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Song Y, He S, Abdallah II, Jopkiewicz A, Setroikromo R, van Merkerk R, Tepper PG, Quax WJ. Engineering of Multiple Modules to Improve Amorphadiene Production in Bacillus subtilis Using CRISPR-Cas9. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:4785-4794. [PMID: 33877851 PMCID: PMC8154554 DOI: 10.1021/acs.jafc.1c00498] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Engineering strategies to improve terpenoids' production in Bacillus subtilis mainly focus on 2C-methyl-d-erythritol-4-phosphate (MEP) pathway overexpression. To systematically engineer the chassis strain for higher amorphadiene (precursor of artemisinin) production, a clustered regularly interspaced short palindromic repeat-Cas9 (CRISPR-Cas9) system was established in B. subtilis to facilitate precise and efficient genome editing. Then, this system was employed to engineer three more modules to improve amorphadiene production, including the terpene synthase module, the branch pathway module, and the central metabolic pathway module. Finally, our combination of all of the useful strategies within one strain significantly increased extracellular amorphadiene production from 81 to 116 mg/L after 48 h flask fermentation without medium optimization. For the first time, we attenuated the FPP-derived competing pathway to improve amorphadiene biosynthesis and investigated how the TCA cycle affects amorphadiene production in B. subtilis. Overall, this study provides a universal strategy for further increasing terpenoids' production in B. subtilis by comprehensive and systematic metabolic engineering.
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Affiliation(s)
- Yafeng Song
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Siqi He
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ingy I. Abdallah
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Department
of Pharmacognosy, Faculty of Pharmacy, Alexandria
University, 21521 Alexandria, Egypt
| | - Anita Jopkiewicz
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rita Setroikromo
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ronald van Merkerk
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Pieter G. Tepper
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Wim J. Quax
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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Malwal SR, Chen L, Hicks H, Qu F, Liu W, Shillo A, Law WX, Zhang J, Chandnani N, Han X, Zheng Y, Chen CC, Guo RT, AbdelKhalek A, Seleem MN, Oldfield E. Discovery of Lipophilic Bisphosphonates That Target Bacterial Cell Wall and Quinone Biosynthesis. J Med Chem 2019; 62:2564-2581. [PMID: 30730737 DOI: 10.1021/acs.jmedchem.8b01878] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report that alkyl-substituted bisphosphonates have activity against Bacillus anthracis Sterne (0.40 μg/mL), Mycobacterium smegmatis (1.4 μg/mL), Bacillus subtilis (1.0 μg/mL), and Staphylococcus aureus (13 μg/mL). In many cases, there is no effect of serum binding, as well as low activity against a human embryonic kidney cell line. Targeting of isoprenoid biosynthesis is involved with 74 having IC50 values of ∼100 nM against heptaprenyl diphosphate synthase and 200 nM against farnesyl diphosphate synthase. B. subtilis growth inhibition was rescued by addition of farnesyl diphosphate, menaquinone-4 (MK-4), or undecaprenyl phosphate (UP), and the combination of MK-4 and UP resulted in a 25× increase in ED50, indicating targeting of both quinone and cell wall biosynthesis. Clostridioides difficile was inhibited by 74, and since this organism does not synthesize quinones, cell wall biosynthesis is the likely target. We also solved three X-ray structures of inhibitors bound to octaprenyl diphosphate and/or undecaprenyl diphosphate synthases.
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Affiliation(s)
| | | | | | | | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 200208 , China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan 430062 , China
| | | | | | | | | | - Xu Han
- Industrial Enzymes National Engineering Laboratory , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 200208 , China
| | - Yingying Zheng
- Industrial Enzymes National Engineering Laboratory , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 200208 , China
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan 430062 , China
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 200208 , China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan 430062 , China
| | - Ahmed AbdelKhalek
- Department of Comparative Pathobiology, College of Veterinary Medicine , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, College of Veterinary Medicine , Purdue University , West Lafayette , Indiana 47907 , United States.,Purdue Institute of Inflammation, Immunology, and Infectious Disease , West Lafayette , Indiana 47907 , United States
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Kurihara K. Molecular Architecture Studied by the Surface Forces Measurement. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:12290-12303. [PMID: 27807975 DOI: 10.1021/acs.langmuir.6b03074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This feature article reviews the surface forces measurement as a tool for studying molecular architecture chemistry. The history of the measurement is briefly described in the Introduction. The general overview covers specific features of the surface forces measurement as a tool for studying and using molecular architecture. This measurement is powerful for understanding interaction forces and for characterizing and discovering the phenomena at solid-liquid interfaces and soft complex matter. An apparatus for opaque samples was developed, which can be used to study not only opaque samples in various media but also electrochemical processes under various electrochemical potentials. Our studies of molecular architecture are reviewed; they include biological molecular recognition especially involved in the enzyme-substrate interaction; polyelectrolyte brushes exhibiting steric repulsion, which can be reproduced by the osmotic pressure of the counterions, and a density-dependent transition; the hydrogen-bonded molecular macrocluster formation of alcohol and carboxylic acids adsorbed on silica in nonpolar solvents such as cyclohexane; and surface forces between ferrocene-modified electrodes under various applied potentials. These studies demonstrate how the forces measurement is used to identify interacting species such as in biological systems to reveal unknown phenomena and to characterize soft complex matter and the effective potential of the electrodes. Readers will be introduced to the broad applications of the force measurement.
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Affiliation(s)
- Kazue Kurihara
- Institute of Multidisciplinary Research for Advanced Materials & Advanced Institute for Materials Research, Tohoku University , Katahira, Aoba-ku, Sendai 980-8577, Japan
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Desai J, Liu YL, Wei H, Liu W, Ko TP, Guo RT, Oldfield E. Structure, Function, and Inhibition of Staphylococcus aureus Heptaprenyl Diphosphate Synthase. ChemMedChem 2016; 11:1915-23. [PMID: 27457559 PMCID: PMC5012948 DOI: 10.1002/cmdc.201600311] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Indexed: 11/07/2022]
Abstract
We report the first structure of heptaprenyl diphosphate synthase from Staphylococcus aureus (SaHepPPS), together with an investigation of its mechanism of action and inhibition. The protein is involved in the formation of menaquinone, a key electron transporter in many bacteria, including pathogens. SaHepPPS consists of a "catalytic " subunit (SaHepPPS-2) having two "DDXXD" motifs and a "regulatory" subunit (SaHepPPS-1) that lacks these motifs. High concentrations of the substrates, isopentenyl diphosphate and farnesyl diphosphate, inhibit the enzyme, which is also potently inhibited by bisphosphonates. The most active inhibitors (Ki ∼200 nm) were N-alkyl analogues of zoledronate containing ∼C6 alkyl side chains. They were modestly active against S. aureus cell growth, and growth inhibition was partially "rescued" by the addition of menaquinone-7. Because SaHepPPS is essential for S. aureus cell growth, its structure is of interest in the context of the development of menaquinone biosynthesis inhibitors as potential antibiotic leads.
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Affiliation(s)
- Janish Desai
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, USA
| | - Yi-Liang Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, IL, 61801, USA
| | - Hongli Wei
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PRC
| | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PRC
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Taipei, 11529, ROC
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PRC
| | - Eric Oldfield
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, USA.
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, IL, 61801, USA.
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Takenaka M, Miyachi Y, Ishii J, Ogino C, Kondo A. The mapping of yeast's G-protein coupled receptor with an atomic force microscope. NANOSCALE 2015; 7:4956-4963. [PMID: 25690872 DOI: 10.1039/c4nr05940a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
An atomic force microscope (AFM) can measure the adhesion force between a sample and a cantilever while simultaneously applying a rupture force during the imaging of a sample. An AFM should be useful in targeting specific proteins on a cell surface. The present study proposes the use of an AFM to measure the adhesion force between targeting receptors and their ligands, and to map the targeting receptors. In this study, Ste2p, one of the G protein-coupled receptors (GPCRs), was chosen as the target receptor. The specific force between Ste2p on a yeast cell surface and a cantilever modified with its ligand, α-factor, was measured and found to be approximately 250 pN. In addition, through continuous measuring of the cell surface, a mapping of the receptors on the cell surface could be performed, which indicated the differences in the Ste2p expression levels. Therefore, the proposed AFM system is accurate for cell diagnosis.
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Affiliation(s)
- Musashi Takenaka
- Department of Chemical and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan.
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Identification of a lysine residue important for the catalytic activity of yeast farnesyl diphosphate synthase. Protein J 2011; 30:334-9. [PMID: 21643844 DOI: 10.1007/s10930-011-9336-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The Saccharomyces cerevisiae ERG20 gene (encoding farnesyl diphosphate synthase) has been subjected to a set of mutations at the catalytic site, at position K254 to determine the in vivo impact. The mutated strains have been shown to exhibit various growth rates, sterol profiles and monoterpenol producing capacities. The results obtained suggest that K at position 254 helps to stabilize one of the three Mg(2+) forming a bridge between the enzyme and DMAPP, and demonstrate that destabilizing two of the three Mg(2+) ions, by introducing a double mutation at positions K197 and K254, results in a loss of FPPS activity and a lethal phenotype.
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Becker B, Cooper MA. A survey of the 2006-2009 quartz crystal microbalance biosensor literature. J Mol Recognit 2011; 24:754-87. [DOI: 10.1002/jmr.1117] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Mori T, Asakura M, Okahata Y. Single-Molecule Force Spectroscopy for Studying Kinetics of Enzymatic Dextran Elongations. J Am Chem Soc 2011; 133:5701-3. [DOI: 10.1021/ja200094f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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MINODA K, ICHIKAWA T, KATSUMATA T, ONOBORI KI, MORI T, SUZUKI Y, ISHII T, NAKAYAMA T. Influence of the Galloyl Moiety in Tea Catechins on Binding Affinity for Human Serum Albumin. J Nutr Sci Vitaminol (Tokyo) 2010; 56:331-4. [DOI: 10.3177/jnsv.56.331] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Casero E, Vázquez L, Parra-Alfambra AM, Lorenzo E. AFM, SECM and QCM as useful analytical tools in the characterization of enzyme-based bioanalytical platforms. Analyst 2010; 135:1878-903. [DOI: 10.1039/c0an00120a] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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11
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Single Molecular Film for Recognizing Biological Molecular Interaction: DNA-Protein Interaction and Enzyme Reaction. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/978-3-540-92233-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Wilner O, Guidotti C, Wieckowska A, Gill R, Willner I. Probing Kinase Activities by Electrochemistry, Contact-Angle Measurements, and Molecular-Force Interactions. Chemistry 2008; 14:7774-81. [DOI: 10.1002/chem.200800765] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Furusawa H, Takano H, Okahata Y. Transient kinetic studies of protein hydrolyses by endo- and exo-proteases on a 27 MHz quartz-crystal microbalance. Org Biomol Chem 2008; 6:727-31. [DOI: 10.1039/b717171d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Suzuki T, Koyama T, Kurihara K. Selectivity in substrate–enzyme complexation studied by surface forces measurement. Colloid Polym Sci 2007. [DOI: 10.1007/s00396-007-1746-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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