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du Preez LL, van der Walt E, Valverde A, Rothmann C, Neser FWC, Cason ED. A metagenomic survey of the fecal microbiome of the African savanna elephant (Loxodonta africana). Anim Genet 2024; 55:621-643. [PMID: 38923598 DOI: 10.1111/age.13458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
The African savanna elephant (Loxodonta africana) is the largest terrestrial animal on Earth and is found primarily in Southern and Eastern Africa. It is a hindgut, colonic fermenter and subsists on a diet of raw plant materials found in its grazing area. In this study the bacterial, archaeal and fungal populations of seven African savanna elephant fecal metagenomes were first characterized using amplicon sequencing. On the genus level it was observed that the p-1088-a5 gut group in the bacteriome, Methanocorpusulum and Methanobrevibacter in the archaeome and Alternaria, Aurobasidium, Didymella and Preussia in the mycome, predominated. Subsequently, metagenomic shotgun sequencing was employed to identify possible functional pathways and carbohydrate-active enzymes (CAZymes). Carbohydrate catabolic pathways represented the main degradation pathways, and the fecal metagenome was enriched in the glycohydroside (GH) class of CAZymes. Additionally, the top GH families identified - GH43, GH2, GH13 and GH3 - are known to be associated with cellulytic, hemicellulytic and pectolytic activities. Finally, the CAZymes families identified in the African savanna elephant were compared with those found in the Asian elephant and it was demonstrated that there is a unique repository of CAZymes that could be leveraged in the biotechnological context such as the degradation of lignocellulose for the production of second-generation biofuels and energy.
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Affiliation(s)
- Louis Lategan du Preez
- Department of Animal Science, University of the Free State, Bloemfontein, Free State, South Africa
| | - Elzette van der Walt
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, Free State, South Africa
| | - Angel Valverde
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, Free State, South Africa
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas, Salamanca, Spain
| | - Christopher Rothmann
- Department of Animal Science, University of the Free State, Bloemfontein, Free State, South Africa
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, Free State, South Africa
| | | | - Errol Duncan Cason
- Department of Animal Science, University of the Free State, Bloemfontein, Free State, South Africa
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2
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Zajki-Zechmeister K, Eibinger M, Kaira GS, Nidetzky B. Mechanochemical Coupling of Catalysis and Motion in a Cellulose-Degrading Multienzyme Nanomachine. ACS Catal 2024; 14:2656-2663. [PMID: 38384941 PMCID: PMC10877591 DOI: 10.1021/acscatal.3c05653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/13/2024] [Accepted: 01/24/2024] [Indexed: 02/23/2024]
Abstract
The cellulosome is a megadalton-size protein complex that functions as a biological nanomachine of cellulosic fiber degradation. We show that the cellulosome behaves as a Brownian ratchet that rectifies protein motions on the cellulose surface into a propulsion mechanism by coupling to the hydrolysis of cellulose chains. Movement on cellulose fibrils is unidirectional and results from "macromolecular crawl" composed of dynamic switches between elongated and compact spatial arrangements of enzyme subunits. Deletion of the main exocellulase Cel48S eliminates conformational bias for aligning the subunits to the long fibril axis, which we reveal as crucial for optimum coupling between directional movement and substrate degradation. Implications of the cellulosome acting as a mechanochemical motor suggest a distinct mechanism of enzymatic machinery in the deconstruction of cellulose assemblies.
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Affiliation(s)
- Krisztina Zajki-Zechmeister
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, Graz 8010, Austria
| | - Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, Graz 8010, Austria
| | - Gaurav Singh Kaira
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, Graz 8010, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, Graz 8010, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, Graz 8010, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, Graz 8010, Austria
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3
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Ichikawa S, Ito D, Asaoka S, Abe R, Katsuo N, Ito T, Ito D, Karita S. The expression of alternative sigma-I7 factor induces the transcription of cellulosomal genes in the cellulolytic bacterium Clostridium thermocellum. Enzyme Microb Technol 2022; 156:110002. [DOI: 10.1016/j.enzmictec.2022.110002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/12/2022] [Accepted: 01/31/2022] [Indexed: 01/07/2023]
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4
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Karki S, Gohain MB, Yadav D, Ingole PG. Nanocomposite and bio-nanocomposite polymeric materials/membranes development in energy and medical sector: A review. Int J Biol Macromol 2021; 193:2121-2139. [PMID: 34780890 DOI: 10.1016/j.ijbiomac.2021.11.044] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 01/13/2023]
Abstract
Nanocomposite and bio-nanocomposite polymer materials/membranes have fascinated prominent attention in the energy as well as the medical sector. Their composites make them appropriate choices for various applications in the medical, energy and industrial sectors. Composite materials are subject of interest in the polymer industry. Different kinds of fillers, such as cellulose-based fillers, carbon black, clay nanomaterials, glass fibers, ceramic nanomaterial, carbon quantum dots, talc and many others have been incorporated into polymers to improve the quality of the final product. These results are dependent on a variety of factors; however, nanoparticle dispersion and distribution are major obstacles to fully using nanocomposites/bio-nanocomposites materials/membranes in various applications. This review examines the various nanocomposite and bio-nanocomposite materials applications in the energy and medical sector. The review also covers the variety of ways for increasing nanocomposite and bio-nanocomposite materials features, each with its own set of applications. Recent researches on composite materials have shown that polymeric nanocomposites and bio-nanocomposites are promising materials that have been intensively explored for many applications that include electronics, environmental remediation, energy, sensing (biosensor) and energy storage devices among other applications. In this review, we studied various nanocomposite and bio-nanocomposite materials, their controlling parameters to develop the product and examine their features and applications in the fields of energy and the medical sector.
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Affiliation(s)
- Sachin Karki
- Chemical Engineering Group, Engineering Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam 785006, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Moucham Borpatra Gohain
- Chemical Engineering Group, Engineering Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam 785006, India
| | - Diksha Yadav
- Chemical Engineering Group, Engineering Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam 785006, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Pravin G Ingole
- Chemical Engineering Group, Engineering Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam 785006, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
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5
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Zajki-Zechmeister K, Kaira GS, Eibinger M, Seelich K, Nidetzky B. Processive Enzymes Kept on a Leash: How Cellulase Activity in Multienzyme Complexes Directs Nanoscale Deconstruction of Cellulose. ACS Catal 2021; 11:13530-13542. [PMID: 34777910 PMCID: PMC8576811 DOI: 10.1021/acscatal.1c03465] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/11/2021] [Indexed: 12/15/2022]
Abstract
Biological deconstruction of polymer materials gains efficiency from the spatiotemporally coordinated action of enzymes with synergetic function in polymer chain depolymerization. To perpetuate enzyme synergy on a solid substrate undergoing deconstruction, the overall attack must alternate between focusing the individual enzymes locally and dissipating them again to other surface sites. Natural cellulases working as multienzyme complexes assembled on a scaffold protein (the cellulosome) maximize the effect of local concentration yet restrain the dispersion of individual enzymes. Here, with evidence from real-time atomic force microscopy to track nanoscale deconstruction of single cellulose fibers, we show that the cellulosome forces the fiber degradation into the transversal direction, to produce smaller fragments from multiple local attacks ("cuts"). Noncomplexed enzymes, as in fungal cellulases or obtained by dissociating the cellulosome, release the confining force so that fiber degradation proceeds laterally, observed as directed ablation of surface fibrils and leading to whole fiber "thinning". Processive cellulases that are enabled to freely disperse evoke the lateral degradation and determine its efficiency. Our results suggest that among natural cellulases, the dispersed enzymes are more generally and globally effective in depolymerization, while the cellulosome represents a specialized, fiber-fragmenting machinery.
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Affiliation(s)
- Krisztina Zajki-Zechmeister
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Gaurav Singh Kaira
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| | - Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Klara Seelich
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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6
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Lee HJ, Kang TG, Kim YW, Lee HS, Kim SK. Functional expression and extracellular secretion of Clostridium thermocellum Cel48S cellulase in Escherichia coli via the signal recognition particle-dependent translocation pathway. Enzyme Microb Technol 2021; 151:109918. [PMID: 34649693 DOI: 10.1016/j.enzmictec.2021.109918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/12/2021] [Accepted: 09/12/2021] [Indexed: 11/17/2022]
Abstract
As the only glycoside hydrolase family 48 member in Clostridium thermocellum, the exoglucanase Cel48S plays a crucial role in the extremely high activity of the cellulosome against crystalline cellulose. Although the importance of Cel48S in the hydrolysis of crystalline cellulose has been widely accepted, an efficient production system has not yet been established because Cel48S is usually expressed in Escherichia coli within inactive inclusion bodies. For unstable proteins like Cel48S, translocation across the inner membrane can be more advantageous than cytoplasmic production due to the presence of folding modulators in the periplasm and the absence of cytoplasmic proteases. In this study, we evaluated whether the production of Cel48S in the periplasmic space of E. coli could enhance its functional expression. To do so, we attached the PelB signal peptide, which mediates post-translational secretion, to the N-terminal end of Cel48S (P-Cel48S). The PelB signal peptide allowed catalytically active Cel48S to be successfully produced in the culture medium. In addition, we investigated the role of an alternative co-translational pathway on the extracellular production of Cel48S, finding that co-translational secretion yielded a specific activity of recombinant Cel48S of 135.1 ± 10.0 U/mg cell in the culture medium, which was 2.2 times higher than that associated with P-Cel48S expression. Therefore, we believe that our approach has potential applications for the cost-effective conversion of lignocellulosic biomass and the industrial production of other unstable proteins.
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Affiliation(s)
- Hyun-Jae Lee
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, 17546, Republic of Korea
| | - Tae-Gu Kang
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, 17546, Republic of Korea
| | - Young-Woo Kim
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, 17546, Republic of Korea
| | - Hee-Seok Lee
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, 17546, Republic of Korea.
| | - Sun-Ki Kim
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, 17546, Republic of Korea.
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7
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Enhanced Activity by Genetic Complementarity: Heterologous Secretion of Clostridial Cellulases by Bacillus licheniformis and Bacillus velezensis. Molecules 2021; 26:molecules26185625. [PMID: 34577096 PMCID: PMC8468253 DOI: 10.3390/molecules26185625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 12/25/2022] Open
Abstract
To adapt to various ecological niches, the members of genus Bacillus display a wide spectrum of glycoside hydrolases (GH) responsible for the hydrolysis of cellulose and lignocellulose. Being abundant and renewable, cellulose-containing plant biomass may be applied as a substrate in second-generation biotechnologies for the production of platform chemicals. The present study aims to enhance the natural cellulase activity of two promising 2,3-butanediol (2,3-BD) producers, Bacillus licheniformis 24 and B. velezensis 5RB, by cloning and heterologous expression of cel8A and cel48S genes of Acetivibrio thermocellus. In B. licheniformis, the endocellulase Cel8A (GH8) was cloned to supplement the action of CelA (GH9), while in B. velezensis, the cellobiohydrolase Cel48S (GH48) successfully complemented the activity of endo-cellulase EglS (GH5). The expression of the natural and heterologous cellulase genes in both hosts was demonstrated by reverse-transcription PCR. The secretion of clostridial cellulases was additionally enhanced by enzyme fusion to the subtilisin-like signal peptide, reaching a significant increase in the cellulase activity of the cell-free supernatants. The results presented are the first to reveal the possibility of genetic complementation for enhancement of cellulase activity in bacilli, thus opening the prospect for genetic improvement of strains with an important biotechnological application.
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8
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Clostridium thermocellum as a Promising Source of Genetic Material for Designer Cellulosomes: An Overview. Catalysts 2021. [DOI: 10.3390/catal11080996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Plant biomass-based biofuels have gradually substituted for conventional energy sources thanks to their obvious advantages, such as renewability, huge quantity, wide availability, economic feasibility, and sustainability. However, to make use of the large amount of carbon sources stored in the plant cell wall, robust cellulolytic microorganisms are highly demanded to efficiently disintegrate the recalcitrant intertwined cellulose fibers to release fermentable sugars for microbial conversion. The Gram-positive, thermophilic, cellulolytic bacterium Clostridium thermocellum possesses a cellulolytic multienzyme complex termed the cellulosome, which has been widely considered to be nature’s finest cellulolytic machinery, fascinating scientists as an auspicious source of saccharolytic enzymes for biomass-based biofuel production. Owing to the supra-modular characteristics of the C. thermocellum cellulosome architecture, the cellulosomal components, including cohesin, dockerin, scaffoldin protein, and the plentiful cellulolytic and hemicellulolytic enzymes have been widely used for constructing artificial cellulosomes for basic studies and industrial applications. In addition, as the well-known microbial workhorses are naïve to biomass deconstruction, several research groups have sought to transform them from non-cellulolytic microbes into consolidated bioprocessing-enabling microbes. This review aims to update and discuss the current progress in these mentioned issues, point out their limitations, and suggest some future directions.
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9
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Araújo EA, Dias AHS, Kadowaki MAS, Piyadov V, Pellegrini VOA, Urio MB, Ramos LP, Skaf MS, Polikarpov I. Impact of cellulose properties on enzymatic degradation by bacterial GH48 enzymes: Structural and mechanistic insights from processive Bacillus licheniformis Cel48B cellulase. Carbohydr Polym 2021; 264:118059. [PMID: 33910709 DOI: 10.1016/j.carbpol.2021.118059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 11/29/2022]
Abstract
Processive cellulases are highly efficient molecular engines involved in the cellulose breakdown process. However, the mechanism that processive bacterial enzymes utilize to recruit and retain cellulose strands in the catalytic site remains poorly understood. Here, integrated enzymatic assays, protein crystallography and computational approaches were combined to study the enzymatic properties of the processive BlCel48B cellulase from Bacillus licheniformis. Hydrolytic efficiency, substrate binding affinity, cleavage patterns, and the apparent processivity of bacterial BlCel48B are significantly impacted by the cellulose size and its surface morphology. BlCel48B crystallographic structure was solved with ligands spanning -5 to -2 and +1 to +2 subsites. Statistical coupling analysis and molecular dynamics show that co-evolved residues on active site are critical for stabilizing ligands in the catalytic tunnel. Our results provide mechanistic insights into BlCel48B molecular-level determinants of activity, substrate binding, and processivity on insoluble cellulose, thus shedding light on structure-activity correlations of GH48 family members in general.
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Affiliation(s)
- Evandro A Araújo
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil; Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials, Campinas 13083-970, São Paulo, Brazil
| | - Artur Hermano Sampaio Dias
- Institute of Chemistry and Center for Computer in Engineering and Sciences, University of Campinas (UNICAMP), Campinas 13084-862, São Paulo, Brazil
| | - Marco A S Kadowaki
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil
| | - Vasily Piyadov
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil
| | - Vanessa O A Pellegrini
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil
| | - Mateus B Urio
- Graduate Programs in Bioenergy, Chemistry and Chemical Engineering, Federal University of Paraná (UFPR), Curitiba 81531-980, Paraná, Brazil
| | - Luiz P Ramos
- Graduate Programs in Bioenergy, Chemistry and Chemical Engineering, Federal University of Paraná (UFPR), Curitiba 81531-980, Paraná, Brazil
| | - Munir S Skaf
- Institute of Chemistry and Center for Computer in Engineering and Sciences, University of Campinas (UNICAMP), Campinas 13084-862, São Paulo, Brazil
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil.
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10
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Eibinger M, Ganner T, Plank H, Nidetzky B. A Biological Nanomachine at Work: Watching the Cellulosome Degrade Crystalline Cellulose. ACS CENTRAL SCIENCE 2020; 6:739-746. [PMID: 32490190 PMCID: PMC7256933 DOI: 10.1021/acscentsci.0c00050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Indexed: 05/14/2023]
Abstract
The cellulosome is a supramolecular multienzymatic protein complex that functions as a biological nanomachine of cellulosic biomass degradation. How the megadalton-size cellulosome adapts to a solid substrate is central to its mechanism of action and is also key for its efficient use in bioconversion applications. We report time-lapse visualization of crystalline cellulose degradation by individual cellulosomes from Clostridium thermocellum by atomic force microscopy. Upon binding to cellulose, the cellulosomes switch to elongated, even filamentous shapes and morph these dynamically at below 1 min time scale according to requirements of the substrate surface under attack. Compared with noncomplexed cellulases that peel off material while sliding along crystalline cellulose surfaces, the cellulosomes remain bound locally for minutes and remove the material lying underneath. The consequent roughening up of the surface leads to an efficient deconstruction of cellulose nanocrystals both from the ends and through fissions within. Distinct modes of cellulose nanocrystal deconstruction by nature's major cellulase systems are thus revealed.
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Affiliation(s)
- Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Thomas Ganner
- Institute
for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Harald Plank
- Institute
for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
- Graz
Centre of Electron Microscopy, Steyrergasse 17, A-8010 Graz, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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11
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Consolidated bio-saccharification: Leading lignocellulose bioconversion into the real world. Biotechnol Adv 2020; 40:107535. [DOI: 10.1016/j.biotechadv.2020.107535] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/03/2020] [Accepted: 02/12/2020] [Indexed: 11/22/2022]
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12
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Ganguly J, Martin‐Pascual M, van Kranenburg R. CRISPR interference (CRISPRi) as transcriptional repression tool for Hungateiclostridium thermocellum DSM 1313. Microb Biotechnol 2020; 13:339-349. [PMID: 31802632 PMCID: PMC7017836 DOI: 10.1111/1751-7915.13516] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/06/2019] [Accepted: 11/12/2019] [Indexed: 01/13/2023] Open
Abstract
Hungateiclostridium thermocellum DSM 1313 has biotechnological potential as a whole-cell biocatalyst for ethanol production using lignocellulosic renewable sources. The full exploitation of H. thermocellum has been hampered due to the lack of simple and high-throughput genome engineering tools. Recently in our research group, a thermophilic bacterial CRISPR-Cas9-based system has been developed as a transcriptional suppression tool for regulation of gene expression. We applied ThermoCas9-based CRISPR interference (CRISPRi) to repress the H. thermocellum central metabolic lactate dehydrogenase (ldh) and phosphotransacetylase (pta) genes. The effects of repression on target genes were studied based on transcriptional expression and product formation. Single-guide RNA (sgRNA) under the control of native intergenic 16S/23S rRNA promoter from H. thermocellum directing the ThermodCas9 to the promoter region of both pta and ldh silencing transformants reduced expression up to 67% and 62% respectively. This resulted in 24% and 17% decrease in lactate and acetate production, correspondingly. Hence, the CRISPRi approach for H. thermocellum to downregulate metabolic genes can be used for remodelling of metabolic pathways without the requisite for genome engineering. These data established for the first time the feasibility of employing CRISPRi-mediated gene repression of metabolic genes in H. thermocellum DSM 1313.
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Affiliation(s)
| | - Maria Martin‐Pascual
- Laboratory of MicrobiologyWageningen UniversityStippeneng 46708WE WageningenThe Netherlands
| | - Richard van Kranenburg
- CorbionArkelsedijk 464206AC GorinchemThe Netherlands
- Laboratory of MicrobiologyWageningen UniversityStippeneng 46708WE WageningenThe Netherlands
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13
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McConnell SA, Cannon KA, Morgan C, McAllister R, Amer BR, Clubb RT, Yeates TO. Designed Protein Cages as Scaffolds for Building Multienzyme Materials. ACS Synth Biol 2020; 9:381-391. [PMID: 31922719 DOI: 10.1021/acssynbio.9b00407] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The functions of enzymes can be strongly affected by their higher-order spatial arrangements. In this study we combine multiple new technologies-designer protein cages and sortase-based enzymatic attachments between proteins-as a novel platform for organizing multiple enzymes (of one or more types) in specified configurations. As a scaffold we employ a previously characterized 24-subunit designed protein cage whose termini are outwardly exposed for attachment. As a first-use case, we test the attachment of two cellulase enzymes known to act synergistically in cellulose degradation. We show that, after endowing the termini of the cage subunits with a short "sort-tag" sequence (LPXTG) and the opposing termini of the cellulase enzymes with a short polyglycine sequence tag, addition of sortase covalently attaches the enzymes to the cage with good reactivity and high copy number. The doubly modified cages show enhanced activity in a cellulose degradation assay compared to enzymes in solution, and compared to a combination of singly modified cages. These new engineering strategies could be broadly useful in the development of enzymatic material and synthetic biology applications.
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Affiliation(s)
- Scott A. McConnell
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Kevin A. Cannon
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Christian Morgan
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095, United States
| | - Rachel McAllister
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Brendan R. Amer
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Robert T. Clubb
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Todd O. Yeates
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
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14
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Chu Y, Hao Z, Wang K, Tu T, Huang H, Wang Y, Bai YG, Wang Y, Luo H, Yao B, Su X. The GH10 and GH48 dual-functional catalytic domains from a multimodular glycoside hydrolase synergize in hydrolyzing both cellulose and xylan. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:279. [PMID: 31827607 PMCID: PMC6892212 DOI: 10.1186/s13068-019-1617-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/23/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Regarding plant cell wall polysaccharides degradation, multimodular glycoside hydrolases (GHs) with two catalytic domains separated by one or multiple carbohydrate-binding domains are rare in nature. This special mode of domain organization endows the Caldicellulosiruptor bescii CelA (GH9-CBM3c-CBM3b-CBM3b-GH48) remarkably high efficiency in hydrolyzing cellulose. CbXyn10C/Cel48B from the same bacterium is also such an enzyme which has, however, evolved to target both xylan and cellulose. Intriguingly, the GH10 endoxylanase and GH48 cellobiohydrolase domains are both dual functional, raising the question if they can act synergistically in hydrolyzing cellulose and xylan, the two major components of plant cell wall. RESULTS In this study, we discovered that CbXyn10C and CbCel48B, which stood for the N- and C-terminal catalytic domains, respectively, cooperatively released much more cellobiose and cellotriose from cellulose. In addition, they displayed intramolecular synergy but only at the early stage of xylan hydrolysis by generating higher amounts of xylooligosaccharides including xylotriose, xylotetraose, and xylobiose. When complex lignocellulose corn straw was used as the substrate, the synergy was found only for cellulose but not xylan hydrolysis. CONCLUSION This is the first report to reveal the synergy between a GH10 and a GH48 domain. The synergy discovered in this study is helpful for understanding how C. bescii captures energy from these recalcitrant plant cell wall polysaccharides. The insight also sheds light on designing robust and multi-functional enzymes for plant cell wall polysaccharides degradation.
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Affiliation(s)
- Yindi Chu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, 5# Dong Dan San Tiao, Beijing, 100005 China
| | - Zhenzhen Hao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Kaikai Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Tao Tu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Huoqing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Yuan Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Ying Guo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Yaru Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
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15
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Kumar S, Sharma S, Thakur S, Mishra T, Negi P, Mishra S, Hesham AEL, Rastegari AA, Yadav N, Yadav AN. Bioprospecting of Microbes for Biohydrogen Production: Current Status and Future Challenges. BIOPROCESSING FOR BIOMOLECULES PRODUCTION 2019:443-471. [DOI: 10.1002/9781119434436.ch22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Affiliation(s)
| | | | | | | | | | | | - Abd El-Latif Hesham
- Genetics Department, Faculty of Agriculture; Assiut University; Assiut Egypt
| | - Ali A. Rastegari
- Department of Molecular and Cell Biochemistry, Falavarjan Branch; Islamic Azad University; Isfahan Iran
| | - Neelam Yadav
- Gopi Nath P.G. College; Veer Bahadur Singh Purvanchal University; India
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16
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Liu S, Liu YJ, Feng Y, Li B, Cui Q. Construction of consolidated bio-saccharification biocatalyst and process optimization for highly efficient lignocellulose solubilization. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:35. [PMID: 30820245 PMCID: PMC6378752 DOI: 10.1186/s13068-019-1374-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/07/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The industrial conversion of biomass to high-value biofuels and biochemical is mainly restricted by lignocellulose solubilization. Consolidated bio-saccharification (CBS) is considered a promising process for lignocellulose solubilization depending on whole-cell biocatalysts that simultaneously perform effective cellulase production and hydrolysis. However, it usually takes a long time to reach a high saccharification level using the current CBS biocatalyst and process. RESULTS To promote the saccharification efficiency and reduce the cost, a Clostridium thermocellum recombinant strain ∆pyrF::KBm was constructed as a new CBS biocatalyst in this study. The key CBS factors, including the medium, inoculum size and cultivation, and substrate load, were investigated and optimized. The saccharification process was also stimulated by adding free hemicellulases, suggesting the need to further enhance hemicellulase activity of the whole-cell catalyst. Under the optimal conditions, the CBS process was shortened by 50% with pretreated wheat straw as the substrate. The sugar yield reached 0.795 g/g and the saccharification level was 89.3%. CONCLUSIONS This work provided a new biocatalyst and an optimized process of CBS and confirmed that CBS is a feasible strategy for cost-efficient solubilization of lignocellulose, which will greatly promote the industrial utilization of lignocellulosic biomass.
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Affiliation(s)
- Shiyue Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
| | - Bin Li
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
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17
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Xiong W, Lo J, Chou KJ, Wu C, Magnusson L, Dong T, Maness P. Isotope-Assisted Metabolite Analysis Sheds Light on Central Carbon Metabolism of a Model Cellulolytic Bacterium Clostridium thermocellum. Front Microbiol 2018; 9:1947. [PMID: 30190711 PMCID: PMC6115520 DOI: 10.3389/fmicb.2018.01947] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/31/2018] [Indexed: 01/01/2023] Open
Abstract
Cellulolytic bacteria have the potential to perform lignocellulose hydrolysis and fermentation simultaneously. The metabolic pathways of these bacteria, therefore, require more comprehensive and quantitative understanding. Using isotope tracer, gas chromatography-mass spectrometry, and metabolic flux modeling, we decipher the metabolic network of Clostridium thermocellum, a model cellulolytic bacterium which represents as an attractive platform for conversion of lignocellulose to dedicated products. We uncover that the Embden-Meyerhof-Parnas (EMP) pathway is the predominant glycolytic route whereas the Entner-Doudoroff (ED) pathway and oxidative pentose phosphate pathway are inactive. We also observe that C. thermocellum's TCA cycle is initiated by both Si- and Re-citrate synthase, and it is disconnected between 2-oxoglutarate and oxaloacetate in the oxidative direction; C. thermocellum uses a citramalate shunt to synthesize isoleucine; and both the one-carbon pathway and the malate shunt are highly active in this bacterium. To gain a quantitative understanding, we further formulate a fluxome map to quantify the metabolic fluxes through central metabolic pathways. This work represents the first global in vivo investigation of the principal carbon metabolism of C. thermocellum. Our results elucidate the unique structure of metabolic network in this cellulolytic bacterium and demonstrate the capability of isotope-assisted metabolite studies in understanding microbial metabolism of industrial interests.
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Affiliation(s)
- Wei Xiong
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Jonathan Lo
- National Renewable Energy Laboratory, Golden, CO, United States
| | | | - Chao Wu
- National Renewable Energy Laboratory, Golden, CO, United States
| | | | - Tao Dong
- National Renewable Energy Laboratory, Golden, CO, United States
| | - PinChing Maness
- National Renewable Energy Laboratory, Golden, CO, United States
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18
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Chen L, Ge X. Correlation Between Size and Activity Enhancement of Recombinantly Assembled Cellulosomes. Appl Biochem Biotechnol 2018; 186:937-948. [PMID: 29797297 DOI: 10.1007/s12010-018-2786-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/15/2018] [Indexed: 11/25/2022]
Abstract
As multienzyme complexes, cellulosomes hydrolyze cellulosic biomass with high efficiency, which is believed to be attributed to either one or both factors: (1) synergy among the catalytic and substrate-binding entities and (2) the large size of cellulosome complexes. Although the former factor has been extensively documented, the correlation between size and specific activity of cellulosomes is still elusive to date. In this study, primary and secondary scaffoldins with 1, 3, or 5 copies of type I/II cohesin domains were recombinantly synthesized and various cellulosomes carrying 1, 3, 5, 9, 15, or 25 molecules of cellulase mixtures of family 5, 9, and 48 glycoside hydrolases were assembled. In addition, the assembled complex was annexed to cellulose with the aid of a family 3a carbohydrate-binding module (CBM3a). Measuring cellulolytic hydrolysis activities of assembled cellulosomes on crystalline Avicel revealed that higher degree of cellulosome complexity resulted in more efficient cellulose hydrolysis with plateaued synergic effects after the cellulosome size reaches certain degree.
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Affiliation(s)
- Long Chen
- Department of Chemical and Environmental Engineering, University of California Riverside, 900 University Ave, Riverside, CA, 92512, USA
| | - Xin Ge
- Department of Chemical and Environmental Engineering, University of California Riverside, 900 University Ave, Riverside, CA, 92512, USA.
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19
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Xiong W, Reyes LH, Michener WE, Maness P, Chou KJ. Engineering cellulolytic bacterium
Clostridium thermocellum
to co‐ferment cellulose‐ and hemicellulose‐derived sugars simultaneously. Biotechnol Bioeng 2018. [DOI: 10.1002/bit.26590] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Wei Xiong
- National Renewable Energy Laboratory BioSciences Center GoldenColorado
| | - Luis H. Reyes
- National Renewable Energy Laboratory BioSciences Center GoldenColorado
- Product and Process Design Group, Department of Chemical Engineering Universidad de los Andes Bogotá D.C. Colombia
| | - William E. Michener
- National Renewable Energy Laboratory National Bioenergy Center GoldenColorado
| | - Pin‐Ching Maness
- National Renewable Energy Laboratory BioSciences Center GoldenColorado
| | - Katherine J. Chou
- National Renewable Energy Laboratory BioSciences Center GoldenColorado
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20
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Genetic diversity detection and gene discovery of novel glycoside hydrolase family 48 from soil environmental genomic DNA. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1327-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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21
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Lee CR, Chi WJ, Lim JH, Dhakshnamoorthy V, Hong SK. Expression and characterization of the processive exo-β-1,4-cellobiohydrolase SCO6546 from Streptomyces coelicolor
A(3). J Basic Microbiol 2018; 58:310-321. [DOI: 10.1002/jobm.201700436] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 11/13/2017] [Accepted: 11/19/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Chang-Ro Lee
- Department of Bioscience and Bioinformatics; Yongin, Gyeoggido Korea
| | - Won-Jae Chi
- Biological and Genetic Resource Assessment Division; National Institute of Biological Resource; Incheon Korea
| | - Ju-Hyeon Lim
- Department of Bioscience and Bioinformatics; Yongin, Gyeoggido Korea
| | | | - Soon-Kwang Hong
- Department of Bioscience and Bioinformatics; Yongin, Gyeoggido Korea
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22
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Wang Y, Okugawa K, Kunitake E, Sakka M, Kimura T, Sakka K. Development of an efficient host-vector system of Ruminiclostridium josui. J Basic Microbiol 2018; 58:448-458. [PMID: 29388680 DOI: 10.1002/jobm.201700620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/23/2017] [Accepted: 12/30/2017] [Indexed: 01/22/2023]
Abstract
Although Ruminiclostridium josui (formerly Clostridium josui), a strictly anaerobic mesophilic cellulolytic bacterium, is a promising candidate for biomass utilization via consolidated bioprocessing, its host-vector system has not yet been established. The existence of a restriction and modification system is a significant barrier to the transformation of R. josui. Here, we partially purified restriction endonuclease RjoI from R. josui cell extract using column chromatography. Further characterization showed that RjoI is an isoschizomer of DpnI, recognizing the sequence 5'-Gmet ATC-3', where the A nucleotide is Dam-methylated. RjoI cleaved the recognition sequence between the A and T nucleotides, producing blunt ends. We then successfully introduced plasmids prepared from Escherichia coli C2925 (dam- /dcm- ) into R. josui by electroporation. The highest transformation efficiency of 6.6 × 103 transformants/μg of DNA was obtained using a square-wave pulse (750 V, 1 ms). When the R. josui cel48A gene, devoid of the dockerin-encoding region, cloned into newly developed plasmid pKKM801 was introduced into R. josui, a truncated form of RjCel48A, RjCel48AΔdoc, was detected in the culture supernatant but not in the intracellular fraction. This is the first report on the establishment of fundamental technology for molecular breeding of R. josui.
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Affiliation(s)
- Yayun Wang
- Graduate School of Bioresources, Mie University, Mie, Japan
| | - Kei Okugawa
- Graduate School of Bioresources, Mie University, Mie, Japan
| | - Emi Kunitake
- Graduate School of Bioresources, Mie University, Mie, Japan
| | - Makiko Sakka
- Graduate School of Bioresources, Mie University, Mie, Japan
| | - Tetsuya Kimura
- Graduate School of Bioresources, Mie University, Mie, Japan
| | - Kazuo Sakka
- Graduate School of Bioresources, Mie University, Mie, Japan
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23
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Liu YJ, Liu S, Dong S, Li R, Feng Y, Cui Q. Determination of the native features of the exoglucanase Cel48S from Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:6. [PMID: 29344087 PMCID: PMC5766998 DOI: 10.1186/s13068-017-1009-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/29/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Clostridium thermocellum is considered one of the most efficient natural cellulose degraders because of its cellulosomal system. As the major exoglucanase of cellulosome in C. thermocellum, Cel48S plays key roles and influences the activity and features of cellulosome to a great extent. Thus, it is of great importance to reveal the enzymatic features of Cel48S. However, Cel48S has not been well performed due to difficulties in purifying either recombinant or native Cel48S proteins. RESULTS We observed that the soluble fraction of the catalytic domain of Cel48S (Cel48S_CD) obtained by heterologous expression in Escherichia coli and denaturation-refolding treatment contained a large portion of incorrectly folded proteins with low activity. Using a previously developed seamless genome-editing system for C. thermocellum, we achieved direct purification of Cel48S_CD from the culture supernatant of C. thermocellum DSM1313 by inserting a sequence encoding 12 successive histidine residues and a TAA stop codon immediately behind the GH domain of Cel48S. Based on the fully active protein, biochemical and structural analyses were performed to reveal its innate characteristics. The native Cel48S_CD showed high activity of 117.61 ± 2.98 U/mg and apparent substrate preference for crystalline cellulose under the assay conditions. The crystal structure of the native GH48 protein revealed substrate-coupled changes in the residue conformation, indicating induced-fit effects between Cel48S_CD and substrates. Mass spectrum and crystal structural analyses suggested no significant posttranslational modification in the native Cel48S_CD protein. CONCLUSION Our results confirmed that the high activity and substrate specificity of Cel48S_CD from C. thermocellum were consistent with its importance in the cellulosome. The structure of the native Cel48S_CD protein revealed evidence of conformational changes during substrate binding. In addition, our study provided a reliable method for in situ purification of cellulosomal and other secretive proteins from C. thermocellum.
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Affiliation(s)
- Ya-Jun Liu
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Shiyue Liu
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Sheng Dong
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Renmin Li
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
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24
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Li M, Liu Z, Wang S, Calatayud DG, Zhu WH, James TD, Wang L, Mao B, Xiao HN. Fluorescence detection and removal of copper from water using a biobased and biodegradable 2D soft material. Chem Commun (Camb) 2018; 54:184-187. [DOI: 10.1039/c7cc08035b] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We have developed a green and robust fluorogenic (λex = 410 nm, λem = 510 nm) cellulose membrane using graphene oxide (GO) as a construct for simultaneous copper ion recognition and filtration at environmentally relevant levels.
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Affiliation(s)
- Meng Li
- Department of Environmental Science and Technology
- North China Electric Power University
- Baoding 071003
- P. R. China
| | - Zhijiang Liu
- Department of Environmental Science and Technology
- North China Electric Power University
- Baoding 071003
- P. R. China
| | - Shuwen Wang
- Shanghai Key Laboratory of Functional Materials Chemistry
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals
- East China University of Science & Technology
- Shanghai 200237
- P. R. China
| | - David G. Calatayud
- Department of Electroceramics
- Instituto de Ceramica y Vidrio CSIC
- Madrid
- Spain
| | - Wei-Hong Zhu
- Shanghai Key Laboratory of Functional Materials Chemistry
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals
- East China University of Science & Technology
- Shanghai 200237
- P. R. China
| | | | - Lidong Wang
- Department of Environmental Science and Technology
- North China Electric Power University
- Baoding 071003
- P. R. China
| | - Boyang Mao
- National Graphene Institute
- The University of Manchester
- Manchester
- UK
- School of Physics and Astronomy
| | - Hui-Ning Xiao
- Department of Environmental Science and Technology
- North China Electric Power University
- Baoding 071003
- P. R. China
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25
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Zhang J, Liu S, Li R, Hong W, Xiao Y, Feng Y, Cui Q, Liu YJ. Efficient whole-cell-catalyzing cellulose saccharification using engineered Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:124. [PMID: 28507596 PMCID: PMC5429504 DOI: 10.1186/s13068-017-0796-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/19/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND Cost-efficient saccharification is one of the main bottlenecks for industrial lignocellulose conversion. Clostridium thermocellum naturally degrades lignocellulose efficiently using the cellulosome, a multiprotein supermolecular complex, and thus can be potentially used as a low-cost catalyst for lignocellulose saccharification. The industrial use of C. thermocellum is restrained due largely to the inhibition of the hydrolysate cellobiose to its cellulosome. Although the supplementation of beta-glucosidase may solve the problem, the production of the enzymes greatly complicates the process and may also increase the cost of saccharification. RESULTS To conquer the feedback inhibition and establish an efficient whole-cell catalyst for highly efficient cellulose saccharification, we constructed a recombinant strain of C. thermocellum ∆pyrF::CaBglA which produced a secretory exoglucanase CelS-bearing heterologous BGL using a newly developed seamless genome editing system. Without the extra addition of enzymes, the relative saccharification level of ∆pyrF::CaBglA was stimulated by over twofolds compared to its parent strain ∆pyrF through a two-stage saccharification process with 100 g/L Avicel as the carbon source. The production of reducing sugars and the relative saccharification level were further enhanced to 490 mM and 79.4%, respectively, with increased cell density. CONCLUSIONS The high cellulose-degrading ability and sugar productivity suggested that the whole-cell-catalysis strategy for cellulose saccharification is promising, and the C. thermocellum strain ∆pyrF::CaBglA could be potentially used as an efficient whole-cell catalyst for industrial cellulose saccharification.
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Affiliation(s)
- Jie Zhang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Shiyue Liu
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Renmin Li
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Wei Hong
- Key Laboratory of Endemic and Ethnic Diseases (Guizhou Medical University), Ministry of Education, Guiyang, 550000 People’s Republic of China
| | - Yan Xiao
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Ya-Jun Liu
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
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26
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Hon S, Lanahan AA, Tian L, Giannone RJ, Hettich RL, Olson DG, Lynd LR. Development of a plasmid-based expression system in Clostridium thermocellum and its use to screen heterologous expression of bifunctional alcohol dehydrogenases ( adhEs). Metab Eng Commun 2016; 3:120-129. [PMID: 29142822 PMCID: PMC5678826 DOI: 10.1016/j.meteno.2016.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 03/15/2016] [Accepted: 04/21/2016] [Indexed: 12/27/2022] Open
Abstract
Clostridium thermocellum is a promising candidate for ethanol production from cellulosic biomass, but requires metabolic engineering to improve ethanol yield. A key gene in the ethanol production pathway is the bifunctional aldehyde and alcohol dehydrogenase, adhE. To explore the effects of overexpressing wild-type, mutant, and exogenous adhEs, we developed a new expression plasmid, pDGO144, that exhibited improved transformation efficiency and better gene expression than its predecessor, pDGO-66. This new expression plasmid will allow for many other metabolic engineering and basic research efforts in C. thermocellum. As proof of concept, we used this plasmid to express 12 different adhE genes (both wild type and mutant) from several organisms. Ethanol production varied between clones immediately after transformation, but tended to converge to a single value after several rounds of serial transfer. The previously described mutant C. thermocellum D494G adhE gave the best ethanol production, which is consistent with previously published results.
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Affiliation(s)
- Shuen Hon
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- BioEnergy Science Center, Oak Ridge, TN, USA
| | - Anthony A. Lanahan
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- BioEnergy Science Center, Oak Ridge, TN, USA
| | - Liang Tian
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- BioEnergy Science Center, Oak Ridge, TN, USA
| | - Richard J. Giannone
- BioEnergy Science Center, Oak Ridge, TN, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Robert L. Hettich
- BioEnergy Science Center, Oak Ridge, TN, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daniel G. Olson
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- BioEnergy Science Center, Oak Ridge, TN, USA
| | - Lee R. Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- BioEnergy Science Center, Oak Ridge, TN, USA
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27
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Advances in Consolidated Bioprocessing Using Clostridium thermocellumand Thermoanaerobacter saccharolyticum. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch10] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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28
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Chen M, Bu L, Alahuhta M, Brunecky R, Xu Q, Lunin VV, Brady JW, Crowley MF, Himmel ME, Bomble YJ. Strategies to reduce end-product inhibition in family 48 glycoside hydrolases. Proteins 2016; 84:295-304. [PMID: 26572060 DOI: 10.1002/prot.24965] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/02/2015] [Accepted: 11/06/2015] [Indexed: 11/07/2022]
Abstract
Family 48 cellobiohydrolases are some of the most abundant glycoside hydrolases in nature. They are able to degrade cellulosic biomass and therefore serve as good enzyme candidates for biofuel production. Family 48 cellulases hydrolyze cellulose chains via a processive mechanism, and produce end products composed primarily of cellobiose as well as other cellooligomers (dp ≤ 4). The challenge of utilizing cellulases in biofuel production lies in their extremely slow turnover rate. A factor contributing to the low enzyme activity is suggested to be product binding to enzyme and the resulting performance inhibition. In this study, we quantitatively evaluated the product inhibitory effect of four family 48 glycoside hydrolases using molecular dynamics simulations and product expulsion free-energy calculations. We also suggested a series of single mutants of the four family 48 glycoside hydrolases with theoretically reduced level of product inhibition. The theoretical calculations provide a guide for future experimental studies designed to produce mutant cellulases with enhanced activity.
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Affiliation(s)
- Mo Chen
- Department of Food Science, Cornell University, Ithaca, New York
| | - Lintao Bu
- National Renewable Energy Laboratory, Golden, Colorado
| | | | | | - Qi Xu
- National Renewable Energy Laboratory, Golden, Colorado
| | | | - John W Brady
- Department of Food Science, Cornell University, Ithaca, New York
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29
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Metatranscriptomic analyses of plant cell wall polysaccharide degradation by microorganisms in the cow rumen. Appl Environ Microbiol 2016; 81:1375-86. [PMID: 25501482 DOI: 10.1128/aem.03682-14] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bovine rumen represents a highly specialized bioreactor where plant cell wall polysaccharides (PCWPs) are efficiently deconstructed via numerous enzymes produced by resident microorganisms. Although a large number of fibrolytic genes from rumen microorganisms have been identified, it remains unclear how they are expressed in a coordinated manner to efficiently degrade PCWPs. In this study, we performed a metatranscriptomic analysis of the rumen microbiomes of adult Holstein cows fed a fiber diet and obtained a total of 1,107,083 high-quality non-rRNA reads with an average length of 483 nucleotides. Transcripts encoding glycoside hydrolases (GHs) and carbohydrate binding modules (CBMs) accounted for 1% and 0.1% of the total non-rRNAs, respectively. The majority (98%) of the putative cellulases belonged to four GH families (i.e., GH5, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus and Fibrobacter. Notably, transcripts for GH48 cellobiohydrolases were relatively abundant compared to the abundance of transcripts for other cellulases. Two-thirds of the putative hemicellulases were of the GH10, GH11, and GH26 types and were produced by members of the genera Ruminococcus, Prevotella, and Fibrobacter. Most (82%) predicted oligosaccharide-degrading enzymes were GH1, GH2, GH3, and GH43 proteins and were from a diverse group of microorganisms. Transcripts for CBM10 and dockerin, key components of the cellulosome, were also relatively abundant. Our results provide metatranscriptomic evidence in support of the notion that members of the genera Ruminococcus, Fibrobacter, and Prevotella are predominant PCWP degraders and point to the significant contribution of GH48 cellobiohydrolases and cellulosome-like structures to efficient PCWP degradation in the cow rumen.
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30
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Chundawat SPS, Paavola CD, Raman B, Nouailler M, Chan SL, Mielenz JR, Receveur-Brechot V, Trent JD, Dale BE. Saccharification of thermochemically pretreated cellulosic biomass using native and engineered cellulosomal enzyme systems. REACT CHEM ENG 2016. [DOI: 10.1039/c6re00172f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Tethering hydrolytic enzymes (e.g., cellulases) to protein scaffolds enhances biomass saccharification to sugars.
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Affiliation(s)
- Shishir P. S. Chundawat
- Department of Chemical & Biochemical Engineering
- The State University of New Jersey
- Piscataway
- USA
- DOE Great Lakes Bioenergy Research Center (GLBRC)
| | | | - Babu Raman
- Biosciences Division and BioEnergy Science Center
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - Matthieu Nouailler
- LISM-UMR 7255 Institut De Microbiologie De La Mediterranee
- CNRS and Aix-Marseille University
- 13402 Marseille Cedex 20
- France
| | | | - Jonathan R. Mielenz
- Biosciences Division and BioEnergy Science Center
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | | | - Jonathan D. Trent
- Bioengineering Branch
- NASA Ames
- Moffett Field
- USA
- Biomolecular Engineering Department
| | - Bruce E. Dale
- DOE Great Lakes Bioenergy Research Center (GLBRC)
- Michigan State University
- East Lansing
- USA
- Chemical Engineering and Materials Science
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31
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de Vries M, Schöler A, Ertl J, Xu Z, Schloter M. Metagenomic analyses reveal no differences in genes involved in cellulose degradation under different tillage treatments. FEMS Microbiol Ecol 2015; 91:fiv069. [DOI: 10.1093/femsec/fiv069] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2015] [Indexed: 11/12/2022] Open
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32
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Olson DG, Maloney M, Lanahan AA, Hon S, Hauser LJ, Lynd LR. Identifying promoters for gene expression in Clostridium thermocellum. Metab Eng Commun 2015; 2:23-29. [PMID: 34150505 PMCID: PMC8193255 DOI: 10.1016/j.meteno.2015.03.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/26/2015] [Accepted: 03/21/2015] [Indexed: 12/03/2022] Open
Abstract
A key tool for metabolic engineering is the ability to express heterologous genes. One obstacle to gene expression in non-model organisms, and especially in relatively uncharacterized bacteria, is the lack of well-characterized promoters. Here we test 17 promoter regions for their ability to drive expression of the reporter genes β-galactosidase (lacZ) and NADPH-alcohol dehydrogenase (adhB) in Clostridium thermocellum, an important bacterium for the production of cellulosic biofuels. Only three promoters have been commonly used for gene expression in C. thermocellum, gapDH, cbp and eno. Of the new promoters tested, 2638, 2926, 966 and 815 showed reliable expression. The 2638 promoter showed relatively higher activity when driving adhB (compared to lacZ), and the 815 promoter showed relatively higher activity when driving lacZ (compared to adhB). Tested 17 different putative promoter sequences with 2 different reporter genes. The eno, cbp, cbp_2, 815, 966, 2638 and 2926 promoters resulted in high enzymatic activity. The gapDH, gapDH_2, 1194 and 3011_2 promoters apparently exacerbate problems with plasmid instability. The 307, 544, 2463, lac and lacUV5 promoters did not result in reporter gene activity. Increasing antibiotic selection pressure did not increase expression of the reporter gene.
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Affiliation(s)
- Daniel G Olson
- Thayer School of Engineering at Dartmouth College, Hanover, NH 03755, United States.,BioEnergy Science Center, TN, United States
| | - Marybeth Maloney
- Thayer School of Engineering at Dartmouth College, Hanover, NH 03755, United States.,BioEnergy Science Center, TN, United States
| | - Anthony A Lanahan
- Thayer School of Engineering at Dartmouth College, Hanover, NH 03755, United States.,BioEnergy Science Center, TN, United States
| | - Shuen Hon
- Thayer School of Engineering at Dartmouth College, Hanover, NH 03755, United States.,BioEnergy Science Center, TN, United States
| | - Loren J Hauser
- Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States.,BioEnergy Science Center, TN, United States
| | - Lee R Lynd
- Thayer School of Engineering at Dartmouth College, Hanover, NH 03755, United States.,Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States.,Mascoma Corporation, NH 37830, United States.,BioEnergy Science Center, TN, United States
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33
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C/N ratio drives soil actinobacterial cellobiohydrolase gene diversity. Appl Environ Microbiol 2015; 81:3016-28. [PMID: 25710367 DOI: 10.1128/aem.00067-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/15/2015] [Indexed: 11/20/2022] Open
Abstract
Cellulose accounts for approximately half of photosynthesis-fixed carbon; however, the ecology of its degradation in soil is still relatively poorly understood. The role of actinobacteria in cellulose degradation has not been extensively investigated despite their abundance in soil and known cellulose degradation capability. Here, the diversity and abundance of the actinobacterial glycoside hydrolase family 48 (cellobiohydrolase) gene in soils from three paired pasture-woodland sites were determined by using terminal restriction fragment length polymorphism (T-RFLP) analysis and clone libraries with gene-specific primers. For comparison, the diversity and abundance of general bacteria and fungi were also assessed. Phylogenetic analysis of the nucleotide sequences of 80 clones revealed significant new diversity of actinobacterial GH48 genes, and analysis of translated protein sequences showed that these enzymes are likely to represent functional cellobiohydrolases. The soil C/N ratio was the primary environmental driver of GH48 community compositions across sites and land uses, demonstrating the importance of substrate quality in their ecology. Furthermore, mid-infrared (MIR) spectrometry-predicted humic organic carbon was distinctly more important to GH48 diversity than to total bacterial and fungal diversity. This suggests a link between the actinobacterial GH48 community and soil organic carbon dynamics and highlights the potential importance of actinobacteria in the terrestrial carbon cycle.
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34
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The bifunctional alcohol and aldehyde dehydrogenase gene, adhE, is necessary for ethanol production in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum. J Bacteriol 2015; 197:1386-93. [PMID: 25666131 DOI: 10.1128/jb.02450-14] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
UNLABELLED Thermoanaerobacterium saccharolyticum and Clostridium thermocellum are anaerobic thermophilic bacteria being investigated for their ability to produce biofuels from plant biomass. The bifunctional alcohol and aldehyde dehydrogenase gene, adhE, is present in these bacteria and has been known to be important for ethanol formation in other anaerobic alcohol producers. This study explores the inactivation of the adhE gene in C. thermocellum and T. saccharolyticum. Deletion of adhE reduced ethanol production by >95% in both T. saccharolyticum and C. thermocellum, confirming that adhE is necessary for ethanol formation in both organisms. In both adhE deletion strains, fermentation products shifted from ethanol to lactate production and resulted in lower cell density and longer time to reach maximal cell density. In T. saccharolyticum, the adhE deletion strain lost >85% of alcohol dehydrogenase (ADH) activity. Aldehyde dehydrogenase (ALDH) activity did not appear to be affected, although ALDH activity was low in cell extracts. Adding ubiquinone-0 to the ALDH assay increased activity in the T. saccharolyticum parent strain but did not increase activity in the adhE deletion strain, suggesting that ALDH activity was inhibited. In C. thermocellum, the adhE deletion strain lost >90% of ALDH and ADH activity in cell extracts. The C. thermocellum adhE deletion strain contained a point mutation in the lactate dehydrogenase gene, which appears to deregulate its activation by fructose 1,6-bisphosphate, leading to constitutive activation of lactate dehydrogenase. IMPORTANCE Thermoanaerobacterium saccharolyticum and Clostridium thermocellum are bacteria that have been investigated for their ability to produce biofuels from plant biomass. They have been engineered to produce higher yields of ethanol, yet questions remain about the enzymes responsible for ethanol formation in these bacteria. The genomes of these bacteria encode multiple predicted aldehyde and alcohol dehydrogenases which could be responsible for alcohol formation. This study explores the inactivation of adhE, a gene encoding a bifunctional alcohol and aldehyde dehydrogenase. Deletion of adhE reduced ethanol production by >95% in both T. saccharolyticum and C. thermocellum, confirming that adhE is necessary for ethanol formation in both organisms. In strains without adhE, we note changes in biochemical activity, product formation, and growth.
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35
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Bhattacharya AS, Bhattacharya A, Pletschke BI. Synergism of fungal and bacterial cellulases and hemicellulases: a novel perspective for enhanced bio-ethanol production. Biotechnol Lett 2015; 37:1117-29. [DOI: 10.1007/s10529-015-1779-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 01/21/2015] [Indexed: 12/15/2022]
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36
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Gardner JG, Crouch L, Labourel A, Forsberg Z, Bukhman YV, Vaaje-Kolstad G, Gilbert HJ, Keating DH. Systems biology defines the biological significance of redox-active proteins during cellulose degradation in an aerobic bacterium. Mol Microbiol 2014; 94:1121-1133. [PMID: 25294408 DOI: 10.1111/mmi.12821] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2014] [Indexed: 11/28/2022]
Abstract
Microbial depolymerization of plant cell walls contributes to global carbon balance and is a critical component of renewable energy. The genomes of lignocellulose degrading microorganisms encode diverse classes of carbohydrate modifying enzymes, although currently there is a paucity of knowledge on the role of these proteins in vivo. We report the comprehensive analysis of the cellulose degradation system in the saprophytic bacterium Cellvibrio japonicus. Gene expression profiling of C. japonicus demonstrated that three of the 12 predicted β-1,4 endoglucanases (cel5A, cel5B, and cel45A) and the sole predicted cellobiohydrolase (cel6A) showed elevated expression during growth on cellulose. Targeted gene disruptions of all 13 predicted cellulase genes showed that only cel5B and cel6A were required for optimal growth on cellulose. Our analysis also identified three additional genes required for cellulose degradation: lpmo10B encodes a lytic polysaccharide monooxygenase (LPMO), while cbp2D and cbp2E encode proteins containing carbohydrate binding modules and predicted cytochrome domains for electron transfer. CjLPMO10B oxidized cellulose and Cbp2D demonstrated spectral properties consistent with redox function. Collectively, this report provides insight into the biological role of LPMOs and redox proteins in cellulose utilization and suggests that C. japonicus utilizes a combination of hydrolytic and oxidative cleavage mechanisms to degrade cellulose.
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Affiliation(s)
- Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, 324 Biological Sciences Building, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
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37
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Akinosho H, Yee K, Close D, Ragauskas A. The emergence of Clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications. Front Chem 2014; 2:66. [PMID: 25207268 PMCID: PMC4143619 DOI: 10.3389/fchem.2014.00066] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 07/28/2014] [Indexed: 01/25/2023] Open
Abstract
First isolated in 1926, Clostridium thermocellum has recently received increased attention as a high utility candidate for use in consolidated bioprocessing (CBP) applications. These applications, which seek to process lignocellulosic biomass directly into useful products such as ethanol, are gaining traction as economically feasible routes toward the production of fuel and other high value chemical compounds as the shortcomings of fossil fuels become evident. This review evaluates C. thermocellum's role in this transitory process by highlighting recent discoveries relating to its genomic, transcriptomic, proteomic, and metabolomic responses to varying biomass sources, with a special emphasis placed on providing an overview of its unique, multivariate enzyme cellulosome complex and the role that this structure performs during biomass degradation. Both naturally evolved and genetically engineered strains are examined in light of their unique attributes and responses to various biomass treatment conditions, and the genetic tools that have been employed for their creation are presented. Several future routes for potential industrial usage are presented, and it is concluded that, although there have been many advances to significantly improve C. thermocellum's amenability to industrial use, several hurdles still remain to be overcome as this unique organism enjoys increased attention within the scientific community.
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Affiliation(s)
- Hannah Akinosho
- School of Chemistry and Biochemistry, Institute of Paper Science and Technology, Georgia Institute of Technology Atlanta, GA, USA ; Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA
| | - Kelsey Yee
- Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA ; Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Dan Close
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Arthur Ragauskas
- Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA ; Department of Chemical and Biomolecular Engineering and Department of Forestry, Wildlife, and Fisheries, University of Tennessee Knoxville, TN, USA
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38
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Hong W, Zhang J, Feng Y, Mohr G, Lambowitz AM, Cui GZ, Liu YJ, Cui Q. The contribution of cellulosomal scaffoldins to cellulose hydrolysis by Clostridium thermocellum analyzed by using thermotargetrons. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:80. [PMID: 24955112 PMCID: PMC4045903 DOI: 10.1186/1754-6834-7-80] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 05/13/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Clostridium thermocellum is a thermophilic anaerobic bacterium that degrades cellulose by using a highly effective cellulosome, a macromolecular complex consisting of multiple cellulose degrading enzymes organized and attached to the cell surface by non-catalytic scaffoldins. However, due largely to lack of efficient methods for genetic manipulation of C. thermocellum, it is still unclear how the different scaffoldins and their functional modules contribute to cellulose hydrolysis. RESULTS We constructed C. thermocellum mutants with the primary scaffoldin CipA (cellulosome-integrating protein A) truncated at different positions or lacking four different secondary scaffoldins by using a newly developed thermotargetron system, and we analyzed cellulose hydrolysis, cellulosome formation, and cellulose binding of the mutants. A CipA truncation that deletes six type I cohesin modules, which bind cellulolytic enzymes, decreased cellulose hydrolysis rates by 46%, and slightly longer truncations that also delete the carbohydrate binding module decreased rates by 89 to 92%, indicating strong cellulosome-substrate synergy. By contrast, a small CipA truncation that deletes only the C-terminal type II dockerin (XDocII) module detached cellulosomes from the cells, but decreased cellulose hydrolysis rates by only 9%, suggesting a relatively small contribution of cellulosome-cell synergy. Disruptants lacking any of four different secondary scaffoldins (OlpB, 7CohII, Orf2p, or SdbA) showed moderately decreased cellulose hydrolysis rates, suggesting additive contributions. Surprisingly, the CipA-ΔXDocII mutant, which lacks cell-associated polycellulosomes, adheres to cellulose almost as strongly as wild-type cells, revealing an alternate, previously unknown cellulose-binding mechanism. CONCLUSIONS Our results emphasize the important role of cellulosome-substrate synergy in cellulose degradation, demonstrate a contribution of secondary scaffoldins, and suggest a previously unknown, non-cellulosomal system for binding insoluble cellulose. Our findings provide new insights into cellulosome function and impact genetic engineering of microorganisms to enhance bioconversions of cellulose substrates.
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Affiliation(s)
- Wei Hong
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, P R China
| | - Jie Zhang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, P R China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
| | - Georg Mohr
- Departments of Molecular Biosciences and Chemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Alan M Lambowitz
- Departments of Molecular Biosciences and Chemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Gu-Zhen Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
| | - Ya-Jun Liu
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
- Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
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Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MWW, Kelly RM. Thermophilic lignocellulose deconstruction. FEMS Microbiol Rev 2014; 38:393-448. [DOI: 10.1111/1574-6976.12044] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 08/20/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022] Open
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40
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Wei H, Fu Y, Magnusson L, Baker JO, Maness PC, Xu Q, Yang S, Bowersox A, Bogorad I, Wang W, Tucker MP, Himmel ME, Ding SY. Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq. Front Microbiol 2014; 5:142. [PMID: 24782837 PMCID: PMC3990059 DOI: 10.3389/fmicb.2014.00142] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/19/2014] [Indexed: 01/01/2023] Open
Abstract
The anaerobic, thermophilic bacterium, Clostridium thermocellum, secretes multi-protein enzyme complexes, termed cellulosomes, which synergistically interact with the microbial cell surface and efficiently disassemble plant cell wall biomass. C. thermocellum has also been considered a potential consolidated bioprocessing (CBP) organism due to its ability to produce the biofuel products, hydrogen, and ethanol. We found that C. thermocellum fermentation of pretreated yellow poplar (PYP) produced 30 and 39% of ethanol and hydrogen product concentrations, respectively, compared to fermentation of cellobiose. RNA-seq was used to analyze the transcriptional profiles of these cells. The PYP-grown cells taken for analysis at the late stationary phase showed 1211 genes up-regulated and 314 down-regulated by more than two-fold compared to the cellobiose-grown cells. These affected genes cover a broad spectrum of specific functional categories. The transcriptional analysis was further validated by sub-proteomics data taken from the literature; as well as by quantitative reverse transcription-PCR (qRT-PCR) analyses of selected genes. Specifically, 47 cellulosomal protein-encoding genes, genes for 4 pairs of SigI-RsgI for polysaccharide sensing, 7 cellodextrin ABC transporter genes, and a set of NAD(P)H hydogenase and alcohol dehydrogenase genes were up-regulated for cells growing on PYP compared to cellobiose. These genes could be potential candidates for future studies aimed at gaining insight into the regulatory mechanism of this organism as well as for improvement of C. thermocellum in its role as a CBP organism.
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Affiliation(s)
- Hui Wei
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Yan Fu
- Center for Plant Genomics, Iowa State University Ames, IA, USA
| | - Lauren Magnusson
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - John O Baker
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Qi Xu
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Andrew Bowersox
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA ; National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Igor Bogorad
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Melvin P Tucker
- National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Shi-You Ding
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
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41
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Thomas L, Joseph A, Gottumukkala LD. Xylanase and cellulase systems of Clostridium sp.: an insight on molecular approaches for strain improvement. BIORESOURCE TECHNOLOGY 2014; 158:343-50. [PMID: 24581864 DOI: 10.1016/j.biortech.2014.01.140] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/23/2014] [Accepted: 01/27/2014] [Indexed: 05/21/2023]
Abstract
Bioethanol and biobutanol hold great promise as alternative biofuels, especially for transport sector, because they can be produced from lignocellulosic agro-industrial residues. From techno-economic point of view, the bioprocess for biofuels production should involve minimal processing steps. Consolidated bioprocessing (CBP), which combines various processing steps such as pretreatment, hydrolysis and fermentation in a single bioreactor, could be of great relevance for the production of bioethanol and biobutanol or solvents (acetone, butanol, ethanol), employing clostridia. For CBP, Clostridium holds best promise because it possesses multi-enzyme system involving cellulosome and xylanosome, which comprise several enzymes such as cellulases and xylanases. The aim of this article was to review the recent developments on enzyme systems of clostridia, especially xylanase and cellulase with an effort to analyse the information available on molecular approaches for the improvement of strains with ultimate aim to improve the efficiencies of hydrolysis and fermentation.
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Affiliation(s)
- Leya Thomas
- Biotechnology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India.
| | - Abhilash Joseph
- Department of Biotechnology & Microbiology, Kannur University, Thalassery Campus, Kannur 670 661, India
| | - Lalitha Devi Gottumukkala
- Biotechnology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
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42
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Li M, Semchonok DA, Boekema EJ, Bruce BD. Characterization and evolution of tetrameric photosystem I from the thermophilic cyanobacterium Chroococcidiopsis sp TS-821. THE PLANT CELL 2014; 26:1230-45. [PMID: 24681621 PMCID: PMC4001380 DOI: 10.1105/tpc.113.120782] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 03/09/2014] [Accepted: 03/13/2014] [Indexed: 05/20/2023]
Abstract
Photosystem I (PSI) is a reaction center associated with oxygenic photosynthesis. Unlike the monomeric reaction centers in green and purple bacteria, PSI forms trimeric complexes in most cyanobacteria with a 3-fold rotational symmetry that is primarily stabilized via adjacent PsaL subunits; however, in plants/algae, PSI is monomeric. In this study, we discovered a tetrameric form of PSI in the thermophilic cyanobacterium Chroococcidiopsis sp TS-821 (TS-821). In TS-821, PSI forms tetrameric and dimeric species. We investigated these species by Blue Native PAGE, Suc density gradient centrifugation, 77K fluorescence, circular dichroism, and single-particle analysis. Transmission electron microscopy analysis of native membranes confirms the presence of the tetrameric PSI structure prior to detergent solubilization. To investigate why TS-821 forms tetramers instead of trimers, we cloned and analyzed its psaL gene. Interestingly, this gene product contains a short insert between the second and third predicted transmembrane helices. Phylogenetic analysis based on PsaL protein sequences shows that TS-821 is closely related to heterocyst-forming cyanobacteria, some of which also have a tetrameric form of PSI. These results are discussed in light of chloroplast evolution, and we propose that PSI evolved stepwise from a trimeric form to tetrameric oligomer en route to becoming monomeric in plants/algae.
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Affiliation(s)
- Meng Li
- Department of Biochemistry, Cellular, and Molecular
Biology, University of Tennessee, Knoxville, Tennessee 37996
- The Bredesen Center for Interdisciplinary Research and
Graduate Education, University of Tennessee, Knoxville, Tennessee 37996
| | - Dmitry A. Semchonok
- Department of Electron Microscopy, Groningen Biomolecular
Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The
Netherlands
| | - Egbert J. Boekema
- Department of Electron Microscopy, Groningen Biomolecular
Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The
Netherlands
| | - Barry D. Bruce
- Department of Biochemistry, Cellular, and Molecular
Biology, University of Tennessee, Knoxville, Tennessee 37996
- The Bredesen Center for Interdisciplinary Research and
Graduate Education, University of Tennessee, Knoxville, Tennessee 37996
- Department of Microbiology, University of Tennessee,
Knoxville, Tennessee 37996
- Sustainable Energy and Education Research Center,
University of Tennessee, Knoxville, Tennessee 37996
- Address correspondence to
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43
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Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes. ISME JOURNAL 2014; 8:1522-33. [PMID: 24477196 DOI: 10.1038/ismej.2013.251] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 12/08/2013] [Accepted: 12/11/2013] [Indexed: 02/08/2023]
Abstract
Most of the lineages of bacteria have remained unknown beyond environmental surveys using molecular markers. Until the recent characterisation of several strains, the phylum Armatimonadetes (formerly known as 'candidate division OP10') was a dominant and globally-distributed lineage within this 'uncultured majority'. Here we report the first Armatimonadetes genome from the thermophile Chthonomonas calidirosea T49(T) and its role as a saccharide scavenger in a geothermal steam-affected soil environment. Phylogenomic analysis indicates T49(T) to be related closely to the phylum Chloroflexi. The predicted genes encoding for carbohydrate transporters (27 carbohydrate ATP-binding cassette transporter-related genes) and carbohydrate-metabolising enzymes (including at least 55 putative enzymes with glycosyl hydrolase domains) within the 3.43 Mb genome help explain its ability to utilise a wide range of carbohydrates as well as its inability to break down extracellular cellulose. The presence of only a single class of branched amino acid transporter appears to be the causative step for the requirement of isoleucine for growth. The genome lacks many commonly conserved operons (for example, lac and trp). Potential causes for this, such as dispersion of functionally related genes via horizontal gene transfer from distant taxa or recent genome recombination, were rejected. Evidence suggests T49(T) relies on the relatively abundant σ-factors, instead of operonic organisation, as the primary means of transcriptional regulation. Examination of the genome with physiological data and environmental dynamics (including interspecific interactions) reveals ecological factors behind the apparent elusiveness of T49(T) to cultivation and, by extension, the remaining 'uncultured majority' that have so far evaded conventional microbiological techniques.
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44
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Xu T, Li Y, He Z, Zhou J. Dockerin-containing protease inhibitor protects key cellulosomal cellulases from proteolysis inClostridium cellulolyticum. Mol Microbiol 2014; 91:694-705. [DOI: 10.1111/mmi.12488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Tao Xu
- Institute for Environmental Genomics; University of Oklahoma; Norman OK 73071 USA
- Department of Microbiology and Plant Biology; University of Oklahoma; Norman OK 73071 USA
| | - Yongchao Li
- Institute for Environmental Genomics; University of Oklahoma; Norman OK 73071 USA
- Department of Microbiology and Plant Biology; University of Oklahoma; Norman OK 73071 USA
| | - Zhili He
- Institute for Environmental Genomics; University of Oklahoma; Norman OK 73071 USA
- Virtual Institute for Microbial Stress and Survival; Berkeley USA
| | - Jizhong Zhou
- Institute for Environmental Genomics; University of Oklahoma; Norman OK 73071 USA
- Virtual Institute for Microbial Stress and Survival; Berkeley USA
- Earth Sciences Division; Lawrence Berkeley National Laboratory; Berkeley CA 94720 USA
- Department of Environmental Science and Engineering; Tsinghua University; Beijing 100084 China
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45
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Young J, Chung D, Bomble YJ, Himmel ME, Westpheling J. Deletion of Caldicellulosiruptor bescii CelA reveals its crucial role in the deconstruction of lignocellulosic biomass. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:142. [PMID: 25317205 PMCID: PMC4195899 DOI: 10.1186/s13068-014-0142-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 09/17/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND Members of the bacterial genus Caldicellulosiruptor are the most thermophilic cellulolytic organisms described to date, and have the ability to grow on lignocellulosic biomass without conventional pretreatment. Different species vary in their abilities to degrade cellulose, and the presence of CelA, a bifunctional glycoside hydrolase that contains a Family 48 and a Family 9 catalytic domain, correlates well with cellulolytic ability in members of this genus. For example, C. hydrothermalis, which does not contain a CelA homolog, or a GH48 Family or GH9 Family glycoside hydrolase, is the least cellulolytic of the Caldicellulosiruptor species so far described. C. bescii, which contains CelA and expresses it constitutively, is among the most cellulolytic. In fact, CelA is the most abundant extracellular protein produced in C. bescii. The enzyme contains two catalytic units, a Family 9A-CBM3c processive endoglucanase and a Family 48 exoglucanase, joined by two Family 3b carbohydrate-binding domains. Although there are two non-reducing end-specific Family 9 and three reducing end-specific Family 48 glycoside hydrolases (producing primarily glucose and cellobiose; and cellobiose and cellotriose, respectively) in C. bescii, CelA is the only protein that combines both enzymatic activities. RESULTS A deletion of the celA gene resulted in a dramatic reduction in the microorganism's ability to grow on crystalline cellulose (Avicel) and diminished growth on lignocellulosic biomass. A comparison of the overall endoglucanase and exoglucanase activities of the mutant compared with the wild-type suggests that the loss of the endoglucanase activity provided by the GH9 family domain is perhaps compensated for by other enzymes produced by the cell. In contrast, it appears that no other enzymes in the C. bescii secretome can compensate for the loss of exoglucanase activity. The change in enzymatic activity in the celA mutant resulted in a 15-fold decrease in sugar release on Avicel compared with the parent and wild-type strains. CONCLUSIONS The exoglucanase activity of the GH48 domain of CelA plays a major role in biomass degradation within the suite of C. bescii biomass-degrading enzymes.
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Affiliation(s)
- Jenna Young
- />Department of Genetics, University of Georgia, Athens, Georgia
- />The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Daehwan Chung
- />Department of Genetics, University of Georgia, Athens, Georgia
- />The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Yannick J Bomble
- />Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
- />The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Michael E Himmel
- />Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
- />The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Janet Westpheling
- />Department of Genetics, University of Georgia, Athens, Georgia
- />The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
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Yi Z, Su X, Revindran V, Mackie RI, Cann I. Molecular and biochemical analyses of CbCel9A/Cel48A, a highly secreted multi-modular cellulase by Caldicellulosiruptor bescii during growth on crystalline cellulose. PLoS One 2013; 8:e84172. [PMID: 24358340 PMCID: PMC3865294 DOI: 10.1371/journal.pone.0084172] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/20/2013] [Indexed: 01/24/2023] Open
Abstract
During growth on crystalline cellulose, the thermophilic bacterium Caldicellulosiruptor bescii secretes several cellulose-degrading enzymes. Among these enzymes is CelA (CbCel9A/Cel48A), which is reported as the most highly secreted cellulolytic enzyme in this bacterium. CbCel9A/Cel48A is a large multi-modular polypeptide, composed of an N-terminal catalytic glycoside hydrolase family 9 (GH9) module and a C-terminal GH48 catalytic module that are separated by a family 3c carbohydrate-binding module (CBM3c) and two identical CBM3bs. The wild-type CbCel9A/Cel48A and its truncational mutants were expressed in Bacillus megaterium and Escherichia coli, respectively. The wild-type polypeptide released twice the amount of glucose equivalents from Avicel than its truncational mutant that lacks the GH48 catalytic module. The truncational mutant harboring the GH9 module and the CBM3c was more thermostable than the wild-type protein, likely due to its compact structure. The main hydrolytic activity was present in the GH9 catalytic module, while the truncational mutant containing the GH48 module and the three CBMs was ineffective in degradation of either crystalline or amorphous cellulose. Interestingly, the GH9 and/or GH48 catalytic modules containing the CBM3bs form low-density particles during hydrolysis of crystalline cellulose. Moreover, TM3 (GH9/CBM3c) and TM2 (GH48 with three CBM3 modules) synergistically hydrolyze crystalline cellulose. Deletion of the CBM3bs or mutations that compromised their binding activity suggested that these CBMs are important during hydrolysis of crystalline cellulose. In agreement with this observation, seven of nine genes in a C. bescii gene cluster predicted to encode cellulose-degrading enzymes harbor CBM3bs. Based on our results, we hypothesize that C. bescii uses the GH48 module and the CBM3bs in CbCel9A/Cel48A to destabilize certain regions of crystalline cellulose for attack by the highly active GH9 module and other endoglucanases produced by this hyperthermophilic bacterium.
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Affiliation(s)
- Zhuolin Yi
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Xiaoyun Su
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Vanessa Revindran
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Roderick I. Mackie
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Isaac Cann
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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47
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Kostylev M, Alahuhta M, Chen M, Brunecky R, Himmel ME, Lunin VV, Brady J, Wilson DB. Cel48A fromThermobifida fusca: Structure and site directed mutagenesis of key residues. Biotechnol Bioeng 2013; 111:664-73. [DOI: 10.1002/bit.25139] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 10/05/2013] [Accepted: 10/21/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Maxim Kostylev
- Department of Molecular Biology and Genetics; Cornell University; 458 Biotechnology Building Ithaca New York 14853
| | - Markus Alahuhta
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - Mo Chen
- Department of Food Science; Cornell University; Ithaca New York
| | - Roman Brunecky
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - Michael E. Himmel
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - Vladimir V. Lunin
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - John Brady
- Department of Food Science; Cornell University; Ithaca New York
| | - David B. Wilson
- Department of Molecular Biology and Genetics; Cornell University; 458 Biotechnology Building Ithaca New York 14853
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48
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Cui GZ, Zhang J, Hong W, Xu C, Feng Y, Cui Q, Liu YJ. Improvement of ClosTron for successive gene disruption in Clostridium cellulolyticum using a pyrF-based screening system. Appl Microbiol Biotechnol 2013; 98:313-23. [DOI: 10.1007/s00253-013-5330-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 10/07/2013] [Accepted: 10/15/2013] [Indexed: 11/28/2022]
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49
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Lin L, Xu J. Dissecting and engineering metabolic and regulatory networks of thermophilic bacteria for biofuel production. Biotechnol Adv 2013; 31:827-37. [DOI: 10.1016/j.biotechadv.2013.03.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/06/2013] [Accepted: 03/10/2013] [Indexed: 01/08/2023]
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50
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St Brice LA, Shao X, Izquierdo JA, Lynd LR. OPTIMIZATION OF AFFINITY DIGESTION FOR THE ISOLATION OF CELLULOSOMES FROMClostridium thermocellum. Prep Biochem Biotechnol 2013; 44:206-16. [DOI: 10.1080/10826068.2013.829494] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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