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Shibata N, Higuchi Y, Kräutler B, Toraya T. Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase. Chemistry 2022; 28:e202202196. [PMID: 35974426 DOI: 10.1002/chem.202202196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Indexed: 11/11/2022]
Abstract
The X-ray structures of coenzyme B12 (AdoCbl)-dependent eliminating isomerases complexed with adenosylmethylcobalamin (AdoMeCbl) have been determined. As judged from geometries, the Co-C bond in diol dehydratase (DD) is not activated even in the presence of substrate. In ethanolamine ammonia-lyase (EAL), the bond is elongated in the absence of substrate; in the presence of substrate, the complex likely exists in both pre- and post-homolysis states. The impacts of incorporating an extra CH2 group are different in the two enzymes: the DD active site is flexible, and AdoMeCbl binding causes large conformational changes that make DD unable to adopt the catalytic state, whereas the EAL active site is rigid, and AdoMeCbl binding does not induce significant conformational changes. Such flexibility and rigidity of the active sites might reflect the tightness of adenine binding. The structures provide good insights into the basis of the very low activity of AdoMeCbl in these enzymes.
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Affiliation(s)
- Naoki Shibata
- Department of Life Science, Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
| | - Bernhard Kräutler
- Institute of Organic Chemistry and, Center of Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria
| | - 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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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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3
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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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Kumar G, Bari NK, Hazra JP, Sinha S. A major shell protein of 1,2-propanediol utilization microcompartment conserves the activity of its signature enzyme at higher temperatures. Chembiochem 2022; 23:e202100694. [PMID: 35229962 DOI: 10.1002/cbic.202100694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/28/2022] [Indexed: 11/11/2022]
Abstract
A classic example of an all-protein natural nano-bioreactor, the bacterial microcompartment is a special kind of prokaryotic organelle that confine enzymes within a small volume enveloped by an outer protein shell. These protein compartments metabolize specific organic molecules, allowing bacteria to survive in restricted nutrient environments. In this work, 1,2-propanediol utilization microcompartment (PduMCP) is used as a model to study the effect of molecular confinement on the stability and catalytic activity of native enzymes in microcompartment. A combination of enzyme assays, spectroscopic techniques, binding assays, and computational analysis are used to evaluate the impact of the major shell protein PduBB' on the stability and activity of PduMCP's signature enzyme, diol dehydratase PduCDE. While free PduCDE shows ~45% reduction in its optimum activity (activity at 37 o C) when exposed to a temperature of 45°C, it retains similar activity up to 50°C when encapsulated within PduMCP. PduBB', a major component of the outer shell of PduMCP, preserves the catalytic efficiency of PduCDE under thermal stress and prevents temperature-induced unfolding and aggregation of PduCDE in vitro . We observe that while both PduB and PduB' interact with the enzyme with micromolar affinity, only the PduBB' combination influences its activity and stability, highlighting the importance of the unique PduBB' combination in the functioning of PduMCP.
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Affiliation(s)
- Gaurav Kumar
- Institute of Nano Science and Technology, Chemical Biology Unit, Sector-81, Knowledge City, 140306, Mohali, INDIA
| | - Naimat Kalim Bari
- Institute of Nano Science and Technology, Chemical Biology Unit, Sector-81, Knowledge City, 140306, Mohali, INDIA
| | - Jagadish P Hazra
- Indian Institute of Science Education and Research Mohali, Chemical Sciences, Sector-81, Knowledge City, 140306, Mohali, INDIA
| | - Sharmistha Sinha
- Institute of Nano Science and Technology, Chemical Biology Unit, Sector-81, Knowledge City, 140306, Mohali, INDIA
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Zhang Y, Li Z, Liu Y, Cen X, Liu D, Chen Z. Systems metabolic engineering of Vibrio natriegens for the production of 1,3-propanediol. Metab Eng 2021; 65:52-65. [PMID: 33722653 DOI: 10.1016/j.ymben.2021.03.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/28/2021] [Accepted: 03/06/2021] [Indexed: 11/18/2022]
Abstract
The economic viability of current bio-production systems is often limited by its low productivity due to slow cell growth and low substrate uptake rate. The fastest-growing bacterium Vibrio natriegens is a highly promising next-generation workhorse of the biotechnology industry which can utilize various industrially relevant carbon sources with high substrate uptake rates. Here, we demonstrate the first systematic engineering example of V. natriegens for the heterologous production of 1,3-propanediol (1,3-PDO) from glycerol. Systems metabolic engineering strategies have been applied in this study to develop a superior 1,3-PDO producer, including: (1) heterologous pathway construction and optimization; (2) engineering cellular transcriptional regulators and global transcriptomic analysis; (3) enhancing intracellular reducing power by cofactor engineering; (4) reducing the accumulation of toxic intermediate by pathway engineering; (5) systematic engineering of glycerol oxidation pathway to eliminate byproduct formation. A final engineered strain can efficiently produce 1,3-PDO with a titer of 56.2 g/L, a yield of 0.61 mol/mol, and an average productivity of 2.36 g/L/h. The strategies described in this study would be useful for engineering V. natriegens as a potential chassis for the production of other useful chemicals and biofuels.
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Affiliation(s)
- Ye Zhang
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Zihua Li
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yu Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xuecong Cen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Dehua Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Tsinghua Innovation Center in Dongguan, Dongguan, 523808, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Zhen Chen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Tsinghua Innovation Center in Dongguan, Dongguan, 523808, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
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Viladomiu M, Metz ML, Lima SF, Jin WB, Chou L, Guo CJ, Diehl GE, Simpson KW, Scherl EJ, Longman RS. Adherent-invasive E. coli metabolism of propanediol in Crohn's disease regulates phagocytes to drive intestinal inflammation. Cell Host Microbe 2021; 29:607-619.e8. [PMID: 33539767 DOI: 10.1016/j.chom.2021.01.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/29/2020] [Accepted: 01/08/2021] [Indexed: 02/06/2023]
Abstract
Adherent-invasive E. coli (AIEC) are enriched in the intestinal microbiota of patients with Crohn's disease (CD) and promote intestinal inflammation. Yet, how AIEC metabolism of nutrients impacts intestinal homeostasis is poorly defined. Here, we show that AIEC encoding the large subunit of propanediol dehydratase (PduC), which facilitates the utilization of fucose fermentation product 1,2-propanediol, are increased in the microbiome of CD patients and drive AIEC-induced intestinal T cell inflammation. In murine models, CX3CR1+ mononuclear phagocytes (MNP) are required for PduC-dependent induction of T helper 17 (Th17) cells and interleukin-1β (IL-1β) production that leads to AIEC-induced inflammatory colitis. Activation of this inflammatory cascade requires the catalytic activity of PduC to generate propionate, which synergizes with lipopolysaccharide (LPS) to induce IL-1β by MNPs. Disrupting fucose availability limits AIEC-induced propionate production and intestinal inflammation. These findings identify MNPs as metabolic sensors linking AIEC metabolism with intestinal inflammation and identify microbial metabolism as a potential therapeutic target in Crohn's disease treatment.
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Affiliation(s)
- Monica Viladomiu
- Jill Roberts Institute for IBD Research, Weill Cornell Medicine, New York, NY 10021, USA
| | - Maeva L Metz
- Jill Roberts Institute for IBD Research, Weill Cornell Medicine, New York, NY 10021, USA
| | - Svetlana F Lima
- Jill Roberts Institute for IBD Research, Weill Cornell Medicine, New York, NY 10021, USA
| | - Wen-Bing Jin
- Jill Roberts Institute for IBD Research, Weill Cornell Medicine, New York, NY 10021, USA
| | - Lance Chou
- Jill Roberts Institute for IBD Research, Weill Cornell Medicine, New York, NY 10021, USA
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- Jill Roberts Institute for IBD Research, Weill Cornell Medicine, New York, NY 10021, USA
| | - Chun-Jun Guo
- Jill Roberts Institute for IBD Research, Weill Cornell Medicine, New York, NY 10021, USA
| | - Gretchen E Diehl
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Kenneth W Simpson
- College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Ellen J Scherl
- Jill Roberts Center for IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Randy S Longman
- Jill Roberts Institute for IBD Research, Weill Cornell Medicine, New York, NY 10021, USA; Jill Roberts Center for IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
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Yun J, Zabed HM, Zhang Y, Parvez A, Zhang G, Qi X. Co-fermentation of glycerol and glucose by a co-culture system of engineered Escherichia coli strains for 1,3-propanediol production without vitamin B 12 supplementation. BIORESOURCE TECHNOLOGY 2021; 319:124218. [PMID: 33049440 DOI: 10.1016/j.biortech.2020.124218] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
The necessity of costly co-enzyme B12 for the activity of glycerol dehydratase (GDHt) is considered as a major bottleneck in sustainable bioproduction of 1,3-propanediol (1,3-PD) from glycerol. Here, an E. coil Rosetta-dhaB1-dhaB2 strain was constructed by overexpressing a B12-independent GDHt (dhaB1) and its activating factor (dhaB2) from Clostridium butyricum. Subsequently, it was used in designing a co-culture with E. coli BL21-dhaT that overexpressed 1,3-PD oxidoreductase (dhaT), to produce 1,3-PD during co-fermentation of glycerol and glucose. The optimum initial ratio of BL21-dhaT to Rosetta-dhaB1-dhaB2 strains in the co-culture was 1.5. Compared to the fermentation of glycerol alone, co-fermentation approach provided 1.3-folds higher 1,3-PD. Finally, co-fermentation was done in a 10 L bioreactor that produced 41.65 g/L 1,3-PD, which corresponded to 0.69 g/L/h productivity and 0.67 mol/mol yield of 1,3-PD. Hence, the developed co-culture could produce 1,3-PD cost-effectively without requiring vitamin B12.
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Affiliation(s)
- Junhua Yun
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Hossain M Zabed
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Yufei Zhang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Amreesh Parvez
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Guoyan Zhang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Xianghui Qi
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China.
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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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Mar MJ, Andersen JM, Kandasamy V, Liu J, Solem C, Jensen PR. Synergy at work: linking the metabolism of two lactic acid bacteria to achieve superior production of 2-butanol. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:45. [PMID: 32180827 PMCID: PMC7065357 DOI: 10.1186/s13068-020-01689-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 02/26/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND The secondary alcohol 2-butanol has many important applications, e.g., as a solvent. Industrially, it is usually made by sulfuric acid-catalyzed hydration of butenes. Microbial production of 2-butanol has also been attempted, however, with little success as witnessed by the low titers and yields reported. Two important reasons for this, are the growth-hampering effect of 2-butanol on microorganisms, and challenges associated with one of the key enzymes involved in its production, namely diol dehydratase. RESULTS We attempt to link the metabolism of an engineered Lactococcus lactis strain, which possesses all enzyme activities required for fermentative production of 2-butanol from glucose, except for diol dehydratase, which acts on meso-2,3-butanediol (mBDO), with that of a Lactobacillus brevis strain which expresses a functional dehydratase natively. We demonstrate growth-coupled production of 2-butanol by the engineered L. lactis strain, when co-cultured with L. brevis. After fine-tuning the co-culture setup, a titer of 80 mM (5.9 g/L) 2-butanol, with a high yield of 0.58 mol/mol is achieved. CONCLUSIONS Here, we demonstrate that it is possible to link the metabolism of two bacteria to achieve redox-balanced production of 2-butanol. Using a simple co-cultivation setup, we achieved the highest titer and yield from glucose in a single fermentation step ever reported. The data highlight the potential that lies in harnessing microbial synergies for producing valuable compounds.
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Affiliation(s)
- Mette J. Mar
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Joakim M. Andersen
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Vijayalakshmi Kandasamy
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Jianming Liu
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Christian Solem
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Peter R. Jensen
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
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Bari NK, Kumar G, Bhatt A, Hazra JP, Garg A, Ali ME, Sinha S. Nanoparticle Fabrication on Bacterial Microcompartment Surface for the Development of Hybrid Enzyme-Inorganic Catalyst. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02322] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Naimat Kalim Bari
- Institute of Nano Science and Technology (INST), Phase-10, Sector-64, Mohali, Punjab 160062, India
| | - Gaurav Kumar
- Institute of Nano Science and Technology (INST), Phase-10, Sector-64, Mohali, Punjab 160062, India
| | - Aashish Bhatt
- Institute of Nano Science and Technology (INST), Phase-10, Sector-64, Mohali, Punjab 160062, India
| | - Jagadish Prasad Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, Mohali, Punjab 140306, India
| | - Ankush Garg
- Institute of Nano Science and Technology (INST), Phase-10, Sector-64, Mohali, Punjab 160062, India
| | - Md. Ehesan Ali
- Institute of Nano Science and Technology (INST), Phase-10, Sector-64, Mohali, Punjab 160062, India
| | - Sharmistha Sinha
- Institute of Nano Science and Technology (INST), Phase-10, Sector-64, Mohali, Punjab 160062, India
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Niu K, Cheng XL, Qin HB, Liu JS, Zheng YG. Investigation of the key factors on 3-hydroxypropionic acid production with different recombinant strains. 3 Biotech 2017; 7:314. [PMID: 28955611 DOI: 10.1007/s13205-017-0966-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/07/2017] [Indexed: 12/26/2022] Open
Abstract
3-Hydroxypropionic acid (3-HP) is an important compound and precursor for a series of chemicals and polymeric materials. In this study, the 3-HP producing bacteria were constructed and studied for efficient synthesis of 3-HP. The results indicated that the instability of glycerol dehydratase (GDHt) affected the 3-HP production significantly, which was successfully solved by the expression of glycerol dehydratase reactivase (GdrB), with fivefold increase in 3-HP yield. Meanwhile, NAD+-regenerating enzymes GPD1 (glycerol-3-phosphate dehydrogenase) was expressed; however, the results showed 3-HP was significantly decreased from 56.73-4 mM, and malic acid was obviously increased. Analysis of the C flux distribution showed that the main reason for the results was the lack of NAD+. The addition of NAD+ further increased the 3-HP production to 23.87 mM, demonstrating that the "regeneration of NAD+" was the major factor for enhancing 3-HP production.
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Affiliation(s)
- Kun Niu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Xiu-Li Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Hai-Bin Qin
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Ji-Song Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
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12
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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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Niu K, Xiong T, Qin HB, Wu H, Liu ZQ, Zheng YG. 3-Hydroxypropionic acid production by recombinant Escherichia coli ZJU-3HP01 using glycerol-glucose dual-substrate fermentative strategy. Biotechnol Appl Biochem 2017; 64:572-578. [PMID: 27189262 DOI: 10.1002/bab.1505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 05/09/2016] [Indexed: 01/23/2023]
Abstract
3-Hydroxypropionic acid (3-HP) is an important platform synthesis block for sets of chemicals, but the relatively low production of 3-HP from biological sources presented major barriers for its industrial applications. In this study, a dual-substrate fermentative strategy by glycerol and glucose was proposed, and the aim was to evaluate the effect of different substrate addition strategies on the fermentation process. The results indicated that the optimal cosubstrate was glucose (20 g/L), and the enzymatic activity of aldehyde dehydrogenase (AldH) could be improved 3.5-fold as compared with no glucose addition. Continuous fed-batch fermentation at a constant speed displayed better 3-HP production of 17.20 g/L and highest specific 3-HP productivity of 1.79 mmol/(g cell·H) than the other fed-batch mode. The addition of glucose could greatly reduce the imbalance of the activity between glycerol dehydratase and AldH and provide a feasible method for improving 3-HP production. These results would be helpful in developing the 3-HP fermentation process.
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Affiliation(s)
- Kun Niu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Tao Xiong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Hai-Bin Qin
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Hao Wu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
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14
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Huang J, Wu Y, Wu W, Zhang Y, Liu D, Chen Z. Cofactor recycling for co-production of 1,3-propanediol and glutamate by metabolically engineered Corynebacterium glutamicum. Sci Rep 2017; 7:42246. [PMID: 28176878 PMCID: PMC5296756 DOI: 10.1038/srep42246] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/05/2017] [Indexed: 01/03/2023] Open
Abstract
Production of 1,3-propanediol (1,3-PDO) from glycerol is a promising route toward glycerol biorefinery. However, the yield of 1,3-PDO is limited due to the requirement of NADH regeneration via glycerol oxidation process, which generates large amounts of undesired byproducts. Glutamate fermentation by Corynebacterium glutamicum is an important oxidation process generating excess NADH. In this study, we proposed a novel strategy to couple the process of 1,3-PDO synthesis with glutamate production for cofactor regeneration. With the optimization of 1,3-PDO synthesis route, C. glutamicum can efficiently convert glycerol into 1,3-PDO with the yield of ~ 1.0 mol/mol glycerol. Co-production of 1,3-PDO and glutamate was also achieved which increased the yield of glutamate by 18% as compared to the control. Since 1,3-PDO and glutamate can be easily separated in downstream process, this study provides a potential green route for coupled production of 1,3-PDO and glutamate to enhance the economic viability of biorefinery process.
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Affiliation(s)
- Jinhai Huang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yao Wu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Wenjun Wu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ye Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Dehua Liu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.,Tsinghua Innovation Center in Dongguan, Dongguan 523808, China
| | - Zhen Chen
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.,Tsinghua Innovation Center in Dongguan, Dongguan 523808, China
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15
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Sankaranarayanan M, Seol E, Kim Y, Chauhan AS, Park S. Measurement of crude-cell-extract glycerol dehydratase activity in recombinant Escherichia coli using coupled-enzyme reactions. J Ind Microbiol Biotechnol 2017; 44:477-488. [PMID: 28093656 DOI: 10.1007/s10295-017-1902-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/04/2017] [Indexed: 11/25/2022]
Abstract
Glycerol dehydratase (GDHt), which converts glycerol to 3-hydroxypropionaldehyde, is essential to the production of 1,3-propanediol (1,3-PDO) or 3-hydroxypropionic acid (3-HP). A reliable GDHt activity assay in crude-cell extract was developed. In the assay, GDHt converted 1,2-propanediol (1,2-PDO) to propionaldehyde, which was further converted to 1-propionic acid by aldehyde dehydrogenase (KGSADH) or to 1-propanol by yeast-alcohol dehydrogenase (yADH), while the NADH concentration change was monitored spectrophotometrically. Cells should be disintegrated by Bead Beater/French Press, not by chemical methods (BugBuster®/B-PER™), because the reagents significantly inactivated GDHt and coupling enzymes. Furthermore, in the assay mixture, a much higher activity of KGSADH (>200-fold) or yADH (>400-fold) than that of GDHt should have been maintained. Under optimal conditions, both KGSADH and yADH showed practically the same activity. The coupled-enzyme assay method established here should prove to be applicable to recombinant strains developed for the production of 3-HP and/or 1,3-PDO from glycerol.
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Affiliation(s)
- Mugesh Sankaranarayanan
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Eunhee Seol
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Yeonhee Kim
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Ashish Singh Chauhan
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Sunghoon Park
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, 46241, Republic of Korea.
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16
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Park ES, Park S, Shin JS. Spectrophotometric assay for sensitive detection of glycerol dehydratase activity using aldehyde dehydrogenase. J Biosci Bioeng 2017; 123:528-533. [PMID: 28052817 DOI: 10.1016/j.jbiosc.2016.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/08/2016] [Accepted: 12/03/2016] [Indexed: 10/20/2022]
Abstract
Glycerol dehydratase (GDHt) is a pivotal enzyme for fermentative utilization of glycerol by catalyzing radical-mediated conversion of glycerol into 3-hydroxypropionaldehyde (3-HPA). Precise and sensitive monitoring of cellular GDHt activity during the fermentation process is a prerequisite for reliable metabolic analysis to afford efficient cellular engineering and process optimization. Here we report a new spectrophotometric assay for the sensitive measurement of the GDHt activity with a sub-nanomolar limit of detection (LOD). The assay method employs aldehyde dehydrogenase (ALDH) as a reporter enzyme, so the readout of the GDHt activity is recorded at 340 nm as an increase in UV absorbance which results from NADH generation accompanied by oxidation of 3-HPA to 3-hydroxypropionic acid (3-HP). The GDHt assay was performed under the reaction conditions where the ALDH activity overwhelms the GDHt activity (i.e., 50-fold higher activity of ALDH relative to GDHt activity), affording sensitive detection of GDHt with 360 pM LOD. The ALDH-coupled assay was used to determine kinetic parameters of GDHt for glycerol, leading to KM = 0.73 ± 0.09 mM and kcat = 400 ± 20 s-1 which are in reasonable agreements with the previous reports. Our assay method allowed measurement of even a 104-fold decrease in the cellular GDHt activity during fermentative production of 3-HP, which demonstrates the detection sensitivity much higher than the previous methods.
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Affiliation(s)
- Eul-Soo Park
- Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea
| | - Sunghoon Park
- Department of Chemical and Biomolecular Engineering, Pusan National University, Busan 609-735, South Korea
| | - Jong-Shik Shin
- Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea.
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17
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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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18
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Abstract
This review summarizes research performed over the last 23 years on the genetics, enzyme structures and functions, and regulation of the expression of the genes encoding functions involved in adenosylcobalamin (AdoCbl, or coenzyme B12) biosynthesis. It also discusses the role of coenzyme B12 in the physiology of Salmonella enterica serovar Typhimurium LT2 and Escherichia coli. John Roth's seminal contributions to the field of coenzyme B12 biosynthesis research brought the power of classical and molecular genetic, biochemical, and structural approaches to bear on the extremely challenging problem of dissecting the steps of what has turned out to be one of the most complex biosynthetic pathways known. In E. coli and serovar Typhimurium, uro'gen III represents the first branch point in the pathway, where the routes for cobalamin and siroheme synthesis diverge from that for heme synthesis. The cobalamin biosynthetic pathway in P. denitrificans was the first to be elucidated, but it was soon realized that there are at least two routes for cobalamin biosynthesis, representing aerobic and anaerobic variations. The expression of the AdoCbl biosynthetic operon is complex and is modulated at different levels. At the transcriptional level, a sensor response regulator protein activates the transcription of the operon in response to 1,2-Pdl in the environment. Serovar Typhimurium and E. coli use ethanolamine as a source of carbon, nitrogen, and energy. In addition, and unlike E. coli, serovar Typhimurium can also grow on 1,2-Pdl as the sole source of carbon and energy.
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19
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Ghiaci P, Lameiras F, Norbeck J, Larsson C. Production of 2-butanol through meso-2,3-butanediol consumption in lactic acid bacteria. FEMS Microbiol Lett 2014; 360:70-5. [PMID: 25175699 DOI: 10.1111/1574-6968.12590] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/13/2014] [Accepted: 08/25/2014] [Indexed: 11/28/2022] Open
Abstract
2-Butanol has been an issue of industries in many areas, for example, biofuel production (as an advanced alternate fuel), fermented beverages, and food (as taste-altering component). Thus, its source of production, the biological pathway, and the enzymes involved are of high interest. In this study, 42 different isolates of lactic acid bacteria from nine different species were screened for their capability to consume meso-2,3-butanediol and produce 2-butanol. Lactobacillus brevis was the only species that showed any production of 2-butanol. Five of ten tested isolates of L. brevis were able to convert meso-2,3-butanediol to 2-butanol in a synthetic medium (SM2). However, none of them showed the same capability in a complex medium such as MRS indicating that the ability to produce 2-butanol is subject to some kind of repression mechanism. Furthermore, by evaluating the performance of the enzymes required to convert meso-2,3-butanediol to 2-butanol, that is, the secondary alcohol dehydrogenase and the diol dehydratase, it was shown that the latter needed the presence of a substrate to be expressed.
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Affiliation(s)
- Payam Ghiaci
- Department of Chemical and Biological Engineering, System and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
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20
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Wei X, Meng X, Chen Y, Wei Y, Du L, Huang R. Cloning, expression, and characterization of coenzyme-B12-dependent diol dehydratase from Lactobacillus diolivorans. Biotechnol Lett 2014; 36:159-65. [PMID: 24078133 DOI: 10.1007/s10529-013-1346-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 09/02/2013] [Indexed: 11/25/2022]
Abstract
The three gldCDE genes from Lactobacillus diolivorans, that encode the three subunits of the glycerol dehydratase, were cloned and the proteins were co-expressed in soluble form in Escherichia coli with added sorbitol and betaine hydrochloride. The purified enzyme exists as a heterohexamer (α2β2γ2) structure with a native molecular mass of 210 kDa. It requires coenzyme B12 for catalytic activity and is subject to suicide inactivation by glycerol during catalysis. The enzyme had maximum activity at pH 8.6 and 37 °C. The apparent K m values for coenzyme B12, 1,2-ethanediol, 1,2-propanediol, and glycerol were 1.5 μM, 10.5 mM, 1.3 mM, and 5.8 mM, respectively. Together, these results indicated that the three genes gldCDE encoding the proteins make up a coenzyme B12-dependent diol dehydratase and not a glycerol dehydratase.
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21
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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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22
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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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23
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Yen HW, Li FT, Chang JS. The effects of dissolved oxygen level on the distribution of 1,3-propanediol and 2,3-butanediol produced from glycerol by an isolated indigenous Klebsiella sp. Ana-WS5. BIORESOURCE TECHNOLOGY 2014; 153:374-8. [PMID: 24369989 DOI: 10.1016/j.biortech.2013.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 11/28/2013] [Accepted: 12/01/2013] [Indexed: 05/03/2023]
Abstract
The rapid accumulation of glycerol during biodiesel synthesis has attracted much interest on the potential usage. One of the promising applications is the conversion of glycerol to 1,3-propanediol (PDO), as well 2,3-butanediol (BDO), by using Klebsiella pneumonia. The results of this study indicate that the dissolved oxygen level (DO) is a determining factor in the distribution of PDO and BDO. The batch with a low DO could achieve a much higher PDO/BDO ratio than the high DO batch, with results of 9.9 and 0.2, respectively. The enzyme activity of glycerol dehydratase (GDHt) in the low DO batch was about three times that of the high DO batch, and this might be the cause of the enhanced PDO production. In conclusion, the results of this work show that high DO was beneficial to the production of BDO when using glycerol as the carbon source, while low DO could enhance PDO production.
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Affiliation(s)
- Hong-Wei Yen
- Department of Chemical and Materials Engineering, Tunghai University, Taichung 407, Taiwan.
| | - Fang-Tzu Li
- Department of Chemical and Materials Engineering, Tunghai University, Taichung 407, Taiwan
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan; Research Center for Energy Technology and Strategy, National Cheng Kung University, Tainan 701, Taiwan; University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
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24
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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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25
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West TP, Peterson JL. Elevated 3-hydroxypropionaldehyde production from glycerol using a Citrobacter freundii mutant. Biotechnol Lett 2013; 36:147-52. [PMID: 24062134 DOI: 10.1007/s10529-013-1343-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 09/05/2013] [Indexed: 11/25/2022]
Abstract
A mutant strain of Citrobacter freundii capable of elevated 3-hydroxypropionaldehyde production from glycerol was isolated using chemical mutagenesis and a screening protocol. The protocol involved screening mutagenized bacterial cells on solid minimal medium containing 5 % (v/v) glycerol. Colonies were picked onto duplicate solid minimal medium plates and one plate was stained with 1 % (w/v) phloroglucinol. Those colonies staining red were further screened and a mutant, HPAO-1, was identified. The mutant strain produced a several-fold higher 3-hydroxypropionaldehyde concentration than did the parent strain when grown on 5 % (v/v) glycerol. The ratio of culture volume to flask volume influenced 3-hydroxypropionaldehyde production by the mutant cells compared to the parent cells. Aldehyde production was highest when the mutant strain was grown on 5 % (v/v) glycerol at a ratio of culture volume to flask volume of 1:3 or 1:12.5.
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Affiliation(s)
- Thomas P West
- Department of Biology and Microbiology, South Dakota State University, Box 2104A, Brookings, SD, 57007, USA,
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26
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Wang Q, Yang P, Liu C, Xue Y, Xian M, Zhao G. Biosynthesis of poly(3-hydroxypropionate) from glycerol by recombinant Escherichia coli. BIORESOURCE TECHNOLOGY 2013; 131:548-551. [PMID: 23414748 DOI: 10.1016/j.biortech.2013.01.096] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/18/2013] [Accepted: 01/19/2013] [Indexed: 06/01/2023]
Abstract
Poly(3-hydroxypropionate) (P3HP) is a biodegradable and biocompatible thermoplastic. In this study, a P3HP biosynthetic pathway from glycerol was constructed in recombinant Escherichia coli. The genes for glycerol dehydratase and its reactivating factor (dhaB123 and gdrAB, from Klebsiella pneumoniae), propionaldehyde dehydrogenase (pduP, from Salmonella typhimurium), and polyhydroxyalkanoate synthase (phaC1, from Cupriavidus necator) were cloned and expressed in E. coli. After culture condition optimization, the final engineered strain accumulated 10.1 g/L P3HP (46.4% of the cell dry weight) using glycerol and glucose as cosubstrates in an aerobic fed-batch fermentation. To date, this is the highest P3HP production without addition of any expensive precursor.
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Affiliation(s)
- Qi Wang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
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27
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Molecular Cloning, Co-expression, and Characterization of Glycerol Dehydratase and 1,3-Propanediol Dehydrogenase from Citrobacter freundii. Mol Biotechnol 2012; 54:469-74. [DOI: 10.1007/s12033-012-9585-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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28
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The effect of cell immobilization on the antibacterial activity of Lactobacillus reuteri DPC16 cells during passage through a simulated gastrointestinal tract system. World J Microbiol Biotechnol 2012; 28:3025-37. [PMID: 22806742 DOI: 10.1007/s11274-012-1113-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 06/15/2012] [Indexed: 01/03/2023]
Abstract
Cell immobilization has the ability to influence the survival and functional characteristics of probiotic bacterial strains in harsh environments. This study investigated the effect of cell immobilization and passage through a simulated gastrointestinal tract (GI) on the antibacterial activity of Lactobacillus reuteri DPC16. Antibacterial activity, reuterin production and diol dehydratase activity were assayed in recovered isolates of L. reuteri that had been immobilized in Ca alginate-skim milk, and incubated in simulated GI fluids. Among all the recovered isolates tested, any that had undergone immobilization followed by immediate recovery of the cells without subsequent incubation in any fluids demonstrated the highest reuterin production, antimicrobial activity and diol dehydratase enzyme activity. L. reuteri DPC16 cells that had been immobilized, incubated in simulated GI fluids, and subsequently recovered from the beads often showed some loss of antimicrobial activity compared to the immobilized cells. The data confirm that the process of immobilization of L. reuteri in Ca alginate-skim milk, rather than the passage through simulated GI fluids, resulted in enhanced antibacterial activity. This is attributed to increased diol dehydratase activity, resulting in increased reuterin production.
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29
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Yamanishi M, Kinoshita K, Fukuoka M, Saito T, Tanokuchi A, Ikeda Y, Obayashi H, Mori K, Shibata N, Tobimatsu T, Toraya T. Redesign of coenzyme B12 dependent diol dehydratase to be resistant to the mechanism-based inactivation by glycerol and act on longer chain 1,2-diols. FEBS J 2012; 279:793-804. [DOI: 10.1111/j.1742-4658.2012.08470.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Celińska E. Klebsiella sppas a 1, 3-propanediol producer – the metabolic engineering approach. Crit Rev Biotechnol 2011; 32:274-88. [DOI: 10.3109/07388551.2011.616859] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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31
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Coproduction of acetaldehyde and hydrogen during glucose fermentation by Escherichia coli. Appl Environ Microbiol 2011; 77:6441-50. [PMID: 21803884 DOI: 10.1128/aem.05358-11] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Escherichia coli K-12 strain MG1655 was engineered to coproduce acetaldehyde and hydrogen during glucose fermentation by the use of exogenous acetyl-coenzyme A (acetyl-CoA) reductase (for the conversion of acetyl-CoA to acetaldehyde) and the native formate hydrogen lyase. A putative acetaldehyde dehydrogenase/acetyl-CoA reductase from Salmonella enterica (SeEutE) was cloned, produced at high levels, and purified by nickel affinity chromatography. In vitro assays showed that this enzyme had both acetaldehyde dehydrogenase activity (68.07 ± 1.63 μmol min(-1) mg(-1)) and the desired acetyl-CoA reductase activity (49.23 ± 2.88 μmol min(-1) mg(-1)). The eutE gene was engineered into an E. coli mutant lacking native glucose fermentation pathways (ΔadhE, ΔackA-pta, ΔldhA, and ΔfrdC). The engineered strain (ZH88) produced 4.91 ± 0.29 mM acetaldehyde while consuming 11.05 mM glucose but also produced 6.44 ± 0.26 mM ethanol. Studies showed that ethanol was produced by an unknown alcohol dehydrogenase(s) that converted the acetaldehyde produced by SeEutE to ethanol. Allyl alcohol was used to select for mutants with reduced alcohol dehydrogenase activity. Three allyl alcohol-resistant mutants were isolated; all produced more acetaldehyde and less ethanol than ZH88. It was also found that modifying the growth medium by adding 1 g of yeast extract/liter and lowering the pH to 6.0 further increased the coproduction of acetaldehyde and hydrogen. Under optimal conditions, strain ZH136 converted glucose to acetaldehyde and hydrogen in a 1:1 ratio with a specific acetaldehyde production rate of 0.68 ± 0.20 g h(-1) g(-1) dry cell weight and at 86% of the maximum theoretical yield. This specific production rate is the highest reported thus far and is promising for industrial application. The possibility of a more efficient "no-distill" ethanol fermentation procedure based on the coproduction of acetaldehyde and hydrogen is discussed.
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Oh BR, Seo JW, Heo SY, Hong WK, Luo LH, Joe MH, Park DH, Kim CH. Efficient production of ethanol from crude glycerol by a Klebsiella pneumoniae mutant strain. BIORESOURCE TECHNOLOGY 2011; 102:3918-22. [PMID: 21186120 DOI: 10.1016/j.biortech.2010.12.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 11/29/2010] [Accepted: 12/01/2010] [Indexed: 05/04/2023]
Abstract
A mutant strain of Klebsiella pneumoniae, termed GEM167, was obtained by γ irradiation, in which glycerol metabolism was dramatically affected on exposure to γ rays. Levels of metabolites of the glycerol reductive pathway, 1,3-propanediol (1,3-PD) and 3-hydroxypropionic acid (3-HP), were decreased in the GEM167 strain compared to a control strain, whereas the levels of metabolites derived from the oxidative pathway, 2,3-butanediol (2,3-BD), ethanol, lactate, and succinate, were increased. Notably, ethanol production from glycerol was greatly enhanced upon fermentation by the mutant strain, to a maximum production level of 21.5 g/l, with a productivity of 0.93 g/l/h. Ethanol production level was further improved to 25.0 g/l upon overexpression of Zymomonas mobilis pdc and adhII genes encoding pyruvate decarboxylase (Pdc) and aldehyde dehydrogenase (Adh), respectively in the mutant strain GEM167.
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Affiliation(s)
- Baek-Rock Oh
- Microbe-based Fusion Technology Research Center, Jeonbuk Branch Institute, KRIBB, Jeongeup, Jeonbuk 580-185, South Korea
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Mori K, Hosokawa Y, Yoshinaga T, Toraya T. Diol dehydratase-reactivating factor is a reactivase--evidence for multiple turnovers and subunit swapping with diol dehydratase. FEBS J 2010; 277:4931-43. [PMID: 21040475 DOI: 10.1111/j.1742-4658.2010.07898.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adenosylcobalamin-dependent diol dehydratase (DD) undergoes suicide inactivation by glycerol, one of its physiological substrates, resulting in the irreversible cleavage of the coenzyme Co-C bond. The damaged cofactor remains tightly bound to the active site. The DD-reactivating factor reactivates the inactivated holoenzyme in the presence of ATP and Mg(2+) by mediating the exchange of the tightly bound damaged cofactor for free intact coenzyme. In this study, we demonstrated that this reactivating factor mediates the cobalamin exchange not stoichiometrically but catalytically in the presence of ATP and Mg(2+). Therefore, we concluded that the reactivating factor is a sort of enzyme. It can be designated DD reactivase. The reactivase showed broad specificity for nucleoside triphosphates in the activation of the enzyme·cyanocobalamin complex. This result is consistent with the lack of specific interaction with the adenine ring of ADP in the crystal structure of the reactivase. The specificities of the reactivase for divalent metal ions were also not strict. DD formed 1:1 and 1:2 complexes with the reactivase in the presence of ADP and Mg(2+). Upon complex formation, one β subunit was released from the (αβ)₂ tetramer of the reactivase. This result, together with the similarity in amino acid sequences and folds between the DD β subunit and the reactivase β subunit, suggests that subunit displacement or swapping takes place upon formation of the enzyme·reactivase complex. This would result in the dissociation of the damaged cofactor from the inactivated holoenzyme, as suggested by the crystal structures of the reactivase and DD.
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Affiliation(s)
- Koichi Mori
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Japan
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Toraya T, Honda S, Mori K. Coenzyme B12-Dependent Diol Dehydratase Is a Potassium Ion-Requiring Calcium Metalloenzyme: Evidence That the Substrate-Coordinated Metal Ion Is Calcium. Biochemistry 2010; 49:7210-7. [DOI: 10.1021/bi100561m] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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
- Department of Industrial Biochemistry, Faculty of Engineering, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Susumu Honda
- Department of Industrial Biochemistry, Faculty of Engineering, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - 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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Akita K, Hieda N, Baba N, Kawaguchi S, Sakamoto H, Nakanishi Y, Yamanishi M, Mori K, Toraya T. Purification and some properties of wild-type and N-terminal-truncated ethanolamine ammonia-lyase of Escherichia coli. J Biochem 2009; 147:83-93. [PMID: 19762342 DOI: 10.1093/jb/mvp145] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The methods of homologous high-level expression and simple large-scale purification for coenzyme B(12)-dependent ethanolamine ammonia-lyase of Escherichia coli were developed. The eutB and eutC genes in the eut operon encoded the large and small subunits of the enzyme, respectively. The enzyme existed as the heterododecamer alpha(6)beta(6). Upon active-site titration with adeninylpentylcobalamin, a strong competitive inhibitor for coenzyme B(12), the binding of 1 mol of the inhibitor per mol of the alphabeta unit caused complete inhibition of enzyme, in consistent with its subunit structure. EPR spectra indicated the formation of substrate-derived radicals during catalysis and the binding of cobalamin in the base-on mode, i.e. with 5,6-dimethylbenzimidazole coordinating to the cobalt atom. The purified wild-type enzyme underwent aggregation and inactivation at high concentrations. Limited proteolysis with trypsin indicated that the N-terminal region is not essential for catalysis. His-tagged truncated enzymes were similar to the wild-type enzyme in catalytic properties, but more resistant to p-chloromercuribenzoate than the wild-type enzyme. A truncated enzyme was highly soluble even in the absence of detergent and resistant to aggregation and oxidative inactivation at high concentrations, indicating that a short N-terminal sequence is sufficient to change the solubility and stability of the enzyme.
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Affiliation(s)
- Keita Akita
- 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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36
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Cloning, expression and reactivating characterization of glycerol dehydratase reactivation factor from Klebsiella pneumoniae XJPD-Li. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0093-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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37
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Pasteris SE, Strasser de Saad AM. Sugar-glycerol cofermentations by Lactobacillus hilgardii isolated from wine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:3853-3858. [PMID: 19323470 DOI: 10.1021/jf803781k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Glycerol catabolism was studied in Lactobacillus hilgardii X(1)B from wine, growing on glycerol and limiting glucose or fructose concentrations in anaerobiosis and microaerophilia. Glycerol consumption occurred simultaneously with sugar use, and it was higher with fructose as a cofermenting sugar in microaerophilia. Enzymatic activities of the glycerol kinase and glycerol dehydratase pathways were detected in both incubation conditions. In anaerobiosis, the main products were lactate, acetate, ethanol, and the intermediary product of the glycerol dehydratase pathway, 3-hydroxypropionaldehyde. However, in microaerophilia, 1,3-propanediol was also detected. In anaerobic glucose + glycerol and fructose + glycerol cultures as in microaerophilic glucose + glycerol cultures, glycerol was degraded mainly through the reductive pathway. However, when L. hilgardii X(1)B was grown on fructose + glycerol cultures in microaerophilia, glycerol dissimilation occurred mainly via the glycerol kinase way. According to these results, L. hilgardii X(1)B can degrade glycerol by producing 3-hydroxypropionaldehyde and acetic acid, both undesirable products for wine sensorial quality.
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Affiliation(s)
- Sergio E Pasteris
- Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Argentina.
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38
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Xu XL, Zhang GL, Wang LW, Ma BB, Li C. Quantitative analysis on inactivation and reactivation of recombinant glycerol dehydratase from Klebsiella pneumoniae XJPD-Li. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2008.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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39
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Characterization of glycerol dehydratase expressed by fusing its alpha- and beta-subunits. Biotechnol Lett 2009; 31:711-7. [PMID: 19152074 DOI: 10.1007/s10529-009-9911-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 12/21/2008] [Indexed: 10/21/2022]
Abstract
The gdh and gdhr genes, encoding B(12)-dependent glycerol dehydratase (GDH) and glycerol dehydratase reactivase (GDHR), respectively, in Klebsiella pneumoniae, were cloned and expressed in E. coli. Part of the beta-subunit was lost during GDH purification when co-expressing alpha, beta and gamma subunit. This was overcome by fusing the beta-subunit to alpha- or gamma-subunit with/without the insertion of a linker peptide between the fusion moieties. The kinetic properties of the fusion enzymes were characterized and compared with wild type enzyme. The results demonstrated that the fusion protein GDHALB/C, constructed by linking the N-terminal of beta-subunit to the C-terminal of alpha subunit through a (Gly(4)Ser)(4) linker peptide, had the greatest catalytic activity. Similar to the wild-type enzyme, GDHALB/C underwent mechanism-based inactivation by glycerol during catalysis and could be reactivated by GDHR.
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40
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Low-solubility glycerol dehydratase, a chimeric enzyme of coenzyme B12-dependent glycerol and diol dehydratases. Arch Microbiol 2008; 191:199-206. [DOI: 10.1007/s00203-008-0443-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Revised: 09/29/2008] [Accepted: 10/27/2008] [Indexed: 11/26/2022]
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41
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Ogura KI, Kunita SI, Mori K, Tobimatsu T, Toraya T. Roles of adenine anchoring and ion pairing at the coenzyme B12-binding site in diol dehydratase catalysis. FEBS J 2008; 275:6204-16. [DOI: 10.1111/j.1742-4658.2008.06745.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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42
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Exogenous or L-rhamnose-derived 1,2-propanediol is metabolized via a pduD-dependent pathway in Listeria innocua. Appl Environ Microbiol 2008; 74:7073-9. [PMID: 18805996 DOI: 10.1128/aem.01074-08] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
1,2-Propanediol (1,2-PD) added exogenously to cultures or produced endogenously from l-rhamnose is metabolized to n-propanol and propionate in Listeria innocua Lin11. The pduD gene, which encodes a diol dehydratase ss subunit homolog, is required for 1,2-PD catabolism. pduD and 16 other genes within the pduA-to-pduF region of a large gene cluster are induced in medium containing 1,2-PD.
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43
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Zheng ZM, Xu YZ, Liu HJ, Guo NN, Cai ZZ, Liu DH. Physiologic mechanisms of sequential products synthesis in 1,3-propanediol fed-batch fermentation by Klebsiella pneumoniae. Biotechnol Bioeng 2008; 100:923-32. [PMID: 18551520 DOI: 10.1002/bit.21830] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The glycerol fed-batch fermentation by Klebsiella pneumoniae CGMCC 1.6366 exhibited the sequential synthesis of products, including acetate, 1,3-propanediol (1,3-PD), 2,3-butanediol, ethanol, succinate, and lactate. The dominant flux distribution was shifted from acetate formation to 1,3-PD formation in early- exponential growth phase and then to lactate synthesis in late-exponential growth phase. The underlying physiological mechanism of the above observations has been investigated via the related enzymes, nucleotide, and intermediary metabolites analysis. The carbon flow shift is dictated by the intrinsic physiological state and enzymatic activity regulation. Especially, the internal redox state could serve as a rate-controlling factor for 1,3-PD production. The q(1,3-PD) formation was the combined outcomes of regulations of glycerol dehydratase activity and internal redox balancing. The q(ethanol)/q(acetate) ratios demonstrated the flexible adaptation mechanism of K. pneumoniae preferring ATP generation in early-exponential growth phase. A low PEP to pyruvate ratio corresponded LDH activity increase, leading to lactate accumulation in stationary phase.
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Affiliation(s)
- Zong-Ming Zheng
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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44
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Toraya T, Tamura N, Watanabe T, Yamanishi M, Hieda N, Mori K. Mechanism-based inactivation of coenzyme B12-dependent diol dehydratase by 3-unsaturated 1,2-diols and thioglycerol. J Biochem 2008; 144:437-46. [PMID: 18586770 DOI: 10.1093/jb/mvn086] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The reactions of diol dehydratase with 3-unsaturated 1,2-diols and thioglycerol were investigated. Holodiol dehydratase underwent rapid and irreversible inactivation by either 3-butene-1,2-diol, 3-butyne-1,2-diol or thioglycerol without catalytic turnovers. In the inactivation, the Co-C bond of adenosylcobalamin underwent irreversible cleavage forming unidentified radicals and cob(II)alamin that resisted oxidation even in the presence of oxygen. Two moles of 5'-deoxyadenosine per mol of enzyme was formed as an inactivation product from the coenzyme adenosyl group. Inactivated holoenzymes underwent reactivation by diol dehydratase-reactivating factor in the presence of ATP, Mg(2+) and adenosylcobalamin. It was thus concluded that these substrate analogues served as mechanism-based inactivators or pseudosubstrates, and that the coenzyme was damaged in the inactivation, whereas apoenzyme was not damaged. In the inactivation by 3-unsaturated 1,2-diols, product radicals stabilized by neighbouring unsaturated bonds might be unable to back-abstract the hydrogen atom from 5'-deoxyadenosine and then converted to unidentified products. In the inactivation by thioglycerol, a product radical may be lost by the elimination of sulphydryl group producing acrolein and unidentified sulphur compound(s). H(2)S or sulphide ion was not formed. The loss or stabilization of product radicals would result in the inactivation of holoenzyme, because the regeneration of the coenzyme becomes impossible.
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Affiliation(s)
- Tetsuo Toraya
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Okayama, Japan.
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45
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Lactobacillus reuteri DSM 20016 produces cobalamin-dependent diol dehydratase in metabolosomes and metabolizes 1,2-propanediol by disproportionation. J Bacteriol 2008; 190:4559-67. [PMID: 18469107 DOI: 10.1128/jb.01535-07] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A Lactobacillus reuteri strain isolated from sourdough is known to produce the vitamin cobalamin. The organism requires this for glycerol cofermentation by a cobalamin-dependent enzyme, usually termed glycerol dehydratase, in the synthesis of the antimicrobial substance reuterin. We show that the cobalamin-synthesizing capacity of another L. reuteri strain (20016, the type strain, isolated from the human gut and recently sequenced as F275) is genetically and phenotypically linked, as in the Enterobacteriaceae, to the production of a cobalamin-dependent enzyme which is associated with a bacterial microcompartment (metabolosome) and known as diol dehydratase. We show that this enzyme allows L. reuteri to carry out a disproportionation reaction converting 1,2-propanediol to propionate and propanol. The wide distribution of this operon suggests that it is adapted to horizontal transmission between bacteria. However, there are significant genetic and phenotypic differences between the Lactobacillus background and the Enterobacteriaceae. Electron microscopy reveals that the bacterial microcompartment in L. reuteri occupies a smaller percentage of the cytoplasm than in gram-negative bacteria. DNA sequence data show evidence of a regulatory control mechanism different from that in gram-negative bacteria, with the presence of a catabolite-responsive element (CRE) sequence immediately upstream of the pdu operon encoding diol dehydratase and metabolosome structural genes in L. reuteri. The metabolosome-associated diol dehydratase we describe is the only candidate glycerol dehydratase present on inspection of the L. reuteri F275 genome sequence.
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46
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Németh A, Sevella B. Development of a new bioprocess for production of 1,3-propanediol I.: Modeling of glycerol bioconversion to 1,3-propanediol with Klebsiella pneumoniae enzymes. Appl Biochem Biotechnol 2008; 144:47-58. [PMID: 18415986 DOI: 10.1007/s12010-007-0040-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Glycerol is a renewable resource for it is formed as a byproduct during biodiesel production. Because of its large volume production, it seems to be a good idea to develop a technology that converts this waste into products of high value, for example, to 1,3-propanediol (1,3-PD). We suggested an enzymatic bioconversion in a membrane reactor in which the NAD coenzyme can be regenerated, and three key enzymes are retained by a 10-kDa ultrafilter membrane. Unfortunately, some byproducts also formed during successful glycerol to 1,3-PD bioconversion runs, as we used crude enzyme solution of Klebsiella pneumoniae. To study the possibilities to avoid this byproduct formation, we built a mathematical description of this system. The model was also used for simulation bioconversions of high glycerol concentration with and without elimination of byproduct formation and of continuous operation.
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Affiliation(s)
- Aron Németh
- Department of Agricultural Chemical Technology, Budapest University of Technology and Economics, Budapest, Hungary
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47
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Wang F, Qu H, Zhang D, Tian P, Tan T. Production of 1,3-propanediol from glycerol by recombinant E. coli using incompatible plasmids system. Mol Biotechnol 2008; 37:112-9. [PMID: 17914171 DOI: 10.1007/s12033-007-0041-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 10/23/2022]
Abstract
1,3-Propanediol (1,3-PD) has numerous applications in polymers, cosmetics, foods, lubricants, and medicines as a bifunctional organic compound. The genes for the production of 1,3-PD in Klebsiella pneumoniae, dhaB, which encodes glycerol dehydratase, and dhaT, which encodes 1,3-PD oxidoreductase, and gdrAB, which encodes glycerol dehydratase reactivating factor, are naturally under the control of different promoters and are transcribed in different directions. These genes were coexpressed in E. coli using two incompatible plasmids (pET28a and pET22b) in the presence of selective pressure. The recombinant E. coli coexpressed the glycerol dehydratase, 1,3-propanediol oxidoreductase and reactivating factor for the glycerol dehydratase at high levels. In a fed-batch fermentation of glycerol and glucose, the recombinant E. coli containing these two incompatible plasmids consumed 14.3 g/l glycerol and produced 8.6 g/l 1,3-propanediol. In the substitution case of yqhD (encoding alcohol dehydrogenase from E. coli) for dhaT, the final 1,3-propanediol concentration of the recombinant E. coli could reach 13.2 g/l.
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Affiliation(s)
- Fenghuan Wang
- Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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48
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Kinoshita K, Kawata M, Ogura KI, Yamasaki A, Watanabe T, Komoto N, Hieda N, Yamanishi M, Tobimatsu T, Toraya T. Histidine-α143 Assists 1,2-Hydroxyl Group Migration and Protects Radical Intermediates in Coenzyme B12-Dependent Diol Dehydratase. Biochemistry 2008; 47:3162-73. [DOI: 10.1021/bi7018095] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Koichiro Kinoshita
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Masahiro Kawata
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Ken-ichi Ogura
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Ai Yamasaki
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Takeshi Watanabe
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Noriaki Komoto
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Naoki Hieda
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Mamoru Yamanishi
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Takamasa Tobimatsu
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
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49
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Kajiura H, Mori K, Shibata N, Toraya T. Molecular basis for specificities of reactivating factors for adenosylcobalamin-dependent diol and glycerol dehydratases. FEBS J 2007; 274:5556-66. [PMID: 17916188 DOI: 10.1111/j.1742-4658.2007.06074.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adenosylcobalamin-dependent diol and glycerol dehydratases are isofunctional enzymes and undergo mechanism-based inactivation by a physiological substrate glycerol during catalysis. Inactivated holoenzymes are reactivated by their own reactivating factors that mediate the ATP-dependent exchange of an enzyme-bound, damaged cofactor for free adenosylcobalamin through intermediary formation of apoenzyme. The reactivation takes place in two steps: (a) ADP-dependent cobalamin release and (b) ATP-dependent dissociation of the resulting apoenzyme-reactivating factor complexes. The in vitro experiments with purified proteins indicated that diol dehydratase-reactivating factor (DDR) cross-reactivates the inactivated glycerol dehydratase, whereas glycerol dehydratase-reactivating factor (GDR) did not cross-reactivate the inactivated diol dehydratase. We investigated the molecular basis of their specificities in vitro by using purified preparations of cognate and noncognate enzymes and reactivating factors. DDR mediated the exchange of glycerol dehydratase-bound cyanocobalamin for free adeninylpentylcobalamin, whereas GDR cannot mediate the exchange of diol dehydratase-bound cyanocobalamin for free adeninylpentylcobalamin. As judged by denaturing PAGE, the glycerol dehydratase-DDR complex was cross-formed, although the diol dehydratase-GDR complex was not formed. There were no specificities of reactivating factors in the ATP-dependent dissociation of enzyme-reactivating factor complexes. Thus, it is very likely that the specificities of reactivating factors are determined by the capability of reactivating factors to form complexes with apoenzymes. A modeling study based on the crystal structures of enzymes and reactivating factors also suggested why DDR cross-forms a complex with glycerol dehydratase, and why GDR does not cross-form a complex with diol dehydratase.
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Affiliation(s)
- Hideki Kajiura
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Japan
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50
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Wang F, Qu H, Tian P, Tan T. Heterologous expression and characterization of recombinant glycerol dehydratase from Klebsiella pneumoniae in Escherichia coli. Biotechnol J 2007; 2:736-42. [PMID: 17373646 DOI: 10.1002/biot.200600101] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Glycerol dehydratase (EC 4.2.1.30), as one of the key enzymes in converting glycerol to the valuable intermediate 1,3-propanediol, is important for biochemical industry. The dhaB genes encoding coenzyme B(12)-dependent glycerol dehydratase in Klebsiella pneumoniae were cloned and expressed in Escherichia coli. An effective co-expression system of multiple subunits protein was constructed. Heterologous expression vectors were constructed using the splicing by overlap extension-PCR technique to co-express the three subunits of the glycerol dehydratase. After induction by isopropyl-beta-D-thiogalactopyranoside, SDS-PAGE analysis revealed that: (i) only the alpha subunit of glycerol dehydratase was expressed in direct expression system, (ii) the three subunits of glycerol dehydratase with predicted molecular massess of 64 (agr;), 22 (beta), and 16 kDa (gamma) were expressed simultaneously in co-expression system, and (iii) the fusion expression system expressed the fusion protein of 99 kDa. Enzyme assay showed that the activities of three heterologous expression products were 27.4, 2.3, and 0.2 U/mg. The highest enzyme activity was almost 17 times of that in K. pneumoniae. The recombinant enzyme was purified and biochemically characterized. The apparent Km values of the enzyme for coenzyme B(12) and 1, 2-propanediol were 8.5 nM and 1.2 mM, respectively. The enzyme showed maximum activity at pH 8.5 and 37 degrees C.
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Affiliation(s)
- Fenghuan Wang
- Beijing key lab of bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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