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Palaniswamy S, Ashoor S, Eskasalam SR, Jang YS. Harnessing lignocellulosic biomass for butanol production through clostridia for sustainable waste management: recent advances and perspectives. Front Bioeng Biotechnol 2023; 11:1272429. [PMID: 37954017 PMCID: PMC10634440 DOI: 10.3389/fbioe.2023.1272429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023] Open
Abstract
The escalating waste generation rates, driven by population growth, urbanization, and consumption patterns, have made waste management a critical global concern with significant environmental, social, and economic repercussions. Among the various waste sources, lignocellulosic biomass represents a significant proportion of agricultural, agro-industrial, and municipal wastes. Biofuels are gaining attention as a promising substitute to fossil fuels, and butanol is one such biofuel that has been identified as a potential candidate due to its compatibility with existing fuel infrastructure, lower volatility, and higher energy density. Sustainable management of lignocellulosic biomass waste and its utilization in fermentation are viable alternatives to produce butanol via the promising microbial catalyst clostridia. This review provides an overview of lignocellulosic biomass waste management, focusing on recent advances in strain development for butanol production from renewable biomass with an emphasis on future perspectives.
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Affiliation(s)
- Sampathkumar Palaniswamy
- Division of Applied Life Science (BK21 Four), Department of Applied Life Chemistry, Institute of Agriculture and Life Science (IALS), Gyeongsang National University (GNU), Jinju, Republic of Korea
| | - Selim Ashoor
- Division of Applied Life Science (BK21 Four), Department of Applied Life Chemistry, Institute of Agriculture and Life Science (IALS), Gyeongsang National University (GNU), Jinju, Republic of Korea
- Department of Agricultural Microbiology, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Syafira Rizqi Eskasalam
- Division of Applied Life Science (BK21 Four), Department of Applied Life Chemistry, Institute of Agriculture and Life Science (IALS), Gyeongsang National University (GNU), Jinju, Republic of Korea
| | - Yu-Sin Jang
- Division of Applied Life Science (BK21 Four), Department of Applied Life Chemistry, Institute of Agriculture and Life Science (IALS), Gyeongsang National University (GNU), Jinju, Republic of Korea
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Joseph RC, Kelley SQ, Kim NM, Sandoval NR. Metabolic Engineering and the Synthetic Biology Toolbox for
Clostridium. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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3
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Li S, Huang L, Ke C, Pang Z, Liu L. Pathway dissection, regulation, engineering and application: lessons learned from biobutanol production by solventogenic clostridia. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:39. [PMID: 32165923 PMCID: PMC7060580 DOI: 10.1186/s13068-020-01674-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/04/2020] [Indexed: 06/01/2023]
Abstract
The global energy crisis and limited supply of petroleum fuels have rekindled the interest in utilizing a sustainable biomass to produce biofuel. Butanol, an advanced biofuel, is a superior renewable resource as it has a high energy content and is less hygroscopic than other candidates. At present, the biobutanol route, employing acetone-butanol-ethanol (ABE) fermentation in Clostridium species, is not economically competitive due to the high cost of feedstocks, low butanol titer, and product inhibition. Based on an analysis of the physiological characteristics of solventogenic clostridia, current advances that enhance ABE fermentation from strain improvement to product separation were systematically reviewed, focusing on: (1) elucidating the metabolic pathway and regulation mechanism of butanol synthesis; (2) enhancing cellular performance and robustness through metabolic engineering, and (3) optimizing the process of ABE fermentation. Finally, perspectives on engineering and exploiting clostridia as cell factories to efficiently produce various chemicals and materials are also discussed.
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Affiliation(s)
- Shubo Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004 China
| | - Li Huang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004 China
| | - Chengzhu Ke
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004 China
| | - Zongwen Pang
- College of Life Science and Technology, Guangxi University, Nanning, 530005 China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
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COMPUTER RECOGNITION OF CHEMICAL SUBSTANCES BASED ON THEIR ELECTROPHYSIOLOGICAL CHARACTERISTICS. BIOTECHNOLOGIA ACTA 2019. [DOI: 10.15407/biotech12.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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de Paula RG, Antoniêto ACC, Ribeiro LFC, Srivastava N, O'Donovan A, Mishra PK, Gupta VK, Silva RN. Engineered microbial host selection for value-added bioproducts from lignocellulose. Biotechnol Adv 2019; 37:107347. [PMID: 30771467 DOI: 10.1016/j.biotechadv.2019.02.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/27/2019] [Accepted: 02/08/2019] [Indexed: 12/12/2022]
Abstract
Lignocellulose is a rich and sustainable globally available carbon source and is considered a prominent alternative raw material for producing biofuels and valuable chemical compounds. Enzymatic hydrolysis is one of the crucial steps of lignocellulose degradation. Cellulolytic and hemicellulolytic enzyme mixes produced by different microorganisms including filamentous fungi, yeasts and bacteria, are used to degrade the biomass to liberate monosaccharides and other compounds for fermentation or conversion to value-added products. During biomass pretreatment and degradation, toxic compounds are produced, and undesirable carbon catabolic repression (CCR) can occur. In order to solve this problem, microbial metabolic pathways and transcription factors involved have been investigated along with the application of protein engineering to optimize the biorefinery platform. Engineered Microorganisms have been used to produce specific enzymes to breakdown biomass polymers and metabolize sugars to produce ethanol as well other biochemical compounds. Protein engineering strategies have been used for modifying lignocellulolytic enzymes to overcome enzymatic limitations and improving both their production and functionality. Furthermore, promoters and transcription factors, which are key proteins in this process, are modified to promote microbial gene expression that allows a maximum performance of the hydrolytic enzymes for lignocellulosic degradation. The present review will present a critical discussion and highlight the aspects of the use of microorganisms to convert lignocellulose into value-added bioproduct as well combat the bottlenecks to make the biorefinery platform from lignocellulose attractive to the market.
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Affiliation(s)
- Renato Graciano de Paula
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Liliane Fraga Costa Ribeiro
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Neha Srivastava
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, U.P, India
| | - Anthonia O'Donovan
- School of Science and Computing, Galway-Mayo Institute of Technology, Galway, Ireland
| | - P K Mishra
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, U.P, India
| | - Vijai K Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia.
| | - Roberto N Silva
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
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Ralston MT, Papoutsakis ET. RNAseq‐based transcriptome assembly of
Clostridium acetobutylicum
for functional genome annotation and discovery. AIChE J 2018. [DOI: 10.1002/aic.16396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Matthew T. Ralston
- Molecular Biotechnology Laboratory, Delaware Biotechnology Institute University of Delaware Newark DE 19711
- Center for Bioinformatics and Computational Biology University of Delaware Newark DE 19711
| | - Eleftherios T. Papoutsakis
- Dept. of Chemical and Biomolecular Engineering University of Delaware Newark DE 19711
- Molecular Biotechnology Laboratory, Delaware Biotechnology Institute University of Delaware Newark DE 19711
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Liao Z, Suo Y, Xue C, Fu H, Wang J. Improving the fermentation performance of Clostridium acetobutylicum ATCC 824 by strengthening the VB1 biosynthesis pathway. Appl Microbiol Biotechnol 2018; 102:8107-8119. [DOI: 10.1007/s00253-018-9208-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/20/2018] [Accepted: 06/27/2018] [Indexed: 11/24/2022]
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Improvement of butanol production by the development and co-culture of C. acetobutylicum TSH1 and B. cereus TSH2. Appl Microbiol Biotechnol 2018; 102:6753-6763. [DOI: 10.1007/s00253-018-9151-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/17/2018] [Accepted: 05/29/2018] [Indexed: 01/07/2023]
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Joseph RC, Kim NM, Sandoval NR. Recent Developments of the Synthetic Biology Toolkit for Clostridium. Front Microbiol 2018; 9:154. [PMID: 29483900 PMCID: PMC5816073 DOI: 10.3389/fmicb.2018.00154] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 01/23/2018] [Indexed: 12/15/2022] Open
Abstract
The Clostridium genus is a large, diverse group consisting of Gram-positive, spore-forming, obligate anaerobic firmicutes. Among this group are historically notorious pathogens as well as several industrially relevant species with the ability to produce chemical commodities, particularly biofuels, from renewable biomass. Additionally, other species are studied for their potential use as therapeutics. Although metabolic engineering and synthetic biology have been instrumental in improving product tolerance, titer, yields, and feed stock consumption capabilities in several organisms, low transformation efficiencies and lack of synthetic biology tools and genetic parts make metabolic engineering within the Clostridium genus difficult. Progress has recently been made to overcome challenges associated with engineering various Clostridium spp. For example, developments in CRISPR tools in multiple species and strains allow greater capability to produce edits with greater precision, faster, and with higher efficiencies. In this mini-review, we will highlight these recent advances and compare them to established methods for genetic engineering in Clostridium. In addition, we discuss the current state and development of Clostridium-based promoters (constitutive and inducible) and reporters. Future progress in this area will enable more rapid development of strain engineering, which would allow for the industrial exploitation of Clostridium for several applications including bioproduction of several commodity products.
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Affiliation(s)
- Rochelle C. Joseph
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, United States
| | - Nancy M. Kim
- Interdisciplinary Bioinnovation PhD Program, Tulane University, New Orleans, LA, United States
| | - Nicholas R. Sandoval
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, United States
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Joseph RC, Kim NM, Sandoval NR. Recent Developments of the Synthetic Biology Toolkit for Clostridium. Front Microbiol 2018. [PMID: 29483900 DOI: 10.3389/fmicb.2018.00154/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
The Clostridium genus is a large, diverse group consisting of Gram-positive, spore-forming, obligate anaerobic firmicutes. Among this group are historically notorious pathogens as well as several industrially relevant species with the ability to produce chemical commodities, particularly biofuels, from renewable biomass. Additionally, other species are studied for their potential use as therapeutics. Although metabolic engineering and synthetic biology have been instrumental in improving product tolerance, titer, yields, and feed stock consumption capabilities in several organisms, low transformation efficiencies and lack of synthetic biology tools and genetic parts make metabolic engineering within the Clostridium genus difficult. Progress has recently been made to overcome challenges associated with engineering various Clostridium spp. For example, developments in CRISPR tools in multiple species and strains allow greater capability to produce edits with greater precision, faster, and with higher efficiencies. In this mini-review, we will highlight these recent advances and compare them to established methods for genetic engineering in Clostridium. In addition, we discuss the current state and development of Clostridium-based promoters (constitutive and inducible) and reporters. Future progress in this area will enable more rapid development of strain engineering, which would allow for the industrial exploitation of Clostridium for several applications including bioproduction of several commodity products.
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Affiliation(s)
- Rochelle C Joseph
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, United States
| | - Nancy M Kim
- Interdisciplinary Bioinnovation PhD Program, Tulane University, New Orleans, LA, United States
| | - Nicholas R Sandoval
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, United States
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Improving cellular robustness and butanol titers of Clostridium acetobutylicum ATCC824 by introducing heat shock proteins from an extremophilic bacterium. J Biotechnol 2017; 252:1-10. [DOI: 10.1016/j.jbiotec.2017.04.031] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 04/07/2017] [Accepted: 04/24/2017] [Indexed: 11/30/2022]
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ARTP mutation and genome shuffling of ABE fermentation symbiotic system for improvement of butanol production. Appl Microbiol Biotechnol 2017; 101:2189-2199. [DOI: 10.1007/s00253-017-8093-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 12/20/2016] [Accepted: 12/23/2016] [Indexed: 12/20/2022]
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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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Fu Y, Chen L, Zhang W. Regulatory mechanisms related to biofuel tolerance in producing microbes. J Appl Microbiol 2016; 121:320-32. [PMID: 27123568 DOI: 10.1111/jam.13162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/20/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Y. Fu
- Laboratory of Synthetic Microbiology; School of Chemical Engineering & Technology; Tianjin University; Tianjin China
- Key Laboratory of Systems Bioengineering (Ministry of Education); Tianjin University; Tianjin China
- SynBio Research Platform; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin China
| | - L. Chen
- Laboratory of Synthetic Microbiology; School of Chemical Engineering & Technology; Tianjin University; Tianjin China
- Key Laboratory of Systems Bioengineering (Ministry of Education); Tianjin University; Tianjin China
- SynBio Research Platform; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin China
| | - W. Zhang
- Laboratory of Synthetic Microbiology; School of Chemical Engineering & Technology; Tianjin University; Tianjin China
- Key Laboratory of Systems Bioengineering (Ministry of Education); Tianjin University; Tianjin China
- SynBio Research Platform; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin China
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Ehsaan M, Kuit W, Zhang Y, Cartman ST, Heap JT, Winzer K, Minton NP. Mutant generation by allelic exchange and genome resequencing of the biobutanol organism Clostridium acetobutylicum ATCC 824. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:4. [PMID: 26732067 PMCID: PMC4700727 DOI: 10.1186/s13068-015-0410-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/04/2015] [Indexed: 05/28/2023]
Abstract
BACKGROUND Clostridium acetobutylicum represents a paradigm chassis for the industrial production of the biofuel biobutanol and a focus for metabolic engineering. We have previously developed procedures for the creation of in-frame, marker-less deletion mutants in the pathogen Clostridium difficile based on the use of pyrE and codA genes as counter selection markers. In the current study we sought to test their suitability for use in C. acetobutylicum. RESULTS Both systems readily allowed the isolation of in-frame deletions of the C. acetobutylicum ATCC 824 spo0A and the cac824I genes, leading to a sporulation minus phenotype and improved transformation, respectively. The pyrE-based system was additionally used to inactivate a putative glycogen synthase (CA_C2239, glgA) and the pSOL1 amylase gene (CA_P0168, amyP), leading to lack of production of granulose and amylase, respectively. Their isolation provided the opportunity to make use of one of the key pyrE system advantages, the ability to rapidly complement mutations at appropriate gene dosages in the genome. In both cases, their phenotypes were restored in terms of production of granulose (glgA) and amylase (amyP). Genome re-sequencing of the ATCC 824 COSMIC consortium laboratory strain used revealed the presence of 177 SNVs and 49 Indels, including a 4916-bp deletion in the pSOL1 megaplasmid. A total of 175 SNVs and 48 Indels were subsequently shown to be present in an 824 strain re-acquired (Nov 2011) from the ATCC and are, therefore, most likely errors in the published genome sequence, NC_003030 (chromosome) and NC_001988 (pSOL1). CONCLUSIONS The codA or pyrE counter selection markers appear equally effective in isolating deletion mutants, but there is considerable merit in using a pyrE mutant as the host as, through the use of ACE (Allele-Coupled Exchange) vectors, mutants created (by whatever means) can be rapidly complemented concomitant with restoration of the pyrE allele. This avoids the phenotypic effects frequently observed with high copy number plasmids and dispenses with the need to add antibiotic to ensure plasmid retention. Our study also revealed a surprising number of errors in the ATCC 824 genome sequence, while at the same time emphasising the need to re-sequence commonly used laboratory strains.
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Affiliation(s)
- Muhammad Ehsaan
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Wouter Kuit
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
- />MicCell Bioservices B.V., Edisonstraat 101, 7006 RB Doetinchem, The Netherlands
| | - Ying Zhang
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Stephen T. Cartman
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
- />Intermediates Sustainability, INVISTA Intermediates, Wilton Centre, Redcar, TS10 4RF UK
| | - John T. Heap
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
- />Department of Life Sciences, Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London, SW7 2AZ 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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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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18
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Wu Y, Yang Y, Ren C, Yang C, Yang S, Gu Y, Jiang W. Molecular modulation of pleiotropic regulator CcpA for glucose and xylose coutilization by solvent-producing Clostridium acetobutylicum. Metab Eng 2015; 28:169-179. [DOI: 10.1016/j.ymben.2015.01.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/05/2014] [Accepted: 01/16/2015] [Indexed: 10/24/2022]
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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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Engineering Clostridium acetobutylicum with a histidine kinase knockout for enhanced n-butanol tolerance and production. Appl Microbiol Biotechnol 2014; 99:1011-22. [DOI: 10.1007/s00253-014-6249-7] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 01/07/2023]
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Wang J, Yang X, Chen CC, Yang ST. Engineering clostridia for butanol production from biorenewable resources: from cells to process integration. Curr Opin Chem Eng 2014. [DOI: 10.1016/j.coche.2014.09.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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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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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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Pyne ME, Bruder M, Moo-Young M, Chung DA, Chou CP. Technical guide for genetic advancement of underdeveloped and intractable Clostridium. Biotechnol Adv 2014; 32:623-41. [DOI: 10.1016/j.biotechadv.2014.04.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/10/2014] [Accepted: 04/15/2014] [Indexed: 02/04/2023]
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Panitz J, Zverlov V, Pham V, Stürzl S, Schieder D, Schwarz W. Isolation of a solventogenic Clostridium sp. strain: Fermentation of glycerol to n-butanol, analysis of the bcs operon region and its potential regulatory elements. Syst Appl Microbiol 2014; 37:1-9. [DOI: 10.1016/j.syapm.2013.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 10/21/2013] [Accepted: 10/28/2013] [Indexed: 12/12/2022]
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Venkataramanan KP, Jones SW, McCormick KP, Kunjeti SG, Ralston MT, Meyers BC, Papoutsakis ET. The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum. BMC Genomics 2013; 14:849. [PMID: 24299206 PMCID: PMC3879012 DOI: 10.1186/1471-2164-14-849] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/14/2013] [Indexed: 01/01/2023] Open
Abstract
Background Small non-coding RNAs (sRNA) are emerging as major components of the cell’s regulatory network, several possessing their own regulons. A few sRNAs have been reported as being involved in general or toxic-metabolite stress, mostly in Gram- prokaryotes, but hardly any in Gram+ prokaryotes. Significantly, the role of sRNAs in the stress response remains poorly understood at the genome-scale level. It was previously shown that toxic-metabolite stress is one of the most comprehensive and encompassing stress responses in the cell, engaging both the general stress (or heat-shock protein, HSP) response as well as specialized metabolic programs. Results Using RNA deep sequencing (RNA-seq) we examined the sRNome of C. acetobutylicum in response to the native but toxic metabolites, butanol and butyrate. 7.5% of the RNA-seq reads mapped to genome outside annotated ORFs, thus demonstrating the richness and importance of the small RNome. We used comparative expression analysis of 113 sRNAs we had previously computationally predicted, and of annotated mRNAs to set metrics for reliably identifying sRNAs from RNA-seq data, thus discovering 46 additional sRNAs. Under metabolite stress, these 159 sRNAs displayed distinct expression patterns, a select number of which was verified by Northern analysis. We identified stress-related expression of sRNAs affecting transcriptional (6S, S-box & solB) and translational (tmRNA & SRP-RNA) processes, and 65 likely targets of the RNA chaperone Hfq. Conclusions Our results support an important role for sRNAs for understanding the complexity of the regulatory network that underlies the stress response in Clostridium organisms, whether related to normophysiology, pathogenesis or biotechnological applications.
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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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Fatehi P. Recent advancements in various steps of ethanol, butanol, and isobutanol productions from woody materials. Biotechnol Prog 2013; 29:297-310. [DOI: 10.1002/btpr.1688] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 11/30/2012] [Indexed: 01/24/2023]
Affiliation(s)
- Pedram Fatehi
- Chemical Engineering Dept.; Lakehead University; Thunder Bay ON Canada P7B5E1
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A genetic system for Clostridium ljungdahlii: a chassis for autotrophic production of biocommodities and a model homoacetogen. Appl Environ Microbiol 2012. [PMID: 23204413 DOI: 10.1128/aem.02891-12] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Methods for genetic manipulation of Clostridium ljungdahlii are of interest because of the potential for production of fuels and other biocommodities from carbon dioxide via microbial electrosynthesis or more traditional modes of autotrophy with hydrogen or carbon monoxide as the electron donor. Furthermore, acetogenesis plays an important role in the global carbon cycle. Gene deletion strategies required for physiological studies of C. ljungdahlii have not previously been demonstrated. An electroporation procedure for introducing plasmids was optimized, and four different replicative origins for plasmid propagation in C. ljungdahlii were identified. Chromosomal gene deletion via double-crossover homologous recombination with a suicide vector was demonstrated initially with deletion of the gene for FliA, a putative sigma factor involved in flagellar biogenesis and motility in C. ljungdahlii. Deletion of fliA yielded a strain that lacked flagella and was not motile. To evaluate the potential utility of gene deletions for functional genomic studies and to redirect carbon and electron flow, the genes for the putative bifunctional aldehyde/alcohol dehydrogenases, adhE1 and adhE2, were deleted individually or together. Deletion of adhE1, but not adhE2, diminished ethanol production with a corresponding carbon recovery in acetate. The double deletion mutant had a phenotype similar to that of the adhE1-deficient strain. Expression of adhE1 in trans partially restored the capacity for ethanol production. These results demonstrate the feasibility of genetic investigations of acetogen physiology and the potential for genetic manipulation of C. ljungdahlii to optimize autotrophic biocommodity production.
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Cai X, Servinsky M, Kiel J, Sund C, Bennett GN. Analysis of redox responses during TNT transformation by Clostridium acetobutylicum ATCC 824 and mutants exhibiting altered metabolism. Appl Microbiol Biotechnol 2012; 97:4651-63. [PMID: 22843424 DOI: 10.1007/s00253-012-4253-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 06/14/2012] [Accepted: 06/15/2012] [Indexed: 11/26/2022]
Abstract
The transformation of trinitrotoluene (TNT) by several mutant strains of Clostridium acetobutylicum has been examined to analyze the maximal rate of initial transformation, determine the effects of metabolic mutations of the host on transformation rate, and to assess the cell metabolic changes brought about during TNT transformation. Little difference in the maximal rate of TNT degradation in early acid phase cultures was found between the parental ATCC 824 strain and strains altered in the acid forming pathways (phosphotransacetylase, or butyrate kinase) or in a high-solvent-producing strain (mutant B). This result is in agreement with the previous findings of a similar degradation rate in a degenerate strain (M5) that had lost the ability to produce solvent. A series of antisense constructs were made that reduced the expression of hydA, encoding the Fe-hydrogenase, or hydE and hydF, genes encoding hydrogenase maturating proteins. While the antisense hydA strain had only ∼30 % of the activity of wild type, the antisense hydE strain exhibited a TNT degradation rate around 70 % that of the parent. Overexpression of hydA modestly increased the TNT degradation rate in acid phase cells, suggesting the amount of reductant flowing into hydrogenase rather than the hydrogenase level itself was a limiting factor in many situations. The redox potential, hydrogen evolution, and organic acid metabolites produced during rapid TNT transformation in early log phase cultures were measured. The redox potential of the acid-producing culture decreased from -370 to -200 mV immediately after addition of TNT and the hydrogen evolution rate decreased, lowering the hydrogen to carbon dioxide ratio from 1.4 to around 1.1 for 15 min. During the time of TNT transformation, the treated acidogenic cells produced less acetate and more butyrate. The results show that during TNT transformation, the cells shift metabolism away from hydrogen formation to reduction of TNT and the resulting effects on cell redox cofactors generate a higher proportion of butyrate.
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Affiliation(s)
- Xianpeng Cai
- Conagen Inc, Suite 238, 1005 North Warson Road, St. Louis, MO 63132, USA.
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Dai Z, Dong H, Zhu Y, Zhang Y, Li Y, Ma Y. Introducing a single secondary alcohol dehydrogenase into butanol-tolerant Clostridium acetobutylicum Rh8 switches ABE fermentation to high level IBE fermentation. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:44. [PMID: 22742819 PMCID: PMC3674747 DOI: 10.1186/1754-6834-5-44] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Accepted: 06/28/2012] [Indexed: 05/07/2023]
Abstract
BACKGROUND Previously we have developed a butanol tolerant mutant of Clostridium acetobutylicum Rh8, from the wild type strain DSM 1731. Strain Rh8 can tolerate up to 19 g/L butanol, with solvent titer improved accordingly, thus exhibiting industrial application potential. To test if strain Rh8 can be used for production of high level mixed alcohols, a single secondary alcohol dehydrogenase from Clostridium beijerinckii NRRL B593 was overexpressed in strain Rh8 under the control of thl promoter. RESULTS The heterogenous gene sADH was functionally expressed in C. acetobutylicum Rh8. This simple, one-step engineering approach switched the traditional ABE (acetone-butanol-ethanol) fermentation to IBE (isopropanol-butanol-ethanol) fermentation. The total alcohol titer reached 23.88 g/l (7.6 g/l isopropanol, 15 g/l butanol, and 1.28 g/l ethanol) with a yield to glucose of 31.42%. The acid (butyrate and acetate) assimilation rate in isopropanol producing strain Rh8(psADH) was increased. CONCLUSIONS The improved butanol tolerance and the enhanced solvent biosynthesis machinery in strain Rh8 is beneficial for production of high concentration of mixed alcohols. Strain Rh8 can thus be considered as a good host for further engineering of solvent/alcohol production.
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Affiliation(s)
- Zongjie Dai
- Department of Biochemistry and Molecular Biology, University of Science and
Technology of China, Hefei, China
- Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen
Road, Chaoyang District, Beijing, 100101, China
| | - Hongjun Dong
- Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen
Road, Chaoyang District, Beijing, 100101, China
| | - Yan Zhu
- Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen
Road, Chaoyang District, Beijing, 100101, China
- Graduate School of the Chinese Academy of Sciences, Beijing China
| | - Yanping Zhang
- Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen
Road, Chaoyang District, Beijing, 100101, China
| | - Yin Li
- Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen
Road, Chaoyang District, Beijing, 100101, China
| | - Yanhe Ma
- Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen
Road, Chaoyang District, Beijing, 100101, China
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Jurgens G, Survase S, Berezina O, Sklavounos E, Linnekoski J, Kurkijärvi A, Väkevä M, van Heiningen A, Granström T. Butanol production from lignocellulosics. Biotechnol Lett 2012; 34:1415-34. [PMID: 22526420 DOI: 10.1007/s10529-012-0926-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 03/27/2012] [Indexed: 12/20/2022]
Abstract
Clostridium spp. produce n-butanol in the acetone/butanol/ethanol process. For sustainable industrial scale butanol production, a number of obstacles need to be addressed including choice of feedstock, the low product yield, toxicity to production strain, multiple-end products and downstream processing of alcohol mixtures. This review describes the use of lignocellulosic feedstocks, bioprocess and metabolic engineering, downstream processing and catalytic refining of n-butanol.
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Affiliation(s)
- German Jurgens
- Department of Biotechnology and Chemical Technology, Aalto University, 00076, Espoo, Finland.
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Gu Y, Jiang Y, Wu H, Liu X, Li Z, Li J, Xiao H, Shen Z, Dong H, Yang Y, Li Y, Jiang W, Yang S. Economical challenges to microbial producers of butanol: Feedstock, butanol ratio and titer. Biotechnol J 2011; 6:1348-57. [DOI: 10.1002/biot.201100046] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Dürre P. Fermentative production of butanol—the academic perspective. Curr Opin Biotechnol 2011; 22:331-6. [DOI: 10.1016/j.copbio.2011.04.010] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 03/16/2011] [Accepted: 04/18/2011] [Indexed: 12/18/2022]
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Bond-Watts BB, Bellerose RJ, Chang MCY. Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways. Nat Chem Biol 2011; 7:222-7. [PMID: 21358636 DOI: 10.1038/nchembio.537] [Citation(s) in RCA: 255] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 01/28/2011] [Indexed: 11/09/2022]
Abstract
Living systems have evolved remarkable molecular functions that can be redesigned for in vivo chemical synthesis as we gain a deeper understanding of the underlying biochemical principles for de novo construction of synthetic pathways. We have focused on developing pathways for next-generation biofuels as they require carbon to be channeled to product at quantitative yields. However, these fatty acid-inspired pathways must manage the highly reversible nature of the enzyme components. For targets in the biodiesel range, the equilibrium can be driven to completion by physical sequestration of an insoluble product, which is a mechanism unavailable to soluble gasoline-sized products. In this work, we report the construction of a chimeric pathway assembled from three different organisms for the high-level production of n-butanol (4,650 ± 720 mg l⁻¹) that uses an enzymatic chemical reaction mechanism in place of a physical step as a kinetic control element to achieve high yields from glucose (28%).
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Affiliation(s)
- Brooks B Bond-Watts
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
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38
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Hu S, Zheng H, Gu Y, Zhao J, Zhang W, Yang Y, Wang S, Zhao G, Yang S, Jiang W. Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018. BMC Genomics 2011; 12:93. [PMID: 21284892 PMCID: PMC3044671 DOI: 10.1186/1471-2164-12-93] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 02/02/2011] [Indexed: 12/17/2022] Open
Abstract
Background Clostridium acetobutylicum, a gram-positive and spore-forming anaerobe, is a major strain for the fermentative production of acetone, butanol and ethanol. But a previously isolated hyper-butanol producing strain C. acetobutylicum EA 2018 does not produce spores and has greater capability of solvent production, especially for butanol, than the type strain C. acetobutylicum ATCC 824. Results Complete genome of C. acetobutylicum EA 2018 was sequenced using Roche 454 pyrosequencing. Genomic comparison with ATCC 824 identified many variations which may contribute to the hyper-butanol producing characteristics in the EA 2018 strain, including a total of 46 deletion sites and 26 insertion sites. In addition, transcriptomic profiling of gene expression in EA 2018 relative to that of ATCC824 revealed expression-level changes of several key genes related to solvent formation. For example, spo0A and adhEII have higher expression level, and most of the acid formation related genes have lower expression level in EA 2018. Interestingly, the results also showed that the variation in CEA_G2622 (CAC2613 in ATCC 824), a putative transcriptional regulator involved in xylose utilization, might accelerate utilization of substrate xylose. Conclusions Comparative analysis of C. acetobutylicum hyper-butanol producing strain EA 2018 and type strain ATCC 824 at both genomic and transcriptomic levels, for the first time, provides molecular-level understanding of non-sporulation, higher solvent production and enhanced xylose utilization in the mutant EA 2018. The information could be valuable for further genetic modification of C. acetobutylicum for more effective butanol production.
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Affiliation(s)
- Shiyuan Hu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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Mainguet SE, Liao JC. Bioengineering of microorganisms for C3 to C5 alcohols production. Biotechnol J 2010; 5:1297-308. [DOI: 10.1002/biot.201000276] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Improving the Clostridium acetobutylicum butanol fermentation by engineering the strain for co-production of riboflavin. J Ind Microbiol Biotechnol 2010; 38:1013-25. [DOI: 10.1007/s10295-010-0875-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 09/13/2010] [Indexed: 11/25/2022]
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41
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Trends and challenges in the microbial production of lignocellulosic bioalcohol fuels. Appl Microbiol Biotechnol 2010; 87:1303-15. [DOI: 10.1007/s00253-010-2707-z] [Citation(s) in RCA: 256] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 05/27/2010] [Accepted: 05/27/2010] [Indexed: 12/30/2022]
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Metabolic engineering for production of biorenewable fuels and chemicals: contributions of synthetic biology. J Biomed Biotechnol 2010; 2010:761042. [PMID: 20414363 PMCID: PMC2857869 DOI: 10.1155/2010/761042] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 12/18/2009] [Accepted: 01/13/2010] [Indexed: 12/18/2022] Open
Abstract
Production of fuels and chemicals through microbial fermentation of plant material is a desirable alternative to petrochemical-based production. Fermentative production of biorenewable fuels and chemicals requires the engineering of biocatalysts that can quickly and efficiently convert sugars to target products at a cost that is competitive with existing petrochemical-based processes. It is also important that biocatalysts be robust to extreme fermentation conditions, biomass-derived inhibitors, and their target products. Traditional metabolic engineering has made great advances in this area, but synthetic biology has contributed and will continue to contribute to this field, particularly with next-generation biofuels. This work reviews the use of metabolic engineering and synthetic biology in biocatalyst engineering for biorenewable fuels and chemicals production, such as ethanol, butanol, acetate, lactate, succinate, alanine, and xylitol. We also examine the existing challenges in this area and discuss strategies for improving biocatalyst tolerance to chemical inhibitors.
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Dellomonaco C, Fava F, Gonzalez R. The path to next generation biofuels: successes and challenges in the era of synthetic biology. Microb Cell Fact 2010; 9:3. [PMID: 20089184 PMCID: PMC2817670 DOI: 10.1186/1475-2859-9-3] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Accepted: 01/20/2010] [Indexed: 01/11/2023] Open
Abstract
Volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. Recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. Metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo pathways for conversion of biomass constituents to short-chain alcohols and advanced biofuels are herewith reviewed. In the foreseeable future, formal integration of functional genomics and systems biology with synthetic biology and metabolic engineering will undoubtedly support the discovery, characterization, and engineering of new metabolic routes and more efficient microbial systems for the production of biofuels.
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Zheng YN, Li LZ, Xian M, Ma YJ, Yang JM, Xu X, He DZ. Problems with the microbial production of butanol. J Ind Microbiol Biotechnol 2009; 36:1127-38. [PMID: 19562394 DOI: 10.1007/s10295-009-0609-9] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Accepted: 06/04/2009] [Indexed: 10/20/2022]
Abstract
With the incessant fluctuations in oil prices and increasing stress from environmental pollution, renewed attention is being paid to the microbial production of biofuels from renewable sources. As a gasoline substitute, butanol has advantages over traditional fuel ethanol in terms of energy density and hygroscopicity. A variety of cheap substrates have been successfully applied in the production of biobutanol, highlighting the commercial potential of biobutanol development. In this review, in order to better understand the process of acetone-butanol-ethanol production, traditional clostridia fermentation is discussed. Sporulation is probably induced by solvent formation, and the molecular mechanism leading to the initiation of sporulation and solventogenesis is also investigated. Different strategies are employed in the metabolic engineering of clostridia that aim to enhancing solvent production, improve selectivity for butanol production, and increase the tolerance of clostridia to solvents. However, it will be hard to make breakthroughs in the metabolic engineering of clostridia for butanol production without gaining a deeper understanding of the genetic background of clostridia and developing more efficient genetic tools for clostridia. Therefore, increasing attention has been paid to the metabolic engineering of E. coli for butanol production. The importation and expression of a non-clostridial butanol-producing pathway in E. coli is probably the most promising strategy for butanol biosynthesis. Due to the lower butanol titers in the fermentation broth, simultaneous fermentation and product removal techniques have been developed to reduce the cost of butanol recovery. Gas stripping is the best technique for butanol recovery found so far.
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Affiliation(s)
- Yan-Ning Zheng
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266071 Qingdao, China.
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Jiang Y, Xu C, Dong F, Yang Y, Jiang W, Yang S. Disruption of the acetoacetate decarboxylase gene in solvent-producing Clostridium acetobutylicum increases the butanol ratio. Metab Eng 2009; 11:284-91. [PMID: 19560551 DOI: 10.1016/j.ymben.2009.06.002] [Citation(s) in RCA: 190] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 05/27/2009] [Accepted: 06/16/2009] [Indexed: 11/18/2022]
Abstract
A possible way to improve the economic efficacy of acetone-butanol-ethanol fermentation is to increase the butanol ratio by eliminating the production of other by-products, such as acetone. The acetoacetate decarboxylase gene (adc) in the hyperbutanol-producing industrial strain Clostridium acetobutylicum EA 2018 was disrupted using TargeTron technology. The butanol ratio increased from 70% to 80.05%, with acetone production reduced to approximately 0.21 g/L in the adc-disrupted mutant (2018adc). pH control was a critical factor in the improvement of cell growth and solvent production in strain 2018adc. The regulation of electron flow by the addition of methyl viologen altered the carbon flux from acetic acid production to butanol production in strain 2018adc, which resulted in an increased butanol ratio of 82% and a corresponding improvement in the overall yield of butanol from 57% to 70.8%. This study presents a general method of blocking acetone production by Clostridium and demonstrates the industrial potential of strain 2018adc.
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Affiliation(s)
- Yu Jiang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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46
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Recent progress on industrial fermentative production of acetone–butanol–ethanol by Clostridium acetobutylicum in China. Appl Microbiol Biotechnol 2009; 83:415-23. [DOI: 10.1007/s00253-009-2003-y] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2009] [Revised: 04/07/2009] [Accepted: 04/07/2009] [Indexed: 10/20/2022]
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47
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Lee SY, Park JH, Jang SH, Nielsen LK, Kim J, Jung KS. Fermentative butanol production by clostridia. Biotechnol Bioeng 2008; 101:209-28. [DOI: 10.1002/bit.22003] [Citation(s) in RCA: 773] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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48
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Papoutsakis ET. Engineering solventogenic clostridia. Curr Opin Biotechnol 2008; 19:420-9. [PMID: 18760360 DOI: 10.1016/j.copbio.2008.08.003] [Citation(s) in RCA: 229] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Revised: 07/23/2008] [Accepted: 08/01/2008] [Indexed: 01/28/2023]
Abstract
Solventogenic clostridia are strictly anaerobic, endospore forming bacteria that produce a large array of primary metabolites, like butanol, by anaerobically degrading simple and complex carbohydrates, including cellulose and hemicellulose. Two genomes have been sequenced and some genetic tools have been developed, but more are now urgently needed. Genomic tools for designing, and assessing the impact of, genetic modifications are well developed. Early efforts to metabolically engineer these organisms suggest that they are promising organisms for biorefinery applications. Pathway engineering efforts have resulted in interesting strains, but global engineering of their transcriptional machinery has produced better outcomes. Future efforts are expected to undertake the development of complex multigenic phenotypes, such as aerotolerance, solvent tolerance, high-cell density fermentations, abolished sporulation without impacting product formation, and genetic stability for continuous bioprocessing.
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Affiliation(s)
- Eleftherios T Papoutsakis
- Department of Chemical Engineering, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
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Abstract
Clostridium acetobutylicum is an anaerobic, spore-forming bacterium with the ability to ferment starch and sugars into solvents. In the past, it has been used for industrial production of acetone and butanol, until cheap crude oil rendered petrochemical synthesis more economically feasible. Both economic (price of crude oil) and environmental aspects (carbon dioxide emissions) have caused the pendulum to swing back again. Molecular biology has allowed a detailed understanding of genes and enzymes, required for solventogenesis. Thus, construction of strains with improved fermentation ability is now possible. Advances in continuous culture technology and improved downstream processing also add to economic advantages of a new biotechnological process. Two major companies have already committed themselves to biobutanol production as a biofuel additive. Thus, butanol fermentation is on the rise again.
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Affiliation(s)
- Peter Dürre
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, 89069 Ulm, Germany.
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