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Metagenomic mining and structure-function studies of a hyper-thermostable cellobiohydrolase from hot spring sediment. Commun Biol 2022; 5:247. [PMID: 35318423 PMCID: PMC8940973 DOI: 10.1038/s42003-022-03195-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/25/2022] [Indexed: 11/09/2022] Open
Abstract
Enzymatic breakdown is an attractive cellulose utilisation method with a low environmental load. Its high temperature operation could promote saccharification and lower contamination risk. Here we report a hyper-thermostable cellobiohydrolase (CBH), named HmCel6A and its variant HmCel6A-3SNP that were isolated metagenomically from hot spring sediments and expressed in Escherichia coli. They are classified into glycoside hydrolases family 6 (GH6). HmCel6A-3SNP had three amino acid replacements to HmCel6A (P88S/L230F/F414S) and the optimum temperature at 95 °C, while HmCel6A did it at 75 °C. Crystal structure showed conserved features among GH6, a (β/α)8-barrel core and catalytic residues, and resembles TfCel6B, a bacterial CBH II of Thermobifida fusca, that had optimum temperature at 60 °C. From structure-function studies, we discuss unique structural features that allow the enzyme to reach its high thermostability level, such as abundance of hydrophobic and charge-charge interactions, characteristic metal bindings and disulphide bonds. Moreover, structure and surface plasmon resonance analysis with oligosaccharides suggested that the contribution of an additional tryptophan located at the tunnel entrance could aid in substrate recognition and thermostability. These results may help to design efficient enzymes and saccharification methods for cellulose working at high temperatures. Bacteria from hot springs are known for highly thermostable enzymes, which may have industrial potential. Here, a unique thermostable cellobiohydrolase is reported that can breakdown cellulose at temperature up to 95 degrees Celsius.
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2
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Araújo EA, Dias AHS, Kadowaki MAS, Piyadov V, Pellegrini VOA, Urio MB, Ramos LP, Skaf MS, Polikarpov I. Impact of cellulose properties on enzymatic degradation by bacterial GH48 enzymes: Structural and mechanistic insights from processive Bacillus licheniformis Cel48B cellulase. Carbohydr Polym 2021; 264:118059. [PMID: 33910709 DOI: 10.1016/j.carbpol.2021.118059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 11/29/2022]
Abstract
Processive cellulases are highly efficient molecular engines involved in the cellulose breakdown process. However, the mechanism that processive bacterial enzymes utilize to recruit and retain cellulose strands in the catalytic site remains poorly understood. Here, integrated enzymatic assays, protein crystallography and computational approaches were combined to study the enzymatic properties of the processive BlCel48B cellulase from Bacillus licheniformis. Hydrolytic efficiency, substrate binding affinity, cleavage patterns, and the apparent processivity of bacterial BlCel48B are significantly impacted by the cellulose size and its surface morphology. BlCel48B crystallographic structure was solved with ligands spanning -5 to -2 and +1 to +2 subsites. Statistical coupling analysis and molecular dynamics show that co-evolved residues on active site are critical for stabilizing ligands in the catalytic tunnel. Our results provide mechanistic insights into BlCel48B molecular-level determinants of activity, substrate binding, and processivity on insoluble cellulose, thus shedding light on structure-activity correlations of GH48 family members in general.
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Affiliation(s)
- Evandro A Araújo
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil; Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials, Campinas 13083-970, São Paulo, Brazil
| | - Artur Hermano Sampaio Dias
- Institute of Chemistry and Center for Computer in Engineering and Sciences, University of Campinas (UNICAMP), Campinas 13084-862, São Paulo, Brazil
| | - Marco A S Kadowaki
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil
| | - Vasily Piyadov
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil
| | - Vanessa O A Pellegrini
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil
| | - Mateus B Urio
- Graduate Programs in Bioenergy, Chemistry and Chemical Engineering, Federal University of Paraná (UFPR), Curitiba 81531-980, Paraná, Brazil
| | - Luiz P Ramos
- Graduate Programs in Bioenergy, Chemistry and Chemical Engineering, Federal University of Paraná (UFPR), Curitiba 81531-980, Paraná, Brazil
| | - Munir S Skaf
- Institute of Chemistry and Center for Computer in Engineering and Sciences, University of Campinas (UNICAMP), Campinas 13084-862, São Paulo, Brazil
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil.
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3
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Glasgow EM, Kemna EI, Bingman CA, Ing N, Deng K, Bianchetti CM, Takasuka TE, Northen TR, Fox BG. A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis. J Biol Chem 2021; 295:17752-17769. [PMID: 33454012 DOI: 10.1074/jbc.ra120.015328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/15/2020] [Indexed: 11/06/2022] Open
Abstract
Broad-specificity glycoside hydrolases (GHs) contribute to plant biomass hydrolysis by degrading a diverse range of polysaccharides, making them useful catalysts for renewable energy and biocommodity production. Discovery of new GHs with improved kinetic parameters or more tolerant substrate-binding sites could increase the efficiency of renewable bioenergy production even further. GH5 has over 50 subfamilies exhibiting selectivities for reaction with β-(1,4)-linked oligo- and polysaccharides. Among these, subfamily 4 (GH5_4) contains numerous broad-selectivity endoglucanases that hydrolyze cellulose, xyloglucan, and mixed-linkage glucans. We previously surveyed the whole subfamily and found over 100 new broad-specificity endoglucanases, although the structural origins of broad specificity remained unclear. A mechanistic understanding of GH5_4 substrate specificity would help inform the best protein design strategies and the most appropriate industrial application of broad-specificity endoglucanases. Here we report structures of 10 new GH5_4 enzymes from cellulolytic microbes and characterize their substrate selectivity using normalized reducing sugar assays and MS. We found that GH5_4 enzymes have the highest catalytic efficiency for hydrolysis of xyloglucan, glucomannan, and soluble β-glucans, with opportunistic secondary reactions on cellulose, mannan, and xylan. The positions of key aromatic residues determine the overall reaction rate and breadth of substrate tolerance, and they contribute to differences in oligosaccharide cleavage patterns. Our new composite model identifies several critical structural features that confer broad specificity and may be readily engineered into existing industrial enzymes. We demonstrate that GH5_4 endoglucanases can have broad specificity without sacrificing high activity, making them a valuable addition to the biomass deconstruction toolset.
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Affiliation(s)
- Evan M Glasgow
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA; Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA
| | - Elias I Kemna
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA; Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA
| | - Nicole Ing
- Joint BioEnergy Institute, Emeryville, California, USA; Sandia National Laboratories, Livermore, California, USA
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, California, USA; Sandia National Laboratories, Livermore, California, USA
| | - Christopher M Bianchetti
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA; Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA
| | | | - Trent R Northen
- Joint BioEnergy Institute, Emeryville, California, USA; Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Brian G Fox
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA; Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA.
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4
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Yamaguchi S, Sunagawa N, Tachioka M, Igarashi K, Samejima M. Thermostable Mutants of Glycoside Hydrolase Family 6 Cellobiohydrolase from the Basidiomycete Phanerochaete chrysosporium. J Appl Glycosci (1999) 2020; 67:79-86. [PMID: 34354533 PMCID: PMC8132074 DOI: 10.5458/jag.jag.jag-2020_0004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 06/09/2020] [Indexed: 11/24/2022] Open
Abstract
Thermal inactivation of saccharifying enzymes is a crucial issue for the efficient utilization of cellulosic biomass as a renewable resource. Cellobiohydrolases (CBHs) are a kind of cellulase. In general, CBHs belonging to glycoside hydrolase (GH) family 6 (Cel6) act synergistically with CBHs of GH family 7 (Cel7) and other carbohydrate-active enzymes during the degradation of cellulosic biomass. However, while the catalytic rate of enzymes generally becomes faster at higher temperatures, Cel6 CBHs are inactivated at lower temperatures than Cel7 CBHs, and this represents a limiting factor for industrial utilization. In this study, we produced a series of mutants of the glycoside hydrolase family 6 cellobiohydrolase Pc Cel6A from the fungus Phanerochaete chrysosporium , and compared their thermal stability. Eight mutants from a random mutagenesis library and one rationally designed mutant were selected as candidate thermostable mutants and produced by heterologous expression in the yeast Pichia pastoris . Comparison of the hydrolytic activities at 50 and 60 °C indicated that the thermal stability of Pc Cel6A is influenced by the number and position of cysteine residues that are not involved in disulfide bonds.
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Affiliation(s)
- Sora Yamaguchi
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Naoki Sunagawa
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Mikako Tachioka
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo.,2 Deep-Sea Nanoscience Research Group, Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology
| | - Kiyohiko Igarashi
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo.,3 VTT Technical Research Centre of Finland
| | - Masahiro Samejima
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo.,4 Faculty of Engineering, Shinshu University
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Abstract
Some cellulases exhibit “processivity”: the ability to degrade crystalline cellulose through successive hydrolytic catalytic reactions without the release of the enzyme from the substrate surface. We previously observed the movement of fungal processive cellulases by high-speed atomic force microscopy, and here, we use the same technique to directly observe the processive movement of bacterial cellobiohydrolases settling a long-standing controversy. Although fungal and bacterial processive cellulases have completely different protein folds, they have evolved to acquire processivity through the same strategy of adding subsites to extend the substrate-binding site and forming a tunnel-like active site by increasing the number of loops covering the active site. This represents an example of protein-level convergent evolution to acquire the same functions from different ancestors. Cellulose is the most abundant biomass on Earth, and many microorganisms depend on it as a source of energy. It consists mainly of crystalline and amorphous regions, and natural degradation of the crystalline part is highly dependent on the degree of processivity of the degrading enzymes (i.e., the extent of continuous hydrolysis without detachment from the substrate cellulose). Here, we report high-speed atomic force microscopic (HS-AFM) observations of the movement of four types of cellulases derived from the cellulolytic bacteria Cellulomonas fimi on various insoluble cellulose substrates. The HS-AFM images clearly demonstrated that two of them (CfCel6B and CfCel48A) slide on crystalline cellulose. The direction of processive movement of CfCel6B is from the nonreducing to the reducing end of the substrate, which is opposite that of processive cellulase Cel7A of the fungus Trichoderma reesei (TrCel7A), whose movement was first observed by this technique, while CfCel48A moves in the same direction as TrCel7A. When CfCel6B and TrCel7A were mixed on the same substrate, “traffic accidents” were observed, in which the two cellulases blocked each other’s progress. The processivity of CfCel6B was similar to those of fungal family 7 cellulases but considerably higher than those of fungal family 6 cellulases. The results indicate that bacteria utilize family 6 cellulases as high-processivity enzymes for efficient degradation of crystalline cellulose, whereas family 7 enzymes have the same function in fungi. This is consistent with the idea of convergent evolution of processive cellulases in fungi and bacteria to achieve similar functionality using different protein foldings.
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Sørlie M, Horn SJ, Vaaje-Kolstad G, Eijsink VG. Using chitosan to understand chitinases and the role of processivity in the degradation of recalcitrant polysaccharides. REACT FUNCT POLYM 2020. [DOI: 10.1016/j.reactfunctpolym.2020.104488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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7
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Røjel N, Kari J, Sørensen TH, Badino SF, Morth JP, Schaller K, Cavaleiro AM, Borch K, Westh P. Substrate binding in the processive cellulase Cel7A: Transition state of complexation and roles of conserved tryptophan residues. J Biol Chem 2020; 295:1454-1463. [PMID: 31848226 PMCID: PMC7008363 DOI: 10.1074/jbc.ra119.011420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/17/2019] [Indexed: 11/06/2022] Open
Abstract
Cellobiohydrolases effectively degrade cellulose and are of biotechnological interest because they can convert lignocellulosic biomass to fermentable sugars. Here, we implemented a fluorescence-based method for real-time measurements of complexation and decomplexation of the processive cellulase Cel7A and its insoluble substrate, cellulose. The method enabled detailed kinetic and thermodynamic analyses of ligand binding in a heterogeneous system. We studied WT Cel7A and several variants in which one or two of four highly conserved Trp residues in the binding tunnel had been replaced with Ala. WT Cel7A had on/off-rate constants of 1 × 105 m-1 s-1 and 5 × 10-3 s-1, respectively, reflecting the slow dynamics of a solid, polymeric ligand. Especially the off-rate constant was many orders of magnitude lower than typical values for small, soluble ligands. Binding rate and strength both were typically lower for the Trp variants, but effects of the substitutions were moderate and sometimes negligible. Hence, we propose that lowering the activation barrier for complexation is not a major driving force for the high conservation of the Trp residues. Using so-called Φ-factor analysis, we analyzed the kinetic and thermodynamic results for the variants. The results of this analysis suggested a transition state for complexation and decomplexation in which the reducing end of the ligand is close to the tunnel entrance (near Trp-40), whereas the rest of the binding tunnel is empty. We propose that this structure defines the highest free-energy barrier of the overall catalytic cycle and hence governs the turnover rate of this industrially important enzyme.
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Affiliation(s)
- Nanna Røjel
- Institut for Naturvidenskab og Miljo, Roskilde University, DK-4000 Roskilde, Denmark
| | - Jeppe Kari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | | | - Silke F Badino
- Institut for Naturvidenskab og Miljo, Roskilde University, DK-4000 Roskilde, Denmark
| | - J Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Kay Schaller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | | | - Kim Borch
- Novozymes A/S, DK-2800 Kgs. Lyngby Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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8
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Hefferon KL, Cantero‐Tubilla B, Brady J, Wilson D. Aromatic residues surrounding the active site tunnel of TfCel48A influence activity, processivity, and synergistic interactions with other cellulases. Biotechnol Bioeng 2019; 116:2463-2472. [DOI: 10.1002/bit.27086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/29/2019] [Accepted: 06/02/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Kathleen L. Hefferon
- Department of Cellular and Molecular GeneticsCornell University Ithaca New York
- Department of Food Science and TechnologyCornell University Ithaca New York
| | - Borja Cantero‐Tubilla
- Robert Frederick Smith School of Chemical and Biomolecular EngineeringCornell University Ithaca New York
| | - John Brady
- Department of Food Science and TechnologyCornell University Ithaca New York
| | - David Wilson
- Department of Cellular and Molecular GeneticsCornell University Ithaca New York
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9
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Christensen SJ, Kari J, Badino SF, Borch K, Westh P. Rate‐limiting step and substrate accessibility of cellobiohydrolase Cel6A from
Trichoderma reesei. FEBS J 2018; 285:4482-4493. [DOI: 10.1111/febs.14668] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 09/11/2018] [Accepted: 09/28/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Stefan J. Christensen
- Research Unit for Functional Biomaterials Department of Science and Environment Roskilde University Denmark
| | - Jeppe Kari
- Research Unit for Functional Biomaterials Department of Science and Environment Roskilde University Denmark
| | - Silke F. Badino
- Research Unit for Functional Biomaterials Department of Science and Environment Roskilde University Denmark
| | | | - Peter Westh
- Research Unit for Functional Biomaterials Department of Science and Environment Roskilde University Denmark
- Department of Biotechnology and Biomedicine Technical University of Denmark Lyngby Denmark
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10
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Effects of mutations of non-catalytic aromatic residues on substrate specificity of Bacillus licheniformis endocellulase cel12A. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.01.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Huang H, Han F, Guan S, Qian M, Wan Y, Shan Y, Zhang H, Wang S. Insight into the process of product expulsion in cellobiohydrolase Cel6A from Trichoderma reesei by computational modeling. J Biomol Struct Dyn 2018. [PMID: 29519213 DOI: 10.1080/07391102.2018.1450164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Glycoside hydrolase cellulase family 6 from Trichoderma reesei (TrCel6A) is an important cellobiohydrolase to hydrolyze cellooligosaccharide into cellobiose. The knowledge of enzymatic mechanisms is critical for improving the conversion efficiency of cellulose into ethanol or other chemicals. However, the process of product expulsion, a key component of enzymatic depolymerization, from TrCel6A has not yet been described in detail. Here, conventional molecular dynamics and steered molecular dynamics (SMD) were applied to study product expulsion from TrCel6A. Tyr103 may be a crucial residue in product expulsion given that it exhibits two different posthydrolytic conformations. In one conformation, Tyr103 rotates to open the -3 subsite. However, Tyr103 does not rotate in the other conformation. Three different routes for product expulsion were proposed on the basis of the two different conformations. The total energy barriers of the three routes were calculated through SMD simulations. The total energy barrier of product expulsion through Route 1, in which Tyr103 does not rotate, was 22.2 kcal·mol-1. The total energy barriers of product expulsion through Routes 2 and 3, in which Tyr103 rotates to open the -3 subsite, were 10.3 and 14.4 kcal·mol-1, respectively. Therefore, Routes 2 and 3 have lower energy barriers than Route 1, and Route 2 is the thermodynamically optimal route for product expulsion. Consequently, the rotation of Tyr103 may be crucial for product release from TrCel6A. Results of this work have potential applications in cellulase engineering.
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Affiliation(s)
- Houhou Huang
- a Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
| | - Fei Han
- a Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
| | - Shanshan Guan
- a Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China.,b National Engineering Laboratory for AIDS Vaccine, School of Life Sciences , Jilin University , Changchun 130012 , People's Republic of China
| | - Mengdan Qian
- c State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering , Jilin University , Changchun , Jilin 130012 , People's Republic of China
| | - Yongfeng Wan
- a Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
| | - Yaming Shan
- b National Engineering Laboratory for AIDS Vaccine, School of Life Sciences , Jilin University , Changchun 130012 , People's Republic of China
| | - Hao Zhang
- a Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
| | - Song Wang
- a Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
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12
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Wu B, Zheng S, Pedroso MM, Guddat LW, Chang S, He B, Schenk G. Processivity and enzymatic mechanism of a multifunctional family 5 endoglucanase from Bacillus subtilis BS-5 with potential applications in the saccharification of cellulosic substrates. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:20. [PMID: 29422948 PMCID: PMC5787917 DOI: 10.1186/s13068-018-1022-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/11/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND Presently, enzymes still constitute a major part of the cost of biofuel production from lignocellulosic biomass. Processive endoglucanases, which possess both endoglucanase and exoglucanase activity, have the potential to reduce the costs of biomass saccharification when used together with commercial cellulases. Therefore, the exploration of new processive endoglucanases has attracted much attention with a view to accelerating the industrialization of biofuels and biochemicals. RESULTS The endoglucanase EG5C and its truncated form EG5C-1 from Bacillus subtilis BS-5 were expressed and characterized. EG5C was a typical endoglucanase, comprised of a family 5 catalytic domain and family 3 carbohydrate-binding domain, and which had high activity toward soluble cellulosic substrates, but low activity toward insoluble cellulosic substrates. Importantly, the truncated form EG5C-1 was a processive endoglucanase that hydrolyzed not only carboxymethyl cellulose (CMC), but also insoluble cellulosic substrates. The hydrolytic activities of EG5C-1 towards CMC, phosphoric acid-swollen cellulose (PASC), p-nitrophenyl-β-d-cellobioside, filter paper and Avicel are 4170, 700, 2550, 405 and 320 U/μmol, respectively. These data demonstrated that EG5C-1 had higher activity ratio of exoglucanase to endoglucanase than other known processive endoglucanases. When PASC was degraded by EG5C-1, the ratio of soluble to insoluble reducing sugars was about 3.7 after 3 h of incubation with cellobiose and cellotriose as the main products. Importantly, EG5C-1 alone was able to hydrolyze filter paper and PASC. At 5% substrate concentration and 10 FPU/g PASC enzyme loading, the saccharification yield was 76.5% after 60 h of incubation. Replacement of a phenylalanine residue (F238) by an alanine at the entrance/exit of the substrate binding cleft significantly reduces the ability of EG5C-1 to degrade filter paper and Avicel, but this mutation has little impact on CMCase activity. The processivity of this mutant was also greatly reduced while its cellulose binding ability was markedly enhanced. CONCLUSIONS The processive endoglucanase EG5C-1 from B. subtilis BS-5 exhibits excellent properties that render it a suitable candidate for use in biofuel and biochemical production from lignocellulosic biomass. In addition, our studies also provide useful information for research on enzyme processivity at the molecular level.
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Affiliation(s)
- Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816 Jiangsu China
- China Jiangsu National Synergetic Innovation Center for Advanced Materials, 30 Puzhunan road, Nanjing, 211816 Jiangsu China
| | - Shan Zheng
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072 Australia
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072 Australia
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072 Australia
| | - Siyuan Chang
- School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816 Jiangsu China
| | - Bingfang He
- China Jiangsu National Synergetic Innovation Center for Advanced Materials, 30 Puzhunan road, Nanjing, 211816 Jiangsu China
- School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816 Jiangsu China
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072 Australia
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13
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Badino SF, Kari J, Christensen SJ, Borch K, Westh P. Direct kinetic comparison of the two cellobiohydrolases Cel6A and Cel7A from Hypocrea jecorina. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1739-1745. [DOI: 10.1016/j.bbapap.2017.08.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/25/2017] [Accepted: 08/14/2017] [Indexed: 01/17/2023]
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14
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Tachioka M, Nakamura A, Ishida T, Igarashi K, Samejima M. Crystal structure of a family 6 cellobiohydrolase from the basidiomycete Phanerochaete chrysosporium. Acta Crystallogr F Struct Biol Commun 2017; 73:398-403. [PMID: 28695848 PMCID: PMC5505244 DOI: 10.1107/s2053230x17008093] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/31/2017] [Indexed: 03/27/2024] Open
Abstract
Cellobiohydrolases belonging to glycoside hydrolase family 6 (CBH II, Cel6A) play key roles in the hydrolysis of crystalline cellulose. CBH II from the white-rot fungus Phanerochaete chrysosporium (PcCel6A) consists of a catalytic domain (CD) and a carbohydrate-binding module connected by a linker peptide, like other known fungal cellobiohydrolases. In the present study, the CD of PcCel6A was crystallized without ligands, and p-nitrophenyl β-D-cellotrioside (pNPG3) was soaked into the crystals. The determined structures of the ligand-free and pNPG3-soaked crystals revealed that binding of cellobiose at substrate subsites +1 and +2 induces a conformational change of the N-terminal and C-terminal loops, switching the tunnel-shaped active site from the open to the closed form.
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Affiliation(s)
- Mikako Tachioka
- 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
| | - Akihiko Nakamura
- 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
| | - Takuya Ishida
- 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
| | - Kiyohiko Igarashi
- 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
- VTT Technical Research Centre of Finland, PO Box 1000, Tietotie 2, Espoo FI-02044 VTT, Finland
| | - Masahiro Samejima
- 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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15
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A bacterial GH6 cellobiohydrolase with a novel modular structure. Appl Microbiol Biotechnol 2017; 101:2943-2952. [PMID: 28120014 DOI: 10.1007/s00253-017-8129-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/19/2016] [Accepted: 12/28/2016] [Indexed: 02/01/2023]
Abstract
Cel6D from Paenibacillus barcinonensis is a modular cellobiohydrolase with a novel molecular architecture among glycosyl hydrolases of family 6. It contains an N-terminal catalytic domain (family 6 of glycosyl hydrolases (GH6)), followed by a fibronectin III-like domain repeat (Fn31,2) and a C-terminal family 3b cellulose-binding domain (CBM3b). The enzyme has been identified and purified showing catalytic activity on cellulosic substrates and cellodextrins, with a marked preference for phosphoric acid swollen cellulose (PASC). Analysis of mode of action of Cel6D shows that it releases cellobiose as the only hydrolysis product from cellulose. Kinetic parameters were determined on PASC showing a K m of 68.73 mg/ml and a V max of 1.73 U/mg. A series of truncated derivatives of Cel6D have been constructed and characterized. Deletion of CBM3b caused a notable reduction in hydrolytic activity, while deletion of the Fn3 domain abolished activity, as the isolated GH6 domain was not active on any of the substrates tested. Mutant enzymes Cel6D-D146A and Cel6D-D97A were constructed in the residues corresponding to the putative acid catalyst and to the network for the nucleophilic attack. The lack of activity of the mutant enzymes indicates the important role of these residues in catalysis. Analysis of cooperative activity of Cel6D with cellulases from the same producing P. barcinonensis strain reveals high synergistic activity with processive endoglucanase Cel9B on hydrolysis of crystalline substrates. The characterized cellobiohydrolase can be a good contribution for depolymerization of cellulosic substrates and for the deconstruction of native cellulose.
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16
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Gusakov AV, Dotsenko AS, Rozhkova AM, Sinitsyn AP. N-Linked glycans are an important component of the processive machinery of cellobiohydrolases. Biochimie 2017; 132:102-108. [DOI: 10.1016/j.biochi.2016.11.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/10/2016] [Indexed: 02/02/2023]
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17
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Damasio ARDL, Rubio MV, Gonçalves TA, Persinoti GF, Segato F, Prade RA, Contesini FJ, de Souza AP, Buckeridge MS, Squina FM. Xyloglucan breakdown by endo-xyloglucanase family 74 from Aspergillus fumigatus. Appl Microbiol Biotechnol 2016; 101:2893-2903. [PMID: 28013403 DOI: 10.1007/s00253-016-8014-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 11/09/2016] [Accepted: 11/12/2016] [Indexed: 12/30/2022]
Abstract
Xyloglucan is the most abundant hemicellulose in primary walls of spermatophytes except for grasses. Xyloglucan-degrading enzymes are important in lignocellulosic biomass hydrolysis because they remove xyloglucan, which is abundant in monocot-derived biomass. Fungal genomes encode numerous xyloglucanase genes, belonging to at least six glycoside hydrolase (GH) families. GH74 endo-xyloglucanases cleave xyloglucan backbones with unsubstituted glucose at the -1 subsite or prefer xylosyl-substituted residues in the -1 subsite. In this work, 137 GH74-related genes were detected by examining 293 Eurotiomycete genomes and Ascomycete fungi contained one or no GH74 xyloglucanase gene per genome. Another interesting feature is that the triad of tryptophan residues along the catalytic cleft was found to be widely conserved among Ascomycetes. The GH74 from Aspergillus fumigatus (AfXEG74) was chosen as an example to conduct comprehensive biochemical studies to determine the catalytic mechanism. AfXEG74 has no CBM and cleaves the xyloglucan backbone between the unsubstituted glucose and xylose-substituted glucose at specific positions, along the XX motif when linked to regions deprived of galactosyl branches. It resembles an endo-processive activity, which after initial random hydrolysis releases xyloglucan-oligosaccharides as major reaction products. This work provides insights on phylogenetic diversity and catalytic mechanism of GH74 xyloglucanases from Ascomycete fungi.
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Affiliation(s)
- André Ricardo de Lima Damasio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil.,Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| | - Marcelo Ventura Rubio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil.,Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| | - Thiago Augusto Gonçalves
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil.,Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| | - Gabriela Felix Persinoti
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | - Fernando Segato
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil.,Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo (USP), Lorena, SP, Brazil
| | - Rolf Alexander Prade
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Fabiano Jares Contesini
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | - Amanda Pereira de Souza
- Laboratório de Fisiologia e Ecologia de Plantas (LAFIECO), Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Marcos Silveira Buckeridge
- Laboratório de Fisiologia e Ecologia de Plantas (LAFIECO), Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Fabio Marcio Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil.
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18
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Kont R, Kari J, Borch K, Westh P, Väljamäe P. Inter-domain Synergism Is Required for Efficient Feeding of Cellulose Chain into Active Site of Cellobiohydrolase Cel7A. J Biol Chem 2016; 291:26013-26023. [PMID: 27780868 DOI: 10.1074/jbc.m116.756007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/21/2016] [Indexed: 01/27/2023] Open
Abstract
Structural polysaccharides like cellulose and chitin are abundant and their enzymatic degradation to soluble sugars is an important route in green chemistry. Processive glycoside hydrolases (GHs), like cellobiohydrolase Cel7A of Trichoderma reesei (TrCel7A) are key components of efficient enzyme systems. TrCel7A consists of a catalytic domain (CD) and a smaller carbohydrate-binding module (CBM) connected through the glycosylated linker peptide. A tunnel-shaped active site rests in the CD and contains 10 glucose unit binding sites. The active site of TrCel7A is lined with four Trp residues with two of them, Trp-40 and Trp-38, in the substrate binding sites near the tunnel entrance. Although addressed in numerous studies the elucidation of the role of CBM and active site aromatics has been obscured by a complex multistep mechanism of processive GHs. Here we studied the role of the CBM-linker and Trp-38 of TrCel7A with respect to binding affinity, on- and off-rates, processivity, and synergism with endoglucanase. The CBM-linker increased the on-rate and substrate affinity of the enzyme. The Trp-38 to Ala substitution resulted in increased off-rates and decreased processivity. The effect of the Trp-38 to Ala substitution on on-rates was strongly dependent on the presence of the CBM-linker. This compensation between CBM-linker and Trp-38 indicates synergism between CBM-linker and CD in feeding the cellulose chain into the active site. The inter-domain synergism was pre-requisite for the efficient degradation of cellulose in the presence of endoglucanase.
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Affiliation(s)
- Riin Kont
- From the Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Jeppe Kari
- the Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark, and
| | - Kim Borch
- Novozymes A/S, Bagsværd DK-2880, Denmark
| | - Peter Westh
- the Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark, and
| | - Priit Väljamäe
- From the Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia,
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19
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Baramee S, Teeravivattanakit T, Phitsuwan P, Waeonukul R, Pason P, Tachaapaikoon C, Kosugi A, Sakka K, Ratanakhanokchai K. A novel GH6 cellobiohydrolase from Paenibacillus curdlanolyticus B-6 and its synergistic action on cellulose degradation. Appl Microbiol Biotechnol 2016; 101:1175-1188. [PMID: 27743043 DOI: 10.1007/s00253-016-7895-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 09/12/2016] [Accepted: 09/25/2016] [Indexed: 11/30/2022]
Abstract
We recently discovered a novel glycoside hydrolase family 6 (GH6) cellobiohydrolase from Paenibacillus curdlanolyticus B-6 (PcCel6A), which is rarely found in bacteria. This enzyme is a true exo-type cellobiohydrolase which exhibits high substrate specificity on amorphous cellulose and low substrate specificity on crystalline cellulose, while this showed no activity on substitution substrates, carboxymethyl cellulose and xylan, distinct from all other known GH6 cellobiohydrolases. Product profiles, HPLC analysis of the hydrolysis products and a schematic drawing of the substrate-binding subsites catalysing cellooligosaccharides can explain the new mode of action of this enzyme which prefers to hydrolyse cellopentaose. PcCel6A was not inhibited by glucose or cellobiose at concentrations up to 300 and 100 mM, respectively. A good synergistic effect for glucose production was found when PcCel6A acted together with processive endoglucanase Cel9R from Clostridium thermocellum and β-glucosidase CglT from Thermoanaerobacter brockii. These properties of PcCel6A make it a suitable candidate for industrial application in the cellulose degradation process.
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Affiliation(s)
- Sirilak Baramee
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Thitiporn Teeravivattanakit
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Paripok Phitsuwan
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, 305-8686, Japan
| | - Kazuo Sakka
- Graduated School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
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20
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Tachioka M, Sugimoto N, Nakamura A, Sunagawa N, Ishida T, Uchiyama T, Igarashi K, Samejima M. Development of simple random mutagenesis protocol for the protein expression system in Pichia pastoris. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:199. [PMID: 27660653 PMCID: PMC5028916 DOI: 10.1186/s13068-016-0613-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/07/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Random mutagenesis is a powerful technique to obtain mutant proteins with different properties from the wild-type molecule. Error-prone PCR is often employed for random mutagenesis in bacterial protein expression systems, but has rarely been used in the methylotrophic yeast Pichia pastoris system, despite its significant advantages, mainly because large (μg-level) amounts of plasmids are required for transformation. RESULTS We developed a quick and easy technique for random mutagenesis in P. pastoris by sequential Phi29 DNA polymerase-based amplification methods, error-prone rolling circle amplification (RCA) and multiple displacement amplification (MDA). The methodology was validated by applying it for random mutation of the gene encoding cellulase from the basidiomycete Phanerochaete chrysosporium (PcCel6A), a key enzyme in degradation of cellulosic biomass. In the error-prone RCA step, the concentrations of manganese ion (Mn(2+)) and cellulase gene-containing plasmid were varied, and the products obtained under each condition were subjected to the second MDA step in the absence of Mn(2+). The maximum error rate was 2.6 mutations/kb, as evaluated from the results of large-scale sequencing. Several μg of MDA products was transformed by electroporation into Pichia cells, and the activities of extracellularly expressed PcCel6A mutants towards crystalline and amorphous celluloses were compared with those of wild-type enzyme to identify key amino acid residues affecting degradation of crystalline cellulose. CONCLUSIONS We present a rapid and convenient random mutagenesis method that does not require laborious steps such as ligation, cloning, and synthesis of specific primers. This method was successfully applied to the protein expression system in P. pastoris.
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Affiliation(s)
- Mikako Tachioka
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Naohisa Sugimoto
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
- Biomaterial in Tokyo Co., Ltd., Fukuoka Lab, Ōnojō, Fukuoka 816-0905 Japan
| | - Akihiko Nakamura
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
- Institute for Molecular Science, National Institute of Natural Sciences, Okazaki, 444-8787 Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Takuya Ishida
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Taku Uchiyama
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Masahiro Samejima
- Department of Biomaterial Sciences, 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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21
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Mayes HB, Knott BC, Crowley MF, Broadbelt LJ, Ståhlberg J, Beckham GT. Who's on base? Revealing the catalytic mechanism of inverting family 6 glycoside hydrolases. Chem Sci 2016; 7:5955-5968. [PMID: 30155195 PMCID: PMC6091422 DOI: 10.1039/c6sc00571c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/29/2016] [Indexed: 12/16/2022] Open
Abstract
In several important classes of inverting carbohydrate-active enzymes, the identity of the catalytic base remains elusive, including in family 6 Glycoside Hydrolase (GH6) enzymes, which are key components of cellulase cocktails for cellulose depolymerization. Despite many structural and kinetic studies with both wild-type and mutant enzymes, especially on the Trichoderma reesei (Hypocrea jecorina) GH6 cellulase (TrCel6A), the catalytic base in the single displacement inverting mechanism has not been definitively identified in the GH6 family. Here, we employ transition path sampling to gain insight into the catalytic mechanism, which provides unbiased atomic-level understanding of key order parameters involved in cleaving the strong glycosidic bond. Our hybrid quantum mechanics and molecular mechanics (QM/MM) simulations reveal a network of hydrogen bonding that aligns two active site water molecules that play key roles in hydrolysis: one water molecule drives the reaction by nucleophilic attack on the substrate and a second shuttles a proton to the putative base (D175) via a short water wire. We also investigated the case where the putative base is mutated to an alanine, an enzyme that is experimentally still partially active. The simulations predict that proton hopping along a water wire via a Grotthuss mechanism provides a mechanism of catalytic rescue. Further simulations reveal that substrate processive motion is 'driven' by strong electrostatic interactions with the protein at the product sites and that the -1 sugar adopts a 2SO ring configuration as it reaches its binding site. This work thus elucidates previously elusive steps in the processive catalytic mechanism of this important class of enzymes.
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Affiliation(s)
- Heather B Mayes
- Department of Chemical and Biological Engineering , Northwestern University , Evanston , IL 60208 , USA
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
| | - Brandon C Knott
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
| | - Michael F Crowley
- Biosciences Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA
| | - Linda J Broadbelt
- Department of Chemical and Biological Engineering , Northwestern University , Evanston , IL 60208 , USA
| | - Jerry Ståhlberg
- Department of Chemistry and Biotechnology , Swedish University of Agricultural Sciences , SE-75007 , Uppsala , Sweden .
| | - Gregg T Beckham
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
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22
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Jana S, Hamre AG, Wildberger P, Holen MM, Eijsink VGH, Beckham GT, Sørlie M, Payne CM. Aromatic-Mediated Carbohydrate Recognition in Processive Serratia marcescens Chitinases. J Phys Chem B 2016; 120:1236-49. [PMID: 26824449 DOI: 10.1021/acs.jpcb.5b12610] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microorganisms use a host of enzymes, including processive glycoside hydrolases, to deconstruct recalcitrant polysaccharides to sugars. Processive glycoside hydrolases closely associate with polymer chains and repeatedly cleave glycosidic linkages without dissociating from the crystalline surface after each hydrolytic step; they are typically the most abundant enzymes in both natural secretomes and industrial cocktails by virtue of their significant hydrolytic potential. The ubiquity of aromatic residues lining the enzyme catalytic tunnels and clefts is a notable feature of processive glycoside hydrolases. We hypothesized that these aromatic residues have uniquely defined roles, such as substrate chain acquisition and binding in the catalytic tunnel, that are defined by their local environment and position relative to the substrate and the catalytic center. Here, we investigated this hypothesis with variants of Serratia marcescens family 18 processive chitinases ChiA and ChiB. We applied molecular simulation and free energy calculations to assess active site dynamics and ligand binding free energies. Isothermal titration calorimetry provided further insight into enthalpic and entropic contributions to ligand binding free energy. Thus, the roles of six aromatic residues, Trp-167, Trp-275, and Phe-396 in ChiA, and Trp-97, Trp-220, and Phe-190 in ChiB, have been examined. We observed that point mutation of the tryptophan residues to alanine results in unfavorable changes in the free energy of binding relative to wild-type. The most drastic effects were observed for residues positioned at the "entrances" of the deep substrate-binding clefts and known to be important for processivity. Interestingly, phenylalanine mutations in ChiA and ChiB had little to no effect on chito-oligomer binding, in accordance with the limited effects of their removal on chitinase functionality.
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Affiliation(s)
- Suvamay Jana
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506-0046, United States
| | - Anne Grethe Hamre
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Patricia Wildberger
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Matilde Mengkrog Holen
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | - Morten Sørlie
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506-0046, United States
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23
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Eibinger M, Zahel T, Ganner T, Plank H, Nidetzky B. Cellular automata modeling depicts degradation of cellulosic material by a cellulase system with single-molecule resolution. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:56. [PMID: 26962329 PMCID: PMC4784381 DOI: 10.1186/s13068-016-0463-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/19/2016] [Indexed: 05/15/2023]
Abstract
BACKGROUND Enzymatic hydrolysis of cellulose involves the spatiotemporally correlated action of distinct polysaccharide chain cleaving activities confined to the surface of an insoluble substrate. Because cellulases differ in preference for attacking crystalline compared to amorphous cellulose, the spatial distribution of structural order across the cellulose surface imposes additional constraints on the dynamic interplay between the enzymes. Reconstruction of total system behavior from single-molecule activity parameters is a longstanding key goal in the field. RESULTS We have developed a stochastic, cellular automata-based modeling approach to describe degradation of cellulosic material by a cellulase system at single-molecule resolution. Substrate morphology was modeled to represent the amorphous and crystalline phases as well as the different spatial orientations of the polysaccharide chains. The enzyme system model consisted of an internally chain-cleaving endoglucanase (EG) as well as two processively acting, reducing and non-reducing chain end-cleaving cellobiohydrolases (CBHs). Substrate preference (amorphous: EG, CBH II; crystalline: CBH I) and characteristic frequencies for chain cleavage, processive movement, and dissociation were assigned from biochemical data. Once adsorbed, enzymes were allowed to reach surface-exposed substrate sites through "random-walk" lateral diffusion or processive motion. Simulations revealed that slow dissociation of processive enzymes at obstacles obstructing further movement resulted in local jamming of the cellulases, with consequent delay in the degradation of the surface area affected. Exploiting validation against evidence from atomic force microscopy imaging as a unique opportunity opened up by the modeling approach, we show that spatiotemporal characteristics of cellulose surface degradation by the system of synergizing cellulases were reproduced quantitatively at the nanometer resolution of the experimental data. This in turn gave useful prediction of the soluble sugar release rate. CONCLUSIONS Salient dynamic features of cellulose surface degradation by different cellulases acting in synergy were reproduced in simulations in good agreement with evidence from high-resolution visualization experiments. Due to the single-molecule resolution of the modeling approach, the utility of the presented model lies not only in predicting system behavior but also in elucidating inherently complex (e.g., stochastic) phenomena involved in enzymatic cellulose degradation. Thus, it creates synergy with experiment to advance the mechanistic understanding for improved application.
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Affiliation(s)
- Manuel Eibinger
- />Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
| | - Thomas Zahel
- />Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
| | - Thomas Ganner
- />Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Harald Plank
- />Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
- />Graz Centre for Electron Microscopy, Steyrergasse 17, 8010 Graz, Austria
| | - Bernd Nidetzky
- />Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
- />Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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24
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Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus. Sci Rep 2015; 5:11666. [PMID: 26133573 PMCID: PMC4488959 DOI: 10.1038/srep11666] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/27/2015] [Indexed: 11/24/2022] Open
Abstract
Previous gene-centric analysis of a cow rumen metagenome revealed the first potentially cellulolytic polysaccharide utilization locus, of which the main catalytic enzyme (AC2aCel5A) was identified as a glycoside hydrolase (GH) family 5 endo-cellulase. Here we present the 1.8 Å three-dimensional structure of AC2aCel5A, and characterization of its enzymatic activities. The enzyme possesses the archetypical (β/α)8-barrel found throughout the GH5 family, and contains the two strictly conserved catalytic glutamates located at the C-terminal ends of β-strands 4 and 7. The enzyme is active on insoluble cellulose and acts exclusively on linear β-(1,4)-linked glucans. Co-crystallization of a catalytically inactive mutant with substrate yielded a 2.4 Å structure showing cellotriose bound in the −3 to −1 subsites. Additional electron density was observed between Trp178 and Trp254, two residues that form a hydrophobic “clamp”, potentially interacting with sugars at the +1 and +2 subsites. The enzyme’s active-site cleft was narrower compared to the closest structural relatives, which in contrast to AC2aCel5A, are also active on xylans, mannans and/or xyloglucans. Interestingly, the structure and function of this enzyme seem adapted to less-substituted substrates such as cellulose, presumably due to the insufficient space to accommodate the side-chains of branched glucans in the active-site cleft.
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25
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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26
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Kari J, Olsen J, Borch K, Cruys-Bagger N, Jensen K, Westh P. Kinetics of cellobiohydrolase (Cel7A) variants with lowered substrate affinity. J Biol Chem 2014; 289:32459-68. [PMID: 25271162 DOI: 10.1074/jbc.m114.604264] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellobiohydrolases are exo-active glycosyl hydrolases that processively convert cellulose to soluble sugars, typically cellobiose. They effectively break down crystalline cellulose and make up a major component in industrial enzyme mixtures used for deconstruction of lignocellulosic biomass. Identification of the rate-limiting step for cellobiohydrolases remains controversial, and recent reports have alternately suggested either association (on-rate) or dissociation (off-rate) as the overall bottleneck. Obviously, this uncertainty hampers both fundamental mechanistic understanding and rational design of enzymes with improved industrial applicability. To elucidate the role of on- and off-rates, respectively, on the overall kinetics, we have expressed a variant in which a tryptophan residue (Trp-38) in the middle of the active tunnel has been replaced with an alanine. This mutation weakens complex formation, and the population of substrate-bound W38A was only about half of the wild type. Nevertheless, the maximal, steady-state rate was twice as high for the variant enzyme. It is argued that these opposite effects on binding and activity can be reconciled if the rate-limiting step is after the catalysis (i.e. in the dissociation process).
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Affiliation(s)
- Jeppe Kari
- From Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark and
| | - Johan Olsen
- From Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark and
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, Bagsværd DK-2880, Denmark
| | - Nicolaj Cruys-Bagger
- From Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark and
| | - Kenneth Jensen
- Novozymes A/S, Krogshøjvej 36, Bagsværd DK-2880, Denmark
| | - Peter Westh
- From Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark and
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27
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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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28
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Knott BC, Crowley MF, Himmel ME, Ståhlberg J, Beckham GT. Carbohydrate-protein interactions that drive processive polysaccharide translocation in enzymes revealed from a computational study of cellobiohydrolase processivity. J Am Chem Soc 2014; 136:8810-9. [PMID: 24869982 DOI: 10.1021/ja504074g] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Translocation of carbohydrate polymers through protein tunnels and clefts is a ubiquitous biochemical phenomenon in proteins such as polysaccharide synthases, glycoside hydrolases, and carbohydrate-binding modules. Although static snapshots of carbohydrate polymer binding in proteins have long been studied via crystallography and spectroscopy, the molecular details of polysaccharide chain processivity have not been elucidated. Here, we employ simulation to examine how a cellulose chain translocates by a disaccharide unit during the processive cycle of a glycoside hydrolase family 7 cellobiohydrolase. Our results demonstrate that these biologically and industrially important enzymes employ a two-step mechanism for chain threading to form a Michaelis complex and that the free energy barrier to chain threading is significantly lower than the hydrolysis barrier. Taken with previous studies, our findings suggest that the rate-limiting step in enzymatic cellulose degradation is the glycosylation reaction, not chain processivity. Based on the simulations, we find that strong electrostatic interactions with polar residues that are conserved in GH7 cellobiohydrolases, but not in GH7 endoglucanases, at the leading glucosyl ring provide the thermodynamic driving force for polysaccharide chain translocation. Also, we consider the role of aromatic-carbohydrate interactions, which are widespread in carbohydrate-active enzymes and have long been associated with processivity. Our analysis suggests that the primary role for these aromatic residues is to provide tunnel shape and guide the carbohydrate chain to the active site. More broadly, this work elucidates the role of common protein motifs found in carbohydrate-active enzymes that synthesize or depolymerize polysaccharides by chain translocation mechanisms coupled to catalysis.
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Affiliation(s)
- Brandon C Knott
- National Bioenergy Center and ‡Biosciences Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States
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29
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Towards a molecular-level theory of carbohydrate processivity in glycoside hydrolases. Curr Opin Biotechnol 2014; 27:96-106. [DOI: 10.1016/j.copbio.2013.12.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 12/04/2013] [Indexed: 10/25/2022]
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30
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Cruys-Bagger N, Badino SF, Tokin R, Gontsarik M, Fathalinejad S, Jensen K, Toscano MD, Sørensen TH, Borch K, Tatsumi H, Väljamäe P, Westh P. A pyranose dehydrogenase-based biosensor for kinetic analysis of enzymatic hydrolysis of cellulose by cellulases. Enzyme Microb Technol 2014; 58-59:68-74. [DOI: 10.1016/j.enzmictec.2014.03.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 03/03/2014] [Accepted: 03/04/2014] [Indexed: 10/25/2022]
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31
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Granum DM, Vyas S, Sambasivarao SV, Maupin CM. Computational Evaluations of Charge Coupling and Hydrogen Bonding in the Active Site of a Family 7 Cellobiohydrolase. J Phys Chem B 2014; 118:434-48. [DOI: 10.1021/jp408536s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David M. Granum
- Chemical and Biological Engineering Department and ‡Chemistry and Geochemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - Shubham Vyas
- Chemical and Biological Engineering Department and ‡Chemistry and Geochemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - Somisetti V. Sambasivarao
- Chemical and Biological Engineering Department and ‡Chemistry and Geochemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - C. Mark Maupin
- Chemical and Biological Engineering Department and ‡Chemistry and Geochemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
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32
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Payne CM, Jiang W, Shirts MR, Himmel ME, Crowley MF, Beckham GT. Glycoside Hydrolase Processivity Is Directly Related to Oligosaccharide Binding Free Energy. J Am Chem Soc 2013; 135:18831-9. [DOI: 10.1021/ja407287f] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Wei Jiang
- Argonne
Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Michael R. Shirts
- Department
of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
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33
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Kostylev M, Alahuhta M, Chen M, Brunecky R, Himmel ME, Lunin VV, Brady J, Wilson DB. Cel48A fromThermobifida fusca: Structure and site directed mutagenesis of key residues. Biotechnol Bioeng 2013; 111:664-73. [DOI: 10.1002/bit.25139] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 10/05/2013] [Accepted: 10/21/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Maxim Kostylev
- Department of Molecular Biology and Genetics; Cornell University; 458 Biotechnology Building Ithaca New York 14853
| | - Markus Alahuhta
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - Mo Chen
- Department of Food Science; Cornell University; Ithaca New York
| | - Roman Brunecky
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - Michael E. Himmel
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - Vladimir V. Lunin
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - John Brady
- Department of Food Science; Cornell University; Ithaca New York
| | - David B. Wilson
- Department of Molecular Biology and Genetics; Cornell University; 458 Biotechnology Building Ithaca New York 14853
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34
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Bianchetti CM, Brumm P, Smith RW, Dyer K, Hura GL, Rutkoski TJ, Phillips GN. Structure, dynamics, and specificity of endoglucanase D from Clostridium cellulovorans. J Mol Biol 2013; 425:4267-85. [PMID: 23751954 PMCID: PMC4039632 DOI: 10.1016/j.jmb.2013.05.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 05/22/2013] [Accepted: 05/30/2013] [Indexed: 11/17/2022]
Abstract
The enzymatic degradation of cellulose is a critical step in the biological conversion of plant biomass into an abundant renewable energy source. An understanding of the structural and dynamic features that cellulases utilize to bind a single strand of crystalline cellulose and hydrolyze the β-1,4-glycosidic bonds of cellulose to produce fermentable sugars would greatly facilitate the engineering of improved cellulases for the large-scale conversion of plant biomass. Endoglucanase D (EngD) from Clostridium cellulovorans is a modular enzyme comprising an N-terminal catalytic domain and a C-terminal carbohydrate-binding module, which is attached via a flexible linker. Here, we present the 2.1-Å-resolution crystal structures of full-length EngD with and without cellotriose bound, solution small-angle X-ray scattering (SAXS) studies of the full-length enzyme, the characterization of the active cleft glucose binding subsites, and substrate specificity of EngD on soluble and insoluble polymeric carbohydrates. SAXS data support a model in which the linker is flexible, allowing EngD to adopt an extended conformation in solution. The cellotriose-bound EngD structure revealed an extended active-site cleft that contains seven glucose-binding subsites, but unlike the majority of structurally determined endocellulases, the active-site cleft of EngD is partially enclosed by Trp162 and Tyr232. EngD variants, which lack Trp162, showed a significant reduction in activity and an alteration in the distribution of cellohexaose degradation products, suggesting that Trp162 plays a direct role in substrate binding.
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Affiliation(s)
- Christopher M. Bianchetti
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706, USA
| | - Phillip Brumm
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706, USA
- Lucigen Corporation and C5-6 Technologies, Madison WI 53562, USA
| | - Robert W. Smith
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706, USA
| | - Kevin Dyer
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Greg L. Hura
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Thomas J. Rutkoski
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706, USA
| | - George N. Phillips
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706, USA
- Department of Biochemistry and Cell Biology Rice University, Houston, TX 77005
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35
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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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36
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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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37
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Affiliation(s)
- Artur Gora
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Centre for Clinical
Research, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
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38
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Ghattyvenkatakrishna PK, Alekozai EM, Beckham GT, Schulz R, Crowley MF, Uberbacher EC, Cheng X. Initial recognition of a cellodextrin chain in the cellulose-binding tunnel may affect cellobiohydrolase directional specificity. Biophys J 2013; 104:904-12. [PMID: 23442969 DOI: 10.1016/j.bpj.2012.12.052] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/14/2012] [Accepted: 12/27/2012] [Indexed: 10/27/2022] Open
Abstract
Cellobiohydrolases processively hydrolyze glycosidic linkages in individual polymer chains of cellulose microfibrils, and typically exhibit specificity for either the reducing or nonreducing end of cellulose. Here, we conduct molecular dynamics simulations and free energy calculations to examine the initial binding of a cellulose chain into the catalytic tunnel of the reducing-end-specific Family 7 cellobiohydrolase (Cel7A) from Hypocrea jecorina. In unrestrained simulations, the cellulose diffuses into the tunnel from the -7 to the -5 positions, and the associated free energy profiles exhibit no barriers for initial processivity. The comparison of the free energy profiles for different cellulose chain orientations show a thermodynamic preference for the reducing end, suggesting that the preferential initial binding may affect the directional specificity of the enzyme by impeding nonproductive (nonreducing end) binding. Finally, the Trp-40 at the tunnel entrance is shown with free energy calculations to have a significant effect on initial chain complexation in Cel7A.
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39
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Kostylev M, Wilson D. Two-parameter kinetic model based on a time-dependent activity coefficient accurately describes enzymatic cellulose digestion. Biochemistry 2013; 52:5656-64. [PMID: 23837567 DOI: 10.1021/bi400358v] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lignocellulosic biomass is a potential source of renewable, low-carbon-footprint liquid fuels. Biomass recalcitrance and enzyme cost are key challenges associated with the large-scale production of cellulosic fuel. Kinetic modeling of enzymatic cellulose digestion has been complicated by the heterogeneous nature of the substrate and by the fact that a true steady state cannot be attained. We present a two-parameter kinetic model based on the Michaelis-Menten scheme ( Michaelis, L., and Menten, M. L. ( 1913 ) Biochem. Z. , 49 , 333 - 369 ) with a time-dependent activity coefficient analogous to fractal-like kinetics formulated by Kopelman ( Kopelman, R. ( 1988 ) Science 241 , 1620 - 1626 ). We provide a mathematical derivation and experimental support to show that one of the parameters is a total activity coefficient and the other is an intrinsic constant that reflects the ability of the cellulases to overcome substrate recalcitrance. The model is applicable to individual cellulases and their mixtures at low-to-medium enzyme loads. Using biomass degrading enzymes from cellulolytic bacterium Thermobifida fusca , we show that the model can be used for mechanistic studies of enzymatic cellulose digestion. We also demonstrate that it applies to the crude supernatant of the widely studied cellulolytic fungus Trichoderma reesei ; thus it can be used to compare cellulases from different organisms. The two parameters may serve a similar role to Vmax, KM, and kcat in classical kinetics. A similar approach may be applicable to other enzymes with heterogeneous substrates and where a steady state is not achievable.
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Affiliation(s)
- Maxim Kostylev
- Department of Molecular Biology and Genetics, 460 Biotechnology Building, Cornell University, Ithaca, NY 14853, USA.
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40
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Taylor CB, Payne CM, Himmel ME, Crowley MF, McCabe C, Beckham GT. Binding Site Dynamics and Aromatic–Carbohydrate Interactions in Processive and Non-Processive Family 7 Glycoside Hydrolases. J Phys Chem B 2013; 117:4924-33. [DOI: 10.1021/jp401410h] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Courtney B. Taylor
- Department
of Chemical and Biomolecular
Engineering, Vanderbilt University, Nashville,
Tennessee 37235, United States
| | - Christina M. Payne
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
80401, United States
- Department
of Chemical and Materials
Engineering, University of Kentucky, Lexington,
Kentucky 40506, United States
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
80401, United States
| | - Michael F. Crowley
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
80401, United States
| | - Clare McCabe
- Department
of Chemical and Biomolecular
Engineering, Vanderbilt University, Nashville,
Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235,
United States
| | - Gregg T. Beckham
- National
Bioenergy Center, National
Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Department of Chemical Engineering, Colorado School of Mines, Golden, Colorado 80401, United
States
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41
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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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42
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Miyauchi S, Te'o VS, Bergquist PL, Nevalainen KMH. Expression of a bacterial xylanase in Trichoderma reesei under the egl2 and cbh2 glycosyl hydrolase gene promoters. N Biotechnol 2013; 30:523-30. [PMID: 23467195 DOI: 10.1016/j.nbt.2013.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 02/24/2013] [Accepted: 02/25/2013] [Indexed: 11/17/2022]
Abstract
Expression vectors were constructed for Trichoderma reesei using the promoters, secretion signals and the modular structure of the efficiently expressed and secreted cellulase enzymes EGL2 (Cel5A) and CBH2 (Cel6A) as a prelude to establishing a platform where a gene of interest can be expressed under several promoters simultaneously. The designs featured (i) EGL2sigpro (egl2 promoter and secretion signal), (ii) EGL2cbmlin (egl2 promoter, secretion signal, EGL2 cellulose binding module and linker), (iii) CBH2sigpro (cbh2 promoter and secretion signal) and (iv) CBH2cbmlin (cbh2 promoter, secretion signal, CBH2 cellulose binding module and linker). Recombinant vectors were introduced individually into the high protein-secreting T. reesei RUT-C30 strain to generate single-promoter transformants expressing the Dictyoglomus thermophilum xynB gene that encodes a thermophilic xylanase enzyme (XynB). Ten transformants producing XynB representing each of the four different types of vectors were selected for further testing and the highest XynB production was achieved from a transformant containing 1-2copies of the EGL2cbmlin vector. Best xylanase producers did not show any particular pattern in terms of the number of gene copies and their mode of integration into the chromosomal DNA. Transformants generated with the cbmlin-type vectors produced multiple forms of XynB which were decorated with various N- and O-glycans. One of the O-glycans was identified as hexuronic acid, whose presence had not been observed previously in the glycosylation patterns of T. reesei.
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Affiliation(s)
- Shingo Miyauchi
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia
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Sandgren M, Wu M, Karkehabadi S, Mitchinson C, Kelemen BR, Larenas EA, Ståhlberg J, Hansson H. The Structure of a Bacterial Cellobiohydrolase: The Catalytic Core of the Thermobifida fusca Family GH6 Cellobiohydrolase Cel6B. J Mol Biol 2013; 425:622-35. [DOI: 10.1016/j.jmb.2012.11.039] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/26/2012] [Accepted: 11/28/2012] [Indexed: 10/27/2022]
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Momeni MH, Payne CM, Hansson H, Mikkelsen NE, Svedberg J, Engström Å, Sandgren M, Beckham GT, Ståhlberg J. Structural, biochemical, and computational characterization of the glycoside hydrolase family 7 cellobiohydrolase of the tree-killing fungus Heterobasidion irregulare. J Biol Chem 2013; 288:5861-72. [PMID: 23303184 DOI: 10.1074/jbc.m112.440891] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Root rot fungi of the Heterobasidion annosum complex are the most damaging pathogens in temperate forests, and the recently sequenced Heterobasidion irregulare genome revealed over 280 carbohydrate-active enzymes. Here, H. irregulare was grown on biomass, and the most abundant protein in the culture filtrate was identified as the only family 7 glycoside hydrolase in the genome, which consists of a single catalytic domain, lacking a linker and carbohydrate-binding module. The enzyme, HirCel7A, was characterized biochemically to determine the optimal conditions for activity. HirCel7A was crystallized and the structure, refined at 1.7 Å resolution, confirms that HirCel7A is a cellobiohydrolase rather than an endoglucanase, with a cellulose-binding tunnel that is more closed than Phanerochaete chrysosporium Cel7D and more open than Hypocrea jecorina Cel7A, suggesting intermediate enzyme properties. Molecular simulations were conducted to ascertain differences in enzyme-ligand interactions, ligand solvation, and loop flexibility between the family 7 glycoside hydrolase cellobiohydrolases from H. irregulare, H. jecorina, and P. chrysosporium. The structural comparisons and simulations suggest significant differences in enzyme-ligand interactions at the tunnel entrance in the -7 to -4 binding sites and suggest that a tyrosine residue at the tunnel entrance of HirCel7A may serve as an additional ligand-binding site. Additionally, the loops over the active site in H. jecorina Cel7A are more closed than loops in the other two enzymes, which has implications for the degree of processivity, endo-initiation, and substrate dissociation. Overall, this study highlights molecular level features important to understanding this biologically and industrially important family of glycoside hydrolases.
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Affiliation(s)
- Majid Haddad Momeni
- Department of Molecular Biology, Swedish University of Agricultural Sciences, SE-751 24 Uppsala, Sweden
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Ganner T, Bubner P, Eibinger M, Mayrhofer C, Plank H, Nidetzky B. Dissecting and reconstructing synergism: in situ visualization of cooperativity among cellulases. J Biol Chem 2012; 287:43215-22. [PMID: 23118223 PMCID: PMC3527909 DOI: 10.1074/jbc.m112.419952] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellulose is the most abundant biopolymer and a major reservoir of fixed carbon on earth. Comprehension of the elusive mechanism of its enzymatic degradation represents a fundamental problem at the interface of biology, biotechnology, and materials science. The interdependence of cellulose disintegration and hydrolysis and the synergistic interplay among cellulases is yet poorly understood. Here we report evidence from in situ atomic force microscopy (AFM) that delineates degradation of a polymorphic cellulose substrate as a dynamic cycle of alternating exposure and removal of crystalline fibers. Direct observation shows that chain-end-cleaving cellobiohydrolases (CBH I, CBH II) and an internally chain-cleaving endoglucanase (EG), the major components of cellulase systems, take on distinct roles: EG and CBH II make the cellulose surface accessible for CBH I by removing amorphous-unordered substrate areas, thus exposing otherwise embedded crystalline-ordered nanofibrils of the cellulose. Subsequently, these fibrils are degraded efficiently by CBH I, thereby uncovering new amorphous areas. Without prior action of EG and CBH II, CBH I was poorly active on the cellulosic substrate. This leads to the conclusion that synergism among cellulases is morphology-dependent and governed by the cooperativity between enzymes degrading amorphous regions and those targeting primarily crystalline regions. The surface-disrupting activity of cellulases therefore strongly depends on mesoscopic structural features of the substrate: size and packing of crystalline fibers are key determinants of the overall efficiency of cellulose degradation.
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Affiliation(s)
- Thomas Ganner
- Institute for Electron Microscopy and Fine Structure Research, Graz University of Technology, Steyrergasse 17, A-8010 Graz, Austria
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Payne CM, Baban J, Horn SJ, Backe PH, Arvai AS, Dalhus B, Bjørås M, Eijsink VGH, Sørlie M, Beckham GT, Vaaje-Kolstad G. Hallmarks of processivity in glycoside hydrolases from crystallographic and computational studies of the Serratia marcescens chitinases. J Biol Chem 2012; 287:36322-30. [PMID: 22952223 DOI: 10.1074/jbc.m112.402149] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Degradation of recalcitrant polysaccharides in nature is typically accomplished by mixtures of processive and nonprocessive glycoside hydrolases (GHs), which exhibit synergistic activity wherein nonprocessive enzymes provide new sites for productive attachment of processive enzymes. GH processivity is typically attributed to active site geometry, but previous work has demonstrated that processivity can be tuned by point mutations or removal of single loops. To gain additional insights into the differences between processive and nonprocessive enzymes that give rise to their synergistic activities, this study reports the crystal structure of the catalytic domain of the GH family 18 nonprocessive endochitinase, ChiC, from Serratia marcescens. This completes the structural characterization of the co-evolved chitinolytic enzymes from this bacterium and enables structural analysis of their complementary functions. The ChiC catalytic module reveals a shallow substrate-binding cleft that lacks aromatic residues vital for processivity, a calcium-binding site not previously seen in GH18 chitinases, and, importantly, a displaced catalytic acid (Glu-141), suggesting flexibility in the catalytic center. Molecular dynamics simulations of two processive chitinases (ChiA and ChiB), the ChiC catalytic module, and an endochitinase from Lactococcus lactis show that the nonprocessive enzymes have more flexible catalytic machineries and that their bound ligands are more solvated and flexible. These three features, which relate to the more dynamic on-off ligand binding processes associated with nonprocessive action, correlate to experimentally measured differences in processivity of the S. marcescens chitinases. These newly defined hallmarks thus appear to be key dynamic metrics in determining processivity in GH enzymes complementing structural insights.
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Affiliation(s)
- Christina M Payne
- Biosciences Center, National Renewable Energy Laboratory, Golden Colorado 80401, USA
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Thompson AJ, Heu T, Shaghasi T, Benyamino R, Jones A, Friis EP, Wilson KS, Davies GJ. Structure of the catalytic core module of theChaetomium thermophilumfamily GH6 cellobiohydrolase Cel6A. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:875-82. [DOI: 10.1107/s0907444912016496] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 04/16/2012] [Indexed: 11/11/2022]
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Sørlie M, Zakariassen H, Norberg AL, Eijsink VGH. Processivity and substrate-binding in family 18 chitinases. BIOCATAL BIOTRANSFOR 2012. [DOI: 10.3109/10242422.2012.676282] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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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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Jakobsson E, Schwarzer D, Jokilammi A, Finne J. Endosialidases: Versatile Tools for the Study of Polysialic Acid. Top Curr Chem (Cham) 2012; 367:29-73. [PMID: 22851159 DOI: 10.1007/128_2012_349] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Polysialic acid is an α2,8-linked N-acetylneuraminic acid polymer found on the surface of both bacterial and eukaryotic cells. Endosialidases are bacteriophage-borne glycosyl hydrolases that specifically cleave polysialic acid. The crystal structure of an endosialidase reveals a trimeric mushroom-shaped molecule which, in addition to the active site, harbors two additional polysialic acid binding sites. Folding of the protein crucially depends on an intramolecular C-terminal chaperone domain that is proteolytically released in an intramolecular reaction. Based on structural data and previous considerations, an updated catalytic mechanism is discussed. Endosialidases degrade polysialic acid in a processive mode of action, and a model for its mechanism is suggested. The review summarizes the structural and biochemical elucidations of the last decade and the importance of endosialidases in biochemical and medical applications. Active endosialidases are important tools in studies on the biological roles of polysialic acid, such as the pathogenesis of septicemia and meningitis by polysialic acid-encapsulated bacteria, or its role as a modulator of the adhesion and interactions of neural and other cells. Endosialidase mutants that have lost their polysialic acid cleaving activity while retaining their polysialic acid binding capability have been fused to green fluorescent protein to provide an efficient tool for the specific detection of polysialic acid.
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Affiliation(s)
- Elina Jakobsson
- Department of Medical Biochemistry and Genetics, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
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