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Klemm BP, Singh D, Smith CE, Hsu AL, Dillard LB, Krahn JM, London RE, Mueller GA, Borgnia MJ, Schaaper RM. Mechanism by which T7 bacteriophage protein Gp1.2 inhibits Escherichia coli dGTPase. Proc Natl Acad Sci U S A 2022; 119:e2123092119. [PMID: 36067314 PMCID: PMC9478638 DOI: 10.1073/pnas.2123092119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
Levels of the cellular dNTPs, the direct precursors for DNA synthesis, are important for DNA replication fidelity, cell cycle control, and resistance against viruses. Escherichia coli encodes a dGTPase (2'-deoxyguanosine-5'-triphosphate [dGTP] triphosphohydrolase [dGTPase]; dgt gene, Dgt) that establishes the normal dGTP level required for accurate DNA replication but also plays a role in protecting E. coli against bacteriophage T7 infection by limiting the dGTP required for viral DNA replication. T7 counteracts Dgt using an inhibitor, the gene 1.2 product (Gp1.2). This interaction is a useful model system for studying the ongoing evolutionary virus/host "arms race." We determined the structure of Gp1.2 by NMR spectroscopy and solved high-resolution cryo-electron microscopy structures of the Dgt-Gp1.2 complex also including either dGTP substrate or GTP coinhibitor bound in the active site. These structures reveal the mechanism by which Gp1.2 inhibits Dgt and indicate that Gp1.2 preferentially binds the GTP-bound form of Dgt. Biochemical assays reveal that the two inhibitors use different modes of inhibition and bind to Dgt in combination to yield enhanced inhibition. We thus propose an in vivo inhibition model wherein the Dgt-Gp1.2 complex equilibrates with GTP to fully inactivate Dgt, limiting dGTP hydrolysis and preserving the dGTP pool for viral DNA replication.
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Affiliation(s)
- Bradley P. Klemm
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Deepa Singh
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Cassandra E. Smith
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Allen L. Hsu
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Lucas B. Dillard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Juno M. Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Robert E. London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Geoffrey A. Mueller
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Mario J. Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Roel M. Schaaper
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
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Klemm BP, Sikkema AP, Hsu AL, Horng JC, Hall TMT, Borgnia MJ, Schaaper RM. High-resolution structures of the SAMHD1 dGTPase homolog from Leeuwenhoekiella blandensis reveal a novel mechanism of allosteric activation by dATP. J Biol Chem 2022; 298:102073. [PMID: 35643313 PMCID: PMC9257424 DOI: 10.1016/j.jbc.2022.102073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 10/27/2022] Open
Abstract
Deoxynucleoside triphosphate (dNTP) triphosphohydrolases (dNTPases) are important enzymes that may perform multiple functions in the cell, including regulating the dNTP pools and contributing to innate immunity against viruses. Among the homologs that are best studied are human sterile alpha motif and HD domain-containing protein 1 (SAMHD1), a tetrameric dNTPase, and the hexameric Escherichia coli dGTPase; however, it is unclear whether these are representative of all dNTPases given their wide distribution throughout life. Here, we investigated a hexameric homolog from the marine bacterium Leeuwenhoekiella blandensis, revealing that it is a dGTPase that is subject to allosteric activation by dATP, specifically. Allosteric regulation mediated solely by dATP represents a novel regulatory feature among dNTPases that may facilitate maintenance of cellular dNTP pools in L. blandensis. We present high-resolution X-ray crystallographic structures (1.80-2.26 Å) in catalytically important conformations as well as cryo-EM structures (2.1-2.7 Å) of the enzyme bound to dGTP and dATP ligands. The structures, the highest resolution cryo-EM structures of any SAMHD1-like dNTPase to date, reveal an intact metal-binding site with the dGTP substrate coordinated to three metal ions. These structural and biochemical data yield insights into the catalytic mechanism and support a conserved catalytic mechanism for the tetrameric and hexameric dNTPase homologs. We conclude that the allosteric activation by dATP appears to rely on structural connectivity between the allosteric and active sites, as opposed to the changes in oligomeric state upon ligand binding used by SAMHD1.
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Affiliation(s)
- Bradley P Klemm
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Andrew P Sikkema
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Allen L Hsu
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - James C Horng
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Roel M Schaaper
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA.
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Tinikul R, Trisrivirat D, Chinantuya W, Wongnate T, Watthaisong P, Phonbuppha J, Chaiyen P. Detection of cellular metabolites by redox enzymatic cascades. Biotechnol J 2022; 17:e2100466. [PMID: 35192744 DOI: 10.1002/biot.202100466] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 11/11/2022]
Abstract
Detection of cellular metabolites that are disease biomarkers is important for human healthcare monitoring and assessing prognosis and therapeutic response. Accurate and rapid detection of microbial metabolites and pathway intermediates is also crucial for the process optimization required for development of bioconversion methods using metabolically engineered cells. Various redox enzymes can generate electrons that can be employed in enzyme-based biosensors and in the detection of cellular metabolites. These reactions can directly transform target compounds into various readout signals. By incorporating engineered enzymes into enzymatic cascades, the readout signals can be improved in terms of accuracy and sensitivity. This review critically discusses selected redox enzymatic and chemoenzymatic cascades currently employed for detection of human- and microbe-related cellular metabolites including, amino acids, d-glucose, inorganic ions (pyrophosphate, phosphate, and sulfate), nitro- and halogenated phenols, NAD(P)H, fatty acids, fatty aldehyde, alkane, short chain acids, and cellular metabolites.
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Affiliation(s)
- Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Duangthip Trisrivirat
- Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, School of Biomolecular Science and Engineering, Rayong, Thailand
| | - Wachirawit Chinantuya
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Thanyaporn Wongnate
- Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, School of Biomolecular Science and Engineering, Rayong, Thailand
| | - Pratchaya Watthaisong
- Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, School of Biomolecular Science and Engineering, Rayong, Thailand
| | - Jittima Phonbuppha
- Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, School of Biomolecular Science and Engineering, Rayong, Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, School of Biomolecular Science and Engineering, Rayong, Thailand
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Kaspar F, Giessmann RT, Westarp S, Hellendahl KF, Krausch N, Thiele I, Walczak MC, Neubauer P, Wagner A. Spectral Unmixing-Based Reaction Monitoring of Transformations between Nucleosides and Nucleobases. Chembiochem 2020; 21:2604-2610. [PMID: 32324971 PMCID: PMC7540295 DOI: 10.1002/cbic.202000204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/21/2020] [Indexed: 11/10/2022]
Abstract
The increased interest in (enzymatic) transformations between nucleosides and nucleobases has demanded the development of efficient analytical tools. In this report, we present an update and extension of our recently described method for monitoring these reactions by spectral unmixing. The presented method uses differences in the UV absorption spectra of nucleosides and nucleobases after alkaline quenching to derive their ratio based on spectral shape by fitting normalized reference spectra. It is applicable to a broad compound spectrum comprising more than 35 examples, offers HPLC-like accuracy, ease of handling and significant reductions in both cost and data acquisition time compared to other methods. This contribution details the principle of monitoring reactions by spectral unmixing, gives recommendations regarding solutions to common problems and applications that necessitate special sample treatment. We provide software, workflows and reference spectra that facilitate the straightforward and versatile application of the method.
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Affiliation(s)
- Felix Kaspar
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
- BioNukleo GmbHAckerstraße 7613355BerlinGermany
| | - Robert T. Giessmann
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
| | - Sarah Westarp
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
- BioNukleo GmbHAckerstraße 7613355BerlinGermany
| | - Katja F. Hellendahl
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
| | - Niels Krausch
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
| | - Isabel Thiele
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
| | - Miriam C. Walczak
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
- BioNukleo GmbHAckerstraße 7613355BerlinGermany
| | - Peter Neubauer
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
| | - Anke Wagner
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
- BioNukleo GmbHAckerstraße 7613355BerlinGermany
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Kaspar F, Giessmann RT, Krausch N, Neubauer P, Wagner A, Gimpel M. A UV/Vis Spectroscopy-Based Assay for Monitoring of Transformations Between Nucleosides and Nucleobases. Methods Protoc 2019; 2:E60. [PMID: 31311105 PMCID: PMC6789650 DOI: 10.3390/mps2030060] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 12/25/2022] Open
Abstract
Efficient reaction monitoring is crucial for data acquisition in kinetic and mechanistic studies. However, for conversions of nucleosides to their corresponding nucleobases, as observed in enzymatically catalyzed nucleoside phosphorylation reactions, the current analytical arsenal does not meet modern requirements regarding cost, speed of analysis and high throughput. Herein, we present a UV/Vis spectroscopy-based assay employing an algorithm for spectral unmixing in a 96-well plate format. The algorithm relies on fitting of reference spectra of nucleosides and their bases to experimental spectra and allows determination of nucleoside/nucleobase ratios in solution with high precision. The experimental procedure includes appropriate dilution of a sample into aqueous alkaline solution, transfer to a multi-well plate, measurement of a UV/Vis spectrum and subsequent in silico spectral unmixing. This enables data collection in a high-throughput fashion and reduces costs compared to state-of-the-art HPLC analyses by approximately 5-fold while being 20-fold faster and offering comparable precision. Additionally, the method is robust regarding dilution and sample transfer errors as it only considers spectral form and not absolute intensity. It can be applied to all natural nucleosides and nucleobases and even unnatural ones as demonstrated by several examples.
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Affiliation(s)
- Felix Kaspar
- Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, D-13355 Berlin, Germany
| | - Robert T Giessmann
- Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, D-13355 Berlin, Germany
| | - Niels Krausch
- Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, D-13355 Berlin, Germany
| | - Peter Neubauer
- Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, D-13355 Berlin, Germany
| | - Anke Wagner
- Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, D-13355 Berlin, Germany.
- BioNukleo GmbH, Ackerstraße 76, D-13355 Berlin, Germany.
| | - Matthias Gimpel
- Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, D-13355 Berlin, Germany
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Polyák P, Rácz P, Rózsa P, Nagy GN, Vértessy BG, Pukánszky B. The novel technique of vapor pressure analysis to monitor the enzymatic degradation of PHB by HPLC chromatography. Anal Biochem 2017; 521:20-27. [DOI: 10.1016/j.ab.2017.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 11/16/2022]
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