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Jäger C, Croft AK. If It Is Hard, It Is Worth Doing: Engineering Radical Enzymes from Anaerobes. Biochemistry 2022; 62:241-252. [PMID: 36121716 PMCID: PMC9850924 DOI: 10.1021/acs.biochem.2c00376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
With a pressing need for sustainable chemistries, radical enzymes from anaerobes offer a shortcut for many chemical transformations and deliver highly sought-after functionalizations such as late-stage C-H functionalization, C-C bond formation, and carbon-skeleton rearrangements, among others. The challenges in handling these oxygen-sensitive enzymes are reflected in their limited industrial exploitation, despite what they may deliver. With an influx of structures and mechanistic understanding, the scope for designed radical enzymes to deliver wanted processes becomes ever closer. Combined with new advances in computational methods and workflows for these complex systems, the outlook for an increased use of radical enzymes in future processes is exciting.
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2
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Liang B, Sun G, Zhang X, Nie Q, Zhao Y, Yang J. Recent Advances, Challenges and Metabolic Engineering Strategies in the Biosynthesis of 3-Hydroxypropionic Acid. Biotechnol Bioeng 2022; 119:2639-2668. [PMID: 35781640 DOI: 10.1002/bit.28170] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/26/2022] [Accepted: 06/29/2022] [Indexed: 11/07/2022]
Abstract
As an attractive and valuable platform chemical, 3-hydroxypropionic acid (3-HP) can be used to produce a variety of industrially important commodity chemicals and biodegradable polymers. Moreover, the biosynthesis of 3-HP has drawn much attention in recent years due to its sustainability and environmental friendliness. Here, we focus on recent advances, challenges and metabolic engineering strategies in the biosynthesis of 3-HP. While glucose and glycerol are major carbon sources for its production of 3-HP via microbial fermentation, other carbon sources have also been explored. To increase yield and titer, synthetic biology and metabolic engineering strategies have been explored, including modifying pathway enzymes, eliminating flux blockages due to byproduct synthesis, eliminating toxic byproducts, and optimizing via genome-scale models. This review also provides insights on future directions for 3-HP biosynthesis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Bo Liang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Qingdao Agricultural University, Qingdao, China.,Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Guannan Sun
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Qingdao Agricultural University, Qingdao, China.,Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xinping Zhang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Qingdao Agricultural University, Qingdao, China.,Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Qingjuan Nie
- Foreign Languages School, Qingdao Agricultural University, Qingdao, China
| | - Yukun Zhao
- Pony Testing International Group, Qingdao, China
| | - Jianming Yang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Qingdao Agricultural University, Qingdao, China.,Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
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3
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Toraya T, Tobimatsu T, Shibata N, Mori K. Reactivating chaperones for coenzyme B 12-dependent diol and glycerol dehydratases and ethanolamine ammonia-lyase. Methods Enzymol 2022; 668:243-284. [PMID: 35589195 DOI: 10.1016/bs.mie.2021.11.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Adenosylcobalamin (AdoCbl) or coenzyme B12-dependent enzymes tend to undergo mechanism-based inactivation during catalysis or inactivation in the absence of substrate. Such inactivation may be inevitable because they use a highly reactive radical for catalysis, and side reactions of radical intermediates result in the damage of the coenzyme. How do living organisms address such inactivation when enzymes are inactivated by undesirable side reactions? We discovered reactivating factors for radical B12 eliminases. They function as releasing factors for damaged cofactor(s) from enzymes and thus mediate their exchange for intact AdoCbl. Since multiple turnovers and chaperone functions were demonstrated, they were renamed "reactivases" or "reactivating chaperones." They play an essential role in coenzyme recycling as part of the activity-maintaining systems for B12 enzymes. In this chapter, we describe our investigations on reactivating chaperones, including their discovery, gene cloning, preparation, characterization, activity assays, and mechanistic studies, that have been conducted using a wide range of biochemical and structural methods that we have developed.
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Affiliation(s)
- Tetsuo Toraya
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan.
| | - Takamasa Tobimatsu
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Naoki Shibata
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, Japan
| | - Koichi Mori
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
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4
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Toraya T, Tobimatsu T, Mori K, Yamanishi M, Shibata N. Coenzyme B 12-dependent eliminases: Diol and glycerol dehydratases and ethanolamine ammonia-lyase. Methods Enzymol 2022; 668:181-242. [PMID: 35589194 DOI: 10.1016/bs.mie.2021.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Adenosylcobalamin (AdoCbl) or coenzyme B12-dependent enzymes catalyze intramolecular group-transfer reactions and ribonucleotide reduction in a wide variety of organisms from bacteria to animals. They use a super-reactive primary-carbon radical formed by the homolysis of the coenzyme's Co-C bond for catalysis and thus belong to the larger class of "radical enzymes." For understanding the general mechanisms of radical enzymes, it is of great importance to establish the general mechanism of AdoCbl-dependent catalysis using enzymes that catalyze the simplest reactions-such as diol dehydratase, glycerol dehydratase and ethanolamine ammonia-lyase. These enzymes are often called "eliminases." We have studied AdoCbl and eliminases for more than a half century. Progress has always been driven by the development of new experimental methodologies. In this chapter, we describe our investigations on these enzymes, including their metabolic roles, gene cloning, preparation, characterization, activity assays, and mechanistic studies, that have been conducted using a wide range of biochemical and structural methodologies we have developed.
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Affiliation(s)
- Tetsuo Toraya
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan.
| | - Takamasa Tobimatsu
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Koichi Mori
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Mamoru Yamanishi
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Naoki Shibata
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, Japan
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5
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Bilić L, Barić D, Sandala GM, Smith DM, Kovačević B. Glycerol as a Substrate and Inactivator of Coenzyme B 12 -Dependent Diol Dehydratase. Chemistry 2021; 27:7930-7941. [PMID: 33792120 DOI: 10.1002/chem.202100416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Indexed: 11/09/2022]
Abstract
Diol dehydratase, dependent on coenzyme B12 (B12 -dDDH), displays a peculiar feature of being inactivated by its native substrate glycerol (GOL). Surprisingly, the isofunctional enzyme, B12 -independent glycerol dehydratase (B12 -iGDH), does not undergo suicide inactivation by GOL. Herein we present a series of QM/MM and MD calculations aimed at understanding the mechanisms of substrate-induced suicide inactivation in B12 -dDDH and that of resistance of B12 -iGDH to inactivation. We show that the first step in the enzymatic transformation of GOL, hydrogen abstraction, can occur from both ends of the substrate (either C1 or C3 of GOL). Whereas C1 abstraction in both enzymes leads to product formation, C3 abstraction in B12 -dDDH results in the formation of a low energy radical intermediate, which is effectively trapped within a deep well on the potential energy surface. The long lifetime of this radical intermediate likely enables its side reactions, leading to inactivation. In B12 -iGDH, by comparison, C3 abstraction is an endothermic step; consequently, the resultant radical intermediate is not of low energy, and the reverse process of reforming the reactant is possible.
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Affiliation(s)
- Luka Bilić
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.,PULS Group, Institute for Theoretical Physics FAU Erlangen-Nürnberg, Staudtstraße 7, Erlangen, Germany
| | - Danijela Barić
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Gregory M Sandala
- Department of Chemistry and Biochemistry, Mount Allison University, New Brunswick, E4L 1G8, Sackville, Canada
| | - David Mathew Smith
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Borislav Kovačević
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
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6
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Nasir A, Ashok S, Shim JY, Park S, Yoo TH. Recent Progress in the Understanding and Engineering of Coenzyme B 12-Dependent Glycerol Dehydratase. Front Bioeng Biotechnol 2020; 8:500867. [PMID: 33224925 PMCID: PMC7674605 DOI: 10.3389/fbioe.2020.500867] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 09/17/2020] [Indexed: 01/21/2023] Open
Abstract
Coenzyme B12-dependent glycerol dehydratase (GDHt) catalyzes the dehydration reaction of glycerol in the presence of adenosylcobalamin to yield 3-hydroxypropanal (3-HPA), which can be converted biologically to versatile platform chemicals such as 1,3-propanediol and 3-hydroxypropionic acid. Owing to the increased demand for biofuels, developing biological processes based on glycerol, which is a byproduct of biodiesel production, has attracted considerable attention recently. In this review, we will provide updates on the current understanding of the catalytic mechanism and structure of coenzyme B12-dependent GDHt, and then summarize the results of engineering attempts, with perspectives on future directions in its engineering.
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Affiliation(s)
- Abdul Nasir
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | | | - Jeung Yeop Shim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea.,Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
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7
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Stewart KL, Stewart AM, Bobik TA. Prokaryotic Organelles: Bacterial Microcompartments in E. coli and Salmonella. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0025-2019. [PMID: 33030141 PMCID: PMC7552817 DOI: 10.1128/ecosalplus.esp-0025-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Indexed: 02/07/2023]
Abstract
Bacterial microcompartments (MCPs) are proteinaceous organelles consisting of a metabolic pathway encapsulated within a selectively permeable protein shell. Hundreds of species of bacteria produce MCPs of at least nine different types, and MCP metabolism is associated with enteric pathogenesis, cancer, and heart disease. This review focuses chiefly on the four types of catabolic MCPs (metabolosomes) found in Escherichia coli and Salmonella: the propanediol utilization (pdu), ethanolamine utilization (eut), choline utilization (cut), and glycyl radical propanediol (grp) MCPs. Although the great majority of work done on catabolic MCPs has been carried out with Salmonella and E. coli, research outside the group is mentioned where necessary for a comprehensive understanding. Salient characteristics found across MCPs are discussed, including enzymatic reactions and shell composition, with particular attention paid to key differences between classes of MCPs. We also highlight relevant research on the dynamic processes of MCP assembly, protein targeting, and the mechanisms that underlie selective permeability. Lastly, we discuss emerging biotechnology applications based on MCP principles and point out challenges, unanswered questions, and future directions.
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Affiliation(s)
- Katie L. Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | - Andrew M. Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | - Thomas A. Bobik
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
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8
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Bilić L, Barić D, Banhatti RD, Smith DM, Kovačević B. Computational Study of Glycerol Binding within the Active Site of Coenzyme B12-Dependent Diol Dehydratase. J Phys Chem B 2019; 123:6178-6187. [DOI: 10.1021/acs.jpcb.9b04071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Luka Bilić
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Danijela Barić
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Radha Dilip Banhatti
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - David M. Smith
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Borislav Kovačević
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
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9
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Jers C, Kalantari A, Garg A, Mijakovic I. Production of 3-Hydroxypropanoic Acid From Glycerol by Metabolically Engineered Bacteria. Front Bioeng Biotechnol 2019; 7:124. [PMID: 31179279 PMCID: PMC6542942 DOI: 10.3389/fbioe.2019.00124] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 05/07/2019] [Indexed: 11/13/2022] Open
Abstract
3-hydroxypropanoic acid (3-HP) is a valuable platform chemical with a high demand in the global market. 3-HP can be produced from various renewable resources. It is used as a precursor in industrial production of a number of chemicals, such as acrylic acid and its many derivatives. In its polymerized form, 3-HP can be used in bioplastic production. Several microbes naturally possess the biosynthetic pathways for production of 3-HP, and a number of these pathways have been introduced in some widely used cell factories, such as Escherichia coli and Saccharomyces cerevisiae. Latest advances in the field of metabolic engineering and synthetic biology have led to more efficient methods for bio-production of 3-HP. These include new approaches for introducing heterologous pathways, precise control of gene expression, rational enzyme engineering, redirecting the carbon flux based on in silico predictions using genome scale metabolic models, as well as optimizing fermentation conditions. Despite the fact that the production of 3-HP has been extensively explored in established industrially relevant cell factories, the current production processes have not yet reached the levels required for industrial exploitation. In this review, we explore the state of the art in 3-HP bio-production, comparing the yields and titers achieved in different microbial cell factories and we discuss possible methodologies that could make the final step toward industrially relevant cell factories.
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Affiliation(s)
- Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Aida Kalantari
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
| | - Abhroop Garg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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10
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Kovačević B, Barić D, Babić D, Bilić L, Hanževački M, Sandala GM, Radom L, Smith DM. Computational Tale of Two Enzymes: Glycerol Dehydration With or Without B12. J Am Chem Soc 2018; 140:8487-8496. [DOI: 10.1021/jacs.8b03109] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Borislav Kovačević
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Danijela Barić
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Darko Babić
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Luka Bilić
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Marko Hanževački
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Gregory M. Sandala
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, New Brunswick E4L 1G8, Canada
| | - Leo Radom
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - David M. Smith
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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11
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Shibata N, Sueyoshi Y, Higuchi Y, Toraya T. Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12
Catalysis. Angew Chem Int Ed Engl 2018; 57:7830-7835. [DOI: 10.1002/anie.201803591] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Naoki Shibata
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
- The RIKEN SPring-8 Center; 1-1-1 Koto Sayo-cho, Sato-gun Hyogo 678-5248 Japan
| | - Yui Sueyoshi
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
| | - Yoshiki Higuchi
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
- The RIKEN SPring-8 Center; 1-1-1 Koto Sayo-cho, Sato-gun Hyogo 678-5248 Japan
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology; Graduate School of Natural Science and Technology; Okayama University; Tsushima-naka Okayama 700-8530 Japan
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12
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Shibata N, Sueyoshi Y, Higuchi Y, Toraya T. Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12
Catalysis. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803591] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Naoki Shibata
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
- The RIKEN SPring-8 Center; 1-1-1 Koto Sayo-cho, Sato-gun Hyogo 678-5248 Japan
| | - Yui Sueyoshi
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
| | - Yoshiki Higuchi
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
- The RIKEN SPring-8 Center; 1-1-1 Koto Sayo-cho, Sato-gun Hyogo 678-5248 Japan
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology; Graduate School of Natural Science and Technology; Okayama University; Tsushima-naka Okayama 700-8530 Japan
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13
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Seok JY, Yang J, Choi SJ, Lim HG, Choi UJ, Kim KJ, Park S, Yoo TH, Jung GY. Directed evolution of the 3-hydroxypropionic acid production pathway by engineering aldehyde dehydrogenase using a synthetic selection device. Metab Eng 2018; 47:113-120. [PMID: 29545147 DOI: 10.1016/j.ymben.2018.03.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 12/30/2022]
Abstract
3-Hydroxypropionic acid (3-HP) is an important platform chemical, and biological production of 3-HP from glycerol as a carbon source using glycerol dehydratase (GDHt) and aldehyde dehydrogenase (ALDH) has been revealed to be effective because it involves a relatively simple metabolic pathway and exhibits higher yield and productivity than other biosynthetic pathways. Despite the successful attempts of 3-HP production from glycerol, the biological process suffers from problems arising from low activity and inactivation of the two enzymes. To apply the directed evolutionary approach to engineer the 3-HP production system, we constructed a synthetic selection device using a 3-HP-responsive transcription factor and developed a selection approach for screening 3-HP-producing microorganisms. The method was applied to an ALDH library, specifically aldehyde-binding site library of alpha-ketoglutaric semialdehyde dehydrogenase (KGSADH). Only two serial cultures resulted in enrichment of strains showing increased 3-HP production, and an isolated KGSADH variant enzyme exhibited a 2.79-fold higher catalytic efficiency toward its aldehyde substrate than the wild-type one. This approach will provide the simple and efficient tool to engineer the pathway enzymes in metabolic engineering.
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Affiliation(s)
- Joo Yeon Seok
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jina Yang
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul 08826, Republic of Korea
| | - Sang Jin Choi
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-Ro, Yeongtong-Gu, Suwon 16499, Republic of Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Un Jong Choi
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-Ro, Yeongtong-Gu, Suwon 16499, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-Ro 80, Buk-Ku, Daegu 702-701, Republic of Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-Gil 50, Eonyang-Eup, Ulju-Gun, Ulsan 449419, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-Ro, Yeongtong-Gu, Suwon 16499, Republic of Korea.
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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14
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Dai L, Tao F, Tang H, Guo Y, Shen Y, Xu P. Directing enzyme devolution for biosynthesis of alkanols and 1,n-alkanediols from natural polyhydroxy compounds. Metab Eng 2017; 44:70-80. [DOI: 10.1016/j.ymben.2017.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 09/07/2017] [Accepted: 09/13/2017] [Indexed: 12/01/2022]
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15
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Chen L, Hatti-Kaul R. Exploring Lactobacillus reuteri DSM20016 as a biocatalyst for transformation of longer chain 1,2-diols: Limits with microcompartment. PLoS One 2017; 12:e0185734. [PMID: 28957423 PMCID: PMC5619818 DOI: 10.1371/journal.pone.0185734] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/18/2017] [Indexed: 11/18/2022] Open
Abstract
Lactobacillus reuteri metabolises glycerol efficiently to form 3-hydroxypropionic acid (3-HP) and 1,3-propanediol (1,3PDO) by the same mechanism as that for 1,2-propanediol (1,2PDO) conversion to propionic acid and propanol via its propanediol utilization (pdu) pathway. Pdu enzymes are encoded by the pdu-operon, which also contain genes encoding the shell proteins of the microcompartment housing the metabolic pathway. In this work the selectivity and kinetics of the reactions catalysed by L. reuteri DSM20016 Pdu enzymes glycerol dehydratase (GDH), 1,3-propanediol oxidoreductase (PduQ) and coenzyme-A acylating propionaldehyde dehydrogenase (PduP), produced recombinantly, was investigated against corresponding substrates of different chain lengths. Glycerol dehydratase exhibited activity against C2-C4 polyols, with the highest activity against glycerol and 1,2-propanediol (1,2-PDO). A double mutant of the pduC gene of GDH (PduC-S302A/Q337A) was constructed that displayed lowered activity against glycerol and 1,2PDO but extended the substrate range upto C6-diol. The best substrate for both PduQ and PduP was 3-hydroxypropanal (3HPA), although PduP exhibited nearly 10-fold higher specific activity. The enzymes also showed some activity against C3-C10 aliphatic aldehydes, with PduP having higher relative activity. Subsequently, transformation of polyols using whole cells of L. reuteri containing the wild type- and mutated GDH, respectively, confirmed the reduced activity of the mutant against glycerol and 1,2PDO, but its activity against longer substrates was negligible. In contrast, recombinant Escherichia coli BL21(DE3) cells harboring the GDH variant converted diols with up to C6 carbon chain length to their respective aldehydes, suggesting that the protein shell of the microcompartment in L. reuteri posed a barrier to the passage of longer chain substrate.
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Affiliation(s)
- Lu Chen
- Division of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
- * E-mail:
| | - Rajni Hatti-Kaul
- Division of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
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16
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Wang J, Jain R, Shen X, Sun X, Cheng M, Liao JC, Yuan Q, Yan Y. Rational engineering of diol dehydratase enables 1,4-butanediol biosynthesis from xylose. Metab Eng 2017; 40:148-156. [DOI: 10.1016/j.ymben.2017.02.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/09/2017] [Accepted: 02/10/2017] [Indexed: 11/29/2022]
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17
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Zhang Y, Liu D, Chen Z. Production of C2-C4 diols from renewable bioresources: new metabolic pathways and metabolic engineering strategies. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:299. [PMID: 29255482 PMCID: PMC5727944 DOI: 10.1186/s13068-017-0992-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/05/2017] [Indexed: 05/17/2023]
Abstract
C2-C4 diols classically derived from fossil resource are very important bulk chemicals which have been used in a wide range of areas, including solvents, fuels, polymers, cosmetics, and pharmaceuticals. Production of C2-C4 diols from renewable resources has received significant interest in consideration of the reducing fossil resource and the increasing environmental issues. While bioproduction of certain diols like 1,3-propanediol has been commercialized in recent years, biosynthesis of many other important C2-C4 diol isomers is highly challenging due to the lack of natural synthesis pathways. Recent advances in synthetic biology have enabled the de novo design of completely new pathways to non-natural molecules from renewable feedstocks. In this study, we review recent advances in bioproduction of C2-C4 diols, focusing on new metabolic pathways and metabolic engineering strategies being developed. We also discuss the challenges and future trends toward the development of economically competitive processes for bio-based diol production.
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Affiliation(s)
- Ye Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Key Lab of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084 China
- Tsinghua Innovation Center in Dongguan, Dongguan, 523808 China
| | - Dehua Liu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Key Lab of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084 China
- Tsinghua Innovation Center in Dongguan, Dongguan, 523808 China
- Center of Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China
| | - Zhen Chen
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Key Lab of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084 China
- Tsinghua Innovation Center in Dongguan, Dongguan, 523808 China
- Center of Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China
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18
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LaMattina JW, Keul ND, Reitzer P, Kapoor S, Galzerani F, Koch DJ, Gouvea IE, Lanzilotta WN. 1,2-Propanediol Dehydration in Roseburia inulinivorans: STRUCTURAL BASIS FOR SUBSTRATE AND ENANTIOMER SELECTIVITY. J Biol Chem 2016; 291:15515-26. [PMID: 27252380 DOI: 10.1074/jbc.m116.721142] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Indexed: 11/06/2022] Open
Abstract
Glycyl radical enzymes (GREs) represent a diverse superfamily of enzymes that utilize a radical mechanism to catalyze difficult, but often essential, chemical reactions. In this work we present the first biochemical and structural data for a GRE-type diol dehydratase from the organism Roseburia inulinivorans (RiDD). Despite high sequence (48% identity) and structural similarity to the GRE-type glycerol dehydratase from Clostridium butyricum, we demonstrate that the RiDD is in fact a diol dehydratase. In addition, the RiDD will utilize both (S)-1,2-propanediol and (R)-1,2-propanediol as a substrate, with an observed preference for the S enantiomer. Based on the new structural information we developed and successfully tested a hypothesis that explains the functional differences we observe.
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Affiliation(s)
- Joseph W LaMattina
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
| | - Nicholas D Keul
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
| | - Pierre Reitzer
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
| | - Suraj Kapoor
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
| | - Felipe Galzerani
- BRASKEM S.A., Rua Lemos Moonteiro, 120 Edifício Odebrecht São Paulo, Butantã 05501-050-São Paulo, SP Brasil
| | - Daniel J Koch
- BRASKEM S.A., Rua Lemos Moonteiro, 120 Edifício Odebrecht São Paulo, Butantã 05501-050-São Paulo, SP Brasil
| | - Iuri E Gouvea
- BRASKEM S.A., Rua Lemos Moonteiro, 120 Edifício Odebrecht São Paulo, Butantã 05501-050-São Paulo, SP Brasil
| | - William N Lanzilotta
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
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Toraya T, Tanokuchi A, Yamasaki A, Nakamura T, Ogura K, Tobimatsu T. Diol Dehydratase-Reactivase Is Essential for Recycling of Coenzyme B12 in Diol Dehydratase. Biochemistry 2015; 55:69-78. [PMID: 26704729 DOI: 10.1021/acs.biochem.5b01023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Holoenzymes of adenosylcobalamin-dependent diol and glycerol dehydratases undergo mechanism-based inactivation by glycerol and O2 inactivation in the absence of substrate, which accompanies irreversible cleavage of the coenzyme Co-C bond. The inactivated holodiol dehydratase and the inactive enzyme·cyanocobalamin complex were (re)activated by incubation with NADH, ATP, and Mg(2+) (or Mn(2+)) in crude extracts of Klebsiella oxytoca, suggesting the presence of a reactivating system in the extract. The reducing system with NADH could be replaced by FMNH2. When inactivated holoenzyme or the enzyme·cyanocobalamin complex, a model of inactivated holoenzyme, was incubated with purified recombinant diol dehydratase-reactivase (DD-R) and an ATP:cob(I)alamin adenosyltransferase in the presence of FMNH2, ATP, and Mg(2+), diol dehydratase activity was restored. Among the three adenosyltransferases (PduO, EutT, and CobA) of this bacterium, PduO and CobA were much more efficient for the reactivation than EutT, although PduO showed the lowest adenosyltransfease activity toward free cob(I)alamin. These results suggest that (1) diol dehydratase activity is maintained through coenzyme recycling by a reactivating system for diol dehydratase composed of DD-R, PduO adenosyltransferase, and a reducing system, (2) the releasing factor DD-R is essential for the recycling of adenosycobalamin, a tightly bound, prosthetic group-type coenzyme, and (3) PduO is a specific adenosylating enzyme for the DD reactivation, whereas CobA and EutT exert their effects through free synthesized coenzyme. Although FMNH2 was mainly used as a reductant in this study, a natural reducing system might consist of PduS cobalamin reductase and NADH.
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Affiliation(s)
- Tetsuo Toraya
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University , Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Aya Tanokuchi
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University , Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Ai Yamasaki
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University , Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Takehiro Nakamura
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University , Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Kenichi Ogura
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University , Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Takamasa Tobimatsu
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University , Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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20
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Chen Z, Wu Y, Huang J, Liu D. Metabolic engineering of Klebsiella pneumoniae for the de novo production of 2-butanol as a potential biofuel. BIORESOURCE TECHNOLOGY 2015; 197:260-5. [PMID: 26342337 DOI: 10.1016/j.biortech.2015.08.086] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/14/2015] [Accepted: 08/17/2015] [Indexed: 05/14/2023]
Abstract
Butanol isomers are important bulk chemicals and promising fuel substitutes. The inevitable toxicity of n-butanol and isobutanol to microbial cells hinders their final titers. In this study, we attempt to engineer Klebsiella pneumoniae for the de novo production of 2-butanol, another butanol isomer which shows lower toxicity than n-butanol and isobutanol. 2-Butanol synthesis was realized by the extension of the native meso-2,3-butanediol synthesis pathway with the introduction of diol dehydratase and secondary alcohol dehydrogenase. By the screening of different secondary alcohol dehydrogenases and diol dehydratases, 320mg/L of 2-butanol was produced by the best engineered K. pneumoniae. The production was increased to 720mg/L by knocking out the ldhA gene and appropriate addition of coenzyme B12. Further improvement of 2-butanol to 1030mg/L was achieved by protein engineering of diol dehydratase. This work lays the basis for the metabolic engineering of microorganism for the production of 2-butanol as potential biofuel.
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Affiliation(s)
- Zhen Chen
- Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Tsinghua Innovation Center in Dongguan, Dongguan 523808, China.
| | - Yao Wu
- Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Jinhai Huang
- Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Dehua Liu
- Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Tsinghua Innovation Center in Dongguan, Dongguan 523808, China
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21
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Zhou S, Ainala SK, Seol E, Nguyen TT, Park S. Inducible gene expression system by 3-hydroxypropionic acid. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:169. [PMID: 26500695 PMCID: PMC4617489 DOI: 10.1186/s13068-015-0353-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/02/2015] [Indexed: 05/25/2023]
Abstract
BACKGROUND 3-Hydroxypropionic acid (3-HP) is an important platform chemical that boasts a variety of industrial applications. Gene expression systems inducible by 3-HP, if available, are of great utility for optimization of the pathways of 3-HP production and excretion. RESULTS Here we report the presence of unique inducible gene expression systems in Pseudomonas denitrificans and other microorganisms. In P. denitrificans, transcription of three genes (hpdH, mmsA and hbdH-4) involved in 3-HP degradation was upregulated by 3-HP by the action of a transcriptional regulator protein, LysR, and a cis-acting regulatory site for LysR binding. Similar inducible systems having an LysR transcriptional regulator were identified in other microorganisms that also could degrade 3-HP. A docking study showed that the 3-HP binding pocket is located between the N-terminal helix-turn-helix motif and the C-terminal cofactor-binding domain. CONCLUSIONS This LysR-regulated 3-HP-inducible system should prove useful for control of the level of gene expression in response to 3-HP.
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Affiliation(s)
- Shengfang Zhou
- />School of Chemical and Biomolecular Engineering, Pusan National University, San 30 Jangeon-dong, Geumjeong-gu, Busan, 609-735 Republic of Korea
- />Department of Biochemical Engineering, College of Pharmaceutical and Life Sciences, Changzhou University, Changzhou, 213164 China
| | - Satish Kumar Ainala
- />School of Chemical and Biomolecular Engineering, Pusan National University, San 30 Jangeon-dong, Geumjeong-gu, Busan, 609-735 Republic of Korea
| | - Eunhee Seol
- />School of Chemical and Biomolecular Engineering, Pusan National University, San 30 Jangeon-dong, Geumjeong-gu, Busan, 609-735 Republic of Korea
| | - Trinh Thi Nguyen
- />School of Chemical and Biomolecular Engineering, Pusan National University, San 30 Jangeon-dong, Geumjeong-gu, Busan, 609-735 Republic of Korea
| | - Sunghoon Park
- />School of Chemical and Biomolecular Engineering, Pusan National University, San 30 Jangeon-dong, Geumjeong-gu, Busan, 609-735 Republic of Korea
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22
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Shibata N, Toraya T. Molecular architectures and functions of radical enzymes and their (re)activating proteins. J Biochem 2015; 158:271-92. [PMID: 26261050 DOI: 10.1093/jb/mvv078] [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: 06/15/2015] [Accepted: 07/22/2015] [Indexed: 02/07/2023] Open
Abstract
Certain proteins utilize the high reactivity of radicals for catalysing chemically challenging reactions. These proteins contain or form a radical and therefore named 'radical enzymes'. Radicals are introduced by enzymes themselves or by (re)activating proteins called (re)activases. The X-ray structures of radical enzymes and their (re)activases revealed some structural features of these molecular apparatuses which solved common enigmas of radical enzymes—i.e. how the enzymes form or introduce radicals at the active sites, how they use the high reactivity of radicals for catalysis, how they suppress undesired side reactions of highly reactive radicals and how they are (re)activated when inactivated by extinction of radicals. This review highlights molecular architectures of radical B12 enzymes, radical SAM enzymes, tyrosyl radical enzymes, glycyl radical enzymes and their (re)activating proteins that support their functions. For generalization, comparisons of the recently reported structures of radical enzymes with those of canonical radical enzymes are summarized here.
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Affiliation(s)
- Naoki Shibata
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan and
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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23
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Kitanishi K, Cracan V, Banerjee R. Engineered and Native Coenzyme B12-dependent Isovaleryl-CoA/Pivalyl-CoA Mutase. J Biol Chem 2015; 290:20466-76. [PMID: 26134562 DOI: 10.1074/jbc.m115.646299] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Indexed: 11/06/2022] Open
Abstract
Adenosylcobalamin-dependent isomerases catalyze carbon skeleton rearrangements using radical chemistry. We have recently demonstrated that an isobutyryl-CoA mutase variant, IcmF, a member of this enzyme family that catalyzes the interconversion of isobutyryl-CoA and n-butyryl-CoA also catalyzes the interconversion between isovaleryl-CoA and pivalyl-CoA, albeit with low efficiency and high susceptibility to inactivation. Given the biotechnological potential of the isovaleryl-CoA/pivalyl-CoA mutase (PCM) reaction, we initially attempted to engineer IcmF to be a more proficient PCM by targeting two active site residues predicted based on sequence alignments and crystal structures, to be key to substrate selectivity. Of the eight mutants tested, the F598A mutation was the most robust, resulting in an ∼17-fold increase in the catalytic efficiency of the PCM activity and a concomitant ∼240-fold decrease in the isobutyryl-CoA mutase activity compared with wild-type IcmF. Hence, mutation of a single residue in IcmF tuned substrate specificity yielding an ∼4000-fold increase in the specificity for an unnatural substrate. However, the F598A mutant was even more susceptible to inactivation than wild-type IcmF. To circumvent this limitation, we used bioinformatics analysis to identify an authentic PCM in genomic databases. Cloning and expression of the putative AdoCbl-dependent PCM with an α2β2 heterotetrameric organization similar to that of isobutyryl-CoA mutase and a recently characterized archaeal methylmalonyl-CoA mutase, allowed demonstration of its robust PCM activity. To simplify kinetic analysis and handling, a variant PCM-F was generated in which the αβ subunits were fused into a single polypeptide via a short 11-amino acid linker. The fusion protein, PCM-F, retained high PCM activity and like PCM, was resistant to inactivation. Neither PCM nor PCM-F displayed detectable isobutyryl-CoA mutase activity, demonstrating that PCM represents a novel 5'-deoxyadenosylcobalamin-dependent acyl-CoA mutase. The newly discovered PCM and the derivative PCM-F, have potential applications in bioremediation of pivalic acid found in sludge, in stereospecific synthesis of C5 carboxylic acids and alcohols, and in the production of potential commodity and specialty chemicals.
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Affiliation(s)
- Kenichi Kitanishi
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Valentin Cracan
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Ruma Banerjee
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
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24
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Doitomi K, Tanaka H, Kamachi T, Toraya T, Yoshizawa K. Computational Mutation Design of Diol Dehydratase: Catalytic Ability toward Glycerol beyond the Wild-Type Enzyme. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20140115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kazuki Doitomi
- Institute for Materials Chemistry and Engineering, Kyushu University
- International Research Center for Molecular Systems, Kyushu University
| | - Hiromasa Tanaka
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University
| | - Takashi Kamachi
- Institute for Materials Chemistry and Engineering, Kyushu University
- International Research Center for Molecular Systems, Kyushu University
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology, Okayama University
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering, Kyushu University
- International Research Center for Molecular Systems, Kyushu University
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University
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25
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Rieckenberg F, Ardao I, Rujananon R, Zeng AP. Cell-free synthesis of 1,3-propanediol from glycerol with a high yield. Eng Life Sci 2014. [DOI: 10.1002/elsc.201400034] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Fabian Rieckenberg
- Institute of Bioprocess and Biosystems Engineering; Hamburg University of Technology; Germany
| | - Inés Ardao
- Institute of Bioprocess and Biosystems Engineering; Hamburg University of Technology; Germany
| | - Rosarin Rujananon
- Institute of Bioprocess and Biosystems Engineering; Hamburg University of Technology; Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering; Hamburg University of Technology; Germany
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26
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Cobalamin-dependent dehydratases and a deaminase: Radical catalysis and reactivating chaperones. Arch Biochem Biophys 2014; 544:40-57. [DOI: 10.1016/j.abb.2013.11.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 11/04/2013] [Accepted: 11/08/2013] [Indexed: 01/12/2023]
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27
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Mori K, Obayashi K, Hosokawa Y, Yamamoto A, Yano M, Yoshinaga T, Toraya T. Essential roles of nucleotide-switch and metal-coordinating residues for chaperone function of diol dehydratase-reactivase. Biochemistry 2013; 52:8677-86. [PMID: 24229359 DOI: 10.1021/bi401290j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Diol dehydratase-reactivase (DD-R) is a molecular chaperone that reactivates inactivated holodiol dehydratase (DD) by cofactor exchange. Its ADP-bound and ATP-bound forms are high-affinity and low-affinity forms for DD, respectively. Among DD-Rs mutated at the nucleotide-binding site, neither the Dα8N nor Dα413N mutant was effective as a reactivase. Although Dα413N showed ATPase activity, it did not mediate cyanocobalamin (CN-Cbl) release from the DD·CN-Cbl complex in the presence of ATP or ADP and formed a tight complex with apoDD even in the presence of ATP, suggesting the involvement of Aspα413 in the nucleotide switch. In contrast, Dα8N showed very low ATPase activity and did not mediate CN-Cbl release from the complex in the presence of ATP, but it did cause about 50% release in the presence of ADP. The complex formation of this mutant with DD was partially reversed by ATP, suggesting that Aspα8 is involved in the ATPase activity but only partially in the nucleotide switch. Among DD-Rs mutated at the Mg(2+)-binding site, only Eβ31Q was about 30% as active as wild-type DD-R and formed a tight complex with apoDD, indicating that the DD-R β subunit is not absolutely required for reactivation. If subunit swapping occurs between the DD-R β and DD β subunits, Gluβ97 of DD would coordinate to Mg(2+). The complex of Eβ97Q DD with CN-Cbl was not activated by wild-type DD-R. No complex was formed between this mutant and wild-type DD-R, indicating that the coordination of Gluβ97 to Mg(2+) is essential for subunit swapping and therefore for (re)activation.
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Affiliation(s)
- Koichi Mori
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University , Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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28
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Doitomi K, Kamachi T, Toraya T, Yoshizawa K. Inactivation Mechanism of Glycerol Dehydration by Diol Dehydratase from Combined Quantum Mechanical/Molecular Mechanical Calculations. Biochemistry 2012; 51:9202-10. [DOI: 10.1021/bi300488u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kazuki Doitomi
- Institute for Materials Chemistry and Engineering
and International Research Center for Molecular Systems, Kyushu University, Fukuoka 819-0395, Japan
| | - Takashi Kamachi
- Institute for Materials Chemistry and Engineering
and International Research Center for Molecular Systems, Kyushu University, Fukuoka 819-0395, Japan
| | - Tetsuo Toraya
- Graduate School of Natural Science
and Technology, Okayama University, Okayama
700-8530, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering
and International Research Center for Molecular Systems, Kyushu University, Fukuoka 819-0395, Japan
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29
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Yang J, Roy A, Zhang Y. BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Res 2012; 41:D1096-103. [PMID: 23087378 PMCID: PMC3531193 DOI: 10.1093/nar/gks966] [Citation(s) in RCA: 454] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BioLiP (http://zhanglab.ccmb.med.umich.edu/BioLiP/) is a semi-manually curated database for biologically relevant ligand–protein interactions. Establishing interactions between protein and biologically relevant ligands is an important step toward understanding the protein functions. Most ligand-binding sites prediction methods use the protein structures from the Protein Data Bank (PDB) as templates. However, not all ligands present in the PDB are biologically relevant, as small molecules are often used as additives for solving the protein structures. To facilitate template-based ligand–protein docking, virtual ligand screening and protein function annotations, we develop a hierarchical procedure for assessing the biological relevance of ligands present in the PDB structures, which involves a four-step biological feature filtering followed by careful manual verifications. This procedure is used for BioLiP construction. Each entry in BioLiP contains annotations on: ligand-binding residues, ligand-binding affinity, catalytic sites, Enzyme Commission numbers, Gene Ontology terms and cross-links to the other databases. In addition, to facilitate the use of BioLiP for function annotation of uncharacterized proteins, a new consensus-based algorithm COACH is developed to predict ligand-binding sites from protein sequence or using 3D structure. The BioLiP database is updated weekly and the current release contains 204 223 entries.
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Affiliation(s)
- Jianyi Yang
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA
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