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Vermaas JV, Petridis L, Qi X, Schulz R, Lindner B, Smith JC. Mechanism of lignin inhibition of enzymatic biomass deconstruction. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:217. [PMID: 26697106 PMCID: PMC4687093 DOI: 10.1186/s13068-015-0379-8] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 11/09/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND The conversion of plant biomass to ethanol via enzymatic cellulose hydrolysis offers a potentially sustainable route to biofuel production. However, the inhibition of enzymatic activity in pretreated biomass by lignin severely limits the efficiency of this process. RESULTS By performing atomic-detail molecular dynamics simulation of a biomass model containing cellulose, lignin, and cellulases (TrCel7A), we elucidate detailed lignin inhibition mechanisms. We find that lignin binds preferentially both to the elements of cellulose to which the cellulases also preferentially bind (the hydrophobic faces) and also to the specific residues on the cellulose-binding module of the cellulase that are critical for cellulose binding of TrCel7A (Y466, Y492, and Y493). CONCLUSIONS Lignin thus binds exactly where for industrial purposes it is least desired, providing a simple explanation of why hydrolysis yields increase with lignin removal.
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Affiliation(s)
- Josh V. Vermaas
- />UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN USA
- />Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 61801 Urbana, IL USA
| | - Loukas Petridis
- />UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN USA
| | - Xianghong Qi
- />UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN USA
- />Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, 37996 Knoxville, TN USA
| | - Roland Schulz
- />UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN USA
- />Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, 37996 Knoxville, TN USA
| | - Benjamin Lindner
- />UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN USA
| | - Jeremy. C. Smith
- />UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN USA
- />Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, 37996 Knoxville, TN USA
- />University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, P.O.Box 2008, Oak Ridge, TN 37831-6309 USA
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52
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Greene ER, Himmel ME, Beckham GT, Tan Z. Glycosylation of Cellulases: Engineering Better Enzymes for Biofuels. Adv Carbohydr Chem Biochem 2015; 72:63-112. [PMID: 26613815 DOI: 10.1016/bs.accb.2015.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cellulose in plant cell walls is the largest reservoir of renewable carbon on Earth. The saccharification of cellulose from plant biomass into soluble sugars can be achieved using fungal and bacterial cellulolytic enzymes, cellulases, and further converted into fuels and chemicals. Most fungal cellulases are both N- and O-glycosylated in their native form, yet the consequences of glycosylation on activity and structure are not fully understood. Studying protein glycosylation is challenging as glycans are extremely heterogeneous, stereochemically complex, and glycosylation is not under direct genetic control. Despite these limitations, many studies have begun to unveil the role of cellulase glycosylation, especially in the industrially relevant cellobiohydrolase from Trichoderma reesei, Cel7A. Glycosylation confers many beneficial properties to cellulases including enhanced activity, thermal and proteolytic stability, and structural stabilization. However, glycosylation must be controlled carefully as such positive effects can be dampened or reversed. Encouragingly, methods for the manipulation of glycan structures have been recently reported that employ genetic tuning of glycan-active enzymes expressed from homogeneous and heterologous fungal hosts. Taken together, these studies have enabled new strategies for the exploitation of protein glycosylation for the production of enhanced cellulases for biofuel production.
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53
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Gao D, Haarmeyer C, Balan V, Whitehead TA, Dale BE, Chundawat SPS. Lignin triggers irreversible cellulase loss during pretreated lignocellulosic biomass saccharification. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:175. [PMID: 25530803 PMCID: PMC4272552 DOI: 10.1186/s13068-014-0175-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/27/2014] [Indexed: 05/02/2023]
Abstract
BACKGROUND Non-productive binding of enzymes to lignin is thought to impede the saccharification efficiency of pretreated lignocellulosic biomass to fermentable sugars. Due to a lack of suitable analytical techniques that track binding of individual enzymes within complex protein mixtures and the difficulty in distinguishing the contribution of productive (binding to specific glycans) versus non-productive (binding to lignin) binding of cellulases to lignocellulose, there is currently a poor understanding of individual enzyme adsorption to lignin during the time course of pretreated biomass saccharification. RESULTS In this study, we have utilized an FPLC (fast protein liquid chromatography)-based methodology to quantify free Trichoderma reesei cellulases (namely CBH I, CBH II, and EG I) concentration within a complex hydrolyzate mixture during the varying time course of biomass saccharification. Three pretreated corn stover (CS) samples were included in this study: Ammonia Fiber Expansion(a) (AFEX™-CS), dilute acid (DA-CS), and ionic liquid (IL-CS) pretreatments. The relative fraction of bound individual cellulases varied depending not only on the pretreated biomass type (and lignin abundance) but also on the type of cellulase. Acid pretreated biomass had the highest levels of non-recoverable cellulases, while ionic liquid pretreated biomass had the highest overall cellulase recovery. CBH II has the lowest thermal stability among the three T. reesei cellulases tested. By preparing recombinant family 1 carbohydrate binding module (CBM) fusion proteins, we have shown that family 1 CBMs are highly implicated in the non-productive binding of full-length T. reesei cellulases to lignin. CONCLUSIONS Our findings aid in further understanding the complex mechanisms of non-productive binding of cellulases to pretreated lignocellulosic biomass. Developing optimized pretreatment processes with reduced or modified lignin content to minimize non-productive enzyme binding or engineering pretreatment-specific, low-lignin binding cellulases will improve enzyme specific activity, facilitate enzyme recycling, and thereby permit production of cheaper biofuels.
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Affiliation(s)
- Dahai Gao
- />Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824 USA
- />Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, 164 Food Safety and Toxicology Building, East Lansing, MI 48824 USA
- />Biomass Conversion Research Lab (BCRL), MBI Building, 3900 Collins Road, East Lansing, MI 48910 USA
| | - Carolyn Haarmeyer
- />Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824 USA
| | - Venkatesh Balan
- />Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824 USA
- />Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, 164 Food Safety and Toxicology Building, East Lansing, MI 48824 USA
- />Biomass Conversion Research Lab (BCRL), MBI Building, 3900 Collins Road, East Lansing, MI 48910 USA
| | - Timothy A Whitehead
- />Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824 USA
- />Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824 USA
| | - Bruce E Dale
- />Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824 USA
- />Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, 164 Food Safety and Toxicology Building, East Lansing, MI 48824 USA
- />Biomass Conversion Research Lab (BCRL), MBI Building, 3900 Collins Road, East Lansing, MI 48910 USA
| | - Shishir PS Chundawat
- />Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824 USA
- />Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, 164 Food Safety and Toxicology Building, East Lansing, MI 48824 USA
- />Biomass Conversion Research Lab (BCRL), MBI Building, 3900 Collins Road, East Lansing, MI 48910 USA
- />Department of Chemical & Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Room C-150A, Piscataway, NJ 08854 USA
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54
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Miyamoto H, Schnupf U, Brady JW. Water structuring over the hydrophobic surface of cellulose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:11017-11023. [PMID: 25365241 DOI: 10.1021/jf501763r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Many important biological solutes possess not only polar and hydrogen-bonding functionalities but also weakly hydrating, or hydrophobic, surfaces. While the aggregation of these hydrophobic surfaces has been shown to play an important role in the aggregation of individual chains of cellulose, it is not known whether the water structuring imposed by these hydrophobic surfaces more closely resembles that associated with small hydrophobic solutes like methane and fats or more closely resembles that associated with extended hydrophobic surfaces like mica or waxy planes. By using molecular dynamics simulations to characterize the water molecule orientations over different regions of the 100 surface of cellulose in contact with water, it was found that the hydrophobic strips of the cellulose crystal are sufficiently narrow that they hydrate like a fatty acid chain, rather than like a more extended surface, suggesting that their aggregation would be dominated by entropy rather than enthalpy.
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Affiliation(s)
- Hitomi Miyamoto
- Department of Food Science, Cornell University , Ithaca, New York 14853, United States
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55
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Carbohydrate-binding modules of fungal cellulases: occurrence in nature, function, and relevance in industrial biomass conversion. ADVANCES IN APPLIED MICROBIOLOGY 2014; 88:103-65. [PMID: 24767427 DOI: 10.1016/b978-0-12-800260-5.00004-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this review, the present knowledge on the occurrence of cellulases, with a special emphasis on the presence of carbohydrate-binding modules (CBMs) in various fungal strains, has been summarized. The importance of efficient fungal cellulases is growing due to their potential uses in biorefinery processes where lignocellulosic biomasses are converted to platform sugars and further to biofuels and chemicals. Most secreted cellulases studied in detail have a bimodular structure containing an active core domain attached to a CBM. CBMs are traditionally been considered as essential parts in cellulases, especially in cellobiohydrolases. However, presently available genome data indicate that many cellulases lack the binding domains in cellulose-degrading organisms. Recent data also demonstrate that CBMs are not necessary for the action of cellulases and they solely increase the concentration of enzymes on the substrate surfaces. On the other hand, in practical industrial processes where high substrate concentrations with low amounts of water are employed, the enzymes have been shown to act equally efficiently with and without CBM. Furthermore, available kinetic data show that enzymes without CBMs can desorb more readily from the often lignaceous substrates, that is, they are not stuck on the substrates and are thus available for new actions. In this review, the available data on the natural habitats of different wood-degrading organisms (with emphasis on the amount of water present during wood degradation) and occurrence of cellulose-binding domains in their genome have been assessed in order to identify evolutionary advantages for the development of CBM-less cellulases in nature.
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56
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Specificity of O-glycosylation in enhancing the stability and cellulose binding affinity of Family 1 carbohydrate-binding modules. Proc Natl Acad Sci U S A 2014; 111:7612-7. [PMID: 24821760 DOI: 10.1073/pnas.1402518111] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The majority of biological turnover of lignocellulosic biomass in nature is conducted by fungi, which commonly use Family 1 carbohydrate-binding modules (CBMs) for targeting enzymes to cellulose. Family 1 CBMs are glycosylated, but the effects of glycosylation on CBM function remain unknown. Here, the effects of O-mannosylation are examined on the Family 1 CBM from the Trichoderma reesei Family 7 cellobiohydrolase at three glycosylation sites. To enable this work, a procedure to synthesize glycosylated Family 1 CBMs was developed. Subsequently, a library of 20 CBMs was synthesized with mono-, di-, or trisaccharides at each site for comparison of binding affinity, proteolytic stability, and thermostability. The results show that, although CBM mannosylation does not induce major conformational changes, it can increase the thermolysin cleavage resistance up to 50-fold depending on the number of mannose units on the CBM and the attachment site. O-Mannosylation also increases the thermostability of CBM glycoforms up to 16 °C, and a mannose disaccharide at Ser3 seems to have the largest themostabilizing effect. Interestingly, the glycoforms with small glycans at each site displayed higher binding affinities for crystalline cellulose, and the glycoform with a single mannose at each of three positions conferred the highest affinity enhancement of 7.4-fold. Overall, by combining chemical glycoprotein synthesis and functional studies, we show that specific glycosylation events confer multiple beneficial properties on Family 1 CBMs.
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57
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Wahlström R, Rahikainen J, Kruus K, Suurnäkki A. Cellulose hydrolysis and binding with Trichoderma reesei Cel5A and Cel7A and their core domains in ionic liquid solutions. Biotechnol Bioeng 2013; 111:726-33. [PMID: 24258388 DOI: 10.1002/bit.25144] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 09/26/2013] [Accepted: 10/28/2013] [Indexed: 11/06/2022]
Abstract
Ionic liquids (ILs) dissolve lignocellulosic biomass and have a high potential as pretreatment prior to total enzymatic hydrolysis. ILs are, however, known to inactivate cellulases. In this article, enzymatic hydrolysis of microcrystalline cellulose (MCC) and enzyme binding onto the cellulosic substrate were studied in the presence of cellulose-dissolving ILs. Two different ILs, 1,3-dimethylimidazolium dimethylphosphate ([DMIM]DMP) and 1-ethyl-3-methylimidazolium acetate ([EMIM]AcO), and two monocomponent cellulases, Trichoderma reesei cellobiohydrolase Cel7A and endoglucanase Cel5A, were used in the study. The role and IL sensitivity of the carbohydrate-binding module (CBM) were studied by performing hydrolysis and binding experiments with both the intact cellulases, and their respective core domains (CDs). Based on hydrolysis yields and substrate binding experiments for the intact enzymes and their CDs in the presence of ILs, the function of the CBM appeared to be very IL sensitive. Binding data suggested that the CBM was more important for the substrate binding of endoglucanase Cel5A than for the binding of cellobiohydrolase Cel7A. The CD of Cel7A was able to bind well to cellulose even without a CBM, whereas Cel5A CD had very low binding affinity. Hydrolysis also occurred with Cel5A CD even if this protein had very low binding affinity in all the studied matrices. Binding and hydrolysis were less affected by the studied ILs for Cel7A than for Cel5A. To our knowledge, this is the first systematic study of IL effects on cellulase substrate binding.
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Affiliation(s)
- Ronny Wahlström
- VTT - Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Uusimaa, Finland.
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58
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Haghpanah JS, Tu R, Da Silva S, Yan D, Mueller S, Weder C, Foster EJ, Sacui I, Gilman JW, Montclare JK. Bionanocomposites: Differential Effects of Cellulose Nanocrystals on Protein Diblock Copolymers. Biomacromolecules 2013; 14:4360-7. [DOI: 10.1021/bm401304w] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jennifer S. Haghpanah
- Department
of Chemical and Biomolecular Engineering, Polytechnic Institute of New York University, Brooklyn, New York 11201, United States
| | - Raymond Tu
- Department
of Chemical Engineering, City College of New York, New York, New York 10031, United States
| | - Sandra Da Silva
- Biomaterials
and Biosystems Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Deng Yan
- Skirball
Institute of Biomolecular Medicine, Microscopy Core Facilities, NYU Medical Center, New York, New York, 10016, United States
| | - Silvana Mueller
- Adolphe
Merkle Institute, University of Fribourg, CH-1723 Marly, Switzerland
| | - Christoph Weder
- Adolphe
Merkle Institute, University of Fribourg, CH-1723 Marly, Switzerland
| | - E. Johan Foster
- Adolphe
Merkle Institute, University of Fribourg, CH-1723 Marly, Switzerland
| | - Iulia Sacui
- Materials
Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Jeffery W. Gilman
- Materials
Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Jin Kim Montclare
- Department
of Chemical and Biomolecular Engineering, Polytechnic Institute of New York University, Brooklyn, New York 11201, United States
- Department
of Biochemistry, SUNY Downstate Medical Center, Brooklyn, New York 11203, United States
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59
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Evaluation of drug interactions with nanofibrillar cellulose. Eur J Pharm Biopharm 2013; 85:1238-44. [DOI: 10.1016/j.ejpb.2013.05.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/12/2013] [Accepted: 05/28/2013] [Indexed: 01/21/2023]
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60
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Rahikainen JL, Evans JD, Mikander S, Kalliola A, Puranen T, Tamminen T, Marjamaa K, Kruus K. Cellulase–lignin interactions—The role of carbohydrate-binding module and pH in non-productive binding. Enzyme Microb Technol 2013; 53:315-21. [DOI: 10.1016/j.enzmictec.2013.07.003] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/04/2013] [Accepted: 07/08/2013] [Indexed: 11/17/2022]
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61
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Payne CM, Resch MG, Chen L, Crowley MF, Himmel ME, Taylor LE, Sandgren M, Ståhlberg J, Stals I, Tan Z, Beckham GT. Glycosylated linkers in multimodular lignocellulose-degrading enzymes dynamically bind to cellulose. Proc Natl Acad Sci U S A 2013; 110:14646-51. [PMID: 23959893 PMCID: PMC3767562 DOI: 10.1073/pnas.1309106110] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plant cell-wall polysaccharides represent a vast source of food in nature. To depolymerize polysaccharides to soluble sugars, many organisms use multifunctional enzyme mixtures consisting of glycoside hydrolases, lytic polysaccharide mono-oxygenases, polysaccharide lyases, and carbohydrate esterases, as well as accessory, redox-active enzymes for lignin depolymerization. Many of these enzymes that degrade lignocellulose are multimodular with carbohydrate-binding modules (CBMs) and catalytic domains connected by flexible, glycosylated linkers. These linkers have long been thought to simply serve as a tether between structured domains or to act in an inchworm-like fashion during catalytic action. To examine linker function, we performed molecular dynamics (MD) simulations of the Trichoderma reesei Family 6 and Family 7 cellobiohydrolases (TrCel6A and TrCel7A, respectively) bound to cellulose. During these simulations, the glycosylated linkers bind directly to cellulose, suggesting a previously unknown role in enzyme action. The prediction from the MD simulations was examined experimentally by measuring the binding affinity of the Cel7A CBM and the natively glycosylated Cel7A CBM-linker. On crystalline cellulose, the glycosylated linker enhances the binding affinity over the CBM alone by an order of magnitude. The MD simulations before and after binding of the linker also suggest that the bound linker may affect enzyme action due to significant damping in the enzyme fluctuations. Together, these results suggest that glycosylated linkers in carbohydrate-active enzymes, which are intrinsically disordered proteins in solution, aid in dynamic binding during the enzymatic deconstruction of plant cell walls.
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Affiliation(s)
- Christina M. Payne
- Biosciences Center and
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY 40506
| | | | - Liqun Chen
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80303
| | | | | | | | - Mats Sandgren
- Department of Molecular Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Molecular Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Ingeborg Stals
- Faculty of Applied Bioscience Engineering, University College Ghent, 9000 Ghent, Belgium
- Department of Biochemistry and Molecular Biology, Ghent University, 9000 Ghent, Belgium; and
| | - Zhongping Tan
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80303
| | - Gregg T. Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401
- Department of Chemical Engineering, Colorado School of Mines, Golden, CO 80401
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62
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Engineering chimeric thermostable GH7 cellobiohydrolases in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2013; 98:2991-3001. [DOI: 10.1007/s00253-013-5177-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/29/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
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63
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Shang BZ, Chang R, Chu JW. Systems-level modeling with molecular resolution elucidates the rate-limiting mechanisms of cellulose decomposition by cellobiohydrolases. J Biol Chem 2013; 288:29081-9. [PMID: 23950182 DOI: 10.1074/jbc.m113.497412] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Interprotein and enzyme-substrate couplings in interfacial biocatalysis induce spatial correlations beyond the capabilities of classical mass-action principles in modeling reaction kinetics. To understand the impact of spatial constraints on enzyme kinetics, we developed a computational scheme to simulate the reaction network of enzymes with the structures of individual proteins and substrate molecules explicitly resolved in the three-dimensional space. This methodology was applied to elucidate the rate-limiting mechanisms of crystalline cellulose decomposition by cellobiohydrolases. We illustrate that the primary bottlenecks are slow complexation of glucan chains into the enzyme active site and excessive enzyme jamming along the crowded substrate. Jamming could be alleviated by increasing the decomplexation rate constant but at the expense of reduced processivity. We demonstrate that enhancing the apparent reaction rate required a subtle balance between accelerating the complexation driving force and simultaneously avoiding enzyme jamming. Via a spatiotemporal systems analysis, we developed a unified mechanistic framework that delineates the experimental conditions under which different sets of rate-limiting behaviors emerge. We found that optimization of the complexation-exchange kinetics is critical for overcoming the barriers imposed by interfacial confinement and accelerating the apparent rate of enzymatic cellulose decomposition.
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Affiliation(s)
- Barry Z Shang
- From the Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720
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64
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Increased enzyme binding to substrate is not necessary for more efficient cellulose hydrolysis. Proc Natl Acad Sci U S A 2013; 110:10922-7. [PMID: 23784776 DOI: 10.1073/pnas.1213426110] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Substrate binding is typically one of the rate-limiting steps preceding enzyme catalytic action during homogeneous reactions. However, interfacial-based enzyme catalysis on insoluble crystalline substrates, like cellulose, has additional bottlenecks of individual biopolymer chain decrystallization from the substrate interface followed by its processive depolymerization to soluble sugars. This additional decrystallization step has ramifications on the role of enzyme-substrate binding and its relationship to overall catalytic efficiency. We found that altering the crystalline structure of cellulose from its native allomorph I(β) to III(I) results in 40-50% lower binding partition coefficient for fungal cellulases, but surprisingly, it enhanced hydrolytic activity on the latter allomorph. We developed a comprehensive kinetic model for processive cellulases acting on insoluble substrates to explain this anomalous finding. Our model predicts that a reduction in the effective binding affinity to the substrate coupled with an increase in the decrystallization procession rate of individual cellulose chains from the substrate surface into the enzyme active site can reproduce our anomalous experimental findings.
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65
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Molecular dynamics study of carbohydrate binding module mutants of fungal cellobiohydrolases. Carbohydr Res 2013; 374:96-102. [DOI: 10.1016/j.carres.2013.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 03/31/2013] [Accepted: 04/03/2013] [Indexed: 11/19/2022]
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66
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Guo J, Catchmark JM, Mohamed MNA, Benesi AJ, Tien M, Kao TH, Watts HD, Kubicki JD. Identification and Characterization of a Cellulose Binding Heptapeptide Revealed by Phage Display. Biomacromolecules 2013; 14:1795-805. [DOI: 10.1021/bm4001876] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Jing Guo
- Intercollege
Graduate Degree Program in Plant Biology, ‡Department of Agricultural and
Biological Engineering, and §School of Advanced Sciences, Crystal Growth and Crystallographic
Division, VIT University,
Vellore-632014, India
- Department
of Chemistry, ⊥Department of Biochemistry and Molecular Biology, #Department of Geosciences, ▽Center for NanoCellulosics, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Jeffrey M. Catchmark
- Intercollege
Graduate Degree Program in Plant Biology, ‡Department of Agricultural and
Biological Engineering, and §School of Advanced Sciences, Crystal Growth and Crystallographic
Division, VIT University,
Vellore-632014, India
- Department
of Chemistry, ⊥Department of Biochemistry and Molecular Biology, #Department of Geosciences, ▽Center for NanoCellulosics, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Mohamed Naseer Ali Mohamed
- Intercollege
Graduate Degree Program in Plant Biology, ‡Department of Agricultural and
Biological Engineering, and §School of Advanced Sciences, Crystal Growth and Crystallographic
Division, VIT University,
Vellore-632014, India
- Department
of Chemistry, ⊥Department of Biochemistry and Molecular Biology, #Department of Geosciences, ▽Center for NanoCellulosics, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Alan James Benesi
- Intercollege
Graduate Degree Program in Plant Biology, ‡Department of Agricultural and
Biological Engineering, and §School of Advanced Sciences, Crystal Growth and Crystallographic
Division, VIT University,
Vellore-632014, India
- Department
of Chemistry, ⊥Department of Biochemistry and Molecular Biology, #Department of Geosciences, ▽Center for NanoCellulosics, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Ming Tien
- Intercollege
Graduate Degree Program in Plant Biology, ‡Department of Agricultural and
Biological Engineering, and §School of Advanced Sciences, Crystal Growth and Crystallographic
Division, VIT University,
Vellore-632014, India
- Department
of Chemistry, ⊥Department of Biochemistry and Molecular Biology, #Department of Geosciences, ▽Center for NanoCellulosics, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Teh-hui Kao
- Intercollege
Graduate Degree Program in Plant Biology, ‡Department of Agricultural and
Biological Engineering, and §School of Advanced Sciences, Crystal Growth and Crystallographic
Division, VIT University,
Vellore-632014, India
- Department
of Chemistry, ⊥Department of Biochemistry and Molecular Biology, #Department of Geosciences, ▽Center for NanoCellulosics, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Heath D. Watts
- Intercollege
Graduate Degree Program in Plant Biology, ‡Department of Agricultural and
Biological Engineering, and §School of Advanced Sciences, Crystal Growth and Crystallographic
Division, VIT University,
Vellore-632014, India
- Department
of Chemistry, ⊥Department of Biochemistry and Molecular Biology, #Department of Geosciences, ▽Center for NanoCellulosics, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - James D. Kubicki
- Intercollege
Graduate Degree Program in Plant Biology, ‡Department of Agricultural and
Biological Engineering, and §School of Advanced Sciences, Crystal Growth and Crystallographic
Division, VIT University,
Vellore-632014, India
- Department
of Chemistry, ⊥Department of Biochemistry and Molecular Biology, #Department of Geosciences, ▽Center for NanoCellulosics, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
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67
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Karnaouri AC, Topakas E, Christakopoulos P. Cloning, expression, and characterization of a thermostable GH7 endoglucanase from Myceliophthora thermophila capable of high-consistency enzymatic liquefaction. Appl Microbiol Biotechnol 2013; 98:231-42. [DOI: 10.1007/s00253-013-4895-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 03/28/2013] [Accepted: 04/03/2013] [Indexed: 11/30/2022]
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68
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Thongekkaew J, Ikeda H, Masaki K, Iefuji H. Fusion of cellulose binding domain from Trichoderma reesei CBHI to Cryptococcus sp. S-2 cellulase enhances its binding affinity and its cellulolytic activity to insoluble cellulosic substrates. Enzyme Microb Technol 2013; 52:241-6. [DOI: 10.1016/j.enzmictec.2013.02.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/04/2013] [Accepted: 02/04/2013] [Indexed: 11/24/2022]
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69
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Nakamura A, Tsukada T, Auer S, Furuta T, Wada M, Koivula A, Igarashi K, Samejima M. The tryptophan residue at the active site tunnel entrance of Trichoderma reesei cellobiohydrolase Cel7A is important for initiation of degradation of crystalline cellulose. J Biol Chem 2013; 288:13503-10. [PMID: 23532843 DOI: 10.1074/jbc.m113.452623] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Mutation of Trp-40 in the Cel7A cellobiohydrolase from Trichoderma reesei (TrCel7A) causes a loss of crystalline cellulose-degrading ability. RESULTS Mutant W40A showed reduced specific activity for crystalline cellulose and diffused the cellulose chain from the entrance of the active site tunnel. CONCLUSION Trp-40 is essential for chain end loading to initiate processive hydrolysis of TrCel7A. SIGNIFICANCE The mechanisms of crystalline polysaccharide degradation are clarified. The glycoside hydrolase family 7 cellobiohydrolase Cel7A from Trichoderma reesei is one of the best studied cellulases with the ability to degrade highly crystalline cellulose. The catalytic domain and the cellulose-binding domain (CBD) are both necessary for full activity on crystalline substrates. Our previous high-speed atomic force microscopy studies showed that mutation of Trp-40 at the entrance of the catalytic tunnel drastically decreases the ability to degrade crystalline cellulose. Here, we examined the activities of the WT enzyme and mutant W40A (with and without the CBD) for various substrates. Evaluation and comparison of the specific activities of the enzymes (WT, W40A, and the corresponding catalytic subunits (WTcat and W40Acat)) adsorbed on crystalline cellulose indicated that Trp-40 is involved in recruiting individual substrate chains into the active site tunnel to initiate processive hydrolysis. This was supported by molecular dynamics simulation study, i.e. the reducing end glucose unit was effectively loaded into the active site of WTcat, but not into that of W40Acat, when the simulation was started from subsite -7. However, when similar simulations were carried out starting from subsite -5, both enzymes held the substrate for 50 ns, indicating that the major difference between WTcat and W40Acat is the length of the free chain end of the substrate required to allow initiation of processive movements; this also reflects the difference between crystalline and amorphous celluloses. The CBD is important for enhancing the enzyme population on crystalline substrate, but it also decreases the specific activity of the adsorbed enzyme, possibly by attaching the enzyme to non-optimal places on the cellulose surface and/or hindering processive hydrolysis.
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Affiliation(s)
- Akihiko Nakamura
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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70
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Bubner P, Plank H, Nidetzky B. Visualizing cellulase activity. Biotechnol Bioeng 2013; 110:1529-49. [DOI: 10.1002/bit.24884] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 01/08/2013] [Accepted: 02/22/2013] [Indexed: 11/08/2022]
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71
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Jiang F, Kittle JD, Tan X, Esker AR, Roman M. Effects of sulfate groups on the adsorption and activity of cellulases on cellulose substrates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:3280-91. [PMID: 23452241 DOI: 10.1021/la3040193] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Pretreatment of lignocellulosic biomass with sulfuric acid may leave sulfate groups on its surface that may hinder its biochemical conversion. This study investigates the effects of sulfate groups on cellulase adsorption onto cellulose substrates and the enzymatic hydrolysis of these substrates. Substrates with different sulfate group densities were prepared from H2SO4- and HCl-hydrolyzed and partially and fully desulfated cellulose nanocrystals. Adsorption onto and hydrolysis of the substrates was analyzed by quartz crystal microbalance with dissipation monitoring (QCM-D). The surface roughness of the substrates, measured by atomic force microscopy, increased with decreasing sulfate group density, but their surface accessibilities, measured by QCM-D H2O/D2O exchange experiments, were similar. The adsorption of cellulose binding domains onto sulfated substrates decreased with increasing sulfate group density, but the adsorption of cellulases increased. The rate of hydrolysis of sulfated substrates decreased with increasing sulfate group density. The results indicated an inhibitory effect of sulfate groups on the enzymatic hydrolysis of cellulose, possibly due to nonproductive binding of the cellulases onto the substrates through electrostatic interactions instead of their cellulose binding domains.
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Affiliation(s)
- Feng Jiang
- Macromolecules and Interfaces Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
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72
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Maurer S, Brady N, Fajardo N, Radke C. Surface kinetics for cooperative fungal cellulase digestion of cellulose from quartz crystal microgravimetry. J Colloid Interface Sci 2013; 394:498-508. [DOI: 10.1016/j.jcis.2012.12.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 12/07/2012] [Accepted: 12/08/2012] [Indexed: 10/27/2022]
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73
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Larroque M, Barriot R, Bottin A, Barre A, Rougé P, Dumas B, Gaulin E. The unique architecture and function of cellulose-interacting proteins in oomycetes revealed by genomic and structural analyses. BMC Genomics 2012; 13:605. [PMID: 23140525 PMCID: PMC3532174 DOI: 10.1186/1471-2164-13-605] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 10/25/2012] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Oomycetes are fungal-like microorganisms evolutionary distinct from true fungi, belonging to the Stramenopile lineage and comprising major plant pathogens. Both oomycetes and fungi express proteins able to interact with cellulose, a major component of plant and oomycete cell walls, through the presence of carbohydrate-binding module belonging to the family 1 (CBM1). Fungal CBM1-containing proteins were implicated in cellulose degradation whereas in oomycetes, the Cellulose Binding Elicitor Lectin (CBEL), a well-characterized CBM1-protein from Phytophthora parasitica, was implicated in cell wall integrity, adhesion to cellulosic substrates and induction of plant immunity. RESULTS To extend our knowledge on CBM1-containing proteins in oomycetes, we have conducted a comprehensive analysis on 60 fungi and 7 oomycetes genomes leading to the identification of 518 CBM1-containing proteins. In plant-interacting microorganisms, the larger number of CBM1-protein coding genes is expressed by necrotroph and hemibiotrophic pathogens, whereas a strong reduction of these genes is observed in symbionts and biotrophs. In fungi, more than 70% of CBM1-containing proteins correspond to enzymatic proteins in which CBM1 is associated with a catalytic unit involved in cellulose degradation. In oomycetes more than 90% of proteins are similar to CBEL in which CBM1 is associated with a non-catalytic PAN/Apple domain, known to interact with specific carbohydrates or proteins. Distinct Stramenopile genomes like diatoms and brown algae are devoid of CBM1 coding genes. A CBM1-PAN/Apple association 3D structural modeling was built allowing the identification of amino acid residues interacting with cellulose and suggesting the putative interaction of the PAN/Apple domain with another type of glucan. By Surface Plasmon Resonance experiments, we showed that CBEL binds to glycoproteins through galactose or N-acetyl-galactosamine motifs. CONCLUSIONS This study provides insight into the evolution and biological roles of CBM1-containing proteins from oomycetes. We show that while CBM1s from fungi and oomycetes are similar, they team up with different protein domains, either in proteins implicated in the degradation of plant cell wall components in the case of fungi or in proteins involved in adhesion to polysaccharidic substrates in the case of oomycetes. This work highlighted the unique role and evolution of CBM1 proteins in oomycete among the Stramenopile lineage.
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Affiliation(s)
- Mathieu Larroque
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan F-31326, France
| | - Roland Barriot
- Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaire, Toulouse F-31000, France
- Centre National de la Recherche Scientifique; LMGM, Toulouse F-31000, France
| | - Arnaud Bottin
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan F-31326, France
| | - Annick Barre
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan F-31326, France
- Present address: Université de Toulouse, UPS, Laboratoire PHARMA-DEV IRD UMR 152, 35 Chemin des Maraîchers, Toulouse 31400, France
| | - Pierre Rougé
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan F-31326, France
- Present address: Université de Toulouse, UPS, Laboratoire PHARMA-DEV IRD UMR 152, 35 Chemin des Maraîchers, Toulouse 31400, France
| | - Bernard Dumas
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan F-31326, France
| | - Elodie Gaulin
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan F-31326, France
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74
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Nakanishi A, Bae J, Kuroda K, Ueda M. Construction of a novel selection system for endoglucanases exhibiting carbohydrate-binding modules optimized for biomass using yeast cell-surface engineering. AMB Express 2012; 2:56. [PMID: 23092441 PMCID: PMC3534607 DOI: 10.1186/2191-0855-2-56] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 09/21/2012] [Indexed: 11/13/2022] Open
Abstract
To permit direct cellulose degradation and ethanol fermentation, Saccharomyces cerevisiae BY4741 (Δsed1) codisplaying 3 cellulases (Trichoderma reesei endoglucanase II [EG], T. reesei cellobiohydrolase II [CBH], and Aspergillus aculeatus β-glucosidase I [BG]) was constructed by yeast cell-surface engineering. The EG used in this study consists of a family 1 carbohydrate-binding module (CBM) and a catalytic module. A comparison with family 1 CBMs revealed conserved amino acid residues and flexible amino acid residues. The flexible amino acid residues were at positions 18, 23, 26, and 27, through which the degrading activity for various cellulose structures in each biomass may have been optimized. To select the optimal combination of CBMs of EGs, a yeast mixture with comprehensively mutated CBM was constructed. The mixture consisted of yeasts codisplaying EG with mutated CBMs, in which 4 flexible residues were comprehensively mutated, CBH, and BG. The yeast mixture was inoculated in selection medium with newspaper as the sole carbon source. The surviving yeast consisted of RTSH yeast (the mutant sequence of CBM: N18R, S23T, S26S, and T27H) and wild-type yeast (CBM was the original) in a ratio of 1:46. The mixture (1 RTSH yeast and 46 wild-type yeasts) had a fermentation activity that was 1.5-fold higher than that of wild-type yeast alone in the early phase of saccharification and fermentation, which indicates that the yeast mixture with comprehensively mutated CBM could be used to select the optimal combination of CBMs suitable for the cellulose of each biomass.
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75
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Maurer SA, Bedbrook CN, Radke CJ. Competitive sorption kinetics of inhibited endo- and exoglucanases on a model cellulose substrate. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:14598-608. [PMID: 22966968 DOI: 10.1021/la3024524] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
For the first time, the competitive adsorption of inhibited cellobiohydrolase I (Cel7A, an exoglucanase) and endoglucanase I (Cel7B) from T. longibrachiatum is studied on cellulose. Using quartz crystal microgravimetry (QCM), sorption histories are measured for individual types of cellulases and their mixtures adsorbing to and desorbing from a model cellulose surface. We find that Cel7A has a higher adsorptive affinity for cellulose than does Cel7B. The adsorption of both cellulases becomes irreversible on time scales of 30-60 min, which are much shorter than those typically used for industrial cellulose hydrolysis. A multicomponent Langmuir kinetic model including first-order irreversible binding is proposed. Although adsorption and desorption rate constants differ between the two enzymes, the rate at which each surface enzyme irreversibly binds is identical. Because of the higher affinity of Cel7A for the cellulose surface, when Cel7A and Cel7B compete for surface sites, a significantly higher bulk concentration of Cel7B is required to achieve comparable surface enzyme concentrations. Because cellulose deconstruction benefits significantly from the cooperative activity of endoglucanases and cellobiohydrolases on the cellulose surface, accounting for competitive adsorption is crucial to developing effective cellulase mixtures.
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Affiliation(s)
- Samuel A Maurer
- Department of Chemical and Biomolecular Engineering, University of California-Berkeley, Berkeley, California 94720-1462, USA
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76
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Structural basis for entropy-driven cellulose binding by a type-A cellulose-binding module (CBM) and bacterial expansin. Proc Natl Acad Sci U S A 2012; 109:14830-5. [PMID: 22927418 DOI: 10.1073/pnas.1213200109] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Components of modular cellulases, type-A cellulose-binding modules (CBMs) bind to crystalline cellulose and enhance enzyme effectiveness, but structural details of the interaction are uncertain. We analyzed cellulose binding by EXLX1, a bacterial expansin with ability to loosen plant cell walls and whose domain D2 has type-A CBM characteristics. EXLX1 strongly binds to crystalline cellulose via D2, whereas its affinity for soluble cellooligosaccharides is weak. Calorimetry indicated cellulose binding was largely entropically driven. We solved the crystal structures of EXLX1 complexed with cellulose-like oligosaccharides to find that EXLX1 binds the ligands through hydrophobic interactions of three linearly arranged aromatic residues in D2. The crystal structures revealed a unique form of ligand-mediated dimerization, with the oligosaccharide sandwiched between two D2 domains in opposite polarity. This report clarifies the molecular target of expansin and the specific molecular interactions of a type-A CBM with cellulose.
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77
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Cheng G, Datta S, Liu Z, Wang C, Murton JK, Brown PA, Jablin MS, Dubey M, Majewski J, Halbert CE, Browning JF, Esker AR, Watson BJ, Zhang H, Hutcheson SW, Huber DL, Sale KL, Simmons BA, Kent MS. Interactions of endoglucanases with amorphous cellulose films resolved by neutron reflectometry and quartz crystal microbalance with dissipation monitoring. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:8348-58. [PMID: 22554348 DOI: 10.1021/la300955q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
A study of the interaction of four endoglucanases with amorphous cellulose films by neutron reflectometry (NR) and quartz crystal microbalance with dissipation monitoring (QCM-D) is reported. The endoglucanases include a mesophilic fungal endoglucanase (Cel45A from H. insolens), a processive endoglucanase from a marine bacterium (Cel5H from S. degradans ), and two from thermophilic bacteria (Cel9A from A. acidocaldarius and Cel5A from T. maritima ). The use of amorphous cellulose is motivated by the promise of ionic liquid pretreatment as a second generation technology that disrupts the native crystalline structure of cellulose. The endoglucanases displayed highly diverse behavior. Cel45A and Cel5H, which possess carbohydrate-binding modules (CBMs), penetrated and digested within the bulk of the films to a far greater extent than Cel9A and Cel5A, which lack CBMs. While both Cel45A and Cel5H were active within the bulk of the films, striking differences were observed. With Cel45A, substantial film expansion and interfacial broadening were observed, whereas for Cel5H the film thickness decreased with little interfacial broadening. These results are consistent with Cel45A digesting within the interior of cellulose chains as a classic endoglucanase, and Cel5H digesting predominantly at chain ends consistent with its designation as a processive endoglucanase.
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Affiliation(s)
- Gang Cheng
- Joint BioEnergy Institute, Emeryville, California, USA
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78
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Harnessing glycosylation to improve cellulase activity. Curr Opin Biotechnol 2012; 23:338-45. [DOI: 10.1016/j.copbio.2011.11.030] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 11/24/2011] [Accepted: 11/26/2011] [Indexed: 11/17/2022]
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79
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Nimlos MR, Beckham GT, Matthews JF, Bu L, Himmel ME, Crowley MF. Binding preferences, surface attachment, diffusivity, and orientation of a family 1 carbohydrate-binding module on cellulose. J Biol Chem 2012; 287:20603-12. [PMID: 22496371 PMCID: PMC3370244 DOI: 10.1074/jbc.m112.358184] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Cellulase enzymes often contain carbohydrate-binding modules (CBMs) for binding to cellulose. The mechanisms by which CBMs recognize specific surfaces of cellulose and aid in deconstruction are essential to understand cellulase action. The Family 1 CBM from the Trichoderma reesei Family 7 cellobiohydrolase, Cel7A, is known to selectively bind to hydrophobic surfaces of native cellulose. It is most commonly suggested that three aromatic residues identify the planar binding face of this CBM, but several recent studies have challenged this hypothesis. Here, we use molecular simulation to study the CBM binding orientation and affinity on hydrophilic and hydrophobic cellulose surfaces. Roughly 43 μs of molecular dynamics simulations were conducted, which enables statistically significant observations. We quantify the fractions of the CBMs that detach from crystal surfaces or diffuse to other surfaces, the diffusivity along the hydrophobic surface, and the overall orientation of the CBM on both hydrophobic and hydrophilic faces. The simulations demonstrate that there is a thermodynamic driving force for the Cel7A CBM to bind preferentially to the hydrophobic surface of cellulose relative to hydrophilic surfaces. In addition, the simulations demonstrate that the CBM can diffuse from hydrophilic surfaces to the hydrophobic surface, whereas the reverse transition is not observed. Lastly, our simulations suggest that the flat faces of Family 1 CBMs are the preferred binding surfaces. These results enhance our understanding of how Family 1 CBMs interact with and recognize specific cellulose surfaces and provide insights into the initial events of cellulase adsorption and diffusion on cellulose.
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Affiliation(s)
- Mark R Nimlos
- National Bioenergy Center, National Renewable Energy Center, Golden, Colorado 80401, USA.
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80
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Sugimoto N, Igarashi K, Samejima M. Cellulose affinity purification of fusion proteins tagged with fungal family 1 cellulose-binding domain. Protein Expr Purif 2012; 82:290-6. [PMID: 22305911 DOI: 10.1016/j.pep.2012.01.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 01/11/2012] [Accepted: 01/13/2012] [Indexed: 11/23/2022]
Abstract
N- or C-terminal fusions of red-fluorescent protein (RFP) with various fungal cellulose-binding domains (CBDs) belonging to carbohydrate binding module (CBM) family 1 were expressed in a Pichia pastoris expression system, and the resulting fusion proteins were used to examine the feasibility of large-scale affinity purification of CBD-tagged proteins on cellulose columns. We found that RFP fused with CBD from Trichoderma reesei CBHI (CBD(Tr)(CBHI)) was expressed at up to 1.2g/l in the culture filtrate, which could be directly injected into the cellulose column. The fusion protein was tightly adsorbed on the cellulose column in the presence of a sufficient amount of ammonium sulfate and was efficiently eluted with pure water. Bovine serum albumin (BSA) was not captured under these conditions, whereas both BSA and the fusion protein were adsorbed on a phenyl column, indicating that the cellulose column can be used for the purification of not only hydrophilic proteins but also for hydrophobic proteins. Recovery of various fusion proteins exceeded 80%. Our results indicate that protein purification by expression of a target protein as a fusion with a fungal family 1 CBD tag in a yeast expression system, followed by affinity purification on a cellulose column, is simple, effective and easily scalable.
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Affiliation(s)
- Naohisa Sugimoto
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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81
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Taylor CB, Talib MF, McCabe C, Bu L, Adney WS, Himmel ME, Crowley MF, Beckham GT. Computational investigation of glycosylation effects on a family 1 carbohydrate-binding module. J Biol Chem 2012; 287:3147-55. [PMID: 22147693 PMCID: PMC3270969 DOI: 10.1074/jbc.m111.270389] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 12/01/2011] [Indexed: 11/06/2022] Open
Abstract
Carbohydrate-binding modules (CBMs) are ubiquitous components of glycoside hydrolases, which degrade polysaccharides in nature. CBMs target specific polysaccharides, and CBM binding affinity to cellulose is known to be proportional to cellulase activity, such that increasing binding affinity is an important component of performance improvement. To ascertain the impact of protein and glycan engineering on CBM binding, we use molecular simulation to quantify cellulose binding of a natively glycosylated Family 1 CBM. To validate our approach, we first examine aromatic-carbohydrate interactions on binding, and our predictions are consistent with previous experiments, showing that a tyrosine to tryptophan mutation yields a 2-fold improvement in binding affinity. We then demonstrate that enhanced binding of 3-6-fold over a nonglycosylated CBM is achieved by the addition of a single, native mannose or a mannose dimer, respectively, which has not been considered previously. Furthermore, we show that the addition of a single, artificial glycan on the anterior of the CBM, with the native, posterior glycans also present, can have a dramatic impact on binding affinity in our model, increasing it up to 140-fold relative to the nonglycosylated CBM. These results suggest new directions in protein engineering, in that modifying glycosylation patterns via heterologous expression, manipulation of culture conditions, or introduction of artificial glycosylation sites, can alter CBM binding affinity to carbohydrates and may thus be a general strategy to enhance cellulase performance. Our results also suggest that CBM binding studies should consider the effects of glycosylation on binding and function.
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Affiliation(s)
| | - M. Faiz Talib
- From the Departments of Chemical and Biomolecular Engineering and
| | - Clare McCabe
- From the Departments of Chemical and Biomolecular Engineering and
- Chemistry, Vanderbilt University, Nashville, Tennessee 37235
| | | | - William S. Adney
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - Michael E. Himmel
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - Michael F. Crowley
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - Gregg T. Beckham
- the National Bioenergy Center and
- the Department of Chemical Engineering, Colorado School of Mines, Golden, Colorado 80401
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82
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Marana SR. Structural and mechanistic fundamentals for designing of cellulases. Comput Struct Biotechnol J 2012; 2:e201209006. [PMID: 24688647 PMCID: PMC3962180 DOI: 10.5936/csbj.201209006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/20/2012] [Accepted: 09/23/2012] [Indexed: 11/22/2022] Open
Affiliation(s)
- Sandro R Marana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, São Paulo, 05513-970, SP, Brazil
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83
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Salinas A, Vega M, Lienqueo ME, Garcia A, Carmona R, Salazar O. Cloning of novel cellulases from cellulolytic fungi: Heterologous expression of a family 5 glycoside hydrolase from Trametes versicolor in Pichia pastoris. Enzyme Microb Technol 2011; 49:485-91. [DOI: 10.1016/j.enzmictec.2011.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 09/15/2011] [Accepted: 10/11/2011] [Indexed: 10/16/2022]
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84
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Hall M, Rubin J, Behrens SH, Bommarius AS. The cellulose-binding domain of cellobiohydrolase Cel7A from Trichoderma reesei is also a thermostabilizing domain. J Biotechnol 2011; 155:370-6. [DOI: 10.1016/j.jbiotec.2011.07.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2011] [Revised: 06/04/2011] [Accepted: 07/12/2011] [Indexed: 11/30/2022]
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85
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Novel cellulose-binding-domain protein in Phytophthora is cell wall localized. PLoS One 2011; 6:e23555. [PMID: 21887271 PMCID: PMC3160888 DOI: 10.1371/journal.pone.0023555] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 07/20/2011] [Indexed: 11/19/2022] Open
Abstract
Cellulose binding domains (CBD) in the carbohydrate binding module family 1 (CBM1) are structurally conserved regions generally linked to catalytic regions of cellulolytic enzymes. While widespread amongst saprophytic fungi that subsist on plant cell wall polysaccharides, they are absent amongst most plant pathogenic fungal cellulases. A genome wide survey for CBM1 was performed on the highly destructive plant pathogen Phytophthora infestans, a fungal-like Stramenopile, to determine if it harbored cellulolytic enzymes with CBM1. Only five genes were found to encode CBM1, and none were associated with catalytic domains. Surveys of other genomes indicated that the CBM1-containing proteins, lacking other domains, represent a unique group of proteins largely confined to the Stramenopiles. Immunolocalization of one of these proteins, CBD1, indicated that it is embedded in the hyphal cell wall. Proteins with CBM1 domains can have plant host elicitor activity, but tests with Agrobacterium-mediated in planta expression and synthetic peptide infiltration failed to identify plant hypersensitive elicitation with CBD1. A structural basis for differential elicitor activity is proposed.
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86
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The impact of Trichoderma reesei Cel7A carbohydrate binding domain mutations on its binding to a cellulose surface: a molecular dynamics free energy study. J Mol Model 2011; 18:1355-64. [DOI: 10.1007/s00894-011-1167-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 06/27/2011] [Indexed: 10/18/2022]
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87
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Ogawa Y, Kimura S, Wada M. Electron diffraction and high-resolution imaging on highly-crystalline β-chitin microfibril. J Struct Biol 2011; 176:83-90. [PMID: 21771660 DOI: 10.1016/j.jsb.2011.07.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 07/05/2011] [Accepted: 07/05/2011] [Indexed: 11/16/2022]
Abstract
The ultrastructure of β-chitin microfibrils from a centric diatom, Thalassiosira, and a tubeworm, Lamellibrachia, was studied using electron diffraction and high-resolution electron microscopy. Electron microdiffraction diagrams corresponding to each projection of the β-chitin crystals were obtained, and all the data support the structure model of anhydrous β-chitin crystals proposed by X-ray diffraction experiments. From high-resolution electron microscopy on ultrathin sections, the cross-sectional shapes of the microfibrils from Thalassiosira and Lamellibrachia were observed as a rectangular and parallelogram, respectively. The lattice fringes corresponding to the (010) plane of anhydrous β-chitin crystals were clearly observed in both cross-sections. Based on these observations, we have constructed a molecular packing model for β-chitin microfibrils.
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Affiliation(s)
- Yu Ogawa
- Department of Biomaterials Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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88
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Hall M, Bansal P, Lee JH, Realff MJ, Bommarius AS. Biological pretreatment of cellulose: enhancing enzymatic hydrolysis rate using cellulose-binding domains from cellulases. BIORESOURCE TECHNOLOGY 2011; 102:2910-5. [PMID: 21111611 DOI: 10.1016/j.biortech.2010.11.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 10/27/2010] [Accepted: 11/01/2010] [Indexed: 05/11/2023]
Abstract
In this study, cellulose-binding domains (CBDs) of cellulases from Trichoderma reesei were used in a pretreatment step and were found to effectively reduce the crystallinity of cellulose (both Avicel and fibrous cellulose). This, in turn, led to higher glucose concentrations (up to 25% increase) in subsequent hydrolysis of cellulose using a mixture of cellulases and without the need for any intermediate purification step. CBDs were shown to be active in a range of temperatures (up to 50°C), while cellulase hydrolytic activity was greatly reduced after incubation at 50°C. This was explained by retention of full binding capacity after incubation at 50°C for 15 h. Our findings suggest that CBDs may be a valuable tool in pretreating cellulose and eventually afford faster enzymatic conversion of cellulose to glucose, thus contributing to more affordable processes in the production of biofuels.
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Affiliation(s)
- Mélanie Hall
- Department of Chemistry, Organic and Bioorganic Chemistry, Heinrichstraße 28, 8010 Graz, Austria
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89
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Mohamed MNA, Watts HD, Guo J, Catchmark JM, Kubicki JD. MP2, density functional theory, and molecular mechanical calculations of C–H···π and hydrogen bond interactions in a cellulose-binding module–cellulose model system. Carbohydr Res 2010; 345:1741-51. [DOI: 10.1016/j.carres.2010.05.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 05/10/2010] [Accepted: 05/22/2010] [Indexed: 10/19/2022]
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90
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91
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Promotion of efficient Saccharification of crystalline cellulose by Aspergillus fumigatus Swo1. Appl Environ Microbiol 2010; 76:2556-61. [PMID: 20173066 DOI: 10.1128/aem.02499-09] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Swollenin is a protein from Trichoderma reesei that has a unique activity for disrupting cellulosic materials, and it has sequence similarity to expansins, plant cell wall proteins that have a loosening effect that leads to cell wall enlargement. In this study we cloned a gene encoding a swollenin-like protein, Swo1, from the filamentous fungus Aspergillus fumigatus, and designated the gene Afswo1. AfSwo1 has a bimodular structure composed of a carbohydrate-binding module family 1 (CBM1) domain and a plant expansin-like domain. AfSwo1 was produced using Aspergillus oryzae for heterologous expression and was easily isolated by cellulose-affinity chromatography. AfSwo1 exhibited weak endoglucanase activity toward carboxymethyl cellulose (CMC) and bound not only to crystalline cellulose Avicel but also to chitin, while showing no detectable affinity to xylan. Treatment by AfSwo1 caused disruption of Avicel into smaller particles without any detectable reducing sugar. Furthermore, simultaneous incubation of AfSwo1 with a cellulase mixture facilitated saccharification of Avicel. Our results provide a novel approach for efficient bioconversion of crystalline cellulose into glucose by use of the cellulose-disrupting protein AfSwo1.
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92
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Molecular cloning, gene expression analysis and structural modelling of the cellobiohydrolase I from Penicillium occitanis. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2009.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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93
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Beckham GT, Matthews JF, Bomble YJ, Bu L, Adney WS, Himmel ME, Nimlos MR, Crowley MF. Identification of Amino Acids Responsible for Processivity in a Family 1 Carbohydrate-Binding Module from a Fungal Cellulase. J Phys Chem B 2010; 114:1447-53. [DOI: 10.1021/jp908810a] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gregg T. Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - James F. Matthews
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Yannick J. Bomble
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Lintao Bu
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - William S. Adney
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Michael E. Himmel
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Mark R. Nimlos
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Michael F. Crowley
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
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94
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Igarashi K, Koivula A, Wada M, Kimura S, Penttilä M, Samejima M. High speed atomic force microscopy visualizes processive movement of Trichoderma reesei cellobiohydrolase I on crystalline cellulose. J Biol Chem 2009; 284:36186-36190. [PMID: 19858200 PMCID: PMC2794734 DOI: 10.1074/jbc.m109.034611] [Citation(s) in RCA: 184] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 10/13/2009] [Indexed: 11/06/2022] Open
Abstract
Fungal cellobiohydrolases act at liquid-solid interfaces. They have the ability to hydrolyze cellulose chains of a crystalline substrate because of their two-domain structure, i.e. cellulose-binding domain and catalytic domain, and unique active site architecture. However, the details of the action of the two domains on crystalline cellulose are still unclear. Here, we present real time observations of Trichoderma reesei (Tr) cellobiohydrolase I (Cel7A) molecules sliding on crystalline cellulose, obtained with a high speed atomic force microscope. The average velocity of the sliding movement on crystalline cellulose was 3.5 nm/s, and interestingly, the catalytic domain without the cellulose-binding domain moved with a velocity similar to that of the intact TrCel7A enzyme. However, no sliding of a catalytically inactive enzyme (mutant E212Q) or a variant lacking tryptophan at the entrance of the active site tunnel (mutant W40A) could be detected. This indicates that, besides the hydrolysis of glycosidic bonds, the loading of a cellulose chain into the active site tunnel is also essential for the enzyme movement.
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Affiliation(s)
- Kiyohiko Igarashi
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan.
| | - Anu Koivula
- VTT Technical Research Centre of Finland, Espoo, 02044 VTT, Finland
| | - Masahisa Wada
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Satoshi Kimura
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, Espoo, 02044 VTT, Finland
| | - Masahiro Samejima
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
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95
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Bu L, Beckham GT, Crowley MF, Chang CH, Matthews JF, Bomble YJ, Adney WS, Himmel ME, Nimlos MR. The energy landscape for the interaction of the family 1 carbohydrate-binding module and the cellulose surface is altered by hydrolyzed glycosidic bonds. J Phys Chem B 2009; 113:10994-1002. [PMID: 19594145 DOI: 10.1021/jp904003z] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A multiscale simulation model is used to construct potential and free energy surfaces for the carbohydrate-binding module [CBM] from an industrially important cellulase, Trichoderma reesei cellobiohydrolase I, on the hydrophobic face of a coarse-grained cellulose Ibeta polymorph. We predict from computation that the CBM alone exhibits regions of stability on the hydrophobic face of cellulose every 5 and 10 A, corresponding to a glucose unit and a cellobiose unit, respectively. In addition, we predict a new role for the CBM: specifically, that in the presence of hydrolyzed cellulose chain ends, the CBM exerts a thermodynamic driving force to translate away from the free cellulose chain ends. This suggests that the CBM is not only required for binding to cellulose, as has been known for two decades, but also that it has evolved to both assist the enzyme in recognizing a cellulose chain end and exert a driving force on the enzyme during processive hydrolysis of cellulose.
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Affiliation(s)
- Lintao Bu
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
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96
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Feng Y, Jiang JX, Zhu LW. Recent developments in activities, utilization and sources of cellulase. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s11632-009-0028-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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97
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Voutilainen SP, Puranen T, Siika-Aho M, Lappalainen A, Alapuranen M, Kallio J, Hooman S, Viikari L, Vehmaanperä J, Koivula A. Cloning, expression, and characterization of novel thermostable family 7 cellobiohydrolases. Biotechnol Bioeng 2008; 101:515-28. [PMID: 18512263 DOI: 10.1002/bit.21940] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
As part of the effort to find better cellulases for bioethanol production processes, we were looking for novel GH-7 family cellobiohydrolases, which would be particularly active on insoluble polymeric substrates and participate in the rate-limiting step in the hydrolysis of cellulose. The enzymatic properties were studied and are reported here for family 7 cellobiohydrolases from the thermophilic fungi Acremonium thermophilum, Thermoascus aurantiacus, and Chaetomium thermophilum. The Trichoderma reesei Cel7A enzyme was used as a reference in the experiments. As the native T. aurantiacus Cel7A has no carbohydrate-binding module (CBM), recombinant proteins having the CBM from either the C. thermophilum Cel7A or the T. reesei Cel7A were also constructed. All these novel acidic cellobiohydrolases were more thermostable (by 4-10 degrees C) and more active (two- to fourfold) in hydrolysis of microcrystalline cellulose (Avicel) at 45 degrees C than T. reesei Cel7A. The C. thermophilum Cel7A showed the highest specific activity and temperature optimum when measured on soluble substrates. The most effective enzyme for Avicel hydrolysis at 70 degrees C, however, was the 2-module version of the T. aurantiacus Cel7A, which was also relatively weakly inhibited by cellobiose. These results are discussed from the structural point of view based on the three-dimensional homology models of these enzymes.
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Affiliation(s)
- Sanni P Voutilainen
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Finland
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98
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Nakamura T, Mine S, Hagihara Y, Ishikawa K, Ikegami T, Uegaki K. Tertiary Structure and Carbohydrate Recognition by the Chitin-Binding Domain of a Hyperthermophilic Chitinase from Pyrococcus furiosus. J Mol Biol 2008; 381:670-80. [DOI: 10.1016/j.jmb.2008.06.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 06/02/2008] [Accepted: 06/04/2008] [Indexed: 10/22/2022]
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99
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Wang L, Zhang Y, Gao P. A novel function for the cellulose binding module of cellobiohydrolase I. ACTA ACUST UNITED AC 2008; 51:620-9. [PMID: 18622745 DOI: 10.1007/s11427-008-0088-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 05/21/2008] [Indexed: 11/29/2022]
Abstract
A homogeneous cellulose-binding module (CBM) of cellobiohydrolase I (CBHI) from Trichoderma pseudokoningii S-38 was obtained by the limited proteolysis with papain and a series of chromatographs filtration. Analysis of FT-IR spectra demonstrated that the structural changes result from a weakening and splitting of the hydrogen bond network in cellulose by the action of CBM(CBHI) at 40 degrees C for 24 h. The results of molecular dynamic simulations are consistent with the experimental conclusions, and provide a nanoscopic view of the mechanism that strong and medium H-bonds decreased dramatically when CBM was bound to the cellulose surface. The function of CBM(CBHI) is not only limited to locating intact CBHI in close proximity with cellulose fibrils, but also is involved in the structural disruption at the fibre surface. The present studies provided considerable evidence for the model of the intramolecular synergy between the catalytic domain and their CBMs.
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Affiliation(s)
- Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
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100
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Structural changes of cellobiohydrolase I (1,4-β-D-glucan-cellobiohydrolase I, CBHI) and PNPC (p-nitrophenyl-β-D-cellobioside) during the binding process. ACTA ACUST UNITED AC 2008; 51:459-69. [DOI: 10.1007/s11427-008-0064-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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