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Zhang F, Zhang K, Zhang Z, Chen HQ, Chen XW, Xian XY, Wu YR. Efficient isopropanol-butanol-ethanol (IBE) fermentation by a gene-modified solventogenic Clostridium species under the co-utilization of Fe(III) and butyrate. BIORESOURCE TECHNOLOGY 2023; 373:128751. [PMID: 36805829 DOI: 10.1016/j.biortech.2023.128751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
To elevate the efficiency of acetone-butanol-ethanol (ABE) fermentation by the wild-type strain WK, an optimal co-utilization system (20 mM Fe3+ and 5 g/L butyrate) was established to bring about a 22.22% increment in the yield of ABE mixtures with a significantly enhanced productivity (0.32 g/L/h). With the heterologous introduction of the secondary alcohol dehydrogenase encoded gene (adh), more than 95% of acetone was eliminated to convert 4.5 g/L isopropanol with corresponding increased butanol and ethanol production by 21.08% and 65.45% in the modified strain WK::adh. Under the optimal condition, strain WK::adh was capable of producing a total of 25.46 g/L IBE biosolvents with an enhanced productivity of 0.35 g/L/h by 45.83% over the original conditions. This work for the first time successfully established a synergetic system of co-utilizing Fe(III) and butyrate to demonstrate a feasible and efficient manner for generating the value-added biofuels through the metabolically engineered solventogenic clostridial strain.
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Affiliation(s)
- Feifei Zhang
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd., Guangzhou, Guangdong 510000, China
| | - Kan Zhang
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd., Guangzhou, Guangdong 510000, China
| | - Zhiqian Zhang
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd., Guangzhou, Guangdong 510000, China
| | - Hai-Qi Chen
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd., Guangzhou, Guangdong 510000, China
| | - Xiao-Wei Chen
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd., Guangzhou, Guangdong 510000, China
| | - Xing-You Xian
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd., Guangzhou, Guangdong 510000, China
| | - Yi-Rui Wu
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd., Guangzhou, Guangdong 510000, China.
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Confirmation of Glucose Transporters through Targeted Mutagenesis and Transcriptional Analysis in Clostridium acetobutylicum. FERMENTATION 2023. [DOI: 10.3390/fermentation9010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The solvent-producing bacterium Clostridium acetobutylicum is able to grow on a variety of carbohydrates. The main hexose transport system is the phosphoenolpyruvate-dependent phosphotransferase system (PTS). When the gene glcG that encodes the glucose transporter was inactivated, the resulting mutant glcG::int(1224) grew as well as the wild type, yet its glucose consumption was reduced by 17% in a batch fermentation. Transcriptomics analysis of the phosphate-limited continuous cultures showed that the cellobiose transporter GlcCE was highly up-regulated in the mutant glcG::int(1224). The glcCE mutation did not affect growth and even consumed slightly more glucose during solventogenesis growth compared to wild type, indicating that GlcG is the primary glucose-specific PTS. Poor growth of the double mutant glcG::int(1224)-glcCE::int(193) further revealed that GlcCE was the secondary glucose PTS and that there must be other PTSs capable of glucose uptake. The observations obtained in this study provided a promising foundation to understand glucose transport in C. acetobutylicum.
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Increased Butyrate Production in Clostridium saccharoperbutylacetonicum from Lignocellulose-Derived Sugars. Appl Environ Microbiol 2022; 88:e0241921. [PMID: 35311509 DOI: 10.1128/aem.02419-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Butyrate is produced by chemical synthesis based on crude oil, produced by microbial fermentation, or extracted from animal fats (M. Dwidar, J.-Y. Park, R. J. Mitchell, and B.-I. Sang, The Scientific World Journal, 2012:471417, 2012, https://doi.org/10.1100/2012/471417). Butyrate production by anaerobic bacteria is highly favorable since waste or sustainable resources can be used as the substrates. For this purpose, the native hyper-butanol producer Clostridium saccharoperbutylacetonicum N1-4(HMT) was used as a chassis strain due to its broad substrate spectrum. BLASTp analysis of the predicted proteome of C. saccharoperbutylacetonicum N1-4(HMT) resulted in the identification of gene products potentially involved in acetone-butanol-ethanol (ABE) fermentation. Their participation in ABE fermentation was either confirmed or disproven by the parallel production of acids or solvents and the respective transcript levels obtained by transcriptome analysis of this strain. The genes encoding phosphotransacetylase (pta) and butyraldehyde dehydrogenase (bld) were deleted to reduce acetate and alcohol formation. The genes located in the butyryl-CoA synthesis (bcs) operon encoding crotonase, butyryl-CoA dehydrogenase with electron-transferring protein subunits α and β, and 3-hydroxybutyryl-CoA dehydrogenase were overexpressed to channel the flux further towards butyrate formation. Thereby, the native hyper-butanol producer C. saccharoperbutylacetonicum N1-4(HMT) was converted into the hyper-butyrate producer C. saccharoperbutylacetonicum ΔbldΔpta [pMTL83151_BCS_PbgaL]. The transcription pattern following deletion and overexpression was characterized by a second transcriptomic study, revealing partial compensation for the deletion. Furthermore, this strain was characterized in pH-controlled fermentations with either glucose or Excello, a substrate yielded from spruce biomass. Butyrate was the main product, with maximum butyrate concentrations of 11.7 g·L-1 and 14.3 g·L-1, respectively. Minimal amounts of by-products were detected. IMPORTANCE Platform chemicals such as butyrate are usually produced chemically from crude oil, resulting in the carry-over of harmful compounds. The selective production of butyrate using sustainable resources or waste without harmful by-products can be achieved by bacteria such as clostridia. The hyper-butanol producer Clostridium saccharoperbutylacetonicum N1-4(HMT) was converted into a hyper-butyrate producer. Butyrate production with very small amounts of by-products was established with glucose and the sustainable lignocellulosic sugar substrate Excello extracted from spruce biomass by the biorefinery Borregaard (Sarpsborg, Norway).
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Du G, Wu Y, Kang W, Xu Y, Li S, Xue C. Enhanced butanol production in Clostridium acetobutylicum by manipulating metabolic pathway genes. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.01.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Yoo JI, Sohn YJ, Son J, Jo SY, Pyo J, Park SK, Choi JI, Joo JC, Kim HT, Park SJ. Recent advances in the microbial production of C4 alcohols by metabolically engineered microorganisms. Biotechnol J 2021; 17:e2000451. [PMID: 33984183 DOI: 10.1002/biot.202000451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND The heavy global dependence on petroleum-based industries has led to serious environmental problems, including climate change and global warming. As a result, there have been calls for a paradigm shift towards the use of biorefineries, which employ natural and engineered microorganisms that can utilize various carbon sources from renewable resources as host strains for the carbon-neutral production of target products. PURPOSE AND SCOPE C4 alcohols are versatile chemicals that can be used directly as biofuels and bulk chemicals and in the production of value-added materials such as plastics, cosmetics, and pharmaceuticals. C4 alcohols can be effectively produced by microorganisms using DCEO biotechnology (tools to design, construct, evaluate, and optimize) and metabolic engineering strategies. SUMMARY OF NEW SYNTHESIS AND CONCLUSIONS In this review, we summarize the production strategies and various synthetic tools available for the production of C4 alcohols and discuss the potential development of microbial cell factories, including the optimization of fermentation processes, that offer cost competitiveness and potential industrial commercialization.
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Affiliation(s)
- Jee In Yoo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Yu Jung Sohn
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Jina Son
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Seo Young Jo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Jiwon Pyo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Su Kyeong Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Jong-Il Choi
- Department of Biotechnology and Engineering, Interdisciplinary Program of Bioenergy and Biomaterials, Chonnam National University, Gwangju, Republic of Korea
| | - Jeong Chan Joo
- Department of Biotechnology, The Catholic University of Korea, Bucheon, Gyenggi-do, Republic of Korea
| | - Hee Taek Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
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Aerobic acetone-butanol-isopropanol (ABI) fermentation through a co-culture of Clostridium beijerinckii G117 and recombinant Bacillus subtilis 1A1. Metab Eng Commun 2020; 11:e00137. [PMID: 32612931 PMCID: PMC7322341 DOI: 10.1016/j.mec.2020.e00137] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/14/2020] [Accepted: 06/06/2020] [Indexed: 02/07/2023] Open
Abstract
An engineered B. subtilis 1A1 strain (BsADH2) expressing a secondary alcohol dehydrogenase (CpSADH) was co-cultured with C. beijerinckii G117 under an aerobic condition. During the fermentation on glucose, B. subtilis BsADH2 depleted oxygen in culture media completely and created an anaerobic environment for C. beijerinckii G117, an obligate anaerobe, to grow. Meanwhile, lactate produced by B. subtilis BsADH2 was re-assimilated by C. beijerinckii G117. In return, acetone produced by C. beijerinckii G117 was reduced into isopropanol by B. subtilis BsADH2 via expressing the CpSADH, which helped maintain the redox balance of the engineered B. subtilis. In the symbiotic system consisting of two strains, 1.7 g/L of acetone, 4.8 g/L of butanol, and 0.9 g/L of isopropanol (with an isopropanol/acetone ratio of 0.53) was produced from 60 g/L of glucose. This symbiotic system also worked when oxygen was supplied to the culture, although less isopropanol was produced (0.9 g/L of acetone, 4.9 g/L of butanol, and 0.2 g/L of isopropanol). The isopropanol titer was increased substantially to 2.5 g/L when we increased the inoculum size of B. subtilis BsADH2 and optimized other process parameters. With the Bacillus-Clostridium co-culture, switching from the original acetone-butanol (AB) fermentation to an aerobic acetone-butanol-isopropanol (ABI) fermentation can be easily achieved without genetic engineering of Clostridium. This strategy of employing a recombinant Bacillus to co-culture with Clostridium should be potentially useful to modify traditional acetone-butanol-ethanol fermentation for the production of other value-added chemicals. A secondary alcohol dehydrogenase was expressed in Bacillus subtilis. Acetone-butanol was upgraded into acetone-butanol-isopropanol by B. subtilis. A mutualistic relationship was established between B. subtilis and C. beijerinckii. Aerobic co-culture of B. subtilis and C. beijerinckii was achieved. Clostridium fermentation was improved by introducing a genetically-modified strain.
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Liu D, Yang Z, Wang P, Niu H, Zhuang W, Chen Y, Wu J, Zhu C, Ying H, Ouyang P. Towards acetone-uncoupled biofuels production in solventogenic Clostridium through reducing power conservation. Metab Eng 2018; 47:102-112. [DOI: 10.1016/j.ymben.2018.03.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 03/11/2018] [Accepted: 03/11/2018] [Indexed: 12/22/2022]
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Little GT, Willson BJ, Heap JT, Winzer K, Minton NP. The Butanol Producing MicrobeClostridium beijerinckiiNCIMB 14988 Manipulated Using Forward and Reverse Genetic Tools. Biotechnol J 2018; 13:e1700711. [DOI: 10.1002/biot.201700711] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/15/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Gareth T. Little
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham; University Park, Nottingham NG7 2RD UK
| | - Benjamin J. Willson
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham; University Park, Nottingham NG7 2RD UK
| | - John T. Heap
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham; University Park, Nottingham NG7 2RD UK
| | - Klaus Winzer
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham; University Park, Nottingham NG7 2RD UK
| | - Nigel P. Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham; University Park, Nottingham NG7 2RD UK
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Zhang C, Li T, He J. Characterization and genome analysis of a butanol-isopropanol-producing Clostridium beijerinckii strain BGS1. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:280. [PMID: 30337959 PMCID: PMC6180514 DOI: 10.1186/s13068-018-1274-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/26/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND One of the main challenges of acetone-butanol-ethanol fermentation is to reduce acetone production with high butanol yield. Converting acetone into isopropanol is an alternative pathway to reduce fermentation by-products in the fermentation broth. Here, we aimed to cultivate a wild-type Clostridium strain with high isopropanol and butanol production and reveal its genome information. RESULTS Clostridium beijerinckii strain BGS1 was found to be capable of producing 10.21 g/L butanol and 3.41 g/L isopropanol, higher than previously known wild-type isopropanol-butanol-producing Clostridium species. Moreover, culture BGS1 exhibited a broad carbon spectrum utilizing diverse sugars such as arabinose, xylose, galactose, cellobiose, and sucrose, with 9.61 g/L butanol and 2.57 g/L isopropanol generated from 60 g/L sucrose and less amount from other sugars. Based on genome analysis, protein-based sequence of strain BGS1 was closer to C. beijerinckii NCIMB 8052, reaching 90.82% similarity, while compared to C. beijerinckii DSM 6423, the similarity was 89.53%. In addition, a unique secondary alcohol dehydrogenase (sAdhE) was revealed in the genome of strain BGS1, which distinguished it from other Clostridium species. Average nucleotide identity analysis identified strain BGS1 belonging to C. beijerinckii. The transcription profile and enzymatic activity of sAdhE proved its function of converting acetone into isopropanol. CONCLUSIONS Clostridium beijerinckii strain BGS1 is a potential candidate for industrial isopropanol and butanol production. Its genome provides unique information for genetic engineering of isopropanol-butanol-producing microorganisms.
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Affiliation(s)
- Chen Zhang
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore, 117576 Singapore
| | - Tinggang Li
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore, 117576 Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore, 117576 Singapore
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Genome Editing in Clostridium saccharoperbutylacetonicum N1-4 with the CRISPR-Cas9 System. Appl Environ Microbiol 2017; 83:AEM.00233-17. [PMID: 28258147 DOI: 10.1128/aem.00233-17] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/26/2017] [Indexed: 12/12/2022] Open
Abstract
Clostridium saccharoperbutylacetonicum N1-4 is well known as a hyper-butanol-producing strain. However, the lack of genetic engineering tools hinders further elucidation of its solvent production mechanism and development of more robust strains. In this study, we set out to develop an efficient genome engineering system for this microorganism based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated 9 (CRISPR-Cas9) system. First, the functionality of the CRISPR-Cas9 system previously customized for Clostridium beijerinckii was evaluated in C. saccharoperbutylacetonicum by targeting pta and buk, two essential genes for acetate and butyrate production, respectively. pta and buk single and double deletion mutants were successfully obtained based on this system. However, the genome engineering efficiency was rather low (the mutation rate is <20%). Therefore, the efficiency was further optimized by evaluating various promoters for guide RNA (gRNA) expression. With promoter P J23119 , we achieved a mutation rate of 75% for pta deletion without serial subculturing as suggested previously for C. beijerinckii Thus, this developed CRISPR-Cas9 system is highly desirable for efficient genome editing in C. saccharoperbutylacetonicum Batch fermentation results revealed that both the acid and solvent production profiles were altered due to the disruption of acid production pathways; however, neither acetate nor butyrate production was eliminated with the deletion of the corresponding gene. The butanol production, yield, and selectivity were improved in mutants, depending on the fermentation medium. In the pta buk double deletion mutant, the butanol production in P2 medium reached 19.0 g/liter, which is one of the highest levels ever reported from batch fermentations.IMPORTANCE An efficient CRISPR-Cas9 genome engineering system was developed for C. saccharoperbutylacetonicum N1-4. This paves the way for elucidating the solvent production mechanism in this hyper-butanol-producing microorganism and developing strains with desirable butanol-producing features. This tool can be easily adapted for use in closely related microorganisms. As also reported by others, here we demonstrated with solid data that the highly efficient expression of gRNA is the key factor determining the efficiency of CRISPR-Cas9 for genome editing. The protocol developed in this study can provide essential references for other researchers who work in the areas of metabolic engineering and synthetic biology. The developed mutants can be used as excellent starting strains for development of more robust ones for desirable solvent production.
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Xue C, Zhao J, Chen L, Yang ST, Bai F. Recent advances and state-of-the-art strategies in strain and process engineering for biobutanol production by Clostridium acetobutylicum. Biotechnol Adv 2017; 35:310-322. [DOI: 10.1016/j.biotechadv.2017.01.007] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/06/2017] [Accepted: 01/25/2017] [Indexed: 12/20/2022]
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Towards improved butanol production through targeted genetic modification of Clostridium pasteurianum. Metab Eng 2017; 40:124-137. [PMID: 28119139 PMCID: PMC5367854 DOI: 10.1016/j.ymben.2017.01.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/18/2017] [Accepted: 01/20/2017] [Indexed: 11/23/2022]
Abstract
Declining fossil fuel reserves, coupled with environmental concerns over their continued extraction and exploitation have led to strenuous efforts to identify renewable routes to energy and fuels. One attractive option is to convert glycerol, a by-product of the biodiesel industry, into n-butanol, an industrially important chemical and potential liquid transportation fuel, using Clostridium pasteurianum. Under certain growth conditions this Clostridium species has been shown to predominantly produce n-butanol, together with ethanol and 1,3-propanediol, when grown on glycerol. Further increases in the yields of n-butanol produced by C. pasteurianum could be accomplished through rational metabolic engineering of the strain. Accordingly, in the current report we have developed and exemplified a robust tool kit for the metabolic engineering of C. pasteurianum and used the system to make the first reported in-frame deletion mutants of pivotal genes involved in solvent production, namely hydA (hydrogenase), rex (Redox response regulator) and dhaBCE (glycerol dehydratase). We were, for the first time in C. pasteurianum, able to eliminate 1,3-propanediol synthesis and demonstrate its production was essential for growth on glycerol as a carbon source. Inactivation of both rex and hydA resulted in increased n-butanol titres, representing the first steps towards improving the utilisation of C. pasteurianum as a chassis for the industrial production of this important chemical.
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Bengelsdorf FR, Poehlein A, Flitsch SK, Linder S, Schiel-Bengelsdorf B, Stegmann BA, Krabben P, Green E, Zhang Y, Minton N, Dürre P. Host Organisms: Clostridium acetobutylicum/ Clostridium beijerinckiiand Related Organisms. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Frank R. Bengelsdorf
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Anja Poehlein
- Georg-August University; Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Göttingen, Grisebachstr. 8 37077 Göttingen Germany
| | - Stefanie K. Flitsch
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Sonja Linder
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Bettina Schiel-Bengelsdorf
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Benjamin A. Stegmann
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Preben Krabben
- Green Biologics Limited; 45A Western Avenue, Milton Park Abingdon Oxfordshire OX14 4RU UK
| | - Edward Green
- CHAIN Biotechnology Limited; Imperial College Incubator, Imperial College London; Level 1 Bessemer Building London SW7 2AZ UK
| | - Ying Zhang
- University of Nottingham; BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences; University Park Nottingham NG7 2RD UK
| | - Nigel Minton
- University of Nottingham; BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences; University Park Nottingham NG7 2RD UK
| | - Peter Dürre
- Universität Ulm; Institut für Mikrobiologie und Biotechnologie; Albert-Einstein-Allee 11 89081 Ulm Germany
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Wong SS, Mi L, Liao JC. Microbial Production of Butanols. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807833.ch19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Sio Si Wong
- University of California; Department of Chemical and Biomolecular Engineering; 420 Westwood Plaza, 5531Boelter Hall Los Angeles CA 90095 USA
| | - Luo Mi
- University of California; Department of Chemical and Biomolecular Engineering; 420 Westwood Plaza, 5531Boelter Hall Los Angeles CA 90095 USA
| | - James C. Liao
- University of California; Department of Chemical and Biomolecular Engineering; 420 Westwood Plaza, 5531Boelter Hall Los Angeles CA 90095 USA
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Su H, Zhu J, Liu G, Tan F. Investigation of availability of a high throughput screening method for predicting butanol solvent -producing ability of Clostridium beijerinckii. BMC Microbiol 2016; 16:160. [PMID: 27448996 PMCID: PMC4957875 DOI: 10.1186/s12866-016-0776-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 07/12/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Currently, efficient screening methods for selection of desired bacterial phenotypes from large populations are not easy feasible or readily available due to the complicated physiological and metabolic networks of solventogenic clostridia. In this study, to contribute to the improvement of methods for predicting the butanol-producing ability of Clostridium beijerinckii based on starch substrate, we further investigate a simple, visualization screening method for selecting target strains from mutant library of Clostridium beijerinckii NCIMB 8052 by using trypan blue dye as an indicator in solid starch via statistical survey and validation of fermentation experiment with controlling pH. RESULTS To verify an effective, efficient phenotypic screening method for isolating high butanol-producing mutants, the revalidation process was conducted based on Trypan Blue was used for visualization, and starch was used as the bacterial metabolic substrate. The availability of the screening system was further evaluated based on the relationship between characteristics of mutant strains and their α-amylase activities. Mutant clones were analyzed in detail based on their distinctive growth patterns and rate of fermentation of soluble starch to form butanol and were compared by statistical method. Significant correlations were identified between colony morphology and changes in butanol concentrations. The screening method was validated via statistical analysis for characterizing phenotypic parameters. The fermentation experiment of mutant strains with controlling pH value also demonstrated a positive correlation between increased α-amylase activity and increased solvent production by Clostridium beijerinckii was observed, and therefore indicated that the trypan blue dyeing method can be used as a fast method to screen target mutant strain for better solvent producers from, for instance, a mutant library. CONCLUSIONS The suitability of the novel screening procedure was validated, opening up a new indicator of approach to select mutant solventogenic clostridia with improved fermentation of starch to increase butanol concentrations. The applicability can easily be broadened to a wide range of interesting microbes such as cellulolytic or acetogenic microorganisms, which produce biofuels from feedstock rich in starch.
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Affiliation(s)
- HaiFeng Su
- Enviromentally-Begnin Chemical Process Research Center, Division of Ecological & Enviromental Research on the Three Gorges, Chongqing Institute of Green and Interligent Technology, Chinese Academy of Science, Beijing, China
| | - Jun Zhu
- Rice Research Institute, Sichuan Agricultural University, 611130, Wenjiang, Sichuan, China
| | - Gang Liu
- Sichuan Academy of Grassland Science, Xipu Chengdu, 611731, Sichuan, Peoples Republic of China.
| | - Furong Tan
- Biogas Institute of Ministry of Agriculture, Chengdu, 610041, Sichuan, Peoples Republic of China.
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Chen CT, Liao JC. Frontiers in microbial 1-butanol and isobutanol production. FEMS Microbiol Lett 2016; 363:fnw020. [PMID: 26832641 DOI: 10.1093/femsle/fnw020] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2016] [Indexed: 12/14/2022] Open
Abstract
The heavy dependence on petroleum-derived fuel has raised concerns about energy sustainability and climate change, which have prompted researchers to explore fuel production from renewable sources. 1-Butanol and isobutanol are promising biofuels that have favorable properties and can also serve as solvents or chemical feedstocks. Microbial production of these alcohols provides great opportunities to access a wide spectrum of renewable resources. In recent years, research has improved the native 1-butanol production and has engineered isobutanol production in various organisms to explore metabolic diversity and a broad range of substrates. This review focuses on progress in metabolic engineering for the production of these two compounds using various resources.
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Affiliation(s)
- Chang-Ting Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - James C Liao
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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18
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Youn SH, Lee KM, Kim KY, Lee SM, Woo HM, Um Y. Effective isopropanol-butanol (IB) fermentation with high butanol content using a newly isolated Clostridium sp. A1424. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:230. [PMID: 27800016 PMCID: PMC5080687 DOI: 10.1186/s13068-016-0650-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/18/2016] [Indexed: 05/17/2023]
Abstract
BACKGROUND Acetone-butanol-ethanol fermentation has been studied for butanol production. Alternatively, to achieve acetone-free butanol production, use of clostridium strains producing butanol and 1,3-propanediol (1,3-PDO) from glycerol, natural and engineered isopropanol-butanol-ethanol (IBE) producers has been attempted; however, residual 1,3-PDO and acetone, low IBE production by natural IBE producers, and complicated gene modification are limitations. RESULTS Here, we report an effective isopropanol and butanol (IB) fermentation using a newly isolated Clostridium sp. A1424 capable of producing IB from various substrates with a small residual acetone. Notably, this strain also utilized glycerol and produced butanol and 1,3-PDO. After 46.35 g/L of glucose consumption at pH 5.5-controlled batch fermentation, Clostridium sp. A1424 produced 9.43 g/L of butanol and 13.92 g/L of IB at the productivity of 0.29 and 0.44 g/L/h, respectively, which are the highest values in glucose-based batch fermentations using natural IB producers. More interestingly, using glucose-glycerol mixtures at ratios ranging from 20:2 to 14:8 led to not only acetone-free and 1,3-PDO-free IB fermentation but also enhanced IB production along with a much higher butanol content (butanol/isopropanol ratio of 1.81 with glucose vs. 2.07-6.14 with glucose-glycerol mixture). Furthermore, when the mixture of glucose and crude glycerol at the ratio of 14:8 (total concentration of 35.68 g/L) was used, high butanol/isopropanol ratio (3.44) and butanol titer (9.86 g/L) were achieved with 1.4-fold enhanced butanol yield (0.28 g/g) and productivity (0.41 g/L/h) compared to those with glucose only at pH 5.5. CONCLUSIONS A newly isolated Clostridium sp. A1424 was able to produce butanol and isopropanol from various carbon sources. The productivity and titer of butanol and total alcohol obtained in this study were higher than the previously reported results obtained using other natural IB producers. Use of the mixture of glucose and glycerol was successful to achieve acetone-free, 1,3-PDO-free, and enhanced IB production with higher yield, productivity, and selectivity of butanol compared to those with glucose only, providing great advantages from the perspective of carbon recovery to alcohols. This notable result could be accomplished by isolating an effective IB producer Clostridium sp. A1424 as well as by utilizing glucose-glycerol mixtures.
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Affiliation(s)
- Sung Hun Youn
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Hwarangno 14‑gil 5, Seongbuk‑gu, Seoul, 02792 South Korea
| | - Kyung Min Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Hwarangno 14‑gil 5, Seongbuk‑gu, Seoul, 02792 South Korea
| | - Ki-Yeon Kim
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Hwarangno 14‑gil 5, Seongbuk‑gu, Seoul, 02792 South Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Hwarangno 14‑gil 5, Seongbuk‑gu, Seoul, 02792 South Korea
- Clean Energy and Chemical Engineering, Korea University of Science and Technology, 217 Gajeong‑ro, Yuseong‑gu, Daejeon, 34113 South Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419 South Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Hwarangno 14‑gil 5, Seongbuk‑gu, Seoul, 02792 South Korea
- Clean Energy and Chemical Engineering, Korea University of Science and Technology, 217 Gajeong‑ro, Yuseong‑gu, Daejeon, 34113 South Korea
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19
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Jin Y, Fang Y, Huang M, Sun J, Huang Y, Gao X, Li R, He K, Zhao H. Combination of RNA sequencing and metabolite data to elucidate improved toxic compound tolerance and butanol fermentation of Clostridium acetobutylicum from wheat straw hydrolysate by supplying sodium sulfide. BIORESOURCE TECHNOLOGY 2015; 198:77-86. [PMID: 26364231 DOI: 10.1016/j.biortech.2015.08.139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/21/2015] [Accepted: 08/22/2015] [Indexed: 06/05/2023]
Abstract
Sodium sulfide (SS) was added to the non-detoxified wheat straw hydrolysate for ABE fermentation by Clostridium acetobutylicum CICC8012. Biochemical measurements demonstrated that supplementation with SS promoted earlier and enhanced conversion of acid to ABE and led to a 27.48% improvement in sugar consumption, a 20.48% improvement in the sugar-based ABE yield, a 47.63% improvement in the butanol titer, and a 53.50% improvement in the ABE concentration. The response of C. acetobutylicum CICC8012 at the mRNA level was examined by a transcriptional analysis performed with RNA sequencing. The expression of genes involved in the membrane transport of carbohydrates, glycolysis, and ABE formation increased following SS-supplemented fermentation, whereas the expression of genes encoding enzymes involved in acid formation decreased, which indicates that supplemental SS affected the central fermentative pathway, down-regulated the metabolic flux toward the acid formation branches, and up-regulated the metabolic flux toward the ABE formation branches.
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Affiliation(s)
- Yanling Jin
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Yang Fang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengjun Huang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaolong Sun
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhong Huang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Xiaofeng Gao
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Renqiang Li
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaize He
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Hai Zhao
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China.
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Fermentation and genomic analysis of acetone-uncoupled butanol production by Clostridium tetanomorphum. Appl Microbiol Biotechnol 2015; 100:1523-1529. [DOI: 10.1007/s00253-015-7121-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/21/2015] [Accepted: 10/24/2015] [Indexed: 11/27/2022]
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21
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Liu Z, Qiao K, Tian L, Zhang Q, Liu ZY, Li FL. Spontaneous large-scale autolysis in Clostridium acetobutylicum contributes to generation of more spores. Front Microbiol 2015; 6:950. [PMID: 26441884 PMCID: PMC4563875 DOI: 10.3389/fmicb.2015.00950] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/27/2015] [Indexed: 12/15/2022] Open
Abstract
Autolysis is a widespread phenomenon in bacteria. In batch fermentation of Clostridium acetobutylicum ATCC 824, there is a spontaneous large-scale autolysis phenomenon with significant decrease of cell density immediately after exponential phase. To unravel the role of autolysis, an autolysin-coding gene, CA_C0554, was disrupted by using ClosTron system to obtain the mutant C. acetobutylicum lyc::int(72). The lower final cell density and faster cell density decrease rate of C. acetobutylicum ATCC 824 than those of C. acetobutylicum lyc::int(72) indicates that CA_C0554 was an important but not the sole autolysin-coding gene responding for the large-scale autolysis. Similar glucose utilization and solvents production but obvious lower cell density of C. acetobutylicum ATCC 824 comparing to C. acetobutylicum lyc::int(72) suggests that lysed C. acetobutylicum ATCC 824 cells were metabolic inactive. On the contrary, the spore density of C. acetobutylicum ATCC 824 is 26.1% higher than that of C. acetobutylicum lyc::int(72) in the final culture broth of batch fermentation. We speculated that spontaneous autolysis of metabolic-inactive cells provided nutrients for the sporulating cells. The present study suggests that one important biological role of spontaneous large-scale autolysis in C. acetobutylicum ATCC 824 batch fermentation is contributing to generation of more spores during sporulation.
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Affiliation(s)
- Zhen Liu
- Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology - Chinese Academy of Sciences Qingdao, China
| | - Kai Qiao
- Sinopec Fushun Research Institute of Petroleum and Petrochemicals Fushun, China
| | - Lei Tian
- Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology - Chinese Academy of Sciences Qingdao, China
| | - Quan Zhang
- Sinopec Fushun Research Institute of Petroleum and Petrochemicals Fushun, China
| | - Zi-Yong Liu
- Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology - Chinese Academy of Sciences Qingdao, China
| | - Fu-Li Li
- Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology - Chinese Academy of Sciences Qingdao, China ; Sinopec Fushun Research Institute of Petroleum and Petrochemicals Fushun, China
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22
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High-Level Butanol Production from Cassava Starch by a Newly Isolated Clostridium acetobutylicum. Appl Biochem Biotechnol 2015; 177:831-41. [DOI: 10.1007/s12010-015-1781-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/23/2015] [Indexed: 01/08/2023]
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23
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Integrated, systems metabolic picture of acetone-butanol-ethanol fermentation by Clostridium acetobutylicum. Proc Natl Acad Sci U S A 2015; 112:8505-10. [PMID: 26100881 DOI: 10.1073/pnas.1423143112] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Microbial metabolism involves complex, system-level processes implemented via the orchestration of metabolic reactions, gene regulation, and environmental cues. One canonical example of such processes is acetone-butanol-ethanol (ABE) fermentation by Clostridium acetobutylicum, during which cells convert carbon sources to organic acids that are later reassimilated to produce solvents as a strategy for cellular survival. The complexity and systems nature of the process have been largely underappreciated, rendering challenges in understanding and optimizing solvent production. Here, we present a system-level computational framework for ABE fermentation that combines metabolic reactions, gene regulation, and environmental cues. We developed the framework by decomposing the entire system into three modules, building each module separately, and then assembling them back into an integrated system. During the model construction, a bottom-up approach was used to link molecular events at the single-cell level into the events at the population level. The integrated model was able to successfully reproduce ABE fermentations of the WT C. acetobutylicum (ATCC 824), as well as its mutants, using data obtained from our own experiments and from literature. Furthermore, the model confers successful predictions of the fermentations with various network perturbations across metabolic, genetic, and environmental aspects. From foundation to applications, the framework advances our understanding of complex clostridial metabolism and physiology and also facilitates the development of systems engineering strategies for the production of advanced biofuels.
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24
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Yu L, Zhao J, Xu M, Dong J, Varghese S, Yu M, Tang IC, Yang ST. Metabolic engineering of Clostridium tyrobutyricum for n-butanol production: effects of CoA transferase. Appl Microbiol Biotechnol 2015; 99:4917-30. [DOI: 10.1007/s00253-015-6566-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 03/18/2015] [Accepted: 03/20/2015] [Indexed: 01/31/2023]
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25
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Becerra M, Cerdán ME, González-Siso MI. Biobutanol from cheese whey. Microb Cell Fact 2015; 14:27. [PMID: 25889728 PMCID: PMC4404668 DOI: 10.1186/s12934-015-0200-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/26/2015] [Indexed: 11/17/2022] Open
Abstract
At present, due to environmental and economic concerns, it is urgent to evolve efficient, clean and secure systems for the production of advanced biofuels from sustainable cheap sources. Biobutanol has proved better characteristics than the more widely used bioethanol, however the main disadvantage of biobutanol is that it is produced in low yield and titer by ABE (acetone-butanol-ethanol) fermentation, this process being not competitive from the economic point of view. In this review we summarize the natural metabolic pathways for biobutanol production by Clostridia and yeasts, together with the metabolic engineering efforts performed up to date with the aim of either enhancing the yield of the natural producer Clostridia or transferring the butanol production ability to other hosts with better attributes for industrial use and facilities for genetic manipulation. Molasses and starch-based feedstocks are main sources for biobutanol production at industrial scale hitherto. We also review herewith (and for the first time up to our knowledge) the research performed for the use of whey, the subproduct of cheese making, as another sustainable source for biobutanol production. This represents a promising alternative that still needs further research. The use of an abundant waste material like cheese whey, that would otherwise be considered an environmental pollutant, for biobutanol production, makes economy of the process more profitable.
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Affiliation(s)
- Manuel Becerra
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus de A Coruña, 15071, A Coruña, Spain.
| | - María Esperanza Cerdán
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus de A Coruña, 15071, A Coruña, Spain.
| | - María Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus de A Coruña, 15071, A Coruña, Spain.
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26
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Liu YJ, Zhang J, Cui GZ, Cui Q. Current progress of targetron technology: Development, improvement and application in metabolic engineering. Biotechnol J 2015; 10:855-65. [DOI: 10.1002/biot.201400716] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/22/2015] [Accepted: 01/29/2015] [Indexed: 01/10/2023]
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27
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Sund CJ, Liu S, Germane KL, Servinsky MD, Gerlach ES, Hurley MM. Phosphoketolase flux in Clostridium acetobutylicum during growth on l-arabinose. Microbiology (Reading) 2015; 161:430-440. [DOI: 10.1099/mic.0.000008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Christian J. Sund
- US Army Research Laboratory, Sensors and Electron Devices Directorate, 2800 Powder Mill Road, Adelphi, MD 20783, USA
| | - Sanchao Liu
- Federal Staffing Resources, 2200 Somerville Rd, Annapolis, MD 21401, USA
| | - Katherine L. Germane
- Oak Ridge Associated Universities, 4692 Millennium Drive, Suite 101, Belcamp, MD 21017, USA
| | - Matthew D. Servinsky
- US Army Research Laboratory, Sensors and Electron Devices Directorate, 2800 Powder Mill Road, Adelphi, MD 20783, USA
| | - Elliot S. Gerlach
- Federal Staffing Resources, 2200 Somerville Rd, Annapolis, MD 21401, USA
| | - Margaret M. Hurley
- US Army Research Laboratory, RDRL-WML-B, 4600 Deer Creek Loop, Aberdeen Proving Ground, MD 21005, USA
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28
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Su H, Zhao Y, Wang M, Xu Y. Development and application of a novel screening method and experimental use of the mutant bacterial strain Clostridium beijerinckii NCIMB 8052 for production of butanol via fermentation of fresh cassava. RSC Adv 2015. [DOI: 10.1039/c4ra16576d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Classic chemical mutagenesis has a demonstrated potential to create a strain ofClostridiumwith improved fermentation performance for obtaining high butanol yield.
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Affiliation(s)
- Haifeng Su
- Enviromentally-Begnin Chemical Process Research Center
- Division of Ecological & Enviromental Research on the Three Gorges
- Chongqing Institute of Green and Interligent Technology
- Chinese Academy of Science
- P. R. China
| | - Yun Zhao
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education
- College of Life Sciences
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Maolin Wang
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education
- College of Life Sciences
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Yuanjian Xu
- Enviromentally-Begnin Chemical Process Research Center
- Division of Ecological & Enviromental Research on the Three Gorges
- Chongqing Institute of Green and Interligent Technology
- Chinese Academy of Science
- P. R. China
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29
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Tan Y, Liu ZY, Liu Z, Zheng HJ, Li FL. Comparative transcriptome analysis between csrA-disruption Clostridium acetobutylicum and its parent strain. MOLECULAR BIOSYSTEMS 2015; 11:1434-42. [DOI: 10.1039/c4mb00600c] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This study represented the first attempt to investigate the global regulation of CsrA through transcriptome analysis in Gram-positive bacteria.
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Affiliation(s)
- Yang Tan
- Key Laboratory of Biofuels
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- China
| | - Zi-Yong Liu
- Key Laboratory of Biofuels
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- China
| | - Zhen Liu
- Key Laboratory of Biofuels
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- China
| | - Hua-Jun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics
- Chinese National Human Genome Center at Shanghai
- Shanghai 201203
- China
| | - Fu-Li Li
- Key Laboratory of Biofuels
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- China
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30
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I-SceI-mediated scarless gene modification via allelic exchange in Clostridium. J Microbiol Methods 2015; 108:49-60. [DOI: 10.1016/j.mimet.2014.11.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/21/2014] [Accepted: 11/07/2014] [Indexed: 02/06/2023]
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31
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Liu D, Chen Y, Ding F, Guo T, Xie J, Zhuang W, Niu H, Shi X, Zhu C, Ying H. Simultaneous production of butanol and acetoin by metabolically engineered Clostridium acetobutylicum. Metab Eng 2015; 27:107-114. [DOI: 10.1016/j.ymben.2014.11.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 09/13/2014] [Accepted: 11/12/2014] [Indexed: 12/26/2022]
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32
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Thakker C, Martínez I, Li W, San KY, Bennett GN. Metabolic engineering of carbon and redox flow in the production of small organic acids. J Ind Microbiol Biotechnol 2014; 42:403-22. [PMID: 25502283 DOI: 10.1007/s10295-014-1560-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/24/2014] [Indexed: 11/26/2022]
Abstract
The review describes efforts toward metabolic engineering of production of organic acids. One aspect of the strategy involves the generation of an appropriate amount and type of reduced cofactor needed for the designed pathway. The ability to capture reducing power in the proper form, NADH or NADPH for the biosynthetic reactions leading to the organic acid, requires specific attention in designing the host and also depends on the feedstock used and cell energetic requirements for efficient metabolism during production. Recent work on the formation and commercial uses of a number of small mono- and diacids is discussed with redox differences, major biosynthetic precursors and engineering strategies outlined. Specific attention is given to those acids that are used in balancing cell redox or providing reduction equivalents for the cell, such as formate, which can be used in conjunction with metabolic engineering of other products to improve yields. Since a number of widely studied acids derived from oxaloacetate as an important precursor, several of these acids are covered with the general strategies and particular components summarized, including succinate, fumarate and malate. Since malate and fumarate are less reduced than succinate, the availability of reduction equivalents and level of aerobiosis are important parameters in optimizing production of these compounds in various hosts. Several other more oxidized acids are also discussed as in some cases, they may be desired products or their formation is minimized to afford higher yields of more reduced products. The placement and connections among acids in the typical central metabolic network are presented along with the use of a number of specific non-native enzymes to enhance routes to high production, where available alternative pathways and strategies are discussed. While many organic acids are derived from a few precursors within central metabolism, each organic acid has its own special requirements for high production and best compatibility with host physiology.
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Affiliation(s)
- Chandresh Thakker
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX, USA
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Zhang L, Nie X, Ravcheev DA, Rodionov DA, Sheng J, Gu Y, Yang S, Jiang W, Yang C. Redox-responsive repressor Rex modulates alcohol production and oxidative stress tolerance in Clostridium acetobutylicum. J Bacteriol 2014; 196:3949-63. [PMID: 25182496 PMCID: PMC4248821 DOI: 10.1128/jb.02037-14] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 08/27/2014] [Indexed: 11/20/2022] Open
Abstract
Rex, a transcriptional repressor that modulates its DNA-binding activity in response to NADH/NAD(+) ratio, has recently been found to play a role in the solventogenic shift of Clostridium acetobutylicum. Here, we combined a comparative genomic reconstruction of Rex regulons in 11 diverse clostridial species with detailed experimental characterization of Rex-mediated regulation in C. acetobutylicum. The reconstructed Rex regulons in clostridia included the genes involved in fermentation, hydrogen production, the tricarboxylic acid cycle, NAD biosynthesis, nitrate and sulfite reduction, and CO2/CO fixation. The predicted Rex-binding sites in the genomes of Clostridium spp. were verified by in vitro binding assays with purified Rex protein. Novel members of the C. acetobutylicum Rex regulon were identified and experimentally validated by comparing the transcript levels between the wild-type and rex-inactivated mutant strains. Furthermore, the effects of exposure to methyl viologen or H2O2 on intracellular NADH and NAD(+) concentrations, expression of Rex regulon genes, and physiology of the wild type and rex-inactivated mutant were comparatively analyzed. Our results indicate that Rex responds to NADH/NAD(+) ratio in vivo to regulate gene expression and modulates fermentation product formation and oxidative stress tolerance in C. acetobutylicum. It is suggested that Rex plays an important role in maintaining NADH/NAD(+) homeostasis in clostridia.
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Affiliation(s)
- Lei Zhang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoqun Nie
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dmitry A Ravcheev
- Sanford-Burnham Medical Research Institute, La Jolla, California, USA Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A Rodionov
- Sanford-Burnham Medical Research Institute, La Jolla, California, USA Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Jia Sheng
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yang Gu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chen Yang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Chemostat cultivation and transcriptional analyses of Clostridium acetobutylicum mutants with defects in the acid and acetone biosynthetic pathways. Appl Microbiol Biotechnol 2014; 98:9777-94. [DOI: 10.1007/s00253-014-6040-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 08/13/2014] [Accepted: 08/20/2014] [Indexed: 12/22/2022]
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Fermentation of oxidized hexose derivatives by Clostridium acetobutylicum. Microb Cell Fact 2014; 13:139. [PMID: 25231163 PMCID: PMC4179846 DOI: 10.1186/s12934-014-0139-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 09/07/2014] [Indexed: 01/02/2023] Open
Abstract
Background Clostridium acetobutylicum fermentations are promising for production of commodity chemicals from heterogeneous biomass due to the wide range of substrates the organism can metabolize. Much work has been done to elucidate the pathways for utilization of aldoses, but little is known about metabolism of more oxidized substrates. Two oxidized hexose derivatives, gluconate and galacturonate, are present in low cost feedstocks, and their metabolism will contribute to overall metabolic output of these substrates. Results A complete metabolic network for glucose, gluconate, and galacturonate utilization was generated using online databases, previous studies, genomic context, and experimental data. Gluconate appears to be metabolized via the Entner-Doudoroff pathway, and is likely dehydrated to 2-keto-3-deoxy-gluconate before phosphorylation to 2-keto-3-deoxy-6-P-gluconate. Galacturonate appears to be processed via the Ashwell pathway, converging on a common metabolite for gluconate and galacturonate metabolism, 2-keto-3-deoxygluconate. As expected, increasingly oxidized substrates resulted in increasingly oxidized products with galacturonate fermentations being nearly homoacetic. Calculations of expected ATP and reducing equivalent yields and experimental data suggested galacturonate fermentations were reductant limited. Galacturonate fermentation was incomplete, which was not due solely to product inhibition or the inability to utilize low concentrations of galacturonate. Removal of H2 and CO2 by agitation resulted in faster growth, higher cell densities, formation of relatively more oxidized products, and higher product yields for cultures grown on glucose or gluconate. In contrast, cells grown on galacturonate showed reduced growth rates upon agitation, which was likely due to loss in reductant in the form of H2. The growth advantage seen on agitated glucose or gluconate cultures could not be solely attributed to improved ATP economics, thereby indicating other factors are also important. Conclusions The metabolic network presented in this work should facilitate similar reconstructions in other organisms, and provides a further understanding of the pathways involved in metabolism of oxidized feedstocks and carbohydrate mixtures. The nearly homoacetic fermentation during growth on galacturonate indicates further optimization of this and related organisms could provide a route to an effective biologically derived acetic acid production platform. Furthermore, the pathways could be targeted to decrease production of undesirable products during fermentations of heterogeneous biomass.
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Lütke-Eversloh T. Application of new metabolic engineering tools for Clostridium acetobutylicum. Appl Microbiol Biotechnol 2014; 98:5823-37. [DOI: 10.1007/s00253-014-5785-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 04/22/2014] [Accepted: 04/23/2014] [Indexed: 01/30/2023]
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Jang YS, Im JA, Choi SY, Lee JI, Lee SY. Metabolic engineering of Clostridium acetobutylicum for butyric acid production with high butyric acid selectivity. Metab Eng 2014; 23:165-74. [DOI: 10.1016/j.ymben.2014.03.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 03/22/2014] [Accepted: 03/25/2014] [Indexed: 12/24/2022]
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Jang YS, Han MJ, Lee J, Im JA, Lee YH, Papoutsakis ET, Bennett G, Lee SY. Proteomic analyses of the phase transition from acidogenesis to solventogenesis using solventogenic and non-solventogenic Clostridium acetobutylicum strains. Appl Microbiol Biotechnol 2014; 98:5105-15. [PMID: 24743985 DOI: 10.1007/s00253-014-5738-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 03/27/2014] [Accepted: 03/29/2014] [Indexed: 01/07/2023]
Abstract
The fermentation carried out by the solvent-producing bacterium, Clostridium acetobutylicum, is characterized by two distinct phases: acidogenic and solventogenic phases. Understanding the cellular physiological changes occurring during the phase transition in clostridial fermentation is important for the enhanced production of solvents. To identify protein changes upon entry to stationary phase where solvents are typically produced, we herein analyzed the proteomic profiles of the parental wild type C. acetobutylicum strains, ATCC 824, the non-solventogenic strain, M5 that has lost the solventogenic megaplasmid pSOL1, and the synthetic simplified alcohol forming strain, M5 (pIMP1E1AB) expressing plasmid-based CoA-transferase (CtfAB) and aldehyde/alcohol dehydrogenase (AdhE1). A total of 68 protein spots, corresponding to 56 unique proteins, were unambiguously identified as being differentially present after the phase transitions in the three C. acetobutylicum strains. In addition to changes in proteins known to be involved in solventogenesis (AdhE1 and CtfB), we identified significant alterations in enzymes involved in sugar transport and metabolism, fermentative pathway, heat shock proteins, translation, and amino acid biosynthesis upon entry into the stationary phase. Of these, four increased proteins (AdhE1, CAC0233, CtfB and phosphocarrier protein HPr) and six decreased proteins (butyrate kinase, ferredoxin:pyruvate oxidoreductase, phenylalanyl-tRNA synthetase, adenylosuccinate synthase, pyruvate kinase and valyl-tRNA synthetase) showed similar patterns in the two strains capable of butanol formation. Interestingly, significant changes of several proteins by post-translational modifications were observed in the solventogenic phase. The proteomic data from this study will improve our understanding on how cell physiology is affected through protein levels patterns in clostridia.
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Affiliation(s)
- Yu-Sin Jang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, South Korea
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Zhou X, Lu XH, Li XH, Xin ZJ, Xie JR, Zhao MR, Wang L, Du WY, Liang JP. Radiation induces acid tolerance of Clostridium tyrobutyricum and enhances bioproduction of butyric acid through a metabolic switch. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:22. [PMID: 24533663 PMCID: PMC3931924 DOI: 10.1186/1754-6834-7-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 02/03/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND Butyric acid as a renewable resource has become an increasingly attractive alternative to petroleum-based fuels. Clostridium tyrobutyricum ATCC 25755T is well documented as a fermentation strain for the production of acids. However, it has been reported that butyrate inhibits its growth, and the accumulation of acetate also inhibits biomass synthesis, making production of butyric acid from conventional fermentation processes economically challenging. The present study aimed to identify whether irradiation of C. tyrobutyricum cells makes them more tolerant to butyric acid inhibition and increases the production of butyrate compared with wild type. RESULTS In this work, the fermentation kinetics of C. tyrobutyricum cultures after being classically adapted for growth at 3.6, 7.2 and 10.8 g·L-1 equivalents were studied. The results showed that, regardless of the irradiation used, there was a gradual inhibition of cell growth at butyric acid concentrations above 10.8 g·L-1, with no growth observed at butyric acid concentrations above 3.6 g·L-1 for the wild-type strain during the first 54 h of fermentation. The sodium dodecyl sulfate polyacrylamide gel electrophoresis also showed significantly different expression levels of proteins with molecular mass around the wild-type and irradiated strains. The results showed that the proportion of proteins with molecular weights of 85 and 106 kDa was much higher for the irradiated strains. The specific growth rate decreased by 50% (from 0.42 to 0.21 h-1) and the final concentration of butyrate increased by 68% (from 22.7 to 33.4 g·L-1) for the strain irradiated at 114 AMeV and 40 Gy compared with the wild-type strains. CONCLUSIONS This study demonstrates that butyric acid production from glucose can be significantly improved and enhanced by using 12C6+ heavy ion-irradiated C. tyrobutyricum. The approach is economical, making it competitive compared with similar fermentation processes. It may prove useful as a first step in a combined method employing long-term continuous fermentation of acid-production processes.
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Affiliation(s)
- Xiang Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou, Gansu 730000, PR China
| | - Xi-Hong Lu
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou, Gansu 730000, PR China
| | - Xue-Hu Li
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou, Gansu 730000, PR China
| | - Zhi-Jun Xin
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou, Gansu 730000, PR China
| | - Jia-Rong Xie
- China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, PR China
| | - Mei-Rong Zhao
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou, Gansu 730000, PR China
| | - Liang Wang
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou, Gansu 730000, PR China
| | - Wen-Yue Du
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou, Gansu 730000, PR China
| | - Jian-Ping Liang
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou, Gansu 730000, PR China
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Enyeart PJ, Mohr G, Ellington AD, Lambowitz AM. Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis. Mob DNA 2014; 5:2. [PMID: 24410776 PMCID: PMC3898094 DOI: 10.1186/1759-8753-5-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 11/19/2013] [Indexed: 12/21/2022] Open
Abstract
Mobile group II introns are bacterial retrotransposons that combine the activities of an autocatalytic intron RNA (a ribozyme) and an intron-encoded reverse transcriptase to insert site-specifically into DNA. They recognize DNA target sites largely by base pairing of sequences within the intron RNA and achieve high DNA target specificity by using the ribozyme active site to couple correct base pairing to RNA-catalyzed intron integration. Algorithms have been developed to program the DNA target site specificity of several mobile group II introns, allowing them to be made into ‘targetrons.’ Targetrons function for gene targeting in a wide variety of bacteria and typically integrate at efficiencies high enough to be screened easily by colony PCR, without the need for selectable markers. Targetrons have found wide application in microbiological research, enabling gene targeting and genetic engineering of bacteria that had been intractable to other methods. Recently, a thermostable targetron has been developed for use in bacterial thermophiles, and new methods have been developed for using targetrons to position recombinase recognition sites, enabling large-scale genome-editing operations, such as deletions, inversions, insertions, and ‘cut-and-pastes’ (that is, translocation of large DNA segments), in a wide range of bacteria at high efficiency. Using targetrons in eukaryotes presents challenges due to the difficulties of nuclear localization and sub-optimal magnesium concentrations, although supplementation with magnesium can increase integration efficiency, and directed evolution is being employed to overcome these barriers. Finally, spurred by new methods for expressing group II intron reverse transcriptases that yield large amounts of highly active protein, thermostable group II intron reverse transcriptases from bacterial thermophiles are being used as research tools for a variety of applications, including qRT-PCR and next-generation RNA sequencing (RNA-seq). The high processivity and fidelity of group II intron reverse transcriptases along with their novel template-switching activity, which can directly link RNA-seq adaptor sequences to cDNAs during reverse transcription, open new approaches for RNA-seq and the identification and profiling of non-coding RNAs, with potentially wide applications in research and biotechnology.
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Affiliation(s)
| | | | | | - Alan M Lambowitz
- Departments of Molecular Biosciences and Chemistry, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA.
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Liu D, Chen Y, Ding FY, Zhao T, Wu JL, Guo T, Ren HF, Li BB, Niu HQ, Cao Z, Lin XQ, Xie JJ, He XJ, Ying HJ. Biobutanol production in a Clostridium acetobutylicum biofilm reactor integrated with simultaneous product recovery by adsorption. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:5. [PMID: 24401161 PMCID: PMC3891980 DOI: 10.1186/1754-6834-7-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Accepted: 12/24/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Clostridium acetobutylicum can propagate on fibrous matrices and form biofilms that have improved butanol tolerance and a high fermentation rate and can be repeatedly used. Previously, a novel macroporous resin, KA-I, was synthesized in our laboratory and was demonstrated to be a good adsorbent with high selectivity and capacity for butanol recovery from a model solution. Based on these results, we aimed to develop a process integrating a biofilm reactor with simultaneous product recovery using the KA-I resin to maximize the production efficiency of biobutanol. RESULTS KA-I showed great affinity for butanol and butyrate and could selectively enhance acetoin production at the expense of acetone during the fermentation. The biofilm reactor exhibited high productivity with considerably low broth turbidity during repeated batch fermentations. By maintaining the butanol level above 6.5 g/L in the biofilm reactor, butyrate adsorption by the KA-I resin was effectively reduced. Co-adsorption of acetone by the resin improved the fermentation performance. By redox modulation with methyl viologen (MV), the butanol-acetone ratio and the total product yield increased. An equivalent solvent titer of 96.5 to 130.7 g/L was achieved with a productivity of 1.0 to 1.5 g · L-1 · h-1. The solvent concentration and productivity increased by 4 to 6-fold and 3 to 5-fold, respectively, compared to traditional batch fermentation using planktonic culture. CONCLUSIONS Compared to the conventional process, the integrated process dramatically improved the productivity and reduced the energy consumption as well as water usage in biobutanol production. While genetic engineering focuses on strain improvement to enhance butanol production, process development can fully exploit the productivity of a strain and maximize the production efficiency.
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Affiliation(s)
- Dong Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Yong Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Feng-Ying Ding
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Ting Zhao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Jing-Lan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Ting Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Heng-Fei Ren
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Bing-Bing Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Huan-Qing Niu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Zhi Cao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Xiao-Qing Lin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Jing-Jing Xie
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Xue-Jun He
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Han-Jie Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, No. 30, Puzhu South Road, Nanjing 211816, China
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Bhandiwad A, Shaw AJ, Guss A, Guseva A, Bahl H, Lynd LR. Metabolic engineering of Thermoanaerobacterium saccharolyticum for n-butanol production. Metab Eng 2014; 21:17-25. [DOI: 10.1016/j.ymben.2013.10.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 10/01/2013] [Accepted: 10/30/2013] [Indexed: 11/25/2022]
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The cold-induced two-component system CBO0366/CBO0365 regulates metabolic pathways with novel roles in group I Clostridium botulinum ATCC 3502 cold tolerance. Appl Environ Microbiol 2013; 80:306-19. [PMID: 24162575 DOI: 10.1128/aem.03173-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The two-component system CBO0366/CBO0365 was recently demonstrated to have a role in cold tolerance of group I Clostridium botulinum ATCC 3502. The mechanisms under its control, ultimately resulting in increased sensitivity to low temperature, are unknown. A transcriptomic analysis with DNA microarrays was performed to identify the differences in global gene expression patterns of the wild-type ATCC 3502 and a derivative mutant with insertionally inactivated cbo0365 at 37 and 15°C. Altogether, 150 or 141 chromosomal coding sequences (CDSs) were found to be differently expressed in the cbo0365 mutant at 37 or 15°C, respectively, and thus considered to be under the direct or indirect transcriptional control of the response regulator CBO0365. Of the differentially expressed CDSs, expression of 141 CDSs was similarly affected at both temperatures investigated, suggesting that the putative CBO0365 regulon was practically not affected by temperature. The regulon involved genes related to acetone-butanol-ethanol (ABE) fermentation, motility, arsenic resistance, and phosphate uptake and transport. Deteriorated growth at 17°C was observed for mutants with disrupted ABE fermentation pathway components (crt, bcd, bdh, and ctfA), arsenic detoxifying machinery components (arsC and arsR), or phosphate uptake mechanism components (phoT), suggesting roles for these mechanisms in cold tolerance of group I C. botulinum. Electrophoretic mobility shift assays showed recombinant CBO0365 to bind to the promoter regions of crt, arsR, and phoT, as well as to the promoter region of its own operon, suggesting direct DNA-binding transcriptional activation or repression as a means for CBO0365 in regulating these operons. The results provide insight to the mechanisms group I C. botulinum utilizes in coping with cold.
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Wang Y, Li X, Blaschek HP. Effects of supplementary butyrate on butanol production and the metabolic switch in Clostridium beijerinckii NCIMB 8052: genome-wide transcriptional analysis with RNA-Seq. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:138. [PMID: 24229082 PMCID: PMC3849199 DOI: 10.1186/1754-6834-6-138] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 09/25/2013] [Indexed: 05/26/2023]
Abstract
BACKGROUND Butanol (n-butanol) has high values as a promising fuel source and chemical feedstock. Biobutanol is usually produced by the solventogenic clostridia through a typical biphasic (acidogenesis and solventogenesis phases) acetone-butanol-ethanol (ABE) fermentation process. It is well known that the acids produced in the acidogenic phase are significant and play important roles in the switch to solventogenesis. However, the mechanism that triggers the metabolic switch is still not clear. RESULTS Sodium butyrate (40 mM) was supplemented into the medium for the ABE fermentation with Clostridium beijerinckii NCIMB 8052. With butyrate addition (reactor R1), solvent production was triggered early in the mid-exponential phase and completed quickly in < 50 h, while in the control (reactor R2), solventogenesis was initiated during the late exponential phase and took > 90 h to complete. Butyrate supplementation led to 31% improvement in final butanol titer, 58% improvement in sugar-based yield, and 133% improvement in butanol productivity, respectively. The butanol/acetone ratio was 2.4 versus 1.8 in the control, indicating a metabolic shift towards butanol production due to butyrate addition. Genome-wide transcriptional dynamics was investigated with RNA-Seq analysis. In reactor R1, gene expression related to solventogenesis was induced about 10 hours earlier when compared to that in reactor R2. Although the early sporulation genes were induced after the onset of solventogenesis in reactor R1 (mid-exponential phase), the sporulation events were delayed and uncoupled from the solventogenesis. In contrast, in reactor R2, sporulation genes were induced at the onset of solventogenesis, and highly expressed through the solventogenesis phase. The motility genes were generally down-regulated to lower levels prior to stationary phase in both reactors. However, in reactor R2 this took much longer and gene expression was maintained at comparatively higher levels after entering stationary phase. CONCLUSIONS Supplemented butyrate provided feedback inhibition to butyrate formation and may be re-assimilated through the reversed butyrate formation pathway, thus resulting in an elevated level of intracellular butyryl phosphate, which may act as a phosphate donor to Spo0A and then trigger solventogenesis and sporulation events. High-resolution genome-wide transcriptional analysis with RNA-Seq revealed detailed insights into the biochemical effects of butyrate on solventogenesis related-events at the gene regulation level.
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Affiliation(s)
- Yi Wang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Hans P Blaschek
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Advanced Bioenergy Research (CABER), University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Metabolic engineering of Clostridium acetobutylicum for enhanced production of butyric acid. Appl Microbiol Biotechnol 2013; 97:9355-63. [DOI: 10.1007/s00253-013-5161-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 07/29/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
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Development of a gene knockout system using mobile group II introns (Targetron) and genetic disruption of acid production pathways in Clostridium beijerinckii. Appl Environ Microbiol 2013; 79:5853-63. [PMID: 23872562 DOI: 10.1128/aem.00971-13] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Clostridium beijerinckii is a well-known solvent-producing microorganism with great potential for biofuel and biochemical production. To better understand and improve the biochemical pathway to solvents, the development of genetic tools for engineering C. beijerinckii is highly desired. Based on mobile group II intron technology, a targetron gene knockout system was developed for C. beijerinckii in this study. This system was successfully employed to disrupt acid production pathways in C. beijerinckii, leading to pta (encoding phosphotransacetylase)- and buk (encoding butyrate kinase)-negative mutants. In addition to experimental characterization, the mutant phenotypes were analyzed in the context of our C. beijerinckii genome-scale model. Compared to those of the parental strain (C. beijerinckii 8052), acetate production in the pta mutant was substantially reduced and butyrate production was remarkably increased, while solvent production was dependent on the growth medium. The pta mutant also produced much higher levels of lactate, suggesting that disrupting pta influenced the energy generation and electron flow pathways. In contrast, acetate and butyrate production in the buk mutant was generally similar to that of the wild type, but solvent production was consistently 20 to 30% higher and glucose consumption was more rapid and complete. Our results suggest that the acid and solvent production of C. beijerinckii can be effectively altered by disrupting the acid production pathways. As the gene disruption method developed in this study does not leave any antibiotic marker in a disrupted allele, multiple and high-throughput gene disruption is feasible for elucidating genotype and phenotype relationships in C. beijerinckii.
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Ventura JRS, Hu H, Jahng D. Enhanced butanol production in Clostridium acetobutylicum ATCC 824 by double overexpression of 6-phosphofructokinase and pyruvate kinase genes. Appl Microbiol Biotechnol 2013; 97:7505-16. [PMID: 23838793 DOI: 10.1007/s00253-013-5075-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 06/18/2013] [Accepted: 06/18/2013] [Indexed: 12/19/2022]
Abstract
This study elucidated the importance of two critical enzymes in the regulation of butanol production in Clostridium acetobutylicum ATCC 824. Overexpression of both the 6-phosphofructokinase (pfkA) and pyruvate kinase (pykA) genes increased intracellular concentrations of ATP and NADH and also resistance to butanol toxicity. Marked increases of butanol and ethanol production, but not acetone, were also observed in batch fermentation. The butanol and ethanol concentrations were 29.4 and 85.5 % higher, respectively, in the fermentation by double-overexpressed C. acetobutylicum ATCC 824/pfkA+pykA than the wild-type strain. Furthermore, when fed-batch fermentation using glucose was carried out, the butanol and total solvent (acetone, butanol, and ethanol) concentrations reached as high as 19.12 and 28.02 g/L, respectively. The reason for improved butanol formation was attributed to the enhanced NADH and ATP concentrations and increased tolerance to butanol in the double-overexpressed strain.
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Affiliation(s)
- Jey-R S Ventura
- Department of Environmental Engineering and Energy, Myongji University, 116 Myongji-Ro, Cheoin-Gu, Yongin, Gyeonggi-Do 449-728, Republic of Korea
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Schiel-Bengelsdorf B, Montoya J, Linder S, Dürre P. Butanol fermentation. ENVIRONMENTAL TECHNOLOGY 2013; 34:1691-1710. [PMID: 24350428 DOI: 10.1080/09593330.2013.827746] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This review provides an overview on bacterial butanol production and recent developments concerning strain improvement, newly built butanol production plants, and the importance of alternative substrates, especially lignocellulosic hydrolysates. The butanol fermentation using solventogenic clostridial strains, particularly Clostridium acetobutylicum, is a very old industrial process (acetone-butanol-ethanol-ABE fermentation). The genome of this organism has been sequenced and analysed, leading to important improvements in rational strain construction. As the traditional ABE fermentation process is economically unfavourable, novel butanol production strains are being developed. In this review, some newly engineered solvent-producing Clostridium strains are described and strains of which sequences are available are compared with C. acetobutylicum. Furthermore, the past and present of commercial butanol fermentation are presented, including active plants and companies. Finally, the use of biomass as substrate for butanol production is discussed. Some advances concerning processing of biomass in a biorefinery are highlighted, which would allow lowering the price of the butanol fermentation process at industrial scale.
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Affiliation(s)
- Bettina Schiel-Bengelsdorf
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | - José Montoya
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | - Sonja Linder
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
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Scheel M, Lütke-Eversloh T. New options to engineer biofuel microbes: development and application of a high-throughput screening system. Metab Eng 2013; 17:51-8. [PMID: 23524105 DOI: 10.1016/j.ymben.2013.03.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 02/21/2013] [Accepted: 03/12/2013] [Indexed: 01/03/2023]
Abstract
The number of recent efforts on rational metabolic engineering approaches to increase butanol production in Clostridium acetobutylicum are quite limited, demonstrating the physiological complexity of solventogenic clostridia. Since multiple largely unknown parameters determine a particular phenotype, an inverse strategy to select a phenotype of interest can be useful. However, the major constraint for explorative or combinatorial metabolic engineering approaches is the availability of a feasible screening method to select the desired phenotype from a large population in a high-throughput manner. Therefore, a semi-quantitative assay was developed to monitor alcohol production in microtiter cultures of C. acetobutylicum. The applicability of the screening system was evaluated by two examples. First, C. acetobutylicum ATCC 824 was chemically mutagenized and subjected to high butanol concentrations as a pre-selection step. Screening of the butanol-tolerant population resulted in the identification of mutants with >20% increased butanol production as compared to the wildtype. The second application example was based on a pre-engineered C. acetobutylicum strain with low acetone biosynthetic activity, but concomitantly reduced butanol titer. After chemical mutagenesis, a total of 4390 clones was analyzed and mutants with significantly increased butanol concentrations and similarly low acetone levels as the parental strain were selected. Thus, the suitability of the semi-quantitative screening system was validated, opening up new perspectives for combinatorial strategies to improve solventogenic clostridia and other biofuel microbes.
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Affiliation(s)
- Michael Scheel
- Department of Microbiology, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
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Decreased hydrogen production leads to selective butanol production in co-cultures of Clostridium thermocellum and Clostridium saccharoperbutylacetonicum strain N1-4. J Biosci Bioeng 2013; 115:173-5. [DOI: 10.1016/j.jbiosc.2012.08.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 07/30/2012] [Accepted: 08/26/2012] [Indexed: 11/19/2022]
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