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Yan Z, Hou J, Leng B, Yao G, Ma C, Sun Y, Liu Q, Zhang F, Mu C, Liu X. Genome-Wide Identification and Characterization of Maize Long-Chain Acyl-CoA Synthetases and Their Expression Profiles in Different Tissues and in Response to Multiple Abiotic Stresses. Genes (Basel) 2024; 15:983. [PMID: 39202344 PMCID: PMC11354158 DOI: 10.3390/genes15080983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 09/03/2024] Open
Abstract
Long-chain acyl-CoA synthetases (LACSs) are essential enzymes that activate free fatty acids to fatty acyl-CoA thioesters, playing key roles in fatty acid (FA) catabolism, lipid synthesis and storage, epidermal wax synthesis, and stress tolerance. Despite their importance, comprehensive information about LACS genes in maize, a primary food crop, remains scarce. In the present work, eleven maize LACS genes were identified and mapped across five chromosomes. Three pairs of segmentally duplicated genes were detected in the maize LACS gene family, which underwent significant purifying selection (Ka/Ks < 1). Subsequently, phylogenetic analysis indicated that ZmLACS genes were divided into four subclasses, as supported by highly conserved motifs and gene structures. On the basis of the PlantCARE database, analysis of the ZmLACS promoter regions revealed various cis-regulatory elements related to tissue-specific expression, hormonal regulation, and abiotic stress response. RT-qPCR analysis showed that ZmLACS genes exhibit tissue-specific expression patterns and respond to diverse abiotic stresses including drought and salt, as well as phytohormone abscisic acid. Furthermore, using the STRING database, several proteins involved in fatty acid and complex lipid synthesis were identified to be the potential interaction partners of ZmLACS proteins, which was also confirmed by the yeast two-hybrid (Y2H) assay, enhancing our understanding of wax biosynthesis and regulatory mechanisms in response to abiotic stresses in maize. These findings provide a comprehensive understanding of ZmLACS genes and offer a theoretical foundation for future research on the biological functions of LACS genes in maize environmental adaptability.
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Affiliation(s)
- Zhenwei Yan
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jing Hou
- School of Agriculture, Ludong University, Yantai 264001, China
| | - Bingying Leng
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Guoqi Yao
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan 250300, China
| | - Yue Sun
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Qiantong Liu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Fajun Zhang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Chunhua Mu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xia Liu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
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Kojima H, Yamamoto K, Suzuki T, Hayakawa Y, Niwa T, Tokuhiro K, Katahira S, Higashiyama T, Ishiguro S. Broad Chain-Length Specificity of the Alkane-Forming Enzymes NoCER1A and NoCER3A/B in Nymphaea odorata. PLANT & CELL PHYSIOLOGY 2024; 65:428-446. [PMID: 38174441 PMCID: PMC11020225 DOI: 10.1093/pcp/pcad168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/01/2023] [Accepted: 01/19/2024] [Indexed: 01/05/2024]
Abstract
Many terrestrial plants produce large quantities of alkanes for use in epicuticular wax and the pollen coat. However, their carbon chains must be long to be useful as fuel or as a petrochemical feedstock. Here, we focus on Nymphaea odorata, which produces relatively short alkanes in its anthers. We identified orthologs of the Arabidopsis alkane biosynthesis genes AtCER1 and AtCER3 in N. odorata and designated them NoCER1A, NoCER3A and NoCER3B. Expression analysis of NoCER1A and NoCER3A/B in Arabidopsis cer mutants revealed that the N. odorata enzymes cooperated with the Arabidopsis enzymes and that the NoCER1A produced shorter alkanes than AtCER1, regardless of which CER3 protein it interacted with. These results indicate that AtCER1 frequently uses a C30 substrate, whereas NoCER1A, NoCER3A/B and AtCER3 react with a broad range of substrate chain lengths. The incorporation of shorter alkanes disturbed the formation of wax crystals required for water-repellent activity in stems, suggesting that chain-length specificity is important for surface cleaning. Moreover, cultured tobacco cells expressing NoCER1A and NoCER3A/B effectively produced C19-C23 alkanes, indicating that the introduction of the two enzymes is sufficient to produce alkanes. Taken together, our findings suggest that these N. odorata enzymes may be useful for the biological production of alkanes of specific lengths. 3D modeling revealed that CER1s and CER3s share a similar structure that consists of N- and C-terminal domains, in which their predicted active sites are respectively located. We predicted the complex structure of both enzymes and found a cavity that connects their active sites.
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Affiliation(s)
- Hisae Kojima
- Technical Center, Nagoya University, Nagoya, 464-8601 Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Kanta Yamamoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai, 487-8501 Japan
| | - Yuri Hayakawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Tomoko Niwa
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Kenro Tokuhiro
- Toyota Central R&D Labs., Inc., Nagakute, 480-1192 Japan
| | | | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601 Japan
- Graduate School of Science, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Sumie Ishiguro
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
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Kim YS, Baek H, Yun HS, Lee JH, Lee KI, Kim HS, Yoon HS. The Prokaryotic Microalga Limnothrix redekei KNUA012 to Improve Aldehyde Decarbonylase Expression for Use as a Biological Resource. Pol J Microbiol 2023; 72:307-317. [PMID: 37725893 PMCID: PMC10561079 DOI: 10.33073/pjm-2023-031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/04/2023] [Indexed: 09/21/2023] Open
Abstract
The prokaryotic microalga Limnothrix redekei KNUA012 isolated from a freshwater bloom sample from Lake Hapcheon, Hapcheon-gun, South Korea, was investigated for its potential as a biofuel feedstock. Microalgae produce straight-chain alkanes/alkenes from acyl carrier protein-linked fatty acyls via aldehyde decarbonylase (AD; EC 1.2.1.3), which can convert aldehyde intermediates into various biofuel precursors, such as alkanes and free fatty acids. In L. redekei KNUA012, long-chain ADs can convert fatty aldehyde intermediates into alkanes. After heterologous AD expression in Escherichia coli (pET28-AD), we identified an AD in L. redekei KNUA012 that can synthesize various alkanes, such as pentadecane (C15H32), 8-heptadecene (C17H34), and heptadecane (C17H36). These alkanes can be directly used as fuels without transesterification. Biodiesel constituents including dodecanoic acid (C13H26O2), tetradecanoic acid (C15H30O2), 9-hexa decenoic acid (C17H32O2), palmitoleic acid (C17H32O2), hexadecanoic acid (C17H34O2), 9-octadecenoic acid (C19H36O2), and octadecanoic acid (C19H38O2) are produced by L. redekei KNUA012 as the major fatty acids. Our findings suggest that Korean domestic L. redekei KNUA012 is a promising resource for microalgae-based biofuels and biofuel feedstock.
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Affiliation(s)
- Young-Saeng Kim
- Research Institute of Ulleung-do and Dok-do, Kyungpook National University, Daegu, Republic of Korea
| | - Haeri Baek
- Water Quality Research Institute Daegu Metropolitan City, Daegu, Republic of Korea
| | - Hyun-Sik Yun
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Hak Lee
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Kyoung-In Lee
- Biotechnology Industrialization Center, Dongshin University, Naju, Republic of Korea
| | - Han-Soon Kim
- Research Institute of Ulleung-do and Dok-do, Kyungpook National University, Daegu, Republic of Korea
- Advanced Bio-Resource Research Center, Kyungpook National University, Daegu, Republic of Korea
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Ho-Sung Yoon
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
- Advanced Bio-Resource Research Center, Kyungpook National University, Daegu, Republic of Korea
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
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Han J, Asano K, Matsumoto T, Yamada R, Ogino H. Engineering acyl-ACP reductase with fusion tags enhances alka(e)ne synthesis in Escherichia coli. Enzyme Microb Technol 2023; 168:110262. [PMID: 37224590 DOI: 10.1016/j.enzmictec.2023.110262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/26/2023]
Abstract
Alka(e)nes are high-value chemicals with a potentially broad range of industrial applications because of their following advantages: (1) chemical and structural resemblance to petroleum hydrocarbons and (2) higher energy density and hydrophobicity than those of other biofuels. The low yield of bio-alka(e)nes, however, hinders their commercial application. The activity and solubility of acyl carrier protein (ACP) reductase (AAR) affect alka(e)ne biosynthesis in cyanobacteria. The enhancement of the activity and concentration of soluble AAR through genetic and process engineering can improve bio-alka(e)ne yield. Although fusion tags are used to enhance the expression or solubility of recombinant proteins, their effectiveness in improving the production of bio-alka(e)nes has not yet been reported. Fusion tags can be used to improve the amount or activity of soluble AAR in Escherichia coli and to increase the yield of alka(e)nes in E. coli cells co-expressing aldehyde deformylating oxygenase (ADO). Hence, in the present study, histidine (His6/His12), thioredoxin (Trx), maltose-binding protein (MBP), and N-utilization substance (NusA) were used as AAR fusion tags. The strain expressing SeAAR with His12 tag and NpADO showed a 7.2-fold higher yield of alka(e)nes than the strain expressing AAR without fusion tag and NpADO. The highest titer of alka(e)nes (194.78 mg/L) was achieved with the His12 tag.
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Affiliation(s)
- Jiahu Han
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Koki Asano
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Takuya Matsumoto
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
| | - Ryosuke Yamada
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Hiroyasu Ogino
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
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5
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Biosynthesis of alkanes/alkenes from fatty acids or derivatives (triacylglycerols or fatty aldehydes). Biotechnol Adv 2022; 61:108045. [DOI: 10.1016/j.biotechadv.2022.108045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/27/2022]
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Wohlgemuth R. Selective Biocatalytic Defunctionalization of Raw Materials. CHEMSUSCHEM 2022; 15:e202200402. [PMID: 35388636 DOI: 10.1002/cssc.202200402] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Biobased raw materials, such as carbohydrates, amino acids, nucleotides, or lipids contain valuable functional groups with oxygen and nitrogen atoms. An abundance of many functional groups of the same type, such as primary or secondary hydroxy groups in carbohydrates, however, limits the synthetic usefulness if similar reactivities cannot be differentiated. Therefore, selective defunctionalization of highly functionalized biobased starting materials to differentially functionalized compounds can provide a sustainable access to chiral synthons, even in case of products with fewer functional groups. Selective defunctionalization reactions, without affecting other functional groups of the same type, are of fundamental interest for biocatalytic reactions. Controlled biocatalytic defunctionalizations of biobased raw materials are attractive for obtaining valuable platform chemicals and building blocks. The biocatalytic removal of functional groups, an important feature of natural metabolic pathways, can also be utilized in a systemic strategy for sustainable metabolite synthesis.
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Affiliation(s)
- Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology Łódź, 90-537, Lodz, Poland
- Swiss Coordination Committee Biotechnology (SKB), 8002, Zurich, Switzerland
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Liu Y, Benitez MG, Chen J, Harrison E, Khusnutdinova AN, Mahadevan R. Opportunities and Challenges for Microbial Synthesis of Fatty Acid-Derived Chemicals (FACs). Front Bioeng Biotechnol 2021; 9:613322. [PMID: 33575251 PMCID: PMC7870715 DOI: 10.3389/fbioe.2021.613322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
Global warming and uneven distribution of fossil fuels worldwide concerns have spurred the development of alternative, renewable, sustainable, and environmentally friendly resources. From an engineering perspective, biosynthesis of fatty acid-derived chemicals (FACs) is an attractive and promising solution to produce chemicals from abundant renewable feedstocks and carbon dioxide in microbial chassis. However, several factors limit the viability of this process. This review first summarizes the types of FACs and their widely applications. Next, we take a deep look into the microbial platform to produce FACs, give an outlook for the platform development. Then we discuss the bottlenecks in metabolic pathways and supply possible solutions correspondingly. Finally, we highlight the most recent advances in the fast-growing model-based strain design for FACs biosynthesis.
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Affiliation(s)
- Yilan Liu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Mauricio Garcia Benitez
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Jinjin Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Emma Harrison
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Anna N. Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, Canada
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8
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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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Hu Y, Zhu Z, Nielsen J, Siewers V. Engineering Saccharomyces cerevisiae cells for production of fatty acid-derived biofuels and chemicals. Open Biol 2020; 9:190049. [PMID: 31088249 PMCID: PMC6544985 DOI: 10.1098/rsob.190049] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The yeast Saccharomyces cerevisiae is a widely used cell factory for the production of fuels and chemicals, in particular ethanol, a biofuel produced in large quantities. With a need for high-energy-density fuels for jets and heavy trucks, there is, however, much interest in the biobased production of hydrocarbons that can be derived from fatty acids. Fatty acids also serve as precursors to a number of oleochemicals and hence provide interesting platform chemicals. Here, we review the recent strategies applied to metabolic engineering of S. cerevisiae for the production of fatty acid-derived biofuels and for improvement of the titre, rate and yield (TRY). This includes, for instance, redirection of the flux towards fatty acids through engineering of the central carbon metabolism, balancing the redox power and varying the chain length of fatty acids by enzyme engineering. We also discuss the challenges that currently hinder further TRY improvements and the potential solutions in order to meet the requirements for commercial application.
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Affiliation(s)
- Yating Hu
- 1 Department of Biology and Biological Engineering, Chalmers University of Technology , 41296 Gothenburg , Sweden.,2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , 41296 Gothenburg , Sweden
| | - Zhiwei Zhu
- 1 Department of Biology and Biological Engineering, Chalmers University of Technology , 41296 Gothenburg , Sweden.,2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , 41296 Gothenburg , Sweden
| | - Jens Nielsen
- 1 Department of Biology and Biological Engineering, Chalmers University of Technology , 41296 Gothenburg , Sweden.,2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , 41296 Gothenburg , Sweden.,3 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , 2800 Kgs Lyngby , Denmark.,4 BioInnovation Institute , Ole Måløes Vej, 2200 Copenhagen N , Denmark
| | - Verena Siewers
- 1 Department of Biology and Biological Engineering, Chalmers University of Technology , 41296 Gothenburg , Sweden.,2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , 41296 Gothenburg , Sweden
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Liu Y, Chen J, Khusnutdinova AN, Correia K, Diep P, Batyrova KA, Nemr K, Flick R, Stogios P, Yakunin AF, Mahadevan R. A novel C-terminal degron identified in bacterial aldehyde decarbonylases using directed evolution. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:114. [PMID: 32612677 PMCID: PMC7325246 DOI: 10.1186/s13068-020-01753-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/16/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Aldehyde decarbonylases (ADs), which convert acyl aldehydes into alkanes, supply promising solution for producing alkanes from renewable feedstock. However the instability of ADs impedes their further application. Therefore, the current study aimed to investigate the degradation mechanism of ADs and engineer it towards high stability. RESULTS Here, we describe the discovery of a degradation tag (degron) in the AD from marine cyanobacterium Prochlorococcus marinus using error-prone PCR-based directed evolution system. Bioinformatic analysis revealed that this C-terminal degron is common in bacterial ADs and identified a conserved C-terminal motif, RMSAYGLAAA, representing the AD degron (ADcon). Furthermore, we demonstrated that the ATP-dependent proteases ClpAP and Lon are involved in the degradation of AD-tagged proteins in E. coli, thereby limiting alkane production. Deletion or modification of the degron motif increased alkane production in vivo. CONCLUSION This work revealed the presence of a novel degron in bacterial ADs responsible for its instability. The in vivo experiments proved eliminating or modifying the degron could stabilize AD, thereby producing higher titers of alkanes.
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Affiliation(s)
- Yilan Liu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Jinjin Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Anna N. Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Kevin Correia
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Khorcheska A. Batyrova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Kayla Nemr
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Peter Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, LL57 2UW UK
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
- Institute of Biomedical Engineering, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
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11
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Continuous photoproduction of hydrocarbon drop-in fuel by microbial cell factories. Sci Rep 2019; 9:13713. [PMID: 31548626 PMCID: PMC6757031 DOI: 10.1038/s41598-019-50261-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 09/09/2019] [Indexed: 11/20/2022] Open
Abstract
Use of microbes to produce liquid transportation fuels is not yet economically viable. A key point to reduce production costs is the design a cell factory that combines the continuous production of drop-in fuel molecules with the ability to recover products from the cell culture at low cost. Medium-chain hydrocarbons seem ideal targets because they can be produced from abundant fatty acids and, due to their volatility, can be easily collected in gas phase. However, pathways used to produce hydrocarbons from fatty acids require two steps, low efficient enzymes and/or complex electron donors. Recently, a new hydrocarbon-forming route involving a single enzyme called fatty acid photodecarboxylase (FAP) was discovered in microalgae. Here, we show that in illuminated E. coli cultures coexpression of FAP and a medium-chain fatty acid thioesterase results in continuous release of volatile hydrocarbons. Maximum hydrocarbon productivity was reached under low/medium light while higher irradiance resulted in decreased amounts of FAP. It was also found that the production rate of hydrocarbons was constant for at least 5 days and that 30% of total hydrocarbons could be collected in the gas phase of the culture. This work thus demonstrates that the photochemistry of the FAP can be harnessed to design a simple cell factory that continuously produces hydrocarbons easy to recover and in pure form.
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Bruder S, Moldenhauer EJ, Lemke RD, Ledesma-Amaro R, Kabisch J. Drop-in biofuel production using fatty acid photodecarboxylase from Chlorella variabilis in the oleaginous yeast Yarrowia lipolytica. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:202. [PMID: 31462926 PMCID: PMC6708191 DOI: 10.1186/s13068-019-1542-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/10/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND Oleaginous yeasts are potent hosts for the renewable production of lipids and harbor great potential for derived products, such as biofuels. Several promising processes have been described that produce hydrocarbon drop-in biofuels based on fatty acid decarboxylation and fatty aldehyde decarbonylation. Unfortunately, besides fatty aldehyde toxicity and high reactivity, the most investigated enzyme, aldehyde-deformylating oxygenase, shows unfavorable catalytic properties which hindered high yields in previous metabolic engineering approaches. RESULTS To demonstrate an alternative alkane production pathway for oleaginous yeasts, we describe the production of diesel-like, odd-chain alkanes and alkenes, by heterologously expressing a recently discovered light-driven oxidase from Chlorella variabilis (CvFAP) in Yarrowia lipolytica. Initial experiments showed that only strains engineered to have an increased pool of free fatty acids were susceptible to sufficient decarboxylation. Providing these strains with glucose and light in a synthetic medium resulted in titers of 10.9 mg/L of hydrocarbons. Using custom 3D printed labware for lighting bioreactors, and an automated pulsed glycerol fed-batch strategy, intracellular titers of 58.7 mg/L were achieved. The production of odd-numbered alkanes and alkenes with a length of 17 and 15 carbons shown in previous studies could be confirmed. CONCLUSIONS Oleaginous yeasts such as Yarrowia lipolytica can transform renewable resources such as glycerol into fatty acids and lipids. By heterologously expressing a fatty acid photodecarboxylase from the algae Chlorella variabilis hydrocarbons were produced in several scales from microwell plate to 400 mL bioreactors. The lighting turned out to be a crucial factor in terms of growth and hydrocarbon production, therefore, the evaluation of different conditions was an important step towards a tailor-made process. In general, the developed bioprocess shows a route to the renewable production of hydrocarbons for a variety of applications ranging from being substrates for further enzymatic or chemical modification or as a drop-in biofuel blend.
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Affiliation(s)
- Stefan Bruder
- Computer-Aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 12, 64287 Darmstadt, Germany
| | - Eva Johanna Moldenhauer
- Computer-Aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 12, 64287 Darmstadt, Germany
| | - Robert Denis Lemke
- Computer-Aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 12, 64287 Darmstadt, Germany
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Johannes Kabisch
- Computer-Aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 12, 64287 Darmstadt, Germany
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Kudo H, Hayashi Y, Arai M. Identification of non-conserved residues essential for improving the hydrocarbon-producing activity of cyanobacterial aldehyde-deformylating oxygenase. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:89. [PMID: 31015863 PMCID: PMC6469105 DOI: 10.1186/s13068-019-1409-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 03/14/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Cyanobacteria produce hydrocarbons corresponding to diesel fuels by means of aldehyde-deformylating oxygenase (ADO). ADO catalyzes a difficult and unusual reaction in the conversion of aldehydes to hydrocarbons and has been widely used for biofuel production in metabolic engineering; however, its activity is low. A comparison of the amino acid sequences of highly active and less active ADOs will elucidate non-conserved residues that are essential for improving the hydrocarbon-producing activity of ADOs. RESULTS Here, we measured the activities of ADOs from 10 representative cyanobacterial strains by expressing each of them in Escherichia coli and quantifying the hydrocarbon yield and amount of soluble ADO. We demonstrated that the activity was highest for the ADO from Synechococcus elongatus PCC 7942 (7942ADO). In contrast, the ADO from Gloeobacter violaceus PCC 7421 (7421ADO) had low activity but yielded high amounts of soluble protein, resulting in a high production level of hydrocarbons. By introducing 37 single amino acid substitutions at the non-conserved residues of the less active ADO (7421ADO) to make its sequence more similar to that of the highly active ADO (7942ADO), we found 20 mutations that improved the activity of 7421ADO. In addition, 13 other mutations increased the amount of soluble ADO while maintaining more than 80% of wild-type activity. Correlation analysis showed a solubility-activity trade-off in ADO, in which activity was negatively correlated with solubility. CONCLUSIONS We succeeded in identifying non-conserved residues that are essential for improving ADO activity. Our results may be useful for generating combinatorial mutants of ADO that have both higher activity and higher amounts of the soluble protein in vivo, thereby producing higher yields of biohydrocarbons.
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Affiliation(s)
- Hisashi Kudo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902 Japan
| | - Yuuki Hayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902 Japan
| | - Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902 Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902 Japan
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14
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Wang J, Yu H, Zhu K. Employing metabolic engineered lipolytic microbial platform for 1-alkene one-step conversion. BIORESOURCE TECHNOLOGY 2018; 263:172-179. [PMID: 29738980 DOI: 10.1016/j.biortech.2018.04.119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/29/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
1-Alkenes are traditionally used as basic chemicals with great importance. Biosynthetic 1-alkenes also have the potential to serve as biofuels. In this study, we engineered a Pseudomonas lipolytic microbial platform for 1-alkene production using hydrophobic substrate as sole carbon source. Fatty acid decarboxylase UndA and UndB were cloned and expressed, which successfully produced 1-alkenes. Optimal culturing temperature and the interruption of competitive pathway were proven to be beneficial to 1-alkene synthesis. Chromosomal integration of UndB conferred 177.8 mg/L 1-alkenes (mainly 1-undecene) in lauric acid medium and 128.9 mg/L 1-alkenes (mainly 1-pentadecene) in palm oil medium. Thioesterase expression, adjustments of fatty acid degradation pathway and a second copy of UndB improved 1-alkene titer to 1102.6 mg/L using lauric acid and 778.4 mg/L using palm oil. All in all, this study offers the first demonstration of lipolytic microbial 1-alkene producing platform with highest reported 1-alkene product titer up to date.
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Affiliation(s)
- Juli Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiying Yu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kun Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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15
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Arai M, Hayashi Y, Kudo H. Cyanobacterial Enzymes for Bioalkane Production. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1080:119-154. [PMID: 30091094 DOI: 10.1007/978-981-13-0854-3_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyanobacterial biosynthesis of alkanes is an attractive way of producing substitutes for petroleum-based fuels. Key enzymes for bioalkane production in cyanobacteria are acyl-ACP reductase (AAR) and aldehyde-deformylating oxygenase (ADO). AAR catalyzes the reduction of the fatty acyl-ACP/CoA substrates to fatty aldehydes, which are then converted into alkanes/alkenes by ADO. These enzymes have been widely used for biofuel production by metabolic engineering of cyanobacteria and other organisms. However, both proteins, particularly ADO, have low enzymatic activities, and their catalytic activities are desired to be improved for use in biofuel production. Recently, progress has been made in the basic sciences and in the application of AAR and ADO in alkane production. This chapter provides an overview of recent advances in the study of the structure and function of AAR and ADO, protein engineering of these enzymes for improving activity and modifying substrate specificities, and examples of metabolic engineering of cyanobacteria and other organisms using AAR and ADO for biofuel production.
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Affiliation(s)
- Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.
| | - Yuuki Hayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Hisashi Kudo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
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16
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Zhang Y, Nielsen J, Liu Z. Metabolic engineering ofSaccharomyces cerevisiaefor production of fatty acid–derived hydrocarbons. Biotechnol Bioeng 2018; 115:2139-2147. [DOI: 10.1002/bit.26738] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 05/23/2018] [Accepted: 05/31/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Yiming Zhang
- Beijing Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical Technology Beijing China
| | - Jens Nielsen
- Beijing Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical Technology Beijing China
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburg Sweden
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Hørsholm Denmark
| | - Zihe Liu
- Beijing Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical Technology Beijing China
- College of Life Science and Technology, Beijing University of Chemical TechnologyBeijing China
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17
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Wang J, Zhu K. Microbial production of alka(e)ne biofuels. Curr Opin Biotechnol 2018; 50:11-18. [DOI: 10.1016/j.copbio.2017.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 08/14/2017] [Accepted: 08/14/2017] [Indexed: 10/18/2022]
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18
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Zhou YJ, Hu Y, Zhu Z, Siewers V, Nielsen J. Engineering 1-Alkene Biosynthesis and Secretion by Dynamic Regulation in Yeast. ACS Synth Biol 2018; 7:584-590. [PMID: 29284088 DOI: 10.1021/acssynbio.7b00338] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Microbial production of fatty acid-derived hydrocarbons offers a great opportunity to sustainably supply biofuels and oleochemicals. One challenge is to achieve a high production rate. Besides, low efficiency in secretion will cause high separation costs, and it is therefore desirable to have product secretion. Here, we engineered the budding yeast Saccharomyces cerevisiae to produce and secrete 1-alkenes by manipulation of the fatty acid metabolism, enzyme selection, engineering the electron transfer system and expressing a transporter. Furthermore, we implemented a dynamic regulation strategy to control the expression of membrane enzyme and transporter, which improved 1-alkene production and cell growth by relieving the possible toxicity of overexpressed membrane proteins. With these efforts, the engineered yeast cell factory produced 35.3 mg/L 1-alkenes with more than 80% being secreted. This represents a 10-fold improvement compared with earlier reported hydrocarbon production by S. cerevisiae.
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Affiliation(s)
- Yongjin J. Zhou
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
| | - Yating Hu
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Zhiwei Zhu
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Verena Siewers
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 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, Kemivägen 10, 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-2800 Kgs. Lyngby, Denmark
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Steps towards 'drop-in' biofuels: focusing on metabolic pathways. Curr Opin Biotechnol 2017; 53:26-32. [PMID: 29207330 DOI: 10.1016/j.copbio.2017.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 12/20/2022]
Abstract
The past decade has witnessed rapid advance in microbial production of 'drop-in' biofuels from renewable resources. Various biosynthetic pathways have been constructed to produce biofuels with diverse structures, and multiple metabolic engineering strategies have been developed to increase biofuel titers, yields, productivities and system robustness. In this review, we intend to give a brief but comprehensive overview of the most recent progresses on four essential pathways leading to 'drop-in' biofuel production, with an emphasis on the metabolic pathway efficiencies and biofuel structures. Furthermore, we also provide an insightful discussion on optimization strategies to improve the robustness of the microbial platforms for biofuel production.
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20
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Engineering microbial fatty acid metabolism for biofuels and biochemicals. Curr Opin Biotechnol 2017; 50:39-46. [PMID: 29101852 DOI: 10.1016/j.copbio.2017.10.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 11/22/2022]
Abstract
Traditional oleochemical industry chemically processes animal fats and plant oils to produce detergents, lubricants, biodiesel, plastics, coatings, and other products. Biotechnology offers an alternative process, where the same oleochemicals can be produced from abundant biomass feedstocks using microbial catalysis. This review summarizes the recent advances in the engineering of microbial metabolism for production of fatty acid-derived products. We highlight the efforts in engineering the central carbon metabolism, redox metabolism, controlling the chain length of the products, and obtaining metabolites with different functionalities. The prospects of commercializing microbial oleochemicals are also discussed.
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21
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Fernandez-Moya R, Da Silva NA. Engineering Saccharomyces cerevisiae for high-level synthesis of fatty acids and derived products. FEMS Yeast Res 2017; 17:4111148. [DOI: 10.1093/femsyr/fox071] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/10/2017] [Indexed: 01/16/2023] Open
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