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Kulakovskaya TV, Andreeva NA, Ledova LA, Ryazanova LP, Trilisenko LV, Eldarov MA. Enzymes of Polyphosphate Metabolism in Yeast: Properties, Functions, Practical Significance. BIOCHEMISTRY (MOSCOW) 2021; 86:S96-S108. [PMID: 33827402 DOI: 10.1134/s0006297921140078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Inorganic polyphosphates (polyP) are the linear polymers of orthophosphoric acid varying in the number of phosphate residues linked by the energy-rich phosphoanhydride bonds. PolyP is an essential component in living cells. Knowledge of polyP metabolizing enzymes in eukaryotes is necessary for understanding molecular mechanisms of polyP metabolism in humans and development of new approaches for treating bone and cardiovascular diseases associated with impaired mineral phosphorus metabolism. Yeast cells represent a rational experimental model for this research due to availability of the methods for studying phosphorus metabolism and construction of knockout mutants and strains overexpressing target proteins. Multicomponent system of polyP metabolism in Saccharomyces cerevisiae cells is presented in this review discussing properties, functioning, and practical significance of the enzymes involved in the synthesis and degradation of this important metabolite.
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Affiliation(s)
- Tatiana V Kulakovskaya
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Research Center for Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Nadezhda A Andreeva
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Research Center for Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Larisa A Ledova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Research Center for Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Lubov P Ryazanova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Research Center for Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Ludmila V Trilisenko
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Research Center for Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Michail A Eldarov
- Institute of Bioengineering, Federal Scientific Center for Biotechnology, Russian Academy of Sciences, Moscow, 117312, Russia
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2
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Denoncourt A, Downey M. Model systems for studying polyphosphate biology: a focus on microorganisms. Curr Genet 2021; 67:331-346. [PMID: 33420907 DOI: 10.1007/s00294-020-01148-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 12/19/2022]
Abstract
Polyphosphates (polyP) are polymers of inorganic phosphates joined by high-energy bonds to form long chains. These chains are present in all forms of life but were once disregarded as 'molecular fossils'. PolyP has gained attention in recent years following new links to diverse biological roles ranging from energy storage to cell signaling. PolyP research in humans and other higher eukaryotes is limited by a lack of suitable tools and awaits the identification of enzymatic players that would enable more comprehensive studies. Therefore, many of the most important insights have come from single-cell model systems. Here, we review determinants of polyP metabolism, regulation, and function in major microbial systems, including bacteria, fungi, protozoa, and algae. We highlight key similarities and differences that may aid in our understanding of how polyP impacts cell physiology at a molecular level.
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Affiliation(s)
- Alix Denoncourt
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, Ottawa, K1H 8M5, Canada
| | - Michael Downey
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, K1H 8M5, Canada. .,Ottawa Institute of Systems Biology, Ottawa, K1H 8M5, Canada.
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3
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Nistala H, Dronzek J, Gonzaga-Jauregui C, Chim SM, Rajamani S, Nuwayhid S, Delgado D, Burke E, Karaca E, Franklin MC, Sarangapani P, Podgorski M, Tang Y, Dominguez MG, Withers M, Deckelbaum RA, Scheonherr CJ, Gahl WA, Malicdan MC, Zambrowicz B, Gale NW, Gibbs RA, Chung WK, Lupski JR, Economides AN. NMIHBA results from hypomorphic PRUNE1 variants that lack short-chain exopolyphosphatase activity. Hum Mol Genet 2021; 29:3516-3531. [PMID: 33105479 PMCID: PMC7788287 DOI: 10.1093/hmg/ddaa237] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/24/2020] [Accepted: 10/15/2020] [Indexed: 11/12/2022] Open
Abstract
Neurodevelopmental disorder with microcephaly, hypotonia and variable brain anomalies (NMIHBA) is an autosomal recessive neurodevelopmental and neurodegenerative disorder characterized by global developmental delay and severe intellectual disability. Microcephaly, progressive cortical atrophy, cerebellar hypoplasia and delayed myelination are neurological hallmarks in affected individuals. NMIHBA is caused by biallelic variants in PRUNE1 encoding prune exopolyphosphatase 1. We provide in-depth clinical description of two affected siblings harboring compound heterozygous variant alleles, c.383G > A (p.Arg128Gln), c.520G > T (p.Gly174*) in PRUNE1. To gain insights into disease biology, we biochemically characterized missense variants within the conserved N-terminal aspartic acid-histidine-histidine (DHH) motif and provide evidence that they result in the destabilization of protein structure and/or loss of exopolyphosphatase activity. Genetic ablation of Prune1 results in midgestational lethality in mice, associated with perturbations to embryonic growth and vascular development. Our findings suggest that NMIHBA results from hypomorphic variant alleles in humans and underscore the potential key role of PRUNE1 exopolyphoshatase activity in neurodevelopment.
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Affiliation(s)
| | - John Dronzek
- Regeneron Genetics Center, Tarrytown, NY 10591, USA
| | | | | | | | - Samer Nuwayhid
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Dennis Delgado
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Elizabeth Burke
- Undiagnosed Diseases Program Translational Laboratory, NHGRI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | | | | | - Yajun Tang
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | | | - Marjorie Withers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - William A Gahl
- Undiagnosed Diseases Program Translational Laboratory, NHGRI, National Institutes of Health, Bethesda, MD 20892, USA
| | - May C Malicdan
- Undiagnosed Diseases Program Translational Laboratory, NHGRI, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wendy K Chung
- Columbia University Medical Center, New York, NY 10032, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030, USA
| | - Aris N Economides
- Regeneron Genetics Center, Tarrytown, NY 10591, USA
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
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4
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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: 89] [Impact Index Per Article: 17.8] [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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5
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Christ JJ, Willbold S, Blank LM. Polyphosphate Chain Length Determination in the Range of Two to Several Hundred P-Subunits with a New Enzyme Assay and 31P NMR. Anal Chem 2019; 91:7654-7661. [PMID: 31082217 DOI: 10.1021/acs.analchem.9b00567] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Currently, 31P NMR is the only analytical method that quantitatively determines the average chain length of long inorganic polyphosphate (>80 P-subunits). In this study, an enzyme assay is presented that determines the average chain length of polyphosphate in the range of two to several hundred P-subunits. In the enzyme assay, the average polyP chain length is calculated by dividing the total polyphosphate concentration by the concentration of the polyphosphate chains. The total polyphosphate is determined by enzymatic polyphosphate hydrolysis with Saccharomyces cerevisiae exopolyphosphatase 1 and S. cerevisiae inorganic pyrophosphatase 1, followed by colorimetric orthophosphate detection. Because the exopolyphosphatase leaves one pyrophosphate per polyphosphate chain, the polyphosphate chain concentration is assayed by coupling the enzymes exopolyphosphatase (polyP into pyrophosphate), ATP sulfurylase (pyrophosphate into ATP), hexokinase (ATP into glucose 6-phosphate), and glucose 6-phosphate dehydrogenase (glucose 6-phosphate into NADPH), followed by fluorometric NADPH detection. The ability of 31P NMR and the enzyme assay to size polyP was demonstrated with polyP lengths in the range from 2 to ca. 280 P-subunits (no polyP with a longer chain length was available). The small deviation between methods (-4 ± 4%) indicated that the new enzyme assay performed accurately. The limitations of 31P NMR (i.e., low throughput, high sample concentration, expensive instrument) are overcome by the enzyme assay that is presented here, which allows for high sample throughput and requires only a commonly available plate reader and micromole per liter concentrations of polyphosphate.
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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 , Aachen D-52074 , Germany
| | - Sabine Willbold
- Central Institute for Engineering, Electronics and Analytics, Analytics (ZEA-3) , Wilhelm-Johnen-Straße, Jülich D-52428 , Germany
| | - Lars Mathias Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, Worringer Weg 1 , RWTH Aachen University , Aachen D-52074 , Germany
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6
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Role of DHH superfamily proteins in nucleic acids metabolism and stress tolerance in prokaryotes and eukaryotes. Int J Biol Macromol 2018; 127:66-75. [PMID: 30578903 DOI: 10.1016/j.ijbiomac.2018.12.123] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/14/2018] [Indexed: 01/05/2023]
Abstract
DHH superfamily proteins play pivotal roles in various cellular processes like replication, recombination, repair and nucleic acids metabolism. These proteins are important for homeostasis maintenance and stress tolerance in prokaryotes and eukaryotes. The prominent members of DHH superfamily include single-strand specific exonuclease RecJ, nanoRNases, polyphosphatase PPX1, pyrophosphatase, prune phosphodiesterase and cell cycle protein Cdc45. The mutations of genes coding for DHH superfamily proteins lead to severe growth defects and in some cases, may be lethal. The members of superfamily have a wide substrate spectrum. The spectrum of substrate for DHH superfamily members ranges from smaller molecules like pyrophosphate and cyclic nucleotides to longer single-stranded DNA molecule. Several genetic, structural and biochemical studies have provided interesting insights about roles of DHH superfamily members. However, there are still various unexplored members in both prokaryotes and eukaryotes. Many aspects of this superfamily associated with homeostasis maintenance and stress tolerance are still not clearly understood. A comprehensive understanding is pre-requisite to decipher the physiological significance of members of DHH superfamily. This article provides the current understanding of DHH superfamily members and their significance in nucleic acids metabolism and stress tolerance across diverse forms of life.
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7
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Cruz CS, Costa EP, Machado JA, Silva JN, Romeiro NC, Moraes J, Silva JR, Fonseca RN, Vaz IS, Logullo C, Campos E. A soluble inorganic pyrophosphatase from the cattle tick Rhipicephalus microplus capable of hydrolysing polyphosphates. INSECT MOLECULAR BIOLOGY 2018; 27:260-267. [PMID: 29271528 DOI: 10.1111/imb.12369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Polyphosphates have been found in all cell types examined to date and play diverse roles depending on the cell type. In eukaryotic organisms, polyphosphates have been investigated mainly in mammalian cells, and only a few studies have addressed arthropods. Pyrophosphatases have been shown to regulate polyphosphate metabolism. However, these studies were restricted to trypanosomatids. Here we focus on the tick Rhipicephalus microplus, a haematophagous ectoparasite that is highly harmful to cattle. We produced a recombinant R. microplus pyrophosphatase (rRmPPase) with the aim of investigating its kinetic parameters using polyphosphates as substrate. Molecular docking assays of RmPPase with polyphosphates were also carried out. The kinetic and Hill coefficient parameters indicated that rRmPPase has a greater affinity, higher catalytic efficiency and increased cooperativity for sodium phosphate glass type 15 (polyP15 ) than for sodium tripolyphosphate (polyP3 ). Through molecular docking, we found that polyP3 binds close to the Mg2+ atoms in the catalytic region of the protein, participating in their coordination network, whereas polyP15 interactions involve negatively charged phosphate groups and basic amino acid residues, such as Lys56, Arg58 and Lys193; polyP15 has a more favourable theoretical binding affinity than polyP3 , thus supporting the kinetic data. This study shows, for the first time in arthropods, a pyrophosphatase with polyphosphatase activity, suggesting its participation in polyphosphate metabolism.
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Affiliation(s)
- C S Cruz
- Laboratório Integrado de Bioquímica - Hatisaburo Masuda, UFRJ, NUPEM, São José do Barreto, Macaé, Rio de Janeiro, Brazil
| | - E P Costa
- Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal - CBB - UENF, Horto, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - J A Machado
- Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal - CBB - UENF, Horto, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - J N Silva
- Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal - CBB - UENF, Horto, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - N C Romeiro
- Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal - CBB - UENF, Horto, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - J Moraes
- Laboratório Integrado de Bioquímica - Hatisaburo Masuda, UFRJ, NUPEM, São José do Barreto, Macaé, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
| | - J R Silva
- Laboratório Integrado de Bioquímica - Hatisaburo Masuda, UFRJ, NUPEM, São José do Barreto, Macaé, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
| | - R N Fonseca
- Laboratório Integrado de Bioquímica - Hatisaburo Masuda, UFRJ, NUPEM, São José do Barreto, Macaé, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
| | - I S Vaz
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
- Centro de Biotecnologia e Faculdade de Veterinária, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - C Logullo
- Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal - CBB - UENF, Horto, Campos dos Goytacazes, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
| | - E Campos
- Laboratório Integrado de Bioquímica - Hatisaburo Masuda, UFRJ, NUPEM, São José do Barreto, Macaé, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
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8
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Gutiérrez-Luna FM, Hernández-Domínguez EE, Valencia-Turcotte LG, Rodríguez-Sotres R. Review: "Pyrophosphate and pyrophosphatases in plants, their involvement in stress responses and their possible relationship to secondary metabolism". PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 267:11-19. [PMID: 29362089 DOI: 10.1016/j.plantsci.2017.10.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 10/19/2017] [Accepted: 10/26/2017] [Indexed: 05/14/2023]
Abstract
Pyrophosphate (PPi) is produced as byproduct of biosynthesis in the cytoplasm, nucleus, mitochondria and chloroplast, or in the tonoplast and Golgi by membrane-bound H+-pumping pyrophosphatases (PPv). Inorganic pyrophosphatases (E.C. 3.6.1.1; GO:0004427) impulse various biosynthetic reactions by recycling PPi and are essential to living cells. Soluble and membrane-bound enzymes of high specificity have evolved in different protein families and multiple pyrophosphatases are encoded in all plant genomes known to date. The soluble proteins are present in cytoplasm, extracellular space, inside chloroplasts, and perhaps inside mitochondria, nucleus or vacuoles. The cytoplasmic isoforms may compete for PPi with the PPv enzymes and how PPv and soluble activities are controlled is currently unknown, yet the cytoplasmic PPi concentration is high and fairly constant. Manipulation of the PPi metabolism impacts primary metabolism and vice versa, indicating a tight link between PPi levels and carbohydrate metabolism. These enzymes appear to play a role in germination, development and stress adaptive responses. In addition, the transgenic overexpression of PPv has been used to enhance plant tolerance to abiotic stress, but the reasons behind this tolerance are not completely understood. Finally, the relationship of PPi to stress suggest a currently unexplored link between PPi and secondary metabolism.
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Affiliation(s)
- Francisca Morayna Gutiérrez-Luna
- FACULTAD DE QUÍMICA, UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO, Ave. Universidad 3000, Cd. Universitaria, Del. Coyoacán, P.C. 04510, Mexico City, Mexico.
| | | | - Lilián Gabriela Valencia-Turcotte
- FACULTAD DE QUÍMICA, UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO, Ave. Universidad 3000, Cd. Universitaria, Del. Coyoacán, P.C. 04510, Mexico City, Mexico.
| | - Rogelio Rodríguez-Sotres
- FACULTAD DE QUÍMICA, UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO, Ave. Universidad 3000, Cd. Universitaria, Del. Coyoacán, P.C. 04510, Mexico City, Mexico.
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9
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Zollo M, Ahmed M, Ferrucci V, Salpietro V, Asadzadeh F, Carotenuto M, Maroofian R, Al-Amri A, Singh R, Scognamiglio I, Mojarrad M, Musella L, Duilio A, Di Somma A, Karaca E, Rajab A, Al-Khayat A, Mohan Mohapatra T, Eslahi A, Ashrafzadeh F, Rawlins LE, Prasad R, Gupta R, Kumari P, Srivastava M, Cozzolino F, Kumar Rai S, Monti M, Harlalka GV, Simpson MA, Rich P, Al-Salmi F, Patton MA, Chioza BA, Efthymiou S, Granata F, Di Rosa G, Wiethoff S, Borgione E, Scuderi C, Mankad K, Hanna MG, Pucci P, Houlden H, Lupski JR, Crosby AH, Baple EL. PRUNE is crucial for normal brain development and mutated in microcephaly with neurodevelopmental impairment. Brain 2017; 140:940-952. [PMID: 28334956 PMCID: PMC5382943 DOI: 10.1093/brain/awx014] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/13/2016] [Indexed: 12/22/2022] Open
Abstract
PRUNE is a member of the DHH (Asp-His-His) phosphoesterase protein superfamily of molecules important for cell motility, and implicated in cancer progression. Here we investigated multiple families from Oman, India, Iran and Italy with individuals affected by a new autosomal recessive neurodevelopmental and degenerative disorder in which the cardinal features include primary microcephaly and profound global developmental delay. Our genetic studies identified biallelic mutations of PRUNE1 as responsible. Our functional assays of disease-associated variant alleles revealed impaired microtubule polymerization, as well as cell migration and proliferation properties, of mutant PRUNE. Additionally, our studies also highlight a potential new role for PRUNE during microtubule polymerization, which is essential for the cytoskeletal rearrangements that occur during cellular division and proliferation. Together these studies define PRUNE as a molecule fundamental for normal human cortical development and define cellular and clinical consequences associated with PRUNE mutation.
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Affiliation(s)
- Massimo Zollo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche DMMBM, Università di Napoli Federico II, Via Sergio Pansini 5, Naples, 80131, Italy.,CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, Naples, Italy.,European School of Molecular Medicine, SEMM, University of Milan, Italy
| | - Mustafa Ahmed
- Medical Research (Level 4), RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Veronica Ferrucci
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche DMMBM, Università di Napoli Federico II, Via Sergio Pansini 5, Naples, 80131, Italy.,CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, Naples, Italy.,European School of Molecular Medicine, SEMM, University of Milan, Italy
| | - Vincenzo Salpietro
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Fatemeh Asadzadeh
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche DMMBM, Università di Napoli Federico II, Via Sergio Pansini 5, Naples, 80131, Italy.,CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, Naples, Italy
| | - Marianeve Carotenuto
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche DMMBM, Università di Napoli Federico II, Via Sergio Pansini 5, Naples, 80131, Italy.,CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, Naples, Italy
| | - Reza Maroofian
- Medical Research (Level 4), RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Ahmed Al-Amri
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, UK.,National Genetic Centre, Directorate General of Royal Hospital, Ministry of Health, Muscat, Sultanate of Oman
| | - Royana Singh
- Molecular Genetics, Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University, Varanasi -221005, UP, India
| | - Iolanda Scognamiglio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche DMMBM, Università di Napoli Federico II, Via Sergio Pansini 5, Naples, 80131, Italy.,CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, Naples, Italy
| | - Majid Mojarrad
- Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Medical Genetics Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Luca Musella
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche DMMBM, Università di Napoli Federico II, Via Sergio Pansini 5, Naples, 80131, Italy.,CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, Naples, Italy
| | - Angela Duilio
- Dipartimento di Scienze Chimiche, Università Federico II, Naples, Italy
| | - Angela Di Somma
- Dipartimento di Scienze Chimiche, Università Federico II, Naples, Italy
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Rajab
- National Genetic Centre, Directorate General of Royal Hospital, Ministry of Health, Muscat, Sultanate of Oman
| | - Aisha Al-Khayat
- Department of Biology, Sultan Qaboos University, PO Box 36, Post code 123, Sultanate of Oman
| | - Tribhuvan Mohan Mohapatra
- Molecular Genetics, Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University, Varanasi -221005, UP, India
| | - Atieh Eslahi
- Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farah Ashrafzadeh
- Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Pediatric Neurology, Ghaem Medical Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Zip Code- 9919991766, Iran
| | - Lettie E Rawlins
- Medical Research (Level 4), RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Rajniti Prasad
- Department of Pediatrics, Institute of Medical Sciences, Banaras Hindu University, Varanasi -221005, UP, India
| | - Rashmi Gupta
- Molecular Genetics, Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University, Varanasi -221005, UP, India
| | - Preeti Kumari
- Molecular Genetics, Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University, Varanasi -221005, UP, India
| | - Mona Srivastava
- Molecular Genetics, Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University, Varanasi -221005, UP, India.,Department of Psychiatry, Institute of Medical Sciences, Banaras Hindu University, Varanasi -221005, UP, India
| | - Flora Cozzolino
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, Naples, Italy
| | - Sunil Kumar Rai
- Molecular Genetics, Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University, Varanasi -221005, UP, India
| | - Maria Monti
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, Naples, Italy.,Dipartimento di Scienze Chimiche, Università Federico II, Naples, Italy
| | - Gaurav V Harlalka
- Medical Research (Level 4), RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Michael A Simpson
- Department of Medical and Molecular Genetics, Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Philip Rich
- Department of Neuroradiology, St. George's Hospital, London, UK
| | - Fatema Al-Salmi
- Department of Biology, Sultan Qaboos University, PO Box 36, Post code 123, Sultanate of Oman
| | - Michael A Patton
- Medical Research (Level 4), RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK.,Department of Biology, Sultan Qaboos University, PO Box 36, Post code 123, Sultanate of Oman.,Genetics Research Centre, St. George's, University of London, London, SW17 0RE, UK
| | - Barry A Chioza
- Medical Research (Level 4), RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Stephanie Efthymiou
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Francesca Granata
- Unit of Neuroradiology, Department of Biomedical Science and Morphological and Functional Images, University of Messina, Messina, Italy
| | - Gabriella Di Rosa
- Unit of Child Neurology and Psychiatry, Department of Human Pathology of the Adult and Developmental Age, University of Messina, Messina, Italy
| | - Sarah Wiethoff
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Eugenia Borgione
- Unit of Neuromuscular disorders, IRCCS Oasi Maria SS Troina, Enna, Italy
| | - Carmela Scuderi
- Unit of Neuromuscular disorders, IRCCS Oasi Maria SS Troina, Enna, Italy
| | - Kshitij Mankad
- Department of Neuroradiology, Great Ormond Street Hospital for Children, London WC1N 3JH, UK
| | - Michael G Hanna
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK.,MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Piero Pucci
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, Naples, Italy.,Dipartimento di Scienze Chimiche, Università Federico II, Naples, Italy
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.,Texas Children's Hospital, Houston, TX 77030, USA
| | - Andrew H Crosby
- Medical Research (Level 4), RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Emma L Baple
- Medical Research (Level 4), RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
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10
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Enzymes of yeast polyphosphate metabolism: structure, enzymology and biological roles. Biochem Soc Trans 2016; 44:234-9. [PMID: 26862210 DOI: 10.1042/bst20150213] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Inorganic polyphosphate (polyP) is found in all living organisms. The known polyP functions in eukaryotes range from osmoregulation and virulence in parasitic protozoa to modulating blood coagulation, inflammation, bone mineralization and cellular signalling in mammals. However mechanisms of regulation and even the identity of involved proteins in many cases remain obscure. Most of the insights obtained so far stem from studies in the yeast Saccharomyces cerevisiae. Here, we provide a short overview of the properties and functions of known yeast polyP metabolism enzymes and discuss future directions for polyP research.
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11
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Cheng K, Xu H, Chen X, Wang L, Tian B, Zhao Y, Hua Y. Structural basis for DNA 5´-end resection by RecJ. eLife 2016; 5:e14294. [PMID: 27058167 PMCID: PMC4846377 DOI: 10.7554/elife.14294] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/07/2016] [Indexed: 12/18/2022] Open
Abstract
The resection of DNA strand with a 5´ end at double-strand breaks is an essential step in recombinational DNA repair. RecJ, a member of DHH family proteins, is the only 5´ nuclease involved in the RecF recombination pathway. Here, we report the crystal structures of Deinococcus radiodurans RecJ in complex with deoxythymidine monophosphate (dTMP), ssDNA, the C-terminal region of single-stranded DNA-binding protein (SSB-Ct) and a mechanistic insight into the RecF pathway. A terminal 5´-phosphate-binding pocket above the active site determines the 5´-3´ polarity of the deoxy-exonuclease of RecJ; a helical gateway at the entrance to the active site admits ssDNA only; and the continuous stacking interactions between protein and nine nucleotides ensure the processive end resection. The active site of RecJ in the N-terminal domain contains two divalent cations that coordinate the nucleophilic water. The ssDNA makes a 180° turn at the scissile phosphate. The C-terminal domain of RecJ binds the SSB-Ct, which explains how RecJ and SSB work together to efficiently process broken DNA ends for homologous recombination.
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Affiliation(s)
- Kaiying Cheng
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Hong Xu
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Xuanyi Chen
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Liangyan Wang
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Bing Tian
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Ye Zhao
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Yuejin Hua
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
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12
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Geer MA, Fitzgerald MC. Characterization of the Saccharomyces cerevisiae ATP-Interactome using the iTRAQ-SPROX Technique. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:233-243. [PMID: 26530046 DOI: 10.1007/s13361-015-1290-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/01/2015] [Accepted: 10/05/2015] [Indexed: 06/05/2023]
Abstract
The stability of proteins from rates of oxidation (SPROX) technique was used in combination with an isobaric mass tagging strategy to identify adenosine triphosphate (ATP) interacting proteins in the Saccharomyces cerevisiae proteome. The SPROX methodology utilized in this work enabled 373 proteins in a yeast cell lysate to be assayed for ATP interactions (both direct and indirect) using the non-hydrolyzable ATP analog, adenylyl imidodiphosphate (AMP-PNP). A total of 28 proteins were identified with AMP-PNP-induced thermodynamic stability changes. These protein hits included 14 proteins that were previously annotated as ATP-binding proteins in the Saccharomyces Genome Database (SGD). The 14 non-annotated ATP-binding proteins included nine proteins that were previously found to be ATP-sensitive in an earlier SPROX study using a stable isotope labeling with amino acids in cell culture (SILAC)-based approach. A bioinformatics analysis of the protein hits identified here and in the earlier SILAC-SPROX experiments revealed that many of the previously annotated ATP-binding protein hits were kinases, ligases, and chaperones. In contrast, many of the newly discovered ATP-sensitive proteins were not from these protein classes, but rather were hydrolases, oxidoreductases, and nucleic acid-binding proteins. Graphical Abstract ᅟ.
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Affiliation(s)
- M Ariel Geer
- Department of Chemistry, Duke University, Durham, NC, 27708-0346, USA
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13
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Positively-charged semi-tunnel is a structural and surface characteristic of polyphosphate-binding proteins: an in-silico study. PLoS One 2015; 10:e0123713. [PMID: 25879219 PMCID: PMC4400040 DOI: 10.1371/journal.pone.0123713] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/06/2015] [Indexed: 12/20/2022] Open
Abstract
Phosphate is essential for all major life processes, especially energy metabolism and signal transduction. A linear phosphate polymer, polyphosphate (polyP), linked by high-energy phosphoanhydride bonds, can interact with various proteins, playing important roles as an energy source and regulatory factor. However, polyP-binding structures are largely unknown. Here we proposed a putative polyP binding site, a positively-charged semi-tunnel (PCST), identified by surface electrostatics analyses in polyP kinases (PPKs) and many other polyP-related proteins. We found that the PCSTs in varied proteins were folded in different secondary structure compositions. Molecular docking calculations revealed a significant value for binding affinity to polyP in PCST-containing proteins. Utilizing the PCST identified in the β subunit of PPK3, we predicted the potential polyP-binding domain of PPK3. The discovery of this feature facilitates future searches for polyP-binding proteins and discovery of the mechanisms for polyP-binding activities. This should greatly enhance the understanding of the many physiological functions of protein-bound polyP and the involvement of polyP and polyP-binding proteins in various human diseases.
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14
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Seamon KJ, Stivers JT. A High-Throughput Enzyme-Coupled Assay for SAMHD1 dNTPase. ACTA ACUST UNITED AC 2015; 20:801-9. [PMID: 25755265 DOI: 10.1177/1087057115575150] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/06/2015] [Indexed: 12/22/2022]
Abstract
Sterile alpha motif and histidine-aspartate domain-containing protein 1 (SAMHD1) is a recently discovered enzyme that plays a central role in nucleotide metabolism and innate immunity. SAMHD1 has deoxyribonucleoside triphosphate (dNTP) triphosphohydrolase activity that depletes the dNTP substrates required for DNA synthesis in cells. The involvement of SAMHD1 in biological processes as varied as viral restriction, endogenous retroelement control, cancer, and modulation of anticancer/antiviral nucleoside drug efficacy makes it a valuable target for the development of small-molecule inhibitors. We report a high-throughput colorimetric assay for SAMHD1 dNTP hydrolase activity that takes advantage of Escherichia coli inorganic pyrophosphatase to convert PPPi to 3 Pi. The assay was validated by screening a library of 2653 clinically used compounds. Fifteen primary hits were obtained (0.57% hit rate); 80% of these were confirmed in a direct secondary assay for dNTP hydrolysis. The zinc salt of the antibiotic cephalosporin C was a potent inhibitor of SAMHD1 with an IC50 of 1.1 ± 0.1 µM, and this inhibition was largely attributable to the presence of zinc. The assay also screened a targeted library of nucleosides and their analogs, revealing that the antiviral drug acycloguanosine (acyclovir) is an inhibitor possessing excellent properties for future fragment-based drug development efforts.
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Affiliation(s)
- Kyle J Seamon
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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15
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A continuous enzyme-coupled assay for triphosphohydrolase activity of HIV-1 restriction factor SAMHD1. Antimicrob Agents Chemother 2014; 59:186-92. [PMID: 25331707 PMCID: PMC4291348 DOI: 10.1128/aac.03903-14] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The development of deoxynucleoside triphosphate (dNTP)-based drugs requires a quantitative understanding of any inhibition, activation, or hydrolysis by off-target cellular enzymes. SAMHD1 is a regulatory dNTP-triphosphohydrolase that inhibits HIV-1 replication in human myeloid cells. We describe here an enzyme-coupled assay for quantifying the activation, inhibition, and hydrolysis of dNTPs, nucleotide analogues, and nucleotide analogue inhibitors by triphosphohydrolase enzymes. The assay facilitates mechanistic studies of triphosphohydrolase enzymes and the quantification of off-target effects of nucleotide-based antiviral and chemotherapeutic agents.
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16
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Srivastav R, Kumar D, Grover A, Singh A, Manjasetty BA, Sharma R, Taneja B. Unique subunit packing in mycobacterial nanoRNase leads to alternate substrate recognitions in DHH phosphodiesterases. Nucleic Acids Res 2014; 42:7894-910. [PMID: 24878921 PMCID: PMC4081065 DOI: 10.1093/nar/gku425] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
DHH superfamily includes RecJ, nanoRNases (NrnA), cyclic nucleotide phosphodiesterases and pyrophosphatases. In this study, we have carried out in vitro and in vivo investigations on the bifunctional NrnA-homolog from Mycobacterium smegmatis, MSMEG_2630. The crystal structure of MSMEG_2630 was determined to 2.2-Å resolution and reveals a dimer consisting of two identical subunits with each subunit folding into an N-terminal DHH domain and a C-terminal DHHA1 domain. The overall structure and fold of the individual domains is similar to other members of DHH superfamily. However, MSMEG_2630 exhibits a distinct quaternary structure in contrast to other DHH phosphodiesterases. This novel mode of subunit packing and variations in the linker region that enlarge the domain interface are responsible for alternate recognitions of substrates in the bifunctional nanoRNases. MSMEG_2630 exhibits bifunctional 3′-5′ exonuclease [on both deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) substrates] as well as CysQ-like phosphatase activity (on pAp) in vitro with a preference for nanoRNA substrates over single-stranded DNA of equivalent lengths. A transposon disruption of MSMEG_2630 in M. smegmatis causes growth impairment in the presence of various DNA-damaging agents. Further phylogenetic analysis and genome organization reveals clustering of bacterial nanoRNases into two distinct subfamilies with possible role in transcriptional and translational events during stress.
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Affiliation(s)
- Rajpal Srivastav
- CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India
| | - Dilip Kumar
- CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India
| | - Amit Grover
- CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India
| | - Ajit Singh
- CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India
| | - Babu A Manjasetty
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, Grenoble 38042, France Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, Grenoble 38042, France
| | - Rakesh Sharma
- CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India
| | - Bhupesh Taneja
- CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India
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17
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Szambowska A, Tessmer I, Kursula P, Usskilat C, Prus P, Pospiech H, Grosse F. DNA binding properties of human Cdc45 suggest a function as molecular wedge for DNA unwinding. Nucleic Acids Res 2013; 42:2308-19. [PMID: 24293646 PMCID: PMC3936751 DOI: 10.1093/nar/gkt1217] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The cell division cycle protein 45 (Cdc45) represents an essential replication factor that, together with the Mcm2-7 complex and the four subunits of GINS, forms the replicative DNA helicase in eukaryotes. Recombinant human Cdc45 (hCdc45) was structurally characterized and its DNA-binding properties were determined. Synchrotron radiation circular dichroism spectroscopy, dynamic light scattering, small-angle X-ray scattering and atomic force microscopy revealed that hCdc45 exists as an alpha-helical monomer and possesses a structure similar to its bacterial homolog RecJ. hCdc45 bound long (113-mer or 80-mer) single-stranded DNA fragments with a higher affinity than shorter ones (34-mer). hCdc45 displayed a preference for 3′ protruding strands and bound tightly to single-strand/double-strand DNA junctions, such as those presented by Y-shaped DNA, bubbles and displacement loops, all of which appear transiently during the initiation of DNA replication. Collectively, our findings suggest that hCdc45 not only binds to but also slides on DNA with a 3′–5′ polarity and, thereby acts as a molecular ‘wedge’ to initiate DNA strand displacement.
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Affiliation(s)
- Anna Szambowska
- Research Group Biochemistry, Leibniz Institute for Age Research -Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany, Laboratory of Molecular Biology IBB PAS, Affiliated with University of Gdansk, Wita Stwosza 59 Gdansk, Poland, Rudolf Virchow Center, DFG Research Center for Experimental Biomedicine, Josef Schneider Strasse 2, 7080 Wurzburg, Germany, Department of Biochemistry, Oulu, P.O. Box 3000, University of Oulu, Oulu 90014, Finland, Department of Chemistry, University of Hamburg/DESY, Notkestrasse 85, 22607 Hamburg, Germany, Biocenter Oulu, P.O. Box 3000, University of Oulu, Oulu 90014, Finland and Center for Molecular Biomedicine, Friedrich-Schiller University, Biochemistry Department, Jena, Germany
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18
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Schomburg KT, Ardao I, Götz K, Rieckenberg F, Liese A, Zeng AP, Rarey M. Computational biotechnology: Prediction of competitive substrate inhibition of enzymes by buffer compounds with protein–ligand docking. J Biotechnol 2012; 161:391-401. [DOI: 10.1016/j.jbiotec.2012.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 08/08/2012] [Accepted: 08/10/2012] [Indexed: 01/18/2023]
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19
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Abstract
DNA replication is one of the most ancient of cellular processes and functional similarities among its molecular machinery are apparent across all cellular life. Cdc45 is one of the essential components of the eukaryotic replication fork and is required for the initiation and elongation of DNA replication, but its molecular function is currently unknown. In order to trace its evolutionary history and to identify functional domains, we embarked on a computational sequence analysis of the Cdc45 protein family. Our findings reveal eukaryotic Cdc45 and prokaryotic RecJ to possess a common ancestry and Cdc45 to contain a catalytic site within a predicted exonuclease domain. The likely orthology between Cdc45 and RecJ reveals new lines of enquiry into DNA replication mechanisms in eukaryotes.
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Affiliation(s)
- Luis Sanchez-Pulido
- Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK.
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20
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Luginbuehl E, Kunz S, Wentzinger L, Freimoser F, Seebeck T. The exopolyphosphatase TbrPPX1 of Trypanosoma brucei. BMC Microbiol 2011; 11:4. [PMID: 21208463 PMCID: PMC3022644 DOI: 10.1186/1471-2180-11-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 01/06/2011] [Indexed: 01/14/2023] Open
Abstract
Background Exopolyphosphatases and pyrophosphatases play important but still incompletely understood roles in energy metabolism, and also in other aspects of cell biology such as osmoregulation or signal transduction. Earlier work has suggested that a human exopolyphosphatase, Prune, might exhibit cyclic nucleotide phosphodiesterase activity. Results The kinetoplastida, a large order of unicellular eukaryotes that contains many important pathogens such as Trypanosoma brucei (human sleeping sickness), Trypanosoma cruzi (Chagas disease) or Leishmania ssp (several clinically dinstinct leishmaniases) all contain several exo- and pyrophosphatases. The current study provides a systematic classification of these enzymes, which now allows to situate the information that is already available on some of these enzymes. It then analyses the exopolyphosphatase TbrPPX1 of T. brucei in detail, using RNA interference and genetic knockouts in an attempt to define its function, and immunofluorescence microscopy to study its subcellular localization. TbrPPX1 is an exopolyphosphatase that does hydrolyze pentasodium triphosphate, but not organic triphosphates such as ATP, pyrophosphate or long-chain polyphosphates. Finally, the study investigates the potential cyclic nucleotide phosphodiesterase activity of TbrPPX1. Conclusions All kinetoplastid genomes that are currently available contain genes for an exopolyphosphatase and two classes of pyrophosphatases, one associated with the acidocalcisomes and one cytoplasmic. TbrPPX1 represents the T. brucei exopolyphosphatase. It is located throughout the cytoplasm, and its genetic ablation does not produce a dramatic phenotype. Importantly, TbrPPX1 does not exhibit any cyclic nucleotide specific phosphodiesterase activity, which definitively eliminates it as an additional player in cAMP signalling of the kinetoplastida.
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Affiliation(s)
- Edith Luginbuehl
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, CH-3012 Bern, Switzerland
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21
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Wakamatsu T, Kitamura Y, Kotera Y, Nakagawa N, Kuramitsu S, Masui R. Structure of RecJ exonuclease defines its specificity for single-stranded DNA. J Biol Chem 2010; 285:9762-9769. [PMID: 20129927 PMCID: PMC2843225 DOI: 10.1074/jbc.m109.096487] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 01/29/2010] [Indexed: 11/06/2022] Open
Abstract
RecJ is a single-stranded DNA (ssDNA)-specific 5'-3' exonuclease that plays an important role in DNA repair and recombination. To elucidate how RecJ achieves its high specificity for ssDNA, we determined the entire structures of RecJ both in a ligand-free form and in a complex with Mn(2+) or Mg(2+) by x-ray crystallography. The entire RecJ consists of four domains that form a molecule with an O-like structure. One of two newly identified domains had structural similarities to an oligonucleotide/oligosaccharide-binding (OB) fold. The OB fold domain alone could bind to DNA, indicating that this domain is a novel member of the OB fold superfamily. The truncated RecJ containing only the core domain exhibited much lower affinity for the ssDNA substrate compared with intact RecJ. These results support the hypothesis that these structural features allow specific binding of RecJ to ssDNA. In addition, the structure of the RecJ-Mn(2+) complex suggests that the hydrolysis reaction catalyzed by RecJ proceeds through a two-metal ion mechanism.
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Affiliation(s)
- Taisuke Wakamatsu
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871
| | - Yoshiaki Kitamura
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148
| | - Yutaro Kotera
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Noriko Nakagawa
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148; Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Seiki Kuramitsu
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871; RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148; Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Ryoji Masui
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148; Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
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22
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Rao F, See RY, Zhang D, Toh DC, Ji Q, Liang ZX. YybT is a signaling protein that contains a cyclic dinucleotide phosphodiesterase domain and a GGDEF domain with ATPase activity. J Biol Chem 2009; 285:473-82. [PMID: 19901023 DOI: 10.1074/jbc.m109.040238] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The cyclic dinucleotide c-di-AMP [corrected] synthesized by the diadenylate cyclase domain was discovered recently [corrected] as a messenger molecule for signaling DNA breaks in Bacillus subtilis. By searching bacterial genomes, we identified a family of DHH/DHHA1 domain proteins (COG3387) that co-occur with a subset of the diadenylate cyclase domain proteins. Here we report that the B. subtilis protein YybT, a member of the COG3387 family proteins, exhibits phosphodiesterase activity toward cyclic dinucleotides. The DHH/DHHA1 domain hydrolyzes c-di-AMP and c-di-GMP to generate the linear dinucleotides 5'-pApA and 5'-pGpG. The data suggest that c-di-AMP could be the physiological substrate for YybT given the physiologically relevant Michaelis-Menten constant (K(m)) and the presence of YybT family proteins in the bacteria lacking c-di-GMP signaling network. The bacterial regulator ppGpp was found to be a strong competitive inhibitor of the DHH/DHHA1 domain, suggesting that YybT is under tight control during stringent response. In addition, the atypical GGDEF domain of YybT exhibits unexpected ATPase activity, distinct from the common diguanylate cyclase activity for GGDEF domains. We further demonstrate the participation of YybT in DNA damage and acid resistance by characterizing the phenotypes of the DeltayybT mutant. The novel enzymatic activity and stress resistance together point toward a role for YybT in stress signaling and response.
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Affiliation(s)
- Feng Rao
- School of Biological Sciences, Nanyang Technological University, Singapore
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23
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3'-Phosphoadenosine-5'-phosphate phosphatase activity is required for superoxide stress tolerance in Streptococcus mutans. J Bacteriol 2009; 191:4330-40. [PMID: 19429620 DOI: 10.1128/jb.00184-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Aerobic microorganisms have evolved different strategies to withstand environmental oxidative stresses generated by various reactive oxygen species (ROS). For the facultative anaerobic human oral pathogen Streptococcus mutans, the mechanisms used to protect against ROS are not fully understood, since it does not possess catalase, an enzyme that degrades hydrogen peroxide. In order to elucidate the genes that are essential for superoxide stress response, methyl viologen (MV)-sensitive mutants of S. mutans were generated via ISS1 mutagenesis. Screening of approximately 2,500 mutants revealed six MV-sensitive mutants, each containing an insertion in one of five genes, including a highly conserved hypothetical gene, SMU.1297. Sequence analysis suggests that SMU.1297 encodes a hypothetical protein with a high degree of homology to the Bacillus subtilis YtqI protein, which possesses an oligoribonuclease activity that cleaves nano-RNAs and a phosphatase activity that degrades 3'-phosphoadenosine-5'-phosphate (pAp) and 3'-phosphoadenosine-5'-phosphosulfate (pApS) to produce AMP; the latter activity is similar to the activity of the Escherichia coli CysQ protein, which is required for sulfur assimilation. SMU.1297 was deleted using a markerless Cre-loxP-based strategy; the SMU.1297 deletion mutant was just as sensitive to MV as the ISS1 insertion mutant. Complementation of the deletion mutant with wild-type SMU.1297, in trans, restored the parental phenotype. Biochemical analyses with purified SMU.1297 protein demonstrated that it has pAp phosphatase activity similar to that of YtqI but apparently lacks an oligoribonuclease activity. The ability of SMU.1297 to dephosphorylate pApS in vivo was confirmed by complementation of an E. coli cysQ mutant with SMU.1297 in trans. Thus, our results suggest that SMU.1297 is involved in superoxide stress tolerance in S. mutans. Furthermore, the distribution of homologs of SMU.1297 in streptococci indicates that this protein is essential for superoxide stress tolerance in these organisms.
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Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization. Proc Natl Acad Sci U S A 2009; 106:8489-94. [PMID: 19423669 DOI: 10.1073/pnas.0901572106] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Alanyl-tRNA synthetase (AlaRS) specifically recognizes the major identity determinant, the G3:U70 base pair, in the acceptor stem of tRNA(Ala) by both the tRNA-recognition and editing domains. In this study, we solved the crystal structures of 2 halves of Archaeoglobus fulgidus AlaRS: AlaRS-DeltaC, comprising the aminoacylation, tRNA-recognition, and editing domains, and AlaRS-C, comprising the dimerization domain. The aminoacylation/tRNA-recognition domains contain an insertion incompatible with the class-specific tRNA-binding mode. The editing domain is fixed tightly via hydrophobic interactions to the aminoacylation/tRNA-recognition domains, on the side opposite from that in threonyl-tRNA synthetase. A groove formed between the aminoacylation/tRNA-recognition domains and the editing domain appears to be an alternative tRNA-binding site, which might be used for the aminoacylation and/or editing reactions. Actually, the amino acid residues required for the G3:U70 recognition are mapped in this groove. The dimerization domain consists of helical and globular subdomains. The helical subdomain mediates dimerization by forming a helix-loop-helix zipper. The globular subdomain, which is important for the aminoacylation and editing activities, has a positively-charged face suitable for tRNA binding.
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25
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Orchestration of Haemophilus influenzae RecJ Exonuclease by Interaction with Single-Stranded DNA-Binding Protein. J Mol Biol 2009; 385:1375-96. [DOI: 10.1016/j.jmb.2008.11.041] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 11/17/2008] [Accepted: 11/18/2008] [Indexed: 11/19/2022]
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Jain R, Shuman S. Polyphosphatase activity of CthTTM, a bacterial triphosphate tunnel metalloenzyme. J Biol Chem 2008; 283:31047-57. [PMID: 18782773 DOI: 10.1074/jbc.m805392200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Triphosphate tunnel metalloenzymes (TTMs) are a superfamily of phosphotransferases with a distinctive active site located within an eight-stranded beta barrel. The best understood family members are the eukaryal RNA triphosphatases, which catalyze the initial step in mRNA capping. The RNA triphosphatases characteristically hydrolyze nucleoside 5'-triphosphates in the presence of manganese and are inept at cleaving inorganic tripolyphosphate. We recently identified a TTM protein from the bacterium Clostridium thermocellum (CthTTM) with the opposite substrate preference. Here we report that CthTTM catalyzes hydrolysis of guanosine 5'-tetraphosphate to yield GTP and P(i) (K(m) = 70 microm, k(cat) = 170 s(-1)) much more effectively than it converts GTP to GDP and P(i) (K(m) = 70 microm, k(cat) = 0.3 s(-1)), implying that a nucleoside interferes when positioned too close to the tunnel entrance. CthTTM is capable of quantitatively cleaving diadenosine hexaphosphate but has feeble activity with shorter derivatives diadenosine tetraphosphate and diadenosine pentaphosphate. We propose that the tunnel opens to accommodate the dumbbell-shaped diadenosine hexaphosphate and then closes around it to perform catalysis. We find that CthTTM can exhaustively hydrolyze a long-chain inorganic polyphosphate, a molecule that plays important roles in bacterial physiology. CthTTM differs from other known polyphosphatases in that it yields a approximately 2:1 mixture of P(i) and PP(i) end products. Bacterial/archaeal TTMs have a C-terminal helix located near the tunnel entrance. Deletion of this helix from CthTTM exerts pleiotropic effects. (i) It suppresses hydrolysis of guanosine 5'-tetraphosphate and inorganic PPP(i); (ii) it stimulates NTP hydrolysis; and (iii) it biases the outcome of the long-chain polyphosphatase reaction more strongly in favor of P(i) production. We discuss models for substrate binding in the triphosphate tunnel.
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Affiliation(s)
- Ruchi Jain
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA
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Tammenkoski M, Koivula K, Cusanelli E, Zollo M, Steegborn C, Baykov AA, Lahti R. Human Metastasis Regulator Protein H-Prune is a Short-Chain Exopolyphosphatase. Biochemistry 2008; 47:9707-13. [DOI: 10.1021/bi8010847] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marko Tammenkoski
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Katja Koivula
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Emilio Cusanelli
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Massimo Zollo
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Clemens Steegborn
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Alexander A. Baykov
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Reijo Lahti
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
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Brown MRW, Kornberg A. The long and short of it - polyphosphate, PPK and bacterial survival. Trends Biochem Sci 2008; 33:284-90. [PMID: 18487048 DOI: 10.1016/j.tibs.2008.04.005] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Revised: 04/17/2008] [Accepted: 04/17/2008] [Indexed: 12/12/2022]
Abstract
Inorganic polyphosphate (poly P) is present in all species tested to date, from each of the three kingdoms of life. Studied mainly in prokaryotes, poly P and its associated enzymes are important in diverse basic metabolism, in at least some structural functions and, notably, in stress responses. These numerous and unrelated roles for poly P are probably the consequence of its presence in life-forms from early in evolution. The genomes of many bacterial species, including pathogens, encode a homologue of a major poly P synthetic enzyme, poly P kinase 1 (PPK1). Loss of PPK1 results in reduced poly P levels, and deletion of the ppk1 gene in pathogens also results in a loss of virulence towards protozoa and animals. Thus far, no PPK1 homologue has been identified in higher-order eukaryotes and, therefore, PPK1 exhibits potential as a novel target for chemotherapy.
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Affiliation(s)
- Michael R W Brown
- Research Institute in Healthcare Science, Department of Pharmacy, University of Wolverhampton, Wulfruna Street, Wolverhampton, WV1 1SB, UK.
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Fang J, Ruiz FA, Docampo M, Luo S, Rodrigues JCF, Motta LS, Rohloff P, Docampo R. Overexpression of a Zn2+-sensitive soluble exopolyphosphatase from Trypanosoma cruzi depletes polyphosphate and affects osmoregulation. J Biol Chem 2007; 282:32501-10. [PMID: 17827150 DOI: 10.1074/jbc.m704841200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report the cloning, expression, purification, and characterization of the Trypanosoma cruzi exopolyphosphatase (TcPPX). The product of this gene (TcPPX), has 383 amino acids and a molecular mass of 43.1 kDa. TcPPX differs from most exopolyphosphatases in its preference for short-chain polyphosphate (poly P). Heterologous expression of TcPPX in Escherichia coli produced a functional enzyme that had a neutral optimum pH and was dramatically inhibited by low concentrations of Zn2+, high concentrations of basic amino acids (lysine and arginine), and heparin. TcPPX is a processive enzyme and does not hydrolyze ATP, pyrophosphate, or p-nitrophenyl phosphate, although it hydrolyzes guanosine 5'-tetraphosphate very efficiently. Overexpression of TcPPX resulted in a dramatic decrease in total short-chain poly P and partial decrease in long-chain poly P. This was accompanied by a delayed regulatory volume decrease after hyposmotic stress. These results support the role of poly P in T. cruzi osmoregulation.
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Affiliation(s)
- Jianmin Fang
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Paul D. Coverdell Biomedical and Health Sciences Center, Athens, Georgia 30602, USA
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