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Kaspar F, Wolff DS, Neubauer P, Kurreck A, Arcus VL. pH-Independent Heat Capacity Changes during Phosphorolysis Catalyzed by the Pyrimidine Nucleoside Phosphorylase from Geobacillus thermoglucosidasius. Biochemistry 2021; 60:1573-1577. [PMID: 33955225 DOI: 10.1021/acs.biochem.1c00156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Enzyme-catalyzed reactions sometimes display curvature in their Eyring plots in the absence of denaturation, indicative of a change in activation heat capacity. However, the effects of pH and (de)protonation on this phenomenon have remained unexplored. Herein, we report a kinetic characterization of the thermophilic pyrimidine nucleoside phosphorylase from Geobacillus thermoglucosidasius across a two-dimensional working space covering 35 °C and 3 pH units with two substrates displaying different pKa values. Our analysis revealed the presence of a measurable activation heat capacity change ΔCp⧧ in this reaction system, which showed no significant dependence on medium pH or substrate charge. Our results further describe the remarkable effects of a single halide substitution that has a minor influence on ΔCp⧧ but conveys a significant kinetic effect by decreasing the activation enthalpy, causing a >10-fold rate increase. Collectively, our results present an important piece in the understanding of enzymatic systems across multidimensional working spaces where the choice of reaction conditions can affect the rate, affinity, and thermodynamic phenomena independently of one another.
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Affiliation(s)
- Felix Kaspar
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, D-13355 Berlin, Germany
| | - Darian S Wolff
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, D-13355 Berlin, Germany
| | - Vickery L Arcus
- Te Aka Ma̅tuatua-School of Science, Te Whare Wa̅nanga o Waikato-University of Waikato, Hamilton 3240, New Zealand
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2
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Holanda RJ, Deves C, Moreira-Dill LS, Guimarães CL, Marttinelli LKB, Fernandes CFC, Medeiros PSM, Pereira SS, Honda ER, Stábeli RG, Santos DS, Soares AM, Pereira da Silva LH. Plasmodium falciparum purine nucleoside phosphorylase as a model in the search for new inhibitors by high throughput screening. Int J Biol Macromol 2020; 165:1832-1841. [PMID: 33075341 DOI: 10.1016/j.ijbiomac.2020.10.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/28/2020] [Accepted: 10/09/2020] [Indexed: 10/23/2022]
Abstract
Studies have shown that inhibition of Plasmodium falciparum Purine Nucleoside Phosphorylase (PfPNP) blocks the purine salvage pathway in vitro and in vivo. In this study, PfPNP was evaluated as a model in the search for new inhibitors using surface plasmon resonance (SPR). Its expression, purification, oligomeric state, kinetic constants, calorimetric parameters and kinetic mechanisms were obtained. PfPNP was immobilized on a CM5 sensor chip and sensorgrams were produced through binding the enzyme to the substrate MESG and interactions between molecules contained in 10 fractions of natural extracts. The oligomeric state showed that recombinant PfPNP is a hexamer. The true steady-state kinetic parameters for the substrate inosine were: KM 17 μM, kcat 1.2 s-1, VMax 2.2 U/mg and kcat/KM 7 × 10-4; for MESG they were: KM 131 μM, kcat 2.4 s-1, VMax 4.4 U/mg and kcat/KM 1.8 × 10-4. The thermodynamic parameters for the substrate Phosphate were: ΔG - 5.8 cal mol-1, ΔH - 6.5 cal mol-1 and ΔS - 2.25 cal mol-1/degree. The ITC results demonstrated that the binding of phosphate to free PfPNP led to a significant change in heat and association constants and thermodynamic parameters. A sequential ordered mechanism was proposed as the kinetic mechanism. Three plant extracts contained molecules capable of interacting with PfPNP, showing different levels of affinity. The identification of plant extract fractions containing molecules that interact with recombinant PfPNP using SRP validates this target as a model in the search for new inhibitors. In this study, we showed for the first time the true steady-state kinetic parameters for reactions catalyzed by PfPNP and a model using PfPNP as a target for High-throughput Screening for new inhibitors through SPR. This knowledge will allow for the development of more efficient research methods in the search for new drugs against malaria.
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Affiliation(s)
- Rudson J Holanda
- Universidade Federal do Amazonas, UFAM, campus Humaitá, Amazonas, Brazil; Laboratório de Biotecnologia de Proteínas e Compostos Bioativos da Amazônia Ocidental, LABIOPROT, Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia e Universidade Federal de Rondônia, UNIR, Porto Velho, Rondônia, Brazil.
| | - Candida Deves
- Centro de Pesquisa em Biologia Molecular e Funcional, PUCRS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Leandro S Moreira-Dill
- Laboratório de Biotecnologia de Proteínas e Compostos Bioativos da Amazônia Ocidental, LABIOPROT, Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia e Universidade Federal de Rondônia, UNIR, Porto Velho, Rondônia, Brazil
| | - Cesar L Guimarães
- Laboratório de Biotecnologia de Proteínas e Compostos Bioativos da Amazônia Ocidental, LABIOPROT, Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia e Universidade Federal de Rondônia, UNIR, Porto Velho, Rondônia, Brazil
| | - Leonardo K B Marttinelli
- Centro de Pesquisa em Biologia Molecular e Funcional, PUCRS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Carla F C Fernandes
- Laboratório de Biotecnologia de Proteínas e Compostos Bioativos da Amazônia Ocidental, LABIOPROT, Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia e Universidade Federal de Rondônia, UNIR, Porto Velho, Rondônia, Brazil; Laboratório de Engenharia de Anticorpos, Fiocruz Rondônia, Porto Velho, Rondônia, Brazil; Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Ceará, Fortaleza, Ceará, Brazil
| | - Patrícia S M Medeiros
- Laboratório de Biotecnologia de Proteínas e Compostos Bioativos da Amazônia Ocidental, LABIOPROT, Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia e Universidade Federal de Rondônia, UNIR, Porto Velho, Rondônia, Brazil
| | - Soraya S Pereira
- Laboratório de Biotecnologia de Proteínas e Compostos Bioativos da Amazônia Ocidental, LABIOPROT, Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia e Universidade Federal de Rondônia, UNIR, Porto Velho, Rondônia, Brazil; Laboratório de Engenharia de Anticorpos, Fiocruz Rondônia, Porto Velho, Rondônia, Brazil
| | - Eduardo R Honda
- Instituto de Pesquisa em Patologias Tropicais de Rondônia, IPEPATRO e Laboratório Central, LACEN, Porto Velho, Rondônia, Brazil
| | - Rodrigo G Stábeli
- Laboratório de Biotecnologia de Proteínas e Compostos Bioativos da Amazônia Ocidental, LABIOPROT, Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia e Universidade Federal de Rondônia, UNIR, Porto Velho, Rondônia, Brazil; Fundação Oswaldo Cruz, FIOCRUZ, Plataforma Bi-institucional de Medicina Translacional, Ribeirão Preto, São Paulo, Brazil
| | - Diógenes S Santos
- Centro de Pesquisa em Biologia Molecular e Funcional, PUCRS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Andreimar M Soares
- Laboratório de Biotecnologia de Proteínas e Compostos Bioativos da Amazônia Ocidental, LABIOPROT, Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia e Universidade Federal de Rondônia, UNIR, Porto Velho, Rondônia, Brazil; Centro Universitário São Lucas, UniSL, Porto Velho, Rondônia, Brazil; Instituto Nacional de Ciência e Tecnologia de Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Brazil.
| | - Luiz H Pereira da Silva
- Laboratório de Biotecnologia de Proteínas e Compostos Bioativos da Amazônia Ocidental, LABIOPROT, Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia e Universidade Federal de Rondônia, UNIR, Porto Velho, Rondônia, Brazil
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3
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Timofeev VI, Fateev IV, Kostromina MA, Abramchik YA, Konstantinova ID, Volkov VV, Lykoshin DD, Mikheeva OO, Muravieva TI, Esipov RS, Kuranova IP. The comparative analysis of the properties and structures of purine nucleoside phosphorylases from thermophilic bacterium Thermus thermophilus HB27. J Biomol Struct Dyn 2020; 40:3626-3641. [PMID: 33225840 DOI: 10.1080/07391102.2020.1848628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Two recombinant purine nucleoside phosphorylases from thermophilic bacterium Thermus thermophilus HB27 encoded by genes TT_C1070 (TthPNPI) and TT_C0194 (TthPNPII) were purified and characterized. The comparative analysis of their sequences, molecular weight, enzymes specificity and kinetics of the catalyzed reaction were realized. As a result, it was determined that the TthPNPI is specific to guanosine while the TthPNPII to adenosine. According to the results of the size exclusion chromatography and SAXS study both enzymes are hexameric molecules. Based on the sequence alignment with homologous purine nucleoside phosphorylases (PNPs), Asn was identified as a purine base recognizing residue in the active site of TthPNPI and Asp in TthPNPII. The three-dimensional structure of TthPNPII was solved at 2.5 Å resolution by molecular replacement method using crystals grown in microgravity. Position of phosphate in the active site cavity is located. The possible arrangement of adenosine and guanosine in TthPNPII active site cavity is considered using superposition with the structures of homologous trimeric and hexameric PNPs complexed with corresponding substrates. The peculiarities of oligomeric structure of TthPNPII in comparison with homologous PNPs are described. It is shown that two trimeric molecules of TthPNPII in the asymmetric part of the unit cell are connected by three two-fold axis into a hexamer with 32-point symmetry. This type of hexameric structure of PNP is found for the first time. The interface area between the subunits in trimeric molecule and between the trimers in TthPNPII hexamer is described.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vladimir I Timofeev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation
| | - Ilya V Fateev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maria A Kostromina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yuliya A Abramchik
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Irina D Konstantinova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir V Volkov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry D Lykoshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Olga O Mikheeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana I Muravieva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Roman S Esipov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Inna P Kuranova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation
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4
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Antipov AN, Mordkovich NN, Khijniak TV, Okorokova NA, Veiko VP. Cloning of Nucleoside Phosphorylase Genes from the Extremophilic Bacterium Halomonas chromatireducens AGD 8-3 with the Construction of Recombinant Producer Strains of These Proteins and the Study of Their Enzymatic Properties. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820010020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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5
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Xie Y, Hu F, Xiang D, Lu H, Li W, Zhao A, Huang L, Wang R. The metabolic effect of gut microbiota on drugs. Drug Metab Rev 2020; 52:139-156. [PMID: 32116054 DOI: 10.1080/03602532.2020.1718691] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yuan Xie
- School of Pharmacy, Lanzhou University, Lanzhou, China
- Key Laboratory of the Plateau Medicial, The 940 Hospital of Joint Logistics Support, PLA, Lanzhou, China
| | - Fangdi Hu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Dawei Xiang
- Key Laboratory of the Plateau Medicial, The 940 Hospital of Joint Logistics Support, PLA, Lanzhou, China
| | - Hui Lu
- Key Laboratory of the Plateau Medicial, The 940 Hospital of Joint Logistics Support, PLA, Lanzhou, China
| | - Wenbin Li
- Key Laboratory of the Plateau Medicial, The 940 Hospital of Joint Logistics Support, PLA, Lanzhou, China
| | - Anpeng Zhao
- Key Laboratory of the Plateau Medicial, The 940 Hospital of Joint Logistics Support, PLA, Lanzhou, China
| | - Longji Huang
- School of Pharmacy, Lanzhou University, Lanzhou, China
- Key Laboratory of the Plateau Medicial, The 940 Hospital of Joint Logistics Support, PLA, Lanzhou, China
| | - Rong Wang
- School of Pharmacy, Lanzhou University, Lanzhou, China
- Key Laboratory of the Plateau Medicial, The 940 Hospital of Joint Logistics Support, PLA, Lanzhou, China
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6
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Efficient Synthesis of Purine Nucleoside Analogs by a New Trimeric Purine Nucleoside Phosphorylase from Aneurinibacillus migulanus AM007. Molecules 2019; 25:molecules25010100. [PMID: 31888088 PMCID: PMC6983109 DOI: 10.3390/molecules25010100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/18/2019] [Accepted: 12/24/2019] [Indexed: 11/16/2022] Open
Abstract
Purine nucleoside phosphorylases (PNPs) are promising biocatalysts for the synthesis of purine nucleoside analogs. Although a number of PNPs have been reported, the development of highly efficient enzymes for industrial applications is still in high demand. Herein, a new trimeric purine nucleoside phosphorylase (AmPNP) from Aneurinibacillus migulanus AM007 was cloned and heterologously expressed in Escherichia coli BL21(DE3). The AmPNP showed good thermostability and a broad range of pH stability. The enzyme was thermostable below 55 °C for 12 h (retaining nearly 100% of its initial activity), and retained nearly 100% of the initial activity in alkaline buffer systems (pH 7.0–9.0) at 60 °C for 2 h. Then, a one-pot, two-enzyme mode of transglycosylation reaction was successfully constructed by combining pyrimidine nucleoside phosphorylase (BbPyNP) derived from Brevibacillus borstelensis LK01 and AmPNP for the production of purine nucleoside analogs. Conversions of 2,6-diaminopurine ribonucleoside (1), 2-amino-6-chloropurine ribonucleoside (2), and 6-thioguanine ribonucleoside (3) synthesized still reached >90% on the higher concentrations of substrates (pentofuranosyl donor: purine base; 20:10 mM) with a low enzyme ratio of BbPyNP: AmPNP (2:20 μg/mL). Thus, the new trimeric AmPNP is a promising biocatalyst for industrial production of purine nucleoside analogs.
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7
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Zhou X, Yan W, Zhang C, Yang Z, Neubauer P, Mikhailopulo IA, Huang Z. Biocatalytic synthesis of seleno-, thio- and chloro-nucleobase modified nucleosides by thermostable nucleoside phosphorylases. CATAL COMMUN 2019. [DOI: 10.1016/j.catcom.2018.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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8
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Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Separating host and microbiome contributions to drug pharmacokinetics and toxicity. Science 2019; 363:363/6427/eaat9931. [PMID: 30733391 DOI: 10.1126/science.aat9931] [Citation(s) in RCA: 236] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 11/02/2018] [Accepted: 12/20/2018] [Indexed: 12/24/2022]
Abstract
The gut microbiota is implicated in the metabolism of many medical drugs, with consequences for interpersonal variation in drug efficacy and toxicity. However, quantifying microbial contributions to drug metabolism is challenging, particularly in cases where host and microbiome perform the same metabolic transformation. We combined gut commensal genetics with gnotobiotics to measure brivudine drug metabolism across tissues in mice that vary in a single microbiome-encoded enzyme. Informed by these measurements, we built a pharmacokinetic model that quantitatively predicts microbiome contributions to systemic drug and metabolite exposure, as a function of bioavailability, host and microbial drug-metabolizing activity, drug and metabolite absorption, and intestinal transit kinetics. Clonazepam studies illustrate how this approach disentangles microbiome contributions to metabolism of drugs subject to multiple metabolic routes and transformations.
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Affiliation(s)
- Michael Zimmermann
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Maria Zimmermann-Kogadeeva
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Rebekka Wegmann
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA.
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Sinitsyna EV, Timofeev VI, Zhukhlistova NE, Muravieva TI, Kostromina MA, Esipov RS, Kuranova IP. Crystallization and Preliminary X-ray Diffraction Study of Purine Nucleoside Phosphorylase from the Thermophilic Bacterium Thermus thermophilus Strain HB27. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518050279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Timofeev VI, Zhukhlistova NE, Abramchik YA, Muravieva TI, Esipov RS, Kuranova IP. Crystal structure of Escherichia coli purine nucleoside phosphorylase complexed with acyclovir. Acta Crystallogr F Struct Biol Commun 2018; 74:402-409. [PMID: 29969103 PMCID: PMC6038453 DOI: 10.1107/s2053230x18008087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/31/2018] [Indexed: 11/10/2022] Open
Abstract
Escherichia coli purine nucleoside phosphorylase (PNP), which catalyzes the reversible phosphorolysis of purine ribonucleosides, belongs to the family I hexameric PNPs. Owing to their key role in the purine salvage pathway, PNPs are attractive targets for drug design against some pathogens. Acyclovir (ACV) is an acyclic derivative of the PNP substrate guanosine and is used as an antiviral drug for the treatment of some human viral infections. The crystalline complex of E. coli PNP with acyclovir was prepared by co-crystallization in microgravity using counter-diffusion through a gel layer in a capillary. The structure of the E. coli PNP-ACV complex was solved at 2.32 Å resolution using the molecular-replacement method. The ACV molecule is observed in two conformations and sulfate ions were located in both the nucleoside-binding and phosphate-binding pockets of the enzyme. A comparison with the complexes of other hexameric and trimeric PNPs with ACV shows the similarity in acyclovir binding by these enzymes.
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Affiliation(s)
- Vladimir I. Timofeev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
- Kurchatov Complex of NBICS-Technologies, National Research Center ‘Kurchatov Institute’, Akad. Kurchatova Square 1, Moscow 123182, Russian Federation
| | - Nadezhda E. Zhukhlistova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
| | - Yuliya A. Abramchik
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Tatiana I. Muravieva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Roman S. Esipov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Inna P. Kuranova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
- Kurchatov Complex of NBICS-Technologies, National Research Center ‘Kurchatov Institute’, Akad. Kurchatova Square 1, Moscow 123182, Russian Federation
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11
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A synergistic effect of phosphate, pH and Phe159 substitution on the formycin A association to the E. coli purine nucleoside phosphorylase. Biochimie 2018; 148:80-86. [DOI: 10.1016/j.biochi.2018.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 02/22/2018] [Indexed: 11/22/2022]
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12
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Prokopowicz M, Greń B, Cieśla J, Kierdaszuk B. Towards understanding the E. coli PNP binding mechanism and FRET absence between E. coli PNP and formycin A. Biophys Chem 2017; 230:99-108. [PMID: 28947300 DOI: 10.1016/j.bpc.2017.09.001] [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: 07/11/2017] [Revised: 08/25/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
Abstract
The aim of this study is threefold: (1) augmentation of the knowledge of the E. coli PNP binding mechanism; (2) explanation of the previously observed 'lack of FRET' phenomenon and (3) an introduction of the correction (modified method) for FRET efficiency calculation in the PNP-FA complexes. We present fluorescence studies of the two E. coli PNP mutants (F159Y and F159A) with formycin A (FA), that indicate that the aromatic amino acid is indispensable in the nucleotide binding, additional hydroxyl group at position 159 probably enhances the strength of binding and that the amino acids pair 159-160 has a great impact on the spectroscopic properties of the enzyme. The experiments were carried out in hepes and phosphate buffers, at pH7 and 8.3. Two methods, a conventional and a modified one, that utilizes the dissociation constant, for calculations of the energy transfer efficiency (E) and the acceptor-to-donor distance (r) between FA and the Tyr (energy donor) were employed. Total difference spectra were calculated for emission spectra (λex 280nm, 295nm, 305nm and 313nm) for all studied systems. Time-resolved techniques allowed to conclude the existence of a specific structure formed by amino acids at positions 159 and 160. The results showed an unexpected pattern change of FRET in the mutants, when compared to the wild type enzyme and a probable presence of a structure created between 159 and 160 residue, that might influence the binding efficiency. Additionally, we confirmed the indispensable role of the modification of the FRET efficiency (E) calculation on the fraction of enzyme saturation in PNP-FA systems.
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Affiliation(s)
- Małgorzata Prokopowicz
- Inter-Faculty Interdisciplinary Doctoral Studies in Natural Sciences and Mathematics, University of Warsaw, Stefana Banacha 2C, Warsaw 02-097, Poland; Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Żwirki i Wigury 93, Warsaw 02-089, Poland.
| | - Bartosz Greń
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Żwirki i Wigury 93, Warsaw 02-089, Poland
| | - Joanna Cieśla
- Department of Drug Technology and Biotechnology, Institute of Biotechnology Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, Warsaw 00-664, Poland
| | - Borys Kierdaszuk
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Żwirki i Wigury 93, Warsaw 02-089, Poland
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13
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Verma P, Patel GK, Kar B, Sharma AK. A case of neofunctionalization of a Putranjiva roxburghii PNP protein to trypsin inhibitor by disruption of PNP-UDP domain through an insert containing inhibitory site. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 260:19-30. [PMID: 28554472 DOI: 10.1016/j.plantsci.2017.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/11/2017] [Accepted: 03/25/2017] [Indexed: 05/24/2023]
Abstract
The attainment of new function by a protein is achieved through convergent/divergent evolution. In present work, the sequence analysis of a 34kDa protein from Putranjiva roxburghii, earlier reported as a potent trypsin inhibitor, showed resemblance to some of the wound inducible and vegetative storage proteins. A detailed sequence analysis revealed that these proteins belong to PNP-UDP family. In case of P. roxburghii protein, an approximately 46 residue insert disrupts the PNP domain. Similar disruption of PNP domain is observed in related plant proteins. The characterization of recombinant full length and truncated (without 46 residue insert) forms of P. roxburghii PNP family protein (PRpnp) unraveled that trypsin inhibitory active site is located within the insert. The truncated form containing uninterrupted PNP domain showed strong PNP enzymatic activity where it hydrolyzed the N-glycosidic bond of inosine and guanosine. The full length protein, however, showed weak PNP enzyme activity which may be due to presence of the insert. These results indicate towards the neofunctionalization of PRpnp to a potent trypsin inhibitor through an insert containing inhibitory residue to cater to the needs of plant defense. The similar wound inducible and vegetative storage proteins may have also evolved due to evolutionary needs.
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Affiliation(s)
- Preeti Verma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Girijesh K Patel
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Bibekananda Kar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Ashwani K Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India.
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Suppressors of dGTP Starvation in Escherichia coli. J Bacteriol 2017; 199:JB.00142-17. [PMID: 28373271 DOI: 10.1128/jb.00142-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/23/2017] [Indexed: 11/20/2022] Open
Abstract
dGTP starvation, a newly discovered phenomenon in which Escherichia coli cells are starved specifically for the DNA precursor dGTP, leads to impaired growth and, ultimately, cell death. Phenomenologically, it represents an example of nutritionally induced unbalanced growth: cell mass amplifies normally as dictated by the nutritional status of the medium, but DNA content growth is specifically impaired. The other known example of such a condition, thymineless death (TLD), involves starvation for the DNA precursor dTTP, which has been found to have important chemotherapeutic applications. Experimentally, dGTP starvation is induced by depriving an E. coligpt optA1 strain of its required purine source, hypoxanthine. In our studies of this phenomenon, we noted the emergence of a relatively high frequency of suppressor mutants that proved resistant to the treatment. To study such suppressors, we used next-generation sequencing on a collection of independently obtained mutants. A significant fraction was found to carry a defect in the PurR transcriptional repressor, controlling de novo purine biosynthesis, or in its downstream purEK operon. Thus, upregulation of de novo purine biosynthesis appears to be a major mode of overcoming the lethal effects of dGTP starvation. In addition, another large fraction of the suppressors contained a large tandem duplication of a 250- to 300-kb genomic region that included the purEK operon as well as the acrAB-encoded multidrug efflux system. Thus, the suppressive effects of the duplications could potentially involve beneficial effects of a number of genes/operons within the amplified regions.IMPORTANCE Concentrations of the four precursors for DNA synthesis (2'-deoxynucleoside-5'-triphosphates [dNTPs]) are critical for both the speed of DNA replication and its accuracy. Previously, we investigated consequences of dGTP starvation, where the DNA precursor dGTP was specifically reduced to a low level. Under this condition, E. coli cells continued cell growth but eventually developed a DNA replication defect, leading to cell death due to formation of unresolvable DNA structures. Nevertheless, dGTP-starved cultures eventually resumed growth due to the appearance of resistant mutants. Here, we used whole-genome DNA sequencing to identify the responsible suppressor mutations. We show that the majority of suppressors can circumvent death by upregulating purine de novo biosynthesis, leading to restoration of dGTP to acceptable levels.
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Štefanić Z, Mikleušević G, Luić M, Bzowska A, Leščić Ašler I. Structural characterization of purine nucleoside phosphorylase from human pathogen Helicobacter pylori. Int J Biol Macromol 2017; 101:518-526. [PMID: 28336275 DOI: 10.1016/j.ijbiomac.2017.03.101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/17/2017] [Accepted: 03/18/2017] [Indexed: 10/19/2022]
Abstract
Microaerophilic bacterium Helicobacer pylori is a well known human pathogen involved in the development of many diseases. Due to the evergrowing infection rate and increase of H. pylori antibiotic resistence, it is of utmost importance to find a new way to attack and eradicate H. pylori. The purine metabolism in H. pylori is solely dependant on the salvage pathway and one of the key enzymes in this pathway is purine nucleoside phosphorylase (PNP). In this timely context, we report here the basic biochemical and structural characterization of recombinant PNP from the H. pylori clinical isolate expressed in Escherichia coli. Structure of H. pylori PNP is typical for high molecular mass PNPs. However, its activity towards adenosine is very low, thus resembling more that of low molecular mass PNPs. Understanding the molecular mechanism of this key enzyme may lead to the development of new drug strategies and help in the eradication of H. pylori.
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Affiliation(s)
- Zoran Štefanić
- Division of Physical Chemistry, Ruđer Bošković Institute, POB 180, Bijenička cesta 54, HR-10002 Zagreb, Croatia
| | - Goran Mikleušević
- Division of Physical Chemistry, Ruđer Bošković Institute, POB 180, Bijenička cesta 54, HR-10002 Zagreb, Croatia
| | - Marija Luić
- Division of Physical Chemistry, Ruđer Bošković Institute, POB 180, Bijenička cesta 54, HR-10002 Zagreb, Croatia
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Żwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Ivana Leščić Ašler
- Division of Physical Chemistry, Ruđer Bošković Institute, POB 180, Bijenička cesta 54, HR-10002 Zagreb, Croatia.
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Boyko KM, Timofeev VI, Samygina VR, Kuranova IP, Popov VO, Koval’chuk MV. Protein crystallization under microgravity conditions. Analysis of the results of Russian experiments performed on the International Space Station in 2005−2015. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s1063774516050059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Konstantinova ID, Fateev IV, Miroshnikov AI. The arsenolysis reaction in the biotechnological method of synthesis of modified purine β-D-arabinonucleosides. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016040105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Isaksen GV, Hopmann KH, Åqvist J, Brandsdal BO. Computer Simulations Reveal Substrate Specificity of Glycosidic Bond Cleavage in Native and Mutant Human Purine Nucleoside Phosphorylase. Biochemistry 2016; 55:2153-62. [PMID: 26985580 DOI: 10.1021/acs.biochem.5b01347] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of purine ribonucleosides and 2'-deoxyribonucleosides, yielding the purine base and (2'-deoxy)ribose 1-phosphate as products. While this enzyme has been extensively studied, several questions with respect to the catalytic mechanism have remained largely unanswered. The role of the phosphate and key amino acid residues in the catalytic reaction as well as the purine ring protonation state is elucidated using density functional theory calculations and extensive empirical valence bond (EVB) simulations. Free energy surfaces for adenosine, inosine, and guanosine are fitted to ab initio data and yield quantitative agreement with experimental data when the surfaces are used to model the corresponding enzymatic reactions. The cognate substrates 6-aminopurines (inosine and guanosine) interact with PNP through extensive hydrogen bonding, but the substrate specificity is found to be a direct result of the electrostatic preorganization energy along the reaction coordinate. Asn243 has previously been identified as a key residue providing substrate specificity. Mutation of Asn243 to Asp has dramatic effects on the substrate specificity, making 6-amino- and 6-oxopurines equally good as substrates. The principal effect of this particular mutation is the change in the electrostatic preorganization energy between the native enzyme and the Asn243Asp mutant, clearly favoring adenosine over inosine and guanosine. Thus, the EVB simulations show that this particular mutation affects the electrostatic preorganization of the active site, which in turn can explain the substrate specificity.
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Affiliation(s)
- Geir Villy Isaksen
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, Faculty of Science and Technology, University of Tromsø , N9037 Tromsø, Norway
| | - Kathrin Helen Hopmann
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, Faculty of Science and Technology, University of Tromsø , N9037 Tromsø, Norway
| | - Johan Åqvist
- Department of Cell & Molecular Biology, Uppsala University , SE-75124 Uppsala, Sweden
| | - Bjørn Olav Brandsdal
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, Faculty of Science and Technology, University of Tromsø , N9037 Tromsø, Norway
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Hassan AEA, Abou-Elkhair RAI, Parker WB, Allan PW, Secrist JA. 6-Methylpurine derived sugar modified nucleosides: Synthesis and evaluation of their substrate activity with purine nucleoside phosphorylases. Bioorg Chem 2015; 65:9-16. [PMID: 26745284 DOI: 10.1016/j.bioorg.2015.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 01/10/2023]
Abstract
6-Methylpurine (MeP) is cytotoxic adenine analog that does not exhibit selectivity when administered systemically, and could be very useful in a gene therapy approach to cancer treatment involving Escherichia coli PNP. The prototype MeP releasing prodrug, 9-(β-d-ribofuranosyl)-6-methylpurine, MeP-dR has demonstrated good activity against tumors expressing E. coli PNP, but its antitumor activity is limited due to toxicity resulting from the generation of MeP from gut bacteria. Therefore, we have embarked on a medicinal chemistry program to identify non-toxic MeP prodrugs that could be used in conjunction with E. coli PNP. In this work, we report on the synthesis of 9-(6-deoxy-β-d-allofuranosyl)-6-methylpurine (3) and 9-(6-deoxy-5-C-methyl-β-d-ribo-hexofuranosyl)-6-methylpurine (4), and the evaluation of their substrate activity with several phosphorylases. The glycosyl donors; 1,2-di-O-acetyl-3,5-di-O-benzyl-α-d-allofuranose (10) and 1-O-acetyl-3-O-benzyl-2,5-di-O-benzoyl-6-deoxy-5-C-methyl-β-d-ribohexofuran-ose (15) were prepared from 1,2:5,6-di-O-isopropylidine-α-d-glucofuranose in 9 and 11 steps, respectively. Coupling of 10 and 15 with silylated 6-methylpurine under Vorbrüggen glycosylation conditions followed conventional deprotection of the hydroxyl groups furnished 5'-C-methylated-6-methylpurine nucleosides 3 and 4, respectively. Unlike 9-(6-deoxy-α-l-talo-furanosyl)-6-methylpurine, which showed good substrate activity with E. coli PNP mutant (M64V), the β-d-allo-furanosyl derivative 3 and the 5'-di-C-methyl derivative 4 were poor substrates for all tested glycosidic bond cleavage enzymes.
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Affiliation(s)
- Abdalla E A Hassan
- Southern Research Institute, P.O. Box 55305, Birmingham, AL 35255-5305, USA; Applied Nucleic Acids Research Center, Zagazig University, Egypt.
| | | | - William B Parker
- Southern Research Institute, P.O. Box 55305, Birmingham, AL 35255-5305, USA; PNP Therapeutics Inc., 15 Richard Arrington Jr. Blvd North, Birmingham, AL 35203, USA
| | - Paula W Allan
- Southern Research Institute, P.O. Box 55305, Birmingham, AL 35255-5305, USA
| | - John A Secrist
- Southern Research Institute, P.O. Box 55305, Birmingham, AL 35255-5305, USA
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20
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Hassan AEA, Abou-Elkhair RAI, Parker WB, Allan PW, Secrist JA. 6-Methylpurine derived sugar modified nucleosides: Synthesis and in vivo antitumor activity in D54 tumor expressing M64V-Escherichia coli purine nucleoside phosphorylase. Eur J Med Chem 2015; 108:616-622. [PMID: 26724729 DOI: 10.1016/j.ejmech.2015.12.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 11/24/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
Impressive antitumor activity has been observed with fludarabine phosphate against tumors that express Escherichia coli purine nucleoside phosphorylase (PNP) due to the liberation of 2-fluoroadenine in the tumor tissue. 6-Methylpurine (MeP) is another cytotoxic adenine analog that does not exhibit selectivity when administered systemically, and could be very useful in a gene therapy approach to cancer treatment involving E. coli PNP. The prototype MeP releasing prodrug 9-(2-deoxy-β-d-ribofuranosyl)-6-methylpurine (1) [MeP-dR] has demonstrated good activity against tumors expressing E. coli PNP, but its antitumor activity is limited due to toxicity resulting from the generation of MeP from gut bacteria. Therefore, we have embarked on a medicinal chemistry program to identify a combination of non-toxic MeP prodrugs and non-human adenosine glycosidic bond cleaving enzymes. The two best MeP-based substrates with M64V-E coli PNP, a mutant which was engineered to tolerate modification at the 5'-position of adenosine and its analogs, were 9-(6-deoxy-α-l-talofuranosyl)-6-methylpurine (3) [methyl(talo)-MeP-R] and 9-(α-l-lyxofuranosyl)6-methylpurine (4) [lyxo-MeP-R]. The detailed synthesis methyl(talo)-MeP-R and lyxo-MeP-R, and the evaluation of their substrate activity with 4 enzymes not normally associated with cancer patients is described. In addition, we have determined the intraperitoneal pharmacokinetic (ip-PK) properties of methyl(talo)-MeP-R and have determined its in vivo bystander activity in mice bearing D54 tumors that express M64V PNP. The observed good in vivo bystander activity of [methyl(talo)-MeP-R/M64V-E coli PNP combination suggests that these agents could be useful for the treatment of cancer.
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Affiliation(s)
- Abdalla E A Hassan
- Southern Research Institute, P.O. Box 55305, Birmingham, AL, 35255-5305, USA; Applied Nucleic Acids Research Centre, Zagazig University, Zagazig, PO Box 44519, Egypt.
| | - Reham A I Abou-Elkhair
- Southern Research Institute, P.O. Box 55305, Birmingham, AL, 35255-5305, USA; Applied Nucleic Acids Research Centre, Zagazig University, Zagazig, PO Box 44519, Egypt
| | - William B Parker
- Southern Research Institute, P.O. Box 55305, Birmingham, AL, 35255-5305, USA; PNP Therapeutics Inc., 15 Richard Arrington Jr. Blvd North, Birmingham, AL, 35203, USA
| | - Paula W Allan
- Southern Research Institute, P.O. Box 55305, Birmingham, AL, 35255-5305, USA
| | - John A Secrist
- Southern Research Institute, P.O. Box 55305, Birmingham, AL, 35255-5305, USA
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Abstract
We review literature on the metabolism of ribo- and deoxyribonucleotides, nucleosides, and nucleobases in Escherichia coli and Salmonella,including biosynthesis, degradation, interconversion, and transport. Emphasis is placed on enzymology and regulation of the pathways, at both the level of gene expression and the control of enzyme activity. The paper begins with an overview of the reactions that form and break the N-glycosyl bond, which binds the nucleobase to the ribosyl moiety in nucleotides and nucleosides, and the enzymes involved in the interconversion of the different phosphorylated states of the nucleotides. Next, the de novo pathways for purine and pyrimidine nucleotide biosynthesis are discussed in detail.Finally, the conversion of nucleosides and nucleobases to nucleotides, i.e.,the salvage reactions, are described. The formation of deoxyribonucleotides is discussed, with emphasis on ribonucleotidereductase and pathways involved in fomation of dUMP. At the end, we discuss transport systems for nucleosides and nucleobases and also pathways for breakdown of the nucleobases.
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22
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Abramchik YA, Timofeev VI, Zhukhlistova NE, Muravieva TI, Esipov RS, Kuranova IP. Purification, crystallization, and preliminary X-ray diffraction study of purine nucleoside phosphorylase from E. coli. CRYSTALLOGR REP+ 2015. [DOI: 10.1134/s1063774515040021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Genome shuffling of Lactobacillus brevis for enhanced production of thymidine phosphorylase. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0617-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Campbell ER, Warsko K, Davidson AM, Bill Campbell WH. Determination of phosphate in soil extracts in the field: A green chemistry enzymatic method. MethodsX 2015; 2:211-8. [PMID: 26150991 PMCID: PMC4487730 DOI: 10.1016/j.mex.2015.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 04/21/2015] [Indexed: 11/11/2022] Open
Abstract
Measurement of ortho-phosphate in soil extracts usually involves sending dried samples of soil to a laboratory for analysis and waiting several weeks for the results. Phosphate determination methods often involve use of strong acids, heavy metals, and organic dyes. To overcome limitations of this approach, we have developed a phosphate determination method which can be carried out in the field to obtain results on the spot. This new method uses: Small volumes. An enzymatic reaction. Green chemistry.
First, the soil sample is extracted with deionized water and filtered. Next, an aliquot of the soil extract (0.5 mL) is transferred to a disposable cuvette, containing 0.5 mL of reaction mixture [200 mM HEPES, pH 7.6, 20 mM MgCl2, with 80 nmol 2-amino-6-mercapto-7-methylpurine ribonucleoside (MESG) and 1 unit of recombinant purine nucleoside phosphorylase (PNP; EC 2.4.2.1)], mixed, and incubated for 10 min at field temperature. Absorbance of the completed reaction is measured at 360 nm in open-source, portable photometer linked by bluetooth to a smartphone. The phosphate and phosphorus content of the soil is determined by comparison of its absorbance at 360 nm to a previously prepared standard phosphate curve, which is stored in the smartphone app.
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Li Y, Ding Q, Ou L, Qian Y, Zhang J. One-pot process of 2′-deoxyguanylic acid catalyzed by a multi-enzyme system. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0392-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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26
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Xu YF, Létisse F, Absalan F, Lu W, Kuznetsova E, Brown G, Caudy AA, Yakunin AF, Broach JR, Rabinowitz JD. Nucleotide degradation and ribose salvage in yeast. Mol Syst Biol 2013; 9:665. [PMID: 23670538 PMCID: PMC4039369 DOI: 10.1038/msb.2013.21] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/08/2013] [Indexed: 12/30/2022] Open
Abstract
Nucleotide degradation is a universal metabolic capability. Here we combine metabolomics, genetics and biochemistry to characterize the yeast pathway. Nutrient starvation, via PKA, AMPK/SNF1, and TOR, triggers autophagic breakdown of ribosomes into nucleotides. A protein not previously associated with nucleotide degradation, Phm8, converts nucleotide monophosphates into nucleosides. Downstream steps, which involve the purine nucleoside phosphorylase, Pnp1, and pyrimidine nucleoside hydrolase, Urh1, funnel ribose into the nonoxidative pentose phosphate pathway. During carbon starvation, the ribose-derived carbon accumulates as sedoheptulose-7-phosphate, whose consumption by transaldolase is impaired due to depletion of transaldolase's other substrate, glyceraldehyde-3-phosphate. Oxidative stress increases glyceraldehyde-3-phosphate, resulting in rapid consumption of sedoheptulose-7-phosphate to make NADPH for antioxidant defense. Ablation of Phm8 or double deletion of Pnp1 and Urh1 prevent effective nucleotide salvage, resulting in metabolite depletion and impaired survival of starving yeast. Thus, ribose salvage provides means of surviving nutrient starvation and oxidative stress.
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Affiliation(s)
- Yi-Fan Xu
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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27
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Xie X, Guo J, Kong Y, Xie GX, Li L, Lv N, Xiao X, Tang J, Wang X, Liu P, Yang M, Xie Z, Wei W, Spencer DM, Xie X. Targeted expression of Escherichia coli purine nucleoside phosphorylase and Fludara® for prostate cancer therapy. J Gene Med 2013; 13:680-91. [PMID: 22009763 DOI: 10.1002/jgm.1620] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Previous studies have shown that Herpes Simplex Virus thymidine kinase (HSV-tk)/ganciclovir (GCV) comprised the most commonly used suicide gene therapy for prostate cancer, with modest results being obtained. However, novel suicide genes, such as Escherichia coli purine nucleoside phosphorylase (PNP), have been utilized to demonstrate more potent tumor killing and an enhanced bystander effect on local, non-expressing cells compared to HSV-tk. METHODS PNP/fludarabine (Fludara®; fludarabine phosphate; Berlex Labs, Richmond, CA, USA) was deliveried by prostate-specific, rat probasin-based promoter, ARR2PB. After infection of various cell lines with ADV.ARR(2) PB-PNP and administration of androgen analog, R1881, expression of PNP mRNA was detected; in vivo, the antitumor effect of the ARR(2) PB-PNP/Fludara system was monitored and analyzed, as well as animal survival. RESULTS After in vitro infection with ADV.ARR(2) PB-PNP (multiplicity of infection = 10), LNCaP cells were more sensitive to a lower concentration Fludara (LD(50) , approximately 0.1 µg/ml) in the presence of R1881. Furthermore, robust bystander effects after R1881/Fludara treatment were observed in LNCaP cells after infection with bicistronic vector ADV.ARR2PB/PNP-IRES-EGFP in contrast to a much weaker effect in cells treated with ADV.CMV-HSV-tk/GCV. In vivo, tumor size in the ADV.ARR2PB-PNP/Fludara treatment group was dramatically smaller than in the control groups, and the mice treated with our system had a significantly prolonged survival, with three of eight mice surviving up to the 160-day termination point, as well as no systemic toxicity. CONCLUSIONS The ARR(2) PB-PNP/Fludara system induced massive tumor cell death and a prolonged life span without systemic cytotoxicity; therefore, it might be a more attractive strategy for suicide gene therapy of prostate cancer.
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Affiliation(s)
- Xinhua Xie
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, China; Department of Breast Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
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Unique substrate specificity of purine nucleoside phosphorylases from Thermus thermophilus. Extremophiles 2013; 17:505-14. [DOI: 10.1007/s00792-013-0535-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/14/2013] [Indexed: 11/27/2022]
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Enzymatic characterization of AMP phosphorylase and ribose-1,5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway. J Bacteriol 2012; 194:6847-55. [PMID: 23065974 DOI: 10.1128/jb.01335-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AMP phosphorylase (AMPpase), ribose-1,5-bisphosphate (R15P) isomerase, and type III ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) have been proposed to constitute a novel pathway involved in AMP metabolism in the Archaea. Here we performed a biochemical examination of AMPpase and R15P isomerase from Thermococcus kodakarensis. R15P isomerase was specific for the α-anomer of R15P and did not recognize other sugar compounds. We observed that activity was extremely low with the substrate R15P alone but was dramatically activated in the presence of AMP. Using AMP-activated R15P isomerase, we reevaluated the substrate specificity of AMPpase. AMPpase exhibited phosphorylase activity toward CMP and UMP in addition to AMP. The [S]-v plot (plot of velocity versus substrate concentration) of the enzyme toward AMP was sigmoidal, with an increase in activity observed at concentrations higher than approximately 3 mM. The behavior of the two enzymes toward AMP indicates that the pathway is intrinsically designed to prevent excess degradation of intracellular AMP. We further examined the formation of 3-phosphoglycerate from AMP, CMP, and UMP in T. kodakarensis cell extracts. 3-Phosphoglycerate generation was observed from AMP alone, and from CMP or UMP in the presence of dAMP, which also activates R15P isomerase. 3-Phosphoglycerate was not formed when 2-carboxyarabinitol 1,5-bisphosphate, a Rubisco inhibitor, was added. The results strongly suggest that these enzymes are actually involved in the conversion of nucleoside monophosphates to 3-phosphoglycerate in T. kodakarensis.
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Chai LC, Kong BH, Elemfareji OI, Thong KL. Variable carbon catabolism among Salmonella enterica serovar Typhi isolates. PLoS One 2012; 7:e36201. [PMID: 22662115 PMCID: PMC3360705 DOI: 10.1371/journal.pone.0036201] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 04/03/2012] [Indexed: 12/22/2022] Open
Abstract
Background Salmonella enterica serovar Typhi (S. Typhi) is strictly a human intracellular pathogen. It causes acute systemic (typhoid fever) and chronic infections that result in long-term asymptomatic human carriage. S. Typhi displays diverse disease manifestations in human infection and exhibits high clonality. The principal factors underlying the unique lifestyle of S. Typhi in its human host during acute and chronic infections remain largely unknown and are therefore the main objective of this study. Methodology/Principal Findings To obtain insight into the intracellular lifestyle of S. Typhi, a high-throughput phenotypic microarray was employed to characterise the catabolic capacity of 190 carbon sources in S. Typhi strains. The success of this study lies in the carefully selected library of S. Typhi strains, including strains from two geographically distinct areas oftyphoid endemicity, an asymptomatic human carrier, clinical stools and blood samples and sewage-contaminated rivers. An extremely low carbon catabolic capacity (27% of 190 carbon substrates) was observed among the strains. The carbon catabolic profiles appeared to suggest that S. Typhi strains survived well on carbon subtrates that are found abundantly in the human body but not in others. The strains could not utilise plant-associated carbon substrates. In addition, α-glycerolphosphate, glycerol, L-serine, pyruvate and lactate served as better carbon sources to monosaccharides in the S. Typhi strains tested. Conclusion The carbon catabolic profiles suggest that S. Typhi could survive and persist well in the nutrient depleted metabolic niches in the human host but not in the environment outside of the host. These findings serve as caveats for future studies to understand how carbon catabolism relates to the pathogenesis and transmission of this pathogen.
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Affiliation(s)
- Lay Ching Chai
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Laboratory of Biomedical Science and Molecular Microbiology, Institute of Graduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Boon Hong Kong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Laboratory of Biomedical Science and Molecular Microbiology, Institute of Graduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Omar Ismail Elemfareji
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Laboratory of Biomedical Science and Molecular Microbiology, Institute of Graduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Kwai Lin Thong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Laboratory of Biomedical Science and Molecular Microbiology, Institute of Graduate Studies, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
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Buckoreelall K, Sun Y, Hobrath JV, Wilson L, Parker WB. Identification of Rv0535 as methylthioadenosine phosphorylase from Mycobacterium tuberculosis. Tuberculosis (Edinb) 2012; 92:139-47. [PMID: 22225784 DOI: 10.1016/j.tube.2011.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/21/2011] [Accepted: 11/28/2011] [Indexed: 10/14/2022]
Abstract
5'-methylthioadenosine (MTA) is a natural purine that is metabolized by methylthioadenosine phosphorylase (MTAP, E.C 2.4.2.28) in Eukarya and Archaea but generally not in bacteria. In this work, Rv0535, which has been annotated as a probable MTAP in Mycobacterium tuberculosis, was expressed in and purified from Escherichia coli BL21 (DE3). The purified protein displayed properties of a phosphorylase and MTA was the preferred substrate. Adenosine and S-adenosyl-l-homocysteine were poor substrates and no activity was detected with 5'-methylthioinosine, the other natural purines, or the natural pyrimidines. Kinetic analysis of M. tuberculosis MTAP showed that the K(m) value for MTA was 9 μM. Rv0535 was estimated as a 30 kDa protein on a denaturing SDS-PAGE gel, which agreed with the molecular mass predicted by its gene sequence. Using gel filtration chromatography, the native molecular mass of the enzyme was determined to be 60 ± 4 kDa, and thus indicated that M. tuberculosis MTAP is a dimer. Differences in active site between mycobacterial and human MTAPs were identified by homology modeling based on the crystal of the human enzyme. A complete structure-activity relationship analysis could identify differences in substrate specificity between the two enzymes to aid in the development of purine-based, anti-tuberculosis drugs.
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Affiliation(s)
- Kajal Buckoreelall
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, 1530 Third Avenue South, Birmingham, AL 35294, USA
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Identification and characterization of two adenosine phosphorylase activities in Mycobacterium smegmatis. J Bacteriol 2011; 193:5668-74. [PMID: 21821769 DOI: 10.1128/jb.05394-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purine nucleoside phosphorylase (PNP) is an important enzyme in purine metabolism and cleaves purine nucleosides to their respective bases. Mycobacterial PNP is specific for 6-oxopurines and cannot account for the adenosine (Ado) cleavage activity that has been detected in M. tuberculosis and M. smegmatis cultures. In the current work, two Ado cleavage activities were identified from M. smegmatis cell extracts. The first activity was biochemically determined to be a phosphorylase that could reversibly catalyze adenosine + phosphate ↔ adenine + alpha-D-ribose-1-phosphate. Our purification scheme led to a 30-fold purification of this activity, with the removal of more than 99.9% of total protein. While Ado was the preferred substrate, inosine and guanosine were also cleaved, with 43% and 32% of the Ado activity, respectively. Our data suggest that M. smegmatis expresses two PNPs: a previously described trimeric PNP that can cleave inosine and guanosine only and a second, novel PNP (Ado-PNP) that can cleave Ado, inosine, and guanosine. Ado-PNP had an apparent K(m) (K(m) ( app)) of 98 ± 6 μM (with Ado) and a native molecular mass of 125 ± 7 kDa. The second Ado cleavage activity was identified as 5'-methylthioadenosine phosphorylase (MTAP) based on its biochemical properties and mass spectrometry analysis. Our study marks the first report of the existence of MTAP in any bacterium. Since human cells do not readily convert Ado to Ade, an understanding of the substrate preferences of these enzymes could lead to the identification of Ado analogs that could be selectively activated to toxic products in mycobacteria.
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Luo W, Liu Y, Zhu X, Zhao W, Huang L, Cai J, Xu Z, Cen P. Cloning and characterization of purine nucleoside phosphorylase in Escherichia coli and subsequent ribavirin biosynthesis using immobilized recombinant cells. Enzyme Microb Technol 2011; 48:438-44. [DOI: 10.1016/j.enzmictec.2011.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Revised: 03/15/2011] [Accepted: 03/18/2011] [Indexed: 11/25/2022]
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Accumulation of gene-targeted Bacillus subtilis mutations that enhance fermentative inosine production. Appl Microbiol Biotechnol 2010; 87:2195-207. [PMID: 20524113 DOI: 10.1007/s00253-010-2646-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 04/21/2010] [Accepted: 04/22/2010] [Indexed: 10/19/2022]
Abstract
In order to test a possible approach to enhance fermentative inosine production by Bacillus subtilis, seven gene-targeted mutations were introduced in the laboratory standard strain168 in a stepwise fashion. The mutations were employed in order to prevent inosine 5'-monophosphate (IMP) from being consumed for AMP and GMP synthesis, to minimize inosine degradation, and to expand the intracellular IMP pool. First, the genes for adenylosuccinate synthase (purA) and IMP dehydrogenase (guaB) were inactivated. Second, two genes for purine nucleoside phosphorylase, punA and deoD, were inactivated. Third, to enhance purine nucleotide biosynthesis, the pur operon repressor PurR and the 5'-UTR of the operon, containing the guanine riboswitch, were disrupted. Finally, the -10 sequence of the pur promoter was optimized to elevate its transcription level. The resulting mutant was capable of producing 6 g/L inosine from 30 g/L glucose in culture broth without the detectable by-production of hypoxanthine. This indicates the validity of this approach for the breeding of the next generation of B. subtilis strains for industrial nucleoside production.
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Hassan AEA, Parker WB, Allan PW, Secrist JA. Regioselective metalation of 6-methylpurines: synthesis of fluoromethyl purines and related nucleosides for suicide gene therapy of cancer. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 28:642-56. [PMID: 20183607 DOI: 10.1080/15257770903091938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Metalation of 6-methyl-9-(tetrahydro-2H-pyran-2-yl)purine (10) with lithiating agents of varying basicities such as n-BuLi and LiHMDS in THF at -78 degrees C resulted in metalation at both of the 6-CH(3) moiety and the 8-CH position, irrespective of the molar equivalence of the base. On the other hand, a regioselective metalation at the 6-CH(3) moiety of 10 was observed with NaHMDS or KHMDS, under similar conditions. Treatment of the potassium salts of 10 and of the protected riboside derivative 6-methyl-9-(beta-D-2,3,5-tri-O-tert-butyldimethylsilylribofuranosyl)purine (22) with N-fluorobenzenesulfonamide (NFSI) at -78 degrees C gave the corresponding 6-fluoromethylpurine derivatives 11 and 23, respectively, in good yields. Deprotection of 11 and 23 under standard conditions gave 6-fluoromethylpurine (6-FMeP, 3) and 6-fluoromethyl-9-(beta-D-ribofuranosyl)purine (6-FMePR, 4), respectively, in high yield. Both 3 and 4 demonstrated cytotoxic activity against CCRF-CEM cells in culture. 6-FMePR is a good substrate for E. coli purine nucleoside phosphorylase (E. coli PNP) with a comparable substrate activity to that of the parent nucleoside, 6-methyl-9-(beta-D-ribofuranosyl)purine (6-MePR, 21). The cytotoxic activity of 6-FMeP along with the substrate activity of 6-FMePR with E. coli PNP meet the fundamental requirements for using 6-FMeP as a potential toxin in PNP/prodrug based cancer gene therapy.
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Affiliation(s)
- Abdalla E A Hassan
- Southern Research Institute, Drug Discovery Division, Birmingham, Alabama, USA
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36
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Pal S, Nair V. Enzymatic Synthesis of Thymidine Using Bacterial Whole Cells and Isolated Purine Nucleoside Phosphorylase. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.3109/10242429709003615] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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37
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Ducati RG, Santos DS, Basso LA. Substrate specificity and kinetic mechanism of purine nucleoside phosphorylase from Mycobacterium tuberculosis. Arch Biochem Biophys 2009; 486:155-64. [DOI: 10.1016/j.abb.2009.04.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 04/23/2009] [Accepted: 04/29/2009] [Indexed: 10/20/2022]
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38
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Co-Expression of Recombinant Nucleoside Phosphorylase from Escherichia coli and its Application. Appl Biochem Biotechnol 2008; 159:168-77. [DOI: 10.1007/s12010-008-8429-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Accepted: 10/31/2008] [Indexed: 10/21/2022]
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39
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Fu W, Lan H, Liang S, Gao T, Ren D. Suicide gene/prodrug therapy using salmonella-mediated delivery of Escherichia coli purine nucleoside phosphorylase gene and 6-methoxypurine 2'-deoxyriboside in murine mammary carcinoma 4T1 model. Cancer Sci 2008; 99:1172-9. [PMID: 18429958 PMCID: PMC11158249 DOI: 10.1111/j.1349-7006.2008.00808.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 02/18/2008] [Accepted: 02/20/2008] [Indexed: 11/26/2022] Open
Abstract
Attenuated salmonella have been reported to be capable of both selectively growing in tumors and expressing exogenous genes for tumor-targeted therapy. As 6-methoxypurine 2'-deoxyriboside (MoPdR) is similar to 6-methylpurine 2'-deoxyriboside in structure, we aimed to evaluate the antitumoral effect of the Escherichia coli purine nucleoside phosphorylase (ePNP) gene, using an attenuated salmonella-mediated delivery system, in combination with MoPdR. A novel mutant serovar Typhimurium (SC36) was used to carry the pEGFP-C1-ePNP vector that contains an enhanced green fluorescent protein and an ePNP gene under the control of the cytomegalovirus promoter. The function of the ePNP expression vector was confirmed in vitro using the enzymic conversion of MoPdR into methoxypurine. We also observed a high bystander effect induced by the ePNP/MoPdR system with a very low proportion (1%) of ePNP-positive cells and 5 microg/mL MoPdR, although the growth of parental cells was affected appreciably by MoPdR. The killing effect and increased apoptosis induced by SC36 carrying the ePNP expression vector (SC/ePNP) were detected by cytotoxicity assay and propidium iodide staining flow cytometry analysis, in combination with MoPdR. SC/ePNP was given orally to mice bearing mammary carcinomas, and its antitumor effect was evaluated. SC/ePNP plus MoPdR significantly inhibited tumor growth by approximately 86.6-88.7% and prolonged the survival of tumor-hosting mice. Our data support the view that MoPdR combined with the ePNP gene could be used in gene-directed enzyme prodrug therapy. Attenuated salmonella could be a promising strategy to improve ePNP/MoPdR bystander killing due to its preferential accumulation and anticancer activity in tumors.
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MESH Headings
- Animals
- Apoptosis/physiology
- Blotting, Western
- Bystander Effect
- Caspase 3/metabolism
- Cell Proliferation
- Combined Modality Therapy
- Escherichia coli/enzymology
- Female
- Genes, Transgenic, Suicide
- Genetic Therapy
- Genetic Vectors
- Green Fluorescent Proteins/genetics
- Humans
- Mammary Neoplasms, Experimental/drug therapy
- Mammary Neoplasms, Experimental/pathology
- Mammary Neoplasms, Experimental/therapy
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Prodrugs/therapeutic use
- Promoter Regions, Genetic
- Purine Nucleosides/therapeutic use
- Purine-Nucleoside Phosphorylase/genetics
- Salmonella/genetics
- Transcription, Genetic
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Wei Fu
- The State Key Laboratory of Genetic Engineering, Institute of Genetics, Fudan University, 220 Han Dan Road, Shanghai 200433, China
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40
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Fu W, Lan H, Li S, Han X, Gao T, Ren D. Synergistic antitumor efficacy of suicide/ePNP gene and 6-methylpurine 2'-deoxyriboside via Salmonella against murine tumors. Cancer Gene Ther 2008; 15:474-84. [PMID: 18437183 DOI: 10.1038/cgt.2008.19] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Some anaerobes and facultative anaerobes have been used in tumor-specific gene therapy by reason of their selective growth in tumors. In this work, we aimed to evaluate the anticancer efficacy of attenuated Salmonella typhimurium as a carrier to deliver the Escherichia coli purine nucleoside phosphorylase (ePNP) gene for GDEPT (gene-directed enzyme-prodrug therapy). A live attenuated purine-auxotrophic strain of S. typhimurium (SC36) was used to carry the pEGFP-C1-ePNP vector that contains a green fluorescent protein (GFP) and an ePNP gene under the control of the human cytomegalovirus (CMV) promoter. The function of the ePNP expression vector was confirmed in vitro using the enzymic conversion of 6-methylpurine 2'-deoxyriboside (MePdR) into 6-methylpurine. We also observed a high bystander effect induced by the ePNP/MePdR system with a very low proportion (1%) of ePNP-positive cells. The killing effect and increased apoptosis induced by SC/ePNP (SC36 carrying the ePNP expression vector) infection were detected by cytotoxicity assay and PI staining flow cytometry analysis, in combination with MePdR administration. Furthermore, SC/ePNP was administered orally into mice bearing melanomas or pulmonary tumors, and its anti-tumor effect was evaluated. When the tumor was huge (500 mm(3)) at the beginning of MePdR administration, SC/ePNP plus MepdR significantly inhibited tumor growth by about 59-80% and prolonged survival of mice. Complete tumor regression and long-term cure were achieved by MePdR administration, even when the tumor was large (100 mm(3)) at the beginning of MePdR treatment. Our data support a hopeful view that tumor-targeting SC36 could improve antitumor efficacy of the ePNP/MePdR system due to its preferential accumulation and anticancer activity in tumors.
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Affiliation(s)
- W Fu
- State Key Lab of Genetic Engineering, Department of Genetics, Fudan University, Shanghai, China
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41
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Purine nucleoside phosphorylase from Pseudoalteromonas sp. Bsi590: molecular cloning, gene expression and characterization of the recombinant protein. Extremophiles 2008; 12:325-33. [DOI: 10.1007/s00792-007-0131-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Accepted: 11/22/2007] [Indexed: 10/22/2022]
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42
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Sgarrella F, Frassetto L, Allegrini S, Camici M, Carta MC, Fadda P, Tozzi MG, Ipata PL. Characterization of the adenine nucleoside specific phosphorylase of Bacillus cereus. Biochim Biophys Acta Gen Subj 2007; 1770:1498-505. [PMID: 17707115 DOI: 10.1016/j.bbagen.2007.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Revised: 07/02/2007] [Accepted: 07/05/2007] [Indexed: 11/30/2022]
Abstract
Adenosine phosphorylase, a purine nucleoside phosphorylase endowed with high specificity for adenine nucleosides, was purified 117-fold from vegetative forms of Bacillus cereus. The purification procedure included ammonium sulphate fractionation, pH 4 treatment, ion exchange chromatography on DEAE-Sephacel, gel filtration on Sephacryl S-300 HR and affinity chromatography on N(6)-adenosyl agarose. The enzyme shows a good stability to both temperature and pH. It appears to be a homohexamer of 164+/-5 kDa. Kinetic characterization confirmed the specificity of this phosphorylase for 6-aminopurine nucleosides. Adenosine was the preferred substrate for nucleoside phosphorolysis (k(cat)/K(m) 2.1x10(6) s(-1) M(-1)), followed by 2'-deoxyadenosine (k(cat)/K(m) 4.2x10(5) s(-1) M(-1)). Apparently, the low specificity of adenosine phosphorylase towards 6-oxopurine nucleosides is due to a slow catalytic rate rather than to poor substrate binding.
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Affiliation(s)
- Francesco Sgarrella
- Dipartimento di Scienze del Farmaco, Università di Sassari, via F. Muroni 23a, 07100 Sassari, Italy.
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Modrak-Wójcik A, Kirilenko A, Shugar D, Kierdaszuk B. Role of ionization of the phosphate cosubstrate on phosphorolysis by purine nucleoside phosphorylase (PNP) of bacterial (E. coli) and mammalian (human) origin. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 37:153-64. [PMID: 17639373 DOI: 10.1007/s00249-007-0205-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2007] [Revised: 05/31/2007] [Accepted: 06/12/2007] [Indexed: 10/23/2022]
Abstract
Kinetics of the reactions of purine nucleoside phosphorylases (PNP) from E. coli (PNP-I, the product of the deoD gene) and human erythrocytes with their natural substrates guanosine (Guo), inosine (Ino), a substrate analogue N(7)-methylguanosine (m(7)Guo), and orthophosphate (P(i), natural cosubstrate) and its thiophosphate analogue (SP(i)), found to be a weak cosubstrate, have been studied in the pH range 5-8. In this pH range Guo and Ino exist predominantly in the neutral forms (pK(a) 9.2 and 8.8); m(7)Guo consists of an equilibrium mixture of the cationic and zwitterionic forms (pK(a) 7.0); and P(i) and SP(i) exhibit equilibria between monoanionic and dianionic forms (pK(a) 6.7 and 5.4, respectively). The phosphorolysis of m(7)Guo (at saturated concentration) with both enzymes exhibits Michaelis kinetics with SP(i), independently of pH. With P(i), the human enzyme shows Michaelis kinetics only at pH approximately 5. However, in the pH range 5-8 for the bacterial enzyme, and 6-8 for the human enzyme, enzyme kinetics with P(i) are best described by a model with high- and low-affinity states of the enzymes, denoted as enzyme-substrate complexes with one or two active sites occupied by P(i), characterized by two sets of enzyme-substrate dissociation constants (apparent Michaelis constants, K (m1) and K (m2)) and apparent maximal velocities (V (max1) and V (max2)). Their values, obtained from non-linear least-squares fittings of the Adair equation, were typical for negative cooperativity of both substrate binding (K (m1) < K (m2)) and enzyme kinetics (V (max1)/K (m1) > V (max2)/K (m2)). Comparison of the pH-dependence of the substrate properties of P(i) versus SP(i) points to both monoanionic and dianionic forms of P(i) as substrates, with a marked preference for the dianionic species in the pH range 5-8, where the population of the P(i) dianion varies from 2 to 95%, reflected by enzyme efficiency three orders of magnitude higher at pH 8 than that at pH 5. This is accompanied by an increase in negative cooperativity, characterized by a decrease in the Hill coefficient from n (H) approximately 1 to n (H) approximately 0.7 for Guo with the human enzyme, and to n (H) approximately 0.7 and 0.5 for m(7)Guo with the E. coli and human enzymes, respectively. Possible mechanisms of cooperativity are proposed. Attention is drawn to the substrate properties of SP(i) in relation to its structure.
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Affiliation(s)
- Anna Modrak-Wójcik
- Department of Biophysics, Institute of Experimental Physics, University of Warsaw, Warsaw, Poland
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44
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Nanduri B, Lawrence ML, Boyle CR, Ramkumar M, Burgess SC. Effects of subminimum inhibitory concentrations of antibiotics on the Pasteurella multocida proteome. J Proteome Res 2007; 5:572-80. [PMID: 16512672 DOI: 10.1021/pr050360r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Subminimum inhibitory concentrations (sub-MICs) of antibiotics can be therapeutically effective, but the underlying molecular mechanisms are not well-characterized. We analyzed the Pasteurella multocida proteome response to sub-MICs of amoxicillin, chlortetracycline, and enrofloxacin using isotope-coded affinity tags (ICAT). There were parallel effects on inhibition of growth kinetics and suppression of protein expression by clusters of orthologous groups (COG) categories. Potential compensatory mechanisms enabling antibiotic adaptation were identified, including increased RecA expression caused by enrofloxacin.
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Affiliation(s)
- Bindu Nanduri
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762, USA
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45
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Hansen MR, Tranekjaer Jørgensen J, Dandanell G. Xanthosine utilization in Salmonella enterica serovar Typhimurium is recovered by a single aspartate-to-glycine substitution in xanthosine phosphorylase. J Bacteriol 2006; 188:4153-7. [PMID: 16707709 PMCID: PMC1482901 DOI: 10.1128/jb.01926-05] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
xapABR from Salmonella enterica was analyzed and compared with the corresponding Escherichia coli genes. xapB and xapR, but not xapA, encode functional proteins. An S. enterica XapA(Asp72Gly) mutant that restores the phosphorolytic activity was selected. The purified mutant enzyme has different kinetic constants than the E. coli enzyme but similar substrate specificity.
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Affiliation(s)
- Michael Riis Hansen
- Department of Biological Chemistry, Institute of Molecular Biology and Physiology, University of Copenhagen, Sølvgade 83 H, 1307 Copenhagen K, Denmark
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46
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Modrak-Wójcik A, Stepniak K, Akoev V, Zółkiewski M, Bzowska A. Molecular architecture of E. coli purine nucleoside phosphorylase studied by analytical ultracentrifugation and CD spectroscopy. Protein Sci 2006; 15:1794-800. [PMID: 16751611 PMCID: PMC2242567 DOI: 10.1110/ps.062183206] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Purine nucleoside phosphorylase (PNP) is a key enzyme of the nucleoside salvage pathway and is characterized by complex kinetics. It was suggested that this is due to coexistence of various oligomeric forms that differ in specific activity. In this work, the molecular architecture of Escherichia coli PNP in solution was studied by analytical ultracentrifugation and CD spectroscopy. Sedimentation equilibrium analysis revealed a homohexameric molecule with molecular mass 150+/-10 kDa, regardless of the conditions investigated-protein concentration, 0.18-1.7 mg/mL; presence of up to 10 mM phosphate and up to 100 mM KCl; temperature, 4-20 degrees C. The parameters obtained from the self-associating model also describe the hexameric form. Sedimentation velocity experiments conducted for broad protein concentration range (1 microg/mL-1.3 mg/mL) with boundary (classical) and band (active enzyme) approaches gave s(0)20,w=7.7+/-0.3 and 8.3+/-0.4 S, respectively. The molecular mass of the sedimenting particle (146+/-30 kDa), calculated using the Svedberg equation, corresponds to the mass of the hexamer. Relative values of the CD signal at 220 nm and the catalytic activity of PNP as a function of GdnHCl concentration were found to be correlated. The transition from the native state to the random coil is a single-step process. The sedimentation coefficient determined at 1 M GdnHCl (at which the enzyme is still fully active) is 7.7 S, showing that also under these conditions the hexamer is the only catalytically active form. Hence, in solution similar to the crystal, E. coli PNP is a hexameric molecule and previous suggestions for coexistence of two oligomeric forms are incorrect.
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Affiliation(s)
- Anna Modrak-Wójcik
- Department of Biophysics, Institute of Experimental Physics, University of Warsaw, Poland
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47
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Tozzi MG, Camici M, Mascia L, Sgarrella F, Ipata PL. Pentose phosphates in nucleoside interconversion and catabolism. FEBS J 2006; 273:1089-101. [PMID: 16519676 DOI: 10.1111/j.1742-4658.2006.05155.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribose phosphates are either synthesized through the oxidative branch of the pentose phosphate pathway, or are supplied by nucleoside phosphorylases. The two main pentose phosphates, ribose-5-phosphate and ribose-1-phosphate, are readily interconverted by the action of phosphopentomutase. Ribose-5-phosphate is the direct precursor of 5-phosphoribosyl-1-pyrophosphate, for both de novo and 'salvage' synthesis of nucleotides. Phosphorolysis of deoxyribonucleosides is the main source of deoxyribose phosphates, which are interconvertible, through the action of phosphopentomutase. The pentose moiety of all nucleosides can serve as a carbon and energy source. During the past decade, extensive advances have been made in elucidating the pathways by which the pentose phosphates, arising from nucleoside phosphorolysis, are either recycled, without opening of their furanosidic ring, or catabolized as a carbon and energy source. We review herein the experimental knowledge on the molecular mechanisms by which (a) ribose-1-phosphate, produced by purine nucleoside phosphorylase acting catabolically, is either anabolized for pyrimidine salvage and 5-fluorouracil activation, with uridine phosphorylase acting anabolically, or recycled for nucleoside and base interconversion; (b) the nucleosides can be regarded, both in bacteria and in eukaryotic cells, as carriers of sugars, that are made available though the action of nucleoside phosphorylases. In bacteria, catabolism of nucleosides, when suitable carbon and energy sources are not available, is accomplished by a battery of nucleoside transporters and of inducible catabolic enzymes for purine and pyrimidine nucleosides and for pentose phosphates. In eukaryotic cells, the modulation of pentose phosphate production by nucleoside catabolism seems to be affected by developmental and physiological factors on enzyme levels.
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Affiliation(s)
- Maria G Tozzi
- Dipartimento di Biologia, Laboratorio di Biochimica, Pisa, Italy
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48
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Komatsu H, Araki T. Efficient chemo-enzymatic syntheses of pharmaceutically useful unnatural 2'-deoxynucleosides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:1127-30. [PMID: 16248106 DOI: 10.1081/ncn-200060154] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Our chemo-enzymatic method was successfully applied to the synthesis of 2-chloro-2'-deoxyadenosine (CdA, cladribine) in two ways: 1) direct conversion of chemically synthesized 2-deoxy-alpha-D-ribose 1-phosphate (dRP) to CdA; 2) a two-step route via 9-(2-deoxy-beta-D-ribos-1-yl)-2, 6-dichloropurine (Cl2Pu-dR, 5).
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Affiliation(s)
- Hironori Komatsu
- Catalysis Science Laboratory, Mitsui Chemicals, Inc., Chiba, Japan
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49
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Parker WB, Allan PW, Ealick SE, Sorscher EJ, Hassan AEA, Silamkoti AV, Fowler AT, Waud WR, Secrist JA. Design and evaluation of 5'-modified nucleoside analogs as prodrugs for an E. coli purine nucleoside phosphorylase mutant. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:387-92. [PMID: 16247956 DOI: 10.1081/ncn-200059807] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Our studies have led to the identification of an E. coli PNP mutant (M64V) that is able to cleave numerous 5'-modified nucleoside analogs with much greater efficiency than the wild-type enzyme. The biological activity of the three best substrates of this mutant (9-[6-deoxy-alpha-L-talofuranosyl]-6-methylpurine (methyl(talo)-MeP-R), 9-[6-deoxy-alpha-L-talofuranosyl]-2-F-adenine, and 9-[alpha-L-lyxofuranosyl]-2-F-adenine) were evaluated so that we can optimally utilize these compounds. Our results indicated that the mechanism of toxicity of methyl(talo)-MeP-R to mice was due to its cleavage to MeP by a bacterial enzyme, and that the toxicity of the two F-Ade analogs was due to their cleavage to F-Ade by mammalian methylthioadenosine phosphorylase.
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Affiliation(s)
- William B Parker
- Southern Research Institute, 2000 Ninth Ave., South, Birmingham, AL 35205, USA.
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50
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Bharara S, Sorscher EJ, Gillespie GY, Lindsey JR, Hong JS, Curlee KV, Allan PW, Gadi VK, Alexander SA, Secrist JA, Parker WB, Waud WR. Antibiotic-mediated chemoprotection enhances adaptation of E. coli PNP for herpes simplex virus-based glioma therapy. Hum Gene Ther 2005; 16:339-47. [PMID: 15812229 DOI: 10.1089/hum.2005.16.339] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The E. coli PNP suicide gene sensitizes solid tumors to nucleoside prodrugs, such as 6-methylpurine-2'-deoxyriboside (MeP-dR). In this study using lentiviral, MuLv, and HSV-based gene transfer, we quantified thresholds for inhibition of tumor growth and bystander killing by E. coli PNP and tested the role of intestinal flora in this process. Regressions of human glioma tumors following retroviral transduction exhibited dose dependence on both the level of PNP expression and the dose of MeP-dR administered, including strong tumor inhibition when 90-99% bystander cells comprised the tumor mass. A replication competent, non-neurovirulent herpes simplex virus (HSV) deficient in both copies of the gamma-1 34.5 gene was next engineered to express E. coli PNP under the egr-1 promoter (HSV-PNP). HSV-PNP injected intratumorally (17 million pfu/0.05 ml) in nude mice bearing 300 mg human glioma flank tumors produced a delay in tumor growth (approximately 24 days delay to one doubling). MeP-dR treatment after antibiotic therapy (to eliminate enteric flora encoding PNP enzymes) resulted in antitumor enhancement, with arrest of tumor growth (delay to doubling >50 days). Bystander killing of the magnitude described here has been difficult to accomplish with other suicide genes, such as HSV-tk or cytosine deaminase. The results establish a model for applying E. coli PNP to HSV treatment of glioma.
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Affiliation(s)
- Suman Bharara
- Department of Surgery, University of Alabama at Birmingham, AL 35294, USA
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