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Re A, Mazzoli R. Current progress on engineering microbial strains and consortia for production of cellulosic butanol through consolidated bioprocessing. Microb Biotechnol 2022; 16:238-261. [PMID: 36168663 PMCID: PMC9871528 DOI: 10.1111/1751-7915.14148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/01/2022] [Accepted: 09/07/2022] [Indexed: 01/27/2023] Open
Abstract
In the last decades, fermentative production of n-butanol has regained substantial interest mainly owing to its use as drop-in-fuel. The use of lignocellulose as an alternative to traditional acetone-butanol-ethanol fermentation feedstocks (starchy biomass and molasses) can significantly increase the economic competitiveness of biobutanol over production from non-renewable sources (petroleum). However, the low cost of lignocellulose is offset by its high recalcitrance to biodegradation which generally requires chemical-physical pre-treatment and multiple bioreactor-based processes. The development of consolidated processing (i.e., single-pot fermentation) can dramatically reduce lignocellulose fermentation costs and promote its industrial application. Here, strategies for developing microbial strains and consortia that feature both efficient (hemi)cellulose depolymerization and butanol production will be depicted, that is, rational metabolic engineering of native (hemi)cellulolytic or native butanol-producing or other suitable microorganisms; protoplast fusion of (hemi)cellulolytic and butanol-producing strains; and co-culture of (hemi)cellulolytic and butanol-producing microbes. Irrespective of the fermentation feedstock, biobutanol production is inherently limited by the severe toxicity of this solvent that challenges process economic viability. Hence, an overview of strategies for developing butanol hypertolerant strains will be provided.
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Affiliation(s)
- Angela Re
- Centre for Sustainable Future TechnologiesFondazione Istituto Italiano di TecnologiaTorinoItaly,Department of Applied Science and TechnologyPolitecnico di TorinoTurinItaly
| | - Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems BiologyUniversity of TorinoTorinoItaly
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Kim SR, Eckert CA, Mazzoli R. Editorial: Microorganisms for Consolidated 2nd Generation Biorefining. Front Microbiol 2022; 13:940610. [PMID: 35783433 PMCID: PMC9248810 DOI: 10.3389/fmicb.2022.940610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 05/23/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Soo Rin Kim
- School of Food Science and Biotechnology, Research Institute of Tailored Food Technology, Kyungpook National University, Daegu, South Korea
| | - Carrie A. Eckert
- Synthetic Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- *Correspondence: Roberto Mazzoli
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Bao T, Hou W, Wu X, Lu L, Zhang X, Yang ST. Engineering Clostridium cellulovorans for highly selective n-butanol production from cellulose in consolidated bioprocessing. Biotechnol Bioeng 2021; 118:2703-2718. [PMID: 33844271 DOI: 10.1002/bit.27789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/06/2021] [Accepted: 04/09/2021] [Indexed: 01/05/2023]
Abstract
Cellulosic n-butanol from renewable lignocellulosic biomass has gained increased interest. Previously, we have engineered Clostridium cellulovorans, a cellulolytic acidogen, to overexpress the bifunctional butyraldehyde/butanol dehydrogenase gene adhE2 from C. acetobutylicum for n-butanol production from crystalline cellulose. However, butanol production by this engineered strain had a relatively low yield of approximately 0.22 g/g cellulose due to the coproduction of ethanol and acids. We hypothesized that strengthening the carbon flux through the central butyryl-CoA biosynthesis pathway and increasing intracellular NADH availability in C. cellulovorans adhE2 would enhance n-butanol production. In this study, thiolase (thlACA ) from C. acetobutylicum and 3-hydroxybutyryl-CoA dehydrogenase (hbdCT ) from C. tyrobutyricum were overexpressed in C. cellulovorans adhE2 to increase the flux from acetyl-CoA to butyryl-CoA. In addition, ferredoxin-NAD(P)+ oxidoreductase (fnr), which can regenerate the intracellular NAD(P)H and thus increase butanol biosynthesis, was also overexpressed. Metabolic flux analyses showed that mutants overexpressing these genes had a significantly increased carbon flux toward butyryl-CoA, which resulted in increased production of butyrate and butanol. The addition of methyl viologen as an electron carrier in batch fermentation further directed more carbon flux towards n-butanol biosynthesis due to increased reducing equivalent or NADH. The engineered strain C. cellulovorans adhE2-fnrCA -thlACA -hbdCT produced n-butanol from cellulose at a 50% higher yield (0.34 g/g), the highest ever obtained in batch fermentation by any known bacterial strain. The engineered C. cellulovorans is thus a promising host for n-butanol production from cellulosic biomass in consolidated bioprocessing.
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Affiliation(s)
- Teng Bao
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Wenjie Hou
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA.,College of Life Sciences, Northwest A&F University, Yangling, Shanxi, China
| | - Xuefeng Wu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA.,School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Li Lu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Xian Zhang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Shang-Tian Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
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Wen Z, Li Q, Liu J, Jin M, Yang S. Consolidated bioprocessing for butanol production of cellulolytic Clostridia: development and optimization. Microb Biotechnol 2020; 13:410-422. [PMID: 31448546 PMCID: PMC7017829 DOI: 10.1111/1751-7915.13478] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/02/2019] [Accepted: 08/04/2019] [Indexed: 12/20/2022] Open
Abstract
Butanol is an important bulk chemical, as well as a promising renewable gasoline substitute, that is commonly produced by solventogenic Clostridia. The main cost of cellulosic butanol fermentation is caused by cellulases that are required to saccharify lignocellulose, since solventogenic Clostridia cannot efficiently secrete cellulases. However, cellulolytic Clostridia can natively degrade lignocellulose and produce ethanol, acetate, butyrate and even butanol. Therefore, cellulolytic Clostridia offer an alternative to develop consolidated bioprocessing (CBP), which combines cellulase production, lignocellulose hydrolysis and co-fermentation of hexose/pentose into butanol in one step. This review focuses on CBP advances for butanol production of cellulolytic Clostridia and various synthetic biotechnologies that drive these advances. Moreover, the efforts to optimize the CBP-enabling cellulolytic Clostridia chassis are also discussed. These include the development of genetic tools, pentose metabolic engineering and the improvement of butanol tolerance. Designer cellulolytic Clostridia or consortium provide a promising approach and resource to accelerate future CBP for butanol production.
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Affiliation(s)
- Zhiqiang Wen
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Qi Li
- College of Life SciencesSichuan Normal UniversityLongquan, Chengdu610101China
| | - Jinle Liu
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Mingjie Jin
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Sheng Yang
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
- Huzhou Center of Industrial BiotechnologyShanghai Institutes of Biological SciencesChinese Academy of SciencesShanghai200032China
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Green Production and Biotechnological Applications of Cell Wall Lytic Enzymes. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9235012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
: Energy demand is constantly growing, and, nowadays, fossil fuels still play a dominant role in global energy production, despite their negative effects on air pollution and the emission of greenhouse gases, which are the main contributors to global warming. An alternative clean source of energy is represented by the lignocellulose fraction of plant cell walls, the most abundant carbon source on Earth. To obtain biofuels, lignocellulose must be efficiently converted into fermentable sugars. In this regard, the exploitation of cell wall lytic enzymes (CWLEs) produced by lignocellulolytic fungi and bacteria may be considered as an eco-friendly alternative. These organisms evolved to produce a variety of highly specific CWLEs, even if in low amounts. For an industrial use, both the identification of novel CWLEs and the optimization of sustainable CWLE-expressing biofactories are crucial. In this review, we focus on recently reported advances in the heterologous expression of CWLEs from microbial and plant expression systems as well as some of their industrial applications, including the production of biofuels from agricultural feedstock and of value-added compounds from waste materials. Moreover, since heterologous expression of CWLEs may be toxic to plant hosts, genetic strategies aimed in converting such a deleterious effect into a beneficial trait are discussed.
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Affiliation(s)
- Ee Taek Hwang
- Center for Convergence Bioceramic Materials, Korea Institute of Ceramic Engineering & Technology, Cheongju-si, Chungcheongbuk-do 28160, Republic of Korea
| | - Seonbyul Lee
- Center for Convergence Bioceramic Materials, Korea Institute of Ceramic Engineering & Technology, Cheongju-si, Chungcheongbuk-do 28160, Republic of Korea
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Jiang Y, Zhang T, Lu J, Dürre P, Zhang W, Dong W, Zhou J, Jiang M, Xin F. Microbial co-culturing systems: butanol production from organic wastes through consolidated bioprocessing. Appl Microbiol Biotechnol 2018; 102:5419-5425. [DOI: 10.1007/s00253-018-8970-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/23/2018] [Accepted: 03/24/2018] [Indexed: 12/29/2022]
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Gyulev IS, Willson BJ, Hennessy RC, Krabben P, Jenkinson ER, Thomas GH. Part by Part: Synthetic Biology Parts Used in Solventogenic Clostridia. ACS Synth Biol 2018; 7:311-327. [PMID: 29186949 DOI: 10.1021/acssynbio.7b00327] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solventogenic Clostridia are of interest to the chemical industry because of their natural ability to produce chemicals such as butanol, acetone and ethanol from diverse feedstocks. Their use as whole cell factories presents multiple metabolic engineering targets that could lead to improved sustainability and profitability of Clostridium industrial processes. However, engineering efforts have been held back by the scarcity of genetic and synthetic biology tools. Over the past decade, genetic tools to enable transformation and chromosomal modifications have been developed, but the lack of a broad palette of synthetic biology parts remains one of the last obstacles to the rapid engineered improvement of these species for bioproduction. We have systematically reviewed existing parts that have been used in the modification of solventogenic Clostridia, revealing a narrow range of empirically chosen and nonengineered parts that are in current use. The analysis uncovers elements, such as promoters, transcriptional terminators and ribosome binding sites where increased fundamental knowledge is needed for their reliable use in different applications. Together, the review provides the most comprehensive list of parts used and also presents areas where an improved toolbox is needed for full exploitation of these industrially important bacteria.
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Affiliation(s)
- Ivan S. Gyulev
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Benjamin J. Willson
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Rosanna C. Hennessy
- Department
of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, 1871, Denmark
| | - Preben Krabben
- Green Biologics Limited, Milton Park, Abingdon, Oxfordshire OX14 4RU, United Kingdom
| | | | - Gavin H. Thomas
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
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Nanda S, Golemi-Kotra D, McDermott JC, Dalai AK, Gökalp I, Kozinski JA. Fermentative production of butanol: Perspectives on synthetic biology. N Biotechnol 2017; 37:210-221. [DOI: 10.1016/j.nbt.2017.02.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 02/20/2017] [Accepted: 02/22/2017] [Indexed: 11/25/2022]
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Wen Z, Minton NP, Zhang Y, Li Q, Liu J, Jiang Y, Yang S. Enhanced solvent production by metabolic engineering of a twin-clostridial consortium. Metab Eng 2017; 39:38-48. [DOI: 10.1016/j.ymben.2016.10.013] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/30/2016] [Accepted: 10/25/2016] [Indexed: 12/16/2022]
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Willson BJ, Kovács K, Wilding-Steele T, Markus R, Winzer K, Minton NP. Production of a functional cell wall-anchored minicellulosome by recombinant Clostridium acetobutylicum ATCC 824. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:109. [PMID: 27222664 PMCID: PMC4877998 DOI: 10.1186/s13068-016-0526-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 05/10/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND The use of fossil fuels is no longer tenable. Not only are they a finite resource, their use is damaging the environment through pollution and global warming. Alternative, environmentally friendly, renewable sources of chemicals and fuels are required. To date, the focus has been on using lignocellulose as a feedstock for microbial fermentation. However, its recalcitrance to deconstruction is making the development of economic processes extremely challenging. One solution is the generation of an organism suitable for use in consolidated bioprocessing (CBP), i.e. one able to both hydrolyse lignocellulose and ferment the released sugars, and this represents an important goal for synthetic biology. We aim to use synthetic biology to develop the solventogenic bacterium C. acetobutylicum as a CBP organism through the introduction of a cellulosome, a complex of cellulolytic enzymes bound to a scaffold protein called a scaffoldin. In previous work, we were able to demonstrate the in vivo production of a C. thermocellum-derived minicellulosome by recombinant strains of C. acetobutylicum, and aim to develop on this success, addressing potential issues with the previous strategy. RESULTS The genes for the cellulosomal enzymes Cel9G, Cel48F, and Xyn10A from C. cellulolyticum were integrated into the C. acetobutylicum genome using Allele-Coupled Exchange (ACE) technology, along with a miniscaffoldin derived from C. cellulolyticum CipC. The possibility of anchoring the recombinant cellulosome to the cell surface using the native sortase system was assessed, and the cellulolytic properties of the recombinant strains were assayed via plate growth, batch fermentation and sugar release assays. CONCLUSIONS We have been able to demonstrate the synthesis and in vivo assembly of a four-component minicellulosome by recombinant C. acetobutylicum strains. Furthermore, we have been able to anchor a minicellulosome to the C. acetobutylicum cell wall by the use of the native sortase system. The recombinant strains display an improved growth phenotype on xylan and an increase in released reducing sugar from several substrates including untreated powdered wheat straw. This constitutes an important milestone towards the development of a truly cellulolytic strain suitable for CBP.
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Affiliation(s)
- Benjamin J. Willson
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Katalin Kovács
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Tom Wilding-Steele
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Robert Markus
- />SLIM Imaging Unit, Faculty of Medicine and Health Sciences, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Klaus Winzer
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Nigel P. Minton
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
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Oh YH, Eom GT, Kang KH, Joo JC, Jang YA, Choi JW, Song BK, Lee SH, Park SJ. Construction of heterologous gene expression cassettes for the development of recombinant Clostridium beijerinckii. Bioprocess Biosyst Eng 2016; 39:555-63. [DOI: 10.1007/s00449-016-1537-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 01/05/2016] [Indexed: 02/08/2023]
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Petit E, Coppi MV, Hayes JC, Tolonen AC, Warnick T, Latouf WG, Amisano D, Biddle A, Mukherjee S, Ivanova N, Lykidis A, Land M, Hauser L, Kyrpides N, Henrissat B, Lau J, Schnell DJ, Church GM, Leschine SB, Blanchard JL. Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels. PLoS One 2015; 10:e0118285. [PMID: 26035711 PMCID: PMC4452783 DOI: 10.1371/journal.pone.0118285] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 01/12/2015] [Indexed: 11/18/2022] Open
Abstract
Clostridium phytofermentans was isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways. The objective of the present study was to understand the molecular mechanisms of biomass conversion to ethanol in a single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome during growth on plant carbohydrates. The saccharolytic versatility of C. phytofermentans is reflected in a diversity of genes encoding ATP-binding cassette sugar transporters and glycoside hydrolases, many of which may have been acquired through horizontal gene transfer. These genes are frequently organized as operons that may be controlled individually by the many transcriptional regulators identified in the genome. Preferential ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases and additional pathways maximizing ethanol yield. The genome also encodes three different proteinaceous bacterial microcompartments with the capacity to compartmentalize pathways that divert fermentation intermediates to various products. These characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels.
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Affiliation(s)
- Elsa Petit
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Maddalena V. Coppi
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - James C. Hayes
- Graduate Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Andrew C. Tolonen
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)-Genoscope, Unité Mixte de Recherche (UMR)-8030, National Center for Scientific Research (CNRS), Evry, France
| | - Thomas Warnick
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - William G. Latouf
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Danielle Amisano
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Amy Biddle
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Supratim Mukherjee
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Natalia Ivanova
- Department of Energy (DOE)- Joint Genome Institute, Genome Biology Program, Production Genomics Facility, Walnut Creek, California, United States of America
| | - Athanassios Lykidis
- Department of Energy (DOE)- Joint Genome Institute, Genome Biology Program, Production Genomics Facility, Walnut Creek, California, United States of America
| | - Miriam Land
- Oak Ridge National Laboratory (ORNL), Life Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Loren Hauser
- Oak Ridge National Laboratory (ORNL), Life Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Nikos Kyrpides
- Department of Energy (DOE)- Joint Genome Institute, Genome Biology Program, Production Genomics Facility, Walnut Creek, California, United States of America
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Unité mixte de recherche (UMR)-6098, National Center for Scientific Research (CNRS), and Universités d’Aix-Marseille I and II, Marseille, France
| | - Joanne Lau
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Danny J. Schnell
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Susan B. Leschine
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Jeffrey L. Blanchard
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Graduate Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
- Graduate Program in Organismal and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
- * E-mail:
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Zheng J, Tashiro Y, Wang Q, Sonomoto K. Recent advances to improve fermentative butanol production: Genetic engineering and fermentation technology. J Biosci Bioeng 2015; 119:1-9. [DOI: 10.1016/j.jbiosc.2014.05.023] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 05/19/2014] [Accepted: 05/30/2014] [Indexed: 11/28/2022]
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Wen Z, Wu M, Lin Y, Yang L, Lin J, Cen P. A novel strategy for sequential co-culture of Clostridium thermocellum and Clostridium beijerinckii to produce solvents from alkali extracted corn cobs. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.07.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Wen Z, Wu M, Lin Y, Yang L, Lin J, Cen P. Artificial symbiosis for acetone-butanol-ethanol (ABE) fermentation from alkali extracted deshelled corn cobs by co-culture of Clostridium beijerinckii and Clostridium cellulovorans. Microb Cell Fact 2014; 13:92. [PMID: 25023325 PMCID: PMC4223388 DOI: 10.1186/s12934-014-0092-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 06/17/2014] [Indexed: 02/02/2023] Open
Abstract
Background Butanol is an industrial commodity and also considered to be a more promising gasoline substitute compared to ethanol. Renewed attention has been paid to solvents (acetone, butanol and ethanol) production from the renewable and inexpensive substrates, for example, lignocellulose, on account of the depletion of oil resources, increasing gasoline prices and deteriorating environment. Limited to current tools for genetic manipulation, it is difficult to develop a genetically engineered microorganism with combined ability of lignocellulose utilization and solvents production. Mixed culture of cellulolytic microorganisms and solventogenic bacteria provides a more convenient and feasible approach for ABE fermentation due to the potential for synergistic utilization of the metabolic pathways of two organisms. But few bacteria pairs succeeded in producing biobutanol of high titer or high productivity without adding butyrate. The aim of this work was to use Clostridium cellulovorans 743B to saccharify lignocellulose and produce butyric acid, instead of adding cellulase and butyric acid to the medium, so that the soluble sugars and butyric acid generated can be subsequently utilized by Clostridium beijerinckii NCIMB 8052 to produce butanol in one pot reaction. Results A stable artificial symbiotic system was constructed by co-culturing a celluloytic, anaerobic, butyrate-producing mesophile (C. cellulovorans 743B) and a non-celluloytic, solventogenic bacterium (C. beijerinckii NCIMB 8052) to produce solvents by consolidated bioprocessing (CBP) with alkali extracted deshelled corn cobs (AECC), a low-cost renewable feedstock, as the sole carbon source. Under optimized conditions, the co-culture degraded 68.6 g/L AECC and produced 11.8 g/L solvents (2.64 g/L acetone, 8.30 g/L butanol and 0.87 g/L ethanol) in less than 80 h. Besides, a real-time PCR assay based on the 16S rRNA gene sequence was performed to study the dynamics of the abundance of each strain during the co-culturing process, which figured out the roles of each strain at different periods in the symbiosis. Conclusion Our work illustrated the great potential of artificial symbiosis in biofuel production from lignocellulosic biomass by CBP. The dynamics of the abundance of C. beijerinckii and C. cellulovorans revealed mechanisms of cooperation and competition between the two strains during the co-culture process.
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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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Kellermann SJ, Rentmeister A. Current Developments in Cellulase Engineering. CHEMBIOENG REVIEWS 2014. [DOI: 10.1002/cben.201300006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Xu Q, Ding SY, Brunecky R, Bomble YJ, Himmel ME, Baker JO. Improving activity of minicellulosomes by integration of intra- and intermolecular synergies. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:126. [PMID: 23987588 PMCID: PMC3766687 DOI: 10.1186/1754-6834-6-126] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 08/28/2013] [Indexed: 05/20/2023]
Abstract
BACKGROUND Complete hydrolysis of cellulose to glucose requires the synergistic action of three general types of glycoside hydrolases; endoglucanases, exoglucanases, and cellobiases. Cellulases that are found in Nature vary considerably in their modular diversity and architecture. They include: non-complexed enzymes with single catalytic domains, independent single peptide chains incorporating multiple catalytic modules, and complexed, scaffolded structures, such as the cellulosome. The discovery of the latter two enzyme architectures has led to a generally held hypothesis that these systems take advantage of intramolecular and intermolecular proximity synergies, respectively, to enhance cellulose degradation. We use domain engineering to exploit both of these concepts to improve cellulase activity relative to the activity of mixtures of the separate catalytic domains. RESULTS We show that engineered minicellulosomes can achieve high levels of cellulose conversion on crystalline cellulose by taking advantage of three types of synergism; (1) a complementary synergy produced by interaction of endo- and exo-cellulases, (2) an intramolecular synergy of multiple catalytic modules in a single gene product (this type of synergism being introduced for the first time to minicellulosomes targeting crystalline cellulose), and (3) an intermolecular proximity synergy from the assembly of these cellulases into larger multi-molecular structures called minicellulosomes. The binary minicellulosome constructed in this study consists of an artificial multicatalytic cellulase (CBM4-Ig-GH9-X11-X12-GH8-Doc) and one cellulase with a single catalytic domain (a modified Cel48S with the structure CBM4-Ig-GH48-Doc), connected by a non-catalytic scaffoldin protein. The high level endo-exo synergy and intramolecular synergies within the artificial multifunctional cellulase have been combined with an additional proximity-dependent synergy produced by incorporation into a minicellulosome demonstrating high conversion of crystalline cellulose (Avicel). Our minicellulosome is the first engineered enzyme system confirmed by test to be capable of both operating at temperatures as high as 60°C and converting over 60% of crystalline cellulose to fermentable sugars. CONCLUSION When compared to previously reported minicellulosomes assembled from cellulases containing only one catalytic module each, our novel minicellulosome demonstrates a method for substantial reduction in the number of peptide chains required, permitting improved heterologous expression of minicellulosomes in microbial hosts. In addition, it has been shown to be capable of substantial conversion of actual crystalline cellulose, as well as of the less-well-ordered and more easily digestible fraction of nominally crystalline cellulose.
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Affiliation(s)
- Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Shi-You Ding
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Roman Brunecky
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - John O Baker
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
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Kovács K, Willson BJ, Schwarz K, Heap JT, Jackson A, Bolam DN, Winzer K, Minton NP. Secretion and assembly of functional mini-cellulosomes from synthetic chromosomal operons in Clostridium acetobutylicum ATCC 824. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:117. [PMID: 23962085 PMCID: PMC3765823 DOI: 10.1186/1754-6834-6-117] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 08/02/2013] [Indexed: 05/31/2023]
Abstract
BACKGROUND Consolidated bioprocessing (CBP) is reliant on the simultaneous enzyme production, saccharification of biomass, and fermentation of released sugars into valuable products such as butanol. Clostridial species that produce butanol are, however, unable to grow on crystalline cellulose. In contrast, those saccharolytic species that produce predominantly ethanol, such as Clostridium thermocellum and Clostridium cellulolyticum, degrade crystalline cellulose with high efficiency due to their possession of a multienzyme complex termed the cellulosome. This has led to studies directed at endowing butanol-producing species with the genetic potential to produce a cellulosome, albeit by localising the necessary transgenes to unstable autonomous plasmids. Here we have explored the potential of our previously described Allele-Coupled Exchange (ACE) technology for creating strains of the butanol producing species Clostridium acetobutylicum in which the genes encoding the various cellulosome components are stably integrated into the genome. RESULTS We used BioBrick2 (BB2) standardised parts to assemble a range of synthetic genes encoding C. thermocellum cellulosomal scaffoldin proteins (CipA variants) and glycoside hydrolases (GHs, Cel8A, Cel9B, Cel48S and Cel9K) as well as synthetic cellulosomal operons that direct the synthesis of Cel8A, Cel9B and a truncated form of CipA. All synthetic genes and operons were integrated into the C. acetobutylicum genome using the recently developed ACE technology. Heterologous protein expression levels and mini-cellulosome self-assembly were assayed by western blot and native PAGE analysis. CONCLUSIONS We demonstrate the successful expression, secretion and self-assembly of cellulosomal subunits by the recombinant C. acetobutylicum strains, providing a platform for the construction of novel cellulosomes.
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Affiliation(s)
- Katalin Kovács
- Clostridia Research Group, BBSRC Sustainable BioEnergy Centre, School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Benjamin J Willson
- Clostridia Research Group, BBSRC Sustainable BioEnergy Centre, School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Katrin Schwarz
- Clostridia Research Group, BBSRC Sustainable BioEnergy Centre, School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - John T Heap
- Clostridia Research Group, BBSRC Sustainable BioEnergy Centre, School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
- Current address: Centre for Synthetic Biology and Innovation, Division of Molecular Biosciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Adam Jackson
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - David N Bolam
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Klaus Winzer
- Clostridia Research Group, BBSRC Sustainable BioEnergy Centre, School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Nigel P Minton
- Clostridia Research Group, BBSRC Sustainable BioEnergy Centre, School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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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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Cui Z, Li Y, Xiao Y, Feng Y, Cui Q, Cui Q. Resonance assignments of cohesin and dockerin domains from Clostridium acetobutylicum ATCC824. BIOMOLECULAR NMR ASSIGNMENTS 2013; 7:73-6. [PMID: 22446850 DOI: 10.1007/s12104-012-9381-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 03/12/2012] [Indexed: 05/07/2023]
Abstract
Cohesin and dockerin domains are critical assembling components of cellulosome, a large extracellular multienzyme complex which is used by anaerobic cellulolytic bacteria to efficiently degrade lignocellulose. According to sequence homology, cohesins can be divided into three major groups, whereas cohesins from Clostridium acetobutylicum are beyond these groups and emanate from a branching point between the type I and type III cohesins. Cohesins and dockerins from C. acetobutylicum show low sequence homology to those from other cellulolytic bacteria, and their interactions are specific in corresponding species. Therefore the interactions between cohesins and dockerins from C. acetobutylicum are meaningful to the studies of both cellulosome assembling mechanism and the construction of designer cellulosome. Here we report the NMR resonance assignments of one cohesin from cellulosome scaffoldin cipA and one dockerin from a cellulosomal glycoside hydrolase (family 9) of C. acetobutylicum for further structural determination and functional studies.
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Affiliation(s)
- Zhenling Cui
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
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Currie DH, Herring CD, Guss AM, Olson DG, Hogsett DA, Lynd LR. Functional heterologous expression of an engineered full length CipA from Clostridium thermocellum in Thermoanaerobacterium saccharolyticum. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:32. [PMID: 23448319 PMCID: PMC3598777 DOI: 10.1186/1754-6834-6-32] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 02/08/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Cellulose is highly recalcitrant and thus requires a specialized suite of enzymes to solubilize it into fermentable sugars. In C. thermocellum, these extracellular enzymes are present as a highly active multi-component system known as the cellulosome. This study explores the expression of a critical C. thermocellum cellulosomal component in T. saccharolyticum as a step toward creating a thermophilic bacterium capable of consolidated bioprocessing by employing heterologously expressed cellulosomes. RESULTS We developed an inducible promoter system based on the native T. saccharolyticum xynA promoter, which was shown to be induced by xylan and xylose. The promoter was used to express the cellulosomal component cipA*, an engineered form of the wild-type cipA from C. thermocellum. Expression and localization to the supernatant were both verified for CipA*. When a ΔcipA mutant C. thermocellum strain was cultured with a CipA*-expressing T. saccharolyticum strain, hydrolysis and fermentation of 10 grams per liter SigmaCell 101, a highly crystalline cellulose, were observed. This trans-species complementation of a cipA deletion demonstrated the ability for CipA* to assemble a functional cellulosome. CONCLUSION This study is the first example of an engineered thermophile heterologously expressing a structural component of a cellulosome. To achieve this goal we developed and tested an inducible promoter for controlled expression in T. saccharolyticum as well as a synthetic cipA. In addition, we demonstrate a high degree of hydrolysis (up to 93%) on microcrystalline cellulose.
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Affiliation(s)
- Devin H Currie
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
- Mascoma Corporation, Lebanon, NH 03766, USA
| | | | - Adam M Guss
- Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | | | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
- Mascoma Corporation, Lebanon, NH 03766, USA
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Tracy BP, Jones SW, Fast AG, Indurthi DC, Papoutsakis ET. Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications. Curr Opin Biotechnol 2012; 23:364-81. [DOI: 10.1016/j.copbio.2011.10.008] [Citation(s) in RCA: 313] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 10/06/2011] [Accepted: 10/20/2011] [Indexed: 12/19/2022]
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27
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Designer Xylanosomes: Protein Nanostructures for Enhanced Xylan Hydrolysis. Appl Biochem Biotechnol 2012; 167:395-411. [DOI: 10.1007/s12010-012-9680-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 04/10/2012] [Indexed: 10/28/2022]
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Direct conversion of xylan to ethanol by recombinant Saccharomyces cerevisiae strains displaying an engineered minihemicellulosome. Appl Environ Microbiol 2012; 78:3837-45. [PMID: 22447594 DOI: 10.1128/aem.07679-11] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Arabinoxylan is a heteropolymeric chain of a β-1,4-linked xylose backbone substituted with arabinose residues, representing a principal component of plant cell walls. Here we developed recombinant Saccharomyces cerevisiae strains as whole-cell biocatalysts capable of combining hemicellulase production, xylan hydrolysis, and hydrolysate fermentation into a single step. These strains displayed a series of uni-, bi-, and trifunctional minihemicellulosomes that consisted of a miniscaffoldin (CipA3/CipA1) and up to three chimeric enzymes. The miniscaffoldin derived from Clostridium thermocellum contained one or three cohesin modules and was tethered to the cell surface through the S. cerevisiae a-agglutinin adhesion receptor. Up to three types of hemicellulases, an endoxylanase (XynII), an arabinofuranosidase (AbfB), and a β-xylosidase (XlnD), each bearing a C-terminal dockerin, were assembled onto the miniscaffoldin by high-affinity cohesin-dockerin interactions. Compared to uni- and bifunctional minihemicellulosomes, the resulting quaternary trifunctional complexes exhibited an enhanced rate of hydrolysis of arabinoxylan. Furthermore, with an integrated d-xylose-utilizing pathway, the recombinant yeast displaying the bifunctional minihemicellulosome CipA3-XynII-XlnD could simultaneously hydrolyze and ferment birchwood xylan to ethanol with a yield of 0.31 g per g of sugar consumed.
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Mazzoli R, Lamberti C, Pessione E. Engineering new metabolic capabilities in bacteria: lessons from recombinant cellulolytic strategies. Trends Biotechnol 2012; 30:111-9. [DOI: 10.1016/j.tibtech.2011.08.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Revised: 08/23/2011] [Accepted: 08/23/2011] [Indexed: 01/19/2023]
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31
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Jang YS, Lee J, Malaviya A, Seung DY, Cho JH, Lee SY. Butanol production from renewable biomass: rediscovery of metabolic pathways and metabolic engineering. Biotechnol J 2011; 7:186-98. [PMID: 21818859 DOI: 10.1002/biot.201100059] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 06/21/2011] [Accepted: 07/04/2011] [Indexed: 11/07/2022]
Abstract
Biofuel from renewable biomass is one of the answers to help solve the problems associated with limited fossil resources and climate change. Butanol has superior liquid-fuel characteristics, with similar properties to gasoline, and thus, has the potential to be used as a substitute for gasoline. Clostridia are recognized as a good butanol producers and are employed in the industrial-scale production of solvents. Due to the difficulty of performing genetic manipulations on clostridia, however, strain improvement has been rather slow. Furthermore, complex metabolic characteristics of acidogenesis followed by solventogenesis in this strain have hampered the development of engineered clostridia strains with highly efficient and selective butanol-production capabilities. In recent years, the butanol-producing characteristics in clostridia have been further characterized and alternative pathways discovered. More recently, systems-level metabolic engineering approaches were taken to develop superior strains. Herein, we review recent discoveries of metabolic pathways for butanol production and the metabolic engineering strategies being developed.
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Affiliation(s)
- Yu-Sin Jang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, Republic of Korea
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Scaffoldin modules serving as "cargo" domains to promote the secretion of heterologous cellulosomal cellulases by Clostridium acetobutylicum. Appl Environ Microbiol 2011; 77:6277-80. [PMID: 21764966 DOI: 10.1128/aem.00758-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The secretion of large heterologous cellulases by Clostridium acetobutylicum was formerly shown to be deleterious. To circumvent this issue, various scaffoldins' modules were grafted at their N termini. Family 3a cellulose binding module combined with an X2 module(s) was found to trigger the secretion of Clostridium cellulolyticum cellulases by the solventogenic bacterium.
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Zhang YHP. Substrate channeling and enzyme complexes for biotechnological applications. Biotechnol Adv 2011; 29:715-25. [PMID: 21672618 DOI: 10.1016/j.biotechadv.2011.05.020] [Citation(s) in RCA: 203] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 05/19/2011] [Accepted: 05/30/2011] [Indexed: 12/25/2022]
Abstract
Substrate channeling is a process of transferring the product of one enzyme to an adjacent cascade enzyme or cell without complete mixing with the bulk phase. Such phenomena can occur in vivo, in vitro, or ex vivo. Enzyme-enzyme or enzyme-cell complexes may be static or transient. In addition to enhanced reaction rates through substrate channeling in complexes, numerous potential benefits of such complexes are protection of unstable substrates, circumvention of unfavorable equilibrium and kinetics imposed, forestallment of substrate competition among different pathways, regulation of metabolic fluxes, mitigation of toxic metabolite inhibition, and so on. Here we review numerous examples of natural and synthetic complexes featuring substrate channeling. Constructing synthetic in vivo, in vitro or ex vivo complexes for substrate channeling would have great biotechnological potentials in metabolic engineering, multi-enzyme-mediated biocatalysis, and cell-free synthetic pathway biotransformation (SyPaB).
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Affiliation(s)
- Y-H Percival Zhang
- Biological Systems Engineering Department, 210-A Seitz Hall, Virginia Tech, Blacksburg, VA 24061, USA.
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The issue of secretion in heterologous expression of Clostridium cellulolyticum cellulase-encoding genes in Clostridium acetobutylicum ATCC 824. Appl Environ Microbiol 2011; 77:2831-8. [PMID: 21378034 DOI: 10.1128/aem.03012-10] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The genes encoding the cellulases Cel5A, Cel8C, Cel9E, Cel48F, Cel9G, and Cel9M from Clostridium cellulolyticum were cloned in the C. acetobutylicum expression vector pSOS952 under the control of a Gram-positive constitutive promoter. The DNA encoding the native leader peptide of the heterologous cellulases was maintained. The transformation of the solventogenic bacterium with the corresponding vectors generated clones in the cases of Cel5A, Cel8C, and Cel9M. Analyses of the recombinant strains indicated that the three cellulases are secreted in an active form to the medium. A large fraction of the secreted cellulases, however, lost the C-terminal dockerin module. In contrast, with the plasmids pSOS952-cel9E, pSOS952-cel48F, and pSOS952-cel9G no colonies were obtained, suggesting that the expression of these genes has an inhibitory effect on growth. The deletion of the DNA encoding the leader peptide of Cel48F in pSOS952-cel48F, however, generated strains of C. acetobutylicum in which mature Cel48F accumulates in the cytoplasm. Thus, the growth inhibition observed when the wild-type cel48F gene is expressed seems related to the secretion of the cellulase. The weakening of the promoter, the coexpression of miniscaffoldin-encoding genes, or the replacement of the native signal sequence of Cel48F by that of secreted heterologous or endogenous proteins failed to generate strains secreting Cel48F. Taken together, our data suggest that a specific chaperone(s) involved in the secretion of the key family 48 cellulase, and probably Cel9G and Cel9E, is missing or insufficiently synthesized in C. acetobutylicum.
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Elkins JG, Raman B, Keller M. Engineered microbial systems for enhanced conversion of lignocellulosic biomass. Curr Opin Biotechnol 2010; 21:657-62. [DOI: 10.1016/j.copbio.2010.05.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 05/27/2010] [Indexed: 11/16/2022]
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Huang H, Liu H, Gan YR. Genetic modification of critical enzymes and involved genes in butanol biosynthesis from biomass. Biotechnol Adv 2010; 28:651-7. [DOI: 10.1016/j.biotechadv.2010.05.015] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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la Grange DC, den Haan R, van Zyl WH. Engineering cellulolytic ability into bioprocessing organisms. Appl Microbiol Biotechnol 2010; 87:1195-208. [DOI: 10.1007/s00253-010-2660-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 05/02/2010] [Accepted: 05/02/2010] [Indexed: 10/19/2022]
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38
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Fontes CMGA, Gilbert HJ. Cellulosomes: highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates. Annu Rev Biochem 2010; 79:655-81. [PMID: 20373916 DOI: 10.1146/annurev-biochem-091208-085603] [Citation(s) in RCA: 362] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cellulosomes can be described as one of nature's most elaborate and highly efficient nanomachines. These cell bound multienzyme complexes orchestrate the deconstruction of cellulose and hemicellulose, two of the most abundant polymers on Earth, and thus play a major role in carbon turnover. Integration of cellulosomal components occurs via highly ordered protein:protein interactions between cohesins and dockerins, whose specificity allows the incorporation of cellulases and hemicellulases onto a molecular scaffold. Cellulosome assembly promotes the exploitation of enzyme synergism because of spatial proximity and enzyme-substrate targeting. Recent structural and functional studies have revealed how cohesin-dockerin interactions mediate both cellulosome assembly and cell-surface attachment, while retaining the spatial flexibility required to optimize the catalytic synergy within the enzyme complex. These emerging advances in our knowledge of cellulosome function are reviewed here.
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Affiliation(s)
- Carlos M G A Fontes
- CIISA, Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, 1300-477 Lisboa, Portugal.
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Yeast surface display of trifunctional minicellulosomes for simultaneous saccharification and fermentation of cellulose to ethanol. Appl Environ Microbiol 2009; 76:1251-60. [PMID: 20023102 DOI: 10.1128/aem.01687-09] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
By combining cellulase production, cellulose hydrolysis, and sugar fermentation into a single step, consolidated bioprocessing (CBP) represents a promising technology for biofuel production. Here we report engineering of Saccharomyces cerevisiae strains displaying a series of uni-, bi-, and trifunctional minicellulosomes. These minicellulosomes consist of (i) a miniscaffoldin containing a cellulose-binding domain and three cohesin modules, which was tethered to the cell surface through the yeast a-agglutinin adhesion receptor, and (ii) up to three types of cellulases, an endoglucanase, a cellobiohydrolase, and a beta-glucosidase, each bearing a C-terminal dockerin. Cell surface assembly of the minicellulosomes was dependent on expression of the miniscaffoldin, indicating that formation of the complex was dictated by the high-affinity interactions between cohesins and dockerins. Compared to the unifunctional and bifunctional minicellulosomes, the quaternary trifunctional complexes showed enhanced enzyme-enzyme synergy and enzyme proximity synergy. More importantly, surface display of the trifunctional minicellulosomes gave yeast cells the ability to simultaneously break down and ferment phosphoric acid-swollen cellulose to ethanol with a titer of approximately 1.8 g/liter. To our knowledge, this is the first report of a recombinant yeast strain capable of producing cell-associated trifunctional minicellulosomes. The strain reported here represents a useful engineering platform for developing CBP-enabling microorganisms and elucidating principles of cellulosome construction and mode of action.
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40
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Lilly M, Fierobe HP, van Zyl WH, Volschenk H. Heterologous expression of aClostridiumminicellulosome inSaccharomyces cerevisiae. FEMS Yeast Res 2009; 9:1236-49. [DOI: 10.1111/j.1567-1364.2009.00564.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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41
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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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Heterologous expression and characterization of man gene from Bacillus Subtilis in Pichia Pastoris. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/s11515-008-0002-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Chang MCY. Harnessing energy from plant biomass. Curr Opin Chem Biol 2007; 11:677-84. [PMID: 17942363 DOI: 10.1016/j.cbpa.2007.08.039] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Accepted: 08/30/2007] [Indexed: 11/24/2022]
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Abstract
Carbon metabolism in anaerobic cellulolytic bacteria has been investigated essentially in Clostridium thermocellum, Clostridium cellulolyticum, Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminococcus albus. While cellulose depolymerization into soluble sugars by various cellulases is undoubtedly the first step in bacterial metabolisation of cellulose, it is not the only one to consider. Among anaerobic cellulolytic bacteria, C. cellulolyticum has been investigated metabolically the most in the past few years. Summarizing metabolic flux analyses in continuous culture using either cellobiose (a soluble cellodextrin resulting from cellulose hydrolysis) or cellulose (an insoluble biopolymer), this review aims to stress the importance of the insoluble nature of a carbon source on bacterial metabolism. Furthermore, some general and specific traits of anaerobic cellulolytic bacteria trends, namely, the importance and benefits of (i) cellodextrins with degree of polymerization higher than 2, (ii) intracellular phosphorolytic cleavage, (iii) glycogen cycling on cell bioenergetics, and (iv) carbon overflows in regulation of carbon metabolism, as well as detrimental effects of (i) soluble sugars and (ii) acidic environment on bacterial growth. Future directions for improving bacterial cellulose degradation are discussed.
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Affiliation(s)
- Mickaël Desvaux
- INRA (Institut National de la Recherche Agronomique), Centre de Clermont-Ferrand, UR454 Unité de Microbiologie, Site de Theix, Saint-Genès Champanelle, F-63122 France.
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Shoseyov O, Shani Z, Levy I. Carbohydrate binding modules: biochemical properties and novel applications. Microbiol Mol Biol Rev 2006; 70:283-95. [PMID: 16760304 PMCID: PMC1489539 DOI: 10.1128/mmbr.00028-05] [Citation(s) in RCA: 351] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polysaccharide-degrading microorganisms express a repertoire of hydrolytic enzymes that act in synergy on plant cell wall and other natural polysaccharides to elicit the degradation of often-recalcitrant substrates. These enzymes, particularly those that hydrolyze cellulose and hemicellulose, have a complex molecular architecture comprising discrete modules which are normally joined by relatively unstructured linker sequences. This structure is typically comprised of a catalytic module and one or more carbohydrate binding modules (CBMs) that bind to the polysaccharide. CBMs, by bringing the biocatalyst into intimate and prolonged association with its substrate, allow and promote catalysis. Based on their properties, CBMs are grouped into 43 families that display substantial variation in substrate specificity, along with other properties that make them a gold mine for biotechnologists who seek natural molecular "Velcro" for diverse and unusual applications. In this article, we review recent progress in the field of CBMs and provide an up-to-date summary of the latest developments in CBM applications.
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Affiliation(s)
- Oded Shoseyov
- The Institute of Plant Science and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 76100, Israel.
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Percival Zhang YH, Himmel ME, Mielenz JR. Outlook for cellulase improvement: screening and selection strategies. Biotechnol Adv 2006; 24:452-81. [PMID: 16690241 DOI: 10.1016/j.biotechadv.2006.03.003] [Citation(s) in RCA: 663] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2006] [Revised: 03/06/2006] [Accepted: 03/11/2006] [Indexed: 10/24/2022]
Abstract
Cellulose is the most abundant renewable natural biological resource, and the production of biobased products and bioenergy from less costly renewable lignocellulosic materials is important for the sustainable development of human beings. A reduction in cellulase production cost, an improvement in cellulase performance, and an increase in sugar yields are all vital to reduce the processing costs of biorefineries. Improvements in specific cellulase activities for non-complexed cellulase mixtures can be implemented through cellulase engineering based on rational design or directed evolution for each cellulase component enzyme, as well as on the reconstitution of cellulase components. Here, we review quantitative cellulase activity assays using soluble and insoluble substrates, and focus on their advantages and limitations. Because there are no clear relationships between cellulase activities on soluble substrates and those on insoluble substrates, soluble substrates should not be used to screen or select improved cellulases for processing relevant solid substrates, such as plant cell walls. Cellulase improvement strategies based on directed evolution using screening on soluble substrates have been only moderately successful, and have primarily targeted improvement in thermal tolerance. Heterogeneity of insoluble cellulose, unclear dynamic interactions between insoluble substrate and cellulase components, and the complex competitive and/or synergic relationship among cellulase components limit rational design and/or strategies, depending on activity screening approaches. Herein, we hypothesize that continuous culture using insoluble cellulosic substrates could be a powerful selection tool for enriching beneficial cellulase mutants from the large library displayed on the cell surface.
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Affiliation(s)
- Y-H Percival Zhang
- Biological Systems Engineering Department, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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