1
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Genetic fusion of P450 BM3 and formate dehydrogenase towards self-sufficient biocatalysts with enhanced activity. Sci Rep 2021; 11:21706. [PMID: 34737365 PMCID: PMC8568981 DOI: 10.1038/s41598-021-00957-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/08/2021] [Indexed: 11/09/2022] Open
Abstract
Fusion of multiple enzymes to multifunctional constructs has been recognized as a viable strategy to improve enzymatic properties at various levels such as stability, activity and handling. In this study, the genes coding for cytochrome P450 BM3 from B. megaterium and formate dehydrogenase from Pseudomonas sp. were fused to enable both substrate oxidation catalyzed by P450 BM3 and continuous cofactor regeneration by formate dehydrogenase within one construct. The order of the genes in the fusion as well as the linkers that bridge the enzymes were varied. The resulting constructs were compared to individual enzymes regarding substrate conversion, stability and kinetic parameters to examine whether fusion led to any substantial improvements of enzymatic properties. Most noticeably, an activity increase of up to threefold was observed for the fusion constructs with various substrates which were partly attributed to the increased diflavin reductase activity of the P450 BM3. We suggest that P450 BM3 undergoes conformational changes upon fusion which resulted in altered properties, however, no NADPH channeling was detected for the fusion constructs.
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2
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Valikhani D, Bolivar JM, Pelletier JN. An Overview of Cytochrome P450 Immobilization Strategies for Drug Metabolism Studies, Biosensing, and Biocatalytic Applications: Challenges and Opportunities. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02017] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Donya Valikhani
- Department of Chemistry, Université de Montréal and Center for Green Chemistry and Catalysis (CGCC), 1375 Thérèse-Lavoie-Roux Ave., Montréal, Quebec H2 V 0B3, Canada
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec City Quebec G1 V 0A6, Canada
| | - Juan M. Bolivar
- Chemical and Materials Engineering Department, Faculty of Chemical Sciences, Complutense University of Madrid, Complutense Ave., 28040 Madrid, Spain
| | - Joelle N. Pelletier
- Department of Chemistry, Université de Montréal and Center for Green Chemistry and Catalysis (CGCC), 1375 Thérèse-Lavoie-Roux Ave., Montréal, Quebec H2 V 0B3, Canada
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec City Quebec G1 V 0A6, Canada
- Department of Biochemistry, Université de Montréal, 2900 Édouard-Montpetit ave, Montréal, Quebec H3T 1J4, Canada
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3
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Behrendorff JBYH. Reductive Cytochrome P450 Reactions and Their Potential Role in Bioremediation. Front Microbiol 2021; 12:649273. [PMID: 33936006 PMCID: PMC8081977 DOI: 10.3389/fmicb.2021.649273] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Cytochrome P450 enzymes, or P450s, are haem monooxygenases renowned for their ability to insert one atom from molecular oxygen into an exceptionally broad range of substrates while reducing the other atom to water. However, some substrates including many organohalide and nitro compounds present little or no opportunity for oxidation. Under hypoxic conditions P450s can perform reductive reactions, contributing electrons to drive reductive elimination reactions. P450s can catalyse dehalogenation and denitration of a range of environmentally persistent pollutants including halogenated hydrocarbons and nitroamine explosives. P450-mediated reductive dehalogenations were first discovered in the context of human pharmacology but have since been observed in a variety of organisms. Additionally, P450-mediated reductive denitration of synthetic explosives has been discovered in bacteria that inhabit contaminated soils. This review will examine the distribution of P450-mediated reductive dehalogenations and denitrations in nature and discuss synthetic biology approaches to developing P450-based reagents for bioremediation.
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Affiliation(s)
- James B. Y. H. Behrendorff
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, Canberra, ACT, Australia
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4
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Abstract
Significant advances in enzyme discovery, protein and reaction engineering have transformed biocatalysis into a viable technology for the industrial scale manufacturing of chemicals. Multi-enzyme catalysis has emerged as a new frontier for the synthesis of complex chemicals. However, the in vitro operation of multiple enzymes simultaneously in one vessel poses challenges that require new strategies for increasing the operational performance of enzymatic cascade reactions. Chief among those strategies is enzyme co-immobilization. This review will explore how advances in synthetic biology and protein engineering have led to bioinspired co-localization strategies for the scaffolding and compartmentalization of enzymes. Emphasis will be placed on genetically encoded co-localization mechanisms as platforms for future autonomously self-organizing biocatalytic systems. Such genetically programmable systems could be produced by cell factories or emerging cell-free systems. Challenges and opportunities towards self-assembling, multifunctional biocatalytic materials will be discussed.
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5
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Haslinger K, Prather KLJ. Heterologous caffeic acid biosynthesis in Escherichia coli is affected by choice of tyrosine ammonia lyase and redox partners for bacterial Cytochrome P450. Microb Cell Fact 2020; 19:26. [PMID: 32046741 PMCID: PMC7011507 DOI: 10.1186/s12934-020-01300-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 02/05/2020] [Indexed: 01/03/2023] Open
Abstract
Background Caffeic acid is industrially recognized for its antioxidant activity and therefore its potential to be used as an anti-inflammatory, anticancer, antiviral, antidiabetic and antidepressive agent. It is traditionally isolated from lignified plant material under energy-intensive and harsh chemical extraction conditions. However, over the last decade bottom-up biosynthesis approaches in microbial cell factories have been established, that have the potential to allow for a more tailored and sustainable production. One of these approaches has been implemented in Escherichia coli and only requires a two-step conversion of supplemented l-tyrosine by the actions of a tyrosine ammonia lyase and a bacterial Cytochrome P450 monooxygenase. Although the feeding of intermediates demonstrated the great potential of this combination of heterologous enzymes compared to others, no de novo synthesis of caffeic acid from glucose has been achieved utilizing the bacterial Cytochrome P450 thus far. Results The herein described work aimed at improving the efficiency of this two-step conversion in order to establish de novo caffeic acid formation from glucose. We implemented alternative tyrosine ammonia lyases that were reported to display superior substrate binding affinity and selectivity, and increased the efficiency of the Cytochrome P450 by altering the electron-donating redox system. With this strategy we were able to achieve final titers of more than 300 µM or 47 mg/L caffeic acid over 96 h in an otherwise wild type E. coli MG1655(DE3) strain with glucose as the only carbon source. We observed that the choice and gene dose of the redox system strongly influenced the Cytochrome P450 catalysis. In addition, we were successful in applying a tethering strategy that rendered even a virtually unproductive Cytochrome P450/redox system combination productive. Conclusions The caffeic acid titer achieved in this study is about 10% higher than titers reported for other heterologous caffeic acid pathways in wildtype E. coli without l-tyrosine supplementation. The tethering strategy applied to the Cytochrome P450 appears to be particularly useful for non-natural Cytochrome P450/redox partner combinations and could be useful for other recombinant pathways utilizing bacterial Cytochromes P450.
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Affiliation(s)
- Kristina Haslinger
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, USA
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, USA.
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6
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Liu H, Cao M, Wang Y, Lv B, Li C. Bioengineering oligomerization and monomerization of enzymes: learning from natural evolution to matching the demands for industrial applications. Crit Rev Biotechnol 2020; 40:231-246. [PMID: 31914816 DOI: 10.1080/07388551.2019.1711014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
It is generally accepted that oligomeric enzymes evolve from their monomeric ancestors, and the evolution process generates superior structural benefits for functional advantages. Furthermore, adjusting the transition between different oligomeric states is an important mechanism for natural enzymes to regulate their catalytic functions for adapting environmental fluctuations in nature, which inspires researchers to mimic such a strategy to develop artificially oligomerized enzymes through protein engineering for improved performance under specific conditions. On the other hand, transforming oligomeric enzymes into their monomers is needed in fundamental research for deciphering catalytic mechanisms as well as exploring their catalytic capacities for better industrial applications. In this article, strategies for developing artificially oligomerized and monomerized enzymes are reviewed and highlighted by their applications. Furthermore, advances in the computational prediction of oligomeric structures are introduced, which would accelerate the systematic design of oligomeric and monomeric enzymes. Finally, the current challenges and future directions in this field are discussed.
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Affiliation(s)
- Hu Liu
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Mingming Cao
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Ying Wang
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Bo Lv
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
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7
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Schmid-Dannert C, López-Gallego F. Advances and opportunities for the design of self-sufficient and spatially organized cell-free biocatalytic systems. Curr Opin Chem Biol 2019; 49:97-104. [DOI: 10.1016/j.cbpa.2018.11.021] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/16/2018] [Accepted: 11/27/2018] [Indexed: 11/29/2022]
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8
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Li T, Li J, Pang Q, Ma L, Tong W, Gao C. Construction of Microreactors for Cascade Reaction and Their Potential Applications as Antibacterial Agents. ACS APPLIED MATERIALS & INTERFACES 2019; 11:6789-6795. [PMID: 30702277 DOI: 10.1021/acsami.8b20069] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Enzymatic cascade reactions in confined microenvironments play important roles in cellular chemical transformation. They also have important biotechnological and therapeutic applications. Here, enzymatic cascade microreactors (MRs) coupling glucose oxidase (GOx) and hemoglobin (Hb) (GOx-Hb MRs) were successfully fabricated by co-precipitation of GOx and Hb into a MnCO3 template, followed by the assembly of a multilayer film on a template surface, slight cross-linking, and final removal of MnCO3. In the presence of glucose with blood-relevant concentration, the GOx-Hb MRs exhibited a higher cascade reaction activity under mild acidic conditions than that under neutral conditions at physiological temperature. The GOx-Hb MRs effectively consumed glucose to generate HO· at pH = 5, which significantly inhibited bacterial growth and biofilm formation. This kind of enzymatic cascade microreactors might be useful for applications in biomedical fields.
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Affiliation(s)
- Tong Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Jiawei Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Qian Pang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Lie Ma
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Weijun Tong
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Changyou Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
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9
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Jäger VD, Lamm R, Kloß R, Kaganovitch E, Grünberger A, Pohl M, Büchs J, Jaeger KE, Krauss U. A Synthetic Reaction Cascade Implemented by Colocalization of Two Proteins within Catalytically Active Inclusion Bodies. ACS Synth Biol 2018; 7:2282-2295. [PMID: 30053372 DOI: 10.1021/acssynbio.8b00274] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In nature, enzymatic reaction cascades, i.e., realized in metabolic networks, operate with unprecedented efficacy, with the reactions often being spatially and temporally orchestrated. The principle of "learning from nature" has in recent years inspired the setup of synthetic reaction cascades combining biocatalytic reaction steps to artificial cascades. Hereby, the spatial organization of multiple enzymes, e.g., by coimmobilization, remains a challenging task, as currently no generic principles are available that work for every enzyme. We here present a tunable, genetically programmed coimmobilization strategy that relies on the fusion of a coiled-coil domain as aggregation inducing-tag, resulting in the formation of catalytically active inclusion body coimmobilizates (Co-CatIBs). Coexpression and coimmobilization was proven using two fluorescent proteins, and the strategy was subsequently extended to two enzymes, which enabled the realization of an integrated enzymatic two-step cascade for the production of (1 R,2 R)-1-phenylpropane-1,2-diol (PPD), a precursor of the calicum channel blocker diltiazem. In particular, the easy production and preparation of Co-CatIBs, readily yielding a biologically produced enzyme immobilizate renders the here presented strategy an interesting alternative to existing cascade immobilization techniques.
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Affiliation(s)
- Vera D. Jäger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Robin Lamm
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, D-52074 Aachen, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Ramona Kloß
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Eugen Kaganovitch
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Alexander Grünberger
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Multiscale Bioengineering group, Bielefeld University, D-33615 Bielefeld, Germany
| | - Martina Pohl
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Jochen Büchs
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, D-52074 Aachen, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
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10
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Haga T, Hirakawa H, Nagamune T. Artificial Self‐Sufficient Cytochrome P450 Containing Multiple Auxiliary Proteins Demonstrates Improved Monooxygenase Activity. Biotechnol J 2018; 13:e1800088. [DOI: 10.1002/biot.201800088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/18/2018] [Indexed: 02/04/2023]
Affiliation(s)
- Tomoaki Haga
- Department of Chemistry and BiotechnologySchool of EngineeringThe University of TokyoTokyo 113‐8656Japan
| | - Hidehiko Hirakawa
- Department of Chemistry and BiotechnologySchool of EngineeringThe University of TokyoTokyo 113‐8656Japan
| | - Teruyuki Nagamune
- Department of Chemistry and BiotechnologySchool of EngineeringThe University of TokyoTokyo 113‐8656Japan
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11
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Building a toolbox of protein scaffolds for future immobilization of biocatalysts. Appl Microbiol Biotechnol 2018; 102:8373-8388. [DOI: 10.1007/s00253-018-9252-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 10/28/2022]
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12
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Zhang G, Quin MB, Schmidt-Dannert C. Self-Assembling Protein Scaffold System for Easy in Vitro Coimmobilization of Biocatalytic Cascade Enzymes. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00986] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Guoqiang Zhang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Maureen B. Quin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
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13
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14
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Iwata F, Hirakawa H, Nagamune T. A Stable Artificial Multienzymatic Complex Using a Heterotrimeric Protein From Metallosphaera sedula. Biotechnol J 2018; 13:e1700662. [PMID: 29663675 DOI: 10.1002/biot.201700662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/24/2018] [Indexed: 01/02/2023]
Abstract
Bacterial cytochrome P450 monooxygenases (P450s) are promising biocatalysts for chemical syntheses because they catalyze a variety of oxidations on non-activated hydrocarbons using O2 . However, the requirement of two auxiliary proteins, an electron transfer protein and a reductase, for the catalysis is a major bottleneck for in vitro applications of these monooxygenases. The authors previous study showed that artificial assembly of a bacterial P450 with its auxiliary proteins using a heterotrimeric proliferating cell nuclear antigen (PCNA) from Sulfolobus solfataricus yields a self-sufficient P450, but partial dissociation of P450 from the complex at catalytic concentrations reduces the apparent specific activity of this self-sufficient P450. In this study, a Metallosphaera sedula PCNA is used, which is currently the most stable heterotrimeric PCNA, to assemble a bacterial P450 with its auxiliary proteins at submicromolar protein concentrations. The apparent specific monooxygenase activity of the M. sedula PCNA-assembled P450 with auxiliary proteins is saturated at protein concentrations of 40 nM, and is 2.1-fold higher than that of the S. solfataricus PCNA-assembled P450. Therefore, M. sedula PCNA represents a versatile tool to facilitate multiple enzymatic reactions, including the P450 monooxygenase system.
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Affiliation(s)
- Fumiya Iwata
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Hidehiko Hirakawa
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Teruyuki Nagamune
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
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15
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Wang L, Ji D, Liu Y, Wang Q, Wang X, Zhou YJ, Zhang Y, Liu W, Zhao ZK. Synthetic Cofactor-Linked Metabolic Circuits for Selective Energy Transfer. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03579] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Lei Wang
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Dalian
National Laboratory for Clean Energy, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, Dalian 116023, China
- Institute
of Green Conversion of Biological Bioresource and Metabolic Engineering,
College of Chemical Engineering, Northeast Electric Power University, Jilin 132012, China
| | - Debin Ji
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yuxue Liu
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Qian Wang
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Dalian
National Laboratory for Clean Energy, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xueying Wang
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yongjin J. Zhou
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yixin Zhang
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Wujun Liu
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Dalian
National Laboratory for Clean Energy, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zongbao K. Zhao
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Dalian
National Laboratory for Clean Energy, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key
Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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16
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Quin MB, Wallin KK, Zhang G, Schmidt-Dannert C. Spatial organization of multi-enzyme biocatalytic cascades. Org Biomol Chem 2017; 15:4260-4271. [DOI: 10.1039/c7ob00391a] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multi-enzyme cascades provide a wealth of valuable chemicals. Efficiency of reaction schemes can be improved by spatial organization of biocatalysts. This review will highlight various methods of spatial organization of biocatalysts: fusion, immobilization, scaffolding and encapsulation.
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Affiliation(s)
- M. B. Quin
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - K. K. Wallin
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - G. Zhang
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - C. Schmidt-Dannert
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
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17
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Behrendorff JBYH, Gillam EMJ. Prospects for Applying Synthetic Biology to Toxicology: Future Opportunities and Current Limitations for the Repurposing of Cytochrome P450 Systems. Chem Res Toxicol 2016; 30:453-468. [DOI: 10.1021/acs.chemrestox.6b00396] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Elizabeth M. J. Gillam
- School
of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia
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18
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P450 BM3 fused to phosphite dehydrogenase allows phosphite-driven selective oxidations. Appl Microbiol Biotechnol 2016; 101:2319-2331. [PMID: 27900443 PMCID: PMC5320008 DOI: 10.1007/s00253-016-7993-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/30/2016] [Accepted: 11/05/2016] [Indexed: 11/24/2022]
Abstract
To facilitate the wider application of the NADPH-dependent P450BM3, we fused the monooxygenase with a phosphite dehydrogenase (PTDH). The resulting monooxygenase-dehydrogenase fusion enzyme acts as a self-sufficient bifunctional catalyst, accepting phosphite as a cheap electron donor for the regeneration of NADPH. The well-expressed fusion enzyme was purified and analyzed in comparison to the parent enzymes. Using lauric acid as substrate for P450BM3, it was found that the fusion enzyme had similar substrate affinity and hydroxylation selectivity while it displayed a significantly higher activity than the non-fused monooxygenase. Phosphite-driven conversions of lauric acid at restricted NADPH concentrations confirmed multiple turnovers of the cofactor. Interestingly, both the fusion enzyme and the native P450BM3 displayed enzyme concentration dependent activity and the fused enzyme reached optimal activity at a lower enzyme concentration. This suggests that the fusion enzyme has an improved tendency to form functional oligomers. To explore the constructed phosphite-driven P450BM3 as a biocatalyst, conversions of the drug compounds omeprazole and rosiglitazone were performed. PTDH-P450BM3 driven by phosphite was found to be more efficient in terms of total turnover when compared with P450BM3 driven by NADPH. The results suggest that PTDH-P450BM3 is an attractive system for use in biocatalytic and drug metabolism studies.
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19
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Tan CY, Hirakawa H, Suzuki R, Haga T, Iwata F, Nagamune T. Immobilization of a Bacterial Cytochrome P450 Monooxygenase System on a Solid Support. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Cheau Yuaan Tan
- Department of Bioengineering; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Hidehiko Hirakawa
- Department of Chemistry and Biotechnology; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Risa Suzuki
- Department of Bioengineering; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Department of Biotechnology; Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya, Aichi 464-8603 Japan
| | - Tomoaki Haga
- Department of Chemistry and Biotechnology; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Fumiya Iwata
- Department of Chemistry and Biotechnology; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Teruyuki Nagamune
- Department of Bioengineering; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Department of Chemistry and Biotechnology; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
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20
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Tan CY, Hirakawa H, Suzuki R, Haga T, Iwata F, Nagamune T. Immobilization of a Bacterial Cytochrome P450 Monooxygenase System on a Solid Support. Angew Chem Int Ed Engl 2016; 55:15002-15006. [PMID: 27781345 DOI: 10.1002/anie.201608033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/16/2016] [Indexed: 01/12/2023]
Abstract
Bacterial cytochrome P450s (P450s), which catalyze regio- and stereoselective oxidations of hydrocarbons with high turnover rates, are attractive biocatalysts for fine chemical production. Enzyme immobilization is needed for cost-effective industrial manufacturing. However, immobilization of P450s is difficult because electron-transfer proteins are involved in catalysis and anchoring these can prevent them from functioning as shuttle molecules for carrying electrons. We studied a heterotrimeric protein-mediated co-immobilization of a bacterial P450, and its electron-transfer protein and reductase. Fusion with subunits of a heterotrimeric Sulfolobus solfataricus proliferating cell nuclear antigen (PCNA) enabled immobilization of the three proteins on a solid support. The co-immobilized enzymes catalyzed monooxygenation because the electron-transfer protein fused to PCNA via a single peptide linker retained its electron-transport function.
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Affiliation(s)
- Cheau Yuaan Tan
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Hidehiko Hirakawa
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Risa Suzuki
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
| | - Tomoaki Haga
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Fumiya Iwata
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Teruyuki Nagamune
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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21
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Luo Q, Hou C, Bai Y, Wang R, Liu J. Protein Assembly: Versatile Approaches to Construct Highly Ordered Nanostructures. Chem Rev 2016; 116:13571-13632. [PMID: 27587089 DOI: 10.1021/acs.chemrev.6b00228] [Citation(s) in RCA: 392] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Nature endows life with a wide variety of sophisticated, synergistic, and highly functional protein assemblies. Following Nature's inspiration to assemble protein building blocks into exquisite nanostructures is emerging as a fascinating research field. Dictating protein assembly to obtain highly ordered nanostructures and sophisticated functions not only provides a powerful tool to understand the natural protein assembly process but also offers access to advanced biomaterials. Over the past couple of decades, the field of protein assembly has undergone unexpected and rapid developments, and various innovative strategies have been proposed. This Review outlines recent advances in the field of protein assembly and summarizes several strategies, including biotechnological strategies, chemical strategies, and combinations of these approaches, for manipulating proteins to self-assemble into desired nanostructures. The emergent applications of protein assemblies as versatile platforms to design a wide variety of attractive functional materials with improved performances have also been discussed. The goal of this Review is to highlight the importance of this highly interdisciplinary field and to promote its growth in a diverse variety of research fields ranging from nanoscience and material science to synthetic biology.
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Affiliation(s)
- Quan Luo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Chunxi Hou
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Yushi Bai
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Taipa, Macau SAR 999078, China
| | - Junqiu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
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22
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Visser F, Müller B, Rose J, Prüfer D, Noll GA. Forizymes - functionalised artificial forisomes as a platform for the production and immobilisation of single enzymes and multi-enzyme complexes. Sci Rep 2016; 6:30839. [PMID: 27502156 PMCID: PMC4977538 DOI: 10.1038/srep30839] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/11/2016] [Indexed: 01/27/2023] Open
Abstract
The immobilisation of enzymes plays an important role in many applications, including biosensors that require enzyme activity, stability and recyclability in order to function efficiently. Here we show that forisomes (plant-derived mechanoproteins) can be functionalised with enzymes by translational fusion, leading to the assembly of structures designated as forizymes. When forizymes are expressed in the yeast Saccharomyces cerevisiae, the enzymes are immobilised by the self-assembly of forisome subunits to form well-structured protein bodies. We used glucose-6-phosphate dehydrogenase (G6PDH) and hexokinase 2 (HXK2) as model enzymes for the one-step production and purification of catalytically active forizymes. These structures retain the typical stimulus-response reaction of the forisome and the enzyme remains active even after multiple assay cycles, which we demonstrated using G6PDH forizymes as an example. We also achieved the co-incorporation of both HXK2 and G6PDH in a single forizyme, facilitating a two-step reaction cascade that was 30% faster than the coupled reaction using the corresponding enzymes on different forizymes or in solution. Our novel forizyme immobilisation technique therefore not only combines the sensory properties of forisome proteins with the catalytic properties of enzymes but also allows the development of multi-enzyme complexes for incorporation into technical devices.
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Affiliation(s)
- Franziska Visser
- University of Münster, Institute of Plant Biology and Biotechnology, Münster, 48143, Germany
| | - Boje Müller
- University of Münster, Institute of Plant Biology and Biotechnology, Münster, 48143, Germany
| | - Judith Rose
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Münster, 48143, Germany
| | - Dirk Prüfer
- University of Münster, Institute of Plant Biology and Biotechnology, Münster, 48143, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Münster, 48143, Germany
| | - Gundula A Noll
- University of Münster, Institute of Plant Biology and Biotechnology, Münster, 48143, Germany
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23
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Schmidt-Dannert C, Lopez-Gallego F. A roadmap for biocatalysis - functional and spatial orchestration of enzyme cascades. Microb Biotechnol 2016; 9:601-9. [PMID: 27418373 PMCID: PMC4993178 DOI: 10.1111/1751-7915.12386] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 06/25/2016] [Indexed: 12/23/2022] Open
Abstract
Advances in biological engineering and systems biology have provided new approaches and tools for the industrialization of biology. In the next decade, advanced biocatalytic systems will increasingly be used for the production of chemicals that cannot be made by current processes and/or where the use of enzyme catalysts is more resource efficient with a much reduced environmental impact. We expect that in the future, manufacture of chemicals and materials will utilize both biocatalytic and chemical synthesis synergistically. The realization of such advanced biomanufacturing processes currently faces a number of major challenges. Ready‐to‐deploy portfolios of biocatalysts for design to production must be created from biological diverse sources and through protein engineering. Robust and efficient multi‐step enzymatic reaction cascades must be developed that can operate simultaneously in one‐pot. For this to happen, bio‐orthogonal strategies for spatial and temporal control of biocatalyst activities must be developed. Promising approaches and technologies are emerging that will eventually lead to the design of in vitro biocatalytic systems that mimic the metabolic pathways and networks of cellular systems which will be discussed in this roadmap.
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Affiliation(s)
- Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Fernando Lopez-Gallego
- Heterogeneous Biocatalysis Group, CIC BiomaGUNE, Pase Miramon 182, San Sebastian-Donostia, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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24
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Iwata F, Hirakawa H, Nagamune T. Three proliferating cell nuclear antigen homologues from Metallosphaera sedula form a head-to-tail heterotrimer. Sci Rep 2016; 6:26588. [PMID: 27228945 PMCID: PMC4894655 DOI: 10.1038/srep26588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/04/2016] [Indexed: 11/28/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a sliding clamp that plays a key role in
DNA metabolism. Genome sequence analysis has revealed that some crenarchaea possess
three PCNA genes in their genome, but it has been reported that three PCNAs
do not always form a unique heterotrimer composed of one of each molecule. The
thermoacidophilic archaeon, Metallosphaera sedula, has three PCNA
homologue genes. Here, we demonstrated that the three PCNA homologues, MsePCNA1,
MsePCNA2 and MsePCNA3, exclusively form a heterotrimer in a stepwise fashion;
MsePCNA1 and MsePCNA2 form a heterodimer, and then MsePCNA3 binds to the
heterodimer. We determined that the dissociation constants between MsePCNA1 and
MsePCNA2, and between MsePCNA3 and the MsePCNA1:MsePCNA2 heterodimer are 0.29 and
43 nM, respectively. Moreover, the MsePCNA1, MsePCNA2 and MsePCNA3
heterotrimer stimulated M. sedula DNA ligase 1 activity, suggesting that the
heterotrimer works as a DNA sliding clamp in the organism. The stable and stepwise
heterotrimerization of M. sedula PCNA homologues would be useful to generate
functional protein-based materials such as artificial multi-enzyme complexes,
functional hydrogels and protein fibres, which have recently been achieved by
protein self-assembly.
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Affiliation(s)
- Fumiya Iwata
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hidehiko Hirakawa
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Teruyuki Nagamune
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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25
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Mahanta S, Paul S. Stable Self-Assembly of Bovine α-Lactalbumin Exhibits Target-Specific Antiproliferative Activity in Multiple Cancer Cells. ACS APPLIED MATERIALS & INTERFACES 2015; 7:28177-28187. [PMID: 26440360 DOI: 10.1021/acsami.5b06076] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Self-assembly of a protein is a natural phenomenon; however, the process can be performed under a suitable condition in vitro. Since proteins are nontoxic, biodegradable, and biocompatible in nature, they are used in various industrial applications such as biocatalyst, therapeutic agent, and drug carriers. Moreover, their flexible structural state and specific activity are being used as sensors and immensely attract many new applications. However, the inherent potential of protein self-assembly for various applications is yet to be explored in detail. In this study, spherical self-assembly of bovine α-lactalbumin (nsBLA) was synthesized using an optimized ethanol-mediated desolvation process with an average diameter of approximately 300 nm. The self-assembly was found to be highly stable against thermal, pH, and proteases stress. When nsBLA was administered in various cancer cells, it demonstrated high cytotoxicity in three different cancer cells via reactive oxygen species (ROS) generation, whereas it exhibited negligible toxicity in normal human and murine cells. When nsBLA was conjugated with folic acid, it improved the cytotoxicity and perhaps mediated through enhanced cellular uptake in cancer cells through binding with folate receptors. Further, experimental results confirmed that the cancer cell death induced by nsBLA was not caused by apoptosis but a necrotic-like death mechanism. When compared with a well-known protein-based anticancer agent BAMLET (bovine α-lactalbumin made lethal against tumor cell), the self-assembled BLA clearly exhibited higher cytotoxicity to cancer cells than BAMLET. While BAMLET exhibits poor biocompatibility, our nsBLA demonstrated excellent biocompatibility to normal cells. Therefore, in this study, we prepared self-assembled α-lactalbumin that exhibits strong inherent antiproliferative potential in multiple cancer cells which can be used for efficient therapeutic approach in cancer.
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Affiliation(s)
- Sailendra Mahanta
- Structural Biology and Nanomedicine Laboratory, Department of Biotechnology and Medical Engineering, National Institute of Technology , Rourkela 769008, Odisha, India
| | - Subhankar Paul
- Structural Biology and Nanomedicine Laboratory, Department of Biotechnology and Medical Engineering, National Institute of Technology , Rourkela 769008, Odisha, India
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