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Effendi SW, Ng IS. Non-native Pathway Engineering with CRISPRi for Carbon Dioxide Assimilation and Valued 5-Aminolevulinic Acid Synthesis in Escherichia coli Nissle. ACS Synth Biol 2024; 13:2038-2044. [PMID: 38954490 PMCID: PMC11264323 DOI: 10.1021/acssynbio.4c00318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/04/2024]
Abstract
Carbon dioxide emission and acidification during chemical biosynthesis are critical challenges toward microbial cell factories' sustainability and efficiency. Due to its acidophilic traits among workhorse lineages, the probiotic Escherichia coli Nissle (EcN) has emerged as a promising chemical bioproducer. However, EcN lacks a CO2-fixing system. Herein, EcN was equipped with a simultaneous CO2 fixation system and subsequently utilized to produce low-emission 5-aminolevulinic acid (5-ALA). Two different artificial CO2-assimilating pathways were reconstructed: the novel ribose-1,5-bisphosphate (R15P) route and the conventional ribulose-5-phosphate (Ru5P) route. CRISPRi was employed to target the pfkAB and zwf genes in order to redirect the carbon flux. As expected, the CRISPRi design successfully strengthened the CO2 fixation. The CO2-fixing route via R15P resulted in high biomass, while the engineered Ru5P route acquired the highest 5-ALA and suppressed the CO2 release by 77%. CO2 fixation during 5-ALA production in EcN was successfully synchronized through fine-tuning the non-native pathways with CRISPRi.
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Affiliation(s)
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan
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2
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Gong Z, Chen J, Jiao X, Gong H, Pan D, Liu L, Zhang Y, Tan T. Genome-scale metabolic network models for industrial microorganisms metabolic engineering: Current advances and future prospects. Biotechnol Adv 2024; 72:108319. [PMID: 38280495 DOI: 10.1016/j.biotechadv.2024.108319] [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: 12/03/2023] [Revised: 01/04/2024] [Accepted: 01/18/2024] [Indexed: 01/29/2024]
Abstract
The construction of high-performance microbial cell factories (MCFs) is the centerpiece of biomanufacturing. However, the complex metabolic regulatory network of microorganisms poses great challenges for the efficient design and construction of MCFs. The genome-scale metabolic network models (GSMs) can systematically simulate the metabolic regulation process of microorganisms in silico, providing effective guidance for the rapid design and construction of MCFs. In this review, we summarized the development status of 16 important industrial microbial GSMs, and further outline the technologies or methods that continuously promote high-quality GSMs construction from five aspects: I) Databases and modeling tools facilitate GSMs reconstruction; II) evolving gap-filling technologies; III) constraint-based model reconstruction; IV) advances in algorithms; and V) developed visualization tools. In addition, we also summarized the applications of GSMs in guiding metabolic engineering from four aspects: I) exploring and explaining metabolic features; II) predicting the effects of genetic perturbations on metabolism; III) predicting the optimal phenotype; IV) guiding cell factories construction in practical experiment. Finally, we discussed the development of GSMs, aiming to provide a reference for efficiently reconstructing GSMs and guiding metabolic engineering.
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Affiliation(s)
- Zhijin Gong
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jiayao Chen
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinyu Jiao
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hao Gong
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; College of Mathematics and Physics, Beijing University of Chemical Technology, Beijing 100029, China
| | - Danzi Pan
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; College of Mathematics and Physics, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lingli Liu
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; College of Mathematics and Physics, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yang Zhang
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Tianwei Tan
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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3
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Cai P, Liu S, Zhang D, Hu QN. MCF2Chem: A manually curated knowledge base of biosynthetic compound production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:167. [PMID: 37925500 PMCID: PMC10625697 DOI: 10.1186/s13068-023-02419-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Microbes have been used as cell factories to synthesize various chemical compounds. Recent advances in synthetic biological technologies have accelerated the increase in the number and capacity of microbial cell factories; the variety and number of synthetic compounds produced via these cell factories have also grown substantially. However, no database is available that provides detailed information on the microbial cell factories and the synthesized compounds. RESULTS In this study, we established MCF2Chem, a manually curated knowledge base on the production of biosynthetic compounds using microbial cell factories. It contains 8888 items of production records related to 1231 compounds that were synthesizable by 590 microbial cell factories, including the production data of compounds (titer, yield, productivity, and content), strain culture information (culture medium, carbon source/precursor/substrate), fermentation information (mode, vessel, scale, and condition), and other information (e.g., strain modification method). The database contains statistical analyses data of compounds and microbial species. The data statistics of MCF2Chem showed that bacteria accounted for 60% of the species and that "fatty acids", "terpenoids", and "shikimates and phenylpropanoids" accounted for the top three chemical products. Escherichia coli, Saccharomyces cerevisiae, Yarrowia lipolytica, and Corynebacterium glutamicum synthesized 78% of these chemical compounds. Furthermore, we constructed a system to recommend microbial cell factories suitable for synthesizing target compounds and vice versa by combining MCF2Chem data, additional strain- and compound-related data, the phylogenetic relationships between strains, and compound similarities. CONCLUSIONS MCF2Chem provides a user-friendly interface for querying, browsing, and visualizing detailed statistical information on microbial cell factories and their synthesizable compounds. It is publicly available at https://mcf.lifesynther.com . This database may serve as a useful resource for synthetic biologists.
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Affiliation(s)
- Pengli Cai
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Sheng Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Dachuan Zhang
- Ecological Systems Design, Institute of Environmental Engineering, ETH Zurich, 8093, Zurich, Switzerland
| | - Qian-Nan Hu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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Dinglasan JLN, Doktycz MJ. Rewiring cell-free metabolic flux in E. coli lysates using a block-push-pull approach. Synth Biol (Oxf) 2023; 8:ysad007. [PMID: 37908558 PMCID: PMC10615139 DOI: 10.1093/synbio/ysad007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/27/2023] [Accepted: 04/12/2023] [Indexed: 11/02/2023] Open
Abstract
Cell-free systems can expedite the design and implementation of biomanufacturing processes by bypassing troublesome requirements associated with the use of live cells. In particular, the lack of survival objectives and the open nature of cell-free reactions afford engineering approaches that allow purposeful direction of metabolic flux. The use of lysate-based systems to produce desired small molecules can result in competitive titers and productivities when compared to their cell-based counterparts. However, pathway crosstalk within endogenous lysate metabolism can compromise conversion yields by diverting carbon flow away from desired products. Here, the 'block-push-pull' concept of conventional cell-based metabolic engineering was adapted to develop a cell-free approach that efficiently directs carbon flow in lysates from glucose and toward endogenous ethanol synthesis. The approach is readily adaptable, is relatively rapid and allows for the manipulation of central metabolism in cell extracts. In implementing this approach, a block strategy is first optimized, enabling selective enzyme removal from the lysate to the point of eliminating by-product-forming activity while channeling flux through the target pathway. This is complemented with cell-free metabolic engineering methods that manipulate the lysate proteome and reaction environment to push through bottlenecks and pull flux toward ethanol. The approach incorporating these block, push and pull strategies maximized the glucose-to-ethanol conversion in an Escherichia coli lysate that initially had low ethanologenic potential. A 10-fold improvement in the percent yield is demonstrated. To our knowledge, this is the first report of successfully rewiring lysate carbon flux without source strain optimization and completely transforming the consumed input substrate to a desired output product in a lysate-based, cell-free system.
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Affiliation(s)
- Jaime Lorenzo N Dinglasan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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Long BHD, Matsubara K, Tanaka T, Ohara H, Aso Y. Production of glycerate from glucose using engineered Escherichiacoli. J Biosci Bioeng 2023; 135:375-381. [PMID: 36841726 DOI: 10.1016/j.jbiosc.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/27/2023]
Abstract
In this study, glycerate was produced from glucose using engineered Escherichia coli BW25113. Plasmid pSR3 carrying gpd1 and gpp2 encoding two isoforms of glycerol-3-phosphate dehydrogenase from Saccharomyces cerevisiae and plasmid pLB2 carrying aldO encoding alditol oxidase from Streptomyces violaceoruber were introduced into E. coli to enable the production of glycerate from glucose via glycerol. Disruptions of garK and glxK genes in the E. coli genome were performed to minimize the consumption of glycerate produced. As a result, E. coli carrying these plasmids could produce nearly three times higher concentration of glycerate (0.50 ± 0.01 g/L) from 10 g/L glucose compared to E. coli EG_2 (0.14 ± 0.02 g/L). In M9 medium, disruption of garK and glxK resulted in an impaired growth rate with low production of glycerate, while supplementation of 0.5 g/L casamino acids and 0.5 g/L manganese sulfate to the medium replenished the growth rate and elevated the glycerate titer. Further disruption of glpF, encoding a glycerol transporter, increased the glycerate production to 0.80 ± 0.00 g/L. MR2 medium improved the glycerate production titers and specific productivities of E. coli EG_4, EG_5, and EG_6. Upscale production of glycerate was carried out in a jar fermentor with MR2 medium using E. coli EG_6, resulting in an improvement in glycerate production up to 2.37 ± 0.46 g/L with specific productivity at 0.34 ± 0.11 g-glycerate/g-cells. These results indicate that E. coli is an appropriate host for glycerate production from glucose.
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Affiliation(s)
- Bui Hoang Dang Long
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kotaro Matsubara
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Tomonari Tanaka
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Hitomi Ohara
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Yuji Aso
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
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Yi X, Alper HS. Considering Strain Variation and Non-Type Strains for Yeast Metabolic Engineering Applications. Life (Basel) 2022; 12:life12040510. [PMID: 35455001 PMCID: PMC9032683 DOI: 10.3390/life12040510] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
A variety of yeast species have been considered ideal hosts for metabolic engineering to produce value-added chemicals, including the model organism Saccharomyces cerevisiae, as well as non-conventional yeasts including Yarrowia lipolytica, Kluyveromyces marxianus, and Pichia pastoris. However, the metabolic capacity of these microbes is not simply dictated or implied by genus or species alone. Within the same species, yeast strains can display distinct variations in their phenotypes and metabolism, which affect the performance of introduced pathways and the production of interesting compounds. Moreover, it is unclear how this metabolic potential corresponds to function upon rewiring these organisms. These reports thus point out a new consideration for successful metabolic engineering, specifically: what are the best strains to utilize and how does one achieve effective metabolic engineering? Understanding such questions will accelerate the host selection and optimization process for generating yeast cell factories. In this review, we survey recent advances in studying yeast strain variations and utilizing non-type strains in pathway production and metabolic engineering applications. Additionally, we highlight the importance of employing portable methods for metabolic rewiring to best access this metabolic diversity. Finally, we conclude by highlighting the importance of considering strain diversity in metabolic engineering applications.
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Affiliation(s)
- Xiunan Yi
- Interdisciplinary Life Sciences, The University of Texas at Austin, Austin, TX 78712, USA;
| | - Hal S. Alper
- Interdisciplinary Life Sciences, The University of Texas at Austin, Austin, TX 78712, USA;
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
- Correspondence:
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Vandelook S, Elsacker E, Van Wylick A, De Laet L, Peeters E. Current state and future prospects of pure mycelium materials. Fungal Biol Biotechnol 2021; 8:20. [PMID: 34930476 PMCID: PMC8691024 DOI: 10.1186/s40694-021-00128-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/02/2021] [Indexed: 12/23/2022] Open
Abstract
In the context of the ongoing transition from a linear to a circular economy, ecologically friendly renewable solutions are put in place. Filamentous fungi can be grown on various organic feedstocks and functionalized into a range of diverse material types which are biobased and thus more sustainable in terms of their production, use and recycling. Pure mycelium materials, consisting only of mycelial biomass, can adopt versatile properties and appear promising as a substitute for current petrochemically produced polymeric materials or, in the case of myco-leather, as a substitute for animal-based leather. In recent years, a handful of private companies have been innovating to bring products based on pure mycelium materials to the market while scientific interest in these promising biomaterials is now starting to gain momentum. In this primer, we introduce pure mycelium materials, frame different production methods, review existing and potential future applications, thereby offering a vision on future advances for this emerging fungi-based technology.
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Affiliation(s)
- Simon Vandelook
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Elise Elsacker
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
- Research Group of Architectural Engineering, Department of Architectural Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
- Hub for Biotechnology in the Built Environment, Devonshire Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Aurélie Van Wylick
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
- Research Group of Architectural Engineering, Department of Architectural Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Lars De Laet
- Research Group of Architectural Engineering, Department of Architectural Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.
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Shomar H, Bokinsky G. Towards a Synthetic Biology Toolset for Metallocluster Enzymes in Biosynthetic Pathways: What We Know and What We Need. Molecules 2021; 26:molecules26226930. [PMID: 34834021 PMCID: PMC8617995 DOI: 10.3390/molecules26226930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022] Open
Abstract
Microbes are routinely engineered to synthesize high-value chemicals from renewable materials through synthetic biology and metabolic engineering. Microbial biosynthesis often relies on expression of heterologous biosynthetic pathways, i.e., enzymes transplanted from foreign organisms. Metallocluster enzymes are one of the most ubiquitous family of enzymes involved in natural product biosynthesis and are of great biotechnological importance. However, the functional expression of recombinant metallocluster enzymes in live cells is often challenging and represents a major bottleneck. The activity of metallocluster enzymes requires essential supporting pathways, involved in protein maturation, electron supply, and/or enzyme stability. Proper function of these supporting pathways involves specific protein-protein interactions that remain poorly characterized and are often overlooked by traditional synthetic biology approaches. Consequently, engineering approaches that focus on enzymatic expression and carbon flux alone often overlook the particular needs of metallocluster enzymes. This review highlights the biotechnological relevance of metallocluster enzymes and discusses novel synthetic biology strategies to advance their industrial application, with a particular focus on iron-sulfur cluster enzymes. Strategies to enable functional heterologous expression and enhance recombinant metallocluster enzyme activity in industrial hosts include: (1) optimizing specific maturation pathways; (2) improving catalytic stability; and (3) enhancing electron transfer. In addition, we suggest future directions for developing microbial cell factories that rely on metallocluster enzyme catalysis.
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Affiliation(s)
- Helena Shomar
- INSERM U722, Faculté de Médecine, Université de Paris, Site Xavier Bichat, 75018 Paris, France
- Correspondence: (H.S.); (G.B.)
| | - Gregory Bokinsky
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Correspondence: (H.S.); (G.B.)
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Bahls MO, Platz L, Morgado G, Schmidt GW, Panke S. Directed evolution of biofuel-responsive biosensors for automated optimization of branched-chain alcohol biosynthesis. Metab Eng 2021; 69:98-111. [PMID: 34767976 DOI: 10.1016/j.ymben.2021.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/21/2021] [Accepted: 10/31/2021] [Indexed: 12/18/2022]
Abstract
The biosynthesis of short-chain alcohols is a carbon-neutral alternative to petroleum-derived production, but strain screening operations are encumbered by laborious analytics. Here, we built, characterized and applied whole cell biosensors by directed evolution of the transcription factor AlkS for screening microbial strain libraries producing industrially relevant alcohols. A selected AlkS variant was applied for in situ product detection in two screening applications concerning key steps in alcohol production. Further, the biosensor strains enabled the implementation of an automated, robotic platform-based workflow with data clustering, which readily allowed the identification of significantly improved strain variants for isopentanol production.
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Affiliation(s)
- Maximilian O Bahls
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Lukas Platz
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Gaspar Morgado
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Gregor W Schmidt
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland.
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10
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Round JW, Robeck LD, Eltis LD. An Integrative Toolbox for Synthetic Biology in Rhodococcus. ACS Synth Biol 2021; 10:2383-2395. [PMID: 34428025 DOI: 10.1021/acssynbio.1c00292] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The development of microbial cell factories requires robust synthetic biology tools to reduce design uncertainty and accelerate the design-build-test-learn process. Herein, we developed a suite of integrative genetic tools to facilitate the engineering of Rhodococcus, a genus of bacteria with considerable biocatalytic potential. We first created pRIME, a modular, copy-controlled integrative-vector, to provide a robust platform for strain engineering and characterizing genetic parts. This vector was then employed to benchmark a series of strong promoters. We found PM6 to be the strongest constitutive rhodococcal promoter, 2.5- to 3-fold stronger than the next in our study, while overall promoter activities ranged 23-fold between the weakest and strongest promoters during exponential growth. Next, we used an optimized variant of PM6 to develop hybrid-promoters and integrative vectors to allow for tetracycline-inducible gene expression in Rhodococcus. The best of the resulting hybrid-promoters maintained a maximal activity of ∼50% of PM6 and displayed an induction factor of ∼40-fold. Finally, we developed and implemented a uLoop-derived Golden Gate assembly strategy for high-throughput DNA assembly in Rhodococcus. To demonstrate the utility of our approaches, pRIME was used to engineer Rhodococcus jostii RHA1 to grow on vanillin at concentrations 10-fold higher than what the wild-type strain tolerated. Overall, this study provides a suite of tools that will accelerate the engineering of Rhodococcus for various biocatalytic applications, including the sustainable production of chemicals from lignin-derived aromatics.
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Affiliation(s)
- James W. Round
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Logan D. Robeck
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D. Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Podolsky IA, Schauer EE, Seppälä S, O'Malley MA. Identification of novel membrane proteins for improved lignocellulose conversion. Curr Opin Biotechnol 2021; 73:198-204. [PMID: 34482155 DOI: 10.1016/j.copbio.2021.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 11/28/2022]
Abstract
Lignocellulose processing yields a heterogeneous mixture of substances, which are poorly utilized by current industrial strains. For efficient valorization of recalcitrant biomass, it is critical to identify and engineer new membrane proteins that enable the broad uptake of hydrolyzed substrates. Whereas glucose consumption rarely presents a bottleneck for cell factories, there is also a lack of transporters that allow co-consumption of glucose with other abundant biomass sugars such as xylose. This review discusses recent efforts to bioinformatically identify membrane proteins of high biotech potential for lignocellulose conversion and metabolic engineering in both model and nonconventional organisms. Of particular interest are transporters sourced from anaerobic gut fungi resident to large herbivores, which produce Sugars Will Eventually be Exported Transporters (SWEETs) that enhance xylose transport in the yeast Saccharomyces cerevisiae and enable glucose and xylose co-utilization. Additionally, recently identified fungal cellodextrin transporters are valuable alternatives to mitigate glucose repression and transporter inhibition.
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Affiliation(s)
- Igor A Podolsky
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Elizabeth E Schauer
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA; Joint BioEnergy Institute (JBEI), Emeryville, CA 94608, USA.
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12
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Microbial production of chemicals driven by CRISPR-Cas systems. Curr Opin Biotechnol 2021; 73:34-42. [PMID: 34303184 DOI: 10.1016/j.copbio.2021.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/25/2021] [Accepted: 07/02/2021] [Indexed: 02/07/2023]
Abstract
Microorganisms have provided an attractive route for biosynthesis of various chemicals from renewable resources. CRISPR-Cas systems have served as powerful mechanisms for generating cell factories with desirable properties by manipulating nucleic acids quickly and efficiently. The CRISPR-Cas system provides a toolbox with excellent opportunities for identifying better biocatalysts, multiplexed fine-tuning of metabolic flux, efficient utilization of low-cost substrates, and improvement of metabolic robustness. The overall goal of this review highlights recent advances in the development of microbial cell factories for chemical production using various CRISPR-Cas systems. The perspectives for further development or applications of CRISPR-Cas systems for strain improvement are also discussed.
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Carotenoids produced by the deep-sea bacterium Erythrobacter citreus LAMA 915: detection and proposal of their biosynthetic pathway. Folia Microbiol (Praha) 2021; 66:441-456. [PMID: 33723710 DOI: 10.1007/s12223-021-00858-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/24/2021] [Indexed: 10/21/2022]
Abstract
Technologies based on synthetic biology to produce bacterial natural carotenoids depend on information regarding their biosynthesis. Although the biosynthetic pathway of common carotenoids is known, there are carotenoids whose pathways are not completely described. This work aimed to mine the genome of the deep-sea bacterium Erythrobacter citreus LAMA 915, an uncommon bacterium that forms yellow colonies under cultivation. This work further explores the potential application of the carotenoids found and low-cost substrates for bacterial growth. A combined approach of genome mining and untargeted metabolomics analysis was applied. The carotenoid erythroxanthin sulfate was detected in E. citreus LAMA 915 cell extract. A proposal for carotenoid biosynthesis by this bacterium is provided, involving the genes crtBIYZWG. These are responsible for the biosynthesis of carotenoids from the zeaxanthin pathway and their 2,2'-hydroxylated derivatives. E. citreus LAMA 915 extracts showed antioxidant and sun protection effects. Based on the high content of proteases and lipases, it was possible to rationally select substrates for bacterial growth, with residual oil from fish processing the best low-cost substrate selected. This work advances in the understanding of carotenoid biosynthesis and provides a genetic basis that can be further explored as a biotechnological route for carotenoid production.
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14
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Chang C, Liu B, Bao Y, Tao Y, Liu W. Efficient bioconversion of raspberry ketone in Escherichia coli using fatty acids feedstocks. Microb Cell Fact 2021; 20:68. [PMID: 33706766 PMCID: PMC7953670 DOI: 10.1186/s12934-021-01551-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/21/2021] [Indexed: 02/02/2023] Open
Abstract
Background Phenylpropanoid including raspberry ketone, is a kind of important natural plant product and widely used in pharmaceuticals, chemicals, cosmetics, and healthcare products. Bioproduction of phenylpropanoid in Escherichia coli and other microbial cell factories is an attractive approach considering the low phenylpropanoid contents in plants. However, it is usually difficult to produce high titer phenylpropanoid production when fermentation using glucose as carbon source. Developing novel bioprocess using alternative sources might provide a solution to this problem. In this study, typical phenylpropanoid raspberry ketone was used as the target product to develop a biosynthesis pathway for phenylpropanoid production from fatty acids, a promising alternative low-cost feedstock. Results A raspberry ketone biosynthesis module was developed and optimized by introducing 4-coumarate-CoA ligase (4CL), benzalacetone synthase (BAS), and raspberry ketone reductase (RZS) in Escherichia coli strains CR1–CR4. Then strain CR5 was developed by introducing raspberry ketone biosynthesis module into a fatty acids-utilization chassis FA09 to achieve production of raspberry ketone from fatty acids feedstock. However, the production of raspberry ketone was still limited by the low biomass and unable to substantiate whole-cell bioconversion process. Thus, a process by coordinately using fatty-acids and glycerol was developed. In addition, we systematically screened and optimized fatty acids-response promoters. The optimized promoter Pfrd3 was then successfully used for the efficient expression of key enzymes of raspberry ketone biosynthesis module during bioconversion from fatty acids. The final engineered strain CR8 could efficiently produce raspberry ketone repeatedly using bioconversion from fatty acids feedstock strategy, and was able to produce raspberry ketone to a concentration of 180.94 mg/L from soybean oil in a 1-L fermentation process. Conclusion Metabolically engineered Escherichia coli strains were successfully developed for raspberry ketone production from fatty acids using several strategies, including optimization of bioconversion process and fine-tuning key enzyme expression. This study provides an essential reference to establish the low-cost biological manufacture of phenylpropanoids compounds. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01551-0.
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Affiliation(s)
- Chen Chang
- College of Forestry, Northeast Forestry University, No. 26 Hexing Road, Harbin, Heilongjiang Province, 150040, PR China.,CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, NO. 1 Beichen West Road, Chaoyang District, Beijing, 100101, PR China
| | - Bo Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, NO. 1 Beichen West Road, Chaoyang District, Beijing, 100101, PR China
| | - Yihong Bao
- College of Forestry, Northeast Forestry University, No. 26 Hexing Road, Harbin, Heilongjiang Province, 150040, PR China. .,Heilongjiang Key Laboratory of Forest Food Resources Utilization, No. 26 Hexing Road, Harbin, Heilongjiang Province, 150040, PR China.
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, NO. 1 Beichen West Road, Chaoyang District, Beijing, 100101, PR China. .,University of Chinese Academy of Sciences, Shijingshan District, NO. 19A Yuquan Road, Beijing, 100049, PR China.
| | - Weifeng Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, NO. 1 Beichen West Road, Chaoyang District, Beijing, 100101, PR China. .,University of Chinese Academy of Sciences, Shijingshan District, NO. 19A Yuquan Road, Beijing, 100049, PR China.
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15
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Combining protein and metabolic engineering to construct efficient microbial cell factories. Curr Opin Biotechnol 2020; 66:27-35. [DOI: 10.1016/j.copbio.2020.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 11/17/2022]
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16
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Malcı K, Walls LE, Rios-Solis L. Multiplex Genome Engineering Methods for Yeast Cell Factory Development. Front Bioeng Biotechnol 2020; 8:589468. [PMID: 33195154 PMCID: PMC7658401 DOI: 10.3389/fbioe.2020.589468] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
As biotechnological applications of synthetic biology tools including multiplex genome engineering are expanding rapidly, the construction of strategically designed yeast cell factories becomes increasingly possible. This is largely due to recent advancements in genome editing methods like CRISPR/Cas tech and high-throughput omics tools. The model organism, baker's yeast (Saccharomyces cerevisiae) is an important synthetic biology chassis for high-value metabolite production. Multiplex genome engineering approaches can expedite the construction and fine tuning of effective heterologous pathways in yeast cell factories. Numerous multiplex genome editing techniques have emerged to capitalize on this recently. This review focuses on recent advancements in such tools, such as delta integration and rDNA cluster integration coupled with CRISPR-Cas tools to greatly enhance multi-integration efficiency. Examples of pre-placed gate systems which are an innovative alternative approach for multi-copy gene integration were also reviewed. In addition to multiple integration studies, multiplexing of alternative genome editing methods are also discussed. Finally, multiplex genome editing studies involving non-conventional yeasts and the importance of automation for efficient cell factory design and construction are considered. Coupling the CRISPR/Cas system with traditional yeast multiplex genome integration or donor DNA delivery methods expedites strain development through increased efficiency and accuracy. Novel approaches such as pre-placing synthetic sequences in the genome along with improved bioinformatics tools and automation technologies have the potential to further streamline the strain development process. In addition, the techniques discussed to engineer S. cerevisiae, can be adapted for use in other industrially important yeast species for cell factory development.
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Affiliation(s)
- Koray Malcı
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, United Kingdom
| | - Laura E Walls
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, United Kingdom
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, United Kingdom
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17
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Sedlar K, Vasylkivska M, Musilova J, Branska B, Provaznik I, Patakova P. Phenotypic and genomic analysis of isopropanol and 1,3-propanediol producer Clostridium diolis DSM 15410. Genomics 2020; 113:1109-1119. [PMID: 33166602 DOI: 10.1016/j.ygeno.2020.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/29/2020] [Accepted: 11/04/2020] [Indexed: 12/12/2022]
Abstract
Clostridium diolis DSM 15410 is a type strain of solventogenic clostridium capable of conducting isopropanol-butanol-ethanol fermentation. By studying its growth on different carbohydrates, we verified its ability to utilize glycerol and produce 1,3-propanediol and discovered its ability to produced isopropanol. Complete genome sequencing showed that its genome is a single circular chromosome and belongs to the cluster I (sensu scricto) of the genus Clostridium. By cultivation analysis we highlighted its specific behavior in comparison to two selected closely related strains. Despite the fact that several CRISPR loci were found, 16 putative prophages showed the ability to receive foreign DNA. Thus, the strain has the necessary features for future engineering of its 1,3-propanediol biosynthetic pathway and for the possible industrial utilization in the production of biofuels.
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Affiliation(s)
- Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 12, Brno, Czech Republic.
| | - Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Jana Musilova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 12, Brno, Czech Republic
| | - Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Ivo Provaznik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 12, Brno, Czech Republic
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
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18
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Lee SH, Lee SM, Lee JH, Lee HS, Kang SG. Biological process for coproduction of hydrogen and thermophilic enzymes during CO fermentation. BIORESOURCE TECHNOLOGY 2020; 305:123067. [PMID: 32120234 DOI: 10.1016/j.biortech.2020.123067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 06/10/2023]
Abstract
To develop a thermophilic cell factory system that uses CO gas, we attempted to engineer a hyperthermophilic carboxydotrophic hydrogenic archaeon Thermococcus onnurineus NA1 to be capable of producing thermophilic enzymes along with hydrogen (H2). The mutant strains 156T-AM and 156T-POL were constructed to have another copy of a gene encoding α-amylase or DNA polymerase, respectively, and exhibited growth rates and H2 production rates distinct from those of the parental strain, 156T, in gas fermentation using 100% CO or coal-gasified syngas. Purified α-amylase displayed starch-hydrolyzing activity, and whole-cell extracts of 156T-AM showed saccharifying activity for potato peel waste. PCR amplification was used to demonstrate that purified DNA polymerase was free from bacterial DNA contamination, in contrast to commercial bacteria-made enzymes. This study demonstrated that this archaeal strain could coproduce enzymes and H2 using CO-containing gas, providing a basis for cell factories to upcycle industrial waste gas.
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Affiliation(s)
- Seong Hyuk Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea
| | - Sung-Mok Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea
| | - Jung-Hyun Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea; Department of Marine Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Hyun Sook Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea; Department of Marine Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Sung Gyun Kang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea; Department of Marine Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea.
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19
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Two-Stage Continuous Conversion of Carbon Monoxide to Ethylene by Whole Cells of Azotobacter vinelandii. Appl Environ Microbiol 2020; 86:AEM.00446-20. [PMID: 32198172 DOI: 10.1128/aem.00446-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 03/17/2020] [Indexed: 01/17/2023] Open
Abstract
Azotobacter vinelandii is an obligate aerobic diazotroph with a verified transient ability to reduce carbon monoxide to ethylene by its vanadium nitrogenase. In this study, we implemented an industrially relevant continuous two-stage stirred-tank system for in vivo biotransformation of a controlled supply of air enriched with 5% carbon monoxide to 302 μg ethylene g-1 glucose consumed. To attain this value, the process required overcoming critical oxygen limitations during cell proliferation while simultaneously avoiding the A. vinelandii respiratory protection mechanism that negatively impacts in vivo nitrogenase activity. Additionally, process conditions allowed the demonstration of carbon monoxide's solubility as a reaction-limiting factor and a competitor with dinitrogen for the vanadium nitrogenase active site, implying that excess intracellular carbon monoxide could lead to a cessation of cell proliferation and ethylene formation as shown genetically using a new strain of A. vinelandii deficient in carbon monoxide dehydrogenase.IMPORTANCE Ethylene is an essential commodity feedstock used for the generation of a variety of consumer products, but its generation demands energy-intensive processes and is dependent on nonrenewable substrates. This work describes a continuous biological method for investigating the nitrogenase-mediated carbon monoxide reductive coupling involved in ethylene production using whole cells of Azotobacter vinelandii If eventually adopted by industry, this technology has the potential to significantly reduce the total energy input required and the ethylene recovery costs, as well as decreasing greenhouse gas emissions associated with current production strategies.
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20
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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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21
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Landberg J, Mundhada H, Nielsen AT. An autoinducible trp-T7 expression system for production of proteins and biochemicals in Escherichia coli. Biotechnol Bioeng 2020; 117:1513-1524. [PMID: 32022248 PMCID: PMC7186829 DOI: 10.1002/bit.27297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/11/2020] [Accepted: 02/03/2020] [Indexed: 12/19/2022]
Abstract
Inducible expression systems can be applied to control the expression of proteins or biochemical pathways in cell factories. However, several of the established systems require the addition of expensive inducers, making them unfeasible for large‐scale production. Here, we establish a genome integrated trp‐T7 expression system where tryptophan can be used to control the induction of a gene or a metabolic pathway. We show that the initiation of gene expression from low‐ and high‐copy vectors can be tuned by varying the initial concentration of tryptophan or yeast extract, and that expression is tightly regulated and homogenous when compared with the commonly used lac‐T7 system. Finally, we apply the trp‐T7 expression system for the production of l‐serine, where we reach titers of 26 g/L in fed‐batch fermentation.
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Affiliation(s)
- Jenny Landberg
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Hemanshu Mundhada
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.,CysBio ApS, Hørsholm, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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22
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Dahabieh MS, Thevelein JM, Gibson B. Multimodal Microorganism Development: Integrating Top-Down Biological Engineering with Bottom-Up Rational Design. Trends Biotechnol 2019; 38:241-253. [PMID: 31653446 DOI: 10.1016/j.tibtech.2019.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/28/2019] [Accepted: 09/30/2019] [Indexed: 12/12/2022]
Abstract
Biological engineering has unprecedented potential to solve society's most pressing challenges. Engineering approaches must consider complex technical, economic, and social factors. This requires methods that confer gene/pathway-level functionality and organism-level robustness in rapid and cost-effective ways. This article compares foundational engineering approaches - bottom-up, gene-targeted engineering, and top-down, whole-genome engineering - and identifies significant complementarity between them. Cases drawn from engineering Saccharomyces cerevisiae exemplify the synergy of a combined approach. Indeed, multimodal engineering streamlines strain development by leveraging the complementarity of whole-genome and gene-targeted engineering to overcome the gap in design knowledge that restricts rational design. As biological engineers target more complex systems, this dual-track approach is poised to become an increasingly important tool to realize the promise of synthetic biology.
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Affiliation(s)
- Matthew S Dahabieh
- Renaissance BioScience, 410-2389 Health Sciences Mall, Vancouver, BC V6T1Z3, Canada
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Katholieke Universiteit (KU) Leuven, Leuven, Belgium; Center for Microbiology, Vlaams Instituut voor Biotechnologie (VIB), Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Brian Gibson
- VTT Technical Research Centre of Finland, Tietotie 2, VTT, PO Box 1000, FI-02044 Espoo, Finland.
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23
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García-Jiménez B, García JL, Nogales J. FLYCOP: metabolic modeling-based analysis and engineering microbial communities. Bioinformatics 2019; 34:i954-i963. [PMID: 30423096 PMCID: PMC6129290 DOI: 10.1093/bioinformatics/bty561] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Motivation Synthetic microbial communities begin to be considered as promising multicellular biocatalysts having a large potential to replace engineered single strains in biotechnology applications, in pharmaceutical, chemical and living architecture sectors. In contrast to single strain engineering, the effective and high-throughput analysis and engineering of microbial consortia face the lack of knowledge, tools and well-defined workflows. This manuscript contributes to fill this important gap with a framework, called FLYCOP (FLexible sYnthetic Consortium OPtimization), which contributes to microbial consortia modeling and engineering, while improving the knowledge about how these communities work. FLYCOP selects the best consortium configuration to optimize a given goal, among multiple and diverse configurations, in a flexible way, taking temporal changes in metabolite concentrations into account. Results In contrast to previous systems optimizing microbial consortia, FLYCOP has novel characteristics to face up to new problems, to represent additional features and to analyze events influencing the consortia behavior. In this manuscript, FLYCOP optimizes a Synechococcus elongatus-Pseudomonas putida consortium to produce the maximum amount of bio-plastic (PHA, polyhydroxyalkanoate), and highlights the influence of metabolites exchange dynamics in a four auxotrophic Escherichia coli consortium with parallel growth. FLYCOP can also provide an explanation about biological evolution driving evolutionary engineering endeavors by describing why and how heterogeneous populations emerge from monoclonal ones. Availability and implementation Code reproducing the study cases described in this manuscript are available on-line: https://github.com/beatrizgj/FLYCOP. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Beatriz García-Jiménez
- Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - José Luis García
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas (CIB-CSIC), 28040 Madrid, Spain.,Applied System Biology and Synthetic Biology Department, Institute for Integrative Systems Biology (I2Sysbio-CSIC-UV), 46980 Paterna, Spain
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
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24
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Mazareli RCDS, Sakamoto IK, Silva EL, Varesche MBA. Bacillus sp. isolated from banana waste and analysis of metabolic pathways in acidogenic systems in hydrogen production. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 247:178-186. [PMID: 31247365 DOI: 10.1016/j.jenvman.2019.06.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/13/2019] [Accepted: 06/08/2019] [Indexed: 06/09/2023]
Abstract
The autochthonous bacterial strain was isolated from banana waste (BW) for hydrogen production and organic acids from different pure substrates and BW. The potential production of H2 and metabolic pathways were analyzed at pH 7.0 at 37 °C. Facultative anaerobic bacterium similar to Bacillus sp. was identified, with generation time (Tg) and growth rate (μ) of 0.43 h and 1.60 h-1, respectively, from glucose. The hydrogen production (P) using pure substrates was observed between 10.81 mmol.L-1 and 17.75 mmol.L-1 from xylose and maltose, respectively. The biggest and smallest hydrogen P of 18.77 mmol.L-1 and 1.72 mmol.L-1, were obtained with 3.5 and 0.5 g.L-1 of cellobiose, respectively. The highest hydrogen yield (126.93 mL.g-1carbohydrates added) was obtained with 2 g.L-1 cellobiose. In the assay using banana waste (5 g.L-1) the maximum P and yield (YH2) of 31.7 mmol.L-1 and 94.66 mL H2 g-1carbohydrates added, was obtained respectively. The main metabolic pathway of hydrogen production by Bacillus sp. RM1 from banana waste was acetic-butyric acid of 487.69 g.L-1 and 535.88 g.L-1, respectively. The accessibility of various carbon sources by Bacillus sp. RM1 in fermentation can benefit the hydrogen production from complex organic substrates in the bioaugmentation process.
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Affiliation(s)
- Raissa Cristina da Silva Mazareli
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Av. Trabalhador São Carlense, 400, 13566-590, São Carlos, SP, Brazil.
| | - Isabel Kimiko Sakamoto
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Av. Trabalhador São Carlense, 400, 13566-590, São Carlos, SP, Brazil.
| | - Edson Luiz Silva
- Department of Chemical Engineering, Federal University of São Carlos, Rod Washington Luiz, Km 235, SP 310, 13565-905, São Carlos, SP, Brazil.
| | - Maria Bernadete Amâncio Varesche
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Av. Trabalhador São Carlense, 400, 13566-590, São Carlos, SP, Brazil.
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25
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Zhang C, Too HP. Revalorizing Lignocellulose for the Production of Natural Pharmaceuticals and Other High Value Bioproducts. Curr Med Chem 2019; 26:2475-2484. [PMID: 28901274 DOI: 10.2174/0929867324666170912095755] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/02/2017] [Accepted: 08/25/2017] [Indexed: 01/27/2023]
Abstract
Lignocellulose is the most abundant renewable natural resource on earth and has been successfully used for the production of biofuels. A significant challenge is to develop cost-effective, environmentally friendly and efficient processes for the conversion of lignocellulose materials into suitable substrates for biotransformation. A number of approaches have been explored to convert lignocellulose into sugars, e.g. combining chemical pretreatment and enzymatic hydrolysis. In nature, there are organisms that can transform the complex lignocellulose efficiently, such as wood-degrading fungi (brown rot and white rot fungi), bacteria (e.g. Clostridium thermocellum), arthropods (e.g. termite) and certain animals (e.g. ruminant). Here, we highlight recent case studies of the natural degraders and the mechanisms involved, providing new utilities in biotechnology. The sugars produced from such biotransformations can be used in metabolic engineering and synthetic biology for the complete biosynthesis of natural medicine. The unique opportunities in using lignocellulose directly to produce natural drug molecules with either using mushroom and/or 'industrial workhorse' organisms (Escherichia coli and Saccharomyces cerevisiae) will be discussed.
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Affiliation(s)
- Congqiang Zhang
- Biotransformation Innovation Platform (BioTrans), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Heng-Phon Too
- Biotransformation Innovation Platform (BioTrans), Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Biochemistry, National University of Singapore, Singapore
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26
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Systems Metabolic Engineering Strategies: Integrating Systems and Synthetic Biology with Metabolic Engineering. Trends Biotechnol 2019; 37:817-837. [DOI: 10.1016/j.tibtech.2019.01.003] [Citation(s) in RCA: 226] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/07/2019] [Accepted: 01/10/2019] [Indexed: 12/12/2022]
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27
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López J, Cataldo VF, Peña M, Saa PA, Saitua F, Ibaceta M, Agosin E. Build Your Bioprocess on a Solid Strain-β-Carotene Production in Recombinant Saccharomyces cerevisiae. Front Bioeng Biotechnol 2019; 7:171. [PMID: 31380362 PMCID: PMC6656860 DOI: 10.3389/fbioe.2019.00171] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 07/03/2019] [Indexed: 11/19/2022] Open
Abstract
Robust fermentation performance of microbial cell factories is critical for successful scaling of a biotechnological process. From shake flask cultivations to industrial-scale bioreactors, consistent strain behavior is fundamental to achieve the production targets. To assert the importance of this feature, we evaluated the impact of the yeast strain design and construction method on process scalability -from shake flasks to bench-scale fed-batch fermentations- using two recombinant Saccharomyces cerevisiae strains capable of producing β-carotene; SM14 and βcar1.2 strains. SM14 strain, obtained previously from adaptive evolution experiments, was capable to accumulate up to 21 mg/gDCW of β-carotene in 72 h shake flask cultures; while the βcar1.2, constructed by overexpression of carotenogenic genes, only accumulated 5.8 mg/gDCW of carotene. Surprisingly, fed-batch cultivation of these strains in 1L bioreactors resulted in opposite performances. βcar1.2 strain reached much higher biomass and β-carotene productivities (1.57 g/L/h and 10.9 mg/L/h, respectively) than SM14 strain (0.48 g/L/h and 3.1 mg/L/h, respectively). Final β-carotene titers were 210 and 750 mg/L after 80 h cultivation for SM14 and βcar1.2 strains, respectively. Our results indicate that these substantial differences in fermentation parameters are mainly a consequence of the exacerbated Crabtree effect of the SM14 strain. We also found that the strategy used to integrate the carotenogenic genes into the chromosomes affected the genetic stability of strains, although the impact was significantly minor. Overall, our results indicate that shake flasks fermentation parameters are poor predictors of the fermentation performance under industrial-like conditions, and that appropriate construction designs and performance tests must be conducted to properly assess the scalability of the strain and the bioprocess.
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Affiliation(s)
- Javiera López
- Centro de Aromas and Sabores, DICTUC S.A., Santiago, Chile.,Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Vicente F Cataldo
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Manuel Peña
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pedro A Saa
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Maximiliano Ibaceta
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eduardo Agosin
- Centro de Aromas and Sabores, DICTUC S.A., Santiago, Chile.,Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
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28
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Favaro L, Jansen T, van Zyl WH. Exploring industrial and naturalSaccharomyces cerevisiaestrains for the bio-based economy from biomass: the case of bioethanol. Crit Rev Biotechnol 2019; 39:800-816. [DOI: 10.1080/07388551.2019.1619157] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lorenzo Favaro
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy
| | - Trudy Jansen
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
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Fernández‐Cabezón L, Cros A, Nikel PI. Evolutionary Approaches for Engineering Industrially Relevant Phenotypes in Bacterial Cell Factories. Biotechnol J 2019; 14:e1800439. [DOI: 10.1002/biot.201800439] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/08/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Lorena Fernández‐Cabezón
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
| | - Antonin Cros
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
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30
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Song HS, Lee JY, Haruta S, Nelson WC, Lee DY, Lindemann SR, Fredrickson JK, Bernstein HC. Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities. Front Microbiol 2019; 10:1264. [PMID: 31263456 PMCID: PMC6584816 DOI: 10.3389/fmicb.2019.01264] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/21/2019] [Indexed: 02/01/2023] Open
Abstract
An intriguing aspect in microbial communities is that pairwise interactions can be influenced by neighboring species. This creates context dependencies for microbial interactions that are based on the functional composition of the community. Context dependent interactions are ecologically important and clearly present in nature, yet firmly established theoretical methods are lacking from many modern computational investigations. Here, we propose a novel network inference method that enables predictions for interspecies interactions affected by shifts in community composition and species populations. Our approach first identifies interspecies interactions in binary communities, which is subsequently used as a basis to infer modulation in more complex multi-species communities based on the assumption that microbes minimize adjustments of pairwise interactions in response to neighbor species. We termed this rule-based inference minimal interspecies interaction adjustment (MIIA). Our critical assessment of MIIA has produced reliable predictions of shifting interspecies interactions that are dependent on the functional role of neighbor organisms. We also show how MIIA has been applied to a microbial community composed of competing soil bacteria to elucidate a new finding that – in many cases – adding fewer competitors could impose more significant impact on binary interactions. The ability to predict membership-dependent community behavior is expected to help deepen our understanding of how microbiomes are organized in nature and how they may be designed and/or controlled in the future.
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Affiliation(s)
- Hyun-Seob Song
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Joon-Yong Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - William C Nelson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Dong-Yup Lee
- Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore.,School of Chemical Engineering, Sungkyunkwan University, Suwon, South Korea
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN, United States.,Department of Nutrition Science, Purdue University, West Lafayette, IN, United States
| | - Jim K Fredrickson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Hans C Bernstein
- Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway.,The Arctic Centre for Sustainable Energy, UiT - The Arctic University of Norway, Tromsø, Norway
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31
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Berterame NM, Martani F, Porro D, Branduardi P. Copper homeostasis as a target to improve Saccharomyces cerevisiae tolerance to oxidative stress. Metab Eng 2019; 46:43-50. [PMID: 29477856 DOI: 10.1016/j.ymben.2018.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 01/19/2023]
Abstract
The yeast Saccharomyces cerevisiae is widely used as a cell factory for the biotechnological production of various industrial products. During these processes, yeasts meet different kinds of stressors that often cause oxidative stress and thus impair cell growth. Therefore, the development of robust strains is indispensable to improve production, yield and productivity of fermentative processes. Copper plays a key role in the response to oxidative stress, as cofactor of the cytosolic superoxide dismutase (Sod1) and being contained in metallochaperone and metallothioneines with antioxidant properties. In this work, we observed a higher naturally copper internalization in a robust S. cerevisiae strain engineered to produce the antioxidant l-ascorbic acid (L-AA), compared with the wild type strain. Therefore, we investigated the effect of the alteration of copper homeostasis on cellular stress tolerance. CTR1 and FRE1 genes, codifying for a plasma membrane high-affinity copper transporter and for a cell-surface ferric/cupric reductase, respectively, were overexpressed in both wild type and L-AA cells. Remarkably, we found that the sole FRE1 overexpression was sufficient to increase copper internalization leading to an enhanced stress tolerance toward H2O2 exposure, in both strains under investigation. These findings reveal copper homeostasis as a target for the development of robust cell factories.
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Affiliation(s)
- Nadia Maria Berterame
- Department of Biotechnology and Biosciences, University of Milano Bicocca, 20126 Milan, Italy; Galatea Biotech Srl, Piazza della Scienza 2, 20126 Milan, Italy
| | - Francesca Martani
- Department of Biotechnology and Biosciences, University of Milano Bicocca, 20126 Milan, Italy
| | - Danilo Porro
- Department of Biotechnology and Biosciences, University of Milano Bicocca, 20126 Milan, Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, 20126 Milan, Italy.
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Sha Y, Zhang Y, Qiu Y, Xu Z, Li S, Feng X, Wang M, Xu H. Efficient Biosynthesis of Low-Molecular-Weight Poly-γ-glutamic Acid by Stable Overexpression of PgdS Hydrolase in Bacillus amyloliquefaciens NB. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:282-290. [PMID: 30543111 DOI: 10.1021/acs.jafc.8b05485] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Low-molecular-weight poly-γ-glutamic acid (LMW-γ-PGA) has attracted much attention owing to its great potential in food, agriculture, medicine, and cosmetics. Current methods of LMW-γ-PGA production, including enzymatic hydrolysis, are associated with low operational stability. Here, an efficient method for stable biosynthesis of LMW-γ-PGA was conceived by overexpression of γ-PGA hydrolase in Bacillus amyloliquefaciens NB. To establish stable expression of γ-PGA hydrolase (PgdS) during fermentation, a novel plasmid pNX01 was constructed with a native replicon from endogenous plasmid p2Sip, showing a loss rate of 4% after 100 consecutive passages. Subsequently, this plasmid was applied in a screen of high activity PgdS hydrolase, leading to substantial improvements to γ-PGA titer with concomitant decrease in the molecular weight. Finally, a satisfactory yield of 17.62 ± 0.38 g/L LMW-γ-PGA with a weight-average molecular weight of 20-30 kDa was achieved by direct fermentation of Jerusalem artichoke tuber extract. Our study presents a potential method for commercial production of LMW-γ-PGA.
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Affiliation(s)
- Yuanyuan Sha
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing 211816 , China
- College of Food Science and Light Industry , Nanjing Tech University , Nanjing 211816 , China
| | - Yatao Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing 211816 , China
- College of Food Science and Light Industry , Nanjing Tech University , Nanjing 211816 , China
| | - Yibin Qiu
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing 211816 , China
- College of Food Science and Light Industry , Nanjing Tech University , Nanjing 211816 , China
| | - Zongqi Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing 211816 , China
- College of Food Science and Light Industry , Nanjing Tech University , Nanjing 211816 , China
| | - Sha Li
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing 211816 , China
- College of Food Science and Light Industry , Nanjing Tech University , Nanjing 211816 , China
| | - Xiaohai Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing 211816 , China
- College of Food Science and Light Industry , Nanjing Tech University , Nanjing 211816 , China
| | - Mingxuan Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing 211816 , China
- College of Food Science and Light Industry , Nanjing Tech University , Nanjing 211816 , China
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing 211816 , China
- College of Food Science and Light Industry , Nanjing Tech University , Nanjing 211816 , China
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Lee H, Sugiharto YEC, Lee H, Jeon W, Ahn J, Lee H. Biotransformation of dicarboxylic acids from vegetable oil–derived sources: current methods and suggestions for improvement. Appl Microbiol Biotechnol 2019; 103:1545-1555. [DOI: 10.1007/s00253-018-9571-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/07/2018] [Accepted: 12/07/2018] [Indexed: 11/28/2022]
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Madsen MA, Semerdzhiev S, Amtmann A, Tonon T. Engineering Mannitol Biosynthesis in Escherichia coli and Synechococcus sp. PCC 7002 Using a Green Algal Fusion Protein. ACS Synth Biol 2018; 7:2833-2840. [PMID: 30408953 DOI: 10.1021/acssynbio.8b00238] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The genetic engineering of microbial cell factories is a sustainable alternative to the chemical synthesis of organic compounds. Successful metabolic engineering often depends on manipulating several enzymes, requiring multiple transformation steps and selection markers, as well as protein assembly and efficient substrate channeling. Naturally occurring fusion genes encoding two or more enzymatic functions may offer an opportunity to simplify the engineering process and to generate ready-made protein modules, but their functionality in heterologous systems remains to be tested. Here we show that heterologous expression of a fusion enzyme from the marine alga Micromonas pusilla, comprising a mannitol-1-phosphate dehydrogenase and a mannitol-1-phosphatase, leads to synthesis of mannitol by Escherichia coli and by the cyanobacterium Synechococcus sp. PCC 7002. Neither of the heterologous systems naturally produce this sugar alcohol, which is widely used in food, pharmaceutical, medical, and chemical industries. While the mannitol production rates obtained by single-gene manipulation were lower than those previously achieved after pathway optimization with multiple genes, our findings show that naturally occurring fusion proteins can offer simple building blocks for the assembly and optimization of recombinant metabolic pathways.
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Affiliation(s)
- Mary Ann Madsen
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Stefan Semerdzhiev
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Anna Amtmann
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Thierry Tonon
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
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Lee H, Han C, Lee HW, Park G, Jeon W, Ahn J, Lee H. Development of a promising microbial platform for the production of dicarboxylic acids from biorenewable resources. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:310. [PMID: 30455739 PMCID: PMC6225622 DOI: 10.1186/s13068-018-1310-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND As a sustainable industrial process, the production of dicarboxylic acids (DCAs), used as precursors of polyamides, polyesters, perfumes, plasticizers, lubricants, and adhesives, from vegetable oil has continuously garnered interest. Although the yeast Candida tropicalis has been used as a host for DCA production, additional strains are continually investigated to meet productivity thresholds and industrial needs. In this regard, the yeast Wickerhamiella sorbophila, a potential candidate strain, has been screened. However, the lack of genetic and physiological information for this uncommon strain is an obstacle that merits further research. To overcome this limitation, we attempted to develop a method to facilitate genetic recombination in this strain and produce high amounts of DCAs from methyl laurate using engineered W. sorbophila. RESULTS In the current study, we first developed efficient genetic engineering tools for the industrial application of W. sorbophila. To increase homologous recombination (HR) efficiency during transformation, the cell cycle of the yeast was synchronized to the S/G2 phase using hydroxyurea. The HR efficiency at POX1 and POX2 loci increased from 56.3% and 41.7%, respectively, to 97.9% in both cases. The original HR efficiency at URA3 and ADE2 loci was nearly 0% during the early stationary and logarithmic phases of growth, and increased to 4.8% and 25.6%, respectively. We used the developed tools to construct W. sorbophila UHP4, in which β-oxidation was completely blocked. The strain produced 92.5 g/l of dodecanedioic acid (DDDA) from methyl laurate over 126 h in 5-l fed-batch fermentation, with a productivity of 0.83 g/l/h. CONCLUSIONS Wickerhamiella sorbophila UHP4 produced more DDDA methyl laurate than C. tropicalis. Hence, we demonstrated that W. sorbophila is a powerful microbial platform for vegetable oil-based DCA production. In addition, by using the developed genetic engineering tools, this emerging yeast could be used for the production of a variety of fatty acid derivatives, such as fatty alcohols, fatty aldehydes, and ω-hydroxy fatty acids.
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Affiliation(s)
- Heeseok Lee
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113 Republic of Korea
| | - Changpyo Han
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
| | - Hyeok-Won Lee
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
| | - Gyuyeon Park
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113 Republic of Korea
| | - Wooyoung Jeon
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
| | - Jungoh Ahn
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
| | - Hongweon Lee
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
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Liu B, Xiang S, Zhao G, Wang B, Ma Y, Liu W, Tao Y. Efficient production of 3-hydroxypropionate from fatty acids feedstock in Escherichia coli. Metab Eng 2018; 51:121-130. [PMID: 30343047 DOI: 10.1016/j.ymben.2018.10.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/10/2018] [Accepted: 10/14/2018] [Indexed: 11/25/2022]
Abstract
The production of chemicals from renewable biomass resources is usually limited by factors including high-cost processes and low efficiency of biosynthetic pathways. Fatty acids (FAs) are an ideal alternative biomass. Their advantages include high-efficiently producing acetyl-CoA and reducing power, coupling chemical production with CO2 fixation, and the fact that they are readily obtained from inexpensive feedstocks. The important platform chemical 3-hydroxypropionate (3HP) can be produced from FAs as the feedstock with a theoretical yield of 2.49 g/g, much higher than the theoretical yield from other feedstocks. In this study, we first systematically analyzed the limiting factors in FA-utilization pathways in Escherichia coli. Then, we optimized FA utilization in Escherichia coli by using a combination of metabolic engineering and optimization of fermentation conditions. The 3HP biosynthesis module was introduced into a FA-utilizing strain, and the flux balance was finely optimized to maximize 3HP production. The resulting strain was able to produce 3HP from FAs with a yield of 1.56 g/g, and was able to produce 3HP to a concentration of 52 g/L from FAs in a 5-L fermentation process. The strain also could produce 3HP from various type of FAs feedstock including gutter oil. This is the first report of a technique for the efficient production of the platform chemical 3HP from FAs.
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Affiliation(s)
- Bo Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuman Xiang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Bojun Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhe Ma
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Weifeng Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Kelwick R, Ricci L, Chee SM, Bell D, Webb AJ, Freemont PS. Cell-free prototyping strategies for enhancing the sustainable production of polyhydroxyalkanoates bioplastics. Synth Biol (Oxf) 2018; 3:ysy016. [PMID: 32995523 PMCID: PMC7445755 DOI: 10.1093/synbio/ysy016] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 07/29/2018] [Accepted: 08/21/2018] [Indexed: 12/31/2022] Open
Abstract
The polyhydroxyalkanoates (PHAs) are microbially-produced biopolymers that could potentially be used as sustainable alternatives to oil-derived plastics. However, PHAs are currently more expensive to produce than oil-derived plastics. Therefore, more efficient production processes would be desirable. Cell-free metabolic engineering strategies have already been used to optimize several biosynthetic pathways and we envisioned that cell-free strategies could be used for optimizing PHAs biosynthetic pathways. To this end, we developed several Escherichia coli cell-free systems for in vitro prototyping PHAs biosynthetic operons, and also for screening relevant metabolite recycling enzymes. Furthermore, we customized our cell-free reactions through the addition of whey permeate, an industrial waste that has been previously used to optimize in vivo PHAs production. We found that the inclusion of an optimal concentration of whey permeate enhanced relative cell-free GFPmut3b production by approximately 50%. In cell-free transcription-translation prototyping reactions, gas chromatography-mass spectrometry quantification of cell-free 3-hydroxybutyrate (3HB) production revealed differences between the activities of the Native ΔPhaC_C319A (1.18 ± 0.39 µM), C104 ΔPhaC_C319A (4.62 ± 1.31 µM) and C101 ΔPhaC_C319A (2.65 ± 1.27 µM) phaCAB operons that were tested. Interestingly, the most active operon, C104 produced higher levels of PHAs (or PHAs monomers) than the Native phaCAB operon in both in vitro and in vivo assays. Coupled cell-free biotransformation/transcription-translation reactions produced greater yields of 3HB (32.87 ± 6.58 µM), and these reactions were also used to characterize a Clostridium propionicum Acetyl-CoA recycling enzyme. Together, these data demonstrate that cell-free approaches complement in vivo workflows for identifying additional strategies for optimizing PHAs production.
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Affiliation(s)
- Richard Kelwick
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK
| | - Luca Ricci
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Soo Mei Chee
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- The London DNA Foundry, Imperial College London, London, UK
| | - David Bell
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- The London DNA Foundry, Imperial College London, London, UK
| | - Alexander J Webb
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK
| | - Paul S Freemont
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK
- The London DNA Foundry, Imperial College London, London, UK
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Rathinam NK, Berchmans S, Sani RK, Salem DR. Rewiring the microbe-electrode interfaces with biologically reduced graphene oxide for improved bioelectrocatalysis. BIORESOURCE TECHNOLOGY 2018; 256:195-200. [PMID: 29438920 DOI: 10.1016/j.biortech.2018.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 06/08/2023]
Abstract
The aim of this work was to study biologically reduced graphene oxide (RGO) for engineering the surface architecture of the bioelectrodes to improve the performance of Bioelectrochemical System (BES). Gluconobacter roseus mediates the reduction of graphene oxide (GO). The RGO modified bioelectrodes produced a current density of 1 mA/cm2 and 0.69 mA/cm2 with ethanol and glucose as substrates, respectively. The current density of RGO modified electrodes was nearly 10-times higher than the controls. This study, for the first time, reports a new strategy to improve the yield as well as efficiency of the BES by wrapping and wiring the electroactive microorganisms to the electrode surfaces using RGO. This innovative wrapping approach will decrease the loss of electrons in the microbe-electrolyte interfaces as well as increase the electron transfer rates at the microorganism-electrode interfaces.
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Affiliation(s)
- Navanietha Krishnaraj Rathinam
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, USA; Composite and Nanocomposite Advanced Manufacturing Center - Biomaterials (CNAM-Bio Center), Rapid City, SD 57701, USA.
| | - Sheela Berchmans
- Biosensors Lab, Central Electrochemical Research Institute, Karaikudi, India
| | - Rajesh K Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, USA; Department of Chemistry and Applied Biological Sciences, South Dakota School of Mines and Technology, Rapid City, SD, USA; Composite and Nanocomposite Advanced Manufacturing Center - Biomaterials (CNAM-Bio Center), Rapid City, SD 57701, USA
| | - David R Salem
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, USA; Department of Materials and Metallurgical Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; Composite and Nanocomposite Advanced Manufacturing Center - Biomaterials (CNAM-Bio Center), Rapid City, SD 57701, USA
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39
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Ankrah NYD, Douglas AE. Nutrient factories: metabolic function of beneficial microorganisms associated with insects. Environ Microbiol 2018. [DOI: 10.1111/1462-2920.14097] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
| | - Angela E. Douglas
- Department of MicrobiologyCornell UniversityIthaca NY14853 USA
- Department of Molecular Biology and GeneticsCornell UniversityIthaca NY14853 USA
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40
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Mao X, Liu Z, Sun J, Lee SY. Metabolic engineering for the microbial production of marine bioactive compounds. Biotechnol Adv 2017; 35:1004-1021. [DOI: 10.1016/j.biotechadv.2017.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/01/2017] [Accepted: 03/01/2017] [Indexed: 01/22/2023]
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41
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Hohnholz R, Pohlmann KJ, Achstetter T. Impact of plasmid architecture on stability and yEGFP3 reporter gene expression in a set of isomeric multicopy vectors in yeast. Appl Microbiol Biotechnol 2017; 101:8455-8463. [PMID: 29052760 PMCID: PMC5694506 DOI: 10.1007/s00253-017-8558-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/21/2017] [Accepted: 09/27/2017] [Indexed: 11/25/2022]
Abstract
Multicopy episomal plasmids in yeast, used whenever elevated levels of foreign or homologous gene expression are necessary, are known to be less stable compared to the endogenous 2-μm plasmid they are based on, at least without selective pressure. Considering that rich medium favors growth rate and, simultaneously, is less expensive than selective medium, enhancing stability in non-selective medium is extremely desirable. In this study, we changed the architecture of a multicopy model expression plasmid, creating six isoforms (same size, same DNA content but different positions and orientations of the expression block) and studied mitotic stability, copy number, as well as reporter yEGFP3 expression between isoforms. With one isoform being significantly more stable than the others and another one exhibiting elevated plasmid copy numbers in rich medium, we show that consideration of the arrangement of the plasmid elements might be crucial for productivity employing Saccharomyces cerevisiae as a host. We strongly believe that the ideal architecture has to be assessed for each case and assembly strategy has to begin by evaluating the stability of the vector backbone before insertion of the desired gene. For the plasmid set studied, yEGFP3 reporter production depends more on mitotic stability than on elevated plasmid copy numbers in a small number of cells retaining the plasmid under non-selective conditions.
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Affiliation(s)
- Ruben Hohnholz
- City University of Applied Sciences Bremen, Neustadtswall 30, D-28199, Bremen, Germany.
- Jacobs University Bremen, Campus Ring 1, D-28759, Bremen, Germany.
| | | | - Tilman Achstetter
- City University of Applied Sciences Bremen, Neustadtswall 30, D-28199, Bremen, Germany
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Tomàs-Gamisans M, Ferrer P, Albiol J. Fine-tuning the P. pastoris iMT1026 genome-scale metabolic model for improved prediction of growth on methanol or glycerol as sole carbon sources. Microb Biotechnol 2017; 11:224-237. [PMID: 29160039 PMCID: PMC5743807 DOI: 10.1111/1751-7915.12871] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 07/28/2017] [Accepted: 08/25/2017] [Indexed: 11/30/2022] Open
Abstract
The methylotrophic yeast Pichia pastoris (Komagataella spp.) is widely used as cell factory for recombinant protein production. In the past recent years, important breakthroughs in the systems-level quantitative analysis of its physiology have been achieved. This wealth of information has allowed the development of genome-scale metabolic models, which make new approaches possible for host cell and bioprocess engineering. Nevertheless, the predictive accuracy of the previous consensus model required to be upgraded and validated with new experimental data sets for P. pastoris growing on glycerol or methanol as sole carbon sources, two of the most relevant substrates for this cell factory. In this study, we have characterized P. pastoris growing in chemostat cultures using glycerol or methanol as sole carbon sources over a wide range of growth rates, thereby providing physiological data on the effect of growth rate and culture conditions on biomass macromolecular and elemental composition. In addition, these data sets were used to improve the performance of the P. pastoris consensus genomic-scale metabolic model iMT1026. Thereupon, new experimentally determined bounds, including the representation of biomass composition for these growth conditions, have been incorporated. As a result, here, we present version 3 (v3.0) of the consensus P. pastoris genome-scale metabolic model as an update of the iMT1026 model. The v3.0 model was validated for growth on glycerol and methanol as sole carbon sources, demonstrating improved prediction capabilities over an extended substrate range including two biotechnologically relevant carbon sources.
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Affiliation(s)
- Màrius Tomàs-Gamisans
- Department of Chemical Biological and Environmental Engineering, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Pau Ferrer
- Department of Chemical Biological and Environmental Engineering, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Joan Albiol
- Department of Chemical Biological and Environmental Engineering, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
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43
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Nielsen C, Rahman A, Rehman AU, Walsh MK, Miller CD. Food waste conversion to microbial polyhydroxyalkanoates. Microb Biotechnol 2017; 10:1338-1352. [PMID: 28736901 PMCID: PMC5658610 DOI: 10.1111/1751-7915.12776] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 06/17/2017] [Indexed: 12/16/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are biopolymers with desirable material properties similar to petrochemically derived plastics. PHAs are naturally produced by a wide range of microorganisms as a carbon storage mechanism and can accumulate to significantly high levels. PHAs are an environmentally friendly alternative to their petroleum counterparts because they can be easily degraded, potentially reducing the burden on municipal waste systems. Nevertheless, widespread use of PHAs is not currently realistic due to a variety of factors. One of the major constraints of large-scale PHA production is the cost of carbon substrate for PHA-producing microbes. The cost of production could potentially be reduced with the use of waste carbon from food-related processes. Food wastage is a global issue and therefore harbours immense potential to create valuable bioproducts. This article's main focus is to examine the state of the art of converting food-derived waste into carbon substrates for microbial metabolism and subsequent conversion into PHAs.
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Affiliation(s)
- Chad Nielsen
- Department of Biological EngineeringUtah State University4105 Old Main HillLoganUT84322‐4105USA
| | - Asif Rahman
- Bioengineering BranchSpace BioSciences DivisionNASA Ames Research CenterMoffett FieldCA94035‐1000USA
- COSMIAC Research CenterUniversity of New MexicoAlbuquerqueNM87106USA
| | - Asad Ur Rehman
- Department of Biological EngineeringUtah State University4105 Old Main HillLoganUT84322‐4105USA
- Institute of Industrial BiotechnologyGovernment College UniversityKatchery RoadLahorePakistan
| | - Marie K. Walsh
- Department of Nutrition, Dietetics, and Food SciencesUtah State University8700 Old Main HillLoganUT84322‐8700USA
| | - Charles D. Miller
- Department of Biological EngineeringUtah State University4105 Old Main HillLoganUT84322‐4105USA
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44
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Iman M, Sobati T, Panahi Y, Mobasheri M. Systems Biology Approach to Bioremediation of Nitroaromatics: Constraint-Based Analysis of 2,4,6-Trinitrotoluene Biotransformation by Escherichia coli. Molecules 2017; 22:E1242. [PMID: 28805729 PMCID: PMC6152126 DOI: 10.3390/molecules22081242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 01/02/2023] Open
Abstract
Microbial remediation of nitroaromatic compounds (NACs) is a promising environmentally friendly and cost-effective approach to the removal of these life-threating agents. Escherichia coli (E. coli) has shown remarkable capability for the biotransformation of 2,4,6-trinitro-toluene (TNT). Efforts to develop E. coli as an efficient TNT degrading biocatalyst will benefit from holistic flux-level description of interactions between multiple TNT transforming pathways operating in the strain. To gain such an insight, we extended the genome-scale constraint-based model of E. coli to account for a curated version of major TNT transformation pathways known or evidently hypothesized to be active in E. coli in present of TNT. Using constraint-based analysis (CBA) methods, we then performed several series of in silico experiments to elucidate the contribution of these pathways individually or in combination to the E. coli TNT transformation capacity. Results of our analyses were validated by replicating several experimentally observed TNT degradation phenotypes in E. coli cultures. We further used the extended model to explore the influence of process parameters, including aeration regime, TNT concentration, cell density, and carbon source on TNT degradation efficiency. We also conducted an in silico metabolic engineering study to design a series of E. coli mutants capable of degrading TNT at higher yield compared with the wild-type strain. Our study, therefore, extends the application of CBA to bioremediation of nitroaromatics and demonstrates the usefulness of this approach to inform bioremediation research.
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Affiliation(s)
- Maryam Iman
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, 1477893855 Tehran, Iran.
- Department of Pharmaceutics, School of Pharmacy, Baqiyatallah University of Medical Sciences, 1477893855 Tehran, Iran.
| | - Tabassom Sobati
- Young Researchers and Elite Club, Islamic Azad University, 46115655 Tehran, Iran.
| | - Yunes Panahi
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, 1477893855 Tehran, Iran.
| | - Meysam Mobasheri
- Young Researchers and Elite Club, Islamic Azad University, 46115655 Tehran, Iran.
- Department of Biotechnology, Faculty of Advanced Sciences & Technology, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), 194193311 Tehran, Iran.
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45
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Kang MK, Zhou YJ, Buijs NA, Nielsen J. Functional screening of aldehyde decarbonylases for long-chain alkane production by Saccharomyces cerevisiae. Microb Cell Fact 2017; 16:74. [PMID: 28464872 PMCID: PMC5414326 DOI: 10.1186/s12934-017-0683-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/18/2017] [Indexed: 02/10/2023] Open
Abstract
Background Low catalytic activities of pathway enzymes are often a limitation when using microbial based chemical production. Recent studies indicated that the enzyme activity of aldehyde decarbonylase (AD) is a critical bottleneck for alkane biosynthesis in Saccharomyces cerevisiae. We therefore performed functional screening to identify efficient ADs that can improve alkane production by S. cerevisiae. Results A comparative study of ADs originated from a plant, insects, and cyanobacteria were conducted in S. cerevisiae. As a result, expression of aldehyde deformylating oxygenases (ADOs), which are cyanobacterial ADs, from Synechococcus elongatus and Crocosphaera watsonii converted fatty aldehydes to corresponding Cn−1 alkanes and alkenes. The CwADO showed the highest alkane titer (0.13 mg/L/OD600) and the lowest fatty alcohol production (0.55 mg/L/OD600). However, no measurable alkanes and alkenes were detected in other AD expressed yeast strains. Dynamic expression of SeADO and CwADO under GAL promoters increased alkane production to 0.20 mg/L/OD600 and no fatty alcohols, with even number chain lengths from C8 to C14, were detected in the cells. Conclusions We demonstrated in vivo enzyme activities of ADs by displaying profiles of alkanes and fatty alcohols in S. cerevisiae. Among the AD enzymes evaluated, cyanobacteria ADOs were found to be suitable for alkane biosynthesis in S. cerevisiae. This work will be helpful to decide an AD candidate for alkane biosynthesis in S. cerevisiae and it will provide useful information for further investigation of AD enzymes with improved activities. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0683-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min-Kyoung Kang
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Yongjin J Zhou
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96, Gothenburg, Sweden.,Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Nicolaas A Buijs
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden.,Evolva Biotech, Lersø Parkalle, 40-42, 2100, Copenhagen, Denmark
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle allé, 2970, Hørsholm, Denmark. .,Science for Life Laboratory, Royal Institute of Technology, 17121, Solna, Sweden.
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46
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Gustavsson M, Lee SY. Prospects of microbial cell factories developed through systems metabolic engineering. Microb Biotechnol 2016; 9:610-7. [PMID: 27435545 PMCID: PMC4993179 DOI: 10.1111/1751-7915.12385] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 06/21/2016] [Indexed: 11/27/2022] Open
Abstract
While academic‐level studies on metabolic engineering of microorganisms for production of chemicals and fuels are ever growing, a significantly lower number of such production processes have reached commercial‐scale. In this work, we review the challenges associated with moving from laboratory‐scale demonstration of microbial chemical or fuel production to actual commercialization, focusing on key requirements on the production organism that need to be considered during the metabolic engineering process. Metabolic engineering strategies should take into account techno‐economic factors such as the choice of feedstock, the product yield, productivity and titre, and the cost effectiveness of midstream and downstream processes. Also, it is important to develop an industrial strain through metabolic engineering for pathway construction and flux optimization together with increasing tolerance to products and inhibitors present in the feedstock, and ensuring genetic stability and strain robustness under actual fermentation conditions.
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Affiliation(s)
- Martin Gustavsson
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Korea.,KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, 106 91, Stockholm, Sweden
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Korea
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