1
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Wessner M, Bommarius B, Brandenbusch C, Bommarius AS. Purification of chimeric amine dehydrogenase using a tailor-made aqueous two-phase system - A case study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114991] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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2
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Mascuch SJ, Fakhretaha-Aval S, Bowman JC, Ma MTH, Thomas G, Bommarius B, Ito C, Zhao L, Newnam GP, Matange KR, Thapa HR, Barlow B, Donegan RK, Nguyen NA, Saccuzzo EG, Obianyor CT, Karunakaran SC, Pollet P, Rothschild-Mancinelli B, Mestre-Fos S, Guth-Metzler R, Bryksin AV, Petrov AS, Hazell M, Ibberson CB, Penev PI, Mannino RG, Lam WA, Garcia AJ, Kubanek J, Agarwal V, Hud NV, Glass JB, Williams LD, Lieberman RL. A blueprint for academic laboratories to produce SARS-CoV-2 quantitative RT-PCR test kits. J Biol Chem 2020; 295:15438-15453. [PMID: 32883809 PMCID: PMC7667971 DOI: 10.1074/jbc.ra120.015434] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/24/2020] [Indexed: 01/09/2023] Open
Abstract
Widespread testing for the presence of the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in individuals remains vital for controlling the COVID-19 pandemic prior to the advent of an effective treatment. Challenges in testing can be traced to an initial shortage of supplies, expertise, and/or instrumentation necessary to detect the virus by quantitative RT-PCR (RT-qPCR), the most robust, sensitive, and specific assay currently available. Here we show that academic biochemistry and molecular biology laboratories equipped with appropriate expertise and infrastructure can replicate commercially available SARS-CoV-2 RT-qPCR test kits and backfill pipeline shortages. The Georgia Tech COVID-19 Test Kit Support Group, composed of faculty, staff, and trainees across the biotechnology quad at Georgia Institute of Technology, synthesized multiplexed primers and probes and formulated a master mix composed of enzymes and proteins produced in-house. Our in-house kit compares favorably with a commercial product used for diagnostic testing. We also developed an environmental testing protocol to readily monitor surfaces for the presence of SARS-CoV-2. Our blueprint should be readily reproducible by research teams at other institutions, and our protocols may be modified and adapted to enable SARS-CoV-2 detection in more resource-limited settings.
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Affiliation(s)
- Samantha J. Mascuch
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sara Fakhretaha-Aval
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jessica C. Bowman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Minh Thu H. Ma
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Gwendell Thomas
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Bettina Bommarius
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Chieri Ito
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Liangjun Zhao
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Gary P. Newnam
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Kavita R. Matange
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Hem R. Thapa
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Brett Barlow
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rebecca K. Donegan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nguyet A. Nguyen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Emily G. Saccuzzo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Chiamaka T. Obianyor
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Suneesh C. Karunakaran
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Pamela Pollet
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | | | - Santi Mestre-Fos
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rebecca Guth-Metzler
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Anton V. Bryksin
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Anton S. Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Mallory Hazell
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Carolyn B. Ibberson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Petar I. Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Robert G. Mannino
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
| | - Wilbur A. Lam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
- Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Andrés J. Garcia
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Julia Kubanek
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Vinayak Agarwal
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jennifer B. Glass
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Raquel L. Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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3
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Mascuch SJ, Fakhretaha-Aval S, Bowman JC, Ma MTH, Thomas G, Bommarius B, Ito C, Zhao L, Newnam GP, Matange KR, Thapa HR, Barlow B, Donegan RK, Nguyen NA, Saccuzzo EG, Obianyor CT, Karunakaran SC, Pollet P, Rothschild-Mancinelli B, Mestre-Fos S, Guth-Metzler R, Bryksin AV, Petrov AS, Hazell M, Ibberson CB, Penev PI, Mannino RG, Lam WA, Garcia AJ, Kubanek JM, Agarwal V, Hud NV, Glass JB, Williams LD, Lieberman RL. A blueprint for academic labs to produce SARS-CoV-2 RT-qPCR test kits. medRxiv 2020:2020.07.29.20163949. [PMID: 32766604 PMCID: PMC7402063 DOI: 10.1101/2020.07.29.20163949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Widespread testing for the presence of the novel coronavirus SARS-CoV-2 in individuals remains vital for controlling the COVID-19 pandemic prior to the advent of an effective treatment. Challenges in testing can be traced to an initial shortage of supplies, expertise and/or instrumentation necessary to detect the virus by quantitative reverse transcription polymerase chain reaction (RT-qPCR), the most robust, sensitive, and specific assay currently available. Here we show that academic biochemistry and molecular biology laboratories equipped with appropriate expertise and infrastructure can replicate commercially available SARS-CoV-2 RT-qPCR test kits and backfill pipeline shortages. The Georgia Tech COVID-19 Test Kit Support Group, composed of faculty, staff, and trainees across the biotechnology quad at Georgia Institute of Technology, synthesized multiplexed primers and probes and formulated a master mix composed of enzymes and proteins produced in-house. Our in-house kit compares favorably to a commercial product used for diagnostic testing. We also developed an environmental testing protocol to readily monitor surfaces across various campus laboratories for the presence of SARS-CoV-2. Our blueprint should be readily reproducible by research teams at other institutions, and our protocols may be modified and adapted to enable SARS-CoV-2 detection in more resource-limited settings.
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Affiliation(s)
- Samantha J Mascuch
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Sara Fakhretaha-Aval
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jessica C Bowman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Minh Thu H Ma
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gwendell Thomas
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Bettina Bommarius
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Chieri Ito
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Liangjun Zhao
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gary P Newnam
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kavita R Matange
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Hem R Thapa
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Brett Barlow
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rebecca K Donegan
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Nguyet A Nguyen
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Emily G Saccuzzo
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Chiamaka T Obianyor
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Suneesh C Karunakaran
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Pamela Pollet
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Santi Mestre-Fos
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rebecca Guth-Metzler
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anton V Bryksin
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anton S Petrov
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mallory Hazell
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Carolyn B Ibberson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Petar I Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Robert G Mannino
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Wilbur A Lam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Andrés J Garcia
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Julia M Kubanek
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Vinayak Agarwal
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Nicholas V Hud
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jennifer B Glass
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Loren Dean Williams
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
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4
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Willot SJ, Hoang MD, Paul CE, Alcalde M, Arends IWCE, Bommarius AS, Bommarius B, Hollmann F. FOx News: Towards Methanol‐driven Biocatalytic Oxyfunctionalisation Reactions. ChemCatChem 2020. [DOI: 10.1002/cctc.202000197] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sébastien J.‐P. Willot
- Department of Biotechnology Delft University of Technology van der Maasweg 9 2629 HZ Delft (The Netherlands
| | - Manh Dat Hoang
- Institute of Biochemical Engineering Technical University of Munich Boltzmannstr. 15 85748 Garching Germany
| | - Caroline E. Paul
- Department of Biotechnology Delft University of Technology van der Maasweg 9 2629 HZ Delft (The Netherlands
| | - Miguel Alcalde
- Department of Biocatalysis Institute of Catalysis, CSIC Madrid Spain
| | | | - Andreas S. Bommarius
- School of Chemical and Biomolecular Engineering Georgia Institute of Technology 950 Atlantic Drive, N.W. Atlanta GA 30332 USA
| | - Bettina Bommarius
- School of Chemical and Biomolecular Engineering Georgia Institute of Technology 950 Atlantic Drive, N.W. Atlanta GA 30332 USA
| | - Frank Hollmann
- Department of Biotechnology Delft University of Technology van der Maasweg 9 2629 HZ Delft (The Netherlands
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5
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Tieves F, Willot SJ, van Schie MMCH, Rauch MCR, Younes SHH, Zhang W, Dong J, Gomez de Santos P, Robbins JM, Bommarius B, Alcalde M, Bommarius AS, Hollmann F. Formate Oxidase (FOx) from Aspergillus oryzae: One Catalyst Enables Diverse H 2 O 2 -Dependent Biocatalytic Oxidation Reactions. Angew Chem Int Ed Engl 2019; 58:7873-7877. [PMID: 30945422 PMCID: PMC6563469 DOI: 10.1002/anie.201902380] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Indexed: 12/29/2022]
Abstract
An increasing number of biocatalytic oxidation reactions rely on H2 O2 as a clean oxidant. The poor robustness of most enzymes towards H2 O2 , however, necessitates more efficient systems for in situ H2 O2 generation. In analogy to the well-known formate dehydrogenase to promote NADH-dependent reactions, we here propose employing formate oxidase (FOx) to promote H2 O2 -dependent enzymatic oxidation reactions. Even under non-optimised conditions, high turnover numbers for coupled FOx/peroxygenase catalysis were achieved.
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Affiliation(s)
- Florian Tieves
- Department of BiotechnologyUniversity of Technology Delftvan der Massweg 92629HZDelftThe Netherlands
| | | | | | | | - Sabry Hamdy Hamed Younes
- Department of BiotechnologyUniversity of Technology Delftvan der Massweg 92629HZDelftThe Netherlands
- Chemistry DepartmentFaculty of ScienceSohag UniversitySohag82524Egypt
| | - Wuyuan Zhang
- Department of BiotechnologyUniversity of Technology Delftvan der Massweg 92629HZDelftThe Netherlands
| | - JiaJia Dong
- Department of BiotechnologyUniversity of Technology Delftvan der Massweg 92629HZDelftThe Netherlands
| | | | - John Mick Robbins
- School of Chemical and Biomolecular EngineeringGeorgia Institute of Technology311 Ferst Drive, N.W.AtlantaGA30332USA
| | - Bettina Bommarius
- School of Chemical and Biomolecular EngineeringGeorgia Institute of Technology311 Ferst Drive, N.W.AtlantaGA30332USA
| | - Miguel Alcalde
- Department of BiocatalysisInstitute of CatalysisCSIC28049MadridSpain
| | - Andreas Sebastian Bommarius
- School of Chemical and Biomolecular EngineeringGeorgia Institute of Technology311 Ferst Drive, N.W.AtlantaGA30332USA
- School of Chemistry and BiochemistryGeorgia Institute of Technology901 Atlantic Drive, N.W.AtlantaGA30332USA
| | - Frank Hollmann
- Department of BiotechnologyUniversity of Technology Delftvan der Massweg 92629HZDelftThe Netherlands
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6
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Tieves F, Willot SJ, van Schie MMCH, Rauch MCR, Younes SHH, Zhang W, Dong J, Gomez de Santos P, Robbins JM, Bommarius B, Alcalde M, Bommarius AS, Hollmann F. Formiat‐Oxidase (FOx) aus
Aspergillus oryzae
: ein Katalysator für verschiedene H
2
O
2
‐abhängige biokatalytische Oxidationen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902380] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Florian Tieves
- Department of BiotechnologyUniversity of Technology Delft van der Massweg 9 2629HZ Delft Niederlande
| | | | | | | | - Sabry Hamdy Hamed Younes
- Department of BiotechnologyUniversity of Technology Delft van der Massweg 9 2629HZ Delft Niederlande
- Chemistry DepartmentFaculty of ScienceSohag University Sohag 82524 Ägypten
| | - Wuyuan Zhang
- Department of BiotechnologyUniversity of Technology Delft van der Massweg 9 2629HZ Delft Niederlande
| | - JiaJia Dong
- Department of BiotechnologyUniversity of Technology Delft van der Massweg 9 2629HZ Delft Niederlande
| | | | - John Mick Robbins
- School of Chemical and Biomolecular EngineeringGeorgia Institute of Technology 311 Ferst Drive, N.W. Atlanta GA 30332 USA
| | - Bettina Bommarius
- School of Chemical and Biomolecular EngineeringGeorgia Institute of Technology 311 Ferst Drive, N.W. Atlanta GA 30332 USA
| | - Miguel Alcalde
- Department of BiocatalysisInstitute of CatalysisCSIC 28049 Madrid Spanien
| | - Andreas Sebastian Bommarius
- School of Chemical and Biomolecular EngineeringGeorgia Institute of Technology 311 Ferst Drive, N.W. Atlanta GA 30332 USA
- School of Chemistry and BiochemistryGeorgia Institute of Technology 901 Atlantic Drive, N.W. Atlanta GA 30332 USA
| | - Frank Hollmann
- Department of BiotechnologyUniversity of Technology Delft van der Massweg 9 2629HZ Delft Niederlande
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7
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Affiliation(s)
- Maike Gräff
- Institute of Biochemistry and Technical BiochemistryUniversity of Stuttgart Stuttgart Germany
| | - Patrick C.F. Buchholz
- Institute of Biochemistry and Technical BiochemistryUniversity of Stuttgart Stuttgart Germany
| | - Peter Stockinger
- Institute of Biochemistry and Technical BiochemistryUniversity of Stuttgart Stuttgart Germany
| | - Bettina Bommarius
- Department of Chemical and Biomolecular EngineeringGeorgia Institute of Technology Atlanta Georgia
| | - Andreas S. Bommarius
- Department of Chemical and Biomolecular EngineeringGeorgia Institute of Technology Atlanta Georgia
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical BiochemistryUniversity of Stuttgart Stuttgart Germany
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8
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Gräff M, Buchholz PC, Stockinger P, Bommarius B, Bommarius AS, Pleiss J. The Short‐chain Dehydrogenase/Reductase Engineering Database (SDRED): A classification and analysis system for a highly diverse enzyme family. Proteins 2019; 87:443-451. [DOI: 10.1002/prot.25666] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/26/2019] [Accepted: 01/31/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Maike Gräff
- Institute of Biochemistry and Technical BiochemistryUniversity of Stuttgart Stuttgart Germany
| | - Patrick C.F. Buchholz
- Institute of Biochemistry and Technical BiochemistryUniversity of Stuttgart Stuttgart Germany
| | - Peter Stockinger
- Institute of Biochemistry and Technical BiochemistryUniversity of Stuttgart Stuttgart Germany
| | - Bettina Bommarius
- Department of Chemical and Biomolecular EngineeringGeorgia Institute of Technology Atlanta Georgia
| | - Andreas S. Bommarius
- Department of Chemical and Biomolecular EngineeringGeorgia Institute of Technology Atlanta Georgia
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical BiochemistryUniversity of Stuttgart Stuttgart Germany
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9
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Baldwin PR, Reeves AZ, Powell KR, Napier RJ, Swimm AI, Sun A, Giesler K, Bommarius B, Shinnick TM, Snyder JP, Liotta DC, Kalman D. Monocarbonyl analogs of curcumin inhibit growth of antibiotic sensitive and resistant strains of Mycobacterium tuberculosis. Eur J Med Chem 2015; 92:693-9. [PMID: 25618016 PMCID: PMC4794995 DOI: 10.1016/j.ejmech.2015.01.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/05/2015] [Accepted: 01/10/2015] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) is a major public health concern worldwide with over 2 billion people currently infected. The rise of strains of Mycobacterium tuberculosis (Mtb) that are resistant to some or all first and second line antibiotics, including multidrug-resistant (MDR), extensively drug resistant (XDR) and totally drug resistant (TDR) strains, is of particular concern and new anti-TB drugs are urgently needed. Curcumin, a natural product used in traditional medicine in India, exhibits anti-microbial activity that includes Mtb, however it is relatively unstable and suffers from poor bioavailability. To improve activity and bioavailability, mono-carbonyl analogs of curcumin were synthesized and screened for their capacity to inhibit the growth of Mtb and the related Mycobacterium marinum (Mm). Using disk diffusion and liquid culture assays, we found several analogs that inhibit in vitro growth of Mm and Mtb, including rifampicin-resistant strains. Structure activity analysis of the analogs indicated that Michael acceptor properties are critical for inhibitory activity. However, no synergistic effects were evident between the monocarbonyl analogs and rifampicin on inhibiting growth. Together, these data provide a structural basis for the development of analogs of curcumin with pronounced anti-mycobacterial activity and provide a roadmap to develop additional structural analogs that exhibit more favorable interactions with other anti-TB drugs.
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Affiliation(s)
| | - Analise Z Reeves
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta GA 30333, USA; Microbiology and Molecular Genetics Graduate Program, Emory University School of Medicine, Atlanta GA 30322, USA
| | - Kimberly R Powell
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta GA 30322, USA
| | - Ruth J Napier
- Microbiology and Molecular Genetics Graduate Program, Emory University School of Medicine, Atlanta GA 30322, USA
| | - Alyson I Swimm
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta GA 30322, USA
| | - Aiming Sun
- Department of Chemistry, Emory University, Atlanta GA 30322, USA
| | - Kyle Giesler
- Department of Chemistry, Emory University, Atlanta GA 30322, USA
| | - Bettina Bommarius
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta GA 30322, USA
| | - Thomas M Shinnick
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta GA 30333, USA
| | - James P Snyder
- Department of Chemistry, Emory University, Atlanta GA 30322, USA
| | - Dennis C Liotta
- Department of Chemistry, Emory University, Atlanta GA 30322, USA
| | - Daniel Kalman
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta GA 30322, USA.
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10
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Bommarius A, Abrahamson M, Schuermann M, Au S, Bommarius B. Design of a novel redox biocatalyst to specification (363.3). FASEB J 2014. [DOI: 10.1096/fasebj.28.1_supplement.363.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Jablonski AE, Vegh RB, Hsiang JC, Bommarius B, Chen YC, Solntsev KM, Bommarius AS, Tolbert LM, Dickson RM. Optically modulatable blue fluorescent proteins. J Am Chem Soc 2013; 135:16410-7. [PMID: 24099419 DOI: 10.1021/ja405459b] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Blue fluorescent proteins (BFPs) offer visualization of protein location and behavior, but often suffer from high autofluorescent background and poor signal discrimination. Through dual-laser excitation of bright and photoinduced dark states, mutations to the residues surrounding the BFP chromophore enable long-wavelength optical modulation of BFP emission. Such dark state engineering enables violet-excited blue emission to be increased upon lower energy, green coillumination. Turning this green coillumination on and off at a specific frequency dynamically modulates collected blue fluorescence without generating additional background. Interpreted as transient photoconversion between neutral cis and anionic trans chromophoric forms, mutations tune photoisomerization and ground state tautomerizations to enable long-wavelength depopulation of the millisecond-lived, spectrally shifted dark states. Single mutations to the tyrosine-based blue fluorescent protein T203V/S205V exhibit enhanced modulation depth and varied frequency. Importantly, analogous single point mutations in the nonmodulatable BFP, mKalama1, creates a modulatable variant. Building modulatable BFPs offers opportunities for improved BFP signal discrimination vs background, greatly enhancing their utility.
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Affiliation(s)
- Amy E Jablonski
- School of Chemistry and Biochemistry, ‡School of Chemical and Biomolecular Engineering, and §Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
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Bommarius B, Jenssen H, Elliott M, Kindrachuk J, Pasupuleti M, Gieren H, Jaeger KE, Hancock REW, Kalman D. Cost-effective expression and purification of antimicrobial and host defense peptides in Escherichia coli. Peptides 2010; 31:1957-65. [PMID: 20713107 PMCID: PMC2992949 DOI: 10.1016/j.peptides.2010.08.008] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 08/02/2010] [Accepted: 08/03/2010] [Indexed: 10/19/2022]
Abstract
Cationic antimicrobial host defense peptides (HDPs) combat infection by directly killing a wide variety of microbes, and/or modulating host immunity. HDPs have great therapeutic potential against antibiotic-resistant bacteria, viruses and even parasites, but there are substantial roadblocks to their therapeutic application. High manufacturing costs associated with amino acid precursors have limited the delivery of inexpensive therapeutics through industrial-scale chemical synthesis. Conversely, the production of peptides in bacteria by recombinant DNA technology has been impeded by the antimicrobial activity of these peptides and their susceptibility to proteolytic degradation, while subsequent purification of recombinant peptides often requires multiple steps and has not been cost-effective. Here we have developed methodologies appropriate for large-scale industrial production of HDPs; in particular, we describe (i) a method, using fusions to SUMO, for producing high yields of intact recombinant HDPs in bacteria without significant toxicity and (ii) a simplified 2-step purification method appropriate for industrial use. We have used this method to produce seven HDPs to date (IDR1, MX226, LL37, CRAMP, HHC-10, E5 and E6). Using this technology, pilot-scale fermentation (10L) was performed to produce large quantities of biologically active cationic peptides. Together, these data indicate that this new method represents a cost-effective means to enable commercial enterprises to produce HDPs in large-scale under Good Laboratory Manufacturing Practice (GMP) conditions for therapeutic application in humans.
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Affiliation(s)
- B Bommarius
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
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Bommarius B, Kalman D. Antimicrobial and host defense peptides for therapeutic use against multidrug-resistant pathogens: new hope on the horizon. IDrugs 2009; 12:376-380. [PMID: 19517318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The concept of using antimicrobial peptides (AMPs) and host defense peptides (HDPs) as therapeutics was first introduced in the late 1990s. However, an AMP drug has yet to reach the market. AMPs and HDPs have intriguing potential as therapeutics: the peptides are evolutionary conserved, and are critical components of the innate immune system of all eukaryotes; their evolution pre-dates the appearance of the adaptive immune system; and they do not readily engender bacterial resistance. Nevertheless, there are significant obstacles to the use of AMPs and HDPs in humans, including the need to conduct clinical trials to demonstrate efficacy, and the capacity to manufacture AMPs and HDPs in a cost-effective manner. Progress in both of these areas would support the exciting possibility that AMPs and HDPs could be developed as therapeutics that kill pathogens and facilitate the immune response.
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Affiliation(s)
- Bettina Bommarius
- Emory University, Department of Pathology and Laboratory Medicine, Atlanta, GA 30322, USA.
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Lebeis SL, Bommarius B, Parkos CA, Sherman MA, Kalman D. TLR signaling mediated by MyD88 is required for a protective innate immune response by neutrophils to Citrobacter rodentium. J Immunol 2007; 179:566-77. [PMID: 17579078 DOI: 10.4049/jimmunol.179.1.566] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Enteropathogenic Escherichia coli, enterohemorrhagic E. coli, and Citrobacter rodentium are classified as attaching and effacing pathogens based on their ability to adhere to intestinal epithelium via actin-filled membranous protrusions (pedestals). Infection of mice with C. rodentium causes breach of the colonic epithelial barrier, a vigorous Th1 inflammatory response, and colitis. Ultimately, an adaptive immune response leads to clearance of the bacteria. Whereas much is known about the adaptive response to C. rodentium, the role of the innate immune response remains unclear. In this study, we demonstrate for the first time that the TLR adaptor MyD88 is essential for survival and optimal immunity following infection. MyD88(-/-) mice suffer from bacteremia, gangrenous mucosal necrosis, severe colitis, and death following infection. Although an adaptive response occurs, MyD88-dependent signaling is necessary for efficient clearance of the pathogen. Based on reciprocal bone marrow transplants in conjunction with assessment of intestinal mucosal pathology, repair, and cytokine production, our findings suggest a model in which TLR signaling in hemopoietic and nonhemopoietic cells mediate three distinct processes: 1) induction of an epithelial repair response that maintains the protective barrier and limits access of bacteria to the lamina propria; 2) production of KC or other chemokines that attract neutrophils and thus facilitate killing of bacteria; and 3) efficient activation of an adaptive response that facilitates Ab-mediated clearance of the infection. Taken together, these experiments provide evidence for a protective role of innate immune signaling in infections caused by attaching and effacing pathogens.
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Affiliation(s)
- Sarah L Lebeis
- Microbiology and Molecular Genetics Graduate Program, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 165 Michael Street, Atlanta, GA 30322, USA
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Bommarius B, Maxwell D, Swimm A, Leung S, Corbett A, Bornmann W, Kalman D. Enteropathogenic Escherichia coli Tir is an SH2/3 ligand that recruits and activates tyrosine kinases required for pedestal formation. Mol Microbiol 2007; 63:1748-68. [PMID: 17367393 DOI: 10.1111/j.1365-2958.2007.05626.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enteropathogenic Escherichia coli (EPEC) cause intestinal inflammation, severe diarrhoea and mortality, particularly among children in developing nations. Upon attachment to intestinal epithelial cells, EPEC induces actin-filled membrane protrusions called 'pedestals' and disrupts microvilli to form attaching and effacing (A/E) lesions. EPEC also disrupts epithelial barrier function and causes colitis. Here we have investigated how virulence factors which orchestrate formation of actin pedestals interface with host tyrosine kinases. We show that Tec-family tyrosine kinases localize beneath EPEC and, with Abl-family kinases, comprise a set of redundant host kinases utilized by EPEC to form actin pedestals. We also show that Tir, a virulence factor required for pathogenesis, contains a polyproline region (PPR) that interacts with SH3 domains of redundant kinases, and a phosphorylation site (Y474) that interacts with kinase SH2 domains. These interactions are essential for pedestal formation, and mimic activation of kinases by cellular ligands. Our results suggest that a positive feedback loop exists in which initial phosphorylation of Tir on Y474 by tyrosine kinases causes recruitment of additional redundant kinases via PPR-SH3 interactions and PO(3)-Y474-SH2 interactions, which in turn phosphorylate other Tir molecules as well as proteins that catalyse formation of actin pedestals.
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Affiliation(s)
- Bettina Bommarius
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
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Reeves PM, Bommarius B, Lebeis S, McNulty S, Christensen J, Swimm A, Chahroudi A, Chavan R, Feinberg MB, Veach D, Bornmann W, Sherman M, Kalman D. Disabling poxvirus pathogenesis by inhibition of Abl-family tyrosine kinases. Nat Med 2005; 11:731-9. [PMID: 15980865 DOI: 10.1038/nm1265] [Citation(s) in RCA: 174] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2004] [Accepted: 06/02/2005] [Indexed: 11/09/2022]
Abstract
The Poxviridae family members vaccinia and variola virus enter mammalian cells, replicate outside the nucleus and produce virions that travel to the cell surface along microtubules, fuse with the plasma membrane and egress from infected cells toward apposing cells on actin-filled membranous protrusions. We show that cell-associated enveloped virions (CEV) use Abl- and Src-family tyrosine kinases for actin motility, and that these kinases act in a redundant fashion, perhaps permitting motility in a greater range of cell types. Additionally, release of CEV from the cell requires Abl- but not Src-family tyrosine kinases, and is blocked by STI-571 (Gleevec), an Abl-family kinase inhibitor used to treat chronic myelogenous leukemia in humans. Finally, we show that STI-571 reduces viral dissemination by five orders of magnitude and promotes survival in infected mice, suggesting possible use for this drug in treating smallpox or complications associated with vaccination. This therapeutic approach may prove generally efficacious in treating microbial infections that rely on host tyrosine kinases, and, because the drug targets host but not viral molecules, this strategy is much less likely to engender resistance compared to conventional antimicrobial therapies.
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Affiliation(s)
- Patrick M Reeves
- Microbiology and Molecular Genetics Graduate Program, Emory University School of Medicine, 615 Michael Street, Whitehead Research Building #144, Atlanta, Georgia 30322, USA
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Swimm A, Bommarius B, Li Y, Cheng D, Reeves P, Sherman M, Veach D, Bornmann W, Kalman D. Enteropathogenic Escherichia coli use redundant tyrosine kinases to form actin pedestals. Mol Biol Cell 2004; 15:3520-9. [PMID: 15155808 PMCID: PMC491815 DOI: 10.1091/mbc.e04-02-0093] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) are deadly contaminants in water and food and induce protrusion of actin-rich membrane pedestals beneath themselves upon attachment to intestinal epithelia. EPEC then causes intestinal inflammation, diarrhea, and, among children, death. Here, we show that EPEC uses multiple tyrosine kinases for formation of pedestals, each of which is sufficient but not necessary. In particular, we show that Abl and Arg, members of the Abl family of tyrosine kinases, localize and are activated in pedestals. We also show that pyrido[2,3-d]pyrimidine (PD) compounds, which inhibit Abl, Arg, and related kinases, block pedestal formation. Finally, we show that Abl and Arg are sufficient for pedestal formation in the absence of other tyrosine kinase activity, but they are not necessary. Our results suggest that additional kinases that are sensitive to inhibition by PD also can suffice. Together, these results suggest that EPEC has evolved a mechanism to use any of several functionally redundant tyrosine kinases during pathogenesis, perhaps facilitating its capacity to infect different cell types. Moreover, PD compounds are being developed to treat cancers caused by dysregulated Abl. Our results raise the possibility that PD may be useful in treating EPEC infections, and because PD affects host and not bacterium, selecting resistant strains may be far less likely than with conventional antibiotics.
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Affiliation(s)
- Alyson Swimm
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia 30322, USA
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Brar SS, Corbin Z, Kennedy TP, Hemendinger R, Thornton L, Bommarius B, Arnold RS, Whorton AR, Sturrock AB, Huecksteadt TP, Quinn MT, Krenitsky K, Ardie KG, Lambeth JD, Hoidal JR. NOX5 NAD(P)H oxidase regulates growth and apoptosis in DU 145 prostate cancer cells. Am J Physiol Cell Physiol 2003; 285:C353-69. [PMID: 12686516 DOI: 10.1152/ajpcell.00525.2002] [Citation(s) in RCA: 204] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Reactive oxygen species (ROS) appear to play an important role in regulating growth and survival of prostate cancer. However, the sources for ROS production in prostate cancer cells have not been determined. We report that ROS are generated by intact American Type Culture Collection DU 145 cells and by their membranes through a mechanism blocked by NAD(P)H oxidase inhibitors. ROS are critical for growth in these cells, because NAD(P)H oxidase inhibitors and antioxidants blocked proliferation. Components of the human phagocyte NAD(P)H oxidase, p22phox and gp91phox, as well as the Ca2+ concentration-responsive gp91phox homolog NOX5 were demonstrated in DU 145 cells by RT-PCR and sequencing. Although the protein product for p22phox was not detectable, both gp91phox and NOX5 were identified throughout the cell by immunostaining and confocal microscopy and NOX5 immunostaining was enhanced in a perinuclear location, corresponding to enhanced ROS production adjacent to the nuclear membrane imaged by 2',7'-dichlorofluorescin diacetate oxidation. The calcium ionophore ionomycin dramatically stimulated ferricytochrome c reduction in cell media, further supporting the importance of NOX5 for ROS production. Antisense oligonucleotides for NOX5 inhibited ROS production and cell proliferation in DU 145 cells. In contrast, antisense oligonucleotides to p22phox or gp91phox did not impair cell growth. Inhibition of ROS generation with antioxidants or NAD(P)H oxidase inhibitors increased apoptosis in cells. These results indicate that ROS generated by the newly described NOX5 oxidase are essential for prostate cancer growth, possibly by providing trophic intracellular oxidant tone that retards programmed cell death.
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Affiliation(s)
- Sukhdev S Brar
- Department of Internal Medicine, Carolinas Medical Center, Charlotte, NC 28232, USA
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