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Fan C, Xie Z, Zheng D, Zhang R, Li Y, Shi J, Cheng M, Wang Y, Zhou Y, Zhan Y, Yan Y. Overview of indigo biosynthesis by Flavin-containing Monooxygenases: History, industrialization challenges, and strategies. Biotechnol Adv 2024; 73:108374. [PMID: 38729229 DOI: 10.1016/j.biotechadv.2024.108374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
Indigo is a natural dye extensively used in the global textile industry. However, the conventional synthesis of indigo using toxic compounds like aniline, formaldehyde, and hydrogen cyanide has led to environmental pollution and health risks for workers. This method also faces growing economic, sustainability, and environmental challenges. To address these issues, the concept of bio-indigo or indigo biosynthesis has been proposed as an alternative to aniline-based indigo synthesis. Among various enzymes, Flavin-containing Monooxygenases (FMOs) have shown promise in achieving a high yield of bio-indigo. However, the industrialization of indigo biosynthesis still encounters several challenges. This review focuses on the historical development of indigo biosynthesis mediated by FMOs. It highlights several factors that have hindered industrialization, including the use of unsuitable chassis (Escherichia coli), the toxicity of indole, the high cost of the substrate L-tryptophan, the water-insolubility of the product indigo, the requirement of reducing reagents such as sodium dithionite, and the relatively low yield and high cost compared to chemical synthesis. Additionally, this paper summarizes various strategies to enhance the yield of indigo synthesized by FMOs, including redundant sequence deletion, semi-rational design, cheap precursor research, NADPH regeneration, large-scale fermentation, and enhancement of water solubility of indigo.
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Affiliation(s)
- Changxin Fan
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Ziqi Xie
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Da Zheng
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Ruihan Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Yijin Li
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Jiacheng Shi
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Mingyuan Cheng
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Yifei Wang
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Yu Zhou
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China.
| | - Yi Zhan
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China.
| | - Yunjun Yan
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China.
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2
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Chandel N, Singh BB, Dureja C, Yang YH, Bhatia SK. Indigo production goes green: a review on opportunities and challenges of fermentative production. World J Microbiol Biotechnol 2024; 40:62. [PMID: 38182914 DOI: 10.1007/s11274-023-03871-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024]
Abstract
Indigo is a widely used dye in various industries, such as textile, cosmetics, and food. However, traditional methods of indigo extraction and processing are associated with environmental and economic challenges. Fermentative production of indigo using microbial strains has emerged as a promising alternative that offers sustainability and cost-effectiveness. This review article provides a critical overview of microbial diversity, metabolic pathways, fermentation strategies, and genetic engineering approaches for fermentative indigo production. The advantages and limitations of different indigo production systems and a critique of the current understanding of indigo biosynthesis are discussed. Finally, the potential application of indigo in other sectors is also discussed. Overall, fermentative production of indigo offers a sustainable and bio-based alternative to synthetic methods and has the potential to contribute to the development of sustainable and circular biomanufacturing.
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Affiliation(s)
- Neha Chandel
- School of Medical and Allied Sciences, GD Goenka University, Gurugram, Haryana, 122103, India
| | - Bharat Bhushan Singh
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chetna Dureja
- Center for Inflammatory and Infectious Diseases, Texas A&M Health Science Center, Institute of Bioscience and Technology, Houston, TX, USA
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
- Institute for Ubiquitous Information Technology and Applications, Seoul, 05029, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
- Institute for Ubiquitous Information Technology and Applications, Seoul, 05029, Republic of Korea.
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Liu C, Cheng M, Ma C, Chen J, Tan H. Identification of novel flavin-dependent monooxygenase from Strobilanthes Cusia reveals molecular basis of indoles' biosynthetic logic. BMC PLANT BIOLOGY 2023; 23:527. [PMID: 37904107 PMCID: PMC10617207 DOI: 10.1186/s12870-023-04557-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/23/2023] [Indexed: 11/01/2023]
Abstract
BACKGROUND Strobilanthes cusia (Nees) Kuntze is a traditional medical plant distributed widely in south China. The indole compounds that originated from the plant are responsible for its pharmacological activities. However, the reason why indole ingredients are accumulated in this herb and how it is biosynthesized has remained largely unknown. RESULTS In this study, metabolic and transcriptional profiling measurement experiments of different S. cusia organs were carried out to understand the underlying molecular basis of indoles' biosynthetic logic. A metabolic investigation demonstrated that the indoles are primarily accumulated mainly in aerial parts, particularly in leaves. RNA-seq was employed to reveal the organ specific accumulation of indoles in different S. cusia organs. Meanwhile, a flavin-dependent monooxygenase gene (ScFMO1) was found in S. cusia, and it has capacity to produce indoxyl from indole by the fermentation assay. Finally, we assessed the outcomes of transient expression experiment in tobacco and confirmed that ScFMO1 localizes in cytoplasm. CONCLUSIONS Our results suggest that ScFMO1 plays a key role in biosynthesis of indoles (Indigo, indirubin, indican, etc.), it will be useful for illuminating the molecular basis of the medicinal indoles' biosynthesis and developing strategies for improving their yields.
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Affiliation(s)
- Chang Liu
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China
- Department of Pharmacy, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Mengya Cheng
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Chao Ma
- Department of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Junfeng Chen
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Hexin Tan
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China.
- Department of Pharmacy, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, China.
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Louwen JJR, Kautsar SA, van der Burg S, Medema MH, van der Hooft JJJ. iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures. PLoS Comput Biol 2023; 19:e1010462. [PMID: 36758069 PMCID: PMC9946207 DOI: 10.1371/journal.pcbi.1010462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 02/22/2023] [Accepted: 01/24/2023] [Indexed: 02/11/2023] Open
Abstract
Microbial specialised metabolism is full of valuable natural products that are applied clinically, agriculturally, and industrially. The genes that encode their biosynthesis are often physically clustered on the genome in biosynthetic gene clusters (BGCs). Many BGCs consist of multiple groups of co-evolving genes called sub-clusters that are responsible for the biosynthesis of a specific chemical moiety in a natural product. Sub-clusters therefore provide an important link between the structures of a natural product and its BGC, which can be leveraged for predicting natural product structures from sequence, as well as for linking chemical structures and metabolomics-derived mass features to BGCs. While some initial computational methodologies have been devised for sub-cluster detection, current approaches are not scalable, have only been run on small and outdated datasets, or produce an impractically large number of possible sub-clusters to mine through. Here, we constructed a scalable method for unsupervised sub-cluster detection, called iPRESTO, based on topic modelling and statistical analysis of co-occurrence patterns of enzyme-coding protein families. iPRESTO was used to mine sub-clusters across 150,000 prokaryotic BGCs from antiSMASH-DB. After annotating a fraction of the resulting sub-cluster families, we could predict a substructure for 16% of the antiSMASH-DB BGCs. Additionally, our method was able to confirm 83% of the experimentally characterised sub-clusters in MIBiG reference BGCs. Based on iPRESTO-detected sub-clusters, we could correctly identify the BGCs for xenorhabdin and salbostatin biosynthesis (which had not yet been annotated in BGC databases), as well as propose a candidate BGC for akashin biosynthesis. Additionally, we show for a collection of 145 actinobacteria how substructures can aid in linking BGCs to molecules by correlating iPRESTO-detected sub-clusters to MS/MS-derived Mass2Motifs substructure patterns. This work paves the way for deeper functional and structural annotation of microbial BGCs by improved linking of orphan molecules to their cognate gene clusters, thus facilitating accelerated natural product discovery.
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Affiliation(s)
- Joris J. R. Louwen
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | - Satria A. Kautsar
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | | | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
- * E-mail: (MHM); (JJJvdH)
| | - Justin J. J. van der Hooft
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
- * E-mail: (MHM); (JJJvdH)
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Li Y, Lin Y, Wang F, Wang J, Shoji O, Xu J. Construction of Biocatalysts Using the P450 Scaffold for the Synthesis of Indigo from Indole. Int J Mol Sci 2023; 24:ijms24032395. [PMID: 36768714 PMCID: PMC9917246 DOI: 10.3390/ijms24032395] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
With the increasing demand for blue dyes, it is of vital importance to develop a green and efficient biocatalyst to produce indigo. This study constructed a hydrogen peroxide-dependent catalytic system for the direct conversion of indole to indigo using P450BM3 with the assistance of dual-functional small molecules (DFSM). The arrangements of amino acids at 78, 87, and 268 positions influenced the catalytic activity. F87G/T268V mutant gave the highest catalytic activity with kcat of 1402 min-1 and with a yield of 73%. F87A/T268V mutant was found to produce the indigo product with chemoselectivity as high as 80%. Moreover, F87G/T268A mutant was found to efficiently catalyze indole oxidation with higher activity (kcat/Km = 1388 mM-1 min-1) than other enzymes, such as the NADPH-dependent P450BM3 (2.4-fold), the Ngb (32-fold) and the Mb (117-fold). Computer simulation results indicate that the arrangements of amino acid residues in the active site can significantly affect the catalytic activity of the protein. The DFSM-facilitated P450BM3 peroxygenase system provides an alternative, simple approach for a key step in the bioproduction of indigo.
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Affiliation(s)
- Yanqing Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
| | - Yingwu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Fang Wang
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
| | - Jinghan Wang
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Correspondence: (O.S.); (J.X.)
| | - Jiakun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
- Correspondence: (O.S.); (J.X.)
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6
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Linke JA, Rayat A, Ward JM. Production of indigo by recombinant bacteria. BIORESOUR BIOPROCESS 2023; 10:20. [PMID: 36936720 PMCID: PMC10011309 DOI: 10.1186/s40643-023-00626-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/06/2023] [Indexed: 03/15/2023] Open
Abstract
Indigo is an economically important dye, especially for the textile industry and the dyeing of denim fabrics for jeans and garments. Around 80,000 tonnes of indigo are chemically produced each year with the use of non-renewable petrochemicals and the use and generation of toxic compounds. As many microorganisms and their enzymes are able to synthesise indigo after the expression of specific oxygenases and hydroxylases, microbial fermentation could offer a more sustainable and environmentally friendly manufacturing platform. Although multiple small-scale studies have been performed, several existing research gaps still hinder the effective translation of these biochemical approaches. No article has evaluated the feasibility and relevance of the current understanding and development of indigo biocatalysis for real-life industrial applications. There is no record of either established or practically tested large-scale bioprocess for the biosynthesis of indigo. To address this, upstream and downstream processing considerations were carried out for indigo biosynthesis. 5 classes of potential biocatalysts were identified, and 2 possible bioprocess flowsheets were designed that facilitate generating either a pre-reduced dye solution or a dry powder product. Furthermore, considering the publicly available data on the development of relevant technology and common bioprocess facilities, possible platform and process values were estimated, including titre, DSP yield, potential plant capacities, fermenter size and batch schedule. This allowed us to project the realistic annual output of a potential indigo biosynthesis platform as 540 tonnes. This was interpreted as an industrially relevant quantity, sufficient to provide an annual dye supply to a single industrial-size denim dyeing plant. The conducted sensitivity analysis showed that this anticipated output is most sensitive to changes in the reaction titer, which can bring a 27.8% increase or a 94.4% drop. Thus, although such a biological platform would require careful consideration, fine-tuning and optimization before real-life implementation, the recombinant indigo biosynthesis was found as already attractive for business exploitation for both, luxury segment customers and mass-producers of denim garments. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1186/s40643-023-00626-7.
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Affiliation(s)
- Julia A. Linke
- grid.83440.3b0000000121901201Chemical Engineering Department, University College London (UCL), Torrington Place, London, WC1E 7JE UK
- grid.83440.3b0000000121901201Division of Medicine, University College London (UCL), 5 University Street, London, WC1E 6JF UK
| | - Andrea Rayat
- grid.83440.3b0000000121901201Biochemical Engineering Department, University College London (UCL), Gower St., London, WC1E 6BT UK
| | - John M. Ward
- grid.83440.3b0000000121901201Biochemical Engineering Department, University College London (UCL), Gower St., London, WC1E 6BT UK
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Catucci G, Turella S, Cheropkina H, De Angelis M, Gilardi G, Sadeghi SJ. Green production of indigo and indirubin by an engineered Baeyer–Villiger monooxygenase. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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8
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Lee J, Kim J, Kim H, Park H, Kim JY, Kim EJ, Yang YH, Choi KY, Kim BG. Constructing multi-enzymatic cascade reactions for selective production of 6-bromoindirubin from tryptophan in Escherichia coli. Biotechnol Bioeng 2022; 119:2938-2949. [PMID: 35876239 DOI: 10.1002/bit.28188] [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: 05/26/2022] [Revised: 07/04/2022] [Accepted: 07/17/2022] [Indexed: 11/06/2022]
Abstract
6-Bromoindirubin (6BrIR), found in Murex sea snails, is a precursor of indirubin-derivatives anticancer drugs. However, its synthesis remains limited due to uncharacterized biosynthetic pathways and difficulties in site-specific bromination and oxidation at indole ring. Here, we present an efficient 6BrIR production strategy in E. coli by using four enzymes, i.e., tryptophan 6-halogenase fused with flavin reductase Fre (Fre-L3-SttH), tryptophanase (TnaA), toluene 4-monooxygenase (PmT4MO) and flavin-containing monooxygenase (MaFMO). Although most indole oxygenases preferentially oxygenate the electronically active C3 position of indole, PmT4MO was newly characterized to perform C2 oxygenation of 6-bromoindole with 45 % yield to produce 6-bromo-2-oxindole. In addition, 6BrIR was selectively generated without indigo and indirubin byproducts by controlling the reducing power of cysteine and oxygen supply during the MaFMO reaction. These approaches led to 34.1 mg/L 6BrIR productions, making it possible to produce the critical precursor of the anticancer drugs only from natural ingredients such as tryptophan, NaBr and oxygen. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jeongchan Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea.,Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
| | - Joonwon Kim
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Hyun Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - HyunA Park
- Department of Environmental Engineering, Ajou University, Suwon, Republic of Korea
| | - Jin Young Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea
| | - Eun-Jung Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea.,Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, Konkuk University, Seoul, Republic of Korea
| | - Kwon-Young Choi
- Department of Environmental Engineering, Ajou University, Suwon, Republic of Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea.,Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea.,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea.,Institute of Engineering Research, Seoul National University, Seoul, Republic of Korea
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9
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Qin M, Li Y, Cai L, Yin X, He Z, Kang J. Overexpression of the global regulator FnVeA up-regulates antitumor substances in endophytic Fusarium nematophilum. Can J Microbiol 2022; 68:531-541. [PMID: 35649283 DOI: 10.1139/cjm-2022-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The special niche of endophytic fungi promotes their potential to produce antitumor compounds with novel structure and significant bio-activity for screening of new antitumor drugs. In our previous studies, we isolated a Fusarium strain from the roots of the medicinal plant Nothapodytes pittosporoides and identified it as Fusarium nematophilum. We found that the crude extract of F. nematophilum had significant anti-tumor activity, and overexpressing the global regulatory factor FnVeA resulted in a significant increase in the anti-tumor activity, which was approximately 5-fold higher than wild strain for relative inhibition rate. In FnVeAOE, the accumulation of indole, alkene, alkaloid, steroid and flavonoid metabolites with potential anti-tumor activity were significantly up-regulated as compared with WT via metabolomic analysis. Moreover, the transcriptome analysis showed that 134 differential genes were considered to be closely related to the biosynthesis of anti-tumor substances, of which 59 differential genes were considered as candidate key genes, and related to tryptophan dimethylallyltransferase, cytochrome P450 monooxygenase, polyketide synthases and transcription factor. Taken together, we suggest that FnVeA may regulate the biosynthesis of anti-tumor substances by mediating the expression of genes related to secondary metabolic pathways in F. nematophilum. Key words: Endophytic Fusarium nematophilum; global regulator VeA; anti-tumor; metabolome; transcriptome.
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Affiliation(s)
- Min Qin
- Guizhou University, 71206, Guiyang, Guizhou, China;
| | - Yongjie Li
- Guizhou University, 71206, Guiyang, Guizhou, China;
| | - Lu Cai
- Guizhou University, 71206, Guiyang, Guizhou, China;
| | - Xuemin Yin
- Guizhou University, 71206, Guiyang, Guizhou, China;
| | | | - Jichuan Kang
- Guizhou University, 71206, Guiyang, Guizhou, China;
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10
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Song H, Lee PG, Kim J, Kim J, Lee SH, Kim H, Lee UJ, Kim JY, Kim EJ, Kim BG. Regioselective One-Pot Synthesis of Hydroxy-( S)-Equols Using Isoflavonoid Reductases and Monooxygenases and Evaluation of the Hydroxyequol Derivatives as Selective Estrogen Receptor Modulators and Antioxidants. Front Bioeng Biotechnol 2022; 10:830712. [PMID: 35402392 PMCID: PMC8987157 DOI: 10.3389/fbioe.2022.830712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/31/2022] [Indexed: 12/22/2022] Open
Abstract
Several regiospecific enantiomers of hydroxy-(S)-equol (HE) were enzymatically synthesized from daidzein and genistein using consecutive reduction (four daidzein-to-equol-converting reductases) and oxidation (4-hydroxyphenylacetate 3-monooxygenase, HpaBC). Despite the natural occurrence of several HEs, most of them had not been studied owing to the lack of their preparation methods. Herein, the one-pot synthesis pathway of 6-hydroxyequol (6HE) was developed using HpaBC (EcHpaB) from Escherichia coli and (S)-equol-producing E. coli, previously developed by our group. Based on docking analysis of the substrate or products, a potential active site and several key residues for substrate binding were predicted to interpret the (S)-equol hydroxylation regioselectivity of EcHpaB. Through investigating mutations on the key residues, the T292A variant was verified to display specific mono-ortho-hydroxylation activity at C6 without further 3'-hydroxylation. In the consecutive oxidoreductive bioconversion using T292A, 0.95 mM 6HE could be synthesized from 1 mM daidzein, while 5HE and 3'HE were also prepared from genistein and 3'-hydroxydaidzein (3'HD or 3'-ODI), respectively. In the following efficacy tests, 3'HE and 6HE showed about 30∼200-fold higher EC50 than (S)-equol in both ERα and ERβ, and they did not have significant SERM efficacy except 6HE showing 10% lower β/α ratio response than that of 17β-estradiol. In DPPH radical scavenging assay, 3'HE showed the highest antioxidative activity among the examined isoflavone derivatives: more than 40% higher than the well-known 3'HD. In conclusion, we demonstrated that HEs could be produced efficiently and regioselectively through the one-pot bioconversion platform and evaluated estrogenic and antioxidative activities of each HE regio-isomer for the first time.
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Affiliation(s)
- Hanbit Song
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Pyung-Gang Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
- Institute of Engineering Research, Seoul National University, Seoul, South Korea
| | - Junyeob Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Joonwon Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Sang-Hyuk Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Hyun Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Uk-Jae Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Jin Young Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Eun-Jung Kim
- Bio-MAX/N-Bio Institute, Seoul National University, Seoul, South Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
- Bio-MAX/N-Bio Institute, Seoul National University, Seoul, South Korea
- Institute for Sustainable Development (ISD), Seoul National University, Seoul, South Korea
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11
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Yin H, Chen H, Yan M, Li Z, Yang R, Li Y, Wang Y, Guan J, Mao H, Wang Y, Zhang Y. Efficient Bioproduction of Indigo and Indirubin by Optimizing a Novel Terpenoid Cyclase XiaI in Escherichia coli. ACS OMEGA 2021; 6:20569-20576. [PMID: 34396002 PMCID: PMC8359145 DOI: 10.1021/acsomega.1c02679] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Blue indigo dye, an important natural colorant, is used for textiles and food additives worldwide, while another red isomer, indirubin, is the major active ingredient of a traditional Chinese medicine named "Danggui Longhui Wan" for treating various diseases including granulocytic leukemia, cancer, and Alzheimer's disease. In this work, we constructed a new and highly efficient indigoid production system by optimizing a novel terpenoid cyclase, XiaI, from the xiamycin biosynthetic pathway. Through introducing the flavin-reducing enzyme Fre, tryptophan-lysing and -importing enzymes TnaA and TnaB, and H2O2-degrading enzyme KatE and optimizing the fermentation parameters including temperature, the concentration of isopropyl-β-d-thiogalactopyranoside, and feeding of the l-tryptophan precursor, the final maximum productivity of indigoids by the recombinant strain Escherichia coli BL21(DE3) (XiaI-Fre-TnaAB-KatE) was apparently improved to 101.9 mg/L, an approximately 60-fold improvement to that of the starting strain E. coli BL21(DE3) (XiaI) (1.7 mg/L). In addition, when the fermentation system was enlarged to 1 L in the flask (feeding with 5 mM tryptophan and 10 mM 2-hydroxyindole), the indigoid productivity further increased to 276.7 mg/L at 48 h, including an indigo productivity of 26.0 mg/L and an indirubin productivity of 250.7 mg/L, which has been the highest productivity of indirubin so far. This work provided a basis for the commercial production of bio-indigo and the clinical drug indirubin in the future.
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Affiliation(s)
- Huifang Yin
- School
of Life Sciences and Technology, Xinxiang
Medical University, Xinxiang, 453003 Henan, China
- Synthetic
Biology Engineering Lab of Henan Province, Xinxiang, 453003 Henan, China
| | - Hongping Chen
- School
of Life Sciences and Technology, Xinxiang
Medical University, Xinxiang, 453003 Henan, China
| | - Meng Yan
- School
of Life Sciences and Technology, Xinxiang
Medical University, Xinxiang, 453003 Henan, China
| | - Zhikun Li
- School
of Life Sciences and Technology, Xinxiang
Medical University, Xinxiang, 453003 Henan, China
| | - Rongdi Yang
- School
of Life Sciences and Technology, Xinxiang
Medical University, Xinxiang, 453003 Henan, China
| | - Yanjiao Li
- School
of Life Sciences and Technology, Xinxiang
Medical University, Xinxiang, 453003 Henan, China
| | - Yanfang Wang
- School
of Life Sciences and Technology, Xinxiang
Medical University, Xinxiang, 453003 Henan, China
| | - Jianyi Guan
- School
of Life Sciences and Technology, Xinxiang
Medical University, Xinxiang, 453003 Henan, China
- Synthetic
Biology Engineering Lab of Henan Province, Xinxiang, 453003 Henan, China
| | - Huili Mao
- School
of Life Sciences and Technology, Xinxiang
Medical University, Xinxiang, 453003 Henan, China
| | - Yan Wang
- School
of Life Sciences and Technology, Xinxiang
Medical University, Xinxiang, 453003 Henan, China
- Synthetic
Biology Engineering Lab of Henan Province, Xinxiang, 453003 Henan, China
| | - Yuyang Zhang
- School
of Life Sciences and Technology, Xinxiang
Medical University, Xinxiang, 453003 Henan, China
- Synthetic
Biology Engineering Lab of Henan Province, Xinxiang, 453003 Henan, China
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12
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Choi K. Nitrogen‐Neutral Amino Acids Refinery: Deamination of Amino Acids for Bio‐Alcohol and Ammonia Production. CHEMBIOENG REVIEWS 2021. [DOI: 10.1002/cben.202000031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kwon‐Young Choi
- Ajou University Department of Environmental and Safety Engineering College of Engineering Suwon, Gyeonggi-do South Korea
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13
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14
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Production of Tyrian purple indigoid dye from tryptophan in Escherichia coli. Nat Chem Biol 2020; 17:104-112. [PMID: 33139950 DOI: 10.1038/s41589-020-00684-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022]
Abstract
Tyrian purple, mainly composed of 6,6'-dibromoindigo (6BrIG), is an ancient dye extracted from sea snails and was recently demonstrated as a biocompatible semiconductor material. However, its synthesis remains limited due to uncharacterized biosynthetic pathways and the difficulty of regiospecific bromination. Here, we introduce an effective 6BrIG production strategy in Escherichia coli using tryptophan 6-halogenase SttH, tryptophanase TnaA and flavin-containing monooxygenase MaFMO. Since tryptophan halogenases are expressed in highly insoluble forms in E. coli, a flavin reductase (Fre) that regenerates FADH2 for the halogenase reaction was used as an N-terminal soluble tag of SttH. A consecutive two-cell reaction system was designed to overproduce regiospecifically brominated precursors of 6BrIG by spatiotemporal separation of bromination and bromotryptophan degradation. These approaches led to 315.0 mg l-1 6BrIG production from tryptophan and successful synthesis of regiospecifically dihalogenated indigos. Furthermore, it was demonstrated that 6BrIG overproducing cells can be directly used as a bacterial dye.
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15
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Finnigan JD, Young C, Cook DJ, Charnock SJ, Black GW. Cytochromes P450 (P450s): A review of the class system with a focus on prokaryotic P450s. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:289-320. [PMID: 32951814 DOI: 10.1016/bs.apcsb.2020.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cytochromes P450 (P450s) are a large superfamily of heme-containing monooxygenases. P450s are found in all Kingdoms of life and exhibit incredible diversity, both at sequence level and also on a biochemical basis. In the majority of cases, P450s can be assigned into one of ten classes based on their associated redox partners, domain architecture and cellular localization. Prokaryotic P450s now represent a large diverse collection of annotated/known enzymes, of which many have great potential biocatalytic potential. The self-sufficient P450 classes (Class VII/VIII) have been explored significantly over the past decade, with many annotated and biochemically characterized members. It is clear that the prokaryotic P450 world is expanding rapidly, as the number of published genomes and metagenome studies increases, and more P450 families are identified and annotated (CYP families).
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Affiliation(s)
| | - Carl Young
- Prozomix Limited, Haltwhistle, Northumberland, United Kingdom
| | - Darren J Cook
- Prozomix Limited, Haltwhistle, Northumberland, United Kingdom
| | | | - Gary W Black
- Hub for Biotechnology in the Built Environment, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
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16
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Park H, Yang I, Choi M, Jang KS, Jung JC, Choi KY. Engineering of melanin biopolymer by co-expression of MelC tyrosinase with CYP102G4 monooxygenase: Structural composition understanding by 15 tesla FT-ICR MS analysis. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107530] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Xie L, Chen K, Cui H, Wan N, Cui B, Han W, Chen Y. Characterization of a Self-Sufficient Cytochrome P450 Monooxygenase from Deinococcus apachensis for Enantioselective Benzylic Hydroxylation. Chembiochem 2020; 21:1820-1825. [PMID: 32012422 DOI: 10.1002/cbic.201900691] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/29/2020] [Indexed: 12/22/2022]
Abstract
A self-sufficient cytochrome P450 monooxygenase from Deinococcus apachensis (P450DA) was identified and successfully overexpressed in Escherichia coli BL21(DE3). P450DA would be a member of the CYP102D subfamily and assigned as CYP102D2 according to the phylogenetic tree and sequence alignment. Purification and characterization of the recombinant P450DA indicated both NADH and NADPH could be used by P450DA as a reducing cofactor. The recombinant E. coli (P450DA) strain was functionally active, showing excellent enantioselectivity for benzylic hydroxylation of methyl 2-phenylacetate. Further substrate scope studies revealed that P450DA is able to catalyze benzylic hydroxylation of a variety of compounds, affording the corresponding chiral benzylic alcohols in 86-99 % ee and 130-1020 total turnover numbers.
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Affiliation(s)
- Lingzhi Xie
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563000, China
| | - Ke Chen
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563000, China
| | - Haibo Cui
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563000, China
| | - Nanwei Wan
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563000, China
| | - Baodong Cui
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563000, China
| | - Wenyong Han
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563000, China
| | - Yongzheng Chen
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563000, China
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18
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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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19
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Fabara AN, Fraaije MW. An overview of microbial indigo-forming enzymes. Appl Microbiol Biotechnol 2019; 104:925-933. [PMID: 31834440 PMCID: PMC6962290 DOI: 10.1007/s00253-019-10292-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/23/2019] [Accepted: 11/28/2019] [Indexed: 11/03/2022]
Abstract
Indigo is one of the oldest textile dyes and was originally prepared from plant material. Nowadays, indigo is chemically synthesized at a large scale to satisfy the demand for dyeing jeans. The current indigo production processes are based on fossil feedstocks; therefore, it is highly attractive to develop a more sustainable and environmentally friendly biotechnological process for the production of this popular dye. In the past decades, a number of natural and engineered enzymes have been identified that can be used for the synthesis of indigo. This mini-review provides an overview of the various microbial enzymes which are able to produce indigo and discusses the advantages and disadvantages of each biocatalytic system.
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Affiliation(s)
- Andrea N Fabara
- Molecular Enzymology group, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology group, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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20
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Lončar N, van Beek HL, Fraaije MW. Structure-Based Redesign of a Self-Sufficient Flavin-Containing Monooxygenase towards Indigo Production. Int J Mol Sci 2019; 20:ijms20246148. [PMID: 31817552 PMCID: PMC6940849 DOI: 10.3390/ijms20246148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 12/12/2022] Open
Abstract
Indigo is currently produced by a century-old petrochemical-based process, therefore it is highly attractive to develop a more environmentally benign and efficient biotechnological process to produce this timeless dye. Flavin-containing monooxygenases (FMOs) are able to oxidize a wide variety of substrates. In this paper we show that the bacterial mFMO can be adapted to improve its ability to convert indole into indigo. The improvement was achieved by a combination of computational and structure-inspired enzyme redesign. We showed that the thermostability and the kcat for indole could be improved 1.5-fold by screening a relatively small number of enzyme mutants. This project not only resulted in an improved biocatalyst but also provided an improved understanding of the structural elements that determine the activity of mFMO and provides hints for further improvement of the monooxygenase as biocatalyst.
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Affiliation(s)
| | - Hugo L. van Beek
- Molecular Enzymology group, University of Groningen, 9747 AG Groningen, The Netherlands;
| | - Marco W. Fraaije
- Molecular Enzymology group, University of Groningen, 9747 AG Groningen, The Netherlands;
- Correspondence: ; Tel.: +31-50-3634345
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21
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Kim J, Lee J, Lee PG, Kim EJ, Kroutil W, Kim BG. Elucidating Cysteine-Assisted Synthesis of Indirubin by a Flavin-Containing Monooxygenase. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02613] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | | | | | | | - Wolfgang Kroutil
- Institute of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Graz, 8074, Austria
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