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Takenaka M, Kamasaka K, Daryong K, Tsuchikane K, Miyazawa S, Fujihana S, Hori Y, Vavricka CJ, Hosoyama A, Kawasaki H, Shirai T, Araki M, Nakagawa A, Minami H, Kondo A, Hasunuma T. Integrated pathway mining and selection of an artificial CYP79-mediated bypass to improve benzylisoquinoline alkaloid biosynthesis. Microb Cell Fact 2024; 23:178. [PMID: 38879464 PMCID: PMC11179272 DOI: 10.1186/s12934-024-02453-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/06/2024] [Indexed: 06/19/2024] Open
Abstract
BACKGROUND Computational mining of useful enzymes and biosynthesis pathways is a powerful strategy for metabolic engineering. Through systematic exploration of all conceivable combinations of enzyme reactions, including both known compounds and those inferred from the chemical structures of established reactions, we can uncover previously undiscovered enzymatic processes. The application of the novel alternative pathways enables us to improve microbial bioproduction by bypassing or reinforcing metabolic bottlenecks. Benzylisoquinoline alkaloids (BIAs) are a diverse group of plant-derived compounds with important pharmaceutical properties. BIA biosynthesis has developed into a prime example of metabolic engineering and microbial bioproduction. The early bottleneck of BIA production in Escherichia coli consists of 3,4-dihydroxyphenylacetaldehyde (DHPAA) production and conversion to tetrahydropapaveroline (THP). Previous studies have selected monoamine oxidase (MAO) and DHPAA synthase (DHPAAS) to produce DHPAA from dopamine and oxygen; however, both of these enzymes produce toxic hydrogen peroxide as a byproduct. RESULTS In the current study, in silico pathway design is applied to relieve the bottleneck of DHPAA production in the synthetic BIA pathway. Specifically, the cytochrome P450 enzyme, tyrosine N-monooxygenase (CYP79), is identified to bypass the established MAO- and DHPAAS-mediated pathways in an alternative arylacetaldoxime route to DHPAA with a peroxide-independent mechanism. The application of this pathway is proposed to result in less formation of toxic byproducts, leading to improved production of reticuline (up to 60 mg/L at the flask scale) when compared with that from the conventional MAO pathway. CONCLUSIONS This study showed improved reticuline production using the bypass pathway predicted by the M-path computational platform. Reticuline production in E. coli exceeded that of the conventional MAO-mediated pathway. The study provides a clear example of the integration of pathway mining and enzyme design in creating artificial metabolic pathways and suggests further potential applications of this strategy in metabolic engineering.
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Affiliation(s)
- Musashi Takenaka
- Bacchus Bio innovation Co. Ltd, 6-3-7-505 Minatojima Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Kouhei Kamasaka
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Kim Daryong
- National Institute of Technology and Evaluation, 2-49-10 Nishihara, Shibuya-ku, Tokyo, 1510066, Japan
| | - Keiko Tsuchikane
- National Institute of Technology and Evaluation, 2-49-10 Nishihara, Shibuya-ku, Tokyo, 1510066, Japan
| | - Seiha Miyazawa
- National Institute of Technology and Evaluation, 2-49-10 Nishihara, Shibuya-ku, Tokyo, 1510066, Japan
| | - Saeko Fujihana
- Bacchus Bio innovation Co. Ltd, 6-3-7-505 Minatojima Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Yoshimi Hori
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Christopher J Vavricka
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Akira Hosoyama
- National Institute of Technology and Evaluation, 2-49-10 Nishihara, Shibuya-ku, Tokyo, 1510066, Japan
| | - Hiroko Kawasaki
- National Institute of Technology and Evaluation, 2-49-10 Nishihara, Shibuya-ku, Tokyo, 1510066, Japan
| | - Tomokazu Shirai
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Michihiro Araki
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606- 8501, Japan
- National Cerebral and Cardiovascular Center, 6-1 Kishibe-Shimmachi, Suita, Osaka, 564-8565, Japan
| | - Akira Nakagawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308, Suematsu, Nonoichi city, Ishikawa, Japan
| | - Hiromichi Minami
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308, Suematsu, Nonoichi city, Ishikawa, Japan
| | - Akihiko Kondo
- Bacchus Bio innovation Co. Ltd, 6-3-7-505 Minatojima Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
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Butler ND, Anderson SR, Dickey RM, Nain P, Kunjapur AM. Combinatorial gene inactivation of aldehyde dehydrogenases mitigates aldehyde oxidation catalyzed by E. coli resting cells. Metab Eng 2023; 77:294-305. [PMID: 37100193 DOI: 10.1016/j.ymben.2023.04.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/11/2023] [Accepted: 04/23/2023] [Indexed: 04/28/2023]
Abstract
Aldehydes are attractive chemical targets both as end products in the flavors and fragrances industry and as intermediates due to their propensity for C-C bond formation. Here, we identify and address unexpected oxidation of a model collection of aromatic aldehydes, including many that originate from biomass degradation. When diverse aldehydes are supplemented to E. coli cells grown under aerobic conditions, as expected they are either reduced by the wild-type MG1655 strain or stabilized by a strain engineered for reduced aromatic aldehyde reduction (the E. coli RARE strain). Surprisingly, when these same aldehydes are supplemented to resting cell preparations of either E. coli strain, under many conditions we observe substantial oxidation. By performing combinatorial inactivation of six candidate aldehyde dehydrogenase genes in the E. coli genome using multiplexed automatable genome engineering (MAGE), we demonstrate that this oxidation can be substantially slowed, with greater than 50% retention of 6 out of 8 aldehydes when assayed 4 h after their addition. Given that our newly engineered strain exhibits reduced oxidation and reduction of aromatic aldehydes, we dubbed it the E. coli ROAR strain. We applied the new strain to resting cell biocatalysis for two kinds of reactions - the reduction of 2-furoic acid to furfural and the condensation of 3-hydroxy-benzaldehyde and glycine to form a beta hydroxylated non-standard amino acid. In each case, we observed substantial improvements in product titer 20 h after reaction initiation (9-fold and 10-fold, respectively). Moving forward, the use of this strain to generate resting cells should allow aldehyde product isolation, further enzymatic conversion, or chemical reactivity under cellular contexts that better accommodate aldehyde toxicity.
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Affiliation(s)
- Neil D Butler
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newar, DE, 19716, USA
| | - Shelby R Anderson
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newar, DE, 19716, USA
| | - Roman M Dickey
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newar, DE, 19716, USA
| | - Priyanka Nain
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newar, DE, 19716, USA
| | - Aditya M Kunjapur
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newar, DE, 19716, USA.
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3
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Haas R, Nikel PI. Challenges and opportunities in bringing nonbiological atoms to life with synthetic metabolism. Trends Biotechnol 2023; 41:27-45. [PMID: 35786519 DOI: 10.1016/j.tibtech.2022.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/05/2022] [Accepted: 06/09/2022] [Indexed: 02/06/2023]
Abstract
The relatively narrow spectrum of chemical elements within the microbial 'biochemical palate' limits the reach of biotechnology, because several added-value compounds can only be produced with traditional organic chemistry. Synthetic biology offers enabling tools to tackle this issue by facilitating 'biologization' of non-canonical chemical atoms. The interplay between xenobiology and synthetic metabolism multiplies routes for incorporating nonbiological atoms into engineered microbes. In this review, we survey natural assimilation routes for elements beyond the essential biology atoms [i.e., carbon (C), hydrogen (H), nitrogen (N), oxygen (O), phosphorus (P), and sulfur (S)], discussing how these mechanisms could be repurposed for biotechnology. Furthermore, we propose a computational framework to identify chemical elements amenable to biologization, ranking reactions suitable to build synthetic metabolism. When combined and deployed in robust microbial hosts, these approaches will offer sustainable alternatives for smart chemical production.
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Affiliation(s)
- Robert Haas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
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4
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Zomorrodi AR, Hemez C, Arranz-Gibert P, Wu T, Isaacs FJ, Segrè D. Computational design and engineering of an Escherichia coli strain producing the nonstandard amino acid para-aminophenylalanine. iScience 2022; 25:104562. [PMID: 35789833 PMCID: PMC9249619 DOI: 10.1016/j.isci.2022.104562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/16/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
Introducing heterologous pathways into host cells constitutes a promising strategy for synthesizing nonstandard amino acids (nsAAs) to enable the production of proteins with expanded chemistries. However, this strategy has proven challenging, as the expression of heterologous pathways can disrupt cellular homeostasis of the host cell. Here, we sought to optimize the heterologous production of the nsAA para-aminophenylalanine (pAF) in Escherichia coli. First, we incorporated a heterologous pAF biosynthesis pathway into a genome-scale model of E. coli metabolism and computationally identified metabolic interventions in the host’s native metabolism to improve pAF production. Next, we explored different approaches of imposing these flux interventions experimentally and found that the upregulation of flux in the chorismate biosynthesis pathway through the elimination of feedback inhibition mechanisms could significantly raise pAF titers (∼20-fold) while maintaining a reasonable pAF production-growth rate trade-off. Overall, this study provides a promising strategy for the biosynthesis of nsAAs in engineered cells. Sought to optimize para-aminophenylalanine (pAF) production and growth in E. coli Identified interventions in the host native metabolism using genome-scale models Constructed multiple mutant strains involving gene knockouts and/or overexpressions Flux modification in chorismate biosynthesis pathway significantly raised pAF titer
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Affiliation(s)
- Ali R. Zomorrodi
- Mucosal Immunology and Biology Research Center, Pediatrics Department, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Bioinformatics Graduate Program, Boston University, Boston, MA, USA
| | - Colin Hemez
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Pol Arranz-Gibert
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
| | - Terrence Wu
- Yale West Campus Analytical Core, 600 West Campus Drive, West Haven, USA
| | - Farren J. Isaacs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Corresponding author
| | - Daniel Segrè
- Bioinformatics Graduate Program, Boston University, Boston, MA, USA
- Department of Biology, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- Corresponding author
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Mohareb RM, Megally Abdo NY. Heterocyclic compounds derived from cyclohexane-1,4-dione: synthesis of tetrahydro-4H-chromene and tetrahydrobenzo[d]thiazole derivatives as target SARS-CoV-2 main protease (Mpro) and potential anti-Covid-19. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [PMCID: PMC8370666 DOI: 10.1007/s13738-021-02366-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Tetrahydro-4H-chromene-3-carbonitrile derivatives 4a-c where prepared from the reaction of 1,4-cyclohexane dione (1), malononitrile (2) and either of benzaldehyde (3a), 2-chlorobenzaldehyde (3b) or 4-methoxybenzaldehyde (3c) in ethanol containing triethylamine. Compound 4b was used to prepare pyrazole, pyrimidine and thiazole derivatives. Moreover, tetrahydrobenzo[d]thiazole derivative 18 was prepared from the reaction of 1,4-cyclohexane dione (1) with elemental sulfur followed by phenyl isothiocyanate (12) in absolute ethanol containing triethylamine. The latter compound reacted with ethyl orthoformate and either malononitrile or ethyl cyanoacetate in 1,4-dioxane in the presence of triethylamine to produce the 9-ethoxy-2H-chromeno[6,5-d]thiazole derivatives 20a,b. In addition, fused thiophene and pyran derivatives were synthesized starting from compound 18. The screened compounds were designed as mimics of the transition state of RNA2’-O-methylation were screened against several viral RNA 2’-OMTases from SARS-CoV (nsp10/nsp16 complex), Zika, West Nile, dengue, vaccinia (VP39) viruses. At the same time, the compounds were tested against human RNA N7-MTase (hRNMT) and selected viral N7-MTases such as SARS-CoV nsp14 and vaccinia D1-D12 complex to evaluate their specificity. Compounds 4a, 4b, 6b, 6c, 6e, 9a, 9b, 15, 16, 21b, and 23b showed high % inhibitions against SARs-Cov nsp 14 with values 93.42, 87.49, 98.23, 88.15, 89.24, 96.31, 93.28, 89.25, 89.20, 87.24, and 94.49, respectively.
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Zhao X, Zhang Y, Jiang H, Zang H, Wang Y, Sun S, Li C. Efficient vanillin biosynthesis by recombinant lignin-degrading bacterium Arthrobacter sp. C2 and its environmental profile via life cycle assessment. BIORESOURCE TECHNOLOGY 2022; 347:126434. [PMID: 34838969 DOI: 10.1016/j.biortech.2021.126434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Vanillin is a natural flavoring agent that is widely used in the bioengineering industry. To enable sustainable development, joint consideration of bacterial performance and negative environmental impacts are critical to vanillin biosynthesis. In this study, a cold shock protein (csp) gene was upregulated for maintaining stable growth in Arthrobacter sp. C2 responding to vanillin and cold stress. Furthermore, the recombinant strain C2 was constructed by simultaneously deleting the xylC gene encoding benzaldehyde dehydrase and overexpressing the pchF gene encoding vanillyl alcohol oxidase and achieved a maximum vanillin productivity of 0.85 mg/g DCW/h with alkaline lignin as the substrate. Finally, this process generated an environmental impact value of 25.05, which was the lowest environmental impact achieved according to life cycle assessment (LCA). Improvement strategies included reducing electricity consumption and replacing chemicals. This study achieved the development of an effective strategy, and future studies should focus on precise vanillin biosynthesis methods for large-scale application.
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Affiliation(s)
- Xinyue Zhao
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yuting Zhang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Hanyi Jiang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Hailian Zang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yue Wang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Shanshan Sun
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Chunyan Li
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China.
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7
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Mohareb RM, Bagato NMA, Radwan IT. Design, Synthesis, Molecular Docking and Biological Studies of New Heterocyclic Compounds Derived from -Diketonesas Novel EGFR and Pim-1 Inhibitors Endowed with Antitumor Activity. Anticancer Agents Med Chem 2022; 22:2558-2576. [PMID: 35023461 DOI: 10.2174/1871520622666220112104320] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 10/20/2021] [Accepted: 11/16/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Cancer is a disease illustrated by a shift in the controlled mechanisms that control both cell proliferation and differentiation. It is regarded as a prime health problem worldwide, leading cause of human death-rate exceeded only by cardiovascular diseases. Many reported work was concerned with the discovery of new antitumor compounds this encourage us to synthesis new anticancer agents. OBJECTIVE In this work, we are aiming to synthesize target molecules from 1,3-dicarbonyl compounds through many heterocyclization reactions. METHOD The reaction of either 4-methylaniline (1a) or 1-naphthylamine (1b) with diethyl malonate (2) gave the anilide derivatives 3a and 3b, respectively. The latter products underwent a series of heterocyclization reactions to give the pyridine, pyran andthiazole derivatives which confirmed with the required spectral data. RESULTS Thein-vitro antitumor evaluations of the newly synthesized products against four cancer cell lines MCF-7, NCI-H460, SF-268 and WI 38 as normal cell line were screened and the data revealed that compounds 11a, 18b, 18c and 20d showed high antitumor activity and 20dindividualize with potential antitumor activity towards cell lines with lowest cytotoxicity effect. Both EGFR and PIM-1 enzyme inhibition were investigated for the compound 20d and his inhibition effect was promising for each enzyme showing IC50=45.67 ng and 553.3 ng for EGFR and PIM-1, respectively. CONCLUSION Molecular docking results of compound 20d showed a strong binding interactions on both enzymes, where, good binding modes obtained on case of EGFR, which closely similar to the binding mode of standard Erlotinib. While, 20d showed complete superimposition binding interactions with VRV-cocrystallized ligand of PIM-1 that may expounds the in-vitro antitumor activity.
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Affiliation(s)
- Rafat Milad Mohareb
- Department of Chemistry, Faculty of Science, Cairo University, Giza, A. R. Egypt
| | - Noha M Asaad Bagato
- Egyptian Petroleum Research Institute (EPRI), P.O. Box 11727, Nasr City, Cairo, A. R. Egypt
| | - Ibrahim Taha Radwan
- Supplementary General Sciences Department, Faculty of Oral and Dental Medicine, Future University in Egypt, P.O. Box 11835, Cairo, Egypt
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Dickey RM, Forti AM, Kunjapur AM. Advances in engineering microbial biosynthesis of aromatic compounds and related compounds. BIORESOUR BIOPROCESS 2021; 8:91. [PMID: 38650203 PMCID: PMC10992092 DOI: 10.1186/s40643-021-00434-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/18/2021] [Indexed: 01/14/2023] Open
Abstract
Aromatic compounds have broad applications and have been the target of biosynthetic processes for several decades. New biomolecular engineering strategies have been applied to improve production of aromatic compounds in recent years, some of which are expected to set the stage for the next wave of innovations. Here, we will briefly complement existing reviews on microbial production of aromatic compounds by focusing on a few recent trends where considerable work has been performed in the last 5 years. The trends we highlight are pathway modularization and compartmentalization, microbial co-culturing, non-traditional host engineering, aromatic polymer feedstock utilization, engineered ring cleavage, aldehyde stabilization, and biosynthesis of non-standard amino acids. Throughout this review article, we will also touch on unmet opportunities that future research could address.
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Affiliation(s)
- Roman M Dickey
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, USA
| | - Amanda M Forti
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, USA
| | - Aditya M Kunjapur
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, USA.
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9
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Scherer M, Fleishman SJ, Jones PR, Dandekar T, Bencurova E. Computational Enzyme Engineering Pipelines for Optimized Production of Renewable Chemicals. Front Bioeng Biotechnol 2021; 9:673005. [PMID: 34211966 PMCID: PMC8239229 DOI: 10.3389/fbioe.2021.673005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/06/2021] [Indexed: 11/13/2022] Open
Abstract
To enable a sustainable supply of chemicals, novel biotechnological solutions are required that replace the reliance on fossil resources. One potential solution is to utilize tailored biosynthetic modules for the metabolic conversion of CO2 or organic waste to chemicals and fuel by microorganisms. Currently, it is challenging to commercialize biotechnological processes for renewable chemical biomanufacturing because of a lack of highly active and specific biocatalysts. As experimental methods to engineer biocatalysts are time- and cost-intensive, it is important to establish efficient and reliable computational tools that can speed up the identification or optimization of selective, highly active, and stable enzyme variants for utilization in the biotechnological industry. Here, we review and suggest combinations of effective state-of-the-art software and online tools available for computational enzyme engineering pipelines to optimize metabolic pathways for the biosynthesis of renewable chemicals. Using examples relevant for biotechnology, we explain the underlying principles of enzyme engineering and design and illuminate future directions for automated optimization of biocatalysts for the assembly of synthetic metabolic pathways.
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Affiliation(s)
- Marc Scherer
- Department of Bioinformatics, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Patrik R Jones
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Thomas Dandekar
- Department of Bioinformatics, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Elena Bencurova
- Department of Bioinformatics, Julius-Maximilians University of Würzburg, Würzburg, Germany
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Zhao X, Zhang Y, Cheng Y, Sun H, Bai S, Li C. Identifying environmental hotspots and improvement strategies of vanillin production with life cycle assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 769:144771. [PMID: 33477040 DOI: 10.1016/j.scitotenv.2020.144771] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
Vanillin, an important aroma chemical, can be synthesized through industrial oxidation processes and biotechnological processes. Studying the environmental impacts of synthetic vanillin production processes is fundamental to making these processes feasible and sustainable; however, few studies have focused on such analyses. This study involved performing a life cycle assessment (LCA) to evaluate multiple industrial synthesis and biosynthesis processes for producing synthetic vanillin. The results indicated that human toxicity potential (HTP) appeared to be the most affected indicator among all the impact categories considered. The dominant drivers of the HTP of the vanillin synthesis process were electricity consumption and ultrapure water consumption. Improvement strategies were then proposed to investigate the possibility of reducing the environmental burdens created by vanillin synthesis. Natural gas power generation was determined to be the best choice for replacing traditional coal-fired power generation, thus reducing the negative impacts of these processes on the environment. The best ways to reduce chemical consumption were to recover organic solvents and to replace ultrapure water with industrial or distilled water. All these improvement strategies were demonstrated to be able to effectively reduce the HTP. In addition, suggestions for evaluating scaled-up vanillin production, increasing the LCA coverage to include technological advancements in biosynthesis techniques, and introducing cost-benefit analysis into the LCA were discussed.
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Affiliation(s)
- Xinyue Zhao
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yuting Zhang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yi Cheng
- College of Science, China Agricultural University, Beijing 100083, China
| | - Hongliang Sun
- Changchun Municipal Engineering Design & Research Institute, 130033 Changchun, China
| | - Shunwen Bai
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Chunyan Li
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China.
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Mori Y, Noda S, Shirai T, Kondo A. Direct 1,3-butadiene biosynthesis in Escherichia coli via a tailored ferulic acid decarboxylase mutant. Nat Commun 2021; 12:2195. [PMID: 33850144 PMCID: PMC8044207 DOI: 10.1038/s41467-021-22504-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/18/2021] [Indexed: 12/11/2022] Open
Abstract
The C4 unsaturated compound 1,3-butadiene is an important monomer in synthetic rubber and engineering plastic production. However, microorganisms cannot directly produce 1,3-butadiene when glucose is used as a renewable carbon source via biological processes. In this study, we construct an artificial metabolic pathway for 1,3-butadiene production from glucose in Escherichia coli by combining the cis,cis-muconic acid (ccMA)-producing pathway together with tailored ferulic acid decarboxylase mutations. The rational design of the substrate-binding site of the enzyme by computational simulations improves ccMA decarboxylation and thus 1,3-butadiene production. We find that changing dissolved oxygen (DO) levels and controlling the pH are important factors for 1,3-butadiene production. Using DO-stat fed-batch fermentation, we produce 2.13 ± 0.17 g L-1 1,3-butadiene. The results indicate that we can produce unnatural/nonbiological compounds from glucose as a renewable carbon source via a rational enzyme design strategy.
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Affiliation(s)
- Yutaro Mori
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | - Shuhei Noda
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | - Tomokazu Shirai
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan.
| | - Akihiko Kondo
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
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Nóbile ML, Stricker AM, Marchesano L, Iribarren AM, Lewkowicz ES. N-oxygenation of amino compounds: Early stages in its application to the biocatalyzed preparation of bioactive compounds. Biotechnol Adv 2021; 51:107726. [PMID: 33675955 DOI: 10.1016/j.biotechadv.2021.107726] [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: 11/16/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 10/22/2022]
Abstract
Among the compounds that contain unusual functional groups, nitro is perhaps one of the most interesting due to the valuable properties it confers on pharmaceuticals and explosives. Traditional chemistry has for many years used environmentally unfriendly strategies; in contrast, the biocatalyzed production of this type of products offers a promising alternative. The small family of enzymes formed by N-oxygenases allows the conversion of an amino group to a nitro through the sequential addition of oxygen. These enzymes also make it possible to obtain other less oxidized N-O functions, such as hydroxylamine or nitroso, present in intermediate or final products. The current substrates on which these enzymes are reported to work encompass a few aromatic molecules and sugars. The unique characteristics of N-oxygenases and the great economic value of the products that they could generate, place them in a position of very high scientific and industrial interest. The most important and best studied N-oxygenases will be presented here.
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Affiliation(s)
- Matías L Nóbile
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina.
| | - Abigail M Stricker
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina
| | - Lucas Marchesano
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina
| | - Adolfo M Iribarren
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina
| | - Elizabeth S Lewkowicz
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina
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Katsimpouras C, Stephanopoulos G. Enzymes in biotechnology: Critical platform technologies for bioprocess development. Curr Opin Biotechnol 2021; 69:91-102. [PMID: 33422914 DOI: 10.1016/j.copbio.2020.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/09/2020] [Accepted: 12/08/2020] [Indexed: 01/02/2023]
Abstract
Enzymes are core elements of biosynthetic pathways employed in the synthesis of numerous bioproducts. Here, we review enzyme promiscuity, enzyme engineering, enzyme immobilization, and cell-free systems as fundamental strategies of bioprocess development. Initially, promiscuous enzymes are the first candidates in the quest for new activities to power new, artificial, or bypass pathways that expand substrate range and catalyze the production of new products. If the activity or regulation of available enzymes is unsuitable for a process, protein engineering can be applied to improve them to the required level. When cell toxicity and low productivity cannot be engineered away, cell-free systems are an attractive option, especially in combination with enzyme immobilization that allows extended enzyme use. Overall, the above methods support powerful platforms for bioprocess development and optimization.
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Affiliation(s)
- Constantinos Katsimpouras
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139 MA, USA
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139 MA, USA.
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Nóbile ML, Stricker AM, Iribarren AM, Lewkowicz ES. Streptomyces griseus: A new biocatalyst with N-oxygenase activity. J Biotechnol 2020; 327:36-42. [PMID: 33373628 DOI: 10.1016/j.jbiotec.2020.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/21/2022]
Abstract
Aromatic nitro compounds are key building blocks for many industrial syntheses and are also components of explosives, drugs and pesticides. Due to the environmentally unfriendly experimental conditions involved in their chemical syntheses, industrial processes would benefit from the use of biocatalysts. Among potentially useful enzymes, N-oxygenases, whose role is to oxygenate primary amines, are becoming relevant. These enzymes are involved in different secondary metabolic pathways in Streptomyces and in few other bacteria, forming part of the enzyme pools implicated in antibiotic synthesis. In this work, a group of Streptomyces strains, whose biomass was obtained from simple and novel culture media, were identified as new sources of N-oxygenase activity. Furthermore, the use of unspecific metabolic stimulation strategies allowed substantial improvements in the activity of whole cells as biocatalysts. It is remarkable the 6 to 50-fold increase in nitro compound yields compared to the biotransformation under standard conditions when Streptomyces griseus was the biocatalyst. In addition, biocatalyst substrate acceptance was studied in order to determine the biocatalytic potential of this enzyme.
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Affiliation(s)
- Matías L Nóbile
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, LBB, Roque Sáenz Peña 352, Quilmes, 1876, Argentina.
| | - Abigail M Stricker
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, LBB, Roque Sáenz Peña 352, Quilmes, 1876, Argentina
| | - Adolfo M Iribarren
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, LBB, Roque Sáenz Peña 352, Quilmes, 1876, Argentina
| | - Elizabeth S Lewkowicz
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, LBB, Roque Sáenz Peña 352, Quilmes, 1876, Argentina
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Guirimand G, Kulagina N, Papon N, Hasunuma T, Courdavault V. Innovative Tools and Strategies for Optimizing Yeast Cell Factories. Trends Biotechnol 2020; 39:488-504. [PMID: 33008642 DOI: 10.1016/j.tibtech.2020.08.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/24/2020] [Accepted: 08/27/2020] [Indexed: 12/13/2022]
Abstract
Metabolic engineering (ME) aims to develop efficient microbial cell factories that can produce a wide variety of valuable compounds, ideally at the highest yield and from various feedstocks. We summarize recent developments in ME methods for tailoring different yeast cell factories (YCFs). In particular, we highlight the most timely and cutting-edge molecular tools and strategies for biosynthetic pathway optimization (including genome-editing tools), combinatorial transcriptional and post-transcriptional engineering (cis/trans regulators), dynamic control of metabolic fluxes (e.g., rewiring of primary metabolism), and spatial reconfiguration of metabolic pathways. Finally, we discuss challenges and perspectives for adaptive laboratory evolution (ALE) of yeast to advance ME of microbial cell factories.
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Affiliation(s)
- Gregory Guirimand
- Graduate School of Sciences, Technology and Innovation, Kobe University, Kobe, Japan; Biomolécules et Biotechnologies Végétales (BBV), Équipe d'Accueil (EA) 2106, Université de Tours, Tours, France
| | - Natalja Kulagina
- Biomolécules et Biotechnologies Végétales (BBV), Équipe d'Accueil (EA) 2106, Université de Tours, Tours, France
| | - Nicolas Papon
- Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP), EA 3142, Université Angers and Université Brest, Structure Féderative de Recherche (SFR) 4208 Interactions Cellulaires et Applications Thérapeutiques (ICAT), Angers, France
| | - Tomohisa Hasunuma
- Graduate School of Sciences, Technology and Innovation, Kobe University, Kobe, Japan; Engineering Biology Research Center, Kobe University, Kobe, Japan.
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales (BBV), Équipe d'Accueil (EA) 2106, Université de Tours, Tours, France.
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Mügge C, Heine T, Baraibar AG, van Berkel WJH, Paul CE, Tischler D. Flavin-dependent N-hydroxylating enzymes: distribution and application. Appl Microbiol Biotechnol 2020; 104:6481-6499. [PMID: 32504128 PMCID: PMC7347517 DOI: 10.1007/s00253-020-10705-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/18/2020] [Accepted: 05/24/2020] [Indexed: 02/06/2023]
Abstract
Amino groups derived from naturally abundant amino acids or (di)amines can be used as "shuttles" in nature for oxygen transfer to provide intermediates or products comprising N-O functional groups such as N-hydroxy, oxazine, isoxazolidine, nitro, nitrone, oxime, C-, S-, or N-nitroso, and azoxy units. To this end, molecular oxygen is activated by flavin, heme, or metal cofactor-containing enzymes and transferred to initially obtain N-hydroxy compounds, which can be further functionalized. In this review, we focus on flavin-dependent N-hydroxylating enzymes, which play a major role in the production of secondary metabolites, such as siderophores or antimicrobial agents. Flavoprotein monooxygenases of higher organisms (among others, in humans) can interact with nitrogen-bearing secondary metabolites or are relevant with respect to detoxification metabolism and are thus of importance to understand potential medical applications. Many enzymes that catalyze N-hydroxylation reactions have specific substrate scopes and others are rather relaxed. The subsequent conversion towards various N-O or N-N comprising molecules is also described. Overall, flavin-dependent N-hydroxylating enzymes can accept amines, diamines, amino acids, amino sugars, and amino aromatic compounds and thus provide access to versatile families of compounds containing the N-O motif. Natural roles as well as synthetic applications are highlighted. Key points • N-O and N-N comprising natural and (semi)synthetic products are highlighted. • Flavin-based NMOs with respect to mechanism, structure, and phylogeny are reviewed. • Applications in natural product formation and synthetic approaches are provided. Graphical abstract .
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Affiliation(s)
- Carolin Mügge
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Thomas Heine
- Environmental Microbiology, Faculty of Chemistry and Physics, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Alvaro Gomez Baraibar
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany
- Rottendorf Pharma GmbH, Ostenfelder Str. 51-61, 59320, Ennigerloh, Germany
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, HZ 2629, Delft, The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
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Nieto-Domínguez M, Nikel PI. Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life. Chembiochem 2020; 21:2551-2571. [PMID: 32274875 DOI: 10.1002/cbic.202000091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/09/2020] [Indexed: 12/19/2022]
Abstract
The diversity of life relies on a handful of chemical elements (carbon, oxygen, hydrogen, nitrogen, sulfur and phosphorus) as part of essential building blocks; some other atoms are needed to a lesser extent, but most of the remaining elements are excluded from biology. This circumstance limits the scope of biochemical reactions in extant metabolism - yet it offers a phenomenal playground for synthetic biology. Xenobiology aims to bring novel bricks to life that could be exploited for (xeno)metabolite synthesis. In particular, the assembly of novel pathways engineered to handle nonbiological elements (neometabolism) will broaden chemical space beyond the reach of natural evolution. In this review, xeno-elements that could be blended into nature's biosynthetic portfolio are discussed together with their physicochemical properties and tools and strategies to incorporate them into biochemistry. We argue that current bioproduction methods can be revolutionized by bridging xenobiology and neometabolism for the synthesis of new-to-nature molecules, such as organohalides.
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Affiliation(s)
- Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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