1
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Xu M, Du Y, Hou X, Zhang Z, Yan N. Chemical structures, biosynthesis, bioactivities, and utilisation values for the diterpenes produced in tobacco trichomes. PHYTOCHEMISTRY 2024; 223:114117. [PMID: 38697243 DOI: 10.1016/j.phytochem.2024.114117] [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: 12/10/2023] [Revised: 03/26/2024] [Accepted: 04/28/2024] [Indexed: 05/04/2024]
Abstract
Cembranoids and labdanes are two important types of diterpenes in tobacco (Nicotiana genus) that are predominantly found in the leaf and flower glandular trichome secretions. This is the first systematic review of the biosynthesis, chemical structures, bioactivities, and utilisation values of cembranoid and labdane diterpenes in tobacco. A total of 131 natural cembranoid diterpenes have been reported in tobacco since 1962; these were summarised and classified according to their chemical structure characteristics as isopropyl cembranoids (1-88), seco-cembranoids (89-103), chain cembranoids (104-123), and polycyclic cembranoids (124-131). Forty natural labdane diterpenes reported since 1961 were also summarised and divided into epoxy side chain labdanes (132-150) and epoxy-free side chain labdanes (151-171). Tobacco cembranoid and labdane diterpenes are both formed via the methylerythritol 4-phosphate pathway and are synthesised from geranylgeranyl diphosphate. Their biosynthetic pathways and the four key enzymes (cembratrienol synthase, cytochrome P450 hydroxylase, copalyl diphosphate synthase, and Z-abienol cyclase) that affect their biosynthesis have been described in detail. A systematic summary of the bioactivity and utilisation values of the cembranoid and labdane diterpenes is also provided. The agricultural bioactivities associated with cembranoid and labdane diterpenes include antimicrobial and insecticidal activities as well as induced resistance, while the medical bioactivities include cytotoxic and neuroprotective activities. Further research into the cembranoid and labdane diterpenes will help to promote their development and utilisation as plant-derived pesticides and medicines.
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Affiliation(s)
- Minglei Xu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yongmei Du
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
| | - Xiaodong Hou
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Zhongfeng Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Ning Yan
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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2
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Qiu C, Wang X, Zuo J, Li R, Gao C, Chen X, Liu J, Wei W, Wu J, Hu G, Song W, Xu N, Liu L. Systems engineering Escherichia coli for efficient production p-coumaric acid from glucose. Biotechnol Bioeng 2024; 121:2147-2162. [PMID: 38666765 DOI: 10.1002/bit.28721] [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: 01/30/2024] [Revised: 04/06/2024] [Accepted: 04/12/2024] [Indexed: 06/13/2024]
Abstract
P-coumaric acid (p-CA), a pant metabolite with antioxidant and anti-inflammatory activity, is extensively utilized in biomedicine, food, and cosmetics industry. In this study, a synthetic pathway (PAL) for p-CA was designed, integrating three enzymes (AtPAL2, AtC4H, AtATR2) into a higher l-phenylalanine-producing strain Escherichia coli PHE05. However, the lower soluble expression and activity of AtC4H in the PAL pathway was a bottleneck for increasing p-CA titers. To overcome this limitation, the soluble expression of AtC4H was enhanced through N-terminal modifications. And an optimal mutant, AtC4HL373T/G211H, which exhibited a 4.3-fold higher kcat/Km value compared to the wild type, was developed. In addition, metabolic engineering strategies were employed to increase the intracellular NADPH pool. Overexpression of ppnk in engineered E. coli PHCA20 led to a 13.9-folds, 1.3-folds, and 29.1% in NADPH content, the NADPH/NADP+ ratio and p-CA titer, respectively. These optimizations significantly enhance p-CA production, in a 5-L fermenter using fed-batch fermentation, the p-CA titer, yield and productivity of engineered strain E. coli PHCA20 were 3.09 g/L, 20.01 mg/g glucose, and 49.05 mg/L/h, respectively. The results presented here provide a novel way to efficiently produce the plant metabolites using an industrial strain.
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Affiliation(s)
- Chong Qiu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Xiaoge Wang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Jiaojiao Zuo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Runyang Li
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Cong Gao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Jia Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Wanqing Wei
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Guipeng Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Nan Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Liming Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
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3
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Ndochinwa OG, Wang QY, Amadi OC, Nwagu TN, Nnamchi CI, Okeke ES, Moneke AN. Current status and emerging frontiers in enzyme engineering: An industrial perspective. Heliyon 2024; 10:e32673. [PMID: 38912509 PMCID: PMC11193041 DOI: 10.1016/j.heliyon.2024.e32673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/25/2024] Open
Abstract
Protein engineering mechanisms can be an efficient approach to enhance the biochemical properties of various biocatalysts. Immobilization of biocatalysts and the introduction of new-to-nature chemical reactivities are also possible through the same mechanism. Discovering new protocols that enhance the catalytic active protein that possesses novelty in terms of being stable, active, and, stereoselectivity with functions could be identified as essential areas in terms of concurrent bioorganic chemistry (synergistic relationship between organic chemistry and biochemistry in the context of enzyme engineering). However, with our current level of knowledge about protein folding and its correlation with protein conformation and activities, it is almost impossible to design proteins with specific biological and physical properties. Hence, contemporary protein engineering typically involves reprogramming existing enzymes by mutagenesis to generate new phenotypes with desired properties. These processes ensure that limitations of naturally occurring enzymes are not encountered. For example, researchers have engineered cellulases and hemicellulases to withstand harsh conditions encountered during biomass pretreatment, such as high temperatures and acidic environments. By enhancing the activity and robustness of these enzymes, biofuel production becomes more economically viable and environmentally sustainable. Recent trends in enzyme engineering have enabled the development of tailored biocatalysts for pharmaceutical applications. For instance, researchers have engineered enzymes such as cytochrome P450s and amine oxidases to catalyze challenging reactions involved in drug synthesis. In addition to conventional methods, there has been an increasing application of machine learning techniques to identify patterns in data. These patterns are then used to predict protein structures, enhance enzyme solubility, stability, and function, forecast substrate specificity, and assist in rational protein design. In this review, we discussed recent trends in enzyme engineering to optimize the biochemical properties of various biocatalysts. Using examples relevant to biotechnology in engineering enzymes, we try to expatiate the significance of enzyme engineering with how these methods could be applied to optimize the biochemical properties of a naturally occurring enzyme.
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Affiliation(s)
- Obinna Giles Ndochinwa
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
| | - Qing-Yan Wang
- State Key Laboratory of Biomass Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Oyetugo Chioma Amadi
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
| | - Tochukwu Nwamaka Nwagu
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
| | | | - Emmanuel Sunday Okeke
- Department of Biochemistry, Faculty of Biological Sciences & Natural Science Unit, School of General Studies, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
- Institute of Environmental Health and Ecological Security, School of the Environment and Safety, Jiangsu University, 301 Xuefu Rd., 212013, Zhenjiang, Jiangsu, China
| | - Anene Nwabu Moneke
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
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4
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Jiang F, Wang Z, Cong Z. Tuning the peroxidase activity of artificial P450 peroxygenase by engineering redox-sensitive residues. Faraday Discuss 2024. [PMID: 38836616 DOI: 10.1039/d4fd00008k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Cytochrome P450 monooxygenases (P450s) are well recognized as versatile bio-oxidation catalysts. However, the catalytic functions of P450s are highly dependent on NAD(P)H and redox partner proteins. Our group has recently reported the use of a dual-functional small molecule (DFSM) for generating peroxygenase activity of P450BM3, a long-chain fatty acid hydroxylase from Bacillus megaterium. The DFSM-facilitated P450BM3 peroxygenase system exhibited excellent peroxygenation activity and regio-/enantioselectivity for various organic substrates, such as styrenes, thioanisole, small alkanes, and alkylbenzenes. Very recently, we demonstrated that the DFSM-facilitated P450BM3 peroxygenase could be switched to a peroxidase by engineering the redox-sensitive tyrosine residues in P450BM3. Given the great potential of P450 peroxidase for C-H oxyfunctionalization, we herein report scrutiny of the effect of mutating redox-sensitive residues on peroxidase activity by deeply screening all redox-sensitive residues of P450BM3, namely methionines, tryptophans, cysteines, and phenylalanines. As a result, six beneficial mutations at positions M212, F81, M112, F173, M177, and F77 were screened out from 78 constructed mutants, and significantly enhanced the peroxidase activity of P450BM3 in the presence of Im-C6-Phe, a typical DFSM molecule. Further combination of the beneficial mutations resulted in a more than 100-fold improvement in peroxidase activity compared with that of the combined parent enzyme and DFSM, comparable to or better than most natural peroxidases. In addition, mutations of redox-sensitive residues even dramatically increased, by more than 300-fold, the peroxidase activity of the starting F87A enzyme in the absence of the DFSM, despite the far lower apparent catalytic turnover number compared with the DFSM-P450 system. This study provides new insights and a potential strategy for regulating the catalytic promiscuity of P450 enzymes for multiple functional oxidations.
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Affiliation(s)
- Fengjie Jiang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zihan Wang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
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5
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Beech JL, Maurya AK, Rodrigues da Silva R, Akpoto E, Asundi A, Fecko JA, Yennawar NH, Sarangi R, Tassone C, Weiss TM, DuBois JL. Understanding the stability of a plastic-degrading Rieske iron oxidoreductase system. Protein Sci 2024; 33:e4997. [PMID: 38723110 PMCID: PMC11081424 DOI: 10.1002/pro.4997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/01/2024] [Accepted: 04/06/2024] [Indexed: 05/13/2024]
Abstract
Rieske oxygenases (ROs) are a diverse metalloenzyme class with growing potential in bioconversion and synthetic applications. We postulated that ROs are nonetheless underutilized because they are unstable. Terephthalate dioxygenase (TPADO PDB ID 7Q05) is a structurally characterized heterohexameric α3β3 RO that, with its cognate reductase (TPARED), catalyzes the first intracellular step of bacterial polyethylene terephthalate plastic bioconversion. Here, we showed that the heterologously expressed TPADO/TPARED system exhibits only ~300 total turnovers at its optimal pH and temperature. We investigated the thermal stability of the system and the unfolding pathway of TPADO through a combination of biochemical and biophysical approaches. The system's activity is thermally limited by a melting temperature (Tm) of 39.9°C for the monomeric TPARED, while the independent Tm of TPADO is 50.8°C. Differential scanning calorimetry revealed a two-step thermal decomposition pathway for TPADO with Tm values of 47.6 and 58.0°C (ΔH = 210 and 509 kcal mol-1, respectively) for each step. Temperature-dependent small-angle x-ray scattering and dynamic light scattering both detected heat-induced dissociation of TPADO subunits at 53.8°C, followed by higher-temperature loss of tertiary structure that coincided with protein aggregation. The computed enthalpies of dissociation for the monomer interfaces were most congruent with a decomposition pathway initiated by β-β interface dissociation, a pattern predicted to be widespread in ROs. As a strategy for enhancing TPADO stability, we propose prioritizing the re-engineering of the β subunit interfaces, with subsequent targeted improvements of the subunits.
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Affiliation(s)
- Jessica Lusty Beech
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMontanaUSA
| | - Anjani K. Maurya
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | | | - Emmanuel Akpoto
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMontanaUSA
| | - Arun Asundi
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Julia Ann Fecko
- The Huck Institutes of the Life SciencesThe Pennsylvania State University, University ParkState CollegePennsylvaniaUSA
| | - Neela H. Yennawar
- The Huck Institutes of the Life SciencesThe Pennsylvania State University, University ParkState CollegePennsylvaniaUSA
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Christopher Tassone
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Jennifer L. DuBois
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMontanaUSA
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6
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He J, Liu X, Li C. Engineering Electron Transfer Pathway of Cytochrome P450s. Molecules 2024; 29:2480. [PMID: 38893355 PMCID: PMC11173547 DOI: 10.3390/molecules29112480] [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: 04/15/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Cytochrome P450s (P450s), a superfamily of heme-containing enzymes, existed in animals, plants, and microorganisms. P450s can catalyze various regional and stereoselective oxidation reactions, which are widely used in natural product biosynthesis, drug metabolism, and biotechnology. In a typical catalytic cycle, P450s use redox proteins or domains to mediate electron transfer from NAD(P)H to heme iron. Therefore, the main factors determining the catalytic efficiency of P450s include not only the P450s themselves but also their redox-partners and electron transfer pathways. In this review, the electron transfer pathway engineering strategies of the P450s catalytic system are reviewed from four aspects: cofactor regeneration, selection of redox-partners, P450s and redox-partner engineering, and electrochemically or photochemically driven electron transfer.
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Affiliation(s)
- Jingting He
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, School of Chemistry and Chemical Engineering, Shihezi 832003, China;
| | - Xin Liu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Chun Li
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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7
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Decembrino D, Cannella D. The thin line between monooxygenases and peroxygenases. P450s, UPOs, MMOs, and LPMOs: A brick to bridge fields of expertise. Biotechnol Adv 2024; 72:108321. [PMID: 38336187 DOI: 10.1016/j.biotechadv.2024.108321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Many scientific fields, although driven by similar purposes and dealing with similar technologies, often appear so isolated and far from each other that even the vocabularies to describe the very same phenomenon might differ. Concerning the vast field of biocatalysis, a special role is played by those redox enzymes that employ oxygen-based chemistry to unlock transformations otherwise possible only with metal-based catalysts. As such, greener chemical synthesis methods and environmentally-driven biotechnological approaches were enabled over the last decades by the use of several enzymes and ultimately resulted in the first industrial applications. Among what can be called today the environmental biorefinery sector, biomass transformation, greenhouse gas reduction, bio-gas/fuels production, bioremediation, as well as bulk or fine chemicals and even pharmaceuticals manufacturing are all examples of fields in which successful prototypes have been demonstrated employing redox enzymes. In this review we decided to focus on the most prominent enzymes (MMOs, LPMO, P450 and UPO) capable of overcoming the ∼100 kcal mol-1 barrier of inactivated CH bonds for the oxyfunctionalization of organic compounds. Harnessing the enormous potential that lies within these enzymes is of extreme value to develop sustainable industrial schemes and it is still deeply coveted by many within the aforementioned fields of application. Hence, the ambitious scope of this account is to bridge the current cutting-edge knowledge gathered upon each enzyme. By creating a broad comparison, scientists belonging to the different fields may find inspiration and might overcome obstacles already solved by the others. This work is organised in three major parts: a first section will be serving as an introduction to each one of the enzymes regarding their structural and activity diversity, whereas a second one will be encompassing the mechanistic aspects of their catalysis. In this regard, the machineries that lead to analogous catalytic outcomes are depicted, highlighting the major differences and similarities. Finally, a third section will be focusing on the elements that allow the oxyfunctionalization chemistry to occur by delivering redox equivalents to the enzyme by the action of diverse redox partners. Redox partners are often overlooked in comparison to the catalytic counterparts, yet they represent fundamental elements to better understand and further develop practical applications based on mono- and peroxygenases.
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Affiliation(s)
- Davide Decembrino
- Photobiocatalysis Unit - Crop Production and Biostimulation Lab (CPBL), and Biomass Transformation Lab (BTL), École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Belgium.
| | - David Cannella
- Photobiocatalysis Unit - Crop Production and Biostimulation Lab (CPBL), and Biomass Transformation Lab (BTL), École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Belgium.
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8
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Jones BS, Ross CM, Foley G, Pozhydaieva N, Sharratt JW, Kress N, Seibt LS, Thomson RES, Gumulya Y, Hayes MA, Gillam EMJ, Flitsch SL. Engineering Biocatalysts for the C-H Activation of Fatty Acids by Ancestral Sequence Reconstruction. Angew Chem Int Ed Engl 2024; 63:e202314869. [PMID: 38163289 DOI: 10.1002/anie.202314869] [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: 10/04/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Selective, one-step C-H activation of fatty acids from biomass is an attractive concept in sustainable chemistry. Biocatalysis has shown promise for generating high-value hydroxy acids, but to date enzyme discovery has relied on laborious screening and produced limited hits, which predominantly oxidise the subterminal positions of fatty acids. Herein we show that ancestral sequence reconstruction (ASR) is an effective tool to explore the sequence-activity landscape of a family of multidomain, self-sufficient P450 monooxygenases. We resurrected 11 catalytically active CYP116B ancestors, each with a unique regioselectivity fingerprint that varied from subterminal in the older ancestors to mid-chain in the lineage leading to the extant, P450-TT. In lineages leading to extant enzymes in thermophiles, thermostability increased from ancestral to extant forms, as expected if thermophily had arisen de novo. Our studies show that ASR can be applied to multidomain enzymes to develop active, self-sufficient monooxygenases as regioselective biocatalysts for fatty acid hydroxylation.
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Affiliation(s)
- Bethan S Jones
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Connie M Ross
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Gabriel Foley
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Nadiia Pozhydaieva
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Joseph W Sharratt
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Nico Kress
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Lisa S Seibt
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Raine E S Thomson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Yosephine Gumulya
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Martin A Hayes
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca, Gothenburg, SE
| | - Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Sabine L Flitsch
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
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9
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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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10
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Hwang Y, Hwang HG, Lee JY, Jung GY. Systematic Engineering of Genistein Biosynthetic Pathway through Genetic Regulators and Combinatorial Enzyme Screening. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5842-5848. [PMID: 38441872 DOI: 10.1021/acs.jafc.3c09687] [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: 03/21/2024]
Abstract
Microbial production of genistein, an isoflavonoid primarily found in soybeans, is gaining prominence in the food industry due to its significant nutritional and health benefits. However, challenges arise in redesigning strains due to intricate regulatory nodes between cell growth and genistein production and in systematically exploring core enzymes involving genistein biosynthesis. To address this, this study devised a strategy that simultaneously and precisely rewires flux at both acetyl-CoA and malonyl-CoA nodes toward genistein synthesis. In particular, naringenin, the primary precursor of genistein, was accumulated 2.6 times more than the unoptimized strain through transcriptional repressor-based genetic regulators. Building upon this, a combination of isoflavone synthase and cytochrome P450 reductase with the remarkable conversion of naringenin to genistein was screened from enzyme homologue libraries. The integrated metabolic engineering strategy yields the highest reported production (98 mg/L of genistein) to date, providing a framework for the biosynthesis of diverse flavonoids, including genistein.
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Affiliation(s)
- Yunhee Hwang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
| | - Hyun Gyu Hwang
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Ji Yeon Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
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11
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Iqbal H, Ilyas K, Akash MSH, Rehman K, Hussain A, Iqbal J. Real-time fluorescent monitoring of phase I xenobiotic-metabolizing enzymes. RSC Adv 2024; 14:8837-8870. [PMID: 38495994 PMCID: PMC10941266 DOI: 10.1039/d4ra00127c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/07/2024] [Indexed: 03/19/2024] Open
Abstract
This article explores the intricate landscape of advanced fluorescent probes crafted for the detection and real-time monitoring of phase I xenobiotic-metabolizing enzymes. Employing state-of-the-art technologies, such as fluorescence resonance energy transfer, intramolecular charge transfer, and solid-state luminescence enhancement, this article unfolds a multifaceted approach to unraveling the dynamics of enzymatic processes within living systems. This encompassing study involves the development and application of a diverse range of fluorescent probes, each intricately designed with tailored mechanisms to heighten sensitivity, providing dynamic insights into phase I xenobiotic-metabolizing enzymes. Understanding the role of phase I xenobiotic-metabolizing enzymes in these pathophysiological processes, is essential for both medical research and clinical practice. This knowledge can guide the development of approaches to prevent, diagnose, and treat a broad spectrum of diseases and conditions. This adaptability underscores their potential clinical applications in cancer diagnosis and personalized medicine. Noteworthy are the trifunctional fluorogenic probes, uniquely designed not only for fluorescence-based cellular imaging but also for the isolation of cellular glycosidases. This innovative feature opens novel avenues for comprehensive studies in enzyme biology, paving the way for potential therapeutic interventions. The research accentuates the selectivity and specificity of the probes, showcasing their proficiency in distinguishing various enzymes and their isoforms. The sophisticated design and successful deployment of these fluorescent probes mark significant advancements in enzymology, providing powerful tools for both researchers and clinicians. Beyond their immediate applications, these probes offer illuminating insights into disease mechanisms, facilitating early detection, and catalyzing the development of targeted therapeutic interventions. This work represents a substantial leap forward in the field, promising transformative implications for understanding and addressing complex biological processes. In essence, this research heralds a new era in the development of fluorescent probes, presenting a comprehensive and innovative approach that not only expands the understanding of cellular enzyme activities but also holds great promise for practical applications in clinical settings and therapeutic endeavors.
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Affiliation(s)
- Hajra Iqbal
- Department of Pharmaceutical Chemistry, Government College University Faisalabad Pakistan
| | - Kainat Ilyas
- Department of Pharmaceutical Chemistry, Government College University Faisalabad Pakistan
| | | | - Kanwal Rehman
- Department of Pharmacy, The Women University Multan Pakistan
| | - Amjad Hussain
- Institute of Chemistry, University of Okara Okara Pakistan
| | - Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus Abbottabad 22044 Pakistan
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12
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Jiao R, Zhao G, Zhang T. Structural Insights into the Reaction between Hydrogen Peroxide and Di-iron Complexes at the Ferroxidase Center of Ferritin. Inorg Chem 2024; 63:3359-3365. [PMID: 38315811 DOI: 10.1021/acs.inorgchem.3c03889] [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: 02/07/2024]
Abstract
The Fe(II) oxidation mechanism in the ferroxidase center of heavy chain ferritin has been studied extensively. However, the actual production of H2O2 was found to be substantially lower than expected at low flux of Fe(II) to ferritin subunits. Here, we demonstrated that H2O2 could interact with the di-iron nuclear center, leading to the production of hydroxyl radicals and oxygen. Two reaction intermediates were captured in the ferroxidase center by using the time-lapse crystallographic techniques in a shellfish ferritin. The crystal structures revealed the binding of H2O2 as a μ -1,2-peroxo-diferric species and the binding of O2 to the diferric structure. This investigation sheds light on the reaction between the di-iron nuclear center and H2O2 and provides insights for the exploitation of metalloenzymes.
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Affiliation(s)
- Ruonan Jiao
- Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Guanghua Zhao
- Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Tuo Zhang
- Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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13
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Hendricks AR, Cohen RS, McEwen GA, Tien T, Guilliams BF, Alspach A, Snow CD, Ackerson CJ. Laboratory Evolution of Metalloid Reductase Substrate Recognition and Nanoparticle Product Size. ACS Chem Biol 2024; 19:289-299. [PMID: 38295274 DOI: 10.1021/acschembio.3c00493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Glutathione reductase-like metalloid reductase (GRLMR) is an enzyme that reduces selenodiglutathione (GS-Se-SG), forming zerovalent Se nanoparticles (SeNPs). Error-prone polymerase chain reaction was used to create a library of ∼10,000 GRLMR variants. The library was expressed in BL21Escherichia coli in liquid culture with 50 mM of SeO32- present, under the hypothesis that the enzyme variants with improved GS-Se-SG reduction kinetics would emerge. The selection resulted in a GRLMR variant with two mutations. One of the mutations (D-E) lacks an obvious functional role, whereas the other mutation is L-H within 5 Å of the enzyme active site. This mutation places a second H residue within 5 Å of an active site dicysteine. This GRLMR variant was characterized for NADPH-dependent reduction of GS-Se-SG, GSSG, SeO32-, SeO42-, GS-Te-SG, and TeO32-. The evolved enzyme demonstrated enhanced reduction of SeO32- and gained the ability to reduce SeO42-. This variant is named selenium reductase (SeR) because of its emergent broad activity for a wide variety of Se substrates, whereas the parent enzyme was specific for GS-Se-SG. This study overall suggests that new biosynthetic routes are possible for inorganic nanomaterials using laboratory-directed evolution methods.
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Affiliation(s)
- Alexander R Hendricks
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, United States
| | - Rachel S Cohen
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, United States
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Gavin A McEwen
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, United States
| | - Tony Tien
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, United States
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Bradley F Guilliams
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, United States
| | - Audrey Alspach
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, United States
| | - Christopher D Snow
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, United States
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Christopher J Ackerson
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, United States
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14
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Liu JCT, De La Peña R, Tocol C, Sattely ES. Reconstitution of early paclitaxel biosynthetic network. Nat Commun 2024; 15:1419. [PMID: 38360800 PMCID: PMC10869802 DOI: 10.1038/s41467-024-45574-8] [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: 10/05/2023] [Accepted: 01/25/2024] [Indexed: 02/17/2024] Open
Abstract
Paclitaxel is an anticancer therapeutic produced by the yew tree. Over the last two decades, a significant bottleneck in the reconstitution of early paclitaxel biosynthesis has been the propensity of heterologously expressed pathway cytochromes P450, including taxadiene 5α-hydroxylase (T5αH), to form multiple products. Here, we structurally characterize four new products of T5αH, many of which appear to be over-oxidation of the primary mono-oxidized products. By tuning the promoter strength for T5αH expression in Nicotiana plants, we observe decreased levels of these proposed byproducts with a concomitant increase in the accumulation of taxadien-5α-ol, the paclitaxel precursor, by three-fold. This enables the reconstitution of a six step biosynthetic pathway, which we further show may function as a metabolic network. Our result demonstrates that six previously characterized Taxus genes can coordinatively produce key paclitaxel intermediates and serves as a crucial platform for the discovery of the remaining biosynthetic genes.
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Affiliation(s)
| | - Ricardo De La Peña
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Christian Tocol
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Elizabeth S Sattely
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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15
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Chen W, Lee S, Moon HB. Cyclic and linear siloxane contamination in sediment and invertebrates around a thermal power plant in Korea: Source impact, distribution, seasonal variation, and potential for bioaccumulation. CHEMOSPHERE 2024; 349:140779. [PMID: 38008296 DOI: 10.1016/j.chemosphere.2023.140779] [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: 09/06/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 11/28/2023]
Abstract
Siloxanes have been commonly used as additives in a variety of industrial and consumer products. Media and government investigations have revealed that defoamers containing siloxanes are used in the effluent of thermal power plants in Korea. However, investigations of the source impact of siloxane contamination from the discharge of thermal power plants into coastal environments are scarce. In this study, sediment and invertebrates were collected around a thermal power plant to assess source impact, seasonal variation, and a potential for bioaccumulation. Although siloxanes were detectable in sediment and invertebrates, the spatial distribution and composition (which differed between the siloxanes found in sediment and invertebrates and those in defoamer used in the plant) suggest they were likely transported by long-distance migration as well as the discharge of thermal power plant. Seasonal differences might affect sedimentary contamination and the bioaccumulation potential of siloxanes. Specifically, octamethylcyclotetrasiloxane (D4) may have limited adsorption capacity and potential for long-distance migration, as its contribution in sediment far from the coastline was greater than that of decamethylcyclopentasiloxane (D5) and dodecamethylcyclohexasiloxane (D6). However, higher D5 accumulation in invertebrates, and D5 has a potential bioaccumulation. A molecular docking analysis showed that the binding affinity between D5 and the cytochrome enzyme in invertebrates was weaker than that with other siloxanes, which could lead to higher D5 accumulation in invertebrates.
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Affiliation(s)
- Wenming Chen
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, Hainan, 571158, China.
| | - Sunggyu Lee
- Department of Marine Science and Convergence Engineering, College of Science and Convergence Technology, Hanyang University, Ansan, 15588, Republic of Korea
| | - Hyo-Bang Moon
- Department of Marine Science and Convergence Engineering, College of Science and Convergence Technology, Hanyang University, Ansan, 15588, Republic of Korea.
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16
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Elfakharany HK, Ghoraba HM, Gaweesh KA, Eldeen AAS, Eid AM. Immunohistochemical expression of cytochrome P4A11 (CYP4A11), carbonic anhydrase 9 (CAIX) and Ki67 in renal cell carcinoma; diagnostic relevance and relations to clinicopathological parameters. Pathol Res Pract 2024; 253:155070. [PMID: 38183818 DOI: 10.1016/j.prp.2023.155070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND Cytochrome P4A11 (CYP4A11) is a member of cytochrome p450 family, which is involved in arachidonic acid metabolism that participates in promoting malignant cell proliferation, progression, and angiogenetic capacity. Carbonic Anhydrase 9 (CAIX) is a transmembrane protein that plays an integral part in regulating hypoxia which affects cancer cell metabolism, proliferation and promotes metastasis. The aim of this study was to evaluate the immunohistochemical expression of CYP4A11, CAIX and ki67 in RCC subtypes in relation to clinicopathological parameters and to evaluate the diagnostic significance of CYP4A11 and CAIX in differentiating renal cell carcinoma (RCC) subtypes. MATERIALS AND METHODS one hundred primary RCC cases, collected from Pathology Department, Faculty of Medicine, Tanta University and from private laboratories, were evaluated for immunohistochemical expression of CYP4A11, CAIX and ki67. RESULTS CYP4A11 was expressed in 59% of RCC; with 91.7% sensitivity and 90% specificity in differentiating clear cell and non-clear cell subtypes. CAIX was expressed in 50% of RCC; with 95% sensitivity, 80% specificity. High expression of CYP4A11 was statistically positively associated with higher tumor grade, high expression of CAIX was statistically positively associated with lower tumor grade and absence of necrosis and high ki67 labeling index was significantly associated with clear cell subtype, larger tumor sizes, higher tumor grade, advanced tumor stage, fat invasion and vascular invasion. CONCLUSIONS CYP4A11 and CAIX can be used as diagnostic markers to differentiate clear cell RCC from other subtypes. CYP4A11 is more diagnostically accurate and specific than CAIX. High expression of CYP4A11, low CAIX expression and high ki67 labeling index were related to features of aggressive tumor behavior.
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17
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Taher M, Dubey KD, Mazumdar S. Computationally guided bioengineering of the active site, substrate access pathway, and water channels of thermostable cytochrome P450, CYP175A1, for catalyzing the alkane hydroxylation reaction. Chem Sci 2023; 14:14316-14326. [PMID: 38098704 PMCID: PMC10718072 DOI: 10.1039/d3sc02857g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023] Open
Abstract
Understanding structure-function relationships in proteins is pivotal in their development as industrial biocatalysts. In this regard, rational engineering of protein active site access pathways and various tunnels and channels plays a central role in designing competent enzymes with high stability and enhanced efficiency. Here, we report the rational evolution of a thermostable cytochrome P450, CYP175A1, to catalyze the C-H activation reaction of longer-chain alkanes. A strategy combining computational tools with experiments has shown that the substrate scope and enzymatic activity can be enhanced by rational engineering of certain important channels such as the substrate entry and water channels along with the active site of the enzyme. The evolved enzymes showed an improved catalytic rate for hexadecane hydroxylation with high regioselectivity. The Q67L/Y68F mutation showed binding of the substrate in the active site, water channel mutation L80F/V220T showed improved catalytic activity through the peroxide shunt pathway and substrate entry channel mutation W269F/I270A showed better substrate accessibility to the active pocket. All-atom MD simulations provided the rationale for the inactivity of the wild-type CYP175A1 for hexadecane hydroxylation and predicted the above hot-spot residues to enhance the activity. The reaction mechanism was studied by QM/MM calculations for enzyme-substrate complexes and reaction intermediates. Detailed thermal and thermodynamic stability of all the mutants were analyzed and the results showed that the evolved enzymes were thermally stable. The present strategy showed promising results, and insights gained from this work can be applied to the general enzymatic system to expand substrate scope and improve catalytic activity.
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Affiliation(s)
- Mohd Taher
- Department of Chemical Sciences, Tata Institute of Fundamental Research Homi Bhabha Road, Colaba Mumbai 400005 India
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Science, Shiv Nadar Institution of Eminence Delhi-NCR NH91, Tehsil Dadri Greater Noida Uttar Pradesh 201314 India
| | - Shyamalava Mazumdar
- Department of Chemical Sciences, Tata Institute of Fundamental Research Homi Bhabha Road, Colaba Mumbai 400005 India
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18
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Padayachee T, Lamb DC, Nelson DR, Syed K. Structure-Function Analysis of the Biotechnologically Important Cytochrome P450 107 (CYP107) Enzyme Family. Biomolecules 2023; 13:1733. [PMID: 38136604 PMCID: PMC10741444 DOI: 10.3390/biom13121733] [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: 11/03/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Cytochrome P450 monooxygenases (CYPs; P450s) are a superfamily of heme-containing enzymes that are recognized for their vast substrate range and oxidative multifunctionality. CYP107 family members perform hydroxylation and epoxidation processes, producing a variety of biotechnologically useful secondary metabolites. Despite their biotechnological importance, a thorough examination of CYP107 protein structures regarding active site cavity dynamics and key amino acids interacting with bound ligands has yet to be undertaken. To address this research knowledge gap, 44 CYP107 crystal structures were investigated in this study. We demonstrate that the CYP107 active site cavity is very flexible, with ligand binding reducing the volume of the active site in some situations and increasing volume size in other instances. Polar interactions between the substrate and active site residues result in crucial salt bridges and the formation of proton shuttling pathways. Hydrophobic interactions, however, anchor the substrate within the active site. The amino acid residues within the binding pocket influence substrate orientation and anchoring, determining the position of the hydroxylation site and hence direct CYP107's catalytic activity. Additionally, the amino acid dynamics within and around the binding pocket determine CYP107's multifunctionality. This study serves as a reference for understanding the structure-function analysis of CYP107 family members precisely and the structure-function analysis of P450 enzymes in general. Finally, this work will aid in the genetic engineering of CYP107 enzymes to produce novel molecules of biotechnological interest.
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Affiliation(s)
- Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, KwaDlangezwa 3886, South Africa;
| | - David C. Lamb
- Faculty of Medicine, Health and Life Sciences, Swansea University, Swansea SA2 8PP, UK;
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, KwaDlangezwa 3886, South Africa;
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19
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Adhikari A, Shakya S, Shrestha S, Aryal D, Timalsina KP, Dhakal D, Khatri Y, Parajuli N. Biocatalytic role of cytochrome P450s to produce antibiotics: A review. Biotechnol Bioeng 2023; 120:3465-3492. [PMID: 37691185 DOI: 10.1002/bit.28548] [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: 02/01/2023] [Revised: 08/15/2023] [Accepted: 08/26/2023] [Indexed: 09/12/2023]
Abstract
Cytochrome P450s belong to a family of heme-binding monooxygenases, which catalyze regio- and stereospecific functionalisation of C-H, C-C, and C-N bonds, including heteroatom oxidation, oxidative C-C bond cleavages, and nitrene transfer. P450s are considered useful biocatalysts for the production of pharmaceutical products, fine chemicals, and bioremediating agents. Despite having tremendous biotechnological potential, being heme-monooxygenases, P450s require either autologous or heterologous redox partner(s) to perform chemical transformations. Randomly distributed P450s throughout a bacterial genome and devoid of particular redox partners in natural products biosynthetic gene clusters (BGCs) showed an extra challenge to reveal their pharmaceutical potential. However, continuous efforts have been made to understand their involvement in antibiotic biosynthesis and their modification, and this review focused on such BGCs. Here, particularly, we have discussed the role of P450s involved in the production of macrolides and aminocoumarin antibiotics, nonribosomal peptide (NRPSs) antibiotics, ribosomally synthesized and post-translationally modified peptide (RiPPs) antibiotics, and others. Several reactions catalyzed by P450s, as well as the role of their redox partners involved in the BGCs of various antibiotics and their derivatives, have been primarily addressed in this review, which would be useful in further exploration of P450s for the biosynthesis of new therapeutics.
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Affiliation(s)
- Anup Adhikari
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Sajan Shakya
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Shreesti Shrestha
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Dipa Aryal
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Kavi Prasad Timalsina
- Department of Biotechnology, National College, Tribhuvan University, Kathmandu, Nepal
| | - Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida, USA
| | | | - Niranjan Parajuli
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
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20
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Yang ZJ, Shao Q, Jiang Y, Jurich C, Ran X, Juarez RJ, Yan B, Stull SL, Gollu A, Ding N. Mutexa: A Computational Ecosystem for Intelligent Protein Engineering. J Chem Theory Comput 2023; 19:7459-7477. [PMID: 37828731 PMCID: PMC10653112 DOI: 10.1021/acs.jctc.3c00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Indexed: 10/14/2023]
Abstract
Protein engineering holds immense promise in shaping the future of biomedicine and biotechnology. This Review focuses on our ongoing development of Mutexa, a computational ecosystem designed to enable "intelligent protein engineering". In this vision, researchers will seamlessly acquire sequences of protein variants with desired functions as biocatalysts, therapeutic peptides, and diagnostic proteins through a finely-tuned computational machine, akin to Amazon Alexa's role as a versatile virtual assistant. The technical foundation of Mutexa has been established through the development of a database that combines and relates enzyme structures and their respective functions (e.g., IntEnzyDB), workflow software packages that enable high-throughput protein modeling (e.g., EnzyHTP and LassoHTP), and scoring functions that map the sequence-structure-function relationship of proteins (e.g., EnzyKR and DeepLasso). We will showcase the applications of these tools in benchmarking the convergence conditions of enzyme functional descriptors across mutants, investigating protein electrostatics and cavity distributions in SAM-dependent methyltransferases, and understanding the role of nonelectrostatic dynamic effects in enzyme catalysis. Finally, we will conclude by addressing the future steps and fundamental challenges in our endeavor to develop new Mutexa applications that assist the identification of beneficial mutants in protein engineering.
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Affiliation(s)
- Zhongyue J. Yang
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data
Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Qianzhen Shao
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Yaoyukun Jiang
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Christopher Jurich
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - Xinchun Ran
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Reecan J. Juarez
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - Bailu Yan
- Department
of Biostatistics, Vanderbilt University, Nashville, Tennessee 37205, United States
| | - Sebastian L. Stull
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Anvita Gollu
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ning Ding
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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21
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Gee AR, Stone ISJ, Stockdale TP, Pukala TL, De Voss JJ, Bell SG. Efficient biocatalytic C-H bond oxidation: an engineered heme-thiolate peroxygenase from a thermostable cytochrome P450. Chem Commun (Camb) 2023; 59:13486-13489. [PMID: 37881007 DOI: 10.1039/d3cc04626e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
A highly sought after reaction in chemical synthesis is the activation of unactivated carbon-hydrogen bonds. We demonstrate the hydroxylation of fatty acids using an engineered thermostable archaeal cytochrome P450 enzyme. By replacing a seven amino acid section of the I-helix, the nicotinamide cofactor-dependent monooxygenase was converted into a hydrogen peroxide using peroxygenase, enabling the efficient biocatalytic oxidation of C-H bonds at room temperature to 90 °C.
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Affiliation(s)
- Alecia R Gee
- School of Physics, Chemistry and Earth Sciences, University of Adelaide, Adelaide, SA 5005, Australia.
| | - Isobella S J Stone
- School of Physics, Chemistry and Earth Sciences, University of Adelaide, Adelaide, SA 5005, Australia.
| | - Tegan P Stockdale
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Tara L Pukala
- School of Physics, Chemistry and Earth Sciences, University of Adelaide, Adelaide, SA 5005, Australia.
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Stephen G Bell
- School of Physics, Chemistry and Earth Sciences, University of Adelaide, Adelaide, SA 5005, Australia.
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22
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Yang J, Liu Y, Zhong D, Xu L, Gao H, Keasling JD, Luo X, Chou HH. Combinatorial optimization and spatial remodeling of CYPs to control product profile. Metab Eng 2023; 80:119-129. [PMID: 37703999 DOI: 10.1016/j.ymben.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023]
Abstract
Activating inert substrates is a challenge in nature and synthetic chemistry, but essential for creating functionally active molecules. In this work, we used a combinatorial optimization approach to assemble cytochrome P450 monooxygenases (CYPs) and reductases (CPRs) to achieve a target product profile. By creating 110 CYP-CPR pairs and iteratively screening different pairing libraries, we demonstrated a framework for establishing a CYP network that catalyzes six oxidation reactions at three different positions of a chemical scaffold. Target product titer was improved by remodeling endoplasmic reticulum (ER) size and spatially controlling the CYPs' configuration on the ER. Out of 47 potential products that could be synthesized, 86% of the products synthesized by the optimized network was our target compound quillaic acid (QA), the aglycone backbone of many pharmaceutically important saponins, and fermentation achieved QA titer 2.23 g/L.
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Affiliation(s)
- Jiazeng Yang
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Yuguang Liu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Dacai Zhong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Linlin Xu
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Haixin Gao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Jay D Keasling
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, CA, 94720, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Xiaozhou Luo
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Howard H Chou
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China.
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23
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Sahil M, Singh T, Ghosh S, Mondal J. 3site Multisubstrate-Bound State of Cytochrome P450cam. J Am Chem Soc 2023; 145:23488-23502. [PMID: 37867463 DOI: 10.1021/jacs.3c06144] [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: 10/24/2023]
Abstract
We identified a multisubstrate-bound state, hereby referred as a 3site state, in cytochrome P450cam via integrating molecular dynamics simulation with nuclear magnetic resonance (NMR) pseudocontact shift measurements. The 3site state is a result of simultaneous binding of three camphor molecules in three locations around P450cam: (a) in a well-established "catalytic" site near heme, (b) in a kink-separated "waiting" site along channel-1, and (c) in a previously reported "allosteric" site at E, F, G, and H helical junctions. These three spatially distinct binding modes in the 3site state mutually communicate with each other via homotropic allostery and act cooperatively to render P450cam functional. The 3site state shows a significantly superior fit with NMR pseudo contact shift (PCS) data with a Q-score of 0.045 than previously known bound states and consists of D251 free of salt-bridges with K178 and R186, rendering the enzyme functionally primed. To date, none of the reported cocomplex of P450cam with its redox partner putidaredoxin (pdx) has been able to match solution NMR data and controversial pdx-induced opening of P450cam's channel-1 remains a matter of recurrent discourse. In this regard, inclusion of pdx to the 3site state is able to perfectly fit the NMR PCS measurement with a Q-score of 0.08 and disfavors the pdx-induced opening of channel-1, reconciling previously unexplained remarkably fast hydroxylation kinetics with a koff of 10.2 s-1. Together, our findings hint that previous experimental observations may have inadvertently captured the 3site state as an in vitro solution state, instead of the catalytic state alone, and provided a distinct departure from the conventional understanding of cytochrome P450.
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Affiliation(s)
- Mohammad Sahil
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Tejender Singh
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Soumya Ghosh
- Tata Institute of Fundamental Research, Hyderabad 500046, India
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24
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Zhang Y, Pan X, Shi T, Gu Z, Yang Z, Liu M, Xu Y, Yang Y, Ren L, Song X, Lin H, Deng K. P450Rdb: a manually curated database of reactions catalyzed by cytochrome P450 enzymes. J Adv Res 2023:S2090-1232(23)00316-8. [PMID: 37871773 DOI: 10.1016/j.jare.2023.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 10/03/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023] Open
Abstract
INTRODUCTION Cytochrome P450 enzymes (P450s) are recognized as the most versatile catalysts worldwide, playing vital roles in numerous biological metabolism and biosynthesis processes across all kingdoms of life. Despite the vast number of P450 genes available in databases (over 300,000), only a small fraction of them (less than 0.2%) have undergone functional characterization. OBJECTIVES To provide a convenient platform with abundant information on P450s and their corresponding reactions, we introduce the P450Rdb database, a manually curated resource compiles literature-supported reactions catalyzed by P450s. METHODS All the P450s and Reactions were manually curated from the literature and known databases. Subsequently, the P450 reactions organized and categorized according to their chemical reaction type and site. The website was developed using HTML and PHP languages, with the MySQL server utilized for data storage. RESULTS The current version of P450Rdb catalogs over 1,600 reactions, involving more than 590 P450s across a diverse range of over 200 species. Additionally, it offers a user-friendly interface with comprehensive information, enabling easy querying, browsing, and analysis of P450s and their corresponding reactions. P450Rdb is free available at http://www.cellknowledge.com.cn/p450rdb/. CONCLUSIONS We believe that this database will significantly promote structural and functional research on P450s, thereby fostering advancements in the fields of natural product synthesis, pharmaceutical engineering, biotechnological applications, agricultural and crop improvement, and the chemical industry.
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Affiliation(s)
- Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xianrun Pan
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianyu Shi
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zhifeng Gu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zhaochang Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Minghao Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yi Xu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yu Yang
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China
| | - Liping Ren
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China
| | - Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China.
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Kejun Deng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
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25
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Zhong G. Cytochromes P450 Associated with the Biosyntheses of Ribosomally Synthesized and Post-translationally Modified Peptides. ACS BIO & MED CHEM AU 2023; 3:371-388. [PMID: 37876494 PMCID: PMC10591300 DOI: 10.1021/acsbiomedchemau.3c00026] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 10/26/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a class of exponentially increased natural products with characteristic chemical structures, topologies, and biosynthetic mechanisms as well as exceptional bioactivities including antibacteria, antitumors, and antiviruses. The biosynthesis of RiPP proceeds via a ribosomally assembled precursor peptide that undergoes varied post-translational modifications to generate a mature peptide. Cytochrome P450 (CYP or P450) monooxygenases are a superfamily of heme-containing enzymes that span a wide range of secondary metabolite biosynthetic pathways due to their broad substrate scopes and excellent catalytic versatility. In contrast to the enormous quantities of RiPPs and P450s, the P450 associated RiPP biosynthesis is comparatively limited, with most of their functions and timings remaining mysterious. Herein, this Review aims to provide an overview on the striking roles of P450s in RiPP biosyntheses uncovered to date and to illustrate their remarkable functions, mechanisms, as well as remaining challenges. This will shed light on novel P450 discovery and characterizations in RiPP biosyntheses.
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Affiliation(s)
- Guannan Zhong
- State
Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute of Shandong University, Suzhou 215123, China
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26
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Yu H, Zhang X, Acevedo-Rocha CG, Li A, Reetz MT. Protein engineering using mutability landscapes: Controlling site-selectivity of P450-catalyzed steroid hydroxylation. Methods Enzymol 2023; 693:191-229. [PMID: 37977731 DOI: 10.1016/bs.mie.2023.09.002] [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: 11/19/2023]
Abstract
Directed evolution and rational design have been used widely in engineering enzymes for their application in synthetic organic chemistry and biotechnology. With stereoselectivity playing a crucial role in catalysis for the synthesis of valuable chemical and pharmaceutical compounds, rational design has not achieved such wide success in this specific area compared to directed evolution. Nevertheless, one bottleneck of directed evolution is the laborious screening efforts and the observed trade-offs in catalytic profiles. This has motivated researchers to develop more efficient protein engineering methods. As a prime approach, mutability landscaping avoids such trade-offs by providing more information of sequence-function relationships. Here, we describe an application of this efficient protein engineering method to improve the regio-/stereoselectivity and activity of P450BM3 for steroid hydroxylation, while keeping the mutagenesis libraries small so that they will require only minimal screening.
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Affiliation(s)
- Huili Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of life science, Hubei University, Wuhan, P.R. China
| | - Xiaodong Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of life science, Hubei University, Wuhan, P.R. China
| | - Carlos G Acevedo-Rocha
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of life science, Hubei University, Wuhan, P.R. China.
| | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1, Muelheim, Germany; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, P. R. China.
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27
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Lappe A, Luelf UJ, Keilhammer M, Bokel A, Urlacher VB. Bacterial cytochrome P450 enzymes: Semi-rational design and screening of mutant libraries in recombinant Escherichia coli cells. Methods Enzymol 2023; 693:133-170. [PMID: 37977729 DOI: 10.1016/bs.mie.2023.09.011] [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: 11/19/2023]
Abstract
Bacterial cytochromes P450 (P450s) have been recognized as attractive targets for biocatalysis and protein engineering. They are soluble cytosolic enzymes that demonstrate higher stability and activity than their membrane-associated eukaryotic counterparts. Many bacterial P450s possess broad substrate spectra and can be produced in well-known expression hosts like Escherichia coli at high levels, which enables quick and convenient mutant libraries construction. However, the majority of bacterial P450s interacts with two auxiliary redox partner proteins, which significantly increase screening efforts. We have established recombinant E. coli cells for screening of P450 variants that rely on two separate redox partners. In this chapter, a case study on construction of a selective P450 to synthesize a precursor of several chemotherapeutics, (-)-podophyllotoxin, is described. The procedure includes co-expression of P450 and redox partner genes in E. coli with subsequent whole-cell conversion of the substrate (-)-deoxypodophyllotoxin in 96-deep-well plates. By omitting the chromatographic separation while measuring mass-to-charge ratios specific for the substrate and product via MS in so-called multiple injections in a single experimental run (MISER) LC/MS, the analysis time could be drastically reduced to roughly 1 min per sample. Screening results were verified by using isolated P450 variants and purified redox partners.
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Affiliation(s)
- Alessa Lappe
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - U Joost Luelf
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mirco Keilhammer
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ansgar Bokel
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Vlada B Urlacher
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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28
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Jiang Y, Li S. P450 fatty acid decarboxylase. Methods Enzymol 2023; 693:339-374. [PMID: 37977736 DOI: 10.1016/bs.mie.2023.09.004] [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: 11/19/2023]
Abstract
P450 fatty acid decarboxylases are able to utilize hydrogen peroxide as the sole cofactor to decarboxylate free fatty acids to produce α-olefins with abundant applications as drop-in biofuels and important chemical precursors. In this chapter, we review diverse approaches for discovery, characterization, engineering, and applications of P450 fatty acid decarboxylases. Information gained from structural data has been advancing our understandings of the unique mechanisms underlying alkene production, and providing important insights for exploring new activities. To build an efficient olefin-producing system, various engineering strategies have been proposed and applied to this unusual P450 catalytic system. Furthermore, we highlight a select number of applied examples of P450 fatty acid decarboxylases in enzyme cascades and metabolic engineering.
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Affiliation(s)
- Yuanyuan Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, P.R. China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, P.R. China.
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29
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Ma L, Sun T, Liu Y, Zhao Y, Liu X, Li Y, Chen X, Cao L, Kang Q, Guo J, Du L, Wang W, Li S. Enzymatic synthesis of indigo derivatives by tuning P450 BM3 peroxygenases. Synth Syst Biotechnol 2023; 8:452-461. [PMID: 37448528 PMCID: PMC10336827 DOI: 10.1016/j.synbio.2023.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/25/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Indigoids, a class of bis-indoles, have long been applied in dyeing, food, and pharmaceutical industries. Recently, interest in these 'old' molecules has been renewed in the field of organic semiconductors as functional building blocks for organic electronics due to their excellent chemical and physical properties. However, these indigo derivatives are difficult to access through chemical synthesis. In this study, we engineer cytochrome P450 BM3 from an NADPH-dependent monooxygenase to peroxygenases through directed evolution. A select number of P450 BM3 variants are used for the selective oxidation of indole derivatives to form different indigoid pigments with a spectrum of colors. Among the prepared indigoid organic photocatalysts, a majority of indigoids demonstrate a reduced band gap than indigo due to the increased light capture and improved charge separation, making them promising candidates for the development of new organic electronic devices. Thus, we present a useful enzymatic approach with broad substrate scope and cost-effectiveness by using low-cost H2O2 as a cofactor for the preparation of diversified indigoids, offering versatility in designing and manufacturing new dyestuff and electronic/sensor components.
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Affiliation(s)
- Li Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Tianjian Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yunjie Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yue Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xiaohui Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yuxuan Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xinwei Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Lin Cao
- School of Materials Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Qianqian Kang
- School of Materials Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Jiawei Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Lei Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Wei Wang
- School of Materials Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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30
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Nsele NN, Padayachee T, Nelson DR, Syed K. Pezizomycetes Genomes Reveal Diverse P450 Complements Characteristic of Saprotrophic and Ectomycorrhizal Lifestyles. J Fungi (Basel) 2023; 9:830. [PMID: 37623601 PMCID: PMC10455484 DOI: 10.3390/jof9080830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/25/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
Cytochrome P450 monooxygenases (CYPs/P450s) are heme proteins that play a role in organisms' primary and secondary metabolism. P450s play an important role in organism adaptation since lifestyle influences P450 composition in their genome. This phenomenon is well-documented in bacteria but less so in fungi. This study observed this phenomenon where diverse P450 complements were identified in saprophytic and ectomycorrhizal Pezizomycetes. Genome-wide data mining, annotation, and phylogenetic analysis of P450s in 19 Pezizomycetes revealed 668 P450s that can be grouped into 153 P450 families and 245 P450 subfamilies. Only four P450 families, namely, CYP51, CYP61, CYP5093, and CYP6001, are conserved across 19 Pezizomycetes, indicating their important role in these species. A total of 5 saprophyte Pezizomycetes have 103 P450 families, whereas 14 ectomycorrhizal Pezizomycetes have 89 P450 families. Only 39 P450 families were common, and 50 and 64 P450 families, respectively, were unique to ectomycorrhizal and saprophytic Pezizomycetes. These findings suggest that the switch from a saprophytic to an ectomycorrhizal lifestyle led to both the development of diverse P450 families as well as the loss of P450s, which led to the lowest P450 family diversity, despite the emergence of novel P450 families in ectomycorrhizal Pezizomycetes.
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Affiliation(s)
- Nomfundo Ntombizinhle Nsele
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.N.); (T.P.)
| | - Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.N.); (T.P.)
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.N.); (T.P.)
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31
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Agustinus B, Gillam EMJ. Solar-powered P450 catalysis: Engineering electron transfer pathways from photosynthesis to P450s. J Inorg Biochem 2023; 245:112242. [PMID: 37187017 DOI: 10.1016/j.jinorgbio.2023.112242] [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: 02/02/2023] [Revised: 04/17/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023]
Abstract
With the increasing focus on green chemistry, biocatalysis is becoming more widely used in the pharmaceutical and other chemical industries for sustainable production of high value and structurally complex chemicals. Cytochrome P450 monooxygenases (P450s) are attractive biocatalysts for industrial application due to their ability to transform a huge range of substrates in a stereo- and regiospecific manner. However, despite their appeal, the industrial application of P450s is limited by their dependence on costly reduced nicotinamide adenine dinucleotide phosphate (NADPH) and one or more auxiliary redox partner proteins. Coupling P450s to the photosynthetic machinery of a plant allows photosynthetically-generated electrons to be used to drive catalysis, overcoming this cofactor dependency. Thus, photosynthetic organisms could serve as photobioreactors with the capability to produce value-added chemicals using only light, water, CO2 and an appropriate chemical as substrate for the reaction/s of choice, yielding new opportunities for producing commodity and high-value chemicals in a carbon-negative and sustainable manner. This review will discuss recent progress in using photosynthesis for light-driven P450 biocatalysis and explore the potential for further development of such systems.
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Affiliation(s)
- Bernadius Agustinus
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia
| | - Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia.
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32
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Kato M, Huynh M, Chan N, Elliott J, Trinh A, Lucero K, Vu J, Parker D, Cheruzel LE. A one-pot Pd- and P450-catalyzed chemoenzymatic synthesis of a library of oxyfunctionalized biaryl alkanoic acids leveraging a substrate anchoring approach. J Inorg Biochem 2023; 245:112240. [PMID: 37245283 DOI: 10.1016/j.jinorgbio.2023.112240] [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: 02/02/2023] [Revised: 04/05/2023] [Accepted: 04/27/2023] [Indexed: 05/30/2023]
Abstract
A one-pot chemoenzymatic approach was developed by combining Palladium-catalysis with selective cytochrome P450 enzyme oxyfunctionalization. Various iodophenyl alkanoic acids could be coupled with alkylphenyl boronic acids to generate a series of alkyl substituted biarylalkanoic acids in overall high yield. The identity of the products could be confirmed by various analytical and chromatographic techniques. Addition of an engineered cytochrome P450 heme domain mutant with peroxygenase activity upon completion of the chemical reaction resulted in the selective oxyfunctionalization of those compounds, primarily at the benzylic position. Moreover, in order to increase the biocatalytic product conversion, a reversible substrate engineering approach was developed. This involves the coupling of a bulky amino acid such as L- phenylalanine or tryptophan, to the carboxylic acid moiety. The approach resulted in a 14 to 49% overall biocatalytic product conversion increase associated with a change in regioselectivity of hydroxylation towards less favored positions.
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Affiliation(s)
- Mallory Kato
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101, USA
| | - Michael Huynh
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101, USA
| | - Nicholas Chan
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101, USA
| | - Julien Elliott
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101, USA
| | - Amie Trinh
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101, USA
| | - Kathreena Lucero
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101, USA
| | - Julia Vu
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101, USA
| | - Daniel Parker
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101, USA
| | - Lionel E Cheruzel
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101, USA.
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33
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Zhang P, Wei W, Shang Y, Ye BC. Metabolic engineering of Yarrowia lipolytica for high-level production of scutellarin. BIORESOURCE TECHNOLOGY 2023:129421. [PMID: 37392967 DOI: 10.1016/j.biortech.2023.129421] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023]
Abstract
Scutellarin drugs have been recognized as a key item in the national development of essential clinical emergency drugs for treating cardiovascular and cerebrovascular diseases; therefore, the market demand for scutellarin is growing rapidly. Microbial synthesis based on synthetic biology is a promising method for industrial production of scutellarin. In this study, the highest reported scutellarin titer in the shake flask of 703.01 ± 4.83 mg/L was achieved in Yarrowia lipolytica through the systematic metabolic engineering modifications, including screening for the optimal flavone-6-hydroxylase-cytochrome P450 reductase combination SbF6H-ATR2 to enhance P450 enzyme activity, increasing the copy numbers of rate-limiting enzyme genes, overexpressing ZWF1 and GND1 to increase NADPH supply, enhancing the supply of p-coumaric acid and uridine diphosphate glucose, and introducing the heterologous gene VHb to enhance oxygen supply. This study has significant implications for the industrial production of scutellarin and other valuable flavonoids in green economies.
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Affiliation(s)
- Ping Zhang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wenping Wei
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Yanzhe Shang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
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Ugya AY, Chen H, Wang Q. Microalgae biofilm system as an efficient tool for wastewater remediation and potential bioresources for pharmaceutical product production: an overview. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2023; 26:131-142. [PMID: 37382505 DOI: 10.1080/15226514.2023.2229920] [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: 06/30/2023]
Abstract
The role of microalgae in wastewater remediation and metabolite production has been well documented, but the limitations of microalgae harvesting and low biomass production call for a more sustainable method of microalgae utilization. The current review gives an insight on how microalgae biofilms can be utilized as a more efficient system for wastewater remediation and as potential source of metabolite for pharmaceutical product production. The review affirms that the extracellular polymeric substance (EPS) is the vital component of the microalgae biofilm because it influences the spatial organization of the organisms forming microalgae biofilm. The EPS is also responsible for the ease interaction between organisms forming microalgae biofilm. This review restate the crucial role play by EPS in the removal of heavy metals from water to be due to the presence of binding sites on its surface. This review also attribute the ability of microalgae biofilm to bio-transform organic pollutant to be dependent on enzymatic activities and the production of reactive oxygen species (ROS). The review assert that during the treatment of wastewater, the wastewater pollutants induce oxidative stress on microalgae biofilms. The response of the microalgae biofilm toward counteracting the stress induced by ROS leads to production of metabolites. These metabolites are important tools that can be harness for the production of pharmaceutical products.
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Affiliation(s)
- Adamu Yunusa Ugya
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, China
- Department of Environmental Management, Kaduna State University, Kaduna State, Nigeria
| | - Hui Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, China
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35
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Hou Z, Li Y, Zheng M, Liu X, Zhang Q, Wang W. Regioselective oxidation of heterocyclic aromatic hydrocarbons catalyzed by cytochrome P450: A case study of carbazole. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 258:114964. [PMID: 37121081 DOI: 10.1016/j.ecoenv.2023.114964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/11/2023] [Accepted: 04/26/2023] [Indexed: 05/22/2023]
Abstract
Recently there are increasing interests in accurately evaluating the health effects of heterocyclic PAHs. However, the activation mechanism and possible metabolites of heterocyclic PAHs catalyzed by human CYP1A1 is still elusive to a great extent. Here, leveraged to high level QM/MM calculations, the corresponding activation pathways of a representative heterocyclic PAHs, carbazole, were systematically explored. The first stage is electrophilic addition or hydrogen abstraction from N-H group. Electrophilic addition was evidenced to be more feasible and regioselectivity at C3 and C4 sites were identified. Correlations between energy barriers and key structural/electrostatic parameters reveal that O-Cα distance and Fe-O-Cα angle are the main origin for the catalytic regioselectivity. Electrophilic addition was determined as the rate-determining step and the subsequent possible reactions include epoxidation, NIH shift (the hydrogen migration from the site of hydroxylation to the adjacent carbon) and proton shuttle. The corresponding products are epoxides, ketones and hydroxylated carbazoles, respectively. The main metabolites (hydroxylated carbazoles) are estimated to be more toxic than carbazole. The regioselectivity of carbazole activated by CYP1A1 is different from the environmental processes (gas and aqueous phase). Collectively, these results will inform the in-depth understanding the metabolic processes of heterocyclic PAHs and aid the accurate evaluation of their health effects.
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Affiliation(s)
- Zexi Hou
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, PR China; Shenzhen Research Institute, Shandong University, Shenzhen 518057, PR China.
| | - Mingna Zheng
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Xinning Liu
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
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36
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Liu R, Pan Y, Wang N, Tang D, Urlacher VB, Li S. Comparative biochemical characterization of mammalian-derived CYP11A1s with cholesterol side-chain cleavage activities. J Steroid Biochem Mol Biol 2023; 229:106268. [PMID: 36764495 DOI: 10.1016/j.jsbmb.2023.106268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Steroid drugs, the second largest class of pharmaceuticals after antibiotics, have shown significant anti-inflammatory, anti-allergic, and endocrine-regulating effects. A group of cytochrome P450 enzymes, namely, CYP11A1 isoenzymes from different organisms are capable of converting cholesterol into pregnenolone, which is a pivotal reaction in both steroid metabolism and (bio)synthetic network of steroid products. However, the low activity of CYP11A1s greatly restricts the industrial application of these cholesterol side-chain cleavage enzymes. Herein, we investigate ten CYP11A1 enzymes of different origins and in vitro characterize two CYP11A1s with a relatively higher expression level from Capra hircus and Sus scrofa, together with the CYP11A1s from Homo sapiens and Bos taurus as references. Towards five selected sterol substrates with different side chain structures, S. scrofa CYP11A1 displays relatively higher activities. Through redox partners combination screening, we reveal the optimal redox partner pair of S. scrofa adrenodoxin and C. hircus adrenodoxin reductase. Moreover, the semi-rational mutagenesis for the active sites and substrate entrance channels of human and bovine CYP11A1s is performed based on comparative analysis of their crystal structures. The mutant mBtCYP11A1-Q377A derived from mature B. taurus CYP11A1 shows a 1.46 times higher activity than the wild type enzyme. These results not only demonstrate the tunability of the highly conserved CYP11A1 isoenzymes, but also lay a foundation for the following engineering efforts on these industrially relevant P450 enzymes.
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Affiliation(s)
- Ruxin Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Yunjun Pan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Ning Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China
| | - Dandan Tang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Vlada B Urlacher
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China.
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Hardiyanti Oktavia FAR, Nguyen NA, Park CM, Cha GS, Nguyen THH, Yun CH. CYP102A1 peroxygenase catalyzed reaction via in situ H 2O 2 generation. J Inorg Biochem 2023; 242:112165. [PMID: 36848686 DOI: 10.1016/j.jinorgbio.2023.112165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/17/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023]
Abstract
CYP102A1 is a promiscuous bacterial cytochrome P450 (CYP or P450) known for its diverse substrates and comparable activity with human P450 enzymes. The development of CYP102A1 peroxygenase activity can contribute significantly to human drug development and drug metabolite production. Peroxygenase has recently emerged as an alternative to a dependency of P450 on NADPH-P450 reductase and NADPH cofactor and gives more opportunity for practical application. However, the H2O2 dependency also leads to challenges regarding its practical application, in which the excessive H2O2 concentration causes the activation of the peroxygenases. Therefore, we need the optimization of H2O2 production to minimize oxidative inactivation. In this study, we report the CYP102A1 peroxygenase-catalyzed atorvastatin hydroxylation reaction with an enzymatic H2O2 generation using glucose oxidase. Random mutagenesis at the CYP102A1 heme domain was used to generate mutant libraries with high throughput screening of highly active mutants, which can pair with the in situ H2O2 generation. The setup of the CYP102A1 peroxygenase reaction was also possible for other statin drugs and could be developed to produce drug metabolites. We also found a relationship between enzyme inactivation and product formation during the catalytic reaction, supported by enzymatic in situ H2O2 supply. It can be suggested that the low product formation is due to enzyme inactivation.
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Affiliation(s)
- Fikri A R Hardiyanti Oktavia
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Yongbong-ro 77, Gwangju 61186, Republic of Korea
| | - Ngoc Anh Nguyen
- School of Biological Sciences and Technology, Chonnam National University, Yongbong-ro 77, Gwangju 61186, Republic of Korea
| | - Chan Mi Park
- School of Biological Sciences and Technology, Chonnam National University, Yongbong-ro 77, Gwangju 61186, Republic of Korea
| | - Gun Su Cha
- Namhae Garlic Research Institute, 2465-8 Namhaedaero, Gyeongsangnamdo 52430, Republic of Korea
| | - Thi Huong Ha Nguyen
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Yongbong-ro 77, Gwangju 61186, Republic of Korea
| | - Chul-Ho Yun
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Yongbong-ro 77, Gwangju 61186, Republic of Korea; School of Biological Sciences and Technology, Chonnam National University, Yongbong-ro 77, Gwangju 61186, Republic of Korea.
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Cai N, Li C, Gu X, Zeng W, Zhong J, Liu J, Zeng G, Zhu J, Hong H. CYP2C19 loss-of-function is associated with increased risk of hypertension in a Hakka population: a case-control study. BMC Cardiovasc Disord 2023; 23:185. [PMID: 37024851 PMCID: PMC10080785 DOI: 10.1186/s12872-023-03207-w] [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: 12/26/2022] [Accepted: 03/27/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Genetic factors have a certain proportion in the risk factors of hypertension. The purpose was to investigate the relationship of cytochrome P450 2C19 (CYP2C19) polymorphisms with hypertension in Hakka population. METHODS The study included 1,872 hypertensive patients and 1,110 controls. The genotypes of CYP2C19 rs4244285 and rs4986893 of all individuals were detected and analyzed. RESULTS The genotype and allele distributions of CYP2C19 rs4244285 were significantly different between hypertension group and control group. The CYP2C19 *1/*1 genotype was the most predominant among the subjects (40.8%), followed by the CYP2C19 *1/*2 genotype (40.5%). The percentage of CYP2C19*1, *2, and *3 allele was 64.2%, 30.8%, and 5.0%, respectively. The proportion of intermediate metabolizers (IM) (49.3% vs. 42.9%), poor metabolizers (PM) (14.3% vs. 8.9%) (P < 0.001), and CYP2C19*2 allele (33.8% vs. 25.7%, P < 0.001) in hypertension group was significantly higher than that in control group. Multivariate logistic regression (adjusted for gender, age, smoking, and drinking) indicated that CYP2C19 *1/*2, *1/*3, and *2/*2 genotypes may increase susceptibility to hypertension. And the CYP2C19 IM genotype (IM vs. EM: OR 1.514, 95% CI: 1.291-1.775, P < 0.001), PM genotype (PM vs. EM: OR 2.120, 95% CI: 1.638-2.743, P < 0.001), IM + PM genotypes (IM + PM vs. EM: OR 1.617, 95% CI: 1.390-1.882, P < 0.001) may increase risk of hypertension. CONCLUSIONS CYP2C19 loss-of-function (IM, PM genotypes) is independent risk factor for hypertension susceptibility. Specifically, the risk genotypes include CYP2C19 *1/*2, *1/*3, and *2/*2.
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Affiliation(s)
- Nan Cai
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China.
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China.
- , No. 63 Huangtang Road, Meijiang District, Meizhou, China.
| | - Cunren Li
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
| | - Xianfang Gu
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
| | - Wenfeng Zeng
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
| | - Jiawei Zhong
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
| | - Jingfeng Liu
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
| | - Guopeng Zeng
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
| | - Junxing Zhu
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
| | - Haifeng Hong
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
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Koroleva PI, Gilep AA, Kraevsky SV, Tsybruk TV, Shumyantseva VV. Improving the Efficiency of Electrocatalysis of Cytochrome P450 3A4 by Modifying the Electrode with Membrane Protein Streptolysin O for Studying the Metabolic Transformations of Drugs. BIOSENSORS 2023; 13:bios13040457. [PMID: 37185532 PMCID: PMC10136652 DOI: 10.3390/bios13040457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/30/2023] [Accepted: 04/02/2023] [Indexed: 05/17/2023]
Abstract
In the present work, screen-printed electrodes (SPE) modified with a synthetic surfactant, didodecyldimethylammonium bromide (DDAB) and streptolysin O (SLO) were prepared for cytochrome P450 3A4 (CYP3A4) immobilization, direct non-catalytic and catalytic electrochemistry. The immobilized CYP3A4 demonstrated a pair of redox peaks with a formal potential of -0.325 ± 0.024 V (vs. the Ag/AgCl reference electrode). The electron transfer process showed a surface-controlled mechanism ("protein film voltammetry") with an electron transfer rate constant (ks) of 0.203 ± 0.038 s-1. Electrochemical CYP3A4-mediated reaction of N-demethylation of erythromycin was explored with the following parameters: an applied potential of -0.5 V and a duration time of 20 min. The system with DDAB/SLO as the electrode modifier showed conversion of erythromycin with an efficiency higher than the electrode modified with DDAB only. Confining CYP3A4 inside the protein frame of SLO accelerated the enzymatic reaction. The increases in product formation in the reaction of the electrochemical N-demethylation of erythromycin for SPE/DDAB/CYP3A4 and SPE/DDAB/SLO/CYP3A4 were equal to 100 ± 22% and 297 ± 7%, respectively. As revealed by AFM images, the SPE/DDAB/SLO possessed a more developed surface with protein cavities in comparison with SPE/DDAB for the effective immobilization of the CYP3A4 enzyme.
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Affiliation(s)
- Polina I Koroleva
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Build 8, 119121 Moscow, Russia
| | - Andrei A Gilep
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Build 8, 119121 Moscow, Russia
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | - Sergey V Kraevsky
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Build 8, 119121 Moscow, Russia
| | - Tatiana V Tsybruk
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | - Victoria V Shumyantseva
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Build 8, 119121 Moscow, Russia
- Faculty of Biomedicine, Pirogov Russian National Research Medical University, Ostrovitianov Street, 1, 117997 Moscow, Russia
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Ge J, Wang X, Bai Y, Wang Y, Wang Y, Tu T, Qin X, Su X, Luo H, Yao B, Huang H, Zhang J. Engineering Escherichia coli for efficient assembly of heme proteins. Microb Cell Fact 2023; 22:59. [PMID: 36978060 PMCID: PMC10053478 DOI: 10.1186/s12934-023-02067-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Heme proteins, such as hemoglobin, horseradish peroxidase and cytochrome P450 (CYP) enzyme, are highly versatile and have widespread applications in the fields of food, healthcare, medical and biological analysis. As a cofactor, heme availability plays a pivotal role in proper folding and function of heme proteins. However, the functional production of heme proteins is usually challenging mainly due to the insufficient supply of intracellular heme. RESULTS Here, a versatile high-heme-producing Escherichia coli chassis was constructed for the efficient production of various high-value heme proteins. Initially, a heme-producing Komagataella phaffii strain was developed by reinforcing the C4 pathway-based heme synthetic route. Nevertheless, the analytical results revealed that most of the red compounds generated by the engineered K. phaffii strain were intermediates of heme synthesis which were unable to activate heme proteins. Subsequently, E. coli strain was selected as the host to develop heme-producing chassis. To fine-tune the C5 pathway-based heme synthetic route in E. coli, fifty-two recombinant strains harboring different combinations of heme synthesis genes were constructed. A high-heme-producing mutant Ec-M13 was obtained with negligible accumulation of intermediates. Then, the functional expression of three types of heme proteins including one dye-decolorizing peroxidase (Dyp), six oxygen-transport proteins (hemoglobin, myoglobin and leghemoglobin) and three CYP153A subfamily CYP enzymes was evaluated in Ec-M13. As expected, the assembly efficiencies of heme-bound Dyp and oxygen-transport proteins expressed in Ec-M13 were increased by 42.3-107.0% compared to those expressed in wild-type strain. The activities of Dyp and CYP enzymes were also significantly improved when expressed in Ec-M13. Finally, the whole-cell biocatalysts harboring three CYP enzymes were employed for nonanedioic acid production. High supply of intracellular heme could enhance the nonanedioic acid production by 1.8- to 6.5-fold. CONCLUSION High intracellular heme production was achieved in engineered E. coli without significant accumulation of heme synthesis intermediates. Functional expression of Dyp, hemoglobin, myoglobin, leghemoglobin and CYP enzymes was confirmed. Enhanced assembly efficiencies and activities of these heme proteins were observed. This work provides valuable guidance for constructing high-heme-producing cell factories. The developed mutant Ec-M13 could be employed as a versatile platform for the functional production of difficult-to-express heme proteins.
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Affiliation(s)
- Jianzhong Ge
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yingguo Bai
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yaru Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
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Pan Y, Li G, Liu R, Guo J, Liu Y, Liu M, Zhang X, Chi L, Xu K, Wu R, Zhang Y, Li Y, Gao X, Li S. Unnatural activities and mechanistic insights of cytochrome P450 PikC gained from site-specific mutagenesis by non-canonical amino acids. Nat Commun 2023; 14:1669. [PMID: 36966128 PMCID: PMC10039885 DOI: 10.1038/s41467-023-37288-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/09/2023] [Indexed: 03/27/2023] Open
Abstract
Cytochrome P450 enzymes play important roles in the biosynthesis of macrolide antibiotics by mediating a vast variety of regio- and stereoselective oxidative modifications, thus improving their chemical diversity, biological activities, and pharmaceutical properties. Tremendous efforts have been made on engineering the reactivity and selectivity of these useful biocatalysts. However, the 20 proteinogenic amino acids cannot always satisfy the requirement of site-directed/random mutagenesis and rational protein design of P450 enzymes. To address this issue, herein, we practice the semi-rational non-canonical amino acid mutagenesis for the pikromycin biosynthetic P450 enzyme PikC, which recognizes its native macrolide substrates with a 12- or 14-membered ring macrolactone linked to a deoxyamino sugar through a unique sugar-anchoring mechanism. Based on a semi-rationally designed substrate binding strategy, non-canonical amino acid mutagenesis at the His238 position enables the unnatural activities of several PikC mutants towards the macrolactone precursors without any sugar appendix. With the aglycone hydroxylating activities, the pikromycin biosynthetic pathway is rewired by the representative mutant PikCH238pAcF carrying a p-acetylphenylalanine residue at the His238 position and a promiscuous glycosyltransferase. Moreover, structural analysis of substrate-free and three different enzyme-substrate complexes of PikCH238pAcF provides significant mechanistic insights into the substrate binding and catalytic selectivity of this paradigm biosynthetic P450 enzyme.
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Affiliation(s)
- Yunjun Pan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Guobang Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Ruxin Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Jiawei Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Yunjie Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Mingyu Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xingwang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China
| | - Luping Chi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Kangwei Xu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yuzhong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China.
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China.
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Lautier T, Smith DJ, Yang LK, Chen X, Zhang C, Truan G, Lindley ND. β-Cryptoxanthin Production in Escherichia coli by Optimization of the Cytochrome P450 CYP97H1 Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4683-4695. [PMID: 36888893 DOI: 10.1021/acs.jafc.2c08970] [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: 06/18/2023]
Abstract
Cytochromes P450, forming a superfamily of monooxygenases containing heme as a cofactor, show great versatility in substrate specificity. Metabolic engineering can take advantage of this feature to unlock novel metabolic pathways. However, the cytochromes P450 often show difficulty being expressed in a heterologous chassis. As a case study in the prokaryotic host Escherichia coli, the heterologous synthesis of β-cryptoxanthin was addressed. This carotenoid intermediate is difficult to produce, as its synthesis requires a monoterminal hydroxylation of β-carotene whereas most of the classic carotene hydroxylases are dihydroxylases. This study was focused on the optimization of the in vivo activity of CYP97H1, an original P450 β-carotene monohydroxylase. Engineering the N-terminal part of CYP97H1, identifying the matching redox partners, defining the optimal cellular background and adjusting the culture and induction conditions improved the production by 400 times compared to that of the initial strain, representing 2.7 mg/L β-cryptoxanthin and 20% of the total carotenoids produced.
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Affiliation(s)
- Thomas Lautier
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 138669 Singapore
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
- CNRS@CREATE, 1 Create Way, #08-01 Create Tower, 138602 Singapore
| | - Derek J Smith
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 138669 Singapore
| | - Lay Kien Yang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 138669 Singapore
| | - Xixian Chen
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 138669 Singapore
| | - Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 138669 Singapore
| | - Gilles Truan
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Nic D Lindley
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 138669 Singapore
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
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43
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Wang Z, Diao W, Wu P, Li J, Fu Y, Guo Z, Cao Z, Shaik S, Wang B. How the Conformational Movement of the Substrate Drives the Regioselective C-N Bond Formation in P450 TleB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations. J Am Chem Soc 2023; 145:7252-7267. [PMID: 36943409 DOI: 10.1021/jacs.2c12962] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
P450 TleB catalyzes the oxidative cyclization of the dipeptide N-methylvalyl-tryptophanol into indolactam V through selective intramolecular C-H bond amination at the indole C4 position. Understanding its catalytic mechanism is instrumental for the engineering or design of P450-catalyzed C-H amination reactions. Using multiscale computational methods, we show that the reaction proceeds through a diradical pathway, involving a hydrogen atom transfer (HAT) from N1-H to Cpd I, a conformational transformation of the substrate radical species, and a second HAT from N13-H to Cpd II. Intriguingly, the conformational transformation is found to be the key to enabling efficient and selective C-N coupling between N13 and C4 in the subsequent diradical coupling reaction. The underlined conformational transformation is triggered by the first HAT, which proceeds with an energy-demanding indole ring flip and is followed by the facile approach of the N13-H group to Cpd II. Detailed analysis shows that the internal electric field (IEF) from the protein environment plays key roles in the transformation process, which not only provides the driving force but also stabilizes the flipped conformation of the indole radical. Our simulations provide a clear picture of how the P450 enzyme can smartly modulate the selective C-N coupling reaction. The present findings are in line with all available experimental data, highlighting the crucial role of substrate dynamics in controlling this highly valuable reaction.
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Affiliation(s)
- Zhanfeng Wang
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
| | - Wenwen Diao
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
| | - Peng Wu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Junfeng Li
- College of Chemistry and Chemical Engineering, and Henan Key Laboratory of Functional-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, China
| | - Yuzhuang Fu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhiyong Guo
- State Key Laboratory of Food Science and Technology, School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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44
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Zhao P, Kong F, Jiang Y, Qin X, Tian X, Cong Z. Enabling Peroxygenase Activity in Cytochrome P450 Monooxygenases by Engineering Hydrogen Peroxide Tunnels. J Am Chem Soc 2023; 145:5506-5511. [PMID: 36790023 DOI: 10.1021/jacs.3c00195] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Given prominent physicochemical similarities between H2O2 and water, we report a new strategy for promoting the peroxygenase activity of P450 enzymes by engineering their water tunnels to facilitate H2O2 access to the heme center buried therein. Specifically, the H2O2-driven activities of two native NADH-dependent P450 enzymes (CYP199A4 and CYP153AM.aq) increase significantly (by >183-fold and >15-fold, respectively). Additionally, the amount of H2O2 required for an artificial P450 peroxygenase facilitated by a dual-functional small molecule to obtain the desired product is reduced by 95%-97.5% (with ∼95% coupling efficiency). Structural analysis suggests that mutating the residue at the bottleneck of the water tunnel may open a second pathway for H2O2 to flow to the heme center (in addition to the natural substrate tunnel). This study highlights a promising, generalizable strategy whereby P450 monooxygenases can be modified to adopt peroxygenase activity through H2O2 tunnel engineering, thus broadening the application scope of P450s in synthetic chemistry and synthetic biology.
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Affiliation(s)
- Panxia Zhao
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanhui Kong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiping Jiang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Xiangquan Qin
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Xiaoxia Tian
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Shandong Energy Institute, Qingdao, Shandong 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
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45
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Lv X, Wu C, Hu H, Fu Y, Yan L, Wang Z, Lv G, Wang G, Bai Z. Transcriptome analysis of growth and shell color between two genetic variants of Corbicula fluminea with different shell colors. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101056. [PMID: 36736150 DOI: 10.1016/j.cbd.2023.101056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/07/2023] [Accepted: 01/08/2023] [Indexed: 01/22/2023]
Abstract
To clarify the molecular mechanism of the black and yellow shell coloration, we performed a transcriptome analysis of whole tissue of Corbicula fluminea in Hongze Lake (Jiangsu Province, China). After assembly, 335,247 unigenes were obtained, and 136,804 unigenes were functionally identified using public databases (NR, GO, KEGG, eggnog, and Swissprot). 1567 differentially expressed genes (DEGs) were detected through pairwise comparisons, of which 941 DEGs were up-regulated and 626 were down-regulated in the black-shelled clam. We compared the DEGs between two clams and identified some coloration-related genes. Notably, the black-shelled clam was larger than the yellow-shelled. We speculated that higher digestion and anabolic ability of black-shelled clam might lead to this phenomenon. In contrast, the yellow-shelled clam appeared to be more sensitive to environmental stress. The metabolic energy of the yellow-shelled clam was depleted to maintain or recover from stress, and provide less energy for growth. In summary, our finding provides a theoretical basis for the molecular mechanism of pigmentation and the difference of somatotype in bivalve, as well as promotes the future breeding of more elite varieties.
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Affiliation(s)
- Xuefeng Lv
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China. https://twitter.com/
| | - Congdi Wu
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Honghui Hu
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Yuanshuai Fu
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Ling Yan
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Zhiyan Wang
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Gaolun Lv
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Guiling Wang
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Zhiyi Bai
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shangha Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China.
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Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Anthropogenic activities and industrial effluents are the major sources of petroleum hydrocarbon contamination in different environments. Microbe-based remediation techniques are known to be effective, inexpensive, and environmentally safe. In this review, the metabolic-target-specific pathway engineering processes used for improving the bioremediation of hydrocarbon-contaminated environments have been described. The microbiomes are characterised using environmental genomics approaches that can provide a means to determine the unique structural, functional, and metabolic pathways used by the microbial community for the degradation of contaminants. The bacterial metabolism of aromatic hydrocarbons has been explained via peripheral pathways by the catabolic actions of enzymes, such as dehydrogenases, hydrolases, oxygenases, and isomerases. We proposed that by using microbiome engineering techniques, specific pathways in an environment can be detected and manipulated as targets. Using the combination of metabolic engineering with synthetic biology, systemic biology, and evolutionary engineering approaches, highly efficient microbial strains may be utilised to facilitate the target-dependent bioprocessing and degradation of petroleum hydrocarbons. Moreover, the use of CRISPR-cas and genetic engineering methods for editing metabolic genes and modifying degradation pathways leads to the selection of recombinants that have improved degradation abilities. The idea of growing metabolically engineered microbial communities, which play a crucial role in breaking down a range of pollutants, has also been explained. However, the limitations of the in-situ implementation of genetically modified organisms pose a challenge that needs to be addressed in future research.
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Evolution of Cytochrome P450 Enzymes and Their Redox Partners in Archaea. Int J Mol Sci 2023; 24:ijms24044161. [PMID: 36835573 PMCID: PMC9962201 DOI: 10.3390/ijms24044161] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Cytochrome P450 monooxygenases (CYPs/P450s) and their redox partners, ferredoxins, are ubiquitous in organisms. P450s have been studied in biology for over six decades owing to their distinct catalytic activities, including their role in drug metabolism. Ferredoxins are ancient proteins involved in oxidation-reduction reactions, such as transferring electrons to P450s. The evolution and diversification of P450s in various organisms have received little attention and no information is available for archaea. This study is aimed at addressing this research gap. Genome-wide analysis revealed 1204 P450s belonging to 34 P450 families and 112 P450 subfamilies, where some families and subfamilies are expanded in archaea. We also identified 353 ferredoxins belonging to the four types 2Fe-2S, 3Fe-4S, 7Fe-4S and 2[4Fe-4S] in 40 archaeal species. We found that bacteria and archaea shared the CYP109, CYP147 and CYP197 families, as well as several ferredoxin subtypes, and that these genes are co-present on archaeal plasmids and chromosomes, implying the plasmid-mediated lateral transfer of these genes from bacteria to archaea. The absence of ferredoxins and ferredoxin reductases in the P450 operons suggests that the lateral transfer of these genes is independent. We present different scenarios for the evolution and diversification of P450s and ferredoxins in archaea. Based on the phylogenetic analysis and high affinity to diverged P450s, we propose that archaeal P450s could have diverged from CYP109, CYP147 and CYP197. Based on this study's results, we propose that all archaeal P450s are bacterial in origin and that the original archaea had no P450s.
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Liu Z, Yashiroda Y, Sun P, Ma H, Wang Y, Li L, Yan F, Sun Y. Argenteolides A and B, Glycosylated Polyketide-Peptide Hybrid Macrolides from an Actinomycete Streptomyces argenteolus. Org Lett 2023; 25:571-575. [PMID: 36469481 DOI: 10.1021/acs.orglett.2c03290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Two novel glycosylated polyketide-peptide hybrid macrolides, argenteolides A (1) and B (2), were isolated from an actinomycete Streptomyces argenteolus. Argenteolide A (1) contains a unique 5/5/5 tricyclic system in a 20-membered macrocycle. Their structures were elucidated by extensive spectroscopic analysis, and their stereochemical configurations were established through the application of chemical derivatization, J-based configuration analysis, DP4+ calculation, and electronic circular dichroism calculation. The analysis of the genome sequence revealed a plausible biosynthesis mechanism, and isotope-labeled feeding studies suggested their biogenetic origins. Argenteolides A and B exhibited moderate cytotoxicities against A549, p388, and Hela human carcinoma cell lines as well as antibacterial activities against Staphylococcus aureus and Escherichia coli ATCC25922.
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Affiliation(s)
- Zhiguo Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing100700, China
| | - Yoko Yashiroda
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama351-0198, Japan
| | - Peng Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing100700, China
| | - Hai Ma
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing100700, China
| | - Yanan Wang
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing100050, China
| | - Li Li
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing100050, China
| | - Fu Yan
- Helmholtz International Lab for Antiinfectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong266237, China
| | - Yi Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing100700, China
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Engineering Rieske oxygenase activity one piece at a time. Curr Opin Chem Biol 2023; 72:102227. [PMID: 36410250 PMCID: PMC9939785 DOI: 10.1016/j.cbpa.2022.102227] [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: 09/07/2022] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 11/19/2022]
Abstract
Enzyme engineering plays a central role in the development of biocatalysts for biotechnology, chemical and pharmaceutical manufacturing, and environmental remediation. Rational design of proteins has historically relied on targeting active site residues to confer a protein with desirable catalytic properties. However, additional "hotspots" are also known to exist beyond the active site. Structural elements such as subunit-subunit interactions, entrance tunnels, and flexible loops influence enzyme catalysis and serve as potential "hotspots" for engineering. For the Rieske oxygenases, which use a Rieske cluster and mononuclear iron center to catalyze a challenging set of reactions, these outside of the active site regions are increasingly being shown to drive catalytic outcomes. Therefore, here, we highlight recent work on structurally characterized Rieske oxygenases that implicates architectural pieces inside and outside of the active site as key dictators of catalysis, and we suggest that these features may warrant attention in efforts aimed at Rieske oxygenase engineering.
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Attar A, Altikatoglu Yapaoz M. The analysis of methylxanthine fractions obtained from Camellia sinensis cultivated in Turkey and effects on the in vitro inhibition of CYP2D6 enzyme. Biotechnol Appl Biochem 2023; 70:22-27. [PMID: 35196743 DOI: 10.1002/bab.2325] [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: 11/07/2021] [Accepted: 01/18/2022] [Indexed: 11/11/2022]
Abstract
Tea is a worldwide consumed herbal beverage and it was aimed in this study to reveal the major fractions of green and black tea in order to enlighten the in vitro inhibition potency on the well-known drug metabolizing enzyme CYP2D6 activity. Methylxanthine fractions were extracted from green and black tea and a yield of 0.265 g (1.06%) for 25 g of dried black tea and 0.302 g (1.2%) for 25 g of green tea was calculated. High-performance liquid chromatography analysis represented that the major components of the methylxanthine fractions were caffeine, theobromine, and theophylline. Methylxanthine content of black tea was 368.25 ± 4.6 μg/ml caffeine, 89.30 ± 2.3 μg/ml theobromine, and 3.40 ± 0.5 μg/ml theophylline, whereas that of green tea was 176.50 ± 3.7 μg/ml caffeine, 53.85 ± 1.4 μg/ml theobromine, and 2.06 ± 0.7 μg/ml theophylline. The results of concentration-dependent inhibition studies were 76% green tea, 75% black tea, and 55% caffeine at concentration of 10 mg/ml. The inhibition rates of green and black tea on CYP2D6 activity were 76% and 75%, respectively, where that of quinidine, the well-known inhibitor of CYP2D6, was 82%. Our results indicate that green and black tea is very likely to modify the CYP2D6 enzyme activity.
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Affiliation(s)
- Azade Attar
- Faculty of Chemical & Metallurgical Engineering, Department of Bioengineering, Yildiz Technical University, Istanbul, Turkey
| | - Melda Altikatoglu Yapaoz
- Faculty of Science and Letters, Department of Chemistry, Yildiz Technical University, Istanbul, Turkey
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