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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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2
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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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H +-Translocating Membrane-Bound Pyrophosphatase from Rhodospirillum rubrum Fuels Escherichia coli Cells via an Alternative Pathway for Energy Generation. Microorganisms 2023; 11:microorganisms11020294. [PMID: 36838259 PMCID: PMC9959109 DOI: 10.3390/microorganisms11020294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/24/2023] Open
Abstract
Inorganic pyrophosphatases (PPases) catalyze an essential reaction, namely, the hydrolysis of PPi, which is formed in large quantities as a side product of numerous cellular reactions. In the majority of living species, PPi hydrolysis is carried out by soluble cytoplasmic PPase (S-PPases) with the released energy dissipated in the form of heat. In Rhodospirillum rubrum, part of this energy can be conserved by proton-pumping pyrophosphatase (H+-PPaseRru) in the form of a proton electrochemical gradient for further ATP synthesis. Here, the codon-harmonized gene hppaRru encoding H+-PPaseRru was expressed in the Escherichia coli chromosome. We demonstrate, for the first time, that H+-PPaseRru complements the essential native S-PPase in E. coli cells. 13C-MFA confirmed that replacing native PPase to H+-PPaseRru leads to the re-distribution of carbon fluxes; a statistically significant 36% decrease in tricarboxylic acid (TCA) cycle fluxes was found compared with wild-type E. coli MG1655. Such a flux re-distribution can indicate the presence of an additional method for energy generation (e.g., ATP), which can be useful for the microbiological production of a number of compounds, the biosynthesis of which requires the consumption of ATP.
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4
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Malinen AM, Anashkin VA, Orlov VN, Bogachev AV, Lahti R, Baykov AA. Pre-steady-state kinetics and solvent isotope effects support the "billiard-type" transport mechanism in Na + -translocating pyrophosphatase. Protein Sci 2022; 31:e4394. [PMID: 36040263 PMCID: PMC9405524 DOI: 10.1002/pro.4394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/23/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022]
Abstract
Membrane-bound pyrophosphatase (mPPase) found in microbes and plants is a membrane H+ pump that transports the H+ ion generated in coupled pyrophosphate hydrolysis out of the cytoplasm. Certain bacterial and archaeal mPPases can in parallel transport Na+ via a hypothetical "billiard-type" mechanism, also involving the hydrolysis-generated proton. Here, we present the functional evidence supporting this coupling mechanism. Rapid-quench and pulse-chase measurements with [32 P]pyrophosphate indicated that the chemical step (pyrophosphate hydrolysis) is rate-limiting in mPPase catalysis and is preceded by a fast isomerization of the enzyme-substrate complex. Na+ , whose binding is a prerequisite for the hydrolysis step, is not required for substrate binding. Replacement of H2 O with D2 O decreased the rates of pyrophosphate hydrolysis by both Na+ - and H+ -transporting bacterial mPPases, the effect being more significant than with a non-transporting soluble pyrophosphatase. We also show that the Na+ -pumping mPPase of Thermotoga maritima resembles other dimeric mPPases in demonstrating negative kinetic cooperativity and the requirement for general acid catalysis. The findings point to a crucial role for the hydrolysis-generated proton both in H+ -pumping and Na+ -pumping by mPPases.
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Affiliation(s)
| | - Viktor A. Anashkin
- Belozersky Institute of Physico‐Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
| | - Victor N. Orlov
- Belozersky Institute of Physico‐Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
| | - Alexander V. Bogachev
- Belozersky Institute of Physico‐Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
| | - Reijo Lahti
- Department of Life TechnologiesUniversity of TurkuTurkuFinland
| | - Alexander A. Baykov
- Belozersky Institute of Physico‐Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
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5
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Nitschke W, Schoepp‐Cothenet B, Duval S, Zuchan K, Farr O, Baymann F, Panico F, Minguzzi A, Branscomb E, Russell MJ. Aqueous electrochemistry: The toolbox for life's emergence from redox disequilibria. ELECTROCHEMICAL SCIENCE ADVANCES 2022. [DOI: 10.1002/elsa.202100192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
| | | | - Simon Duval
- CNRS, BIP (UMR 7281), Aix Marseille Univ Marseille France
| | - Kilian Zuchan
- CNRS, BIP (UMR 7281), Aix Marseille Univ Marseille France
| | - Orion Farr
- CNRS, BIP (UMR 7281), Aix Marseille Univ Marseille France
- Aix Marseille Univ CINaM (UMR 7325) Luminy France
| | - Frauke Baymann
- CNRS, BIP (UMR 7281), Aix Marseille Univ Marseille France
| | - Francesco Panico
- Dipartimento di Chimica Università degli Studi di Milano Milan Italy
| | | | - Elbert Branscomb
- Department of Physics Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana Illinois USA
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6
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Higuchi-Takeuchi M, Morisaki K, Numata K. Method for the facile transformation of marine purple photosynthetic bacteria using chemically competent cells. Microbiologyopen 2019; 9:e00953. [PMID: 31638342 PMCID: PMC6957439 DOI: 10.1002/mbo3.953] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 02/03/2023] Open
Abstract
Marine purple photosynthetic bacteria are ideal organisms for the production of useful materials at reduced costs and contributing to a sustainable society because they can utilize sunlight, seawater, and components of air, including carbon dioxide and nitrogen gases, for their growth. However, conjugation is the only applicable method for the transformation of marine purple photosynthetic bacteria so far. Here, we examined a calcium chloride‐mediated method for the transformation of marine purple photosynthetic bacteria. Plasmid DNAs containing the kanamycin resistance gene were successfully transferred into chemically competent cells of two strains of marine purple photosynthetic bacteria (Rhodovulum sulfidophilum and Roseospira marina). Heat shock treatment increased the transformation efficiency in R. sulfidophilum, whereas the addition of cell‐penetrating peptide did not improve it. We also found that prolonged incubation in agar plates containing kanamycin led to spontaneous mutation of the 16S rRNA, resulting in kanamycin resistance in R. marina. Thus, we developed an efficient and facile transformation method using chemically competent cells of marine purple photosynthetic bacteria with calcium chloride.
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Affiliation(s)
- Mieko Higuchi-Takeuchi
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Kumiko Morisaki
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
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7
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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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8
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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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9
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10
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Proton/sodium pumping pyrophosphatases: the last of the primary ion pumps. Curr Opin Struct Biol 2014; 27:38-47. [DOI: 10.1016/j.sbi.2014.03.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 03/18/2014] [Accepted: 03/25/2014] [Indexed: 11/24/2022]
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11
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Liu J, Pace D, Dou Z, King TP, Guidot D, Li ZH, Carruthers VB, Moreno SNJ. A vacuolar-H(+) -pyrophosphatase (TgVP1) is required for microneme secretion, host cell invasion, and extracellular survival of Toxoplasma gondii. Mol Microbiol 2014; 93:698-712. [PMID: 24975633 DOI: 10.1111/mmi.12685] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2014] [Indexed: 01/17/2023]
Abstract
The vacuolar proton pyrophosphatase (H(+) -PPase) of Toxoplasma gondii (TgVP1), a membrane proton pump, localizes to acidocalcisomes and a novel lysosome-like compartment termed plant-like vacuole (PLV) or vacuolar compartment (VAC). We report the characterization of a T. gondii null mutant for the TgVP1 gene. Propagation of these mutants decreased significantly because of deficient attachment and invasion of host cells, which correlated with deficient microneme secretion. Processing of cathepsin L (CPL) in these mutants was deficient only when the parasites were incubated in the presence of low concentrations of the vacuolar H(+) -ATPase (V-H(+) -ATPase) inhibitor bafilomycin A1 , suggesting that either TgVP1 or the T. gondii V-H(+) -ATPase (TgVATPase) are sufficient to support CPL processing. The lack of TgVP1 did not affect processing of micronemal proteins, indicating that it does not contribute to proMIC maturations. The TgVP1 null mutants were more sensitive to extracellular conditions and were less virulent in mice. We demonstrate that T. gondii tachyzoites possess regulatory volume decrease capability during hypo-osmotic stress and this ability is impaired in TgVP1 null mutants implicating TgVP1 in osmoregulation. We hypothesize that osmoregulation is needed for host cell invasion and that TgVP1 plays a role during the normal lytic cycle of T. gondii.
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Affiliation(s)
- Jing Liu
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, GA, 30602-7400, USA; College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
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12
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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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13
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Kajander T, Kellosalo J, Goldman A. Inorganic pyrophosphatases: one substrate, three mechanisms. FEBS Lett 2013; 587:1863-9. [PMID: 23684653 DOI: 10.1016/j.febslet.2013.05.003] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 10/26/2022]
Abstract
Soluble inorganic pyrophosphatases (PPases) catalyse an essential reaction, the hydrolysis of pyrophosphate to inorganic phosphate. In addition, an evolutionarily ancient family of membrane-integral pyrophosphatases couple this hydrolysis to Na(+) and/or H(+) pumping, and so recycle some of the free energy from the pyrophosphate. The structures of the H(+)-pumping mung bean PPase and the Na(+)-pumping Thermotoga maritima PPase solved last year revealed an entirely novel membrane protein containing 16 transmembrane helices. The hydrolytic centre, well above the membrane, is linked by a charged "coupling funnel" to the ionic gate about 20Å away. By comparing the active sites, fluoride inhibition data and the various models for ion transport, we conclude that membrane-integral PPases probably use binding of pyrophosphate to drive pumping.
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Affiliation(s)
- Tommi Kajander
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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14
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Expression patterns reveal niche diversification in a marine microbial assemblage. ISME JOURNAL 2012; 7:281-98. [PMID: 22931830 DOI: 10.1038/ismej.2012.96] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Resolving the ecological niches of coexisting marine microbial taxa is challenging due to the high species richness of microbial communities and the apparent functional redundancy in bacterial genomes and metagenomes. Here, we generated over 11 million Illumina reads of protein-encoding transcripts collected from well-mixed southeastern US coastal waters to characterize gene expression patterns distinguishing the ecological roles of hundreds of microbial taxa sharing the same environment. The taxa with highest in situ growth rates (based on relative abundance of ribosomal protein transcripts) were typically not the greatest contributors to community transcription, suggesting strong top-down ecological control, and their diverse transcriptomes indicated roles as metabolic generalists. The taxa with low in situ growth rates typically had low diversity transcriptomes dominated by specialized metabolisms. By identifying protein-encoding genes with atypically high expression for their level of conservation, unique functional roles of community members emerged related to substrate use (such as complex carbohydrates, fatty acids, methanesulfonate, taurine, tartrate, ectoine), alternative energy-conservation strategies (proteorhodopsin, AAnP, V-type pyrophosphatases, sulfur oxidation, hydrogen oxidation) and mechanisms for negotiating a heterogeneous environment (flagellar motility, gliding motility, adhesion strategies). On average, the heterotrophic bacterioplankton dedicated 7% of their transcriptomes to obtaining energy by non-heterotrophic means. This deep sequencing of a coastal bacterioplankton transcriptome provides the most highly resolved view of bacterioplankton niche dimensions yet available, uncovering a spectrum of unrecognized ecological strategies.
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15
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Kellosalo J, Kajander T, Honkanen R, Goldman A. Crystallization and preliminary X-ray analysis of membrane-bound pyrophosphatases. Mol Membr Biol 2012; 30:64-74. [DOI: 10.3109/09687688.2012.712162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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16
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Dupont CL, Rusch DB, Yooseph S, Lombardo MJ, Richter RA, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH, Halpern AL, Lasken RS, Nealson K, Friedman R, Venter JC. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME JOURNAL 2011; 6:1186-99. [PMID: 22170421 PMCID: PMC3358033 DOI: 10.1038/ismej.2011.189] [Citation(s) in RCA: 358] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of γ-proteobacteria, and the individual genomes display a temperature-dependent distribution. Modestly sized at 1.25-1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack of a retinal biosynthesis pathway may require it to scavenge exogenously-derived pigments to utilize proteorhodopsin. The genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition.
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Affiliation(s)
- Chris L Dupont
- Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, CA 92121, USA.
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Rinta-Kanto JM, Sun S, Sharma S, Kiene RP, Moran MA. Bacterial community transcription patterns during a marine phytoplankton bloom. Environ Microbiol 2011; 14:228-39. [PMID: 21985473 DOI: 10.1111/j.1462-2920.2011.02602.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterioplankton consume a large proportion of photosynthetically fixed carbon in the ocean and control its biogeochemical fate. We used an experimental metatranscriptomics approach to compare bacterial activities that route energy and nutrients during a phytoplankton bloom compared with non-bloom conditions. mRNAs were sequenced from duplicate bloom and control microcosms 1 day after a phytoplankton biomass peak, and transcript copies per litre of seawater were calculated using an internal mRNA standard. Transcriptome analysis revealed a potential novel mechanism for enhanced efficiency during carbon-limited growth, mediated through membrane-bound pyrophosphatases [V-type H(+)-translocating; hppA]; bloom bacterioplankton participated less in this metabolic energy scavenging than non-bloom bacterioplankton, with possible implications for differences in growth yields on organic substrates. Bloom bacterioplankton transcribed more copies of genes predicted to increase cell surface adhesiveness, mediated by changes in bacterial signalling molecules related to biofilm formation and motility; these may be important in microbial aggregate formation. Bloom bacterioplankton also transcribed more copies of genes for organic acid utilization, suggesting an increased importance of this compound class in the bioreactive organic matter released during phytoplankton blooms. Transcription patterns were surprisingly faithful within a taxon regardless of treatment, suggesting that phylogeny broadly predicts the ecological roles of bacterial groups across 'boom' and 'bust' environmental backgrounds.
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Heterologous expression and purification of membrane-bound pyrophosphatases. Protein Expr Purif 2011; 79:25-34. [DOI: 10.1016/j.pep.2011.05.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 05/20/2011] [Accepted: 05/26/2011] [Indexed: 12/18/2022]
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19
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Luoto HH, Belogurov GA, Baykov AA, Lahti R, Malinen AM. Na+-translocating membrane pyrophosphatases are widespread in the microbial world and evolutionarily precede H+-translocating pyrophosphatases. J Biol Chem 2011; 286:21633-42. [PMID: 21527638 DOI: 10.1074/jbc.m111.244483] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Membrane pyrophosphatases (PPases), divided into K(+)-dependent and K(+)-independent subfamilies, were believed to pump H(+) across cell membranes until a recent demonstration that some K(+)-dependent PPases function as Na(+) pumps. Here, we have expressed seven evolutionarily important putative PPases in Escherichia coli and estimated their hydrolytic, Na(+) transport, and H(+) transport activities as well as their K(+) and Na(+) requirements in inner membrane vesicles. Four of these enzymes (from Anaerostipes caccae, Chlorobium limicola, Clostridium tetani, and Desulfuromonas acetoxidans) were identified as K(+)-dependent Na(+) transporters. Phylogenetic analysis led to the identification of a monophyletic clade comprising characterized and predicted Na(+)-transporting PPases (Na(+)-PPases) within the K(+)-dependent subfamily. H(+)-transporting PPases (H(+)-PPases) are more heterogeneous and form at least three independent clades in both subfamilies. These results suggest that rather than being a curious rarity, Na(+)-PPases predominantly constitute the K(+)-dependent subfamily. Furthermore, Na(+)-PPases possibly preceded H(+)-PPases in evolution, and transition from Na(+) to H(+) transport may have occurred in several independent enzyme lineages. Site-directed mutagenesis studies facilitated the identification of a specific Glu residue that appears to be central in the transport mechanism. This residue is located in the cytoplasm-membrane interface of transmembrane helix 6 in Na(+)-PPases but shifted to within the membrane or helix 5 in H(+)-PPases. These results contribute to the prediction of the transport specificity and K(+) dependence for a particular membrane PPase sequence based on its position in the phylogenetic tree, identity of residues in the K(+) dependence signature, and position of the membrane-located Glu residue.
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Affiliation(s)
- Heidi H Luoto
- Department of Biochemistry and Food Chemistry, University of Turku, FIN-20014 Turku, Finland
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Pellitteri-Hahn MC, Halligan BD, Scalf M, Smith L, Hickey WJ. Quantitative proteomic analysis of the chemolithoautotrophic bacterium Nitrosomonas europaea: Comparison of growing- and energy-starved cells. J Proteomics 2011; 74:411-9. [DOI: 10.1016/j.jprot.2010.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 11/01/2010] [Accepted: 12/10/2010] [Indexed: 01/05/2023]
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21
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Hirono M, Nakanishi Y, Maeshima M. Identification of amino acid residues participating in the energy coupling and proton transport of Streptomyces coelicolor A3(2) H+-pyrophosphatase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:1401-11. [DOI: 10.1016/j.bbabio.2007.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2007] [Revised: 09/05/2007] [Accepted: 09/20/2007] [Indexed: 11/30/2022]
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22
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Malinen AM, Belogurov GA, Baykov AA, Lahti R. Na+-Pyrophosphatase: A Novel Primary Sodium Pump. Biochemistry 2007; 46:8872-8. [PMID: 17605473 DOI: 10.1021/bi700564b] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membrane-bound pyrophosphatase (PPase) is commonly believed to couple pyrophosphate (PPi) hydrolysis to H+ transport across the membrane. Here, we demonstrate that two newly isolated bacterial membrane PPases from the mesophile Methanosarcina mazei (Mm-PPase) and the moderate thermophile Moorella thermoacetica and a previously described PPase from the hyperthermophilic bacterium Thermotoga maritima catalyze Na+ rather than H+ transport into Escherichia coli inner membrane vesicles (IMV). When assayed in uncoupled IMV, the three PPases exhibit an absolute requirement for Na+ but display the highest hydrolyzing activity in the presence of both Na+ and K+. Steady-state kinetic analysis of PPi hydrolysis by Mm-PPase revealed two Na+ binding sites. One of these sites can also bind K+, resulting in a 10-fold increase in the affinity of the other site for Na+ and a 2-fold increase in maximal velocity. PPi-driven 22Na+ transport into IMV containing Mm-PPase was unaffected by the protonophore carbonyl cyanide m-chlorophenylhydrazone, inhibited by the Na+ ionophore monensin, and activated by the K+ ionophore valinomycin. The Na+ transport was accompanied by the generation of a positive inside membrane potential as reported by Oxonol VI. These findings define Na+-dependent PPases as electrogenic Na+ pumps. Phylogenetic analysis suggests that ancient gene duplication preceded the split of Na+- and H+-PPases.
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Affiliation(s)
- Anssi M Malinen
- Department of Biochemistry and Food Chemistry, University of Turku, FIN-20014 Turku, Finland
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23
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Hirono M, Nakanishi Y, Maeshima M. Essential amino acid residues in the central transmembrane domains and loops for energy coupling of Streptomyces coelicolor A3(2) H+-pyrophosphatase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:930-9. [PMID: 17498645 DOI: 10.1016/j.bbabio.2007.03.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Revised: 03/20/2007] [Accepted: 03/29/2007] [Indexed: 01/30/2023]
Abstract
The H+-translocating inorganic pyrophosphatase is a proton pump that hydrolyzes inorganic pyrophosphate. It consists of a single polypeptide with 14-17 transmembrane domains, and is found in a range of organisms. We focused on the second quarter region of Streptomyces coelicolor A3(2) H+-pyrophosphatase, which contains long conserved cytoplasmic loops. We prepared a library of 1536 mutants that were assayed for pyrophosphate hydrolysis and proton translocation. Mutant enzymes with low substrate hydrolysis and proton-pump activities were selected and their DNAs sequenced. Of these, 34 were single-residue substitution mutants. We generated 29 site-directed mutant enzymes and assayed their activity. The mutation of 10 residues in the fifth transmembrane domain resulted in low coupling efficiencies, and a mutation of Gly198 showed neither hydrolysis nor pumping activity. Four residues in cytoplasmic loop e were essential for substrate hydrolysis and efficient H+ translocation. Pro189, Asp281, and Val351 in the periplasmic loops were critical for enzyme function. Mutation of Ala357 in periplasmic loop h caused a selective reduction of proton-pump activity. These low-efficiency mutants reflect dysfunction of the energy-conversion and/or proton-translocation activities of H+-pyrophosphatase. Four critical residues were also found in transmembrane domain 6, three in transmembrane domain 7, and five in transmembrane domains 8 and 9. These results suggest that transmembrane domain 5 is involved in enzyme function, and that energy coupling is affected by several residues in the transmembrane domains, as well as in the cytoplasmic and periplasmic loops. H+-pyrophosphatase activity might involve dynamic linkage between the hydrophilic and transmembrane domains.
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Affiliation(s)
- Megumi Hirono
- Laboratory of Cell Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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24
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Au KM, Barabote RD, Hu KY, Saier MH. Evolutionary appearance of H+-translocating pyrophosphatases. Microbiology (Reading) 2006; 152:1243-1247. [PMID: 16622041 DOI: 10.1099/mic.0.28581-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ka M Au
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Ravi D Barabote
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Kuang Yu Hu
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Milton H Saier
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
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Mimura H, Nakanishi Y, Maeshima M. Oligomerization of H(+)-pyrophosphatase and its structural and functional consequences. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1708:393-403. [PMID: 15953583 DOI: 10.1016/j.bbabio.2005.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2005] [Revised: 04/18/2005] [Accepted: 05/10/2005] [Indexed: 11/23/2022]
Abstract
The H(+)-pyrophosphatase (H(+)-PPase) consists of a single polypeptide, containing 16 or 17 transmembrane domains. To determine the higher order oligomeric state of Streptomyces coelicolor H(+)-PPase, we constructed a series of cysteine substitution mutants and expressed them in Escherichia coli. Firstly, we analyzed the formation of disulfide bonds, promoted by copper, in mutants with single cysteine substitutions. 28 of 39 mutants formed disulfide bonds, including S545C, a substitution at the periplasmic side. The formation of intermolecular disulfide bonds suppressed the enzyme activity of several, where the substituted residues were located in the cytosol. Creating disulfide links in the cytosol may interfere with the enzyme's catalytic function. Secondly, we prepared double mutants by introducing second cysteine substitutions into the S545C mutant. These double-cysteine mutants produced cross-linked complexes, estimated to be at least tetramers and possibly hexamers. Thirdly, we co-expressed epitope-tagged, wild type, and inactive mutant H(+)-PPases in E. coli and confirmed the formation of oligomers by co-purifying one subunit using the epitope tag used to label the other. The enzyme activity of these oligomers was markedly suppressed. We propose that H(+)-PPase is present as an oligomer made up of at least two or three sets of dimers.
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Affiliation(s)
- Hisatoshi Mimura
- Laboratory of Cell Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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26
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Mimura H, Nakanishi Y, Maeshima M. Disulfide-bond formation in the H+-pyrophosphatase ofStreptomyces coelicolorand its implications for redox control and enzyme structure. FEBS Lett 2005; 579:3625-31. [PMID: 15963991 DOI: 10.1016/j.febslet.2005.05.045] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2005] [Revised: 05/11/2005] [Accepted: 05/11/2005] [Indexed: 11/16/2022]
Abstract
Redox control of disulfide-bond formation in the H+-pyrophosphatase of Streptomyces coelicolor was investigated using cysteine mutants expressed in Escherichia coli. The wild-type enzyme, but not a cysteine-less mutant, was reversibly inactivated by oxidation. To determine the residues involved in oxidative inactivation, different cysteine residues were replaced. Analysis with a cysteine-modifying reagent revealed that the formation of a disulfide bond between cysteines 253 and 621 was responsible for enzyme inactivation. This result suggests that residues in different cytoplasmic loops are close to each other in the tertiary structure. Both cysteine residues are conserved in K+-independent (type II) H+-pyrophosphatases.
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Affiliation(s)
- Hisatoshi Mimura
- Laboratory of Cell Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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