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Kato J, Matsuo T, Takemura K, Kato S, Fujii T, Wada K, Nakamichi Y, Watanabe M, Aoi Y, Morita T, Murakami K, Nakashimada Y. Isopropanol production via the thermophilic bioconversion of sugars and syngas using metabolically engineered Moorella thermoacetica. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:13. [PMID: 38281982 PMCID: PMC10823632 DOI: 10.1186/s13068-024-02460-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
BACKGROUND Isopropanol (IPA) is a commodity chemical used as a solvent or raw material for polymeric products, such as plastics. Currently, IPA production depends largely on high-CO2-emission petrochemical methods that are not sustainable. Therefore, alternative low-CO2 emission methods are required. IPA bioproduction using biomass or waste gas is a promising method. RESULTS Moorella thermoacetica, a thermophilic acetogenic microorganism, was genetically engineered to produce IPA. A metabolic pathway related to acetone reduction was selected, and acetone conversion to IPA was achieved via the heterologous expression of secondary alcohol dehydrogenase (sadh) in the thermophilic bacterium. sadh-expressing strains were combined with acetone-producing strains, to obtain an IPA-producing strain. The strain produced IPA as a major product using hexose and pentose sugars as substrates (81% mol-IPA/mol-sugar). Furthermore, IPA was produced from CO, whereas acetate was an abundant byproduct. Fermentation using syngas containing both CO and H2 resulted in higher IPA production at the specific rate of 0.03 h-1. The supply of reducing power for acetone conversion from the gaseous substrates was examined by supplementing acetone to the culture, and the continuous and rapid conversion of acetone to IPA showed a sufficient supply of NADPH for Sadh. CONCLUSIONS The successful engineering of M. thermoacetica resulted in high IPA production from sugars. M. thermoacetica metabolism showed a high capacity for acetone conversion to IPA in the gaseous substrates, indicating acetone production as the bottleneck in IPA production for further improving the strain. This study provides a platform for IPA production via the metabolic engineering of thermophilic acetogens.
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Affiliation(s)
- Junya Kato
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8530, Japan
- National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashihiroshima, Hiroshima, 739-0046, Japan
| | - Takeshi Matsuo
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Kaisei Takemura
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Setsu Kato
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Tatsuya Fujii
- National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashihiroshima, Hiroshima, 739-0046, Japan
| | - Keisuke Wada
- National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Yusuke Nakamichi
- National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashihiroshima, Hiroshima, 739-0046, Japan
| | - Masahiro Watanabe
- National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashihiroshima, Hiroshima, 739-0046, Japan
| | - Yoshiteru Aoi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Tomotake Morita
- National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashihiroshima, Hiroshima, 739-0046, Japan
| | - Katsuji Murakami
- National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashihiroshima, Hiroshima, 739-0046, Japan
| | - Yutaka Nakashimada
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8530, Japan.
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Yang M, Meng F, Gu W, Fu L, Zhang F, Li F, Tao Y, Zhang Z, Wang X, Yang X, Li J, Yu J. Influence of Polysaccharides From Polygonatum kingianum on Short-Chain Fatty Acid Production and Quorum Sensing in Lactobacillus faecis. Front Microbiol 2021; 12:758870. [PMID: 34867887 PMCID: PMC8635744 DOI: 10.3389/fmicb.2021.758870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/19/2021] [Indexed: 01/09/2023] Open
Abstract
Polysaccharide is one of the main active ingredients of Polygonatum kingianum, which has been proven to regulate the balance of gut microbiota. For the first time, this study focused on the regulation of polysaccharides from Polygonatum kingianum (PS) on Lactobacillus faecis, a specific probiotic in the intestinal tract. PS effectively promoted the biomass, biofilm and acetic acid production in L. faecis 2-84, and enhanced quorum sensing (QS) signaling. The characteristics of gene sequence were analyzed using genomics approaches, and L. faecis 2-84 was found to encode 18 genes that are closely related to QS and 10 genes related to short-chain fatty acids (SCFAs). Additionally, transcriptome and proteome analysis demonstrated that PS could promote the QS system of L. faecis by enhancing the transcription of oppA gene and expression of oppD protein. PS also regulated the production and metabolism of SCFAs of L. faecis by upregulating the expression of ldh and metE gene and adh2 protein, and downregulating the expression of mvK gene. In conclusion, it was speculated that PS could affect intestinal SCFAs production by affecting the QS system and SCFAs production in L. faecis. The present study implied that PS might have a role in promoting the growth of intestinal probiotics, where the QS system and SCFAs might be two of the important mechanisms for the probiotic activity of PS.
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Affiliation(s)
- Min Yang
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China.,Kunming Third People's Hospital, Kunming, China
| | - Fanying Meng
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Wen Gu
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Lihui Fu
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Fan Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Fengjiao Li
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Yating Tao
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Zhengyang Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Xi Wang
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Xingxin Yang
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Jingping Li
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Jie Yu
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
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3
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Hitschler L, Nissen LS, Kuntz M, Basen M. Alcohol dehydrogenases AdhE and AdhB with broad substrate ranges are important enzymes for organic acid reduction in Thermoanaerobacter sp. strain X514. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:187. [PMID: 34563250 PMCID: PMC8466923 DOI: 10.1186/s13068-021-02038-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The industrial production of various alcohols from organic carbon compounds may be performed at high rates and with a low risk of contamination using thermophilic microorganisms as whole-cell catalysts. Thermoanaerobacter species that thrive around 50-75 °C not only perform fermentation of sugars to alcohols, but some also utilize different organic acids as electron acceptors, reducing them to their corresponding alcohols. RESULTS We purified AdhE as the major NADH- and AdhB as the major NADPH-dependent alcohol dehydrogenase (ADH) from the cell extract of the organic acid-reducing Thermoanaerobacter sp. strain X514. Both enzymes were present in high amounts during growth on glucose with and without isobutyrate, had broad substrate spectra including different aldehydes, with high affinities (< 1 mM) for acetaldehyde and for NADH (AdhE) or NADPH (AdhB). Both enzymes were highly thermostable at the physiological temperature of alcohol production. In addition to AdhE and AdhB, we identified two abundant AdhA-type ADHs based on their genes, which were recombinantly produced and biochemically characterized. The other five ADHs encoded in the genome were only expressed at low levels. CONCLUSIONS According to their biochemical and kinetic properties, AdhE and AdhB are most important for ethanol formation from sugar and reduction of organic acids to alcohols, while the role of the two AdhA-type enzymes is less clear. AdhE is the only abundant aldehyde dehydrogenase for the acetyl-CoA reduction to aldehydes, however, acid reduction may also proceed directly by aldehyde:ferredoxin oxidoreductase. The role of the latter in bio-alcohol formation from sugar and in organic acid reduction needs to be elucidated in future studies.
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Affiliation(s)
- Lisa Hitschler
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue Str. 9, 60438, Frankfurt/Main, Germany
- Department of Membrane Biochemistry, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115, Bonn, Germany
| | - Laura Sofie Nissen
- Microbiology, Institute of Biological Sciences, University of Rostock, Albert-Einstein Str. 3, 18059, Rostock, Germany
| | - Michelle Kuntz
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue Str. 9, 60438, Frankfurt/Main, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, University of Tübingen, Auf der Morgenstelle 24, 72076, Tübingen, Germany
| | - Mirko Basen
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue Str. 9, 60438, Frankfurt/Main, Germany.
- Microbiology, Institute of Biological Sciences, University of Rostock, Albert-Einstein Str. 3, 18059, Rostock, Germany.
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4
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Kato J, Takemura K, Kato S, Fujii T, Wada K, Iwasaki Y, Aoi Y, Matsushika A, Murakami K, Nakashimada Y. Metabolic engineering of Moorella thermoacetica for thermophilic bioconversion of gaseous substrates to a volatile chemical. AMB Express 2021; 11:59. [PMID: 33891189 PMCID: PMC8065083 DOI: 10.1186/s13568-021-01220-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 04/09/2021] [Indexed: 11/26/2022] Open
Abstract
Gas fermentation is one of the promising bioprocesses to convert CO2 or syngas to important chemicals. Thermophilic gas fermentation of volatile chemicals has the potential for the development of consolidated bioprocesses that can simultaneously separate products during fermentation. This study reports the production of acetone from CO2 and H2, CO, or syngas by introducing the acetone production pathway using acetyl–coenzyme A (Ac-CoA) and acetate produced via the Wood–Ljungdahl pathway in Moorella thermoacetica. Reducing the carbon flux from Ac-CoA to acetate through genetic engineering successfully enhanced acetone productivity, which varied on the basis of the gas composition. The highest acetone productivity was obtained with CO–H2, while autotrophic growth collapsed with CO2–H2. By adding H2 to CO, the acetone productivity from the same amount of carbon source increased compared to CO gas only, and the maximum specific acetone production rate also increased from 0.04 to 0.09 g-acetone/g-dry cell/h. Our development of the engineered thermophilic acetogen M. thermoacetica, which grows at a temperature higher than the boiling point of acetone (58 °C), would pave the way for developing a consolidated process with simplified and cost-effective recovery via condensation following gas fermentation.
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5
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Suresh A, Shravan Ramgopal D, Panchamoorthy Gopinath K, Arun J, SundarRajan P, Bhatnagar A. Recent advancements in the synthesis of novel thermostable biocatalysts and their applications in commercially important chemoenzymatic conversion processes. BIORESOURCE TECHNOLOGY 2021; 323:124558. [PMID: 33383359 DOI: 10.1016/j.biortech.2020.124558] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 06/12/2023]
Abstract
Thermostable enzymes are a field of growing interest in bioremediation, pharmaceuticals, food industry etc., due to their ability to catalyze bio reactions at high temperatures. This review aims to provide an overview on extremophiles with a special focus on thermophiles and enzymes produced from extremophilic bacteria. Novel thermostable catalysts, used in producing commercially important chemicals, are discussed in this review. Various classes of enzymes produced by microbes, synthesis of thermozymes and comparison with enzymes produced at optimal conditions are critically discussed. A detailed discussion on immobilized enzymes in comparisons with free enzymes, produced by extremozymes, is included. Different parameters which affect enzyme production are also discussed. The current industrial trends along with the future of biocatalysts in the production of chemicals using efficient methods are also discussed.
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Affiliation(s)
- Aravind Suresh
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam - 603110, Chennai, Tamil Nadu, India
| | - Dhakshin Shravan Ramgopal
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam - 603110, Chennai, Tamil Nadu, India
| | - Kannappan Panchamoorthy Gopinath
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam - 603110, Chennai, Tamil Nadu, India
| | - Jayaseelan Arun
- Centre for Waste Management, International Research Centre, Sathyabama Institute of Science and Technology, Jeppiaar Nagar (OMR), Chennai 600119, Tamil Nadu, India
| | - Panneerselvam SundarRajan
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam - 603110, Chennai, Tamil Nadu, India
| | - Amit Bhatnagar
- Department of Separation Science, LUT School of Engineering Science, LUT University, Sammonkatu 12, FI-50130 Mikkeli, Finland.
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6
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Rollin JA, Bomble YJ, St. John PC, Stark AK. Biochemical Production with Purified Cell-Free Systems. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2018.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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7
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Mandal S, Debnath U, Sarkar J. Structural-Genetic Characterization Of Novel Butaryl co-A Dehydrogenase and Proposition of Butanol Biosynthesis Pathway in Pusillimonas ginsengisoli SBSA. J Mol Evol 2021; 89:81-94. [PMID: 33462639 DOI: 10.1007/s00239-020-09989-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 12/21/2020] [Indexed: 01/02/2023]
Abstract
Despite extensive use in the biofuel industry, only butyryl co-A dehydrogenase enzymes from the Clostridia group have undergone extensive structural and genetic characterization. The present study, portrays the characterization of structural, functional and phylogenetic properties of butyryl co-A dehydrogenase identified within the genome of Pusillimonas ginsengisoli SBSA. In silico characterization, homology modelling and docking data indicates that this protein is a homo-tetramer and 388 amino acid residue long, rich in alanine and leucine residue; having molecular weight of 42347.69 dalton. Its isoelectric point value is 5.78; indicate its neutral nature while 38.38 instability index value indicate its stable nature. Its thermostable nature evidenced by its high aliphatic index (93.14); makes its suitable for industry-based use. The secondary structure prediction analysis of butyryl co-A dehydrogenase unveiled that the proteins has secondary arrangements of 54% α-helix, 13% β-stand and 5% disordered conformation. However, phylogenetic analysis clearly indicates that probably horizontal gene transfer is the primary mechanism of spreading of this gene in this organism. Notably, multiple sequence alignment study of phylogenetically diverse butyryl co-A dehydrogenase sequence highlighted the presence of conserved amino acid residues i.e. YXV/LGXKXWXS/T. Physicochemical characterization of other relevant proteins involved in butanol metabolism of SBSA also has been carried out. However, metabolic construction of functional butanol biosynthesis pathway in SBSA, enlightened its cost-effective potential use in biofuel industry as an alternate to Clostridia system.
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Affiliation(s)
- Subhrangshu Mandal
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India.
| | - Utsab Debnath
- School of Health Science, University of Petroleum and Energy Studies, Dehradun, 248007, India
| | - Jagannath Sarkar
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
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8
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Garcia S, Thompson RA, Giannone RJ, Dash S, Maranas CD, Trinh CT. Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design. Front Bioeng Biotechnol 2020; 8:772. [PMID: 32974289 PMCID: PMC7471609 DOI: 10.3389/fbioe.2020.00772] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/18/2020] [Indexed: 01/29/2023] Open
Abstract
Solving environmental and social challenges such as climate change requires a shift from our current non-renewable manufacturing model to a sustainable bioeconomy. To lower carbon emissions in the production of fuels and chemicals, plant biomass feedstocks can replace petroleum using microorganisms as biocatalysts. The anaerobic thermophile Clostridium thermocellum is a promising bacterium for bioconversion due to its capability to efficiently degrade lignocellulosic biomass. However, the complex metabolism of C. thermocellum is not fully understood, hindering metabolic engineering to achieve high titers, rates, and yields of targeted molecules. In this study, we developed an updated genome-scale metabolic model of C. thermocellum that accounts for recent metabolic findings, has improved prediction accuracy, and is standard-conformant to ensure easy reproducibility. We illustrated two applications of the developed model. We first formulated a multi-omics integration protocol and used it to understand redox metabolism and potential bottlenecks in biofuel (e.g., ethanol) production in C. thermocellum. Second, we used the metabolic model to design modular cells for efficient production of alcohols and esters with broad applications as flavors, fragrances, solvents, and fuels. The proposed designs not only feature intuitive push-and-pull metabolic engineering strategies, but also present novel manipulations around important central metabolic branch-points. We anticipate the developed genome-scale metabolic model will provide a useful tool for system analysis of C. thermocellum metabolism to fundamentally understand its physiology and guide metabolic engineering strategies to rapidly generate modular production strains for effective biosynthesis of biofuels and biochemicals from lignocellulosic biomass.
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Affiliation(s)
- Sergio Garcia
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, United States.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - R Adam Thompson
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville, TN, United States.,Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Richard J Giannone
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Satyakam Dash
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Costas D Maranas
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Cong T Trinh
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, United States.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville, TN, United States.,Oak Ridge National Laboratory, Oak Ridge, TN, United States
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9
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Extreme thermophiles as emerging metabolic engineering platforms. Curr Opin Biotechnol 2019; 59:55-64. [DOI: 10.1016/j.copbio.2019.02.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/31/2019] [Accepted: 02/09/2019] [Indexed: 02/06/2023]
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10
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Yang J, Zhang CT, Yuan XJ, Zhang M, Mo XH, Tan LL, Zhu LP, Chen WJ, Yao MD, Hu B, Yang S. Metabolic engineering of Methylobacterium extorquens AM1 for the production of butadiene precursor. Microb Cell Fact 2018; 17:194. [PMID: 30572892 PMCID: PMC6300920 DOI: 10.1186/s12934-018-1042-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/10/2018] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Butadiene is a platform chemical used as an industrial feedstock for the manufacture of automobile tires, synthetic resins, latex and engineering plastics. Currently, butadiene is predominantly synthesized as a byproduct of ethylene production from non-renewable petroleum resources. Although the idea of biological synthesis of butadiene from sugars has been discussed in the literature, success for that goal has so far not been reported. As a model system for methanol assimilation, Methylobacterium extorquens AM1 can produce several unique metabolic intermediates for the production of value-added chemicals, including crotonyl-CoA as a potential precursor for butadiene synthesis. RESULTS In this work, we focused on constructing a metabolic pathway to convert crotonyl-CoA into crotyl diphosphate, a direct precursor of butadiene. The engineered pathway consists of three identified enzymes, a hydroxyethylthiazole kinase (THK) from Escherichia coli, an isopentenyl phosphate kinase (IPK) from Methanothermobacter thermautotrophicus and an aldehyde/alcohol dehydrogenase (ADHE2) from Clostridium acetobutylicum. The Km and kcat of THK, IPK and ADHE2 were determined as 8.35 mM and 1.24 s-1, 1.28 mM and 153.14 s-1, and 2.34 mM and 1.15 s-1 towards crotonol, crotyl monophosphate and crotonyl-CoA, respectively. Then, the activity of one of rate-limiting enzymes, THK, was optimized by random mutagenesis coupled with a developed high-throughput screening colorimetric assay. The resulting variant (THKM82V) isolated from over 3000 colonies showed 8.6-fold higher activity than wild-type, which helped increase the titer of crotyl diphosphate to 0.76 mM, corresponding to a 7.6% conversion from crotonol in the one-pot in vitro reaction. Overexpression of native ADHE2, IPK with THKM82V under a strong promoter mxaF in M. extorquens AM1 did not produce crotyl diphosphate from crotonyl-CoA, but the engineered strain did generate 0.60 μg/mL of intracellular crotyl diphosphate from exogenously supplied crotonol at mid-exponential phase. CONCLUSIONS These results represent the first step in producing a butadiene precursor in recombinant M. extorquens AM1. It not only demonstrates the feasibility of converting crotonol to key intermediates for butadiene biosynthesis, it also suggests future directions for improving catalytic efficiency of aldehyde/alcohol dehydrogenase to produce butadiene precursor from methanol.
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Affiliation(s)
- Jing Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong China
| | - Chang-Tai Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong China
| | - Xiao-Jie Yuan
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong China
| | - Min Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong China
| | - Xu-Hua Mo
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong China
| | - Ling-Ling Tan
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong China
| | - Li-Ping Zhu
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong China
| | - Wen-Jing Chen
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong China
| | - Ming-Dong Yao
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Bo Hu
- Industrial Product Division, Intrexon Corporation, South San Francisco, CA 94080 USA
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, Shandong China
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11
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Zeldes BM, Straub CT, Otten JK, Adams MW, Kelly RM. A synthetic enzymatic pathway for extremely thermophilic acetone production based on the unexpectedly thermostable acetoacetate decarboxylase from Clostridium acetobutylicum. Biotechnol Bioeng 2018; 115:2951-2961. [PMID: 30199090 PMCID: PMC6231964 DOI: 10.1002/bit.26829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/25/2018] [Accepted: 09/05/2018] [Indexed: 01/02/2023]
Abstract
One potential advantage of an extremely thermophilic metabolic engineering host (T opt ≥ 70°C) is facilitated recovery of volatile chemicals from the vapor phase of an active fermenting culture. This process would reduce purification costs and concomitantly alleviate toxicity to the cells by continuously removing solvent fermentation products such as acetone or ethanol, a process we are calling "bio-reactive distillation." Although extremely thermophilic heterologous metabolic pathways can be inspired by existing mesophilic versions, they require thermostable homologs of the constituent enzymes if they are to be utilized in extremely thermophilic bacteria or archaea. Production of acetone from acetyl-CoA and acetate in the mesophilic bacterium Clostridium acetobutylicum utilizes three enzymes: thiolase, acetoacetyl-CoA: acetate CoA transferase (CtfAB), and acetoacetate decarboxylase (Adc). Previously reported biocatalytic pathways for acetone production were demonstrated only as high as 55°C. Here, we demonstrate a synthetic enzymatic pathway for acetone production that functions up to at least 70°C in vitro, made possible by the unusual thermostability of Adc from the mesophile C. acetobutylicum, and heteromultimeric acetoacetyl-CoA:acetate CoA-transferase (CtfAB) complexes from Thermosipho melanesiensis and Caldanaerobacter subterraneus, composed of a highly thermostable α-subunit and a thermally labile β-subunit. The three enzymes produce acetone in vitro at temperatures of at least 70°C, paving the way for bio-reactive distillation of acetone using a metabolically engineered extreme thermophile as a production host.
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Affiliation(s)
- Benjamin M. Zeldes
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Christopher T. Straub
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Jonathan K. Otten
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Michael W.W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
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Becher E, Heese A, Claußen L, Eisen S, Jehmlich N, Rohwerder T, Purswani J. Active site alanine preceding catalytic cysteine determines unique substrate specificity in bacterial CoA-acylating prenal dehydrogenase. FEBS Lett 2018; 592:1150-1160. [PMID: 29485713 DOI: 10.1002/1873-3468.13019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/08/2018] [Accepted: 02/19/2018] [Indexed: 11/06/2022]
Abstract
In detoxification and fermentation processes, acylating dehydrogenases catalyze the reversible oxidation of aldehydes to their corresponding acyl-CoA esters. Here, we characterize an enzyme from Aquincola tertiaricarbonis L108 responsible for prenal (3-methyl-2-butenal) to 3-methylcrotonyl-CoA oxidation. Enzyme kinetics demonstrate a preference for C5 substrates not yet observed in aldehyde dehydrogenases. Compared to acetaldehyde and acetyl-CoA, conversion of valeraldehyde and valeryl-CoA is > 100- and 8-fold more efficient, respectively. Enzyme variants with A254I, A254P, and A254G mutations indicate that active site Ala preceding the catalytic C255 is crucial for this unique specificity. These results shed new light on evolutionary adaptation of aldehyde dehydrogenases toward xenobiotics and structure-guided design of highly specific enzymes for production of biofuels, such as linear or iso-branched butanols and pentanols.
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Affiliation(s)
- Ellen Becher
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Alexander Heese
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Laura Claußen
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Sebastian Eisen
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Thore Rohwerder
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jessica Purswani
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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13
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Straub CT, Zeldes BM, Schut GJ, Adams MWW, Kelly RM. Extremely thermophilic energy metabolisms: biotechnological prospects. Curr Opin Biotechnol 2017; 45:104-112. [DOI: 10.1016/j.copbio.2017.02.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/14/2017] [Accepted: 02/24/2017] [Indexed: 12/16/2022]
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Keller MW, Lipscomb GL, Nguyen DM, Crowley AT, Schut GJ, Scott I, Kelly RM, Adams MWW. Ethanol production by the hyperthermophilic archaeon Pyrococcus furiosus by expression of bacterial bifunctional alcohol dehydrogenases. Microb Biotechnol 2017; 10:1535-1545. [PMID: 28194879 PMCID: PMC5658578 DOI: 10.1111/1751-7915.12486] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/03/2016] [Accepted: 11/14/2016] [Indexed: 01/25/2023] Open
Abstract
Ethanol is an important target for the renewable production of liquid transportation fuels. It can be produced biologically from pyruvate, via pyruvate decarboxylase, or from acetyl‐CoA, by alcohol dehydrogenase E (AdhE). Thermophilic bacteria utilize AdhE, which is a bifunctional enzyme that contains both acetaldehyde dehydrogenase and alcohol dehydrogenase activities. Many of these organisms also contain a separate alcohol dehydrogenase (AdhA) that generates ethanol from acetaldehyde, although the role of AdhA in ethanol production is typically not clear. As acetyl‐CoA is a key central metabolite that can be generated from a wide range of substrates, AdhE can serve as a single gene fuel module to produce ethanol through primary metabolic pathways. The focus here is on the hyperthermophilic archaeon Pyrococcus furiosus, which grows by fermenting sugar to acetate, CO2 and H2. Previously, by the heterologous expression of adhA from a thermophilic bacterium, P. furiosus was shown to produce ethanol by a novel mechanism from acetate, mediated by AdhA and the native enzyme aldehyde oxidoreductase (AOR). In this study, the AOR gene was deleted from P. furiosus to evaluate ethanol production directly from acetyl‐CoA by heterologous expression of the adhE gene from eight thermophilic bacteria. Only AdhEs from two Thermoanaerobacter strains showed significant activity in cell‐free extracts of recombinant P. furiosus and supported ethanol production in vivo. In the AOR deletion background, the highest amount of ethanol (estimated 61% theoretical yield) was produced when adhE and adhA from Thermoanaerobacter were co‐expressed.
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Affiliation(s)
- Matthew W Keller
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Gina L Lipscomb
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Diep M Nguyen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Alexander T Crowley
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Israel Scott
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
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Loder AJ, Zeldes BM, Conway JM, Counts JA, Straub CT, Khatibi PA, Lee LL, Vitko NP, Keller MW, Rhaesa AM, Rubinstein GM, Scott IM, Lipscomb GL, Adams MW, Kelly RM. Extreme Thermophiles as Metabolic Engineering Platforms: Strategies and Current Perspective. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Andrew J. Loder
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Benjamin M. Zeldes
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Jonathan M. Conway
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - James A. Counts
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Christopher T. Straub
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Piyum A. Khatibi
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Laura L. Lee
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Nicholas P. Vitko
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Matthew W. Keller
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Amanda M. Rhaesa
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Gabe M. Rubinstein
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Israel M. Scott
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Gina L. Lipscomb
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Michael W.W. Adams
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Robert M. Kelly
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
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Reaction kinetic analysis of the 3-hydroxypropionate/4-hydroxybutyrate CO 2 fixation cycle in extremely thermoacidophilic archaea. Metab Eng 2016; 38:446-463. [PMID: 27771364 DOI: 10.1016/j.ymben.2016.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/07/2016] [Accepted: 10/17/2016] [Indexed: 12/21/2022]
Abstract
The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle fixes CO2 in extremely thermoacidophilic archaea and holds promise for metabolic engineering because of its thermostability and potentially rapid pathway kinetics. A reaction kinetics model was developed to examine the biological and biotechnological attributes of the 3HP/4HB cycle as it operates in Metallosphaera sedula, based on previous information as well as on kinetic parameters determined here for recombinant versions of five of the cycle enzymes (malonyl-CoA/succinyl-CoA reductase, 3-hydroxypropionyl-CoA synthetase, 3-hydroxypropionyl-CoA dehydratase, acryloyl-CoA reductase, and succinic semialdehyde reductase). The model correctly predicted previously observed features of the cycle: the 35-65% split of carbon flux through the acetyl-CoA and succinate branches, the high abundance and relative ratio of acetyl-CoA/propionyl-CoA carboxylase (ACC) and MCR, and the significance of ACC and hydroxybutyryl-CoA synthetase (HBCS) as regulated control points for the cycle. The model was then used to assess metabolic engineering strategies for incorporating CO2 into chemical intermediates and products of biotechnological importance: acetyl-CoA, succinate, and 3-hydroxypropionate.
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17
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Lian H, Zeldes BM, Lipscomb GL, Hawkins AB, Han Y, Loder AJ, Nishiyama D, Adams MWW, Kelly RM. Ancillary contributions of heterologous biotin protein ligase and carbonic anhydrase for CO 2 incorporation into 3-hydroxypropionate by metabolically engineered Pyrococcus furiosus. Biotechnol Bioeng 2016; 113:2652-2660. [PMID: 27315782 DOI: 10.1002/bit.26033] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/11/2016] [Accepted: 06/05/2016] [Indexed: 12/18/2022]
Abstract
Acetyl-Coenzyme A carboxylase (ACC), malonyl-CoA reductase (MCR), and malonic semialdehyde reductase (MRS) convert HCO3- and acetyl-CoA into 3-hydroxypropionate (3HP) in the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation cycle resident in the extremely thermoacidophilic archaeon Metallosphaera sedula. These three enzymes, when introduced into the hyperthermophilic archaeon Pyrococcus furiosus, enable production of 3HP from maltose and CO2 . Sub-optimal function of ACC was hypothesized to be limiting for production of 3HP, so accessory enzymes carbonic anhydrase (CA) and biotin protein ligase (BPL) from M. sedula were produced recombinantly in Escherichia coli to assess their function. P. furiosus lacks a native, functional CA, while the M. sedula CA (Msed_0390) has a specific activity comparable to other microbial versions of this enzyme. M. sedula BPL (Msed_2010) was shown to biotinylate the β-subunit (biotin carboxyl carrier protein) of the ACC in vitro. Since the native BPLs in E. coli and P. furiosus may not adequately biotinylate the M. sedula ACC, the carboxylase was produced in P. furiosus by co-expression with the M. sedula BPL. The baseline production strain, containing only the ACC, MCR, and MSR, grown in a CO2 -sparged bioreactor reached titers of approximately 40 mg/L 3HP. Strains in which either the CA or BPL accessory enzyme from M. sedula was added to the pathway resulted in improved titers, 120 or 370 mg/L, respectively. The addition of both M. sedula CA and BPL, however, yielded intermediate titers of 3HP (240 mg/L), indicating that the effects of CA and BPL on the engineered 3HP pathway were not additive, possible reasons for which are discussed. While further efforts to improve 3HP production by regulating gene dosage, improving carbon flux and optimizing bioreactor operation are needed, these results illustrate the ancillary benefits of accessory enzymes for incorporating CO2 into 3HP production in metabolically engineered P. furiosus, and hint at the important role that CA and BPL likely play in the native 3HP/4HB pathway in M. sedula. Biotechnol. Bioeng. 2016;113: 2652-2660. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Hong Lian
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27587
| | - Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27587
| | - Gina L Lipscomb
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| | - Aaron B Hawkins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27587
| | - Yejun Han
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27587
| | - Andrew J Loder
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27587
| | - Declan Nishiyama
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27587
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27587.
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