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Frazão CJR, Wagner N, Rabe K, Walther T. Construction of a synthetic metabolic pathway for biosynthesis of 2,4-dihydroxybutyric acid from ethylene glycol. Nat Commun 2023; 14:1931. [PMID: 37024485 PMCID: PMC10079672 DOI: 10.1038/s41467-023-37558-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 03/22/2023] [Indexed: 04/08/2023] Open
Abstract
Ethylene glycol is an attractive two-carbon alcohol substrate for biochemical product synthesis as it can be derived from CO2 or syngas at no sacrifice to human food stocks. Here, we disclose a five-step synthetic metabolic pathway enabling the carbon-conserving biosynthesis of the versatile platform molecule 2,4-dihydroxybutyric acid (DHB) from this compound. The linear pathway chains ethylene glycol dehydrogenase, D-threose aldolase, D-threose dehydrogenase, D-threono-1,4-lactonase, D-threonate dehydratase and 2-oxo-4-hydroxybutyrate reductase enzyme activities in succession. We screen candidate enzymes with D-threose dehydrogenase and D-threonate dehydratase activities on cognate substrates with conserved carbon-centre stereochemistry. Lastly, we show the functionality of the pathway by its expression in an Escherichia coli strain and production of 1 g L-1 and 0.8 g L-1 DHB from, respectively, glycolaldehyde or ethylene glycol.
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Affiliation(s)
- Cláudio J R Frazão
- Institute of Natural Materials Technology, TU Dresden, 01062, Dresden, Germany
| | - Nils Wagner
- Institute of Natural Materials Technology, TU Dresden, 01062, Dresden, Germany
| | - Kenny Rabe
- Institute of Natural Materials Technology, TU Dresden, 01062, Dresden, Germany
| | - Thomas Walther
- Institute of Natural Materials Technology, TU Dresden, 01062, Dresden, Germany.
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2
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Molecular evolutionary insight of structural zinc atom in yeast xylitol dehydrogenases and its application in bioethanol production by lignocellulosic biomass. Sci Rep 2023; 13:1920. [PMID: 36732376 PMCID: PMC9895041 DOI: 10.1038/s41598-023-29195-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/31/2023] [Indexed: 02/04/2023] Open
Abstract
Xylitol dehydrogenase (XDH) catalyzes the NAD+-dependent oxidization of xylitol into D-xylulose, and belongs to a zinc-dependent medium-chain dehydrogenase/reductase family. This protein family consists of enzymes with one or two zinc atoms per subunit, among which catalytic zinc is necessary for the activity. Among many XDHs from yeast and fungi, XDH from Pichia stipitis is one of the key enzymes for bioethanol production by lignocellulosic biomass, and possesses only a catalytic zinc atom. Despite its importance in bioindustry, a structural data of XDH has not yet been available, and little insight into the role of a second zinc atom in this protein family is known. We herein report the crystal structure of XDH from P. stipitis using a thermostabilized mutant. In the refined structure, a second zinc atom clearly coordinated with four artificially introduced cysteine ligands. Homologous mutations in XDH from Saccharomyces cerevisiae also stabilized and enhanced activity. The substitution of each of the four cysteine ligands with an aspartate in XDH from Schizosaccharomyces pombe contributed to the significantly better maintenance of activity and thermostability than their substitution with a serine, providing a novel hypothesis for how this zinc atom was eliminated.
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3
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Ren Y, Eronen V, Blomster Andberg M, Koivula A, Hakulinen N. Structure and function of aldopentose catabolism enzymes involved in oxidative non-phosphorylative pathways. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:147. [PMID: 36578086 PMCID: PMC9795676 DOI: 10.1186/s13068-022-02252-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022]
Abstract
Platform chemicals and polymer precursors can be produced via enzymatic pathways starting from lignocellulosic waste materials. The hemicellulose fraction of lignocellulose contains aldopentose sugars, such as D-xylose and L-arabinose, which can be enzymatically converted into various biobased products by microbial non-phosphorylated oxidative pathways. The Weimberg and Dahms pathways convert pentose sugars into α-ketoglutarate, or pyruvate and glycolaldehyde, respectively, which then serve as precursors for further conversion into a wide range of industrial products. In this review, we summarize the known three-dimensional structures of the enzymes involved in oxidative non-phosphorylative pathways of pentose catabolism. Key structural features and reaction mechanisms of a diverse set of enzymes responsible for the catalytic steps in the reactions are analysed and discussed.
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Affiliation(s)
- Yaxin Ren
- grid.9668.10000 0001 0726 2490Department of Chemistry, University of Eastern Finland, 111, 80101 Joensuu, Finland
| | - Veikko Eronen
- grid.9668.10000 0001 0726 2490Department of Chemistry, University of Eastern Finland, 111, 80101 Joensuu, Finland
| | | | - Anu Koivula
- grid.6324.30000 0004 0400 1852VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Nina Hakulinen
- grid.9668.10000 0001 0726 2490Department of Chemistry, University of Eastern Finland, 111, 80101 Joensuu, Finland
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4
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Stark F, Loderer C, Petchey M, Grogan G, Ansorge-Schumacher M. Advanced Insights into Catalytic and Structural Features of the Zinc-Dependent Alcohol Dehydrogenase from Thauera aromatica. Chembiochem 2022; 23:e202200149. [PMID: 35557486 PMCID: PMC9400901 DOI: 10.1002/cbic.202200149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/12/2022] [Indexed: 11/10/2022]
Abstract
The asymmetric reduction of ketones to chiral hydroxyl compounds by alcohol dehydrogenases (ADHs) is an established strategy for the provision of valuable precursors for fine chemicals and pharmaceutics. However, most ADHs favor linear aliphatic and aromatic carbonyl compounds, and suitable biocatalysts with preference for cyclic ketones and diketones are still scarce. Among the few candidates, the alcohol dehydrogenase from Thauera aromatica (ThaADH) stands out with a high activity for the reduction of the cyclic α‐diketone 1,2‐cyclohexanedione to the corresponding α‐hydroxy ketone. This study elucidates catalytic and structural features of the enzyme. ThaADH showed a remarkable thermal and pH stability as well as stability in the presence of polar solvents. A thorough description of the substrate scope combined with the resolution and description of the crystal structure, demonstrated a strong preference of ThaADH for cyclic α‐substituted cyclohexanones, and indicated structural determinants responsible for the unique substrate acceptance.
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Affiliation(s)
- Frances Stark
- TU Dresden: Technische Universitat Dresden, Molecular Biotechnology, GERMANY
| | - Christoph Loderer
- TU Dresden: Technische Universitat Dresden, Molecular Biotechnology, GERMANY
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Jiang Z, Xu C, Wang L, Hong K, Ma C, Lv C. Potential enzymes involved in beer monoterpenoids transformation: structures, functions and challenges. Crit Rev Food Sci Nutr 2021; 63:2082-2092. [PMID: 34459289 DOI: 10.1080/10408398.2021.1970510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Monoterpenes are important flavor and fragrance compounds in food. In beer, the monoterpenes mainly come from hops added during boiling process. Biotransformations of monoterpene which occurred during fermentation conferred beer with various kinds of aroma profiles, which can be mainly attributed to the contribution of enzymes in yeast. However, there are few reports on the identification and characterization of these enzymes in yeast. Illustrating the structure and functions of key enzymes related to transformations will broaden their potential applications in beer or other foodstuffs. Monoterpenoids including terpene hydrocarbons (limonene, myrcene, and pinene) and terpene alcohol (linalool, geraniol, nerol, and citronellol) gave the beer flower-like or fruit-like aroma. The biotransformation of monoterpenes and monoterpene alcohols in bacteria and yeast, and potential enzymes related to the transformation of them are reviewed here. Enzymes primarily are dehydrogenases including linalool dehydrogenase/isomerase, geraniol/geranial dehydrogenase, nerol dehydrogenase and citronellol dehydrogenase. Most of them are substrate-specific or substrate-specific after modifications by biotechnology methods, and part of them have been expressed in E. coli, while the purification and catalytic rate is very low. Efforts should be made to acquire abundant enzymes, and to fabricate enzyme-expressing yeast, which can be further applied in beer fermentation system.highlightsMonoterpenoids contributed to the flavor of food, especially beer.Transformation of monoterpenoids occurred during fermentation.Various kinds of enzymes are involved in the transformation of monoterpenoids in bacteria, yeast, etc.Crystal structures of these enzymes have been partially resolved.Few enzymes are further applied in food system to obtain abundant flavor.
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Affiliation(s)
- Zhenghui Jiang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, China
| | - Chen Xu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, China
| | - Limin Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, China
| | - Kai Hong
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, China
| | - Changwei Ma
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, China
| | - Chenyan Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, China
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6
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Watanabe S, Fukumori F, Nishiwaki H, Sakurai Y, Tajima K, Watanabe Y. Novel non-phosphorylative pathway of pentose metabolism from bacteria. Sci Rep 2019; 9:155. [PMID: 30655589 PMCID: PMC6336799 DOI: 10.1038/s41598-018-36774-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 09/30/2018] [Indexed: 11/09/2022] Open
Abstract
Pentoses, including D-xylose, L-arabinose, and D-arabinose, are generally phosphorylated to D-xylulose 5-phosphate in bacteria and fungi. However, in non-phosphorylative pathways analogous to the Entner-Dodoroff pathway in bacteria and archaea, such pentoses can be converted to pyruvate and glycolaldehyde (Route I) or α-ketoglutarate (Route II) via a 2-keto-3-deoxypentonate (KDP) intermediate. Putative gene clusters related to these metabolic pathways were identified on the genome of Herbaspirillum huttiense IAM 15032 using a bioinformatic analysis. The biochemical characterization of C785_RS13685, one of the components encoded to D-arabinonate dehydratase, differed from the known acid-sugar dehydratases. The biochemical characterization of the remaining components and a genetic expression analysis revealed that D- and L-KDP were converted not only to α-ketoglutarate, but also pyruvate and glycolate through the participation of dehydrogenase and hydrolase (Route III). Further analyses revealed that the Route II pathway of D-arabinose metabolism was not evolutionally related to the analogous pathway from archaea.
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Affiliation(s)
- Seiya Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan. .,Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan. .,Center for Marine Environmental Studies (CMES), Ehime University, 2-5 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan.
| | - Fumiyasu Fukumori
- Faculty of Food and Nutritional Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan
| | - Hisashi Nishiwaki
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.,Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
| | - Yasuhiro Sakurai
- Department of Bio-molecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Kunihiko Tajima
- Department of Bio-molecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Yasuo Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.,Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
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7
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Tan CS, Hassan M, Mohamed Hussein ZA, Ismail I, Ho KL, Ng CL, Zainal Z. Structural and kinetic studies of a novel nerol dehydrogenase from Persicaria minor, a nerol-specific enzyme for citral biosynthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 123:359-368. [PMID: 29304481 DOI: 10.1016/j.plaphy.2017.12.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/23/2017] [Accepted: 12/20/2017] [Indexed: 06/07/2023]
Abstract
Geraniol degradation pathway has long been elucidated in microorganisms through bioconversion studies, yet weakly characterised in plants; enzyme with specific nerol-oxidising activity has not been reported. A novel cDNA encodes nerol dehydrogenase (PmNeDH) was isolated from Persicaria minor. The recombinant PmNeDH (rPmNeDH) is a homodimeric enzyme that belongs to MDR (medium-chain dehydrogenases/reductases) superfamily that catalyses the first oxidative step of geraniol degradation pathway in citral biosynthesis. Kinetic analysis revealed that rPmNeDH has a high specificity for allylic primary alcohols with backbone ≤10 carbons. rPmNeDH has ∼3 fold higher affinity towards nerol (cis-3,7-dimethyl-2,6-octadien-1-ol) than its trans-isomer, geraniol. To our knowledge, this is the first alcohol dehydrogenase with higher preference towards nerol, suggesting that nerol can be effective substrate for citral biosynthesis in P. minor. The rPmNeDH crystal structure (1.54 Å) showed high similarity with enzyme structures from MDR superfamily. Structure guided mutation was conducted to describe the relationships between substrate specificity and residue substitutions in the active site. Kinetics analyses of wild-type rPmNeDH and several active site mutants demonstrated that the substrate specificity of rPmNeDH can be altered by changing any selected active site residues (Asp280, Leu294 and Ala303). Interestingly, the L294F, A303F and A303G mutants were able to revamp the substrate preference towards geraniol. Furthermore, mutant that exhibited a broader substrate range was also obtained. This study demonstrates that P. minor may have evolved to contain enzyme that optimally recognise cis-configured nerol as substrate. rPmNeDH structure provides new insights into the substrate specificity and active site plasticity in MDR superfamily.
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Affiliation(s)
- Cheng Seng Tan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Maizom Hassan
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Zeti Azura Mohamed Hussein
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Ismanizan Ismail
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Chyan Leong Ng
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia.
| | - Zamri Zainal
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia.
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8
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McClintock MK, Wang J, Zhang K. Application of Nonphosphorylative Metabolism as an Alternative for Utilization of Lignocellulosic Biomass. Front Microbiol 2017; 8:2310. [PMID: 29218038 PMCID: PMC5703739 DOI: 10.3389/fmicb.2017.02310] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/08/2017] [Indexed: 01/28/2023] Open
Abstract
Production of chemicals via fermentation has been evolving over the past 30 years in search of economically viable systems. Thus far, there have been few industrially relevant chemicals that have seen commercialization, examples being lactic acid and ethanol. Currently, many of these fermentation processes still compete with food sources. In order to reduce this competition fermentation of alternative feedstocks, such as lignocellulosic biomass must to be utilized. Hemicellulosic sugars can be employed effectively for the production of chemicals by incorporating nonphosphorylative metabolism. This review covers nonphosphorylative metabolism, the pathways and enzymes involved, as well as the products that have been produced using nonphosphorylative metabolism.
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Affiliation(s)
- Maria K McClintock
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, United States
| | - Jilong Wang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, United States
| | - Kechun Zhang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, United States
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Wolf J, Stark H, Fafenrot K, Albersmeier A, Pham TK, Müller KB, Meyer BH, Hoffmann L, Shen L, Albaum SP, Kouril T, Schmidt-Hohagen K, Neumann-Schaal M, Bräsen C, Kalinowski J, Wright PC, Albers SV, Schomburg D, Siebers B. A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeon Sulfolobus solfataricus in response to the carbon source L-fucose versus D-glucose. Mol Microbiol 2016; 102:882-908. [PMID: 27611014 DOI: 10.1111/mmi.13498] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2016] [Indexed: 12/01/2022]
Abstract
Archaea are characterised by a complex metabolism with many unique enzymes that differ from their bacterial and eukaryotic counterparts. The thermoacidophilic archaeon Sulfolobus solfataricus is known for its metabolic versatility and is able to utilize a great variety of different carbon sources. However, the underlying degradation pathways and their regulation are often unknown. In this work, the growth on different carbon sources was analysed, using an integrated systems biology approach. The comparison of growth on L-fucose and D-glucose allows first insights into the genome-wide changes in response to the two carbon sources and revealed a new pathway for L-fucose degradation in S. solfataricus. During growth on L-fucose major changes in the central carbon metabolic network, as well as an increased activity of the glyoxylate bypass and the 3-hydroxypropionate/4-hydroxybutyrate cycle were observed. Within the newly discovered pathway for L-fucose degradation the following key reactions were identified: (i) L-fucose oxidation to L-fuconate via a dehydrogenase, (ii) dehydration to 2-keto-3-deoxy-L-fuconate via dehydratase, (iii) 2-keto-3-deoxy-L-fuconate cleavage to pyruvate and L-lactaldehyde via aldolase and (iv) L-lactaldehyde conversion to L-lactate via aldehyde dehydrogenase. This pathway as well as L-fucose transport shows interesting overlaps to the D-arabinose pathway, representing another example for pathway promiscuity in Sulfolobus species.
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Affiliation(s)
- Jacqueline Wolf
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Helge Stark
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Katharina Fafenrot
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
| | - Andreas Albersmeier
- Center for Biotechnology - CeBiTec, Universität Bielefeld, Bielefeld, 33615, Germany
| | - Trong K Pham
- Departement of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD, UK
| | - Katrin B Müller
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Benjamin H Meyer
- Molecular Biology of Archaea, Institute for Biology II - Microbiology, Universität Freiburg, Freiburg, 79104, Germany
| | - Lena Hoffmann
- Molecular Biology of Archaea, Institute for Biology II - Microbiology, Universität Freiburg, Freiburg, 79104, Germany
| | - Lu Shen
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
| | - Stefan P Albaum
- Center for Biotechnology - CeBiTec, Universität Bielefeld, Bielefeld, 33615, Germany
| | - Theresa Kouril
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
| | - Kerstin Schmidt-Hohagen
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Meina Neumann-Schaal
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, Universität Bielefeld, Bielefeld, 33615, Germany
| | - Phillip C Wright
- Departement of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD, UK
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute for Biology II - Microbiology, Universität Freiburg, Freiburg, 79104, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
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10
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Identification and characterization of 2-keto-3-deoxy-l-rhamnonate dehydrogenase belonging to the MDR superfamily from the thermoacidophilic bacterium Sulfobacillus thermosulfidooxidans: implications to l-rhamnose metabolism in archaea. Extremophiles 2015; 19:469-78. [DOI: 10.1007/s00792-015-0731-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/09/2015] [Indexed: 10/24/2022]
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11
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Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. Microbiol Mol Biol Rev 2014; 78:89-175. [PMID: 24600042 DOI: 10.1128/mmbr.00041-13] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The metabolism of Archaea, the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya. However, this metabolic complexity in Archaea is accompanied by the absence of many "classical" pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of "new," unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea. In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya. Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.
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Molecular characterization of an NADPH-dependent acetoin reductase/2,3-butanediol dehydrogenase from Clostridium beijerinckii NCIMB 8052. Appl Environ Microbiol 2014; 80:2011-20. [PMID: 24441158 DOI: 10.1128/aem.04007-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acetoin reductase is an important enzyme for the fermentative production of 2,3-butanediol, a chemical compound with a very broad industrial use. Here, we report on the discovery and characterization of an acetoin reductase from Clostridium beijerinckii NCIMB 8052. An in silico screen of the C. beijerinckii genome revealed eight potential acetoin reductases. One of them (CBEI_1464) showed substantial acetoin reductase activity after expression in Escherichia coli. The purified enzyme (C. beijerinckii acetoin reductase [Cb-ACR]) was found to exist predominantly as a homodimer. In addition to acetoin (or 2,3-butanediol), other secondary alcohols and corresponding ketones were converted as well, provided that another electronegative group was attached to the adjacent C-3 carbon. Optimal activity was at pH 6.5 (reduction) and 9.5 (oxidation) and around 68°C. Cb-ACR accepts both NADH and NADPH as electron donors; however, unlike closely related enzymes, NADPH is preferred (Km, 32 μM). Cb-ACR was compared to characterized close homologs, all belonging to the "threonine dehydrogenase and related Zn-dependent dehydrogenases" (COG1063). Metal analysis confirmed the presence of 2 Zn(2+) atoms. To gain insight into the substrate and cofactor specificity, a structural model was constructed. The catalytic zinc atom is likely coordinated by Cys37, His70, and Glu71, while the structural zinc site is probably composed of Cys100, Cys103, Cys106, and Cys114. Residues determining NADP specificity were predicted as well. The physiological role of Cb-ACR in C. beijerinckii is discussed.
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13
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Kort JC, Esser D, Pham TK, Noirel J, Wright PC, Siebers B. A cool tool for hot and sour Archaea: Proteomics of Sulfolobus solfataricus. Proteomics 2013; 13:2831-50. [DOI: 10.1002/pmic.201300088] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/23/2013] [Accepted: 05/03/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Julia Christin Kort
- Molecular Enzyme Technology and Biochemistry; Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen; Essen Germany
| | - Dominik Esser
- Molecular Enzyme Technology and Biochemistry; Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen; Essen Germany
| | - Trong Khoa Pham
- Department of Chemical and Biological Engineering; ChELSI Institute, The University of Sheffield; Sheffield UK
| | - Josselin Noirel
- Department of Chemical and Biological Engineering; ChELSI Institute, The University of Sheffield; Sheffield UK
| | - Phillip C. Wright
- Department of Chemical and Biological Engineering; ChELSI Institute, The University of Sheffield; Sheffield UK
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry; Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen; Essen Germany
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Napora-Wijata K, Strohmeier GA, Sonavane MN, Avi M, Robins K, Winkler M. Enantiocomplementary Yarrowia lipolytica Oxidoreductases: Alcohol Dehydrogenase 2 and Short Chain Dehydrogenase/Reductase. Biomolecules 2013; 3:449-60. [PMID: 24970175 PMCID: PMC4030946 DOI: 10.3390/biom3030449] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 07/31/2013] [Accepted: 08/02/2013] [Indexed: 11/16/2022] Open
Abstract
Enzymes of the non-conventional yeast Yarrowia lipolytica seem to be tailor-made for the conversion of lipophilic substrates. Herein, we cloned and overexpressed the Zn-dependent alcohol dehydrogenase ADH2 from Yarrowia lipolytica in Escherichia coli. The purified enzyme was characterized in vitro. The substrate scope for YlADH2 mediated oxidation and reduction was investigated spectrophotometrically and the enzyme showed a broader substrate range than its homolog from Saccharomyces cerevisiae. A preference for secondary compared to primary alcohols in oxidation direction was observed for YlADH2. 2-Octanone was investigated in reduction mode in detail. Remarkably, YlADH2 displays perfect (S)-selectivity and together with a highly (R)-selective short chain dehydrogenase/ reductase from Yarrowia lipolytica it is possible to access both enantiomers of 2-octanol in >99% ee with Yarrowia lipolytica oxidoreductases.
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Affiliation(s)
- Kamila Napora-Wijata
- ACIB (Austrian Centre of Industrial Biotechnology) GmbH, Petersgasse 14/III, Graz 8010, Austria.
| | - Gernot A Strohmeier
- ACIB (Austrian Centre of Industrial Biotechnology) GmbH, Petersgasse 14/III, Graz 8010, Austria.
| | - Manoj N Sonavane
- ACIB (Austrian Centre of Industrial Biotechnology) GmbH, Petersgasse 14/III, Graz 8010, Austria.
| | - Manuela Avi
- LONZA AG, Rottenstrasse 6, Visp 3930, Switzerland.
| | - Karen Robins
- LONZA AG, Rottenstrasse 6, Visp 3930, Switzerland.
| | - Margit Winkler
- ACIB (Austrian Centre of Industrial Biotechnology) GmbH, Petersgasse 14/III, Graz 8010, Austria.
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Abstract
Sulfolobus belongs to the hyperthermophilic archaea and it serves as a model organism to study archaeal molecular biology and evolution. In the last few years, we have focused on developing genetic systems for Sulfolobus islandicus using pyrEF as a selection marker and versatile genetic tools have been developed, including methods for constructing gene knockouts and for identifying essential genes. These genetic tools enable us to conduct genetic analysis on the functions of the genes involved in DNA replication and repair processes in S. islandicus and they should also facilitate in vivo analysis of functions of other genes in this model organism.
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