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Lin Y, Yin Y, Oger P, Gong Y, Zhou X, Bai Y, Zhang L. New insights into thermostable iron-containing/activated alcohol dehydrogenases from hyperthermophiles. Int J Biol Macromol 2024; 275:133707. [PMID: 38972651 DOI: 10.1016/j.ijbiomac.2024.133707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/21/2024] [Accepted: 07/05/2024] [Indexed: 07/09/2024]
Abstract
Alcohol dehydrogenase (ADH) is an important enzyme that catalyzes alcohol oxidation and/or aldehyde reduction. As one of NAD+-dependent ADH types, iron-containing/activated ADH (Fe-ADH) is ubiquitous in Bacteria, Archaea, and Eukaryotes, possessing a similar "tunnel-like" structure that is composed of a domain A in its N-terminus and a domain B in its C-terminus. A conserved "GGGS" sequence in the domain A of Fe-ADH associates with NAD+, and one conserved Asp residue and three conserved His residues in the domain B are its catalytic active sites by surrounding with Fe atom, suggesting that it might employ similar catalytic mechanism. Notably, all the biochemically characterized Fe-ADHs from hyperthermophiles that thrive in above 80 °C possess two unique characteristics that are absent in other Fe-ADHs: thermophilicity and thermostability, thereby demonstrating that they can oxidize alcohol and reduce aldehyde at high temperature. Considering these two unique characteristics, Fe-ADHs from hyperthermophiles are potentially industrial biocatalysts for alcohol and aldehyde biotransformation at high temperature. Herein, we reviewed structural and biochemical characteristics of Fe-ADHs from hyperthermophiles, focusing on similarity and difference between Fe-ADHs from hyperthermophiles and their homologs from non-hyperthermophiles, and between hyperthermophilic archaeal Fe-ADHs and bacterial homologs. Furthermore, we proposed future directions of Fe-ADHs from hyperthermophiles.
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Affiliation(s)
- Yushan Lin
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou City, China
| | - Youcheng Yin
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou City, China
| | - Philippe Oger
- Univ Lyon, INSA De Lyon, CNRS UMR 5240, Lyon, France
| | - Yong Gong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, China
| | - Xiaojian Zhou
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou City, China.
| | - Yanchao Bai
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou City, China.
| | - Likui Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou City, China.
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2
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Hao L, Ayinla Z, Ma K. Molecular Characterization of the Iron-Containing Alcohol Dehydrogenase from the Extremely Thermophilic Bacterium Pseudothermotoga hypogea. Microorganisms 2024; 12:311. [PMID: 38399715 PMCID: PMC10891854 DOI: 10.3390/microorganisms12020311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
Pseudothermotoga hypogea is an extremely thermophilic bacterium capable of growing at 90 °C and producing ethanol, which is catalyzed by an alcohol dehydrogenase (ADH). The gene encoding P. hypogea ADH (PhADH) was cloned, sequenced and over-expressed. The gene sequence (1164 bp) was obtained by sequencing all fragments of the gene, which were amplified from the genomic DNA. The deduced amino acid sequence showed high identity to iron-containing ADHs from other Thermotoga species and harbored typical iron- and NADP-binding motifs, Asp195His199His268His282 and Gly39Gly40Gly41Ser42, respectively. Structural modeling showed that the N-terminal domain of PhADH contains an α/β-dinucleotide-binding motif and that its C-terminal domain is an α-helix-rich region containing the iron-binding motif. The recombinant PhADH was soluble, active, and thermostable, with a subunit size of 43 ± 1 kDa revealed by SDS-PAGE analyses. The recombinant PhADH (69 ± 2 U/mg) was shown to have similar properties to the native enzyme. The optimal pH values for alcohol oxidation and aldehyde reduction were 11.0 and 8.0, respectively. It was also thermostable, with a half-life of 5 h at 70 °C. The successful expression of the recombinant PhADH in E. coli significantly enhanced the yield of enzyme production and thus will facilitate further investigation of the catalytic mechanisms of iron-containing ADHs.
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Affiliation(s)
| | | | - Kesen Ma
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada (Z.A.)
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Chen S, Liu J, Gao G, Li M, Cao L, Liu T, Li G, Ma T. An NAD +-dependent group Ⅲ alcohol dehydrogenase involved in long-chain alkane degradation in Acinetobacter venetianus RAG-1. Enzyme Microb Technol 2024; 172:110343. [PMID: 37890395 DOI: 10.1016/j.enzmictec.2023.110343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023]
Abstract
Alcohol dehydrogenases (ADHs) are a class of key enzymes responsible for the oxidation of alkyl alcohols in the aerobic alkane metabolic pathway. Currently, the degradation mechanisms of short- and medium-chain alkanes are commonly reported, while those of long-chain alkanes have received less attention. In this work, a putative long-chain ADH was screened from Acinetobacter venetianus RAG-1 via RNA-seq with n-octacosane (C28) as the sole carbon source. Conserved sequence analysis revealed that it is a group III (Fe-containing/activated) ADH, which is widespread in the genus Acinetobacter. The deletion of adhA led to a significant reduction in the degradation of C28. AdhA exhibited optimal oxidative activity at pH 8.0 and 50 °C with NAD+ as coenzyme, while showing better tolerability to chemical reagents. Enzyme activity assay showed that AdhA owed the oxidative activity to a wide range of substrates including alkyl alcohols (C1-C32) and some isomeric alcohols, such as isopropanol, isobutanol, isoamyl alcohol, and propanetriol, and could reduce the alkyl aldehyde (C1-C12). Meanwhile, the binding of AdhA to different alkyl alcohols was mediated by different amino acids. AdhA is an ADH with an extremely broad substrate utilization range and excellent biochemical characteristics. These results provided important insights in the subsequent investigation of long-chain alkane degradation and petroleum pollution bioremediation.
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Affiliation(s)
- Shuai Chen
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Jia Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ge Gao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Mingchang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Lu Cao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Tongtong Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Guoqiang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China; Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin, China.
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China; Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin, China.
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4
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Wu L, Zhang L. Biochemical and Functional Characterization of an Iron-Containing Alcohol Dehydrogenase from Thermococcus barophilus Ch5. Appl Biochem Biotechnol 2022; 194:5537-5555. [DOI: 10.1007/s12010-022-04052-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2022] [Indexed: 11/29/2022]
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5
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Shanbhag AP, Ghatak A, Rajagopal S. Industrial light at the end of the Iron-containing (group III) alcohol dehydrogenase tunnel. Biotechnol Appl Biochem 2022; 70:537-552. [PMID: 35751426 DOI: 10.1002/bab.2376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 06/10/2022] [Indexed: 11/05/2022]
Abstract
There are three prominent alcohol dehydrogenases superfamilies: Short-chain, Medium-chain, and Iron-containing alcohol dehydrogenases (FeADHs). Many members are valuable catalysts for producing industrially relevant products such as Active pharmaceutical Intermediates, Chiral synthons, Biopolymers, Biofuels and secondary metabolites. However, FeADHs are the least explored enzymes among the superfamilies for commercial tenacities. They portray a conserved structure having a 'tunnel-like' cofactor and substrate binding site with particular functions, despite representing high sequence diversity. Interestingly, phylogenetic analysis demarcates enzymes catalyzing distinct native substrates where closely related clades convert similar molecules. Further, homologs from various mesophilic and thermophilic microbes have been explored for designing a solvent and temperature resistant enzyme for industrial purposes. The review explores different Iron-containing alcohol dehydrogenases potential engineering of the enzymes and substrates helpful in manufacturing commercial products. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Anirudh P Shanbhag
- Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK Campus, Bangalore, 560065.,Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India
| | - Arindam Ghatak
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India.,Biomoneta Research Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK Campus, Bangalore, 560065
| | - Sreenath Rajagopal
- Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK Campus, Bangalore, 560065
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Zhang L, Jiang D, Li Y, Wu L, Liu Q, Dong K, Oger P. Characterization of a novel type III alcohol dehydrogenase from Thermococcus barophilus Ch5. Int J Biol Macromol 2021; 171:491-501. [PMID: 33428959 DOI: 10.1016/j.ijbiomac.2020.12.197] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/25/2020] [Accepted: 12/26/2020] [Indexed: 12/27/2022]
Abstract
The genome of the hyperthermophilic and piezophilic euryarchaeaon Thermococcus barophilus Ch5 encodes three putative alcohol dehydrogenases (Tba ADHs). Herein, we characterized Tba ADH547 biochemically and probed its catalytic mechanism by mutational studies. Our data demonstrate that Tba ADH547 can oxidize ethanol and reduce acetaldehyde at high temperature with the same optimal temperature (75 °C) and exhibit similar thermostability for oxidization and reduction reactions. However, Tba ADH547 has different optimal pH for oxidation and reduction: 8.5 for oxidation and 7.0 for reduction. Tba ADH547 is dependent on a divalent ion for its oxidation activity, among which Mn2+ is optimal. However, Tba ADH547 displays about 20% reduction activity without a divalent ion, and the maximal activity with Fe2+. Furthermore, Tba ADH547 showcases a strong substrate preference for 1-butanol and 1-hexanol over ethanol and other alcohols. Similarly, Tba ADH547 prefers butylaldehyde to acetaldehyde as its reduction substrate. Mutational studies showed that the mutations of residues D195, H199, H262 and H274 to Ala result in the significant activity loss of Tba ADH547, suggesting that residues D195, H199, H262 and H274 are responsible for catalysis. Overall, Tba ADH547 is a thermoactive ADH with novel biochemical characteristics, thereby allowing this enzyme to be a potential biocatalyst.
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Affiliation(s)
- Likui Zhang
- Guangling College, Yangzhou University, China; College of Environmental Science and Engineering, Marine Science & Technology Institute, Yangzhou University, China.
| | - Donghao Jiang
- College of Environmental Science and Engineering, Marine Science & Technology Institute, Yangzhou University, China
| | - Yuting Li
- College of Environmental Science and Engineering, Marine Science & Technology Institute, Yangzhou University, China
| | - Leilei Wu
- College of Environmental Science and Engineering, Marine Science & Technology Institute, Yangzhou University, China
| | - Qing Liu
- College of Environmental Science and Engineering, Marine Science & Technology Institute, Yangzhou University, China
| | - Kunming Dong
- College of Environmental Science and Engineering, Marine Science & Technology Institute, Yangzhou University, China
| | - Philippe Oger
- Univ Lyon, INSA de Lyon, CNRS UMR 5240, Villeurbanne, France.
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7
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Sugimoto C, Takeda K, Kariya Y, Matsumura H, Yohda M, Ohno H, Nakamura N. A method of expression for an oxygen-tolerant group III alcohol dehydrogenase from Pyrococcus horikoshii OT3. J Biol Inorg Chem 2017; 22:527-534. [PMID: 28084552 DOI: 10.1007/s00775-017-1439-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/28/2016] [Indexed: 05/29/2023]
Abstract
NAD(P)-dependent group III alcohol dehydrogenases (ADHs), well known as iron-activated enzymes, generally lose their activities under aerobic conditions due to their oxygen-sensitivities. In this paper, we expressed an extremely thermostable group III ADH from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 (PhADH) heterologously in Escherichia coli. When purified from a culture medium containing nickel, the recombinant PhADH (Ni-PhADH) contained 0.85 ± 0.01 g-atoms of nickel per subunit. Ni-PhADH retained high activity under aerobic conditions (9.80 U mg-1), while the enzyme expressed without adding nickel contained 0.46 ± 0.01 g-atoms of iron per subunit and showed little activity (0.27 U mg-1). In the presence of oxygen, the activity of the Fe2+-reconstituted PhADH prepared from the Ni-PhADH was gradually decreased, whereas the Ni2+-reconstituted PhADH maintained enzymatic activity. These results indicated that PhADH with bound nickel ion was stable in oxygen. The activity of the Ni2+-reconstituted PhADH prepared from the expression without adding nickel was significantly lower than that from the Ni-PhADH, suggesting that binding a nickel ion to PhADH in this expression system contributed to protecting against inactivation during the expression and purification processes. Unlike other thermophilic group III ADHs, Ni-PhADH showed high affinity for NAD(H) rather than NADP(H). Furthermore, it showed an unusually high k cat value toward aldehyde reduction. The activity of Ni-PhADH for butanal reduction was increased to 60.7 U mg-1 with increasing the temperature to 95 °C. These findings provide a new strategy to obtain oxygen-sensitive group III ADHs.
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Affiliation(s)
- Chikanobu Sugimoto
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo, 184-8588, Japan
| | - Kouta Takeda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo, 184-8588, Japan
| | - Yumi Kariya
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo, 184-8588, Japan
| | - Hirotoshi Matsumura
- Department of Life Science, Graduate School and Faculty of Engineering Science, Akita University, Akita, 010-8502, Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo, 184-8588, Japan
| | - Hiroyuki Ohno
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo, 184-8588, Japan
| | - Nobuhumi Nakamura
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo, 184-8588, Japan.
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Gaona-López C, Julián-Sánchez A, Riveros-Rosas H. Diversity and Evolutionary Analysis of Iron-Containing (Type-III) Alcohol Dehydrogenases in Eukaryotes. PLoS One 2016; 11:e0166851. [PMID: 27893862 PMCID: PMC5125639 DOI: 10.1371/journal.pone.0166851] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/05/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Alcohol dehydrogenase (ADH) activity is widely distributed in the three domains of life. Currently, there are three non-homologous NAD(P)+-dependent ADH families reported: Type I ADH comprises Zn-dependent ADHs; type II ADH comprises short-chain ADHs described first in Drosophila; and, type III ADH comprises iron-containing ADHs (FeADHs). These three families arose independently throughout evolution and possess different structures and mechanisms of reaction. While types I and II ADHs have been extensively studied, analyses about the evolution and diversity of (type III) FeADHs have not been published yet. Therefore in this work, a phylogenetic analysis of FeADHs was performed to get insights into the evolution of this protein family, as well as explore the diversity of FeADHs in eukaryotes. PRINCIPAL FINDINGS Results showed that FeADHs from eukaryotes are distributed in thirteen protein subfamilies, eight of them possessing protein sequences distributed in the three domains of life. Interestingly, none of these protein subfamilies possess protein sequences found simultaneously in animals, plants and fungi. Many FeADHs are activated by or contain Fe2+, but many others bind to a variety of metals, or even lack of metal cofactor. Animal FeADHs are found in just one protein subfamily, the hydroxyacid-oxoacid transhydrogenase (HOT) subfamily, which includes protein sequences widely distributed in fungi, but not in plants), and in several taxa from lower eukaryotes, bacteria and archaea. Fungi FeADHs are found mainly in two subfamilies: HOT and maleylacetate reductase (MAR), but some can be found also in other three different protein subfamilies. Plant FeADHs are found only in chlorophyta but not in higher plants, and are distributed in three different protein subfamilies. CONCLUSIONS/SIGNIFICANCE FeADHs are a diverse and ancient protein family that shares a common 3D scaffold with a patchy distribution in eukaryotes. The majority of sequenced FeADHs from eukaryotes are distributed in just two subfamilies, HOT and MAR (found mainly in animals and fungi). These two subfamilies comprise almost 85% of all sequenced FeADHs in eukaryotes.
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Affiliation(s)
- Carlos Gaona-López
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM). Cd. Universitaria, Ciudad de México, México
| | - Adriana Julián-Sánchez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM). Cd. Universitaria, Ciudad de México, México
| | - Héctor Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM). Cd. Universitaria, Ciudad de México, México
- * E-mail:
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Hensley SA, Jung JH, Park CS, Holden JF. Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. of hyperthermophilic heterotrophs from deep-sea hydrothermal vents. Int J Syst Evol Microbiol 2014; 64:3655-3659. [DOI: 10.1099/ijs.0.066100-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two heterotrophic hyperthermophilic strains, ES1T and CL1T, were isolated from Paralvinella sp. polychaete worms collected from active hydrothermal vent chimneys in the north-eastern Pacific Ocean. Both were obligately anaerobic and produced H2S in the presence of elemental sulfur and H2. Complete genome sequences are available for both strains. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strains are more than 97 % similar to most other species of the genus
Thermococcus
. Therefore, overall genome relatedness index analyses were performed to establish that these strains are novel species. For each analysis, strain ES1T was determined to be most similar to
Thermococcus barophilus
MPT, while strain CL1T was determined to be most similar to
Thermococcus sp.
4557. The average nucleotide identity scores for these strains were 84 % for strain ES1T and 81 % for strain CL1T, genome-to-genome direct comparison scores were 23 % for strain ES1T and 47 % for strain CL1T, and the species identification scores were 89 % for strain ES1T and 88 % for strain CL1T. For each analysis, strains ES1T and CL1T were below the species delineation cut-off. Therefore, based on their whole genome sequences, strains ES1T and CL1T are suggested to represent novel species of the genus
Thermococcus
for which the names Thermococcus
paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. are proposed, respectively. The type strains are ES1T ( = DSM 27261T = KACC 17923T) and CL1T ( = DSM 27260T = KACC 17922T).
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Affiliation(s)
- Sarah A. Hensley
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Jong-Hyun Jung
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Cheon-Seok Park
- Graduate School of Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - James F. Holden
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
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The bifunctional pyruvate decarboxylase/pyruvate ferredoxin oxidoreductase from Thermococcus guaymasensis. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:349379. [PMID: 24982594 PMCID: PMC4058850 DOI: 10.1155/2014/349379] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 04/29/2014] [Indexed: 11/18/2022]
Abstract
The hyperthermophilic archaeon Thermococcus guaymasensis produces ethanol as a metabolic end product, and an alcohol dehydrogenase (ADH) catalyzing the reduction of acetaldehyde to ethanol has been purified and characterized. However, the enzyme catalyzing the formation of acetaldehyde has not been identified. In this study an enzyme catalyzing the production of acetaldehyde from pyruvate was purified and characterized from T. guaymasensis under strictly anaerobic conditions. The enzyme had both pyruvate decarboxylase (PDC) and pyruvate ferredoxin oxidoreductase (POR) activities. It was oxygen sensitive, and the optimal temperatures were 85°C and >95°C for the PDC and POR activities, respectively. The purified enzyme had activities of 3.8 ± 0.22 U mg(-1) and 20.2 ± 1.8 U mg(-1), with optimal pH-values of 9.5 and 8.4 for each activity, respectively. Coenzyme A was essential for both activities, although it did not serve as a substrate for the former. Enzyme kinetic parameters were determined separately for each activity. The purified enzyme was a heterotetramer. The sequences of the genes encoding the subunits of the bifunctional PDC/POR were determined. It is predicted that all hyperthermophilic β -keto acids ferredoxin oxidoreductases are bifunctional, catalyzing the activities of nonoxidative and oxidative decarboxylation of the corresponding β -keto acids.
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Jung JH, Kim YT, Jeon EJ, Seo DH, Hensley SA, Holden JF, Lee JH, Park CS. Complete genome sequence of hyperthermophilic archaeon Thermococcus sp. ES1. J Biotechnol 2014; 174:14-5. [DOI: 10.1016/j.jbiotec.2014.01.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 01/14/2014] [Indexed: 10/25/2022]
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12
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Characterization of an allylic/benzyl alcohol dehydrogenase from Yokenella sp. strain WZY002, an organism potentially useful for the synthesis of α,β-unsaturated alcohols from allylic aldehydes and ketones. Appl Environ Microbiol 2014; 80:2399-409. [PMID: 24509923 DOI: 10.1128/aem.03980-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel whole-cell biocatalyst with high allylic alcohol-oxidizing activities was screened and identified as Yokenella sp. WZY002, which chemoselectively reduced the C=O bond of allylic aldehydes/ketones to the corresponding α,β-unsaturated alcohols at 30°C and pH 8.0. The strain also had the capacity of stereoselectively reducing aromatic ketones to (S)-enantioselective alcohols. The enzyme responsible for the predominant allylic/benzyl alcohol dehydrogenase activity was purified to homogeneity and designated YsADH (alcohol dehydrogenase from Yokenella sp.), which had a calculated subunit molecular mass of 36,411 Da. The gene encoding YsADH was subsequently expressed in Escherichia coli, and the purified recombinant YsADH protein was characterized. The enzyme strictly required NADP(H) as a coenzyme and was putatively zinc dependent. The optimal pH and temperature for crotonaldehyde reduction were pH 6.5 and 65°C, whereas those for crotyl alcohol oxidation were pH 8.0 and 55°C. The enzyme showed moderate thermostability, with a half-life of 6.2 h at 55°C. It was robust in the presence of organic solvents and retained 87.5% of the initial activity after 24 h of incubation with 20% (vol/vol) dimethyl sulfoxide. The enzyme preferentially catalyzed allylic/benzyl aldehydes as the substrate in the reduction of aldehydes/ketones and yielded the highest activity of 427 U mg(-1) for benzaldehyde reduction, while the alcohol oxidation reaction demonstrated the maximum activity of 79.9 U mg(-1) using crotyl alcohol as the substrate. Moreover, kinetic parameters of the enzyme showed lower Km values and higher catalytic efficiency for crotonaldehyde/benzaldehyde and NADPH than for crotyl alcohol/benzyl alcohol and NADP(+), suggesting the nature of being an aldehyde reductase.
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13
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Eram MS, Ma K. Decarboxylation of pyruvate to acetaldehyde for ethanol production by hyperthermophiles. Biomolecules 2013; 3:578-96. [PMID: 24970182 PMCID: PMC4030962 DOI: 10.3390/biom3030578] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/02/2013] [Accepted: 08/15/2013] [Indexed: 11/16/2022] Open
Abstract
Pyruvate decarboxylase (PDC encoded by pdc) is a thiamine pyrophosphate (TPP)-containing enzyme responsible for the conversion of pyruvate to acetaldehyde in many mesophilic organisms. However, no pdc/PDC homolog has yet been found in fully sequenced genomes and proteomes of hyper/thermophiles. The only PDC activity reported in hyperthermophiles was a bifunctional, TPP- and CoA-dependent pyruvate ferredoxin oxidoreductase (POR)/PDC enzyme from the hyperthermophilic archaeon Pyrococcus furiosus. Another enzyme known to be involved in catalysis of acetaldehyde production from pyruvate is CoA-acetylating acetaldehyde dehydrogenase (AcDH encoded by mhpF and adhE). Pyruvate is oxidized into acetyl-CoA by either POR or pyruvate formate lyase (PFL), and AcDH catalyzes the reduction of acetyl-CoA to acetaldehyde in mesophilic organisms. AcDH is present in some mesophilic (such as clostridia) and thermophilic bacteria (e.g., Geobacillus and Thermoanaerobacter). However, no AcDH gene or protein homologs could be found in the released genomes and proteomes of hyperthermophiles. Moreover, no such activity was detectable from the cell-free extracts of different hyperthermophiles under different assay conditions. In conclusion, no commonly-known PDCs was found in hyperthermophiles. Instead of the commonly-known PDC, it appears that at least one multifunctional enzyme is responsible for catalyzing the non-oxidative decarboxylation of pyruvate to acetaldehyde in hyperthermophiles.
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Affiliation(s)
- Mohammad S Eram
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.
| | - Kesen Ma
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.
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Tan Y, Liu J, Liu Z, Li F. Characterization of two novel butanol dehydrogenases involved in butanol degradation in syngas-utilizing bacterium Clostridium ljungdahlii DSM 13528. J Basic Microbiol 2013; 54:996-1004. [PMID: 23720212 DOI: 10.1002/jobm.201300046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 04/24/2013] [Indexed: 11/06/2022]
Abstract
Syngas utilizing bacterium Clostridium ljungdahlii DSM 13528 is a promising platform organism for a whole variety of different biofuels and biochemicals production from syngas. During syngas fermentation, C. ljungdahlii DSM 13528 could convert butanol into butyrate, which significantly reduces productivity of butanol. However, there has been no any enzyme involved in the degradation of butanol characterized in C. ljungdahlii DSM 13528. In this study two genes, CLJU_c24880 and CLJU_c39950, encoding putative butanol dehydrogenase (designated as BDH1 and BDH2) were identified in the genome of C. ljungdahlii DSM 13528 and qRT-PCR analysis showed the expression of bdh1 and bdh2 was significantly upregulated in the presence of 0.25% butanol. And the deduced amino acid sequence for BDH1 and BDH2 showed 69.85 and 68.04% identity with Clostridium acetobutylicum ADH1, respectively. Both BDH1 and BDH2 were oxygen-sensitive and preferred NADP(+) as cofactor and butanol as optimal substrate. The optimal temperature and pH for BDH1 were at 55 °C and pH 7.5 and specific activity was 18.07 ± 0.01 µmol min(-1) mg(-1) . BDH2 was a thermoactive dehydrogenase with maximum activity at 65 °C and at pH 7.0. The specific activity for BDH2 was 11.21 ± 0.02 µmol min(-1) mg(-1) . This study provided important information for understanding the molecular mechanism of butanol degradation and determining the targets for gene knockout to improve the productivity of butanol from syngas in C. ljungdahlii DSM 13528 in future.
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Affiliation(s)
- Yang Tan
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; University of Chinese Academy of Sciences, Beijing, 100039, China
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Wang Z, Song Q, Yu M, Wang Y, Xiong B, Zhang Y, Zheng J, Ying X. Characterization of a stereospecific acetoin(diacetyl) reductase from Rhodococcus erythropolis WZ010 and its application for the synthesis of (2S,3S)-2,3-butanediol. Appl Microbiol Biotechnol 2013; 98:641-50. [PMID: 23568047 DOI: 10.1007/s00253-013-4870-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 03/12/2013] [Accepted: 03/19/2013] [Indexed: 10/27/2022]
Abstract
Rhodococcus erythropolis WZ010 was capable of producing optically pure (2S,3S)-2,3-butanediol in alcoholic fermentation. The gene encoding an acetoin(diacetyl) reductase from R. erythropolis WZ010 (ReADR) was cloned, overexpressed in Escherichia coli, and subsequently purified by Ni-affinity chromatography. ReADR in the native form appeared to be a homodimer with a calculated subunit size of 26,864, belonging to the family of the short-chain dehydrogenase/reductases. The enzyme accepted a broad range of substrates including aliphatic and aryl alcohols, aldehydes, and ketones. It exhibited remarkable tolerance to dimethyl sulfoxide (DMSO) and retained 53.6 % of the initial activity after 4 h incubation with 30 % (v/v) DMSO. The enzyme displayed absolute stereospecificity in the reduction of diacetyl to (2S,3S)-2,3-butanediol via (S)-acetoin. The optimal pH and temperature for diacetyl reduction were pH 7.0 and 30 °C, whereas those for (2S,3S)-2,3-butanediol oxidation were pH 9.5 and 25 °C. Under the optimized conditions, the activity of diacetyl reduction was 11.9-fold higher than that of (2S,3S)-2,3-butanediol oxidation. Kinetic parameters of the enzyme showed lower K(m) values and higher catalytic efficiency for diacetyl and NADH in comparison to those for (2S,3S)-2,3-butanediol and NAD⁺, suggesting its physiological role in favor of (2S,3S)-2,3-butanediol formation. Interestingly, the enzyme showed higher catalytic efficiency for (S)-1-phenylethanol oxidation than that for acetophenone reduction. ReADR-catalyzed asymmetric reduction of diacetyl was coupled with stereoselective oxidation of 1-phenylethanol, which simultaneously formed both (2S,3S)-2,3-butanediol and (R)-1-phenylethanol in great conversions and enantiomeric excess values.
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Affiliation(s)
- Zhao Wang
- College of Biological and Environmental Engineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, Zhejiang, 310014, China
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Elleuche S, Fodor K, Klippel B, von der Heyde A, Wilmanns M, Antranikian G. Structural and biochemical characterisation of a NAD⁺-dependent alcohol dehydrogenase from Oenococcus oeni as a new model molecule for industrial biotechnology applications. Appl Microbiol Biotechnol 2013; 97:8963-75. [PMID: 23385476 DOI: 10.1007/s00253-013-4725-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 01/14/2013] [Accepted: 01/16/2013] [Indexed: 01/18/2023]
Abstract
Alcohol dehydrogenases are highly diverse enzymes catalysing the interconversion of alcohols and aldehydes or ketones. Due to their versatile specificities, these biocatalysts are of great interest for industrial applications. The adh3-gene encoding a group III alcohol dehydrogenase was isolated from the gram-positive bacterium Oenococcus oeni and was characterised after expression in the heterologous host Escherichia coli. Adh3 has been identified by genome BLASTP analyses using the amino acid sequence of 1,3-propanediol dehydrogenase DhaT from Klebsiella pneumoniae and group III alcohol dehydrogenases with known activity towards 1,3-propanediol as target sequences. The recombinant protein was purified in a two-step column chromatography approach. Crystal structure determination and biochemical characterisation confirmed that Adh3 forms a Ni(2+)-containing homodimer in its active form. Adh3 catalyses the interconversion of ethanol and its corresponding aldehyde acetaldyhyde and is also capable of using other alcoholic compounds as substrates, such as 1,3-propanediol, 1,2-propanediol and 1-propanol. In the presence of Ni(2+), activity increases towards 1,3-propanediol and 1,2-propanediol. Adh3 is strictly dependent on NAD(+)/NADH, whereas no activity has been observed with NADP(+)/NADPH as co-factor. The enzyme exhibits a specific activity of 1.1 U/mg using EtOH as substrate with an optimal pH value of 9.0 for ethanol oxidation and 8.0 for aldehyde reduction. Moreover, Adh3 exhibits tolerance to several metal ions and organic solvents, but is completely inhibited in the presence of Zn(2+). The present study demonstrates that O. oeni is a group III alcohol dehydrogenase with versatile substrate specificity, including Ni(2+)-dependent activity towards 1,3-propanediol.
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Affiliation(s)
- Skander Elleuche
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, 21073, Hamburg, Germany
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17
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Thermostable alcohol dehydrogenase from Thermococcus kodakarensis KOD1 for enantioselective bioconversion of aromatic secondary alcohols. Appl Environ Microbiol 2013; 79:2209-17. [PMID: 23354700 DOI: 10.1128/aem.03873-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel thermostable alcohol dehydrogenase (ADH) showing activity toward aromatic secondary alcohols was identified from the hyperthermophilic archaeon Thermococcus kodakarensis KOD1 (TkADH). The gene, tk0845, which encodes an aldo-keto reductase, was heterologously expressed in Escherichia coli. The enzyme was found to be a monomer with a molecular mass of 31 kDa. It was highly thermostable with an optimal temperature of 90°C and a half-life of 4.5 h at 95°C. The apparent K(m) values for the cofactors NAD(P)(+) and NADPH were similar within a range of 66 to 127 μM. TkADH preferred secondary alcohols and accepted various ketones and aldehydes as substrates. Interestingly, the enzyme could oxidize 1-phenylethanol and its derivatives having substituents at the meta and para positions with high enantioselectivity, yielding the corresponding (R)-alcohols with optical purities of greater than 99.8% enantiomeric excess (ee). TkADH could also reduce 2,2,2-trifluoroacetophenone to (R)-2,2,2-trifluoro-1-phenylethanol with high enantioselectivity (>99.6% ee). Furthermore, the enzyme showed high resistance to organic solvents and was particularly highly active in the presence of H2O-20% 2-propanol and H2O-50% n-hexane or n-octane. This ADH is expected to be a useful tool for the production of aromatic chiral alcohols.
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Yang C, Ying X, Yu M, Zhang Y, Xiong B, Song Q, Wang Z. Towards the discovery of alcohol dehydrogenases: NAD(P)H fluorescence-based screening and characterization of the newly isolated Rhodococcus erythropolis WZ010 in the preparation of chiral aryl secondary alcohols. J Ind Microbiol Biotechnol 2012; 39:1431-43. [PMID: 22743788 DOI: 10.1007/s10295-012-1160-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 06/11/2012] [Indexed: 10/28/2022]
Abstract
A simple and reliable procedure was developed to screen biocatalysts with high alcohol dehydrogenase activity, efficient internal coenzyme regeneration, and high stereoselectivity. The strategy of activity screening in a microtitre plate format was based on the detection of fluorescence of NAD(P)H originating from the oxidation of alcohols. The primary and secondary screenings from soil samples yielded a versatile bacterial biocatalyst Rhodococcus erythropolis WZ010 demonstrating potential for the preparation of chiral aryl secondary alcohols. In terms of activity and stereoselectivity, the optimized reaction conditions in the stereoselective oxidation were 30 °C, pH 10.5, and 250 rpm, whereas bioreduction using glucose as co-substrate was the most favorable at 35 °C and pH 7.5 in the static reaction mixture. Under the optimized conditions, fresh cells of the strain stereoselectively oxidized the (S)-enantiomer of racemic 1-phenylethanol (120 mM) to acetophenone and afforded the unoxidized (R)-1-phenylethanol in 49.4 % yield and >99.9 % enantiomeric excess (e.e.). In the reduction of 10 mM acetophenone, the addition of 100 mM glucose significantly increased the conversion rate from 3.1 to 97.4 %. In the presence of 800 mM glucose, acetophenone and other aromatic ketones (80 mM) were enantioselectively reduced to corresponding (S)-alcohols with excellent e.e. values. Both stereoselective oxidation and asymmetric reduction required no external cofactor regeneration system.
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Affiliation(s)
- Chi Yang
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou, 310014 Zhejiang, China
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Vinckier NK, Chworos A, Parsons SM. Improved isolation of proteins tagged with glutathione S-transferase. Protein Expr Purif 2011; 75:161-4. [DOI: 10.1016/j.pep.2010.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 09/03/2010] [Accepted: 09/08/2010] [Indexed: 11/26/2022]
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