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Vtc5 Is Localized to the Vacuole Membrane by the Conserved AP-3 Complex to Regulate Polyphosphate Synthesis in Budding Yeast. mBio 2021; 12:e0099421. [PMID: 34544285 PMCID: PMC8510523 DOI: 10.1128/mbio.00994-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Polyphosphates (polyP) are energy-rich polymers of inorganic phosphates assembled into chains ranging from 3 residues to thousands of residues in length. They are thought to exist in all cells on earth and play roles in an eclectic mix of functions ranging from phosphate homeostasis to cell signaling, infection control, and blood clotting. In the budding yeast Saccharomyces cerevisiae, polyP chains are synthesized by the vacuole-bound vacuolar transporter chaperone (VTC) complex, which synthesizes polyP while simultaneously translocating it into the vacuole lumen, where it is stored at high concentrations. VTC’s activity is promoted by an accessory subunit called Vtc5. In this work, we found that the conserved AP-3 complex is required for proper Vtc5 localization to the vacuole membrane. In human cells, previous work has demonstrated that mutation of AP-3 subunits gives rise to Hermansky-Pudlak syndrome, a rare disease with molecular phenotypes that include decreased polyP accumulation in platelet dense granules. In yeast AP-3 mutants, we found that Vtc5 is rerouted to the vacuole lumen by the endosomal sorting complex required for transport (ESCRT), where it is degraded by the vacuolar protease Pep4. Cells lacking functional AP-3 have decreased levels of polyP, demonstrating that membrane localization of Vtc5 is required for its VTC stimulatory activity in vivo. Our work provides insight into the molecular trafficking of a critical regulator of polyP metabolism in yeast. We speculate that AP-3 may also be responsible for the delivery of polyP regulatory proteins to platelet dense granules in higher eukaryotes.
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2
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Semenyuk PI. Effect of Polyphosphorylation on Behavior of Protein Disordered Regions. Int J Mol Sci 2021; 22:ijms22157883. [PMID: 34360648 PMCID: PMC8345927 DOI: 10.3390/ijms22157883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 11/25/2022] Open
Abstract
Proteins interact with many charged biological macromolecules (polyelectrolytes), including inorganic polyphosphates. Recently a new protein post-translational modification, polyphosphorylation, or a covalent binding of polyphosphate chain to lysine, was demonstrated in human and yeast. Herein, we performed the first molecular modeling study of a possible effect of polyphosphorylation on behavior of the modified protein using replica exchange molecular dynamics simulations in atomistic force field with explicit water. Human endoplasmin (GRP-94), a member of heat shock protein 90 family, was selected as a model protein. Intrinsically disordered region in N-terminal domain serving as a charged linker between domains and containing a polyacidic serine and lysine-rich motif, was selected as a potent polyphosphorylation site according to literature data. Polyphosphorylation, depending on exact modification site, has been shown to influence on the disordered loop flexibility and induce its further expanding, as well as induce changes in interaction with ordered part of the molecule. As a result, polyphosphorylation in N-terminal domain might affect interaction of HSP90 with client proteins since these chaperones play a key role in protein folding.
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Affiliation(s)
- Pavel I Semenyuk
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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3
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Rosigkeit H, Kneißle L, Obruča S, Jendrossek D. The Multiple Roles of Polyphosphate in Ralstonia eutropha and Other Bacteria. Microb Physiol 2021; 31:163-177. [PMID: 34015783 DOI: 10.1159/000515741] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/06/2021] [Indexed: 11/19/2022]
Abstract
An astonishing variety of functions has been attributed to polyphosphate (polyP) in prokaryotes. Besides being a reservoir of phosphorus, functions in exopolysaccharide formation, motility, virulence and in surviving various forms of stresses such as exposure to heat, extreme pH, oxidative agents, high osmolarity, heavy metals and others have been ascribed to polyP. In this contribution, we will provide a historical overview on polyP, will then describe the key proteins of polyP synthesis, the polyP kinases, before we will critically assess of the underlying data on the multiple functions of polyP and provide evidence that - with the exception of a P-storage-function - most other functions of polyP are not relevant for survival of Ralstonia eutropha, a biotechnologically important beta-proteobacterial species.
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Affiliation(s)
- Hanna Rosigkeit
- Institute of Microbiology, University of Stuttgart, Stuttgart, Germany
| | - Lea Kneißle
- Institute of Microbiology, University of Stuttgart, Stuttgart, Germany
| | - Stanislav Obruča
- Faculty of Chemistry, Brno University of Technology, Brno, Czechia
| | - Dieter Jendrossek
- Institute of Microbiology, University of Stuttgart, Stuttgart, Germany
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4
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Baijal K, Downey M. The promises of lysine polyphosphorylation as a regulatory modification in mammals are tempered by conceptual and technical challenges. Bioessays 2021; 43:e2100058. [PMID: 33998006 DOI: 10.1002/bies.202100058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 12/17/2022]
Abstract
Polyphosphate (polyP) is a ubiquitous biomolecule thought to be present in all cells on Earth. PolyP is deceivingly simple, consisting of repeated units of inorganic phosphates polymerized in long energy-rich chains. PolyP is involved in diverse functions in mammalian systems-from cell signaling to blood clotting. One exciting avenue of research is a new nonenzymatic post-translational modification, termed lysine polyphosphorylation, wherein polyP chains are covalently attached to lysine residues of target proteins. While the modification was first characterized in budding yeast, recent work has now identified the first human targets. There is significant promise in this area of biomedical research, but a number of technical issues and knowledge gaps present challenges to rapid progress. In this review, the current state of the field is summarized and existing roadblocks related to the study of lysine polyphosphorylation in higher eukaryotes are introduced. It is discussed how limited methods to identify targets of polyphosphorylation are further impacted by low concentration, unknown regulatory enzymes, and sequestration of polyP into compartments in mammalian systems. Furthermore, suggestions on how these obstacles could be addressed or what their physiological relevance may be within mammalian cells are presented.
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Affiliation(s)
- Kanchi Baijal
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Downey
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
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5
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McCarthy L, Bentley‐DeSousa A, Denoncourt A, Tseng Y, Gabriel M, Downey M. Proteins required for vacuolar function are targets of lysine polyphosphorylation in yeast. FEBS Lett 2019; 594:21-30. [DOI: 10.1002/1873-3468.13588] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/22/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Liam McCarthy
- Department of Cellular and Molecular Medicine University of Ottawa Canada
- Ottawa Institute of Systems Biology University of Ottawa Canada
| | - Amanda Bentley‐DeSousa
- Department of Cellular and Molecular Medicine University of Ottawa Canada
- Ottawa Institute of Systems Biology University of Ottawa Canada
| | - Alix Denoncourt
- Department of Cellular and Molecular Medicine University of Ottawa Canada
- Ottawa Institute of Systems Biology University of Ottawa Canada
| | - Yi‐Chieh Tseng
- Department of Cellular and Molecular Medicine University of Ottawa Canada
- Ottawa Institute of Systems Biology University of Ottawa Canada
| | - Matthew Gabriel
- Department of Cellular and Molecular Medicine University of Ottawa Canada
- Ottawa Institute of Systems Biology University of Ottawa Canada
| | - Michael Downey
- Department of Cellular and Molecular Medicine University of Ottawa Canada
- Ottawa Institute of Systems Biology University of Ottawa Canada
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6
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Ogawa M, Uyeda A, Harada K, Sato Y, Kato Y, Watanabe H, Honda K, Matsuura T. Class III Polyphosphate Kinase 2 Enzymes Catalyze the Pyrophosphorylation of Adenosine-5'-Monophosphate. Chembiochem 2019; 20:2961-2967. [PMID: 31206993 DOI: 10.1002/cbic.201900303] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Indexed: 11/09/2022]
Abstract
Polyphosphate kinase 2 (PPK2) transfer phosphate from inorganic polyphosphate to nucleotides. According to their activity, PPK2 enzymes are classified into three groups. Among them, class III enzymes catalyze both the phosphorylation of nucleotide mono- to diphosphates and di- to triphosphates by using polyphosphate, which is a very inexpensive substrate. Therefore, class III enzymes are very attractive for use in biotechnological applications. Despite several studies on class III enzymes, a detailed mechanism of how phosphate is transferred from the polyphosphate to the nucleotide remains to be elucidated. Herein, it is reported that PPK2 class III enzymes from two different bacterial species catalyze the phosphorylation of adenosine mono- (AMP) into triphosphate (ATP) not only through step-by-step phosphorylation, but also by pyrophosphorylation. These are the first PPK2 enzymes that have been shown to possess polyphosphate-dependent pyrophosphorylation activity.
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Affiliation(s)
- Marin Ogawa
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Atsuko Uyeda
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kazuo Harada
- Department of Applied Environmental Biology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yu Sato
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yasuhiko Kato
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hajime Watanabe
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kohsuke Honda
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomoaki Matsuura
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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7
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A Stringent Analysis of Polyphosphate Dynamics in Escherichia coli. J Bacteriol 2019; 201:JB.00070-19. [PMID: 30782636 DOI: 10.1128/jb.00070-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
During stress, bacterial cells activate a conserved pathway called the stringent response that promotes survival. Polyphosphates are long chains of inorganic phosphates that modulate this response in diverse bacterial species. In this issue, Michael J. Gray provides an important correction to the model of how polyphosphate accumulation is regulated during the stringent response in Escherichia coli (M. J. Gray, J. Bacteriol, 201:e00664-18, 2019, https://doi.org/10.1128/JB.00664-18). With other recent publications, this study provides a revised framework for understanding how bacterial polyphosphate dynamics might be exploited in infection control and industrial applications.
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Sofronova A, Semenyuk P, Muronetz V. The influence of β-casein glycation on its interaction with natural and synthetic polyelectrolytes. Food Hydrocoll 2019. [DOI: 10.1016/j.foodhyd.2018.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Petkowski JJ, Bains W, Seager S. Natural Products Containing 'Rare' Organophosphorus Functional Groups. Molecules 2019; 24:E866. [PMID: 30823503 PMCID: PMC6429109 DOI: 10.3390/molecules24050866] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/13/2019] [Accepted: 02/22/2019] [Indexed: 12/25/2022] Open
Abstract
Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.
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Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
| | - William Bains
- Rufus Scientific, 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK.
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
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10
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Azevedo C, Singh J, Steck N, Hofer A, Ruiz FA, Singh T, Jessen HJ, Saiardi A. Screening a Protein Array with Synthetic Biotinylated Inorganic Polyphosphate To Define the Human PolyP-ome. ACS Chem Biol 2018; 13:1958-1963. [PMID: 29924597 DOI: 10.1021/acschembio.8b00357] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Phenotypes are established by tight regulation on protein functions. This regulation can be mediated allosterically, through protein binding, and covalently, through post-translational modification (PTM). The integration of an ever-increasing number of PTMs into regulatory networks enables and defines the proteome complexity. Protein PTMs can occur enzymatically and nonenzymatically. Polyphosphorylation, which is a recently discovered PTM that belongs to the latter category, is the covalent attachment of the linear ortho-phosphate polymer called inorganic polyphosphate (polyP) to lysine residues. PolyP, which is ubiquitously present in nature, is also known to allosterically control protein function. To date, lack of reagents has prevented the systematic analysis of proteins covalently and/or allosterically associated with polyP. Here, we report on the chemical synthesis of biotin-modified monodisperse short-chain polyP (bio-polyP8-bio) and its subsequent use to screen a human proteome array to identify proteins that associate with polyP, thereby starting to define the human polyP-ome.
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Affiliation(s)
- Cristina Azevedo
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Jyoti Singh
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Nicole Steck
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Alexandre Hofer
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Felix A. Ruiz
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, United Kingdom
- Research Unit, “Puerta del Mar” University Hospital, School of Medicine, and Institute of Biomedical Research Cadiz (INiBICA), University of Cadiz, Cadiz, Spain
| | - Tanya Singh
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Henning J. Jessen
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, United Kingdom
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11
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Wang X, Ackermann M, Neufurth M, Wang S, Li Q, Feng Q, Schröder HC, Müller WEG. Restoration of Impaired Metabolic Energy Balance (ATP Pool) and Tube Formation Potential of Endothelial Cells under "high glucose", Diabetic Conditions by the Bioinorganic Polymer Polyphosphate. Polymers (Basel) 2017; 9:E575. [PMID: 30965879 PMCID: PMC6418735 DOI: 10.3390/polym9110575] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/01/2017] [Accepted: 11/02/2017] [Indexed: 12/15/2022] Open
Abstract
Micro-vascularization is a fast, energy-dependent process that is compromised by elevated glucose concentrations such as in diabetes mellitus disease. Here, we studied the effect of the physiological bioinorganic polymer, polyphosphate (polyP), on the reduced ATP content and impaired function of endothelial cells cultivated under "high glucose" (35 mM diabetes mellitus conditions) concentrations. This high-energy biopolymer has been shown to provide a source of metabolic energy, stored in its phosphoanhydride bonds. We show that exposure of human umbilical vein endothelial cells (HUVEC cells) to "high glucose" levels results in reduced cell viability, increased apoptotic cell death, and a decline in intracellular ATP level. As a consequence, the ability of HUVEC cells to form tube-like structures in the in vitro cell tube formation assay was almost completely abolished under "high glucose" conditions. Those cells were grown onto a physiological collagen scaffold (collagen/basement membrane extract). We demonstrate that these adverse effects of increased glucose levels can be reversed by administration of polyP to almost normal values. Using Na-polyP, complexed in a stoichiometric (molar) ratio to Ca2+ ions and in the physiological concentration range between 30 and 300 µM, an almost complete restoration of the reduced ATP pool of cells exposed to "high glucose" was found, as well as a normalization of the number of apoptotic cells and energy-dependent tube formation. It is concluded that the adverse effects on endothelial cells caused by the metabolic energy imbalance at elevated glucose concentrations can be counterbalanced by polyP, potentially opening new strategies for treatment of the micro-vascular complications in diabetic patients.
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Affiliation(s)
- Xiaohong Wang
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Duesbergweg 6, 55128 Mainz, Germany.
| | - Maximilian Ackermann
- Institute of Functional and Clinical Anatomy, University Medical Center of the Johannes Gutenberg University, Johann Joachim Becher Weg 13, D-55099 Mainz, Germany.
| | - Meik Neufurth
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Duesbergweg 6, 55128 Mainz, Germany.
| | - Shunfeng Wang
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Duesbergweg 6, 55128 Mainz, Germany.
| | - Qiang Li
- Institute of Karst Geology, Chinese Academy of Geological Sciences, No. 50, Qixing Road, Guilin 541004, China.
| | - Qingling Feng
- Key Laboratory of Advanced Materials of Ministry of Education of China, School of Materials Science and Engineering, Tsinghua University, Beijing 100084, China.
| | - Heinz C Schröder
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Duesbergweg 6, 55128 Mainz, Germany.
| | - Werner E G Müller
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Duesbergweg 6, 55128 Mainz, Germany.
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12
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Differential regulation of polyphosphate genes in Pseudomonas aeruginosa. Mol Genet Genomics 2016; 292:105-116. [PMID: 27744562 DOI: 10.1007/s00438-016-1259-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/11/2016] [Indexed: 12/17/2022]
Abstract
Phosphate homeostasis is tightly regulated in bacteria. Phosphate scarcity is overcome by inducing the expression of genes associated with the scavenging of phosphate and phosphate-containing molecules, while phosphate surplus is stored in the form of polyphosphate (polyP). Regulation of the genes involved in polyP metabolism was investigated. Knockout of the most distal gene of the pstSCAB-phoU operon that encodes a Pi-transport system results in large accumulation of polyphosphate (polyP). Here, we show that the phoU mutation differentially affects the transcription of ppk and ppx, that respectively, encode a polyP kinase and a polyP exopolyphosphatase, by increasing the former and reducing the latter, further contributing the accumulation of polyP. We also show that ppk forms an operon with the upstream gene hemB and that neither ppk nor ppx positively respond to Pi starvation. Furthermore, a putative PHO-box sequence in ppx regulatory region did not show a strong affinity for the PHO response regulator PhoB, while the promoter of hemB does not carry a PHO-box sequence. Altogether, the data indicate that the main genes involved in polyP metabolism, ppk and ppx, are differentially regulated in the absence of phoU, but neither gene belongs to the PHO regulon.
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