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Zhu F, Xia L, Wen J, Zhang L. Recent Advances in the Biosynthesis of Mid- and Long-Chain Dicarboxylic Acids Using Terminally Oxidizing Unconventional Yeasts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:19566-19580. [PMID: 39207200 DOI: 10.1021/acs.jafc.4c05028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
As high-performance monomers for the manufacture of polyamide materials, mid- and long-chain dicarboxylic acids (DCAi, i ≥ 6) have received extensive attention from researchers. Biosynthesis is gradually replacing chemical synthesis due to its outstanding advantages in the industrial production of mid- and long-chain dicarboxylic acids, which is mostly achieved by using the strong terminal oxidation ability of nonmodel microorganisms such as Candida tropicalis to oxidize hydrophobic substrates such as alkanes. Here, we first summarize the metabolic pathways of oxidative alkane conversion into dicarboxylic acid by terminally oxidizing unconventional yeasts and the corresponding metabolic engineering strategies. Then, we summarize the research progress on new dicarboxylic acid production processes. Finally, the future development directions in the biosynthesis of mid- and long-chain dicarboxylic acids are prospected from synthetic biology and bioprocess engineering, which can also provide a reference for the synthesis of other biobased chemicals and biomaterials.
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Affiliation(s)
- Fuzhou Zhu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Li Xia
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Lin Zhang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian 116045, China
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2
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Pham NN, Chang CW, Chang YH, Tu Y, Chou JY, Wang HY, Hu YC. Rational genome and metabolic engineering of Candida viswanathii by split CRISPR to produce hundred grams of dodecanedioic acid. Metab Eng 2023; 77:76-88. [PMID: 36948241 DOI: 10.1016/j.ymben.2023.03.007] [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: 06/09/2022] [Revised: 01/29/2023] [Accepted: 03/14/2023] [Indexed: 03/24/2023]
Abstract
Candida viswanathii is a promising cell factory for producing dodecanedioic acid (DDA) and other long chain dicarboxylic acids. However, metabolic engineering of C. viswanathii is difficult partly due to the lack of synthetic biology toolkits. Here we developed CRISPR-based approaches for rational genome and metabolic engineering of C. viswanathii. We first optimized the CRISPR system and protocol to promote the homozygous gene integration efficiency to >60%. We also designed a split CRISPR system for one-step integration of multiple genes into C. viswanathii. We uncovered that co-expression of CYP52A19, CPRb and FAO2 that catalyze different steps in the biotransformation enhances DDA production and abolishes accumulation of intermediates. We also unveiled that co-expression of additional enzyme POS5 further promotes DDA production and augments cell growth. We harnessed the split CRISPR system to co-integrate these 4 genes (13.6 kb) into C. viswanathii and generated a stable strain that doubles the DDA titer (224 g/L), molar conversion (83%) and productivity (1.87 g/L/h) when compared with the parent strain. This study altogether identifies appropriate enzymes/promoters to augment dodecane conversion to DDA and implicates the potential of split CRISPR system for metabolic engineering of C. viswanathii.
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Affiliation(s)
- Nam Ngoc Pham
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Chin-Wei Chang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Hao Chang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi Tu
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - June-Yen Chou
- Innovation and R&D Division, Chang Chun Group, Taipei, Taiwan; Dairen Chemical Corp, Taipei, Taiwan
| | | | - Yu-Chen Hu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan; Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan.
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3
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Price CL, Warrilow AGS, Rolley NJ, Parker JE, Thoss V, Kelly DE, Corcionivoschi N, Kelly SL. Cytochrome P450 168A1 from Pseudomonas aeruginosa is involved in the hydroxylation of biologically relevant fatty acids. PLoS One 2022; 17:e0265227. [PMID: 35312722 PMCID: PMC8936499 DOI: 10.1371/journal.pone.0265227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 02/24/2022] [Indexed: 11/26/2022] Open
Abstract
The cytochrome P450 CYP168A1 from Pseudomonas aeruginosa was cloned and expressed in Escherichia coli followed by purification and characterization of function. CYP168A1 is a fatty acid hydroxylase that hydroxylates saturated fatty acids, including myristic (0.30 min-1), palmitic (1.61 min-1) and stearic acids (1.24 min-1), at both the ω-1- and ω-2-positions. However, CYP168A1 only hydroxylates unsaturated fatty acids, including palmitoleic (0.38 min-1), oleic (1.28 min-1) and linoleic acids (0.35 min-1), at the ω-1-position. CYP168A1 exhibited a catalytic preference for palmitic, oleic and stearic acids as substrates in keeping with the phosphatidylcholine-rich environment deep in the lung that is colonized by P. aeruginosa.
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Affiliation(s)
- Claire L. Price
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
| | - Andrew G. S. Warrilow
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
| | - Nicola J. Rolley
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
| | - Josie E. Parker
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
| | - Vera Thoss
- Plant Chemistry Group, School of Chemistry, Bangor University, Bangor, Gwynedd, Wales, United Kingdom
| | - Diane E. Kelly
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
| | - Nicolae Corcionivoschi
- Agri-Food and Biosciences Institute, Veterinary Science Division, Bacteriology Branch, Stoney Road, Stormont, Belfast, Northern Ireland, United Kingdom
- Faculty of Bioengineering of Animal Resources, Banat University of Agricultural Sciences and Veterinary Medicine, King Michael I of Romania, Timisoara, Romania
| | - Steven L. Kelly
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
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Sun J, Karuppiah V, Li Y, Pandian S, Kumaran S, Chen J. Role of cytochrome P450 genes of Trichoderma atroviride T23 on the resistance and degradation of dichlorvos. CHEMOSPHERE 2022; 290:133173. [PMID: 34914953 DOI: 10.1016/j.chemosphere.2021.133173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 11/28/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
The Trichoderma has been extensively used to degrade the xenobiotics. In the present study, thirty-nine open reading frames of cytochrome P450 genes from T. atroviride T23 genome was cloned and it was found to be distributed in 29 families under 21 clades. Among them, 21 cytochrome P450 genes were involved in the degradation of xenobiotics. The quantitative expression of P450 genes in the presence of dichlorvos at 24 h showed 7 different expression patterns in the presence of 100 μg/mL, 300 μg/mL, 500 μg/mL and 1000 μg/mL of dichlorvos. The relative expression of P450 genes belongs to the family of TaCyp548, TaCyp620, TaCyp52, TaCyp528, TaCyp504 were upregulated at least 1-fold compared to the control. Significantly, the deletion of TaCyp548-2 reduced the concentration of 2,2-dichloroethanol. Further, it was observed that TaCyp548-2 belongs to the ω-hydroxylase family was responsible for fatty acid oxidation and the production of acetic acid, propionic acid, isobutyric acid and dibutyric acid to convert the 2,2-dichloroethanol to 2,2-dichloroethanolacetate. This study evidenced the involvement of Trichoderma P450 genes on dichlorvos degradation as an environmentally significant Biological control agent for the sustainable agriculture.
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Affiliation(s)
- Jianan Sun
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China; The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China
| | - Valliappan Karuppiah
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China; The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China
| | - Yaqian Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China; The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China
| | - Sivakumar Pandian
- School of Petroleum Technology, Pandit Deendayal Energy University, Gandhinagar, 382421, Gujarat, India
| | - Subramanian Kumaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600119, Tamilnadu, India
| | - Jie Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China; The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China.
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Park H, Bak D, Jeon W, Jang M, Ahn JO, Choi KY. Engineering of CYP153A33 With Enhanced Ratio of Hydroxylation to Overoxidation Activity in Whole-Cell Biotransformation of Medium-Chain 1-Alkanols. Front Bioeng Biotechnol 2022; 9:817455. [PMID: 35059390 PMCID: PMC8764613 DOI: 10.3389/fbioe.2021.817455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/13/2021] [Indexed: 12/21/2022] Open
Abstract
α,ω-Dodecanediol is a versatile material that has been widely used not only as an adhesive and crosslinking reagent, but also as a building block in the pharmaceutical and polymer industries. The biosynthesis of α,ω-dodecanediol from fatty derivatives, such as dodecane and dodecanol, requires an ω-specific hydroxylation step using monooxygenase enzymes. An issue with the whole-cell biotransformation of 1-dodecanol using cytochrome P450 monooxygenase (CYP) with ω-specific hydroxylation activity was the low conversion and production of the over-oxidized product of dodecanoic acid. In this study, CYP153A33 from Marinobacter aquaeolei was engineered to obtain higher ω-specific hydroxylation activity through site-directed mutagenesis. The target residue was mutated to increase flux toward α,ω-dodecanediol synthesis, while reducing the generation of the overoxidation product of dodecanoic acid and α,ω-dodecanedioic acid. Among the evaluated variants, CYP153A33 P136A showed a significant increase in 1-dodecanol conversion, i.e., 71.2% (7.12 mM from 10 mM 1-dodecanol), with an increased hydroxylation to over-oxidation activity ratio, i.e., 32.4. Finally, the applicability of this engineered enzyme for ω-specific hydroxylation against several 1-alkanols, i.e., from C6 to C16, was investigated and discussed based on the structure-activity relationship.
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Affiliation(s)
- Hyuna Park
- Department of Environmental Engineering, College of Engineering, Ajou University, Suwon, South Korea
| | - Doyeong Bak
- Department of Environmental and Safety Engineering, College of Engineering, Ajou University, Suwon, South Korea
| | - Wooyoung Jeon
- Biotechnology Process Engineering Center, Korea Research Institute of Biosceince and Biotechnology (KRIBB), Cheongju, South Korea
| | - Minjung Jang
- Biotechnology Process Engineering Center, Korea Research Institute of Biosceince and Biotechnology (KRIBB), Cheongju, South Korea
| | - Jung-Oh Ahn
- Biotechnology Process Engineering Center, Korea Research Institute of Biosceince and Biotechnology (KRIBB), Cheongju, South Korea.,Department of Bioprocess Engineering, University of Science and Technology (UST), Daejeon, South Korea
| | - Kwon-Young Choi
- Department of Environmental Engineering, College of Engineering, Ajou University, Suwon, South Korea.,Department of Environmental and Safety Engineering, College of Engineering, Ajou University, Suwon, South Korea
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6
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Bauwelinck J, Caluwé M, Wijnants M, Wittner N, Broos W, Dries J, Akkermans V, Tavernier S, Cornet I. Chocolate industry side streams as a valuable feedstock for microbial long-chain dicarboxylic acid production. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2020.107888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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7
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Whole-Cell Biotransformation of 1,12-Dodecanedioic Acid from Coconut Milk Factory Wastewater by Recombinant CYP52A17SS Expressing Saccharomyces cerevisiae. Processes (Basel) 2020. [DOI: 10.3390/pr8080969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Biotransformation of fatty acids from renewable wastewater as feedstock to value-added chemicals is a fascinating commercial opportunity. α,ω-Dicarboxylic acids (DCAs) are building blocks in many industries, such as polymers, cosmetic intermediates, and pharmaceuticals, and can be obtained by chemical synthesis under extreme conditions. However, biological synthesis can replace the traditional chemical synthesis using cytochrome P450 enzymes to oxidize fatty acids to DCAs. Saccharomyces cerevisiae BY(2R)/pYeDP60-CYP52A17SS (BCM), a transgenic strain expressing the galactose-inducible CYP52A17SS cytochrome P450 enzyme, was able to grow in a coconut milk factory wastewater (CCW) medium and produced 12-hydroxydodecanoic acid (HDDA) and 1,12-dodecanedioic acid (DDA). The supplementation of CCW with 10 g/L yeast extract and 20 g/L peptone (YPCCW) markedly increased the yeast growth rate and the yields of 12-HDDA and 1,12-DDA, with the highest levels of approximately 60 and 38 µg/L, respectively, obtained at 30 °C and pH 5. The incubation temperature and medium pH strongly influenced the yeast growth and 1,12-DDA yield, with the highest 1,12-DDA formation at 30 °C and pH 5–5.5. Hence, the S. cerevisiae BCM strain can potentially be used for producing value-added products from CCW.
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8
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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9
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Whole-cell biocatalysis using cytochrome P450 monooxygenases for biotransformation of sustainable bioresources (fatty acids, fatty alkanes, and aromatic amino acids). Biotechnol Adv 2020; 40:107504. [PMID: 31926255 DOI: 10.1016/j.biotechadv.2020.107504] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/09/2019] [Accepted: 01/06/2020] [Indexed: 12/25/2022]
Abstract
Cytochrome P450s (CYPs) are heme-thiolated enzymes that catalyze the oxidation of CH bonds in a regio and stereoselective manner. Activation of the non-activated carbon atom can be further enhanced by multistep chemo-enzymatic reactions; moreover, several useful chemicals can be synthesized to provide alternative organic synthesis routes. Given their versatile functionality, CYPs show promise in a number of biotechnological fields. Recently, various CYPs, along with their sequences and functionalities, have been identified owing to rapid developments in sequencing technology and molecular biotechnology. In addition to these discoveries, attempts have been made to utilize CYPs to industrially produce biochemicals from available and sustainable bioresources such as oil, amino acids, carbohydrates, and lignin. Here, these accomplishments, particularly those involving the use of CYP enzymes as whole-cell biocatalysts for bioresource biotransformation, will be reviewed. Further, recently developed biotransformation pathways that result in gram-scale yields of fatty acids and fatty alkanes as well as aromatic amino acids, which depend on the hosts used for CYP expression, and the nature of the multistep reactions will be discussed. These pathways are similar regardless of whether the hosts are CYP-producing or non-CYP-producing; the limitations of these methods and the ways to overcome them are reviewed here.
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10
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Sultana N, Guria C, Saxena VK. Selective conversion of stearic acid into high-added value octadecanedioic acid using air and transition metal acetate bromide catalyst: Kinetics, pathway and process optimization. ARAB J CHEM 2020. [DOI: 10.1016/j.arabjc.2018.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
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11
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Li G, Huang D, Sui X, Li S, Huang B, Zhang X, Wu H, Deng Y. Advances in microbial production of medium-chain dicarboxylic acids for nylon materials. REACT CHEM ENG 2020. [DOI: 10.1039/c9re00338j] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Medium-chain dicarboxylic acids (MDCAs) are widely used in the production of nylon materials, and among which, succinic, glutaric, adipic, pimelic, suberic, azelaic and sebacic acids are particularly important for that purpose.
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Affiliation(s)
- Guohui Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
| | - Dixuan Huang
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
| | - Xue Sui
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
| | - Shiyun Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
| | - Bing Huang
- State Key Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology
| | - Xiaojuan Zhang
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
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12
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Biochemical and structural insights into the cytochrome P450 reductase from Candida tropicalis. Sci Rep 2019; 9:20088. [PMID: 31882753 PMCID: PMC6934812 DOI: 10.1038/s41598-019-56516-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/04/2019] [Indexed: 12/15/2022] Open
Abstract
Cytochrome P450 reductases (CPRs) are diflavin oxidoreductases that supply electrons to type II cytochrome P450 monooxygenases (CYPs). In addition, it can also reduce other proteins and molecules, including cytochrome c, ferricyanide, and different drugs. Although various CPRs have been functionally and structurally characterized, the overall mechanism and its interaction with different redox acceptors remain elusive. One of the main problems regarding electron transfer between CPRs and CYPs is the so-called “uncoupling”, whereby NAD(P)H derived electrons are lost due to the reduced intermediates’ (FAD and FMN of CPR) interaction with molecular oxygen. Additionally, the decay of the iron-oxygen complex of the CYP can also contribute to loss of reducing equivalents during an unproductive reaction cycle. This phenomenon generates reactive oxygen species (ROS), leading to an inefficient reaction. Here, we present the study of the CPR from Candida tropicalis (CtCPR) lacking the hydrophobic N-terminal part (Δ2–22). The enzyme supports the reduction of cytochrome c and ferricyanide, with an estimated 30% uncoupling during the reactions with cytochrome c. The ROS produced was not influenced by different physicochemical conditions (ionic strength, pH, temperature). The X-ray structures of the enzyme were solved with and without its cofactor, NADPH. Both CtCPR structures exhibited the closed conformation. Comparison with the different solved structures revealed an intricate ionic network responsible for the regulation of the open/closed movement of CtCPR.
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13
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Ebrecht AC, van der Bergh N, Harrison STL, Smit MS, Sewell BT, Opperman DJ. Biochemical and structural insights into the cytochrome P450 reductase from Candida tropicalis. Sci Rep 2019; 9:20088. [PMID: 31882753 DOI: 10.1101/711317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/04/2019] [Indexed: 05/28/2023] Open
Abstract
Cytochrome P450 reductases (CPRs) are diflavin oxidoreductases that supply electrons to type II cytochrome P450 monooxygenases (CYPs). In addition, it can also reduce other proteins and molecules, including cytochrome c, ferricyanide, and different drugs. Although various CPRs have been functionally and structurally characterized, the overall mechanism and its interaction with different redox acceptors remain elusive. One of the main problems regarding electron transfer between CPRs and CYPs is the so-called "uncoupling", whereby NAD(P)H derived electrons are lost due to the reduced intermediates' (FAD and FMN of CPR) interaction with molecular oxygen. Additionally, the decay of the iron-oxygen complex of the CYP can also contribute to loss of reducing equivalents during an unproductive reaction cycle. This phenomenon generates reactive oxygen species (ROS), leading to an inefficient reaction. Here, we present the study of the CPR from Candida tropicalis (CtCPR) lacking the hydrophobic N-terminal part (Δ2-22). The enzyme supports the reduction of cytochrome c and ferricyanide, with an estimated 30% uncoupling during the reactions with cytochrome c. The ROS produced was not influenced by different physicochemical conditions (ionic strength, pH, temperature). The X-ray structures of the enzyme were solved with and without its cofactor, NADPH. Both CtCPR structures exhibited the closed conformation. Comparison with the different solved structures revealed an intricate ionic network responsible for the regulation of the open/closed movement of CtCPR.
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Affiliation(s)
- Ana C Ebrecht
- Department of Microbial, Biochemical, and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
- South African DST-NRF Centre of Excellence in Catalysis (c*Change), University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Naadia van der Bergh
- Centre for Bioprocess Engineering Research (CeBER), Department of Chemical Engineering, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
- South African DST-NRF Centre of Excellence in Catalysis (c*Change), University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Susan T L Harrison
- Centre for Bioprocess Engineering Research (CeBER), Department of Chemical Engineering, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
- South African DST-NRF Centre of Excellence in Catalysis (c*Change), University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Martha S Smit
- Department of Microbial, Biochemical, and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
- South African DST-NRF Centre of Excellence in Catalysis (c*Change), University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - B Trevor Sewell
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7700, South Africa.
| | - Diederik J Opperman
- Department of Microbial, Biochemical, and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa.
- South African DST-NRF Centre of Excellence in Catalysis (c*Change), University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa.
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14
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De Graeve M, Van de Velde I, Saey L, Chys M, Oorts H, Kahriman H, Mincke S, Stevens C, De Maeseneire SL, Roelants SLKW, Soetaert WKG. Production of long-chain hydroxy fatty acids by Starmerella bombicola. FEMS Yeast Res 2019; 19:5584341. [PMID: 31598679 DOI: 10.1093/femsyr/foz067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 10/08/2019] [Indexed: 01/15/2023] Open
Abstract
To decrease our dependency for the diminishing source of fossils resources, bio-based alternatives are being explored for the synthesis of commodity and high-value molecules. One example in this ecological initiative is the microbial production of the biosurfactant sophorolipids by the yeast Starmerella bombicola. Sophorolipids are surface-active molecules mainly used as household and laundry detergents. Because S. bombicola is able to produce high titers of sophorolipids, the yeast is also used to increase the portfolio of lipophilic compounds through strain engineering. Here, the one-step microbial production of hydroxy fatty acids by S. bombicola was accomplished by the selective blockage of three catabolic pathways through metabolic engineering. Successful production of 17.39 g/l (ω-1) linked hydroxy fatty acids was obtained by the successive blockage of the sophorolipid biosynthesis, the β-oxidation and the ω-oxidation pathways. Minor contamination of dicarboxylic acids and fatty aldehydes were successfully removed using flash chromatography. This way, S. bombicola was further expanded into a flexible production platform of economical relevant compounds in the chemical, food and cosmetic industries.
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Affiliation(s)
- Marilyn De Graeve
- Department of Biotechnology, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Isabelle Van de Velde
- Department of Biotechnology, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Lien Saey
- Department of Biotechnology, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Maarten Chys
- Department of Biotechnology, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Hanne Oorts
- Department of Biotechnology, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Hümeyra Kahriman
- Department of Biotechnology, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Stein Mincke
- Department of Green Chemistry and Technology, Sustainable Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Christian Stevens
- Department of Green Chemistry and Technology, Sustainable Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Sofie L De Maeseneire
- Department of Biotechnology, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Sophie L K W Roelants
- Department of Biotechnology, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Wim K G Soetaert
- Department of Biotechnology, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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He Q, Bennett GN, San KY, Wu H. Biosynthesis of Medium-Chain ω-Hydroxy Fatty Acids by AlkBGT of Pseudomonas putida GPo1 With Native FadL in Engineered Escherichia coli. Front Bioeng Biotechnol 2019; 7:273. [PMID: 31681749 PMCID: PMC6812396 DOI: 10.3389/fbioe.2019.00273] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/01/2019] [Indexed: 12/19/2022] Open
Abstract
Hydroxy fatty acids (HFAs) are valuable compounds that are widely used in medical, cosmetic and food fields. Production of ω-HFAs via bioconversion by engineered Escherichia coli has received a lot of attention because this process is environmentally friendly. In this study, a whole-cell bio-catalysis strategy was established to synthesize medium-chain ω-HFAs based on the AlkBGT hydroxylation system from Pseudomonas putida GPo1. The effects of blocking the β-oxidation of fatty acids (FAs) and enhancing the transportation of FAs on ω-HFAs bio-production were also investigated. When fadE and fadD were deleted, the consumption of decanoic acid decreased, and the yield of ω-hydroxydecanoic acid was enhanced remarkably. Additionally, the co-expression of the FA transporter protein, FadL, played an important role in increasing the conversion rate of ω-hydroxydecanoic acid. As a result, the concentration and yield of ω-hydroxydecanoic acid in NH03(pBGT-fadL) increased to 309 mg/L and 0.86 mol/mol, respectively. This whole-cell bio-catalysis system was further applied to the biosynthesis of ω-hydroxyoctanoic acid and ω-hydroxydodecanoic acid using octanoic acid and dodecanoic acid as substrates, respectively. The concentrations of ω-hydroxyoctanoic acid and ω-hydroxydodecanoic acid reached 275.48 and 249.03 mg/L, with yields of 0.63 and 0.56 mol/mol, respectively. This study demonstrated that the overexpression of AlkBGT coupled with native FadL is an efficient strategy to synthesize medium-chain ω-HFAs from medium-chain FAs in fadE and fadD mutant E. coli strains.
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Affiliation(s)
- Qiaofei He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - George N. Bennett
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States
| | - Ka-Yiu San
- Department of Bioengineering, Rice University, Houston, TX, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, China
- Key Laboratory of Bio-based Material Engineering of China National Light Industry Council, Shanghai, China
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Lee H, Sugiharto YEC, Lee H, Jeon W, Ahn J, Lee H. Biotransformation of dicarboxylic acids from vegetable oil–derived sources: current methods and suggestions for improvement. Appl Microbiol Biotechnol 2019; 103:1545-1555. [DOI: 10.1007/s00253-018-9571-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/07/2018] [Accepted: 12/07/2018] [Indexed: 11/28/2022]
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Biosynthesis of ω-hydroxy fatty acids and related chemicals from natural fatty acids by recombinant Escherichia coli. Appl Microbiol Biotechnol 2018; 103:191-199. [DOI: 10.1007/s00253-018-9503-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/01/2018] [Accepted: 11/05/2018] [Indexed: 10/27/2022]
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Lee H, Han C, Lee HW, Park G, Jeon W, Ahn J, Lee H. Development of a promising microbial platform for the production of dicarboxylic acids from biorenewable resources. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:310. [PMID: 30455739 PMCID: PMC6225622 DOI: 10.1186/s13068-018-1310-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND As a sustainable industrial process, the production of dicarboxylic acids (DCAs), used as precursors of polyamides, polyesters, perfumes, plasticizers, lubricants, and adhesives, from vegetable oil has continuously garnered interest. Although the yeast Candida tropicalis has been used as a host for DCA production, additional strains are continually investigated to meet productivity thresholds and industrial needs. In this regard, the yeast Wickerhamiella sorbophila, a potential candidate strain, has been screened. However, the lack of genetic and physiological information for this uncommon strain is an obstacle that merits further research. To overcome this limitation, we attempted to develop a method to facilitate genetic recombination in this strain and produce high amounts of DCAs from methyl laurate using engineered W. sorbophila. RESULTS In the current study, we first developed efficient genetic engineering tools for the industrial application of W. sorbophila. To increase homologous recombination (HR) efficiency during transformation, the cell cycle of the yeast was synchronized to the S/G2 phase using hydroxyurea. The HR efficiency at POX1 and POX2 loci increased from 56.3% and 41.7%, respectively, to 97.9% in both cases. The original HR efficiency at URA3 and ADE2 loci was nearly 0% during the early stationary and logarithmic phases of growth, and increased to 4.8% and 25.6%, respectively. We used the developed tools to construct W. sorbophila UHP4, in which β-oxidation was completely blocked. The strain produced 92.5 g/l of dodecanedioic acid (DDDA) from methyl laurate over 126 h in 5-l fed-batch fermentation, with a productivity of 0.83 g/l/h. CONCLUSIONS Wickerhamiella sorbophila UHP4 produced more DDDA methyl laurate than C. tropicalis. Hence, we demonstrated that W. sorbophila is a powerful microbial platform for vegetable oil-based DCA production. In addition, by using the developed genetic engineering tools, this emerging yeast could be used for the production of a variety of fatty acid derivatives, such as fatty alcohols, fatty aldehydes, and ω-hydroxy fatty acids.
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Affiliation(s)
- Heeseok Lee
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113 Republic of Korea
| | - Changpyo Han
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
| | - Hyeok-Won Lee
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
| | - Gyuyeon Park
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113 Republic of Korea
| | - Wooyoung Jeon
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
| | - Jungoh Ahn
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
| | - Hongweon Lee
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
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Chadha S, Mehetre ST, Bansal R, Kuo A, Aerts A, Grigoriev IV, Druzhinina IS, Mukherjee PK. Genome-wide analysis of cytochrome P450s of Trichoderma spp.: annotation and evolutionary relationships. Fungal Biol Biotechnol 2018; 5:12. [PMID: 29881631 PMCID: PMC5985579 DOI: 10.1186/s40694-018-0056-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/18/2018] [Indexed: 01/21/2023] Open
Abstract
Background Cytochrome P450s form an important group of enzymes involved in xenobiotics degradation and metabolism, both primary and secondary. These enzymes are also useful in industry as biotechnological tools for bioconversion and a few are reported to be involved in pathogenicity. Trichoderma spp. are widely used in industry and agriculture and are known for their biosynthetic potential of a large number of secondary metabolites. For realising the full biosynthetic potential of an organism, it is important to do a genome-wide annotation and cataloguing of these enzymes. Results Here, we have studied the genomes of seven species (T. asperellum, T. atroviride, T. citrinoviride, T. longibrachiatum, T. reesei , T. harzianum and T. virens) and identified a total of 477 cytochrome P450s. We present here the classification, evolution and structure as well as predicted function of these proteins. This study would pave the way for functional characterization of these groups of enzymes and will also help in realization of their full economic potential. Conclusion Our CYPome annotation and evolutionary studies of the seven Trichoderma species now provides opportunities for exploration of research-driven strategies to select Trichoderma species for various applications especially in relation to secondary metabolism and degradation of environmental pollutants.
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Affiliation(s)
- Sonia Chadha
- 1Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085 India
| | - Sayaji T Mehetre
- 1Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085 India
| | - Ravindra Bansal
- 1Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085 India
| | - Alan Kuo
- 2U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Andrea Aerts
- 2U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Igor V Grigoriev
- 2U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Irina S Druzhinina
- 3Research Area Biochemical Technology, Institute of Chemical and Biological Engineering, TU Wien, 1060 Vienna, Austria
| | - Prasun K Mukherjee
- 1Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085 India
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Sugiharto YEC, Lee H, Fitriana AD, Lee H, Jeon W, Park K, Ahn J, Lee H. Effect of decanoic acid and 10-hydroxydecanoic acid on the biotransformation of methyl decanoate to sebacic acid. AMB Express 2018; 8:75. [PMID: 29730843 PMCID: PMC5936482 DOI: 10.1186/s13568-018-0605-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 04/28/2018] [Indexed: 01/23/2023] Open
Abstract
Biotransformation of fatty acid methyl esters to dicarboxylic acids has attracted much attention in recent years; however, reports of sebacic acid production using such biotransformation remain few. The toxicity of decanoic acid is the main challenge for this process. Decane induction has been reported to be essential to activate the enzymes involved in the α,ω-oxidation pathway before initiating the biotransformation of methyl decanoate to sebacic acid. However, we observed the accumulation of intermediates (decanoic acid and 10-hydroxydecanoic acid) during the induction period. In this study, we examined the effects of these intermediates on the biotransformation process. The presence of decanoic acid, even at a low concentration (0.2 g/L), inhibited the transformation of 10-hydroxydecanoic acid to sebacic acid. Moreover, about 24–32% reduction in the decanoic acid oxidation was observed in the presence of 0.5–1.5 g/L 10-hydroxydecanoic acid. To eliminate these inhibitory effects, we applied substrate-limiting conditions during the decane induction process, which eliminated the accumulation of decanoic acid. Although the productivity of sebacic acid (34.5 ± 1.10 g/L) was improved, by 28% over that achieved using the previously methods, after 54 h, the accumulation of 10-hydroxydecanoic acid was still detected. The accumulation of 10-hydroxydecanoic acid even under the decane limiting conditions could be an evidence that oxidation of 10-hydroxydecanoic acid could be the rate-limiting step in this process. The improvement of this reaction should be an important objective for further development of the production of sebacic acid using biotransformation.
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Mishra P, Lee NR, Lakshmanan M, Kim M, Kim BG, Lee DY. Genome-scale model-driven strain design for dicarboxylic acid production in Yarrowia lipolytica. BMC SYSTEMS BIOLOGY 2018; 12:12. [PMID: 29560822 PMCID: PMC5861505 DOI: 10.1186/s12918-018-0542-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Background Recently, there have been several attempts to produce long-chain dicarboxylic acids (DCAs) in various microbial hosts. Of these, Yarrowia lipolytica has great potential due to its oleaginous characteristics and unique ability to utilize hydrophobic substrates. However, Y. lipolytica should be further engineered to make it more competitive: the current approaches are mostly intuitive and cumbersome, thus limiting its industrial application. Results In this study, we proposed model-guided metabolic engineering strategies for enhanced production of DCAs in Y. lipolytica. At the outset, we reconstructed genome-scale metabolic model (GSMM) of Y. lipolytica (iYLI647) by substantially expanding the previous models. Subsequently, the model was validated using three sets of published culture experiment data. It was finally exploited to identify genetic engineering targets for overexpression, knockout, and cofactor modification by applying several in silico strain design methods, which potentially give rise to high yield production of the industrially relevant long-chain DCAs, e.g., dodecanedioic acid (DDDA). The resultant targets include (1) malate dehydrogenase and malic enzyme genes and (2) glutamate dehydrogenase gene, in silico overexpression of which generated additional NADPH required for fatty acid synthesis, leading to the increased DDDA fluxes by 48% and 22% higher, respectively, compared to wild-type. We further investigated the effect of supplying branched-chain amino acids on the acetyl-CoA turn-over rate which is key metabolite for fatty acid synthesis, suggesting their significance for production of DDDA in Y. lipolytica. Conclusion In silico model-based strain design strategies allowed us to identify several metabolic engineering targets for overproducing DCAs in lipid accumulating yeast, Y. lipolytica. Thus, the current study can provide a methodological framework that is applicable to other oleaginous yeasts for value-added biochemical production. Electronic supplementary material The online version of this article (10.1186/s12918-018-0542-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pranjul Mishra
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Na-Rae Lee
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Meiyappan Lakshmanan
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, Singapore, 138668, Singapore
| | - Minsuk Kim
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742, Republic of Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742, Republic of Korea
| | - Dong-Yup Lee
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore. .,Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, Singapore, 138668, Singapore. .,School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Republic of Korea.
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Shin J, Kim JE, Lee YW, Son H. Fungal Cytochrome P450s and the P450 Complement (CYPome) of Fusarium graminearum. Toxins (Basel) 2018; 10:E112. [PMID: 29518888 PMCID: PMC5869400 DOI: 10.3390/toxins10030112] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/02/2018] [Accepted: 03/03/2018] [Indexed: 12/19/2022] Open
Abstract
Cytochrome P450s (CYPs), heme-containing monooxygenases, play important roles in a wide variety of metabolic processes important for development as well as biotic/trophic interactions in most living organisms. Functions of some CYP enzymes are similar across organisms, but some are organism-specific; they are involved in the biosynthesis of structural components, signaling networks, secondary metabolisms, and xenobiotic/drug detoxification. Fungi possess more diverse CYP families than plants, animals, or bacteria. Various fungal CYPs are involved in not only ergosterol synthesis and virulence but also in the production of a wide array of secondary metabolites, which exert toxic effects on humans and other animals. Although few studies have investigated the functions of fungal CYPs, a recent systematic functional analysis of CYP genes in the plant pathogen Fusarium graminearum identified several novel CYPs specifically involved in virulence, asexual and sexual development, and degradation of xenobiotics. This review provides fundamental information on fungal CYPs and a new platform for further metabolomic and biochemical studies of CYPs in toxigenic fungi.
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Affiliation(s)
| | | | | | - Hokyoung Son
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (J.S.); (J.-E.K.); (Y.-W.L.)
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Production of 1-Dodecanol, 1-Tetradecanol, and 1,12-Dodecanediol through Whole-Cell Biotransformation in Escherichia coli. Appl Environ Microbiol 2018; 84:AEM.01806-17. [PMID: 29180361 DOI: 10.1128/aem.01806-17] [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] [Received: 08/16/2017] [Accepted: 11/16/2017] [Indexed: 12/18/2022] Open
Abstract
Medium- and long-chain 1-alkanol and α,ω-alkanediols are used in personal care products, in industrial lubricants, and as precursors for polymers synthesized for medical applications. The industrial production of α,ω-alkanediols by alkane hydroxylation primarily occurs at high temperature and pressure using heavy metal catalysts. However, bioproduction has recently emerged as a more economical and environmentally friendly alternative. Among alkane monooxygenases, CYP153A from Marinobacter aquaeolei VT8 (CYP153A M.aq ; the strain is also known as Marinobacter hydrocarbonoclasticus VT8) possesses low overoxidation activity and high regioselectivity and thus has great potential for use in terminal hydroxylation. However, the application of CYP153A M.aq is limited because it is encoded by a dysfunctional operon. In this study, we demonstrated that the operon regulator AlkR M.aq is functional, can be induced by alkanes of various lengths, and does not suffer from product inhibition. Additionally, we identified a transposon insertion in the CYP153A M.aq operon. When the transposon was removed, the expression of the operon genes could be induced by alkanes, and the alkanes could then be oxyfunctionalized by the resulting proteins. To increase the accessibility of medium- and long-chain alkanes, we coexpressed a tunable alkane facilitator (AlkL) from Pseudomonas putida GPo1. Using a recombinant Escherichia coli strain, we produced 1.5 g/liter 1-dodecanol in 20 h and 2 g/liter 1-tetradecanol in 50 h by adding dodecane and tetradecane, respectively. Furthermore, in 68 h, we generated 3.76 g/liter of 1,12-dodecanediol by adding a dodecane-1-dodecanol substrate mixture. This study reports a very efficient method of producing C12/C14 alkanols and C12 1,12-alkanediol by whole-cell biotransformation.IMPORTANCE To produce terminally hydroxylated medium- to long-chain alkane compounds by whole-cell biotransformation, substrate permeability, enzymatic activity, and the control of overoxidability should be considered. Due to difficulties in production, small amounts of 1-dodecanol, 1-tetradecanol, and 1,12-dodecanediol are typically produced. In this study, we identified an alkane-inducible monooxygenase operon that can efficiently catalyze the conversion of alkane to 1-alkanol with no detection of the overoxidation product. By coexpressing an alkane membrane facilitator, high levels of 1-dodecanol, 1-tetradecanol, and 1,12-dodecanediol could be generated. This study is significant for the bioproduction of medium- and long-chain 1-alkanol and α,ω-alkanediols.
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Effects of glucose concentration on 1,18-cis-octadec-9-enedioic acid biotransformation efficiency and lipid body formation in Candida tropicalis. Sci Rep 2017; 7:13842. [PMID: 29062119 PMCID: PMC5653835 DOI: 10.1038/s41598-017-14173-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 10/06/2017] [Indexed: 11/08/2022] Open
Abstract
The unsaturated long-chain α,ω-dicarboxylic acid 1,18-cis-octadec-9-enedioic acid (cis-ODA) is a versatile precursor of various valuable compounds, such as polymers, and can be obtained from renewable resources. This makes cis-ODA highly attractive for the chemical industry where there is a growing interest in sustainable processes. However, chemical synthesis of the cis isomers is currently not feasible. In contrast, biotechnological production allows for highly specific and selective reactions. Therefore, we developed an efficient production strategy for cis-ODA using Candida tropicalis as a whole-cell biocatalyst for the biotransformation of oleic acid, which naturally occurs in various fats and oils. Applying a bench-top system comprising eight parallel bioreactors, the production process was characterised and optimised for high productivity. Glucose feed rate was identified as the most crucial process parameter influencing product yield, with high rates inducing oleic acid incorporation into triacylglycerols and storage in lipid bodies. Conversely, application of medium-chain length fatty acid as a substrate did not show any occurrence of lipid bodies. Applying the lowest possible molar ratio of glucose to oleic acid (1.5) resulted in marginal lipid body formation, but led to a peak volumetric productivity of 0.56 g/L/h and a final titre of approximately 45 g/L with a corresponding yield of 70%.
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Werner N, Zibek S. Biotechnological production of bio-based long-chain dicarboxylic acids with oleogenious yeasts. World J Microbiol Biotechnol 2017; 33:194. [PMID: 28983758 DOI: 10.1007/s11274-017-2360-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/26/2017] [Indexed: 01/15/2023]
Abstract
Long-chain α,ω-dicarboxylic acids (DCAs) are versatile chemical intermediates of industrial importance used as building blocks for the production of polymers, lubricants, or adhesives. The majority of industrial long-chain DCAs is produced from petro-chemical resources. An alternative is their biotechnological production from renewable materials like plant oil fatty acids by microbial fermentation using oleogenious yeasts. Oleogenious yeasts are natural long-chain DCA producers, which have to be genetically engineered for high-yield DCA production. Although, some commercialized fermentation processes using engineered yeasts are reported, bio-based long-chain DCAs are still far from being a mass product. Further progress in bioprocess engineering and rational strain design is necessary to advance their further commercialization. The present article reviews the basic strategies, as well as novel approaches in the strain design of oleogenious yeasts, such as the combination of traditional metabolic engineering with system biology strategies for high-yield long-chain DCA production. Therefore a detailed overview of the involved metabolic processes for the biochemical long-chain DCA synthesis is given.
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Affiliation(s)
- Nicole Werner
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Susanne Zibek
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany.
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Combinatorial Engineering of Yarrowia lipolytica as a Promising Cell Biorefinery Platform for the de novo Production of Multi-Purpose Long Chain Dicarboxylic Acids. FERMENTATION-BASEL 2017. [DOI: 10.3390/fermentation3030040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Funk I, Rimmel N, Schorsch C, Sieber V, Schmid J. Production of dodecanedioic acid via biotransformation of low cost plant-oil derivatives using Candida tropicalis. J Ind Microbiol Biotechnol 2017; 44:1491-1502. [PMID: 28756564 DOI: 10.1007/s10295-017-1972-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/20/2017] [Indexed: 01/09/2023]
Abstract
Dodecanedioic acid (DDA) is highly useful to the chemical industry as a versatile precursor for producing the polyamide nylon-6,12, which is used for many technical applications, such as heat and chemical-resistant sheaths. However, DDA synthesis has several drawbacks, such as high energy input and cost-intensive removal of by-products. Therefore, alternative bio-based production routes are required due to increasing industrial demand for green chemicals and renewable products. Candida tropicalis converts petrochemical-based n-dodecanes to the corresponding dicarboxylic acids by targeted functionalization. To increase sustainability of the DDA production process, we tested dodecanoic acid methyl ester, which can be easily obtained from transesterification of coconut oil, in whole-cell biotransformation by C. tropicalis. By modifying selected process parameters, a final DDA concentration of 66 g/L was achieved using a highly reliable, small-scale bioreactor system. Crucial process development included a gradual pH shift, an optimized substrate feeding strategy, and monitoring the transcriptional profile.
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Affiliation(s)
- Irina Funk
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Nina Rimmel
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Christoph Schorsch
- Evonik Creavis GmbH, Science & Technology, Paul-Baumann-Straße 1, 45772, Marl, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Jochen Schmid
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany.
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Cho YH, Kim SJ, Kim HW, Kim JY, Gwak JS, Chung D, Kim KH, Park K, Park YC. Continuous supply of glucose and glycerol enhances biotransformation of ricinoleic acid to ( E )-11-(heptanoyloxy) undec-9-enoic acid in recombinant Escherichia coli. J Biotechnol 2017; 253:34-39. [DOI: 10.1016/j.jbiotec.2017.05.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/29/2017] [Accepted: 05/19/2017] [Indexed: 11/25/2022]
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29
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Lee H, Sugiharto YEC, Lee S, Park G, Han C, Jang H, Jeon W, Park H, Ahn J, Kang K, Lee H. Characterization of the newly isolated ω-oxidizing yeast Candida sorbophila DS02 and its potential applications in long-chain dicarboxylic acid production. Appl Microbiol Biotechnol 2017; 101:6333-6342. [PMID: 28589225 DOI: 10.1007/s00253-017-8321-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/18/2017] [Accepted: 04/29/2017] [Indexed: 12/13/2022]
Abstract
α, ω-Dicarboxylic acids (DCAs) are multipurpose chemicals widely used in polymers, perfumes, plasticizers, lubricants, and adhesives. The biotransformation of DCAs from alkanes and fatty acids by microorganisms has attracted recent interest, since synthesis via chemical oxidation causes problems in terms of the environment and safety. We isolated an ω-oxidizing yeast from a wastewater disposal facility of a petrochemical factory by chemostat enrichment culture. The haploid strain identified as Candida sorbophila DS02 grew on glucose and dodecane, exhibiting greater cell shrinkage on the latter. In flask cultures with mixed alkanes (C10-16) and fatty acid methyl esters (C10-16), DS02 used mixed alkanes simultaneously unlike Candida tropicalis and Yarrowia lipolytica and showed high substrate resistance. In flask cultures with acrylic acid-a known inhibitor of β-oxidation-DS02 produced 0.28 g/l dodecanedioic acid (DDDA) from dodecane, similar to wild-type C. tropicalis ATCC 20336. In fed-batch fermentation, DS02 produced 9.87 g/l DDDA, which was 5.7-fold higher than wild-type C. tropicalis. These results suggest that C. sorbophila strain DS02 has potential applications for the large-scale production of DCA.
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Affiliation(s)
- Heeseok Lee
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 28116, Republic of Korea
| | - Yohanes Eko Chandra Sugiharto
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 28116, Republic of Korea
| | - Seunghoon Lee
- R&D Center, Lotte Chemical Corporation, 115 Gajeongbuk-ro, Yuseong-gu, Daejeon, 34110, Republic of Korea
| | - Gyuyeon Park
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 28116, Republic of Korea
| | - Changpyo Han
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 28116, Republic of Korea
| | - Hyeran Jang
- R&D Center, Lotte Chemical Corporation, 115 Gajeongbuk-ro, Yuseong-gu, Daejeon, 34110, Republic of Korea
| | - Wooyoung Jeon
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 28116, Republic of Korea
| | - Heejoon Park
- R&D Center, Lotte Chemical Corporation, 115 Gajeongbuk-ro, Yuseong-gu, Daejeon, 34110, Republic of Korea
| | - Jungoh Ahn
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 28116, Republic of Korea
| | - Kyungbo Kang
- R&D Center, Lotte Chemical Corporation, 115 Gajeongbuk-ro, Yuseong-gu, Daejeon, 34110, Republic of Korea
| | - Hongwoen Lee
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 28116, Republic of Korea.
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30
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Winnacker M, Rieger B. Biobased Polyamides: Recent Advances in Basic and Applied Research. Macromol Rapid Commun 2016; 37:1391-413. [DOI: 10.1002/marc.201600181] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/15/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Malte Winnacker
- WACKER-Lehrstuhl für Makromolekulare Chemie; Technische Universität München; Lichtenbergstraße 4 85474 Garching bei München Germany
| | - Bernhard Rieger
- WACKER-Lehrstuhl für Makromolekulare Chemie; Technische Universität München; Lichtenbergstraße 4 85474 Garching bei München Germany
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31
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Zhao R, Zhang Y, Chung J, Shea KJ. Convenient Controlled Aqueous C1 Synthesis of Long-Chain Aliphatic AB, AA, and BB Macromonomers for the Synthesis of Polyesters with Tunable Hydrocarbon Chain Segments. ACS Macro Lett 2016; 5:854-857. [PMID: 35614751 DOI: 10.1021/acsmacrolett.6b00427] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The insertion of long hydrocarbon chains between ester groups in polyester allows for introduction and modulation of crystallinity, which can result in enhanced performance approaching high-density polyethylene. We report a convenient synthesis of building blocks for long-chain aliphatic polyesters via an aqueous C1 polymerization. The macromonomers include ω-hydroxyacid esters, α,ω-diols and α,ω-diacids. The length of hydrocarbon chain segment (C20-C60) can be controlled by the ratio of monomer/initiator in the C1 polymerization. The obtained polyesters from condensation of the long-chain ω-hydroxyacid esters have thermal and mechanical properties indistinguishable from related materials derived from biomass.
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Affiliation(s)
- Ruobing Zhao
- Department
of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Yan Zhang
- Key
Laboratory for Ultrafine Materials of Ministry of Education, School
of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jaeyoon Chung
- Department
of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Kenneth J. Shea
- Department
of Chemistry, University of California, Irvine, Irvine, California 92697, United States
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32
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Iwama R, Kobayashi S, Ishimaru C, Ohta A, Horiuchi H, Fukuda R. Functional roles and substrate specificities of twelve cytochromes P450 belonging to CYP52 family in n-alkane assimilating yeast Yarrowia lipolytica. Fungal Genet Biol 2016; 91:43-54. [PMID: 27039152 DOI: 10.1016/j.fgb.2016.03.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/16/2016] [Accepted: 03/29/2016] [Indexed: 11/26/2022]
Abstract
Yarrowia lipolytica possesses twelve ALK genes, which encode cytochromes P450 in the CYP52 family. In this study, using a Y. lipolytica strain from which all twelve ALK genes had been deleted, strains individually expressing each of the ALK genes were constructed and their roles and substrate specificities were determined by observing their growth on n-alkanes and analyzing fatty acid metabolism. The results suggested that the twelve Alk proteins can be categorized into four groups based on their substrate specificity: Alk1p, Alk2p, Alk9p, and Alk10p, which have significant activities to hydroxylate n-alkanes; Alk4p, Alk5p, and Alk7p, which have significant activities to hydroxylate the ω-terminal end of dodecanoic acid; Alk3p and Alk6p, which have significant activities to hydroxylate both n-alkanes and dodecanoic acid; and Alk8p, Alk11p, and Alk12p, which showed faint or no activities to oxidize these substrates. The involvement of Alk proteins in the oxidation of fatty alcohols and fatty aldehydes was also analyzed by measuring viability of the mutant deleted for twelve ALK genes in medium containing dodecanol and by observing growth on dodecanal of a mutant strain, in which twelve ALK genes were deleted along with four fatty aldehyde dehydrogenase genes. It was suggested that ALK gene(s) is/are involved in the detoxification of dodecanol and the assimilation of dodecanal. These results imply that genes encoding CYP52-family P450s have undergone multiplication and diversification in Y. lipolytica for assimilation of various hydrophobic compounds.
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Affiliation(s)
- Ryo Iwama
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Satoshi Kobayashi
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Chiaki Ishimaru
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akinori Ohta
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Hiroyuki Horiuchi
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryouichi Fukuda
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.
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33
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Stempfle F, Ortmann P, Mecking S. Long-Chain Aliphatic Polymers To Bridge the Gap between Semicrystalline Polyolefins and Traditional Polycondensates. Chem Rev 2016; 116:4597-641. [DOI: 10.1021/acs.chemrev.5b00705] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Florian Stempfle
- Chair of
Chemical Materials
Science, Department of Chemistry, University of Konstanz, Universitätsstrasse
10, D-78457 Konstanz, Germany
| | - Patrick Ortmann
- Chair of
Chemical Materials
Science, Department of Chemistry, University of Konstanz, Universitätsstrasse
10, D-78457 Konstanz, Germany
| | - Stefan Mecking
- Chair of
Chemical Materials
Science, Department of Chemistry, University of Konstanz, Universitätsstrasse
10, D-78457 Konstanz, Germany
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34
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Mishra P, Park GY, Lakshmanan M, Lee HS, Lee H, Chang MW, Ching CB, Ahn J, Lee DY. Genome-scale metabolic modeling and in silico analysis of lipid accumulating yeast Candida tropicalis for dicarboxylic acid production. Biotechnol Bioeng 2016; 113:1993-2004. [PMID: 26915092 DOI: 10.1002/bit.25955] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/25/2015] [Accepted: 02/14/2016] [Indexed: 02/02/2023]
Abstract
Recently, the bio-production of α,ω-dicarboxylic acids (DCAs) has gained significant attention, which potentially leads to the replacement of the conventional petroleum-based products. In this regard, the lipid accumulating yeast Candida tropicalis, has been recognized as a promising microbial host for DCA biosynthesis: it possess the unique ω-oxidation pathway where the terminal carbon of α-fatty acids is oxidized to form DCAs with varying chain lengths. However, despite such industrial importance, its cellular physiology and lipid accumulation capability remain largely uncharacterized. Thus, it is imperative to better understand the metabolic behavior of this lipogenic yeast, which could be achieved by a systems biological approach. To this end, herein, we reconstructed the genome-scale metabolic model of C. tropicalis, iCT646, accounting for 646 unique genes, 945 metabolic reactions, and 712 metabolites. Initially, the comparative network analysis of iCT646 with other yeasts revealed several distinctive metabolic reactions, mainly within the amino acid and lipid metabolism including the ω-oxidation pathway. Constraints-based flux analysis was, then, employed to predict the in silico growth rates of C. tropicalis which are highly consistent with the cellular phenotype observed in glucose and xylose minimal media chemostat cultures. Subsequently, the lipid accumulation capability of C. tropicalis was explored in comparison with Saccharomyces cerevisiae, indicating that the formation of "citrate pyruvate cycle" is essential to the lipid accumulation in oleaginous yeasts. The in silico flux analysis also highlighted the enhanced ability of pentose phosphate pathway as NADPH source rather than malic enzyme during lipogenesis. Finally, iCT646 was successfully utilized to highlight the key directions of C. tropicalis strain design for the whole cell biotransformation application to produce long-chain DCAs from alkanes. Biotechnol. Bioeng. 2016;113: 1993-2004. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Pranjul Mishra
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore
| | - Gyu-Yeon Park
- Biotechnology Process Engineering Center, KRIBB, 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju, 363-883, Korea.,Bioprocess Department, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Korea
| | - Meiyappan Lakshmanan
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, 138668, Singapore
| | - Hee-Seok Lee
- Biotechnology Process Engineering Center, KRIBB, 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju, 363-883, Korea.,Bioprocess Department, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Korea
| | - Hongweon Lee
- Biotechnology Process Engineering Center, KRIBB, 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju, 363-883, Korea.,Bioprocess Department, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Korea
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Chi Bun Ching
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore
| | - Jungoh Ahn
- Biotechnology Process Engineering Center, KRIBB, 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju, 363-883, Korea. .,Bioprocess Department, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Korea.
| | - Dong-Yup Lee
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore. .,Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, 138668, Singapore. .,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore.
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35
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Seo JH, Lee SM, Lee J, Park JB. Adding value to plant oils and fatty acids: Biological transformation of fatty acids into ω-hydroxycarboxylic, α,ω-dicarboxylic, and ω-aminocarboxylic acids. J Biotechnol 2015; 216:158-66. [PMID: 26546054 DOI: 10.1016/j.jbiotec.2015.10.024] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/22/2015] [Accepted: 10/30/2015] [Indexed: 10/22/2022]
Abstract
Not only short chain ω-hydroxycarboxylic acids, α,ω-dicarboxylic acids, and ω-aminocarboxylic acids but also medium to long chain carboxylic acids are widely used as building blocks and intermediates in the chemical, pharmaceutical, and food industries. Thereby, recent achievements in biological production of medium to long chain carboxylic acids are addressed here. ω-Hydroxycarboxylic and α,ω-dicarboxylic acids were synthesized via terminal CH bond oxygenation of fatty acids and/or internal oxidative cleavage of the fatty acid carbon skeletons. ω-Aminocarboxylic acids were enzymatically produced from ω-hydroxycarboxylic acids via ω-oxocarboxylic acids. Productivities and product yields of some of the products are getting close to the industrial requirements for large scale production.
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Affiliation(s)
- Joo-Hyun Seo
- Department of Food Science and Engineering, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Sun-Mee Lee
- Division of Food Science, Kyungil University, Gyeongsan 712-701, Republic of Korea
| | - Jinwon Lee
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 121-742, Republic of Korea
| | - Jin-Byung Park
- Department of Food Science and Engineering, Ewha Womans University, Seoul 120-750, Republic of Korea.
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36
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Sathesh-Prabu C, Lee SK. Production of Long-Chain α,ω-Dicarboxylic Acids by Engineered Escherichia coli from Renewable Fatty Acids and Plant Oils. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:8199-8208. [PMID: 26359801 DOI: 10.1021/acs.jafc.5b03833] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Long-chain α,ω-dicarboxylic acids (LDCAs, ≥ C12) are widely used as a raw material for preparing various commodities and polymers. In this study, a CYP450-monooxygenase-mediated ω-oxidation pathway system with high ω-regioselectivity was heterologously expressed in Escherichia coli to produce DCAs from fatty acids. The resulting engineered E. coli produced a maximum of 41 mg/L of C12 DCA and 163 mg/L of C14 DCA from fatty acids (1 g/L), following 20 h of whole cell biotransformation. Addition of a heme precursor and the hydroxyl radical scavenger, thiourea, increased product concentration (159 mg/L of C12 DCA and 410 mg/L of C14 DCA) in a shorter culture duration than that of the corresponding controls. DCAs of various chain lengths were synthesized from coconut oil hydrolysate using the engineered E. coli. This novel synthetic biocatalytic system could be applied to produce high value DCAs in a cost-effective manner from renewable plant oils.
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Affiliation(s)
- Chandran Sathesh-Prabu
- School of Energy and Chemical Engineering, and ‡School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST) , Ulsan 689-798, Republic of Korea
| | - Sung Kuk Lee
- School of Energy and Chemical Engineering, and ‡School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST) , Ulsan 689-798, Republic of Korea
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37
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Dennig A, Kuhn M, Tassoti S, Thiessenhusen A, Gilch S, Bülter T, Haas T, Hall M, Faber K. Oxidative Decarboxylation of Short-Chain Fatty Acids to 1-Alkenes. Angew Chem Int Ed Engl 2015; 54:8819-22. [PMID: 26095212 DOI: 10.1002/anie.201502925] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Indexed: 01/11/2023]
Abstract
The enzymatic oxidative decarboxylation of linear short-chain fatty acids (C4:0-C9:0) employing the P450 monooxygenase OleT, O2 as the oxidant, and NAD(P)H as the electron donor gave the corresponding terminal C3 to C8 alkenes with product titers of up to 0.93 g L(-1) and TTNs of >2000. Key to this process was the construction of an efficient electron-transfer chain employing putidaredoxin CamAB in combination with NAD(P)H recycling at the expense of glucose, formate, or phosphite. This system allows for the biocatalytic production of industrially important 1-alkenes, such as propene and 1-octene, from renewable resources for the first time.
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Affiliation(s)
- Alexander Dennig
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz (Austria)
| | - Miriam Kuhn
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz (Austria)
| | - Sebastian Tassoti
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz (Austria)
| | - Anja Thiessenhusen
- Creavis, Evonik Industries, Bau 1420, Paul Baumann Strasse 1, 45772 Marl (Germany)
| | - Stefan Gilch
- Creavis, Evonik Industries, Bau 1420, Paul Baumann Strasse 1, 45772 Marl (Germany)
| | - Thomas Bülter
- Creavis, Evonik Industries, Bau 1420, Paul Baumann Strasse 1, 45772 Marl (Germany)
| | - Thomas Haas
- Creavis, Evonik Industries, Bau 1420, Paul Baumann Strasse 1, 45772 Marl (Germany)
| | - Mélanie Hall
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz (Austria)
| | - Kurt Faber
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz (Austria).
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38
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Dennig A, Kuhn M, Tassoti S, Thiessenhusen A, Gilch S, Bülter T, Haas T, Hall M, Faber K. Oxidative Decarboxylierung von kurzkettigen Fettsäuren zu 1-Alkenen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502925] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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39
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Holtmann D, Fraaije MW, Arends IWCE, Opperman DJ, Hollmann F. The taming of oxygen: biocatalytic oxyfunctionalisations. Chem Commun (Camb) 2015; 50:13180-200. [PMID: 24902635 DOI: 10.1039/c3cc49747j] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The scope and limitations of oxygenases as catalysts for preparative organic synthesis is discussed.
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Affiliation(s)
- Dirk Holtmann
- DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
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40
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Durairaj P, Malla S, Nadarajan SP, Lee PG, Jung E, Park HH, Kim BG, Yun H. Fungal cytochrome P450 monooxygenases of Fusarium oxysporum for the synthesis of ω-hydroxy fatty acids in engineered Saccharomyces cerevisiae. Microb Cell Fact 2015; 14:45. [PMID: 25880760 PMCID: PMC4387584 DOI: 10.1186/s12934-015-0228-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 03/12/2015] [Indexed: 01/03/2023] Open
Abstract
Background Omega hydroxy fatty acids (ω-OHFAs) are multifunctional compounds that act as the basis for the production of various industrial products with broad commercial and pharmaceutical implications. However, the terminal oxygenation of saturated or unsaturated fatty acids for the synthesis of ω-OHFAs is intricate to accomplish through chemocatalysis, due to the selectivity and controlled reactivity in C-H oxygenation reactions. Cytochrome P450, the ubiquitous enzyme is capable of catalyzing the selective terminal omega hydroxylation naturally in biological kingdom. Results To gain a deep insight on the biochemical role of fungal P450s towards the production of omega hydroxy fatty acids, two cytochrome P450 monooxygenases from Fusarium oxysporum (FoCYP), FoCYP539A7 and FoCYP655C2; were identified, cloned, and heterologously expressed in Saccharomyces cerevisiae. For the efficient production of ω-OHFAs, the S. cerevisiae was engineered to disrupt the acyl-CoA oxidase enzyme and the β-oxidation pathway inactivated (ΔPox1) S. cerevisiae mutant was generated. To elucidate the significance of the interaction of redox mechanism, FoCYPs were reconstituted with the heterologous and homologous reductase systems - S. cerevisiae CPR (ScCPR) and F. oxysporum CPR (FoCPR). To further improve the yield, the effect of pH was analyzed and the homologous FoCYP-FoCPR system efficiently hydroxylated caprylic acid, capric acid and lauric acid into their respective ω-hydroxy fatty acids with 56%, 79% and 67% conversion. Furthermore, based on computational simulations, we identified the key residues (Asn106 of FoCYP539A7 and Arg235 of FoCYP655C2) responsible for the recognition of fatty acids and demonstrated the structural insights of the active site of FoCYPs. Conclusion Fungal CYP monooxygenases, FoCYP539A7 and FoCYP655C2 with its homologous redox partner, FoCPR constitutes a promising catalyst due to its high regio- and stereo-selectivity in the hydroxylation of fatty acids and in the substantial production of industrially valuable ω-hydroxy fatty acids. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0228-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Sailesh Malla
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea. .,Current position: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark.
| | | | - Pyung-Gang Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea.
| | - Eunok Jung
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea.
| | - Hyun Ho Park
- School of Biotechnology, Yeungnam University, Gyeongsan, South Korea.
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea.
| | - Hyungdon Yun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea.
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Novak M, Lah L, Šala M, Stojan J, Bohlmann J, Komel R. Oleic acid metabolism via a conserved cytochrome P450 system-mediated ω-hydroxylation in the bark beetle-associated fungus Grosmannia clavigera. PLoS One 2015; 10:e0120119. [PMID: 25794012 PMCID: PMC4368105 DOI: 10.1371/journal.pone.0120119] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 01/22/2015] [Indexed: 12/27/2022] Open
Abstract
The bark beetle-associated fungus Grosmannia clavigera participates in the large-scale destruction of pine forests. In the tree, it must tolerate saturating levels of toxic conifer defense chemicals (e.g. monoterpenes). The fungus can metabolize some of these compounds through the ß-oxidation pathway and use them as a source of carbon. It also uses carbon from pine triglycerides, where oleic acid is the most common fatty acid. High levels of free fatty acids, however, are toxic and can cause additional stress during host colonization. Fatty acids induce expression of neighboring genes encoding a cytochrome P450 (CYP630B18) and its redox partner, cytochrome P450 reductase (CPR2). The aim of this work was to study the function of this novel P450 system. Using LC/MS, we biochemically characterized CYP630 as a highly specific oleic acid ω-hydroxylase. We explain oleic acid specificity using protein interaction modeling. Our results underscore the importance of ω-oxidation when the main ß-oxidation pathway may be overwhelmed by other substrates such as host terpenoid compounds. Because this CYP-CPR gene cluster is evolutionarily conserved, our work has implications for metabolism studies in other fungi.
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Affiliation(s)
- Metka Novak
- National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Ljerka Lah
- National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- * E-mail: (LL); (RK)
| | - Martin Šala
- National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Jure Stojan
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000, Ljubljana, Slovenia
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Radovan Komel
- National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- * E-mail: (LL); (RK)
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Iwama R, Kobayashi S, Ohta A, Horiuchi H, Fukuda R. Fatty aldehyde dehydrogenase multigene family involved in the assimilation of n-alkanes in Yarrowia lipolytica. J Biol Chem 2014; 289:33275-86. [PMID: 25315778 DOI: 10.1074/jbc.m114.596890] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the n-alkane assimilating yeast Yarrowia lipolytica, n-alkanes are oxidized to fatty acids via fatty alcohols and fatty aldehydes, after which they are utilized as carbon sources. Here, we show that four genes (HFD1-HFD4) encoding fatty aldehyde dehydrogenases (FALDHs) are involved in the metabolism of n-alkanes in Y. lipolytica. A mutant, in which all of four HFD genes are deleted (Δhfd1-4 strain), could not grow on n-alkanes of 12-18 carbons; however, the expression of one of those HFD genes restored its growth on n-alkanes. Production of Hfd2Ap or Hfd2Bp, translation products of transcript variants generated from HFD2 by the absence or presence of splicing, also supported the growth of the Δhfd1-4 strain on n-alkanes. The FALDH activity in the extract of the wild-type strain was increased when cells were incubated in the presence of n-decane, whereas this elevation in FALDH activity by n-decane was not observed in Δhfd1-4 strain extract. Substantial FALDH activities were detected in the extracts of Escherichia coli cells expressing the HFD genes. Fluorescent microscopic observation suggests that Hfd3p and Hfd2Bp are localized predominantly in the peroxisome, whereas Hfd1p and Hfd2Ap are localized in both the endoplasmic reticulum and the peroxisome. These results suggest that the HFD multigene family is responsible for the oxidation of fatty aldehydes to fatty acids in the metabolism of n-alkanes, and raise the possibility that Hfd proteins have diversified by gene multiplication and RNA splicing to efficiently assimilate or detoxify fatty aldehydes in Y. lipolytica.
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Affiliation(s)
- Ryo Iwama
- From the Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 and
| | - Satoshi Kobayashi
- From the Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 and
| | - Akinori Ohta
- the Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Hiroyuki Horiuchi
- From the Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 and
| | - Ryouichi Fukuda
- From the Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 and
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Metabolism of Hydrophobic Carbon Sources and Regulation of It inn-Alkane-Assimilating YeastYarrowia lipolytica. Biosci Biotechnol Biochem 2014; 77:1149-54. [DOI: 10.1271/bbb.130164] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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44
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Comparative analysis of P450 signature motifs EXXR and CXG in the large and diverse kingdom of fungi: identification of evolutionarily conserved amino acid patterns characteristic of P450 family. PLoS One 2014; 9:e95616. [PMID: 24743800 PMCID: PMC3990721 DOI: 10.1371/journal.pone.0095616] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/28/2014] [Indexed: 11/25/2022] Open
Abstract
Cytochrome P450 monooxygenases (P450s) are heme-thiolate proteins distributed across the biological kingdoms. P450s are catalytically versatile and play key roles in organisms primary and secondary metabolism. Identification of P450s across the biological kingdoms depends largely on the identification of two P450 signature motifs, EXXR and CXG, in the protein sequence. Once a putative protein has been identified as P450, it will be assigned to a family and subfamily based on the criteria that P450s within a family share more than 40% homology and members of subfamilies share more than 55% homology. However, to date, no evidence has been presented that can distinguish members of a P450 family. Here, for the first time we report the identification of EXXR- and CXG-motifs-based amino acid patterns that are characteristic of the P450 family. Analysis of P450 signature motifs in the under-explored fungal P450s from four different phyla, ascomycota, basidiomycota, zygomycota and chytridiomycota, indicated that the EXXR motif is highly variable and the CXG motif is somewhat variable. The amino acids threonine and leucine are preferred as second and third amino acids in the EXXR motif and proline and glycine are preferred as second and third amino acids in the CXG motif in fungal P450s. Analysis of 67 P450 families from biological kingdoms such as plants, animals, bacteria and fungi showed conservation of a set of amino acid patterns characteristic of a particular P450 family in EXXR and CXG motifs. This suggests that during the divergence of P450 families from a common ancestor these amino acids patterns evolve and are retained in each P450 family as a signature of that family. The role of amino acid patterns characteristic of a P450 family in the structural and/or functional aspects of members of the P450 family is a topic for future research.
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45
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Expression and characterization of CYP52 genes involved in the biosynthesis of sophorolipid and alkane metabolism from Starmerella bombicola. Appl Environ Microbiol 2013; 80:766-76. [PMID: 24242247 DOI: 10.1128/aem.02886-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Three cytochrome P450 monooxygenase CYP52 gene family members were isolated from the sophorolipid-producing yeast Starmerella bombicola (former Candida bombicola), namely, CYP52E3, CYP52M1, and CYP52N1, and their open reading frames were cloned into the pYES2 vector for expression in Saccharomyces cerevisiae. The functions of the recombinant proteins were analyzed with a variety of alkane and fatty acid substrates using microsome proteins or a whole-cell system. CYP52M1 was found to oxidize C16 to C20 fatty acids preferentially. It converted oleic acid (C18:1) more efficiently than stearic acid (C18:0) and linoleic acid (C18:2) and much more effectively than α-linolenic acid (C18:3). No products were detected when C10 to C12 fatty acids were used as the substrates. Moreover, CYP52M1 hydroxylated fatty acids at their ω- and ω-1 positions. CYP52N1 oxidized C14 to C20 saturated and unsaturated fatty acids and preferentially oxidized palmitic acid, oleic acid, and linoleic acid. It only catalyzed ω-hydroxylation of fatty acids. Minor ω-hydroxylation activity against myristic acid, palmitic acid, palmitoleic acid, and oleic acid was shown for CYP52E3. Furthermore, the three P450s were coassayed with glucosyltransferase UGTA1. UGTA1 glycosylated all hydroxyl fatty acids generated by CYP52E3, CYP52M1, and CYP52N1. The transformation efficiency of fatty acids into glucolipids by CYP52M1/UGTA1 was much higher than those by CYP52N1/UGTA1 and CYP52E3/UGTA1. Taken together, CYP52M1 is demonstrated to be involved in the biosynthesis of sophorolipid, whereas CYP52E3 and CYP52N1 might be involved in alkane metabolism in S. bombicola but downstream of the initial oxidation steps.
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Kim KR, Oh DK. Production of hydroxy fatty acids by microbial fatty acid-hydroxylation enzymes. Biotechnol Adv 2013; 31:1473-85. [PMID: 23860413 DOI: 10.1016/j.biotechadv.2013.07.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 07/03/2013] [Accepted: 07/06/2013] [Indexed: 10/26/2022]
Abstract
Hydroxy fatty acids are widely used in chemical, food, and cosmetic industries as starting materials for the synthesis of polymers and as additives for the manufacture of lubricants, emulsifiers, and stabilizers. They have antibiotic, anti-inflammatory, and anticancer activities and therefore can be applied for medicinal uses. Microbial fatty acid-hydroxylation enzymes, including P450, lipoxygenase, hydratase, 12-hydroxylase, and diol synthase, synthesize regio-specific hydroxy fatty acids. In this article, microbial fatty acid-hydroxylation enzymes, with a focus on region-specificity and diversity, are summarized and the production of mono-, di-, and tri-hydroxy fatty acids is introduced. Finally, the production methods of regio-specific and diverse hydroxy fatty acids, such as gene screening, protein engineering, metabolic engineering, and combinatory biosynthesis, are suggested.
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Affiliation(s)
- Kyoung-Rok Kim
- Department of Bioscience and Biotechnology, Konkuk University, 1 Hwayang-Dong Gwangjin-Gu, Seoul 143-701, Republic of Korea
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47
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Gessler NN, Filippovich SY, Bachurina GP, Groza NV, Dorodnikova EA, Belozerskaya TA. Effect of oxylipins on Neurospora crassa growth and differentiation. Microbiology (Reading) 2012. [DOI: 10.1134/s0026261712050074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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48
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Lu W, Ness JE, Xie W, Zhang X, Liu F, Cai J, Minshull J, Gross RA. Biosynthesis of Monomers for Plastics from Renewable Oils. ACS SYMPOSIUM SERIES 2012. [DOI: 10.1021/bk-2012-1105.ch006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Wenhua Lu
- Polytechnic Institute of New York University, 6 Metrotech Center, Brooklyn, NY 11201
- DNA2.0 Inc, 1430 O'Brien Drive, Menlo Park, CA 94025
| | - Jon E. Ness
- Polytechnic Institute of New York University, 6 Metrotech Center, Brooklyn, NY 11201
- DNA2.0 Inc, 1430 O'Brien Drive, Menlo Park, CA 94025
| | - Wenchun Xie
- Polytechnic Institute of New York University, 6 Metrotech Center, Brooklyn, NY 11201
- DNA2.0 Inc, 1430 O'Brien Drive, Menlo Park, CA 94025
| | - Xiaoyan Zhang
- Polytechnic Institute of New York University, 6 Metrotech Center, Brooklyn, NY 11201
- DNA2.0 Inc, 1430 O'Brien Drive, Menlo Park, CA 94025
| | - Fei Liu
- Polytechnic Institute of New York University, 6 Metrotech Center, Brooklyn, NY 11201
- DNA2.0 Inc, 1430 O'Brien Drive, Menlo Park, CA 94025
| | - Jiali Cai
- Polytechnic Institute of New York University, 6 Metrotech Center, Brooklyn, NY 11201
- DNA2.0 Inc, 1430 O'Brien Drive, Menlo Park, CA 94025
| | - Jeremy Minshull
- Polytechnic Institute of New York University, 6 Metrotech Center, Brooklyn, NY 11201
- DNA2.0 Inc, 1430 O'Brien Drive, Menlo Park, CA 94025
| | - Richard A. Gross
- Polytechnic Institute of New York University, 6 Metrotech Center, Brooklyn, NY 11201
- DNA2.0 Inc, 1430 O'Brien Drive, Menlo Park, CA 94025
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49
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Joo YC, Jeong KW, Yeom SJ, Kim YS, Kim Y, Oh DK. Biochemical characterization and FAD-binding analysis of oleate hydratase from Macrococcus caseolyticus. Biochimie 2011; 94:907-15. [PMID: 22203098 DOI: 10.1016/j.biochi.2011.12.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 12/13/2011] [Indexed: 11/15/2022]
Abstract
A putative fatty acid hydratase gene from Macrococcus caseolyticus was cloned and expressed in Escherichia coli. The recombinant enzyme was a 68 kDa dimer with a molecular mass of 136 kDa. The enzymatic products formed from fatty acid substrates by the putative enzyme were isolated with high purity (>99%) by solvent fractional crystallization at low temperature. After the identification by GC-MS, the purified hydroxy fatty acids were used as standards to quantitatively determine specific activities and kinetic parameters for fatty acids as substrates. Among the fatty acids evaluated, specific activity and catalytic efficiency (k(cat)/K(m)) were highest for oleic acid, indicating that the putative fatty acid hydratase was an oleate hydratase. Hydration occurred only for cis-9-double and cis-12-double bonds of unsaturated fatty acids without any trans-configurations. The maximum activity for oleate hydration was observed at pH 6.5 and 25 °C with 2% (v/v) ethanol and 0.2 mM FAD. Without FAD, all catalytic activity was abolished. Thus, the oleate hydratase is an FAD-dependent enzyme. The residues G29, G31, S34, E50, and E56, which are conserved in the FAD-binding motif of fatty acid hydratases (GXGXXG((A/S))X((15-21))E((D))), were selected by alignment, and the spectral properties and kinetic parameters of their alanine-substituted variants were analyzed. Among the five variants, G29A, G31A, and E56A showed no interaction with FAD and exhibited no activity. These results indicate that G29, G31, and E56 are essential for FAD-binding.
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Affiliation(s)
- Young-Chul Joo
- Department of Bioscience and Biotechnology, Konkuk University, 1 Hayang-dong Gangjin-gu, Seoul 143-701, Republic of Korea
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50
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Takai H, Iwama R, Kobayashi S, Horiuchi H, Fukuda R, Ohta A. Construction and characterization of a Yarrowia lipolytica mutant lacking genes encoding cytochromes P450 subfamily 52. Fungal Genet Biol 2011; 49:58-64. [PMID: 22119766 DOI: 10.1016/j.fgb.2011.11.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 11/07/2011] [Accepted: 11/09/2011] [Indexed: 11/16/2022]
Abstract
The initial hydroxylation of n-alkane is catalyzed by cytochrome P450ALK of the CYP52 family in the n-alkane-assimilating yeast Yarrowia lipolytica. A mutant with a deletion of all 12 genes, ALK1 to ALK12, which are deduced to encode cytochromes P450 of the CYP52 family in Y. lipolytica, was successfully constructed. This deletion mutant, Δalk1-12, completely lost the ability to grow on n-alkanes of 10-16 carbons. In contrast, Δalk1-12 grew on the metabolite of n-dodecane, i.e., n-dodecanol, n-dodecanal, or n-dodecanoic acid, as well as the wild-type strain. In addition, production of n-dodecanoic acid was not observed when Δalk1-12 was incubated in the presence of n-dodecane. These results indicate the essential roles of P450ALKs in the oxidation of n-alkane. Δalk1-12 will be valuable as a host strain to express an individual ALK gene to elucidate the molecular function and substrate specificity of each P450ALK. Transcriptional activation of the ALK1 promoter by n-alkanes was observed in Δalk1-12 as in the wild-type strain, implying that n-alkanes per se, but not their metabolites, trigger n-alkane-induced transcriptional activation in Y. lipolytica.
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Affiliation(s)
- Hiroshi Takai
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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