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Pfeiffer M, Ribar A, Nidetzky B. A selective and atom-economic rearrangement of uridine by cascade biocatalysis for production of pseudouridine. Nat Commun 2023; 14:2261. [PMID: 37081027 PMCID: PMC10116470 DOI: 10.1038/s41467-023-37942-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/06/2023] [Indexed: 04/22/2023] Open
Abstract
As a crucial factor of their therapeutic efficacy, the currently marketed mRNA vaccines feature uniform substitution of uridine (U) by the corresponding C-nucleoside, pseudouridine (Ψ), in 1-N-methylated form. Synthetic supply of the mRNA building block (1-N-Me-Ψ-5'-triphosphate) involves expedient access to Ψ as the principal challenge. Here, we show selective and atom-economic 1N-5C rearrangement of β-D-ribosyl on uracil to obtain Ψ from unprotected U in quantitative yield. One-pot cascade transformation of U in four enzyme-catalyzed steps, via D-ribose (Rib)-1-phosphate, Rib-5-phosphate (Rib5P) and Ψ-5'-phosphate (ΨMP), gives Ψ. Coordinated function of the coupled enzymes in the overall rearrangement necessitates specific release of phosphate from the ΨMP, but not from the intermediary ribose phosphates. Discovery of Yjjg as ΨMP-specific phosphatase enables internally controlled regeneration of phosphate as catalytic reagent. With driving force provided from the net N-C rearrangement, the optimized U reaction yields a supersaturated product solution (∼250 g/L) from which the pure Ψ crystallizes (90% recovery). Scale up to 25 g isolated product at enzyme turnovers of ∼105 mol/mol demonstrates a robust process technology, promising for Ψ production. Our study identifies a multistep rearrangement reaction, realized by cascade biocatalysis, for C-nucleoside synthesis in high efficiency.
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Affiliation(s)
- Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010, Graz, Austria
- Austrian Centre of Industrial Biotechnology (acib), Krenngasse 37, A-8010, Graz, Austria
| | - Andrej Ribar
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010, Graz, Austria
- Austrian Centre of Industrial Biotechnology (acib), Krenngasse 37, A-8010, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010, Graz, Austria.
- Austrian Centre of Industrial Biotechnology (acib), Krenngasse 37, A-8010, Graz, Austria.
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2
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Baek YY, Sung B, Choi JS, Go HK, Kim DH, Hyon JY, You JC. In Vivo Efficacy of Imatinib Mesylate, a Tyrosine Kinase Inhibitor, in the Treatment of Chemically Induced Dry Eye in Animal Models. Transl Vis Sci Technol 2021; 10:14. [PMID: 34520512 PMCID: PMC8444463 DOI: 10.1167/tvst.10.11.14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Purpose Dry eye disease (DED) is a multifactorial disorder of the tears and ocular surface accompanied by ocular discomfort, visual disturbance, tear film instability, and ocular surface inflammation. In the present study, we evaluated the efficacy of the tyrosine kinase inhibitor imatinib mesylate for the treatment of DED. Methods Experimental models of DED were generated in Sprague Dawley rats using a combination of benzalkonium chloride (BAC) with atropine sulfate and in New Zealand White rabbits using BAC. The animals were treated twice daily with eye drops of vehicle, imatinib (0.01%-0.3%), or a positive control (Restasis). The improvement in DED due to imatinib was assessed by staining with fluorescein, lissamine green, impression cytology, and histological analysis. In addition, immunofluorescence staining was performed at the end of the study to evaluate the inflammatory response in the ocular surface. Results Topical application of imatinib significantly reduced ocular surface damage compared with vehicle-treated animals. Imatinib restored the morphology and structure of the conjunctival epithelium and reduced the recruitment of immune cells in the corneal epithelium. Furthermore, imatinib significantly reduced the impression cytology score, thus demonstrating that imatinib prevents the loss of goblet cells in DED animal models. The therapeutic efficacy of imatinib was similar to or better than that of cyclosporine treatment. Conclusions In this study, we provide an animal in vivo proof of concept of the therapeutic potential of imatinib for the treatment of DED. Translational Relevance With this study we show the possibility of developing imatinib as a new ophthalmic drop to treat DED.
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Affiliation(s)
| | | | | | | | | | - Joon Young Hyon
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Ji Chang You
- Avixgen Inc., Seoul, Republic of Korea.,National Research Laboratory for Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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3
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Smith JP, Obligacion JV, Dance ZEX, Lomont JP, Ralbovsky NM, Bu X, Mann BF. Investigation of Lithium Acetyl Phosphate Synthesis Using Process Analytical Technology. Org Process Res Dev 2021. [DOI: 10.1021/acs.oprd.1c00091] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Joseph P. Smith
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Jennifer V. Obligacion
- Small Molecule Process Research & Development, MRL, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Zachary E. X. Dance
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Justin P. Lomont
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Nicole M. Ralbovsky
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Xiaodong Bu
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Benjamin F. Mann
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
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4
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Patel NR, Huffman MA, Wang X, Ding B, McLaughlin M, Newman JA, Andreani T, Maloney KM, Johnson HC, Whittaker AM. Five-Step Enantioselective Synthesis of Islatravir via Asymmetric Ketone Alkynylation and an Ozonolysis Cascade. Chemistry 2020; 26:14118-14123. [PMID: 32710473 DOI: 10.1002/chem.202003091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/20/2020] [Indexed: 11/10/2022]
Abstract
A 5-step enantioselective synthesis of the potent anti-HIV nucleoside islatravir is reported. The highly efficient route was enabled by a novel enantioselective alkynylation of an α,β-unsaturated ketone, a unique ozonolysis-dealkylation cascade in water, and an enzymatic aldol-glycosylation cascade.
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Affiliation(s)
- Niki R Patel
- Department of Process Research and Development, MRL, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Mark A Huffman
- Department of Process Research and Development, MRL, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Xiao Wang
- Department of Process Research and Development, MRL, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Bangwei Ding
- Department of Process Research and Development, MRL, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Mark McLaughlin
- Department of Process Research and Development, MRL, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Justin A Newman
- Department of Process Research and Development, MRL, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Teresa Andreani
- Department of Process Research and Development, MRL, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Kevin M Maloney
- Department of Process Research and Development, MRL, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Heather C Johnson
- Department of Process Research and Development, MRL, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Aaron M Whittaker
- Department of Process Research and Development, MRL, Merck & Co., Inc., Rahway, NJ, 07065, USA
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5
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Nawrat CC, Whittaker AM, Huffman MA, McLaughlin M, Cohen RD, Andreani T, Ding B, Li H, Weisel M, Tschaen DM. Nine-Step Stereoselective Synthesis of Islatravir from Deoxyribose. Org Lett 2020; 22:2167-2172. [PMID: 32108487 DOI: 10.1021/acs.orglett.0c00239] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A stereoselective nine-step synthesis of the potent HIV nucleoside reverse transcriptase translocation inhibitor (NRTTI) islatravir (EfdA, MK-8591) from 2-deoxyribose is described. Key findings include a diastereodivergent addition of an acetylide nucleophile to an enolizable ketone, a chemoselective ozonolysis of a terminal olefin and a biocatalytic glycosylation cascade that uses a unique strategy of byproduct precipitation to drive an otherwise-reversible transformation forward.
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Affiliation(s)
- Christopher C Nawrat
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Aaron M Whittaker
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Mark A Huffman
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Mark McLaughlin
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ryan D Cohen
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Teresa Andreani
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Bangwei Ding
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Hongming Li
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Mark Weisel
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - David M Tschaen
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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6
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Huffman MA, Fryszkowska A, Alvizo O, Borra-Garske M, Campos KR, Canada KA, Devine PN, Duan D, Forstater JH, Grosser ST, Halsey HM, Hughes GJ, Jo J, Joyce LA, Kolev JN, Liang J, Maloney KM, Mann BF, Marshall NM, McLaughlin M, Moore JC, Murphy GS, Nawrat CC, Nazor J, Novick S, Patel NR, Rodriguez-Granillo A, Robaire SA, Sherer EC, Truppo MD, Whittaker AM, Verma D, Xiao L, Xu Y, Yang H. Design of an in vitro biocatalytic cascade for the manufacture of islatravir. Science 2019; 366:1255-1259. [DOI: 10.1126/science.aay8484] [Citation(s) in RCA: 238] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/24/2019] [Indexed: 12/14/2022]
Abstract
Enzyme-catalyzed reactions have begun to transform pharmaceutical manufacturing, offering levels of selectivity and tunability that can dramatically improve chemical synthesis. Combining enzymatic reactions into multistep biocatalytic cascades brings additional benefits. Cascades avoid the waste generated by purification of intermediates. They also allow reactions to be linked together to overcome an unfavorable equilibrium or avoid the accumulation of unstable or inhibitory intermediates. We report an in vitro biocatalytic cascade synthesis of the investigational HIV treatment islatravir. Five enzymes were engineered through directed evolution to act on non-natural substrates. These were combined with four auxiliary enzymes to construct islatravir from simple building blocks in a three-step biocatalytic cascade. The overall synthesis requires fewer than half the number of steps of the previously reported routes.
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Affiliation(s)
- Mark A. Huffman
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Anna Fryszkowska
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Oscar Alvizo
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | | | - Kevin R. Campos
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Keith A. Canada
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Paul N. Devine
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Da Duan
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Jacob H. Forstater
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Shane T. Grosser
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Holst M. Halsey
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Gregory J. Hughes
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Junyong Jo
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Leo A. Joyce
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Joshua N. Kolev
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Jack Liang
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Kevin M. Maloney
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Benjamin F. Mann
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Mark McLaughlin
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Jeffrey C. Moore
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Grant S. Murphy
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Jovana Nazor
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Scott Novick
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Niki R. Patel
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Sandra A. Robaire
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Edward C. Sherer
- Computational and Structural Chemistry, Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Matthew D. Truppo
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Aaron M. Whittaker
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Deeptak Verma
- Computational and Structural Chemistry, Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Li Xiao
- Computational and Structural Chemistry, Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Yingju Xu
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Hao Yang
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
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The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism. Microbiol Mol Biol Rev 2018; 83:83/1/e00040-18. [PMID: 30567937 DOI: 10.1128/mmbr.00040-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ribosyl 1,5-bisphosphate (PRibP) was discovered 65 years ago and was believed to be an important intermediate in ribonucleotide metabolism, a role immediately taken over by its "big brother" phosphoribosyldiphosphate. Only recently has PRibP come back into focus as an important player in the metabolism of ribonucleotides with the discovery of the pentose bisphosphate pathway that comprises, among others, the intermediates PRibP and ribulose 1,5-bisphosphate (cf. ribose 5-phosphate and ribulose 5-phosphate of the pentose phosphate pathway). Enzymes of several pathways produce and utilize PRibP not only in ribonucleotide metabolism but also in the catabolism of phosphonates, i.e., compounds containing a carbon-phosphorus bond. Pathways for PRibP metabolism are found in all three domains of life, most prominently among organisms of the archaeal domain, where they have been identified either experimentally or by bioinformatic analysis within all of the four main taxonomic groups, Euryarchaeota, TACK, DPANN, and Asgard. Advances in molecular genetics of archaea have greatly improved the understanding of the physiology of PRibP metabolism, and reconciliation of molecular enzymology and three-dimensional structure analysis of enzymes producing or utilizing PRibP emphasize the versatility of the compound. Finally, PRibP is also an effector of several metabolic activities in many organisms, including higher organisms such as mammals. In the present review, we describe all aspects of PRibP metabolism, with emphasis on the biochemical, genetic, and physiological aspects of the enzymes that produce or utilize PRibP. The inclusion of high-resolution structures of relevant enzymes that bind PRibP provides evidence for the flexibility and importance of the compound in metabolism.
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8
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Meyer F, Keller P, Hartl J, Gröninger OG, Kiefer P, Vorholt JA. Methanol-essential growth of Escherichia coli. Nat Commun 2018; 9:1508. [PMID: 29666370 PMCID: PMC5904121 DOI: 10.1038/s41467-018-03937-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/22/2018] [Indexed: 12/22/2022] Open
Abstract
Methanol represents an attractive substrate for biotechnological applications. Utilization of reduced one-carbon compounds for growth is currently limited to methylotrophic organisms, and engineering synthetic methylotrophy remains a major challenge. Here we apply an in silico-guided multiple knockout approach to engineer a methanol-essential Escherichia coli strain, which contains the ribulose monophosphate cycle for methanol assimilation. Methanol conversion to biomass was stoichiometrically coupled to the metabolization of gluconate and the designed strain was subjected to laboratory evolution experiments. Evolved strains incorporate up to 24% methanol into core metabolites under a co-consumption regime and utilize methanol at rates comparable to natural methylotrophs. Genome sequencing reveals mutations in genes coding for glutathione-dependent formaldehyde oxidation (frmA), NAD(H) homeostasis/biosynthesis (nadR), phosphopentomutase (deoB), and gluconate metabolism (gntR). This study demonstrates a successful metabolic re-routing linked to a heterologous pathway to achieve methanol-dependent growth and represents a crucial step in generating a fully synthetic methylotrophic organism. Engineering synthetic methylotrophy remains challenging. Here, the authors engineer a methanol-essential E. coli by an in silico-guided multiple knockout approach and show a laboratory evolved strain can incorporate up to 24% methanol into core metabolites during growth.
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Affiliation(s)
- Fabian Meyer
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Philipp Keller
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Johannes Hartl
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Olivier G Gröninger
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Patrick Kiefer
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Julia A Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, 8093, Switzerland.
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9
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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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Rivero CW, De Benedetti EC, Gallego FL, Pessela BC, Guisán JM, Trelles JA. Biosynthesis of an antiviral compound using a stabilized phosphopentomutase by multipoint covalent immobilization. J Biotechnol 2017; 249:34-41. [DOI: 10.1016/j.jbiotec.2017.03.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 10/19/2022]
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Abstract
This chapter focuses on transition metals. All transition metal cations are toxic-those that are essential for Escherichia coli and belong to the first transition period of the periodic system of the element and also the "toxic-only" metals with higher atomic numbers. Common themes are visible in the metabolism of these ions. First, there is transport. High-rate but low-affinity uptake systems provide a variety of cations and anions to the cells. Control of the respective systems seems to be mainly through regulation of transport activity (flux control), with control of gene expression playing only a minor role. If these systems do not provide sufficient amounts of a needed ion to the cell, genes for ATP-hydrolyzing high-affinity but low-rate uptake systems are induced, e.g., ABC transport systems or P-type ATPases. On the other hand, if the amount of an ion is in surplus, genes for efflux systems are induced. By combining different kinds of uptake and efflux systems with regulation at the levels of gene expression and transport activity, the concentration of a single ion in the cytoplasm and the composition of the cellular ion "bouquet" can be rapidly adjusted and carefully controlled. The toxicity threshold of an ion is defined by its ability to produce radicals (copper, iron, chromate), to bind to sulfide and thiol groups (copper, zinc, all cations of the second and third transition period), or to interfere with the metabolism of other ions. Iron poses an exceptional metabolic problem due its metabolic importance and the low solubility of Fe(III) compounds, combined with the ability to cause dangerous Fenton reactions. This dilemma for the cells led to the evolution of sophisticated multi-channel iron uptake and storage pathways to prevent the occurrence of unbound iron in the cytoplasm. Toxic metals like Cd2+ bind to thiols and sulfide, preventing assembly of iron complexes and releasing the metal from iron-sulfur clusters. In the unique case of mercury, the cation can be reduced to the volatile metallic form. Interference of nickel and cobalt with iron is prevented by the low abundance of these metals in the cytoplasm and their sequestration by metal chaperones, in the case of nickel, or by B12 and its derivatives, in the case of cobalt. The most dangerous metal, copper, catalyzes Fenton-like reactions, binds to thiol groups, and interferes with iron metabolism. E. coli solves this problem probably by preventing copper uptake, combined with rapid efflux if the metal happens to enter the cytoplasm.
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Fateev IV, Antonov KV, Konstantinova ID, Muravyova TI, Seela F, Esipov RS, Miroshnikov AI, Mikhailopulo IA. The chemoenzymatic synthesis of clofarabine and related 2'-deoxyfluoroarabinosyl nucleosides: the electronic and stereochemical factors determining substrate recognition by E. coli nucleoside phosphorylases. Beilstein J Org Chem 2014; 10:1657-69. [PMID: 25161724 PMCID: PMC4142866 DOI: 10.3762/bjoc.10.173] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 06/16/2014] [Indexed: 12/25/2022] Open
Abstract
Two approaches to the synthesis of 2-chloro-9-(2-deoxy-2-fluoro-β-D-arabinofuranosyl)adenine (1, clofarabine) were studied. The first approach consists in the chemical synthesis of 2-deoxy-2-fluoro-α-D-arabinofuranose-1-phosphate (12a, (2F)Ara-1P) via three step conversion of 1,3,5-tri-O-benzoyl-2-deoxy-2-fluoro-α-D-arabinofuranose (9) into the phosphate 12a without isolation of intermediary products. Condensation of 12a with 2-chloroadenine catalyzed by the recombinant E. coli purine nucleoside phosphorylase (PNP) resulted in the formation of clofarabine in 67% yield. The reaction was also studied with a number of purine bases (2-aminoadenine and hypoxanthine), their analogues (5-aza-7-deazaguanine and 8-aza-7-deazahypoxanthine) and thymine. The results were compared with those of a similar reaction with α-D-arabinofuranose-1-phosphate (13a, Ara-1P). Differences of the reactivity of various substrates were analyzed by ab initio calculations in terms of the electronic structure (natural purines vs analogues) and stereochemical features ((2F)Ara-1P vs Ara-1P) of the studied compounds to determine the substrate recognition by E. coli nucleoside phosphorylases. The second approach starts with the cascade one-pot enzymatic transformation of 2-deoxy-2-fluoro-D-arabinose into the phosphate 12a, followed by its condensation with 2-chloroadenine thereby affording clofarabine in ca. 48% yield in 24 h. The following recombinant E. coli enzymes catalyze the sequential conversion of 2-deoxy-2-fluoro-D-arabinose into the phosphate 12a: ribokinase (2-deoxy-2-fluoro-D-arabinofuranose-5-phosphate), phosphopentomutase (PPN; no 1,6-diphosphates of D-hexoses as co-factors required) (12a), and finally PNP. The substrate activities of D-arabinose, D-ribose and D-xylose in the similar cascade syntheses of the relevant 2-chloroadenine nucleosides were studied and compared with the activities of 2-deoxy-2-fluoro-D-arabinose. As expected, D-ribose exhibited the best substrate activity [90% yield of 2-chloroadenosine (8) in 30 min], D-arabinose reached an equilibrium at a concentration of ca. 1:1 of a starting base and the formed 2-chloro-9-(β-D-arabinofuranosyl)adenine (6) in 45 min, the formation of 2-chloro-9-(β-D-xylofuranosyl)adenine (7) proceeded very slowly attaining ca. 8% yield in 48 h.
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Affiliation(s)
- Ilja V Fateev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 GSP, Moscow B-437, Russia
| | - Konstantin V Antonov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 GSP, Moscow B-437, Russia
| | - Irina D Konstantinova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 GSP, Moscow B-437, Russia
| | - Tatyana I Muravyova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 GSP, Moscow B-437, Russia
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, D-48149 Münster, Germany
| | - Roman S Esipov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 GSP, Moscow B-437, Russia
| | - Anatoly I Miroshnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 GSP, Moscow B-437, Russia
| | - Igor A Mikhailopulo
- Institute of Bioorganic Chemistry, National Academy of Sciences, Acad. Kuprevicha 5/2, 220141 Minsk, Belarus
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Aklujkar M, Haveman SA, DiDonato R, Chertkov O, Han CS, Land ML, Brown P, Lovley DR. The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features. BMC Genomics 2012; 13:690. [PMID: 23227809 PMCID: PMC3543383 DOI: 10.1186/1471-2164-13-690] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 11/22/2012] [Indexed: 11/24/2022] Open
Abstract
Background The bacterium Pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically. The genome of P. carbinolicus was sequenced in order to understand its metabolic capabilities and physiological features in comparison with its relatives, acetate-oxidizing Geobacter species. Results Pathways were predicted for catabolism of known substrates: 2,3-butanediol, acetoin, glycerol, 1,2-ethanediol, ethanolamine, choline and ethanol. Multiple isozymes of 2,3-butanediol dehydrogenase, ATP synthase and [FeFe]-hydrogenase were differentiated and assigned roles according to their structural properties and genomic contexts. The absence of asparagine synthetase and the presence of a mutant tRNA for asparagine encoded among RNA-active enzymes suggest that P. carbinolicus may make asparaginyl-tRNA in a novel way. Catabolic glutamate dehydrogenases were discovered, implying that the tricarboxylic acid (TCA) cycle can function catabolically. A phosphotransferase system for uptake of sugars was discovered, along with enzymes that function in 2,3-butanediol production. Pyruvate:ferredoxin/flavodoxin oxidoreductase was identified as a potential bottleneck in both the supply of oxaloacetate for oxidation of acetate by the TCA cycle and the connection of glycolysis to production of ethanol. The P. carbinolicus genome was found to encode autotransporters and various appendages, including three proteins with similarity to the geopilin of electroconductive nanowires. Conclusions Several surprising metabolic capabilities and physiological features were predicted from the genome of P. carbinolicus, suggesting that it is more versatile than anticipated.
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Affiliation(s)
- Muktak Aklujkar
- University of Massachusetts Amherst, Amherst, MA 01003, USA.
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14
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Iverson TM, Panosian TD, Birmingham WR, Nannemann DP, Bachmann BO. Molecular differences between a mutase and a phosphatase: investigations of the activation step in Bacillus cereus phosphopentomutase. Biochemistry 2012; 51:1964-75. [PMID: 22329805 DOI: 10.1021/bi201761h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Prokaryotic phosphopentomutases (PPMs) are di-Mn(2+) enzymes that catalyze the interconversion of α-D-ribose 5-phosphate and α-D-ribose 1-phosphate at an active site located between two independently folded domains. These prokaryotic PPMs belong to the alkaline phosphatase superfamily, but previous studies of Bacillus cereus PPM suggested adaptations of the conserved alkaline phosphatase catalytic cycle. Notably, B. cereus PPM engages substrates when the active site nucleophile, Thr-85, is phosphorylated. Further, the phosphoenzyme is stable throughout purification and crystallization. In contrast, alkaline phosphatase engages substrates when the active site nucleophile is dephosphorylated, and the phosphoenzyme reaction intermediate is only stably trapped in a catalytically compromised enzyme. Studies were undertaken to understand the divergence of these mechanisms. Crystallographic and biochemical investigations of the PPM(T85E) phosphomimetic variant and the neutral corollary PPM(T85Q) determined that the side chain of Lys-240 underwent a change in conformation in response to active site charge, which modestly influenced the affinity for the small molecule activator α-D-glucose 1,6-bisphosphate. More strikingly, the structure of unphosphorylated B. cereus PPM revealed a dramatic change in the interdomain angle and a new hydrogen bonding interaction between the side chain of Asp-156 and the active site nucleophile, Thr-85. This hydrogen bonding interaction is predicted to align and activate Thr-85 for nucleophilic addition to α-D-glucose 1,6-bisphosphate, favoring the observed equilibrium phosphorylated state. Indeed, phosphorylation of Thr-85 is severely impaired in the PPM(D156A) variant even under stringent activation conditions. These results permit a proposal for activation of PPM and explain some of the essential features that distinguish between the catalytic cycles of PPM and alkaline phosphatase.
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Affiliation(s)
- T M Iverson
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States.
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15
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Panosian TD, Nannemann DP, Watkins GR, Phelan VV, McDonald WH, Wadzinski BE, Bachmann BO, Iverson TM. Bacillus cereus phosphopentomutase is an alkaline phosphatase family member that exhibits an altered entry point into the catalytic cycle. J Biol Chem 2011; 286:8043-8054. [PMID: 21193409 PMCID: PMC3048691 DOI: 10.1074/jbc.m110.201350] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2010] [Revised: 12/14/2010] [Indexed: 11/06/2022] Open
Abstract
Bacterial phosphopentomutases (PPMs) are alkaline phosphatase superfamily members that interconvert α-D-ribose 5-phosphate (ribose 5-phosphate) and α-D-ribose 1-phosphate (ribose 1-phosphate). We investigated the reaction mechanism of Bacillus cereus PPM using a combination of structural and biochemical studies. Four high resolution crystal structures of B. cereus PPM revealed the active site architecture, identified binding sites for the substrate ribose 5-phosphate and the activator α-D-glucose 1,6-bisphosphate (glucose 1,6-bisphosphate), and demonstrated that glucose 1,6-bisphosphate increased phosphorylation of the active site residue Thr-85. The phosphorylation of Thr-85 was confirmed by Western and mass spectroscopic analyses. Biochemical assays identified Mn(2+)-dependent enzyme turnover and demonstrated that glucose 1,6-bisphosphate treatment increases enzyme activity. These results suggest that protein phosphorylation activates the enzyme, which supports an intermolecular transferase mechanism. We confirmed intermolecular phosphoryl transfer using an isotope relay assay in which PPM reactions containing mixtures of ribose 5-[(18)O(3)]phosphate and [U-(13)C(5)]ribose 5-phosphate were analyzed by mass spectrometry. This intermolecular phosphoryl transfer is seemingly counter to what is anticipated from phosphomutases employing a general alkaline phosphatase reaction mechanism, which are reported to catalyze intramolecular phosphoryl transfer. However, the two mechanisms may be reconciled if substrate encounters the enzyme at a different point in the catalytic cycle.
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Affiliation(s)
| | - David P Nannemann
- the Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235
| | | | - Vanessa V Phelan
- the Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235
| | - W Hayes McDonald
- Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee 37232 and
| | | | - Brian O Bachmann
- the Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235; Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee 37232 and.
| | - Tina M Iverson
- From the Departments of Pharmacology and; Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee 37232 and.
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16
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Biologically important nucleosides: modern trends in biotechnology and application. MENDELEEV COMMUNICATIONS 2011. [DOI: 10.1016/j.mencom.2011.03.001] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Panosian TD, Nannemann DP, Bachmann BO, Iverson TM. Crystallization and preliminary X-ray analysis of a phosphopentomutase from Bacillus cereus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:811-4. [PMID: 20606280 DOI: 10.1107/s1744309110017549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Accepted: 05/12/2010] [Indexed: 11/10/2022]
Abstract
Phosphopentomutases (PPMs) interconvert D-ribose 5-phosphate and alpha-D-ribose 1-phosphate to link glucose and nucleotide metabolism. PPM from Bacillus cereus was overexpressed in Escherichia coli, purified to homogeneity and crystallized. Bacterial PPMs are predicted to contain a di-metal reaction center, but the catalytically relevant metal has not previously been identified. Sparse-matrix crystallization screening was performed in the presence or absence of 50 mM MnCl(2). This strategy resulted in the formation of two crystal forms from two chemically distinct conditions. The crystals that formed with 50 mM MnCl(2) were more easily manipulated and diffracted to higher resolution. These results suggest that even if the catalytically relevant metal is not known, the crystallization of putative metalloproteins may still benefit from supplementation of the crystallization screens with potential catalytic metals.
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Affiliation(s)
- Timothy D Panosian
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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18
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Horinouchi N, Kawano T, Sakai T, Matsumoto S, Sasaki M, Mikami Y, Ogawa J, Shimizu S. Screening and characterization of a phosphopentomutase useful for enzymatic production of 2′-deoxyribonucleoside. N Biotechnol 2009; 26:75-82. [DOI: 10.1016/j.nbt.2009.03.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 03/20/2009] [Accepted: 03/27/2009] [Indexed: 10/20/2022]
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19
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Horzempa J, Carlson PE, O'Dee DM, Shanks RMQ, Nau GJ. Global transcriptional response to mammalian temperature provides new insight into Francisella tularensis pathogenesis. BMC Microbiol 2008; 8:172. [PMID: 18842136 PMCID: PMC2576331 DOI: 10.1186/1471-2180-8-172] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 10/08/2008] [Indexed: 01/06/2023] Open
Abstract
Background After infecting a mammalian host, the facultative intracellular bacterium, Francisella tularensis, encounters an elevated environmental temperature. We hypothesized that this temperature change may regulate genes essential for infection. Results Microarray analysis of F. tularensis LVS shifted from 26°C (environmental) to 37°C (mammalian) showed ~11% of this bacterium's genes were differentially-regulated. Importantly, 40% of the protein-coding genes that were induced at 37°C have been previously implicated in virulence or intracellular growth of Francisella in other studies, associating the bacterial response to this temperature shift with pathogenesis. Forty-four percent of the genes induced at 37°C encode proteins of unknown function, suggesting novel Francisella virulence traits are regulated by mammalian temperature. To explore this possibility, we generated two mutants of loci induced at 37°C [FTL_1581 and FTL_1664 (deoB)]. The FTL_1581 mutant was attenuated in a chicken embryo infection model, which was likely attributable to a defect in survival within macrophages. FTL_1581 encodes a novel hypothetical protein that we suggest naming temperature-induced, virulence-associated locus A, tivA. Interestingly, the deoB mutant showed diminished entry into mammalian cells compared to wild-type LVS, including primary human macrophages and dendritic cells, the macrophage-like RAW 264.7 line, and non-phagocytic HEK-293 cells. This is the first study identifying a Francisella gene that contributes to uptake into both phagocytic and non-phagocytic host cells. Conclusion Our results provide new insight into mechanisms of Francisella virulence regulation and pathogenesis. F. tularensis LVS undergoes considerable gene expression changes in response to mammalian body temperature. This temperature shift is important for the regulation of genes that are critical for the pathogenesis of Francisella. Importantly, the compilation of temperature-regulated genes also defines a rich collection of novel candidate virulence determinants, including tivA (FTL_1581). An analysis of tivA and deoB (FTL_1664) revealed that these genes contribute to intracellular survival and entry into mammalian cells, respectively.
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Affiliation(s)
- Joseph Horzempa
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
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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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21
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Ouwerkerk N, Steenweg M, de Ruijter M, Brouwer J, van Boom JH, Lugtenburg J, Raap J. One-pot two-step enzymatic coupling of pyrimidine bases to 2-deoxy-D-ribose-5-phosphate. A new strategy in the synthesis of stable isotope labeled deoxynucleosides. J Org Chem 2002; 67:1480-9. [PMID: 11871876 DOI: 10.1021/jo0107249] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzymatic synthesis of thymidine from 2-deoxy-D-ribose-5-phosphate is achieved, in a one-pot two-step reaction using phosphoribomutase (PRM) and commercially available thymidine phosphorylase (TP). In the first step the sugar-5-phosphate is enzymatically rearranged to alpha-2-deoxy-D-ribose-1-phosphate. Highly active PRM is easily obtained from genetically modified overproducing E. coli cells (12,000 units/84 mg protein) and is used without further purification. In the second step thymine is coupled to the sugar-1-phosphate. The thermodynamically unfavorable equilibrium is shifted to the product by addition of MnCl(2) to precipitate inorganic phosphate. In this way the overall yield of the beta-anomeric pure nucleoside increases from 14 to 60%. In contrast to uracil, cytosine is not accepted by TP as a substrate. Therefore, 2'-deoxy-cytidine is obtained by functional group transformations of the enzymatically prepared 2'-deoxy-uridine. The method has been demonstrated by the synthesis of [2',5'-(13)C(2)]- and [1',2',5'-(13)C(3)]thymidine as well as [1',2',5'-(13)C(3)]2'-deoxyuridine and [3',4'-(13)C(2)]2'-deoxycytidine. In addition the nucleoside bases thymine and uracil are tetralabeled at the (1,3-(15)N(2),2,4-(13)C(2))-atomic positions. All compounds are prepared without any scrambling or dilution of the labeled material and are thus obtained with a very high isotope enrichment (96-99%). In combination with the methods that have been developed earlier it is concluded that each of the (13)C- and (15)N-positions and combination of positions of the pyrimidine deoxynucleosides can be efficiently labeled starting from commercially available and highly (13)C- or (15)N-enriched formaldehyde, acetaldehyde, acetic acid, potassium cyanide, methylamine hydrochloride, and ammonia.
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Affiliation(s)
- N Ouwerkerk
- Leiden University, Leiden Institute of Chemistry, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Carta MC, Mattana A, Camici M, Allegrini S, Tozzi MG, Sgarrella F. Catabolism of exogenous deoxyinosine in cultured epithelial amniotic cells. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1528:74-80. [PMID: 11687292 DOI: 10.1016/s0304-4165(01)00175-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Uptake and catabolism of purine nucleosides have been commonly considered as means to salvage the purine ring for nucleic acid synthesis, usually neglecting the destiny of the pentose moiety. With the aim to ascertain if deoxyribose derived from exogenous DNA can be utilised as a carbon and energy source, we studied the catabolism of exogenous deoxyinosine in a cell line derived from human amnion epithelium (WISH). Intact WISH cells catabolise deoxyinosine by conversion into hypoxanthine. The nucleoside enters the cell through a nitrobenzylthioinosine-insensitive equilibrative transport. Deoxyinosine undergoes a phosphorolytic cleavage inside the cell. The purine base diffuses back to the external medium, while the phosphorylated pentose moiety can be further catabolised to glycolysis and citric acid cycle intermediates. Our results indicate that the catabolism of the deoxynucleoside can be considered mainly as a means to meet the carbon and energy requirements of growing cells.
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Affiliation(s)
- M C Carta
- Dipartimento di Scienze del Farmaco, Università di Sassari, Italy
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23
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Nixon AE, Hunter JL, Bonifacio G, Eccleston JF, Webb MR. Purine nucleoside phosphorylase: its use in a spectroscopic assay for inorganic phosphate and for removing inorganic phosphate with the aid of phosphodeoxyribomutase. Anal Biochem 1998; 265:299-307. [PMID: 9882406 DOI: 10.1006/abio.1998.2916] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The kinetics of the phosphorolysis of 7-methylated guanosine analogues catalyzed by purine nucleoside phosphorylase has been analyzed to understand the use of this system as a "Pi mop" to remove Pi from solutions and as a spectroscopic assay for Pi at micromolar concentrations. An expression system was developed for the phosphorylase from Escherichia coli: this protein (subunit molecular mass 26 kDa) and one from a commercial source (29 kDa) were used in this study. Rates of >50 s-1 were obtained for the phosphorolysis at 30 degrees C, so that when the phosphorylase is coupled to the phosphatase being studied, rates of Pi release from the phosphatase can be measured close to this rate. The kinetic mechanism appears to obey the Michaelis-Menten model in the steady state with the bond cleavage rate limiting. Slow hydrolysis of ribose-1-phosphate to Pi catalyzed by the phosphorylase limits the efficiency of the Pi mop. To overcome this, phosphodeoxyribomutase was used to catalyze the conversion of ribose-1-phosphate to ribose-5-phosphate, enabling the Pi mop to remove large amounts of Pi quantitatively. Acyclovir diphosphate provides a simple method to switch off the Pi mop as it is a tight inhibitor (Kd 12 nM) of purine nucleoside phosphorylase.
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Affiliation(s)
- A E Nixon
- National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
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Galperin MY, Bairoch A, Koonin EV. A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases. Protein Sci 1998; 7:1829-35. [PMID: 10082381 PMCID: PMC2144072 DOI: 10.1002/pro.5560070819] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Sequence analysis of the probable archaeal phosphoglycerate mutase resulted in the identification of a superfamily of metalloenzymes with similar metal-binding sites and predicted conserved structural fold. This superfamily unites alkaline phosphatase, N-acetylgalactosamine-4-sulfatase, and cerebroside sulfatase, enzymes with known three-dimensional structures, with phosphopentomutase, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, phosphoglycerol transferase, phosphonate monoesterase, streptomycin-6-phosphate phosphatase, alkaline phosphodiesterase/nucleotide pyrophosphatase PC-1, and several closely related sulfatases. In addition to the metal-binding motifs, all these enzymes contain a set of conserved amino acid residues that are likely to be required for the enzymatic activity. Mutational changes in the vicinity of these residues in several sulfatases cause mucopolysaccharidosis (Hunter, Maroteaux-Lamy, Morquio, and Sanfilippo syndromes) and metachromatic leucodystrophy.
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Affiliation(s)
- M Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
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25
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Overexpression and substrate specificity studies of phosphodeoxyribomutase and thymidine phosphorylase. Bioorg Chem 1991. [DOI: 10.1016/0045-2068(91)90051-p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Guha SK, Rose ZB. The enzymic synthesis of ribose-1,5-bisphosphate: studies of its role in metabolism. Arch Biochem Biophys 1986; 250:513-8. [PMID: 3022651 DOI: 10.1016/0003-9861(86)90756-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ribose-1,5-bisphosphate is synthesized in a reaction that uses ribose-1(or 5)-P as the phosphoryl acceptor and the acyl-P of 3-phosphoglyceryl phosphate as the donor. Glucose-1,6-bisphosphate is synthesized in a similar reaction. The relative activity with the two substrates remains unchanged over almost 300-fold purification of the enzyme, indicating that glucose-1,6-bisphosphate synthase catalyzes both reactions. The relative V/Km values for alternative phosphoryl acceptors are ribose-1-P (1); glucose-1-P (0.30); mannose-1-P and ribose-5-P (0.11); glucose-6-P (0.10); 2-deoxyglucose-6-P (0.03); and 2-deoxyribose-5-P (0.02). Fructose-1- and 6-phosphates are not substrates. The synthesis of both ribose-1,5-bisphosphate and glucose-1,6-bisphosphate is inhibited by physiologically significant levels of fructose-1,6-bisphosphate, glycerate-2,3-bisphosphate, glycerate-3-phosphate, citrate, and inorganic phosphate. Ribose-1,5-bisphosphate is a strong activator of brain phosphofructokinase.
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Pérignon JL, Houllier AM, Cartier PH. A facile radio-isotopic assay for phosphoribomutase activity in human red blood cells. Clin Chim Acta 1983; 129:365-70. [PMID: 6303632 DOI: 10.1016/0009-8981(83)90041-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Barsky DL, Hoffee PA. Purification and characterization of phosphopentomutase from rat liver. BIOCHIMICA ET BIOPHYSICA ACTA 1983; 743:162-71. [PMID: 6297594 DOI: 10.1016/0167-4838(83)90430-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Hammer-Jespersen K, Buxton RS, Hansen TD. A second purine nucleoside phosphorylase in Escherichia coli K-12. II. Properties of xanthosine phosphorylase and its induction by xanthosine. MOLECULAR & GENERAL GENETICS : MGG 1980; 179:341-8. [PMID: 7007809 DOI: 10.1007/bf00425462] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The presence of a second purine nucleoside phosphorylase in wild-type strains of E. coli K-12 after growth on xanthosine has been demonstrated. Like other purine nucleoside phosphorylase it is able to carry out both phosphorylosis and synthesis of purine deoxy- and ribonucleosides whilst pyrimidine nucleosides cannot act as substrates. In contrast to the well characterised purine nucleoside phosphorylase of E. coli K-12 (encoded by the deoD gene) this new enzyme could act on xanthosine and is hence called xanthosine phosphorylase. Studies of its substrate specificity showed that xanthosine phosphorylase, like the mammalian purine nucleoside phosphorylases, has no activity towards adenine and the corresponding nucleosides. Determinations of Km and gel filtration behaviour was carried out on crude dialysed extracts. The presence of xanthosine phosphorylase enables E. coli to grow on xanthosine as carbon source. Xanthosine was the only compound found which induce xanthosine phosphorylase. No other known nucleoside catabolising enzyme was induced by xanthosine. The implications of non-linear induction kinetics of xanthosine phosphorylase is discussed.
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Valentin-Hansen P, Hammer-Jespersen K, Buxton RS. Evidence for the existence of three promoters for the deo operon of Escherichia coli K12 in vitro. J Mol Biol 1979; 133:1-17. [PMID: 231107 DOI: 10.1016/0022-2836(79)90248-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Leer JC, Hammer-Jespersen K, Schwartz M. Uridine phosphorylase from Escherichia coli. Physical and chemical characterization. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 75:217-24. [PMID: 16751 DOI: 10.1111/j.1432-1033.1977.tb11520.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Uridine phosphorylase from Escherichia coli has been purified to homogeneity. The enzyme was found to have a molecular weight of 176000 and to consist of 8 probably identical subunits with molecular weights of 22000. These numbers were determined from equilibrium centrifugations in the analytical ultracentrifuge, from dodecylsulphate gel electrophoresis and from amino acid analysis. Moreover the following physico-chemical constants were determined: s020,w = 8.2 x 10(-13) s, upsilon2 = 0.751 cm3/g, A1%280 (1 cm) = 6.73 and a specific activity of 183 units/mg towards uridine. The enzyme shows some activity towards deoxyuridine and thymidine. The activity is not impaired through substitution by bromo, fluoro or methyl groups in the 5-position of the uracil base, but no enzymatic activity is observed when cytosine base is used in the nucleoside substrate.
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Albrechtsen H, Hammer-Jespersen K, Munch-Petersen A, Fiil N. Multiple regulation of nucleoside catabolizing enzymes: effects of a polar dra mutation on the deo enzymes. MOLECULAR & GENERAL GENETICS : MGG 1976; 146:139-45. [PMID: 822276 DOI: 10.1007/bf00268082] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Strains with an amber, polar mutation in the dra1 gene have been isolated. The mutation was introduced into a set of isogenic strains, wild type or with concurrent regulatory mutations, and further characterized by suppression and heat inactivation experiments. The effect of the polar dra mutation on the three remaining genes of the deo operon, the tpp, drm and pup genes, was determined by estimating the enzyme levels in the various dra-mutants. The effect was found to be non-coordinate, indicating the formation in the cells of two types of transcripts: A tetracistronic unit, containing the message from all four genes, and a dicistronic unit, covering the two distal genes only.
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Jensen KF, Nygaard P. Purine nucleoside phosphorylase from Escherichia coli and Salmonella typhimurium. Purification and some properties. EUROPEAN JOURNAL OF BIOCHEMISTRY 1975; 51:253-65. [PMID: 235429 DOI: 10.1111/j.1432-1033.1975.tb03925.x] [Citation(s) in RCA: 158] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The purine nucleoside phosphorylases from Escherichia coli and from Salmonella typhimurium have been purified to electrophoretic homogeneity and crystallized. Comparative studies revealed that the two enzymes are very much alike. They obey simple Michaelis-Menten kinetics for their substrates with the exception of phosphate for which they show negative cooperativity. Gel filtration on Sephadex G-200 of the native enzymes revealed a molecular weight for both enzymes of 138000 plus or minus 10%. By use of dodecylsulphate gel electrophoresis a subunit molecular weight of 23700 plus or minus 5% was determined, suggesting that both enzymes consist of six subunits of equal molecular weight. When the subunits were partially crosslinked with dimethyl suberimidate before dodecylsulphate electrophoresis six protein bands were observed in agreement with the proposed oligomeric state of the enzyme, consisting of six subunits of equal molecular weight. Analysis of the amino acid composition also indicates that the subunits are identical. 6M guanidinium chloride dissociates the enzymes; association experiments with native and succinylated enzymes suggested that only the hexameric form is active. Both enzymes could be dissociated into subunits by p-chloromercuribenzoate; this dissociation is prevented by the substrates: the nucleosides, the pentose 1-phosphates, and mixtures of phosphate and purine bases.
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Rowley GL, Kenyon GL. PEI-cellulose thin-layer chromatography. Product studies of the creatine kinase and pyruvate kinase reactions. Anal Biochem 1974; 58:525-33. [PMID: 4827394 DOI: 10.1016/0003-2697(74)90220-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Jensen KF, Leer JC, Nygaard P. Thymine utilization in Escherichia coli K12 on the role of deoxyribose 1-phosphate and thymidine phosphorylase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 40:345-54. [PMID: 4592648 DOI: 10.1111/j.1432-1033.1973.tb03203.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Munch-Petersen A, Schwartz M. Inhibition of the catabolism of deoxyribonucleosides in Escherichia coli after infection by T 4 phage. EUROPEAN JOURNAL OF BIOCHEMISTRY 1972; 27:443-7. [PMID: 4559177 DOI: 10.1111/j.1432-1033.1972.tb01858.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Schwartz M. Thymidine phosphorylase from Escherichia coli. Properties and kinetics. EUROPEAN JOURNAL OF BIOCHEMISTRY 1971; 21:191-8. [PMID: 4935199 DOI: 10.1111/j.1432-1033.1971.tb01455.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Hammer-Jespersen K, Munch-Petersen A, Schwartz M, Nygaard P. Induction of enzymes involed in the catabolism of deoxyribonucleosides and ribonucleosides in Escherichia coli K 12. EUROPEAN JOURNAL OF BIOCHEMISTRY 1971; 19:533-8. [PMID: 4931185 DOI: 10.1111/j.1432-1033.1971.tb01345.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Hoffmeyer J, Neuhard J. Metabolism of exogenous purine bases and nucleosides by Salmonella typhimurium. J Bacteriol 1971; 106:14-24. [PMID: 4928005 PMCID: PMC248638 DOI: 10.1128/jb.106.1.14-24.1971] [Citation(s) in RCA: 49] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Purine-requiring mutants of Salmonella typhimurium LT2 containing additional mutations in either adenosine deaminase or purine nucleoside phosphorylase have been constructed. From studies of the ability of these mutants to utilize different purine compounds as the sole source of purines, the following conclusions may be drawn. (i) S. typhimurium does not contain physiologically significant amounts of adenine deaminase and adenosine kinase activities. (ii) The presence of inosine and guanosine kinase activities in vivo was established, although the former activity appears to be of minor significance for inosine metabolism. (iii) The utilization of exogenous purine deoxyribonucleosides is entirely dependent on a functional purine nucleoside phosphorylase. (iv) The pathway by which exogenous adenine is converted to guanine nucleotides in the presence of histidine requires a functional purine nucleoside phosphorylase. Evidence is presented that this pathway involves the conversion of adenine to adenosine, followed by deamination to inosine and subsequent phosphorolysis to hypoxanthine. Hypoxanthine is then converted to inosine monophosphate by inosine monophosphate pyrophosphorylase. The rate-limiting step in this pathway is the synthesis of adenosine from adenine due to lack of endogenous ribose-l-phosphate.
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