1
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Holmes AOM, Goldman A, Kalli AC. mPPases create a conserved anionic membrane fingerprint as identified via multi-scale simulations. PLoS Comput Biol 2022; 18:e1010578. [PMID: 36191052 PMCID: PMC9560603 DOI: 10.1371/journal.pcbi.1010578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 10/13/2022] [Accepted: 09/16/2022] [Indexed: 11/06/2022] Open
Abstract
Membrane-integral pyrophosphatases (mPPases) are membrane-bound enzymes responsible for hydrolysing inorganic pyrophosphate and translocating a cation across the membrane. Their function is essential for the infectivity of clinically relevant protozoan parasites and plant maturation. Recent developments have indicated that their mechanism is more complicated than previously thought and that the membrane environment may be important for their function. In this work, we use multiscale molecular dynamics simulations to demonstrate for the first time that mPPases form specific anionic lipid interactions at 4 sites at the distal and interfacial regions of the protein. These interactions are conserved in simulations of the mPPases from Thermotoga maritima, Vigna radiata and Clostridium leptum and characterised by interactions with positive residues on helices 1, 2, 3 and 4 for the distal site, or 9, 10, 13 and 14 for the interfacial site. Due to the importance of these helices in protein stability and function, these lipid interactions may play a crucial role in the mPPase mechanism and enable future structural and functional studies.
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Affiliation(s)
- Alexandra O. M. Holmes
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Adrian Goldman
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- Research Program in Molecular and Integrative Biosciences, University of Helsinki, Helsinki, Finland
| | - Antreas C. Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine and Astbury Centre for Structural Biology, University of Leeds, Leeds, United Kingdom
- * E-mail:
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2
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Holmes AOM, Kalli AC, Goldman A. The Function of Membrane Integral Pyrophosphatases From Whole Organism to Single Molecule. Front Mol Biosci 2019; 6:132. [PMID: 31824962 PMCID: PMC6882861 DOI: 10.3389/fmolb.2019.00132] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/08/2019] [Indexed: 12/02/2022] Open
Abstract
Membrane integral pyrophosphatases (mPPases) are responsible for the hydrolysis of pyrophosphate. This enzymatic mechanism is coupled to the pumping of H+ or Na+ across membranes in a process that can be K+ dependent or independent. Understanding the movements and dynamics throughout the mPPase catalytic cycle is important, as this knowledge is essential for improving or impeding protein function. mPPases have been shown to play a crucial role in plant maturation and abiotic stress tolerance, and so have the potential to be engineered to improve plant survival, with implications for global food security. mPPases are also selectively toxic drug targets, which could be pharmacologically modulated to reduce the virulence of common human pathogens. The last few years have seen the publication of many new insights into the function and structure of mPPases. In particular, there is a new body of evidence that the catalytic cycle is more complex than originally proposed. There are structural and functional data supporting a mechanism involving half-of-the-sites reactivity, inter-subunit communication, and exit channel motions. A more advanced and in-depth understanding of mPPases has begun to be uncovered, leaving the field of research with multiple interesting avenues for further exploration and investigation.
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Affiliation(s)
- Alexandra O. M. Holmes
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Antreas C. Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine and Astbury Centre for Structural Biology, University of Leeds, Leeds, United Kingdom
| | - Adrian Goldman
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- Research Program in Molecular and Integrative Biosciences, University of Helsinki, Helsinki, Finland
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3
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Strauss J, Wilkinson C, Vidilaseris K, Harborne SPD, Goldman A. A Simple Strategy to Determine the Dependence of Membrane-Bound Pyrophosphatases on K + as a Cofactor. Methods Enzymol 2018; 607:131-156. [PMID: 30149856 DOI: 10.1016/bs.mie.2018.04.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Membrane-bound pyrophosphatases (mPPases) couple pyrophosphate hydrolysis to H+ and/or Na+ pumping across membranes and are found in all domains of life except for multicellular animals including humans. They are important for development and stress resistance in plants. Furthermore, mPPases play a role in virulence of human pathogens that cause severe diseases such as malaria and African sleeping sickness. Sequence analysis, functional studies, and recently solved crystal structures have contributed to the understanding of the mPPase catalytic cycle. However, several key mechanistic features remain unknown. During evolution, several subgroups of mPPases differing in their pumping specificity and cofactor dependency arose. mPPases are classified into one of five subgroups, usually by sequence analysis. However, classification based solely on sequence has been inaccurate in several instances due to our limited understanding of the molecular mechanism of mPPases. Thus, pumping specificity and cofactor dependency of mPPases require experimental confirmation. Here, we describe a simple method for the determination of K+ dependency in mPPases using a hydrolytic activity assay. By coupling these dependency studies with site-directed mutagenesis, we have begun to build a better understanding of the molecular mechanisms of mPPases. We optimized the assay for thermostable mPPases that are commonly used as model systems in our lab, but the method is equally applicable to mesophilic mPPases with minor modifications.
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Affiliation(s)
- Jannik Strauss
- Astbury Centre for Structural Biology, University of Leeds, Leeds, United Kingdom
| | - Craig Wilkinson
- Astbury Centre for Structural Biology, University of Leeds, Leeds, United Kingdom
| | - Keni Vidilaseris
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Steven P D Harborne
- Astbury Centre for Structural Biology, University of Leeds, Leeds, United Kingdom.
| | - Adrian Goldman
- Astbury Centre for Structural Biology, University of Leeds, Leeds, United Kingdom; Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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4
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Zhao Q, Chen W, Bian J, Xie H, Li Y, Xu C, Ma J, Guo S, Chen J, Cai X, Wang X, Wang Q, She Y, Chen S, Zhou Z, Dai S. Proteomics and Phosphoproteomics of Heat Stress-Responsive Mechanisms in Spinach. FRONTIERS IN PLANT SCIENCE 2018; 9:800. [PMID: 29997633 PMCID: PMC6029058 DOI: 10.3389/fpls.2018.00800] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/24/2018] [Indexed: 05/02/2023]
Abstract
Elevated temperatures limit plant growth and reproduction and pose a growing threat to agriculture. Plant heat stress response is highly conserved and fine-tuned in multiple pathways. Spinach (Spinacia oleracea L.) is a cold tolerant but heat sensitive green leafy vegetable. In this study, heat adaptation mechanisms in a spinach sibling inbred heat-tolerant line Sp75 were investigated using physiological, proteomic, and phosphoproteomic approaches. The abundance patterns of 911 heat stress-responsive proteins, and phosphorylation level changes of 45 phosphoproteins indicated heat-induced calcium-mediated signaling, ROS homeostasis, endomembrane trafficking, and cross-membrane transport pathways, as well as more than 15 transcription regulation factors. Although photosynthesis was inhibited, diverse primary and secondary metabolic pathways were employed for defense against heat stress, such as glycolysis, pentose phosphate pathway, amino acid metabolism, fatty acid metabolism, nucleotide metabolism, vitamin metabolism, and isoprenoid biosynthesis. These data constitute a heat stress-responsive metabolic atlas in spinach, which will springboard further investigations into the sophisticated molecular mechanisms of plant heat adaptation and inform spinach molecular breeding initiatives.
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Affiliation(s)
- Qi Zhao
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
- Key Laboratory of Forest Plant Ecology, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Wenxin Chen
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Jiayi Bian
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Hao Xie
- Key Laboratory of Forest Plant Ecology, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
| | - Ying Li
- Key Laboratory of Forest Plant Ecology, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
| | - Chenxi Xu
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Jun Ma
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - Siyi Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
| | - Jiaying Chen
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaofeng Cai
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaoli Wang
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Quanhua Wang
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Yimin She
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - Sixue Chen
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
- Plant Molecular and Cellular Biology Program, Department of Biology, Genetics Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Zhiqiang Zhou
- Key Laboratory of Forest Plant Ecology, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
- *Correspondence: Shaojun Dai, Zhiqiang Zhou,
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
- Key Laboratory of Forest Plant Ecology, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
- *Correspondence: Shaojun Dai, Zhiqiang Zhou,
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5
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Shah NR, Wilkinson C, Harborne SPD, Turku A, Li KM, Sun YJ, Harris S, Goldman A. Insights into the mechanism of membrane pyrophosphatases by combining experiment and computer simulation. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:032105. [PMID: 28345008 PMCID: PMC5336470 DOI: 10.1063/1.4978038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/20/2017] [Indexed: 05/06/2023]
Abstract
Membrane-integral pyrophosphatases (mPPases) couple the hydrolysis of pyrophosphate (PPi) to the pumping of Na+, H+, or both these ions across a membrane. Recently solved structures of the Na+-pumping Thermotoga maritima mPPase (TmPPase) and H+-pumping Vigna radiata mPPase revealed the basis of ion selectivity between these enzymes and provided evidence for the mechanisms of substrate hydrolysis and ion-pumping. Our atomistic molecular dynamics (MD) simulations of TmPPase demonstrate that loop 5-6 is mobile in the absence of the substrate or substrate-analogue bound to the active site, explaining the lack of electron density for this loop in resting state structures. Furthermore, creating an apo model of TmPPase by removing ligands from the TmPPase:IDP:Na structure in MD simulations resulted in increased dynamics in loop 5-6, which results in this loop moving to uncover the active site, suggesting that interactions between loop 5-6 and the imidodiphosphate and its associated Mg2+ are important for holding a loop-closed conformation. We also provide further evidence for the transport-before-hydrolysis mechanism by showing that the non-hydrolyzable substrate analogue, methylene diphosphonate, induces low levels of proton pumping by VrPPase.
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Affiliation(s)
- Nita R Shah
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds, United Kingdom
| | - Craig Wilkinson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds, United Kingdom
| | - Steven P D Harborne
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds, United Kingdom
| | - Ainoleena Turku
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki , Helsinki, Finland
| | - Kun-Mou Li
- Department of Life Sciences and Institute of Bioinformatics and Structural Biology, College of Life Sciences, National Tsing Hua University , Hsinchu 30013, Taiwan
| | - Yuh-Ju Sun
- Department of Life Sciences and Institute of Bioinformatics and Structural Biology, College of Life Sciences, National Tsing Hua University , Hsinchu 30013, Taiwan
| | - Sarah Harris
- School of Physics and Astronomy and Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds, United Kingdom
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6
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Suzuki N, Bassil E, Hamilton JS, Inupakutika MA, Zandalinas SI, Tripathy D, Luo Y, Dion E, Fukui G, Kumazaki A, Nakano R, Rivero RM, Verbeck GF, Azad RK, Blumwald E, Mittler R. ABA Is Required for Plant Acclimation to a Combination of Salt and Heat Stress. PLoS One 2016; 11:e0147625. [PMID: 26824246 PMCID: PMC4733103 DOI: 10.1371/journal.pone.0147625] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/06/2016] [Indexed: 11/30/2022] Open
Abstract
Abiotic stresses such as drought, heat or salinity are a major cause of yield loss worldwide. Recent studies revealed that the acclimation of plants to a combination of different environmental stresses is unique and cannot be directly deduced from studying the response of plants to each of the different stresses applied individually. Here we report on the response of Arabidopsis thaliana to a combination of salt and heat stress using transcriptome analysis, physiological measurements and mutants deficient in abscisic acid, salicylic acid, jasmonic acid or ethylene signaling. Arabidopsis plants were found to be more susceptible to a combination of salt and heat stress compared to each of the different stresses applied individually. The stress combination resulted in a higher ratio of Na+/K+ in leaves and caused the enhanced expression of 699 transcripts unique to the stress combination. Interestingly, many of the transcripts that specifically accumulated in plants in response to the salt and heat stress combination were associated with the plant hormone abscisic acid. In accordance with this finding, mutants deficient in abscisic acid metabolism and signaling were found to be more susceptible to a combination of salt and heat stress than wild type plants. Our study highlights the important role abscisic acid plays in the acclimation of plants to a combination of two different abiotic stresses.
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Affiliation(s)
- Nobuhiro Suzuki
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7–1 Kioi-cho, Chiyoda-ku, 102–8554, Tokyo, Japan
- * E-mail: (NS); (RM)
| | - Elias Bassil
- Department of Plant Sciences, Mail Stop 5, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, United States of America
| | - Jason S. Hamilton
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203–5017, United States of America
| | - Madhuri A. Inupakutika
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203–5017, United States of America
| | - Sara Izquierdo Zandalinas
- Departamento de Ciencias Agrarias y del Medio Natural, Universitat Jaume I, Campus Riu Sec, E- 12071, Castello de la Plana, Spain
| | - Deesha Tripathy
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203–5017, United States of America
| | - Yuting Luo
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203–5017, United States of America
| | - Erin Dion
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203–5017, United States of America
| | - Ginga Fukui
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7–1 Kioi-cho, Chiyoda-ku, 102–8554, Tokyo, Japan
| | - Ayana Kumazaki
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7–1 Kioi-cho, Chiyoda-ku, 102–8554, Tokyo, Japan
| | - Ruka Nakano
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7–1 Kioi-cho, Chiyoda-ku, 102–8554, Tokyo, Japan
| | - Rosa M. Rivero
- Centro de Edafología y Biología Aplicada del Segura, Campus Universitario de Espinardo, Espinardo, Murcia, 30100, Spain
| | - Guido F. Verbeck
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203–5017, United States of America
| | - Rajeev K. Azad
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203–5017, United States of America
- Department of Mathematics, University of North Texas, Denton, TX, 76203, United States of America
| | - Eduardo Blumwald
- Department of Plant Sciences, Mail Stop 5, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, United States of America
| | - Ron Mittler
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203–5017, United States of America
- * E-mail: (NS); (RM)
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7
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R. Shah N, Vidilaseris K, Xhaard H, Goldman A. Integral membrane pyrophosphatases: a novel drug target for human pathogens? AIMS BIOPHYSICS 2016. [DOI: 10.3934/biophy.2016.1.171] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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8
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Yang Y, Liu Y, Yuan H, Liu X, Gao Y, Gong M, Zou Z. Membrane-bound pyrophosphatase of human gut microbe Clostridium methylpentosum confers improved salt tolerance in Escherichia coli, Saccharomyces cerevisiae and tobacco. Mol Membr Biol 2016; 33:39-50. [PMID: 29025361 DOI: 10.1080/09687688.2017.1370145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Membrane-bound pyrophosphatases (PPases) are involved in the adaption of organisms to stress conditions, which was substantiated by numerous plant transgenic studies with H+-PPase yet devoid of any correlated evidences for other two subfamilies, Na+-PPase and Na+,H+-PPase. Herein, we demonstrate the gene cloning and functional evaluation of the membrane-bound PPase (CmPP) of the human gut microbe Clostridium methylpentosum. The CmPP gene encodes a single polypeptide of 699 amino acids that was predicted as a multi-spanning membrane and K+-dependent Na+,H+-PPase. Heterologous expression of CmPP could significantly enhance the salt tolerance of both Escherichia coli and Saccharomyces cerevisiae, and this effect in yeast could be fortified by N-terminal addition of a vacuole-targeting signal peptide from the H+-PPase of Trypanosoma cruzi. Furthermore, introduction of CmPP could remarkably improve the salt tolerance of tobacco, implying its potential use in constructing salt-resistant transgenic crops. Consequently, the possible mechanisms of CmPP to underlie salt tolerance are discussed.
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Affiliation(s)
- Yumei Yang
- a School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy , Ministry of Education, Key Laboratory of Biomass Energy and Environmental Biotechnology of Yunnan Province, Yunnan Normal University , Kunming , Yunnan , China
| | - Yanjuan Liu
- a School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy , Ministry of Education, Key Laboratory of Biomass Energy and Environmental Biotechnology of Yunnan Province, Yunnan Normal University , Kunming , Yunnan , China
| | - Hang Yuan
- a School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy , Ministry of Education, Key Laboratory of Biomass Energy and Environmental Biotechnology of Yunnan Province, Yunnan Normal University , Kunming , Yunnan , China
| | - Xian Liu
- a School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy , Ministry of Education, Key Laboratory of Biomass Energy and Environmental Biotechnology of Yunnan Province, Yunnan Normal University , Kunming , Yunnan , China
| | - Yanxiu Gao
- a School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy , Ministry of Education, Key Laboratory of Biomass Energy and Environmental Biotechnology of Yunnan Province, Yunnan Normal University , Kunming , Yunnan , China
| | - Ming Gong
- a School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy , Ministry of Education, Key Laboratory of Biomass Energy and Environmental Biotechnology of Yunnan Province, Yunnan Normal University , Kunming , Yunnan , China
| | - Zhurong Zou
- a School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy , Ministry of Education, Key Laboratory of Biomass Energy and Environmental Biotechnology of Yunnan Province, Yunnan Normal University , Kunming , Yunnan , China
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9
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Molecular Cloning, Expression Analysis, and Functional Characterization of the H(+)-Pyrophosphatase from Jatropha curcas. Appl Biochem Biotechnol 2015; 178:1273-85. [PMID: 26643082 DOI: 10.1007/s12010-015-1944-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
Abstract
H(+)-pyrophosphatase (H(+)-PPase) is a primary pyrophosphate (PPi)-energized proton pump to generate electrochemical H(+) gradient for ATP production and substance translocations across membranes. It plays an important role in stress adaptation that was intensively substantiated by numerous transgenic plants overexpressing H(+)-PPases yet devoid of any correlated studies pointing to the elite energy plant, Jatropha curcas. Herein, we cloned the full length of J. curcas H(+)-PPase (JcVP1) complementary DNA (cDNA) by reverse transcription PCR, based on the assembled sequence of its ESTs highly matched to Hevea brasiliensis H(+)-PPase. This gene encodes a polypeptide of 765 amino acids that was predicted as a K(+)-dependent H(+)-PPase evolutionarily closest to those of other Euphorbiaceae plants. Many cis-regulatory elements relevant to environmental stresses, molecular signals, or tissue-specificity were identified by promoter prediction within the 1.5-kb region upstream of JcVP1 coding sequence. Meanwhile, the responses of JcVP1 expression to several common abiotic stresses (salt, drought, heat, cold) were characterized with a considerable accordance with the inherent stress tolerance of J. curcas. Moreover, we found that the heterologous expression of JcVP1 could significantly improve the salt tolerance in both recombinant Escherichia coli and Saccharomyces cerevisiae, and this effect could be further fortified in yeast by N-terminal addition of a vacuole-targeting signal peptide from the H(+)-PPase of Trypanosoma cruzi.
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10
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Mirete S, Mora-Ruiz MR, Lamprecht-Grandío M, de Figueras CG, Rosselló-Móra R, González-Pastor JE. Salt resistance genes revealed by functional metagenomics from brines and moderate-salinity rhizosphere within a hypersaline environment. Front Microbiol 2015; 6:1121. [PMID: 26528268 PMCID: PMC4602150 DOI: 10.3389/fmicb.2015.01121] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
Hypersaline environments are considered one of the most extreme habitats on earth and microorganisms have developed diverse molecular mechanisms of adaptation to withstand these conditions. The present study was aimed at identifying novel genes from the microbial communities of a moderate-salinity rhizosphere and brine from the Es Trenc saltern (Mallorca, Spain), which could confer increased salt resistance to Escherichia coli. The microbial diversity assessed by pyrosequencing of 16S rRNA gene libraries revealed the presence of communities that are typical in such environments and the remarkable presence of three bacterial groups never revealed as major components of salt brines. Metagenomic libraries from brine and rhizosphere samples, were transferred to the osmosensitive strain E. coli MKH13, and screened for salt resistance. Eleven genes that conferred salt resistance were identified, some encoding for well-known proteins previously related to osmoadaptation such as a glycerol transporter and a proton pump, whereas others encoded proteins not previously related to this function in microorganisms such as DNA/RNA helicases, an endonuclease III (Nth) and hypothetical proteins of unknown function. Furthermore, four of the retrieved genes were cloned and expressed in Bacillus subtilis and they also conferred salt resistance to this bacterium, broadening the spectrum of bacterial species in which these genes can function. This is the first report of salt resistance genes recovered from metagenomes of a hypersaline environment.
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Affiliation(s)
- Salvador Mirete
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología, Consejo Superior de Investigaciones Científicas - Instituto Nacional de Técnica Aeroespacial, Madrid Spain
| | - Merit R Mora-Ruiz
- Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies, Consejo Superior de Investigaciones Científicas - Universidad de las Islas Baleares, Esporles Spain
| | - María Lamprecht-Grandío
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología, Consejo Superior de Investigaciones Científicas - Instituto Nacional de Técnica Aeroespacial, Madrid Spain
| | - Carolina G de Figueras
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología, Consejo Superior de Investigaciones Científicas - Instituto Nacional de Técnica Aeroespacial, Madrid Spain
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies, Consejo Superior de Investigaciones Científicas - Universidad de las Islas Baleares, Esporles Spain
| | - José E González-Pastor
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología, Consejo Superior de Investigaciones Científicas - Instituto Nacional de Técnica Aeroespacial, Madrid Spain
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11
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Evolutionarily divergent, Na+-regulated H+-transporting membrane-bound pyrophosphatases. Biochem J 2015; 467:281-91. [DOI: 10.1042/bj20141434] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Membrane-bound pyrophosphatase (mPPases) of various types consume pyrophosphate (PPi) to drive active H+ or Na+ transport across membranes. H+-transporting PPases are divided into phylogenetically distinct K+-independent and K+-dependent subfamilies. In the present study, we describe a group of 46 bacterial proteins and one archaeal protein that are only distantly related to known mPPases (23%–34% sequence identity). Despite this evolutionary divergence, these proteins contain the full set of 12 polar residues that interact with PPi, the nucleophilic water and five cofactor Mg2+ ions found in ‘canonical’ mPPases. They also contain a specific lysine residue that confers K+ independence on canonical mPPases. Two of the proteins (from Chlorobium limicola and Cellulomonas fimi) were expressed in Escherichia coli and shown to catalyse Mg2+-dependent PPi hydrolysis coupled with electrogenic H+, but not Na+ transport, in inverted membrane vesicles. Unique features of the new H+-PPases include their inhibition by Na+ and inhibition or activation, depending on PPi concentration, by K+ ions. Kinetic analyses of PPi hydrolysis over wide ranges of cofactor (Mg2+) and substrate (Mg2–PPi) concentrations indicated that the alkali cations displace Mg2+ from the enzyme, thereby arresting substrate conversion. These data define the new proteins as a novel subfamily of H+-transporting mPPases that partly retained the Na+ and K+ regulation patterns of their precursor Na+-transporting mPPases.
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Emmerstorfer A, Wriessnegger T, Hirz M, Pichler H. Overexpression of membrane proteins from higher eukaryotes in yeasts. Appl Microbiol Biotechnol 2014; 98:7671-98. [PMID: 25070595 DOI: 10.1007/s00253-014-5948-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 02/08/2023]
Abstract
Heterologous expression and characterisation of the membrane proteins of higher eukaryotes is of paramount interest in fundamental and applied research. Due to the rather simple and well-established methods for their genetic modification and cultivation, yeast cells are attractive host systems for recombinant protein production. This review provides an overview on the remarkable progress, and discusses pitfalls, in applying various yeast host strains for high-level expression of eukaryotic membrane proteins. In contrast to the cell lines of higher eukaryotes, yeasts permit efficient library screening methods. Modified yeasts are used as high-throughput screening tools for heterologous membrane protein functions or as benchmark for analysing drug-target relationships, e.g., by using yeasts as sensors. Furthermore, yeasts are powerful hosts for revealing interactions stabilising and/or activating membrane proteins. We also discuss the stress responses of yeasts upon heterologous expression of membrane proteins. Through co-expression of chaperones and/or optimising yeast cultivation and expression strategies, yield-optimised hosts have been created for membrane protein crystallography or efficient whole-cell production of fine chemicals.
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Affiliation(s)
- Anita Emmerstorfer
- ACIB-Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
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Rivero RM, Mestre TC, Mittler R, Rubio F, Garcia-Sanchez F, Martinez V. The combined effect of salinity and heat reveals a specific physiological, biochemical and molecular response in tomato plants. PLANT, CELL & ENVIRONMENT 2014; 37:1059-73. [PMID: 24028172 DOI: 10.1111/pce.12199] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 09/04/2013] [Accepted: 09/04/2013] [Indexed: 05/18/2023]
Abstract
Many studies have described the response mechanisms of plants to salinity and heat applied individually; however, under field conditions some abiotic stresses often occur simultaneously. Recent studies revealed that the response of plants to a combination of two different stresses is specific and cannot be deduced from the stresses applied individually. Here, we report on the response of tomato plants to a combination of heat and salt stress. Interestingly, and in contrast to the expected negative effect of the stress combination on plant growth, our results show that the combination of heat and salinity provides a significant level of protection to tomato plants from the effects of salinity. We observed a specific response of plants to the stress combination that included accumulation of glycine betaine and trehalose. The accumulation of these compounds under the stress combination was linked to the maintenance of a high K(+) concentration and thus a lower Na(+) /K(+) ratio, with a better performance of the cell water status and photosynthesis as compared with salinity alone. Our findings unravel new and unexpected aspects of the response of plants to stress combination and provide a proposed list of enzymatic targets for improving crop tolerance to the abiotic field environment.
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Affiliation(s)
- Rosa M Rivero
- Centro de Edafología y Biología Aplicada del Segura, Campus Universitario de Espinardo, Espinardo, Murcia, 30100, Spain
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Sehrawat A, Abat JK, Deswal R. RuBisCO depletion improved proteome coverage of cold responsive S-nitrosylated targets in Brassica juncea. FRONTIERS IN PLANT SCIENCE 2013; 4:342. [PMID: 24032038 PMCID: PMC3759006 DOI: 10.3389/fpls.2013.00342] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/13/2013] [Indexed: 05/21/2023]
Abstract
Although in the last few years good number of S-nitrosylated proteins are identified but information on endogenous targets is still limiting. Therefore, an attempt is made to decipher NO signaling in cold treated Brassica juncea seedlings. Treatment of seedlings with substrate, cofactor and inhibitor of Nitric-oxide synthase and nitrate reductase (NR), indicated NR mediated NO biosynthesis in cold. Analysis of the in vivo thiols showed depletion of low molecular weight thiols and enhancement of available protein thiols, suggesting redox changes. To have a detailed view, S-nitrosylation analysis was done using biotin switch technique (BST) and avidin-affinity chromatography. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is S-nitrosylated and therefore, is identified as target repeatedly due to its abundance. It also competes out low abundant proteins which are important NO signaling components. Therefore, RuBisCO was removed (over 80%) using immunoaffinity purification. Purified S-nitrosylated RuBisCO depleted proteins were resolved on 2-D gel as 110 spots, including 13 new, which were absent in the crude S-nitrosoproteome. These were identified by nLC-MS/MS as thioredoxin, fructose biphosphate aldolase class I, myrosinase, salt responsive proteins, peptidyl-prolyl cis-trans isomerase and malate dehydrogenase. Cold showed differential S-nitrosylation of 15 spots, enhanced superoxide dismutase activity (via S-nitrosylation) and promoted the detoxification of superoxide radicals. Increased S-nitrosylation of glyceraldehyde-3-phosphate dehydrogenase sedoheptulose-biphosphatase, and fructose biphosphate aldolase, indicated regulation of Calvin cycle by S-nitrosylation. The results showed that RuBisCO depletion improved proteome coverage and provided clues for NO signaling in cold.
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Affiliation(s)
| | | | - Renu Deswal
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of DelhiDelhi, India
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Baykov AA, Malinen AM, Luoto HH, Lahti R. Pyrophosphate-fueled Na+ and H+ transport in prokaryotes. Microbiol Mol Biol Rev 2013; 77:267-76. [PMID: 23699258 PMCID: PMC3668671 DOI: 10.1128/mmbr.00003-13] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In its early history, life appeared to depend on pyrophosphate rather than ATP as the source of energy. Ancient membrane pyrophosphatases that couple pyrophosphate hydrolysis to active H(+) transport across biological membranes (H(+)-pyrophosphatases) have long been known in prokaryotes, plants, and protists. Recent studies have identified two evolutionarily related and widespread prokaryotic relics that can pump Na(+) (Na(+)-pyrophosphatase) or both Na(+) and H(+) (Na(+),H(+)-pyrophosphatase). Both these transporters require Na(+) for pyrophosphate hydrolysis and are further activated by K(+). The determination of the three-dimensional structures of H(+)- and Na(+)-pyrophosphatases has been another recent breakthrough in the studies of these cation pumps. Structural and functional studies have highlighted the major determinants of the cation specificities of membrane pyrophosphatases and their potential use in constructing transgenic stress-resistant organisms.
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Affiliation(s)
- Alexander A. Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anssi M. Malinen
- Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland
| | - Heidi H. Luoto
- Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland
| | - Reijo Lahti
- Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland
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