1
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Fansher D, Besna JN, Fendri A, Pelletier JN. Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants. ACS Catal 2024; 14:5560-5592. [PMID: 38660610 PMCID: PMC11036407 DOI: 10.1021/acscatal.4c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.
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Affiliation(s)
- Douglas
J. Fansher
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Jonathan N. Besna
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| | - Ali Fendri
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Joelle N. Pelletier
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
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2
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Yang H, Chen Y, Zeng M, Wu H, Zou X, Fang T, Zhai L, Liang H, Luo H, Tian G, Liu Q, Tang H. Long non-coding RNA LINC01480 is activated by Foxo3a and promotes hydroquinone-induced TK6 cell apoptosis by inhibiting the PI3K/AKT pathway. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 255:114786. [PMID: 36934544 DOI: 10.1016/j.ecoenv.2023.114786] [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: 10/19/2022] [Revised: 03/04/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been shown to play a critical role in the damage caused to the body by environmental exogenous chemicals; however, few studies have explored their effects during exposure to benzene and its metabolite, hydroquinone (HQ). An emerging lncRNA, LINC01480, was found to be associated with the immune microenvironment of some cancers, but its specific function remains unknown. Therefore, this study aimed to investigate the role of LINC01480 in HQ-induced apoptosis. The biological function of LINC01480 was investigated through gain-of-function and loss-of-function experiments. Mechanically, nuclear-cytoplasmic fractionation experiment, chromatin immunoprecipitation (ChIP), dual-luciferase reporter assay, and rescue experiments were performed. In this study, when TK6 cells were treated with HQ (0, 5, 10, and 20 μM) for 12, 24, 48, and 72 h, the expression of LINC01480 was increased in a dose-dependent manner. Meanwhile, the phosphorylation levels of PI3K and AKT decreased, and apoptosis increased. As compared to the control group, HQ-induced apoptosis was significantly reduced, and the relative survival rate of TK6 cells increased after silencing LINC01480, while overexpression of LINC01480 further sensitized TK6 cells to HQ-induced apoptotic cell death. LINC01480 negatively regulated the PI3K/AKT pathway in TK6 cells, and the apoptosis-inhibiting effect of LINC01480 silencing was reversed after inhibition of the PI3K/AKT pathway. In addition, ChIP and the dual-luciferase reporter assays showed that the transcription factor Foxo3a promoted LINC01480 transcription by directly binding to the promoter regions - 149 to - 138 of LINC01480. Moreover, short-term HQ exposure promoted the expression of Foxo3a. From these findings, we can conclude that LINC01480 is activated by Foxo3a, and promotes HQ-induced apoptosis by inhibiting the PI3K/AKT pathway, suggesting that LINC01480 might become a possible target for therapeutic intervention of HQ-induced toxicity.
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Affiliation(s)
- Hui Yang
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, Guangdong, China; Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Yuting Chen
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, Guangdong, China; Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Minjuan Zeng
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Haipeng Wu
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Xiangli Zou
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Tiantian Fang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Lu Zhai
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Hairong Liang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Hao Luo
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Gaiqin Tian
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Qizhan Liu
- Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Huanwen Tang
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, Guangdong, China; Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China.
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3
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Lee UJ, Sohng JK, Kim BG, Choi KY. Recent trends in the modification of polyphenolic compounds using hydroxylation and glycosylation. Curr Opin Biotechnol 2023; 80:102914. [PMID: 36857963 DOI: 10.1016/j.copbio.2023.102914] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/08/2023] [Accepted: 01/31/2023] [Indexed: 03/02/2023]
Abstract
Polyphenols are bioactive molecules that are used in therapeutics. Polyphenol hydroxylation and glycosylation have been shown to increase their bioavailability, solubility, bioactivity, and stability for use in various applications. Ortho-hydroxylation of polyphenols using tyrosinase allows high selectivity and yield without requiring a cofactor, while meta- and para-hydroxylation of polyphenols are mediated by site-specific hydroxylases and cytochrome P450s, although these processes are somewhat rare. O-glycosylation of polyphenols proceeds further after hydroxylation. The O-glycosylation reaction typically requires nucleotide diphosphate (NDP) sugar. However, amylosucrase (AS) has emerged as a promising enzyme for polyphenol glycosylation in large-scale production without requiring NDP-sugar. Overall, this review describes recent findings on the enzymatic mechanisms, enzyme engineering, and applications of enzymatic reactions.
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Affiliation(s)
- Uk-Jae Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea; Bio-MAX/N-Bio, Institute of BioEngineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jae Kyung Sohng
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea; Department of Biotechnology and Pharmaceutical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea; Bio-MAX/N-Bio, Institute of BioEngineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Kwon-Young Choi
- Department of Environmental and Safety Engineering, College of Engineering, Ajou University, Republic of Korea; Department of Energy Systems Research, Ajou University, Republic of Korea.
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4
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Ji J, Zeng C, Wu P, Wang Y, Chen X, Yan X. Improved Whole-Cell Biocatalyst for the Synthesis of Vitamin E Precursor 2,3,5-Trimethylhydroquinone. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:1162-1169. [PMID: 36621524 DOI: 10.1021/acs.jafc.2c07768] [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: 06/17/2023]
Abstract
2,3,5-Trimethylhydroquinone (2,3,5-TMHQ) is the key precursor in the synthesis of vitamin E. It is still a major challenge to produce 2,3,5-TMHQ under mild reaction conditions by chemical methods. The monooxygenase system MpdAB can specifically catalyze the conversion of 2,3,6-trimethylphenol (2,3,6-TMP) to 2,3,5-TMHQ. However, the weak catalytic capacity of wild-type MpdA and the cytotoxicity of the substrate limited the production efficiency of 2,3,5-TMHQ. Here, homologous modeling and saturation mutation were performed to increase the catalytic activity of MpdA. Two variants, L128A and L128K, with higher activity toward 2,3,6-TMP (1.86-1.87-fold) were obtained. On the other hand, an evolved strain B5-4M-evolved with enhanced resistance to 2,3,6-TMP (8.15-fold higher for 1000 μM 2,3,6-TMP) was obtained through adaptive laboratory evolution. Subsequently, a 5.29-fold (or 4.87-fold) improvement in 2,3,5-TMHQ production was achieved by a strain B5-4M-evolved harboring L128K (or L128A) and MpdB, in comparison with that of the wild type (strain B5-4M expressing MpdAB). This study provides better genetic resources for producing 2,3,5-TMHQ and proves that the synthesis efficiency of 2,3,5-TMHQ can be improved through enzyme modification and adaptive laboratory evolution.
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Affiliation(s)
- Junbin Ji
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
- Nanjing Key Laboratory of Quality and Safety of Agricultural Products, College of Food Science, Nanjing XiaoZhuang University, Nanjing 211171, Jiangsu, People's Republic of China
| | - Caiting Zeng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
| | - Panpan Wu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
| | - Yuying Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
| | - Xueting Chen
- Shanghai Fisheries Research Institute, Shanghai Fisheries Technical Extension Station, Shanghai 200433, People's Republic of China
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
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5
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Meng S, Ji Y, Zhu L, Dhoke GV, Davari MD, Schwaneberg U. The molecular basis and enzyme engineering strategies for improvement of coupling efficiency in cytochrome P450s. Biotechnol Adv 2022; 61:108051. [DOI: 10.1016/j.biotechadv.2022.108051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/26/2022] [Accepted: 10/13/2022] [Indexed: 11/28/2022]
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6
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Characterization of the 2,6-Dimethylphenol Monooxygenase MpdAB and Evaluation of Its Potential in Vitamin E Precursor Synthesis. Appl Environ Microbiol 2022; 88:e0011022. [PMID: 35380460 DOI: 10.1128/aem.00110-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2,6-Dimethylphenol (2,6-DMP) is a widely used chemical intermediate whose residue has been frequently detected in the environment, posing a threat to some aquatic organisms. Microbial degradation is an effective method to eliminate 2,6-DMP in nature. However, the genetic and biochemical mechanisms of 2,6-DMP metabolism remain unknown. Mycobacterium neoaurum B5-4 is a 2,6-DMP-degrading bacterium isolated in our previous study. Here, a 2,6-DMP degradation-deficient mutant of strain B5-4 was screened. Comparative genomic, transcriptomic, gene disruption, and genetic complementation data indicated that mpdA and mpdB are responsible for the initial step of 2,6-DMP degradation in M. neoaurum B5-4. MpdAB was predicted to be a two-component flavin-dependent monooxygenase system, which shows 32% and 36% identities with HsaAB from Mycobacterium tuberculosis CDC1551. The transcription of mpdA and mpdB was substantially increased upon exposure to 2,6-DMP. Nuclear magnetic resonance analysis showed that purified 6×His-MpdA and 6×His-MpdB hydroxylated 2,6-DMP and 2,3,6-trimethylphenol (2,3,6-TMP) at the para-position using NADH and flavin adenine dinucleotide (FAD) as cofactors. The apparent Km values of MpdAB for 2,6-DMP and 2,3,6-TMP were 0.12 ± 0.01 and 0.17 ± 0.01 mM, respectively, and the corresponding kcat/Km values were 4.02 and 2.84 s-1 mM-1, respectively. Since para-hydroxylated 2,3,6-TMP is a major precursor for vitamin E synthesis, the potential of MpdAB in vitamin E synthesis was preliminarily evaluated using whole-cell catalysis. Low expression levels of MpdA and 2,3,6-TMP cytotoxicity limited the efficiency of whole-cell catalysis. Together, this study reveals the genetic and biochemical basis for the initial step of 2,6-DMP biodegradation and provides candidate enzymes for vitamin E synthesis. IMPORTANCE Although the microbial degradation of the six isomers of dimethylphenol has been extensively studied, the genetic and biochemical mechanisms of 2,6-DMP degradation remain unclear. This study identified the genes responsible for the initial step in the 2,6-DMP catabolic pathway in M. neoaurum B5-4. Moreover, MpdAB also catalyzed the transformation of 2,3,6-TMP to 2,3,5-trimethylhydroquinone (2,3,5-TMHQ), a crucial step in vitamin E synthesis. Overall, this study provides candidate enzymes for both the bioremediation of 2,6-DMP contamination and the development of a green method to synthesize vitamin E.
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7
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Huang L, Ye J, Jiang K, Wang Y, Li Y. Oil contamination drives the transformation of soil microbial communities: Co-occurrence pattern, metabolic enzymes and culturable hydrocarbon-degrading bacteria. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 225:112740. [PMID: 34482066 DOI: 10.1016/j.ecoenv.2021.112740] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/12/2021] [Accepted: 08/30/2021] [Indexed: 05/16/2023]
Abstract
The land-based oil extraction activity has led to serious pollution of the soil. While microbes may play an important role in the remediation of contaminated soils, ecological effects of oil pollution on soil microbial relationships remain poorly understood. Here, typical contaminated soils and undisturbed soils from seven oilfields of China were investigated in terms of their physicochemical characteristics, indigenous microbial assemblages, bacterial co-occurrence patterns, and metabolic enzymes. Network visualization based on k-core decomposition illustrated that oil pollution reduced correlations between co-existing bacteria. The core genera were altered to those related with oil metabolism (Pseudarthrobacter, Alcanivorax, Sphingomonas, Chromohalobacter and Nocardioides). Under oil pollution pressure, the indigenous bacteria Gammaproteobacteria was domesticated as biomarker and the enzyme expression associated with the metabolism of toxic benzene, toluene, ethylbenzene, xylene and polycyclic aromatic hydrocarbons was enhanced. Functional pathways of xenobiotics biodegradation were also stimulated under oil contamination. Finally, twelve culturable hydrocarbon-degrading microbes were isolated from these polluted soils and classified into Stenotrophomonas, Delftia, Pseudomonas and Bacillus. These results show that the soil microbial communities are transformed under oil pollution stress, and also provide useful information for future bioremediation processes.
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Affiliation(s)
- Liping Huang
- College of Environment and Ecology, Chongqing University, Chongqing 400045, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Jiangyu Ye
- College of Environment and Ecology, Chongqing University, Chongqing 400045, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
| | - Kemei Jiang
- College of Environment and Ecology, Chongqing University, Chongqing 400045, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Yichao Wang
- College of Environment and Ecology, Chongqing University, Chongqing 400045, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Yunyi Li
- College of Environment and Ecology, Chongqing University, Chongqing 400045, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
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8
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Kardashliev T, Weingartner A, Romero E, Schwaneberg U, Fraaije M, Panke S, Held M. Whole-cell screening of oxidative enzymes using genetically encoded sensors. Chem Sci 2021; 12:14766-14772. [PMID: 34820092 PMCID: PMC8597865 DOI: 10.1039/d1sc02578c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/20/2021] [Indexed: 11/23/2022] Open
Abstract
Biocatalysis is increasingly used for synthetic purposes in the chemical and especially the pharmaceutical industry. Enzyme discovery and optimization which is frequently needed to improve biocatalytic performance rely on high-throughput methods for activity determination. These methods should ideally be generic and applicable to entire enzyme families. Hydrogen peroxide (H2O2) is a product of several biocatalytic oxidations and its formation can serve as a proxy for oxidative activity. We designed a genetically encoded sensor for activity measurement of oxidative biocatalysts via the amount of intracellularly-formed H2O2. A key component of the sensor is an H2O2-sensitive transcriptional regulator, OxyR, which is used to control the expression levels of fluorescent proteins. We employed the OxyR sensor to monitor the oxidation of glycerol to glyceraldehyde and of toluene to o-cresol catalysed by recombinant E. coli expressing an alcohol oxidase and a P450 monooxygenase, respectively. In case of the P450 BM3-catalysed reaction, we additionally monitored o-cresol formation via a second genetically encoded sensor based on the phenol-sensitive transcriptional activator, DmpR, and an orthogonal fluorescent reporter protein. Single round screens of mutant libraries by flow cytometry or by visual inspection of colonies on agar plates yielded significantly improved oxidase and oxygenase variants thus exemplifying the suitability of the sensor system to accurately assess whole-cell oxidations in a high-throughput manner.
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Affiliation(s)
- Tsvetan Kardashliev
- Department of Biosystems Science and Engineering ETH Zurich, Mattenstrasse 26 4058 Basel Switzerland
| | - Alexandra Weingartner
- Institute of Biotechnology, RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Elvira Romero
- Faculty of Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Marco Fraaije
- Faculty of Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Sven Panke
- Department of Biosystems Science and Engineering ETH Zurich, Mattenstrasse 26 4058 Basel Switzerland
| | - Martin Held
- Department of Biosystems Science and Engineering ETH Zurich, Mattenstrasse 26 4058 Basel Switzerland
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A Promiscuous Bacterial P450: The Unparalleled Diversity of BM3 in Pharmaceutical Metabolism. Int J Mol Sci 2021; 22:ijms222111380. [PMID: 34768811 PMCID: PMC8583553 DOI: 10.3390/ijms222111380] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022] Open
Abstract
CYP102A1 (BM3) is a catalytically self-sufficient flavocytochrome fusion protein isolated from Bacillus megaterium, which displays similar metabolic capabilities to many drug-metabolizing human P450 isoforms. BM3's high catalytic efficiency, ease of production and malleable active site makes the enzyme a desirable tool in the production of small molecule metabolites, especially for compounds that exhibit drug-like chemical properties. The engineering of select key residues within the BM3 active site vastly expands the catalytic repertoire, generating variants which can perform a range of modifications. This provides an attractive alternative route to the production of valuable compounds that are often laborious to synthesize via traditional organic means. Extensive studies have been conducted with the aim of engineering BM3 to expand metabolite production towards a comprehensive range of drug-like compounds, with many key examples found both in the literature and in the wider industrial bioproduction setting of desirable oxy-metabolite production by both wild-type BM3 and related variants. This review covers the past and current research on the engineering of BM3 to produce drug metabolites and highlights its crucial role in the future of biosynthetic pharmaceutical production.
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10
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Maxel S, Saleh S, King E, Aspacio D, Zhang L, Luo R, Li H. Growth-Based, High-Throughput Selection for NADH Preference in an Oxygen-Dependent Biocatalyst. ACS Synth Biol 2021; 10:2359-2370. [PMID: 34469126 PMCID: PMC10362907 DOI: 10.1021/acssynbio.1c00258] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclohexanone monooxygenases (CHMO) consume molecular oxygen and NADPH to catalyze the valuable oxidation of cyclic ketones. However, CHMO usage is restricted by poor stability and stringent specificity for NADPH. Efforts to engineer CHMO have been limited by the sensitivity of the enzyme to perturbations in conformational dynamics and long-range interactions that cannot be predicted. We demonstrate an aerobic, high-throughput growth selection platform in Escherichia coli for oxygenase evolution based on NADH redox balance. We applied this NADH-dependent selection to alter the cofactor specificity of CHMO to accept NADH, a less expensive cofactor than NADPH. We first identified the variant CHMO DTNP (S208D-K326T-K349N-L143P) with a ∼1200-fold relative cofactor specificity switch from NADPH to NADH compared to the wild type through semirational design. Molecular modeling suggests CHMO DTNP activity is driven by cooperative fine-tuning of cofactor contacts. Additional evolution of CHMO DTNP through random mutagenesis yielded the variant CHMO DTNPY with a ∼2900-fold relative specificity switch compared to the wild type afforded by an additional distal mutation, H163Y. These results highlight the difficulty in engineering functionally innovative variants from static models and rational designs, and the need for high throughput selection methods. Our introduced tools for oxygenase engineering accelerate the advancements of characteristics essential for industrial feasibility.
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Affiliation(s)
- Sarah Maxel
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
| | - Samer Saleh
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
| | - Edward King
- Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Derek Aspacio
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
| | - Linyue Zhang
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
| | - Ray Luo
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
- Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
- Biomedical Engineering, University of California, Irvine, California 92697, United States
| | - Han Li
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
- Biomedical Engineering, University of California, Irvine, California 92697, United States
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11
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King E, Maxel S, Li H. Engineering natural and noncanonical nicotinamide cofactor-dependent enzymes: design principles and technology development. Curr Opin Biotechnol 2020; 66:217-226. [PMID: 32956903 PMCID: PMC7744333 DOI: 10.1016/j.copbio.2020.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/14/2020] [Accepted: 08/16/2020] [Indexed: 12/20/2022]
Abstract
Nicotinamide cofactors enable oxidoreductases to catalyze a myriad of important reactions in biomanufacturing. Decades of research has focused on optimizing enzymes which utilize natural nicotinamide cofactors, namely nicotinamide adenine dinucleotide (phosphate) (NAD(P)+). Recent findings reignite the interest in engineering enzymes to utilize noncanonical cofactors, the mimetics of NAD+ (mNADs), which exhibit superior industrial properties in vitro and enable specific electron delivery in vivo. We compare recent advances in engineering natural versus noncanonical cofactor-utilizing enzymes, discuss design principles discovered, and survey emerging high-throughput platforms beyond the traditional 96-well plate-based methods. Obtaining mNAD-dependent enzymes remains challenging with a limited toolkit. To this end, we highlight design principles and technologies which can potentially be translated from engineering natural to noncanonical cofactor-dependent enzymes.
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Affiliation(s)
- Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Sarah Maxel
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697, USA
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697, USA.
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12
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Winning the numbers game in enzyme evolution - fast screening methods for improved biotechnology proteins. Curr Opin Struct Biol 2020; 63:123-133. [PMID: 32615371 DOI: 10.1016/j.sbi.2020.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/28/2020] [Accepted: 05/08/2020] [Indexed: 01/02/2023]
Abstract
The booming demand for environmentally benign industrial processes relies on the ability to quickly find or engineer a biocatalyst suitable to ideal process conditions. Both metagenomic approaches and directed evolution involve the screening of huge libraries of protein variants, which can only be managed reasonably by flexible platforms for (ultra)high-throughput profiling against the desired criteria. Here, we review the most recent additions toward a growing toolbox of versatile assays using fluorescence, absorbance and mass spectrometry readouts. While conventional solution based high-throughput screening in microtiter plate formats is still important, the implementation of novel screening protocols for microfluidic cell or droplet sorting systems supports technological advances for ultra-high-frequency screening that now can dramatically reduce the timescale of engineering projects. We discuss practical issues of scope, scalability, sensitivity and stereoselectivity for the improvement of biotechnologically relevant enzymes from different classes.
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Brands S, Brass HUC, Klein AS, Pietruszka J, Ruff AJ, Schwaneberg U. A colourimetric high-throughput screening system for directed evolution of prodigiosin ligase PigC. Chem Commun (Camb) 2020; 56:8631-8634. [DOI: 10.1039/d0cc02181d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A colourimetric high-throughput screening system was developed for the first directed evolution campaign on PigC towards production of artificial prodiginines.
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Affiliation(s)
- Stefanie Brands
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Hannah U. C. Brass
- Institute of Bioorganic Chemistry
- Heinrich Heine University Düsseldorf located at Forschungszentrum Jülich
- Stetternicher Forst
- 52426 Jülich
- Germany
| | - Andreas S. Klein
- Institute of Bioorganic Chemistry
- Heinrich Heine University Düsseldorf located at Forschungszentrum Jülich
- Stetternicher Forst
- 52426 Jülich
- Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry
- Heinrich Heine University Düsseldorf located at Forschungszentrum Jülich
- Stetternicher Forst
- 52426 Jülich
- Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
- DWI-Leibniz Institut für Interaktive Materialien
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A 96-multiplex capillary electrophoresis screening platform for product based evolution of P450 BM3. Sci Rep 2019; 9:15479. [PMID: 31664146 PMCID: PMC6820799 DOI: 10.1038/s41598-019-52077-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/04/2019] [Indexed: 11/08/2022] Open
Abstract
The main challenge that prevents a broader application of directed enzyme evolution is the lack of high-throughput screening systems with universal product analytics. Most directed evolution campaigns employ screening systems based on colorimetric or fluorogenic surrogate substrates or universal quantification methods such as nuclear magnetic resonance spectroscopy or mass spectrometry, which have not been advanced to achieve a high-throughput. Capillary electrophoresis with a universal UV-based product detection is a promising analytical tool to quantify product formation. Usage of a multiplex system allows the simultaneous measurement with 96 capillaries. A 96-multiplexed capillary electrophoresis (MP-CE) enables a throughput that is comparable to traditional direct evolution campaigns employing 96-well microtiter plates. Here, we report for the first time the usage of a MP-CE system for directed P450 BM3 evolution towards increased product formation (oxidation of alpha-isophorone to 4-hydroxy-isophorone; highest reached total turnover number after evolution campaign: 7120 mol4-OH molP450−1). The MP-CE platform was 3.5-fold more efficient in identification of beneficial variants than the standard cofactor (NADPH) screening system.
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Santos GDA, Dhoke GV, Davari MD, Ruff AJ, Schwaneberg U. Directed Evolution of P450 BM3 towards Functionalization of Aromatic O-Heterocycles. Int J Mol Sci 2019; 20:E3353. [PMID: 31288417 PMCID: PMC6651506 DOI: 10.3390/ijms20133353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 02/04/2023] Open
Abstract
The O-heterocycles, benzo-1,4-dioxane, phthalan, isochroman, 2,3-dihydrobenzofuran, benzofuran, and dibenzofuran are important building blocks with considerable medical application for the production of pharmaceuticals. Cytochrome P450 monooxygenase (P450) Bacillus megaterium 3 (BM3) wild type (WT) from Bacillus megaterium has low to no conversion of the six O-heterocycles. Screening of in-house libraries for active variants yielded P450 BM3 CM1 (R255P/P329H), which was subjected to directed evolution and site saturation mutagenesis of four positions. The latter led to the identification of position R255, which when introduced in the P450 BM3 WT, outperformed all other variants. The initial oxidation rate of nicotinamide adenine dinucleotide phosphate (NADPH) consumption increased ≈140-fold (WT: 8.3 ± 1.3 min-1; R255L: 1168 ± 163 min-1), total turnover number (TTN) increased ≈21-fold (WT: 40 ± 3; R255L: 860 ± 15), and coupling efficiency, ≈2.9-fold (WT: 8.8 ± 0.1%; R255L: 25.7 ± 1.0%). Computational analysis showed that substitution R255L (distant from the heme-cofactor) does not have the salt bridge formed with D217 in WT, which introduces flexibility into the I-helix and leads to a heme rearrangement allowing for efficient hydroxylation.
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Affiliation(s)
| | - Gaurao V Dhoke
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
- DWI-Leibniz-Institut für Interaktive Materialien e.V., Forckenbeckstraße 50, 52074 Aachen, Germany.
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