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Foldi J, Connolly JA, Takano E, Breitling R. Synthetic Biology of Natural Products Engineering: Recent Advances Across the Discover-Design-Build-Test-Learn Cycle. ACS Synth Biol 2024; 13:2684-2692. [PMID: 39163395 PMCID: PMC11421215 DOI: 10.1021/acssynbio.4c00391] [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] [Indexed: 08/22/2024]
Abstract
Advances in genome engineering and associated technologies have reinvigorated natural products research. Here we highlight the latest developments in the field across the discover-design-build-test-learn cycle of bioengineering, from recent progress in computational tools for AI-supported genome mining, enzyme and pathway engineering, and compound identification to novel host systems and new techniques for improving production levels, and place these trends in the context of responsible research and innovation, emphasizing the importance of anticipatory analysis at the early stages of process development.
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Affiliation(s)
- Jonathan Foldi
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Jack A Connolly
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Eriko Takano
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M1 7DN, United Kingdom
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2
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Schwarze FWMR, Carvalho T, Reina G, Greca LG, Buenter U, Gholam Z, Krupnik L, Neels A, Boesel L, Morris H, Heeb M, Huch A, Nyström G, Giovannini G. Taming the Production of Bioluminescent Wood Using the White Rot Fungus Desarmillaria Tabescens. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403215. [PMID: 39263934 DOI: 10.1002/advs.202403215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/19/2024] [Indexed: 09/13/2024]
Abstract
Although bioluminescence is documented both anecdotally and experimentally, the parameters involved in the production of fungal bioluminescence during wood colonization have not been identified to date. Here, for the first time, this work develops a methodology to produce a hybrid living material by manipulating wood colonization through merging the living fungus Desarmillaria tabescens with nonliving balsa (Ochroma pyramidale) wood to achieve and control the autonomous emission of bioluminescence. The hybrid material with the highest bioluminescence is produced by soaking the wood blocks before co-cultivating them with the fungus for 3 months. Regardless of the incubation period, the strongest bioluminescence is evident from balsa wood blocks with a moisture content of 700-1200%, highlighting the fundamental role of moisture content for bioluminescence production. Further characterization reveals that D. tabescens preferentially degraded hemicelluloses and lignin in balsa wood. Fourier-transform infrared spectroscopy reveals a decrease in lignin, while X-ray diffraction analysis confirms that the cellulose crystalline structure is not altered during the colonization process. This information will enable the design of ad-hoc synthetic materials that use fungi as tools to maximize bioluminescence production, paving the way for an innovative hybrid material that could find application in the sustainable production of light.
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Affiliation(s)
- Francis W M R Schwarze
- Laboratory for Cellulose and Wood Materials, Empa, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Tiago Carvalho
- Laboratory for Cellulose and Wood Materials, Empa, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Giacomo Reina
- Laboratory for Particles-Biology Interactions, Empa, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Luiz Garcia Greca
- Laboratory for Cellulose and Wood Materials, Empa, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Urs Buenter
- Laboratory for Cellulose and Wood Materials, Empa, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Zennat Gholam
- Laboratory for Cellulose and Wood Materials, Empa, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Leonard Krupnik
- Center for X-ray Analytics, Empa, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Antonia Neels
- Center for X-ray Analytics, Empa, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Luciano Boesel
- Giorgia Giovannini, Laboratory for Biomimetic Membranes and Textiles Empa, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Hugh Morris
- Integrated Land Management Department, SRUC, Barony, Parkgate, Dumfries, DG1 3NE, UK
| | - Markus Heeb
- Laboratory for Cellulose and Wood Materials, Empa, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Anja Huch
- Laboratory for Cellulose and Wood Materials, Empa, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Gustav Nyström
- Laboratory for Cellulose and Wood Materials, Empa, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Giorgia Giovannini
- Giorgia Giovannini, Laboratory for Biomimetic Membranes and Textiles Empa, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
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3
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Mao J, Zhang H, Chen Y, Wei L, Liu J, Nielsen J, Chen Y, Xu N. Relieving metabolic burden to improve robustness and bioproduction by industrial microorganisms. Biotechnol Adv 2024; 74:108401. [PMID: 38944217 DOI: 10.1016/j.biotechadv.2024.108401] [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: 02/01/2024] [Revised: 05/04/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024]
Abstract
Metabolic burden is defined by the influence of genetic manipulation and environmental perturbations on the distribution of cellular resources. The rewiring of microbial metabolism for bio-based chemical production often leads to a metabolic burden, followed by adverse physiological effects, such as impaired cell growth and low product yields. Alleviating the burden imposed by undesirable metabolic changes has become an increasingly attractive approach for constructing robust microbial cell factories. In this review, we provide a brief overview of metabolic burden engineering, focusing specifically on recent developments and strategies for diminishing the burden while improving robustness and yield. A variety of examples are presented to showcase the promise of metabolic burden engineering in facilitating the design and construction of robust microbial cell factories. Finally, challenges and limitations encountered in metabolic burden engineering are discussed.
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Affiliation(s)
- Jiwei Mao
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Hongyu Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yu Chen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, PR China
| | - Liang Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Jun Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Jens Nielsen
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden; BioInnovation Institute, Ole Maaløes Vej 3, DK2200 Copenhagen, Denmark.
| | - Yun Chen
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Kongens Lyngby, Denmark.
| | - Ning Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China.
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4
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Burbano DA, Kiattisewee C, Karanjia AV, Cardiff RAL, Faulkner ID, Sugianto W, Carothers JM. CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications. Annu Rev Chem Biomol Eng 2024; 15:389-430. [PMID: 38598861 DOI: 10.1146/annurev-chembioeng-100522-114706] [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] [Indexed: 04/12/2024]
Abstract
In the past decades, the broad selection of CRISPR-Cas systems has revolutionized biotechnology by enabling multimodal genetic manipulation in diverse organisms. Rooted in a molecular engineering perspective, we recapitulate the different CRISPR components and how they can be designed for specific genetic engineering applications. We first introduce the repertoire of Cas proteins and tethered effectors used to program new biological functions through gene editing and gene regulation. We review current guide RNA (gRNA) design strategies and computational tools and how CRISPR-based genetic circuits can be constructed through regulated gRNA expression. Then, we present recent advances in CRISPR-based biosensing, bioproduction, and biotherapeutics across in vitro and in vivo prokaryotic systems. Finally, we discuss forthcoming applications in prokaryotic CRISPR technology that will transform synthetic biology principles in the near future.
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Affiliation(s)
- Diego Alba Burbano
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Cholpisit Kiattisewee
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ava V Karanjia
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ryan A L Cardiff
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ian D Faulkner
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Widianti Sugianto
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - James M Carothers
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
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5
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Chua J, Hanko EK, Yiakoumetti A, Stoney RA, Chromy J, Valdehuesa KNG, Hollywood KA, Yan C, Takano E, Breitling R. Bioproduction of methylated phenylpropenes and isoeugenol in Escherichia coli. Metab Eng Commun 2024; 18:e00237. [PMID: 38799229 PMCID: PMC11127157 DOI: 10.1016/j.mec.2024.e00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/28/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024] Open
Abstract
Phenylpropenes are a class of natural products that are synthesised by a vast range of plant species and hold considerable promise in the flavour and fragrance industries. Many in vitro studies have been carried out to elucidate and characterise the enzymes responsible for the production of these volatile compounds. However, there is a scarcity of studies demonstrating the in vivo production of phenylpropenes in microbial cell factories. In this study, we engineered Escherichia coli to produce methylchavicol, methyleugenol and isoeugenol from their respective phenylacrylic acid precursors. We achieved this by extending and modifying a previously optimised heterologous pathway for the biosynthesis of chavicol and eugenol. We explored the potential of six S-adenosyl l-methionine (SAM)-dependent O-methyltransferases to produce methylchavicol and methyleugenol from chavicol and eugenol, respectively. Additionally, we examined two isoeugenol synthases for the production of isoeugenol from coniferyl acetate. The best-performing strains in this study were able to achieve titres of 13 mg L-1 methylchavicol, 59 mg L-1 methyleugenol and 361 mg L-1 isoeugenol after feeding with their appropriate phenylacrylic acid substrates. We were able to further increase the methyleugenol titre to 117 mg L-1 by supplementation with methionine to facilitate SAM recycling. Moreover, we report the biosynthesis of methylchavicol and methyleugenol from l-tyrosine through pathways involving six and eight enzymatic steps, respectively.
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Affiliation(s)
- Jeremy Chua
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Erik K.R. Hanko
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Andrew Yiakoumetti
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Ruth A. Stoney
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Jakub Chromy
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Kris Niño G. Valdehuesa
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Katherine A. Hollywood
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Cunyu Yan
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Eriko Takano
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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6
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Marsan CB, Lee SG, Nguyen A, Gordillo Sierra AR, Coleman SM, Brooks SM, Alper HS. Leveraging a Y. lipolytica naringenin chassis for biosynthesis of apigenin and associated glucoside. Metab Eng 2024; 83:1-11. [PMID: 38447910 DOI: 10.1016/j.ymben.2024.02.018] [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: 12/16/2023] [Revised: 02/01/2024] [Accepted: 02/26/2024] [Indexed: 03/08/2024]
Abstract
Flavonoids are a diverse set of natural products with promising bioactivities including anti-inflammatory, anti-cancer, and neuroprotective properties. Previously, the oleaginous host Yarrowia lipolytica has been engineered to produce high titers of the base flavonoid naringenin. Here, we leverage this host along with a set of E. coli bioconversion strains to produce the flavone apigenin and its glycosylated derivative isovitexin, two potential nutraceutical and pharmaceutical candidates. Through downstream strain selection, co-culture optimization, media composition, and mutant isolation, we were able to produce168 mg/L of apigenin, representing a 46% conversion rate of 2-(R/S)-naringenin to apigenin. This apigenin platform was modularly extended to produce isovitexin by addition of a second bioconversion strain. Together, these results demonstrate the promise of microbial production and modular bioconversion to access diversified flavonoids.
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Affiliation(s)
- Celeste B Marsan
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Sung Gyung Lee
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ankim Nguyen
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Angela R Gordillo Sierra
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Sarah M Coleman
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Sierra M Brooks
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA; Interdisciplinary Life Sciences Program, The University of Texas at Austin, Austin, TX, 78712, USA.
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7
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Lv Y, Chang J, Zhang W, Dong H, Chen S, Wang X, Zhao A, Zhang S, Alam MA, Wang S, Du C, Xu J, Wang W, Xu P. Improving Microbial Cell Factory Performance by Engineering SAM Availability. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3846-3871. [PMID: 38372640 DOI: 10.1021/acs.jafc.3c09561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Methylated natural products are widely spread in nature. S-Adenosyl-l-methionine (SAM) is the secondary abundant cofactor and the primary methyl donor, which confer natural products with structural and functional diversification. The increasing demand for SAM-dependent natural products (SdNPs) has motivated the development of microbial cell factories (MCFs) for sustainable and efficient SdNP production. Insufficient and unsustainable SAM availability hinders the improvement of SdNP MCF performance. From the perspective of developing MCF, this review summarized recent understanding of de novo SAM biosynthesis and its regulatory mechanism. SAM is just the methyl mediator but not the original methyl source. Effective and sustainable methyl source supply is critical for efficient SdNP production. We compared and discussed the innate and relatively less explored alternative methyl sources and identified the one involving cheap one-carbon compound as more promising. The SAM biosynthesis is synergistically regulated on multilevels and is tightly connected with ATP and NAD(P)H pools. We also covered the recent advancement of metabolic engineering in improving intracellular SAM availability and SdNP production. Dynamic regulation is a promising strategy to achieve accurate and dynamic fine-tuning of intracellular SAM pool size. Finally, we discussed the design and engineering constraints underlying construction of SAM-responsive genetic circuits and envisioned their future applications in developing SdNP MCFs.
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Affiliation(s)
- Yongkun Lv
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Jinmian Chang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Weiping Zhang
- Bloomage Biotechnology Corporation Limited, 678 Tianchen Street, Jinan, Shandong 250101, China
| | - Hanyu Dong
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Song Chen
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Xian Wang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Anqi Zhao
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, China
| | - Shen Zhang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Md Asraful Alam
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Shilei Wang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Chaojun Du
- Nanyang Research Institute of Zhengzhou University, Nanyang Institute of Technology, No. 80 Changjiang Road, Nanyang 473004, China
| | - Jingliang Xu
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
- National Key Laboratory of Biobased Transportation Fuel Technology, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Weigao Wang
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Palo Alto, California 94305, United States
| | - Peng Xu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong 515063, China
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8
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Zhu Z, Chen R, Zhang L. Simple phenylpropanoids: recent advances in biological activities, biosynthetic pathways, and microbial production. Nat Prod Rep 2024; 41:6-24. [PMID: 37807808 DOI: 10.1039/d3np00012e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Covering: 2000 to 2023Simple phenylpropanoids are a large group of natural products with primary C6-C3 skeletons. They are not only important biomolecules for plant growth but also crucial chemicals for high-value industries, including fragrances, nutraceuticals, biomaterials, and pharmaceuticals. However, with the growing global demand for simple phenylpropanoids, direct plant extraction or chemical synthesis often struggles to meet current needs in terms of yield, titre, cost, and environmental impact. Benefiting from the rapid development of metabolic engineering and synthetic biology, microbial production of natural products from inexpensive and renewable sources provides a feasible solution for sustainable supply. This review outlines the biological activities of simple phenylpropanoids, compares their biosynthetic pathways in different species (plants, bacteria, and fungi), and summarises key research on the microbial production of simple phenylpropanoids over the last decade, with a focus on engineering strategies that seem to hold most potential for further development. Moreover, constructive solutions to the current challenges and future perspectives for industrial production of phenylpropanoids are presented.
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Affiliation(s)
- Zhanpin Zhu
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China.
| | - Ruibing Chen
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China.
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China.
- Institute of Interdisciplinary Integrative Medicine Research, Medical School of Nantong University, Nantong 226001, China
- Innovative Drug R&D Centre, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
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9
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Wierzchowski K, Nowak B, Kawka M, Sykłowska-Baranek K, Pilarek M. Effect of Silica Xerogel Functionalization on Intensification of Rindera graeca Transgenic Roots Proliferation and Boosting Naphthoquinone Production. Life (Basel) 2024; 14:159. [PMID: 38276288 PMCID: PMC10817608 DOI: 10.3390/life14010159] [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: 11/29/2023] [Revised: 01/15/2024] [Accepted: 01/20/2024] [Indexed: 01/27/2024] Open
Abstract
Secondary metabolites derived from plants are recognized as valuable products with several successful applications in the pharmaceutical, cosmetic, and food industries. The major limitation to the broader implementation of these compounds is their low manufacturing efficiency. Current efforts to overcome unprofitability depend mainly on biotechnological methods, especially through the application of plant in vitro cultures. This concept allows unprecedented bioengineering opportunities for culture system modifications with in situ product removal. The silica-based xerogels can be used as a novel, porous biomaterial characterized by a large surface area and high affinity to lipophilic secondary metabolites produced by plant tissue. This study aimed to investigate the influence of xerogel-based biomaterials functionalized with methyl, hydroxyl, carboxylic, and amine groups on Rindera graeca transgenic root growth and the production of naphthoquinone derivatives. The application of xerogel-based scaffolds functionalized with the methyl group resulted in more than 1.5 times higher biomass proliferation than for reference untreated culture. The naphthoquinone derivatives' production was noted exclusively in culture systems supplemented with xerogel functionalized with methyl and hydroxyl groups. Applying chemically functionalized xerogels as in situ adsorbents allowed for the enhanced growth and productivity of in vitro cultured R. graeca transgenic roots, facilitating product isolation due to their selective and efficient accumulation.
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Affiliation(s)
- Kamil Wierzchowski
- Faculty of Chemical and Process Engineering, Warsaw University of Technology, Waryńskiego 1, 00-645 Warsaw, Poland; (K.W.); (B.N.)
| | - Bartosz Nowak
- Faculty of Chemical and Process Engineering, Warsaw University of Technology, Waryńskiego 1, 00-645 Warsaw, Poland; (K.W.); (B.N.)
| | - Mateusz Kawka
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland; (M.K.); (K.S.-B.)
| | - Katarzyna Sykłowska-Baranek
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland; (M.K.); (K.S.-B.)
| | - Maciej Pilarek
- Faculty of Chemical and Process Engineering, Warsaw University of Technology, Waryńskiego 1, 00-645 Warsaw, Poland; (K.W.); (B.N.)
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10
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Boob AG, Chen J, Zhao H. Enabling pathway design by multiplex experimentation and machine learning. Metab Eng 2024; 81:70-87. [PMID: 38040110 DOI: 10.1016/j.ymben.2023.11.006] [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: 09/14/2023] [Revised: 11/01/2023] [Accepted: 11/25/2023] [Indexed: 12/03/2023]
Abstract
The remarkable metabolic diversity observed in nature has provided a foundation for sustainable production of a wide array of valuable molecules. However, transferring the biosynthetic pathway to the desired host often runs into inherent failures that arise from intermediate accumulation and reduced flux resulting from competing pathways within the host cell. Moreover, the conventional trial and error methods utilized in pathway optimization struggle to fully grasp the intricacies of installed pathways, leading to time-consuming and labor-intensive experiments, ultimately resulting in suboptimal yields. Considering these obstacles, there is a pressing need to explore the enzyme expression landscape and identify the optimal pathway configuration for enhanced production of molecules. This review delves into recent advancements in pathway engineering, with a focus on multiplex experimentation and machine learning techniques. These approaches play a pivotal role in overcoming the limitations of traditional methods, enabling exploration of a broader design space and increasing the likelihood of discovering optimal pathway configurations for enhanced production of molecules. We discuss several tools and strategies for pathway design, construction, and optimization for sustainable and cost-effective microbial production of molecules ranging from bulk to fine chemicals. We also highlight major successes in academia and industry through compelling case studies.
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Affiliation(s)
- Aashutosh Girish Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Junyu Chen
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.
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11
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Chacόn M, Percival E, Bugg TDH, Dixon N. Engineered co-culture for consolidated production of phenylpropanoids directly from aromatic-rich biomass. BIORESOURCE TECHNOLOGY 2024; 391:129935. [PMID: 37923228 DOI: 10.1016/j.biortech.2023.129935] [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: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023]
Abstract
Consolidated bioprocesses for the in situ hydrolysis and conversion of biomass feedstocks into value-added products offers great potential for both process and cost reduction. However, to date few consolidated bioprocesses have been developed that target aromatic rich feedstock fractions. Reported here is the development of synthetic co-cultivation for the consolidated hydrolysis and valorisation of corncob hydroxycinnamic acids. Biomass hydrolysis was achieved via a secretion module developed in B. subtilis using a genetically encoded biosensor-actuator to secrete hydrolytic enzymes. Conversion was achieved via a biotransformation module developed in E. coli using a suite of plug-and-play encoded enzymes to convert the released hydroxycinnamic acids into high-value phenylpropanoid target compounds. Finally, employing cellulolytic pre-treatment, extractive fermentation and in situ product recovery multiple aromatic products, coniferol and chavicol, were isolated from the same process in high purity.
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Affiliation(s)
- Micaela Chacόn
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, University of Manchester, Manchester M1 7DN, UK
| | - Ellen Percival
- Department of Chemistry, University of Warwick, Coventry CV4 7AK, UK
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AK, UK
| | - Neil Dixon
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, University of Manchester, Manchester M1 7DN, UK.
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Hanko EKR, Valdehuesa KNG, Verhagen KJA, Chromy J, Stoney RA, Chua J, Yan C, Roubos JA, Schmitz J, Breitling R. Carboxylic acid reductase-dependent biosynthesis of eugenol and related allylphenols. Microb Cell Fact 2023; 22:238. [PMID: 37980525 PMCID: PMC10656918 DOI: 10.1186/s12934-023-02246-4] [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: 08/30/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023] Open
Abstract
BACKGROUND (Hydroxy)cinnamyl alcohols and allylphenols, including coniferyl alcohol and eugenol, are naturally occurring aromatic compounds widely utilised in pharmaceuticals, flavours, and fragrances. Traditionally, the heterologous biosynthesis of (hydroxy)cinnamyl alcohols from (hydroxy)cinnamic acids involved CoA-dependent activation of the substrate. However, a recently explored alternative pathway involving carboxylic acid reductase (CAR) has proven efficient in generating the (hydroxy)cinnamyl aldehyde intermediate without the need for CoA activation. In this study, we investigated the application of the CAR pathway for whole-cell bioconversion of a range of (hydroxy)cinnamic acids into their corresponding (hydroxy)cinnamyl alcohols. Furthermore, we sought to extend the pathway to enable the production of a variety of allylphenols and allylbenzene. RESULTS By screening the activity of several heterologously expressed enzymes in crude cell lysates, we identified the combination of Segniliparus rugosus CAR (SrCAR) and Medicago sativa cinnamyl alcohol dehydrogenase (MsCAD2) as the most efficient enzymatic cascade for the two-step reduction of ferulic acid to coniferyl alcohol. To optimise the whole-cell bioconversion in Escherichia coli, we implemented a combinatorial approach to balance the gene expression levels of SrCAR and MsCAD2. This optimisation resulted in a coniferyl alcohol yield of almost 100%. Furthermore, we extended the pathway by incorporating coniferyl alcohol acyltransferase and eugenol synthase, which allowed for the production of eugenol with a titre of up to 1.61 mM (264 mg/L) from 3 mM ferulic acid. This improvement in titre surpasses previous achievements in the field employing a CoA-dependent coniferyl alcohol biosynthesis pathway. Our study not only demonstrated the successful utilisation of the CAR pathway for the biosynthesis of diverse (hydroxy)cinnamyl alcohols, such as p-coumaryl alcohol, caffeyl alcohol, cinnamyl alcohol, and sinapyl alcohol, from their corresponding (hydroxy)cinnamic acid precursors but also extended the pathway to produce allylphenols, including chavicol, hydroxychavicol, and methoxyeugenol. Notably, the microbial production of methoxyeugenol from sinapic acid represents a novel achievement. CONCLUSION The combination of SrCAR and MsCAD2 enzymes offers an efficient enzymatic cascade for the production of a wide array of (hydroxy)cinnamyl alcohols and, ultimately, allylphenols from their respective (hydroxy)cinnamic acids. This expands the range of value-added molecules that can be generated using microbial cell factories and creates new possibilities for applications in industries such as pharmaceuticals, flavours, and fragrances. These findings underscore the versatility of the CAR pathway, emphasising its potential in various biotechnological applications.
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Affiliation(s)
- Erik K R Hanko
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Kris Niño G Valdehuesa
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Koen J A Verhagen
- dsm-firmenich, Science & Research, P.O. Box 1, Delft, 2600 MA, The Netherlands
| | - Jakub Chromy
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Ruth A Stoney
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jeremy Chua
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Cunyu Yan
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Johannes A Roubos
- dsm-firmenich, Science & Research, P.O. Box 1, Delft, 2600 MA, The Netherlands
| | - Joep Schmitz
- dsm-firmenich, Science & Research, P.O. Box 1, Delft, 2600 MA, The Netherlands
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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