1
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Gurdo N, Volke DC, Nikel PI. Merging automation and fundamental discovery into the design–build–test–learn cycle of nontraditional microbes. Trends Biotechnol 2022; 40:1148-1159. [DOI: 10.1016/j.tibtech.2022.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/12/2022] [Accepted: 03/16/2022] [Indexed: 12/29/2022]
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2
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Choi BH, Kang HJ, Kim SC, Lee PC. Organelle Engineering in Yeast: Enhanced Production of Protopanaxadiol through Manipulation of Peroxisome Proliferation in Saccharomyces cerevisiae. Microorganisms 2022; 10:microorganisms10030650. [PMID: 35336225 PMCID: PMC8950469 DOI: 10.3390/microorganisms10030650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 12/15/2022] Open
Abstract
Isoprenoids, which are natural compounds with diverse structures, possess several biological activities that are beneficial to humans. A major consideration in isoprenoid production in microbial hosts is that the accumulation of biosynthesized isoprenoid within intracellular membranes may impede balanced cell growth, which may consequently reduce the desired yield of the target isoprenoid. As a strategy to overcome this suggested limitation, we selected peroxisome membranes as depots for the additional storage of biosynthesized isoprenoids to facilitate increased isoprenoid production in Saccharomyces cerevisiae. To maximize the peroxisome membrane storage capacity of S.cerevisiae, the copy number and size of peroxisomes were increased through genetic engineering of the expression of three peroxisome biogenesis-related peroxins (Pex11p, Pex34p, and Atg36p). The genetically enlarged and high copied peroxisomes in S.cerevisiae were stably maintained under a bioreactor fermentation condition. The peroxisome-engineered S.cerevisiae strains were then utilized as host strains for metabolic engineering of heterologous protopanaxadiol pathway. The yields of protopanaxadiol from the engineered peroxisome strains were ca 78% higher than those of the parent strain, which strongly supports the rationale for harnessing the storage capacity of the peroxisome membrane to accommodate the biosynthesized compounds. Consequently, this study presents in-depth knowledge on peroxisome biogenesis engineering in S.cerevisiae and could serve as basic information for improvement in ginsenosides production and as a potential platform to be utilized for other isoprenoids.
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Affiliation(s)
- Bo Hyun Choi
- Department of Molecular Science and Technology, Ajou University, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea; (B.H.C.); (H.J.K.)
| | - Hyun Joon Kang
- Department of Molecular Science and Technology, Ajou University, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea; (B.H.C.); (H.J.K.)
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea;
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology, Ajou University, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea; (B.H.C.); (H.J.K.)
- Correspondence: ; Tel.: +82-31-219-2461
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3
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Gosalawit C, Imsoonthornruksa S, Gilroyed BH, Mcnea L, Boontawan A, Ketudat-Cairns M. The potential of the oleaginous yeast Rhodotorula paludigena CM33 to produce biolipids. J Biotechnol 2021; 329:56-64. [PMID: 33549673 DOI: 10.1016/j.jbiotec.2021.01.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 01/04/2021] [Accepted: 01/28/2021] [Indexed: 10/22/2022]
Abstract
Sixty-seven yeast strains were isolated from castor beans then their endogenous lipids were stained by Nile Red (NR) fluorescence dye, and flow cytometry was used to obtain a strain with a high relative mean fluorescence intensity (MFI) value. The highest MFI value was obtained for strain CM33, which produced a maximum lipid content of 20.8 % dry cell weight (DCW). Based on the sequence of the ITS-5.8S-ITS rDNA and D1/D2 26S rDNA regions, CM33 showed 99 % identity with Rhodotorula paludigena. The potential of CM33 to assimilate various carbon sources was examined by growth on minimal media using glucose, glycerol, sucrose or xylose. CM33 was grown in glucose-based medium for 96 h and exhibited a maximum lipid content of 23.9 % DCW. Furthermore, when cells were cultured on molasses waste, their biomass, lipid content and lipid concentration reached 16.5 g/L, 37.1 % DCW and 6.1 g/L, respectively. These results demonstrated the potential of R. paludigena CM33 to contribute to a value-added carbon chain by converting renewable waste materials for biolipid production.
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Affiliation(s)
- Chotika Gosalawit
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Suranaree Sub-district, Muang District, Nakhon Ratchasima, 30000, Thailand.
| | - Sumeth Imsoonthornruksa
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Suranaree Sub-district, Muang District, Nakhon Ratchasima, 30000, Thailand.
| | - Brandon H Gilroyed
- School of Environmental Sciences, University of Guelph Ridgetown Campus, 120 Main Street East, Ridgetown, Ontario, N0P 2C0, Canada.
| | - Lucas Mcnea
- School of Environmental Sciences, University of Guelph Ridgetown Campus, 120 Main Street East, Ridgetown, Ontario, N0P 2C0, Canada.
| | - Apichat Boontawan
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Suranaree Sub-district, Muang District, Nakhon Ratchasima, 30000, Thailand.
| | - Mariena Ketudat-Cairns
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Suranaree Sub-district, Muang District, Nakhon Ratchasima, 30000, Thailand.
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4
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Krishnan A, McNeil BA, Stuart DT. Biosynthesis of Fatty Alcohols in Engineered Microbial Cell Factories: Advances and Limitations. Front Bioeng Biotechnol 2020; 8:610936. [PMID: 33344437 PMCID: PMC7744569 DOI: 10.3389/fbioe.2020.610936] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/10/2020] [Indexed: 11/19/2022] Open
Abstract
Concerns about climate change and environmental destruction have led to interest in technologies that can replace fossil fuels and petrochemicals with compounds derived from sustainable sources that have lower environmental impact. Fatty alcohols produced by chemical synthesis from ethylene or by chemical conversion of plant oils have a large range of industrial applications. These chemicals can be synthesized through biological routes but their free forms are produced in trace amounts naturally. This review focuses on how genetic engineering of endogenous fatty acid metabolism and heterologous expression of fatty alcohol producing enzymes have come together resulting in the current state of the field for production of fatty alcohols by microbial cell factories. We provide an overview of endogenous fatty acid synthesis, enzymatic methods of conversion to fatty alcohols and review the research to date on microbial fatty alcohol production. The primary focus is on work performed in the model microorganisms, Escherichia coli and Saccharomyces cerevisiae but advances made with cyanobacteria and oleaginous yeasts are also considered. The limitations to production of fatty alcohols by microbial cell factories are detailed along with consideration to potential research directions that may aid in achieving viable commercial scale production of fatty alcohols from renewable feedstock.
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Affiliation(s)
- Anagha Krishnan
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Bonnie A McNeil
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - David T Stuart
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
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5
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Basri RS, Rahman RNZRA, Kamarudin NHA, Ali MSM. Cyanobacterial aldehyde deformylating oxygenase: Structure, function, and potential in biofuels production. Int J Biol Macromol 2020; 164:3155-3162. [PMID: 32841666 DOI: 10.1016/j.ijbiomac.2020.08.162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/04/2020] [Accepted: 08/20/2020] [Indexed: 11/27/2022]
Abstract
The conversion of aldehydes to valuable alkanes via cyanobacterial aldehyde deformylating oxygenase is of great interest. The availability of fossil reserves that keep on decreasing due to human exploitation is worrying, and even more troubling is the combustion emission from the fuel, which contributes to the environmental crisis and health issues. Hence, it is crucial to use a renewable and eco-friendly alternative that yields compound with the closest features as conventional petroleum-based fuel, and that can be used in biofuels production. Cyanobacterial aldehyde deformylating oxygenase (ADO) is a metal-dependent enzyme with an α-helical structure that contains di‑iron at the active site. The substrate enters the active site of every ADO through a hydrophobic channel. This enzyme exhibits catalytic activity toward converting Cn aldehyde to Cn-1 alkane and formate as a co-product. These cyanobacterial enzymes are small and easy to manipulate. Currently, ADOs are broadly studied and engineered for improving their enzymatic activity and substrate specificity for better alkane production. This review provides a summary of recent progress in the study of the structure and function of ADO, structural-based engineering of the enzyme, and highlight its potential in producing biofuels.
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Affiliation(s)
- Rose Syuhada Basri
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
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6
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Passarini MRZ, E Silva TR, Bernal SPF, Cecchet NL, Sartoratto A, Boroski M, Duarte AWF, Ottoni JR, Rosa LH, de Oliveira VM. Undecane production by cold-adapted bacteria from Antarctica. Extremophiles 2020; 24:863-873. [PMID: 32944821 DOI: 10.1007/s00792-020-01200-1] [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: 05/20/2020] [Accepted: 09/03/2020] [Indexed: 11/27/2022]
Abstract
In the last decades, efforts to reduce the use of fossil fuels have increased the search for alternative sustainable sources of renewable energy. In this scenario, hydrocarbons derived from fatty acids are among the compounds that have been drawing attention. The intracellular production of hydrocarbons by bacteria derived from cold environments such as the Antarctic continent is currently poorly investigated, as extremophilic microorganisms provide a great range of metabolic capabilities and may represent a key tool in the production of biofuels. The aim of this study was to explore the ability of bacterial cells derived from extreme environments to produce hydrocarbons with potential for further use as biofuels. Seven bacteria isolated from Antarctic samples were evaluated for hydrocarbon production using GC-MS approaches. Two isolates, identified as Arthrobacter livingstonensis 593 and Pseudoalteromonas arctica 628, were able to produce the hydrocarbon undecane (CH3-(CH2)9-CH3) in concentrations of 1.39 mg L-1 and 1.81 mg L-1, respectively. Results from the present work encourage further research focusing on the optimization of hydrocarbon production by the isolates identified as producers, which may be used in further aircraft biofuel production. This is the first report on the production of the undecane compound by bacteria isolated from waterlogged soil and sponge from Antarctica.
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Affiliation(s)
- Michel Rodrigo Zambrano Passarini
- UNILA-Universidade Federal da Integração Latino-Americana. Laboratório de Biotecnologia Ambiental, Av. Tarquínio Joslin dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil.
| | - Tiago Rodrigues E Silva
- CPQBA/UNICAMP-Divisão de Recursos Microbianos, Rua Alexandre Caselatto 999, Vila Betel, CP 6171, Campinas, SP, 13083-970, Brazil
| | - Suzan Prado Fernandes Bernal
- UNILA-Universidade Federal da Integração Latino-Americana. Laboratório de Biotecnologia Ambiental, Av. Tarquínio Joslin dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | - Nathália Luana Cecchet
- UNILA-Universidade Federal da Integração Latino-Americana. Laboratório de Biotecnologia Ambiental, Av. Tarquínio Joslin dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | - Adilson Sartoratto
- CPQBA/UNICAMP-Divisão de Química Orgânica e Farmacêutica, Rua Alexandre Caselatto 999, Vila Betel, CP 6171, Campinas, SP, 13083-970, Brazil
| | - Marcela Boroski
- UNILA-Universidade Federal da Integração Latino-Americana. Laboratório de Química, Av. Tancredo Neves 6731- Conjunto B, Foz do Iguaçu, PR, 85867-970, Brazil
| | - Alysson Wagner Fernandes Duarte
- UFAL-Universidade Federal de Alagoas, Av. Manoel Severino Barbosa-Rodovia AL-115, Bom Sucesso, Arapiraca, AL, 57309-005, Brazil
| | - Júlia Ronzella Ottoni
- UDC-Centro Universitário Dinâmica das Cataratas, Rua Castelo Branco, 349, Centro, Foz do Iguaçu, PR, Brazil
| | - Luiz Henrique Rosa
- UFMG-Departamento de Microbiologia, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | - Valéria Maia de Oliveira
- CPQBA/UNICAMP-Divisão de Recursos Microbianos, Rua Alexandre Caselatto 999, Vila Betel, CP 6171, Campinas, SP, 13083-970, Brazil
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7
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Zhou L, Wen Z, Wang Z, Zhang Y, Ledesma-Amaro R, Jin M. Evolutionary Engineering Improved d-Glucose/Xylose Cofermentation of Yarrowia lipolytica. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c00896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Linlin Zhou
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Zhiqiang Wen
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Zedi Wang
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Yuwei Zhang
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | | | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
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8
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Enriching the Production of 2-Methyl-1-Butanol in Fermentation Process Using Corynebacterium crenatum. Curr Microbiol 2020; 77:1699-1706. [PMID: 32300924 DOI: 10.1007/s00284-020-01961-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/21/2020] [Indexed: 10/24/2022]
Abstract
Non-natural 2-methyl-1-butanol (2 MB) has been biosynthesized through the modification of metabolic pathways using Corynebacterium crenatum, a non-model host. However, its production capacity is not effectively improved. In this study, the fermentation process was strengthened through factor combination design (FCD) for enhancing the production of 2 MB. Our results showed that the highest production of 2 MB, 3-methyl-1-butanol (3 MB), ethanol, and total solvent was 4.87 ± 0.39 g/L, 3.57 ± 0.21 g/L, 5.74 ± 0.43 g/L, and 14.18 g/L, respectively, under the optimal fermentation conditions. The optimal fermentation conditions were determined through the FCD to be as follows: pH of 6.5, IPTG concentration of 1.2 mM, fermentation temperature of 32 °C, and fermentation time of 96 h. This study provides a significant guidance for the optimal control technology of the genetically engineered C. crenatum, and also a useful reference for the industrial production of 2 MB via the microbial fermentation approach.
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9
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Discovery of a Regulatory Subunit of the Yeast Fatty Acid Synthase. Cell 2020; 180:1130-1143.e20. [DOI: 10.1016/j.cell.2020.02.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/23/2019] [Accepted: 02/12/2020] [Indexed: 11/23/2022]
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10
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Liu D, Geiselman GM, Coradetti S, Cheng YF, Kirby J, Prahl JP, Jacobson O, Sundstrom ER, Tanjore D, Skerker JM, Gladden J. Exploiting nonionic surfactants to enhance fatty alcohol production in Rhodosporidium toruloides. Biotechnol Bioeng 2020; 117:1418-1425. [PMID: 31981215 PMCID: PMC7187362 DOI: 10.1002/bit.27285] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/23/2019] [Accepted: 01/22/2020] [Indexed: 01/13/2023]
Abstract
Fatty alcohols (FOHs) are important feedstocks in the chemical industry to produce detergents, cosmetics, and lubricants. Microbial production of FOHs has become an attractive alternative to production in plants and animals due to growing energy demands and environmental concerns. However, inhibition of cell growth caused by intracellular FOH accumulation is one major issue that limits FOH titers in microbial hosts. In addition, identification of FOH‐specific exporters remains a challenge and previous studies towards this end are limited. To alleviate the toxicity issue, we exploited nonionic surfactants to promote the export of FOHs in Rhodosporidium toruloides, an oleaginous yeast that is considered an attractive next‐generation host for the production of fatty acid‐derived chemicals. Our results showed FOH export efficiency was dramatically improved and the growth inhibition was alleviated in the presence of small amounts of tergitol and other surfactants. As a result, FOH titers increase by 4.3‐fold at bench scale to 352.6 mg/L. With further process optimization in a 2‐L bioreactor, the titer was further increased to 1.6 g/L. The method we show here can potentially be applied to other microbial hosts and may facilitate the commercialization of microbial FOH production.
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Affiliation(s)
- Di Liu
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California.,Department of Energy, Agile BioFoundry, Emeryville, California
| | - Gina M Geiselman
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California.,Department of Energy, Agile BioFoundry, Emeryville, California
| | - Samuel Coradetti
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California.,Department of Energy, Agile BioFoundry, Emeryville, California
| | - Ya-Fang Cheng
- QB3-Berkeley, University of California, Berkeley, California
| | - James Kirby
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California.,Department of Energy, Agile BioFoundry, Emeryville, California
| | - Jan-Philip Prahl
- Department of Energy, Agile BioFoundry, Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, California
| | - Oslo Jacobson
- Department of Energy, Agile BioFoundry, Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, California
| | - Eric R Sundstrom
- Department of Energy, Agile BioFoundry, Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, California
| | - Deepti Tanjore
- Department of Energy, Agile BioFoundry, Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, California
| | | | - John Gladden
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California.,Department of Energy, Agile BioFoundry, Emeryville, California.,Joint BioEnergy Institute, Emeryville, California
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11
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Jiang Y, Li Z, Zheng S, Xu H, Zhou YJ, Gao Z, Meng C, Li S. Establishing an enzyme cascade for one-pot production of α-olefins from low-cost triglycerides and oils without exogenous H 2O 2 addition. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:52. [PMID: 32190117 PMCID: PMC7075034 DOI: 10.1186/s13068-020-01684-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 02/21/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Biological α-olefins can be used as both biofuels and high value-added chemical precursors to lubricants, polymers, and detergents. The prototypic CYP152 peroxygenase family member OleTJE from Jeotgalicoccus sp. ATCC 8456 catalyzes a single-step decarboxylation of free fatty acids (FFAs) to form α-olefins using H2O2 as a cofactor, thus attracting much attention since its discovery. To improve the productivity of α-olefins, significant efforts on protein engineering, electron donor engineering, and metabolic engineering of OleTJE have been made. However, little success has been achieved in obtaining α-olefin high-producer microorganisms due to multiple reasons such as the tight regulation of FFA biosynthesis, the difficulty of manipulating multi-enzyme metabolic network, and the poor catalytic performance of OleTJE. RESULTS In this study, a novel enzyme cascade was developed for one-pot production of α-olefins from low-cost triacylglycerols (TAGs) and natural oils without exogenous H2O2 addition. This artificial biocatalytic route consists of a lipase (CRL, AOL or Lip2) for TAG hydrolysis to produce glycerol and free fatty acids (FFAs), an alditol oxidase (AldO) for H2O2 generation upon glycerol oxidation, and the P450 fatty acid decarboxylase OleTJE for FFA decarboxylation using H2O2 generated in situ. The multi-enzyme system was systematically optimized leading to the production of α-olefins with the conversion rates ranging from 37.2 to 68.5%. Furthermore, a reaction using lyophilized CRL/OleTJE/AldO enzymes at an optimized ratio (5 U/6 μM/30 μM) gave a promising α-olefin yield of 0.53 g/L from 1500 μM (~1 g/L) coconut oil. CONCLUSIONS The one-pot enzyme cascade was successfully established and applied to prepare high value-added α-olefins from low-cost and renewable TAGs/natural oils. This system is independent of exogenous addition of H2O2, thus not only circumventing the detrimental effect of H2O2 on the stability and activity of involved enzymes, but also lower the overall costs on the TAG-to-olefin transformation. It is anticipated that this biotransformation system will become industrially relevant in the future upon more engineering efforts based on this proof-of-concept work.
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Affiliation(s)
- Yuanyuan Jiang
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhong Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shanmin Zheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
- School of Life Sciences, Shandong University of Technology, Zibo, 255000 Shandong China
| | - Huifang Xu
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
| | - Yongjin J. Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 Liaoning China
| | - Zhengquan Gao
- School of Life Sciences, Shandong University of Technology, Zibo, 255000 Shandong China
| | - Chunxiao Meng
- School of Life Sciences, Shandong University of Technology, Zibo, 255000 Shandong China
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 Shandong China
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12
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Liu GS, Li T, Zhou W, Jiang M, Tao XY, Liu M, Zhao M, Ren YH, Gao B, Wang FQ, Wei DZ. The yeast peroxisome: A dynamic storage depot and subcellular factory for squalene overproduction. Metab Eng 2020; 57:151-161. [DOI: 10.1016/j.ymben.2019.11.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/19/2019] [Accepted: 11/05/2019] [Indexed: 02/06/2023]
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13
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Khairuddin NFM, Idris A, Hock LW. Harvesting Nannochloropsis sp. using PES/MWCNT/LiBr membrane with good antifouling properties. Sep Purif Technol 2019. [DOI: 10.1016/j.seppur.2018.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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14
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Lee SY, Kim HU, Chae TU, Cho JS, Kim JW, Shin JH, Kim DI, Ko YS, Jang WD, Jang YS. A comprehensive metabolic map for production of bio-based chemicals. Nat Catal 2019. [DOI: 10.1038/s41929-018-0212-4] [Citation(s) in RCA: 282] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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15
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Kieliszek M, Błażejak S, Bzducha-Wróbel A, Kot AM. Effect of Selenium on Lipid and Amino Acid Metabolism in Yeast Cells. Biol Trace Elem Res 2019; 187:316-327. [PMID: 29675568 PMCID: PMC6315055 DOI: 10.1007/s12011-018-1342-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 04/09/2018] [Indexed: 12/27/2022]
Abstract
This article discusses the effect of selenium in aqueous solutions on aspects of lipid and amino acid metabolism in the cell biomass of Saccharomyces cerevisiae MYA-2200 and Candida utilis ATCC 9950 yeasts. The yeast biomass was obtained by using waste products (potato wastewater and glycerol). Selenium, at a dose of 20 mg/L of aqueous solution, affected the differentiation of cellular morphology. Yeast enriched with selenium was characterized by a large functional diversity in terms of protein and amino acid content. The protein content in the biomass of S. cerevisiae enriched with selenium (42.6%) decreased slightly as compared to that in the control sample without additional selenium supplementation (48.4%). Moreover, yeasts of both strains enriched with selenium contained a large amount of glutamic acid, aspartic acid, lysine, and leucine. Analysis of fatty acid profiles in S. cerevisiae yeast supplemented with selenium showed an increase in the unsaturated fatty acid content (e.g., C18:1). The presence of margaric acid (C17:0) and hexadecanoic acid (C17:1) was found in the C. utilis biomass enriched with selenium, in contrast to that of S. cerevisiae. These results indicate that selenium may induce lipid peroxidation, which consequently affects the loss of integrity of the cytoplasmic membrane. Yeast enriched with selenium with optimal amino acid and lipid composition can be used to prepare a novel formula of dietary supplements, which can be applied directly to various diets for both humans and animals.
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Affiliation(s)
- Marek Kieliszek
- Faculty of Food Sciences, Department of Biotechnology, Microbiology and Food Evaluation, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159 C, 02-776, Warsaw, Poland.
| | - Stanisław Błażejak
- Faculty of Food Sciences, Department of Biotechnology, Microbiology and Food Evaluation, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159 C, 02-776, Warsaw, Poland
| | - Anna Bzducha-Wróbel
- Faculty of Food Sciences, Department of Biotechnology, Microbiology and Food Evaluation, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159 C, 02-776, Warsaw, Poland
| | - Anna M Kot
- Faculty of Food Sciences, Department of Biotechnology, Microbiology and Food Evaluation, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159 C, 02-776, Warsaw, Poland
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He Q, Yang Y, Yang S, Donohoe BS, Van Wychen S, Zhang M, Himmel ME, Knoshaug EP. Oleaginicity of the yeast strain Saccharomyces cerevisiae D5A. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:258. [PMID: 30258492 PMCID: PMC6151946 DOI: 10.1186/s13068-018-1256-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/10/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND The model yeast, Saccharomyces cerevisiae, is not known to be oleaginous. However, an industrial wild-type strain, D5A, was shown to accumulate over 20% storage lipids from glucose when growth is nitrogen-limited compared to no more than 7% lipid accumulation without nitrogen stress. METHODS AND RESULTS To elucidate the mechanisms of S. cerevisiae D5A oleaginicity, we compared physiological and metabolic changes; as well as the transcriptional profiles of the oleaginous industrial strain, D5A, and a non-oleaginous laboratory strain, BY4741, under normal and nitrogen-limited conditions using analytic techniques and next-generation sequencing-based RNA-Seq transcriptomics. Transcriptional levels for genes associated with fatty acid biosynthesis, nitrogen metabolism, amino acid catabolism, as well as the pentose phosphate pathway and ethanol oxidation in central carbon (C) metabolism, were up-regulated in D5A during nitrogen deprivation. Despite increased carbon flux to lipids, most gene-encoding enzymes involved in triacylglycerol (TAG) assembly were expressed at similar levels regardless of the varying nitrogen concentrations in the growth media and strain backgrounds. Phospholipid turnover also contributed to TAG accumulation through increased precursor production with the down-regulation of subsequent phospholipid synthesis steps. Our results also demonstrated that nitrogen assimilation via the glutamate-glutamine pathway and amino acid metabolism, as well as the fluxes of carbon and reductants from central C metabolism, are integral to the general oleaginicity of D5A, which resulted in the enhanced lipid storage during nitrogen deprivation. CONCLUSION This work demonstrated the disequilibrium and rebalance of carbon and nitrogen contribution to the accumulation of lipids in the oleaginous yeast S. cerevisiae D5A. Rather than TAG assembly from acyl groups, the major switches for the enhanced lipid accumulation of D5A (i.e., fatty acid biosynthesis) are the increases of cytosolic pools of acetyl-CoA and NADPH, as well as alternative nitrogen assimilation.
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Affiliation(s)
- Qiaoning He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yongfu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | | | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | - Eric P. Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, 80401 USA
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17
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Motwalli O, Essack M, Salhi A, Hanks J, Mijakovic I, Bajic VB. BioPS: System for screening and assessment of biofuel-production potential of cyanobacteria. PLoS One 2018; 13:e0202002. [PMID: 30096176 PMCID: PMC6086437 DOI: 10.1371/journal.pone.0202002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 07/26/2018] [Indexed: 01/03/2023] Open
Abstract
Background Cyanobacteria are one of the target groups of organisms explored for production of free fatty acids (FFAs) as biofuel precursors. Experimental evaluation of cyanobacterial potential for FFA production is costly and time consuming. Thus, computational approaches for comparing and ranking cyanobacterial strains for their potential to produce biofuel based on the characteristics of their predicted proteomes can be of great importance. Results To enable such comparison and ranking, and to assist biotechnology developers and researchers in selecting strains more likely to be successfully engineered for the FFA production, we developed the Biofuel Producer Screen (BioPS) platform (http://www.cbrc.kaust.edu.sa/biops). BioPS relies on the estimation of the predicted proteome makeup of cyanobacterial strains to produce and secrete FFAs, based on the analysis of well-studied cyanobacterial strains with known FFA production profiles. The system links results back to various external repositories such as KEGG, UniProt and GOLD, making it easier for users to explore additional related information. Conclusion To our knowledge, BioPS is the first tool that screens and evaluates cyanobacterial strains for their potential to produce and secrete FFAs based on strain’s predicted proteome characteristics, and rank strains based on that assessment. We believe that the availability of such a platform (comprising both a prediction tool and a repository of pre-evaluated stains) would be of interest to biofuel researchers. The BioPS system will be updated annually with information obtained from newly sequenced cyanobacterial genomes as they become available, as well as with new genes that impact FFA production or secretion.
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Affiliation(s)
- Olaa Motwalli
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
- Saudi Electronic University (SEU), College of Computing and Informatics, Madinah, Kingdom of Saudi Arabia
| | - Magbubah Essack
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
| | - Adil Salhi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
| | - John Hanks
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
| | - Ivan Mijakovic
- Chalmers University of Technology, Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Vladimir B. Bajic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
- * E-mail:
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Petronikolou N, Nair SK. Structural and Biochemical Studies of a Biocatalyst for the Enzymatic Production of Wax Esters. ACS Catal 2018; 8:6334-6344. [PMID: 31559109 DOI: 10.1021/acscatal.8b00787] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Wax esters are high-value products whose enzymatic synthesis is of increasing biotechnological interest. The fabrication of cell factories that mass-produce wax esters may provide a facile route towards a sustainable, and environment-friendly approach to a large-scale process for this commodity chemical. An expedient route for wax-ester biocatalysis may be facilitated by the action of enzymes termed wax ester synthases/diacylglycerol acyltransferases (WS/DGAT), which produce wax esters using fatty acids and alcohols as a precursor. In this work, we report the structure for a member of the WS/DGAT superfamily. The structural data in conjunction with bioinformatics and mutational analyses allowed us to identify the substrate binding pockets, and residues that may be important for catalysis. Using this information as a guide, we generated a mutant with preference towards shorter acyl-substrates. This study demonstrates the efficacy of a structure-guided engineering effort towards a WS/DGAT variant with preference towards wax esters of desired lengths.
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Kurokawa Y, Nagai K, Huan PD, Shimazaki K, Qu H, Mori Y, Toda Y, Kuroha T, Hayashi N, Aiga S, Itoh JI, Yoshimura A, Sasaki-Sekimoto Y, Ohta H, Shimojima M, Malik AI, Pedersen O, Colmer TD, Ashikari M. Rice leaf hydrophobicity and gas films are conferred by a wax synthesis gene (LGF1) and contribute to flood tolerance. THE NEW PHYTOLOGIST 2018; 218:1558-1569. [PMID: 29498045 DOI: 10.1111/nph.15070] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/14/2018] [Indexed: 06/08/2023]
Abstract
Floods impede gas (O2 and CO2 ) exchange between plants and the environment. A mechanism to enhance plant gas exchange under water comprises gas films on hydrophobic leaves, but the genetic regulation of this mechanism is unknown. We used a rice mutant (dripping wet leaf 7, drp7) which does not retain gas films on leaves, and its wild-type (Kinmaze), in gene discovery for this trait. Gene complementation was tested in transgenic lines. Functional properties of leaves as related to gas film retention and underwater photosynthesis were evaluated. Leaf Gas Film 1 (LGF1) was identified as the gene determining leaf gas films. LGF1 regulates C30 primary alcohol synthesis, which is necessary for abundant epicuticular wax platelets, leaf hydrophobicity and gas films on submerged leaves. This trait enhanced underwater photosynthesis 8.2-fold and contributes to submergence tolerance. Gene function was verified by a complementation test of LGF1 expressed in the drp7 mutant background, which restored C30 primary alcohol synthesis, wax platelet abundance, leaf hydrophobicity, gas film retention, and underwater photosynthesis. The discovery of LGF1 provides an opportunity to better understand variation amongst rice genotypes for gas film retention ability and to target various alleles in breeding for improved submergence tolerance for yield stability in flood-prone areas.
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Affiliation(s)
- Yusuke Kurokawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Phung Danh Huan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
- Crops Research and Development Institute, Vietnam National University of Agriculture, Trau Quy, Gia Lam, Ha Noi, Vietnam
| | - Kousuke Shimazaki
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8503, Japan
| | - Huangqi Qu
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
| | - Yoshinao Mori
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
| | - Yosuke Toda
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
| | - Takeshi Kuroha
- Graduate School of Life Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba, Sendai, Miyagi, 980-8578, Japan
| | - Nagao Hayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Saori Aiga
- Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Jun-Ichi Itoh
- Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Atsushi Yoshimura
- Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi, Fukuoka, 812-8581, Japan
| | - Yuko Sasaki-Sekimoto
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8503, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Japan
| | - Hiroyuki Ohta
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8503, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8503, Japan
| | - Mie Shimojima
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8503, Japan
| | - Al Imran Malik
- Centre for Plant Genetics and Breeding, UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Ole Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3rd floor, Copenhagen, 2100, Denmark
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Timothy David Colmer
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
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Chimeric Fatty Acyl-Acyl Carrier Protein Thioesterases Provide Mechanistic Insight into Enzyme Specificity and Expression. Appl Environ Microbiol 2018; 84:AEM.02868-17. [PMID: 29549102 DOI: 10.1128/aem.02868-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 03/12/2018] [Indexed: 12/27/2022] Open
Abstract
Medium-chain fatty acids are commodity chemicals. Increasing and modifying the activity of thioesterases (TEs) on medium-chain fatty acyl-acyl carrier protein (acyl-ACP) esters may enable a high-yield microbial production of these molecules. The plant Cuphea palustris harbors two distinct TEs: C. palustris FatB1 (CpFatB1) (C8 specificity, lower activity) and CpFatB2 (C14 specificity, higher activity) with 78% sequence identity. We combined structural features from these two enzymes to create several chimeric TEs, some of which showed nonnatural fatty acid production as measured by an enzymatic assay and gas chromatography-mass spectrometry (GC-MS). Notably, chimera 4 exhibited an increased C8 fatty acid production in correlation with improved microbial expression. This chimera led us to identify CpFatB2-specific amino acids between positions 219 and 272 that lead to higher protein levels. Chimera 7 produced a broad range of fatty acids and appeared to combine a fatty acid binding pocket with long-chain specificity and an ACP interaction site that may activate fatty acid extrusion. Using homology modeling and in silico docking with ACP, we identified a "positive patch" within amino acids 162 to 218, which may direct the ACP interaction and regulate access to short-chain fatty acids. On the basis of this modeling, we transplanted putative ACP interaction sequences from CpFatB1 into CpFatB2 and created a chimeric thioesterase that produced medium-chain as well as long-chain fatty acids. Thus, the engineering of chimeric enzymes and characterizing their microbial activity and chain-length specificity suggested mechanistic insights into TE functions and also generated thioesterases with potentially useful properties. These observations may inform a rational engineering of TEs to allow alkyl chain length control.IMPORTANCE Medium-chain fatty acids are important commodity chemicals. These molecules are used as plastic precursors and in shampoos and other detergents and could be used as biofuel precursors if production economics were favorable. Hydrocarbon-based liquid fuels must be optimized to have a desired boiling point, low freezing point, low viscosity, and other physical characteristics. Similarly, the solubility and harshness of detergents and the flexibility of plastic polymers can be modulated. The length and distribution of the carbon chains in the hydrophobic tails determine these properties. The biological synthesis of cell membranes and fatty acids produces chains of primarily 16 to 18 carbons, which give rise to current biofuels. The ultimate goal of the work presented here is to engineer metabolic pathways to produce designer molecules with the correct number of carbons in a chain, so that such molecules could be used directly as specialty commodity chemicals or as fuels after minimal processing.
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Hu Y, Zhu Z, Nielsen J, Siewers V. Heterologous transporter expression for improved fatty alcohol secretion in yeast. Metab Eng 2018; 45:51-58. [DOI: 10.1016/j.ymben.2017.11.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/01/2017] [Accepted: 11/18/2017] [Indexed: 11/25/2022]
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Feng Y, Wang Y, Liu J, Liu Y, Cao X, Xue S. Structural Insight into Acyl-ACP Thioesterase toward Substrate Specificity Design. ACS Chem Biol 2017; 12:2830-2836. [PMID: 28991437 DOI: 10.1021/acschembio.7b00641] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acyl-ACP thioesterase (TE) catalyzes the hydrolysis of thioester bonds during type II fatty acid synthesis and directly determines fatty acid chain length. Most TEs are responsible for recognition of 16:0 and 18:1 substrates, while specific TEs interrupt acyl-ACP elongation at C8-C14. However, the acyl selection mechanism of TE has not been thoroughly elucidated to date. In this study, the crystal structure of the C12-specific thioesterase FatB from Umbellularia californica, which consists of two independent hotdog domains, was determined. An uncanonical Asp-His-Glu catalytic network was identified on the C-terminal hotdog domain, whereas the substrate binding pocket was determined to be on the N-terminal hotdog domain. Moreover, we elucidated UcFatB's substrate selection mechanism, which is accommodated by several unconservative amino acids on the β5, β2, and β4 sheets and enclosed by T137 on the α1 helix. On this basis, the C12-specific TE was rationally redesigned toward C14 selectivity by tuning the substrate binding pocket capacity. The T137G mutant demonstrated comparative relative activity on C14 substrates compared to C12 substrates in vitro. Furthermore, the reconstructed UcFatB_T137G achieved C14 fatty acid content up to 40% in contrast to 10% C14 from the wild type in engineered E. coli cells. The unraveled substrate selection mechanism of TE provides a new strategy for tailoring fatty acid synthesis.
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Affiliation(s)
- Yanbin Feng
- Marine
Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yayue Wang
- Marine
Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiao Liu
- Marine
Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yinghui Liu
- Marine
Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xupeng Cao
- Marine
Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Song Xue
- Marine
Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Vermaas JV, Beckham GT, Crowley MF. Membrane Permeability of Fatty Acyl Compounds Studied via Molecular Simulation. J Phys Chem B 2017; 121:11311-11324. [PMID: 29040809 DOI: 10.1021/acs.jpcb.7b08233] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interest in fatty acid-derived products as fuel and chemical precursors has grown substantially. Microbes can be genetically engineered to produce fatty acid-derived products that are able to cross host membranes and can be extracted into an applied organic overlay. This process is thought to be passive, with a rate dependent on the chemistry of the crossing compound. The relationship between the chemical composition and the energetics and kinetics of product accumulation within the overlay is not well understood. Through biased and unbiased molecular simulation, we compute the membrane permeability coefficients from production to extraction for different fatty acyl products, including fatty acids, fatty alcohols, fatty aldehydes, alkanes, and alkenes. These simulations identify specific interactions that accelerate the transit of aldehydes across the membrane bilayer relative to other oxidized products, specifically the lack of hydrogen bonds to the surrounding membrane environment. However, since extraction from the outer membrane leaflet into the organic phase is found to be rate limiting for the entire process, we find that fatty alcohols and fatty aldehydes would both manifest similar fluxes into a dodecane overlay under equivalent conditions, outpacing the accumulation of acids or alkanes into the organic phase. Since aldehydes are known to be highly reactive as well as toxic in high quantities, the findings suggest that indeed fatty alcohols are the optimal long-tail fatty acyl product for extraction.
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Affiliation(s)
- Josh V Vermaas
- Biosciences Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | - Michael F Crowley
- Biosciences Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States
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Metabolic engineering of Saccharomyces cerevisiae for production of very long chain fatty acid-derived chemicals. Nat Commun 2017; 8:15587. [PMID: 28548095 PMCID: PMC5458556 DOI: 10.1038/ncomms15587] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 04/04/2017] [Indexed: 12/27/2022] Open
Abstract
Production of chemicals and biofuels through microbial fermentation is an economical and sustainable alternative for traditional chemical synthesis. Here we present the construction of a Saccharomyces cerevisiae platform strain for high-level production of very-long-chain fatty acid (VLCFA)-derived chemicals. Through rewiring the native fatty acid elongation system and implementing a heterologous Mycobacteria FAS I system, we establish an increased biosynthesis of VLCFAs in S. cerevisiae. VLCFAs can be selectively modified towards the fatty alcohol docosanol (C22H46O) by expressing a specific fatty acid reductase. Expression of this enzyme is shown to impair cell growth due to consumption of VLCFA-CoAs. We therefore implement a dynamic control strategy for separating cell growth from docosanol production. We successfully establish high-level and selective docosanol production of
83.5 mg l−1 in yeast. This approach will provide a universal strategy towards the production of similar high value chemicals in a more scalable, stable and sustainable manner. Production of chemicals by microbial fermentation is an economical alternative to chemical synthesis. Here the authors re-engineer the yeast S. cerevisiae to produce the very long chain fatty alcohol docosanol by expressing a heterologous Mycobacteria fatty acid synthase and a specific fatty acid reductase.
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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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Xu P, Qiao K, Stephanopoulos G. Engineering oxidative stress defense pathways to build a robust lipid production platform in Yarrowia lipolytica. Biotechnol Bioeng 2017; 114:1521-1530. [PMID: 28295166 DOI: 10.1002/bit.26285] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/05/2017] [Accepted: 03/09/2017] [Indexed: 12/22/2022]
Abstract
Microbially derived lipids have recently attracted renewed interests due to their broad applications in production of green diesels, cosmetic additives, and oleochemicals. Metabolic engineering efforts have targeted a large portfolio of biosynthetic pathways to efficiently convert sugar to lipids in oleaginous yeast. In the engineered overproducing strains, endogenous cell metabolism typically generates harmful electrophilic molecules that compromise cell fitness and productivity. Lipids, particularly unsaturated fatty acids, are highly susceptible to oxygen radical attack and the resulting oxidative species are detrimental to cell metabolism and limit lipid productivity. In this study, we investigated cellular oxidative stress defense pathways in Yarrowia lipolytica to further improve the lipid titer, yield, and productivity. Specifically, we determined that coupling glutathione disulfide reductase and glucose-6-phosphate dehydrogenase along with aldehyde dehydrogenase are efficient solutions to combat reactive oxygen and aldehyde stress in Y. lipolytica. With the reported engineering strategies, we were able to synchronize cell growth and lipid production, improve cell fitness and morphology, and achieved industrially-relevant level of lipid titer (72.7 g/L), oil content (81.4%) and productivity (0.97 g/L/h) in controlled bench-top bioreactors. The strategies reported here represent viable steps in the development of sustainable biorefinery platforms that potentially upgrade low value carbons to high value oleochemicals and biofuels. Biotechnol. Bioeng. 2017;114: 1521-1530. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Peng Xu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.,Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland
| | - Kangjian Qiao
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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27
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Yu P, Chen X, Li P. Enhancing microbial production of biofuels by expanding microbial metabolic pathways. Biotechnol Appl Biochem 2017; 64:606-619. [PMID: 27507087 DOI: 10.1002/bab.1529] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 07/31/2016] [Indexed: 12/29/2022]
Abstract
Fatty acid, isoprenoid, and alcohol pathways have been successfully engineered to produce biofuels. By introducing three genes, atfA, adhE, and pdc, into Escherichia coli to expand fatty acid pathway, up to 1.28 g/L of fatty acid ethyl esters can be achieved. The isoprenoid pathway can be expanded to produce bisabolene with a high titer of 900 mg/L in Saccharomyces cerevisiae. Short- and long-chain alcohols can also be effectively biosynthesized by extending the carbon chain of ketoacids with an engineered "+1" alcohol pathway. Thus, it can be concluded that expanding microbial metabolic pathways has enormous potential for enhancing microbial production of biofuels for future industrial applications. However, some major challenges for microbial production of biofuels should be overcome to compete with traditional fossil fuels: lowering production costs, reducing the time required to construct genetic elements and to increase their predictability and reliability, and creating reusable parts with useful and predictable behavior. To address these challenges, several aspects should be further considered in future: mining and transformation of genetic elements related to metabolic pathways, assembling biofuel elements and coordinating their functions, enhancing the tolerance of host cells to biofuels, and creating modular subpathways that can be easily interconnected.
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Affiliation(s)
- Ping Yu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Xingge Chen
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Peng Li
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, People's Republic of China
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28
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Dasgupta D, Sharma T, Bhatt A, Bandhu S, Ghosh D. Cultivation of oleaginous yeast Rhodotorula mucilaginosa IIPL32 in split column airlift reactor and its influence on fuel properties. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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29
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Teixeira PG, Ferreira R, Zhou YJ, Siewers V, Nielsen J. Dynamic regulation of fatty acid pools for improved production of fatty alcohols in Saccharomyces cerevisiae. Microb Cell Fact 2017; 16:45. [PMID: 28298234 PMCID: PMC5353878 DOI: 10.1186/s12934-017-0663-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 03/10/2017] [Indexed: 01/05/2023] Open
Abstract
Background In vivo production of fatty acid-derived chemicals in Saccharomyces cerevisiae requires strategies to increase the intracellular supply of either acyl-CoA or free fatty acids (FFAs), since their cytosolic concentrations are quite low in a natural state for this organism. Deletion of the fatty acyl-CoA synthetase genes FAA1 and FAA4 is an effective and straightforward way to disable re-activation of fatty acids and drastically increase FFA levels. However, this strategy causes FFA over-accumulation and consequential release to the extracellular medium, which results in a significant loss of precursors that compromises the process yield. In the present study, we aimed for dynamic expression of the fatty acyl-CoA synthetase gene FAA1 to regulate FFA and acyl-CoA pools in order to improve fatty alcohol production yields. Results We analyzed the metabolite dynamics of a faa1Δ faa4Δ strain constitutively expressing a carboxylic acid reductase from Mycobacterium marinum (MmCAR) and an endogenous alcohol dehydrogenase (Adh5) for in vivo production of fatty alcohols from FFAs. We observed production of fatty acids and fatty alcohols with different rates leading to high levels of FFAs not being converted to the final product. To address the issue, we expressed the MmCAR + Adh5 pathway together with a fatty acyl-CoA reductase from Marinobacter aquaeolei to enable fatty alcohol production simultaneously from FFA and acyl-CoA, respectively. Then, we expressed FAA1 under the control of different promoters in order to balance FFA and acyl-CoA interconversion rates and to achieve optimal levels for conversion to fatty alcohols. Expressing FAA1 under control of the HXT1 promoter led to an increased accumulation of fatty alcohols per OD600 up to 41% while FFA levels were decreased by 63% compared with the control strain. Conclusions Fine-tuning and dynamic regulation of key metabolic steps can be used to improve cell factories when the rates of downstream reactions are limiting. This avoids loss of precursors to the extracellular medium or to competing reactions, hereby potentially improving the process yield. The study also provides knowledge of a key point of fatty acid regulation and homeostasis, which can be used for future design of cells factories for fatty acid-derived chemicals. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0663-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paulo Gonçalves Teixeira
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Raphael Ferreira
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Yongjin J Zhou
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, 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, 2800, Kgs. Lyngby, Denmark.
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30
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Uehling J, Gryganskyi A, Hameed K, Tschaplinski T, Misztal PK, Wu S, Desirò A, Vande Pol N, Du Z, Zienkiewicz A, Zienkiewicz K, Morin E, Tisserant E, Splivallo R, Hainaut M, Henrissat B, Ohm R, Kuo A, Yan J, Lipzen A, Nolan M, LaButti K, Barry K, Goldstein AH, Labbé J, Schadt C, Tuskan G, Grigoriev I, Martin F, Vilgalys R, Bonito G. Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens. Environ Microbiol 2017; 19:2964-2983. [PMID: 28076891 DOI: 10.1111/1462-2920.13669] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/05/2017] [Accepted: 01/07/2017] [Indexed: 12/13/2022]
Abstract
Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well-known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. We sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within a lineage of endofungal symbionts that are sister clade to Burkholderia. The genome of M. elongata strain AG77 features a core set of primary metabolic pathways for degradation of simple carbohydrates and lipid biosynthesis, while the M. cysteinexigens (AG77) genome is reduced in size and function. Experiments using antibiotics to cure the endobacterium from the host demonstrate that the fungal host metabolism is highly modulated by presence/absence of M. cysteinexigens. Independent comparative phylogenomic analyses of fungal and bacterial genomes are consistent with an ancient origin for M. elongata - M. cysteinexigens symbiosis, most likely over 350 million years ago and concomitant with the terrestrialization of Earth and diversification of land fungi and plants.
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Affiliation(s)
- J Uehling
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - A Gryganskyi
- LF Lambert Spawn Company Coatesville, PA, 19320, USA
| | - K Hameed
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - T Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - P K Misztal
- University of California Berkeley, Berkeley, CA, 94720, USA
| | - S Wu
- Arizona State University Tempe, AZ, 85281, USA
| | - A Desirò
- Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - N Vande Pol
- Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Z Du
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - A Zienkiewicz
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - K Zienkiewicz
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA.,Department of Plant Biochemistry, Georg-August University, Göttingen, 37073, Germany
| | - E Morin
- Institut National de la Recherche Agronomique, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'excellence ARBRE, INRA-Nancy, Champenoux, 54280, France
| | - E Tisserant
- Institut National de la Recherche Agronomique, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'excellence ARBRE, INRA-Nancy, Champenoux, 54280, France
| | - R Splivallo
- Goethe University Frankfurt, Institute for Molecular Biosciences, 60438 Frankfurt, Germany Integrative Fungal Research Cluster (IPF), Frankfurt, 60325, Germany
| | - M Hainaut
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France
| | - B Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France
| | - R Ohm
- Microbiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - A Kuo
- Department of Energy, Joint Genome Institute, Oakland, CA, 94598, USA
| | - J Yan
- Department of Energy, Joint Genome Institute, Oakland, CA, 94598, USA
| | - A Lipzen
- Department of Energy, Joint Genome Institute, Oakland, CA, 94598, USA
| | - M Nolan
- Department of Energy, Joint Genome Institute, Oakland, CA, 94598, USA
| | - K LaButti
- Department of Energy, Joint Genome Institute, Oakland, CA, 94598, USA
| | - K Barry
- Department of Energy, Joint Genome Institute, Oakland, CA, 94598, USA
| | - A H Goldstein
- University of California Berkeley, Berkeley, CA, 94720, USA
| | - J Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - C Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - G Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - I Grigoriev
- Department of Energy, Joint Genome Institute, Oakland, CA, 94598, USA
| | - F Martin
- Institut National de la Recherche Agronomique, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'excellence ARBRE, INRA-Nancy, Champenoux, 54280, France
| | - R Vilgalys
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - G Bonito
- Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
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31
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Zhou YJ, Buijs NA, Zhu Z, Gómez DO, Boonsombuti A, Siewers V, Nielsen J. Harnessing Yeast Peroxisomes for Biosynthesis of Fatty-Acid-Derived Biofuels and Chemicals with Relieved Side-Pathway Competition. J Am Chem Soc 2016; 138:15368-15377. [DOI: 10.1021/jacs.6b07394] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | | | | | | | | | | | - Jens Nielsen
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
- Science
for Life Laboratory, Royal Institute of Technology, SE-17121 Stockholm, Sweden
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32
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Bommareddy RR, Sabra W, Zeng AP. Glucose-mediated regulation of glycerol uptake in Rhodosporidium toruloides: Insights through transcriptomic analysis on dual substrate fermentation. Eng Life Sci 2016; 17:282-291. [PMID: 32624774 DOI: 10.1002/elsc.201600010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/17/2016] [Accepted: 04/27/2016] [Indexed: 12/13/2022] Open
Abstract
Rhodosporidium toruloides is a robust oleaginous yeast that can accumulate lipids to more than 70% of its dry cell mass. Even though it is extensively studied for its fermentation of substrates like glucose and glycerol, limited information is available about its metabolism of mixture of glucose and glycerol. During growth on mixture of glucose and glycerol a typical diauxic growth and higher lipid yields were observed. To understand this phenomenon, RNA-seq analysis was implemented to study the gene expression profiles during growth on mixtures mainly to elucidate regulation of glycerol metabolism. Insights into lipid biosynthesis on mixed substrates are provided at a systems level. Among others, transcriptional profiles showed that glycerol might be produced intracellularly and glycerol kinase (GUT1) and glycerol 3-phosphate dehydrogenase (GUT2) enzymes were not downregulated in the presence of glucose. Transcriptional analysis also showed that the regulation of glycerol uptake in the presence of glucose at transcriptional level is different from that observed in Saccharomyces cerevisiae.
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Affiliation(s)
- Rajesh Reddy Bommareddy
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - Wael Sabra
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany
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33
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Zhou YJ, Buijs NA, Zhu Z, Qin J, Siewers V, Nielsen J. Production of fatty acid-derived oleochemicals and biofuels by synthetic yeast cell factories. Nat Commun 2016; 7:11709. [PMID: 27222209 PMCID: PMC4894961 DOI: 10.1038/ncomms11709] [Citation(s) in RCA: 243] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/21/2016] [Indexed: 12/18/2022] Open
Abstract
Sustainable production of oleochemicals requires establishment of cell factory platform strains. The yeast Saccharomyces cerevisiae is an attractive cell factory as new strains can be rapidly implemented into existing infrastructures such as bioethanol production plants. Here we show high-level production of free fatty acids (FFAs) in a yeast cell factory, and the production of alkanes and fatty alcohols from its descendants. The engineered strain produces up to 10.4 g l(-1) of FFAs, which is the highest reported titre to date. Furthermore, through screening of specific pathway enzymes, endogenous alcohol dehydrogenases and aldehyde reductases, we reconstruct efficient pathways for conversion of fatty acids to alkanes (0.8 mg l(-1)) and fatty alcohols (1.5 g l(-1)), to our knowledge the highest titres reported in S. cerevisiae. This should facilitate the construction of yeast cell factories for production of fatty acids derived products and even aldehyde-derived chemicals of high value.
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Affiliation(s)
- Yongjin J Zhou
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg SE-41296, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg SE41296, Sweden
| | - Nicolaas A Buijs
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg SE-41296, Sweden
| | - Zhiwei Zhu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg SE-41296, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg SE41296, Sweden
| | - Jiufu Qin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg SE-41296, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg SE-41296, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg SE41296, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg SE-41296, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg SE41296, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm DK2970, Denmark.,Science for Life Laboratory, Royal Institute of Technology, Stockholm SE-17121, Sweden
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34
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Luo X, Zhao S, Huan T, Sun D, Friis RMN, Schultz MC, Li L. High-Performance Chemical Isotope Labeling Liquid Chromatography-Mass Spectrometry for Profiling the Metabolomic Reprogramming Elicited by Ammonium Limitation in Yeast. J Proteome Res 2016; 15:1602-12. [PMID: 26947805 DOI: 10.1021/acs.jproteome.6b00070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Information about how yeast metabolism is rewired in response to internal and external cues can inform the development of metabolic engineering strategies for food, fuel, and chemical production in this organism. We report a new metabolomics workflow for the characterization of such metabolic rewiring. The workflow combines efficient cell lysis without using chemicals that may interfere with downstream sample analysis and differential chemical isotope labeling liquid chromatography mass spectrometry (CIL LC-MS) for in-depth yeast metabolome profiling. Using (12)C- and (13)C-dansylation (Dns) labeling to analyze the amine/phenol submetabolome, we detected and quantified a total of 5719 peak pairs or metabolites. Among them, 120 metabolites were positively identified using a library of 275 Dns-metabolite standards, and 2980 metabolites were putatively identified based on accurate mass matches to metabolome databases. We also applied (12)C- and (13)C-dimethylaminophenacyl (DmPA) labeling to profile the carboxylic acid submetabolome and detected over 2286 peak pairs, from which 33 metabolites were positively identified using a library of 188 DmPA-metabolite standards, and 1595 metabolites were putatively identified. Using this workflow for metabolomic profiling of cells challenged by ammonium limitation revealed unexpected links between ammonium assimilation and pantothenate accumulation that might be amenable to engineering for better acetyl-CoA production in yeast. We anticipate that efforts to improve other schemes of metabolic engineering will benefit from application of this workflow to multiple cell types.
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Affiliation(s)
- Xian Luo
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Shuang Zhao
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Tao Huan
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Difei Sun
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - R Magnus N Friis
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Michael C Schultz
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Liang Li
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
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35
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Kerkhoven EJ, Pomraning KR, Baker SE, Nielsen J. Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica. NPJ Syst Biol Appl 2016; 2:16005. [PMID: 28725468 PMCID: PMC5516929 DOI: 10.1038/npjsba.2016.5] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/23/2015] [Accepted: 12/07/2015] [Indexed: 01/01/2023] Open
Abstract
Yarrowia lipolytica is a promising microbial cell factory for the production of lipids to be used as fuels and chemicals, but there are few studies on regulation of its metabolism. Here we performed the first integrated data analysis of Y. lipolytica grown in carbon and nitrogen limited chemostat cultures. We first reconstructed a genome-scale metabolic model and used this for integrative analysis of multilevel omics data. Metabolite profiling and lipidomics was used to quantify the cellular physiology, while regulatory changes were measured using RNAseq. Analysis of the data showed that lipid accumulation in Y. lipolytica does not involve transcriptional regulation of lipid metabolism but is associated with regulation of amino-acid biosynthesis, resulting in redirection of carbon flux during nitrogen limitation from amino acids to lipids. Lipid accumulation in Y. lipolytica at nitrogen limitation is similar to the overflow metabolism observed in many other microorganisms, e.g. ethanol production by Sacchromyces cerevisiae at nitrogen limitation.
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Affiliation(s)
- Eduard J Kerkhoven
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Kyle R Pomraning
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Scott E Baker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jens Nielsen
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
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36
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de Jong BW, Siewers V, Nielsen J. Physiological and transcriptional characterization of Saccharomyces cerevisiae engineered for production of fatty acid ethyl esters. FEMS Yeast Res 2015; 16:fov105. [PMID: 26590613 DOI: 10.1093/femsyr/fov105] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2015] [Indexed: 01/06/2023] Open
Abstract
Saccharomyces cerevisiae has previously been engineered to become a cell factory for the production of fatty acid ethyl esters (FAEEs), molecules suitable for crude diesel replacement. To find new metabolic engineering targets for the improvement of FAEE cell factories, three different FAEE-producing strains of S. cerevisiae, constructed previously, were compared and characterized by quantification of key fluxes and genome-wide transcription analysis. From both the physiological and the transcriptional data, it was indicated that strain CB2I20, with high expression of a heterologous wax ester synthase gene (ws2) and strain BdJ15, containing disruptions of genes DGA1, LRO1, ARE1, ARE2 and POX1, which prevent the conversion of acyl-CoA to sterol esters, triacylglycerides and the degradation to acetyl-CoA, triggered oxidative stress that consequently influenced cellular growth. In the latter strain, stress was possibly triggered by disabling the buffering capacity of lipid droplets in encapsulating toxic fatty acids such as oleic acid. Additionally, it was indicated that there was an increased demand for NADPH required for the reduction steps in fatty acid biosynthesis. In conclusion, our analysis clearly shows that engineering of fatty acid biosynthesis results in transcriptional reprogramming and has a significant effect on overall cellular metabolism.
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Affiliation(s)
- Bouke Wim de Jong
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
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37
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Jin Z, Wong A, Foo JL, Ng J, Cao Y, Chang MW, Yuan Y. Engineering
Saccharomyces cerevisiae
to produce odd chain‐length fatty alcohols. Biotechnol Bioeng 2015; 113:842-51. [DOI: 10.1002/bit.25856] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 09/15/2015] [Accepted: 10/08/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Zhu Jin
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringSchool of Chemical Engineering and Technology, Tianjin UniversityTianjin300072PR China
- Department of BiochemistryYong Loo Lin School of MedicineNational University of Singapore14 Medical Drive117599Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)Life Sciences InstituteNational University of Singapore, 28 Medical Drive117456Singapore
| | - Adison Wong
- Department of BiochemistryYong Loo Lin School of MedicineNational University of Singapore14 Medical Drive117599Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)Life Sciences InstituteNational University of Singapore, 28 Medical Drive117456Singapore
| | - Jee Loon Foo
- Department of BiochemistryYong Loo Lin School of MedicineNational University of Singapore14 Medical Drive117599Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)Life Sciences InstituteNational University of Singapore, 28 Medical Drive117456Singapore
| | - Joey Ng
- Department of BiochemistryYong Loo Lin School of MedicineNational University of Singapore14 Medical Drive117599Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)Life Sciences InstituteNational University of Singapore, 28 Medical Drive117456Singapore
| | - Ying‐Xiu Cao
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringSchool of Chemical Engineering and Technology, Tianjin UniversityTianjin300072PR China
| | - Matthew Wook Chang
- Department of BiochemistryYong Loo Lin School of MedicineNational University of Singapore14 Medical Drive117599Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)Life Sciences InstituteNational University of Singapore, 28 Medical Drive117456Singapore
| | - Ying‐Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringSchool of Chemical Engineering and Technology, Tianjin UniversityTianjin300072PR China
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38
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Synthetic biology for microbial production of lipid-based biofuels. Curr Opin Chem Biol 2015; 29:58-65. [PMID: 26479184 DOI: 10.1016/j.cbpa.2015.09.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 11/22/2022]
Abstract
The risks of maintaining current CO2 emission trends have led to interest in producing biofuels using engineered microbes. Microbial biofuels reduce emissions because CO2 produced by fuel combustion is offset by CO2 captured by growing biomass, which is later used as feedstock for biofuel fermentation. Hydrocarbons found in petroleum fuels share striking similarity with biological lipids. Here we review synthetic metabolic pathways based on fatty acid and isoprenoid metabolism to produce alkanes and other molecules suitable as biofuels. We further discuss engineering strategies to optimize engineered biosynthetic routes, as well as the potential of synthetic biology for sustainable manufacturing.
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39
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Fletcher E, Feizi A, Kim S, Siewers V, Nielsen J. RNA-seq analysis of Pichia anomala reveals important mechanisms required for survival at low pH. Microb Cell Fact 2015; 14:143. [PMID: 26376644 PMCID: PMC4574170 DOI: 10.1186/s12934-015-0331-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/31/2015] [Indexed: 02/08/2023] Open
Abstract
Background The product yield and titers of biological processes involving the conversion of biomass to desirable chemicals can be limited by environmental stresses encountered by the microbial hosts used for the bioconversion. One of these main stresses is growth inhibition due to exposure to low pH conditions. In order to circumvent this problem, understanding the biological mechanisms involved in acid stress response and tolerance is essential. Characterisation of wild yeasts that have a natural ability to resist such harsh conditions will pave the way to understand the biological basis underlying acid stress resistance. Pichia anomala possesses a unique ability to adapt to and tolerate a number of environmental stresses particularly low pH stress giving it the advantage to outcompete other microorganisms under such conditions. However, the genetic basis of this resistance has not been previously studied. Results To this end, we isolated an acid resistant strain of P. anomala, performed a gross phenotypic characterisation at low pH and also performed a whole genome and total RNA sequencing. By integrating the RNA-seq data with the genome sequencing data, we found that several genes associated with different biological processes including proton efflux, the electron transfer chain and oxidative phosphorylation were highly expressed in P. anomala cells grown in low pH media. We therefore present data supporting the notion that a high expression of proton pumps in the plasma membrane coupled with an increase in mitochondrial ATP production enables the high level of acid stress tolerance of P. anomala. Conclusions Our findings provide insight into the molecular and genetic basis of low pH tolerance in P. anomala which was previously unknown. Ultimately, this is a step towards developing non-conventional yeasts such as P. anomala for the production of industrially relevant chemicals under low pH conditions. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0331-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eugene Fletcher
- 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, Kemivägen 10, 412 96, Gothenburg, Sweden.
| | - Amir Feizi
- 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, Kemivägen 10, 412 96, Gothenburg, Sweden.
| | - SungSoo Kim
- Samsung Advanced Institute of Technology, 130 Samsung-Ro YoungTong-Ku, Suwon, Kyunggi-do, South Korea. .,Biotech Research Team, Dongbu Farm Hannong Co., Ltd., Daejeon, 305-708, Republic of Korea.
| | - Verena Siewers
- 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, Kemivägen 10, 412 96, Gothenburg, Sweden.
| | - 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, Kemivägen 10, 412 96, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark.
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40
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Petrovič U. Next-generation biofuels: a new challenge for yeast. Yeast 2015; 32:583-93. [DOI: 10.1002/yea.3082] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/16/2015] [Accepted: 06/16/2015] [Indexed: 11/11/2022] Open
Affiliation(s)
- Uroš Petrovič
- Jožef Stefan Institute; Department of Molecular and Biomedical Sciences; Ljubljana Slovenia
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41
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Tang X, Lee J, Chen WN. Engineering the fatty acid metabolic pathway in Saccharomyces cerevisiae for advanced biofuel production. Metab Eng Commun 2015; 2:58-66. [PMID: 34150509 PMCID: PMC8193251 DOI: 10.1016/j.meteno.2015.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 06/22/2015] [Accepted: 06/22/2015] [Indexed: 11/30/2022] Open
Abstract
Fatty acid-derived fuels and chemicals have attracted a great deal of attention in recent decades, due to their following properties of high compatibility to gasoline-based fuels and existing infrastructure for their direct utilization, storage and distribution. The yeast Saccharomyces cerevisiae is the ideal biofuel producing candidate, based on the wealth of available genetic information and versatile tools designed to manipulate its metabolic pathways. Engineering the fatty acid metabolic pathways in S. cerevisiae is an effective strategy to increase its fatty acid biosynthesis and provide more pathway precursors for production of targeted products. This review summarizes the recent progress in metabolic engineering of yeast cells for fatty acids and fatty acid derivatives production, including the regulation of acetyl-CoA biosynthesis, NADPH production, fatty acid elongation, and the accumulation of activated precursors of fatty acids for converting enzymes. By introducing specific enzymes in the engineered strains, a powerful platform with a scalable, controllable and economic route for advanced biofuel production has been established. Recent progress in metabolic engineering for enhanced fatty acid production. Regulation of acetyl-CoA, NADPH pathway for fatty acid synthesis. Regulation of elongation and catabolic pathway to strength fatty acid synthesis. Enhanced production of activated precursors for fatty acid derivatives production.
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Affiliation(s)
- Xiaoling Tang
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Jaslyn Lee
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Wei Ning Chen
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
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42
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Sheng J, Feng X. Metabolic engineering of yeast to produce fatty acid-derived biofuels: bottlenecks and solutions. Front Microbiol 2015; 6:554. [PMID: 26106371 PMCID: PMC4459083 DOI: 10.3389/fmicb.2015.00554] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/20/2015] [Indexed: 12/14/2022] Open
Abstract
Fatty acid-derived biofuels can be a better solution than bioethanol to replace petroleum fuel, since they have similar energy content and combustion properties as current transportation fuels. The environmentally friendly microbial fermentation process has been used to synthesize advanced biofuels from renewable feedstock. Due to their robustness as well as the high tolerance to fermentation inhibitors and phage contamination, yeast strains such as Saccharomyces cerevisiae and Yarrowia lipolytica have attracted tremendous attention in recent studies regarding the production of fatty acid-derived biofuels, including fatty acids, fatty acid ethyl esters, fatty alcohols, and fatty alkanes. However, the native yeast strains cannot produce fatty acids and fatty acid-derived biofuels in large quantities. To this end, we have summarized recent publications in this review on metabolic engineering of yeast strains to improve the production of fatty acid-derived biofuels, identified the bottlenecks that limit the productivity of biofuels, and categorized the appropriate approaches to overcome these obstacles.
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Affiliation(s)
- Jiayuan Sheng
- Biomolecular Engineering Lab, Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
| | - Xueyang Feng
- Biomolecular Engineering Lab, Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
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43
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Biosynthesis of odd-chain fatty alcohols in Escherichia coli. Metab Eng 2015; 29:113-123. [PMID: 25773521 DOI: 10.1016/j.ymben.2015.03.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/16/2015] [Accepted: 03/04/2015] [Indexed: 11/21/2022]
Abstract
Engineered microbes offer the opportunity to design and implement artificial molecular pathways for renewable production of tailored chemical commodities. Targeted biosynthesis of odd-chain fatty alcohols is very challenging in microbe, due to the specificity of fatty acids synthase for two-carbon unit elongation. Here, we developed a novel strategy to directly tailor carbon number in fatty aldehydes formation step by incorporating α-dioxygenase (αDOX) from Oryza sativa (rice) into Escherichia coli αDOX oxidizes Cn fatty acids (even-chain) to form Cn-1 fatty aldehydes (odd-chain). Through combining αDOX with fatty acyl-acyl carrier protein (-ACP) thioesterase (TE) and aldehyde reductase (AHR), the medium odd-chain fatty alcohols profile (C11, C13, C15) was firstly established in E. coli. Also, medium even-chain alkanes (C12, C14) were obtained by substitution of AHR to aldehyde decarbonylase (AD). The titer of odd-chain fatty alcohols was improved from 7.4mg/L to 101.5mg/L in tube cultivation by means of fine-tuning endogenous fatty acyl-ACP TE (TesA'), αDOX, AHRs and the genes involved in fatty acids metabolism pathway. Through high cell density fed-batch fermentation, a titer of 1.95g/L odd-chain fatty alcohols was achieved, which was the highest reported titer in E. coli. Our system has greatly expanded the current microbial fatty alcohols profile that provides a new brand solution for producing complex and desired molecules in microbes.
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44
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Pfleger BF, Gossing M, Nielsen J. Metabolic engineering strategies for microbial synthesis of oleochemicals. Metab Eng 2015; 29:1-11. [PMID: 25662836 DOI: 10.1016/j.ymben.2015.01.009] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/27/2015] [Accepted: 01/28/2015] [Indexed: 11/30/2022]
Abstract
Microbial synthesis of oleochemicals has advanced significantly in the last decade. Microbes have been engineered to convert renewable substrates to a wide range of molecules that are ordinarily made from plant oils. This approach is attractive because it can reduce a motivation for converting tropical rainforest into farmland while simultaneously enabling access to molecules that are currently expensive to produce from oil crops. In the last decade, enzymes responsible for producing oleochemicals in nature have been identified, strategies to circumvent native regulation have been developed, and high yielding strains have been designed, built, and successfully demonstrated. This review will describe the metabolic pathways that lead to the diverse molecular features found in natural oleochemicals, highlight successful metabolic engineering strategies, and comment on areas where future work could further advance the field.
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Affiliation(s)
- Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States.
| | - Michael Gossing
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
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45
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Buijs NA, Zhou YJ, Siewers V, Nielsen J. Long-chain alkane production by the yeast Saccharomyces cerevisiae. Biotechnol Bioeng 2015; 112:1275-9. [PMID: 25545362 DOI: 10.1002/bit.25522] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/17/2014] [Accepted: 12/08/2014] [Indexed: 11/10/2022]
Abstract
In the past decade industrial-scale production of renewable transportation biofuels has been developed as an alternative to fossil fuels, with ethanol as the most prominent biofuel and yeast as the production organism of choice. However, ethanol is a less efficient substitute fuel for heavy-duty and maritime transportation as well as aviation due to its low energy density. Therefore, new types of biofuels, such as alkanes, are being developed that can be used as drop-in fuels and can substitute gasoline, diesel, and kerosene. Here, we describe for the first time the heterologous biosynthesis of long-chain alkanes by the yeast Saccharomyces cerevisiae. We show that elimination of the hexadecenal dehydrogenase Hfd1 and expression of a redox system are essential for alkane biosynthesis in yeast. Deletion of HFD1 together with expression of an alkane biosynthesis pathway resulted in the production of the alkanes tridecane, pentadecane, and heptadecane. Our study provides a proof of principle for producing long-chain alkanes in the industrial workhorse S. cerevisiae, which was so far limited to bacteria. We anticipate that these findings will be a key factor for further yeast engineering to enable industrial production of alkane based drop-in biofuels, which can allow the biofuel industry to diversify beyond bioethanol.
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Affiliation(s)
- Nicolaas A Buijs
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
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