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Bai X, Xu K, Zhao Z, Qin H, Nam KH, Quan C, Ha NC, Xu Y. Structural and Biochemical Analysis of Butanol Dehydrogenase From Thermotoga maritima. Proteins 2024. [PMID: 39023292 DOI: 10.1002/prot.26731] [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: 01/18/2024] [Revised: 06/10/2024] [Accepted: 07/02/2024] [Indexed: 07/20/2024]
Abstract
Butanol dehydrogenase (BDH) plays a crucial role in butanol biosynthesis by catalyzing the conversion of butanal to butanol using the coenzyme NAD(P)H. In this study, we observed that BDH from Thermotoga maritima (TmBDH) exhibits dual coenzyme specificity and catalytic activity with NADPH as the coenzyme under highly alkaline conditions. Additionally, a thermal stability analysis on TmBDH demonstrated its excellent activity retention even at elevated temperatures of 80°C. These findings demonstrate the superior thermal stability of TmBDH and suggest that it is a promising candidate for large-scale industrial butanol production. Furthermore, we discovered that TmBDH effectively catalyzes the conversion of aldehydes to alcohols and exhibits a wide range of substrate specificities toward aldehydes, while excluding alcohols. The dimeric state of TmBDH was observed using rapid online buffer exchange native mass spectrometry. Additionally, we analyzed the coenzyme-binding sites and inferred the possible locations of the substrate-binding sites. These results provide insights that improve our understanding of BDHs.
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Affiliation(s)
- Xue Bai
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, Liaoning, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian, China
| | - Ke Xu
- Department of Ophthalmology, The Fourth People's Hospital of Shenyang, Shenyang, China
| | - Zhidan Zhao
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, Liaoning, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian, China
| | - Huiwen Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China
| | - Ki Hyun Nam
- College of General Education, Kookmin University, Seoul, South Korea
| | - Chunshan Quan
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, Liaoning, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian, China
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, Liaoning, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian, China
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He Y, Kennes C, Lens PNL. Enhanced solventogenesis in syngas bioconversion: Role of process parameters and thermodynamics. CHEMOSPHERE 2022; 299:134425. [PMID: 35351479 DOI: 10.1016/j.chemosphere.2022.134425] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Biofuels, such as ethanol and butanol, obtained from carbon monoxide-rich gas or syngas bioconversion (solventogenesis) are an attractive alternative to traditional fermentation processes with merits of no competition with food production and sustainability. However, there is a lack of comprehensive understanding of some key process parameters and mechanisms enhancing solventogenesis during the fermentation process. This review provides an overview of the current state of the art of the main influencing factors during the syngas fermentation process catalyzed by acetogenic species as well as undefined mixed cultures. The role of syngas pressure, syngas components, fermentation pH, temperature, trace metals, organic compounds and additional materials is overviewed. As a so far hardly considered approach, thermodynamic calculations of the Gibbs free energy of CO conversion to acetic acid, ethanol, butyric acid and butanol under different CO pressures and pH at 25, 33 and 55 °C are also addressed and reviewed. Strategies for enhancing mass transfer and longer carbon chain solvent production are considered as well.
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Affiliation(s)
- Yaxue He
- National University of Ireland Galway, H91 TK33, Galway, Ireland; Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research - Centro de Investigaciones Científicas Avanzadas (CICA), BIOENGIN Group, University of La Coruña (UDC), E-15008, La Coruña, Spain.
| | - Christian Kennes
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research - Centro de Investigaciones Científicas Avanzadas (CICA), BIOENGIN Group, University of La Coruña (UDC), E-15008, La Coruña, Spain
| | - Piet N L Lens
- National University of Ireland Galway, H91 TK33, Galway, Ireland
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Lauer I, Philipps G, Jennewein S. Metabolic engineering of Clostridium ljungdahlii for the production of hexanol and butanol from CO 2 and H 2. Microb Cell Fact 2022; 21:85. [PMID: 35568911 PMCID: PMC9107641 DOI: 10.1186/s12934-022-01802-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The replacement of fossil fuels and petrochemicals with sustainable alternatives is necessary to mitigate the effects of climate change and also to counteract diminishing fossil resources. Acetogenic microorganisms such as Clostridium spp. are promising sources of fuels and basic chemical precursors because they efficiently utilize CO and CO2 as carbon source. However the conversion into high titers of butanol and hexanol is challenging. RESULTS Using a metabolic engineering approach we transferred a 17.9-kb gene cluster via conjugation, containing 13 genes from C. kluyveri and C. acetobutylicum for butanol and hexanol biosynthesis, into C. ljungdahlii. Plasmid-based expression resulted in 1075 mg L-1 butanol and 133 mg L-1 hexanol from fructose in complex medium, and 174 mg L-1 butanol and 15 mg L-1 hexanol from gaseous substrate (20% CO2 and 80% H2) in minimal medium. Product formation was increased by the genomic integration of the heterologous gene cluster. We confirmed the expression of all 13 enzymes by targeted proteomics and identified potential rate-limiting steps. Then, we removed the first-round selection marker using CRISPR/Cas9 and integrated an additional 7.8 kb gene cluster comprising 6 genes from C. carboxidivorans. This led to a significant increase in the hexanol titer (251 mg L-1) at the expense of butanol (158 mg L-1), when grown on CO2 and H2 in serum bottles. Fermentation of this strain at 2-L scale produced 109 mg L-1 butanol and 393 mg L-1 hexanol. CONCLUSIONS We thus confirmed the function of the butanol/hexanol biosynthesis genes and achieved hexanol biosynthesis in the syngas-fermenting species C. ljungdahlii for the first time, reaching the levels produced naturally by C. carboxidivorans. The genomic integration strain produced hexanol without selection and is therefore suitable for continuous fermentation processes.
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Affiliation(s)
- Ira Lauer
- Department for Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, 52074, Aachen, Germany
| | - Gabriele Philipps
- Department for Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, 52074, Aachen, Germany
| | - Stefan Jennewein
- Department for Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, 52074, Aachen, Germany.
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Abstract
Microbes that can recycle one-carbon (C1) greenhouse gases into fuels and chemicals are vital for the biosustainability of future industries. Acetogens are the most efficient known microbes for fixing carbon oxides CO2 and CO. Understanding proteome allocation is important for metabolic engineering as it dictates metabolic fitness. Here, we use absolute proteomics to quantify intracellular concentrations for >1,000 proteins in the model acetogen Clostridium autoethanogenum grown autotrophically on three gas mixtures (CO, CO+H2, or CO+CO2+H2). We detect the prioritization of proteome allocation for C1 fixation and the significant expression of proteins involved in the production of acetate and ethanol as well as proteins with unclear functions. The data also revealed which isoenzymes are likely relevant in vivo for CO oxidation, H2 metabolism, and ethanol production. The integration of proteomic and metabolic flux data demonstrated that enzymes catalyze high fluxes with high concentrations and high in vivo catalytic rates. We show that flux adjustments were dominantly accompanied by changing enzyme catalytic rates rather than concentrations. IMPORTANCE Acetogen bacteria are important for maintaining biosustainability as they can recycle gaseous C1 waste feedstocks (e.g., industrial waste gases and syngas from gasified biomass or municipal solid waste) into fuels and chemicals. Notably, the acetogen Clostridium autoethanogenum is being used as a cell factory in industrial-scale gas fermentation. Here, we perform reliable absolute proteome quantification for the first time in an acetogen. This is important as our work advances both rational metabolic engineering of acetogen cell factories and accurate in silico reconstruction of their phenotypes. Furthermore, this absolute proteomics data set serves as a reference toward a better systems-level understanding of the ancient metabolism of acetogens.
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Effectively Converting Cane Molasses into 2,3-Butanediol Using Clostridium ljungdahlii by an Integrated Fermentation and Membrane Separation Process. Molecules 2022; 27:molecules27030954. [PMID: 35164219 PMCID: PMC8839846 DOI: 10.3390/molecules27030954] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 11/16/2022] Open
Abstract
Firstly, 2,3-butanediol (2,3-BDO) is a chemical platform used in several applications. However, the pathogenic nature of its producers and the expensive feedstocks used limit its scale production. In this study, cane molasses was used for 2,3-BDO production by a nonpathogenic Clostridium ljungdahlii. It was found that cane molasses alone, without the addition of other ingredients, was favorable for use as the culture medium for 2,3-BDO production. Compared with the control (i.e., the modified DSMZ 879 medium), the differential genes are mainly involved in the pathways of carbohydrate metabolism, membrane transport, and amino acid metabolism in the case of the cane molasses alone. However, when cane molasses alone was used, cell growth was significantly inhibited by KCl in cane molasses. Similarly, a high concentration of sugars (i.e., above 35 g/L) can inhibit cell growth and 2,3-BDO production. More seriously, 2,3-BDO production was inhibited by itself. As a result, cane molasses alone with an initial 35 g/L total sugars was suitable for 2,3-BDO production in batch culture. Finally, an integrated fermentation and membrane separation process was developed to maintain high 2,3-BDO productivity of 0.46 g·L−1·h−1. Meanwhile, the varied fouling mechanism indicated that the fermentation properties changed significantly, especially for the cell properties. Therefore, the integrated fermentation and membrane separation process was favorable for 2,3-BDO production by C. ljungdahlii using cane molasses.
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Fan YX, Zhang JZ, Zhang Q, Ma XQ, Liu ZY, Lu M, Qiao K, Li FL. Biofuel and chemical production from carbon one industry flux gas by acetogenic bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2021; 117:1-34. [PMID: 34742365 DOI: 10.1016/bs.aambs.2021.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Carbon one industry flux gas generated from fossil fuels, various industrial and domestic waste, as well as lignocellulosic biomass provides an innovative raw material to lead the sustainable development. Through the chemical and biological processing, the gas mixture composed of CO, CO2, and H2, also termed as syngas, is converted to biofuels and high-value chemicals. Here, the syngas fermentation process is elaborated to provide an overview. Sources of syngas are summarized and the influences of impurities on biological fermentation are exhibited. Acetogens and carboxydotrophs are the two main clusters of syngas utilizing microorganisms, their essential characters are presented, especially the energy metabolic scheme with CO, CO2, and H2. Synthetic biology techniques and microcompartment regulation are further discussed and proposed to create a high-efficiency cell factory. Moreover, the influencing factors in fermentation and products in carboxylic acids, alcohols, and others such like polyhydroxyalkanoate and poly-3-hydroxybutyrate are addressed. Biological fermentation from carbon one industry flux gas is a promising alternative, the latest scientific advances are expatiated hoping to inspire more creative transformation.
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Affiliation(s)
- Yi-Xuan Fan
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Zhe Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Quan Zhang
- Sinopec Dalian (Fushun) Research Institute of Petroleum and Petrochemicals, Dalian, China
| | - Xiao-Qing Ma
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China
| | - Zi-Yong Liu
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China
| | - Ming Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China
| | - Kai Qiao
- Sinopec Dalian (Fushun) Research Institute of Petroleum and Petrochemicals, Dalian, China.
| | - Fu-Li Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Dalian National Laboratory for Clean Energy, Dalian, China.
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Kuang X, Ouyang Y, Guo Y, Li Q, Wang H, Abrha GT, Ayepa E, Gu Y, Li X, Chen Q, Ma M. New insights into two yeast BDHs from the PDH subfamily as aldehyde reductases in context of detoxification of lignocellulosic aldehyde inhibitors. Appl Microbiol Biotechnol 2020; 104:6679-6692. [PMID: 32556414 DOI: 10.1007/s00253-020-10722-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/25/2020] [Accepted: 06/04/2020] [Indexed: 12/30/2022]
Abstract
At least 24 aldehyde reductases from Saccharomyces cerevisiae have been characterized and most function in in situ detoxification of lignocellulosic aldehyde inhibitors, but none is classified into the polyol dehydrogenase (PDH) subfamily of the medium-chain dehydrogenase/reductase (MDR) superfamily. This study confirmed that two (2R,3R)-2,3-butanediol dehydrogenases (BDHs) from industrial (denoted Y)/laboratory (denoted B) strains of S. cerevisiae, Bdh1p(Y)/Bdh1p(B) and Bdh2p(Y)/Bdh2p(B), were members of the PDH subfamily with an NAD(P)H binding domain and a catalytic zinc binding domain, and exhibited reductive activities towards lignocellulosic aldehyde inhibitors, such as acetaldehyde, glycolaldehyde, and furfural. Especially, the highest enzyme activity towards acetaldehyde by Bdh2p(Y) was 117.95 U/mg with cofactor nicotinamide adenine dinucleotide reduced (NADH). Based on the comparative kinetic property analysis, Bdh2p(Y)/Bdh2p(B) possessed higher specific activity, substrate affinity, and catalytic efficiency towards glycolaldehyde than Bdh1p(Y)/Bdh1p(B). This was speculated to be related to their 49% sequence differences and five nonsynonymous substitutions (Ser41Thr, Glu173Gln, Ile270Leu, Ile316Met, and Gly317Cys) occurred in their conserved NAD(P)H binding domains. Compared with BDHs from a laboratory strain, Bdh1p(Y) and Bdh2p(Y) from an industrial strain displayed five nonsynonymous mutations (Thr12, Asn61, Glu168, Val222, and Ala235) and three nonsynonymous mutations (Ala34, Ile96, and Ala369), respectively. From a first analysis with selected aldehydes, their reductase activities were different from BDHs of laboratory strain, and their catalytic efficiency was higher towards glycolaldehyde and lower towards acetaldehyde. Comparative investigation of kinetic properties of BDHs from S. cerevisiae as aldehyde reductases provides a guideline for their practical applications in in situ detoxification of aldehyde inhibitors during lignocellulose bioconversion.Key Points• Two yeast BDHs have enzyme activities for reduction of aldehydes.• Overexpression of BDHs slightly improves yeast tolerance to acetaldehyde and glycolaldehyde.• Bdh1p and Bdh2p differ in enzyme kinetic properties.• BDHs from strains with different genetic backgrounds differ in enzyme kinetic properties.
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Affiliation(s)
- Xiaolin Kuang
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Yidan Ouyang
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Yaping Guo
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China.,Patent Examination Cooperation Sichuan Center of the Patent Office, SIPO, Chengdu, 610213, Sichuan, People's Republic of China
| | - Qian Li
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Hanyu Wang
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Getachew Tafere Abrha
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Ellen Ayepa
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Yunfu Gu
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Xi Li
- College of Landscape Architecture, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Qiang Chen
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Menggen Ma
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China. .,Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China.
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8
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Yang B, Nie X, Gu Y, Jiang W, Yang C. Control of solvent production by sigma-54 factor and the transcriptional activator AdhR in Clostridium beijerinckii. Microb Biotechnol 2019; 13:328-338. [PMID: 31691520 PMCID: PMC7017808 DOI: 10.1111/1751-7915.13505] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 10/09/2019] [Accepted: 10/09/2019] [Indexed: 11/30/2022] Open
Abstract
Clostridia are obligate anaerobic bacteria that can produce solvents such as acetone, butanol and ethanol. Alcohol dehydrogenases (ADHs) play a key role in solvent production; however, their regulatory mechanisms remain largely unknown. In this study, we characterized the regulatory mechanisms of two ADH-encoding genes in C. beijerinckii. SigL (sigma factor σ54 ) was found to be required for transcription of adhA1 and adhA2 genes. Moreover, a novel transcriptional activator AdhR was identified, which binds to the σ54 promoter and activates σ54 -dependent transcription of adhA1 and adhA2. Clostridia beijerinckii mutants deficient in SigL or AdhR showed severely impaired butanol and ethanol production as well as altered acetone and butyrate synthesis. Overexpression of SigL resulted in significantly improved solvent production by C. beijerinckii when butyrate was added to cultures. Our results reveal SigL as a novel engineering target for improving solvent production by C. beijerinckii and other solvent-producing clostridia. Moreover, this study gains an insight into regulation of alcohol metabolism in diverse clostridia.
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Affiliation(s)
- Bin Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoqun Nie
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yang Gu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Weihong Jiang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Chen Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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9
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Patakova P, Kolek J, Sedlar K, Koscova P, Branska B, Kupkova K, Paulova L, Provaznik I. Comparative analysis of high butanol tolerance and production in clostridia. Biotechnol Adv 2018; 36:721-738. [DOI: 10.1016/j.biotechadv.2017.12.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/05/2017] [Accepted: 12/12/2017] [Indexed: 12/24/2022]
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10
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Jiang Y, Guo D, Lu J, Dürre P, Dong W, Yan W, Zhang W, Ma J, Jiang M, Xin F. Consolidated bioprocessing of butanol production from xylan by a thermophilic and butanologenic Thermoanaerobacterium sp. M5. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:89. [PMID: 29619085 PMCID: PMC5879998 DOI: 10.1186/s13068-018-1092-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/21/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Consolidated bioprocessing (CBP) has attracted increasing attention since it can accomplish hydrolytic enzymes production, lignocellulose degradation and microbial fermentation in one single step. Currently, biobutanol is mainly produced by mesophilic and solventogenic clostridia, such as Clostridium beijerinckii and C. acetobutylicum, which cannot directly utilize lignocellulose, an abundant, renewable and economic feedstock. Hence, metabolic construction or isolation of novel cellulolytic/hemicellulolytic and solventogenic bacteria to achieve direct butanol production from lignocellulose offers a promising alternative. RESULTS In this study, a newly isolated Thermoanaerobacterium sp. M5 could directly produce butanol from xylan through CBP at 55 °C via the butanol-ethanol pathway. Further genomic and proteomic analysis showed that the capabilities of efficient xylan degradation and butanol synthesis were attributed to the efficient expression of xylanase, β-xylosidase and the bifunctional alcohol/aldehyde dehydrogenase (AdhE). Process optimization based on the characteristic of AdhE could further improve the final butanol titer to 1.17 g/L from xylan through CBP. Furthermore, a new co-cultivation system consisting of Thermoanaerobacterium sp. M5 which could release xylose from xylan efficiently and C. acetobutylicum NJ4 which possesses the capacity of high butanol production was established. This microbial co-cultivation system could improve the butanol titer to 8.34 g/L, representing the highest butanol titer from xylan through CBP. CONCLUSIONS A newly thermophilic and butanogenic bacterium Thermoanaerobacterium sp. M5 was isolated and key enzymes responsible for butanol production were characterized in this study. High butanol titer was obtained from xylan through process optimization. In addition, the newly set up microbial co-cultivation system, consisting of Thermoanaerobacterium sp. M5 and C. acetobutylicum NJ4, achieved the highest butanol production from xylan compared with the reported co-cultivation systems.
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Affiliation(s)
- Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
| | - Dong Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
| | - Jiasheng Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Wei Yan
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
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11
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Bengelsdorf FR, Beck MH, Erz C, Hoffmeister S, Karl MM, Riegler P, Wirth S, Poehlein A, Weuster-Botz D, Dürre P. Bacterial Anaerobic Synthesis Gas (Syngas) and CO 2+H 2 Fermentation. ADVANCES IN APPLIED MICROBIOLOGY 2018; 103:143-221. [PMID: 29914657 DOI: 10.1016/bs.aambs.2018.01.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Anaerobic bacterial gas fermentation gains broad interest in various scientific, social, and industrial fields. This microbial process is carried out by a specific group of bacterial strains called acetogens. All these strains employ the Wood-Ljungdahl pathway but they belong to different taxonomic groups. Here we provide an overview of the metabolism of acetogens and naturally occurring products. Characteristics of 61 strains were summarized and selected acetogens described in detail. Acetobacterium woodii, Clostridium ljungdahlii, and Moorella thermoacetica serve as model organisms. Results of approaches such as genome-scale modeling, proteomics, and transcriptomics are discussed. Metabolic engineering of acetogens can be used to expand the product portfolio to platform chemicals and to study different aspects of cell physiology. Moreover, the fermentation of gases requires specific reactor configurations and the development of the respective technology, which can be used for an industrial application. Even though the overall process will have a positive effect on climate, since waste and greenhouse gases could be converted into commodity chemicals, some legislative barriers exist, which hamper successful exploitation of this technology.
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Affiliation(s)
- Frank R Bengelsdorf
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany.
| | - Matthias H Beck
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Catarina Erz
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Sabrina Hoffmeister
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Michael M Karl
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Peter Riegler
- Technical University of Munich, Institute of Biochemical Engineering, Garching, Germany
| | - Steffen Wirth
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
| | - Dirk Weuster-Botz
- Technical University of Munich, Institute of Biochemical Engineering, Garching, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
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Dürre P. Butanol formation from gaseous substrates. FEMS Microbiol Lett 2016; 363:fnw040. [PMID: 26903012 DOI: 10.1093/femsle/fnw040] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2016] [Indexed: 01/24/2023] Open
Abstract
Mostly, butanol is formed as a product by saccharolytic anaerobes, employing the so-called ABE fermentation (for acetone-butanol-ethanol). However, this alcohol can also be produced from gaseous substrates such as syn(thesis) gas (major components are carbon monoxide and hydrogen) by autotrophic acetogens. In view of economic considerations, a biotechnological process based on cheap and abundant gases such as CO and CO2 as a carbon source is preferable to more expensive sugar or starch fermentation. In addition, any conflict for use of substrates that can also serve as human nutrition is avoided. Natural formation of butanol has been found with, e.g. Clostridium carboxidivorans, while metabolic engineering for butanol production was successful using, e.g. C. ljungdahlii. Production of butanol from CO2 under photoautotrophic conditions was also possible by recombinant DNA construction of a respective cyanobacterial Synechococcus sp. PCC 7942 strain.
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Affiliation(s)
- Peter Dürre
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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Bertsch J, Siemund AL, Kremp F, Müller V. A novel route for ethanol oxidation in the acetogenic bacterium Acetobacterium woodii: the acetaldehyde/ethanol dehydrogenase pathway. Environ Microbiol 2015; 18:2913-22. [PMID: 26472176 DOI: 10.1111/1462-2920.13082] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ethanol is a common substrate for anaerobic microorganisms despite its high redox potential (E0' etha- nol/acetaldehyde = -190mV), which does not allow for NAD(+) reduction. How this thermodynamic barrier is overcome is largely unknown. The acetogenic bacterium Acetobacterium woodii can also grow on ethanol. The genome harbours 11 genes encoding putative alcohol dehydrogenases, but only one, adhE, was upregulated during growth on ethanol. The bifunctional acetaldehyde/ethanol dehydrogenase (AdhE) was purified from ethanol-grown cells. It catalysed the NAD(+) - and CoA-dependent oxidation of ethanol via acetaldehyde to acetyl-CoA. The enzyme was regulated by free coenzyme A: in the absence of coenzyme A, the Km value for ethanol was shifted from 3.4 to 40 mM. The alcohol dehydrogenase domain could also oxidize 1-propanol and 1-butanol; however, the aldehyde dehydrogenase domain was highly specific for acetaldehyde as substrate. Apparently, the bifunctional AdhE allows for NAD(+) reduction by lowering the concentration of acetaldehyde, which makes the first oxidation reaction thermodynamically feasible.
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Affiliation(s)
- Johannes Bertsch
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Anna Lena Siemund
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Florian Kremp
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany.
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Metabolic response of Clostridium ljungdahlii to oxygen exposure. Appl Environ Microbiol 2015; 81:8379-91. [PMID: 26431975 DOI: 10.1128/aem.02491-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/23/2015] [Indexed: 12/31/2022] Open
Abstract
Clostridium ljungdahlii is an important synthesis gas-fermenting bacterium used in the biofuels industry, and a preliminary investigation showed that it has some tolerance to oxygen when cultured in rich mixotrophic medium. Batch cultures not only continue to grow and consume H2, CO, and fructose after 8% O2 exposure, but fermentation product analysis revealed an increase in ethanol concentration and decreased acetate concentration compared to non-oxygen-exposed cultures. In this study, the mechanisms for higher ethanol production and oxygen/reactive oxygen species (ROS) detoxification were identified using a combination of fermentation, transcriptome sequencing (RNA-seq) differential expression, and enzyme activity analyses. The results indicate that the higher ethanol and lower acetate concentrations were due to the carboxylic acid reductase activity of a more highly expressed predicted aldehyde oxidoreductase (CLJU_c24130) and that C. ljungdahlii's primary defense upon oxygen exposure is a predicted rubrerythrin (CLJU_c39340). The metabolic responses of higher ethanol production and oxygen/ROS detoxification were found to be linked by cofactor management and substrate and energy metabolism. This study contributes new insights into the physiology and metabolism of C. ljungdahlii and provides new genetic targets to generate C. ljungdahlii strains that produce more ethanol and are more tolerant to syngas contaminants.
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Mock J, Zheng Y, Mueller AP, Ly S, Tran L, Segovia S, Nagaraju S, Köpke M, Dürre P, Thauer RK. Energy Conservation Associated with Ethanol Formation from H2 and CO2 in Clostridium autoethanogenum Involving Electron Bifurcation. J Bacteriol 2015; 197:2965-80. [PMID: 26148714 PMCID: PMC4542177 DOI: 10.1128/jb.00399-15] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 06/29/2015] [Indexed: 02/01/2023] Open
Abstract
UNLABELLED Most acetogens can reduce CO2 with H2 to acetic acid via the Wood-Ljungdahl pathway, in which the ATP required for formate activation is regenerated in the acetate kinase reaction. However, a few acetogens, such as Clostridium autoethanogenum, Clostridium ljungdahlii, and Clostridium ragsdalei, also form large amounts of ethanol from CO2 and H2. How these anaerobes with a growth pH optimum near 5 conserve energy has remained elusive. We investigated this question by determining the specific activities and cofactor specificities of all relevant oxidoreductases in cell extracts of H2/CO2-grown C. autoethanogenum. The activity studies were backed up by transcriptional and mutational analyses. Most notably, despite the presence of six hydrogenase systems of various types encoded in the genome, the cells appear to contain only one active hydrogenase. The active [FeFe]-hydrogenase is electron bifurcating, with ferredoxin and NADP as the two electron acceptors. Consistently, most of the other active oxidoreductases rely on either reduced ferredoxin and/or NADPH as the electron donor. An exception is ethanol dehydrogenase, which was found to be NAD specific. Methylenetetrahydrofolate reductase activity could only be demonstrated with artificial electron donors. Key to the understanding of this energy metabolism is the presence of membrane-associated reduced ferredoxin:NAD(+) oxidoreductase (Rnf), of electron-bifurcating and ferredoxin-dependent transhydrogenase (Nfn), and of acetaldehyde:ferredoxin oxidoreductase, which is present with very high specific activities in H2/CO2-grown cells. Based on these findings and on thermodynamic considerations, we propose metabolic schemes that allow, depending on the H2 partial pressure, the chemiosmotic synthesis of 0.14 to 1.5 mol ATP per mol ethanol synthesized from CO2 and H2. IMPORTANCE Ethanol formation from syngas (H2, CO, and CO2) and from H2 and CO2 that is catalyzed by bacteria is presently a much-discussed process for sustainable production of biofuels. Although the process is already in use, its biochemistry is only incompletely understood. The most pertinent question is how the bacteria conserve energy for growth during ethanol formation from H2 and CO2, considering that acetyl coenzyme A (acetyl-CoA), is an intermediate. Can reduction of the activated acetic acid to ethanol with H2 be coupled with the phosphorylation of ADP? Evidence is presented that this is indeed possible, via both substrate-level phosphorylation and electron transport phosphorylation. In the case of substrate-level phosphorylation, acetyl-CoA reduction to ethanol proceeds via free acetic acid involving acetaldehyde:ferredoxin oxidoreductase (carboxylate reductase).
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Affiliation(s)
- Johanna Mock
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Yanning Zheng
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - San Ly
- LanzaTech Inc., Skokie, Illinois, USA
| | - Loan Tran
- LanzaTech Inc., Skokie, Illinois, USA
| | | | | | | | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Converting carbon dioxide to butyrate with an engineered strain of Clostridium ljungdahlii. mBio 2014; 5:e01636-14. [PMID: 25336453 PMCID: PMC4212834 DOI: 10.1128/mbio.01636-14] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Microbial conversion of carbon dioxide to organic commodities via syngas metabolism or microbial electrosynthesis is an attractive option for production of renewable biocommodities. The recent development of an initial genetic toolbox for the acetogen Clostridium ljungdahlii has suggested that C. ljungdahlii may be an effective chassis for such conversions. This possibility was evaluated by engineering a strain to produce butyrate, a valuable commodity that is not a natural product of C. ljungdahlii metabolism. Heterologous genes required for butyrate production from acetyl-coenzyme A (CoA) were identified and introduced initially on plasmids and in subsequent strain designs integrated into the C. ljungdahlii chromosome. Iterative strain designs involved increasing translation of a key enzyme by modifying a ribosome binding site, inactivating the gene encoding the first step in the conversion of acetyl-CoA to acetate, disrupting the gene which encodes the primary bifunctional aldehyde/alcohol dehydrogenase for ethanol production, and interrupting the gene for a CoA transferase that potentially represented an alternative route for the production of acetate. These modifications yielded a strain in which ca. 50 or 70% of the carbon and electron flow was diverted to the production of butyrate with H2 or CO as the electron donor, respectively. These results demonstrate the possibility of producing high-value commodities from carbon dioxide with C. ljungdahlii as the catalyst. Importance: The development of a microbial chassis for efficient conversion of carbon dioxide directly to desired organic products would greatly advance the environmentally sustainable production of biofuels and other commodities. Clostridium ljungdahlii is an effective catalyst for microbial electrosynthesis, a technology in which electricity generated with renewable technologies, such as solar or wind, powers the conversion of carbon dioxide and water to organic products. Other electron donors for C. ljungdahlii include carbon monoxide, which can be derived from industrial waste gases or the conversion of recalcitrant biomass to syngas, as well as hydrogen, another syngas component. The finding that carbon and electron flow in C. ljungdahlii can be diverted from the production of acetate to butyrate synthesis is an important step toward the goal of renewable commodity production from carbon dioxide with this organism.
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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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