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Molinari F, Salini A, Vittore A, Santoro O, Izzo L, Fusco S, Pollegioni L, Rosini E. Bio-based production of cis,cis-muconic acid as platform for a sustainable polymers production. BIORESOURCE TECHNOLOGY 2024; 408:131190. [PMID: 39094966 DOI: 10.1016/j.biortech.2024.131190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
Production of the high industrial value cis,cis-muconic acid (ccMA) from renewable biomasses is of main interest especially when biological (green) processes are used. We recently generated a E. coli strain expressing five recombinant enzymes to convert vanillin (VA, from lignin) into ccMA. Here, we optimized a growing cell approach in bioreactor for the ccMA production. The medium composition, fermentation conditions, and VA addition were tuned: pulse-feeding VA at 1 mmol/h allowed to reach 5.2 g/L of ccMA in 48 h (0.86 g ccMA/g VA), with a productivity 4-fold higher compared to the resting cells approach, thus resulting in significantly lower E-factor and Process Mass Intensity green metric parameters. The recovered ccMA has been used as building block to produce a fully bioderived polymer with rubber-like properties. The sustainable optimized bioprocess can be considered an integrated approach to develop a platform for bio-based polymers production from renewable feedstocks.
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Affiliation(s)
- Filippo Molinari
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Andrea Salini
- Biochemistry and Industrial Biotechnology (BIB) Laboratory, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Aniello Vittore
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Orlando Santoro
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Lorella Izzo
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Salvatore Fusco
- Biochemistry and Industrial Biotechnology (BIB) Laboratory, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Elena Rosini
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy.
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Liu Y, Xue B, Liu H, Wang S, Su H. Rational construction of synthetic consortia: Key considerations and model-based methods for guiding the development of a novel biosynthesis platform. Biotechnol Adv 2024; 72:108348. [PMID: 38531490 DOI: 10.1016/j.biotechadv.2024.108348] [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: 02/04/2024] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
The rapid development of synthetic biology has significantly improved the capabilities of mono-culture systems in converting different substrates into various value-added bio-chemicals through metabolic engineering. However, overexpression of biosynthetic pathways in recombinant strains can impose a heavy metabolic burden on the host, resulting in imbalanced energy distribution and negatively affecting both cell growth and biosynthesis capacity. Synthetic consortia, consisting of two or more microbial species or strains with complementary functions, have emerged as a promising and efficient platform to alleviate the metabolic burden and increase product yield. However, research on synthetic consortia is still in its infancy, with numerous challenges regarding the design and construction of stable synthetic consortia. This review provides a comprehensive comparison of the advantages and disadvantages of mono-culture systems and synthetic consortia. Key considerations for engineering synthetic consortia based on recent advances are summarized, and simulation and computational tools for guiding the advancement of synthetic consortia are discussed. Moreover, further development of more efficient and cost-effective synthetic consortia with emerging technologies such as artificial intelligence and machine learning is highlighted.
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Affiliation(s)
- Yu Liu
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Boyuan Xue
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Hao Liu
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Shaojie Wang
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China.
| | - Haijia Su
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China.
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Kordesedehi R, Shahpiri A, Asadollahi MA, Biria D, Nikel PI. Enhanced chaotrope tolerance and (S)-2-hydroxypropiophenone production by recombinant Pseudomonas putida engineered with Pprl from Deinococcus radiodurans. Microb Biotechnol 2024; 17:e14448. [PMID: 38498302 PMCID: PMC10946676 DOI: 10.1111/1751-7915.14448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
Pseudomonas putida is a soil bacterium with multiple uses in fermentation and biotransformation processes. P. putida ATCC 12633 can biotransform benzaldehyde and other aldehydes into valuable α-hydroxyketones, such as (S)-2-hydroxypropiophenone. However, poor tolerance of this strain toward chaotropic aldehydes hampers efficient biotransformation processes. To circumvent this problem, we expressed the gene encoding the global regulator PprI from Deinococcus radiodurans, an inducer of pleiotropic proteins promoting DNA repair, in P. putida. Fine-tuned gene expression was achieved using an expression plasmid under the control of the LacIQ /Ptrc system, and the cross-protective role of PprI was assessed against multiple stress treatments. Moreover, the stress-tolerant P. putida strain was tested for 2-hydroxypropiophenone production using whole resting cells in the presence of relevant aldehyde substrates. P. putida cells harbouring the global transcriptional regulator exhibited high tolerance toward benzaldehyde, acetaldehyde, ethanol, butanol, NaCl, H2 O2 and thermal stress, thereby reflecting the multistress protection profile conferred by PprI. Additionally, the engineered cells converted aldehydes to 2-hydroxypropiophenone more efficiently than the parental P. putida strain. 2-Hydroxypropiophenone concentration reached 1.6 g L-1 upon a 3-h incubation under optimized conditions, at a cell concentration of 0.033 g wet cell weight mL-1 in the presence of 20 mM benzaldehyde and 600 mM acetaldehyde. Product yield and productivity were 0.74 g 2-HPP g-1 benzaldehyde and 0.089 g 2-HPP g cell dry weight-1 h-1 , respectively, 35% higher than the control experiments. Taken together, these results demonstrate that introducing PprI from D. radiodurans enhances chaotrope tolerance and 2-HPP production in P. putida ATCC 12633.
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Affiliation(s)
- Reihaneh Kordesedehi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Azar Shahpiri
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Mohammad Ali Asadollahi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Davoud Biria
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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Yan Z, Pan Y, Huang M, Liu JZ. De Novo Pterostilbene Production from Glucose Using Modular Coculture Engineering in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:516-528. [PMID: 38130104 DOI: 10.1021/acs.jafc.3c06629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Pterostilbene, a derivative of resveratrol, is of increasing interest due to its increased bioavailability and potential health benefits. Sustainable production of pterostilbene is important, especially given the challenges of traditional plant extraction and chemical synthesis methods. While engineered microbial cell factories provide a potential alternative for pterostilbene production, most approaches necessitate feeding intermediate compounds. To address these limitations, we adopted a modular coculture engineering strategy, dividing the pterostilbene biosynthetic pathway between two engineered E. coli strains. Using a combination of gene knockout, atmospheric and room-temperature plasma mutagenesis, and error-prone PCR-based whole genome shuffling to engineer strains for the coculture system, we achieved a pterostilbene production titer of 134.84 ± 9.28 mg/L from glucose using a 1:3 inoculation ratio and 0.1% dimethyl sulfoxide supplementation. This represents the highest reported de novo production titer. Our results underscore the potential of coculture systems and metabolic balance in microbial biosynthesis.
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Affiliation(s)
- Zhibo Yan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
| | - Yuyang Pan
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
| | - Mingtao Huang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
| | - Jian-Zhong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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Lignin Valorization: Production of High Value-Added Compounds by Engineered Microorganisms. Catalysts 2023. [DOI: 10.3390/catal13030555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
Lignin is the second most abundant polymer in nature, which is also widely generated during biomass fractionation in lignocellulose biorefineries. At present, most of technical lignin is simply burnt for energy supply although it represents the richest natural source of aromatics, and thus it is a promising feedstock for generation of value-added compounds. Lignin is heterogeneous in composition and recalcitrant to degradation, with this substantially hampering its use. Notably, microbes have evolved particular enzymes and specialized metabolic pathways to degrade this polymer and metabolize its various aromatic components. In recent years, novel pathways have been designed allowing to establish engineered microbial cell factories able to efficiently funnel the lignin degradation products into few metabolic intermediates, representing suitable starting points for the synthesis of a variety of valuable molecules. This review focuses on recent success cases (at the laboratory/pilot scale) based on systems metabolic engineering studies aimed at generating value-added and specialty chemicals, with much emphasis on the production of cis,cis-muconic acid, a building block of recognized industrial value for the synthesis of plastic materials. The upgrade of this global waste stream promises a sustainable product portfolio, which will become an industrial reality when economic issues related to process scale up will be tackled.
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Mittermeier F, Bäumler M, Arulrajah P, García Lima JDJ, Hauke S, Stock A, Weuster‐Botz D. Artificial microbial consortia for bioproduction processes. Eng Life Sci 2023; 23:e2100152. [PMID: 36619879 PMCID: PMC9815086 DOI: 10.1002/elsc.202100152] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/03/2022] [Accepted: 03/24/2022] [Indexed: 01/11/2023] Open
Abstract
The application of artificial microbial consortia for biotechnological production processes is an emerging field in research as it offers great potential for the improvement of established as well as the development of novel processes. In this review, we summarize recent highlights in the usage of various microbial consortia for the production of, for example, platform chemicals, biofuels, or pharmaceutical compounds. It aims to demonstrate the great potential of co-cultures by employing different organisms and interaction mechanisms and exploiting their respective advantages. Bacteria and yeasts often offer a broad spectrum of possible products, fungi enable the utilization of complex lignocellulosic substrates via enzyme secretion and hydrolysis, and microalgae can feature their abilities to fixate CO2 through photosynthesis for other organisms as well as to form lipids as potential fuelstocks. However, the complexity of interactions between microbes require methods for observing population dynamics within the process and modern approaches such as modeling or automation for process development. After shortly discussing these interaction mechanisms, we aim to present a broad variety of successfully established co-culture processes to display the potential of artificial microbial consortia for the production of biotechnological products.
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Affiliation(s)
- Fabian Mittermeier
- Department of Energy and Process EngineeringTUM School of Engineering and DesignChair of Biochemical EngineeringTechnical University of MunichGarchingGermany
| | - Miriam Bäumler
- Department of Energy and Process EngineeringTUM School of Engineering and DesignChair of Biochemical EngineeringTechnical University of MunichGarchingGermany
| | - Prasika Arulrajah
- TUM School of Engineering and DesignTechnical University of MunichGarchingGermany
| | | | - Sebastian Hauke
- TUM School of Engineering and DesignTechnical University of MunichGarchingGermany
| | - Anna Stock
- TUM School of Engineering and DesignTechnical University of MunichGarchingGermany
| | - Dirk Weuster‐Botz
- Department of Energy and Process EngineeringTUM School of Engineering and DesignChair of Biochemical EngineeringTechnical University of MunichGarchingGermany
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7
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Recent advances and perspectives on production of value-added organic acids through metabolic engineering. Biotechnol Adv 2023; 62:108076. [PMID: 36509246 DOI: 10.1016/j.biotechadv.2022.108076] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
Organic acids are important consumable materials with a wide range of applications in the food, biopolymer and chemical industries. The global consumer organic acids market is estimated to increase to $36.86 billion by 2026. Conventionally, organic acids are produced from the chemical catalysis process with petrochemicals as raw materials, which posts severe environmental concerns and conflicts with our sustainable development goals. Most of the commonly used organic acids can be produced from various organisms. As a state-of-the-art technology, large-scale fermentative production of important organic acids with genetically-modified microbes has become an alternative to the chemical route to meet the market demand. Despite the fact that bio-based organic acid production from renewable cheap feedstock provides a viable solution, low productivity has impeded their industrial-scale application. With our deeper understanding of strain genetics, physiology and the availability of strain engineering tools, new technologies including synthetic biology, various metabolic engineering strategies, omics-based system biology tools, and high throughput screening methods are gradually established to bridge our knowledge gap. And they were further applied to modify the cellular reaction networks of potential microbial hosts and improve the strain performance, which facilitated the commercialization of consumable organic acids. Here we present the recent advances of metabolic engineering strategies to improve the production of important organic acids including fumaric acid, citric acid, itaconic acid, adipic acid, muconic acid, and we also discuss the current challenges and future perspectives on how we can develop a cost-efficient, green and sustainable process to produce these important chemicals from low-cost feedstocks.
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Zhao S, Li F, Yang F, Ma Q, Liu L, Huang Z, Fan X, Li Q, Liu X, Gu P. Microbial production of valuable chemicals by modular co-culture strategy. World J Microbiol Biotechnol 2022; 39:6. [PMID: 36346491 DOI: 10.1007/s11274-022-03447-6] [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: 09/09/2022] [Accepted: 10/22/2022] [Indexed: 11/11/2022]
Abstract
Nowadays, microbial synthesis has become a common way for producing valuable chemicals. Traditionally, microbial production of valuable chemicals is accomplished by a single strain. For the purpose of increasing the production titer and yield of a recombinant strain, complicated pathways and regulation layers should be fine-tuned, which also brings a heavy metabolic burden to the host. In addition, utilization of various complex and mixed substrates further interferes with the normal growth of the host strain and increases the complexity of strain engineering. As a result, modular co-culture technology, which aims to divide a target complex pathway into separate modules located at different single strains, poses an alternative solution for microbial production. Recently, modular co-culture strategy has been employed for the synthesis of different natural products. Therefore, in this review, various chemicals produced with application of co-cultivation technology are summarized, including co-culture with same species or different species, and regulation of population composition between the co-culture members. In addition, development prospects and challenges of this promising field are also addressed, and possible solution for these issues were also provided.
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Affiliation(s)
- Shuo Zhao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Fangfang Li
- Yantai Food and Drug Control and Test Center, Yantai, 264003, People's Republic of China
| | - Fan Yang
- Tsingtao Brewery Co., Ltd., Qingdao, 266071, People's Republic of China
| | - Qianqian Ma
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Liwen Liu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Zhaosong Huang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Xiangyu Fan
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Xiaoli Liu
- Key Laboratory of Marine Biotechnology in Universities of Shandong, School of Life Sciences, Ludong University, Yantai, 264025, People's Republic of China
| | - Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China.
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9
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Atkinson E, Tuza Z, Perrino G, Stan GB, Ledesma-Amaro R. Resource-aware whole-cell model of division of labour in a microbial consortium for complex-substrate degradation. Microb Cell Fact 2022; 21:115. [PMID: 35698129 PMCID: PMC9195437 DOI: 10.1186/s12934-022-01842-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Low-cost sustainable feedstocks are essential for commercially viable biotechnologies. These feedstocks, often derived from plant or food waste, contain a multitude of different complex biomolecules which require multiple enzymes to hydrolyse and metabolise. Current standard biotechnology uses monocultures in which a single host expresses all the proteins required for the consolidated bioprocess. However, these hosts have limited capacity for expressing proteins before growth is impacted. This limitation may be overcome by utilising division of labour (DOL) in a consortium, where each member expresses a single protein of a longer degradation pathway. RESULTS Here, we model a two-strain consortium, with one strain expressing an endohydrolase and a second strain expressing an exohydrolase, for cooperative degradation of a complex substrate. Our results suggest that there is a balance between increasing expression to enhance degradation versus the burden that higher expression causes. Once a threshold of burden is reached, the consortium will consistently perform better than an equivalent single-cell monoculture. CONCLUSIONS We demonstrate that resource-aware whole-cell models can be used to predict the benefits and limitations of using consortia systems to overcome burden. Our model predicts the region of expression where DOL would be beneficial for growth on starch, which will assist in making informed design choices for this, and other, complex-substrate degradation pathways.
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Affiliation(s)
- Eliza Atkinson
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK
| | - Zoltan Tuza
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK
| | - Giansimone Perrino
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK
| | - Guy-Bart Stan
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK.
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK.
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10
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Thuan NH, Tatipamula VB, Canh NX, Van Giang N. Recent advances in microbial co-culture for production of value-added compounds. 3 Biotech 2022; 12:115. [PMID: 35547018 PMCID: PMC9018925 DOI: 10.1007/s13205-022-03177-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/31/2022] [Indexed: 02/06/2023] Open
Abstract
Micro-organisms have often been used to produce bioactive compounds as antibiotics, antifungals, and anti-tumors, etc. due to their easy and applicable culture, genetic manipulation, and extraction, etc. Mainly, microbial mono-cultures have been applied to produce value-added compounds and gotten numerous valuable results. However, mono-culture also has several complicated problems, such as metabolic burdens affecting the growth and development of the host, leading to a decrease in titer of the target compound. To circumvent those limitations, microbial co-culture has been technically developed and gained much interest compared to mono-culture. For example, co-culture simplifies the design of artificial biosynthetic pathways and restricts the recombinant host's metabolic burden, causing increased titer of desired compounds. This paper summarizes the recent advanced progress in applying microbial platform co-culture to produce natural products, such as flavonoid, terpenoid, alkaloid, etc. Furthermore, importantly different strategies for enhancing production, overcoming the metabolic burdens, building autonomous modulation of cell growth rate and culture composition in response to a quorum-sensing signal, etc., were also described in detail.
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Affiliation(s)
- Nguyen Huy Thuan
- Center for Molecular Biology, Duy Tan University, Da Nang, 550000 Vietnam
| | | | - Nguyen Xuan Canh
- Faculty of Biotechnology, Vietnam National University of Agriculture, Gialam, Hanoi Vietnam
| | - Nguyen Van Giang
- Faculty of Biotechnology, Vietnam National University of Agriculture, Gialam, Hanoi Vietnam
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Kohlstedt M, Weimer A, Weiland F, Stolzenberger J, Selzer M, Sanz M, Kramps L, Wittmann C. Biobased PET from lignin using an engineered cis, cis-muconate-producing Pseudomonas putida strain with superior robustness, energy and redox properties. Metab Eng 2022; 72:337-352. [DOI: 10.1016/j.ymben.2022.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/18/2022] [Accepted: 05/04/2022] [Indexed: 11/26/2022]
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12
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Zhu Y, Ai M, Jia X. Optimization of a Two-Species Microbial Consortium for Improved Mcl-PHA Production From Glucose-Xylose Mixtures. Front Bioeng Biotechnol 2022; 9:794331. [PMID: 35083203 PMCID: PMC8784772 DOI: 10.3389/fbioe.2021.794331] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) have attracted much attention as a good substitute for petroleum-based plastics, especially mcl-PHA due to their superior physical and mechanical properties with broader applications. Artificial microbial consortia can solve the problems of low metabolic capacity of single engineered strains and low conversion efficiency of natural consortia while expanding the scope of substrate utilization. Therefore, the use of artificial microbial consortia is considered a promising method for the production of mcl-PHA. In this work, we designed and constructed a microbial consortium composed of engineered Escherichia coli MG1655 and Pseudomonas putida KT2440 based on the "nutrition supply-detoxification" concept, which improved mcl-PHA production from glucose-xylose mixtures. An engineered E. coli that preferentially uses xylose was engineered with an enhanced ability to secrete acetic acid and free fatty acids (FFAs), producing 6.44 g/L acetic acid and 2.51 g/L FFAs with 20 g/L xylose as substrate. The mcl-PHA producing strain of P. putida in the microbial consortium has been engineered to enhance its ability to convert acetic acid and FFAs into mcl-PHA, producing 0.75 g/L mcl-PHA with mixed substrates consisting of glucose, acetic acid, and octanoate, while also reducing the growth inhibition of E. coli by acetic acid. The further developed artificial microbial consortium finally produced 1.32 g/L of mcl-PHA from 20 g/L of a glucose-xylose mixture (1:1) after substrate competition control and process optimization. The substrate utilization and product synthesis functions were successfully divided into the two strains in the constructed artificial microbial consortium, and a mutually beneficial symbiosis of "nutrition supply-detoxification" with a relatively high mcl-PHA titer was achieved, enabling the efficient accumulation of mcl-PHA. The consortium developed in this study is a potential platform for mcl-PHA production from lignocellulosic biomass.
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Affiliation(s)
- Yinzhuang Zhu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Mingmei Ai
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
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13
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Vila-Santa A, Mendes FC, Ferreira FC, Prather KLJ, Mira NP. Implementation of Synthetic Pathways to Foster Microbe-Based Production of Non-Naturally Occurring Carboxylic Acids and Derivatives. J Fungi (Basel) 2021; 7:jof7121020. [PMID: 34947002 PMCID: PMC8706239 DOI: 10.3390/jof7121020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/15/2021] [Accepted: 11/20/2021] [Indexed: 11/20/2022] Open
Abstract
Microbially produced carboxylic acids (CAs) are considered key players in the implementation of more sustainable industrial processes due to their potential to replace a set of oil-derived commodity chemicals. Most CAs are intermediates of microbial central carbon metabolism, and therefore, a biochemical production pathway is described and can be transferred to a host of choice to enable/improve production at an industrial scale. However, for some CAs, the implementation of this approach is difficult, either because they do not occur naturally (as is the case for levulinic acid) or because the described production pathway cannot be easily ported (as it is the case for adipic, muconic or glucaric acids). Synthetic biology has been reshaping the range of molecules that can be produced by microbial cells by setting new-to-nature pathways that leverage on enzyme arrangements not observed in vivo, often in association with the use of substrates that are not enzymes’ natural ones. In this review, we provide an overview of how the establishment of synthetic pathways, assisted by computational tools for metabolic retrobiosynthesis, has been applied to the field of CA production. The translation of these efforts in bridging the gap between the synthesis of CAs and of their more interesting derivatives, often themselves non-naturally occurring molecules, is also reviewed using as case studies the production of methacrylic, methylmethacrylic and poly-lactic acids.
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Affiliation(s)
- Ana Vila-Santa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Department of Bioengineering, University of Lisbon, 1049-001 Lisbon, Portugal; (A.V.-S.); (F.C.M.); (F.C.F.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Fernão C. Mendes
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Department of Bioengineering, University of Lisbon, 1049-001 Lisbon, Portugal; (A.V.-S.); (F.C.M.); (F.C.F.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Frederico C. Ferreira
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Department of Bioengineering, University of Lisbon, 1049-001 Lisbon, Portugal; (A.V.-S.); (F.C.M.); (F.C.F.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Kristala L. J. Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
| | - Nuno P. Mira
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Department of Bioengineering, University of Lisbon, 1049-001 Lisbon, Portugal; (A.V.-S.); (F.C.M.); (F.C.F.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Correspondence:
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14
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Conversion of Carbon Monoxide to Chemicals Using Microbial Consortia. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 180:373-407. [PMID: 34811579 DOI: 10.1007/10_2021_180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Syngas, a gaseous mixture of CO, H2 and CO2, can be produced by gasification of carbon-containing materials, including organic waste materials or lignocellulosic biomass. The conversion of bio-based syngas to chemicals is foreseen as an important process in circular bioeconomy. Carbon monoxide is also produced as a waste gas in many industrial sectors (e.g., chemical, energy, steel). Often, the purity level of bio-based syngas and waste gases is low and/or the ratios of syngas components are not adequate for chemical conversion (e.g., by Fischer-Tropsch). Microbes are robust catalysts to transform impure syngas into a broad spectrum of products. Fermentation of CO-rich waste gases to ethanol has reached commercial scale (by axenic cultures of Clostridium species), but production of other chemical building blocks is underexplored. Currently, genetic engineering of carboxydotrophic acetogens is applied to increase the portfolio of products from syngas/CO, but the limited energy metabolism of these microbes limits product yields and applications (for example, only products requiring low levels of ATP for synthesis can be produced). An alternative approach is to explore microbial consortia, including open mixed cultures and synthetic co-cultures, to create a metabolic network based on CO conversion that can yield products such as medium-chain carboxylic acids, higher alcohols and other added-value chemicals.
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15
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Kayastha S, Sagwan-Barkdoll L, Anterola A, Jayakody LN. Developing synthetic microbes to produce indirubin-derivatives. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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16
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Yuan X, Chen F. Cocultivation Study of Monascus spp. and Aspergillus niger Inspired From Black-Skin-Red-Koji by a Double-Sided Petri Dish. Front Microbiol 2021; 12:670684. [PMID: 34177849 PMCID: PMC8221429 DOI: 10.3389/fmicb.2021.670684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Cocultivation is an emerging and potential way to investigate microbial interaction in the laboratory. Extensive researches has been carried out over the years, but some microorganism cocultivation are not easy to implement in the laboratory, especially the fungus-fungus (FF) cocultivation, owing to the obstacles such as fungal different growth rate, limited growing space, hyphae intertwining, and difficulty of sample separation, etc. In this research, a double-sided petri dish (DSPD) was designed and carried out as a tool to study FF cocultivation in the laboratory. A natural FF cocultivation of Monascus spp. and Aspergillus niger inspired from black-skin-red-koji (BSRK), were studied. By using DSPD, the aforementioned obstacles in the FF cocultivation study were overcome through co-culturing Monascus spp. and A. niger on each side of DSPD. The characteristics of monocultured and co-cultured Monascus spp. and A. niger were compared and analyzed, including colonial and microscopic morphologies, and main secondary metabolites (SMs) of Monascus spp. analyzed by high performance liquid chromatography. And a novel SM was found to be produced by Monascus ruber M7 when co-cultured with A. niger CBS 513.88. Since the above mentioned obstacles, were overcome, we obtained good quality of transcriptome data for further analysis. These results indicate that DSPD might be an efficient tool for investigation of microbial interaction, in particular, for FF interaction.
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Affiliation(s)
- Xi Yuan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fusheng Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
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17
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Bretschneider L, Wegner M, Bühler K, Bühler B, Karande R. One-pot synthesis of 6-aminohexanoic acid from cyclohexane using mixed-species cultures. Microb Biotechnol 2021; 14:1011-1025. [PMID: 33369139 PMCID: PMC8085927 DOI: 10.1111/1751-7915.13744] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022] Open
Abstract
6-Aminohexanoic acid (6AHA) is a vital polymer building block for Nylon 6 production and an FDA-approved orphan drug. However, its production from cyclohexane is associated with several challenges, including low conversion and yield, and severe environmental issues. We aimed at overcoming these challenges by developing a bioprocess for 6AHA synthesis. A mixed-species approach turned out to be most promising. Thereby, Pseudomonas taiwanensis VLB120 strains harbouring an upstream cascade converting cyclohexane to either є-caprolactone (є-CL) or 6-hydroxyhexanoic acid (6HA) were combined with Escherichia coli JM101 strains containing the corresponding downstream cascade for the further conversion to 6AHA. ε-CL was found to be a better 'shuttle molecule' than 6HA enabling higher 6AHA formation rates and yields. Mixed-species reaction performance with 4 g l-1 biomass, 10 mM cyclohexane, and an air-to-aqueous phase ratio of 23 combined with a repetitive oxygen feeding strategy led to complete substrate conversion with 86% 6AHA yield and an initial specific 6AHA formation rate of 7.7 ± 0.1 U gCDW -1 . The same cascade enabled 49% 7-aminoheptanoic acid yield from cycloheptane. This combination of rationally engineered strains allowed direct 6AHA production from cyclohexane in one pot with high conversion and yield under environmentally benign conditions.
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Affiliation(s)
- Lisa Bretschneider
- Department of Solar MaterialsHelmholtz‐Centre for Environmental Research –UFZPermoserstrasse 15Leipzig04318Germany
| | - Martin Wegner
- Department of Solar MaterialsHelmholtz‐Centre for Environmental Research –UFZPermoserstrasse 15Leipzig04318Germany
| | - Katja Bühler
- Department of Solar MaterialsHelmholtz‐Centre for Environmental Research –UFZPermoserstrasse 15Leipzig04318Germany
| | - Bruno Bühler
- Department of Solar MaterialsHelmholtz‐Centre for Environmental Research –UFZPermoserstrasse 15Leipzig04318Germany
| | - Rohan Karande
- Department of Solar MaterialsHelmholtz‐Centre for Environmental Research –UFZPermoserstrasse 15Leipzig04318Germany
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18
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Petch JE, Gurnani P, Yilmaz G, Mastrotto F, Alexander C, Heeb S, Cámara M, Mantovani G. Combining Inducible Lectin Expression and Magnetic Glyconanoparticles for the Selective Isolation of Bacteria from Mixed Populations. ACS APPLIED MATERIALS & INTERFACES 2021; 13:19230-19243. [PMID: 33852268 DOI: 10.1021/acsami.1c00907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The selective isolation of bacteria from mixed populations has been investigated in varied applications ranging from differential pathogen identification in medical diagnostics and food safety to the monitoring of microbial stress dynamics in industrial bioreactors. Selective isolation techniques are generally limited to the confinement of small populations in defined locations, may be unable to target specific bacteria, or rely on immunomagnetic separation, which is not universally applicable. In this proof-of-concept work, we describe a novel strategy combining inducible bacterial lectin expression with magnetic glyconanoparticles (MGNPs) as a platform technology to enable selective bacterial isolation from cocultures. An inducible mutant of the type 1 fimbriae, displaying the mannose-specific lectin FimH, was constructed in Escherichia coli allowing for "on-demand" glycan-binding protein presentation following external chemical stimulation. Binding to glycopolymers was only observed upon fimbrial induction and was specific for mannosylated materials. A library of MGNPs was produced via the grafting of well-defined catechol-terminal glycopolymers prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization to magnetic nanoparticles. Thermal analysis revealed high functionalization (≥85% polymer by weight). Delivery of MGNPs to cocultures of fluorescently labeled bacteria followed by magnetic extraction resulted in efficient depletion of type 1 fimbriated target cells from wild-type or afimbriate E. coli. Extraction efficiency was found to be dependent on the molecular weight of the glycopolymers utilized to engineer the nanoparticles, with MGNPs decorated with shorter Dopa-(ManAA)50 mannosylated glycopolymers found to perform better than those assembled from a longer Dopa-(ManAA)200 analogue. The extraction efficiency of fimbriated E. coli was also improved when the counterpart strain did not harbor the genetic apparatus for the expression of the type 1 fimbriae. Overall, this work suggests that the modulation of the genetic apparatus encoding bacterial surface-associated lectins coupled with capture through MGNPs could be a versatile tool for the extraction of bacteria from mixed populations.
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Affiliation(s)
- Joshua E Petch
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
- Nottingham University Biodiscovery Institute, National Biofilms Innovation Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Pratik Gurnani
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Gokhan Yilmaz
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Francesca Mastrotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | - Cameron Alexander
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Stephan Heeb
- Nottingham University Biodiscovery Institute, National Biofilms Innovation Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Miguel Cámara
- Nottingham University Biodiscovery Institute, National Biofilms Innovation Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Giuseppe Mantovani
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
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19
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Diender M, Parera Olm I, Sousa DZ. Synthetic co-cultures: novel avenues for bio-based processes. Curr Opin Biotechnol 2021; 67:72-79. [PMID: 33517194 DOI: 10.1016/j.copbio.2021.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/23/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023]
Abstract
In nature, microorganisms live in multi-species communities allowing microbial interactions. These interactions are lost upon establishing a pure culture, increasing the metabolic burden and limiting the metabolic potential of the isolated microbe. In the past years, synthetic microbial co-cultivation, using well-defined consortia of two or more microbes, was increasingly explored for innovative applications in biotechnology. As such, interspecies interactions take place without the complexity of an open mixed culture, minimizing undesired side reactions. Ultimately, synthetic co-cultivation allows to take well-characterized microbes 'off-the-shelf' to create ecosystems with improved process capabilities. This review highlights some of the recent developments on co-cultivation, focusing on waste-to-chemicals conversions. It also addresses fundamental knowledge on microbial interactions deriving from these studies, which is important to further develop our ability to engineer functional co-cultures for bioproduction.
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Affiliation(s)
- Martijn Diender
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ivette Parera Olm
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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20
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Ai M, Zhu Y, Jia X. Recent advances in constructing artificial microbial consortia for the production of medium-chain-length polyhydroxyalkanoates. World J Microbiol Biotechnol 2021; 37:2. [PMID: 33392870 DOI: 10.1007/s11274-020-02986-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/20/2020] [Indexed: 11/29/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are a class of high-molecular-weight polyesters made from hydroxy fatty acid monomers. PHAs produced by microorganisms have diverse structures, variable physical properties, and good biodegradability. They exhibit similar physical properties to petroleum-based plastics but are much more environmentally friendly. Medium-chain-length polyhydroxyalkanoates (mcl-PHAs), in particular, have attracted much interest because of their low crystallinity, low glass transition temperature, low tensile strength, high elongation at break, and customizable structure. Nevertheless, high production costs have hindered their practical application. The use of genetically modified organisms can reduce production costs by expanding the scope of substrate utilization, improving the conversion efficiency of substrate to product, and increasing the yield of mcl-PHAs. The yield of mcl-PHAs produced by a pure culture of an engineered microorganism was not high enough because of the limitations of the metabolic capacity of a single microorganism. The construction of artificial microbial consortia and the optimization of microbial co-cultivation have been studied. This type of approach avoids the addition of precursor substances and helps synthesize mcl-PHAs more efficiently. In this paper, we reviewed the design and construction principles and optimized control strategies for artificial microbial consortia that produce mcl-PHAs. We described the metabolic advantages of co-cultivating artificial microbial consortia using low-value substrates and discussed future perspectives on the production of mcl-PHAs using artificial microbial consortia.
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Affiliation(s)
- Mingmei Ai
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yinzhuang Zhu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072, China.
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21
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Yun J, Zabed HM, Zhang Y, Parvez A, Zhang G, Qi X. Co-fermentation of glycerol and glucose by a co-culture system of engineered Escherichia coli strains for 1,3-propanediol production without vitamin B 12 supplementation. BIORESOURCE TECHNOLOGY 2021; 319:124218. [PMID: 33049440 DOI: 10.1016/j.biortech.2020.124218] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
The necessity of costly co-enzyme B12 for the activity of glycerol dehydratase (GDHt) is considered as a major bottleneck in sustainable bioproduction of 1,3-propanediol (1,3-PD) from glycerol. Here, an E. coil Rosetta-dhaB1-dhaB2 strain was constructed by overexpressing a B12-independent GDHt (dhaB1) and its activating factor (dhaB2) from Clostridium butyricum. Subsequently, it was used in designing a co-culture with E. coli BL21-dhaT that overexpressed 1,3-PD oxidoreductase (dhaT), to produce 1,3-PD during co-fermentation of glycerol and glucose. The optimum initial ratio of BL21-dhaT to Rosetta-dhaB1-dhaB2 strains in the co-culture was 1.5. Compared to the fermentation of glycerol alone, co-fermentation approach provided 1.3-folds higher 1,3-PD. Finally, co-fermentation was done in a 10 L bioreactor that produced 41.65 g/L 1,3-PD, which corresponded to 0.69 g/L/h productivity and 0.67 mol/mol yield of 1,3-PD. Hence, the developed co-culture could produce 1,3-PD cost-effectively without requiring vitamin B12.
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Affiliation(s)
- Junhua Yun
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Hossain M Zabed
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Yufei Zhang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Amreesh Parvez
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Guoyan Zhang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Xianghui Qi
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China.
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22
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Yuan X, Chen F. Cocultivation Study of Monascus spp. and Aspergillus niger Inspired From Black-Skin-Red-Koji by a Double-Sided Petri Dish. Front Microbiol 2021. [PMID: 34177849 DOI: 10.3389/fmicb.2021.6706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
Cocultivation is an emerging and potential way to investigate microbial interaction in the laboratory. Extensive researches has been carried out over the years, but some microorganism cocultivation are not easy to implement in the laboratory, especially the fungus-fungus (FF) cocultivation, owing to the obstacles such as fungal different growth rate, limited growing space, hyphae intertwining, and difficulty of sample separation, etc. In this research, a double-sided petri dish (DSPD) was designed and carried out as a tool to study FF cocultivation in the laboratory. A natural FF cocultivation of Monascus spp. and Aspergillus niger inspired from black-skin-red-koji (BSRK), were studied. By using DSPD, the aforementioned obstacles in the FF cocultivation study were overcome through co-culturing Monascus spp. and A. niger on each side of DSPD. The characteristics of monocultured and co-cultured Monascus spp. and A. niger were compared and analyzed, including colonial and microscopic morphologies, and main secondary metabolites (SMs) of Monascus spp. analyzed by high performance liquid chromatography. And a novel SM was found to be produced by Monascus ruber M7 when co-cultured with A. niger CBS 513.88. Since the above mentioned obstacles, were overcome, we obtained good quality of transcriptome data for further analysis. These results indicate that DSPD might be an efficient tool for investigation of microbial interaction, in particular, for FF interaction.
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Affiliation(s)
- Xi Yuan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fusheng Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
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23
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Antoniewicz MR. A guide to metabolic flux analysis in metabolic engineering: Methods, tools and applications. Metab Eng 2020; 63:2-12. [PMID: 33157225 DOI: 10.1016/j.ymben.2020.11.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 10/28/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022]
Abstract
The field of metabolic engineering is primarily concerned with improving the biological production of value-added chemicals, fuels and pharmaceuticals through the design, construction and optimization of metabolic pathways, redirection of intracellular fluxes, and refinement of cellular properties relevant for industrial bioprocess implementation. Metabolic network models and metabolic fluxes are central concepts in metabolic engineering, as was emphasized in the first paper published in this journal, "Metabolic fluxes and metabolic engineering" (Metabolic Engineering, 1: 1-11, 1999). In the past two decades, a wide range of computational, analytical and experimental approaches have been developed to interrogate the capabilities of biological systems through analysis of metabolic network models using techniques such as flux balance analysis (FBA), and quantify metabolic fluxes using constrained-based modeling approaches such as metabolic flux analysis (MFA) and more advanced experimental techniques based on the use of stable-isotope tracers, i.e. 13C-metabolic flux analysis (13C-MFA). In this review, we describe the basic principles of metabolic flux analysis, discuss current best practices in flux quantification, highlight potential pitfalls and alternative approaches in the application of these tools, and give a broad overview of pragmatic applications of flux analysis in metabolic engineering practice.
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Affiliation(s)
- Maciek R Antoniewicz
- Department of Chemical Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Michigan, Ann Arbor, MI, 48109, USA.
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24
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Choi S, Lee HN, Park E, Lee SJ, Kim ES. Recent Advances in Microbial Production of cis,cis-Muconic Acid. Biomolecules 2020; 10:biom10091238. [PMID: 32854378 PMCID: PMC7564838 DOI: 10.3390/biom10091238] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
cis,cis-Muconic acid (MA) is a valuable C6 dicarboxylic acid platform chemical that is used as a starting material for the production of various valuable polymers and drugs, including adipic acid and terephthalic acid. As an alternative to traditional chemical processes, bio-based MA production has progressed to the establishment of de novo MA pathways in several microorganisms, such as Escherichia coli, Corynebacterium glutamicum, Pseudomonas putida, and Saccharomyces cerevisiae. Redesign of the metabolic pathway, intermediate flux control, and culture process optimization were all pursued to maximize the microbial MA production yield. Recently, MA production from biomass, such as the aromatic polymer lignin, has also attracted attention from researchers focusing on microbes that are tolerant to aromatic compounds. This paper summarizes recent microbial MA production strategies that involve engineering the metabolic pathway genes as well as the heterologous expression of some foreign genes involved in MA biosynthesis. Microbial MA production will continue to play a vital role in the field of bio-refineries and a feasible way to complement various petrochemical-based chemical processes.
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Affiliation(s)
- Sisun Choi
- Department of Biological Engineering, Inha University, Incheon 22212, Korea; (S.C.); (H.-N.L.); (E.P.)
| | - Han-Na Lee
- Department of Biological Engineering, Inha University, Incheon 22212, Korea; (S.C.); (H.-N.L.); (E.P.)
- STR Biotech Co., Ltd., Chuncheon-si, Gangwon-do 24232, Korea;
| | - Eunhwi Park
- Department of Biological Engineering, Inha University, Incheon 22212, Korea; (S.C.); (H.-N.L.); (E.P.)
| | - Sang-Jong Lee
- STR Biotech Co., Ltd., Chuncheon-si, Gangwon-do 24232, Korea;
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University, Incheon 22212, Korea; (S.C.); (H.-N.L.); (E.P.)
- Correspondence: ; Tel.: +82-32-860-8318; Fax: +82-32-872-4046
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25
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Bioconversion of Plant Hydrolysate Biomass into Biofuels Using an Engineered Bacillus subtilis and Escherichia coli Mixed-whole Cell Biotransformation. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0487-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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26
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Wang X, Policarpio L, Prajapati D, Li Z, Zhang H. Developing E. coli-E. coli co-cultures to overcome barriers of heterologous tryptamine biosynthesis. Metab Eng Commun 2020; 10:e00110. [PMID: 31853442 PMCID: PMC6911970 DOI: 10.1016/j.mec.2019.e00110] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/28/2019] [Accepted: 11/13/2019] [Indexed: 11/29/2022] Open
Abstract
Tryptamine is an alkaloid compound with demonstrated bioactivities and is also a precursor molecule to many important hormones and neurotransmitters. The high efficiency biosynthesis of tryptamine from inexpensive and renewable carbon substrates is of great research and application significance. In the present study, a tryptamine biosynthesis pathway was established in a metabolically engineered E. coli-E. coli co-culture. The upstream and downstream strains of the co-culture were dedicated to tryptophan provision and conversion to tryptamine, respectively. The constructed co-culture was cultivated using either glucose or glycerol as carbon source for de novo production of tryptamine. The manipulation of the co-culture strains' inoculation ratio was adapted to balance the biosynthetic strengths of the pathway modules for bioproduction optimization. Moreover, a biosensor-assisted cell selection strategy was adapted to improve the pathway intermediate tryptophan provision by the upstream strain, which further enhanced the tryptamine biosynthesis. The resulting biosensor-assisted modular co-culture produced 194 mg/L tryptamine with a yield of 0.02 g/g glucose using shake flask cultivation. The findings of this work demonstrate that the biosensor-assisted modular co-culture engineering offers a new perspective for conducting microbial biosynthesis.
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Affiliation(s)
| | | | | | | | - Haoran Zhang
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Rd, Piscataway, NJ, 08854, USA
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27
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Qian X, Chen L, Sui Y, Chen C, Zhang W, Zhou J, Dong W, Jiang M, Xin F, Ochsenreither K. Biotechnological potential and applications of microbial consortia. Biotechnol Adv 2020; 40:107500. [DOI: 10.1016/j.biotechadv.2019.107500] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 11/13/2019] [Accepted: 12/17/2019] [Indexed: 12/20/2022]
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28
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Wang G, Øzmerih S, Guerreiro R, Meireles AC, Carolas A, Milne N, Jensen MK, Ferreira BS, Borodina I. Improvement of cis, cis-Muconic Acid Production in Saccharomyces cerevisiae through Biosensor-Aided Genome Engineering. ACS Synth Biol 2020; 9:634-646. [PMID: 32058699 PMCID: PMC8457548 DOI: 10.1021/acssynbio.9b00477] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Muconic acid is a potential platform chemical for the production of nylon, polyurethanes, and terephthalic acid. It is also an attractive functional copolymer in plastics due to its two double bonds. At this time, no economically viable process for the production of muconic acid exists. To harness novel genetic targets for improved production of cis,cis-muconic acid (CCM) in the yeast Saccharomyces cerevisiae, we employed a CCM-biosensor coupled to GFP expression with a broad dynamic response to screen UV-mutagenesis libraries of CCM-producing yeast. Via fluorescence activated cell sorting we identified a clone Mut131 with a 49.7% higher CCM titer and 164% higher titer of biosynthetic intermediate-protocatechuic acid (PCA). Genome resequencing of the Mut131 and reverse engineering identified seven causal missense mutations of the native genes (PWP2, EST2, ATG1, DIT1, CDC15, CTS2, and MNE1) and a duplication of two CCM biosynthetic genes, encoding dehydroshikimate dehydratase and catechol 1,2-dioxygenase, which were not recognized as flux controlling before. The Mut131 strain was further rationally engineered by overexpression of the genes encoding for PCA decarboxylase and AROM protein without shikimate dehydrogenase domain (Aro1pΔE), and by restoring URA3 prototrophy. The resulting engineered strain produced 20.8 g/L CCM in controlled fed-batch fermentation, with a yield of 66.2 mg/g glucose and a productivity of 139 mg/L/h, representing the highest reported performance metrics in a yeast for de novo CCM production to date and the highest production of an aromatic compound in yeast. The study illustrates the benefit of biosensor-based selection and brings closer the prospect of biobased muconic acid.
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Affiliation(s)
- Guokun Wang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK-2800 Kgs, Denmark
| | - Süleyman Øzmerih
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK-2800 Kgs, Denmark
| | - Rogério Guerreiro
- Biotrend-Inovação e Engenharia em Biotecnologia SA, Cantanhede, 3060-197, Portugal
| | - Ana C. Meireles
- Biotrend-Inovação e Engenharia em Biotecnologia SA, Cantanhede, 3060-197, Portugal
| | - Ana Carolas
- Biotrend-Inovação e Engenharia em Biotecnologia SA, Cantanhede, 3060-197, Portugal
| | - Nicholas Milne
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK-2800 Kgs, Denmark
| | - Michael K. Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK-2800 Kgs, Denmark
| | - Bruno S. Ferreira
- Biotrend-Inovação e Engenharia em Biotecnologia SA, Cantanhede, 3060-197, Portugal
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK-2800 Kgs, Denmark
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Cao M, Gao M, Suástegui M, Mei Y, Shao Z. Building microbial factories for the production of aromatic amino acid pathway derivatives: From commodity chemicals to plant-sourced natural products. Metab Eng 2020; 58:94-132. [DOI: 10.1016/j.ymben.2019.08.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/03/2019] [Accepted: 08/07/2019] [Indexed: 01/23/2023]
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Metabolic engineering of Escherichia coli for shikimate pathway derivative production from glucose-xylose co-substrate. Nat Commun 2020; 11:279. [PMID: 31937786 PMCID: PMC6959354 DOI: 10.1038/s41467-019-14024-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/13/2019] [Indexed: 11/08/2022] Open
Abstract
Glucose and xylose are the major components of lignocellulose. Effective utilization of both sugars can improve the efficiency of bioproduction. Here, we report a method termed parallel metabolic pathway engineering (PMPE) for producing shikimate pathway derivatives from glucose–xylose co-substrate. In this method, we seek to use glucose mainly for target chemical production, and xylose for supplying essential metabolites for cell growth. Glycolysis and the pentose phosphate pathway are completely separated from the tricarboxylic acid (TCA) cycle. To recover cell growth, we introduce a xylose catabolic pathway that directly flows into the TCA cycle. As a result, we can produce 4.09 g L−1cis,cis-muconic acid using the PMPE Escherichia coli strain with high yield (0.31 g g−1 of glucose) and produce l-tyrosine with 64% of the theoretical yield. The PMPE strategy can contribute to the development of clean processes for producing various valuable chemicals from lignocellulosic resources. In lignocellulose biomass, microbes prefer consuming glucose over xylose, which affects target compound production. Here, the authors achieve simultaneous utilization of glucose and xylose for target chemical production and cell growth, respectively, and realize high-level production of shikimate pathway derivatives.
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Wang R, Zhao S, Wang Z, Koffas MA. Recent advances in modular co-culture engineering for synthesis of natural products. Curr Opin Biotechnol 2019; 62:65-71. [PMID: 31605875 DOI: 10.1016/j.copbio.2019.09.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/22/2019] [Accepted: 09/06/2019] [Indexed: 01/13/2023]
Abstract
The microbial production of natural products has been traditionally accomplished in a single organism engineered to accommodate target biosynthetic pathways. Often times, such approaches result in large metabolic burdens as key cofactors, precursor metabolites and energy are channeled to pathways of structurally complex chemicals. Recently, modular co-culture engineering has emerged as a new approach to efficiently conduct heterologous biosynthesis and greatly enhance the production of natural products. This review highlights recent advances that leverage Escherichia coli-based modular co-culture engineering for making natural products. Potential future perspectives for studies in this promising field are addressed as well.
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Affiliation(s)
- Rufeng Wang
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shujuan Zhao
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhengtao Wang
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Mattheos Ag Koffas
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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Madhavan A, Arun KB, Sindhu R, Binod P, Kim SH, Pandey A. Tailoring of microbes for the production of high value plant-derived compounds: From pathway engineering to fermentative production. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140262. [PMID: 31404685 DOI: 10.1016/j.bbapap.2019.140262] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 08/03/2019] [Accepted: 08/05/2019] [Indexed: 12/20/2022]
Abstract
Plant natural products have been an attracting platform for the isolation of various active drugs and other bioactives. However large-scale extraction of these compounds is affected by the difficulty in mass cultivation of these plants and absence of strategies for successful extraction. Even though, synthesis by chemical method is an alternative method; it is less efficient as their chemical structure is highly complex which involve enantio-selectivity. Thus an alternate bio-system for heterologous production of plant natural products using microbes has emerged. Advent of various omics, synthetic and metabolic engineering strategies revolutionised the field of heterologous plant metabolite production. In this context, various engineering methods taken to synthesise plant natural products are described with an additional focus to fermentation strategies.
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Affiliation(s)
- Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | | | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR- NIIST), Trivandrum 695 019, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR- NIIST), Trivandrum 695 019, India
| | - Sang Hyoun Kim
- Department of Civil and Environmental Engineering, Yonsei University, Seoul, South Korea
| | - Ashok Pandey
- Department of Civil and Environmental Engineering, Yonsei University, Seoul, South Korea; Center for Innovation and Translational Research, CSIR- Indian Institute of Toxicology Research (CSIR-IITR), Lucknow 226 001, India.
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Li Z, Wang X, Zhang H. Balancing the non-linear rosmarinic acid biosynthetic pathway by modular co-culture engineering. Metab Eng 2019; 54:1-11. [PMID: 30844431 DOI: 10.1016/j.ymben.2019.03.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 03/01/2019] [Accepted: 03/03/2019] [Indexed: 11/20/2022]
Abstract
Pathway balancing is a critical and common challenge for microbial biosynthesis using metabolic engineering approaches. Non-linear biosynthetic pathways, such as diverging and converging pathways, are particularly difficult for bioproduction optimization, because they require delicate balancing between all interconnected constituent pathway modules. The emergence of modular co-culture engineering offers a new perspective for biosynthetic pathways modularization and balancing, as the biosynthetic capabilities of individual pathway modules can be coordinated by flexible adjustment of the subpopulation ratio of the co-culture strains carrying the designated modules. This study developed microbial co-cultures composed of multiple metabolically engineered E. coli strains for heterologous biosynthesis of complex natural product rosmarinic acid (RA) whose biosynthesis involves a complex diverging-converging pathway. Our results showed that, compared with the conventional mono-culture strategy, the engineered two-strain co-cultures significantly improved the RA production. Further pathway modularization and balancing in the context of three-strain co-cultures resulted in additional production improvement. Moreover, metabolically engineered co-culture strains utilizing different carbon substrates were recruited to improve the three-strain co-culture stability. The optimized co-culture based on these efforts produced 172 mg/L RA, exhibiting 38-fold biosynthesis improvement over the parent strain used in mono-culture biosynthesis. The findings of this work demonstrate the strong potentials of modular co-culture engineering for overcoming the challenges of complex natural product biosynthesis involving non-linear pathways.
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Affiliation(s)
- Zhenghong Li
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Rd, Piscataway, NJ 08854, USA
| | - Xiaonan Wang
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Rd, Piscataway, NJ 08854, USA
| | - Haoran Zhang
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Rd, Piscataway, NJ 08854, USA.
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Jiang Y, Wu R, Zhou J, He A, Xu J, Xin F, Zhang W, Ma J, Jiang M, Dong W. Recent advances of biofuels and biochemicals production from sustainable resources using co-cultivation systems. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:155. [PMID: 31285755 PMCID: PMC6588928 DOI: 10.1186/s13068-019-1495-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 06/11/2019] [Indexed: 05/09/2023]
Abstract
Microbial communities are ubiquitous in nature and exhibit several attractive features, such as sophisticated metabolic capabilities and strong environment robustness. Inspired by the advantages of natural microbial consortia, diverse artificial co-cultivation systems have been metabolically constructed for biofuels, chemicals and natural products production. In these co-cultivation systems, especially genetic engineering ones can reduce the metabolic burden caused by the complex of metabolic pathway through labor division, and improve the target product production significantly. This review summarized the most up-to-dated co-cultivation systems used for biofuels, chemicals and nature products production. In addition, major challenges associated with co-cultivation systems are also presented and discussed for meeting further industrial demands.
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Affiliation(s)
- Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
| | - Ruofan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Aiyong He
- Jiangsu Key Laboratory for Biomass-based Energy and Enzyme Technology, Huaiyin Normal University, Huaian, 223300 People’s Republic of China
| | - Jiaxing Xu
- Jiangsu Key Laboratory for Biomass-based Energy and Enzyme Technology, Huaiyin Normal University, Huaian, 223300 People’s Republic of China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
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35
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Flores AD, Ayla EZ, Nielsen DR, Wang X. Engineering a Synthetic, Catabolically Orthogonal Coculture System for Enhanced Conversion of Lignocellulose-Derived Sugars to Ethanol. ACS Synth Biol 2019; 8:1089-1099. [PMID: 30979337 DOI: 10.1021/acssynbio.9b00007] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fermentation of lignocellulosic sugar mixtures is often suboptimal due to inefficient xylose catabolism and sequential sugar utilization caused by carbon catabolite repression. Unlike in conventional applications employing a single engineered strain, the alternative development of synthetic microbial communities facilitates the execution of complex metabolic tasks by exploiting the unique community features, including modularity, division of labor, and facile tunability. A series of synthetic, catabolically orthogonal coculture systems were systematically engineered, as derived from either wild-type Escherichia coli W or ethanologenic LY180. Net catabolic activities were effectively balanced by simple tuning of the inoculum ratio between specialist strains, which enabled coutilization (98% of 100 g L-1 total sugars) of glucose-xylose mixtures (2:1 by mass) for both culture systems in simple batch fermentations. The engineered ethanologenic cocultures achieved ethanol titer (46 g L-1), productivity (488 mg L-1 h-1), and yield (∼90% of theoretical maximum), which were all significantly increased compared to LY180 monocultures.
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Affiliation(s)
- Andrew D. Flores
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, ECG 301, 501 E. Tyler Mall, Tempe, Arizona 85287, United States
| | - E. Zeynep Ayla
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, ECG 301, 501 E. Tyler Mall, Tempe, Arizona 85287, United States
| | - David R. Nielsen
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, ECG 301, 501 E. Tyler Mall, Tempe, Arizona 85287, United States
| | - Xuan Wang
- School of Life Sciences, Arizona State University, 427 E. Tyler Mall, Tempe, Arizona 85287, United States
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36
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Zhou Y, Li Z, Wang X, Zhang H. Establishing microbial co-cultures for 3-hydroxybenzoic acid biosynthesis on glycerol. Eng Life Sci 2019; 19:389-395. [PMID: 32625017 DOI: 10.1002/elsc.201800195] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/25/2019] [Accepted: 03/22/2019] [Indexed: 12/25/2022] Open
Abstract
Converting renewable feedstocks to aromatic compounds using engineered microbes offers a robust approach for sustainable, environment-friendly, and cost-effective production of these value-added products without the reliance on petroleum. In this study, rationally designed E. coli-E. coli co-culture systems were established for converting glycerol to 3-hydroxybenzoic acid (3HB). Specifically, the 3HB pathway was modularized and accommodated by two metabolically engineered E. coli strains. The co-culture biosynthesis was optimized by using different cultivation temperatures, varying the inoculum ratio between the co-culture strains, recruitment of a key pathway intermediate transporter, strengthening the critical pathway enzyme expression, and adjusting the timing for inducing pathway gene expression. Compared with the E. coli mono-culture, the optimized co-culture showed 5.3-fold improvement for 3HB biosynthesis. This study demonstrated the applicability of modular co-culture engineering for addressing the challenges of aromatic compound biosynthesis.
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Affiliation(s)
- Yiyao Zhou
- Department of Chemical and Biochemical Engineering Rutgers the State University of New Jersey Piscataway NJ USA
| | - Zhenghong Li
- Department of Chemical and Biochemical Engineering Rutgers the State University of New Jersey Piscataway NJ USA
| | - Xiaonan Wang
- Department of Chemical and Biochemical Engineering Rutgers the State University of New Jersey Piscataway NJ USA
| | - Haoran Zhang
- Department of Chemical and Biochemical Engineering Rutgers the State University of New Jersey Piscataway NJ USA
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37
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Modular Metabolic Engineering for Biobased Chemical Production. Trends Biotechnol 2019; 37:152-166. [DOI: 10.1016/j.tibtech.2018.07.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/03/2018] [Accepted: 07/05/2018] [Indexed: 11/21/2022]
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38
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Fujiwara R, Noda S, Tanaka T, Kondo A. Muconic Acid Production Using Gene-Level Fusion Proteins in Escherichia coli. ACS Synth Biol 2018; 7:2698-2705. [PMID: 30350569 DOI: 10.1021/acssynbio.8b00380] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study reports on the improving of muconic acid (MA) production by using metabolically engineered Escherichia coli. Three MA synthesis pathways separately were introduced into E. coli. After 72 h of cultivation, two of the three strains, i.e., one carrying the Pathway 1 (1.00 g/L) and the other carrying the Pathway 3 (1.34 g/L) produced MA. To increase MA production, the enzymes of the shikimate pathway (AroC and AroD) were overexpressed in these strains. Although the overexpression of AroC increased the MA production (1.59 g/L) by the Pathway 1, AroD overexpression decreased it by the Pathway 3. The metabolic channeling using gene-level fusion proteins additionally increased the MA production. In the pathway 1 and pH-controlled cultures, the overexpression of a fusion protein (AroC and MenF) increased the MA production from 20 g/L glucose to >3 and 4.45 g/L, respectively. These results suggest that the metabolic channeling approach is a promising strategy to increase the yield of the target compound.
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Affiliation(s)
- Ryosuke Fujiwara
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Japan
| | - Shuhei Noda
- Center for Sustainable Resource Science, RIKEN, Wako, Saitama 351-0198, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
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Charubin K, Papoutsakis ET. Direct cell-to-cell exchange of matter in a synthetic Clostridium syntrophy enables CO 2 fixation, superior metabolite yields, and an expanded metabolic space. Metab Eng 2018; 52:9-19. [PMID: 30391511 DOI: 10.1016/j.ymben.2018.10.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/19/2018] [Accepted: 10/25/2018] [Indexed: 11/24/2022]
Abstract
In microbial fermentations at least 33% of the sugar-substrate carbon is lost as CO2 during pyruvate decarboxylation to acetyl-CoA, with the corresponding electrons lost in the form of H2. Previous attempts to reduce this carbon and electron loss focused on engineering of a single organism. In nature, most microorganisms live in complex communities where syntrophic interactions result in superior resource utilization. Here, we show that a synthetic syntrophy consisting of the solventogen Clostridium acetobutylicum, which converts simple and complex carbohydrates into a variety of chemicals, and the acetogen C. ljungdahlii which fixes CO2, achieved carbon recoveries into C2-C4 alcohols almost to the limit of substrate-electron availability, with minimal H2 and CO2 release. The syntrophic co-culture produced robust metabolic outcomes over a broad range of starting population ratios of the two organisms. We show that direct cell-to-cell interactions and material exchange among the two microbes enabled unforeseen rearrangements in the metabolism of the individual species that resulted in the production of non-native metabolites, namely isopropanol and 2,3-butanediol. This was accomplished by pathway-specific alterations of gene expression brought about by one organism on the other, and vice versa. While some of these gene-expression alterations can be explained by the exchange of metabolites that induce specific gene expression patterns, others, as demonstrated by co-culture setup in a transwell system, cannot. The latter, for now, would be attributed to complex direct physical interactions among the two organisms, thus providing a glimpse of the potential microbial complexity of simple or multicomponent microbiomes. Such direct material-transfer phenomena have not been documented in the literature. Furthermore, our study shows that syntrophic cultures offer a flexible platform for metabolite production with superior carbon recovery that can also be applied to electron-enhanced fermentations enabling even higher carbon recoveries.
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Affiliation(s)
- Kamil Charubin
- Department of Chemical and Biomolecular Engineering, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA; Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
| | - Eleftherios Terry Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA; Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
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Charubin K, Bennett RK, Fast AG, Papoutsakis ET. Engineering Clostridium organisms as microbial cell-factories: challenges & opportunities. Metab Eng 2018; 50:173-191. [DOI: 10.1016/j.ymben.2018.07.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 11/25/2022]
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41
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Escherichia coli as a host for metabolic engineering. Metab Eng 2018; 50:16-46. [DOI: 10.1016/j.ymben.2018.04.008] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 12/21/2022]
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42
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Metabolically engineered Corynebacterium glutamicum for bio-based production of chemicals, fuels, materials, and healthcare products. Metab Eng 2018; 50:122-141. [DOI: 10.1016/j.ymben.2018.07.008] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 01/15/2023]
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43
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Jones JA, Wang X. Use of bacterial co-cultures for the efficient production of chemicals. Curr Opin Biotechnol 2018; 53:33-38. [DOI: 10.1016/j.copbio.2017.11.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 11/22/2017] [Accepted: 11/23/2017] [Indexed: 01/03/2023]
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Sensor-regulator and RNAi based bifunctional dynamic control network for engineered microbial synthesis. Nat Commun 2018; 9:3043. [PMID: 30072730 PMCID: PMC6072776 DOI: 10.1038/s41467-018-05466-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/06/2018] [Indexed: 11/10/2022] Open
Abstract
Writing artificial logic and dynamic function into complex cellular background to achieve desired phenotypes or improved outputs calls for the development of new genetic tools as well as their innovative use. In this study, we present a sensor-regulator and RNAi-based bifunctional dynamic control network that can provide simultaneous upregulation and downregulation of cellular metabolism for engineered biosynthesis. The promoter-regulator-mediated upregulation function and its transduced downregulation function through RNAi are systematically verified and characterized. We apply this dynamic control network to regulate the phosphoenolpyruvate metabolic node in Escherichia coli and achieve autonomous distribution of carbon flux between its native metabolism and the engineered muconic acid biosynthetic pathway. This allows muconic acid biosynthesis to reach 1.8 g L−1. This study also suggests the circumstances where dynamic control approaches are likely to take effects. Engineering dynamic control can improve microbial production of target chemicals. Here, the authors design a sensor-regulator and RNAi based bifunctional dynamic control network that can simultaneously and independently turn up and down cellular metabolism for engineered muconic acid production in E. coli.
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Becker J, Kuhl M, Kohlstedt M, Starck S, Wittmann C. Metabolic engineering of Corynebacterium glutamicum for the production of cis, cis-muconic acid from lignin. Microb Cell Fact 2018; 17:115. [PMID: 30029656 PMCID: PMC6054733 DOI: 10.1186/s12934-018-0963-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/13/2018] [Indexed: 11/25/2022] Open
Abstract
Background Cis, cis-muconic acid (MA) is a dicarboxylic acid of recognized industrial value. It provides direct access to adipic acid and terephthalic acid, prominent monomers of commercial plastics. Results In the present work, we engineered the soil bacterium Corynebacterium glutamicum into a stable genome-based cell factory for high-level production of bio-based MA from aromatics and lignin hydrolysates. The elimination of muconate cycloisomerase (catB) in the catechol branch of the β-ketoadipate pathway provided a mutant, which accumulated MA at 100% molar yield from catechol, phenol, and benzoic acid, using glucose as additional growth substrate. The production of MA was optimized by constitutive overexpression of catA, which increased the activity of the encoded catechol 1,2-dioxygenase, forming MA from catechol, tenfold. Intracellular levels of catechol were more than 30-fold lower than extracellular levels, minimizing toxicity, but still saturating the high affinity CatA enzyme. In a fed-batch process, the created strain C. glutamicum MA-2 accumulated 85 g L−1 MA from catechol in 60 h and achieved a maximum volumetric productivity of 2.4 g L−1 h−1. The strain was furthermore used to demonstrate the production of MA from lignin in a cascade process. Following hydrothermal depolymerization of softwood lignin into small aromatics, the MA-2 strain accumulated 1.8 g L−1 MA from the obtained hydrolysate. Conclusions Our findings open the door to valorize lignin, the second most abundant polymer on earth, by metabolically engineered C. glutamicum for industrial production of MA and potentially other chemicals. Electronic supplementary material The online version of this article (10.1186/s12934-018-0963-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Judith Becker
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Martin Kuhl
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Sören Starck
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany.
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Salmela M, Lehtinen T, Efimova E, Santala S, Mangayil R. Metabolic pairing of aerobic and anaerobic production in a one-pot batch cultivation. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:187. [PMID: 29988745 PMCID: PMC6029424 DOI: 10.1186/s13068-018-1186-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 06/25/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND The versatility of microbial metabolic pathways enables their utilization in vast number of applications. However, the electron and carbon recovery rates, essentially constrained by limitations of cell energetics, are often too low in terms of process feasibility. Cocultivation of divergent microbial species in a single process broadens the metabolic landscape, and thus, the possibilities for more complete carbon and energy utilization. RESULTS In this study, we integrated the metabolisms of two bacteria, an obligate anaerobe Clostridium butyricum and an obligate aerobe Acinetobacter baylyi ADP1. In the process, a glucose-negative mutant of A. baylyi ADP1 first deoxidized the culture allowing C. butyricum to grow and produce hydrogen from glucose. In the next phase, ADP1 produced long chain alkyl esters (wax esters) utilizing the by-products of C. butyricum, namely acetate and butyrate. The coculture produced 24.5 ± 0.8 mmol/l hydrogen (1.7 ± 0.1 mol/mol glucose) and 28 mg/l wax esters (10.8 mg/g glucose). CONCLUSIONS The cocultivation of strictly anaerobic and aerobic bacteria allowed the production of both hydrogen gas and long-chain alkyl esters in a simple one-pot batch process. The study demonstrates the potential of 'metabolic pairing' using designed microbial consortia for more optimal electron and carbon recovery.
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Affiliation(s)
- Milla Salmela
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, Tampere, Finland
| | - Tapio Lehtinen
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, Tampere, Finland
| | - Elena Efimova
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, Tampere, Finland
| | - Suvi Santala
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, Tampere, Finland
| | - Rahul Mangayil
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, Tampere, Finland
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Wang S, Bilal M, Zong Y, Hu H, Wang W, Zhang X. Development of a Plasmid-Free Biosynthetic Pathway for Enhanced Muconic Acid Production in Pseudomonas chlororaphis HT66. ACS Synth Biol 2018; 7:1131-1142. [PMID: 29608278 DOI: 10.1021/acssynbio.8b00047] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Muconic acid is a platform chemical and an important intermediate in the degradation process of a series of aromatic compounds. Herein, a plasmid-free synthetic pathway in Pseudomonas chlororaphis HT66 is constructed for the enhanced biosynthesis of muconic acid by connecting endogenous ubiquinone biosynthesis pathway with protocatechuate degradation pathway using chromosomal integration. Instead of being plasmid and inducer dependent, the engineered strains could steadily produce the high muconic acid using glycerol as a carbon source. The engineered strain HT66-MA6 achieved a 3376 mg/L muconic acid production with a yield of 187.56 mg/g glycerol via the following strategies: (1) block muconic acid conversion and enhance muconic acid efflux pumping with phenazine biosynthesis cluster; (2) increase the muconic acid precursors supply through overexpressing the rate-limiting step, and (3) coexpress the "3-dehydroshikimate-derived" route in parallel with the "4-hydroxybenzoic acid-derived" route to create a synthetic "metabolic funnel". Finally, on the basis of the glycerol feeding strategies, the muconic acid yield reached 0.122 mol/mol glycerol. The results suggest that the construction of synthetic pathway with a plasmid-free strategy in P. chlororaphis displays a high biotechnological perspective.
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Convergent engineering of syntrophic Escherichia coli coculture for efficient production of glycosides. Metab Eng 2018; 47:243-253. [PMID: 29596994 DOI: 10.1016/j.ymben.2018.03.016] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 03/21/2018] [Accepted: 03/24/2018] [Indexed: 11/23/2022]
Abstract
Synthetic microbial coculture to express heterologous biosynthetic pathway for de novo production of medicinal ingredients is an emerging strategy for metabolic engineering and synthetic biology. Here, taking efficient production of salidroside as an example of glycosides, we design and construct a syntrophic Escherichia coli-E. coli coculture composed of the aglycone (AG) strain and the glycoside (GD) strain, which convergently accommodate biosynthetic pathways of tyrosol and salidroside, respectively. To accomplish this the phenylalanine-deficient AG strain was engineered to utilize xylose preferentially and to overproduce precursor tyrosol, while the tyrosine-deficient GD strain was constructed to consume glucose exclusively and to enhance another precursor UDP-glucose availability for synthesis of salidroside. The AG and GD strains in the synthetic consortium are obligatory cooperators through crossfeeding of tyrosine and phenylalanine and compatible in glucose and xylose mixture. Through balancing the metabolic pathway strength, we show that the syntrophic coculture was robust and stable, and produced 6.03 g/L of salidroside. It was the de novo production of salidroside for the first time in E. coli coculture system, which would be applicable for production of other important glycosides and natural products.
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Thompson B, Pugh S, Machas M, Nielsen DR. Muconic Acid Production via Alternative Pathways and a Synthetic "Metabolic Funnel". ACS Synth Biol 2018; 7:565-575. [PMID: 29053259 DOI: 10.1021/acssynbio.7b00331] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Muconic acid is a promising platform biochemical and precursor to adipic acid, which can be used to synthesize various plastics and polymers. In this study, the systematic construction and comparative evaluation of a modular network of non-natural pathways for muconic acid biosynthesis was investigated in Escherichia coli, including via three distinct and novel pathways proceeding via phenol as a common intermediate. However, poor recombinant activity and high promiscuity of phenol hydroxylase ultimately limited "phenol-dependent" muconic acid production. A fourth pathway proceeding via p-hydroxybenzoate, protocatechuate, and catechol was accordingly developed, though with muconic acid titers by this route reaching just 819 mg/L, its performance lagged behind that of the established, "3-dehydroshikimiate-derived" route. Finally, these two most promising pathways were coexpressed in parallel to create a synthetic "metabolic funnel" that, by enabling maximal net precursor assimilation and flux while preserving native chorismate biosynthesis, nearly doubled muconic acid production to up to >3.1 g/L at a glucose yield of 158 mg/g while introducing only a single auxotrophy. This generalizable, "funneling" strategy is expected to have broad applications in metabolic engineering for further enhancing production of muconic acid, as well as other important bioproducts of interest.
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Affiliation(s)
- Brian Thompson
- Chemical Engineering, School for Engineering
of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - Shawn Pugh
- Chemical Engineering, School for Engineering
of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - Michael Machas
- Chemical Engineering, School for Engineering
of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - David R. Nielsen
- Chemical Engineering, School for Engineering
of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
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Averesch NJH, Martínez VS, Nielsen LK, Krömer JO. Toward Synthetic Biology Strategies for Adipic Acid Production: An in Silico Tool for Combined Thermodynamics and Stoichiometric Analysis of Metabolic Networks. ACS Synth Biol 2018; 7:490-509. [PMID: 29237121 DOI: 10.1021/acssynbio.7b00304] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adipic acid, a nylon-6,6 precursor, has recently gained popularity in synthetic biology. Here, 16 different production routes to adipic acid were evaluated using a novel tool for network-embedded thermodynamic analysis of elementary flux modes. The tool distinguishes between thermodynamically feasible and infeasible modes under determined metabolite concentrations, allowing the thermodynamic feasibility of theoretical yields to be assessed. Further, patterns that always caused infeasible flux distributions were identified, which will aid the development of tailored strain design. A review of cellular efflux mechanisms revealed that significant accumulation of extracellular product is only possible if coupled with ATP hydrolysis. A stoichiometric analysis demonstrated that the maximum theoretical product carbon yield heavily depends on the metabolic route, ranging from 32 to 99% on glucose and/or palmitate in Escherichia coli and Saccharomyces cerevisiae metabolic models. Equally important, metabolite concentrations appeared to be thermodynamically restricted in several pathways. Consequently, the number of thermodynamically feasible flux distributions was reduced, in some cases even rendering whole pathways infeasible, highlighting the importance of pathway choice. Only routes based on the shikimate pathway were thermodynamically favorable over a large concentration and pH range. The low pH capability of S. cerevisiae shifted the thermodynamic equilibrium of some pathways toward product formation. One identified infeasible-pattern revealed that the reversibility of the mitochondrial malate dehydrogenase contradicted the current state of knowledge, which imposes a major restriction on the metabolism of S. cerevisiae. Finally, the evaluation of industrially relevant constraints revealed that two shikimate pathway-based routes in E. coli were the most robust.
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Affiliation(s)
- Nils J. H. Averesch
- Centre
for Microbial Electrochemical Systems (CEMES), Advanced Water Management
Centre (AWMC), The University of Queensland, Brisbane 4072, Australia
- Universities Space Research Association at NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Verónica S. Martínez
- Systems
and Synthetic Biology Group, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
- ARC
Training Centre for Biopharmaceutical Innovation (CBI), Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
| | - Lars K. Nielsen
- Systems
and Synthetic Biology Group, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
- DTU
BIOSUSTAIN, Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Jens O. Krömer
- Centre
for Microbial Electrochemical Systems (CEMES), Advanced Water Management
Centre (AWMC), The University of Queensland, Brisbane 4072, Australia
- Department
for Solar Materials, Helmholtz Centre of Environmental Research−UFZ, 04318 Leipzig, Germany
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