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Chen J, Guo L, Zhang Y, Zhao M, Li M, Zhao Z, Qi Q, Xian M, Liu M, Zhao G. Metabolic Engineering of Escherichia coli for Bioproduction of ( R)-3-Hydroxybutyric Acid through a Three-Pronged Approach. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39024463 DOI: 10.1021/acs.jafc.4c04123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
(R)-3-Hydroxybutyric acid (R-3HB) is an important chiral chemical with extensive applications in the agricultural, food, and chemical industries. The synthesis of R-3HB by microbial fermentation is of interest due to its remarkable stereoselectivity and economy. However, the low production of R-3HB failed to meet the needs of large-scale industrial production. In this study, an engineered strain for the efficient biosynthesis of R-3HB was constructed through a three-pronged approach encompassing biosynthetic pathway optimization, engineering of NADPH regenerators, and central metabolism regulation. The engineered strain Q5081 produced 75.7 g/L R-3HB, with a productivity of 1.26 g/L/h and a yield of 0.34 g/g glucose in fed-batch fermentation, showing the highest reported titer and productivity of R-3HB to date. We also performed transcriptome sequencing and annotation to illustrate the mechanism underlying the enhanced R-3HB production. The systematic metabolic engineering by a three-pronged approach demonstrated the feasibility of improving the biosynthesis, and the engineered strain Q5081 has the potential for widespread applications in the industrial production of R-3HB.
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Affiliation(s)
- Jinhong Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Likun Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Mohan Zhao
- Qingdao No. 2 Middle School, Qingdao 266061, China
| | - Meijie Li
- Energy-Rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhe Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Mo Xian
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Min Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Guang Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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2
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Islam T, Nguyen-Vo TP, Cho S, Lee J, Gaur VK, Park S. Metabolic engineering of Escherichia coli for enhanced production of 1,3-butanediol from glucose. BIORESOURCE TECHNOLOGY 2023; 389:129814. [PMID: 37783239 DOI: 10.1016/j.biortech.2023.129814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
1,3-Butanediol (1,3-BDO) finds versatile applications in the cosmetic, chemical, and food industries. This study focuses on the metabolic engineering of Escherichia coli K12 to achieve efficient production of 1,3-BDO from glucose via acetoacetyl-CoA, 3-hydroxybutyryl-CoA, and 3-hydroxybutyraldehyde. The accumulation of an intermediary metabolite (pyruvate) and a byproduct (3-hydroxybutyric acid) was reduced by disruption of the negative transcription factor (PdhR) for pyruvate dehydrogenase complex (PDHc) and employing an efficient alcohol dehydrogenase (YjgB), respectively. Additionally, to improve NADPH availability, carbon flux was redirected from the Embden-Meyerhof-Parnas (EMP) pathway to the Entner-Doudoroff (ED) pathway. One resulting strain achieved a record-high titer of 790 mM (∼71.1 g/L) with a yield of 0.65 mol/mol for optically pure (R)-1,3-BDO, with an enantiomeric excess (e.e.) value of 98.5 %. These findings are useful in the commercial production of 1,3-BDO and provide valuable insights into the development of an efficient cell factory for other acetyl-CoA derivatives.
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Affiliation(s)
- Tayyab Islam
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Thuan Phu Nguyen-Vo
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Seunghyun Cho
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Junhak Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; R&D Center, ACTIVON Co., Ltd., Cheongju 28104, Republic of Korea
| | - Vivek Kumar Gaur
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
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3
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Kee PE, Chiang YC, Ng HS, Lan JCW. Expression of His-tagged NADPH-dependent acetoacetyl-CoA reductase in recombinant Escherichia coli BL-21(DE3). J Biosci Bioeng 2023; 136:312-319. [PMID: 37500302 DOI: 10.1016/j.jbiosc.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/14/2023] [Accepted: 07/01/2023] [Indexed: 07/29/2023]
Abstract
Poly-3-hydroxybutyrate (P(3HB)), a member of the polyhydroxyalkanoate (PHA) family, is a biodegradable polyester with diverse industrial applications. NADPH-dependent acetoacetyl-CoA reductase (phaB) is the enzyme which plays an essential role in P(3HB) synthesis by catalyzing the conversion of the intermediates. The expression of phaB enzyme using the recombinant Escherichia coli BL-21(DE3) and the purification of the synthesized enzyme were studied. The pET-B3 plasmid harbouring the phaB gene derived from Ralstonia eutropha H16, was driven by the lac promoter in E. coli BL-21(DE3). The enzyme was expressed with different induction time, temperatures and cell age. Results showed that the cell age of 4 h, induction time of 12 h at 37°C were identified as the optimal conditions for the enzyme reductase expression. A specific activity of 0.151 U mg-1 protein and total protein concentration of 0.518 mg mg-1 of dry cell weight (DCW) were attained. Affinity chromatography was performed to purify the His-tagged phaB enzyme, in which enhanced the specific activity (14.44 U mg-1) and purification fold (38-fold), despite relative low yield (44.6%) of the enzyme was obtained. The purified phaB showed an optimal enzyme activity at 30°C and pH 8.0. The findings provide an alternative for the synthesis of the reductase enzyme which can be used in the industrial-scale production of the biodegradable polymers.
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Affiliation(s)
- Phei Er Kee
- Centre for Research and Graduate Studies, University of Cyberjaya, Persiaran Bestari, Cyberjaya, 63000 Selangor, Malaysia
| | - Yi-Cheng Chiang
- Biorefinery and Bioprocess Engineering Laboratory, Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-Li 32003, Taiwan
| | - Hui Suan Ng
- Centre for Research and Graduate Studies, University of Cyberjaya, Persiaran Bestari, Cyberjaya, 63000 Selangor, Malaysia
| | - John Chi-Wei Lan
- Biorefinery and Bioprocess Engineering Laboratory, Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-Li 32003, Taiwan; Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Chung-Li 32003, Taiwan.
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4
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Collas F, Dronsella BB, Kubis A, Schann K, Binder S, Arto N, Claassens NJ, Kensy F, Orsi E. Engineering the biological conversion of formate into crotonate in Cupriavidus necator. Metab Eng 2023; 79:49-65. [PMID: 37414134 DOI: 10.1016/j.ymben.2023.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/08/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
To advance the sustainability of the biobased economy, our society needs to develop novel bioprocesses based on truly renewable resources. The C1-molecule formate is increasingly proposed as carbon and energy source for microbial fermentations, as it can be efficiently generated electrochemically from CO2 and renewable energy. Yet, its biotechnological conversion into value-added compounds has been limited to a handful of examples. In this work, we engineered the natural formatotrophic bacterium C. necator as cell factory to enable biological conversion of formate into crotonate, a platform short-chain unsaturated carboxylic acid of biotechnological relevance. First, we developed a small-scale (150-mL working volume) cultivation setup for growing C. necator in minimal medium using formate as only carbon and energy source. By using a fed-batch strategy with automatic feeding of formic acid, we could increase final biomass concentrations 15-fold compared to batch cultivations in flasks. Then, we engineered a heterologous crotonate pathway in the bacterium via a modular approach, where each pathway section was assessed using multiple candidates. The best performing modules included a malonyl-CoA bypass for increasing the thermodynamic drive towards the intermediate acetoacetyl-CoA and subsequent conversion to crotonyl-CoA through partial reverse β-oxidation. This pathway architecture was then tested for formate-based biosynthesis in our fed-batch setup, resulting in a two-fold higher titer, three-fold higher productivity, and five-fold higher yield compared to the strain not harboring the bypass. Eventually, we reached a maximum product titer of 148.0 ± 6.8 mg/L. Altogether, this work consists in a proof-of-principle integrating bioprocess and metabolic engineering approaches for the biological upgrading of formate into a value-added platform chemical.
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Affiliation(s)
| | - Beau B Dronsella
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Karin Schann
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | | | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands
| | | | - Enrico Orsi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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Batt SM, Toth S, Rodriguez B, Abrahams KA, Veerapen N, Chiodarelli G, Cox LR, Moynihan PJ, Lelievre J, Fütterer K, Besra GS. Assay development and inhibition of the Mt-DprE2 essential reductase from Mycobacterium tuberculosis. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001288. [PMID: 36748627 PMCID: PMC9993113 DOI: 10.1099/mic.0.001288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
DprE2 is an essential enzyme in the synthesis of decaprenylphosphoryl-β-d-arabinofuranose (DPA) and subsequently arabinogalactan, and is a significant new drug target for M. tuberculosis. Two compounds from the GSK-177 box set, GSK301A and GSK032A, were identified through Mt-DprE2-target overexpression studies. The Mt-DprE1-DprE2 complex was co-purified and a new in vitro DprE2 assay developed, based on the oxidation of the reduced nicotinamide adenine dinucleotide cofactor of DprE2 (NADH/NADPH). The Mt-DprE1-DprE2 complex showed interesting kinetics in both the DprE1 resazurin-based assay, where Mt-DprE2 was found to enhance Mt-DprE1 activity and reduce substrate inhibition; and also in the DprE2 assay, which similarly exhibited substrate inhibition and a difference in kinetics of the two potential cofactors, NADH and NADPH. Although, no inhibition was observed in the DprE2 assay by the two GSK set compounds, spontaneous mutant generation indicated a possible explanation in the form of a pro-drug activation pathway, involving fgd1 and fbiC.
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Affiliation(s)
- Sarah M Batt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Szilvi Toth
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Beatriz Rodriguez
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Katherine A Abrahams
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Natacha Veerapen
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | | | - Liam R Cox
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, UK
| | - Patrick J Moynihan
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Joel Lelievre
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Klaus Fütterer
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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Rueda E, Álvarez-González A, Vila J, Díez-Montero R, Grifoll M, García J. Inorganic carbon stimulates the metabolic routes related to the polyhdroxybutyrate production in a Synechocystis sp. strain (cyanobacteria) isolated from wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154691. [PMID: 35318053 DOI: 10.1016/j.scitotenv.2022.154691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Cyanobacteria are capable of transforming CO2 into polyhydroxybutyrate (PHB). In this study, different inorganic carbon concentrations (0-2 gC L-1) were evaluated for a Synechocystis sp. strain isolated from wastewater. Quantitative RT-qPCR was also performed to decipher the links between inorganic carbon and PHB and glycogen metabolism. 2 gC L-1 of bicarbonate stimulated cell growth, nutrients consumption and production of PHB. Using this concentration, a 14%dcw of PHB and an average productivity of 2.45 mgPHB L-1 d-1 were obtained. Gene expression analysis revelated that these conditions caused the overexpression of genes related to glycogen and PHB synthesis. Moreover, a positive correlation between the genes codifying for the glycogen phosphorylase, the acetyl-CoA reductase and the poly(3-hydroxyalkanoate) polymerase was found, meaning that PHB synthesis and glycogen catabolism are strongly related. These results provide an exhaustive evaluation of the effect of carbon on the PHB production and cyanobacterial metabolism.
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Affiliation(s)
- Estel Rueda
- GEMMA-Group of Environmental Engineering and Microbiology, Department of Civil and Environmental Engineering, Escola d'Enginyeria de Barcelona Est (EEBE), Universitat Politècnica de Catalunya-BarcelonaTech, Av. Eduard Maristany 16, Building C5.1, E-08019 Barcelona, Spain
| | - Ana Álvarez-González
- GEMMA-Group of Environmental Engineering and Microbiology, Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya-BarcelonaTech, c/ Jordi Girona 1-3, Building D1, E-08034 Barcelona, Spain
| | - Joaquim Vila
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Diagonal 643, Barcelona E-08028, Spain
| | - Rubén Díez-Montero
- GEMMA-Group of Environmental Engineering and Microbiology, Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya-BarcelonaTech, c/ Jordi Girona 1-3, Building D1, E-08034 Barcelona, Spain
| | - Magdalena Grifoll
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Diagonal 643, Barcelona E-08028, Spain
| | - Joan García
- GEMMA-Group of Environmental Engineering and Microbiology, Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya-BarcelonaTech, c/ Jordi Girona 1-3, Building D1, E-08034 Barcelona, Spain.
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7
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Adaptive Laboratory Evolution of Halomonas bluephagenesis Enhances Acetate Tolerance and Utilization to Produce Poly(3-hydroxybutyrate). Molecules 2022; 27:molecules27093022. [PMID: 35566371 PMCID: PMC9103988 DOI: 10.3390/molecules27093022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022] Open
Abstract
Acetate is a promising economical and sustainable carbon source for bioproduction, but it is also a known cell-growth inhibitor. In this study, adaptive laboratory evolution (ALE) with acetate as selective pressure was applied to Halomonas bluephagenesis TD1.0, a fast-growing and contamination-resistant halophilic bacterium that naturally accumulates poly(3-hydroxybutyrate) (PHB). After 71 transfers, the evolved strain, B71, was isolated, which not only showed better fitness (in terms of tolerance and utilization rate) to high concentrations of acetate but also produced a higher PHB titer compared with the parental strain TD1.0. Subsequently, overexpression of acetyl-CoA synthetase (ACS) in B71 resulted in a further increase in acetate utilization but a decrease in PHB production. Through whole-genome resequencing, it was speculated that genetic mutations (single-nucleotide variation (SNV) in phaB, mdh, and the upstream of OmpA, and insertion of TolA) in B71 might contribute to its improved acetate adaptability and PHB production. Finally, in a 5 L bioreactor with intermittent feeding of acetic acid, B71 was able to produce 49.79 g/L PHB and 70.01 g/L dry cell mass, which were 147.2% and 82.32% higher than those of TD1.0, respectively. These results highlight that ALE provides a reliable method to harness H. bluephagenesis to metabolize acetate for the production of PHB or other high-value chemicals more efficiently.
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Olavarria K, Pijman YO, Cabrera R, van Loosdrecht MCM, Wahl SA. Engineering an acetoacetyl-CoA reductase from Cupriavidus necator toward NADH preference under physiological conditions. Sci Rep 2022; 12:3757. [PMID: 35260659 PMCID: PMC8904767 DOI: 10.1038/s41598-022-07663-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/21/2022] [Indexed: 11/09/2022] Open
Abstract
The coupling of PHB generation with NADH reoxidation is required to generate PHB as a fermentation product. A fundamental trait to accomplish this feature is to express a functional NADH-preferring acetoacetyl-CoA reductase, engaged in PHB accumulation. One way to obtain such a reductase is by engineering the cofactor preference of the acetoacetyl-CoA reductase encoded by the phaB1 gene from Cupriavidus necator (AARCn1). Aiming to have a deeper understanding of the structural determinants of the cofactor preference in AARCn1, and to obtain an NADH-preferring acetoacetyl-CoA reductase derived from this protein, some engineered enzymes were expressed, purified and kinetically characterized, together with the parental AARCn1. One of these engineered enzymes, Chimera 5, experimentally showed a selectivity ratio ((kcat/KM)NADH/(kcat/KM)NADPH) ≈ 18, which is 160 times higher than the selectivity ratio experimentally observed in the parental AARCn1. A thermodynamic-kinetic approach was employed to estimate the cofactor preference and flux capacity of Chimera 5 under physiological conditions. According to this approach, Chimera 5 could prefer NADH over NADPH between 25 and 150 times. Being a derivative of AARCn1, Chimera 5 should be readily functional in Escherichia coli and C. necator. Moreover, with the expected expression level, its activity should be enough to sustain PHB accumulation fluxes similar to the fluxes previously observed in these biotechnologically relevant cell factories.
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Affiliation(s)
- Karel Olavarria
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands. .,Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6700 EH, Wageningen, The Netherlands.
| | - Yared O Pijman
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Ricardo Cabrera
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Región Metropolitana, Chile
| | - Mark C M van Loosdrecht
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - S Aljoscha Wahl
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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Li M, Ma Y, Zhang X, Zhang L, Chen X, Ye JW, Chen GQ. Tailor-Made Polyhydroxyalkanoates by Reconstructing Pseudomonas Entomophila. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2102766. [PMID: 34322928 DOI: 10.1002/adma.202102766] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/29/2021] [Indexed: 06/13/2023]
Abstract
Microbial polyhydroxyalkanoates (PHA) containing short- and medium/long-chain-length monomers, abbreviated as SCL-co-MCL/LCL PHAs, generate suitable thermal and mechanical properties. However, SCL-co-MCL/LCL PHAs with carbon chain longer than nine are difficult to synthesize due to the low specificity of PHA synthase PhaC and the lack of either SCL- or MCL/LCL monomer precursor fluxes. This study succeeds in reprogramming a β-oxidation weakened Pseudomonas entomophila containing synthesis pathways of SCL 3-hydroxybutyryl-CoA (3HB) from glucose and MCL/LCL 3-hydroxyalkanoyl-CoA from fatty acids with carbon chain lengths from 9 to 18, respectively, that are polymerized under a low specificity PhaC61-3 to form P(3HB-co-MCL/LCL 3HA) copolymers. Through rational flux-tuning approaches, the optimized recombinant P. entomophila accumulates 55 wt% poly-3-hydroxybutyrate in 8.4 g L-1 cell dry weight. Combined with weakened β-oxidation, a series of novel P(3HB-co-MCL/LCL 3HA) copolymers with over 60 wt% PHA in 9 g L-1 cell dry weight have been synthesized for the first time. P. entomophila has become a high-performing platform to generate tailor-made new SCL-co-MCL/LCL PHAs.
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Affiliation(s)
- Mengyi Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yueyuan Ma
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xu Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lizhan Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xinyu Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jian-Wen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center of Life Sciences, Tsinghua University, Beijing, 100084, China
- MOE Key Lab of Industrial Biocatalysts, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
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10
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Yu Z, Cao W, Gao X, Aleem MT, Liu J, Luo J, Yan R, Xu L, Song X, Li X. With Chitosan and PLGA as the Delivery Vehicle, Toxoplasma gondii Oxidoreductase-Based DNA Vaccines Decrease Parasite Burdens in Mice. Front Immunol 2021; 12:726615. [PMID: 34512659 PMCID: PMC8430031 DOI: 10.3389/fimmu.2021.726615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/06/2021] [Indexed: 01/02/2023] Open
Abstract
Toxoplasma gondii (T. gondii) is an intracellular parasitic protozoan that can cause serious public health problems. However, there is no effectively preventive or therapeutic strategy available for human and animals. In the present study, we developed a DNA vaccine encoding T. gondii oxidoreductase from short-chain dehydrogenase/reductase family (TgSDRO-pVAX1) and then entrapped in chitosan and poly lactic-co-glycolic acid (PLGA) to improve the efficacy. When encapsulated in chitosan (TgSDRO-pVAX1/CS nanospheres) and PLGA (TgSDRO-pVAX1/PLGA nanospheres), adequate plasmids were loaded and released stably. Before animal immunizations, the DNA vaccine was transfected into HEK 293-T cells and examined by western blotting and laser confocal microscopy. Th1/Th2 cellular and humoral immunity was induced in immunized mice, accompanied by modulated secretion of antibodies and cytokines, promoted the maturation and MHC expression of dendritic cells, and enhanced the percentages of CD4+ and CD8+ T lymphocytes. Immunization with TgSDRO-pVAX1/CS and TgSDRO-pVAX1/PLGA nanospheres conferred significant immunity with lower parasite burden in the mice model of acute toxoplasmosis. Furthermore, our results also lent credit to the idea that TgSDRO-pVAX1/CS and TgSDRO-pVAX1/PLGA nanospheres are substitutes for each other. In general, the current study proposed that TgSDRO-pVAX1 with chitosan or PLGA as the delivery vehicle is a promising vaccine candidate against acute toxoplasmosis.
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Affiliation(s)
- Zhengqing Yu
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wandi Cao
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xuchen Gao
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Tahir Aleem
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Junlong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ruofeng Yan
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Lixin Xu
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiaokai Song
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiangrui Li
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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11
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Liu Y, Cen X, Liu D, Chen Z. Metabolic Engineering of Escherichia coli for High-Yield Production of ( R)-1,3-Butanediol. ACS Synth Biol 2021; 10:1946-1955. [PMID: 34264647 DOI: 10.1021/acssynbio.1c00144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
1,3-Butanediol (1,3-BDO) is an important C4 platform chemical widely used as a solvent in cosmetics and a key intermediate for the synthesis of fragrances, pheromones, and pharmaceuticals. The development of sustainable bioprocesses to produce enantiopure 1,3-BDO from renewable bioresources by fermentation is a promising alternative to conventional chemical routes and has aroused great interest in recent years. Although two metabolic pathways have been previously established for the biosynthesis of (R)-1,3-PDO, the reported titer and yield are too low for cost-competitive production. In this study, we report the combination of different metabolic engineering strategies to improve the production of (R)-1,3-BDO by Escherichia coli, including (1) screening of key pathway enzymes; (2) increasing NADPH supply by cofactor engineering; (3) optimization of fermentation conditions to divert more flux into 1,3-BDO pathway; (4) reduction of byproducts formation by pathway engineering. With these efforts, the best engineered E. coli strain can efficiently produce (R)-1,3-BDO with a yield of 0.6 mol/mol glucose, corresponding to 60% of the theoretical yield. Besides, we also showed the feasibility of aerobically producing 1,3-BDO via a new pathway using 3-hydroxybutyrate as an intermediate.
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Affiliation(s)
- Yu Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Xuecong Cen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Dehua Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Tsinghua Innovation Center in Dongguan, Dongguan 523808, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Zhen Chen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Tsinghua Innovation Center in Dongguan, Dongguan 523808, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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12
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Dong H, Chang MCY. Structural Basis for Branched Substrate Selectivity in a Ketoreductase from Ascaris suum. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Hongjun Dong
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
| | - Michelle C. Y. Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
- Department of Molecular & Cell Biology, University of California, Berkeley, California 94720-3200, United States
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California 94720-1462, United States
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13
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Grosse-Honebrink A, Little GT, Bean Z, Heldt D, Cornock RHM, Winzer K, Minton NP, Green E, Zhang Y. Development of Clostridium saccharoperbutylacetonicum as a Whole Cell Biocatalyst for Production of Chirally Pure ( R)-1,3-Butanediol. Front Bioeng Biotechnol 2021; 9:659895. [PMID: 34055760 PMCID: PMC8155681 DOI: 10.3389/fbioe.2021.659895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Chirally pure (R)-1,3-butanediol ((R)-1,3-BDO) is a valuable intermediate for the production of fragrances, pheromones, insecticides and antibiotics. Biotechnological production results in superior enantiomeric excess over chemical production and is therefore the preferred production route. In this study (R)-1,3-BDO was produced in the industrially important whole cell biocatalyst Clostridium saccharoperbutylacetonicum through expression of the enantio-specific phaB gene from Cupriavidus necator. The heterologous pathway was optimised in three ways: at the transcriptional level choosing strongly expressed promoters and comparing plasmid borne with chromosomal gene expression, at the translational level by optimising the codon usage of the gene to fit the inherent codon adaptation index of C. saccharoperbutylacetonicum, and at the enzyme level by introducing point mutations which led to increased enzymatic activity. The resulting whole cell catalyst produced up to 20 mM (1.8 g/l) (R)-1,3-BDO in non-optimised batch fermentation which is a promising starting position for economical production of this chiral chemical.
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Affiliation(s)
- Alexander Grosse-Honebrink
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Gareth T Little
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Zak Bean
- CHAIN Biotechnology Ltd., MediCity, Nottingham, United Kingdom
| | - Dana Heldt
- CHAIN Biotechnology Ltd., MediCity, Nottingham, United Kingdom
| | - Ruth H M Cornock
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Klaus Winzer
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Nigel P Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Edward Green
- CHAIN Biotechnology Ltd., MediCity, Nottingham, United Kingdom
| | - Ying Zhang
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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14
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Olavarria K, Carnet A, van Renselaar J, Quakkelaar C, Cabrera R, Guedes da Silva L, Smids AL, Villalobos PA, van Loosdrecht MCM, Wahl SA. An NADH preferring acetoacetyl-CoA reductase is engaged in poly-3-hydroxybutyrate accumulation in Escherichia coli. J Biotechnol 2020; 325:207-216. [PMID: 33122026 DOI: 10.1016/j.jbiotec.2020.10.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/16/2020] [Accepted: 10/18/2020] [Indexed: 01/08/2023]
Abstract
Oxygen supply implies higher production cost and reduction of maximum theoretical yields. Thus, generation of fermentation products is more cost-effective. Aiming to find a key piece for the production of (poly)-3-hydroxybutyrate (PHB) as a fermentation product, here we characterize an acetoacetyl-CoA reductase, isolated from a Candidatus Accumulibacter phosphatis-enriched mixed culture, showing a (kcatNADH/KMNADH)/(kcatNADPH/KMNADPH)>500. Further kinetic analyses indicate that, at physiological concentrations, this enzyme clearly prefers NADH, presenting the strongest NADH preference so far observed among the acetoacetyl-CoA reductases. Structural and kinetic analyses indicate that residues between E37 and P41 have an important role for the observed NADH preference. Moreover, an operon was assembled combining the phaCA genes from Cupriavidus necator and the gene encoding for this NADH-preferring acetoacetyl-CoA reductase. Escherichia coli cells expressing that assembled operon showed continuous accumulation of PHB under oxygen limiting conditions and PHB titer increased when decreasing the specific oxygen consumption rate. Taken together, these results show that it is possible to generate PHB as a fermentation product in E. coli, opening opportunities for further protein/metabolic engineering strategies envisioning a more efficient anaerobic production of PHB.
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Affiliation(s)
- Karel Olavarria
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Netherlands.
| | - Alexandre Carnet
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Netherlands.
| | - Joachim van Renselaar
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Netherlands.
| | - Caspar Quakkelaar
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Netherlands.
| | - Ricardo Cabrera
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Región Metropolitana, Chile.
| | - Leonor Guedes da Silva
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Netherlands.
| | - Aron L Smids
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Netherlands.
| | - Pablo Andres Villalobos
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Región Metropolitana, Chile.
| | - Mark C M van Loosdrecht
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Netherlands.
| | - S Aljoscha Wahl
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Netherlands.
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15
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Song HS, Jeon JM, Bhatia SK, Choi TR, Lee SM, Park SL, Lee HS, Yoon JJ, Ahn J, Lee H, Brigham CJ, Choi KY, Yang YH. Enhanced isobutanol production by co-production of polyhydroxybutyrate and cofactor engineering. J Biotechnol 2020; 320:66-73. [DOI: 10.1016/j.jbiotec.2020.06.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 05/29/2020] [Accepted: 06/18/2020] [Indexed: 01/17/2023]
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16
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Yang Z, Ye W, Xie Y, Liu Q, Chen R, Wang H, Wei D. Efficient Asymmetric Synthesis of Ethyl (S)-4-Chloro-3-hydroxybutyrate Using Alcohol Dehydrogenase SmADH31 with High Tolerance of Substrate and Product in a Monophasic Aqueous System. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00088] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Zeyu Yang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Wenjie Ye
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Youyu Xie
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Qinghai Liu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Rong Chen
- School of Medicine, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
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17
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Ellis GA, Klein WP, Lasarte-Aragonés G, Thakur M, Walper SA, Medintz IL. Artificial Multienzyme Scaffolds: Pursuing in Vitro Substrate Channeling with an Overview of Current Progress. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02413] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gregory A. Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - William P. Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20001, United States
| | - Guillermo Lasarte-Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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18
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Ostafe R, Fontaine N, Frank D, Ng Fuk Chong M, Prodanovic R, Pandjaitan R, Offmann B, Cadet F, Fischer R. One-shot optimization of multiple enzyme parameters: Tailoring glucose oxidase for pH and electron mediators. Biotechnol Bioeng 2019; 117:17-29. [PMID: 31520472 DOI: 10.1002/bit.27169] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/20/2019] [Accepted: 09/08/2019] [Indexed: 01/03/2023]
Abstract
Enzymes are biological catalysts with many industrial applications, but natural enzymes are usually unsuitable for industrial processes because they are not optimized for the process conditions. The properties of enzymes can be improved by directed evolution, which involves multiple rounds of mutagenesis and screening. By using mathematical models to predict the structure-activity relationship of an enzyme, and by defining the optimal combination of mutations in silico, we can significantly reduce the number of bench experiments needed, and hence the time and investment required to develop an optimized product. Here, we applied our innovative sequence-activity relationship methodology (innov'SAR) to improve glucose oxidase activity in the presence of different mediators across a range of pH values. Using this machine learning approach, a predictive model was developed and the optimal combination of mutations was determined, leading to a glucose oxidase mutant (P1) with greater specificity for the mediators ferrocene-methanol (12-fold) and nitrosoaniline (8-fold), compared to the wild-type enzyme, and better performance in three pH-adjusted buffers. The kcat /KM ratio of P1 increased by up to 121 folds compared to the wild type enzyme at pH 5.5 in the presence of ferrocene methanol.
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Affiliation(s)
- Raluca Ostafe
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Molecular Evolution, Protein Engineering and Production, Purdue University, West Lafayette, Indiana.,Institute of Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | | | - David Frank
- Institute of Molecular Biotechnology, RWTH Aachen University, Aachen, Germany.,Aquila Biolabs GmbH, Baesweiler, Germany
| | | | | | | | | | - Frédéric Cadet
- PEACCEL - Protein Engineering Accelerator, Paris, France
| | - Rainer Fischer
- Institute of Molecular Biotechnology, RWTH Aachen University, Aachen, Germany.,Departments of Biological Sciences and Chemistry, Purdue University, West Lafayette, Indiana
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19
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Dong H, Liffland S, Hillmyer MA, Chang MCY. Engineering in Vivo Production of α-Branched Polyesters. J Am Chem Soc 2019; 141:16877-16883. [DOI: 10.1021/jacs.9b08585] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | - Stephanie Liffland
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Marc A. Hillmyer
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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20
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Modification of acetoacetyl-CoA reduction step in Ralstonia eutropha for biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) from structurally unrelated compounds. Microb Cell Fact 2019; 18:147. [PMID: 31466527 PMCID: PMC6716841 DOI: 10.1186/s12934-019-1197-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/22/2019] [Indexed: 12/24/2022] Open
Abstract
Background Poly((R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate) [P(3HB-co-3HHx)] is a bacterial polyester with high biodegradability, even in marine environments. Ralstonia eutropha has been engineered for the biosynthesis of P(3HB-co-3HHx) from vegetable oils, but its production from structurally unrelated carbon sources remains unsatisfactory. Results Ralstonia eutropha strains capable of synthesizing P(3HB-co-3HHx) from not only fructose but also glucose and glycerol were constructed by integrating previously established engineering strategies. Further modifications were made at the acetoacetyl-CoA reduction step determining flux distribution responsible for the copolymer composition. When the major acetoacetyl-CoA reductase (PhaB1) was replaced by a low-activity paralog (PhaB2) or enzymes for reverse β-oxidation, copolyesters with high 3HHx composition were efficiently synthesized from glucose, possibly due to enhanced formation of butyryl-CoA from acetoacetyl-CoA via (S)-3HB-CoA. P(3HB-co-3HHx) composed of 7.0 mol% and 12.1 mol% 3HHx fractions, adequate for practical applications, were produced at cellular contents of 71.4 wt% and 75.3 wt%, respectively. The replacement by low-affinity mutants of PhaB1 had little impact on the PHA biosynthesis on glucose, but slightly affected those on fructose, suggesting altered metabolic regulation depending on the sugar-transport machinery. PhaB1 mostly acted in the conversion of acetoacetyl-CoA when the cells were grown on glycerol, as copolyester biosynthesis was severely impaired by the lack of phaB1. Conclusions The present results indicate the importance of flux distribution at the acetoacetyl-CoA node in R. eutropha for the biosynthesis of the PHA copolyesters with regulated composition from structurally unrelated compounds.
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21
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Perez-Zabaleta M, Guevara-Martínez M, Gustavsson M, Quillaguamán J, Larsson G, van Maris AJA. Comparison of engineered Escherichia coli AF1000 and BL21 strains for (R)-3-hydroxybutyrate production in fed-batch cultivation. Appl Microbiol Biotechnol 2019; 103:5627-5639. [PMID: 31104101 PMCID: PMC6597613 DOI: 10.1007/s00253-019-09876-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/18/2019] [Accepted: 04/24/2019] [Indexed: 02/06/2023]
Abstract
Accumulation of acetate is a limiting factor in recombinant production of (R)-3-hydroxybutyrate (3HB) by Escherichia coli in high-cell-density processes. To alleviate this limitation, this study investigated two approaches: (i) deletion of phosphotransacetylase (pta), pyruvate oxidase (poxB), and/or the isocitrate lyase regulator (iclR), known to decrease acetate formation, on bioreactor cultivations designed to achieve high 3HB concentrations. (ii) Screening of different E. coli strain backgrounds (B, BL21, W, BW25113, MG1655, W3110, and AF1000) for their potential as low acetate-forming, 3HB-producing platforms. Deletion of pta and pta-poxB in the AF1000 strain background was to some extent successful in decreasing acetate formation, but also dramatically increased excretion of pyruvate and did not result in increased 3HB production in high-cell-density fed-batch cultivations. Screening of the different E. coli strains confirmed BL21 as a low acetate-forming background. Despite low 3HB titers in low-cell-density screening, 3HB-producing BL21 produced five times less acetic acid per mole of 3HB, which translated into a 2.3-fold increase in the final 3HB titer and a 3-fold higher volumetric 3HB productivity over 3HB-producing AF1000 strains in nitrogen-limited fed-batch cultivations. Consequently, the BL21 strain achieved the hitherto highest described volumetric productivity of 3HB (1.52 g L−1 h−1) and the highest 3HB concentration (16.3 g L−1) achieved by recombinant E. coli. Screening solely for 3HB titers in low-cell-density batch cultivations would not have identified the potential of this strain, reaffirming the importance of screening with the final production conditions in mind.
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Affiliation(s)
- Mariel Perez-Zabaleta
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
- Center of Biotechnology, Faculty of Science and Technology, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Mónica Guevara-Martínez
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
- Center of Biotechnology, Faculty of Science and Technology, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Martin Gustavsson
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
| | - Jorge Quillaguamán
- Center of Biotechnology, Faculty of Science and Technology, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Gen Larsson
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
| | - Antonius J. A. van Maris
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
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22
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Takenoya M, Taguchi S, Yajima S. Crystal structure and kinetic analyses of a hexameric form of (S)-3-hydroxybutyryl-CoA dehydrogenase from Clostridium acetobutylicum. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2018; 74:733-740. [PMID: 30387779 DOI: 10.1107/s2053230x18014814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/19/2018] [Indexed: 11/11/2022]
Abstract
(S)-3-Hydroxybutyryl-CoA dehydrogenase (HBD) has been gaining increased attention recently as it is a key enzyme in the enantiomeric formation of (S)-3-hydroxybutyryl-CoA [(S)-3HB-CoA]. It converts acetoacetyl-CoA to (S)-3HB-CoA in the synthetic metabolic pathway. (S)-3HB-CoA is further modified to form (S)-3-hydroxybutyrate, which is a source of biodegradable polymers. During the course of a study to develop biodegradable polymers, attempts were made to determine the crystal structure of HBD from Clostridium acetobutylicum (CacHBD), and the crystal structures of both apo and NAD+-bound forms of CacHBD were determined. The crystals belonged to different space groups: P212121 and P21. However, both structures adopted a hexamer composed of three dimers in the asymmetric unit, and this oligomerization was additionally confirmed by gel-filtration column chromatography. Furthermore, to investigate the catalytic residues of CacHBD, the enzymatic activities of the wild type and of three single-amino-acid mutants were analyzed, in which the Ser, His and Asn residues that are conserved in the HBDs from C. acetobutylicum, C. butyricum and Ralstonia eutropha, as well as in the L-3-hydroxyacyl-CoA dehydrogenases from Homo sapiens and Escherichia coli, were substituted by alanines. The S117A and N188A mutants abolished the activity, while the H138A mutant showed a slightly lower Km value and a significantly lower kcat value than the wild type. Therefore, in combination with the crystal structures, it was shown that His138 is involved in catalysis and that Ser117 and Asn188 may be important for substrate recognition to place the keto group of the substrate in the correct position for reaction.
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Affiliation(s)
- Mihoko Takenoya
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Seiichi Taguchi
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Shunsuke Yajima
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
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23
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Segawa M, Wen C, Orita I, Nakamura S, Fukui T. Two NADH-dependent (S)-3-hydroxyacyl-CoA dehydrogenases from polyhydroxyalkanoate-producing Ralstonia eutropha. J Biosci Bioeng 2018; 127:294-300. [PMID: 30243533 DOI: 10.1016/j.jbiosc.2018.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/20/2018] [Accepted: 08/22/2018] [Indexed: 12/28/2022]
Abstract
Ralstonia eutropha H16 contains both NADH- and NADPH-dependent reduction activities to acetoacetyl-CoA, and the NADPH-dependent activity is mediated by PhaB paralogs with (R)-stereospecificity providing (R)-3-hydroxybutyryl (3HB)-CoA monomer for poly((R)-3-hydroxybutyrate) synthesis. In contrast, the gene encoding the NADH-dependent enzyme has not been identified to date. This study focused on the NADH-dependent dehydrogenase with (S)-stereospecificity in R. eutropha, as the (S)-specific reduction of acetoacetyl-CoA potentially competed with the polyester biosynthesis via (R)-3HB-CoA. The NADH-dependent reduction activity decreased to one-half when the gene for H16_A0282 (PaaH1), one of two homologs of clostridial NADH-3HB-CoA dehydrogenase, was deleted. The enzyme responsible for the remaining activity was partially purified and identified as H16_A0602 (Had) belonging to a different family from PaaH1. Gene disruption analysis elucidated that most of the NADH-dependent activity was mediated by PaaH1 and Had. The kinetic analysis using the recombinant enzymes indicated that PaaH1 and Had were both NADH-dependent 3-hydroxyacyl-CoA dehydrogenases with rather broad substrate specificity to 3-oxoacyl-CoAs of C4 to C8. The deletion of had in the R. eutropha strain previously engineered for biosynthesis of poly((R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate) led to decrease in the C6 composition of the copolyester synthesized from soybean oil, suggesting the role of Had in (S)-specific reduction of 3-oxohexanoyl-CoA with reverse β-oxidation direction. Crotonase ((S)-specific enoyl-CoA hydratase) in R. eutropha H16 was also partially purified and identified as H16_A3307.
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Affiliation(s)
- Mutsumi Segawa
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Cheng Wen
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Izumi Orita
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Satoshi Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
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24
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Engineering NADH/NAD + ratio in Halomonas bluephagenesis for enhanced production of polyhydroxyalkanoates (PHA). Metab Eng 2018; 49:275-286. [PMID: 30219528 DOI: 10.1016/j.ymben.2018.09.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/12/2018] [Accepted: 09/12/2018] [Indexed: 11/20/2022]
Abstract
Halomonas bluephagenesis has been developed as a platform strain for the next generation industrial biotechnology (NGIB) with advantages of resistances to microbial contamination and high cell density growth (HCD), especially for production of polyhydroxyalkanoates (PHA) including poly(3-hydroxybutyrate) (PHB), poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P34HB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). However, little is known about the mechanism behind PHA accumulation under oxygen limitation. This study for the first time found that H. bluephagenesis utilizes NADH instead of NADPH as a cofactor for PHB production, thus revealing the rare situation of enhanced PHA accumulation under oxygen limitation. To increase NADH/NAD+ ratio for enhanced PHA accumulation under oxygen limitation, an electron transport pathway containing electron transfer flavoprotein subunits α and β encoded by etf operon was blocked to increase NADH supply, leading to 90% PHB accumulation in the cell dry weight (CDW) of H. bluephagenesis compared with 84% by the wild type. Acetic acid, a cost-effective carbon source, was used together with glucose to balance the redox state and reduce inhibition on pyruvate metabolism, resulting in 22% more CDW and 94% PHB accumulation. The cellular redox state changes induced by the addition of acetic acid increased 3HV ratio in its copolymer PHBV from 4% to 8%, 4HB in its copolymer P34HB from 8% to 12%, respectively, by engineered H. bluephagenesis. The strategy of systematically modulation on the redox potential of H. bluephagenesis led to enhanced PHA accumulation and controllable monomer ratios in PHA copolymers under oxygen limitation, reducing energy consumption and scale-up complexity.
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25
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Sagong HY, Son HF, Choi SY, Lee SY, Kim KJ. Structural Insights into Polyhydroxyalkanoates Biosynthesis. Trends Biochem Sci 2018; 43:790-805. [PMID: 30139647 DOI: 10.1016/j.tibs.2018.08.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/27/2018] [Accepted: 08/04/2018] [Indexed: 12/25/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are diverse biopolyesters produced by numerous microorganisms and have attracted much attention as a substitute for petroleum-based polymers. Despite several decades of study, the detailed molecular mechanisms of PHA biosynthesis have remained unknown due to the lack of structural information on the key PHA biosynthetic enzyme PHA synthase. The recently determined crystal structure of PHA synthase, together with the structures of acetyl-coenzyme A (CoA) acetyltransferase and reductase, have changed this situation. Structural and biochemical studies provided important clues for the molecular mechanisms of each enzyme as well as the overall mechanism of PHA biosynthesis from acetyl-CoA. This new information and knowledge is expected to facilitate production of designed novel PHAs and also enhanced production of PHAs.
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Affiliation(s)
- Hye-Young Sagong
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyeoncheol Francis Son
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea.
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26
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Dalwadi MP, Garavaglia M, Webb JP, King JR, Minton NP. Applying asymptotic methods to synthetic biology: Modelling the reaction kinetics of the mevalonate pathway. J Theor Biol 2017; 439:39-49. [PMID: 29199089 PMCID: PMC5764709 DOI: 10.1016/j.jtbi.2017.11.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/26/2017] [Accepted: 11/29/2017] [Indexed: 11/26/2022]
Abstract
We investigate a kinetic model for the mevalonate pathway which includes inhibition effects and a sink of acetyl-CoA. Of the enzymes in the pathway, upregulating HMG-CoA reductase has the most significant positive effect on improving pathway efficiency. Upregulating pyruvate dehydrogenase complex and HMG-CoA synthase can also help, but only in conjunction with the upregulation of HMG-CoA reductase. We confirm our theoretical predictions by introducing the mevalonate pathway into Cupriavidus necator.
The mevalonate pathway is normally found in eukaryotes, and allows for the production of isoprenoids, a useful class of organic compounds. This pathway has been successfully introduced to Escherichia coli, enabling a biosynthetic production route for many isoprenoids. In this paper, we develop and solve a mathematical model for the concentration of metabolites in the mevalonate pathway over time, accounting for the loss of acetyl-CoA to other metabolic pathways. Additionally, we successfully test our theoretical predictions experimentally by introducing part of the pathway into Cupriavidus necator. In our model, we exploit the natural separation of time scales as well as of metabolite concentrations to make significant asymptotic progress in understanding the system. We confirm that our asymptotic results agree well with numerical simulations, the former enabling us to predict the most important reactions to increase isopentenyl diphosphate production whilst minimizing the levels of HMG-CoA, which inhibits cell growth. Thus, our mathematical model allows us to recommend the upregulation of certain combinations of enzymes to improve production through the mevalonate pathway.
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Affiliation(s)
- Mohit P Dalwadi
- Synthetic Biology Research Centre, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Marco Garavaglia
- Synthetic Biology Research Centre, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Joseph P Webb
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - John R King
- Synthetic Biology Research Centre, University of Nottingham, University Park, Nottingham NG7 2RD, UK; School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Nigel P Minton
- Synthetic Biology Research Centre, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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27
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Lin YY, Chen PT. Development of polyhydroxybutyrate biosynthesis in Bacillus subtilis with combination of PHB-associated genes derived from Ralstonia eutropha and Bacillus megaterium. J Taiwan Inst Chem Eng 2017. [DOI: 10.1016/j.jtice.2017.02.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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28
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Wang P, Cao HY, Chen XL, Li CY, Li PY, Zhang XY, Qin QL, Todd JD, Zhang YZ. Mechanistic insight into acrylate metabolism and detoxification in marine dimethylsulfoniopropionate-catabolizing bacteria. Mol Microbiol 2017; 105:674-688. [PMID: 28598523 DOI: 10.1111/mmi.13727] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2017] [Indexed: 12/24/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) cleavage, yielding dimethyl sulfide (DMS) and acrylate, provides vital carbon sources to marine bacteria, is a key component of the global sulfur cycle and effects atmospheric chemistry and potentially climate. Acrylate and its metabolite acryloyl-CoA are toxic if allowed to accumulate within cells. Thus, organisms cleaving DMSP require effective systems for both the utilization and detoxification of acrylate. Here, we examine the mechanism of acrylate utilization and detoxification in Roseobacters. We propose propionate-CoA ligase (PrpE) and acryloyl-CoA reductase (AcuI) as the key enzymes involved and through structural and mutagenesis analyses, provide explanations of their catalytic mechanisms. In most cases, DMSP lyases and DMSP demethylases (DmdAs) have low substrate affinities, but AcuIs have very high substrate affinities, suggesting that an effective detoxification system for acylate catabolism exists in DMSP-catabolizing Roseobacters. This study provides insight on acrylate metabolism and detoxification and a possible explanation for the high Km values that have been noted for some DMSP lyases. Since acrylate/acryloyl-CoA is probably produced by other metabolism, and AcuI and PrpE are conserved in many organisms across all domains of life, the detoxification system is likely relevant to many metabolic processes and environments beyond DMSP catabolism.
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Affiliation(s)
- Peng Wang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Hai-Yan Cao
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Chun-Yang Li
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Ping-Yi Li
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Xi-Ying Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Qi-Long Qin
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Yu-Zhong Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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29
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Binding of NADP + triggers an open-to-closed transition in a mycobacterial FabG β-ketoacyl-ACP reductase. Biochem J 2017; 474:907-921. [PMID: 28126742 DOI: 10.1042/bcj20161052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/11/2017] [Accepted: 01/25/2017] [Indexed: 02/07/2023]
Abstract
The ketoacyl-acyl carrier protein (ACP) reductase FabG catalyzes the NADPH/NADH dependent reduction of β-ketoacyl-ACP substrates to β-hydroxyacyl-ACP products, the first reductive step in the fatty acid biosynthesis elongation cycle. FabG proteins are ubiquitous in bacteria and are part of the type II fatty acid synthase system. Mining the Mycobacterium smegmatis genome uncovered several putative FabG-like proteins. Among them, we identified M. smegmatis MSMEG_6753 whose gene was found adjacent to MSMEG_6754, encoding a recently characterized enoyl-CoA dehydratase, and to MSMEG_6755, encoding another potential reductase. Recombinantly expressed and purified MSMEG_6753 exhibits ketoacyl reductase activity in the presence of acetoacetyl-CoA and NADPH. This activity was subsequently confirmed by functional complementation studies in a fabG thermosensitive Escherichia coli mutant. Furthermore, comparison of the apo and the NADP+-bound MSMEG_6753 crystal structures showed that cofactor binding induces a closed conformation of the protein. A ΔMSMEG_6753 deletion mutant could be generated in M. smegmatis, indicating that this gene is dispensable for mycobacterial growth. Overall, these results showcase the diversity of FabG-like proteins in mycobacteria and new structural features regarding the catalytic mechanism of this important family of enzymes that may be of importance for the rational design of specific FabG inhibitors.
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Tippmann S, Anfelt J, David F, Rand JM, Siewers V, Uhlén M, Nielsen J, Hudson EP. Affibody Scaffolds Improve Sesquiterpene Production in Saccharomyces cerevisiae. ACS Synth Biol 2017; 6:19-28. [PMID: 27560952 DOI: 10.1021/acssynbio.6b00109] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Enzyme fusions have been widely used as a tool in metabolic engineering to increase pathway efficiency by reducing substrate loss and accumulation of toxic intermediates. Alternatively, enzymes can be colocalized through attachment to a synthetic scaffold via noncovalent interactions. Here we describe the use of affibodies for enzyme tagging and scaffolding. The scaffolding is based on the recognition of affibodies to their anti-idiotypic partners in vivo, and was first employed for colocalization of farnesyl diphosphate synthase and farnesene synthase in S. cerevisiae. Different parameters were modulated to improve the system, and the enzyme:scaffold ratio was most critical for its functionality. Ultimately, the yield of farnesene on glucose YSFar could be improved by 135% in fed-batch cultivations using a 2-site affibody scaffold. The scaffolding strategy was then extended to a three-enzyme polyhydroxybutyrate (PHB) pathway, heterologously expressed in E. coli. Within a narrow range of enzyme and scaffold induction, the affibody tagging and scaffolding increased PHB production 7-fold. This work demonstrates how the versatile affibody can be used for metabolic engineering purposes.
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Affiliation(s)
- Stefan Tippmann
- Department
of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Josefine Anfelt
- Division
of Proteomics and Nanobiotechnology, School of Biotechnology, Royal Institute of Technology (KTH), Science for Life Laboratory, SE171 21 Stockholm, Sweden
| | - Florian David
- Department
of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Jacqueline M. Rand
- Department
of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Verena Siewers
- Department
of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Mathias Uhlén
- Division
of Proteomics and Nanobiotechnology, School of Biotechnology, Royal Institute of Technology (KTH), Science for Life Laboratory, SE171 21 Stockholm, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2970 Hørsholm, Denmark
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2970 Hørsholm, Denmark
| | - Elton P. Hudson
- Division
of Proteomics and Nanobiotechnology, School of Biotechnology, Royal Institute of Technology (KTH), Science for Life Laboratory, SE171 21 Stockholm, Sweden
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31
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de Las Heras AM, Portugal-Nunes DJ, Rizza N, Sandström AG, Gorwa-Grauslund MF. Anaerobic poly-3-D-hydroxybutyrate production from xylose in recombinant Saccharomyces cerevisiae using a NADH-dependent acetoacetyl-CoA reductase. Microb Cell Fact 2016; 15:197. [PMID: 27863495 PMCID: PMC5116212 DOI: 10.1186/s12934-016-0598-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/10/2016] [Indexed: 11/19/2022] Open
Abstract
Background Poly-3-d-hydroxybutyrate (PHB) that is a promising precursor for bioplastic with similar physical properties as polypropylene, is naturally produced by several bacterial species. The bacterial pathway is comprised of the three enzymes β-ketothiolase, acetoacetyl-CoA reductase (AAR) and PHB synthase, which all together convert acetyl-CoA into PHB. Heterologous expression of the pathway genes from Cupriavidus necator has enabled PHB production in the yeast Saccharomyces cerevisiae from glucose as well as from xylose, after introduction of the fungal xylose utilization pathway from Scheffersomyces stipitis including xylose reductase (XR) and xylitol dehydrogenase (XDH). However PHB titers are still low. Results In this study the acetoacetyl-CoA reductase gene from C. necator (CnAAR), a NADPH-dependent enzyme, was replaced by the NADH-dependent AAR gene from Allochromatium vinosum (AvAAR) in recombinant xylose-utilizing S. cerevisiae and PHB production was compared. A. vinosum AAR was found to be active in S. cerevisiae and able to use both NADH and NADPH as cofactors. This resulted in improved PHB titers in S. cerevisiae when xylose was used as sole carbon source (5-fold in aerobic conditions and 8.4-fold under oxygen limited conditions) and PHB yields (4-fold in aerobic conditions and up to 5.6-fold under oxygen limited conditions). Moreover, the best strain was able to accumulate up to 14% of PHB per cell dry weight under fully anaerobic conditions. Conclusions This study reports a novel approach for boosting PHB accumulation in S. cerevisiae by replacement of the commonly used AAR from C. necator with the NADH-dependent alternative from A. vinosum. Additionally, to the best of our knowledge, it is the first demonstration of anaerobic PHB synthesis from xylose. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0598-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Diogo J Portugal-Nunes
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden
| | - Nathasha Rizza
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden.,Vattenhallen Science Center, John Ericssons väg 1, 223 63, Lund, Sweden
| | - Anders G Sandström
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden.,Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark
| | - Marie F Gorwa-Grauslund
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden.
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Characterization of mutants of a tyrosine ammonia-lyase from Rhodotorula glutinis. Appl Microbiol Biotechnol 2016; 100:10443-10452. [DOI: 10.1007/s00253-016-7672-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 05/09/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022]
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Inahashi Y, Shiraishi T, Palm K, Takahashi Y, Ōmura S, Kuzuyama T, Nakashima T. Biosynthesis of Trehangelin in Polymorphospora rubra K07-0510: Identification of Metabolic Pathway to Angelyl-CoA. Chembiochem 2016; 17:1442-7. [PMID: 27311629 DOI: 10.1002/cbic.201600208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Indexed: 11/09/2022]
Abstract
Trehangelins are trehalose angelates discovered from endophytic actinomycete Polymorphospora rubra K07-0510. We identified the trehangelin biosynthetic gene cluster, including genes that encode a glycoside hydrolase-like protein (thgC), α-amylase (thgD), 3-ketoacyl-ACP synthase III (thgI), 3-ketoacyl-ACP reductase (thgK), enoyl-CoA hydratase (thgH) and acyl transferase (thgJ). Heterologous expression of thgH, thgI, thgJ and thgK confirmed the importance of these genes in the biosynthesis of trehangelin A. Enzymatic activity studies showed that ThgI catalyses the condensation of acetyl-CoA and methylmalonyl-CoA to 2-methylacetoacetyl-CoA (MAA-CoA), ThgK catalyses NADPH-dependent reduction of MAA-CoA to 3-hydroxy-2-methylbutyryl-CoA (HMB-CoA) and ThgH catalyses the dehydration of HMB-CoA to angelyl-CoA (AN-CoA). This is the first report on the elucidation of the enzymatic formation of AN-CoA.
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Affiliation(s)
- Yuki Inahashi
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
| | - Taro Shiraishi
- Laboratory of Cell Biotechnology, Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kaia Palm
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.,Protobios Llc, Mäealuse 4, Tallinn, 12618, Estonia
| | - Yoko Takahashi
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Satoshi Ōmura
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Tomohisa Kuzuyama
- Laboratory of Cell Biotechnology, Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takuji Nakashima
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
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Molina-Espeja P, Viña-Gonzalez J, Gomez-Fernandez BJ, Martin-Diaz J, Garcia-Ruiz E, Alcalde M. Beyond the outer limits of nature by directed evolution. Biotechnol Adv 2016; 34:754-767. [PMID: 27064127 DOI: 10.1016/j.biotechadv.2016.03.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/22/2016] [Accepted: 03/27/2016] [Indexed: 01/19/2023]
Abstract
For more than thirty years, biotechnology has borne witness to the power of directed evolution in designing molecules of industrial relevance. While scientists all over the world discuss the future of molecular evolution, dozens of laboratory-designed products are being released with improved characteristics in terms of turnover rates, substrate scope, catalytic promiscuity or stability. In this review we aim to present the most recent advances in this fascinating research field that are allowing us to surpass the limits of nature and apply newly gained attributes to a range of applications, from gene therapy to novel green processes. The use of directed evolution in non-natural environments, the generation of catalytic promiscuity for non-natural reactions, the insertion of unnatural amino acids into proteins or the creation of unnatural DNA, is described comprehensively, together with the potential applications in bioremediation, biomedicine and in the generation of new bionanomaterials. These successful case studies show us that the limits of directed evolution will be defined by our own imagination, and in some cases, stretching beyond that.
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Affiliation(s)
- Patricia Molina-Espeja
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Javier Viña-Gonzalez
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain
| | | | - Javier Martin-Diaz
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Eva Garcia-Ruiz
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61801, USA
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain.
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35
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Kadoya R, Matsumoto K, Ooi T, Taguchi S. MtgA Deletion-Triggered Cell Enlargement of Escherichia coli for Enhanced Intracellular Polyester Accumulation. PLoS One 2015; 10:e0125163. [PMID: 26039058 PMCID: PMC4454544 DOI: 10.1371/journal.pone.0125163] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 03/12/2015] [Indexed: 11/18/2022] Open
Abstract
Bacterial polyester polyhydroxyalkanoates (PHAs) have been produced in engineered Escherichia coli, which turned into an efficient and versatile platform by applying metabolic and enzyme engineering approaches. The present study aimed at drawing out the latent potential of this organism using genome-wide mutagenesis. To meet this goal, a transposon-based mutagenesis was carried out on E. coli, which was transformed to produce poly(lactate-co-3-hydroxybutyrate) from glucose. A high-throughput screening of polymer-accumulating cells on Nile red-containing plates isolated one mutant that produced 1.8-fold higher quantity of polymer without severe disadvantages in the cell growth and monomer composition of the polymer. The transposon was inserted into the locus within the gene encoding MtgA that takes part, as a non-lethal component, in the formation of the peptidoglycan backbone. Accordingly, the mtgA-deleted strain E. coli JW3175, which was a derivate of superior PHA-producing strain BW25113, was examined for polymer production, and exhibited an enhanced accumulation of the polymer (7.0 g/l) compared to the control (5.2 g/l). Interestingly, an enlargement in cell width associated with polymer accumulation was observed in this strain, resulting in a 1.6-fold greater polymer accumulation per cell compared to the control. This result suggests that the increase in volumetric capacity for accumulating intracellular material contributed to the enhanced polymer production. The mtgA deletion should be combined with conventional engineering approaches, and thus, is a promising strategy for improved production of intracellularly accumulated biopolymers.
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Affiliation(s)
- Ryosuke Kadoya
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Ken'ichiro Matsumoto
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Toshihiko Ooi
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Seiichi Taguchi
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
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Enhanced cellular content and lactate fraction of the poly(lactate-co-3-hydroxybutyrate) polyester produced in recombinant Escherichia coli by the deletion of σ factor RpoN. J Biosci Bioeng 2015; 119:427-9. [DOI: 10.1016/j.jbiosc.2014.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 08/25/2014] [Accepted: 09/03/2014] [Indexed: 11/13/2022]
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Yokoo T, Matsumoto K, Ooba T, Morimoto K, Taguchi S. Enhanced poly(3-hydroxybutyrate) production in transgenic tobacco BY-2 cells using engineered acetoacetyl-CoA reductase. Biosci Biotechnol Biochem 2015; 79:986-8. [PMID: 25647430 DOI: 10.1080/09168451.2014.1002448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Highly active mutant of NADPH-dependent acetoacetyl-CoA reductase (PhaB) was expressed in Nicotiana tabacum cv. Bright Yellow-2 cultured cells to produce poly(3-hydroxybutyrate) [P(3HB)]. The mutated PhaB increased P(3HB) content by three-fold over the control, indicating that the mutant was a versatile tool for P(3HB) production. Additionally, the PhaB-catalyzed reaction was suggested to be a rate-limiting step of P(3HB) biosynthesis in tobacco BY-2 cells.
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Affiliation(s)
- Toshinori Yokoo
- a Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering , Hokkaido University , Sapporo , Japan
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Engineering of Escherichia coli for the biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) from glucose. Appl Microbiol Biotechnol 2015; 99:2593-602. [PMID: 25586585 DOI: 10.1007/s00253-015-6380-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 12/28/2014] [Accepted: 12/31/2014] [Indexed: 12/28/2022]
Abstract
The copolymer poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) [P(HB-co-HHx)] has the potential to serve as a biodegradable tissue engineering material. However, the production of this kind of copolymer still suffers from high cost and uncertainty. We describe here the design of metabolic pathways to synthesize P(HB-co-HHx) directly from glucose using recombinant Escherichia coli. By combining the BktB-dependent condensation pathway with the inverted β-oxidation cycle pathway, we were able to synthesize a P(HB-co-HHx) copolymer with a 10 mol% HHx fraction in recombinant E. coli. After optimizing the host strain and employing thioesterase mutant strains, the engineered E. coli produced 12.9 wt% P(HB-co-HHx) with a 13.2 mol% 3HHx fraction.
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Matsumoto K, Tobitani K, Aoki S, Song Y, Ooi T, Taguchi S. Improved production of poly(lactic acid)-like polyester based on metabolite analysis to address the rate-limiting step. AMB Express 2014; 4:83. [PMID: 26267112 PMCID: PMC4884051 DOI: 10.1186/s13568-014-0083-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 11/06/2014] [Indexed: 01/19/2023] Open
Abstract
The biosynthesis of poly(lactic acid) (PLA)-like polymers, composed of >99 mol% lactate and a trace amount of 3-hydroxybutyrate, in engineered Corynebacterium glutamicum consists of two steps; the generation of the monomer substrate lactyl-coenzyme A (CoA) and the polyhydroxyalkanoate (PHA) synthase-catalyzed polymerization of lactyl-CoA. In order to increase polymer productivity, we explored the rate-limiting step in PLA-like polymer synthesis based on quantitative metabolite analysis using liquid chromatography mass spectroscopy (LC-MS). A significant pool of lactyl-CoA was found during polymer synthesis. This result suggested that the rate-limitation occurred at the polymerization step. Accordingly, the expression level of PHA synthase was increased by means of codon-optimization of the corresponding gene that consequently led to an increase in polymer content by 4.4-fold compared to the control. Notably, the codon-optimization did not significantly affect the concentration of lactyl-CoA, suggesting that the polymerization reaction was still the rate-limiting step upon the overexpression of PHA synthase. Another important finding was that the generation of lactyl-CoA was concomitant with a decrease in the acetyl-CoA level, indicating that acetyl-CoA served as a CoA donor for lactyl-CoA synthesis. These results show that obtaining information on the metabolite concentrations is highly useful for improving PLA-like polymer production. This strategy should be applicable to a wide range of PHA-producing systems.
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Insomphun C, Xie H, Mifune J, Kawashima Y, Orita I, Nakamura S, Fukui T. Improved artificial pathway for biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) with high C6-monomer composition from fructose in Ralstonia eutropha. Metab Eng 2014; 27:38-45. [PMID: 25446974 DOI: 10.1016/j.ymben.2014.10.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/25/2014] [Accepted: 10/06/2014] [Indexed: 02/06/2023]
Abstract
Poly((R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate) [P(3HB-co-3HHx)], a flexible and practical kind of polyhydroxyalkanoates, is generally produced from plant oils and fatty acids by several wild and recombinant bacteria. This study established an improved artificial pathway for the biosynthesis of P(3HB-co-3HHx) with high 3HHx composition from structurally unrelated fructose in Ralstonia eutropha. Depression of (R)-specific reduction of acetoacetyl-CoA by the deletion of phaB1 was an effective modification for formation of the C6-monomer unit from fructose driven by crotonyl-CoA carboxylase/reductase (Ccr). Co-overexpression of phaJ4a, which encodes medium-chain-length (R)-enoyl-CoA hydratase, with ccr promoted the incorporation of both 3HB and 3HHx units. Further introduction of emdMm, a synthetic gene encoding ethylmalonyl-CoA decarboxylase derived from mouse, was remarkably effective for P(3HB-co-3HHx) biosynthesis, probably by converting ethylmalonyl-CoA generated by the reductive carboxylase activity of Ccr back into butyryl-CoA. A high cellular content of P(3HB-co-3HHx) composed of 22mol% 3HHx could be produced from fructose by the engineered strain of R. eutropha with ΔphaB1 genotype expressing ccr, phaJ4a, and emd.
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Affiliation(s)
- Chayatip Insomphun
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Huan Xie
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Jun Mifune
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Yui Kawashima
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Izumi Orita
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Satoshi Nakamura
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Toshiaki Fukui
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
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