1
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Son SY, Bae DW, Kim E, Jeong BG, Kim MY, Youn SY, Yi S, Kim G, Hahn JS, Lee NK, Yoon YJ, Cha SS. Structural investigation of the docking domain assembly from trans-AT polyketide synthases. Structure 2024; 32:1477-1487.e4. [PMID: 38908377 DOI: 10.1016/j.str.2024.05.017] [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: 01/30/2024] [Revised: 05/02/2024] [Accepted: 05/28/2024] [Indexed: 06/24/2024]
Abstract
Docking domains (DDs) located at the C- and N-termini of polypeptides play a crucial role in directing the assembly of polyketide synthases (PKSs), which are multienzyme complexes. Here, we determined the crystal structure of a complex comprising the C-terminal DD (CDDMlnB) and N-terminal DD (NDDMlnC) of macrolactin trans-acyltransferase (AT) PKS that were fused to a functional enzyme, AmpC EC2 β-lactamase. Interface analyses of the CDDMlnB/NDDMlnC complex revealed the molecular intricacies in the core section underpinning the precise DD assembly. Additionally, circular dichroism and steady-state kinetics demonstrated that the formation of the CDDMlnB/NDDMlnC complex had no influence on the structural and functional fidelity of the fusion partner, AmpC EC2. This inspired us to apply the CDDMlnB/NDDMlnC assembly to metabolon engineering. Indeed, DD assembly induced the formation of a complex between 4-coumarate-CoA ligase and chalcone synthase both involved in flavonoid biosynthesis, leading to a remarkable increase in naringenin production in vitro.
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Affiliation(s)
- Se-Young Son
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Da-Woon Bae
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Eunji Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Bo-Gyeong Jeong
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Myeong-Yeon Kim
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - So-Yeon Youn
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Soojung Yi
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Gyeongmin Kim
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji-Sook Hahn
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 08826, Republic of Korea
| | - Nam Ki Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, Republic of Korea.
| | - Sun-Shin Cha
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
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2
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Benninghaus L, Schwardmann LS, Jilg T, Wendisch VF. Establishment of synthetic microbial consortia with Corynebacterium glutamicum and Pseudomonas putida: Design, construction, and application to production of γ-glutamylisopropylamide and l-theanine. Microb Biotechnol 2024; 17:e14400. [PMID: 38206115 PMCID: PMC10832564 DOI: 10.1111/1751-7915.14400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Microbial synthetic consortia are a promising alternative to classical monoculture for biotechnological applications and fermentative processes. Their versatile use offers advantages in the degradation of complex substrates, the allocation of the metabolic burden between individual partners, or the division of labour in energy utilisation, substrate supply or product formation. Here, stable synthetic consortia between the two industrially relevant production hosts, Pseudomonas putida KT2440 and Corynebacterium glutamicum ATCC13032, were established for the first time. By applying arginine auxotrophy/overproduction and/or formamidase-based utilisation of the rare nitrogen source formamide, different types of interaction were realised, such as commensal relationships (+/0 and 0/+) and mutualistic cross-feeding (+/+). These consortia did not only show stable growth but could also be used for fermentative production of the γ-glutamylated amines theanine and γ-glutamyl-isopropylamide (GIPA). The consortia produced up to 2.8 g L-1 of GIPA and up to 2.6 g L-1 of theanine, a taste-enhancing constituent of green tea leaves. Thus, the advantageous approach of using synthetic microbial consortia for fermentative production of value-added compounds was successfully demonstrated.
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Affiliation(s)
- Leonie Benninghaus
- Genetics of Prokaryotes, Faculty of Biology and CeBiTecBielefeld UniversityBielefeldGermany
| | - Lynn S. Schwardmann
- Genetics of Prokaryotes, Faculty of Biology and CeBiTecBielefeld UniversityBielefeldGermany
- Present address:
Aminoverse B.V.Daelderweg 9Nuth6361 HKthe Netherlands
| | - Tatjana Jilg
- Genetics of Prokaryotes, Faculty of Biology and CeBiTecBielefeld UniversityBielefeldGermany
- Present address:
Symrise AGMühlenfeldstraße 1Holzminden37603Germany
| | - Volker F. Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTecBielefeld UniversityBielefeldGermany
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3
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Pan R, Yang X, Qiu M, Jiang W, Zhang W, Jiang Y, Xin F, Jiang M. Construction of Coculture System Containing Escherichia coli with Different Microbial Species for Biochemical Production. ACS Synth Biol 2023; 12:2208-2216. [PMID: 37506399 DOI: 10.1021/acssynbio.3c00329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Microbial synthesis of target chemicals usually involves multienzymatic reactions in vivo, especially for compounds with a long metabolic pathway. However, when various genes are introduced into one single strain, it leads to a heavy metabolic burden. In contrast, the microbial coculture system can allocate metabolic pathways into different hosts, which will relieve the metabolic burdens. Escherichia coli is the most used chassis to synthesize biofuels and chemicals owing to its well-known genetics, high transformation efficiency, and easy cultivation. Accordingly, cocultures containing the cooperative E. coli with other microbial species have received great attention. In this review, the individual applications and boundedness of different combinations will be summarized. Additionally, the strategies for the self-regulation of population composition, which can help enhance the stability of a coculture system, will also be discussed. Finally, perspectives for the cocultures will be proposed.
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Affiliation(s)
- Runze Pan
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
| | - Xinyi Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
| | - Min Qiu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
- Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, P. R. China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
- Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, P. R. China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
- Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, P. R. China
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4
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Thuan NH, Tatipamula VB, Trung NT, Van Giang N. Metabolic engineering and optimization of Escherichia coli co-culture for the de novo synthesis of genkwanin. J Ind Microbiol Biotechnol 2023; 50:kuad030. [PMID: 37738435 PMCID: PMC10565888 DOI: 10.1093/jimb/kuad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Genkwanin has various significant roles in nutrition, biomedicine, and pharmaceutical biology. Previously, this compound was chiefly produced by plant-originated extraction or chemical synthesis. However, due to increasing concern and demand for safe food and environmental issues, the biotechnological production of genkwanin and other bioactive compounds based on safe, cheap, and renewable substrates has gained much interest. This paper described recombinant Escherichia coli-based co-culture engineering that was reconstructed for the de novo production of genkwanin from d-glucose. The artificial genkwanin biosynthetic chain was divided into 2 modules in which the upstream strain contained the genes for synthesizing p-coumaric acid from d-glucose, and the downstream module contained a gene cluster that produced the precursor apigenin and the final product, genkwanin. The Box-Behnken design, a response surface methodology, was used to empirically model the production of genkwanin and optimize its productivity. As a result, the application of the designed co-culture improved the genkwanin production by 48.8 ± 1.3 mg/L or 1.7-fold compared to the monoculture. In addition, the scale-up of genkwanin bioproduction by a bioreactor resulted in 68.5 ± 1.9 mg/L at a 48 hr time point. The combination of metabolic engineering and fermentation technology was therefore a very efficient and applicable approach to enhance the production of other bioactive compounds.
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Affiliation(s)
- Nguyen Huy Thuan
- Center for Pharmaceutical Biotechnology, Duy Tan University, Da Nang 550000, Vietnam
| | | | - Nguyen Thanh Trung
- Center for Pharmaceutical Biotechnology, Duy Tan University, Da Nang 550000, Vietnam
| | - Nguyen Van Giang
- Faculty of Biotechnology, Vietnam National University of Agriculture, Trau Quy, Hanoi 100000, Vietnam
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5
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Wiles D, Shanbhag BK, O'Brien M, Doblin MS, Bacic A, Beddoe T. Heterologous production of Cannabis sativa-derived specialised metabolites of medicinal significance - Insights into engineering strategies. PHYTOCHEMISTRY 2022; 203:113380. [PMID: 36049526 DOI: 10.1016/j.phytochem.2022.113380] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/08/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
Cannabis sativa L. has been known for at least 2000 years as a source of important, medically significant specialised metabolites and several bio-active molecules have been enriched from multiple chemotypes. However, due to the many levels of complexity in both the commercial cultivation of cannabis and extraction of its specialised metabolites, several heterologous production approaches are being pursued in parallel. In this review, we outline the recent achievements in engineering strategies used for heterologous production of cannabinoids, terpenes and flavonoids along with their strength and weakness. We provide an overview of the specialised metabolism pathway in C. sativa and a comprehensive list of the specialised metabolites produced along with their medicinal significance. We highlight cannabinoid-like molecules produced by other species. We discuss the key biosynthetic enzymes and their heterologous production using various hosts such as microbial and eukaryotic systems. A brief discussion on complementary production strategies using co-culturing and cell-free systems is described. Various approaches to optimise specialised metabolite production through co-expression, enzyme engineering and pathway engineering are discussed. We derive insights from recent advances in metabolic engineering of hosts with improved precursor supply and suggest their application for the production of C. sativa speciality metabolites. We present a collation of non-conventional hosts with speciality traits that can improve the feasibility of commercial heterologous production of cannabis-based specialised metabolites. We provide a perspective of emerging research in synthetic biology, allied analytical techniques and plant heterologous platforms as focus areas for heterologous production of cannabis specialised metabolites in the future.
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Affiliation(s)
- Danielle Wiles
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Bhuvana K Shanbhag
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Martin O'Brien
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Monika S Doblin
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia; La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, Australia
| | - Antony Bacic
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia; La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, Australia
| | - Travis Beddoe
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia.
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6
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Dippe M, Davari MD, Weigel B, Heinke R, Vogt T, Wessjohann LA. Altering the Regiospecificity of a Catechol
O
‐methyltransferase through Rational Design: Vanilloid vs. Isovanilloid Motifs in the B‐ring of Flavonoids. ChemCatChem 2022. [DOI: 10.1002/cctc.202200511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Martin Dippe
- Department of Bioorganic Chemistry Leibniz-Institute of Plant Biochemistry Weinberg 3 D-06120 Halle Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry Leibniz-Institute of Plant Biochemistry Weinberg 3 D-06120 Halle Germany
| | - Benjamin Weigel
- Department of Bioorganic Chemistry Leibniz-Institute of Plant Biochemistry Weinberg 3 D-06120 Halle Germany
| | - Ramona Heinke
- Department of Bioorganic Chemistry Leibniz-Institute of Plant Biochemistry Weinberg 3 D-06120 Halle Germany
| | - Thomas Vogt
- Department of Cell and Metabolic Biology Leibniz-Institute of Plant Biochemistry Weinberg 3 D-06120 Halle Germany
| | - Ludger A. Wessjohann
- Department of Bioorganic Chemistry Leibniz-Institute of Plant Biochemistry Weinberg 3 D-06120 Halle Germany
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7
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Sun Q, Gao S, Yu S, Zheng P, Zhou J. Production of (2S)-sakuranetin from (2S)-naringenin in Escherichia coli by strengthening methylation process and cell resistance. Synth Syst Biotechnol 2022; 7:1117-1125. [PMID: 36017331 PMCID: PMC9399173 DOI: 10.1016/j.synbio.2022.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/15/2022] Open
Abstract
(2S)-Sakuranetin is a 7-O-methylflavonoid that has anticancer, antiviral, and antimicrobial activities. Methylation process is involved in biosynthesizing (2S)-sakuranetin from (2S)-naringenin, in which S-adenosylmethionine (SAM) serves as the methyl donor. In this study, after methyl donor and substrate inhibition were identified as limiting factors for (2S)-sakuranetin biosynthesis, an efficient (2S)-sakuranetin-producing strain was constructed by enhancing methyl donor supply and cell tolerance to (2S)-naringenin. Firstly, PfOMT3 from Perilla frutescens was selected as the optimal flavonoid 7-O-methyltransferase (F7-OMT) for the conversion of (2S)-naringenin to (2S)-sakuranetin. Then, the methylation process was upregulated by regulating pyridoxal 5′-phosphate (PLP) content, key enzymes in methionine synthesis pathway, and the availability of ATP. Furthermore, genes that can enhance cell resistance to (2S)-naringenin were identified from molecular chaperones and sRNAs. Finally, by optimizing the fermentation process, 681.44 mg/L of (2S)-sakuranetin was obtained in 250-mL shake flasks. The titer of (2S)-sakuranetin reached 2642.38 mg/L in a 5-L bioreactor, which is the highest titer ever reported. This work demonstrates the importance of cofactor PLP in methylation process, and provides insights to biosynthesize other O-methylated flavonoids efficiently in E. coli.
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Affiliation(s)
- Qiumeng Sun
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Song Gao
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Shiqin Yu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Pu Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Corresponding author. School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, 214122, China
- Corresponding author. Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
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8
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Sun J, Sun W, Zhang G, Lv B, Li C. High efficient production of plant flavonoids by microbial cell factories: Challenges and opportunities. Metab Eng 2022; 70:143-154. [DOI: 10.1016/j.ymben.2022.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 01/12/2022] [Accepted: 01/21/2022] [Indexed: 12/27/2022]
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9
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Fidan O, Zhan J, Ren J. Engineered production of bioactive natural products from medicinal plants. WORLD JOURNAL OF TRADITIONAL CHINESE MEDICINE 2022. [DOI: 10.4103/wjtcm.wjtcm_66_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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10
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Fidan O, Zhan J, Ren J. Engineered production of bioactive natural products from medicinal plants. WORLD JOURNAL OF TRADITIONAL CHINESE MEDICINE 2022. [DOI: 10.4103/2311-8571.336839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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11
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Liao YL, Niu FX, Liu JZ. Recent Progress in Microbial Biosynthesis by Coculture Engineering. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821100033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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12
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Optimization of Pre-Inoculum, Fermentation Process Parameters and Precursor Supplementation Conditions to Enhance Apigenin Production by a Recombinant Streptomyces albus Strain. FERMENTATION 2021. [DOI: 10.3390/fermentation7030161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Streptomyces albus J1074-pAPI (Streptomyces albus-pAPI) is a recombinant strain constructed to biotechnologically produce apigenin, a flavonoid with interesting bioactive features that up to now has been manufactured by extraction from plants with long and not environmentally friendly procedures. So far, in literature, only a maximum apigenin concentration of 80.0 µg·L−1 has been obtained in shake flasks. In this paper, three integrated fermentation strategies were exploited to enhance the apigenin production by Streptomyces albus J1074-pAPI, combining specific approaches for pre-inoculum conditions, optimization of fermentation process parameters and supplementation of precursors. Using a pre-inoculum of mycelium, the apigenin concentration increased of 1.8-fold in shake flask physiological studies. In 2L batch fermentation, the aeration and stirring conditions were optimized and integrated with the new inoculum approach and the apigenin production reached 184.8 ± 4.0 µg·L−1, with a productivity of 2.6 ± 0.1 μg·L−1·h−1. The supplementation of 1.5 mM L-tyrosine in batch fermentations allowed to obtain an apigenin production of 343.3 ± 3.0 µg·L−1 in only 48 h, with an increased productivity of 7.1 ± 0.1 μg·L−1·h−1. This work demonstrates that the optimization of fermentation process conditions is a crucial requirement to increase the apigenin concentration and productivity by up to 4.3- and 10.7-fold.
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13
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Kim JH, Lee N, Hwang S, Kim W, Lee Y, Cho S, Palsson BO, Cho BK. Discovery of novel secondary metabolites encoded in actinomycete genomes through coculture. J Ind Microbiol Biotechnol 2021; 48:6119915. [PMID: 33825906 PMCID: PMC9113425 DOI: 10.1093/jimb/kuaa001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/02/2020] [Indexed: 01/23/2023]
Abstract
Actinomycetes are a rich source of bioactive natural products important for novel drug leads. Recent genome mining approaches have revealed an enormous number of secondary metabolite biosynthetic gene clusters (smBGCs) in actinomycetes. However, under standard laboratory culture conditions, many smBGCs are silent or cryptic. To activate these dormant smBGCs, several approaches, including culture-based or genetic engineering-based strategies, have been developed. Above all, coculture is a promising approach to induce novel secondary metabolite production from actinomycetes by mimicking an ecological habitat where cryptic smBGCs may be activated. In this review, we introduce coculture studies that aim to expand the chemical diversity of actinomycetes, by categorizing the cases by the type of coculture partner. Furthermore, we discuss the current challenges that need to be overcome to support the elicitation of novel bioactive compounds from actinomycetes.
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Affiliation(s)
- Ji Hun Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Namil Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongjae Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,Intelligent Synthetic Biology Center, Daejeon 34141, Republic of Korea
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14
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Ibrahim M, Raajaraam L, Raman K. Modelling microbial communities: Harnessing consortia for biotechnological applications. Comput Struct Biotechnol J 2021; 19:3892-3907. [PMID: 34584635 PMCID: PMC8441623 DOI: 10.1016/j.csbj.2021.06.048] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Microbes propagate and thrive in complex communities, and there are many benefits to studying and engineering microbial communities instead of single strains. Microbial communities are being increasingly leveraged in biotechnological applications, as they present significant advantages such as the division of labour and improved substrate utilisation. Nevertheless, they also present some interesting challenges to surmount for the design of efficient biotechnological processes. In this review, we discuss key principles of microbial interactions, followed by a deep dive into genome-scale metabolic models, focussing on a vast repertoire of constraint-based modelling methods that enable us to characterise and understand the metabolic capabilities of microbial communities. Complementary approaches to model microbial communities, such as those based on graph theory, are also briefly discussed. Taken together, these methods provide rich insights into the interactions between microbes and how they influence microbial community productivity. We finally overview approaches that allow us to generate and test numerous synthetic community compositions, followed by tools and methodologies that can predict effective genetic interventions to further improve the productivity of communities. With impending advancements in high-throughput omics of microbial communities, the stage is set for the rapid expansion of microbial community engineering, with a significant impact on biotechnological processes.
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Affiliation(s)
- Maziya Ibrahim
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Lavanya Raajaraam
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Karthik Raman
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
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Sun X, Li X, Shen X, Wang J, Yuan Q. Recent advances in microbial production of phenolic compounds. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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16
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Naturally Occurring Flavonoids and Isoflavonoids and Their Microbial Transformation: A Review. Molecules 2020; 25:molecules25215112. [PMID: 33153224 PMCID: PMC7663748 DOI: 10.3390/molecules25215112] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 10/31/2020] [Accepted: 11/01/2020] [Indexed: 02/06/2023] Open
Abstract
Flavonoids and isoflavonoids are polyphenolic secondary metabolites usually produced by plants adapting to changing ecological environments over a long period of time. Therefore, their biosynthesis pathways are considered as the most distinctive natural product pathway in plants. Seemingly, the flavonoids and isoflavones from fungi and actinomycetes have been relatively overlooked. In this review, we summarized and classified the isoflavones and flavonoids derived from fungi and actinomycetes and described their biological activities. Increasing attention has been paid to bioactive substances derived from microorganism whole-cell biotransformation. Additionally, we described the utilization of isoflavones and flavonoids as substrates by fungi and actinomycetes for biotransformation through hydroxylation, methylation, halogenation, glycosylation, dehydrogenation, cyclisation, and hydrogenation reactions to obtain rare and highly active biofunctional derivatives. Overall, among all microorganisms, actinomycetes are the main producers of flavonoids. In our review, we also summarized the functional genes involved in flavonoid biosynthesis.
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17
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Sgobba E, Wendisch VF. Synthetic microbial consortia for small molecule production. Curr Opin Biotechnol 2019; 62:72-79. [PMID: 31627138 DOI: 10.1016/j.copbio.2019.09.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/06/2019] [Accepted: 09/11/2019] [Indexed: 11/26/2022]
Abstract
Microbial consortia were designed for the production of small molecules with 'labor' being divided between two or more microorganisms. Examples of linear designs are substrate conversion preceding target molecule production or subdivision of two consecutive steps of target molecule production. Here, we review synthetic biology design approaches for microbial consortia based on ecological principles and microbial interactions that is, mutualism, and commensalism. Besides highlighting the technical challenges regarding industrial application of synthetic microbial consortia, we forecast the extension of the concept from binary linear to ternary linear and more complex microbial consortia in biotechnological applications. Microbial consortia are here reviewed and proposed as a rational solution toward feedstock accessibility as it has been shown for production of l-lysine, l-pipecolic acid and cadaverine from starch or production of fumarate from microcrystalline cellulose and alkaline pre-treated corn, or alternatively to establish new multi-step pathway for the production of rosmarinic acid from xylose and glucose.
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Affiliation(s)
- Elvira Sgobba
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University Bielefeld, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University Bielefeld, Germany.
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18
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Wang R, Zhao S, Wang Z, Koffas MA. Recent advances in modular co-culture engineering for synthesis of natural products. Curr Opin Biotechnol 2019; 62:65-71. [PMID: 31605875 DOI: 10.1016/j.copbio.2019.09.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/22/2019] [Accepted: 09/06/2019] [Indexed: 01/13/2023]
Abstract
The microbial production of natural products has been traditionally accomplished in a single organism engineered to accommodate target biosynthetic pathways. Often times, such approaches result in large metabolic burdens as key cofactors, precursor metabolites and energy are channeled to pathways of structurally complex chemicals. Recently, modular co-culture engineering has emerged as a new approach to efficiently conduct heterologous biosynthesis and greatly enhance the production of natural products. This review highlights recent advances that leverage Escherichia coli-based modular co-culture engineering for making natural products. Potential future perspectives for studies in this promising field are addressed as well.
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Affiliation(s)
- Rufeng Wang
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shujuan Zhao
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhengtao Wang
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Mattheos Ag Koffas
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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Microbial production of O-methylated flavanones from methylated phenylpropanoic acids in engineered Escherichia coli. J Ind Microbiol Biotechnol 2019; 46:1707-1713. [PMID: 31595455 DOI: 10.1007/s10295-019-02239-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/26/2019] [Indexed: 10/25/2022]
Abstract
Methylated flavonoids possess improved bioactivities compared to their unmethylated counterparts. In this study, for the efficient production of O-methylated flavonoids from simple methylated phenylpropanoic acids, a recombinant Escherichia coli strain expressing 4-coumarate:coenzyme A ligase (4CL) from Oryza sativa and chalcone synthase (CHS) from Hordeum vulgare was constructed; this strain produced significant amount of homoeriodictyol (~ 52 mg/L) as well as a few amount of hesperetin (0.4 mg/L), respectively, from ferulic acid and 4-methylcaffeic acid. This demonstrates, for the first time, that the scarce but valuable methylated flavanones can be successfully produced from methylated phenylpropanoic acids in a microbial host via an artificial biosynthetic pathway consisting of 4CL and CHS that can accept O-methylated precursors.
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