1
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Wittmund M, Cadet F, Davari MD. Learning Epistasis and Residue Coevolution Patterns: Current Trends and Future Perspectives for Advancing Enzyme Engineering. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marcel Wittmund
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Frederic Cadet
- Laboratory of Excellence LABEX GR, DSIMB, Inserm UMR S1134, University of Paris city & University of Reunion, Paris 75014, France
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
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2
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Zheng Y, Zhang B, Xie Y, Lin J, Wei D. Using a novel data-driven combinatorial mutagenesis strategy to engineer an alcohol dehydrogenase for efficient geraniol synthesis. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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Computational enzyme redesign: large jumps in function. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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4
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Sankara Narayanan P, Runthala A. Accurate computational evolution of proteins and its dependence on deep learning and machine learning strategies. BIOCATAL BIOTRANSFOR 2022. [DOI: 10.1080/10242422.2022.2030317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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5
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Revolutionizing enzyme engineering through artificial intelligence and machine learning. Emerg Top Life Sci 2021; 5:113-125. [PMID: 33835131 DOI: 10.1042/etls20200257] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 12/20/2022]
Abstract
The combinatorial space of an enzyme sequence has astronomical possibilities and exploring it with contemporary experimental techniques is arduous and often ineffective. Multi-target objectives such as concomitantly achieving improved selectivity, solubility and activity of an enzyme have narrow plausibility under approaches of restricted mutagenesis and combinatorial search. Traditional enzyme engineering approaches have a limited scope for complex optimization due to the requirement of a priori knowledge or experimental burden of screening huge protein libraries. The recent surge in high-throughput experimental methods including Next Generation Sequencing and automated screening has flooded the field of molecular biology with big-data, which requires us to re-think our concurrent approaches towards enzyme engineering. Artificial Intelligence (AI) and Machine Learning (ML) have great potential to revolutionize smart enzyme engineering without the explicit need for a complete understanding of the underlying molecular system. Here, we portray the role and position of AI techniques in the field of enzyme engineering along with their scope and limitations. In addition, we explain how the traditional approaches of directed evolution and rational design can be extended through AI tools. Recent successful examples of AI-assisted enzyme engineering projects and their deviation from traditional approaches are highlighted. A comprehensive picture of current challenges and future avenues for AI in enzyme engineering are also discussed.
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6
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Affiliation(s)
- Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International Centre for Clinical Research, St. Ann’s Hospital, 602 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International Centre for Clinical Research, St. Ann’s Hospital, 602 00 Brno, Czech Republic
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7
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Structure-Based Engineering of Amidase from Pantoea sp. for Efficient 2-Chloronicotinic Acid Biosynthesis. Appl Environ Microbiol 2019; 85:AEM.02471-18. [PMID: 30578259 DOI: 10.1128/aem.02471-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/08/2018] [Indexed: 11/20/2022] Open
Abstract
2-Chloronicotinic acid is a key intermediate of pharmaceuticals and pesticides. Amidase-catalyzed hydrolysis provides a promising enzymatic method for 2-chloronicotinic acid production from 2-chloronicotinamide. However, biocatalytic hydrolysis of 2-chloronicotinamide is difficult due to the strong steric and electronic effect caused by 2-position chlorine substituent of the pyridine ring. In this study, an amidase from a Pantoea sp. (Pa-Ami) was designed and engineered to have improved catalytic properties. Single mutant G175A and double mutant G175A/A305T strains exhibited 3.2- and 3.7-fold improvements in their specific activity for 2-chloronicotinamide, and the catalytic efficiency was significantly increased, with k cat/Km values 3.1 and 10.0 times higher than that of the wild type, respectively. Structure-function analysis revealed that the distance between Oγ of Ser177 (involved in the catalytic triad) and the carbonyl carbon of 2-chloronicotinamide was shortened in the G175A mutant, making the nucleophilic attack on the Oγ of Ser177 easier by virtue of proper orientation. In addition, the A305T mutation contributed to a suitable tunnel formation to facilitate the substrate entry and product release, resulting in improved catalytic efficiency. With the G175A/A305T double mutant as a biocatalyst, a maximum of 1,220 mM 2-chloronicotinic acid was produced with a 94% conversion, and the space-time yield reached as high as 575 gproduct liter-1 day-1 These results provide not only a novel robust biocatalyst for the production of 2-chloronicotinic acid but also new insights into amidase structure-function relationships.IMPORTANCE In recent years, the demand for 2-chloronicotinic acid has been greatly increased. To date, several chemical methods have been used for the synthesis of 2-chloronicotinic acid, but all include tedious steps and/or drastic reaction conditions, resulting in both economic and environmental issues. It is requisite to develop an efficient and green synthesis route. We recently screened Pa-Ami and demonstrated its potential for synthesis of 2-chloronicotinic acid from 2-chloronicotinamide. However, chlorine substitution on the pyridine ring of nicotinamide significantly affected the activity of Pa-Ami. Especially for 2-chloronicotinamide, the enzyme activity and catalytic efficiency were relatively low. In this study, based on structure-function analysis, we succeeded in engineering the amidase by structure-guided saturation mutagenesis. The engineered Pa-Ami exhibited quite high catalytic activity toward 2-chloronicotinamide and could serve as a promising biocatalyst for the biosynthesis of 2-chloronicotinic acid.
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Bioconversion of p-Tyrosol into Hydroxytyrosol under Bench-Scale Fermentation. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7390751. [PMID: 30105240 PMCID: PMC6076966 DOI: 10.1155/2018/7390751] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/19/2018] [Indexed: 11/17/2022]
Abstract
Tyrosol hydroxylating Pseudomonas strain was previously isolated from olive mill wastewaters-irrigated soil. In the present work, experimental design was used to study the bioconversion of tyrosol in laboratory fermenters aiming at the recovery of the highest yields of hydroxytyrosol. The effects of biocatalyst loading and tyrosol concentration were studied. The bioconversion yield reached 86.9% (37.3 mM hydroxytyrosol) starting from a tyrosol concentration of 43 mM. Under these conditions, the specific productivity relative to the biocatalyst was 4.78 μM/min/g. The established model to predict bioconversion yield was validated in two bench-scale fermenters. At the downstream stage, the reaction product was recovered as a hydroxytyrosol rich solution after microfiltration and concentration under vacuum. Subsequent to this operation, hydroxytyrosol composition yielded 73.8% of the total dry matter.
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9
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Lock M, Nichol T, Murrell JC, Smith TJ. Mutagenesis and expression of methane monooxygenase to alter regioselectivity with aromatic substrates. FEMS Microbiol Lett 2017; 364:3906680. [PMID: 28854685 PMCID: PMC5812538 DOI: 10.1093/femsle/fnx137] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/27/2017] [Indexed: 11/13/2022] Open
Abstract
Soluble methane monooxygenase (sMMO) from methane-oxidising bacteria can oxygenate more than 100 hydrocarbons and is one of the most catalytically versatile biological oxidation catalysts. Expression of recombinant sMMO has to date not been achieved in Escherichia coli and so an alternative expression system must be used to manipulate it genetically. Here we report substantial improvements to the previously described system for mutagenesis of sMMO and expression of recombinant enzymes in a methanotroph (Methylosinus trichosporium OB3b) expression system. This system has been utilised to make a number of new mutants and to engineer sMMO to increase its catalytic precision with a specific substrate whilst increasing activity by up to 6-fold. These results are the first 'proof-of-principle' experiments illustrating the feasibility of developing sMMO-derived catalysts for diverse applications.
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Affiliation(s)
- Malcolm Lock
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield S1 1WB, UK
| | - Tim Nichol
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield S1 1WB, UK
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Thomas J. Smith
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield S1 1WB, UK
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10
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Towards Understanding the Catalytic Mechanism of Human Paraoxonase 1: Experimental and In Silico Mutagenesis Studies. Appl Biochem Biotechnol 2017; 182:1642-1662. [DOI: 10.1007/s12010-017-2424-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 01/23/2017] [Indexed: 12/23/2022]
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11
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Kurt C, Sönmez B, Vardar N, Yanık-Yıldırım KC, Vardar-Schara G. Cavity residue leucine 95 and channel residues glutamine 204, aspartic acid 211, and phenylalanine 269 of toluene o-xylene monooxygenase influence catalysis. Appl Microbiol Biotechnol 2016; 100:7599-609. [PMID: 27311562 DOI: 10.1007/s00253-016-7658-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
Abstract
Structural analysis of toluene-o-xylene monooxygenase (ToMO) hydroxylase revealed the presence of three hydrophobic cavities, a channel, and a pore leading from the protein surface to the active site. Here, saturation mutagenesis was used to investigate the catalytic roles of alpha-subunit (TouA) second cavity residue L95 and TouA channel residues Q204, D211, and F269. By testing the substrates toluene, phenol, nitrobenzene, and/or naphthalene, these positions were found to influence the catalytic activity of ToMO. Several regiospecific variants were identified from TouA positions Q204, F269, and L95. For example, TouA variant Q204H had the regiospecificity of nitrobenzene changed significantly from 30 to 61 % p-nitrophenol. Interestingly, a combination of mutations at Q204H and A106V altered the regiospecificity of nitrobenzene back to 27 % p-nitrophenol. TouA variants F269Y, F269P, Q204E, and L95D improved the meta-hydroxylating capability of nitrobenzene by producing 87, 85, 82, and 77 % m-nitrophenol, respectively. For naphthalene oxidation, TouA variants F269V, Q204A, Q204S/S222N, and F269T had the regiospecificity changed from 16 to 9, 10, 23, and 25 % 2-naphthol, respectively. Here, two additional TouA residues, S222 and A106, were also identified that may have important roles in catalysis. Most of the isolated variants from D211 remained active, whereas having a hydrophobic residue at this position appeared to diminish the catalytic activity toward naphthalene. The mutational effects on the ToMO regiospecificity described here suggest that it is possible to further fine tune and engineer the reactivity of multicomponent diiron monooxygenases toward different substrates at positions that are relatively distant from the active site.
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Affiliation(s)
- Cansu Kurt
- Department of Genetics and Biongineering, Fatih University, Buyukcekmece, 34500, Istanbul, Turkey
| | - Burcu Sönmez
- Department of Genetics and Biongineering, Fatih University, Buyukcekmece, 34500, Istanbul, Turkey
| | - Nurcan Vardar
- Department of Genetics and Biongineering, Fatih University, Buyukcekmece, 34500, Istanbul, Turkey
| | - K Cansu Yanık-Yıldırım
- Department of Genetics and Biongineering, Fatih University, Buyukcekmece, 34500, Istanbul, Turkey
| | - Gönül Vardar-Schara
- Department of Genetics and Biongineering, Fatih University, Buyukcekmece, 34500, Istanbul, Turkey.
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12
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Achmon Y, Fishman A. The antioxidant hydroxytyrosol: biotechnological production challenges and opportunities. Appl Microbiol Biotechnol 2014; 99:1119-30. [PMID: 25547836 DOI: 10.1007/s00253-014-6310-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/06/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
Abstract
Hydroxytyrosol (HT) is a highly potent antioxidant originating in nature as a second metabolite of plants, most abundantly in olives (Olea europaea). In the last decade, numerous research studies showed the health benefits of antioxidants in general and those of HT in particular. As olive oil is a prime constituent of the health-promoting Mediterranean diet, HT has obtained recognition for its attributes, supported by a recent health claim of the European Food Safety Authority. HT is already used as a food supplement and in cosmetic products, but it has the potential to be used as a food additive and drug, based on its anticarcinogenic, anti-inflammatory, antiapoptotic and neuroprotective activity. Nevertheless, there is a large gap between the potential of HT and its current availability in the market due to its high price tag. In this review, the challenges of producing HT using biotechnological methods are described with an emphasis on the substrate source, the biocatalyst and the process parameters, in order to narrow the gap towards an efficient bio-based industrial process.
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Affiliation(s)
- Yigal Achmon
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
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Saturation mutagenesis of Bradyrhizobium sp. BTAi1 toluene 4-monooxygenase at alpha-subunit residues proline 101, proline 103, and histidine 214 for regiospecific oxidation of aromatics. Appl Microbiol Biotechnol 2014; 98:8975-86. [DOI: 10.1007/s00253-014-5913-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 06/20/2014] [Accepted: 06/24/2014] [Indexed: 10/25/2022]
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14
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Hosseini A, Brouk M, Lucas MF, Glaser F, Fishman A, Guallar V. Atomic picture of ligand migration in toluene 4-monooxygenase. J Phys Chem B 2014; 119:671-8. [PMID: 24798294 DOI: 10.1021/jp502509a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Computational modeling combined with mutational and activity assays was used to underline the substrate migration pathways in toluene 4-monooxygenase, a member of the important family of bacterial multicomponent monooxygenases (BMMs). In all structurally defined BMM hydroxylases, several hydrophobic cavities in the α-subunit map a preserved path from the protein surface to the diiron active site. Our results confirm the presence of two pathways by which different aromatic molecules can enter/escape the active site. While the substrate is observed to enter from both channels, the more hydrophilic product is withdrawn mainly from the shorter channel ending at residues D285 and E214. The long channel ends in the vicinity of S395, whose variants have been seen to affect activity and specificity. These mutational effects are clearly reproduced and rationalized by the in silico studies. Furthermore, the combined computational and experimental results highlight the importance of residue F269, which is located at the intersection of the two channels.
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Affiliation(s)
- Ali Hosseini
- Department of Life Sciences, Barcelona Supercomputing Center , Nexus II Building, 08034 Barcelona, Spain
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15
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Directed evolution of nitrobenzene dioxygenase for the synthesis of the antioxidant hydroxytyrosol. Appl Microbiol Biotechnol 2014; 98:4975-85. [DOI: 10.1007/s00253-013-5505-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/20/2013] [Accepted: 12/26/2013] [Indexed: 01/07/2023]
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16
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Probabilistic methods in directed evolution: library size, mutation rate, and diversity. Methods Mol Biol 2014; 1179:261-78. [PMID: 25055784 DOI: 10.1007/978-1-4939-1053-3_18] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Directed evolution has emerged as an important tool for engineering proteins with improved or novel properties. Because of their inherent reliance on randomness, directed evolution protocols are amenable to probabilistic modeling and analysis. This chapter summarizes and reviews in a nonmathematical way some of the probabilistic works related to directed evolution, with particular focus on three of the most widely used methods: saturation mutagenesis, error-prone PCR, and in vitro recombination. The ultimate aim is to provide the reader with practical information to guide the planning and design of directed evolution studies. Importantly, the applications and locations of freely available computational resources to assist with this process are described in detail.
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Nov Y. Fitness loss and library size determination in saturation mutagenesis. PLoS One 2013; 8:e68069. [PMID: 23844158 PMCID: PMC3700877 DOI: 10.1371/journal.pone.0068069] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/24/2013] [Indexed: 01/31/2023] Open
Abstract
Saturation mutagenesis is a widely used directed evolution technique, in which a large number of protein variants, each having random amino acids in certain predetermined positions, are screened in order to discover high-fitness variants among them. Several metrics for determining the library size (the number of variants screened) have been suggested in the literature, but none of them incorporates the actual fitness of the variants discovered in the experiment. We present the results of an extensive simulation study, which is based on probabilistic models for protein fitness landscape, and which investigates how the result of a saturation mutagenesis experiment – the fitness of the best variant discovered – varies as a function of the library size. In particular, we study the loss of fitness in the experiment: the difference between the fitness of the best variant discovered, and the fitness of the best variant in variant space. Our results are that the existing criteria for determining the library size are conservative, so smaller libraries are often satisfactory. Reducing the library size can save labor, time, and expenses in the laboratory.
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Affiliation(s)
- Yuval Nov
- Department of Statistics, University of Haifa, Haifa, Israel.
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18
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19
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Brouk M, Fishman A. Improving process conditions of hydroxytyrosol synthesis by toluene-4-monooxygenase. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2012.05.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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20
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Dror A, Fishman A. Engineering non-heme mono- and dioxygenases for biocatalysis. Comput Struct Biotechnol J 2012; 2:e201209011. [PMID: 24688652 PMCID: PMC3962191 DOI: 10.5936/csbj.201209011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Revised: 10/02/2012] [Accepted: 10/12/2012] [Indexed: 11/25/2022] Open
Abstract
Oxygenases are ubiquitous enzymes that catalyze the introduction of one or two oxygen atoms to unreactive chemical compounds. They require reduction equivalents from NADH or NADPH and comprise metal ions, metal ion complexes, or coenzymes in their active site. Thus, for industrial purposes, oxygenases are most commonly employed using whole cell catalysis, to alleviate the need for co-factor regeneration. Biotechnological applications include bioremediation, chiral synthesis, biosensors, fine chemicals, biofuels, pharmaceuticals, food ingredients and polymers. Controlling activity and selectivity of oxygenases is therefore of great importance and of growing interest to the scientific community. This review focuses on protein engineering of non-heme monooxygenases and dioxygenases for generating improved or novel functionalities. Rational mutagenesis based on x-ray structures and sequence alignment, as well as random methods such as directed evolution, have been utilized. It is concluded that knowledge-based protein engineering accompanied with targeted libraries, is most efficient for the design and tuning of biocatalysts towards novel substrates and enhanced catalytic activity while minimizing the screening efforts.
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Affiliation(s)
- Adi Dror
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Ayelet Fishman
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
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Goldsmith M, Tawfik DS. Directed enzyme evolution: beyond the low-hanging fruit. Curr Opin Struct Biol 2012; 22:406-12. [DOI: 10.1016/j.sbi.2012.03.010] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 03/14/2012] [Accepted: 03/14/2012] [Indexed: 12/26/2022]
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Dennig A, Shivange AV, Marienhagen J, Schwaneberg U. OmniChange: the sequence independent method for simultaneous site-saturation of five codons. PLoS One 2011; 6:e26222. [PMID: 22039444 PMCID: PMC3198389 DOI: 10.1371/journal.pone.0026222] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 09/22/2011] [Indexed: 12/20/2022] Open
Abstract
Focused mutant library generation methods have been developed to improve mainly "localizable" enzyme properties such as activity and selectivity. Current multi-site saturation methods are restricted by the gene sequence, require subsequent PCR steps and/or additional enzymatic modifications. Here we report, a multiple site saturation mutagenesis method, OmniChange, which simultaneously and efficiently saturates five independent codons. As proof of principle, five chemically cleaved DNA fragments, each carrying one NNK-degenerated codon, were generated and assembled to full gene length in a one-pot-reaction without additional PCR-amplification or use of restriction enzymes or ligases. Sequencing revealed the presence of up to 27 different codons at individual positions, corresponding to 84.4% of the theoretical diversity offered by NNK-degeneration. OmniChange is absolutely sequence independent, does not require a minimal distance between mutated codons and can be accomplished within a day.
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Affiliation(s)
- Alexander Dennig
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | - Amol V. Shivange
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | - Jan Marienhagen
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
- * E-mail:
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Behrens GA, Hummel A, Padhi SK, Schätzle S, Bornscheuer UT. Discovery and Protein Engineering of Biocatalysts for Organic Synthesis. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100446] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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24
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Notomista E, Scognamiglio R, Troncone L, Donadio G, Pezzella A, Di Donato A, Izzo V. Tuning the specificity of the recombinant multicomponent toluene o-xylene monooxygenase from Pseudomonas sp. strain OX1 for the biosynthesis of tyrosol from 2-phenylethanol. Appl Environ Microbiol 2011; 77:5428-37. [PMID: 21666013 PMCID: PMC3147462 DOI: 10.1128/aem.00461-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 06/01/2011] [Indexed: 12/27/2022] Open
Abstract
Biocatalysis is today a standard technology for the industrial production of several chemicals, and the number of biotransformation processes running on a commercial scale is constantly increasing. Among biocatalysts, bacterial multicomponent monooxygenases (BMMs), a diverse group of nonheme diiron enzymes that activate dioxygen, are of primary interest due to their ability to catalyze a variety of complex oxidations, including reactions of mono- and dihydroxylation of phenolic compounds. In recent years, both directed evolution and rational design have been successfully used to identify the molecular determinants responsible for BMM regioselectivity and to improve their activity toward natural and nonnatural substrates. Toluene o-xylene monooxygenase (ToMO) is a BMM isolated from Pseudomonas sp. strain OX1 which hydroxylates a wide spectrum of aromatic compounds. In this work we investigate the use of recombinant ToMO for the biosynthesis in recombinant cells of Escherichia coli strain JM109 of 4-hydroxyphenylethanol (tyrosol), an antioxidant present in olive oil, from 2-phenylethanol, a cheap and commercially available substrate. We initially found that wild-type ToMO is unable to convert 2-phenylethanol to tyrosol. This was explained by using a computational model which analyzed the interactions between ToMO active-site residues and the substrate. We found that residue F176 is the major steric hindrance for the correct positioning of the reaction intermediate leading to tyrosol production into the active site of the enzyme. Several mutants were designed and prepared, and we found that the combination of different mutations at position F176 with mutation E103G allows ToMO to convert up to 50% of 2-phenylethanol into tyrosol in 2 h.
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Affiliation(s)
- Eugenio Notomista
- Dipartimento di Biologia Strutturale e Funzionale, Università di Napoli Federico II, Via Cinthia, I-80126 Naples, and CEINGE-Biotecnologie Avanzate s.c.ar.l., Naples, Italy
| | - Roberta Scognamiglio
- Dipartimento di Biologia Strutturale e Funzionale, Università di Napoli Federico II, Via Cinthia, I-80126 Naples, and CEINGE-Biotecnologie Avanzate s.c.ar.l., Naples, Italy
| | - Luca Troncone
- Dipartimento di Biologia Strutturale e Funzionale, Università di Napoli Federico II, Via Cinthia, I-80126 Naples, and CEINGE-Biotecnologie Avanzate s.c.ar.l., Naples, Italy
| | - Giuliana Donadio
- Dipartimento di Biologia Strutturale e Funzionale, Università di Napoli Federico II, Via Cinthia, I-80126 Naples, and CEINGE-Biotecnologie Avanzate s.c.ar.l., Naples, Italy
| | - Alessandro Pezzella
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, Via Cinthia, 80126 Naples, Italy
| | - Alberto Di Donato
- Dipartimento di Biologia Strutturale e Funzionale, Università di Napoli Federico II, Via Cinthia, I-80126 Naples, and CEINGE-Biotecnologie Avanzate s.c.ar.l., Naples, Italy
| | - Viviana Izzo
- Dipartimento di Biologia Strutturale e Funzionale, Università di Napoli Federico II, Via Cinthia, I-80126 Naples, and CEINGE-Biotecnologie Avanzate s.c.ar.l., Naples, Italy
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