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Guan J, Jakob U. The Protein Scaffolding Functions of Polyphosphate. J Mol Biol 2024; 436:168504. [PMID: 38423453 DOI: 10.1016/j.jmb.2024.168504] [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: 12/05/2023] [Revised: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
Inorganic polyphosphate (polyP), one of the first high-energy compound on earth, defies its extreme compositional and structural simplicity with an astoundingly wide array of biological activities across all domains of life. However, the underlying mechanism of such functional pleiotropy remains largely elusive. In this review, we will summarize recent studies demonstrating that this simple polyanion stabilizes protein folding intermediates and scaffolds select native proteins. These functions allow polyP to act as molecular chaperone that protects cells against protein aggregation, as pro-amyloidogenic factor that accelerates both physiological and disease-associated amyloid formation, and as a modulator of liquid-liquid phase separation processes. These activities help to explain polyP's known roles in bacterial stress responses and pathogenicity, provide the mechanistic foundation for its potential role in human neurodegenerative diseases, and open a new direction regarding its influence on gene expression through condensate formation. We will highlight critical unanswered questions and point out potential directions that will help to further understand the pleiotropic functions of this ancient and ubiquitous biopolymer.
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Affiliation(s)
- Jian Guan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA; Biological Chemistry Department, University of Michigan Medical School, Ann Arbor, MI, USA.
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2
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Meng Z, Li X, Lu S, Hua Y, Yin B, Qian B, Li Z, Zhou Y, Sergeeva I, Fu Y, Ma Y. A comprehensive analysis of m6A/m7G/m5C/m1A-related gene expression and immune infiltration in liver ischemia-reperfusion injury by integrating bioinformatics and machine learning algorithms. Eur J Med Res 2024; 29:326. [PMID: 38867322 PMCID: PMC11170855 DOI: 10.1186/s40001-024-01928-y] [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: 10/28/2023] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Liver ischemia-reperfusion injury (LIRI) is closely associated with immune infiltration, which commonly occurs after liver surgery, especially liver transplantation. Therefore, it is crucial to identify the genes responsible for LIRI and develop effective therapeutic strategies that target immune response. Methylation modifications in mRNA play various crucial roles in different diseases. This study aimed to identify potential methylation-related markers in patients with LIRI and evaluate the corresponding immune infiltration. METHODS Two Gene Expression Omnibus datasets containing human liver transplantation data (GSE12720 and GSE151648) were downloaded for integrated analysis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were conducted to investigate the functional enrichment of differentially expressed genes (DEGs). Differentially expressed methylation-related genes (DEMRGs) were identified by overlapping DEG sets and 65 genes related to N6-methyladenosine (m6A), 7-methylguanine (m7G), 5-methylcytosine (m5C), and N1-methyladenosine (m1A). To evaluate the relationship between DEMRGs, a protein-protein interaction (PPI) network was utilized. The core DEMRGs were screened using three machine learning algorithms: least absolute shrinkage and selection operator, random forest, and support vector machine-recursive feature elimination. After verifying the diagnostic efficacy using the receiver operating characteristic curve, we validated the expression of the core DEMRGs in clinical samples and performed relative cell biology experiments. Additionally, the immune status of LIRI was comprehensively assessed using the single sample gene set enrichment analysis algorithm. The upstream microRNA and transcription factors of the core DEMRGs were also predicted. RESULTS In total, 2165 upregulated and 3191 downregulated DEGs were identified, mainly enriched in LIRI-related pathways. The intersection of DEGs and methylation-related genes yielded 28 DEMRGs, showing high interaction in the PPI network. Additionally, the core DEMRGs YTHDC1, METTL3, WTAP, and NUDT3 demonstrated satisfactory diagnostic efficacy and significant differential expression and corresponding function based on cell biology experiments. Furthermore, immune infiltration analyses indicated that several immune cells correlated with all core DEMRGs in the LIRI process to varying extents. CONCLUSIONS We identified core DEMRGs (YTHDC1, METTL3, WTAP, and NUDT3) associated with immune infiltration in LIRI through bioinformatics and validated them experimentally. This study may provide potential methylation-related gene targets for LIRI immunotherapy.
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Affiliation(s)
- Zhanzhi Meng
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinglong Li
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shounan Lu
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yongliang Hua
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
- Department of Pediatric Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bing Yin
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Baolin Qian
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhongyu Li
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yongzhi Zhou
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Irina Sergeeva
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yao Fu
- Department of Ultrasound, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yong Ma
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China.
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Khan A, Mallick M, Ladke JS, Bhandari R. The ring rules the chain - inositol pyrophosphates and the regulation of inorganic polyphosphate. Biochem Soc Trans 2024; 52:567-580. [PMID: 38629621 DOI: 10.1042/bst20230256] [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: 02/13/2024] [Revised: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
The maintenance of phosphate homeostasis serves as a foundation for energy metabolism and signal transduction processes in all living organisms. Inositol pyrophosphates (PP-InsPs), composed of an inositol ring decorated with monophosphate and diphosphate moieties, and inorganic polyphosphate (polyP), chains of orthophosphate residues linked by phosphoanhydride bonds, are energy-rich biomolecules that play critical roles in phosphate homeostasis. There is a complex interplay between these two phosphate-rich molecules, and they share an interdependent relationship with cellular adenosine triphosphate (ATP) and inorganic phosphate (Pi). In eukaryotes, the enzymes involved in PP-InsP synthesis show some degree of conservation across species, whereas distinct enzymology exists for polyP synthesis among different organisms. In fact, the mechanism of polyP synthesis in metazoans, including mammals, is still unclear. Early studies on PP-InsP and polyP synthesis were conducted in the slime mould Dictyostelium discoideum, but it is in the budding yeast Saccharomyces cerevisiae that a clear understanding of the interplay between polyP, PP-InsPs, and Pi homeostasis has now been established. Recent research has shed more light on the influence of PP-InsPs on polyP in mammals, and the regulation of both these molecules by cellular ATP and Pi levels. In this review we will discuss the cross-talk between PP-InsPs, polyP, ATP, and Pi in the context of budding yeast, slime mould, and mammals. We will also highlight the similarities and differences in the relationship between these phosphate-rich biomolecules among this group of organisms.
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Affiliation(s)
- Azmi Khan
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | - Manisha Mallick
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Jayashree S Ladke
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
- Graduate Studies, Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
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4
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Zhuo L, Stöckl JB, Fröhlich T, Moser S, Vollmar AM, Zahler S. A Novel Interaction of Slug (SNAI2) and Nuclear Actin. Cells 2024; 13:696. [PMID: 38667311 PMCID: PMC11049500 DOI: 10.3390/cells13080696] [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: 02/28/2024] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Actin is a protein of central importance to many cellular functions. Its localization and activity are regulated by interactions with a high number of actin-binding proteins. In a yeast two-hybrid (Y2H) screening system, snail family transcriptional repressor 2 (SNAI2 or slug) was identified as a yet unknown potential actin-binding protein. We validated this interaction using immunoprecipitation and analyzed the functional relation between slug and actin. Since both proteins have been reported to be involved in DNA double-strand break (DSB) repair, we focused on their interaction during this process after treatment with doxorubicin or UV irradiation. Confocal microscopy elicits that the overexpression of actin fused to an NLS stabilizes complexes of slug and γH2AX, an early marker of DNA damage repair.
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Affiliation(s)
- Ling Zhuo
- Center for Drug Research, Ludwig-Maximilians-University Munich, Butenandtstr, 5-13, 81377 Munich, Germany; (L.Z.); (A.M.V.)
| | - Jan B. Stöckl
- Laboratory for Functional Genome Analysis, Gene Center Munich, Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany; (J.B.S.); (T.F.)
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis, Gene Center Munich, Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany; (J.B.S.); (T.F.)
| | - Simone Moser
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria;
| | - Angelika M. Vollmar
- Center for Drug Research, Ludwig-Maximilians-University Munich, Butenandtstr, 5-13, 81377 Munich, Germany; (L.Z.); (A.M.V.)
| | - Stefan Zahler
- Center for Drug Research, Ludwig-Maximilians-University Munich, Butenandtstr, 5-13, 81377 Munich, Germany; (L.Z.); (A.M.V.)
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5
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Garcés P, Amaro A, Montecino M, van Zundert B. Inorganic polyphosphate: from basic research to diagnostic and therapeutic opportunities in ALS/FTD. Biochem Soc Trans 2024; 52:123-135. [PMID: 38323662 DOI: 10.1042/bst20230257] [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: 11/22/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/08/2024]
Abstract
Inorganic polyphosphate (polyP) is a simple, negatively charged biopolymer with chain lengths ranging from just a few to over a thousand ortho-phosphate (Pi) residues. polyP is detected in every cell type across all organisms in nature thus far analyzed. Despite its structural simplicity, polyP has been shown to play important roles in a remarkably broad spectrum of biological processes, including blood coagulation, bone mineralization and inflammation. Furthermore, polyP has been implicated in brain function and the neurodegenerative diseases amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Alzheimer's disease and Parkinson's disease. In this review, we first address the challenges associated with identifying mammalian polyP metabolizing enzymes, such as Nudt3, and quantifying polyP levels in brain tissue, cultured neural cells and cerebrospinal fluid. Subsequently, we focus on recent studies that unveil how the excessive release of polyP by human and mouse ALS/FTD astrocytes contributes to these devastating diseases by inducing hyperexcitability, leading to motoneuron death. Potential implications of elevated polyP levels in ALS/FTD patients for innovative diagnostic and therapeutic approaches are explored. It is emphasized, however, that caution is required in targeting polyP in the brain due to its diverse physiological functions, serving as an energy source, a chelator for divalent cations and a scaffold for amyloidogenic proteins. Reducing polyP levels, especially in neurons, might thus have adverse effects in brain functioning. Finally, we discuss how activated mast cells and platelets also can significantly contribute to ALS progression, as they can massively release polyP.
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Affiliation(s)
- Polett Garcés
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Armando Amaro
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Martin Montecino
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
- Millennium Nucleus of Neuroepigenetics and Plasticity (EpiNeuro), Santiago, Chile
| | - Brigitte van Zundert
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
- Millennium Nucleus of Neuroepigenetics and Plasticity (EpiNeuro), Santiago, Chile
- Department of Neurology, University of Massachusetts Chan Medical School (UMMS), Worcester, MA, U.S.A
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6
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Da Costa RT, Riggs LM, Solesio ME. Inorganic polyphosphate and the regulation of mitochondrial physiology. Biochem Soc Trans 2023; 51:2153-2161. [PMID: 37955101 PMCID: PMC10842919 DOI: 10.1042/bst20230735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023]
Abstract
Inorganic polyphosphate (polyP) is an ancient polymer that is well-conserved throughout evolution. It is formed by multiple subunits of orthophosphates linked together by phosphoanhydride bonds. The presence of these bonds, which are structurally similar to those found in ATP, and the high abundance of polyP in mammalian mitochondria, suggest that polyP could be involved in the regulation of the physiology of the organelle, especially in the energy metabolism. In fact, the scientific literature shows an unequivocal role for polyP not only in directly regulating oxidative a phosphorylation; but also in the regulation of reactive oxygen species metabolism, mitochondrial free calcium homeostasis, and the formation and opening of mitochondrial permeability transitions pore. All these processes are closely interconnected with the status of mitochondrial bioenergetics and therefore play a crucial role in maintaining mitochondrial and cell physiology. In this invited review, we discuss the main scientific literature regarding the regulatory role of polyP in mammalian mitochondrial physiology, placing a particular emphasis on its impact on energy metabolism. Although the effects of polyP on the physiology of the organelle are evident; numerous aspects, particularly within mammalian cells, remain unclear and require further investigation. These aspects encompass, for example, advancing the development of more precise analytical methods, unraveling the mechanism responsible for sensing polyP levels, and understanding the exact molecular mechanism that underlies the effects of polyP on mitochondrial physiology. By increasing our understanding of the biology of this ancient and understudied polymer, we could unravel new pharmacological targets in diseases where mitochondrial dysfunction, including energy metabolism dysregulation, has been broadly described.
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Affiliation(s)
- Renata T Da Costa
- Department of Biology; and Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, NJ, U.S.A
| | - Lindsey M Riggs
- Department of Biology; and Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, NJ, U.S.A
| | - Maria E Solesio
- Department of Biology; and Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, NJ, U.S.A
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7
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Takado M, Komamura T, Nishimura T, Ohkubo I, Ohuchi K, Matsumoto T, Takeda K. Phosphate uptake restriction, phosphate export, and polyphosphate synthesis contribute synergistically to cellular proliferation and survival. J Biol Chem 2023; 299:105454. [PMID: 37949217 PMCID: PMC10704438 DOI: 10.1016/j.jbc.2023.105454] [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: 03/09/2023] [Revised: 10/22/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Abstract
Phosphate (Pi) is a macronutrient, and Pi homeostasis is essential for life. Pi homeostasis has been intensively studied; however, many questions remain, even at the cellular level. Using Schizosaccharomyces pombe, we sought to better understand cellular Pi homeostasis and showed that three Pi regulators with SPX domains, Xpr1/Spx2, Pqr1, and the VTC complex synergistically contribute to Pi homeostasis to support cell proliferation and survival. SPX domains bind to inositol pyrophosphate and modulate activities of Pi-related proteins. Xpr1 is a plasma membrane protein and its Pi-exporting activity has been demonstrated in metazoan orthologs, but not in fungi. We first found that S. pombe Xpr1 is a Pi exporter, activity of which is regulated and accelerated in the mutants of Pqr1 and the VTC complex. Pqr1 is the ubiquitin ligase downregulating the Pi importers, Pho84 and Pho842. The VTC complex synthesizes polyphosphate in vacuoles. Triple deletion of Xpr1, Pqr1, and Vtc4, the catalytic core of the VTC complex, was nearly lethal in normal medium but survivable at lower [Pi]. All double-deletion mutants of the three genes were viable at normal Pi, but Δpqr1Δxpr1 showed severe viability loss at high [Pi], accompanied by hyper-elevation of cellular total Pi and free Pi. This study suggests that the three cellular processes, restriction of Pi uptake, Pi export, and polyP synthesis, contribute synergistically to cell proliferation through maintenance of Pi homeostasis, leading to the hypothesis that cooperation between Pqr1, Xpr1, and the VTC complex protects the cytoplasm and/or the nucleus from lethal elevation of free Pi.
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Affiliation(s)
- Masahiro Takado
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Tochi Komamura
- Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Tomoki Nishimura
- Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Ikkei Ohkubo
- Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Keita Ohuchi
- Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Tomohiro Matsumoto
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kojiro Takeda
- Graduate School of Natural Science, Konan University, Kobe, Japan; Institute of Integrative Neurobiology, Konan University, Kobe, Japan.
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8
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Borghi F, Saiardi A. Evolutionary perspective on mammalian inorganic polyphosphate (polyP) biology. Biochem Soc Trans 2023; 51:1947-1956. [PMID: 37844192 PMCID: PMC10657179 DOI: 10.1042/bst20230483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023]
Abstract
Inorganic polyphosphate (polyP), the polymeric form of phosphate, is attracting ever-growing attention due to the many functions it appears to perform within mammalian cells. This essay does not aim to systematically review the copious mammalian polyP literature. Instead, we examined polyP synthesis and functions in various microorganisms and used an evolutionary perspective to theorise key issues of this field and propose solutions. By highlighting the presence of VTC4 in distinct species of very divergent eucaryote clades (Opisthokonta, Viridiplantae, Discoba, and the SAR), we propose that whilst polyP synthesising machinery was present in the ancestral eukaryote, most lineages subsequently lost it during evolution. The analysis of the bacteria-acquired amoeba PPK1 and its unique polyP physiology suggests that eukaryote cells must have developed mechanisms to limit cytosolic polyP accumulation. We reviewed the literature on polyP in the mitochondria from the perspective of its endosymbiotic origin from bacteria, highlighting how mitochondria could possess a polyP physiology reminiscent of their 'bacterial' beginning that is not yet investigated. Finally, we emphasised the similarities that the anionic polyP shares with the better-understood negatively charged polymers DNA and RNA, postulating that the nucleus offers an ideal environment where polyP physiology might thrive.
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Affiliation(s)
- Filipy Borghi
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, U.K
| | - Adolfo Saiardi
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, U.K
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Neville N, Lehotsky K, Yang Z, Klupt KA, Denoncourt A, Downey M, Jia Z. Modification of histidine repeat proteins by inorganic polyphosphate. Cell Rep 2023; 42:113082. [PMID: 37660293 DOI: 10.1016/j.celrep.2023.113082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/29/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023] Open
Abstract
Inorganic polyphosphate (polyP) is a linear polymer of orthophosphate that is present in nearly all organisms studied to date. A remarkable function of polyP involves its attachment to lysine residues via non-enzymatic post-translational modification (PTM), which is presumed to be covalent. Here, we show that proteins containing tracts of consecutive histidine residues exhibit a similar modification by polyP, which confers an electrophoretic mobility shift on NuPAGE gels. Our screen uncovers 30 human and yeast histidine repeat proteins that undergo histidine polyphosphate modification (HPM). This polyP modification is histidine dependent and non-covalent in nature, although remarkably it withstands harsh denaturing conditions-a hallmark of covalent PTMs. Importantly, we show that HPM disrupts phase separation and the phosphorylation activity of the human protein kinase DYRK1A, and inhibits the activity of the transcription factor MafB, highlighting HPM as a potential protein regulatory mechanism.
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Affiliation(s)
- Nolan Neville
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Kirsten Lehotsky
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Zhiyun Yang
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Kody A Klupt
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Alix Denoncourt
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
| | - Michael Downey
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
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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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11
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Zaza G, Neri F, Bruschi M, Granata S, Petretto A, Bartolucci M, di Bella C, Candiano G, Stallone G, Gesualdo L, Furian L. Proteomics reveals specific biological changes induced by the normothermic machine perfusion of donor kidneys with a significant up-regulation of Latexin. Sci Rep 2023; 13:5920. [PMID: 37041202 PMCID: PMC10090051 DOI: 10.1038/s41598-023-33194-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 04/08/2023] [Indexed: 04/13/2023] Open
Abstract
Renal normothermic machine perfusion (NMP) is an organ preservation method based on the circulation of a warm (35-37 °C) perfusion solution through the renal vasculature to deliver oxygen and nutrients. However, its biological effects on marginal kidneys are unclear. We therefore used mass spectrometry to determine the proteomic profile of kidney tissue and urine from eight organs reconditioned for 120 min using a Kidney Assist device. Biopsies were taken during the pre-implantation histological evaluation (T-1), at the start of back table preparation (T0), and after 60 and 120 min of perfusion (T60, T120). Urine samples were collected at T0 (urine produced in the first 15 min after the beginning of normothermic reperfusion), T30, T60 and T120. Multiple algorithms, support vector machine learning and partial least squares discriminant analysis were used to select the most discriminative proteins during NMP. Statistical analysis revealed the upregulation of 169 proteins and the downregulation of 196 during NMP. Machine learning algorithms identified the top 50 most discriminative proteins, five of which were concomitantly upregulated (LXN, ETFB, NUDT3, CYCS and UQCRC1) and six downregulated (CFHR3, C1S, CFI, KNG1, SERPINC1 and F9) in the kidney and urine after NMP. Latexin (LXN), an endogenous carboxypeptidase inhibitor, resulted the most-upregulated protein at T120, and this result was confirmed by ELISA. In addition, functional analysis revealed that the most strongly upregulated proteins were involved in the oxidative phosphorylation system and ATP synthesis, whereas the downregulated proteins represented the complement system and coagulation cascade. Our proteomic analysis demonstrated that even brief periods of NMP induce remarkable metabolic and biochemical changes in marginal organs, which supports the use of this promising technique in the clinic.
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Affiliation(s)
- Gianluigi Zaza
- Nephrology, Dialysis and Transplantation Unit, Department of Medical and Surgical Sciences, University-Hospital of Foggia, Via L. Pinto 1, 71122, Foggia, Italy.
| | - Flavia Neri
- Kidney and Pancreas Transplantation Unit, University of Padua, Padua, Italy
| | - Maurizio Bruschi
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy
| | - Simona Granata
- Nephrology, Dialysis and Transplantation Unit, Department of Medical and Surgical Sciences, University-Hospital of Foggia, Via L. Pinto 1, 71122, Foggia, Italy
| | - Andrea Petretto
- Core Facilities - Proteomica E Metabolomica Clinica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Martina Bartolucci
- Core Facilities - Proteomica E Metabolomica Clinica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Caterina di Bella
- Kidney and Pancreas Transplantation Unit, University of Padua, Padua, Italy
| | - Giovanni Candiano
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Giovanni Stallone
- Nephrology, Dialysis and Transplantation Unit, Department of Medical and Surgical Sciences, University-Hospital of Foggia, Via L. Pinto 1, 71122, Foggia, Italy
| | - Loreto Gesualdo
- Nephrology, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", Bari, Italy
| | - Lucrezia Furian
- Kidney and Pancreas Transplantation Unit, University of Padua, Padua, Italy
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12
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Krenzlin V, Roewe J, Strueve M, Martínez-Negro M, Sharma A, Reinhardt C, Morsbach S, Bosmann M. Bacterial-Type Long-Chain Polyphosphates Bind Human Proteins in the Phosphatidylinositol Signaling Pathway. Thromb Haemost 2022; 122:1943-1947. [PMID: 35909349 PMCID: PMC9798540 DOI: 10.1055/s-0042-1751280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Viola Krenzlin
- Center for Thrombosis and Hemostasis, University Medical Center Mainz, Mainz, Germany
| | - Julian Roewe
- Center for Thrombosis and Hemostasis, University Medical Center Mainz, Mainz, Germany
| | - Marcel Strueve
- Center for Thrombosis and Hemostasis, University Medical Center Mainz, Mainz, Germany
| | - María Martínez-Negro
- Department of Physical Chemistry of Polymers, Max Planck Institute for Polymer Research, Mainz, Germany
| | - Arjun Sharma
- Center for Thrombosis and Hemostasis, University Medical Center Mainz, Mainz, Germany
- Department of Medicine, Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States
| | - Christoph Reinhardt
- Center for Thrombosis and Hemostasis, University Medical Center Mainz, Mainz, Germany
| | - Svenja Morsbach
- Department of Physical Chemistry of Polymers, Max Planck Institute for Polymer Research, Mainz, Germany
| | - Markus Bosmann
- Center for Thrombosis and Hemostasis, University Medical Center Mainz, Mainz, Germany
- Department of Medicine, Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States
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13
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Song Q, Yang Y, Jiang D, Qin Z, Xu C, Wang H, Huang J, Chen L, Luo R, Zhang X, Huang Y, Xu L, Yu Z, Tan S, Deng M, Xue R, Qie J, Li K, Yin Y, Yue X, Sun X, Su J, He F, Ding C, Hou Y. Proteomic analysis reveals key differences between squamous cell carcinomas and adenocarcinomas across multiple tissues. Nat Commun 2022; 13:4167. [PMID: 35851595 PMCID: PMC9293992 DOI: 10.1038/s41467-022-31719-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 06/24/2022] [Indexed: 12/24/2022] Open
Abstract
Squamous cell carcinoma (SCC) and adenocarcinoma (AC) are two main histological subtypes of solid cancer; however, SCCs are derived from different organs with similar morphologies, and it is challenging to distinguish the origin of metastatic SCCs. Here we report a deep proteomic analysis of 333 SCCs of 17 organs and 69 ACs of 7 organs. Proteomic comparison between SCCs and ACs identifies distinguishable pivotal pathways and molecules in those pathways play consistent adverse or opposite prognostic roles in ACs and SCCs. A comparison between common and rare SCCs highlights lipid metabolism may reinforce the malignancy of rare SCCs. Proteomic clusters reveal anatomical features, and kinase-transcription factor networks indicate differential SCC characteristics, while immune subtyping reveals diverse tumor microenvironments across and within diagnoses and identified potential druggable targets. Furthermore, tumor-specific proteins provide candidates with differentially diagnostic values. This proteomics architecture represents a public resource for researchers seeking a better understanding of SCCs and ACs. Squamous cell carcinomas are an aggressive cancer type which can occur in multiple organ systems. Here, the authors analyse the proteome of SCC cancers from 17 organs and show commonly dysregulated proteins independent of location.
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Affiliation(s)
- Qi Song
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Ye Yang
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Dongxian Jiang
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Zhaoyu Qin
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Chen Xu
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Haixing Wang
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Jie Huang
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Lingli Chen
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Rongkui Luo
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Xiaolei Zhang
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Yufeng Huang
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Lei Xu
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Zixiang Yu
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Subei Tan
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Minying Deng
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Ruqun Xue
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Jingbo Qie
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Kai Li
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Yanan Yin
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Xuetong Yue
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Xiaogang Sun
- State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis, (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Jieakesu Su
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
| | - Chen Ding
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China. .,State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis, (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan, China. .,Academy of Medical Science, Zhengzhou University, Zhengzhou, China.
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China.
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14
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Ddp1 Cooperates with Ppx1 to Counter a Stress Response Initiated by Nonvacuolar Polyphosphate. mBio 2022; 13:e0039022. [PMID: 35862758 PMCID: PMC9426566 DOI: 10.1128/mbio.00390-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In diverse cells from bacterial to mammalian species, inorganic phosphate is stored in long chains called polyphosphate (polyP). These nearly universal polymers, ranging from three to thousands of phosphate moieties in length, are associated with molecular functions, including energy homeostasis, protein folding, and cell signaling. In many cell types, polyphosphate is concentrated in subcellular compartments or organelles. In the budding yeast Saccharomyces cerevisiae, polyP synthesis by the membrane-bound vacuolar transporter chaperone (VTC) complex is coupled to its translocation into the lumen of the vacuole, a lysosome-like organelle, where it is stored at high concentrations. In contrast, the ectopic expression of the bacterial polyphosphate kinase (PPK) results in the toxic accumulation of polyP outside the vacuole. In this study, we used label-free mass spectrometry to investigate the mechanisms underlying this toxicity. We find that PPK expression results in the activation of a stress response mediated in part by the Hog1 and Yak1 kinases and the Msn2/Msn4 transcription factors as well as by changes in protein kinase A (PKA) activity. This response is countered by the combined action of the Ddp1 and Ppx1 polyphosphatases that function together to counter polyP accumulation and downstream toxicity. In contrast, the ectopic expression of previously proposed mammalian polyphosphatases did not impact PPK-mediated toxicity in this model, suggesting either that these enzymes do not function directly as polyphosphatases in vivo or that they require cofactors unique to higher eukaryotes. Our work provides insight into why polyP accumulation outside lysosome-like organelles is toxic. Furthermore, it serves as a resource for exploring how polyP may impact conserved biological processes at a molecular level.
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15
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Jiménez J, Lázaro B, Sarrias A, Tadeo FJ, Pérez-Montero M, Clotet J, Bru S. Protocol to quantify polyphosphate in human cell lines using a tagged PPBD peptide. STAR Protoc 2022; 3:101363. [PMID: 35542178 PMCID: PMC9079103 DOI: 10.1016/j.xpro.2022.101363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Polyphosphate (polyP) is an evolutionarily conserved polymer of phosphates that is difficult to study in human cells because of its low concentration and high lability. First, we described how to express and purify Xpress-tagged PPBD (Ppx1 PolyP Binding Domain). We describe the detection and quantification of nuclear polyP in HEK293T cells using Xpress-PPBD, Xpress antibody, and Alexa-conjugated secondary antibodies. We have also used this protocol in SH-SY5Y HeLa and HEK293 cells. For complete details on the use and execution of this protocol, please refer to Samper-Martín et al. (2021). E. coli PPBD peptide to localize polyP in human cells cultures PPBD purification and storage is a critical step for polyP staining Detection of nuclear polyP fraction that can be degraded by the endopolyPase Nudt3 Quantification of relative polyP amounts using a free image analysis software
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Affiliation(s)
- Javier Jiménez
- Basic Sciences Department, Universitat International de Catalunya, 08195 Barcelona, Spain
- Corresponding author
| | - Blanca Lázaro
- Basic Sciences Department, Universitat International de Catalunya, 08195 Barcelona, Spain
| | - Ana Sarrias
- Basic Sciences Department, Universitat International de Catalunya, 08195 Barcelona, Spain
| | - Francisco J. Tadeo
- Basic Sciences Department, Universitat International de Catalunya, 08195 Barcelona, Spain
| | - Marta Pérez-Montero
- Basic Sciences Department, Universitat International de Catalunya, 08195 Barcelona, Spain
| | - Josep Clotet
- Basic Sciences Department, Universitat International de Catalunya, 08195 Barcelona, Spain
| | - Samuel Bru
- Basic Sciences Department, Universitat International de Catalunya, 08195 Barcelona, Spain
- Corresponding author
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16
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Hambardikar V, Guitart-Mampel M, Scoma ER, Urquiza P, Nagana GGA, Raftery D, Collins JA, Solesio ME. Enzymatic Depletion of Mitochondrial Inorganic Polyphosphate (polyP) Increases the Generation of Reactive Oxygen Species (ROS) and the Activity of the Pentose Phosphate Pathway (PPP) in Mammalian Cells. Antioxidants (Basel) 2022; 11:685. [PMID: 35453370 PMCID: PMC9029763 DOI: 10.3390/antiox11040685] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 01/27/2023] Open
Abstract
Inorganic polyphosphate (polyP) is an ancient biopolymer that is well preserved throughout evolution and present in all studied organisms. In mammals, it shows a high co-localization with mitochondria, and it has been demonstrated to be involved in the homeostasis of key processes within the organelle, including mitochondrial bioenergetics. However, the exact extent of the effects of polyP on the regulation of cellular bioenergetics, as well as the mechanisms explaining these effects, still remain poorly understood. Here, using HEK293 mammalian cells under Wild-type (Wt) and MitoPPX (cells enzymatically depleted of mitochondrial polyP) conditions, we show that depletion of polyP within mitochondria increased oxidative stress conditions. This is characterized by enhanced mitochondrial O2- and intracellular H2O2 levels, which may be a consequence of the dysregulation of oxidative phosphorylation (OXPHOS) that we have demonstrated in MitoPPX cells in our previous work. These findings were associated with an increase in basal peroxiredoxin-1 (Prx1), superoxide dismutase-2 (SOD2), and thioredoxin (Trx) antioxidant protein levels. Using 13C-NMR and immunoblotting, we assayed the status of glycolysis and the pentose phosphate pathway (PPP) in Wt and MitoPPX cells. Our results show that MitoPPX cells display a significant increase in the activity of the PPP and an increase in the protein levels of transaldolase (TAL), which is a crucial component of the non-oxidative phase of the PPP and is involved in the regulation of oxidative stress. In addition, we observed a trend towards increased glycolysis in MitoPPX cells, which corroborates our prior work. Here, for the first time, we show the crucial role played by mitochondrial polyP in the regulation of mammalian redox homeostasis. Moreover, we demonstrate a significant effect of mitochondrial polyP on the regulation of global cellular bioenergetics in these cells.
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Affiliation(s)
- Vedangi Hambardikar
- Department of Biology and Center for Computational and Integrative Biology (CCIB), College of Arts and Sciences, Rutgers University, Camden, NJ 08103, USA; (V.H.); (M.G.-M.); (E.R.S.); (P.U.)
| | - Mariona Guitart-Mampel
- Department of Biology and Center for Computational and Integrative Biology (CCIB), College of Arts and Sciences, Rutgers University, Camden, NJ 08103, USA; (V.H.); (M.G.-M.); (E.R.S.); (P.U.)
| | - Ernest R. Scoma
- Department of Biology and Center for Computational and Integrative Biology (CCIB), College of Arts and Sciences, Rutgers University, Camden, NJ 08103, USA; (V.H.); (M.G.-M.); (E.R.S.); (P.U.)
| | - Pedro Urquiza
- Department of Biology and Center for Computational and Integrative Biology (CCIB), College of Arts and Sciences, Rutgers University, Camden, NJ 08103, USA; (V.H.); (M.G.-M.); (E.R.S.); (P.U.)
| | - Gowda G. A. Nagana
- Mitochondrial and Metabolism Center, University of Washington, Seattle, WA 98109, USA; (G.G.A.N.); (D.R.)
| | - Daniel Raftery
- Mitochondrial and Metabolism Center, University of Washington, Seattle, WA 98109, USA; (G.G.A.N.); (D.R.)
| | - John A. Collins
- Department of Orthopedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Maria E. Solesio
- Department of Biology and Center for Computational and Integrative Biology (CCIB), College of Arts and Sciences, Rutgers University, Camden, NJ 08103, USA; (V.H.); (M.G.-M.); (E.R.S.); (P.U.)
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17
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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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