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Basallo O, Perez L, Lucido A, Sorribas A, Marin-Saguino A, Vilaprinyo E, Perez-Fons L, Albacete A, Martínez-Andújar C, Fraser PD, Christou P, Capell T, Alves R. Changing biosynthesis of terpenoid percursors in rice through synthetic biology. FRONTIERS IN PLANT SCIENCE 2023; 14:1133299. [PMID: 37465386 PMCID: PMC10350630 DOI: 10.3389/fpls.2023.1133299] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/30/2023] [Indexed: 07/20/2023]
Abstract
Many highly valued chemicals in the pharmaceutical, biotechnological, cosmetic, and biomedical industries belong to the terpenoid family. Biosynthesis of these chemicals relies on polymerization of Isopentenyl di-phosphate (IPP) and/or dimethylallyl diphosphate (DMAPP) monomers, which plants synthesize using two alternative pathways: a cytosolic mevalonic acid (MVA) pathway and a plastidic methyleritritol-4-phosphate (MEP) pathway. As such, developing plants for use as a platform to use IPP/DMAPP and produce high value terpenoids is an important biotechnological goal. Still, IPP/DMAPP are the precursors to many plant developmental hormones. This creates severe challenges in redirecting IPP/DMAPP towards production of non-cognate plant metabolites. A potential solution to this problem is increasing the IPP/DMAPP production flux in planta. Here, we aimed at discovering, understanding, and predicting the effects of increasing IPP/DMAPP production in plants through modelling. We used synthetic biology to create rice lines containing an additional ectopic MVA biosynthetic pathway for producing IPP/DMAPP. The rice lines express three alternative versions of the additional MVA pathway in the plastid, in addition to the normal endogenous pathways. We collected data for changes in macroscopic and molecular phenotypes, gene expression, isoprenoid content, and hormone abundance in those lines. To integrate the molecular and macroscopic data and develop a more in depth understanding of the effects of engineering the exogenous pathway in the mutant rice lines, we developed and analyzed data-centric, line-specific, multilevel mathematical models. These models connect the effects of variations in hormones and gene expression to changes in macroscopic plant phenotype and metabolite concentrations within the MVA and MEP pathways of WT and mutant rice lines. Our models allow us to predict how an exogenous IPP/DMAPP biosynthetic pathway affects the flux of terpenoid precursors. We also quantify the long-term effect of plant hormones on the dynamic behavior of IPP/DMAPP biosynthetic pathways in seeds, and predict plant characteristics, such as plant height, leaf size, and chlorophyll content from molecular data. In addition, our models are a tool that can be used in the future to help in prioritizing re-engineering strategies for the exogenous pathway in order to achieve specific metabolic goals.
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Affiliation(s)
- Orio Basallo
- Systems Biology Group, Department Ciències Mèdiques Bàsiques, Faculty of Medicine, Universitat de Lleida, Lleida, Spain
- Institut de Recerca Biomedica de Lleida (IRBLleida), Lleida, Spain
| | - Lucia Perez
- Applied Plant Biotechnology Group, Department de Producció Vegetal I Ciència Florestal, Escola Tècnica Superior d'Enginyeria Agroalimentària i Forestal i de Veterinària (ETSEAFiV), Universitat de Lleida, Lleida, Spain
- Agrotecnio Centres de Recerca de Catalunya (CERCA) Center, Lleida, Spain
| | - Abel Lucido
- Systems Biology Group, Department Ciències Mèdiques Bàsiques, Faculty of Medicine, Universitat de Lleida, Lleida, Spain
- Institut de Recerca Biomedica de Lleida (IRBLleida), Lleida, Spain
| | - Albert Sorribas
- Systems Biology Group, Department Ciències Mèdiques Bàsiques, Faculty of Medicine, Universitat de Lleida, Lleida, Spain
- Institut de Recerca Biomedica de Lleida (IRBLleida), Lleida, Spain
| | - Alberto Marin-Saguino
- Systems Biology Group, Department Ciències Mèdiques Bàsiques, Faculty of Medicine, Universitat de Lleida, Lleida, Spain
- Institut de Recerca Biomedica de Lleida (IRBLleida), Lleida, Spain
| | - Ester Vilaprinyo
- Systems Biology Group, Department Ciències Mèdiques Bàsiques, Faculty of Medicine, Universitat de Lleida, Lleida, Spain
- Institut de Recerca Biomedica de Lleida (IRBLleida), Lleida, Spain
| | - Laura Perez-Fons
- School of Biological Sciences, Royal Holloway University of London, Egham Hill, United Kingdom
| | - Alfonso Albacete
- Departament of Plant Nutrition, Center of Edaphology and Applied Biology of the Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Murcia, Murcia, Spain
- Department of Plant Production and Agrotechnology, Institute for Agri-Food Research and Development of Murcia, Murcia, Spain
| | - Cristina Martínez-Andújar
- Departament of Plant Nutrition, Center of Edaphology and Applied Biology of the Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Murcia, Murcia, Spain
| | - Paul D. Fraser
- School of Biological Sciences, Royal Holloway University of London, Egham Hill, United Kingdom
| | - Paul Christou
- Applied Plant Biotechnology Group, Department de Producció Vegetal I Ciència Florestal, Escola Tècnica Superior d'Enginyeria Agroalimentària i Forestal i de Veterinària (ETSEAFiV), Universitat de Lleida, Lleida, Spain
- Agrotecnio Centres de Recerca de Catalunya (CERCA) Center, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain
| | - Teresa Capell
- Applied Plant Biotechnology Group, Department de Producció Vegetal I Ciència Florestal, Escola Tècnica Superior d'Enginyeria Agroalimentària i Forestal i de Veterinària (ETSEAFiV), Universitat de Lleida, Lleida, Spain
- Agrotecnio Centres de Recerca de Catalunya (CERCA) Center, Lleida, Spain
| | - Rui Alves
- Systems Biology Group, Department Ciències Mèdiques Bàsiques, Faculty of Medicine, Universitat de Lleida, Lleida, Spain
- Institut de Recerca Biomedica de Lleida (IRBLleida), Lleida, Spain
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Pan H, Wang J, Wu H, Li Z, Lian J. Synthetic biology toolkit for engineering Cupriviadus necator H16 as a platform for CO 2 valorization. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:212. [PMID: 34736496 PMCID: PMC8570001 DOI: 10.1186/s13068-021-02063-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 10/25/2021] [Indexed: 06/09/2023]
Abstract
BACKGROUND CO2 valorization is one of the effective methods to solve current environmental and energy problems, in which microbial electrosynthesis (MES) system has proved feasible and efficient. Cupriviadus necator (Ralstonia eutropha) H16, a model chemolithoautotroph, is a microbe of choice for CO2 conversion, especially with the ability to be employed in MES due to the presence of genes encoding [NiFe]-hydrogenases and all the Calvin-Benson-Basham cycle enzymes. The CO2 valorization strategy will make sense because the required hydrogen can be produced from renewable electricity independently of fossil fuels. MAIN BODY In this review, synthetic biology toolkit for C. necator H16, including genetic engineering vectors, heterologous gene expression elements, platform strain and genome engineering, and transformation strategies, is firstly summarized. Then, the review discusses how to apply these tools to make C. necator H16 an efficient cell factory for converting CO2 to value-added products, with the examples of alcohols, fatty acids, and terpenoids. The review is concluded with the limitation of current genetic tools and perspectives on the development of more efficient and convenient methods as well as the extensive applications of C. necator H16. CONCLUSIONS Great progress has been made on genetic engineering toolkit and synthetic biology applications of C. necator H16. Nevertheless, more efforts are expected in the near future to engineer C. necator H16 as efficient cell factories for the conversion of CO2 to value-added products.
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Affiliation(s)
- Haojie Pan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jia Wang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Haoliang Wu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Zhongjian Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China.
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Dalwadi MP, Orol D, Walter F, Minton NP, King JR, Kovács K. Using singular perturbation theory to determine kinetic parameters in a non-standard coupled enzyme assay. J Math Biol 2020; 81:649-690. [PMID: 32761360 PMCID: PMC7427744 DOI: 10.1007/s00285-020-01524-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 06/29/2020] [Indexed: 11/27/2022]
Abstract
We investigate how to characterize the kinetic parameters of an aminotransaminase using a non-standard coupled (or auxiliary) enzyme assay, where the peculiarity arises for two reasons. First, one of the products of the auxiliary enzyme is a substrate for the primary enzyme and, second, we explicitly account for the reversibility of the auxiliary enzyme reaction. Using singular perturbation theory, we characterize the two distinguished asymptotic limits in terms of the strength of the reverse reaction, which allows us to determine how to deduce the kinetic parameters of the primary enzyme for a characterized auxiliary enzyme. This establishes a parameter-estimation algorithm that is applicable more generally to similar reaction networks. We demonstrate the applicability of our theory by performing enzyme assays to characterize a novel putative aminotransaminase enzyme, CnAptA (UniProtKB Q0KEZ8) from Cupriavidus necator H16, for two different omega-amino acid substrates.
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Affiliation(s)
- Mohit P Dalwadi
- Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Oxford, OX2 6GG, UK.
- Synthetic Biology Research Centre, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Diego Orol
- Synthetic Biology Research Centre, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Frederik Walter
- Synthetic Biology Research Centre, 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
| | - 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
| | - Katalin Kovács
- Synthetic Biology Research Centre, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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Dalwadi MP, King JR. An Asymptotic Analysis of the Malonyl-CoA Route to 3-Hydroxypropionic Acid in Genetically Engineered Microbes. Bull Math Biol 2020; 82:36. [PMID: 32140941 PMCID: PMC7058581 DOI: 10.1007/s11538-020-00714-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/24/2020] [Indexed: 11/23/2022]
Abstract
There has been recent interest in creating an efficient microbial production route for 3-hydroxypropionic acid, an important platform chemical. We develop and solve a mathematical model for the time-dependent metabolite concentrations in the malonyl-CoA pathway for 3-hydroxypropionic acid production in microbes, using a combination of numerical and asymptotic methods. This allows us to identify the most important targets for enzyme regulation therein under conditions of plentiful and sparse pyruvate, and to quantify their relative importance. In our model, we account for sinks of acetyl-CoA and malonyl-CoA to, for example, the citric acid cycle and fatty acid biosynthesis, respectively. Notably, in the plentiful pyruvate case we determine that there is a bifurcation in the asymptotic structure of the system, the crossing of which corresponds to a significant increase in 3-hydroxypropionic acid production. Moreover, we deduce that the most significant increases to 3-hydroxypropionic acid production can be obtained by up-regulating two specific enzymes in tandem, as the inherent nonlinearity of the system means that a solo up-regulation of either does not result in large increases in production. The types of issue arising here are prevalent in synthetic biology applications, and it is hoped that the system considered provides an instructive exemplar for broader applications.
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Affiliation(s)
- Mohit P Dalwadi
- Mathematical Institute, University of Oxford, Oxford, OX2 6GG, UK. .,Synthetic Biology Research Centre, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - John R King
- Synthetic Biology Research Centre, University of Nottingham, Nottingham, NG7 2RD, UK.,School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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