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Yang X, Gao R, Zhang Q, Yung CCM, Yin H, Li J. Quantification of Polyphosphate in Environmental Planktonic Samples Using a Novel Fluorescence Dye JC-D7. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:14249-14259. [PMID: 39079691 PMCID: PMC11325646 DOI: 10.1021/acs.est.4c04545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Polyphosphate (polyP) is found in plankton of diverse aquatic ecosystems and is important for plankton ecology and biogeochemical cycling. However, our knowledge of polyP in aquatic environments is hindered by a lack of data due to the limitations of quantification methods. The estimate of polyP in model organisms using phenol-chloroform extraction followed by enzymatic hydrolysis is complicated and fails for environmental samples. The commonly used 4',6-diamidino-2-phenylindole (DAPI) fluorescence method for environmental studies, on the contrary, severely overestimates polyP due to interference. In this paper, we develop a plankton lysis buffer to extract polyP and a quantification method using a novel polyP-specific fluorescence dye JC-D7. We test the methods using cultured algae and bacteria, as well as natural samples from marine and freshwater environments. We show that our plankton lysis extracts polyP with high recovery while requiring substantially less time and effort. Subsequent polyP quantification using JC-D7 fluorescence overcomes the interference encountered by the DAPI method and provides an accurate measurement of polyP down to <0.5 μmol L-1. This novel method enables more accurate quantification of polyP in aquatic environments and will profoundly enhance our knowledge of polyP, plankton ecology, and biogeochemistry.
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Affiliation(s)
- Xingyu Yang
- Department of Ocean Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong SAR, China
- Center for Ocean Research in Hong Kong and Macau, Hong Kong 999077, Hong Kong SAR, China
| | - Rixuan Gao
- Department of Ocean Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong SAR, China
- Center for Ocean Research in Hong Kong and Macau, Hong Kong 999077, Hong Kong SAR, China
| | - Qiong Zhang
- Department of Ocean Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong SAR, China
- Center for Ocean Research in Hong Kong and Macau, Hong Kong 999077, Hong Kong SAR, China
| | - Charmaine C M Yung
- Department of Ocean Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong SAR, China
| | - Hongbin Yin
- Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China
| | - Jiying Li
- Department of Ocean Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong SAR, China
- Center for Ocean Research in Hong Kong and Macau, Hong Kong 999077, Hong Kong SAR, China
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2
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Jiang H, Milanov M, Jüngert G, Angebauer L, Flender C, Smudde E, Gather F, Vogel T, Jessen HJ, Koch HG. Control of a chemical chaperone by a universally conserved ATPase. iScience 2024; 27:110215. [PMID: 38993675 PMCID: PMC11237923 DOI: 10.1016/j.isci.2024.110215] [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: 12/19/2023] [Revised: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 07/13/2024] Open
Abstract
The universally conserved YchF/Ola1 ATPases regulate stress response pathways in prokaryotes and eukaryotes. Deletion of YchF/Ola1 leads to increased resistance against environmental stressors, such as reactive oxygen species, while their upregulation is associated with tumorigenesis in humans. The current study shows that in E. coli, the absence of YchF stimulates the synthesis of the alternative sigma factor RpoS by a transcription-independent mechanism. Elevated levels of RpoS then enhance the transcription of major stress-responsive genes. In addition, the deletion of ychF increases the levels of polyphosphate kinase, which in turn boosts the production of the evolutionary conserved and ancient chemical chaperone polyphosphate. This potentially provides a unifying concept for the increased stress resistance in bacteria and eukaryotes upon YchF/Ola1 deletion. Intriguingly, the simultaneous deletion of ychF and the polyphosphate-degrading enzyme exopolyphosphatase causes synthetic lethality in E. coli, demonstrating that polyphosphate production needs to be fine-tuned to prevent toxicity.
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Affiliation(s)
- Hong Jiang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Martin Milanov
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Gabriela Jüngert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Larissa Angebauer
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Clara Flender
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Eva Smudde
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Fabian Gather
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Tanja Vogel
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Henning J. Jessen
- Institute for Organic Chemistry, Faculty of Chemistry and Pharmacy, University Freiburg 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
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Borghi F, Azevedo C, Johnson E, Burden JJ, Saiardi A. A mammalian model reveals inorganic polyphosphate channeling into the nucleolus and induction of a hyper-condensate state. CELL REPORTS METHODS 2024; 4:100814. [PMID: 38981472 PMCID: PMC11294840 DOI: 10.1016/j.crmeth.2024.100814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/23/2024] [Accepted: 06/13/2024] [Indexed: 07/11/2024]
Abstract
Inorganic polyphosphate (polyP) is a ubiquitous polymer that controls fundamental processes. To overcome the absence of a genetically tractable mammalian model, we developed an inducible mammalian cell line expressing Escherichia coli polyphosphate kinase 1 (EcPPK1). Inducing EcPPK1 expression prompted polyP synthesis, enabling validation of polyP analytical methods. Virtually all newly synthesized polyP accumulates within the nucleus, mainly in the nucleolus. The channeled polyP within the nucleolus results in the redistribution of its markers, leading to altered rRNA processing. Ultrastructural analysis reveals electron-dense polyP structures associated with a hyper-condensed nucleolus resulting from an exacerbation of the liquid-liquid phase separation (LLPS) phenomena controlling this membraneless organelle. The selective accumulation of polyP in the nucleoli could be interpreted as an amplification of polyP channeling to where its physiological function takes place. Indeed, quantitative analysis of several mammalian cell lines confirms that endogenous polyP accumulates within the nucleolus.
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Affiliation(s)
- Filipy Borghi
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Cristina Azevedo
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Errin Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Jemima J Burden
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Adolfo Saiardi
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK.
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Hambardikar V, Akosah YA, Scoma ER, Guitart-Mampel M, Urquiza P, Da Costa RT, Perez MM, Riggs LM, Patel R, Solesio ME. Toolkit for cellular studies of mammalian mitochondrial inorganic polyphosphate. Front Cell Dev Biol 2023; 11:1302585. [PMID: 38161329 PMCID: PMC10755588 DOI: 10.3389/fcell.2023.1302585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction: Inorganic polyphosphate (polyP) is an ancient polymer which is extremely well-conserved throughout evolution, and found in every studied organism. PolyP is composed of orthophosphates linked together by high-energy bonds, similar to those found in ATP. The metabolism and the functions of polyP in prokaryotes and simple eukaryotes are well understood. However, little is known about its physiological roles in mammalian cells, mostly due to its unknown metabolism and lack of systematic methods and effective models for the study of polyP in these organisms. Methods: Here, we present a comprehensive set of genetically modified cellular models to study mammalian polyP. Specifically, we focus our studies on mitochondrial polyP, as previous studies have shown the potent regulatory role of mammalian polyP in the organelle, including bioenergetics, via mechanisms that are not yet fully understood. Results: Using SH-SY5Y cells, our results show that the enzymatic depletion of mitochondrial polyP affects the expression of genes involved in the maintenance of mitochondrial physiology, as well as the structure of the organelle. Furthermore, this depletion has deleterious effects on mitochondrial respiration, an effect that is dependent on the length of polyP. Our results also show that the depletion of mammalian polyP in other subcellular locations induces significant changes in gene expression and bioenergetics; as well as that SH-SY5Y cells are not viable when the amount and/or the length of polyP are increased in mitochondria. Discussion: Our findings expand on the crucial role of polyP in mammalian mitochondrial physiology and place our cell lines as a valid model to increase our knowledge of both mammalian polyP and mitochondrial physiology.
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Affiliation(s)
- Vedangi Hambardikar
- Department of Biology, and Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, NJ, United States
| | - Yaw A. Akosah
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York City, NY, United States
| | - Ernest R. Scoma
- Department of Biology, and Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, NJ, United States
| | - Mariona Guitart-Mampel
- Department of Biology, and Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, NJ, United States
| | - Pedro Urquiza
- Department of Biology, and Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, NJ, United States
| | - Renata T. Da Costa
- Department of Biology, and Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, NJ, United States
| | - Matheus M. Perez
- Department of Biology, and Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, NJ, United States
| | - Lindsey M. Riggs
- Department of Biology, and Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, NJ, United States
| | - Rajesh Patel
- Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, United States
| | - Maria E. Solesio
- Department of Biology, and Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, NJ, United States
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Scoma ER, Da Costa RT, Leung HH, Urquiza P, Guitart-Mampel M, Hambardikar V, Riggs LM, Wong CO, Solesio ME. Human Prune Regulates the Metabolism of Mammalian Inorganic Polyphosphate and Bioenergetics. Int J Mol Sci 2023; 24:13859. [PMID: 37762163 PMCID: PMC10531210 DOI: 10.3390/ijms241813859] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 08/30/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Inorganic polyphosphate (polyP) is an evolutionarily conserved and ubiquitous polymer that is present in all studied organisms. PolyP consists of orthophosphates (Pi) linked together by phosphoanhydride bonds. The metabolism of polyP still remains poorly understood in higher eukaryotes. Currently, only F0F1-ATP synthase, Nudt3, and Prune have been proposed to be involved in this metabolism, although their exact roles and regulation in the context of polyP biology have not been fully elucidated. In the case of Prune, in vitro studies have shown that it exhibits exopolyphosphatase activity on very short-chain polyP (up to four units of Pi), in addition to its known cAMP phosphodiesterase (PDE) activity. Here, we expand upon studies regarding the effects of human Prune (h-Prune) on polyP metabolism. Our data show that recombinant h-Prune is unable to hydrolyze short (13-33 Pi) and medium (45-160 Pi) chains of polyP, which are the most common chain lengths of the polymer in mammalian cells. Moreover, we found that the knockdown of h-Prune (h-Prune KD) results in significantly decreased levels of polyP in HEK293 cells. Likewise, a reduction in the levels of polyP is also observed in Drosophila melanogaster loss-of-function mutants of the h-Prune ortholog. Furthermore, while the activity of ATP synthase, and the levels of ATP, are decreased in h-Prune KD HEK293 cells, the expression of ATP5A, which is a main component of the catalytic subunit of ATP synthase, is upregulated in the same cells, likely as a compensatory mechanism. Our results also show that the effects of h-Prune on mitochondrial bioenergetics are not a result of a loss of mitochondrial membrane potential or of significant changes in mitochondrial biomass. Overall, our work corroborates the role of polyP in mitochondrial bioenergetics. It also demonstrates a conserved effect of h-Prune on the metabolism of short- and medium-chain polyP (which are the predominant chain lengths found in mammalian cells). The effects of Prune in polyP are most likely exerted via the regulation of the activity of ATP synthase. Our findings pave the way for modifying the levels of polyP in mammalian cells, which could have pharmacological implications in many diseases where dysregulated bioenergetics has been demonstrated.
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Affiliation(s)
- Ernest R. Scoma
- Department of Biology, and Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08103, USA
| | - Renata T. Da Costa
- Department of Biology, and Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08103, USA
| | - Ho Hang Leung
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (H.H.L.)
| | - Pedro Urquiza
- Department of Biology, and Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08103, USA
| | - Mariona Guitart-Mampel
- Department of Biology, and Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08103, USA
| | - Vedangi Hambardikar
- Department of Biology, and Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08103, USA
| | - Lindsey M. Riggs
- Department of Biology, and Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08103, USA
| | - Ching-On Wong
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (H.H.L.)
| | - Maria E. Solesio
- Department of Biology, and Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08103, USA
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6
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Umeda C, Nakajima T, Maruhashi T, Tanigawa M, Maeda T, Mukai Y. Overexpression of polyphosphate polymerases and deletion of polyphosphate phosphatases shorten the replicative lifespan in yeast. FEBS Lett 2023; 597:2316-2333. [PMID: 37574219 DOI: 10.1002/1873-3468.14715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/29/2023] [Accepted: 08/03/2023] [Indexed: 08/15/2023]
Abstract
We previously found that overexpression of phosphate starvation-responsive genes by disrupting PHO80 led to a shortened replicative lifespan in yeast. To identify lifespan-related genes, we screened upregulated genes in the pho80Δ mutant and focused on the VTC genes, which encode the vacuolar polyphosphate (polyP) polymerase complex. VTC1/VTC2/VTC4 deletion restored the lifespan and intracellular polyP levels in pho80Δ. In the wild type, overexpression of VTC5 or a combination of the other VTCs caused high polyP accumulation and shortened lifespan. Similar phenotypes were caused by the deletion of polyP phosphatase genes-vacuolar PPN1 and cytosolic PPX1. The polyP-accumulating strains exhibited stress sensitivities. Thus, we demonstrated that polyP metabolic enzymes participate in replicative lifespan, and extreme polyP accumulation shortens the lifespan.
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Affiliation(s)
- Chiharu Umeda
- Department of Frontier Bioscience, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | - Toshio Nakajima
- Department of Frontier Bioscience, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | - Tsubasa Maruhashi
- Department of Frontier Bioscience, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | - Mirai Tanigawa
- Department of Biology, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Tatsuya Maeda
- Department of Biology, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Yukio Mukai
- Department of Frontier Bioscience, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
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7
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Manoukian L, Stein RS, Correa JA, Frigon D, Omelon S. Short-chain polyphosphates: Extraction effects on migration and size estimation of Saccharomyces cerevisiae extracts with polyacrylamide gel electrophoresis. Electrophoresis 2023; 44:1197-1205. [PMID: 37353918 DOI: 10.1002/elps.202300055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 06/25/2023]
Abstract
Polyacrylamide gel electrophoresis is commonly used to characterize the chain length of polyphosphates (polyP), more generally called condensed phosphates. After separation, nonradioactive, optical polyP staining is limited to chain lengths greater than 15PO 3 - ${\rm{PO}}_3^ - $ monomers with toluidine blue or 4',6-diamidino-2-phenylindole. PolyP chain lengths longer than 62PO 3 - $\;{\rm{PO}}_3^ - $ monomers were correlated to the shortest DNA ladders. In this study, synthetic linear polyPs (Sigma-Aldrich "Type 45", estimated mean length of 45PO 3 - ${\rm{PO}}_3^ - $ monomers), trimetaphosphate (trimetaP: 3PO 3 - ${\rm{PO}}_3^ - $ ring), tripolyphosphate (tripolyP), pyrophosphate (PPi ), and inorganic orthophosphate (o-Pi ) were visualized after separation by an in situ hydrolytic degradation process to o-Pi that was subsequently stained with methyl green. Statistically insignificant migration reduction of synthetic short-chain polyP after perchloric acid or phenol-chloroform extraction was confirmed with the Friedman test. 31 P diffusion-ordered NMR spectroscopy confirmed that extraction also reduced PPi diffusivity by <10%. Linear regression between the Rf peak migration value and the logarithm of synthetic polyP molecular weights enabled estimation of extracted polyP chain lengths from 2 to 45PO 3 - ${\rm{PO}}_3^ - $ monomers. Linear polyP extracts from Saccharomyces cerevisiae grown in aerobic conditions were generally shorter than extracts cultured in anaerobic conditions. Extractions from both aerobic and anaerobic S. cerevisiae included tripolyP and o-Pi , but no PPi .
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Affiliation(s)
- Lori Manoukian
- Department of Mining and Materials Engineering, McGill University, Montreal, Quebec, Canada
| | - Robin S Stein
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - José A Correa
- Department of Mathematics and Statistics, McGill University, Montreal, Quebec, Canada
| | - Dominic Frigon
- Department of Civil Engineering, McGill University, Montreal, Quebec, Canada
| | - Sidney Omelon
- Department of Mining and Materials Engineering, McGill University, Montreal, Quebec, Canada
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8
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Kawase T, Suzuki K, Kamimura M, Mochizuki T, Ushiki T. Optimized Protocol for Preservation of Human Platelet Samples for Fluorometric Polyphosphate Quantification. Methods Protoc 2023; 6:59. [PMID: 37489426 PMCID: PMC10366864 DOI: 10.3390/mps6040059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/30/2023] [Accepted: 06/20/2023] [Indexed: 07/26/2023] Open
Abstract
Platelet polyphosphate (polyP) can be conveniently quantified by exploiting a recent methodological breakthrough using 4',6-diamidino-2-phenylindole (DAPI). However, the preservation of these biological samples has not yet been standardized. In a preliminary study, potential protocols were screened, while accepted protocols were further tested in this study. Pure-platelet-rich plasma (P-PRP) samples and washed platelet suspensions were prepared using blood obtained from non-smoking healthy male donors and were fixed with ThromboFix for 20-24 h at 4 °C. Mass polyP levels were determined using a fluorometer at wavelengths of 425 and 525 nm. Platelet polyP levels were normalized to platelet counts. Statistical analyses were performed using non-parametric tests. Platelet polyP levels significantly decreased by 20% after 7 days in the platelet suspension maintained under fixed conditions at 4 °C (control). In contrast, the platelet polyP levels in both the P-PRP and washed platelet suspensions were maintained without a significant reduction for up to 6 weeks by removing ThromboFix after fixation and subsequent freezing in pure water at -80 °C. Fluorometric polyP quantification often interferes with the low specificity of DAPI binding and the wavelength used. Our validated protocols will enable long-term preservation and high-throughput polyP quantification and can be applied to relatively large cohort studies.
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Affiliation(s)
- Tomoyuki Kawase
- Division of Oral Bioengineering, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8514, Japan
| | - Katsuya Suzuki
- Department of Transfusion Medicine, Cell Therapy and Regenerative Medicine, Niigata University Medical and Dental Hospital, Niigata 951-8520, Japan
| | - Masami Kamimura
- Department of Transfusion Medicine, Cell Therapy and Regenerative Medicine, Niigata University Medical and Dental Hospital, Niigata 951-8520, Japan
| | - Tomoharu Mochizuki
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Takashi Ushiki
- Department of Transfusion Medicine, Cell Therapy and Regenerative Medicine, Niigata University Medical and Dental Hospital, Niigata 951-8520, Japan
- Division of Hematology and Oncology, Graduate School of Health Sciences, Niigata University, Niigata 951-8518, Japan
- Department of Hematology, Endocrinology and Metabolism, Faculty of Medicine, Niigata University, Niigata 951-8510, Japan
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9
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Liu W, Wang J, Comte‐Miserez V, Zhang M, Yu X, Chen Q, Jessen HJ, Mayer A, Wu S, Ye S. Cryo-EM structure of the polyphosphate polymerase VTC reveals coupling of polymer synthesis to membrane transit. EMBO J 2023; 42:e113320. [PMID: 37066886 PMCID: PMC10183816 DOI: 10.15252/embj.2022113320] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/18/2023] [Accepted: 03/27/2023] [Indexed: 04/18/2023] Open
Abstract
The eukaryotic vacuolar transporter chaperone (VTC) complex acts as a polyphosphate (polyP) polymerase that synthesizes polyP from adenosine triphosphate (ATP) and translocates polyP across the vacuolar membrane to maintain an intracellular phosphate (Pi ) homeostasis. To discover how the VTC complex performs its function, we determined a cryo-electron microscopy structure of an endogenous VTC complex (Vtc4/Vtc3/Vtc1) purified from Saccharomyces cerevisiae at 3.1 Å resolution. The structure reveals a heteropentameric architecture of one Vtc4, one Vtc3, and three Vtc1 subunits. The transmembrane region forms a polyP-selective channel, likely adopting a resting state conformation, in which a latch-like, horizontal helix of Vtc4 limits the entrance. The catalytic Vtc4 central domain is located on top of the pseudo-symmetric polyP channel, creating a strongly electropositive pathway for nascent polyP that can couple synthesis to translocation. The SPX domain of the catalytic Vtc4 subunit positively regulates polyP synthesis by the VTC complex. The noncatalytic Vtc3 regulates VTC through a phosphorylatable loop. Our findings, along with the functional data, allow us to propose a mechanism of polyP channel gating and VTC complex activation.
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Affiliation(s)
- Wei Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life SciencesTianjin UniversityTianjinChina
| | - Jiening Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life SciencesHubei UniversityWuhanChina
| | | | - Mengyu Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life SciencesTianjin UniversityTianjinChina
| | - Xuejing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life SciencesHubei UniversityWuhanChina
| | - Qingfeng Chen
- School of Life SciencesYunnan UniversityKunmingChina
| | - Henning Jacob Jessen
- Institute of Organic ChemistryUniversity of FreiburgFreiburgGermany
- CIBSS – Centre for Integrative Biological Signalling StudiesUniversity of FreiburgFreiburgGermany
| | - Andreas Mayer
- Département d'ImmunobiologieUniversité de LausanneEpalingesSwitzerland
| | - Shan Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life SciencesHubei UniversityWuhanChina
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life SciencesTianjin UniversityTianjinChina
- Life Sciences Institute, Zhejiang UniversityHangzhouChina
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10
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Llop A, Labella JI, Borisova M, Forchhammer K, Selim KA, Contreras A. Pleiotropic effects of PipX, PipY, or RelQ overexpression on growth, cell size, photosynthesis, and polyphosphate accumulation in the cyanobacterium Synechococcus elongatus PCC7942. Front Microbiol 2023; 14:1141775. [PMID: 37007489 PMCID: PMC10060972 DOI: 10.3389/fmicb.2023.1141775] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
The cyanobacterial protein PipY belongs to the Pyridoxal-phosphate (PLP)-binding proteins (PLPBP/COG0325) family of pyridoxal-phosphate-binding proteins, which are represented in all three domains of life. These proteins share a high degree of sequence conservation, appear to have purely regulatory functions, and are involved in the homeostasis of vitamin B6 vitamers and amino/keto acids. Intriguingly, the genomic context of the pipY gene in cyanobacteria connects PipY with PipX, a protein involved in signaling the intracellular energy status and carbon-to-nitrogen balance. PipX regulates its cellular targets via protein–protein interactions. These targets include the PII signaling protein, the ribosome assembly GTPase EngA, and the transcriptional regulators NtcA and PlmA. PipX is thus involved in the transmission of multiple signals that are relevant for metabolic homeostasis and stress responses in cyanobacteria, but the exact function of PipY is still elusive. Preliminary data indicated that PipY might also be involved in signaling pathways related to the stringent stress response, a pathway that can be induced in the unicellular cyanobacterium Synechococcus elongatus PCC7942 by overexpression of the (p)ppGpp synthase, RelQ. To get insights into the cellular functions of PipY, we performed a comparative study of PipX, PipY, or RelQ overexpression in S. elongatus PCC7942. Overexpression of PipY or RelQ caused similar phenotypic responses, such as growth arrest, loss of photosynthetic activity and viability, increased cell size, and accumulation of large polyphosphate granules. In contrast, PipX overexpression decreased cell length, indicating that PipX and PipY play antagonistic roles on cell elongation or cell division. Since ppGpp levels were not induced by overexpression of PipY or PipX, it is apparent that the production of polyphosphate in cyanobacteria does not require induction of the stringent response.
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Affiliation(s)
- Antonio Llop
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
- Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Jose I. Labella
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Marina Borisova
- Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Khaled A. Selim
- Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
- *Correspondence: Asunción Contreras,
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11
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Kumar D, Mandal S, Bailey JV, Flood BE, Jones RS. Fluoride and gallein inhibit polyphosphate accumulation by oral pathogen Rothia dentocariosa. Lett Appl Microbiol 2023; 76:ovad017. [PMID: 36715153 PMCID: PMC9990172 DOI: 10.1093/lambio/ovad017] [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: 09/11/2022] [Accepted: 01/27/2023] [Indexed: 01/31/2023]
Abstract
The uptake and storage of extracellular orthophosphate (Pi) by polyphosphate (polyP) accumulating bacteria may contribute to mineral dissolution in the oral cavity. To test the effect of potential inhibitors of polyP kinases on Rothia dentocariosa, gallein (0, 25, 50, and 100 μM) and fluoride (0, 50, and 100 ppm) were added to R. dentocariosa cultures grown in brain-heart infusion broth. At a late log growth phase (8 h), extracellular Pi was measured using an ascorbic acid assay, and polyP was isolated from bacterial cells treated with RNA/DNAases using a neutral phenol/chloroform extraction. Extracts were hydrolyzed and quantified as above. Gallein and fluoride had minor effects on bacterial growth with NaF having a direct effect on media pH. Gallein (≥25 μM) and fluoride (≥50 ppm) attenuated the bacterial drawdown of extracellular Pi by 56.7% (P < 0.05) and 37.3% (P < 0.01). There was a corresponding polyP synthesis decrease of 73.2% (P < 0.0001) from gallein and 83.1% (P < 0.0001) from fluoride. Attenuated total reflectance-Fourier-transform infrared spectroscopy validated the presence of polyP and its reduced concentration in R. dentocariosa bacterial cells following gallein and fluoride treatment. Rothia dentocariosa can directly change extracellular Pi and accumulate intracellular polyP, but the mechanism is attenuated by gallein and NaF.
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Affiliation(s)
- Dhiraj Kumar
- Department of Developmental and Surgical Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Subhrangshu Mandal
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jake V Bailey
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Beverly E Flood
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert S Jones
- Department of Developmental and Surgical Sciences, University of Minnesota, Minneapolis, MN 55455, USA
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12
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Manoukian L, Correa JA, Stein RS, Frigon D, Omelon S. Extraction processes reduce polyphosphate ion migration, dispersion and diffusion as detected with gel electrophoresis and
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P DOSY NMR. Electrophoresis 2022; 43:2014-2022. [DOI: 10.1002/elps.202100364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 07/10/2022] [Accepted: 08/08/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Lori Manoukian
- Department of Mining and Materials Engineering McGill University Montreal Quebec Canada
| | - José A. Correa
- Department of Mathematics and Statistics McGill University Montreal Quebec Canada
| | - Robin S. Stein
- Department of Chemistry McGill University Montreal Quebec Canada
| | - Dominic Frigon
- Department of Civil Engineering McGill University Montreal Quebec Canada
| | - Sidney Omelon
- Department of Mining and Materials Engineering McGill University Montreal Quebec Canada
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13
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Arredondo C, Cefaliello C, Dyrda A, Jury N, Martinez P, Díaz I, Amaro A, Tran H, Morales D, Pertusa M, Stoica L, Fritz E, Corvalán D, Abarzúa S, Méndez-Ruette M, Fernández P, Rojas F, Kumar MS, Aguilar R, Almeida S, Weiss A, Bustos FJ, González-Nilo F, Otero C, Tevy MF, Bosco DA, Sáez JC, Kähne T, Gao FB, Berry JD, Nicholson K, Sena-Esteves M, Madrid R, Varela D, Montecino M, Brown RH, van Zundert B. Excessive release of inorganic phosphate by ALS/FTD astrocytes causes non-cell-autonomous toxicity to motoneurons. Neuron 2022; 110:1656-1670.e12. [PMID: 35276083 DOI: 10.1016/j.neuron.2022.02.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/01/2021] [Accepted: 02/15/2022] [Indexed: 12/13/2022]
Abstract
Non-cell-autonomous mechanisms contribute to neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), in which astrocytes release unidentified factors that are toxic to motoneurons (MNs). We report here that mouse and patient iPSC-derived astrocytes with diverse ALS/FTD-linked mutations (SOD1, TARDBP, and C9ORF72) display elevated levels of intracellular inorganic polyphosphate (polyP), a ubiquitous, negatively charged biopolymer. PolyP levels are also increased in astrocyte-conditioned media (ACM) from ALS/FTD astrocytes. ACM-mediated MN death is prevented by degrading or neutralizing polyP in ALS/FTD astrocytes or ACM. Studies further reveal that postmortem familial and sporadic ALS spinal cord sections display enriched polyP staining signals and that ALS cerebrospinal fluid (CSF) exhibits increased polyP concentrations. Our in vitro results establish excessive astrocyte-derived polyP as a critical factor in non-cell-autonomous MN degeneration and a potential therapeutic target for ALS/FTD. The CSF data indicate that polyP might serve as a new biomarker for ALS/FTD.
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Affiliation(s)
- Cristian Arredondo
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile; CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Carolina Cefaliello
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Agnieszka Dyrda
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile; CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Nur Jury
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile; CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Pablo Martinez
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile; CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Iván Díaz
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile; CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Armando Amaro
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile; CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Helene Tran
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Danna Morales
- Program of Physiology and Biophysics, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Santiago 9160000, Chile
| | - Maria Pertusa
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Santiago 9160000, Chile; Millennium Nucleus for the Study of Pain (MiNuSPain), Santiago 9160000, Chile; Department of Biology, Faculty of Chemistry and Biology, Universidad de Santiago de Chile, Santiago 9160000, Chile
| | - Lorelei Stoica
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA; Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Elsa Fritz
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile; CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Daniela Corvalán
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile; CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Sebastián Abarzúa
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile; CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; FONDAP Center for Genome Regulation, Santiago 8370146, Chile
| | - Maxs Méndez-Ruette
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile; CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Paola Fernández
- Instituto de Neurociencias, Centro Interdisciplinario de Neurociencias de Valparaíso, Universidad de Valparaíso, Valparaíso 2340000, Chile
| | - Fabiola Rojas
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile; CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Meenakshi Sundaram Kumar
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Rodrigo Aguilar
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile
| | - Sandra Almeida
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Alexandra Weiss
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Fernando J Bustos
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile
| | - Fernando González-Nilo
- Instituto de Neurociencias, Centro Interdisciplinario de Neurociencias de Valparaíso, Universidad de Valparaíso, Valparaíso 2340000, Chile; Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile
| | - Carolina Otero
- School of Chemistry and Pharmacy, Faculty of Medicine, Universidad Andres Bello, Santiago 8320000, Chile
| | - Maria Florencia Tevy
- Cell Biology Laboratory, INTA, University of Chile and GEDIS Biotech, Santiago 7810000, Chile
| | - Daryl A Bosco
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Juan C Sáez
- Instituto de Neurociencias, Centro Interdisciplinario de Neurociencias de Valparaíso, Universidad de Valparaíso, Valparaíso 2340000, Chile
| | - Thilo Kähne
- Institute of Experimental Internal Medicine, Medical School, Otto von Guericke University Magdeburg, Magdeburg 39120, Germany
| | - Fen-Biao Gao
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - James D Berry
- Massachusetts General Hospital Neurological Clinical Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Katharine Nicholson
- Massachusetts General Hospital Neurological Clinical Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Miguel Sena-Esteves
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA; Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Rodolfo Madrid
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Santiago 9160000, Chile; Millennium Nucleus for the Study of Pain (MiNuSPain), Santiago 9160000, Chile; Department of Biology, Faculty of Chemistry and Biology, Universidad de Santiago de Chile, Santiago 9160000, Chile
| | - Diego Varela
- Program of Physiology and Biophysics, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Santiago 9160000, Chile
| | - Martin Montecino
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile; FONDAP Center for Genome Regulation, Santiago 8370146, Chile
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Brigitte van Zundert
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile; CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
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14
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Cleavage-Polyadenylation Factor Cft1 and SPX Domain Proteins Are Agents of Inositol Pyrophosphate Toxicosis in Fission Yeast. mBio 2022; 13:e0347621. [PMID: 35012333 PMCID: PMC8749416 DOI: 10.1128/mbio.03476-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Inositol pyrophosphate (IPP) dynamics govern expression of the fission yeast phosphate homeostasis regulon via their effects on lncRNA-mediated transcription interference. The growth defects (ranging from sickness to lethality) elicited by fission yeast mutations that inactivate IPP pyrophosphatase enzymes are exerted via the agonistic effects of too much 1,5-IP8 on RNA 3'-processing and transcription termination. To illuminate determinants of IPP toxicosis, we conducted a genetic screen for spontaneous mutations that suppressed the sickness of Asp1 pyrophosphatase mutants. We identified a missense mutation, C823R, in the essential Cft1 subunit of the cleavage and polyadenylation factor complex that suppresses even lethal Asp1 IPP pyrophosphatase mutations, thereby fortifying the case for 3'-processing/termination as the target of IPP toxicity. The suppressor screen also identified Gde1 and Spx1 (SPAC6B12.07c), both of which have an IPP-binding SPX domain and both of which are required for lethality elicited by Asp1 mutations. A survey of other SPX proteins in the proteome identified the Vtc4 and Vtc2 subunits of the vacuolar polyphosphate polymerase as additional agents of IPP toxicosis. Gde1, Spx1, and Vtc4 contain enzymatic modules (glycerophosphodiesterase, RING finger ubiquitin ligase, and polyphosphate polymerase, respectively) fused to their IPP-sensing SPX domains. Structure-guided mutagenesis of the IPP-binding sites and the catalytic domains of Gde1 and Spx1 indicated that both modules are necessary to elicit IPP toxicity. Whereas Vtc4 polymerase catalytic activity is required for IPP toxicity, its IPP-binding site is not. Epistasis analysis, transcriptome profiling, and assays of Pho1 expression implicate Spx1 as a transducer of IP8 signaling to the 3'-processing/transcription termination machinery. IMPORTANCE Impeding the catabolism of the inositol pyrophosphate (IPP) signaling molecule IP8 is cytotoxic to fission yeast. Here, by performing a genetic suppressor screen, we identified several cellular proteins required for IPP toxicosis. Alleviation of IPP lethality by a missense mutation in the essential Cft1 subunit of the cleavage and polyadenylation factor consolidates previous evidence that toxicity results from IP8 action as an agonist of RNA 3'-processing and transcription termination. Novel findings are that IP8 toxicity depends on IPP-sensing SPX domain proteins with associated enzymatic functions: Gde1 (glycerophosphodiesterase), Spx1 (ubiquitin ligase), and Vtc2/4 (polyphosphate polymerase). The effects of Spx1 deletion on phosphate homeostasis imply a role for Spx1 in communicating an IP8-driven signal to the transcription and RNA processing apparatus.
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15
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Samper-Martín B, Sarrias A, Lázaro B, Pérez-Montero M, Rodríguez-Rodríguez R, Ribeiro MPC, Bañón A, Wolfgeher D, Jessen HJ, Alsina B, Clotet J, Kron SJ, Saiardi A, Jiménez J, Bru S. Polyphosphate degradation by Nudt3-Zn 2+ mediates oxidative stress response. Cell Rep 2021; 37:110004. [PMID: 34788624 DOI: 10.1016/j.celrep.2021.110004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/08/2021] [Accepted: 10/22/2021] [Indexed: 02/06/2023] Open
Abstract
Polyphosphate (polyP) is a polymer of hundreds of phosphate residues present in all organisms. In mammals, polyP is involved in crucial physiological processes, including coagulation, inflammation, and stress response. However, after decades of research, the metabolic enzymes are still unknown. Here, we purify and identify Nudt3, a NUDIX family member, as the enzyme responsible for polyP phosphatase activity in mammalian cells. We show that Nudt3 shifts its substrate specificity depending on the cation; specifically, Nudt3 is active on polyP when Zn2+ is present. Nudt3 has in vivo polyP phosphatase activity in human cells, and importantly, we show that cells with altered polyP levels by modifying Nudt3 protein amount present reduced viability upon oxidative stress and increased DNA damage, suggesting that polyP and Nudt3 play a role in oxidative stress protection. Finally, we show that Nudt3 is involved in the early stages of embryo development in zebrafish.
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Affiliation(s)
- Bàrbara Samper-Martín
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain
| | - Ana Sarrias
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain
| | - Blanca Lázaro
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain
| | - Marta Pérez-Montero
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain
| | - Rosalía Rodríguez-Rodríguez
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain
| | - Mariana P C Ribeiro
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain
| | - Aitor Bañón
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra-Parc de Recerca Biomèdica, 08003 Barcelona, Spain
| | - Don Wolfgeher
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Berta Alsina
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra-Parc de Recerca Biomèdica, 08003 Barcelona, Spain
| | - Josep Clotet
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain
| | - Stephen J Kron
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E6BT, UK
| | - Javier Jiménez
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain.
| | - Samuel Bru
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain; Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Cerdanyola del Vallès, Spain.
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16
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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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17
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Correa Deza MA, Rodríguez de Olmos A, Suárez NE, Font de Valdez G, Salva S, Gerez CL. Inorganic polyphosphate from the immunobiotic Lactobacillus rhamnosus CRL1505 prevents inflammatory response in the respiratory tract. Saudi J Biol Sci 2021; 28:5684-5692. [PMID: 34588880 PMCID: PMC8459082 DOI: 10.1016/j.sjbs.2021.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022] Open
Abstract
Lactobacillus (L.) rhamnosus CRL1505 accumulates inorganic polyphosphate (polyP) in its cytoplasm in response to environmental stress. The aim of this study was to evaluate the potential effects of polyP from the immunobiotic CRL1505 on an acute respiratory inflammation murine animal model induced by lipopolysaccharide (LPS). First, the presence of polyP granules in the cytoplasm of CRL1505 strain was evidenced by specific staining. Then, it was demonstrated in the intracellular extracts (ICE) of CRL1505 that polyP chain length is greater than 45 phosphate residues. In addition, the functionality of the genes involved in the polyP metabolism (ppk, ppx1 and ppx2) was corroborated by RT-PCR. Finally, the possible effect of the ICE of CRL1505 strain containing polyP and a synthetic polyP was evaluated in vivo using a murine model of acute lung inflammation. It was observed that the level of cytokines pro-inflammatory (IL-17, IL-6, IL-2, IL-4, INF-γ) in serum was normalized in mice treated with ICE, which would indicate that polyP prevents the local inflammatory response in the respiratory tract. The potential application of ICE from L. rhamnosus CRL1505 as a novel bioproduct for the treatment of respiratory diseases is one of the projections of this work.
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Affiliation(s)
- María A Correa Deza
- Centro de Referencia para Lactobacilos (CERELA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Miguel de Tucumán, Tucumán, Argentina
| | - Antonieta Rodríguez de Olmos
- Centro de Referencia para Lactobacilos (CERELA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Miguel de Tucumán, Tucumán, Argentina
| | - Nadia E Suárez
- Centro de Referencia para Lactobacilos (CERELA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Miguel de Tucumán, Tucumán, Argentina
| | - Graciela Font de Valdez
- Centro de Referencia para Lactobacilos (CERELA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Miguel de Tucumán, Tucumán, Argentina
| | - Susana Salva
- Centro de Referencia para Lactobacilos (CERELA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Miguel de Tucumán, Tucumán, Argentina
| | - Carla L Gerez
- Centro de Referencia para Lactobacilos (CERELA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Miguel de Tucumán, Tucumán, Argentina
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18
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Regulation of inorganic polyphosphate is required for proper vacuolar proteolysis in fission yeast. J Biol Chem 2021; 297:100891. [PMID: 34147496 PMCID: PMC8294586 DOI: 10.1016/j.jbc.2021.100891] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 06/07/2021] [Accepted: 06/16/2021] [Indexed: 02/08/2023] Open
Abstract
Regulation of cellular proliferation and quiescence is a central issue in biology that has been studied using model unicellular eukaryotes, such as the fission yeast Schizosaccharomyces pombe. We previously reported that the ubiquitin/proteasome pathway and autophagy are essential to maintain quiescence induced by nitrogen deprivation in S. pombe; however, specific ubiquitin ligases that maintain quiescence are not fully understood. Here we investigated the SPX-RING-type ubiquitin ligase Pqr1, identified as required for quiescence in a genetic screen. Pqr1 is found to be crucial for vacuolar proteolysis, the final step of autophagy, through proper regulation of phosphate and its polymer polyphosphate. Pqr1 restricts phosphate uptake into the cell through ubiquitination and subsequent degradation of phosphate transporters on plasma membranes. We hypothesized that Pqr1 may act as the central regulator for phosphate control in S. pombe, through the function of the SPX domain involved in phosphate sensing. Deletion of pqr1+ resulted in hyperaccumulation of intracellular phosphate and polyphosphate and in improper autophagy-dependent proteolysis under conditions of nitrogen starvation. Polyphosphate hyperaccumulation in pqr1+-deficient cells was mediated by the polyphosphate synthase VTC complex in vacuoles. Simultaneous deletion of VTC complex subunits rescued Pqr1 mutant phenotypes, including defects in proteolysis and loss of viability during quiescence. We conclude that excess polyphosphate may interfere with proteolysis in vacuoles by mechanisms that as yet remain unknown. The present results demonstrate a connection between polyphosphate metabolism and vacuolar functions for proper autophagy-dependent proteolysis, and we propose that polyphosphate homeostasis contributes to maintenance of cellular viability during quiescence.
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19
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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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20
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Mandala VS, Loh DM, Shepard SM, Geeson MB, Sergeyev IV, Nocera DG, Cummins CC, Hong M. Bacterial Phosphate Granules Contain Cyclic Polyphosphates: Evidence from 31P Solid-State NMR. J Am Chem Soc 2020; 142:18407-18421. [PMID: 33075224 DOI: 10.1021/jacs.0c06335] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Polyphosphates (polyPs) are ubiquitous polymers in living organisms from bacteria to mammals. They serve a wide variety of biological functions, ranging from energy storage to stress response. In the last two decades, polyPs have been primarily viewed as linear polymers with varying chain lengths. However, recent biochemical data show that small metaphosphates, cyclic oligomers of [PO3](-), can bind to the enzymes ribonuclease A and NAD kinase, raising the question of whether metaphosphates can occur naturally as products of biological activity. Before the 1980s, metaphosphates had been reported in polyPs extracted from various organisms, but these results are considered artifactual due to the extraction and purification protocols. Here, we employ nondestructive 31P solid-state NMR spectroscopy to investigate the chemical structure of polyphosphates in whole cells as well as insoluble fractions of the bacterium Xanthobacter autotrophicus. Isotropic and anisotropic 31P chemical shifts of hydrated whole cells indicate the coexistence of linear and cyclic phosphates. Under our cell growth conditions and the concentrated conditions of the solid-state NMR samples, we found substantial amounts of cyclic phosphates in X. autotrophicus, suggesting that in fresh cells metaphosphate concentrations can be significant. The cellular metaphosphates are identified by comparison with the 31P chemical shift anisotropy of synthetic metaphosphates of known structures. In X. autotrophicus, the metaphosphates have a chemical shift anisotropy that is consistent with an average size of 3-8 phosphate units. These metaphosphates are enriched in insoluble and electron-dense granules. Exogenous hexametaphosphate added to X. autotrophicus cell extracts is metabolized to trimetaphosphates, supporting the presence and biological role of metaphosphates in cells. The definitive evidence for the presence of metaphosphates, reported here in whole bacterial cells for the first time, opens the path for future investigations of the biological function of metaphosphates in many organisms.
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Affiliation(s)
- Venkata S Mandala
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Daniel M Loh
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Scott M Shepard
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Michael B Geeson
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Ivan V Sergeyev
- Bruker Biospin, Billerica, Massachusetts 01821, United States
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Christopher C Cummins
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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21
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Sanz-Luque E, Saroussi S, Huang W, Akkawi N, Grossman AR. Metabolic control of acclimation to nutrient deprivation dependent on polyphosphate synthesis. SCIENCE ADVANCES 2020; 6:6/40/eabb5351. [PMID: 32998900 PMCID: PMC7556998 DOI: 10.1126/sciadv.abb5351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/07/2020] [Indexed: 05/05/2023]
Abstract
Polyphosphate, an energy-rich polymer conserved in all kingdoms of life, is integral to many cellular stress responses, including nutrient deprivation, and yet, the mechanisms that underlie its biological roles are not well understood. In this work, we elucidate the physiological function of this polymer in the acclimation of the model alga Chlamydomonas reinhardtii to nutrient deprivation. Our data reveal that polyphosphate synthesis is vital to control cellular adenosine 5'-triphosphate homeostasis and maintain both respiratory and photosynthetic electron transport upon sulfur deprivation. Using both genetic and pharmacological approaches, we show that electron flow in the energy-generating organelles is essential to induce and sustain acclimation to sulfur deprivation at the transcriptional level. These previously unidentified links among polyphosphate synthesis, photosynthetic and respiratory electron flow, and the acclimation of cells to nutrient deprivation could unveil the mechanism by which polyphosphate helps organisms cope with a myriad of stress conditions in a fluctuating environment.
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Affiliation(s)
- E Sanz-Luque
- Department of Plant Biology, The Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA.
| | - S Saroussi
- Department of Plant Biology, The Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA
| | - W Huang
- Department of Plant Biology, The Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA
| | - N Akkawi
- Department of Plant Biology, The Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA
| | - A R Grossman
- Department of Plant Biology, The Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA.
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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22
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Sanz-Luque E, Bhaya D, Grossman AR. Polyphosphate: A Multifunctional Metabolite in Cyanobacteria and Algae. FRONTIERS IN PLANT SCIENCE 2020; 11:938. [PMID: 32670331 PMCID: PMC7332688 DOI: 10.3389/fpls.2020.00938] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/09/2020] [Indexed: 05/19/2023]
Abstract
Polyphosphate (polyP), a polymer of orthophosphate (PO4 3-) of varying lengths, has been identified in all kingdoms of life. It can serve as a source of chemical bond energy (phosphoanhydride bond) that may have been used by biological systems prior to the evolution of ATP. Intracellular polyP is mainly stored as granules in specific vacuoles called acidocalcisomes, and its synthesis and accumulation appear to impact a myriad of cellular functions. It serves as a reservoir for inorganic PO4 3- and an energy source for fueling cellular metabolism, participates in maintaining adenylate and metal cation homeostasis, functions as a scaffold for sequestering cations, exhibits chaperone function, covalently binds to proteins to modify their activity, and enables normal acclimation of cells to stress conditions. PolyP also appears to have a role in symbiotic and parasitic associations, and in higher eukaryotes, low polyP levels seem to impact cancerous proliferation, apoptosis, procoagulant and proinflammatory responses and cause defects in TOR signaling. In this review, we discuss the metabolism, storage, and function of polyP in photosynthetic microbes, which mostly includes research on green algae and cyanobacteria. We focus on factors that impact polyP synthesis, specific enzymes required for its synthesis and degradation, sequestration of polyP in acidocalcisomes, its role in cellular energetics, acclimation processes, and metal homeostasis, and then transition to its potential applications for bioremediation and medical purposes.
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Affiliation(s)
- Emanuel Sanz-Luque
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA, United States
- Department of Biochemistry and Molecular Biology, University of Cordoba, Cordoba, Spain
| | - Devaki Bhaya
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA, United States
| | - Arthur R. Grossman
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA, United States
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23
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Zhu J, Loubéry S, Broger L, Zhang Y, Lorenzo-Orts L, Utz-Pugin A, Fernie AR, Young-Tae C, Hothorn M. A genetically validated approach for detecting inorganic polyphosphates in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:507-516. [PMID: 31816134 DOI: 10.1111/tpj.14642] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 11/08/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
Inorganic polyphosphates (polyPs) are linear polymers of orthophosphate units linked by phosphoanhydride bonds. Polyphosphates represent important stores of phosphate and energy, and are abundant in many pro- and eukaryotic organisms. In plants, the existence of polyPs has been established using microscopy and biochemical extraction methods that are now known to produce artifacts. Here we use a polyP-specific dye and a polyP-binding domain to detect polyPs in plant and algal cells. To develop the staining protocol, we induced polyP granules in Nicotiana benthamiana and Arabidopsis cells by heterologous expression of Escherichia coli polyphosphate kinase 1 (PPK1). Over-expression of PPK1 but not of a catalytically impaired version of the enzyme leads to severe growth phenotypes, suggesting that ATP-dependent synthesis and accumulation of polyPs in the plant cytosol is toxic. We next crossed stable PPK1-expressing Arabidopsis lines with plants expressing the polyP-binding domain of E. coli exopolyphosphatase (PPX1c), which co-localized with PPK1-generated polyP granules. These granules were stained by the polyP-specific dye JC-D7 and appeared as electron-dense structures in transmission electron microscopy sections. Using the polyP staining protocol derived from these experiments, we screened for polyP stores in different organs and tissues of both mono- and dicotyledonous plants. While we could not detect polyP granules in higher plants, we could visualize the polyP-rich acidocalcisomes in the green alga Chlamydomonas reinhardtii.
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Affiliation(s)
- Jinsheng Zhu
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
| | - Sylvain Loubéry
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
| | - Larissa Broger
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
| | - Youjun Zhang
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
- Center of Plant System Biology and Biotechnology, Ruski Blvd. 139, Plovdiv, 4000, Bulgaria
| | - Laura Lorenzo-Orts
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
| | - Anne Utz-Pugin
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
| | - Alisdair R Fernie
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Chang Young-Tae
- Center for Self-assembly and Complexity, IBS and Department of Chemistry, POSTECH, 50, Jigok-ro 127beon-gil, Nam-gu, Pohang-si, Gyeongsangbuk-do, Pohang, 37673, Republic of Korea
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
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24
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Christ JJ, Willbold S, Blank LM. Methods for the Analysis of Polyphosphate in the Life Sciences. Anal Chem 2020; 92:4167-4176. [PMID: 32039586 DOI: 10.1021/acs.analchem.9b05144] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Inorganic polyphosphate (polyP) is the polymer of orthophosphate and can be found in all living organisms. For polyP characterization, one or more of six parameters are of interest: the molecular structure (linear, cyclic, or branched), the concentration, the average chain length, the chain length distribution, the cellular localization, and the cation composition. Here, the merits, limitations, and critical parameters of the state-of-the-art methods for the analysis of the six parameters from the life sciences are discussed. With this contribution, we aim to lower the entry barrier into the analytics of polyP, a molecule with prominent, yet often incompletely understood, contributions to cellular function.
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Affiliation(s)
- Jonas Johannes Christ
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, Worringer Weg 1, RWTH Aachen University, D-52074 Aachen, Germany
| | - Sabine Willbold
- Central Institute for Engineering, Electronics and Analytics, Analytics (ZEA-3), Wilhelm-Johnen-Straße, D-52428 Jülich, Germany
| | - Lars Mathias Blank
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, Worringer Weg 1, RWTH Aachen University, D-52074 Aachen, Germany
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25
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Feng C, Welles L, Zhang X, Pronk M, de Graaff D, van Loosdrecht M. Stress-induced assays for polyphosphate quantification by uncoupling acetic acid uptake and anaerobic phosphorus release. WATER RESEARCH 2020; 169:115228. [PMID: 31698149 DOI: 10.1016/j.watres.2019.115228] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/14/2019] [Accepted: 10/23/2019] [Indexed: 05/19/2023]
Abstract
Phosphorus has been successfully eliminated from wastewater by biological techniques of enhanced biological phosphorus removal (EBPR) process, which relies on a specific microbiota of polyphosphate accumulating organisms (PAOs) that accumulate phosphate as polyphosphates (poly-P). Most methods for quantification of poly-P pools suffer from low accuracy and specificity. More powerful and implementable P-analysis tools are required for poly-P quantification, which will help in improved evaluation of processes in laboratory and full-scale EBPR systems. This study developed two methods to quantify poly-P pools by releasing the poly-P from the cell. During experimental optimization, it was observed that two different methods resulted in the highest phosphate release: acetate addition at a pH of 4.8 and exposure to EDTA solution with a concentration of 1% (w/v). Treatment with EDTA resulted in a higher amount of phosphate release from all sludge samples. This was characterized by P-release of 1.5-2.5 times higher than the control tests. In contrast, treatments with acetate addition at a low pH exhibited that P-release depended upon the types of the sludge samples. The highest P-release amount and rate were found in highly-enriched PAO sludge samples, but with fewer influences on the sludge collected from WWTP, which may be attributed to the lower fraction of PAOs in the sludge. Overall, the proposed approaches to quantify the poly-P concentration can be applied in simple, user-friendly, and cost-effective ways.
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Affiliation(s)
- Cuijie Feng
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands; Department of Civil and Environmental Engineering, Polytechnic University of Milano, Piazza Leonardo da Vinci 32, 20133, Milan, Italy.
| | - Laurens Welles
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands; Environmental Engineering and Water Technology Department, IHE Institute for Water Education, Westvest 7, 2611 AX, Delft, the Netherlands.
| | - Xuedong Zhang
- Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN, Delft, the Netherlands
| | - Mario Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Danny de Graaff
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Mark van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
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26
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Lorenzo‐Orts L, Couto D, Hothorn M. Identity and functions of inorganic and inositol polyphosphates in plants. THE NEW PHYTOLOGIST 2020; 225:637-652. [PMID: 31423587 PMCID: PMC6973038 DOI: 10.1111/nph.16129] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/22/2019] [Indexed: 05/08/2023]
Abstract
Inorganic polyphosphates (polyPs) and inositol pyrophosphates (PP-InsPs) form important stores of inorganic phosphate and can act as energy metabolites and signaling molecules. Here we review our current understanding of polyP and inositol phosphate (InsP) metabolism and physiology in plants. We outline methods for polyP and InsP detection, discuss the known plant enzymes involved in their synthesis and breakdown, and summarize the potential physiological and signaling functions for these enigmatic molecules in plants.
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Affiliation(s)
- Laura Lorenzo‐Orts
- Structural Plant Biology LaboratoryDepartment of Botany and Plant BiologyUniversity of Geneva30 Quai E. AnsermetGeneva1211Switzerland
| | - Daniel Couto
- Structural Plant Biology LaboratoryDepartment of Botany and Plant BiologyUniversity of Geneva30 Quai E. AnsermetGeneva1211Switzerland
| | - Michael Hothorn
- Structural Plant Biology LaboratoryDepartment of Botany and Plant BiologyUniversity of Geneva30 Quai E. AnsermetGeneva1211Switzerland
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27
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Müller WE, Schröder HC, Wang X. Inorganic Polyphosphates As Storage for and Generator of Metabolic Energy in the Extracellular Matrix. Chem Rev 2019; 119:12337-12374. [PMID: 31738523 PMCID: PMC6935868 DOI: 10.1021/acs.chemrev.9b00460] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Indexed: 12/14/2022]
Abstract
Inorganic polyphosphates (polyP) consist of linear chains of orthophosphate residues, linked by high-energy phosphoanhydride bonds. They are evolutionarily old biopolymers that are present from bacteria to man. No other molecule concentrates as much (bio)chemically usable energy as polyP. However, the function and metabolism of this long-neglected polymer are scarcely known, especially in higher eukaryotes. In recent years, interest in polyP experienced a renaissance, beginning with the discovery of polyP as phosphate source in bone mineralization. Later, two discoveries placed polyP into the focus of regenerative medicine applications. First, polyP shows morphogenetic activity, i.e., induces cell differentiation via gene induction, and, second, acts as an energy storage and donor in the extracellular space. Studies on acidocalcisomes and mitochondria provided first insights into the enzymatic basis of eukaryotic polyP formation. In addition, a concerted action of alkaline phosphatase and adenylate kinase proved crucial for ADP/ATP generation from polyP. PolyP added extracellularly to mammalian cells resulted in a 3-fold increase of ATP. The importance and mechanism of this phosphotransfer reaction for energy-consuming processes in the extracellular matrix are discussed. This review aims to give a critical overview about the formation and function of this unique polymer that is capable of storing (bio)chemically useful energy.
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Affiliation(s)
- Werner E.G. Müller
- ERC Advanced Investigator
Grant Research
Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Duesbergweg 6, D-55128 Mainz, Germany
| | - Heinz C. Schröder
- ERC Advanced Investigator
Grant Research
Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Duesbergweg 6, D-55128 Mainz, Germany
| | - Xiaohong Wang
- ERC Advanced Investigator
Grant Research
Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Duesbergweg 6, D-55128 Mainz, Germany
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28
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Polyphosphate Initiates Tau Aggregation through Intra- and Intermolecular Scaffolding. Biophys J 2019; 117:717-728. [PMID: 31400913 DOI: 10.1016/j.bpj.2019.07.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/28/2019] [Accepted: 07/08/2019] [Indexed: 12/20/2022] Open
Abstract
The aggregation and deposition of tau is a hallmark of a class of neurodegenerative diseases called tauopathies. Despite intensive study, cellular and molecular factors that trigger tau aggregation are not well understood. Here, we provide evidence for two mechanisms relevant to the initiation of tau aggregation in the presence of cytoplasmic polyphosphates (polyP): changes in the conformational ensemble of monomer tau and noncovalent cross-linking of multiple tau monomers. We identified conformational changes throughout full-length tau, most notably diminishment of long-range interactions between the termini coupled with compaction of the microtubule binding and proline- rich regions. We found that while the proline-rich and microtubule binding regions both contain polyP binding sites, the proline-rich region is a requisite for compaction of the microtubule binding region upon binding. Additionally, both the magnitude of the conformational change and the aggregation of tau are dependent on the chain length of the polyP polymer. Longer polyP chains are more effective at intermolecular, noncovalent cross-linking of tau. These observations provide an understanding of the initial steps of tau aggregation through interaction with a physiologically relevant aggregation inducer.
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29
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Lorenzo-Orts L, Hohmann U, Zhu J, Hothorn M. Molecular characterization of CHAD domains as inorganic polyphosphate-binding modules. Life Sci Alliance 2019; 2:2/3/e201900385. [PMID: 31133615 PMCID: PMC6537752 DOI: 10.26508/lsa.201900385] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 12/23/2022] Open
Abstract
A domain of unknown function termed CHAD, present in all kingdoms of life, is characterized as a specific inorganic polyphosphate-binding domain. Inorganic polyphosphates (polyPs) are linear polymers of orthophosphate units linked by phosphoanhydride bonds. Here, we report that bacterial, archaeal, and eukaryotic conserved histidine α-helical (CHAD) domains are specific polyP-binding modules. Crystal structures reveal that CHAD domains are formed by two four-helix bundles, giving rise to a central pore surrounded by conserved basic surface patches. Different CHAD domains bind polyPs with dissociation constants ranging from the nano- to mid-micromolar range, but not nucleic acids. A CHAD—polyP complex structure reveals the phosphate polymer binding across the central pore and along the two basic patches. Mutational analysis of CHAD—polyP interface residues validates the complex structure. The presence of a CHAD domain in the polyPase ygiF enhances its enzymatic activity. The only known CHAD protein from the plant Ricinus communis localizes to the nucleus/nucleolus when expressed in Arabidopsis and tobacco, suggesting that plants may harbor polyPs in these compartments. We propose that CHAD domains may be used to engineer the properties of polyP-metabolizing enzymes and to specifically localize polyP stores in eukaryotic cells and tissues.
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Affiliation(s)
- Laura Lorenzo-Orts
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Ulrich Hohmann
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Jinsheng Zhu
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
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30
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Pokhrel A, Lingo JC, Wolschendorf F, Gray MJ. Assaying for Inorganic Polyphosphate in Bacteria. J Vis Exp 2019. [PMID: 30735204 DOI: 10.3791/58818] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Inorganic polyphosphate (polyP) is a biological polymer found in cells from all domains of life, and is required for virulence and stress response in many bacteria. There are a variety of methods for quantifying polyP in biological materials, many of which are either labor-intensive or insensitive, limiting their usefulness. We present here a streamlined method for polyP quantification in bacteria, using a silica membrane column extraction optimized for rapid processing of multiple samples, digestion of polyP with the polyP-specific exopolyphosphatase ScPPX, and detection of the resulting free phosphate with a sensitive ascorbic acid-based colorimetric assay. This procedure is straightforward, inexpensive, and allows reliable polyP quantification in diverse bacterial species. We present representative polyP quantification from the Gram-negative bacterium (Escherichia coli), the Gram-positive lactic acid bacterium (Lactobacillus reuteri), and the mycobacterial species (Mycobacterium smegmatis). We also include a simple protocol for nickel affinity purification of mg quantities of ScPPX, which is not currently commercially available.
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Affiliation(s)
- Arya Pokhrel
- Department of Microbiology, University of Alabama at Birmingham
| | - Jordan C Lingo
- Division of Infectious Diseases, University of Alabama at Birmingham
| | | | - Michael J Gray
- Department of Microbiology, University of Alabama at Birmingham;
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31
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Christ JJ, Blank LM. Analytical polyphosphate extraction from Saccharomyces cerevisiae. Anal Biochem 2018; 563:71-78. [DOI: 10.1016/j.ab.2018.09.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/27/2018] [Accepted: 09/27/2018] [Indexed: 10/28/2022]
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Christ JJ, Blank LM. Enzymatic quantification and length determination of polyphosphate down to a chain length of two. Anal Biochem 2018; 548:82-90. [DOI: 10.1016/j.ab.2018.02.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 10/18/2022]
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Rudat AK, Pokhrel A, Green TJ, Gray MJ. Mutations in Escherichia coli Polyphosphate Kinase That Lead to Dramatically Increased In Vivo Polyphosphate Levels. J Bacteriol 2018; 200:e00697-17. [PMID: 29311274 PMCID: PMC5826030 DOI: 10.1128/jb.00697-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 12/20/2017] [Indexed: 11/20/2022] Open
Abstract
Bacteria synthesize inorganic polyphosphate (polyP) in response to a wide variety of stresses, and production of polyP is essential for stress response and survival in many important pathogens and bacteria used in biotechnological processes. However, surprisingly little is known about the molecular mechanisms that control polyP synthesis. We have therefore developed a novel genetic screen that specifically links growth of Escherichia coli to polyP synthesis, allowing us to isolate mutations leading to enhanced polyP production. Using this system, we have identified mutations in the polyP-synthesizing enzyme polyP kinase (PPK) that lead to dramatic increases in in vivo polyP synthesis but do not substantially affect the rate of polyP synthesis by PPK in vitro These mutations are distant from the PPK active site and found in interfaces between monomers of the PPK tetramer. We have also shown that high levels of polyP lead to intracellular magnesium starvation. Our results provide new insights into the control of bacterial polyP accumulation and suggest a simple, novel strategy for engineering bacteria with increased polyP contents.IMPORTANCE PolyP is an ancient, universally conserved biomolecule and is important for stress response, energy metabolism, and virulence in a remarkably broad range of microorganisms. PolyP accumulation by bacteria is also important in biotechnology applications. For example, it is critical to enhanced biological phosphate removal (EBPR) from wastewater. Understanding how bacteria control polyP synthesis is therefore of broad importance in both the fields of bacterial pathogenesis and biological engineering. Using Escherichia coli as a model organism, we have identified the first known mutations in polyP kinase that lead to increases in cellular polyP content.
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Affiliation(s)
- Amanda K Rudat
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Arya Pokhrel
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Todd J Green
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael J Gray
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Moudříková Š, Sadowsky A, Metzger S, Nedbal L, Mettler-Altmann T, Mojzeš P. Quantification of Polyphosphate in Microalgae by Raman Microscopy and by a Reference Enzymatic Assay. Anal Chem 2017; 89:12006-12013. [PMID: 29099580 DOI: 10.1021/acs.analchem.7b02393] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Polyphosphates have occurred in living cells early in evolution and microalgae contain these important polymers in their cells. Progress in research of polyphosphate metabolism of these ecologically as well as biotechnologically important microorganisms is hampered by the lack of rapid quantification methods. Experiments with the green alga Chlorella vulgaris presented here compared polyphosphate extraction in water, methanol-chloroform, and phenol-chloroform followed by polyphosphate purification by binding to silica columns or ethanol precipitation. The phenol-chloroform extraction of C. vulgaris followed by ethanol precipitation of polyphosphate was shown to be superior to the other tested method variants. Recovery test of added polyphosphate standard to algal biomass showed that the method is accurate. Using this biochemical assay as a validated reference, we show that 2-dimensional, confocal Raman microscopy can serve as a linear proxy for polyphosphate in C. vulgaris with R2 up to 0.956. With this, polyphosphate quantification can be shortened by use of Raman microscopy from days to hours and, additionally, information about intracellular distribution of polyphosphate and heterogeneity among individual cells in algal culture can be obtained. This offers new insights into the dynamics and role of these polymers crucial for phosphorus uptake and storage. This analytical capability is of particular practical importance because algae aid phosphorus sequestration from wastewater and the thus enriched biomass may serve as organic fertilizer. Both these applications have a strong potential in a future sustainable, circular bioeconomy.
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Affiliation(s)
- Šárka Moudříková
- Institute of Bio- and Geosciences/Plant Sciences (IBG-2), Forschungszentrum Jülich , Wilhelm-Johnen-Straße, D-52428 Jülich, Germany.,Institute of Physics, Faculty of Mathematics and Physics, Charles University , Ke Karlovu 5, CZ-12116 Prague 2, Czech Republic
| | - Andres Sadowsky
- CEPLAS Plant Metabolism and Metabolomics Laboratory, Institute of Plant Biochemistry, Heinrich Heine University Düsseldorf , Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Sabine Metzger
- CEPLAS Plant Metabolism and Metabolomics Laboratory, Botanical Institute, University of Cologne , Zülpicher Str. 47b, D-50674 Cologne, Germany
| | - Ladislav Nedbal
- Institute of Physics, Faculty of Mathematics and Physics, Charles University , Ke Karlovu 5, CZ-12116 Prague 2, Czech Republic
| | - Tabea Mettler-Altmann
- CEPLAS Plant Metabolism and Metabolomics Laboratory, Institute of Plant Biochemistry, Heinrich Heine University Düsseldorf , Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Peter Mojzeš
- Institute of Bio- and Geosciences/Plant Sciences (IBG-2), Forschungszentrum Jülich , Wilhelm-Johnen-Straße, D-52428 Jülich, Germany.,Institute of Physics, Faculty of Mathematics and Physics, Charles University , Ke Karlovu 5, CZ-12116 Prague 2, Czech Republic
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Bru S, Samper-Martín B, Quandt E, Hernández-Ortega S, Martínez-Laínez JM, Garí E, Rafel M, Torres-Torronteras J, Martí R, Ribeiro MPC, Jiménez J, Clotet J. Polyphosphate is a key factor for cell survival after DNA damage in eukaryotic cells. DNA Repair (Amst) 2017; 57:171-178. [PMID: 28822913 DOI: 10.1016/j.dnarep.2017.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 07/30/2017] [Accepted: 08/04/2017] [Indexed: 12/11/2022]
Abstract
Cells require extra amounts of dNTPs to repair DNA after damage. Polyphosphate (polyP) is an evolutionary conserved linear polymer of up to several hundred inorganic phosphate (Pi) residues that is involved in many functions, including Pi storage. In the present article, we report on findings demonstrating that polyP functions as a source of Pi when required to sustain the dNTP increment essential for DNA repair after damage. We show that mutant yeast cells without polyP produce less dNTPs upon DNA damage and that their survival is compromised. In contrast, when polyP levels are ectopically increased, yeast cells become more resistant to DNA damage. More importantly, we show that when polyP is reduced in HEK293 mammalian cell line cells and in human dermal primary fibroblasts (HDFa), these cells become more sensitive to DNA damage, suggesting that the protective role of polyP against DNA damage is evolutionary conserved. In conclusion, we present polyP as a molecule involved in resistance to DNA damage and suggest that polyP may be a putative target for new approaches in cancer treatment or prevention.
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Affiliation(s)
- Samuel Bru
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Bàrbara Samper-Martín
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Eva Quandt
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Sara Hernández-Ortega
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Joan M Martínez-Laínez
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Eloi Garí
- Institut de Recerca Biomèdica de Lleida (IRBLleida), Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Universitat de Lleida, Lleida, Spain
| | - Marta Rafel
- Institut de Recerca Biomèdica de Lleida (IRBLleida), Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Universitat de Lleida, Lleida, Spain
| | - Javier Torres-Torronteras
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Ramón Martí
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Mariana P C Ribeiro
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Javier Jiménez
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain.
| | - Josep Clotet
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain.
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