses, which leads to stomatal closure. This phenomenon involves a complex network of ion channels and their regulation. It is well-established that the turgor pressure of guard cells is regulated by ions transportation across the membrane, such as anions and potassium ions. In this review, the guard cell ion channels are discussed, highlighting the structure and functions of key ion channels; the SLAC1 anion channel and KAT1 potassium channel, and their regulatory components, emphasizing their significance in guard cell response to various stimuli.
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7
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Subba A, Tomar S, Pareek A, Singla-Pareek SL. The chloride channels: Silently serving the plants. PHYSIOLOGIA PLANTARUM 2021; 171:688-702. [PMID: 33034380 DOI: 10.1111/ppl.13240] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 05/12/2023]
Abstract
Chloride channels (CLCs), member of anion transporting proteins, are present ubiquitously in all life forms. Diverging from its name, the CLC family includes both channel and exchanger (proton-coupled) proteins; nevertheless, they share conserved structural organization. They are engaged in diverse indispensable functions such as acid and fluoride tolerance in prokaryotes to muscle stabilization, transepithelial transport, and neuronal development in mammals. Mutations in genes encoding CLCs lead to several physiological disorders in different organisms, including severe diseases in humans. Even in plants, loss of CLC protein function severely impairs various cellular processes critical for normal growth and development. These proteins sequester Cl- into the vacuole, thus, making them an attractive target for improving salinity tolerance in plants caused by high abundance of salts, primarily NaCl. Besides, some CLCs are involved in NO3 - transport and storage function in plants, thus, influencing their nitrogen use efficiency. However, despite their high significance, not many studies have been carried out in plants. Here, we have attempted to concisely highlight the basic structure of CLC proteins and critical residues essential for their function and classification. We also present the diverse functions of CLCs in plants from their first cloning back in 1996 to the knowledge acquired as of now. We stress the need for carrying out more in-depth studies on CLCs in plants, for they may have future applications towards crop improvement.
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Affiliation(s)
- Ashish Subba
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Surabhi Tomar
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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Cubero-Font P, De Angeli A. Connecting vacuolar and plasma membrane transport networks. THE NEW PHYTOLOGIST 2021; 229:755-762. [PMID: 33007120 DOI: 10.1111/nph.16983] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/01/2020] [Indexed: 05/12/2023]
Abstract
The coordinated control of ion transport across the two major membranes of differentiated plant cells, the plasma and the vacuolar membranes, is fundamental in cell physiology. The stomata responses to the fluctuating environmental conditions are an illustrative example. Indeed, they rely on the coordination of ion fluxes between the different cell compartments. The cytosolic environment, which is an interface between intracellular compartments, and the activity of the ion transporters localised in the different membranes influence one each other. Here we analyse the molecular mechanisms connecting and modulating the transport processes at both the plasma and the vacuolar membranes of guard cells.
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Affiliation(s)
- Paloma Cubero-Font
- BPMP, Université de Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, 34060, France
| | - Alexis De Angeli
- BPMP, Université de Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, 34060, France
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9
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Feng H, Fan X, Miller AJ, Xu G. Plant nitrogen uptake and assimilation: regulation of cellular pH homeostasis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4380-4392. [PMID: 32206788 PMCID: PMC7382382 DOI: 10.1093/jxb/eraa150] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/19/2020] [Indexed: 05/10/2023]
Abstract
The enzymatic controlled metabolic processes in cells occur at their optimized pH ranges, therefore cellular pH homeostasis is fundamental for life. In plants, the nitrogen (N) source for uptake and assimilation, mainly in the forms of nitrate (NO3-) and ammonium (NH4+) quantitatively dominates the anion and cation equilibrium and the pH balance in cells. Here we review ionic and pH homeostasis in plant cells and regulation by N source from the rhizosphere to extra- and intracellular pH regulation for short- and long-distance N distribution and during N assimilation. In the process of N transport across membranes for uptake and compartmentation, both proton pumps and proton-coupled N transporters are essential, and their proton-binding sites may sense changes of apoplastic or intracellular pH. In addition, during N assimilation, carbon skeletons are required to synthesize amino acids, thus the combination of NO3- or NH4+ transport and assimilation results in different net charge and numbers of protons in plant cells. Efficient maintenance of N-controlled cellular pH homeostasis may improve N uptake and use efficiency, as well as enhance the resistance to abiotic stresses.
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Affiliation(s)
- Huimin Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, China
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, China
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
| | - Anthony J Miller
- Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, China
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
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10
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Grieschat M, Guzman RE, Langschwager K, Fahlke C, Alekov AK. Metabolic energy sensing by mammalian CLC anion/proton exchangers. EMBO Rep 2020; 21:e47872. [PMID: 32390228 PMCID: PMC7271328 DOI: 10.15252/embr.201947872] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 01/26/2020] [Accepted: 01/29/2020] [Indexed: 12/13/2022] Open
Abstract
CLC anion/proton exchangers control the pH and [Cl- ] of the endolysosomal system that is essential for cellular nutrient uptake. Here, we use heterologous expression and whole-cell electrophysiology to investigate the regulation of the CLC isoforms ClC-3, ClC-4, and ClC-5 by the adenylic system components ATP, ADP, and AMP. Our results show that cytosolic ATP and ADP but not AMP and Mg2+ -free ADP enhance CLC ion transport. Biophysical analysis reveals that adenine nucleotides alter the ratio between CLC ion transport and CLC gating charge and shift the CLC voltage-dependent activation. The latter effect is suppressed by blocking the intracellular entrance of the proton transport pathway. We suggest, therefore, that adenine nucleotides regulate the internal proton delivery into the CLC transporter machinery and alter the probability of CLC transporters to undergo silent non-transporting cycles. Our findings suggest that the CBS domains in mammalian CLC transporters serve as energy sensors that regulate vesicular Cl- /H+ exchange by detecting changes in the cytosolic ATP/ADP/AMP equilibrium. Such sensing mechanism links the endolysosomal activity to the cellular metabolic state.
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Affiliation(s)
| | - Raul E Guzman
- Institute of Complex SystemsZelluläre Biophysik (ICS‐4), Forschungszentrum JülichJülichGermany
| | | | - Christoph Fahlke
- Institute of Complex SystemsZelluläre Biophysik (ICS‐4), Forschungszentrum JülichJülichGermany
| | - Alexi K Alekov
- Institute of NeurophysiologyHannover Medical SchoolHannoverGermany
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Chatterjee A, Singh S, Rai R, Rai S, Rai L. Functional Characterization of Alr0765, A Hypothetical Protein from Anabaena PCC 7120 Involved in Cellular Energy Status Sensing, Iron Acquisition and Abiotic Stress Management in E. coli Using Molecular, Biochemical and Computational Approaches. Curr Genomics 2020; 21:295-310. [PMID: 33071622 PMCID: PMC7521041 DOI: 10.2174/1389202921999200424181239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Cyanobacteria are excellent model to understand the basic metabolic processes taking place in response to abiotic stress. The present study involves the characterization of a hypothetical protein Alr0765 of Anabaena PCC7120 comprising the CBS-CP12 domain and deciphering its role in abiotic stress tolerance. METHODS Molecular cloning, heterologous expression and protein purification using affinity chromatography were performed to obtain native purified protein Alr0765. The energy sensing property of Alr0765 was inferred from its binding affinity with different ligand molecules as analyzed by FTIR and TNP-ATP binding assay. AAS and real time-PCR were applied to evaluate the iron acquisition property and cyclic voltammetry was employed to check the redox sensitivity of the target protein. Transcript levels under different abiotic stresses, as well as spot assay, CFU count, ROS level and cellular H2O2 level, were used to show the potential role of Alr0765 in abiotic stress tolerance. In-silico analysis of Alr0765 included molecular function probability analysis, multiple sequence analysis, protein domain and motif finding, secondary structure analysis, protein-ligand interaction, homologous modeling, model refinement and verification and molecular docking was performed with COFACTOR, PROMALS-3D, InterProScan, MEME, TheaDomEx, COACH, Swiss modeller, Modrefiner, PROCHECK, ERRAT, MolProbity, ProSA, TM-align, and Discovery studio, respectively. RESULTS Transcript levels of alr0765 significantly increased by 20, 13, 15, 14.8, 12, 7, 6 and 2.5 fold when Anabaena PCC7120 treated with LC50 dose of heat, arsenic, cadmium, butachlor, salt, mannitol (drought), UV-B, and methyl viologen respectively, with respect to control (untreated). Heterologous expression resulted in 23KDa protein observed on the SDS-PAGE. Immunoblotting and MALDI-TOF-MS/MS, followed by MASCOT search analysis, confirmed the identity of the protein and ESI/MS revealed that the purified protein was a dimer. Binding possibility of Alr0765 with ATP was observed with an almost 6-fold increment in relative fluorescence during TNP-ATP binding assay with a λ max of 538 nm. FTIR spectra revealed modification in protein confirmation upon binding of Alr0765 with ATP, ADP, AMP and NADH. A 10-fold higher accumulation of iron was observed in digests of E. coli with recombinant vector after induction as compared to control, which affirms the iron acquisition property of the protein. Moreover, the generation of the redox potential of 146 mV by Alr0765 suggested its probable role in maintaining the redox status of the cell under environmental constraints. As per CFU count recombinant, E. coli BL21 cells showed about 14.7, 7.3, 6.9, 1.9, 3 and 4.9 fold higher number of colonies under heat, cadmium (CdCl2), arsenic (Na3AsO4), salt (NaCl), UV-B and drought (mannitol) respectively compared to pET21a harboring E. coli BL21 cells. Deterioration in the cellular ROS level and total cellular H2O2 concentration validated the stress tolerance ability of Alr0765. In-silico analysis unraveled novel findings and attested experimental findings in determining the role of Alr0765. CONCLUSION Alr0765 is a novel CBS-CP12 domain protein that maintains cellular energy level and iron homeostasis which provides tolerance against multiple abiotic stresses.
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Affiliation(s)
- Antra Chatterjee
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi-221005, India
| | - Shilpi Singh
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi-221005, India
| | - Ruchi Rai
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi-221005, India
| | - Shweta Rai
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi-221005, India
| | - L.C. Rai
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi-221005, India
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Wang Y, Liu X, Zhao J, Ouyang S, Li W, Zhu J, Zhu Y, Zhu X. Molecular cloning of ESR1, BMPR1B, and FOXL2 and differential expressions depend on maternal age and size during breeding season in cultured Asian yellow pond turtle (Mauremys mutica). Comp Biochem Physiol B Biochem Mol Biol 2019; 232:108-120. [DOI: 10.1016/j.cbpb.2019.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 02/06/2023]
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Asaoka M, Inoue SI, Gunji S, Kinoshita T, Maeshima M, Tsukaya H, Ferjani A. Excess Pyrophosphate within Guard Cells Delays Stomatal Closure. PLANT & CELL PHYSIOLOGY 2019; 60:875-887. [PMID: 30649470 DOI: 10.1093/pcp/pcz002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/28/2018] [Indexed: 05/08/2023]
Abstract
A variety of cellular metabolic reactions generate inorganic pyrophosphate (PPi) as an ATP hydrolysis byproduct. The vacuolar H+-translocating pyrophosphatase (H+-PPase) loss-of-function fugu5 mutant is susceptible to drought and displays pleotropic postgerminative growth defects due to excess PPi. It was recently reported that stomatal closure after abscisic acid (ABA) treatment is delayed in vhp1-1, a fugu5 allele. In contrast, we found that specific removal of PPi rescued all of the above fugu5 developmental and growth defects. Hence, we speculated that excess PPi itself, rather than vacuolar acidification, might delay stomatal closure. To test this hypothesis, we constructed transgenic plants expressing the yeast IPP1 gene (encoding a cytosolic pyrophosphatase) driven by a guard cell-specific promoter (pGC1::IPP1) in the fugu5 background. Our measurements confirmed stomatal closure defects in fugu5, further supporting a role for H+-PPase in stomatal functioning. Importantly, while pGC1::IPP1 transgenics morphologically mimicked fugu5, stomatal closure was restored in response to ABA and darkness. Quantification of water loss revealed that fugu5 stomata were almost completely insensitive to ABA. In addition, growth of pGC1::IPP1 plants was promoted compared to fugu5 throughout their life; however, it did not reach the wild type level. fugu5 also displayed an increased stomatal index, in violation of the one-cell-spacing rule, and phenotypes recovered upon removal of PPi by pAVP1::IPP1 (FUGU5, VHP1 and AVP1 are the same gene encoding H+-PPase), but not in the pGC1::IPP1 line. Taken together, these results clearly support our hypothesis that dysfunction in stomata is triggered by excess PPi within guard cells, probably via perturbed guard cell metabolism.
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Affiliation(s)
- Mariko Asaoka
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Tokyo, Japan
| | - Shin-Ichiro Inoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Shizuka Gunji
- United Graduated School of Education, Tokyo Gakugei University, Tokyo, Japan
| | - Toshinori Kinoshita
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Masayoshi Maeshima
- Laboratory of Cell Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, Aichi, Japan
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Tokyo, Japan
- United Graduated School of Education, Tokyo Gakugei University, Tokyo, Japan
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Saito S, Uozumi N. Guard Cell Membrane Anion Transport Systems and Their Regulatory Components: An Elaborate Mechanism Controlling Stress-Induced Stomatal Closure. PLANTS 2019; 8:plants8010009. [PMID: 30609843 PMCID: PMC6359458 DOI: 10.3390/plants8010009] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/19/2018] [Accepted: 12/16/2018] [Indexed: 02/07/2023]
Abstract
When plants are exposed to drastic environmental changes such as drought, salt or bacterial invasion, rapid stomatal movement confers tolerance to these stresses. This process involves a variety of guard cell expressed ion channels and their complex regulation network. Inward K+ channels mainly function in stomatal opening. On the other hand, guard cell anion channels play a crucial role in the closing of stomata, which is vital in terms of preventing water loss and bacterial entrance. Massive progress has been made on the research of these anion channels in the last decade. In this review, we focus on the function and regulation of Arabidopsis guard cell anion channels. Starting from SLAC1, a main contributor of stomatal closure, members of SLAHs (SLAC1 homologues), AtNRTs (Nitrate transporters), AtALMTs (Aluminum-activated malate transporters), ABC transporters, AtCLCs (Chloride channels), DTXs (Detoxification efflux carriers), SULTRs (Sulfate transporters), and their regulator components are reviewed. These membrane transport systems are the keys to maintaining cellular ion homeostasis against fluctuating external circumstances.
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Affiliation(s)
- Shunya Saito
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan.
| | - Nobuyuki Uozumi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan.
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He Q, Tang QY, Sun YF, Zhou M, Gärtner W, Zhao KH. Chromophorylation of cyanobacteriochrome Slr1393 from Synechocystis sp. PCC 6803 is regulated by protein Slr2111 through allosteric interaction. J Biol Chem 2018; 293:17705-17715. [PMID: 30242127 DOI: 10.1074/jbc.ra118.003830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 08/13/2018] [Indexed: 11/06/2022] Open
Abstract
Cyanobacteriochromes (CBCRs) are photochromic proteins in cyanobacteria that act as photosensors. CBCRs bind bilins as chromophores and sense nearly the entire visible spectrum of light, but the regulation of the chromophorylation of CBCRs is unknown. Slr1393 from Synechocystis sp. PCC 6803 is a CBCR containing three consecutive GAF (cGMP phosphodiesterase, adenylyl cyclase, and FhlA protein) domains, of which only the third one (Slr1393g3) can be phycocyanobilin-chromophorylated. The protein Slr2111 from Synechocystis sp. PCC 6803 includes a cystathionine β-synthase (CBS) domain pair of an as yet unknown function at its N terminus. CBS domains are often characterized as sensors of cellular energy status by binding nucleotides. In this work, we demonstrate that Slr2111 strongly interacts with Slr1393 in vivo and in vitro, which generates a complex in a 1:1 molar ratio. This tight interaction inhibits the chromophorylation of Slr1393g3, even if the chromophore is present. Instead, the complex stability and thereby the chromophorylation of Slr1393 are regulated by the binding of nucleotides (ATP, ADP, AMP) to the CBS domains of Slr2111 with varying affinities. It is demonstrated that residues Asp-53 and Arg-97 of Slr2111 are involved in nucleotide binding. While ATP binds to Slr2111, the association between the two proteins gets weaker and chromophorylation of Slr1393 are enabled. In contrast, AMP binding to Slr2111 leads to a stronger association, thereby inhibiting the chromophorylation. It is concluded that Slr2111 acts as a sensor of the cellular energy status that regulates the chromophorylation of Slr1393 and thereby its function as a light-driven histidine kinase.
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Affiliation(s)
- Qi He
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Qi-Ying Tang
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Ya-Fang Sun
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Ming Zhou
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry, University of Leipzig, 04103 Leipzig, Germany
| | - Kai-Hong Zhao
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
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16
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Maia CMF, Machado RA, Gil-da-Silva-Lopes VL, Lustosa-Mendes E, Rim PHH, Dias VO, Martelli DRB, Nasser LS, Coletta RD, Martelli-Júnior H. Report of two unrelated families with Jalili syndrome and a novel nonsense heterozygous mutation in CNNM4 gene. Eur J Med Genet 2018; 61:384-387. [PMID: 29421602 DOI: 10.1016/j.ejmg.2018.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/10/2018] [Accepted: 02/03/2018] [Indexed: 12/18/2022]
Abstract
Jalili syndrome (JS) is an autosomal recessive disease characterized by a combination of cone-rode retinal dytrophy (CRD) and amelogenesis imperfect (AI). Mutations in cyclin and CBS domain divalent metal cation transport mediator 4 (CNNM4) gene cause JS. Here we described 2 families (3 members) affected by JS. In the first family, JS was caused by the homozygous p.Leu324Pro (c.971T > C) missense mutation and the affected patient developed both CRD and AI. In the second family, a specific combination of a compound heterozygous mutation was found - the p.Leu324Pro (c.971T > C) missense transition and the novel p.Tyr581* (c.1743C > G) nonsense mutation. The proband showed CRD and AI, but her father just developed eye alterations. Together, these findings suggest that the p.Leu324Pro mutation in homozygosis induces a complete phenotype with both CRD and AI, but in heterozygosis and in composition with the novel p.Tyr581* nonsense mutation in CNNM4 promotes variable clinical expressivity, particularly with lack of dental phenotypes. These different phenotypes could be explained by deletions affecting the proband's homologous allele, epistasia or interactions with environmental factors leading to residual activity of protein.
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Affiliation(s)
| | - Renato Assis Machado
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil.
| | | | - Elaine Lustosa-Mendes
- Department of Medical Genetics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Priscila Hae Hyun Rim
- Department of Medical Genetics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Verônica Oliveira Dias
- Health Science Program, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil
| | | | - Luciano Sólia Nasser
- Health Science Program, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil
| | - Ricardo D Coletta
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Hercílio Martelli-Júnior
- Health Science Program, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil; Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
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17
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Tomita A, Zhang M, Jin F, Zhuang W, Takeda H, Maruyama T, Osawa M, Hashimoto KI, Kawasaki H, Ito K, Dohmae N, Ishitani R, Shimada I, Yan Z, Hattori M, Nureki O. ATP-dependent modulation of MgtE in Mg 2+ homeostasis. Nat Commun 2017; 8:148. [PMID: 28747715 PMCID: PMC5529423 DOI: 10.1038/s41467-017-00082-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 05/26/2017] [Indexed: 11/09/2022] Open
Abstract
Magnesium is an essential ion for numerous physiological processes. MgtE is a Mg2+ selective channel involved in the maintenance of intracellular Mg2+ homeostasis, whose gating is regulated by intracellular Mg2+ levels. Here, we report that ATP binds to MgtE, regulating its Mg2+-dependent gating. Crystal structures of MgtE–ATP complex show that ATP binds to the intracellular CBS domain of MgtE. Functional studies support that ATP binding to MgtE enhances the intracellular domain affinity for Mg2+ within physiological concentrations of this divalent cation, enabling MgtE to function as an in vivo Mg2+ sensor. ATP dissociation from MgtE upregulates Mg2+ influx at both high and low intracellular Mg2+ concentrations. Using site-directed mutagenesis and structure based-electrophysiological and biochemical analyses, we identify key residues and main structural changes involved in the process. This work provides the molecular basis of ATP-dependent modulation of MgtE in Mg2+ homeostasis. MgtE is an Mg2+ transporter involved in Mg2+ homeostasis. Here, the authors report that ATP regulates the Mg+2-dependent gating of MgtE and use X-ray crystallography combined with functional studies to propose the molecular mechanisms involved in this process.
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Affiliation(s)
- Atsuhiro Tomita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Mingfeng Zhang
- State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center of Genetics and Development, Institute of Brain Science, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai, 200438, China
| | - Fei Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai, 200438, China
| | - Wenhui Zhuang
- State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center of Genetics and Development, Institute of Brain Science, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai, 200438, China
| | - Hironori Takeda
- Faculty of Life Science, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Tatsuro Maruyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ken-Ichi Hashimoto
- Department of Green and Sustainable Chemistry, Tokyo Denki University, 5 Asahi-cho, Senju, Adachi-ku, Tokyo, 120-8551, Japan
| | - Hisashi Kawasaki
- Department of Green and Sustainable Chemistry, Tokyo Denki University, 5 Asahi-cho, Senju, Adachi-ku, Tokyo, 120-8551, Japan
| | - Koichi Ito
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Zhiqiang Yan
- State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center of Genetics and Development, Institute of Brain Science, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai, 200438, China. .,Department of Human Anatomy, School of Basic Medicine Sciences, Southwest Medical University, Luzhou, Sichuan, 646000, China.
| | - Motoyuki Hattori
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai, 200438, China.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
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18
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Bose J, Munns R, Shabala S, Gilliham M, Pogson B, Tyerman SD. Chloroplast function and ion regulation in plants growing on saline soils: lessons from halophytes. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3129-3143. [PMID: 28472512 DOI: 10.1093/jxb/erx142] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Salt stress impacts multiple aspects of plant metabolism and physiology. For instance it inhibits photosynthesis through stomatal limitation, causes excessive accumulation of sodium and chloride in chloroplasts, and disturbs chloroplast potassium homeostasis. Most research on salt stress has focused primarily on cytosolic ion homeostasis with few studies of how salt stress affects chloroplast ion homeostasis. This review asks the question whether membrane-transport processes and ionic relations are differentially regulated between glycophyte and halophyte chloroplasts and whether this contributes to the superior salt tolerance of halophytes. The available literature indicates that halophytes can overcome stomatal limitation by switching to CO2 concentrating mechanisms and increasing the number of chloroplasts per cell under saline conditions. Furthermore, salt entry into the chloroplast stroma may be critical for grana formation and photosystem II activity in halophytes but not in glycophytes. Salt also inhibits some stromal enzymes (e.g. fructose-1,6-bisphosphatase) to a lesser extent in halophyte species. Halophytes accumulate more chloride in chloroplasts than glycophytes and appear to use sodium in functional roles. We propose the molecular identities of candidate transporters that move sodium, chloride and potassium across chloroplast membranes and discuss how their operation may regulate photochemistry and photosystem I and II activity in chloroplasts.
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Affiliation(s)
- Jayakumar Bose
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia
| | - Rana Munns
- Australian Research Council Centre of Excellence in Plant Energy Biology, and School of Agriculture and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Sergey Shabala
- School of Land and Food, University of Tasmania, Private Bag 54, Hobart, TAS 7001, Australia
| | - Matthew Gilliham
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia
| | - Barry Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Stephen D Tyerman
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia
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Jezek M, Blatt MR. The Membrane Transport System of the Guard Cell and Its Integration for Stomatal Dynamics. PLANT PHYSIOLOGY 2017; 174:487-519. [PMID: 28408539 PMCID: PMC5462021 DOI: 10.1104/pp.16.01949] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/11/2017] [Indexed: 05/17/2023]
Abstract
Stomatal guard cells are widely recognized as the premier plant cell model for membrane transport, signaling, and homeostasis. This recognition is rooted in half a century of research into ion transport across the plasma and vacuolar membranes of guard cells that drive stomatal movements and the signaling mechanisms that regulate them. Stomatal guard cells surround pores in the epidermis of plant leaves, controlling the aperture of the pore to balance CO2 entry into the leaf for photosynthesis with water loss via transpiration. The position of guard cells in the epidermis is ideally suited for cellular and subcellular research, and their sensitivity to endogenous signals and environmental stimuli makes them a primary target for physiological studies. Stomata underpin the challenges of water availability and crop production that are expected to unfold over the next 20 to 30 years. A quantitative understanding of how ion transport is integrated and controlled is key to meeting these challenges and to engineering guard cells for improved water use efficiency and agricultural yields.
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Affiliation(s)
- Mareike Jezek
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Michael R Blatt
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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Eisenach C, De Angeli A. Ion Transport at the Vacuole during Stomatal Movements. PLANT PHYSIOLOGY 2017; 174:520-530. [PMID: 28381500 PMCID: PMC5462060 DOI: 10.1104/pp.17.00130] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/03/2017] [Indexed: 05/19/2023]
Abstract
Recent research on vacuolar ion channels, transporters, and pumps of Arabidopsis highlight their function and roles in stomatal opening and closure.
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Affiliation(s)
- Cornelia Eisenach
- Department of Plant and Microbial Biology, University of Zurich, Zurich CH-8008, Switzerland (C.E.); and
- Institut de Biologie Intégrative de la Cellule, Centre National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France (A.D.A.)
| | - Alexis De Angeli
- Department of Plant and Microbial Biology, University of Zurich, Zurich CH-8008, Switzerland (C.E.); and
- Institut de Biologie Intégrative de la Cellule, Centre National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France (A.D.A.)
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21
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Poroca DR, Pelis RM, Chappe VM. ClC Channels and Transporters: Structure, Physiological Functions, and Implications in Human Chloride Channelopathies. Front Pharmacol 2017; 8:151. [PMID: 28386229 PMCID: PMC5362633 DOI: 10.3389/fphar.2017.00151] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/09/2017] [Indexed: 02/04/2023] Open
Abstract
The discovery of ClC proteins at the beginning of the 1990s was important for the development of the Cl- transport research field. ClCs form a large family of proteins that mediate voltage-dependent transport of Cl- ions across cell membranes. They are expressed in both plasma and intracellular membranes of cells from almost all living organisms. ClC proteins form transmembrane dimers, in which each monomer displays independent ion conductance. Eukaryotic members also possess a large cytoplasmic domain containing two CBS domains, which are involved in transport modulation. ClC proteins function as either Cl- channels or Cl-/H+ exchangers, although all ClC proteins share the same basic architecture. ClC channels have two gating mechanisms: a relatively well-studied fast gating mechanism, and a slow gating mechanism, which is poorly defined. ClCs are involved in a wide range of physiological processes, including regulation of resting membrane potential in skeletal muscle, facilitation of transepithelial Cl- reabsorption in kidneys, and control of pH and Cl- concentration in intracellular compartments through coupled Cl-/H+ exchange mechanisms. Several inherited diseases result from C1C gene mutations, including myotonia congenita, Bartter's syndrome (types 3 and 4), Dent's disease, osteopetrosis, retinal degeneration, and lysosomal storage diseases. This review summarizes general features, known or suspected, of ClC structure, gating and physiological functions. We also discuss biophysical properties of mammalian ClCs that are directly involved in the pathophysiology of several human inherited disorders, or that induce interesting phenotypes in animal models.
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Affiliation(s)
- Diogo R Poroca
- Department of Physiology and Biophysics, Dalhousie University, Halifax NS, Canada
| | - Ryan M Pelis
- Department of Pharmacology, Dalhousie University, Halifax NS, Canada
| | - Valérie M Chappe
- Department of Physiology and Biophysics, Dalhousie University, Halifax NS, Canada
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Li B, Tester M, Gilliham M. Chloride on the Move. TRENDS IN PLANT SCIENCE 2017; 22:236-248. [PMID: 28081935 DOI: 10.1016/j.tplants.2016.12.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 11/21/2016] [Accepted: 12/11/2016] [Indexed: 05/20/2023]
Abstract
Chloride (Cl-) is an essential plant nutrient but under saline conditions it can accumulate to toxic levels in leaves; limiting this accumulation improves the salt tolerance of some crops. The rate-limiting step for this process - the transfer of Cl- from root symplast to xylem apoplast, which can antagonize delivery of the macronutrient nitrate (NO3-) to shoots - is regulated by abscisic acid (ABA) and is multigenic. Until recently the molecular mechanisms underpinning this salt-tolerance trait were poorly defined. We discuss here how recent advances highlight the role of newly identified transport proteins, some that directly transfer Cl- into the xylem, and others that act on endomembranes in 'gatekeeper' cell types in the root stele to control root-to-shoot delivery of Cl-.
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Affiliation(s)
- Bo Li
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Mark Tester
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Matthew Gilliham
- Plant Transport and Signalling Group, Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia.
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23
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Rodríguez-Celma J, Tsai YH, Wen TN, Wu YC, Curie C, Schmidt W. Systems-wide analysis of manganese deficiency-induced changes in gene activity of Arabidopsis roots. Sci Rep 2016; 6:35846. [PMID: 27804982 PMCID: PMC5090222 DOI: 10.1038/srep35846] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/06/2016] [Indexed: 11/09/2022] Open
Abstract
Manganese (Mn) is pivotal for plant growth and development, but little information is available regarding the strategies that evolved to improve Mn acquisition and cellular homeostasis of Mn. Using an integrated RNA-based transcriptomic and high-throughput shotgun proteomics approach, we generated a comprehensive inventory of transcripts and proteins that showed altered abundance in response to Mn deficiency in roots of the model plant Arabidopsis. A suite of 22,385 transcripts was consistently detected in three RNA-seq runs; LC-MS/MS-based iTRAQ proteomics allowed the unambiguous determination of 11,606 proteins. While high concordance between mRNA and protein expression (R = 0.87) was observed for transcript/protein pairs in which both gene products accumulated differentially upon Mn deficiency, only approximately 10% of the total alterations in the abundance of proteins could be attributed to transcription, indicating a large impact of protein-level regulation. Differentially expressed genes spanned a wide range of biological functions, including the maturation, translation, and transport of mRNAs, as well as primary and secondary metabolic processes. Metabolic analysis by UPLC-qTOF-MS revealed that the steady-state levels of several major glucosinolates were significantly altered upon Mn deficiency in both roots and leaves, possibly as a compensation for increased pathogen susceptibility under conditions of Mn deficiency.
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Affiliation(s)
- Jorge Rodríguez-Celma
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, Taiwan
| | - Yi-Hsiu Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, Taiwan
| | - Tuan-Nan Wen
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, Taiwan
| | - Yu-Ching Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, Taiwan
| | - Catherine Curie
- Biochimie et Physiologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Institut National pour la Recherche Agronomique, Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, INRA/SupAgro, Université Montpellier 2, Montpellier, France
| | - Wolfgang Schmidt
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, Taiwan
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De Angeli A, Thomine S, Frachisse JM. Anion Channel Blockage by ATP as a Means for Membranes to Perceive the Energy Status of the Cell. MOLECULAR PLANT 2016; 9:320-322. [PMID: 26785050 DOI: 10.1016/j.molp.2016.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/25/2015] [Accepted: 01/08/2016] [Indexed: 05/08/2023]
Affiliation(s)
- Alexis De Angeli
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Sébastien Thomine
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Jean-Marie Frachisse
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.
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Mhashal AR, Choudhury CK, Roy S. Probing the ATP-induced conformational flexibility of the PcrA helicase protein using molecular dynamics simulation. J Mol Model 2016; 22:54. [PMID: 26860503 DOI: 10.1007/s00894-016-2922-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 01/24/2016] [Indexed: 11/26/2022]
Abstract
Helicases are enzymes that unwind double-stranded DNA (dsDNA) into its single-stranded components. It is important to understand the binding and unbinding of ATP from the active sites of helicases, as this knowledge can be used to elucidate the functionality of helicases during the unwinding of dsDNA. In this work, we investigated the unbinding of ATP and its effect on the active-site residues of the helicase PcrA using molecular dynamic simulations. To mimic the unbinding process of ATP from the active site of the helicase, we simulated the application of an external force that pulls ATP from the active site and computed the free-energy change during this process. We estimated an energy cost of ~85 kJ/mol for the transformation of the helicase from the ATP-bound state (1QHH) to the ATP-free state (1PJR). Unbinding led to conformational changes in the residues of the protein at the active site. Some of the residues at the ATP-binding site were significantly reoriented when the ATP was pulled. We observed a clear competition between reorientation of the residues and energy stabilization by hydrogen bonds between the ATP and active-site residues. We also checked the flexibility of the PcrA protein using a principal component analysis of domain motion. We found that the ATP-free state of the helicase is more flexible than the ATP-bound state.
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Affiliation(s)
- Anil R Mhashal
- Physical Chemistry Division, National Chemical Laboratory, Pune, 411008, India
| | | | - Sudip Roy
- Physical Chemistry Division, National Chemical Laboratory, Pune, 411008, India.
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26
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Herdean A, Nziengui H, Zsiros O, Solymosi K, Garab G, Lundin B, Spetea C. The Arabidopsis Thylakoid Chloride Channel AtCLCe Functions in Chloride Homeostasis and Regulation of Photosynthetic Electron Transport. FRONTIERS IN PLANT SCIENCE 2016; 7:115. [PMID: 26904077 PMCID: PMC4746265 DOI: 10.3389/fpls.2016.00115] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/21/2016] [Indexed: 05/20/2023]
Abstract
Chloride ions can be translocated across cell membranes through Cl(-) channels or Cl(-)/H(+) exchangers. The thylakoid-located member of the Cl(-) channel CLC family in Arabidopsis thaliana (AtCLCe) was hypothesized to play a role in photosynthetic regulation based on the initial photosynthetic characterization of clce mutant lines. The reduced nitrate content of Arabidopsis clce mutants suggested a role in regulation of plant nitrate homeostasis. In this study, we aimed to further investigate the role of AtCLCe in the regulation of ion homeostasis and photosynthetic processes in the thylakoid membrane. We report that the size and composition of proton motive force were mildly altered in two independent Arabidopsis clce mutant lines. Most pronounced effects in the clce mutants were observed on the photosynthetic electron transport of dark-adapted plants, based on the altered shape and associated parameters of the polyphasic OJIP kinetics of chlorophyll a fluorescence induction. Other alterations were found in the kinetics of state transition and in the macro-organization of photosystem II supercomplexes, as indicated by circular dichroism measurements. Pre-treatment with KCl but not with KNO3 restored the wild-type photosynthetic phenotype. Analyses by transmission electron microscopy revealed a bow-like arrangement of the thylakoid network and a large thylakoid-free stromal region in chloroplast sections from the dark-adapted clce plants. Based on these data, we propose that AtCLCe functions in Cl(-) homeostasis after transition from light to dark, which affects chloroplast ultrastructure and regulation of photosynthetic electron transport.
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Affiliation(s)
- Andrei Herdean
- Department of Biological and Environmental Sciences, University of GothenburgGothenburg, Sweden
| | - Hugues Nziengui
- Department of Biological and Environmental Sciences, University of GothenburgGothenburg, Sweden
| | - Ottó Zsiros
- Biological Research Center, Hungarian Academy of SciencesSzeged, Hungary
| | - Katalin Solymosi
- Department of Plant Anatomy, Eötvös Loránd UniversityBudapest, Hungary
| | - Győző Garab
- Biological Research Center, Hungarian Academy of SciencesSzeged, Hungary
| | - Björn Lundin
- Department of Biological and Environmental Sciences, University of GothenburgGothenburg, Sweden
| | - Cornelia Spetea
- Department of Biological and Environmental Sciences, University of GothenburgGothenburg, Sweden
- *Correspondence: Cornelia Spetea
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27
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Accardi A. Structure and gating of CLC channels and exchangers. J Physiol 2015; 593:4129-38. [PMID: 26148215 DOI: 10.1113/jp270575] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 06/28/2015] [Indexed: 11/08/2022] Open
Abstract
Since their serendipitous discovery the CLC family of Cl(-) transporting proteins has been a never ending source of surprises. From their double-barrelled architecture to their complex structure and divergence as channels and transporters, the CLCs never cease to amaze biophysicists, biochemists and physiologists alike. These unusual functional properties allow the CLCs to fill diverse physiological niches, regulating processes that range from muscle contraction to acidification of intracellular organelles, nutrient accumulation and survival of bacteria to environmental stresses. Over the last 15 years, the availability of atomic-level information on the structure of the CLCs, coupled to the discovery that the family is divided into passive channels and secondary active transporters, has revolutionized our understanding of their function. These breakthroughs led to the identification of the key structural elements regulating gating, transport, selectivity and regulation by ligands. Unexpectedly, many lines of evidence indicate that the CLC exchangers function according to a non-conventional transport mechanism that defies the fundamental tenets of the alternating-access paradigm for exchange transport, paving the way for future unexpected insights into the principles underlying active transport and channel gating.
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Affiliation(s)
- Alessio Accardi
- Departments of Anaesthesiology, Physiology & Biophysics, and Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA
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28
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Reddy MM, Ulaganathan K. Nitrogen Nutrition, Its Regulation and Biotechnological Approaches to Improve Crop Productivity. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/ajps.2015.618275] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Coneva V, Simopoulos C, Casaretto JA, El-Kereamy A, Guevara DR, Cohn J, Zhu T, Guo L, Alexander DC, Bi YM, McNicholas PD, Rothstein SJ. Metabolic and co-expression network-based analyses associated with nitrate response in rice. BMC Genomics 2014; 15:1056. [PMID: 25471115 PMCID: PMC4301927 DOI: 10.1186/1471-2164-15-1056] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/27/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding gene expression and metabolic re-programming that occur in response to limiting nitrogen (N) conditions in crop plants is crucial for the ongoing progress towards the development of varieties with improved nitrogen use efficiency (NUE). To unravel new details on the molecular and metabolic responses to N availability in a major food crop, we conducted analyses on a weighted gene co-expression network and metabolic profile data obtained from leaves and roots of rice plants adapted to sufficient and limiting N as well as after shifting them to limiting (reduction) and sufficient (induction) N conditions. RESULTS A gene co-expression network representing clusters of rice genes with similar expression patterns across four nitrogen conditions and two tissue types was generated. The resulting 18 clusters were analyzed for enrichment of significant gene ontology (GO) terms. Four clusters exhibited significant correlation with limiting and reducing nitrate treatments. Among the identified enriched GO terms, those related to nucleoside/nucleotide, purine and ATP binding, defense response, sugar/carbohydrate binding, protein kinase activities, cell-death and cell wall enzymatic activity are enriched. Although a subset of functional categories are more broadly associated with the response of rice organs to limiting N and N reduction, our analyses suggest that N reduction elicits a response distinguishable from that to adaptation to limiting N, particularly in leaves. This observation is further supported by metabolic profiling which shows that several compounds in leaves change proportionally to the nitrate level (i.e. higher in sufficient N vs. limiting N) and respond with even higher levels when the nitrate level is reduced. Notably, these compounds are directly involved in N assimilation, transport, and storage (glutamine, asparagine, glutamate and allantoin) and extend to most amino acids. Based on these data, we hypothesize that plants respond by rapidly mobilizing stored vacuolar nitrate when N deficit is perceived, and that the response likely involves phosphorylation signal cascades and transcriptional regulation. CONCLUSIONS The co-expression network analysis and metabolic profiling performed in rice pinpoint the relevance of signal transduction components and regulation of N mobilization in response to limiting N conditions and deepen our understanding of N responses and N use in crops.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Steven J Rothstein
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
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Hu Y, Fernández V, Ma L. Nitrate transporters in leaves and their potential roles in foliar uptake of nitrogen dioxide. FRONTIERS IN PLANT SCIENCE 2014; 5:360. [PMID: 25126090 PMCID: PMC4115617 DOI: 10.3389/fpls.2014.00360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 07/04/2014] [Indexed: 05/07/2023]
Abstract
While plant roots are specialized organs for the uptake and transport of water and nutrients, the absorption of gaseous or liquid mineral elements by aerial plant parts has been recognized since more than one century. Nitrogen (N) is an essential macronutrient which generally absorbed either as nitrate (NO(-) 3) or ammonium (NH(+) 4) by plant roots. Gaseous nitrogen pollutants like N dioxide (NO2) can also be absorbed by plant surfaces and assimilated via the NO(-) 3 assimilation pathway. The subsequent NO(-) 3 flux may induce or repress the expression of various NO(-) 3-responsive genes encoding for instance, the transmembrane transporters, NO(-) 3/NO(-) 2 (nitrite) reductase, or assimilatory enzymes involved in N metabolism. Based on the existing information, the aim of this review was to theoretically analyze the potential link between foliar NO2 absorption and N transport and metabolism. For such purpose, an overview of the state of knowledge on the NO(-) 3 transporter genes identified in leaves or shoots of various species and their roles for NO(-) 3 transport across the tonoplast and plasma membrane, in addition to the process of phloem loading is briefly provided. It is assumed that a NO2-induced accumulation of NO(-) 3/NO(-) 2 may alter the expression of such genes, hence linking transmembrane NO(-) 3 transporters and foliar uptake of NO2. It is likely that NRT1/NRT2 gene expression and species-dependent apoplastic buffer capacity may be also related to the species-specific foliar NO2 uptake process. It is concluded that further work focusing on the expression of NRT1 (NRT1.1, NRT1.7, NRT1.11, and NRT1.12), NRT2 (NRT2.1, NRT2.4, and NRT2.5) and chloride channel family genes (CLCa and CLCd) may help us elucidate the physiological and metabolic response of plants fumigated with NO2.
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Affiliation(s)
- Yanbo Hu
- College of Life Science, Northeast Forestry UniversityHarbin, China
| | - Victoria Fernández
- Forest Genetics and Ecophysiology Research Group, School of Forest Engineering, Technical University of MadridMadrid, Spain
| | - Ling Ma
- School of Forestry, Northeast Forestry UniversityHarbin, China
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Zhang J, Martinoia E, De Angeli A. Cytosolic nucleotides block and regulate the Arabidopsis vacuolar anion channel AtALMT9. J Biol Chem 2014; 289:25581-9. [PMID: 25028514 DOI: 10.1074/jbc.m114.576108] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The aluminum-activated malate transporters (ALMTs) form a membrane protein family exhibiting different physiological roles in plants, varying from conferring tolerance to environmental Al(3+) to the regulation of stomatal movement. The regulation of the anion channels of the ALMT family is largely unknown. Identifying intracellular modulators of the activity of anion channels is fundamental to understanding their physiological functions. In this study we investigated the role of cytosolic nucleotides in regulating the activity of the vacuolar anion channel AtALMT9. We found that cytosolic nucleotides modulate the transport activity of AtALMT9. This modulation was based on a direct block of the pore of the channel at negative membrane potentials (open channel block) by the nucleotide and not by a phosphorylation mechanism. The block by nucleotides of AtALMT9-mediated currents was voltage dependent. The blocking efficiency of intracellular nucleotides increased with the number of phosphate groups and ATP was the most effective cellular blocker. Interestingly, the ATP block induced a marked modification of the current-voltage characteristic of AtALMT9. In addition, increased concentrations of vacuolar anions were able to shift the ATP block threshold to a more negative membrane potential. The block of AtALMT9-mediated anion currents by ATP at negative membrane potentials acts as a gate of the channel and vacuolar anion tune this gating mechanism. Our results suggest that anion transport across the vacuolar membrane in plant cells is controlled by cytosolic nucleotides and the energetic status of the cell.
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Affiliation(s)
- Jingbo Zhang
- From the Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland and
| | - Enrico Martinoia
- From the Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland and
| | - Alexis De Angeli
- From the Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland and the Institut des Sciences du Végétal, CNRS, 91198 Gif-sur-Yvette, France
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32
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Wege S, De Angeli A, Droillard MJ, Kroniewicz L, Merlot S, Cornu D, Gambale F, Martinoia E, Barbier-Brygoo H, Thomine S, Leonhardt N, Filleur S. Phosphorylation of the vacuolar anion exchanger AtCLCa is required for the stomatal response to abscisic acid. Sci Signal 2014; 7:ra65. [PMID: 25005229 DOI: 10.1126/scisignal.2005140] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Eukaryotic anion/proton exchangers of the CLC (chloride channel) family mediate anion fluxes across intracellular membranes. The Arabidopsis thaliana anion/proton exchanger AtCLCa is involved in vacuolar accumulation of nitrate. We investigated the role of AtCLCa in leaf guard cells, a specialized plant epidermal cell that controls gas exchange and water loss through pores called stomata. We showed that AtCLCa not only fulfilled the expected role of accumulating anions in the vacuole during stomatal opening but also mediated anion release during stomatal closure in response to the stress hormone abscisic acid (ABA). We found that this dual role resulted from a phosphorylation-dependent change in the activity of AtCLCa. The protein kinase OST1 (also known as SnRK2.6) is a key signaling player and central regulator in guard cells in response to ABA. Phosphorylation of Thr(38) in the amino-terminal cytoplasmic domain of AtCLCa by OST1 increased the outward anion fluxes across the vacuolar membrane, which are essential for stomatal closure. We provide evidence that bidirectional activities of an intracellular CLC exchanger are physiologically relevant and that phosphorylation regulates the transport mode of this exchanger.
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Affiliation(s)
- Stefanie Wege
- CNRS-UPR 2355, Institut des Sciences du Végétal, Saclay Plant Sciences Labex, Bât. 22, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France
| | - Alexis De Angeli
- CNRS-UPR 2355, Institut des Sciences du Végétal, Saclay Plant Sciences Labex, Bât. 22, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France. Istituto di Biofisica, C.N.R., Via De Marini 6, 16149 Genova, Italy. Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
| | - Marie-Jo Droillard
- CNRS-UPR 2355, Institut des Sciences du Végétal, Saclay Plant Sciences Labex, Bât. 22, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France
| | - Laetitia Kroniewicz
- Laboratoire de Biologie du Développement des Plantes, Unité Mixte de Recherche 7265, Centre National de la Recherche Scientifique-Commissariat à l'Energie Atomique-Université Aix-Marseille II, Commissariat à l'Energie Atomique Cadarache Bât. 156, 13108 St Paul-lez-Durance, France
| | - Sylvain Merlot
- CNRS-UPR 2355, Institut des Sciences du Végétal, Saclay Plant Sciences Labex, Bât. 22, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France
| | - David Cornu
- CNRS-FRC5115, Centre de Recherche de Gif, Imagif, Bât. 21, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France
| | - Franco Gambale
- Istituto di Biofisica, C.N.R., Via De Marini 6, 16149 Genova, Italy
| | - Enrico Martinoia
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
| | - Hélène Barbier-Brygoo
- CNRS-UPR 2355, Institut des Sciences du Végétal, Saclay Plant Sciences Labex, Bât. 22, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France
| | - Sébastien Thomine
- CNRS-UPR 2355, Institut des Sciences du Végétal, Saclay Plant Sciences Labex, Bât. 22, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France
| | - Nathalie Leonhardt
- Laboratoire de Biologie du Développement des Plantes, Unité Mixte de Recherche 7265, Centre National de la Recherche Scientifique-Commissariat à l'Energie Atomique-Université Aix-Marseille II, Commissariat à l'Energie Atomique Cadarache Bât. 156, 13108 St Paul-lez-Durance, France
| | - Sophie Filleur
- CNRS-UPR 2355, Institut des Sciences du Végétal, Saclay Plant Sciences Labex, Bât. 22, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France. Université Paris 7 Denis Diderot, U.F.R. Sciences du Vivant, 35 rue Hélène Brion, 75205 Paris Cedex 13, France.
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Le Deunff E, Malagoli P. An updated model for nitrate uptake modelling in plants. I. Functional component: cross-combination of flow-force interpretation of nitrate uptake isotherms, and environmental and in planta regulation of nitrate influx. ANNALS OF BOTANY 2014; 113:991-1005. [PMID: 24638820 PMCID: PMC3997639 DOI: 10.1093/aob/mcu021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 01/21/2014] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS In spite of major breakthroughs in the last three decades in the identification of root nitrate uptake transporters in plants and the associated regulation of nitrate transport activities, a simplified and operational modelling approach for nitrate uptake is still lacking. This is due mainly to the difficulty in linking the various regulations of nitrate transport that act at different levels of time and on different spatial scales. METHODS A cross-combination of a Flow-Force approach applied to nitrate influx isotherms and experimentally determined environmental and in planta regulation is used to model nitrate in oilseed rape, Brassica napus. In contrast to 'Enzyme-Substrate' interpretations, a Flow-Force modelling approach considers the root as a single catalytic structure and does not infer hypothetical cellular processes among nitrate transporter activities across cellular layers in the mature roots. In addition, this approach accounts for the driving force on ion transport based on the gradient of electrochemical potential, which is more appropriate from a thermodynamic viewpoint. KEY RESULTS AND CONCLUSIONS Use of a Flow-Force formalism on nitrate influx isotherms leads to the development of a new conceptual mechanistic basis to model more accurately N uptake by a winter oilseed rape crop under field conditions during the whole growth cycle. This forms the functional component of a proposed new structure-function mechanistic model of N uptake.
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Affiliation(s)
- Erwan Le Deunff
- Université de Caen Basse-Normandie, UMR EVA, F-14032 Caen cedex, France
- INRA, UMR 950, Écophysiologie Végétale & Agronomie Nutritions NCS, F-14032 Caen cedex, France
| | - Philippe Malagoli
- Clermont Universités, Université Blaise Pascal, UMR 547 PIAF, BP 10448, F-63000 Clermont Ferrand, France
- INRA, UMR 547 PIAF, F-63100 Clermont Ferrand, France
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34
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Conformational changes required for H(+)/Cl(-) exchange mediated by a CLC transporter. Nat Struct Mol Biol 2014; 21:456-63. [PMID: 24747941 PMCID: PMC4040230 DOI: 10.1038/nsmb.2814] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 03/26/2014] [Indexed: 11/08/2022]
Abstract
CLC-type exchangers mediate transmembrane Cl(-) transport. Mutations altering their gating properties cause numerous genetic disorders. However, their transport mechanism remains poorly understood. In conventional models, two gates alternatively expose substrates to the intra- or extracellular solutions. A glutamate was identified as the only gate in the CLCs, suggesting that CLCs function by a nonconventional mechanism. Here we show that transport in CLC-ec1, a prokaryotic homolog, is inhibited by cross-links constraining movement of helix O far from the transport pathway. Cross-linked CLC-ec1 adopts a wild-type-like structure, indicating stabilization of a native conformation. Movements of helix O are transduced to the ion pathway via a direct contact between its C terminus and a tyrosine that is a constitutive element of the second gate of CLC transporters. Therefore, the CLC exchangers have two gates that are coupled through conformational rearrangements outside the ion pathway.
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35
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Ereño-Orbea J, Oyenarte I, Martínez-Cruz LA. CBS domains: Ligand binding sites and conformational variability. Arch Biochem Biophys 2013; 540:70-81. [DOI: 10.1016/j.abb.2013.10.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/08/2013] [Accepted: 10/11/2013] [Indexed: 02/07/2023]
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36
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Yamada T, Bhate MP, Strange K. Regulatory phosphorylation induces extracellular conformational changes in a CLC anion channel. Biophys J 2013; 104:1893-904. [PMID: 23663832 DOI: 10.1016/j.bpj.2013.03.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 03/15/2013] [Accepted: 03/19/2013] [Indexed: 10/26/2022] Open
Abstract
CLH-3b is a CLC-1/2/Ka/Kb channel homolog activated by meiotic cell cycle progression and cell swelling. Channel inhibition occurs by GCK-3 kinase-mediated phosphorylation of serine residues on the cytoplasmic C-terminus linker connecting CBS1 and CBS2. Two conserved aromatic amino acid residues located on the intracellular loop connecting membrane helices H and I and α1 of CBS2 are required for transducing phosphorylation changes into changes in channel activity. Helices H and I form part of the interface between the two subunits that comprise functional CLC channels. Using a cysteine-less CLH-3b mutant, we demonstrate that the sulfhydryl reagent reactivity of substituted cysteines at the subunit interface changes dramatically during GCK-3-mediated channel inhibition and that these changes are prevented by mutation of the H-I loop/CBS2 α1 signal transduction domain. We also show that GCK-3 modifies Zn(2+) inhibition, which is thought to be mediated by the common gating process. These and other results suggest that phosphorylation of the cytoplasmic C-terminus inhibits CLH-3b by inducing subunit interface conformation changes that activate the common gate. Our findings have important implications for understanding CLC regulation by diverse signaling mechanisms and for understanding the structure/function relationships that mediate intraprotein communication in this important family of Cl(-) transport proteins.
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Affiliation(s)
- Toshiki Yamada
- Boylan Center for Cellular and Molecular Physiology, Mount Desert Island Biological Laboratory, Salisbury Cove, Maine, USA
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NO₃⁻/H⁺ antiport in the tonoplast of cucumber root cells is stimulated by nitrate supply: evidence for a reversible nitrate-induced phosphorylation of vacuolar NO₃⁻/H⁺ antiport. PLoS One 2013; 8:e73972. [PMID: 24040130 PMCID: PMC3770621 DOI: 10.1371/journal.pone.0073972] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 07/25/2013] [Indexed: 11/19/2022] Open
Abstract
Studies in the last few years have shed light on the process of nitrate accumulation within plant cells, achieving molecular identification and partial characterization of the genes and proteins involved in this process. However, contrary to the plasma membrane-localized nitrate transport activities, the kinetics of active nitrate influx into the vacuole and its adaptation to external nitrate availability remain poorly understood. In this work, we have investigated the activity and regulation of the tonoplast-localized H+/NO3− antiport in cucumber roots in response to N starvation and NO3− induction. The time course of nitrate availability strongly influenced H+/NO3− antiport activity at the tonoplast of root cells. However, under N starvation active nitrate accumulation within the vacuole still occurred. Hence, either a constitutive H+-coupled transport system specific for nitrate operates at the tonoplast, or nitrate uses another transport protein of broader specificity to different anions to enter the vacuole via a proton-dependent process. H+/NO3− antiport in cucumber was significantly stimulated in NO3−-induced plants that were supplied with nitrate for 24 hours following 6-day-long N starvation. The cytosolic fraction isolated from the roots of NO3−-induced plants significantly stimulated H+/NO3− antiport in tonoplast membranes isolated from cucumbers growing on nitrate. The stimulatory effect of the cytosolic fraction was completely abolished by EGTA and the protein kinase inhibitor staurosporine and slightly enhanced by the phosphatase inhibitors okadaic acid and cantharidin. Hence, we conclude that stimulation of H+/NO3− antiport at the tonoplast of cucumber roots in response to nitrate provision may occur through the phosphorylation of a membrane antiporter involving Ca-dependent, staurosporine-sensitive protein kinase.
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Anantharaman V, Iyer LM, Aravind L. Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing. MOLECULAR BIOSYSTEMS 2013; 8:3142-65. [PMID: 23044854 DOI: 10.1039/c2mb25239b] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The mode of action of the bacterial ter cluster and TelA genes, implicated in natural resistance to tellurite and other xenobiotic toxic compounds, pore-forming colicins and several bacteriophages, has remained enigmatic for almost two decades. Using comparative genomics, sequence-profile searches and structural analysis we present evidence that the ter gene products and their functional partners constitute previously underappreciated, chemical stress response and anti-viral defense systems of bacteria. Based on contextual information from conserved gene neighborhoods and domain architectures, we show that the ter gene products and TelA lie at the center of membrane-linked metal recognition complexes with regulatory ramifications encompassing phosphorylation-dependent signal transduction, RNA-dependent regulation, biosynthesis of nucleoside-like metabolites and DNA processing. Our analysis suggests that the multiple metal-binding and non-binding TerD paralogs and TerC are likely to constitute a membrane-associated complex, which might also include TerB and TerY, and feature several, distinct metal-binding sites. Versions of the TerB domain might also bind small molecule ligands and link the TerD paralog-TerC complex to biosynthetic modules comprising phosphoribosyltransferases (PRTases), ATP grasp amidoligases, TIM-barrel carbon-carbon lyases, and HAD phosphoesterases, which are predicted to synthesize novel nucleoside-like molecules. One of the PRTases is also likely to interact with RNA by means of its Pelota/Ribosomal protein L7AE-like domain. The von Willebrand factor A domain protein, TerY, is predicted to be part of a distinct phosphorylation switch, coupling a protein kinase and a PP2C phosphatase. We show, based on the evidence from numerous conserved gene neighborhoods and domain architectures, that both the TerB and TelA domains have been linked to diverse lipid-interaction domains, such as two novel PH-like and the Coq4 domains, in different bacteria, and are likely to comprise membrane-associated sensory complexes that might additionally contain periplasmic binding-protein-II and OmpA domains. We also show that the TerD and TerB domains and the TerY-associated phosphorylation system are functionally linked to many distinct DNA-processing complexes, which feature proteins with SWI2/SNF2 and RecQ-like helicases, multiple AAA+ ATPases, McrC-N-terminal domain proteins, several restriction endonuclease fold DNases, DNA-binding domains and a type-VII/Esx-like system, which is at the center of a predicted DNA transfer apparatus. These DNA-processing modules and associated genes are predicted to be involved in restriction or suicidal action in response to phages and possibly repairing xenobiotic-induced DNA damage. In some eukaryotes, certain components of the ter system appear to be recruited to function in conjunction with the ubiquitin system and calcium-signaling pathways.
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Affiliation(s)
- Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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39
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Garcia-Celma J, Szydelko A, Dutzler R. Functional characterization of a ClC transporter by solid-supported membrane electrophysiology. ACTA ACUST UNITED AC 2013; 141:479-91. [PMID: 23478993 PMCID: PMC3607819 DOI: 10.1085/jgp.201210927] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
EcClC, a prokaryotic member of the ClC family of chloride channels and transporters, works as coupled H+/Cl− exchanger. With a known structure and the possibility of investigating its behavior with different biochemical and biophysical techniques, the protein has become an important model system for the family. Although many aspects of its function have been previously characterized, it was difficult to measure transport on the same sample under different environmental conditions. To overcome this experimental limitation, we have studied EcClC by solid-supported membrane electrophysiology. The large transport-related transient currents and a simple way of relating transport rates to the measured signal have allowed a thorough investigation of ion selectivity, inhibition, and the dependence of transport on changes in ion concentration and pH. Our results confirm that the protein transports larger anions with about similar rates, whereas the smaller fluoride is not a substrate. We also show that 4,4′-diisothiocyano-2,2’-stilbenedisulfonic acid (DIDS), a known inhibitor of other anion transport protein, irreversibly inhibits EcClC from the intracellular side. The chloride dependence shows an apparent saturation at millimolar concentrations that resembles a similar behavior in eukaryotic ClC channels. Our experiments have also allowed us to quantify the pH dependence of transport. EcClC shows a strong activation at low pH with an apparent pKa of 4.6. The pronounced pH dependence is lost by the mutation of a conserved glutamate facing the extracellular solution that was previously shown to be an acceptor for transported protons, whereas it is largely retained by the mutation of an equivalent residue at the intracellular side. Our results have provided a quantitative basis for the transport behavior of EcClC, and they will serve as a reference for future investigations of novel electrogenic transporters with still-uncharacterized properties.
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Affiliation(s)
- Juan Garcia-Celma
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
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40
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Moran O, Grottesi A, Chadburn AJ, Tammaro P. Parametrisation of the free energy of ATP binding to wild-type and mutant Kir6.2 potassium channels. Biophys Chem 2012; 171:76-83. [PMID: 23219002 DOI: 10.1016/j.bpc.2012.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 10/30/2012] [Accepted: 10/30/2012] [Indexed: 11/28/2022]
Abstract
ATP-sensitive K(+) (K(ATP)) channels, comprised of pore-forming Kir6.x and regulatory SURx subunits, play important roles in many cellular functions; because of their sensitivity to inhibition by intracellular ATP, K(ATP) channels provide a link between cell metabolism and membrane electrical activity. We constructed structural homology models of Kir6.2 and a series of Kir6.2 channels carrying mutations within the putative ATP-binding site. Computational docking was carried out to determine the conformation of ATP in its binding site. The Linear Interaction Energy (LIE) method was used to estimate the free-energy of ATP binding to wild-type and mutant Kir6.2 channels. Comparisons of the theoretical binding free energies for ATP with those determined from mutational experiments enabled the identification of the most probable conformation of ATP bound to the Kir6.2 channel. A set of LIE parameters was defined that may enable prediction of the effects of additional Kir6.2 mutations within the ATP binding site on the affinity for ATP.
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Miyazaki H, Yamada T, Parton A, Morrison R, Kim S, Beth AH, Strange K. CLC anion channel regulatory phosphorylation and conserved signal transduction domains. Biophys J 2012; 103:1706-18. [PMID: 23083714 DOI: 10.1016/j.bpj.2012.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/20/2012] [Accepted: 09/04/2012] [Indexed: 12/01/2022] Open
Abstract
The signaling mechanisms that regulate CLC anion channels are poorly understood. Caenorhabditis elegans CLH-3b is a member of the CLC-1/2/Ka/Kb channel subfamily. CLH-3b is activated by meiotic cell-cycle progression and cell swelling. Inhibition is brought about by GCK-3 kinase-mediated phosphorylation of S742 and S747 located on a ∼176 amino acid disordered domain linking CBS1 and CBS2. Much of the inter-CBS linker is dispensable for channel regulation. However, deletion of a 14 amino acid activation domain encompassing S742 and S747 inhibits channel activity to the same extent as GCK-3. The crystal structure of CmCLC demonstrated that CBS2 interfaces extensively with an intracellular loop connecting membrane helices H and I, the C-terminus of helix D, and a short linker connecting helix R to CBS1. Point mutagenesis of this interface identified two highly conserved aromatic amino acid residues located in the H-I loop and the first α-helix (α1) of CBS2. Mutation of either residue to alanine rendered CLH-3b insensitive to GCK-3 inhibition. We suggest that the dephosphorylated activation domain normally interacts with CBS1 and/or CBS2, and that conformational information associated with this interaction is transduced through a conserved signal transduction module comprising the H-I loop and CBS2 α1.
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Affiliation(s)
- Hiroaki Miyazaki
- Boylan Center for Cellular and Molecular Physiology, Mount Desert Island Biological Laboratory, Salisbury Cove, Maine, USA
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42
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Gómez-García I, Stuiver M, Ereño J, Oyenarte I, Corral-Rodríguez MA, Müller D, Martínez-Cruz LA. Purification, crystallization and preliminary crystallographic analysis of the CBS-domain pair of cyclin M2 (CNNM2). Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1198-203. [PMID: 23027747 PMCID: PMC3497979 DOI: 10.1107/s1744309112035348] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 08/09/2012] [Indexed: 05/13/2024]
Abstract
This work describes the purification and preliminary crystallographic analysis of the CBS-domain pair of the murine CNNM2 magnesium transporter (formerly known as ancient domain protein 2; ACDP2), which consists of a pair of cystathionine β-synthase (CBS) motifs and has 100% sequence identity to its human homologue. CNNM proteins represent the least-studied members of the eight different types of magnesium transporters identified to date in mammals. In humans, the CNNM family is encoded by four genes: CNNM1-4. CNNM1 acts as a cytosolic copper chaperone, whereas CNNM2 and CNNM4 have been associated with magnesium handling. Interestingly, mutations in the CNNM2 gene cause familial dominant hypomagnesaemia (MIM:607803), a rare human disorder characterized by renal and intestinal magnesium (Mg(2+)) wasting, which may lead to symptoms of Mg(2+) depletion such as tetany, seizures and cardiac arrhythmias. This manuscript describes the preliminary crystallographic analysis of two different crystal habits of a truncated form of the protein containing its regulatory CBS-domain pair, which has been reported to host the pathological mutation T568I in humans. The crystals belonged to space groups P2(1)2(1)2 and I222 (or I2(1)2(1)2(1)) and diffracted X-rays to 2.0 and 3.6 Å resolution, respectively, using synchrotron radiation.
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Affiliation(s)
- Inmaculada Gómez-García
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Bizkaia, Spain
| | - Marchel Stuiver
- Department of Pediatric Nephrology, Charité Universitätsmedizin, 13353 Berlin, Germany
| | - June Ereño
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Bizkaia, Spain
| | - Iker Oyenarte
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Bizkaia, Spain
| | | | - Dominik Müller
- Department of Pediatric Nephrology, Charité Universitätsmedizin, 13353 Berlin, Germany
| | - Luis Alfonso Martínez-Cruz
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Bizkaia, Spain
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Wang YY, Hsu PK, Tsay YF. Uptake, allocation and signaling of nitrate. TRENDS IN PLANT SCIENCE 2012; 17:458-67. [PMID: 22658680 DOI: 10.1016/j.tplants.2012.04.006] [Citation(s) in RCA: 321] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 04/20/2012] [Accepted: 04/26/2012] [Indexed: 05/18/2023]
Abstract
Plants need to acquire nitrogen (N) efficiently from the soil for growth. Nitrate is one of the major N sources for higher plants. Therefore, nitrate uptake and allocation are key factors in efficient N utilization. Membrane-bound transporters are required for nitrate uptake from the soil and for the inter- and intracellular movement of nitrate inside the plants. Four gene families, nitrate transporter 1/peptide transporter (NRT1/PTR), NRT2, chloride channel (CLC), and slow anion channel-associated 1 homolog 3 (SLAC1/SLAH), are involved in nitrate uptake, allocation, and storage in higher plants. Recent studies of these transporters or channels have provided new insights into the molecular mechanisms of nitrate uptake and allocation. Interestingly, several of these transporters also play versatile roles in nitrate sensing, plant development, pathogen defense, and/or stress response.
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Affiliation(s)
- Ya-Yun Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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44
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Bennetts B, Yu Y, Chen TY, Parker MW. Intracellular β-nicotinamide adenine dinucleotide inhibits the skeletal muscle ClC-1 chloride channel. J Biol Chem 2012; 287:25808-20. [PMID: 22689570 DOI: 10.1074/jbc.m111.327551] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
ClC-1 is the dominant sarcolemmal chloride channel and plays an important role in regulating membrane excitability that is underscored by ClC-1 mutations in congenital myotonia. Here we show that the coenzyme β-nicotinamide adenine dinucleotide (NAD), an important metabolic regulator, robustly inhibits ClC-1 when included in the pipette solution in whole cell patch clamp experiments and when transiently applied to inside-out patches. The oxidized (NAD(+)) form of the coenzyme was more efficacious than the reduced (NADH) form, and inhibition by both was greatly enhanced by acidification. Molecular modeling, based on the structural coordinates of the homologous ClC-5 and CmClC proteins and in silico docking, suggest that NAD(+) binds with the adenine base deep in a cleft formed by ClC-1 intracellular cystathionine β-synthase domains, and the nicotinamide base interacts with the membrane-embedded channel domain. Consistent with predictions from the models, mutation of residues in cystathionine β-synthase and channel domains either attenuated (G200R, T636A, H847A) or abrogated (L848A) the effect of NAD(+). In addition, the myotonic mutations G200R and Y261C abolished potentiation of NAD(+) inhibition at low pH. Our results identify a new biological role for NAD and suggest that the main physiological relevance may be the exquisite sensitivity to intracellular pH that NAD(+) inhibition imparts to ClC-1 gating. These findings are consistent with the reduction of sarcolemmal chloride conductance that occurs upon acidification of skeletal muscle and suggest a previously unexplored mechanism in the pathophysiology of myotonia.
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Affiliation(s)
- Brett Bennetts
- Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia.
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Costa A, Gutla PVK, Boccaccio A, Scholz-Starke J, Festa M, Basso B, Zanardi I, Pusch M, Schiavo FL, Gambale F, Carpaneto A. The Arabidopsis central vacuole as an expression system for intracellular transporters: functional characterization of the Cl-/H+ exchanger CLC-7. J Physiol 2012; 590:3421-30. [PMID: 22641774 DOI: 10.1113/jphysiol.2012.230227] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Functional characterization of intracellular transporters is hampered by the inaccessibility of animal endomembranes to standard electrophysiological techniques. Here, we used Arabidopsis mesophyll protoplasts as a novel heterologous expression system for the lysosomal chloride–proton exchanger CLC-7 from rat. Following transient expression of a rCLC-7:EGFP construct in isolated protoplasts, the fusion protein efficiently targeted to the membrane of the large central vacuole, the lytic compartment of plant cells. Membrane currents recorded from EGFP-positive vacuoles were almost voltage independent and showed time-dependent activation at elevated positive membrane potentials as a hallmark. The shift in the reversal potential of the current induced by a decrease of cytosolic pH was compatible with a 2Cl(-)/1H(+) exchange stoichiometry. Mutating the so-called gating glutamate into alanine (E245A) uncoupled chloride fluxes from the movement of protons, transforming the transporter into a chloride channel-like protein. Importantly, CLC-7 transport activity in the vacuolar expression system was recorded in the absence of the auxiliary subunit Ostm1, differently to recent data obtained in Xenopus oocytes using a CLC-7 mutant with partial plasma membrane expression. We also show that plasma membrane-targeted CLC-7(E245A) is non-functional in Xenopus oocytes when expressed without Ostm1. In summary, our data suggest the existence of an alternative CLC-7 operating mode, which is active when the protein is not in complex with Ostm1. The vacuolar expression system has the potential to become a valuable tool for functional studies on intracellular ion channels and transporters from animal cells.
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Affiliation(s)
- Alex Costa
- University of Padova, Via U. Bassi 58/B, 35131 Padova, Italy
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Tampieri E, Baraldi E, Carnevali F, Frascaroli E, De Santis A. The activity of plant inner membrane anion channel (PIMAC) can be performed by a chloride channel (CLC) protein in mitochondria from seedlings of maize populations divergently selected for cold tolerance. J Bioenerg Biomembr 2011; 43:611-21. [PMID: 21989547 DOI: 10.1007/s10863-011-9386-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 08/21/2011] [Indexed: 10/17/2022]
Abstract
The proteins performing the activity of the inner membrane anion channel (IMAC) and its plant counterpart (PIMAC) are still unknown. Lurin et al. (Biochem J 348: 291-295, 2000) indicated that a chloride channel (CLC) protein corresponds to PIMAC activity in tobacco seedling mitochondria. In this study, we investigated: (i) the presence of a CLC protein in maize seedling mitochondria; (ii) the involvement of this protein in plant cold tolerance; and (iii) its possible role in PIMAC activity. We validated the presence of a CLC protein (ZmCLCc) in maize mitochondria by immunoassay using a polyclonal antibody against its C-terminus. The differential expression of the ZmCLCc protein in mitochondria was measured in seedlings of maize populations divergently selected for cold tolerance and grown at different temperatures. The ZmCLCc protein level was higher in cold stressed than in non-stressed growing conditions. Moreover, the ZmCLCc level showed a direct relationship with the cold sensitivity level of the populations under both growing conditions, suggesting that selection for cold tolerance induced a constitutive change of the ZmCLCc protein amount in mitochondria. The anti-ZmCLCc antibody inhibited (about 60%) the channel-mediated anion translocations by PIMAC, whereas the same antibody did not affect the free diffusion of potassium thiocyanide through the inner mitochondrial membrane. For this reason, we conclude that the mitochondrial ZmCLCc protein can perform the PIMAC activity in maize seedlings.
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Affiliation(s)
- Elisabetta Tampieri
- Laboratory of Plant Physiology, Dipartimento di Scienze del Mare, Università Politecnica delle Marche, Via Brecce Bianche, 60123, Ancona, Italy
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Baykov AA, Tuominen HK, Lahti R. The CBS domain: a protein module with an emerging prominent role in regulation. ACS Chem Biol 2011; 6:1156-63. [PMID: 21958115 DOI: 10.1021/cb200231c] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Regulatory CBS (cystathionine β-synthase) domains exist as two or four tandem copies in thousands of cytosolic and membrane-associated proteins from all kingdoms of life. Mutations in the CBS domains of human enzymes and membrane channels are associated with an array of hereditary diseases. Four CBS domains encoded within a single polypeptide or two identical polypeptides (each having a pair of CBS domains at the subunit interface) form a highly conserved disk-like structure. CBS domains act as autoinhibitory regulatory units in some proteins and activate or further inhibit protein function upon binding to adenosine nucleotides (AMP, ADP, ATP, S-adenosyl methionine, NAD, diadenosine polyphosphates). As a result of the differential effects of the nucleotides, CBS domain-containing proteins can sense cell energy levels. Significant conformational changes are induced in CBS domains by bound ligands, highlighting the structural basis for their effects.
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Affiliation(s)
- Alexander A. Baykov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Heidi K. Tuominen
- Department of Biochemistry and Food Chemistry, University of Turku, Turku FIN-20014, Finland
| | - Reijo Lahti
- Department of Biochemistry and Food Chemistry, University of Turku, Turku FIN-20014, Finland
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Schulz A, Beyhl D, Marten I, Wormit A, Neuhaus E, Poschet G, Büttner M, Schneider S, Sauer N, Hedrich R. Proton-driven sucrose symport and antiport are provided by the vacuolar transporters SUC4 and TMT1/2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 68:129-36. [PMID: 21668536 DOI: 10.1111/j.1365-313x.2011.04672.x] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The vacuolar membrane is involved in solute uptake into and release from the vacuole, which is the largest plant organelle. In addition to inorganic ions and metabolites, large quantities of protons and sugars are shuttled across this membrane. Current models suggest that the proton gradient across the membrane drives the accumulation and/or release of sugars. Recent studies have associated AtSUC4 with the vacuolar membrane. Some members of the SUC family are plasma membrane proton/sucrose symporters. In addition, the sugar transporters TMT1 and TMT2, which are localized to the vacuolar membrane, have been suggested to function in proton-driven glucose antiport. Here we used the patch-clamp technique to monitor carrier-mediated sucrose transport by AtSUC4 and AtTMTs in intact Arabidopsis thaliana mesophyll vacuoles. In the whole-vacuole configuration with wild-type material, cytosolic sucrose-induced proton currents were associated with a proton/sucrose antiport mechanism. To identify the related transporter on one hand, and to enable the recording of symporter-mediated currents on the other hand, we electrophysiologically characterized vacuolar proteins recognized by Arabidopsis mutants of partially impaired sugar compartmentation. To our surprise, the intrinsic sucrose/proton antiporter activity was greatly reduced when vacuoles were isolated from plants lacking the monosaccharide transporter AtTMT1/TMT2. Transient expression of AtSUC4 in this mutant background resulted in proton/sucrose symport activity. From these studies, we conclude that, in the natural environment within the Arabidopsis cell, AtSUC4 most likely catalyses proton-coupled sucrose export from the vacuole. However, TMT1/2 probably represents a proton-coupled antiporter capable of high-capacity loading of glucose and sucrose into the vacuole.
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Affiliation(s)
- Alexander Schulz
- University of Wuerzburg, Institute for Molecular Plant Physiology and Biophysics, Julius von Sachs Platz 2, D-97082 Wuerzburg, Germany
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Tseng PY, Yu WP, Liu HY, Zhang XD, Zou X, Chen TY. Binding of ATP to the CBS domains in the C-terminal region of CLC-1. ACTA ACUST UNITED AC 2011; 137:357-68. [PMID: 21444658 PMCID: PMC3068280 DOI: 10.1085/jgp.201010495] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The common gating of CLC-1 has been shown to be inhibited by intracellular adenosine triphosphate (ATP) in acidic pH conditions. Such modulation is thought to be mediated by direct binding of ATP to the cystathionine β-synthase (CBS) domains at the C-terminal cytoplasmic region of CLC-1. Guided by the crystal structure of the C-terminal domain of CLC-5, we constructed a homology model of CLC-1’s C terminus and mutated critical amino acid residues lining the potential ATP-binding site. The CLC-1 mutations V634A and E865A completely abolished the ATP inhibition of CLC-1, consistent with the loss of ATP binding seen with the corresponding mutations in CLC-5. Mutating two other residues, V613 and V860, also disrupted the ATP modulation of CLC-1. However, placing aromatic amino acids at position 634 increases the apparent ATP affinity. Mutant cycle analyses showed that the modulation effects of ATP and cytidine triphosphate on wild-type CLC-1 and the V634F mutant were nonadditive, suggesting that the side chain of amino acid at position 634 interacts with the base moiety of the nucleotide. The mutation effects of V634F and V613A on the ATP modulation were also nonadditive, which is consistent with the assertion suggested from the homology model that these two residues may both interact with the bound nucleotide. These results provide evidence for a direct ATP binding for modulating the function of CLC-1 and suggest an overall conserved architecture of the ATP-binding sites in CLC-1 and CLC-5. This study also demonstrates that CLC-1 is a convenient experimental model for studying the interaction of nucleotides/nucleosides with the CBS domain.
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Affiliation(s)
- Pang-Yen Tseng
- Center for Neuroscience, University of California, Davis, Davis, CA 95618, USA
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Spetea C, Schoefs B. Solute transporters in plant thylakoid membranes: Key players during photosynthesis and light stress. Commun Integr Biol 2011; 3:122-9. [PMID: 20585503 DOI: 10.4161/cib.3.2.10909] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 12/09/2009] [Indexed: 11/19/2022] Open
Abstract
Plants utilize sunlight to drive photosynthetic energy conversion in the chloroplast thylakoid membrane. Here are located four major photosynthetic complexes, about which we have great knowledge in terms of structure and function. However, much less we know about auxiliary proteins, such as transporters, ensuring an optimum function and turnover of these complexes. The most prominent thylakoid transporter is the proton-translocating ATP-synthase. Recently, four additional transporters have been identified in the thylakoid membrane of Arabidopsis thaliana, namely one copper-transporting P-ATPase, one chloride channel, one phosphate transporter, and one ATP/ADP carrier. Here, we review the current knowledge on the function and physiological role of these transporters during photosynthesis and light stress in plants. Subsequently, we make a survey on the outlook of thylakoid activities awaiting identification of responsible proteins. Such knowledge is necessary to understand the thylakoid network of transporters, and to design strategies for bioengineering crop plants in the future.
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