1
|
Biodegradation of Polymers Used in Oil and Gas Operations: Towards Enzyme Biotechnology Development and Field Application. Polymers (Basel) 2022; 14:polym14091871. [PMID: 35567040 PMCID: PMC9100872 DOI: 10.3390/polym14091871] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 12/04/2022] Open
Abstract
Linear and crosslinked polymers are commonly used in the oil and gas industry. Guar-derived polymers have been extensively utilized in hydraulic fracturing processes, and recently polyacrylamide and cellulose-based polymers have also found utility. As these polymers are used during various phases of the hydraulic fracturing process, they can accumulate at formation fracture faces, resulting in undesired filter cakes that impede oil and gas recovery. Although acids and chemical oxidizers are often added in the fracturing fluids to degrade or ‘break’ polymer filter cakes, the constant use of these chemicals can be hazardous and can result in formation damage and corrosion of infrastructure. Alternately, the use of enzymes is an attractive and environmentally friendly technology that can be used to treat polymer accumulations. While guar-linkage-specific enzyme breakers isolated from bacteria have been shown to successfully cleave guar-based polymers and decrease their molecular weight and viscosity at reservoir conditions, new enzymes that target a broader range of polymers currently used in hydraulic fracturing operations still require research and development for effective application. This review article describes the current state-of-knowledge on the mechanisms and enzymes involved in biodegradation of guar gum, polyacrylamide (and hydrolyzed polyacrylamide), and carboxymethyl cellulose polymers. In addition, advantages and challenges in the development and application of enzyme breaker technologies are discussed.
Collapse
|
2
|
Abuajah CI, Ogbonna AC, Chukeze EJ, Ikpeme CA, Asogwa KK. A glucose oxidase peroxidase-coupled continuous assay protocol for the determination of cellulase activity in the laboratory. Anal Biochem 2022; 647:114649. [DOI: 10.1016/j.ab.2022.114649] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/01/2022] [Accepted: 03/09/2022] [Indexed: 11/01/2022]
|
3
|
Obeng EM, Adam SNN, Budiman C, Ongkudon CM, Maas R, Jose J. Lignocellulases: a review of emerging and developing enzymes, systems, and practices. BIORESOUR BIOPROCESS 2017. [DOI: 10.1186/s40643-017-0146-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
4
|
Eibinger M, Sigl K, Sattelkow J, Ganner T, Ramoni J, Seiboth B, Plank H, Nidetzky B. Functional characterization of the native swollenin from Trichoderma reesei: study of its possible role as C1 factor of enzymatic lignocellulose conversion. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:178. [PMID: 27570542 PMCID: PMC5000517 DOI: 10.1186/s13068-016-0590-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/15/2016] [Indexed: 05/28/2023]
Abstract
BACKGROUND Through binding to cellulose, expansin-like proteins are thought to loosen the structural order of crystalline surface material, thus making it more accessible for degradation by hydrolytic enzymes. Swollenin SWO1 is the major expansin-like protein from the fungus Trichoderma reesei. Here, we have performed a detailed characterization of a recombinant native form of SWO1 with respect to its possible auxiliary role in the enzymatic saccharification of lignocellulosic substrates. RESULTS The swo1 gene was overexpressed in T. reesei QM9414 Δxyr1 mutant, featuring downregulated cellulase production, and the protein was purified from culture supernatant. SWO1 was N-glycosylated and its circular dichroism spectrum suggested a folded protein. Adsorption isotherms (25 °C, pH 5.0, 1.0 mg substrate/mL) revealed SWO1 to be 120- and 20-fold more specific for binding to birchwood xylan and kraft lignin, respectively, than for binding to Avicel PH-101. The SWO1 binding capacity on lignin (25 µmol/g) exceeded 12-fold that on Avicel PH-101 (2.1 µmol/g). On xylan, not only the binding capacity (22 µmol/g) but also the affinity of SWO1 (K d = 0.08 µM) was enhanced compared to Avicel PH-101 (K d = 0.89 µM). SWO1 caused rapid release of a tiny amount of reducing sugars (<1 % of total) from different substrates (Avicel PH-101, nanocrystalline cellulose, steam-pretreated wheat straw, barley β-glucan, cellotetraose) but did not promote continued saccharification. Atomic force microscopy revealed that amorphous cellulose films were not affected by SWO1. Also with AFM, binding of SWO1 to cellulose nanocrystallites was demonstrated at the single-molecule level, but adsorption did not affect this cellulose. SWO1 exhibited no synergy with T. reesei cellulases in the hydrolysis of the different celluloses. However, SWO1 boosted slightly (1.5-fold) the reducing sugar release from a native grass substrate. CONCLUSIONS SWO1 is a strongly glycosylated protein, which has implications for producing it in heterologous hosts. Although SWO1 binds to crystalline cellulose, its adsorption to xylan is much stronger. SWO1 is not an auxiliary factor of the enzymatic degradation of a variety of cellulosic substrates. Effect of SWO1 on sugar release from intact plant cell walls might be exploitable with certain (e.g., mildly pretreated) lignocellulosic feedstocks.
Collapse
Affiliation(s)
- Manuel Eibinger
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010 Graz, Austria
| | - Karin Sigl
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010 Graz, Austria
| | - Jürgen Sattelkow
- Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Thomas Ganner
- Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Jonas Ramoni
- Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstrasse 1A/166, 1060 Vienna, Austria
| | - Bernhard Seiboth
- Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstrasse 1A/166, 1060 Vienna, Austria
| | - Harald Plank
- Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
- Graz Centre for Electron Microscopy, Steyrergasse 17, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010 Graz, Austria
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| |
Collapse
|
5
|
Cellulases: Classification, Methods of Determination and Industrial Applications. Appl Biochem Biotechnol 2016; 179:1346-80. [PMID: 27068832 DOI: 10.1007/s12010-016-2070-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 03/31/2016] [Indexed: 10/22/2022]
Abstract
Microbial cellulases have been receiving worldwide attention, as they have enormous potential to process the most abundant cellulosic biomass on this planet and transform it into sustainable biofuels and other value added products. The synergistic action of endoglucanases, exoglucanases, and β-glucosidases is required for the depolymerization of cellulose to fermentable sugars for transformation in to useful products using suitable microorganisms. The lack of a better understanding of the mechanisms of individual cellulases and their synergistic actions is the major hurdles yet to be overcome for large-scale commercial applications of cellulases. We have reviewed various microbial cellulases with a focus on their classification with mechanistic aspects of cellulase hydrolytic action, insights into novel approaches for determining cellulase activity, and potential industrial applications of cellulases.
Collapse
|
6
|
Naqvi S, Moerschbacher BM. The cell factory approach toward biotechnological production of high-value chitosan oligomers and their derivatives: an update. Crit Rev Biotechnol 2015; 37:11-25. [DOI: 10.3109/07388551.2015.1104289] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
7
|
Deng K, Takasuka TE, Bianchetti CM, Bergeman LF, Adams PD, Northen TR, Fox BG. Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases. Front Bioeng Biotechnol 2015; 3:165. [PMID: 26579511 PMCID: PMC4621489 DOI: 10.3389/fbioe.2015.00165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/02/2015] [Indexed: 12/20/2022] Open
Abstract
Chemically synthesized nanostructure-initiator mass spectrometry (NIMS) probes derivatized with tetrasaccharides were used to study the reactivity of representative Clostridium thermocellum β-glucosidase, endoglucanases, and cellobiohydrolase. Diagnostic patterns for reactions of these different classes of enzymes were observed. Results show sequential removal of glucose by the β-glucosidase and a progressive increase in specificity of reaction from endoglucanases to cellobiohydrolase. Time-dependent reactions of these polysaccharide-selective enzymes were modeled by numerical integration, which provides a quantitative basis to make functional distinctions among a continuum of naturally evolved catalytic properties. Consequently, our method, which combines automated protein translation with high-sensitivity and time-dependent detection of multiple products, provides a new approach to annotate glycoside hydrolase phylogenetic trees with functional measurements.
Collapse
Affiliation(s)
- Kai Deng
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Taichi E Takasuka
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA
| | - Christopher M Bianchetti
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA ; Department of Chemistry, University of Wisconsin-Oshkosh , Oshkosh, WI , USA
| | - Lai F Bergeman
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA
| | - Paul D Adams
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA ; Department of Bioengineering, University of California Berkeley , Berkeley, CA , USA
| | - Trent R Northen
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Brian G Fox
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA ; Department of Biochemistry, University of Wisconsin-Madison , Madison, WI , USA
| |
Collapse
|
8
|
Deng K, Guenther JM, Gao J, Bowen BP, Tran H, Reyes-Ortiz V, Cheng X, Sathitsuksanoh N, Heins R, Takasuka TE, Bergeman LF, Geertz-Hansen H, Deutsch S, Loqué D, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR. Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS. Front Bioeng Biotechnol 2015; 3:153. [PMID: 26528471 PMCID: PMC4603251 DOI: 10.3389/fbioe.2015.00153] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/21/2015] [Indexed: 12/26/2022] Open
Abstract
Cost-effective hydrolysis of biomass into sugars for biofuel production requires high-performance low-cost glycoside hydrolase (GH) cocktails that are active under demanding process conditions. Improving the performance of GH cocktails depends on knowledge of many critical parameters, including individual enzyme stabilities, optimal reaction conditions, kinetics, and specificity of reaction. With this information, rate- and/or yield-limiting reactions can be potentially improved through substitution, synergistic complementation, or protein engineering. Given the wide range of substrates and methods used for GH characterization, it is difficult to compare results across a myriad of approaches to identify high performance and synergistic combinations of enzymes. Here, we describe a platform for systematic screening of GH activities using automatic biomass handling, bioconjugate chemistry, robotic liquid handling, and nanostructure-initiator mass spectrometry (NIMS). Twelve well-characterized substrates spanning the types of glycosidic linkages found in plant cell walls are included in the experimental workflow. To test the application of this platform and substrate panel, we studied the reactivity of three engineered cellulases and their synergy of combination across a range of reaction conditions and enzyme concentrations. We anticipate that large-scale screening using the standardized platform and substrates will generate critical datasets to enable direct comparison of enzyme activities for cocktail design.
Collapse
Affiliation(s)
- Kai Deng
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Joel M Guenther
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Jian Gao
- Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | | | - Huu Tran
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Vimalier Reyes-Ortiz
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Xiaoliang Cheng
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Noppadon Sathitsuksanoh
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Richard Heins
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Taichi E Takasuka
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin , Madison, WI , USA
| | - Lai F Bergeman
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin , Madison, WI , USA
| | | | - Samuel Deutsch
- Lawrence Berkeley National Laboratory , Berkeley, CA , USA ; Joint Genome Institute , Walnut Creek, CA , USA
| | - Dominique Loqué
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Kenneth L Sale
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Blake A Simmons
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Paul D Adams
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA ; Department of Bioengineering, University of California Berkeley , Berkeley, CA , USA
| | - Anup K Singh
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Brian G Fox
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin , Madison, WI , USA ; Department of Biochemistry, University of Wisconsin , Madison, WI , USA
| | - Trent R Northen
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| |
Collapse
|
9
|
Grate JW, Mo KF, Shin Y, Vasdekis A, Warner MG, Kelly RT, Orr G, Hu D, Dehoff KJ, Brockman FJ, Wilkins MJ. Alexa Fluor-Labeled Fluorescent Cellulose Nanocrystals for Bioimaging Solid Cellulose in Spatially Structured Microenvironments. Bioconjug Chem 2015; 26:593-601. [DOI: 10.1021/acs.bioconjchem.5b00048] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jay W. Grate
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Kai-For Mo
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Yongsoon Shin
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Andreas Vasdekis
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Marvin G. Warner
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Ryan T. Kelly
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Galya Orr
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Dehong Hu
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Karl J. Dehoff
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Fred J. Brockman
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Michael J. Wilkins
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| |
Collapse
|
10
|
Takasuka TE, Walker JA, Bergeman LF, Vander Meulen KA, Makino SI, Elsen NL, Fox BG. Cell-free translation of biofuel enzymes. Methods Mol Biol 2014; 1118:71-95. [PMID: 24395410 DOI: 10.1007/978-1-62703-782-2_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In nature, bacteria and fungi are able to utilize recalcitrant plant materials by secreting a diverse set of enzymes. While genomic sequencing efforts offer exhaustive lists of genes annotated as potential polysaccharide-degrading enzymes, biochemical and functional characterizations of the encoded proteins are still needed to realize the full potential of this natural genomic diversity. This chapter outlines an application of wheat germ cell-free translation to the study of biofuel enzymes using genes from Clostridium thermocellum, a model cellulolytic organism. Since wheat germ extract lacks enzymatic activities that can hydrolyze insoluble polysaccharide substrates and is likewise devoid of enzymes that consume the soluble sugar products, the cell-free translation reactions provide a clean background for production and study of the reactions of biofuel enzymes. Examples of assays performed with individual enzymes or with small sets of enzymes obtained directly from cell-free translation are provided.
Collapse
Affiliation(s)
- Taichi E Takasuka
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | | | | | | | | | | | | |
Collapse
|
11
|
Extracellular secretion of β-glucosidase in ethanologenic E. coli enhances ethanol fermentation of cellobiose. Appl Biochem Biotechnol 2014; 174:772-83. [PMID: 25096392 DOI: 10.1007/s12010-014-1108-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/22/2014] [Indexed: 01/11/2023]
Abstract
Consolidated bioprocessing of lignocellulose for ethanol production is realized by expressing cellulase enzymes on ethanologenic strain. In this study, an ethanologenic Escherichia coli ZY81 was constructed by integrating pyruvate decarboxylase gene pdc and alcohol dehydrogenase gene adhB from Zymomonas mobilis into the genome of E. coli JM109 to obtain the capability of ethanol production. Then, the β-glucosidase gene bglB from Bacillus polymyxa was cloned and secretively expressed in E. coli ZY81. The recombinant strain E. coli ZY81/bglB showed an obvious activity of β-glucosidase in extracellular location with more than half in periplasmic space. EDTA was found to promote the release of the periplasmic proteins by approximately tenfold. E. coli ZY81/bglB utilized cellobiose as sole carbon source for ethanol production with 33.99 % of theoretical yield.
Collapse
|
12
|
Uniform cross-linked cellulase aggregates prepared in millifluidic reactors. J Colloid Interface Sci 2014; 428:146-51. [DOI: 10.1016/j.jcis.2014.04.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 04/02/2014] [Accepted: 04/13/2014] [Indexed: 11/22/2022]
|
13
|
Sharma PR, Rajamohanan PR, Varma AJ. Supramolecular transitions in native cellulose-I during progressive oxidation reaction leading to quasi-spherical nanoparticles of 6-carboxycellulose. Carbohydr Polym 2014; 113:615-23. [PMID: 25256525 DOI: 10.1016/j.carbpol.2014.07.056] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 07/22/2014] [Accepted: 07/23/2014] [Indexed: 11/25/2022]
Abstract
Cellulose-I swells considerably in phosphoric acid, and converts to amorphous cellulose via a cellulose-II transition state. Controlled oxidation of cellulose-I to 6-carboxycellulose (6 CC) using HNO3-H3PO4-NaNO2 oxidation system led to the selective production of 6 CC's of varying carboxyl contents (1.7-22%) as well as various shapes and sizes (macro-sized fibrils of several micron length and/or spherical nanoparticles of 25-35 nm), depending on the reaction conditions. 6 CC's having less than 14% carboxyl content were largely in cellulose-II form (WAXRD values in-between cellulose I and cellulose II), whereas at 14-22% the 6 CC's were largely amorphous; only trace crystallinity was observed at 19% and 22% carboxyl 6 CC. Spherical nanoparticles retained a high degree of crystallinity having cellulose-I structure, whereas the macro-sized fibrils were largely converted to cellulose-II structure. Analysis by WAXRD as well as by CP-MAS (13)C NMR studies gave similar conclusions. Reduced molecular weight with progressive oxidation, including presence of oligomers, was also evident from an increase in the reducing-end carbon peak at ∼ 92 ppm. For high oxidation levels (>14%) the NMR 92-96 ppm peaks disappeared on extracting with dilute alkali, due to soluble oligomers being removed.
Collapse
Affiliation(s)
- Priyanka R Sharma
- Polymer Science & Engineering Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | | | - Anjani J Varma
- Polymer Science & Engineering Division, CSIR-National Chemical Laboratory, Pune 411008, India.
| |
Collapse
|
14
|
Cheng X, Hiras J, Deng K, Bowen B, Simmons BA, Adams PD, Singer SW, Northen TR. High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal β-glucosidase production. Front Microbiol 2013; 4:365. [PMID: 24367356 PMCID: PMC3854461 DOI: 10.3389/fmicb.2013.00365] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/17/2013] [Indexed: 11/13/2022] Open
Abstract
Production of biofuels via enzymatic hydrolysis of complex plant polysaccharides is a subject of intense global interest. Microbial communities are known to express a wide range of enzymes necessary for the saccharification of lignocellulosic feedstocks and serve as a powerful reservoir for enzyme discovery. However, the growth temperature and conditions that yield high cellulase activity vary widely, and the throughput to identify optimal conditions has been limited by the slow handling and conventional analysis. A rapid method that uses small volumes of isolate culture to resolve specific enzyme activity is needed. In this work, a high throughput nanostructure-initiator mass spectrometry (NIMS)-based approach was developed for screening a thermophilic cellulolytic actinomycete, Thermobispora bispora, for β-glucosidase production under various growth conditions. Media that produced high β-glucosidase activity were found to be I/S + glucose or microcrystalline cellulose (MCC), Medium 84 + rolled oats, and M9TE + MCC at 45°C. Supernatants of cell cultures grown in M9TE + 1% MCC cleaved 2.5 times more substrate at 45°C than at all other temperatures. While T. bispora is reported to grow optimally at 60°C in Medium 84 + rolled oats and M9TE + 1% MCC, approximately 40% more conversion was observed at 45°C. This high throughput NIMS approach may provide an important tool in discovery and characterization of enzymes from environmental microbes for industrial and biofuel applications.
Collapse
Affiliation(s)
- Xiaoliang Cheng
- 1Technology Division, Joint BioEnergy Institute Emeryville, CA, USA ; 2Department of Bioenergy/GTL & Structural Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jennifer Hiras
- 3Deconstruction Division, Joint BioEnergy Institute Emeryville, CA, USA ; 4Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Kai Deng
- 1Technology Division, Joint BioEnergy Institute Emeryville, CA, USA ; 5Biological and Materials Science Center, Sandia National Laboratories Livermore, CA, USA
| | - Benjamin Bowen
- 2Department of Bioenergy/GTL & Structural Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Blake A Simmons
- 3Deconstruction Division, Joint BioEnergy Institute Emeryville, CA, USA ; 5Biological and Materials Science Center, Sandia National Laboratories Livermore, CA, USA
| | - Paul D Adams
- 1Technology Division, Joint BioEnergy Institute Emeryville, CA, USA ; 4Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Steven W Singer
- 3Deconstruction Division, Joint BioEnergy Institute Emeryville, CA, USA ; 6Department of Geochemistry, Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; 7Department of Ecology, Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Trent R Northen
- 1Technology Division, Joint BioEnergy Institute Emeryville, CA, USA ; 2Department of Bioenergy/GTL & Structural Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| |
Collapse
|
15
|
Nyyssönen M, Tran HM, Karaoz U, Weihe C, Hadi MZ, Martiny JBH, Martiny AC, Brodie EL. Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries. Front Microbiol 2013; 4:282. [PMID: 24069019 PMCID: PMC3779933 DOI: 10.3389/fmicb.2013.00282] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 09/02/2013] [Indexed: 12/13/2022] Open
Abstract
Recent advances in sequencing technologies generate new predictions and hypotheses about the functional roles of environmental microorganisms. Yet, until we can test these predictions at a scale that matches our ability to generate them, most of them will remain as hypotheses. Function-based mining of metagenomic libraries can provide direct linkages between genes, metabolic traits and microbial taxa and thus bridge this gap between sequence data generation and functional predictions. Here we developed high-throughput screening assays for function-based characterization of activities involved in plant polymer decomposition from environmental metagenomic libraries. The multiplexed assays use fluorogenic and chromogenic substrates, combine automated liquid handling and use a genetically modified expression host to enable simultaneous screening of 12,160 clones for 14 activities in a total of 170,240 reactions. Using this platform we identified 374 (0.26%) cellulose, hemicellulose, chitin, starch, phosphate and protein hydrolyzing clones from fosmid libraries prepared from decomposing leaf litter. Sequencing on the Illumina MiSeq platform, followed by assembly and gene prediction of a subset of 95 fosmid clones, identified a broad range of bacterial phyla, including Actinobacteria, Bacteroidetes, multiple Proteobacteria sub-phyla in addition to some Fungi. Carbohydrate-active enzyme genes from 20 different glycoside hydrolase (GH) families were detected. Using tetranucleotide frequency (TNF) binning of fosmid sequences, multiple enzyme activities from distinct fosmids were linked, demonstrating how biochemically-confirmed functional traits in environmental metagenomes may be attributed to groups of specific organisms. Overall, our results demonstrate how functional screening of metagenomic libraries can be used to connect microbial functionality to community composition and, as a result, complement large-scale metagenomic sequencing efforts.
Collapse
Affiliation(s)
- Mari Nyyssönen
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Strategy for screening metagenomic resources for exocellulase activity using a robotic, high-throughput screening system. J Microbiol Methods 2013; 94:311-6. [DOI: 10.1016/j.mimet.2013.07.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 07/16/2013] [Accepted: 07/16/2013] [Indexed: 11/17/2022]
|
17
|
Pribowo AY, Hu J, Arantes V, Saddler JN. The development and use of an ELISA-based method to follow the distribution of cellulase monocomponents during the hydrolysis of pretreated corn stover. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:80. [PMID: 23687947 PMCID: PMC3666928 DOI: 10.1186/1754-6834-6-80] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 05/10/2013] [Indexed: 05/11/2023]
Abstract
BACKGROUND It is widely recognised that fast, effective hydrolysis of pretreated lignocellulosic substrates requires the synergistic action of multiple types of hydrolytic and some non-hydrolytic proteins. However, due to the complexity of the enzyme mixture, the enzymes interaction with and interference from the substrate and a lack of specific methods to follow the distribution of individual enzymes during hydrolysis, most of enzyme-substrate interaction studies have used purified enzymes and pure cellulose model substrates. As the enzymes present in a typical "cellulase mixture" need to work cooperatively to achieve effective hydrolysis, the action of one enzyme is likely to influence the behaviour of others. The action of the enzymes will be further influenced by the nature of the lignocellulosic substrate. Therefore, it would be beneficial if a method could be developed that allowed us to follow some of the individual enzymes present in a cellulase mixture during hydrolysis of more commercially realistic biomass substrates. RESULTS A high throughput immunoassay that could quantitatively and specifically follow individual cellulase enzymes during hydrolysis was developed. Using monoclonal and polyclonal antibodies (MAb and PAb, respectively), a double-antibody sandwich enzyme-linked immunosorbent assay (ELISA) was developed to specifically quantify cellulase enzymes from Trichoderma reesei: cellobiohydrolase I (Cel7A), cellobiohydrolase II (Cel6A), and endoglucanase I (Cel7B). The interference from substrate materials present in lignocellulosic supernatants could be minimized by dilution. CONCLUSION A double-antibody sandwich ELISA was able to detect and quantify individual enzymes when present in cellulase mixtures. The assay was sensitive over a range of relatively low enzyme concentration (0 - 1 μg/ml), provided the enzymes were first pH adjusted and heat treated to increase their antigenicity. The immunoassay was employed to quantitatively monitor the adsorption of cellulase monocomponents, Cel7A, Cel6A, and Cel7B, that were present in both Celluclast and Accellerase 1000, during the hydrolysis of steam-pretreated corn stover (SPCS). All three enzymes exhibited different individual adsorption profiles. The specific and quantitative adsorption profiles observed with the ELISA method were in agreement with earlier work where more labour intensive enzyme assay techniques were used.
Collapse
Affiliation(s)
- Amadeus Y Pribowo
- Forest Products Biotechnology/Bioenergy Group, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, V6T1Z4, Canada
| | - Jinguang Hu
- Forest Products Biotechnology/Bioenergy Group, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, V6T1Z4, Canada
| | - Valdeir Arantes
- Forest Products Biotechnology/Bioenergy Group, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, V6T1Z4, Canada
| | - Jack N Saddler
- Forest Products Biotechnology/Bioenergy Group, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, V6T1Z4, Canada
| |
Collapse
|
18
|
Assessment of the biomass hydrolysis potential in bacterial isolates from a volcanic environment: biosynthesis of the corresponding activities. World J Microbiol Biotechnol 2012; 28:2889-902. [DOI: 10.1007/s11274-012-1100-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 06/05/2012] [Indexed: 11/25/2022]
|
19
|
Reindl W, Deng K, Cheng X, Singh AK, Simmons BA, Adams PD, Northen TR. Nanostructure‐Initiator Mass Spectrometry (NIMS) for the Analysis of Enzyme Activities. ACTA ACUST UNITED AC 2012. [DOI: 10.1002/9780470559277.ch110221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Wolfgang Reindl
- Joint BioEnergy Institute (JBEI), Lawrence Berkeley National Laboratory Berkeley California
- Department of Bioenergy/GTL & Structural Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley California
| | - Kai Deng
- Joint BioEnergy Institute (JBEI), Lawrence Berkeley National Laboratory Berkeley California
- Biotechnology and Bioengineering & Biomass Science and Conversion Technology Departments, Sandia National Laboratories Livermore California
| | - Xiaoliang Cheng
- Joint BioEnergy Institute (JBEI), Lawrence Berkeley National Laboratory Berkeley California
- Department of Bioenergy/GTL & Structural Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley California
| | - Anup K. Singh
- Joint BioEnergy Institute (JBEI), Lawrence Berkeley National Laboratory Berkeley California
- Biotechnology and Bioengineering & Biomass Science and Conversion Technology Departments, Sandia National Laboratories Livermore California
| | - Blake A. Simmons
- Joint BioEnergy Institute (JBEI), Lawrence Berkeley National Laboratory Berkeley California
- Biotechnology and Bioengineering & Biomass Science and Conversion Technology Departments, Sandia National Laboratories Livermore California
| | - Paul D. Adams
- Joint BioEnergy Institute (JBEI), Lawrence Berkeley National Laboratory Berkeley California
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley California
| | - Trent R. Northen
- Joint BioEnergy Institute (JBEI), Lawrence Berkeley National Laboratory Berkeley California
- Department of Bioenergy/GTL & Structural Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley California
| |
Collapse
|
20
|
Langston JA, Brown K, Xu F, Borch K, Garner A, Sweeney MD. Cloning, expression, and characterization of a cellobiose dehydrogenase from Thielavia terrestris induced under cellulose growth conditions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:802-12. [PMID: 22484439 DOI: 10.1016/j.bbapap.2012.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 03/14/2012] [Accepted: 03/16/2012] [Indexed: 11/19/2022]
Abstract
The enzyme cellobiose dehydrogenase (CDH) is of considerable interest, not only for its biotechnological applications, but also its potential biological role in lignocellulosic biomass breakdown. The enzyme catalyzes the oxidation of cellobiose and other cellodextrins, utilizing a variety of one- and two-electron acceptors, although the electron acceptor employed in nature is still unknown. In this study we show that a CDH is present in the secretome of the thermophilic ascomycete Thielavia terrestris when grown with cellulose, along with a mixture of cellulases and hemicellulases capable of breaking down lignocellulosic biomass. We report the cloning of this T. terrestris CDH gene (cbdA), its recombinant expression in Aspergillus oryzae, and purification and characterization of the T. terrestris CDH protein (TtCDH). The TtCDH shows spectral properties and enzyme activity similar to other characterized CDH enzymes. Substrate specificity was determined for a number of carbohydrate electron donors in the presence of the two-electron acceptor 2,6-dichlorophenol-indophenol. The TtCDH also shows dramatic synergy with Thermoascus aurantiacus glycoside hydrolase family 61A protein in the presence of a β-glucosidase for the cleavage of cellulose.
Collapse
|
21
|
Greving M, Cheng X, Reindl W, Bowen B, Deng K, Louie K, Nyman M, Cohen J, Singh A, Simmons B, Adams P, Siuzdak G, Northen T. Acoustic deposition with NIMS as a high-throughput enzyme activity assay. Anal Bioanal Chem 2012; 403:707-11. [DOI: 10.1007/s00216-012-5908-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 02/22/2012] [Accepted: 02/24/2012] [Indexed: 10/28/2022]
|
22
|
Murphy L, Cruys-Bagger N, Damgaard HD, Baumann MJ, Olsen SN, Borch K, Lassen SF, Sweeney M, Tatsumi H, Westh P. Origin of initial burst in activity for Trichoderma reesei endo-glucanases hydrolyzing insoluble cellulose. J Biol Chem 2012; 287:1252-60. [PMID: 22110134 PMCID: PMC3256860 DOI: 10.1074/jbc.m111.276485] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 11/10/2011] [Indexed: 11/06/2022] Open
Abstract
The kinetics of cellulose hydrolysis have long been described by an initial fast hydrolysis rate, tapering rapidly off, leading to a process that takes days rather than hours to complete. This behavior has been mainly attributed to the action of cellobiohydrolases and often linked to the processive mechanism of this exo-acting group of enzymes. The initial kinetics of endo-glucanases (EGs) is far less investigated, partly due to a limited availability of quantitative assay technologies. We have used isothermal calorimetry to monitor the early time course of the hydrolysis of insoluble cellulose by the three main EGs from Trichoderma reesei (Tr): TrCel7B (formerly EG I), TrCel5A (EG II), and TrCel12A (EG III). These endo-glucanases show a distinctive initial burst with a maximal rate that is about 5-fold higher than the rate after 5 min of hydrolysis. The burst is particularly conspicuous for TrCel7B, which reaches a maximal turnover of about 20 s(-1) at 30 °C and conducts about 1200 catalytic cycles per enzyme molecule in the initial fast phase. For TrCel5A and TrCel12A the extent of the burst is 2-300 cycles per enzyme molecule. The availability of continuous data on EG activity allows an analysis of the mechanisms underlying the initial kinetics, and it is suggested that the slowdown is linked to transient inactivation of enzyme on the cellulose surface. We propose, therefore, that the frequency of structures on the substrate surface that cause transient inactivation determine the extent of the burst phase.
Collapse
Affiliation(s)
- Leigh Murphy
- From Roskilde University, NSM, Biomaterials, 1 Universitetsvej, DK-4000 Roskilde, Denmark
- Novozymes A/S, Krogshøjvej 36, DK-2880 Denmark
| | - Nicolaj Cruys-Bagger
- From Roskilde University, NSM, Biomaterials, 1 Universitetsvej, DK-4000 Roskilde, Denmark
| | | | | | | | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880 Denmark
| | | | | | - Hirosuke Tatsumi
- International Young Researchers Empowerment Center, Shinshu University, Matsumoto, Nagano 390-8621, Japan
| | - Peter Westh
- From Roskilde University, NSM, Biomaterials, 1 Universitetsvej, DK-4000 Roskilde, Denmark
| |
Collapse
|
23
|
|
24
|
Cloning of Thermostable Cellulase Genes of Clostridium thermocellum and Their Secretive Expression in Bacillus subtilis. Appl Biochem Biotechnol 2011; 166:652-62. [DOI: 10.1007/s12010-011-9456-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 11/07/2011] [Indexed: 10/15/2022]
|
25
|
Mewis K, Taupp M, Hallam SJ. A high throughput screen for biomining cellulase activity from metagenomic libraries. J Vis Exp 2011:2461. [PMID: 21307835 DOI: 10.3791/2461] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Cellulose, the most abundant source of organic carbon on the planet, has wide-ranging industrial applications with increasing emphasis on biofuel production (1). Chemical methods to modify or degrade cellulose typically require strong acids and high temperatures. As such, enzymatic methods have become prominent in the bioconversion process. While the identification of active cellulases from bacterial and fungal isolates has been somewhat effective, the vast majority of microbes in nature resist laboratory cultivation. Environmental genomic, also known as metagenomic, screening approaches have great promise in bridging the cultivation gap in the search for novel bioconversion enzymes. Metagenomic screening approaches have successfully recovered novel cellulases from environments as varied as soils (2), buffalo rumen (3) and the termite hind-gut (4) using carboxymethylcellulose (CMC) agar plates stained with congo red dye (based on the method of Teather and Wood (5)). However, the CMC method is limited in throughput, is not quantitative and manifests a low signal to noise ratio (6). Other methods have been reported (7,8) but each use an agar plate-based assay, which is undesirable for high-throughput screening of large insert genomic libraries. Here we present a solution-based screen for cellulase activity using a chromogenic dinitrophenol (DNP)-cellobioside substrate (9). Our library was cloned into the pCC1 copy control fosmid to increase assay sensitivity through copy number induction (10). The method uses one-pot chemistry in 384-well microplates with the final readout provided as an absorbance measurement. This readout is quantitative, sensitive and automated with a throughput of up to 100X 384-well plates per day using a liquid handler and plate reader with attached stacking system.
Collapse
Affiliation(s)
- Keith Mewis
- Microbiology and Immunology, University of British Columbia - UBC
| | | | | |
Collapse
|
26
|
Bharadwaj R, Wong A, Knierim B, Singh S, Holmes BM, Auer M, Simmons BA, Adams PD, Singh AK. High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration. BIORESOURCE TECHNOLOGY 2011; 102:1329-37. [PMID: 20884206 DOI: 10.1016/j.biortech.2010.08.108] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 07/29/2010] [Accepted: 08/27/2010] [Indexed: 05/09/2023]
Abstract
The high cost of lignocellulolytic enzymes is one of the main barriers towards the development of economically competitive biorefineries. Enzyme engineering can be used to significantly increase the production rate as well as specific activity of enzymes. However, the success of enzyme optimization efforts is currently limited by a lack of robust high-throughput (HTP) cellulase screening platforms for insoluble pretreated lignocellulosic substrates. We have developed a cost-effective microplate based HTP enzyme-screening platform for ionic liquid (IL) pretreated lignocellulose. By performing in-situ biomass regeneration in micro-volumes, we can volumetrically meter biomass (sub-mg loading) and also precisely control the amount of residual IL for engineering novel IL-tolerant cellulases. Our platform only requires straightforward liquid-handling steps and allows the integration of biomass regeneration, washing, saccharification, and imaging steps in a single microtiter plate. The proposed method can be used to screen individual cellulases as well as to develop novel cellulase cocktails.
Collapse
Affiliation(s)
- Rajiv Bharadwaj
- Technology Division, Joint BioEnergy Institute, Emeryville, CA, United States.
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Gupta R, Baldock SJ, Fielden PR, Grieve BD. A specific, robust, and automated method for routine at-line monitoring of the concentration of cellulases in genetically modified sugarcane plants. Appl Biochem Biotechnol 2010; 163:528-39. [PMID: 21136205 DOI: 10.1007/s12010-010-9059-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 08/09/2010] [Indexed: 11/28/2022]
Abstract
Bagasse is one of the waste crop materials highlighted as commercially viable for cellulosic bio-ethanol production via enzymatic conversion to release fermentable sugars. Genetically modified sugarcane expressing cellobiohydrolases (CBH), endoglucanase (EG), and β-glucosidases (BG) provide a more cost-effective route to cellulose breakdown compared to culturing these enzymes in microbial tanks. Hence, process monitoring of the concentration profile of these key cellulases in incoming batches of sugarcane is required for fiscal measures and bio-ethanol process control. The existing methods due to their non-specificity, requirement of trained analysts, low sample throughput, and low amenability to automation are unsuitable for this purpose. Therefore, this paper explores a membrane-based sample preparation method coupled to capillary zone electrophoresis (CZE) to quantify these enzymes. The maximum enzyme extraction efficiency was obtained by using a polyethersulfone membrane with molecular cut-off of 10 kDa. The use of 15 mM, pH 7.75, phosphate buffer resulted in CZE separation and quantification of CBH, EG, and BG within 10 min. Migration time reproducibility was between 0.56% and 0.7% and hence, suitable for use with automatic peak detection software. Therefore, the developed CZE method is suitable for at-line analysis of BG, CBH, and EG in every batch of harvested sugarcane.
Collapse
Affiliation(s)
- Ruchi Gupta
- School of Electrical and Electronics Engineering, The University of Manchester, Sackville Street Building, Manchester M139PL, UK.
| | | | | | | |
Collapse
|
28
|
Isotachophoresis-based sample preparation of cellulases in sugarcane juice using bovine serum albumin as a model protein. J Chromatogr A 2010; 1217:8026-31. [DOI: 10.1016/j.chroma.2010.08.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 08/15/2010] [Accepted: 08/18/2010] [Indexed: 11/18/2022]
|
29
|
Bharadwaj R, Chen Z, Datta S, Holmes BM, Sapra R, Simmons BA, Adams PD, Singh AK. Microfluidic Glycosyl Hydrolase Screening for Biomass-to-Biofuel Conversion. Anal Chem 2010; 82:9513-20. [DOI: 10.1021/ac102243f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rajiv Bharadwaj
- Technology and Deconstruction Divisions, The Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, Department of Bioengineering, University of California, Berkeley, California 94720, and Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Zhiwei Chen
- Technology and Deconstruction Divisions, The Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, Department of Bioengineering, University of California, Berkeley, California 94720, and Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Supratim Datta
- Technology and Deconstruction Divisions, The Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, Department of Bioengineering, University of California, Berkeley, California 94720, and Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Bradley M. Holmes
- Technology and Deconstruction Divisions, The Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, Department of Bioengineering, University of California, Berkeley, California 94720, and Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Rajat Sapra
- Technology and Deconstruction Divisions, The Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, Department of Bioengineering, University of California, Berkeley, California 94720, and Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Blake A. Simmons
- Technology and Deconstruction Divisions, The Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, Department of Bioengineering, University of California, Berkeley, California 94720, and Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Paul D. Adams
- Technology and Deconstruction Divisions, The Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, Department of Bioengineering, University of California, Berkeley, California 94720, and Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Anup K. Singh
- Technology and Deconstruction Divisions, The Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, Department of Bioengineering, University of California, Berkeley, California 94720, and Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
30
|
Characterization of commercial cellulases and their use in the saccharification of a sugarcane bagasse sample pretreated with dilute sulfuric acid. J Ind Microbiol Biotechnol 2010; 38:1089-98. [DOI: 10.1007/s10295-010-0888-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 09/29/2010] [Indexed: 10/18/2022]
|
31
|
Jimenez-Flores R, Fake G, Carroll J, Hood E, Howard J. A novel method for evaluating the release of fermentable sugars from cellulosic biomass. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2010.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
32
|
Dashtban M, Maki M, Leung KT, Mao C, Qin W. Cellulase activities in biomass conversion: measurement methods and comparison. Crit Rev Biotechnol 2010; 30:302-9. [DOI: 10.3109/07388551.2010.490938] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
33
|
Chandrasekaran A, Bharadwaj R, Park JI, Sapra R, Adams PD, Singh AK. A Microscale Platform for Integrated Cell-Free Expression and Activity Screening of Cellulases. J Proteome Res 2010; 9:5677-83. [DOI: 10.1021/pr1003938] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aarthi Chandrasekaran
- Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Rajiv Bharadwaj
- Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Joshua I. Park
- Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Rajat Sapra
- Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Anup K. Singh
- Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| |
Collapse
|
34
|
Deng W, Tan X, Fang W, Zhang Q, Wang Y. Conversion of Cellulose into Sorbitol over Carbon Nanotube-Supported Ruthenium Catalyst. Catal Letters 2009. [DOI: 10.1007/s10562-009-0136-3] [Citation(s) in RCA: 258] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
35
|
Adden R, Melander C, Brinkmalm G, Knarr M, Engelhardt J, Mischnick P. The Applicability of Enzymes in Cellulose Ether Analysis. ACTA ACUST UNITED AC 2009. [DOI: 10.1002/masy.200950605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
36
|
Ivanen DR, Rongjina NL, Shishlyannikov SM, Litviakova GI, Isaeva-Ivanova LS, Shabalin KA, Kulminskaya AA. Novel precipitated fluorescent substrates for the screening of cellulolytic microorganisms. J Microbiol Methods 2008; 76:295-300. [PMID: 19150471 DOI: 10.1016/j.mimet.2008.12.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2008] [Revised: 12/11/2008] [Accepted: 12/15/2008] [Indexed: 12/01/2022]
Abstract
New substrates, 2-(2'-benzothiazolyl)-phenyl (BTP) cellooligosaccharides with degree of polymerization (d.p.) 2-4 (BTPG(2-4)) were synthesized for the screening of microbial cellulolytic activity in plate assays. The substrates were very efficient that was shown for several cellulolytic bacteria, including yeast-like isolates from Kamchatka hot springs. Three tested bacterial strains and eighteen of 30 of the yeast isolates showed ability to degrade cellulose with cellobiohydrolase, beta-glucosidase and endo-cellulase activities measured with standard substrates. The structures of 2-(2'-benzothiazolyl)-phenyl oligosaccharides were solved by NMR- and mass-spectrometry. The usefulness of the 2-(2'-benzothiazolyl)-phenyl substrates were also shown during purification of the B. polymyxa cellulolytic complex, which consists of at least three types of the enzymes: cellobiohydrolase, endo-beta-d-glucanase and beta-glucosidase.
Collapse
Affiliation(s)
- Dina R Ivanen
- Petersburg Nuclear Physics Institute, Russian Academy of Science, Molecular and Radiation Biophysics Division, 188300, Orlova roscha 1, Gatchina, Leningrad District, Russia
| | | | | | | | | | | | | |
Collapse
|
37
|
Chundawat SPS, Balan V, Dale BE. High-throughput microplate technique for enzymatic hydrolysis of lignocellulosic biomass. Biotechnol Bioeng 2008; 99:1281-94. [PMID: 18306256 DOI: 10.1002/bit.21805] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Several factors will influence the viability of a biochemical platform for manufacturing lignocellulosic based fuels and chemicals, for example, genetically engineering energy crops, reducing pre-treatment severity, and minimizing enzyme loading. Past research on biomass conversion has focused largely on acid based pre-treatment technologies that fractionate lignin and hemicellulose from cellulose. However, for alkaline based (e.g., AFEX) and other lower severity pre-treatments it becomes critical to co-hydrolyze cellulose and hemicellulose using an optimized enzyme cocktail. Lignocellulosics are appropriate substrates to assess hydrolytic activity of enzyme mixtures compared to conventional unrealistic substrates (e.g., filter paper, chromogenic, and fluorigenic compounds) for studying synergistic hydrolysis. However, there are few, if any, high-throughput lignocellulosic digestibility analytical platforms for optimizing biomass conversion. The 96-well Biomass Conversion Research Lab (BCRL) microplate method is a high-throughput assay to study digestibility of lignocellulosic biomass as a function of biomass composition, pre-treatment severity, and enzyme composition. The most suitable method for delivering milled biomass to the microplate was through multi-pipetting slurry suspensions. A rapid bio-enzymatic, spectrophotometric assay was used to determine fermentable sugars. The entire procedure was automated using a robotic pipetting workstation. Several parameters that affect hydrolysis in the microplate were studied and optimized (i.e., particle size reduction, slurry solids concentration, glucan loading, mass transfer issues, and time period for hydrolysis). The microplate method was optimized for crystalline cellulose (Avicel) and ammonia fiber expansion (AFEX) pre-treated corn stover.
Collapse
Affiliation(s)
- Shishir P S Chundawat
- Biomass Conversion Research Lab, Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, USA.
| | | | | |
Collapse
|
38
|
Sun Y, Cheng JJ, Himmel ME, Skory CD, Adney WS, Thomas SR, Tisserat B, Nishimura Y, Yamamoto YT. Expression and characterization of Acidothermus cellulolyticus E1 endoglucanase in transgenic duckweed Lemna minor 8627. BIORESOURCE TECHNOLOGY 2007; 98:2866-72. [PMID: 17127051 DOI: 10.1016/j.biortech.2006.09.055] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 09/25/2006] [Accepted: 09/28/2006] [Indexed: 05/04/2023]
Abstract
Endoglucanase E1 from Acidothermus cellulolyticus was expressed cytosolically under control of the cauliflower mosaic virus 35S promoter in transgenic duckweed, Lemna minor 8627 without any obvious observable phenotypic effects on morphology or rate of growth. The recombinant enzyme co-migrated with the purified catalytic domain fraction of the native E1 protein on western blot analysis, revealing that the cellulose-binding domain was cleaved near or in the linker region. The duckweed-expressed enzyme was biologically active and the expression level was up to 0.24% of total soluble protein. The endoglucanase activity with carboxymethylcellulose averaged 0.2 units mg protein(-1) extracted from fresh duckweed. The optimal temperature and pH for E1 enzyme activity were about 80 degrees C and pH 5, respectively. While extraction with HEPES (N-[2-hydroxyethyl]piperazine-N'-[2-ethanesulfonic acid]) buffer (pH 8) resulted in the highest recovery of total soluble proteins and E1 enzyme, extraction with citrate buffer (pH 4.8) at 65 degrees C enriched relative amounts of E1 enzyme in the extract. This study demonstrates that duckweed may offer new options for the expression of cellulolytic enzymes in transgenic plants.
Collapse
Affiliation(s)
- Ye Sun
- Department of Biological and Agricultural Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Cook DM, DeCrescenzo Henriksen E, Upchurch R, Peterson JBD. Isolation of polymer-degrading bacteria and characterization of the hindgut bacterial community from the detritus-feeding larvae of Tipula abdominalis (Diptera: Tipulidae). Appl Environ Microbiol 2007; 73:5683-6. [PMID: 17630316 PMCID: PMC2042085 DOI: 10.1128/aem.00213-07] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Accepted: 06/28/2007] [Indexed: 02/01/2023] Open
Abstract
The Tipula abdominalis larval hindgut microbial community presumably facilitates digestion of the lignocellulosic diet. The microbial community was investigated through characterization of bacterial isolates and analysis of 16S rRNA gene clone libraries. This initial study revealed novel bacteria and provides a framework for future studies of this symbiosis.
Collapse
Affiliation(s)
- Dana M Cook
- University of Georgia, Department of Microbiology, 1000 Cedar St., 204 Biological Sciences, Athens, GA 30602, USA
| | | | | | | |
Collapse
|
40
|
Wu B, Zhao Y, Gao PJ. Estimation of cellobiohydrolase I activity by numerical differentiation of dynamic ultraviolet spectroscopy. Acta Biochim Biophys Sin (Shanghai) 2006; 38:372-8. [PMID: 16761094 DOI: 10.1111/j.1745-7270.2006.00179.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
1,4-beta-D-glucan cellobiohydrolase I (CBH I), p-nitrophenyl beta-D-cellobioside, p-nitrophenol and cellobiose show distinct ultraviolet spectra, allowing the design of an assay to track the dynamic process of p-nitrophenyl beta-D-cellobioside hydrolysis by CBH I. Based on the linear relationship between p-nitrophenol formation in the hydrolysate and its first derivative absorption curve of AUC340-400 nm (area under the curve), a new sensitive assay for the determination of CBH I activity was developed. The dynamic parameters of catalysis reaction, such as Vm and kcat, can all be derived from this result. The influence of beta-glucosidase and endoglucanase in crude enzyme sample on the assay was discussed in detail. This approach is useful for accurate determination of the activity of CBHs.
Collapse
Affiliation(s)
- Bin Wu
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | | | | |
Collapse
|
41
|
Percival Zhang YH, Himmel ME, Mielenz JR. Outlook for cellulase improvement: screening and selection strategies. Biotechnol Adv 2006; 24:452-81. [PMID: 16690241 DOI: 10.1016/j.biotechadv.2006.03.003] [Citation(s) in RCA: 663] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2006] [Revised: 03/06/2006] [Accepted: 03/11/2006] [Indexed: 10/24/2022]
Abstract
Cellulose is the most abundant renewable natural biological resource, and the production of biobased products and bioenergy from less costly renewable lignocellulosic materials is important for the sustainable development of human beings. A reduction in cellulase production cost, an improvement in cellulase performance, and an increase in sugar yields are all vital to reduce the processing costs of biorefineries. Improvements in specific cellulase activities for non-complexed cellulase mixtures can be implemented through cellulase engineering based on rational design or directed evolution for each cellulase component enzyme, as well as on the reconstitution of cellulase components. Here, we review quantitative cellulase activity assays using soluble and insoluble substrates, and focus on their advantages and limitations. Because there are no clear relationships between cellulase activities on soluble substrates and those on insoluble substrates, soluble substrates should not be used to screen or select improved cellulases for processing relevant solid substrates, such as plant cell walls. Cellulase improvement strategies based on directed evolution using screening on soluble substrates have been only moderately successful, and have primarily targeted improvement in thermal tolerance. Heterogeneity of insoluble cellulose, unclear dynamic interactions between insoluble substrate and cellulase components, and the complex competitive and/or synergic relationship among cellulase components limit rational design and/or strategies, depending on activity screening approaches. Herein, we hypothesize that continuous culture using insoluble cellulosic substrates could be a powerful selection tool for enriching beneficial cellulase mutants from the large library displayed on the cell surface.
Collapse
Affiliation(s)
- Y-H Percival Zhang
- Biological Systems Engineering Department, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
| | | | | |
Collapse
|
42
|
Cao Y, Tan H. Improvement of alkali solubility of cellulose with enzymatic treatment. Appl Microbiol Biotechnol 2006; 70:176-82. [PMID: 16059687 DOI: 10.1007/s00253-005-0069-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Revised: 06/19/2005] [Accepted: 06/20/2005] [Indexed: 11/25/2022]
Abstract
Cellulose was treated with different extracellular microbial enzymes. The treatment of cellulose with the enzymes can improve alkaline solubility. Both endoglucanase and crude cellulase decreased the average degrees of polymerization ([see text]) and improved the alkaline solubility of cellulose most efficiently. The composition of the enzyme, the type of cellulosic materials, pretreatment, and the treatment conditions are the key factors for its effective processing, using the enzymes to improve on alkaline solubility of cellulose. The improvement in the alkaline solubility is caused by the decrease in [see text] and hydrogen bond because of enzymatic hydrolysis.
Collapse
Affiliation(s)
- Yu Cao
- State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, People's Republic of China.
| | | |
Collapse
|
43
|
Reinhold-Hurek B, Maes T, Gemmer S, Van Montagu M, Hurek T. An endoglucanase is involved in infection of rice roots by the not-cellulose-metabolizing endophyte Azoarcus sp. strain BH72. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2006; 19:181-8. [PMID: 16529380 DOI: 10.1094/mpmi-19-0181] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The nitrogen-fixing endophyte Azoarcus sp. strain BH72 infects roots of Kallar grass and rice inter- and intra-cellularly and can spread systemically into shoots without causing symptoms of plant disease. Although cellulose or its breakdown products do not support growth, this strain expresses an endoglucanase, which might be involved in infection. Sequence analysis of eglA places the secreted 34-kDa protein into the glycosyl hydrolases family 5, with highest relatedness (40% identity) to endoglucanases of the phytopathogenic bacteria Xanthomonas campestris and Ralstonia solanacearum. Transcriptional regulation studied by eglA:: gusA fusion was not significantly affected by cellulose or its breakdown products or by microaerobiosis. Strongest induction (threefold) was obtained in bacteria grown in close vicinity to rice roots. Visible sites of expression were the emergence points of lateral roots and root tips, which are the primary regions of ingress into the root. To study the role in endophytic colonization, eglA was inactivated by transposon mutagenesis. Systemic spreading of the eglA mutant and of a pilAB mutant into the rice shoot could no longer be detected by polymerase chain reaction. Microscopic inspection of infection revealed that the intracellular colonization of root epidermis cells was significantly reduced in the eglA- mutant BHE6 compared with the wild type and partially restored in the complementation mutant BHRE2 expressing eglA. This provides evidence that Azoarcus sp. endoglucanase is an important determinant for successful endophytic colonization of rice roots, suggesting an active bacterial colonization process.
Collapse
Affiliation(s)
- Barbara Reinhold-Hurek
- Laboratory of General Microbiology, University Bremen, P.O. Box 33 04 40, D-28334 Bremen, Germany.
| | | | | | | | | |
Collapse
|
44
|
Zhang YHP, Cui J, Lynd LR, Kuang LR. A Transition from Cellulose Swelling to Cellulose Dissolution byo-Phosphoric Acid: Evidence from Enzymatic Hydrolysis and Supramolecular Structure. Biomacromolecules 2006; 7:644-8. [PMID: 16471942 DOI: 10.1021/bm050799c] [Citation(s) in RCA: 340] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Y-H Percival Zhang
- Biological Systems Engineering Department, Virginia Polytechnic Institute and State University, Blacksburg, 24060, USA.
| | | | | | | |
Collapse
|
45
|
Cao Y, Tan H. Study on crystal structures of enzyme-hydrolyzed cellulosic materials by X-ray diffraction. Enzyme Microb Technol 2005. [DOI: 10.1016/j.enzmictec.2004.09.002] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
46
|
|
47
|
|
48
|
Meeuwsen PJ, Vincken JP, Beldman G, Voragen AG. A universal assay for screening expression libraries for carbohydrases. J Biosci Bioeng 2000; 89:107-9. [PMID: 16232711 DOI: 10.1016/s1389-1723(00)88062-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/1999] [Accepted: 11/07/1999] [Indexed: 11/16/2022]
Abstract
Although many assays are available for the screening of expression libraries for carbohydrases, some enzymes cannot be detected because their substrates are incompatible with the existing assays. One thing that all carbohydrases have in common is that they increase the number of reducing ends when degrading their substrates. In this paper we explore the possibility of detecting this increase with the highly sensitive bicinchoninic acid (BCA) reducing value assay. This assay can be used for the detection of all carbohydrases degrading any polysaccharide; enzymes with either an exo- or an endo-type of mechanism can be detected at the same time. A cDNA library of Aspergillus tubigensis expressed in Kluyveromyces lactis clones, was screened with this assay for the presence of xylogalacturonan degrading enzyme(s). High background absorbances caused by culture medium, by proteins produced by the clones and by substrate could be dealt with by using the precautions described in this note. Three xylogalacturonase producing clones were found using this procedure.
Collapse
Affiliation(s)
- P J Meeuwsen
- Food Chemistry Group, Department of Food Technology and Nutritional Sciences, Wageningen Agricultural University, Bomenweg 2, NL-6703 HD Wageningen, The Netherlands
| | | | | | | |
Collapse
|
49
|
Vlasenko EY, Ryan AI, Shoemaker CF, Shoemaker SP. The use of capillary viscometry, reducing end-group analysis, and size exclusion chromatography combined with multi-angle laser light scattering to characterize endo-1,4-β-d-glucanases on carboxymethylcellulose: a comparative evaluation of the three methods. Enzyme Microb Technol 1998. [DOI: 10.1016/s0141-0229(98)00052-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
50
|
Thomas L, Crawford DL. Cloning of clustered Streptomyces viridosporus T7A lignocellulose catabolism genes encoding peroxidase and endoglucanase and their extracellular expression in Pichia pastoris. Can J Microbiol 1998; 44:364-72. [PMID: 9674109 DOI: 10.1139/w98-010] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A 4.1-kb fragment of chromosomal DNA from the lignocellulose-decomposing actinomycete Streptomyces viridosporus T7A was previously found to encode a lignin peroxidase gene. However, when cloned into Escherichia coli in pBSKS+, peroxidase activity was not expressed. When cloned in pIJ702 in Streptomyces lividans, the gene was expressed in a peroxidase positive background, owing to the production by S. lividans of its own extracellular peroxidase. To circumvent these problems, the DNA was cloned into the commercial expression vector pIC9 for extracellular expression in the yeast Pichia pastoris. Yeast transformants, however, expressed two activities, extracellular peroxidase and an extracellular endoglucanase. The enzymes were not expressed by the yeast cells alone or by yeast cells with pIC9 without the insert. Expression of the enzymes by only those transformants expressing the 4.1-kb DNA was confirmed by Western blot analyses, by nondenaturing activity gel staining, and by spectrophotometric enzyme assays of extracellular culture filtrates. Activity gel staining showed that the two activities resided in different proteins and the peroxidase expressed was similar to ALip-P3, one of the isoenzymes of lignin peroxidase of the S. viridosporus T7A wildtype. Other evidence indicated that in the transformants, the peroxidase and endoglucanase genes in the 4.1-kb insert were controlled by the methanol-inducible AOX1 yeast promoter in pIC9, since their expression was induced by methanol. In the best transformants, extracellular production of peroxidase by recombinant P. pastoris cultures was significantly higher than typically observed in S. viridosporus. The results also indicate that lignocellulose catabolism genes may be clustered on the S. viridosporus chromosome.
Collapse
Affiliation(s)
- L Thomas
- Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow 83844-3052, USA
| | | |
Collapse
|