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Luo J, Yuan Q, Mao Y, Wei F, Zhao J, Yu W, Kong S, Guo Y, Cai J, Liao X, Wang Z, Ma H. Reconstruction of a Genome-Scale Metabolic Network for Shewanella oneidensis MR-1 and Analysis of its Metabolic Potential for Bioelectrochemical Systems. Front Bioeng Biotechnol 2022; 10:913077. [PMID: 35646853 PMCID: PMC9133699 DOI: 10.3389/fbioe.2022.913077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/26/2022] [Indexed: 11/28/2022] Open
Abstract
Bioelectrochemical systems (BESs) based on Shewanella oneidensis MR-1 offer great promise for sustainable energy/chemical production, but the low rate of electron generation remains a crucial bottleneck preventing their industrial application. Here, we reconstructed a genome-scale metabolic model of MR-1 to provide a strong theoretical basis for novel BES applications. The model iLJ1162, comprising 1,162 genes, 1,818 metabolites and 2,084 reactions, accurately predicted cellular growth using a variety of substrates with 86.9% agreement with experimental results, which is significantly higher than the previously published models iMR1_799 and iSO783. The simulation of microbial fuel cells indicated that expanding the substrate spectrum of MR-1 to highly reduced feedstocks, such as glucose and glycerol, would be beneficial for electron generation. In addition, 31 metabolic engineering targets were predicted to improve electricity production, three of which have been experimentally demonstrated, while the remainder are potential targets for modification. Two potential electron transfer pathways were identified, which could be new engineering targets for increasing the electricity production capacity of MR-1. Finally, the iLJ1162 model was used to simulate the optimal biosynthetic pathways for six platform chemicals based on the MR-1 chassis in microbial electrosynthesis systems. These results offer guidance for rational design of novel BESs.
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Affiliation(s)
- Jiahao Luo
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Frontier Science Center for Synthetic Biology (Ministry of Education), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Qianqian Yuan
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yufeng Mao
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Fan Wei
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Juntao Zhao
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Frontier Science Center for Synthetic Biology (Ministry of Education), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Wentong Yu
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Frontier Science Center for Synthetic Biology (Ministry of Education), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Shutian Kong
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Frontier Science Center for Synthetic Biology (Ministry of Education), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yanmei Guo
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jingyi Cai
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xiaoping Liao
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhiwen Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Frontier Science Center for Synthetic Biology (Ministry of Education), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- *Correspondence: Zhiwen Wang, ; Hongwu Ma,
| | - Hongwu Ma
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- *Correspondence: Zhiwen Wang, ; Hongwu Ma,
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Korth B, Harnisch F. Modeling Microbial Electrosynthesis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 167:273-325. [PMID: 29119203 DOI: 10.1007/10_2017_35] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mathematical modeling is an overarching approach for assessing the complexity of microbial electrosynthesis (MES) and for complementing the relevant experimental research. By describing and linking compartments, components, and processes with appropriate mathematical equations, MES and the corresponding bioelectrodes and complete bioelectrochemical systems can be analyzed and predicted across several temporal and local scales. Thereby, insights into fundamental phenomena and mechanisms, in addition to process engineering and design can be obtained. However, a substantial lack of knowledge about extracellular electron transfer mechanisms and electrotrophic microorganisms presumably prevented the development of adequate models of MES, especially of biocathodes, so far. To propel efforts regarding this demanding task, this chapter provides a comprehensive overview of the relevant compartments, components and processes, appropriate model strategies, and a discussion on potential modeling pitfalls. By adapting an established approach to assessing the energetics of microorganism, an instruction for calculating stoichiometry, thermodynamics, and kinetics, with the example of electro-autotrophic growth at cathodes, is presented. Models of bioanodes and fundamental electrochemical equations are described to provided strategies for calculating cathodic electron-uptake reactions and connecting them to the microbial metabolism. Finally, differential equations are detailed for coupling the distinct compartments of a bioelectrochemical system. Although MES comprises anodic and cathodic reactions, the present chapter focuses on biocathodes representing a functional connection between cathode and electron-accepting microorganisms. Graphical Abstract.
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Affiliation(s)
- Benjamin Korth
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Falk Harnisch
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
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Lu M, Chan S, Babanova S, Bretschger O. Effect of oxygen on the per-cell extracellular electron transfer rate of Shewanella oneidensis MR-1 explored in bioelectrochemical systems. Biotechnol Bioeng 2016; 114:96-105. [PMID: 27399911 PMCID: PMC5132103 DOI: 10.1002/bit.26046] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/06/2016] [Indexed: 02/03/2023]
Abstract
Extracellular electron transfer (EET) is a mechanism that enables microbes to respire solid‐phase electron acceptors. These EET reactions most often occur in the absence of oxygen, since oxygen can act as a competitive electron acceptor for many facultative microbes. However, for Shewanella oneidensis MR‐1, oxygen may increase biomass development, which could result in an overall increase in EET activity. Here, we studied the effect of oxygen on S. oneidensis MR‐1 EET rates using bioelectrochemical systems (BESs). We utilized optically accessible BESs to monitor real‐time biomass growth, and studied the per‐cell EET rate as a function of oxygen and riboflavin concentrations in BESs of different design and operational conditions. Our results show that oxygen exposure promotes biomass development on the electrode, but significantly impairs per‐cell EET rates even though current production does not always decrease with oxygen exposure. Additionally, our results indicated that oxygen can affect the role of riboflavin in EET. Under anaerobic conditions, both current density and per‐cell EET rate increase with the riboflavin concentration. However, as the dissolved oxygen (DO) value increased to 0.42 mg/L, riboflavin showed very limited enhancement on per‐cell EET rate and current generation. Since it is known that oxygen can promote flavins secretion in S. oneidensis, the role of riboflavin may change under anaerobic and aerobic conditions. Biotechnol. Bioeng. 2017;114: 96–105. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Mengqian Lu
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037
| | - Shirley Chan
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037
| | - Sofia Babanova
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037.,Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico
| | - Orianna Bretschger
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037
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Luo S, Guo W, Nealson KH, Feng X, He Z. ¹³C Pathway Analysis for the Role of Formate in Electricity Generation by Shewanella Oneidensis MR-1 Using Lactate in Microbial Fuel Cells. Sci Rep 2016; 6:20941. [PMID: 26868848 PMCID: PMC4751489 DOI: 10.1038/srep20941] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/14/2016] [Indexed: 12/16/2022] Open
Abstract
Microbial fuel cell (MFC) is a promising technology for direct electricity generation from organics by microorganisms. The type of electron donors fed into MFCs affects the electrical performance, and mechanistic understanding of such effects is important to optimize the MFC performance. In this study, we used a model organism in MFCs, Shewanella oneidensis MR-1, and (13)C pathway analysis to investigate the role of formate in electricity generation and the related microbial metabolism. Our results indicated a synergistic effect of formate and lactate on electricity generation, and extra formate addition on the original lactate resulted in more electrical output than using formate or lactate as a sole electron donor. Based on the (13)C tracer analysis, we discovered decoupled cell growth and electricity generation in S. oneidensis MR-1 during co-utilization of lactate and formate (i.e., while the lactate was mainly metabolized to support the cell growth, the formate was oxidized to release electrons for higher electricity generation). To our best knowledge, this is the first time that (13)C tracer analysis was applied to study microbial metabolism in MFCs and it was demonstrated to be a valuable tool to understand the metabolic pathways affected by electron donors in the selected electrochemically-active microorganisms.
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Affiliation(s)
- Shuai Luo
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Weihua Guo
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Xueyang Feng
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Zhen He
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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Mao L, Nicolae A, Oliveira MAP, He F, Hachi S, Fleming RMT. A constraint-based modelling approach to metabolic dysfunction in Parkinson's disease. Comput Struct Biotechnol J 2015; 13:484-91. [PMID: 26504511 PMCID: PMC4579274 DOI: 10.1016/j.csbj.2015.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 08/05/2015] [Accepted: 08/09/2015] [Indexed: 12/18/2022] Open
Abstract
One of the hallmarks of sporadic Parkinson's disease is degeneration of dopaminergic neurons in the pars compacta of the substantia nigra. The aetiopathogenesis of this degeneration is still not fully understood, with dysfunction of many biochemical pathways in different subsystems suggested to be involved. Recent advances in constraint-based modelling approaches hold great potential to systematically examine the relative contribution of dysfunction in disparate pathways to dopaminergic neuronal degeneration, but few studies have employed these methods in Parkinson's disease research. Therefore, this review outlines a framework for future constraint-based modelling of dopaminergic neuronal metabolism to decipher the multi-factorial mechanisms underlying the neuronal pathology of Parkinson's disease.
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Affiliation(s)
- Longfei Mao
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-Belval, Luxembourg
| | - Averina Nicolae
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-Belval, Luxembourg
| | - Miguel A P Oliveira
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-Belval, Luxembourg
| | - Feng He
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-Belval, Luxembourg ; Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29, rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - Siham Hachi
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-Belval, Luxembourg
| | - Ronan M T Fleming
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-Belval, Luxembourg
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