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Azubuike CC, Gatehouse AMR, Howard TP. pCAT vectors overcome inefficient electroporation of Cupriavidus necator H16. N Biotechnol 2021; 65:20-30. [PMID: 34333160 DOI: 10.1016/j.nbt.2021.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/06/2021] [Accepted: 07/24/2021] [Indexed: 10/20/2022]
Abstract
Cupriavidus necator H16 is a chemolithoautotroph with a range of industrial biotechnological applications. Advanced metabolic engineering in the bacterium, however, is impeded by low transformation efficiency, making it difficult to introduce and screen new genetic functions rapidly. This study systematically characterized the broad host range plasmids pBHR1, pBBR1MCS-2 and pKT230 used frequently for C. necator engineering. Kanamycin resistance cassette (KanR) and a truncated sequence of the replication origin (Rep) are contributing factors to C. necator low electroporation transformation efficiency. Consequently, a series of modular minimal plasmids, named pCAT, were constructed. pCAT vectors transform C. necator H16 with a > 3000-fold higher efficiency (up to 107 CFU/μg DNA) compared to control plasmids. Further, pCAT vectors are highly stable, expressing reporter proteins over several days of serial cultivation in the absence of selection pressure. Finally, they can be assembled rapidly from PCR or synthesized DNA fragments, and restriction-ligation reactions can be efficiently electroporated directly into C. necator, circumventing the requirement to use Escherichia coli for plasmid maintenance or propagation. This study demonstrates that an understanding of the behaviour of the constituent parts of plasmids in a host is key to efficient propagation of genetic information, while offering new methods for engineering a bacterium with desirable industrial biotechnological features.
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Affiliation(s)
- Christopher C Azubuike
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle-upon-Tyne, NE1 7RX, United Kingdom; Department of Microbiology, Faculty of Science, University of Port Harcourt, East-West Road, P.M.B. 5323, Choba, Port Harcourt, Rivers State, Nigeria
| | - Angharad M R Gatehouse
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle-upon-Tyne, NE1 7RX, United Kingdom
| | - Thomas P Howard
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle-upon-Tyne, NE1 7RX, United Kingdom.
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Applying Statistical Design of Experiments To Understanding the Effect of Growth Medium Components on Cupriavidus necator H16 Growth. Appl Environ Microbiol 2020; 86:AEM.00705-20. [PMID: 32561588 PMCID: PMC7440812 DOI: 10.1128/aem.00705-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/31/2020] [Indexed: 01/06/2023] Open
Abstract
Chemically defined media (CDM) for cultivation of C. necator vary in components and compositions. This lack of consensus makes it difficult to optimize new processes for the bacterium. This study employed statistical design of experiments (DOE) to understand how basic components of defined media affect C. necator growth. Our growth model predicts that C. necator can be cultivated to high cell density with components held at low concentrations, arguing that CDM for large-scale cultivation of the bacterium for industrial purposes will be economically competitive. Although existing CDM for the bacterium are without amino acids, addition of a few amino acids to growth medium shortened lag phase of growth. The interactions highlighted by our growth model show how factors can interact with each other during a process to positively or negatively affect process output. This approach is efficient, relying on few well-structured experimental runs to gain maximum information on a biological process, growth. Cupriavidus necator H16 is gaining significant attention as a microbial chassis for range of biotechnological applications. While the bacterium is a major producer of bioplastics, its lithoautotrophic and versatile metabolic capabilities make the bacterium a promising microbial chassis for biofuels and chemicals using renewable resources. It remains necessary to develop appropriate experimental resources to permit controlled bioengineering and system optimization of this microbe. In this study, we employed statistical design of experiments to gain understanding of the impact of components of defined media on C. necator growth and built a model that can predict the bacterium’s cell density based on medium components. This highlighted medium components, and interaction between components, having the most effect on growth: fructose, amino acids, trace elements, CaCl2, and Na2HPO4 contributed significantly to growth (t values of <−1.65 or >1.65); copper and histidine were found to interact and must be balanced for robust growth. Our model was experimentally validated and found to correlate well (r2 = 0.85). Model validation at large culture scales showed correlations between our model-predicted growth ranks and experimentally determined ranks at 100 ml in shake flasks (ρ = 0.87) and 1 liter in a bioreactor (ρ = 0.90). Our approach provides valuable and quantifiable insights on the impact of medium components on cell growth and can be applied to model other C. necator responses that are crucial for its deployment as a microbial chassis. This approach can be extended to other nonmodel microbes of medical and industrial biotechnological importance. IMPORTANCE Chemically defined media (CDM) for cultivation of C. necator vary in components and compositions. This lack of consensus makes it difficult to optimize new processes for the bacterium. This study employed statistical design of experiments (DOE) to understand how basic components of defined media affect C. necator growth. Our growth model predicts that C. necator can be cultivated to high cell density with components held at low concentrations, arguing that CDM for large-scale cultivation of the bacterium for industrial purposes will be economically competitive. Although existing CDM for the bacterium are without amino acids, addition of a few amino acids to growth medium shortened lag phase of growth. The interactions highlighted by our growth model show how factors can interact with each other during a process to positively or negatively affect process output. This approach is efficient, relying on few well-structured experimental runs to gain maximum information on a biological process, growth.
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Assil-Companioni L, Schmidt S, Heidinger P, Schwab H, Kourist R. Hydrogen-Driven Cofactor Regeneration for Stereoselective Whole-Cell C=C Bond Reduction in Cupriavidus necator. CHEMSUSCHEM 2019; 12:2361-2365. [PMID: 30889304 DOI: 10.1002/cssc.201900327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/18/2019] [Indexed: 06/09/2023]
Abstract
The coupling of recombinantly expressed oxidoreductases to endogenous hydrogenases for cofactor recycling permits the omission of organic cosubstrates as sacrificial electron donors in whole-cell biotransformations. This increases atom efficiency and simplifies the reaction. A recombinant ene-reductase was expressed in the hydrogen-oxidizing proteobacterium Cupriavidus necator H16. In hydrogen-driven biotransformations, whole cells catalyzed asymmetric C=C bond reduction of unsaturated cyclic ketones with stereoselectivities up to >99 % enantiomeric excess. The use of hydrogen as a substrate for growth and cofactor regeneration is particularly attractive because it represents a strategy for improving atom efficiency and reducing side product formation associated with the recycling of organic cofactors.
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Affiliation(s)
- Leen Assil-Companioni
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/I, 8010, Graz, Austria
| | - Sandy Schmidt
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/I, 8010, Graz, Austria
| | - Petra Heidinger
- ACIB-Austrian Centre of Industrial Biotechnology, Petersgasse 14/V, 8010, Graz, Austria
| | - Helmut Schwab
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/I, 8010, Graz, Austria
| | - Robert Kourist
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/I, 8010, Graz, Austria
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Lauterbach L, Lenz O. How to make the reducing power of H 2 available for in vivo biosyntheses and biotransformations. Curr Opin Chem Biol 2018; 49:91-96. [PMID: 30544016 DOI: 10.1016/j.cbpa.2018.11.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/15/2018] [Accepted: 11/27/2018] [Indexed: 12/22/2022]
Abstract
Solar-driven electrolysis enables sustainable production of molecular hydrogen (H2), which represents a cheap and carbon-free reductant. Knallgas bacteria like Ralstonia eutropha are able to split H2 to supply energy in form of ATP and NADH, which can be subsequently used to power reactions of interest. R. eutropha employs the Calvin-Benson-Bassham cycle for the fixation of CO2, which is considered as an abundant and non-competing raw material. In this article, we summarize state-of-the-art approaches for H2-driven biosyntheses using engineered R. eutropha. Furthermore, we describe strategies for synthetic H2-driven NADH recycling. Major challenges for technical application and future perspectives are discussed.
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Affiliation(s)
- Lars Lauterbach
- Technische Universität Berlin, Department of Chemistry, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Oliver Lenz
- Technische Universität Berlin, Department of Chemistry, Straße des 17. Juni 135, 10623 Berlin, Germany
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Kutralam-Muniasamy G, Peréz-Guevara F. Genome characteristics dictate poly-R-(3)-hydroxyalkanoate production in Cupriavidus necator H16. World J Microbiol Biotechnol 2018; 34:79. [DOI: 10.1007/s11274-018-2460-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/19/2018] [Indexed: 11/28/2022]
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Magomedova Z, Grecu A, Sensen CW, Schwab H, Heidinger P. Characterization of two novel alcohol short-chain dehydrogenases/reductases from Ralstonia eutropha H16 capable of stereoselective conversion of bulky substrates. J Biotechnol 2016; 221:78-90. [DOI: 10.1016/j.jbiotec.2016.01.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 12/19/2022]
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Lonsdale TH, Lauterbach L, Honda Malca S, Nestl BM, Hauer B, Lenz O. H2-driven biotransformation of n-octane to 1-octanol by a recombinant Pseudomonas putida strain co-synthesizing an O2-tolerant hydrogenase and a P450 monooxygenase. Chem Commun (Camb) 2015; 51:16173-5. [DOI: 10.1039/c5cc06078h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A bacterial whole-cell system was designed for hydroxylation of n-octane to 1-octanol at the expense of molecular hydrogen and oxygen.
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Affiliation(s)
- Thomas H. Lonsdale
- Department of Chemistry
- Technische Universität Berlin
- 10623 Berlin
- Germany
- Department of Chemistry
| | - Lars Lauterbach
- Department of Chemistry
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Sumire Honda Malca
- Institute of Technical Biochemistry
- Universität Stuttgart
- Stuttgart
- Germany
| | - Bettina M. Nestl
- Institute of Technical Biochemistry
- Universität Stuttgart
- Stuttgart
- Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry
- Universität Stuttgart
- Stuttgart
- Germany
| | - Oliver Lenz
- Department of Chemistry
- Technische Universität Berlin
- 10623 Berlin
- Germany
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Biotransformation of 1,3-propanediol cyclic sulfate and its derivatives to diols by Rhodococcus sp. Biotechnol Lett 2014; 37:183-8. [PMID: 25214230 DOI: 10.1007/s10529-014-1670-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 09/02/2014] [Indexed: 10/24/2022]
Abstract
Rhodococcus sp. CGMCC 4911 transformed 1,3-propanediol cyclic sulfate (1,3-PDS) and its derivatives into corresponding diols. Ethylene sulfate, glycol sulfide, 1,3-PDS, and 1,2-propanediol cyclic sulfate were effectively hydrolyzed with growing cells. (R)-1,2-Propanediol (>99 % e.e.) was obtained at 44 % yield with growing cells. Glycol sulfide, ethylene sulfate, and 1,3-PDS were converted into the corresponding diols at 94.6, 96.3, and 98.3 %, respectively. Optimal reaction conditions with lyophilized resting cells were 30 °C, pH 7.5, and cell dosage 17.9 mg cell dry wt/ml. 1,3-Propanediol was obtained from 50 mM 1,3-PDS at 97.2 % yield by lyophilized cells after 16 h. Lyophilized cells were entrapped in calcium alginate with a half-life of 263 h at 30 °C, and the total operational time of the immobilized biocatalysts could reach over 192 h with a high conversion rate.
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Ramanjooloo A, Cresteil T, Lebrasse C, Beedessee G, Oogarah P, van Soest RW, Marie DE. α-Glucosidase inhibitory activity of marine sponges collected in Mauritius waters. Nat Prod Res 2014; 29:383-7. [DOI: 10.1080/14786419.2014.945173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Fesenko E, Edwards R. Plant synthetic biology: a new platform for industrial biotechnology. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1927-37. [PMID: 24638901 DOI: 10.1093/jxb/eru070] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Thirty years after the production of the first generation of genetically modified plants we are now set to move into a new era of recombinant crop technology through the application of synthetic biology to engineer new and complex input and output traits. The use of synthetic biology technologies will represent more than incremental additions of transgenes, but rather the directed design of completely new metabolic pathways, physiological traits, and developmental control strategies. The need to enhance our ability to improve crops through new engineering capability is now increasingly pressing as we turn to plants not just for food, but as a source of renewable feedstocks for industry. These accelerating and diversifying demands for new output traits coincide with a need to reduce inputs and improve agricultural sustainability. Faced with such challenges, existing technologies will need to be supplemented with new and far-more-directed approaches to turn valuable resources more efficiently into usable agricultural products. While these objectives are challenging enough, the use of synthetic biology in crop improvement will face public acceptance issues as a legacy of genetically modified technologies in many countries. Here we review some of the potential benefits of adopting synthetic biology approaches in improving plant input and output traits for their use as industrial chemical feedstocks, as linked to the rapidly developing biorefining industry. Several promising technologies and biotechnological targets are identified along with some of the key regulatory and societal challenges in the safe and acceptable introduction of such technology.
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Affiliation(s)
- Elena Fesenko
- Food and Environment Research Agency, Sand Hutton, York, YO41 1LZ, UK
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Lauterbach L, Lenz O, Vincent KA. H₂-driven cofactor regeneration with NAD(P)⁺-reducing hydrogenases. FEBS J 2013; 280:3058-68. [PMID: 23497170 DOI: 10.1111/febs.12245] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 03/05/2013] [Accepted: 03/08/2013] [Indexed: 12/15/2022]
Abstract
A large number of industrially relevant enzymes depend upon nicotinamide cofactors, which are too expensive to be added in stoichiometric amounts. Existing NAD(P)H-recycling systems suffer from low activity, or the generation of side products. H₂-driven cofactor regeneration has the advantage of 100% atom efficiency and the use of H₂ as a cheap reducing agent, in a world where sustainable energy carriers are increasingly attractive. The state of development of H₂-driven cofactor-recycling systems and examples of their integration with enzyme reactions are summarized in this article. The O₂-tolerant NAD⁺-reducing hydrogenase from Ralstonia eutropha is a particularly attractive candidate for this approach, and we therefore discuss its catalytic properties that are relevant for technical applications.
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