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García-Contreras R, de la Mora J, Mora-Montes HM, Martínez-Álvarez JA, Vicente-Gómez M, Padilla-Vaca F, Vargas-Maya NI, Franco B. The inorganic pyrophosphatases of microorganisms: a structural and functional review. PeerJ 2024; 12:e17496. [PMID: 38938619 PMCID: PMC11210485 DOI: 10.7717/peerj.17496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/09/2024] [Indexed: 06/29/2024] Open
Abstract
Pyrophosphatases (PPases) are enzymes that catalyze the hydrolysis of pyrophosphate (PPi), a byproduct of the synthesis and degradation of diverse biomolecules. The accumulation of PPi in the cell can result in cell death. Although the substrate is the same, there are variations in the catalysis and features of these enzymes. Two enzyme forms have been identified in bacteria: cytoplasmic or soluble pyrophosphatases and membrane-bound pyrophosphatases, which play major roles in cell bioenergetics. In eukaryotic cells, cytoplasmic enzymes are the predominant form of PPases (c-PPases), while membrane enzymes (m-PPases) are found only in protists and plants. The study of bacterial cytoplasmic and membrane-bound pyrophosphatases has slowed in recent years. These enzymes are central to cell metabolism and physiology since phospholipid and nucleic acid synthesis release important amounts of PPi that must be removed to allow biosynthesis to continue. In this review, two aims were pursued: first, to provide insight into the structural features of PPases known to date and that are well characterized, and to provide examples of enzymes with novel features. Second, the scientific community should continue studying these enzymes because they have many biotechnological applications. Additionally, in this review, we provide evidence that there are m-PPases present in fungi; to date, no examples have been characterized. Therefore, the diversity of PPase enzymes is still a fruitful field of research. Additionally, we focused on the roles of H+/Na+ pumps and m-PPases in cell bioenergetics. Finally, we provide some examples of the applications of these enzymes in molecular biology and biotechnology, especially in plants. This review is valuable for professionals in the biochemistry field of protein structure-function relationships and experts in other fields, such as chemistry, nanotechnology, and plant sciences.
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Affiliation(s)
- Rodolfo García-Contreras
- Departamento de Microbiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Javier de la Mora
- Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Héctor Manuel Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - José A. Martínez-Álvarez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Marcos Vicente-Gómez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Felipe Padilla-Vaca
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Naurú Idalia Vargas-Maya
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Bernardo Franco
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
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Strauss J, Wilkinson C, Vidilaseris K, de Castro Ribeiro OM, Liu J, Hillier J, Wichert M, Malinen AM, Gehl B, Jeuken LJ, Pearson AR, Goldman A. Functional and structural asymmetry suggest a unifying principle for catalysis in membrane-bound pyrophosphatases. EMBO Rep 2024; 25:853-875. [PMID: 38182815 PMCID: PMC10897367 DOI: 10.1038/s44319-023-00037-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 01/07/2024] Open
Abstract
Membrane-bound pyrophosphatases (M-PPases) are homodimeric primary ion pumps that couple the transport of Na+- and/or H+ across membranes to the hydrolysis of pyrophosphate. Their role in the virulence of protist pathogens like Plasmodium falciparum makes them an intriguing target for structural and functional studies. Here, we show the first structure of a K+-independent M-PPase, asymmetric and time-dependent substrate binding in time-resolved structures of a K+-dependent M-PPase and demonstrate pumping-before-hydrolysis by electrometric studies. We suggest how key residues in helix 12, 13, and the exit channel loops affect ion selectivity and K+-activation due to a complex interplay of residues that are involved in subunit-subunit communication. Our findings not only explain ion selectivity in M-PPases but also why they display half-of-the-sites reactivity. Based on this, we propose, for the first time, a unified model for ion-pumping, hydrolysis, and energy coupling in all M-PPases, including those that pump both Na+ and H+.
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Affiliation(s)
- Jannik Strauss
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
- Numaferm GmbH, Düsseldorf, Germany
| | - Craig Wilkinson
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
| | - Keni Vidilaseris
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland
| | - Orquidea M de Castro Ribeiro
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland
| | - Jianing Liu
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland
| | - James Hillier
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
- Bio-Rad Laboratories Ltd., Watford, UK
| | - Maximilian Wichert
- Leiden Institute of Chemistry, University Leiden, PO Box 9502, 2300 RA, Leiden, The Netherlands
| | - Anssi M Malinen
- Department of Life Technologies, University of Turku, FIN-20014, Turku, Finland
| | - Bernadette Gehl
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland
- Department of Applied Physics, Aalto University, FI-00076, AALTO, Espoo, Finland
| | - Lars Jc Jeuken
- Leiden Institute of Chemistry, University Leiden, PO Box 9502, 2300 RA, Leiden, The Netherlands
| | - Arwen R Pearson
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22761, Hamburg, Germany
| | - Adrian Goldman
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK.
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland.
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3
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The Mechanism of Energy Coupling in H +/Na +-Pumping Membrane Pyrophosphatase-Possibilities and Probabilities. Int J Mol Sci 2022; 23:ijms23169504. [PMID: 36012762 PMCID: PMC9408878 DOI: 10.3390/ijms23169504] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/12/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
Membrane pyrophosphatases (mPPases) found in plant vacuoles and some prokaryotes and protists are ancient cation pumps that couple pyrophosphate hydrolysis with the H+ and/or Na+ transport out of the cytoplasm. Because this function is reversible, mPPases play a role in maintaining the level of cytoplasmic pyrophosphate, a known regulator of numerous metabolic reactions. mPPases arouse interest because they are among the simplest membrane transporters and have no homologs among known ion pumps. Detailed phylogenetic studies have revealed various subtypes of mPPases and suggested their roles in the evolution of the "sodium" and "proton" bioenergetics. This treatise focuses on the mechanistic aspects of the transport reaction, namely, the coupling step, the role of the chemically produced proton, subunit cooperation, and the relationship between the proton and sodium ion transport. The available data identify H+-PPases as the first non-oxidoreductase pump with a "direct-coupling" mechanism, i.e., the transported proton is produced in the coupled chemical reaction. They also support a "billiard" hypothesis, which unifies the H+ and Na+ transport mechanisms in mPPase and, probably, other transporters.
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Refojo PN, Sena FV, Calisto F, Sousa FM, Pereira MM. The plethora of membrane respiratory chains in the phyla of life. Adv Microb Physiol 2019; 74:331-414. [PMID: 31126533 DOI: 10.1016/bs.ampbs.2019.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The diversity of microbial cells is reflected in differences in cell size and shape, motility, mechanisms of cell division, pathogenicity or adaptation to different environmental niches. All these variations are achieved by the distinct metabolic strategies adopted by the organisms. The respiratory chains are integral parts of those strategies especially because they perform the most or, at least, most efficient energy conservation in the cell. Respiratory chains are composed of several membrane proteins, which perform a stepwise oxidation of metabolites toward the reduction of terminal electron acceptors. Many of these membrane proteins use the energy released from the oxidoreduction reaction they catalyze to translocate charges across the membrane and thus contribute to the establishment of the membrane potential, i.e. they conserve energy. In this work we illustrate and discuss the composition of the respiratory chains of different taxonomic clades, based on bioinformatic analyses and on biochemical data available in the literature. We explore the diversity of the respiratory chains of Animals, Plants, Fungi and Protists kingdoms as well as of Prokaryotes, including Bacteria and Archaea. The prokaryotic phyla studied in this work are Gammaproteobacteria, Betaproteobacteria, Epsilonproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria, Chlamydiae, Verrucomicrobia, Acidobacteria, Planctomycetes, Cyanobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Aquificae, Thermotogae, Deferribacteres, Nitrospirae, Euryarchaeota, Crenarchaeota and Thaumarchaeota.
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Affiliation(s)
- Patrícia N Refojo
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipa Calisto
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal; University of Lisboa, Faculty of Sciences, BIOISI- Biosystems & Integrative Sciences Institute, Lisboa, Portugal
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5
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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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6
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Role of the potassium/lysine cationic center in catalysis and functional asymmetry in membrane-bound pyrophosphatases. Biochem J 2018. [PMID: 29519958 DOI: 10.1042/bcj20180071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Membrane-bound pyrophosphatases (mPPases), which couple pyrophosphate hydrolysis to transmembrane transport of H+ and/or Na+ ions, are divided into K+,Na+-independent, Na+-regulated, and K+-dependent families. The first two families include H+-transporting mPPases (H+-PPases), whereas the last family comprises one Na+-transporting, two Na+- and H+-transporting subfamilies (Na+-PPases and Na+,H+-PPases, respectively), and three H+-transporting subfamilies. Earlier studies of the few available model mPPases suggested that K+ binds to a site located adjacent to the pyrophosphate-binding site, but is substituted by the ε-amino group of an evolutionarily acquired lysine residue in the K+-independent mPPases. Here, we performed a systematic analysis of the K+/Lys cationic center across all mPPase subfamilies. An Ala → Lys replacement in K+-dependent mPPases abolished the K+ dependence of hydrolysis and transport activities and decreased these activities close to the level (4-7%) observed for wild-type enzymes in the absence of monovalent cations. In contrast, a Lys → Ala replacement in K+,Na+-independent mPPases conferred partial K+ dependence on the enzyme by unmasking an otherwise conserved K+-binding site. Na+ could partially replace K+ as an activator of K+-dependent mPPases and the Lys → Ala variants of K+,Na+-independent mPPases. Finally, we found that all mPPases were inhibited by excess substrate, suggesting strong negative co-operativity of active site functioning in these homodimeric enzymes; moreover, the K+/Lys center was identified as part of the mechanism underlying this effect. These findings suggest that the mPPase homodimer possesses an asymmetry of active site performance that may be an ancient prototype of the rotational binding-change mechanism of F-type ATPases.
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7
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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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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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