1
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Guo Y, Hu SY, Wu C, Gao CX, Hui CY. Biosynthesis of Indigo Dyes and Their Application in Green Chemical and Visual Biosensing for Heavy Metals. ACS OMEGA 2024; 9:33868-33881. [PMID: 39130558 PMCID: PMC11308077 DOI: 10.1021/acsomega.4c03613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 08/13/2024]
Abstract
Fermentative production of natural colorants using microbial strains has emerged as a cost-effective and sustainable alternative to chemical synthesis. Visual pigments are used as signal outputs in colorimetric bacterial biosensors, a promising method for monitoring environmental pollutants. In this study, we engineered four self-sufficient indigo-forming enzymes, including HbpAv, bFMO, cFMO, and rFPMO, in a model bacterium E. coli. TrxA-bFMO was chosen for its strong ability to produce indigo under T7 lac and mer promoters' regulation. The choice of bacterial hosts, the supplementation of substrate l-tryptophan, and ventilation were crucial factors affecting indigo production. The indigo reporter validated the biosensors for Hg(II), Pb(II), As(III), and Cd(II). The biosensors reported Hg(II) as low as 14.1 nM, Pb(II) as low as 1.5 nM, and As(III) as low as 4.5 nM but increased to 25 μM for Cd(II). The detection ranges for Hg(II), Pb(II), As(III), and Cd(II) were quantified from 14.1 to 225 nM, 1.5 to 24.4 nM, 4.5 to 73.2 nM, and 25 to 200 μM, respectively. The sensitivity, responsive concentration range, and selectivity are comparable to β-galactosidase and luciferase reporter enzymes. This study suggests that engineered enzymes for indigo production have great potential for green chemical synthesis. Additionally, heterologous biosynthesis of indigo production can lead to the development of novel, low-cost, and mini-equipment bacterial biosensors with zero background noise for visual monitoring of pollutant heavy metals.
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Affiliation(s)
- Yan Guo
- National
Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen 518020, China
| | - Shun-Yu Hu
- Department
of Pathology and Toxicology, Shenzhen Prevention
and Treatment Center for Occupational Diseases, Shenzhen 518020, China
- Department
of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Can Wu
- Department
of Pathology and Toxicology, Shenzhen Prevention
and Treatment Center for Occupational Diseases, Shenzhen 518020, China
- Department
of Environmental Health, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Chao-Xian Gao
- Department
of Pathology and Toxicology, Shenzhen Prevention
and Treatment Center for Occupational Diseases, Shenzhen 518020, China
| | - Chang-Ye Hui
- Department
of Pathology and Toxicology, Shenzhen Prevention
and Treatment Center for Occupational Diseases, Shenzhen 518020, China
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2
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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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3
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Du J, Li Y, Chen Z, Wang C, Huang Y, Li L. Functional characterization of a novel flavin reductase from a deep-sea sediment metagenomic library and its application for indirubin production. Appl Environ Microbiol 2024; 90:e0042924. [PMID: 38780258 PMCID: PMC11218617 DOI: 10.1128/aem.00429-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Microbial synthesis is a desirable approach to produce indirubin but suffers from low synthetic efficiency. Insufficient supply of reduced flavins is one major factor limiting synthetic efficiency. To address this, a novel flavin reductase, MoxB, was discovered through screening of the metagenomic library. MoxB showed a strong preference for NADH over NADPH as the electron source for FMN/FAD reduction and exhibited the highest activity at pH 8.0 and 30°C. It displayed remarkable thermostability by maintaining 80% of full activity after incubation at 60°C for 1 h. Furthermore, MoxB showed great organic solvent tolerance and its activity could be significantly increased by bivalent metal ions. In addition, heterologous expression of the moxB gene in the indirubin-producing E. coli significantly improved indirubin production up to 15.12-fold. This discovery expands the understanding of flavin reductases and provides a promising catalytic tool for microbial indirubin production.IMPORTANCEMuch effort has been exerted to produce indirubin using engineered Escherichia coli, but high-level production has not been achieved so far. Insufficient supply of reduced flavins is one key factor limiting the catalytic efficiency. However, the flavin reductases involved in indirubin biosynthesis have not been hitherto reported. Discovery of the novel flavin reductase MoxB provides a useful tool for enhancing indirubin production by E. coli. Overexpression of MoxB in indirubin-producing E. coli increased indirubin production by 15.12-fold in comparison to the control strain. Our results document the function of flavin reductase that reduces flavins during indirubin biosynthesis and provide an important foundation for using the flavin reductases to improve indirubin production by engineered microorganisms.
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Affiliation(s)
- Jikun Du
- Central Research Laboratory, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
| | - Yuanhua Li
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Zhengzhuang Chen
- Central Research Laboratory, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
- Postgraduate Training Base of Guangzhou University of Chinese Medicine, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
| | - Chang Wang
- Central Research Laboratory, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
- Postgraduate Training Base of Guangzhou University of Chinese Medicine, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
| | - Yali Huang
- Basic Medical Science College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Li Li
- Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China
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4
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Kim HJ, Ham S, Shin N, Hwang JH, Oh SJ, Choi TR, Joo JC, Bhatia SK, Yang YH. Tryptophan-Based Hyperproduction of Bioindigo by Combinatorial Overexpression of Two Different Tryptophan Transporters. J Microbiol Biotechnol 2024; 34:969-977. [PMID: 38213292 PMCID: PMC11091664 DOI: 10.4014/jmb.2308.08039] [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: 08/21/2023] [Revised: 11/18/2023] [Accepted: 11/22/2023] [Indexed: 01/13/2024]
Abstract
Indigo is a valuable, natural blue dye that has been used for centuries in the textile industry. The large-scale commercial production of indigo relies on its extraction from plants and chemical synthesis. Studies are being conducted to develop methods for environment-friendly and sustainable production of indigo using genetically engineered microbes. Here, to enhance the yield of bioindigo from an E. coli whole-cell system containing tryptophanase (TnaA) and flavin-containing monooxygenase (FMO), we evaluated tryptophan transporters to improve the transport of aromatic compounds, such as indole and tryptophan, which are not easily soluble and passable through cell walls. Among the three transporters, Mtr, AroP, and TnaB, AroP enhanced indigo production the most. The combination of each transporter with AroP was also evaluated, and the combination of AroP and TnaB showed the best performance compared to the single transporters and two transporters. Bioindigo production was then optimized by examining the culture medium, temperature, isopropyl β-D-1-thiogalactopyranoside concentration, shaking speed (rpm), and pH. The novel strain containing aroP and tnaB plasmid with tnaA and FMO produced 8.77 mM (2.3 g/l) of bioindigo after 66 h of culture. The produced bioindigo was further recovered using a simple method and used as a watercolor dye, showing good mixing with other colors and color retention for a relatively long time. This study presents an effective strategy for enhancing indigo production using a combination of transporters.
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Affiliation(s)
- Hyun Jin Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Sion Ham
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Nara Shin
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jeong Hyeon Hwang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Suk Jin Oh
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Tae-Rim Choi
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jeong Chan Joo
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, 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 Application, Konkuk University, Seoul 05029, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
- Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul 05029, Republic of Korea
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5
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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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6
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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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7
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Du J, Li Y, Huang Y, Zhang D, Li L. Characterization of a novel monooxygenase originating from a deep-sea sediment metagenomic library. Appl Microbiol Biotechnol 2023; 107:6237-6249. [PMID: 37581624 DOI: 10.1007/s00253-023-12719-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/12/2023] [Accepted: 08/01/2023] [Indexed: 08/16/2023]
Abstract
Oxygenases are important biocatalysts to produce many industrially important biomolecules. Here, a novel oxygenase, named MoxA, was identified through screening of a deep-sea sediment metagenomic library. Sequence analysis showed MoxA contains 424 amino acid residues with a predicated molecular mass of 46.9 kDa. Multiple sequence alignment and phylogenetic analysis indicated the sequence might be a new member of monooxygenase subfamily. A recombinant MoxA was obtained through the functional expression of moxA gene in Escherichia coli. Characterization of the purified MoxA indicated that it is an alkaline oxygenase showing maximal activity at pH 8.0. The optimal temperature of MoxA was 37 ℃, and it retained more than 70% of its initial activity after 1 h at 20-50 ℃ exhibiting good thermostability. Furthermore, effect of metal ions and organic solvents on enzymatic activity was investigated, and the results showed that the activity of MoxA was enhanced by Cu2+, Zn2+, Co2+ and Mg2+ at 1 mM, and by Co2+, Ca2+ and Mg2+ at 5 mM. Moreover, the recombinant strain harboring MoxA was used as a whole-cell biocatalyst for the efficient biosynthesis of indigo showing promising conversion efficiency. The biochemical properties of MoxA indicated that it would provide great contribution for the indigo bioproduction. KEY POINTS: • A novel monooxygenase from a metagenomic library was characterized. • The activity of MoxA was enhanced by metal ions at 1 mM and 5 mM. • MoxA has an optimal temperature of 37 ℃ and exhibited high conversion capacity.
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Affiliation(s)
- Jikun Du
- Central Research Laboratory, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, 518104, China.
| | - Yuanhua Li
- Central Research Laboratory, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, 518104, China
- Traditional Chinese Medicine and New Drug Research Institute, Department of Pharmacology, Guangdong Medical University, Dongguan, 523808, China
| | - Yali Huang
- College of Fundamental Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Dawei Zhang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Li Li
- Traditional Chinese Medicine and New Drug Research Institute, Department of Pharmacology, Guangdong Medical University, Dongguan, 523808, China.
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Deng JJ, Hu JY, Han XY, Li Y, Luo XC, Wang ZL, Li JZ. Degradation of indole via a two-component indole oxygenase system from Enterococcus hirae GDIAS-5. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131707. [PMID: 37379596 DOI: 10.1016/j.jhazmat.2023.131707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/30/2023]
Abstract
Animal farming copiously generates indoles, which contribute to odor and pose a challenge for deodorization. While biodegradation is widely accepted, there is a lack of suitable indole-degrading bacteria for animal husbandry. In this study, we aimed to construct genetically engineered strains with indole-degrading abilities. Enterococcus hirae GDIAS-5 is a highly efficient indole-degrading bacterium, which functions via a monooxygenase YcnE presumably contributes to indole oxidation. However, the efficiency of engineered Escherichia coli expressing YcnE for indole degradation is lower than that of GDIAS-5. To improve its efficacy, the underlying indole-degradation mechanisms in GDIAS-5 were analyzed. An ido operon that responds to a two-component indole oxygenase system was identified. In vitro experiments showed that the reductase component of YcnE, YdgI, can improve the catalytic efficiency. The reconstruction of the two-component system in E. coli exhibited higher indole removal efficiency than GDIAS-5. Furthermore, isatin, the key intermediate metabolite in indole degradation, might be degraded via a novel isatin-acetaminophen-aminophenol pathway involving an amidase whose coding gene is located near the ido operon. The two-component anaerobic oxidation system, upstream degradation pathway, and engineering strains investigated in this study provide important insights into indole degradation metabolism and offer efficient resources for achieving bacterial odor elimination.
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Affiliation(s)
- Jun-Jin Deng
- Agro-Biological Gene Research Center, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangdong Academy of Agricultural Sciences, No. 20 Jinying Road, Tianhe, Guangzhou, Guangdong 510640, China; Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, The Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Animal Breeding and Nutrition, No. 1 Dafeng Street, Wushan Road, Tianhe, Guangzhou, Guangdong 510640, China
| | - Jing-Yi Hu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu, Guangzhou, Guangdong 510006, China
| | - Xue-Ying Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu, Guangzhou, Guangdong 510006, China
| | - Yang Li
- Agro-Biological Gene Research Center, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangdong Academy of Agricultural Sciences, No. 20 Jinying Road, Tianhe, Guangzhou, Guangdong 510640, China
| | - Xiao-Chun Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu, Guangzhou, Guangdong 510006, China
| | - Zhi-Lin Wang
- Agro-Biological Gene Research Center, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangdong Academy of Agricultural Sciences, No. 20 Jinying Road, Tianhe, Guangzhou, Guangdong 510640, China.
| | - Jia-Zhou Li
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, The Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Animal Breeding and Nutrition, No. 1 Dafeng Street, Wushan Road, Tianhe, Guangzhou, Guangdong 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture Heyuan Sub-center, Heyuan, Guangdong 517000, China.
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9
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Cho DH, Kim HJ, Oh SJ, Hwang JH, Shin N, Bhatia SK, Yoon JJ, Jeon JM, Yang YH. Strategy for efficiently utilizing Escherichia coli cells producing isobutanol by combining isobutanol and indigo production systems. J Biotechnol 2023; 367:62-70. [PMID: 37019156 DOI: 10.1016/j.jbiotec.2023.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023]
Abstract
Isobutanol is a potential biofuel, and its microbial production systems have demonstrated promising results. In a microbial system, the isobutanol produced is secreted into the media; however, the cells remaining after fermentation cannot be used efficiently during the isobutanol recovery process and are discarded as waste. To address this, we aimed to investigate the strategy of utilizing these remaining cells by combining the isobutanol production system with the indigo production system, wherein the product accumulates intracellularly. Accordingly, we constructed E. coli systems with genes, such as acetolactate synthase gene (alsS), ketol-acid reductoisomerase gene (ilvC), dihydroxyl-acid dehydratase (ilvD), and alpha-ketoisovalerate decarboxylase gene (kivD), for isobutanol production and genes, such as tryptophanase gene (tnaA) and flavin-containing monooxygenase gene (FMO), for indigo production. This system produced isobutanol and indigo simultaneously while accumulating indigo within cells. The production of isobutanol and indigo exhibited a strong linear correlation up to 72 h of production time; however, the pattern of isobutanol and indigo production varied. To our knowledge, this study is the first to simultaneously produce isobutanol and indigo and can potentially enhance the economy of biochemical production.
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Affiliation(s)
- Do Hyun Cho
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Hyun Jin Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Suk Jin Oh
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jeong Hyeon Hwang
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Nara Shin
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Applications, Konkuk University, Seoul, South Korea
| | - Jeong-Jun Yoon
- Green & Sustainable Materials R&D Department, Korea Institute of Industrial Technology (KITECH), Cheonan, Republic of Korea
| | - Jong-Min Jeon
- Green & Sustainable Materials R&D Department, Korea Institute of Industrial Technology (KITECH), Cheonan, Republic of Korea.
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Applications, Konkuk University, Seoul, South Korea.
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10
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Ham S, Cho DH, Oh SJ, Hwang JH, Kim HJ, Shin N, Ahn J, Choi KY, Bhatia SK, Yang YH. Enhanced production of bio-indigo in engineered Escherichia coli, reinforced by cyclopropane-fatty acid-acyl-phospholipid synthase from psychrophilic Pseudomonas sp. B14-6. J Biotechnol 2023; 366:1-9. [PMID: 36849085 DOI: 10.1016/j.jbiotec.2023.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/29/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Indigo dye is an organic compound with a distinctive blue color. Most of the indigo currently used in industry is produced via chemical synthesis, which generates a large amount of wastewater. Therefore, several studies have recently been conducted to find ways to produce indigo eco-friendly using microorganisms. Here, we produced indigo using recombinant Escherichia coli with both an indigo-producing plasmid and a cyclopropane fatty acid (CFA)-regulating plasmid. The CFA-regulating plasmid contains the cfa gene, and its expression increases the CFA composition of the phospholipid fatty acids of the cell membrane. Overexpression of cfa showed cytotoxicity resistance of indole, an intermediate product formed during the indigo production process. This had a positive effect on indigo production and cfa originated from Pseudomonas sp. B 14-6 was used. Optimal conditions for indigo production were determined by adjusting the expression strain, culture temperature, shaking speed, and isopropyl β-D-1-thiogalactopyranoside concentration. Treatment with Tween 80 at a particular concentration to increase the permeability of the cell membrane had a positive effect on indigo production. The strain with the CFA plasmid produced 4.1 mM of indigo after 24 h of culture and produced 1.5-fold higher indigo than the control strain without the CFA plasmid that produced 2.7 mM.
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Affiliation(s)
- Sion Ham
- Department of Biological Engineering, College of Engineering, Konkuk University, the Republic of Korea
| | - Do-Hyun Cho
- Department of Biological Engineering, College of Engineering, Konkuk University, the Republic of Korea
| | - Suk Jin Oh
- Department of Biological Engineering, College of Engineering, Konkuk University, the Republic of Korea
| | - Jeong Hyeon Hwang
- Department of Biological Engineering, College of Engineering, Konkuk University, the Republic of Korea
| | - Hyun Jin Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, the Republic of Korea
| | - Nara Shin
- Department of Biological Engineering, College of Engineering, Konkuk University, the Republic of Korea
| | - Jungoh Ahn
- Biotechnology Process Engineering Center, Korea Research Institute Bioscience Biotechnology (KRIBB), the Republic of Korea
| | - Kwon-Young Choi
- Department of Environmental and Safety Engineering, College of Engineering, Ajou University, the Republic of Korea; Department of Energy Systems Research, Ajou University, the Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, the Republic of Korea.
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, the Republic of Korea.
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11
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Li F, Deng H, Zhong B, Ruan B, Zhao X, Luo X. Identification of an indole biodegradation gene cluster from Providencia rettgeri and its contribution in selectively biosynthesizing Tyrian purple. Front Bioeng Biotechnol 2023; 10:1109929. [PMID: 36704308 PMCID: PMC9871250 DOI: 10.3389/fbioe.2022.1109929] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023] Open
Abstract
Tyrian purple, mainly composed of 6, 6'-dibromoindigo, is a precious dye extracted from sea snails. In this study, we found Tyrian purple can be selectively produced by a bacterial strain GS-2 when fed with 6-bromotryptophan in the presence of tryptophan. This GS-2 strain was then identified as Providencia rettgeri based on bacterial genome sequencing analysis. An indole degradation gene cluster for indole metabolism was identified from this GS-2 strain. The heterologous expression of the indole degradation gene cluster in Escherichia coli BL21 (DE3) and in vitro enzymatic reaction demonstrated that the indole biodegradation gene cluster may contribute to selectively biosynthesizing Tyrian purple. To further explore the underlying mechanism of the selectivity, we explored the intermediates in this indole biodegradation pathway using liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry (LC-ESI-QTOF-MS/MS), which indicated that the indole biodegradation pathway in Providencia rettgeri is the catechol pathway. Interestingly, the monooxygenase GS-C co-expressed with its corresponding reductase GS-D in the cluster has better activity for the biosynthesis of Tyrian purple compared with the previously reported monooxygenase from Methylophaga aminisulfidivorans (MaFMO) or Streptomyces cattleya cytochrome P450 enzyme (CYP102G4). This is the first study to show the existence of an indole biodegradation pathway in Providencia rettgeri, and the indole biodegradation gene cluster can contribute to the selective production of Tyrian purple.
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Affiliation(s)
- Feifei Li
- School of Life Sciences, Inner Mongolia University, Hohhot, China,Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Huaxiang Deng
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Biming Zhong
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Banlai Ruan
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xixi Zhao
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,*Correspondence: Xixi Zhao, ; Xiaozhou Luo,
| | - Xiaozhou Luo
- School of Life Sciences, Inner Mongolia University, Hohhot, China,Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,*Correspondence: Xixi Zhao, ; Xiaozhou Luo,
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12
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Mellor SB, Behrendorff JBYH, Ipsen JØ, Crocoll C, Laursen T, Gillam EMJ, Pribil M. Exploiting photosynthesis-driven P450 activity to produce indican in tobacco chloroplasts. FRONTIERS IN PLANT SCIENCE 2023; 13:1049177. [PMID: 36743583 PMCID: PMC9890960 DOI: 10.3389/fpls.2022.1049177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/14/2022] [Indexed: 05/28/2023]
Abstract
Photosynthetic organelles offer attractive features for engineering small molecule bioproduction by their ability to convert solar energy into chemical energy required for metabolism. The possibility to couple biochemical production directly to photosynthetic assimilation as a source of energy and substrates has intrigued metabolic engineers. Specifically, the chemical diversity found in plants often relies on cytochrome P450-mediated hydroxylations that depend on reductant supply for catalysis and which often lead to metabolic bottlenecks for heterologous production of complex molecules. By directing P450 enzymes to plant chloroplasts one can elegantly deal with such redox prerequisites. In this study, we explore the capacity of the plant photosynthetic machinery to drive P450-dependent formation of the indigo precursor indoxyl-β-D-glucoside (indican) by targeting an engineered indican biosynthetic pathway to tobacco (Nicotiana benthamiana) chloroplasts. We show that both native and engineered variants belonging to the human CYP2 family are catalytically active in chloroplasts when driven by photosynthetic reducing power and optimize construct designs to improve productivity. However, while increasing supply of tryptophan leads to an increase in indole accumulation, it does not improve indican productivity, suggesting that P450 activity limits overall productivity. Co-expression of different redox partners also does not improve productivity, indicating that supply of reducing power is not a bottleneck. Finally, in vitro kinetic measurements showed that the different redox partners were efficiently reduced by photosystem I but plant ferredoxin provided the highest light-dependent P450 activity. This study demonstrates the inherent ability of photosynthesis to support P450-dependent metabolic pathways. Plants and photosynthetic microbes are therefore uniquely suited for engineering P450-dependent metabolic pathways regardless of enzyme origin. Our findings have implications for metabolic engineering in photosynthetic hosts for production of high-value chemicals or drug metabolites for pharmacological studies.
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Affiliation(s)
- Silas B. Mellor
- Section for Plant Biochemistry, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - James B. Y. H. Behrendorff
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
- Australian Research Council (ARC) Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia
| | - Johan Ø. Ipsen
- Section for Forest, Nature and Biomass, Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Christoph Crocoll
- DynaMo Center, Section for Molecular Plant Biology, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Tomas Laursen
- Section for Plant Biochemistry, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Elizabeth M. J. Gillam
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Mathias Pribil
- Section for Molecular Plant Biology, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
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Xiao S, Wang Z, Wang B, Hou B, Cheng J, Bai T, Zhang Y, Wang W, Yan L, Zhang J. Expanding the application of tryptophan: Industrial biomanufacturing of tryptophan derivatives. Front Microbiol 2023; 14:1099098. [PMID: 37032885 PMCID: PMC10076799 DOI: 10.3389/fmicb.2023.1099098] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
Tryptophan derivatives are various aromatic compounds produced in the tryptophan metabolic pathway, such as 5-hydroxytryptophan, 5-hydroxytryptamine, melatonin, 7-chloro-tryptophan, 7-bromo-tryptophan, indigo, indirubin, indole-3-acetic acid, violamycin, and dexoyviolacein. They have high added value, widely used in chemical, food, polymer and pharmaceutical industry and play an important role in treating diseases and improving life. At present, most tryptophan derivatives are synthesized by biosynthesis. The biosynthesis method is to combine metabolic engineering with synthetic biology and system biology, and use the tryptophan biosynthesis pathway of Escherichia coli, Corynebacterium glutamicum and other related microorganisms to reconstruct the artificial biosynthesis pathway, and then produce various tryptophan derivatives. In this paper, the characteristics, applications and specific biosynthetic pathways and methods of these derivatives were reviewed, and some strategies to increase the yield of derivatives and reduce the production cost on the basis of biosynthesis were introduced in order to make some contributions to the development of tryptophan derivatives biosynthesis industry.
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Affiliation(s)
- Shujian Xiao
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Zhen Wang
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
| | - Bangxu Wang
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Bo Hou
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Jie Cheng
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, China
- *Correspondence: Jie Cheng, ; Lixiu Yan, ; Jiamin Zhang,
| | - Ting Bai
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yin Zhang
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Wei Wang
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Lixiu Yan
- Chongqing Academy of Metrology and Quality Inspection, Chongqing, China
- *Correspondence: Jie Cheng, ; Lixiu Yan, ; Jiamin Zhang,
| | - Jiamin Zhang
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, China
- *Correspondence: Jie Cheng, ; Lixiu Yan, ; Jiamin Zhang,
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14
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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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15
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Aukema KG, Bygd MD, Tassoulas LJ, Richman JE, Wackett LP. Fluoro-recognition: New in vivo fluorescent assay for toluene dioxygenase probing induction by and metabolism of polyfluorinated compounds. Environ Microbiol 2022; 24:5202-5216. [PMID: 36054238 PMCID: PMC9828342 DOI: 10.1111/1462-2920.16187] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/30/2022] [Indexed: 01/12/2023]
Abstract
The present study examined the regulatory and metabolic response of the aromatic degrader Pseudomonas putida F1 and its tod operon, controlling toluene degradation, to fluorinated aromatic and aliphatic compounds. The tod operon is upregulated by inducer binding to the TodS sensing domain of a two-component regulator. The induced enzymes include toluene dioxygenase that initiates catabolic assimilation of benzenoid hydrocarbons. Toluene dioxygenase was shown to oxidize 6-fluoroindole to a meta-stable fluorescent product, 6-fluoroindoxyl. The fluorescent output allowed monitoring relative levels of tod operon induction in whole cells using microtiter well plates. Mono- and polyfluorinated aromatic compounds were shown to induce toluene dioxygenase, in some cases to a greater extent than compounds serving as growth substrates. Compounds that are oxidized by toluene dioxygenase and undergoing defluorination were shown to induce their own metabolism. 1,2,4-Trifluorobenzene caused significant induction and computational modelling indicated productive binding to the TodS sensor domain of the TodST regulator. Toluene dioxygenase also showed preferential binding of 1,2,4-trifluorobenzene such that defluorination was favoured. Fluorinated aliphatic compounds were shown to induce toluene dioxygenase. An aliphatic ether with seven fluorine atoms, 1,1,1,2-tetrafluoro-2-trifluoromethoxy-4-iodobutane (TTIB), was an excellent inducer of toluene dioxygenase activity and shown to undergo transformation in cultures of P. putida F1.
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Affiliation(s)
- Kelly G. Aukema
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology InstituteUniversity of Minnesota, Twin CitiesMinnesotaUSA
| | - Madison D. Bygd
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology InstituteUniversity of Minnesota, Twin CitiesMinnesotaUSA
| | - Lambros J. Tassoulas
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology InstituteUniversity of Minnesota, Twin CitiesMinnesotaUSA
| | - Jack E. Richman
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology InstituteUniversity of Minnesota, Twin CitiesMinnesotaUSA
| | - Lawrence P. Wackett
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology InstituteUniversity of Minnesota, Twin CitiesMinnesotaUSA
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16
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Núñez-Navarro N, Salazar Muñoz J, Castillo F, Ramírez-Sarmiento CA, Poblete-Castro I, Zacconi FC, Parra LP. Discovery of New Phenylacetone Monooxygenase Variants for the Development of Substituted Indigoids through Biocatalysis. Int J Mol Sci 2022; 23:ijms232012544. [PMID: 36293414 PMCID: PMC9604523 DOI: 10.3390/ijms232012544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/15/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
Indigoids are natural pigments obtained from plants by ancient cultures. Romans used them mainly as dyes, whereas Asian cultures applied these compounds as treatment agents for several diseases. In the modern era, the chemical industry has made it possible to identify and develop synthetic routes to obtain them from petroleum derivatives. However, these processes require high temperatures and pressures and large amounts of solvents, acids, and alkali agents. Thus, enzyme engineering and the development of bacteria as whole-cell biocatalysts emerges as a promising green alternative to avoid the use of these hazardous materials and consequently prevent toxic waste generation. In this research, we obtained two novel variants of phenylacetone monooxygenase (PAMO) by iterative saturation mutagenesis. Heterologous expression of these two enzymes, called PAMOHPCD and PAMOHPED, in E. coli was serendipitously found to produce indigoids. These interesting results encourage us to characterize the thermal stability and enzyme kinetics of these new variants and to evaluate indigo and indirubin production in a whole-cell system by HPLC. The highest yields were obtained with PAMOHPCD supplemented with L-tryptophan, producing ~3000 mg/L indigo and ~130.0 mg/L indirubin. Additionally, both enzymes could oxidize and produce several indigo derivatives from substituted indoles, with PAMOHPCD being able to produce the well-known Tyrian purple. Our results indicate that the PAMO variants described herein have potential application in the textile, pharmaceutics, and semiconductors industries, prompting the use of environmentally friendly strategies to obtain a diverse variety of indigoids.
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Affiliation(s)
- Nicolás Núñez-Navarro
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Javier Salazar Muñoz
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Center for Nanomedicine, Diagnostic & Drug Development (ND3), Universidad de Talca, Talca 3460000, Chile
| | - Francisco Castillo
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Department of Chemical and Bioprocess Engineering, Universidad de Santiago de Chile (USACH), Santiago 8350709, Chile
| | - Flavia C. Zacconi
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Center for Nanomedicine, Diagnostic & Drug Development (ND3), Universidad de Talca, Talca 3460000, Chile
- Correspondence: (F.C.Z.); (L.P.P.)
| | - Loreto P. Parra
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Correspondence: (F.C.Z.); (L.P.P.)
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17
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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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18
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Solubility enhancement of indigo dye through biochemical reduction and structural modification. KOREAN J CHEM ENG 2022. [DOI: 10.1007/s11814-022-1165-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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19
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Mindt M, Beyraghdar Kashkooli A, Suarez-Diez M, Ferrer L, Jilg T, Bosch D, Martins Dos Santos V, Wendisch VF, Cankar K. Production of indole by Corynebacterium glutamicum microbial cell factories for flavor and fragrance applications. Microb Cell Fact 2022; 21:45. [PMID: 35331232 PMCID: PMC8944080 DOI: 10.1186/s12934-022-01771-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/01/2022] [Indexed: 02/07/2023] Open
Abstract
Background The nitrogen containing aromatic compound indole is known for its floral odor typical of jasmine blossoms. Due to its characteristic scent, it is frequently used in dairy products, tea drinks and fine fragrances. The demand for natural indole by the flavor and fragrance industry is high, yet, its abundance in essential oils isolated from plants such as jasmine and narcissus is low. Thus, there is a strong demand for a sustainable method to produce food-grade indole. Results Here, we established the biotechnological production of indole upon l-tryptophan supplementation in the bacterial host Corynebacterium glutamicum. Heterologous expression of the tryptophanase gene from E. coli enabled the conversion of supplemented l-tryptophan to indole. Engineering of the substrate import by co-expression of the native aromatic amino acid permease gene aroP increased whole-cell biotransformation of l-tryptophan to indole by two-fold. Indole production to 0.2 g L−1 was achieved upon feeding of 1 g L−1l-tryptophan in a bioreactor cultivation, while neither accumulation of side-products nor loss of indole were observed. To establish an efficient and robust production process, new tryptophanases were recruited by mining of bacterial sequence databases. This search retrieved more than 400 candidates and, upon screening of tryptophanase activity, nine new enzymes were identified as most promising. The highest production of indole in vivo in C. glutamicum was achieved based on the tryptophanase from Providencia rettgeri. Evaluation of several biological aspects identified the product toxicity as major bottleneck of this conversion. In situ product recovery was applied to sequester indole in a food-grade organic phase during the fermentation to avoid inhibition due to product accumulation. This process enabled complete conversion of l-tryptophan and an indole product titer of 5.7 g L−1 was reached. Indole partitioned to the organic phase which contained 28 g L−1 indole while no other products were observed indicating high indole purity. Conclusions The bioconversion production process established in this study provides an attractive route for sustainable indole production from tryptophan in C. glutamicum. Industrially relevant indole titers were achieved within 24 h and indole was concentrated in the organic layer as a pure product after the fermentation. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01771-y.
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Affiliation(s)
- Melanie Mindt
- Business Unit Bioscience, Wageningen Plant Research, Wageningen University & Research, Wageningen, The Netherlands.,Axxence Aromatic GmbH, Emmerich am Rhein, Germany
| | - Arman Beyraghdar Kashkooli
- Business Unit Bioscience, Wageningen Plant Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Lenny Ferrer
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Tatjana Jilg
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Dirk Bosch
- Business Unit Bioscience, Wageningen Plant Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Vitor Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands.,Laboratory of Bioprocess Engineering, Wageningen University & Research, Wageningen, The Netherlands
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Katarina Cankar
- Business Unit Bioscience, Wageningen Plant Research, Wageningen University & Research, Wageningen, The Netherlands.
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Feng J, Huang D, Yang Y, Chen J, Qiu S, Lv Z, Ma X, Li Y, Li R, Xiao Y, Chen W. Isatis indigotica: from (ethno) botany, biochemistry to synthetic biology. MOLECULAR HORTICULTURE 2021; 1:17. [PMID: 37789475 PMCID: PMC8668392 DOI: 10.1186/s43897-021-00021-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/25/2021] [Indexed: 05/20/2023]
Abstract
Isatis indigotica Fort. (Chinese woad) is a species with an ancient and well-documented history as an indigo dye and medicinal plant. It is often confused with Isatis tinctoria L. (European woad), a medicinal plant in Europe. Here, the differences between I. indigotica and I. tinctoria are systematically described. The usage development history, clinical applications and pharmacological activities, and chemical components of I. indigotica are also summarized. Lignans, indole alkaloids, and their corresponding derivatives have been identified as the major active ingredients of I. indigotica and are associated with anti-viral, anti-inflammatory, anti-cancer, and other health-promoting activities. Notable progress has been made in understanding the biosynthetic pathway and regulation mechanism of lignans and indole alkaloids in I. indigotica, the results from which should facilitate the process of targeted metabolic engineering or synthetic biology. Moreover, multiple biotechnology methods such as polyploid breeding and genetic engineering have been used with I. indigotica to result in, for example, greater yields, higher levels of bioactive component accumulation, and enhanced stress tolerance to salt, drought, and insects. Some issues require additional analyses, and suggestions for future research on I. indigotica are also discussed.
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Affiliation(s)
- Jingxian Feng
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Doudou Huang
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yingbo Yang
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Jiangsu Kanion Pharmaceutical Co., Ltd, Jiangsu, 222001, Lianyungang, China
| | - Junfeng Chen
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Shi Qiu
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Zongyou Lv
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xueqi Ma
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yuanyu Li
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Rongrong Li
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Ying Xiao
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Wansheng Chen
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
- Medical Guarantee Center, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China.
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21
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Kayastha S, Sagwan-Barkdoll L, Anterola A, Jayakody LN. Developing synthetic microbes to produce indirubin-derivatives. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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22
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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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23
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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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Inoue S, Morita R, Minami Y. An indigo-producing plant, Polygonum tinctorium, possesses a flavin-containing monooxygenase capable of oxidizing indole. Biochem Biophys Res Commun 2020; 534:199-205. [PMID: 33303189 DOI: 10.1016/j.bbrc.2020.11.112] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 11/27/2020] [Indexed: 11/17/2022]
Abstract
Polygonum tinctorium (P. tinctorium) is an indigo plant that is cultivated for a specific metabolite that it produces i.e., indoxyl β-D-glucoside (indican). In this study, flavin-containing monooxygenase (PtFMO) from P. tinctorium was cloned. When recombinant PtFMO was expressed in E. coli in the presence of tryptophan, indigo production was observed. Furthermore, we measured the activity of PtFMO using the membrane fraction from E. coli and found that it could produce indigo using indole as a substrate. The co-expression of PtFMO with indoxyl β-D-glucoside synthase (PtIGS), which catalyzes the glucosylation of indoxyl, brought about the formation of indican in E. coli. The results showed that indican was synthesized by sequential reactions of PtFMO and PtIGS. In three-week-old P. tinctorium specimens, the first leaves demonstrated higher levels of PtFMO expression than the subsequent leaves. This result coincided with that of our prior study on PtIGS expression level. Our study provides evidence that PtFMO might contribute to indican biosynthesis.
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Affiliation(s)
- Shintaro Inoue
- Okayama University of Science, Department of Biochemistry, Faculty of Science, 1-1 Ridai-cho, Kita-ku, Okayama, 700-0005, Japan
| | - Rihito Morita
- Okayama University of Science, Department of Biochemistry, Faculty of Science, 1-1 Ridai-cho, Kita-ku, Okayama, 700-0005, Japan
| | - Yoshiko Minami
- Okayama University of Science, Department of Biochemistry, Faculty of Science, 1-1 Ridai-cho, Kita-ku, Okayama, 700-0005, Japan.
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25
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Use of Flavin-Containing Monooxygenases for Conversion of Trimethylamine in Salmon Protein Hydrolysates. Appl Environ Microbiol 2020; 86:AEM.02105-20. [PMID: 32978141 PMCID: PMC7688232 DOI: 10.1128/aem.02105-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 09/23/2020] [Indexed: 11/20/2022] Open
Abstract
Enzyme-based conversion of marine biomass to high-quality peptide ingredients leaves a distinct smell of “fish” caused by the presence of trimethylamine, which limits their economic potential. We suggest an enzymatic solution for converting trimethylamine to the odorless trimethylamine N-oxide as a novel strategy to improve the smell quality of marine protein hydrolysates. Following a systematic investigation of 45 putative bacterial trimethylamine monooxygenases from several phyla, we expand the repertoire of known active trimethylamine monooxygenases. As a proof-of-concept, we demonstrate that three of these enzymes oxidized trimethylamine in an industry-relevant salmon protein hydrolysate. Our results add new oxidoreductases to the industrial biocatalytic toolbox and provide a new point of departure for enzyme process developments in marine biorefineries. Enzymatic processing of fish by-products for recovery of peptides (hydrolysates) is a promising technology to reach food grade ingredients of high nutritional quality. Despite this, their bitter taste and “fish” odor block implementation in food products and limit their economic potential. Trimethylamine (TMA) is a known contributor to malodor in fish. Current strategies to mask or remove the odor either are not effective or give rise to undesirable side effects. As an alternative approach to remediate TMA, we propose a novel enzymatic strategy to convert TMA into the odorless trimethylamine N-oxide (TMAO) using TMA monooxygenases (Tmms). We identified a diverse set of bacterial Tmms using a sequence similarity network. Purified, recombinant enzymes were assessed for their biocatalytic capacity by monitoring NADPH consumption and TMAO generation. Selected Tmms were subjected to biochemical characterization and investigated for their ability to oxidize TMA in an industry-relevant substrate. From the 45 bacterial Tmm candidates investigated, eight enzymes from four different taxa were selected for their high activity toward TMA. The three most active enzymes were shown to vary in temperature optimum, with the highest being 45°C. Enzymatic activity dropped at high temperatures, likely due to structural unfolding. The enzymes were all active from pH 6.0 to 8.5, with functional stability being lowest around the optimal pH. All three Tmms, given sufficient NADPH cofactor, were found to generate TMAO in the TMA-rich salmon protein hydrolysate. The Tmms serve as unique starting points for engineering and should be useful for guiding process development for marine biorefineries. IMPORTANCE Enzyme-based conversion of marine biomass to high-quality peptide ingredients leaves a distinct smell of “fish” caused by the presence of trimethylamine, which limits their economic potential. We suggest an enzymatic solution for converting trimethylamine to the odorless trimethylamine N-oxide as a novel strategy to improve the smell quality of marine protein hydrolysates. Following a systematic investigation of 45 putative bacterial trimethylamine monooxygenases from several phyla, we expand the repertoire of known active trimethylamine monooxygenases. As a proof-of-concept, we demonstrate that three of these enzymes oxidized trimethylamine in an industry-relevant salmon protein hydrolysate. Our results add new oxidoreductases to the industrial biocatalytic toolbox and provide a new point of departure for enzyme process developments in marine biorefineries.
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26
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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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27
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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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28
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Cheng L, Yue J, Yin S, Ren M, Wang C. Expression of styAB is regulated by a two-component system during indigo biosynthesis in Pseudomonas putida. Biochem Biophys Res Commun 2019; 519:198-203. [PMID: 31492500 DOI: 10.1016/j.bbrc.2019.08.142] [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: 08/07/2019] [Accepted: 08/25/2019] [Indexed: 11/26/2022]
Abstract
A two-component regulatory system involving StyS and StyR is involved in the regulation of indigo synthesis in Pseudomonas sp. However, the function of the styR gene in indigo synthesis and the detailed mechanisms through which StyR enhances the expression of the styAB operon are unclear. Accordingly, in this study, we constructed a styR/styS gene knockout mutant strain. By comparing the differences in indigo yields between the wild-type and mutant strains, we found that the styR gene mutant strain had no indigo synthesis ability, whereas the yield in the wild-type strain was 5.4 mg/L. Thus, these findings indicate that the styR gene plays a key role in the regulation of indigo synthesis. The interactions among StyS, StyR, and the styAB promoter were verified by electrophoresis mobility shift assays. The results showed that StyR interacts with the styAB promoter by binding to the palindrome in the styAB promoter. Moreover, the kinase function of StyS regulated StyR by transphosphorylating StyR during indigo biosynthesis in P. putida B3. Taken together, these findings provide important insights into the establishment of environmentally friendly indigo synthesis methods using P. putida.
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Affiliation(s)
- Lei Cheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048, People's Republic of China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, 100048, People's Republic of China
| | - Jianming Yue
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048, People's Republic of China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, 100048, People's Republic of China
| | - Sheng Yin
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048, People's Republic of China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, 100048, People's Republic of China
| | - Mingjing Ren
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048, People's Republic of China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, 100048, People's Republic of China
| | - Chengtao Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048, People's Republic of China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, 100048, People's Republic of China.
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29
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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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30
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Characterization of a thermostable flavin-containing monooxygenase from Nitrincola lacisaponensis (NiFMO). Appl Microbiol Biotechnol 2019; 103:1755-1764. [DOI: 10.1007/s00253-018-09579-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/06/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022]
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31
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Fiorentini F, Hatzl AM, Schmidt S, Savino S, Glieder A, Mattevi A. The Extreme Structural Plasticity in the CYP153 Subfamily of P450s Directs Development of Designer Hydroxylases. Biochemistry 2018; 57:6701-6714. [DOI: 10.1021/acs.biochem.8b01052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Filippo Fiorentini
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, Pavia 27100, Italy
| | - Anna-Maria Hatzl
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Sandy Schmidt
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Simone Savino
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, Pavia 27100, Italy
| | - Anton Glieder
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, Pavia 27100, Italy
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32
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Ma Q, Zhang X, Qu Y. Biodegradation and Biotransformation of Indole: Advances and Perspectives. Front Microbiol 2018; 9:2625. [PMID: 30443243 PMCID: PMC6221969 DOI: 10.3389/fmicb.2018.02625] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/15/2018] [Indexed: 11/17/2022] Open
Abstract
Indole is long regarded as a typical N-heterocyclic aromatic pollutant in industrial and agricultural wastewater, and recently it has been identified as a versatile signaling molecule with wide environmental distributions. An exponentially growing number of researches have been reported on indole due to its significant roles in bacterial physiology, pathogenesis, animal behavior and human diseases. From the viewpoint of both environmental bioremediation and biological studies, the researches on metabolism and fates of indole are important to realize environmental treatment and illuminate its biological function. Indole can be produced from tryptophan by tryptophanase in many bacterial species. Meanwhile, various bacterial strains have obtained the ability to transform and degrade indole. The characteristics and pathways for indole degradation have been investigated for a century, and the functional genes for indole aerobic degradation have also been uncovered recently. Interestingly, many oxygenases have proven to be able to oxidize indole to indigo, and this historic and motivating case for biological applications has attracted intensive attention for decades. Herein, the bacteria, enzymes and pathways for indole production, biodegradation and biotransformation are systematically summarized, and the future researches on indole-microbe interactions are also prospected.
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Affiliation(s)
- Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, China
| | - Xuwang Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Food and Environment, Dalian University of Technology, Panjin, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
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33
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Metabolic engineering of Escherichia coli for the production of indirubin from glucose. J Biotechnol 2018; 267:19-28. [DOI: 10.1016/j.jbiotec.2017.12.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/22/2017] [Accepted: 12/31/2017] [Indexed: 11/19/2022]
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34
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Complete Genome Sequence of Indigo-Producing Bacterium Celeribacter sp. Strain TSPH2. GENOME ANNOUNCEMENTS 2017; 5:5/45/e01124-17. [PMID: 29122863 PMCID: PMC5679796 DOI: 10.1128/genomea.01124-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Celeribacter sp. strain TSPH2, a novel producer of indigo, was isolated from oil-contaminated sediment. We present here its genome sequence consisting of one circular chromosome (4 Mb) and one plasmid (0.15 Mb), with an overall G+C content of 60.9%. This strain contains oxygenase genes involved in indigo synthesis, such as flavin-containing monooxygenase.
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35
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Shivlata L, Satyanarayana T. Thermophilic and alkaliphilic Actinobacteria: biology and potential applications. Front Microbiol 2015; 6:1014. [PMID: 26441937 PMCID: PMC4585250 DOI: 10.3389/fmicb.2015.01014] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/07/2015] [Indexed: 11/13/2022] Open
Abstract
Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive compounds, which find multifarious applications.
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