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Zhu Q, Huang Y, Yang Z, Wu X, Zhu Q, Zheng H, Zhu D, Lv Z, Yin Y. A Recombinant Thermophilic and Glucose-Tolerant GH1 β-Glucosidase Derived from Hehua Hot Spring. Molecules 2024; 29:1017. [PMID: 38474529 DOI: 10.3390/molecules29051017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/18/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
As a crucial enzyme for cellulose degradation, β-glucosidase finds extensive applications in food, feed, and bioethanol production; however, its potential is often limited by inadequate thermal stability and glucose tolerance. In this study, a functional gene (lq-bg5) for a GH1 family β-glucosidase was obtained from the metagenomic DNA of a hot spring sediment sample and heterologously expressed in E. coli and the recombinant enzyme was purified and characterized. The optimal temperature and pH of LQ-BG5 were 55 °C and 4.6, respectively. The relative residual activity of LQ-BG5 exceeded 90% at 55 °C for 9 h and 60 °C for 6 h and remained above 100% after incubation at pH 5.0-10.0 for 12 h. More importantly, LQ-BG5 demonstrated exceptional glucose tolerance with more than 40% activity remaining even at high glucose concentrations of 3000 mM. Thus, LQ-BG5 represents a thermophilic β-glucosidase exhibiting excellent thermal stability and remarkable glucose tolerance, making it highly promising for lignocellulose development and utilization.
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Affiliation(s)
- Qian Zhu
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Yuying Huang
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
- Key Laboratory of Bioinformatics and Computational Biology, Department of Education of Yunnan Province, Dali University, Dali 671003, China
| | - Zhengfeng Yang
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Xingci Wu
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Qianru Zhu
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Hongzhao Zheng
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Dan Zhu
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Zhihua Lv
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
- Cangshan Forest Ecosystem Observation and Research Station of Yunnan Province, Dali University, Dali 671003, China
| | - Yirui Yin
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
- Key Laboratory of Bioinformatics and Computational Biology, Department of Education of Yunnan Province, Dali University, Dali 671003, China
- Cangshan Forest Ecosystem Observation and Research Station of Yunnan Province, Dali University, Dali 671003, China
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2
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Haataja T, Gado JE, Nutt A, Anderson NT, Nilsson M, Momeni MH, Isaksson R, Väljamäe P, Johansson G, Payne CM, Ståhlberg J. Enzyme kinetics by GH7 cellobiohydrolases on chromogenic substrates is dictated by non-productive binding: insights from crystal structures and MD simulation. FEBS J 2023; 290:379-399. [PMID: 35997626 PMCID: PMC10087753 DOI: 10.1111/febs.16602] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/30/2022] [Accepted: 08/17/2022] [Indexed: 02/05/2023]
Abstract
Cellobiohydrolases (CBHs) in the glycoside hydrolase family 7 (GH7) (EC3.2.1.176) are the major cellulose degrading enzymes both in industrial settings and in the context of carbon cycling in nature. Small carbohydrate conjugates such as p-nitrophenyl-β-d-cellobioside (pNPC), p-nitrophenyl-β-d-lactoside (pNPL) and methylumbelliferyl-β-d-cellobioside have commonly been used in colorimetric and fluorometric assays for analysing activity of these enzymes. Despite the similar nature of these compounds the kinetics of their enzymatic hydrolysis vary greatly between the different compounds as well as among different enzymes within the GH7 family. Through enzyme kinetics, crystallographic structure determination, molecular dynamics simulations, and fluorometric binding studies using the closely related compound o-nitrophenyl-β-d-cellobioside (oNPC), in this work we examine the different hydrolysis characteristics of these compounds on two model enzymes of this class, TrCel7A from Trichoderma reesei and PcCel7D from Phanerochaete chrysosporium. Protein crystal structures of the E212Q mutant of TrCel7A with pNPC and pNPL, and the wildtype TrCel7A with oNPC, reveal that non-productive binding at the product site is the dominating binding mode for these compounds. Enzyme kinetics results suggest the strength of non-productive binding is a key determinant for the activity characteristics on these substrates, with PcCel7D consistently showing higher turnover rates (kcat ) than TrCel7A, but higher Michaelis-Menten (KM ) constants as well. Furthermore, oNPC turned out to be useful as an active-site probe for fluorometric determination of the dissociation constant for cellobiose on TrCel7A but could not be utilized for the same purpose on PcCel7D, likely due to strong binding to an unknown site outside the active site.
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Affiliation(s)
- Topi Haataja
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Japheth E Gado
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA.,Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Anu Nutt
- Department of Chemistry, Uppsala University, Sweden.,Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Nolan T Anderson
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA
| | - Mikael Nilsson
- Institute of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Majid Haddad Momeni
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Roland Isaksson
- Institute of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | | | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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3
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Molecular recognition in the product site of cellobiohydrolase Cel7A regulates processive step length. Biochem J 2020; 477:99-110. [PMID: 31816027 DOI: 10.1042/bcj20190770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 11/17/2022]
Abstract
Cellobiohydrolase Cel7A is an industrial important enzyme that breaks down cellulose by a complex processive mechanism. The enzyme threads the reducing end of a cellulose strand into its tunnel-shaped catalytic domain and progresses along the strand while sequentially releasing the disaccharide cellobiose. While some molecular details of this intricate process have emerged, general structure-function relationships for Cel7A remain poorly elucidated. One interesting aspect is the occurrence of particularly strong ligand interactions in the product binding site. In this work, we analyze these interactions in Cel7A from Trichoderma reesei with special emphasis on the Arg251 and Arg394 residues. We made extensive biochemical characterization of enzymes that were mutated in these two positions and showed that the arginine residues contributed strongly to product binding. Specifically, ∼50% of the total standard free energy of product binding could be ascribed to four hydrogen bonds to Arg251 and Arg394, which had previously been identified in crystal structures. Mutation of either Arg251 or Arg394 lowered production inhibition of Cel7A, but at the same time altered the enzyme product profile and resulted in ∼50% reduction in both processivity and hydrolytic activity. The position of the two arginine residues closely matches the two-fold screw axis symmetry of the substrate, and this energetically favors the productive enzyme-substrate complex. Our results indicate that the strong and specific ligand interactions of Arg251 and Arg394 provide a simple proofreading system that controls the step length during consecutive hydrolysis and minimizes dead time associated with transient, non-productive complexes.
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4
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Kalbarczyk KZ, Mazeau EJ, Rapp KM, Marchand N, Koffas MAG, Collins CH. Engineering Bacillus megaterium Strains To Secrete Cellulases for Synergistic Cellulose Degradation in a Microbial Community. ACS Synth Biol 2018; 7:2413-2422. [PMID: 30226981 DOI: 10.1021/acssynbio.8b00186] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recent environmental concerns have intensified the need to develop systems to degrade waste biomass for use as an inexpensive carbon source for microbial chemical production. Current approaches to biomass utilization rely on pretreatment processes that include expensive enzymatic purification steps for the requisite cellulases. We aimed to engineer a synthetic microbial community to synergistically degrade cellulose by compartmentalizing the system with multiple specialized Bacillus megaterium strains. EGI1, an endoglucanase, and Cel9AT, a multimodular cellulase, were targeted for secretion from B. megaterium. A small library of signal peptides (SPs) with five amino acid linkers was selected to tag each cellulase for secretion from B. megaterium. Cellulase activity against amorphous cellulose was confirmed through a series of bioassays, and the most active SP constructs were identified as EGI1 with the LipA SP and Cel9AT with the YngK SP. The activity of the optimized cellulase secretion strains was characterized individually and in tandem to assess synergistic cellulolytic activity. The combination of EGI1 and Cel9AT yielded higher activity than either single cellulase. A coculture of EGI1 and Cel9AT secreting B. megaterium strains demonstrated synergistic behavior with higher activity than either monoculture. This cellulose degradation module can be further integrated with bioproduct synthesis modules to build complex systems for the production of high value molecules.
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Affiliation(s)
- Karolina Z. Kalbarczyk
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Emily J. Mazeau
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Kent M. Rapp
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Nicholas Marchand
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Mattheos A. G. Koffas
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Cynthia H. Collins
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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5
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Rabinovich ML, Melnik MS, Herner ML, Voznyi YV, Vasilchenko LG. Predominant Nonproductive Substrate Binding by Fungal Cellobiohydrolase I and Implications for Activity Improvement. Biotechnol J 2018; 14:e1700712. [PMID: 29781240 DOI: 10.1002/biot.201700712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 05/08/2018] [Indexed: 12/20/2022]
Abstract
Enzymatic conversion of the most abundant renewable source of organic compounds, cellulose to fermentable sugars is attractive for production of green fuels and chemicals. The major component of industrial enzyme systems, cellobiohydrolase I from Hypocrea jecorina (Trichoderma reesei) (HjCel7A) processively splits disaccharide units from the reducing ends of tightly packed cellulose chains. HjCel7A consists of a catalytic domain (CD) and a carbohydrate-binding module (CBM) separated by a linker peptide. A tunnel-shaped substrate-binding site in the CD includes nine subsites for β-d-glucose units, seven of which (-7 to -1) precede the catalytic center. Low catalytic activity of Cel7A is the bottleneck and the primary target for improvement. Here it is shown for the first time that, in spite of much lower apparent kcat of HjCel7A at the hydrolysis of β-1,4-glucosidic linkages in the fluorogenic cellotetra- and -pentaose compared to the structurally related endoglucanase I (HjCel7B), the specificity constants (catalytic efficiency) kcat /Km for both enzymes are almost equal in these reactions. The observed activity difference appears from strong nonproductive substrate binding by HjCel7A, particularly significant for MU-β-cellotetraose (MUG4 ). Interaction of substrates with the subsites -6 and -5 proximal to the nonconserved Gln101 residue in HjCel7A decreases Km,ap by >1500 times. HjCel7A can be nonproductively bound onto cellulose surface with Kd ≈2-9 nM via CBM and CD that captures six terminal glucose units of cellulose chain. Decomposition of this nonproductive complex can determine the rate of cellulose conversion. MUG4 is a promising substrate to select active cellobiohydrolase I variants with reduced nonproductive substrate binding.
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Affiliation(s)
- Mikhail L Rabinovich
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Maria S Melnik
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Mikhail L Herner
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Yakov V Voznyi
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia
| | - Lilia G Vasilchenko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
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6
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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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7
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Kuusk S, Väljamäe P. When substrate inhibits and inhibitor activates: implications of β-glucosidases. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:7. [PMID: 28053666 PMCID: PMC5209912 DOI: 10.1186/s13068-016-0690-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/16/2016] [Indexed: 05/15/2023]
Abstract
BACKGROUND β-glucosidases (BGs) catalyze the hydrolysis of β-glycosidic bonds in glucose derivatives. They constitute an important group of enzymes with biotechnological interest like supporting cellulases in degradation of lignocellulose to fermentable sugars. In the latter context, the glucose tolerant BGs are of particular interest. These BGs often show peculiar kinetics, including inhibitory effects of substrates and activating effects of inhibitors, such as glucose or xylose. The mechanisms behind the activating/inhibiting effects are poorly understood. The nonproductive binding of substrate is expected in cases where enzymes with multiple consecutive binding subsites are studied on substrates with a low degree of polymerization. The effects of inhibitors to BGs exerting nonproductive binding of substrate have not been discussed in the literature before. RESULTS Here, we performed analyses of different reaction schemes using the catalysis by retaining BGs as a model. We found that simple competition of inhibitor with nonproductive binding of substrate can account for the activation of enzyme by inhibitor without involving any allosteric effects. The transglycosylation to inhibitor was also able to explain the activating effect of inhibitor. For both mechanisms, the activation was caused by the increase of kcat with increasing inhibitor concentration, while kcat/Km always decreased. Therefore, the activation by inhibitor was more pronounced at high substrate concentrations. The possible contribution of the two mechanisms in the activation by inhibitor was dependent on the rate-limiting step of glycosidic bond hydrolysis as well as on whether and which glucose-unit-binding subsites are interacting. CONCLUSION Knowledge on the mechanisms of the activating/inhibiting effects of inhibitors helps the rational engineering and selection of BGs for biotechnological applications. Provided that the catalysis is consistent with the reaction schemes addressed here and underlying assumptions, the mechanism of activation by inhibitor reported here is applicable for all enzymes exerting nonproductive binding of substrate.
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Affiliation(s)
- Silja Kuusk
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b – 202, 51010 Tartu, Estonia
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b – 202, 51010 Tartu, Estonia
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8
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Wang X, Rong L, Wang M, Pan Y, Zhao Y, Tao F. Improving the activity of endoglucanase I (EGI) from Saccharomyces cerevisiae by DNA shuffling. RSC Adv 2017. [DOI: 10.1039/c6ra26508a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
To enhance the endo-β-1,4-glucanase activity of three mixedTrichodermasp. (Trichoderma reesei, Trichoderma longibrachiatum, andTrichoderma pseudokoningii), we optimized the efficiency of the encoding gene using DNA shuffling andSaccharomyces cerevisiaeINVSc1 as a host.
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Affiliation(s)
- Xu Wang
- College of Food Science and Technology
- Shanghai Ocean University
- Shanghai
- China
- School of Life Sciences
| | - Liang Rong
- USC School of Pharmacy
- University of Southern California
- Los Angeles
- USA
| | - Mingfu Wang
- College of Food Science and Technology
- Shanghai Ocean University
- Shanghai
- China
| | - Yingjie Pan
- College of Food Science and Technology
- Shanghai Ocean University
- Shanghai
- China
| | - Yong Zhao
- College of Food Science and Technology
- Shanghai Ocean University
- Shanghai
- China
| | - Fang Tao
- School of Life Sciences
- Anhui Agricultural University
- China
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9
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Kari J, Kont R, Borch K, Buskov S, Olsen JP, Cruyz-Bagger N, Väljamäe P, Westh P. Anomeric Selectivity and Product Profile of a Processive Cellulase. Biochemistry 2016; 56:167-178. [PMID: 28026938 DOI: 10.1021/acs.biochem.6b00636] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cellobiohydrolases (CBHs) make up an important group of enzymes for both natural carbon cycling and industrial deconstruction of lignocellulosic biomass. The consecutive hydrolysis of one cellulose strand relies on an intricate pattern of enzyme-substrate interactions in the long, tunnel-shaped binding site of the CBH. In this work, we have investigated the initial complexation mode with cellulose of the most thoroughly studied CBH, Cel7A from Hypocrea jecorina (HjCel7A). We found that HjCel7A predominantly produces glucose when it initiates a processive run on insoluble microcrystalline cellulose, confirming the validity of an even and odd product ratio as an estimate of processivity. Moreover, the glucose released from cellulose was predominantly α-glucose. A link between the initial binding mode of the enzyme and the reducing end configuration was investigated by inhibition studies with the two anomers of cellobiose. A clear preference for β-cellobiose in product binding site +2 was observed for HjCel7A, but not the homologous endoglucanase, HjCe7B. Possible relationships between this anomeric preference in the product site and the prevalence of odd-numbered initial-cut products are discussed, and a correlation between processivity and anomer selectivity is proposed.
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Affiliation(s)
- Jeppe Kari
- Research Unit for Functional Biomaterials, Roskilde University , Roskilde, Denmark
| | - Riin Kont
- Institute of Molecular and Cell Biology, University of Tartu , Tartu, Estonia
| | - Kim Borch
- Novozymes A/S , Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | - Steen Buskov
- Novozymes A/S , Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | - Johan Pelck Olsen
- Research Unit for Functional Biomaterials, Roskilde University , Roskilde, Denmark
| | | | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu , Tartu, Estonia
| | - Peter Westh
- Research Unit for Functional Biomaterials, Roskilde University , Roskilde, Denmark
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10
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Wang Y, Zhang S, Song X, Yao L. Cellulose chain binding free energy drives the processive move of cellulases on the cellulose surface. Biotechnol Bioeng 2016; 113:1873-80. [DOI: 10.1002/bit.25970] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/17/2016] [Accepted: 02/21/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Yefei Wang
- Shandong Provincial Key Laboratory of Synthetic Biology; Chinese Academy of Sciences; Qingdao China
- Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266061 China
| | - Shujun Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology; Chinese Academy of Sciences; Qingdao China
- Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266061 China
| | - Xiangfei Song
- Shandong Provincial Key Laboratory of Synthetic Biology; Chinese Academy of Sciences; Qingdao China
- Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266061 China
| | - Lishan Yao
- Shandong Provincial Key Laboratory of Synthetic Biology; Chinese Academy of Sciences; Qingdao China
- Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266061 China
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11
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Olsen JP, Alasepp K, Kari J, Cruys-Bagger N, Borch K, Westh P. Mechanism of product inhibition for cellobiohydrolase Cel7A during hydrolysis of insoluble cellulose. Biotechnol Bioeng 2016; 113:1178-86. [DOI: 10.1002/bit.25900] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/23/2015] [Accepted: 11/29/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Johan P. Olsen
- Research Unit for Functional Biomaterials; Roskilde University; NSM, 1 Universitetsvej, Build. 28 DK-4000 Roskilde Denmark
| | - Kadri Alasepp
- Research Unit for Functional Biomaterials; Roskilde University; NSM, 1 Universitetsvej, Build. 28 DK-4000 Roskilde Denmark
| | - Jeppe Kari
- Research Unit for Functional Biomaterials; Roskilde University; NSM, 1 Universitetsvej, Build. 28 DK-4000 Roskilde Denmark
| | - Nicolaj Cruys-Bagger
- Research Unit for Functional Biomaterials; Roskilde University; NSM, 1 Universitetsvej, Build. 28 DK-4000 Roskilde Denmark
- Novozymes A/S; Bagsvaerd Denmark
| | | | - Peter Westh
- Research Unit for Functional Biomaterials; Roskilde University; NSM, 1 Universitetsvej, Build. 28 DK-4000 Roskilde Denmark
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12
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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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13
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Momeni MH, Ubhayasekera W, Sandgren M, Ståhlberg J, Hansson H. Structural insights into the inhibition of cellobiohydrolase Cel7A by xylo-oligosaccharides. FEBS J 2015; 282:2167-77. [PMID: 25765184 DOI: 10.1111/febs.13265] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 03/06/2015] [Accepted: 03/10/2015] [Indexed: 11/28/2022]
Abstract
UNLABELLED The filamentous fungus Hypocrea jecorina (anamorph of Trichoderma reesei) is the predominant source of enzymes for industrial saccharification of lignocellulose biomass. The major enzyme, cellobiohydrolase Cel7A, constitutes nearly half of the total protein in the secretome. The performance of such enzymes is susceptible to inhibition by compounds liberated by physico-chemical pre-treatment if the biomass is kept unwashed. Xylan and xylo-oligosaccharides (XOS) have been proposed to play a key role in inhibition of cellobiohydrolases of glycoside hydrolase family 7. To elucidate the mechanism behind this inhibition at a molecular level, we used X-ray crystallography to determine structures of H. jecorina Cel7A in complex with XOS. Structures with xylotriose, xylotetraose and xylopentaose revealed a predominant binding mode at the entrance of the substrate-binding tunnel of the enzyme, in which each xylose residue is shifted ~ 2.4 Å towards the catalytic center compared with binding of cello-oligosaccharides. Furthermore, partial occupancy of two consecutive xylose residues at subsites -2 and -1 suggests an alternative binding mode for XOS in the vicinity of the catalytic center. Interestingly, the -1 xylosyl unit exhibits an open aldehyde conformation in one of the structures and a ring-closed pyranoside in another complex. Complementary inhibition studies with p-nitrophenyl lactoside as substrate indicate mixed inhibition rather than pure competitive inhibition. DATABASE The atomic coordinates and structure factors are available in the Protein Data Bank under accession number 4D5I (H. jecorina Cel7A E212Q variant, complex with xylotriose), 4D5J (H. jecorina Cel7A E217Q variant, complex with xylotriose), 4D5O (H. jecorina Cel7A E212Q variant, complex with xylopentaose), 4D5P (H. jecorina Cel7A E217Q variant, complex with xylopentaose), 4D5Q (wild-type H. jecorina Cel7A, complex with xylopentaose) and 4D5V (H. jecorina Cel7A E217Q variant, complex with xylotetraose).
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Affiliation(s)
- Majid Haddad Momeni
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Wimal Ubhayasekera
- Institute of Medicinal Chemistry, University of Copenhagen, Denmark.,MAX-Lab, Lund University, Sweden
| | - Mats Sandgren
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Henrik Hansson
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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14
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Kuusk S, Sørlie M, Väljamäe P. The predominant molecular state of bound enzyme determines the strength and type of product inhibition in the hydrolysis of recalcitrant polysaccharides by processive enzymes. J Biol Chem 2015; 290:11678-91. [PMID: 25767120 DOI: 10.1074/jbc.m114.635631] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Indexed: 11/06/2022] Open
Abstract
Processive enzymes are major components of the efficient enzyme systems that are responsible for the degradation of the recalcitrant polysaccharides cellulose and chitin. Despite intensive research, there is no consensus on which step is rate-limiting for these enzymes. Here, we performed a comparative study of two well characterized enzymes, the cellobiohydrolase Cel7A from Hypocrea jecorina and the chitinase ChiA from Serratia marcescens. Both enzymes were inhibited by their disaccharide product, namely chitobiose for ChiA and cellobiose for Cel7A. The products behaved as noncompetitive inhibitors according to studies using the (14)C-labeled crystalline polymeric substrates (14)C chitin nanowhiskers and (14)C-labeled bacterial microcrystalline cellulose for ChiA and Cel7A, respectively. The resulting observed Ki (obs) values were 0.45 ± 0.08 mm for ChiA and 0.17 ± 0.02 mm for Cel7A. However, in contrast to ChiA, the Ki (obs) of Cel7A was an order of magnitude higher than the true Ki value governed by the thermodynamic stability of the enzyme-inhibitor complex. Theoretical analysis of product inhibition suggested that the inhibition strength and pattern can be accounted for by assuming different rate-limiting steps for ChiA and Cel7A. Measuring the population of enzymes whose active site was occupied by a polymer chain revealed that Cel7A was bound predominantly via its active site. Conversely, the active-site-mediated binding of ChiA was slow, and most ChiA exhibited a free active site, even when the substrate concentration was saturating for the activity. Collectively, our data suggest that complexation with the polymer chain is rate-limiting for ChiA, whereas Cel7A is limited by dissociation.
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Affiliation(s)
- Silja Kuusk
- From the Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia and
| | - Morten Sørlie
- the Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Priit Väljamäe
- From the Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia and
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15
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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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16
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Colussi F, Sørensen TH, Alasepp K, Kari J, Cruys-Bagger N, Windahl MS, Olsen JP, Borch K, Westh P. Probing substrate interactions in the active tunnel of a catalytically deficient cellobiohydrolase (Cel7). J Biol Chem 2014; 290:2444-54. [PMID: 25477511 DOI: 10.1074/jbc.m114.624163] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellobiohydrolases break down cellulose sequentially by sliding along the crystal surface with a single cellulose strand threaded through the catalytic tunnel of the enzyme. This so-called processive mechanism relies on a complex pattern of enzyme-substrate interactions, which need to be addressed in molecular descriptions of processivity and its driving forces. Here, we have used titration calorimetry to study interactions of cellooligosaccharides (COS) and a catalytically deficient variant (E212Q) of the enzyme Cel7A from Trichoderma reesei. This enzyme has ∼10 glucopyranose subsites in the catalytic tunnel, and using COS ligands with a degree of polymerization (DP) from 2 to 8, different regions of the tunnel could be probed. For COS ligands with a DP of 2-3 the binding constants were around 10(5) m(-1), and for longer ligands (DP 5-8) this value was ∼10(7) m(-1). Within each of these groups we did not find increased affinity as the ligands got longer and potentially filled more subsites. On the contrary, we found a small but consistent affinity loss as DP rose from 6 to 8, particularly at the higher investigated temperatures. Other thermodynamic functions (ΔH, ΔS, and ΔCp) decreased monotonously with both temperature and DP. Combined interpretation of these thermodynamic results and previously published structural data allowed assessment of an affinity profile along the length axis of the active tunnel.
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Affiliation(s)
- Francieli Colussi
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Trine H Sørensen
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Kadri Alasepp
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Jeppe Kari
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Nicolaj Cruys-Bagger
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Michael S Windahl
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and Novozymes A/S, Krogshøjvej 36, DK-2880, Bagsværd, Denmark
| | - Johan P Olsen
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880, Bagsværd, Denmark
| | - Peter Westh
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
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17
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Shang BZ, Chu JW. Kinetic Modeling at Single-Molecule Resolution Elucidates the Mechanisms of Cellulase Synergy. ACS Catal 2014. [DOI: 10.1021/cs500126q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Barry Z. Shang
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Jhih-Wei Chu
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department
of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, ROC
- Institute
of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, ROC
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18
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RETRACTED ARTICLE: The effects of each beta-glucosidase gene deletion on cellulase gene regulation in Neurospora crassa (online publication: DOI 10.1007/s10482-013- 9972-7). Antonie Van Leeuwenhoek 2013; 105:269. [PMID: 24000093 DOI: 10.1007/s10482-013-9972-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 07/09/2013] [Indexed: 11/26/2022]
Abstract
Takao Kasuga and Zhiliang Fan were listed as co-authors without their acknowledgement and would like to be removed from the authors list. This article is retracted on request of Weihua Wu due to inconsistent errors of intracellular and total beta-glucosidase activities assay and the mycelia weight measurement in this paper. These errors led to inaccurate results of total and intracellular beta-glucosidase activities, and the normalized endoglucanases and exoglucanases activities and therefore compromise the partial conclusions of this publication.
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19
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Zhang Y, Yan S, Yao L. A Mechanistic Study of Trichoderma reesei Cel7B Catalyzed Glycosidic Bond Cleavage. J Phys Chem B 2013; 117:8714-22. [DOI: 10.1021/jp403999s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Yu Zhang
- Laboratory
of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Shihai Yan
- Laboratory
of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Lishan Yao
- Laboratory
of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
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20
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Murphy L, Bohlin C, Baumann MJ, Olsen SN, Sørensen TH, Anderson L, Borch K, Westh P. Product inhibition of five Hypocrea jecorina cellulases. Enzyme Microb Technol 2013; 52:163-9. [DOI: 10.1016/j.enzmictec.2013.01.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 01/02/2013] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
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21
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Textor LC, Colussi F, Silveira RL, Serpa V, de Mello BL, Muniz JRC, Squina FM, Pereira N, Skaf MS, Polikarpov I. Joint X-ray crystallographic and molecular dynamics study of cellobiohydrolase I fromTrichoderma harzianum: deciphering the structural features of cellobiohydrolase catalytic activity. FEBS J 2012; 280:56-69. [DOI: 10.1111/febs.12049] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/18/2012] [Accepted: 10/19/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Larissa C. Textor
- Instituto de Física de São Carlos; Universidade de São Paulo; São Carlos; SP; Brazil
| | - Francieli Colussi
- Instituto de Física de São Carlos; Universidade de São Paulo; São Carlos; SP; Brazil
| | - Rodrigo L. Silveira
- Institute of Chemistry; State University of Campinas - UNICAMP; Campinas; SP; Brazil
| | - Viviane Serpa
- Instituto de Física de São Carlos; Universidade de São Paulo; São Carlos; SP; Brazil
| | - Bruno L. de Mello
- Instituto de Física de São Carlos; Universidade de São Paulo; São Carlos; SP; Brazil
| | - João Renato C. Muniz
- Instituto de Física de São Carlos; Universidade de São Paulo; São Carlos; SP; Brazil
| | - Fabio M. Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE); Centro Nacional de Pesquisa em Energia e Materiais (CNPEM); Campinas; SP; Brazil
| | - Nei Pereira
- Centro de Tecnologia, Escola de Química, Laboratório de Desenvolvimento de Bioprocessos (LaDeBio); Universidade Federal do Rio de Janeiro; RJ; Brazil
| | - Munir S. Skaf
- Institute of Chemistry; State University of Campinas - UNICAMP; Campinas; SP; Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos; Universidade de São Paulo; São Carlos; SP; Brazil
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22
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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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23
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Bu L, Nimlos MR, Shirts MR, Ståhlberg J, Himmel ME, Crowley MF, Beckham GT. Product binding varies dramatically between processive and nonprocessive cellulase enzymes. J Biol Chem 2012; 287:24807-13. [PMID: 22648408 DOI: 10.1074/jbc.m112.365510] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellulases hydrolyze β-1,4 glycosidic linkages in cellulose, which are among the most prevalent and stable bonds in Nature. Cellulases comprise many glycoside hydrolase families and exist as processive or nonprocessive enzymes. Product inhibition negatively impacts cellulase action, but experimental measurements of product-binding constants vary significantly, and there is little consensus on the importance of this phenomenon. To provide molecular level insights into cellulase product inhibition, we examine the impact of product binding on processive and nonprocessive cellulases by calculating the binding free energy of cellobiose to the product sites of catalytic domains of processive and nonprocessive enzymes from glycoside hydrolase families 6 and 7. The results suggest that cellobiose binds to processive cellulases much more strongly than nonprocessive cellulases. We also predict that the presence of a cellodextrin bound in the reactant site of the catalytic domain, which is present during enzymatic catalysis, has no effect on product binding in nonprocessive cellulases, whereas it significantly increases product binding to processive cellulases. This difference in product binding correlates with hydrogen bonding between the substrate-side ligand and the cellobiose product in processive cellulase tunnels and the additional stabilization from the longer tunnel-forming loops. The hydrogen bonds between the substrate- and product-side ligands are disrupted by water in nonprocessive cellulase clefts, and the lack of long tunnel-forming loops results in lower affinity of the product ligand. These findings provide new insights into the large discrepancies reported for binding constants for cellulases and suggest that product inhibition will vary significantly based on the amount of productive binding for processive cellulases on cellulose.
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Affiliation(s)
- Lintao Bu
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA.
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24
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Chen HL, Chen YC, Lu MYJ, Chang JJ, Wang HTC, Ke HM, Wang TY, Ruan SK, Wang TY, Hung KY, Cho HY, Lin WT, Shih MC, Li WH. A highly efficient β-glucosidase from the buffalo rumen fungus Neocallimastix patriciarum W5. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:24. [PMID: 22515264 PMCID: PMC3403894 DOI: 10.1186/1754-6834-5-24] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 04/19/2012] [Indexed: 05/07/2023]
Abstract
BACKGROUND Cellulose, which is the most abundant renewable biomass on earth, is a potential bio-resource of alternative energy. The hydrolysis of plant polysaccharides is catalyzed by microbial cellulases, including endo-β-1,4-glucanases, cellobiohydrolases, cellodextrinases, and β-glucosidases. Converting cellobiose by β-glucosidases is the key factor for reducing cellobiose inhibition and enhancing the efficiency of cellulolytic enzymes for cellulosic ethanol production. RESULTS In this study, a cDNA encoding β-glucosidase was isolated from the buffalo rumen fungus Neocallimastix patriciarum W5 and is named NpaBGS. It has a length of 2,331 bp with an open reading frame coding for a protein of 776 amino acid residues, corresponding to a theoretical molecular mass of 85.1 kDa and isoelectric point of 4.4. Two GH3 catalytic domains were found at the N and C terminals of NpaBGS by sequence analysis. The cDNA was expressed in Pichia pastoris and after protein purification, the enzyme displayed a specific activity of 34.5 U/mg against cellobiose as the substrate. Enzymatic assays showed that NpaBGS was active on short cello-oligosaccharides from various substrates. A weak activity in carboxymethyl cellulose (CMC) digestion indicated that the enzyme might also have the function of an endoglucanase. The optimal activity was detected at 40°C and pH 5 ~ 6, showing that the enzyme prefers a weak acid condition. Moreover, its activity could be enhanced at 50°C by adding Mg2+ or Mn2+ ions. Interestingly, in simultaneous saccharification and fermentation (SSF) experiments using Saccharomyces cerevisiae BY4741 or Kluyveromyces marxianus KY3 as the fermentation yeast, NpaBGS showed advantages in cell growth, glucose production, and ethanol production over the commercial enzyme Novo 188. Moreover, we showed that the KY3 strain engineered with the NpaNGS gene can utilize 2 % dry napiergrass as the sole carbon source to produce 3.32 mg/ml ethanol when Celluclast 1.5 L was added to the SSF system. CONCLUSION Our characterizations of the novel β-glucosidase NpaBGS revealed that it has a preference of weak acidity for optimal yeast fermentation and an optimal temperature of ~40°C. Since NpaBGS performs better than Novo 188 under the living conditions of fermentation yeasts, it has the potential to be a suitable enzyme for SSF.
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Affiliation(s)
- Hsin-Liang Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Yo-Chia Chen
- Department of Biological Science & Technology, National Pingtung University of Science & Technology, Neipu Hsiang, Pingtung, 91201, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Jui-Jen Chang
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | | | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
- Program in Microbial Genomics, National Chung-Hsing University, Taichung, 402, Taiwan
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Sz-Kai Ruan
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Tao-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Kuo-Yen Hung
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Hsing-Yi Cho
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University – Academia Sinica, Taipei, 115, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, 402, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Wan-Ting Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Ming-Che Shih
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University – Academia Sinica, Taipei, 115, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, 402, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, 402, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
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25
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Tamura M, Miyazaki T, Tanaka Y, Yoshida M, Nishikawa A, Tonozuka T. Comparison of the structural changes in two cellobiohydrolases, CcCel6A and CcCel6C, from Coprinopsis cinerea--a tweezer-like motion in the structure of CcCel6C. FEBS J 2012; 279:1871-82. [PMID: 22429290 DOI: 10.1111/j.1742-4658.2012.08568.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The basidiomycete Coprinopsis cinerea produces five cellobiohydrolases belonging to glycoside hydrolase family 6 (GH6). Among these enzymes, C. cinerea cellulase 6C (CcCel6C), but not C. cinerea cellulase 6A (CcCel6A), can efficiently hydrolyze carboxymethyl cellulose and is constitutively expressed in C. cinerea. In contrast, CcCel6A possesses a cellulose-binding domain, and is strongly induced by cellobiose. Here, we determined the crystal structures of the CcCel6A catalytic domain complexed with a Hepes buffer molecule, with cellobiose, and with p-nitrophenyl β-D-cellotrioside (pNPG3). A notable feature of the GH6 cellobiohydrolases is that the active site is enclosed by two loops to form a tunnel, and the loops have been demonstrated to open and close in response to ligand binding. The enclosed tunnel of CcCel6A-Hepes is seen as the open form, whereas the tunnels of CcCel6A-cellobiose and CcCel6A-pNPG3 adopt the closed form. pNPG3 was not hydrolyzed by CcCel6A, and bound in subsites +1 to +4. On the basis of this observation, we constructed two mutants, CcCel6A D164A and CcCel6C D102A. Neither CcCel6A D164A nor CcCel6C D102A hydrolyze phosphoric acid-swollen cellulose. We have previously determined the crystal structures of CcCel6C unbound and in complex with ligand, both of which adopt the open form. In the present study, both CcCel6A and CcCel6C mutants were identified as the closed form. However, the motion angle of CcCel6C was more than 10-fold greater than that of CcCel6A. The width of the active site cleft of CcCel6C was narrowed, owing to a tweezer-like motion.
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Affiliation(s)
- Mizuki Tamura
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
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Ogata M, Kameshima Y, Hattori T, Michishita K, Suzuki T, Kawagishi H, Totani K, Hiratake J, Usui T. Lactosylamidine-based affinity purification for cellulolytic enzymes EG I and CBH I from Hypocrea jecorina and their properties. Carbohydr Res 2010; 345:2623-9. [DOI: 10.1016/j.carres.2010.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 10/15/2010] [Accepted: 10/15/2010] [Indexed: 10/18/2022]
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27
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Abstract
Fungi secrete many different enzymes to deconstruct lignocellulosic biomass, including several families of hydrolases, oxidative enzymes, and many uncharacterized proteins. Here we describe the isolation, characterization, and primary sequence analysis of an extracellular aldonolactonase from the thermophilic fungus Myceliophthora thermophila (synonym Sporotrichum thermophile). The lactonase is a 48-kDa glycoprotein with a broad pH optimum. The enzyme catalyzes the hydrolysis of glucono-δ-lactone and cellobiono-δ-lactone with an apparent second-order rate constant, k(cat)/K(m), of ~1 × 10(6) M(-1) s(-1) at pH 5.0 and 25°C but is unable to hydrolyze xylono-γ-lactone or arabino-γ-lactone. Sequence analyses of the lactonase show that it has distant homology to cis-carboxy-muconate lactonizing enzymes (CMLE) as well as 6-phosphogluconolactonases present in some bacteria. The M. thermophila genome contains two predicted extracellular lactonase genes, and expression of both genes is induced by the presence of pure cellulose. Homologues of the M. thermophila lactonase, which are also predicted to be extracellular, are present in nearly all known cellulolytic ascomycetes.
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Chakraborty S, Aniket, Gaikwad A. Mixing Effects in Cellulase-Mediated Hydrolysis of Cellulose for Bio-Ethanol Production. Ind Eng Chem Res 2010. [DOI: 10.1021/ie100466h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Saikat Chakraborty
- Department of Chemical Engineering Indian Institute of Technology, Kharagpur, Kharagpur 721302, India
| | - Aniket
- Department of Chemical Engineering Indian Institute of Technology, Kharagpur, Kharagpur 721302, India
| | - Ashwin Gaikwad
- Department of Chemical Engineering Indian Institute of Technology, Kharagpur, Kharagpur 721302, India
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Jalak J, Väljamäe P. Mechanism of initial rapid rate retardation in cellobiohydrolase catalyzed cellulose hydrolysis. Biotechnol Bioeng 2010; 106:871-83. [DOI: 10.1002/bit.22779] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Zakariassen H, Aam BB, Horn SJ, Vårum KM, Sørlie M, Eijsink VGH. Aromatic residues in the catalytic center of chitinase A from Serratia marcescens affect processivity, enzyme activity, and biomass converting efficiency. J Biol Chem 2009; 284:10610-7. [PMID: 19244232 DOI: 10.1074/jbc.m900092200] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The processive Serratia marcescens chitinases A (ChiA) and B (ChiB) are thought to degrade chitin in the opposite directions. A recent study of ChiB suggested that processivity is governed by aromatic residues in the +1 and +2 (aglycon) subsites close to the catalytic center. To further investigate the roles of aromatic residues in processivity and to gain insight into the structural basis of directionality, we have mutated Trp(167), Trp(275), and Phe(396) in the -3, +1, and +2 subsites of ChiA, respectively, and characterized the hydrolytic activities of the mutants toward beta-chitin and the soluble chitin-derivative chitosan. Although the W275A and F396A mutants showed only modest reductions in processivity, it was almost abolished by the W167A mutation. Thus, although aglycon subsites seem to steer processivity in ChiB, a glycon (-3) subsite seems to be adapted to do so in ChiA, in line with the notion that the two enzymes have different directionalities. Remarkably, whereas all three single mutants and the W167A/W275A double mutant showed reduced efficiency toward chitin, they showed up to 20-fold higher activities toward chitosan. These results show that the processive mechanism is essential for an efficient conversion of crystalline substrates but comes at a large cost in terms of intrinsic enzyme speed. This needs to be taken into account when devising enzymatic strategies for biomass turnover.
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Affiliation(s)
- Henrik Zakariassen
- Department of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences, 1432 As, Norway
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31
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Voutilainen SP, Puranen T, Siika-Aho M, Lappalainen A, Alapuranen M, Kallio J, Hooman S, Viikari L, Vehmaanperä J, Koivula A. Cloning, expression, and characterization of novel thermostable family 7 cellobiohydrolases. Biotechnol Bioeng 2008; 101:515-28. [PMID: 18512263 DOI: 10.1002/bit.21940] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
As part of the effort to find better cellulases for bioethanol production processes, we were looking for novel GH-7 family cellobiohydrolases, which would be particularly active on insoluble polymeric substrates and participate in the rate-limiting step in the hydrolysis of cellulose. The enzymatic properties were studied and are reported here for family 7 cellobiohydrolases from the thermophilic fungi Acremonium thermophilum, Thermoascus aurantiacus, and Chaetomium thermophilum. The Trichoderma reesei Cel7A enzyme was used as a reference in the experiments. As the native T. aurantiacus Cel7A has no carbohydrate-binding module (CBM), recombinant proteins having the CBM from either the C. thermophilum Cel7A or the T. reesei Cel7A were also constructed. All these novel acidic cellobiohydrolases were more thermostable (by 4-10 degrees C) and more active (two- to fourfold) in hydrolysis of microcrystalline cellulose (Avicel) at 45 degrees C than T. reesei Cel7A. The C. thermophilum Cel7A showed the highest specific activity and temperature optimum when measured on soluble substrates. The most effective enzyme for Avicel hydrolysis at 70 degrees C, however, was the 2-module version of the T. aurantiacus Cel7A, which was also relatively weakly inhibited by cellobiose. These results are discussed from the structural point of view based on the three-dimensional homology models of these enzymes.
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Affiliation(s)
- Sanni P Voutilainen
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Finland
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32
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Yoon JJ, Kim KY, Cha CJ. Purification and characterization of thermostable β-glucosidase from the brown-rot basidiomycete Fomitopsis palustris grown on microcrystalline cellulose. J Microbiol 2008; 46:51-5. [DOI: 10.1007/s12275-007-0230-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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33
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Mertz B, Hill AD, Mulakala C, Reilly PJ. Automated docking to explore subsite binding by glycoside hydrolase family 6 cellobiohydrolases and endoglucanases. Biopolymers 2007; 87:249-60. [PMID: 17724729 DOI: 10.1002/bip.20831] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cellooligosaccharides were computationally docked using AutoDock into the active sites of the glycoside hydrolase Family 6 enzymes Hypocrea jecorina (formerly Trichoderma reesei) cellobiohydrolase and Thermobifida fusca endoglucanase. Subsite -2 exerts the greatest intermolecular energy in binding beta-glucosyl residues, with energies progressively decreasing to either side. Cumulative forces imparting processivity exerted by these two enzymes are significantly less than by the equivalent glycoside hydrolase Family 7 enzymes studied previously. Putative subsites -4, -3, +3, and +4 exist in H. jecorina cellobiohydrolase, along with putative subsites -4, -3, and +3 in T. fusca endoglucanase, but they are less important than subsites -2, -1, +1, and +2. In general, binding adds 3-7 kcal/mol to ligand intramolecular energies because of twisting of scissile glycosidic bonds. Distortion of beta-glucosyl residues to the (2)S(O) conformation by binding in subsite -1 adds approximately 7 kcal/mol to substrate intramolecular energies.
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Affiliation(s)
- Blake Mertz
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
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34
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Den Haan R, Mcbride JE, Grange DCL, Lynd LR, Van Zyl WH. Functional expression of cellobiohydrolases in Saccharomyces cerevisiae towards one-step conversion of cellulose to ethanol. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2006.09.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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35
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Fagerström A, Nilsson M, Berg U, Isaksson R. pH dependency of ligand binding to cellobiohydrolase 1 (Cel7A). J Chromatogr A 2007; 1138:276-83. [PMID: 17141791 DOI: 10.1016/j.chroma.2006.10.098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Revised: 10/16/2006] [Accepted: 10/19/2006] [Indexed: 11/23/2022]
Abstract
The affinity and enantioselectivity have been determined for designed propranolol derivatives as ligands for Cel7A by capillary electrophoresis (CE) at pH 7.0. These results have been compared to measurements at pH 5.0. In agreement with previous studies, the affinity increased at the higher pH. However, the affinity was not as dependent of the ligand structure at pH 7.0 as at pH 5.0, and the selectivity was generally decreased. Instead, at pH 7.0, the changes in binding were mainly dependent on the presence of additional dihydroxyl groups, indicating an increased importance of the electrostatic interactions. To evaluate the pH dependent variations in binding, changes in both the ligand and in the enzyme had to be taken into account. To ensure that the ligands had the same charge in all measurements, pKa-values of all compounds were determined. The ligand-protein interaction has also been studied by inhibition experiments at both pHs to evaluate the specific binding to the active site when competing with the substrate p-nitrophenyl lactoside (pNPL). With support of docking computations we propose a hypothesis on the effect of the ligand structure and pH dependency of the binding and selectivity of amino alcohols to Cel7A.
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Affiliation(s)
- Alexandra Fagerström
- Organic Chemistry, Department of Chemistry, P.O. Box 124, Lund University, S-221 00 Lund, Sweden
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36
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Markov AV, Gusakov AV, Kondratyeva EG, Okunev ON, Bekkarevich AO, Sinitsyn AP. New effective method for analysis of the component composition of enzyme complexes from Trichoderma reesei. BIOCHEMISTRY (MOSCOW) 2005; 70:657-63. [PMID: 16038608 DOI: 10.1007/s10541-005-0166-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A method for analysis of the component composition of multienzyme complexes secreted by the filamentous fungus Trichoderma reesei was developed. The method is based on chromatofocusing followed by further identification of protein fractions according to their substrate specificity and molecular characteristics of the proteins. The method allows identifying practically all known cellulases and hemicellulases of T. reesei: endoglucanase I (EG I), EG II, EG III, cellobiohydrolase I (CBH I), CBH II, xylanase I (XYL I), XYL II, beta-xylosidase, alpha-L-arabinofuranosidase, acetyl xylan esterase, mannanase, alpha-galactosidase, xyloglucanase, polygalacturonase, and exo-beta-1,3-glucosidase. The component composition of several laboratory and commercial T. reesei preparations was studied and the content of the individual enzymes in these preparations was quantified. The influence of fermentation conditions on the component composition of secreted enzyme complexes was revealed. The characteristic features of enzyme preparations obtained in "cellulase" and "xylanase" fermentation conditions are shown.
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Affiliation(s)
- A V Markov
- Faculty of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russia.
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37
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Zhang YHP, Lynd LR. Toward an aggregated understanding of enzymatic hydrolysis of cellulose: noncomplexed cellulase systems. Biotechnol Bioeng 2005; 88:797-824. [PMID: 15538721 DOI: 10.1002/bit.20282] [Citation(s) in RCA: 883] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Information pertaining to enzymatic hydrolysis of cellulose by noncomplexed cellulase enzyme systems is reviewed with a particular emphasis on development of aggregated understanding incorporating substrate features in addition to concentration and multiple cellulase components. Topics considered include properties of cellulose, adsorption, cellulose hydrolysis, and quantitative models. A classification scheme is proposed for quantitative models for enzymatic hydrolysis of cellulose based on the number of solubilizing activities and substrate state variables included. We suggest that it is timely to revisit and reinvigorate functional modeling of cellulose hydrolysis, and that this would be highly beneficial if not necessary in order to bring to bear the large volume of information available on cellulase components on the primary applications that motivate interest in the subject.
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38
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Ubhayasekera W, Muñoz IG, Vasella A, Ståhlberg J, Mowbray SL. Structures of Phanerochaete chrysosporium Cel7D in complex with product and inhibitors. FEBS J 2005; 272:1952-64. [PMID: 15819888 DOI: 10.1111/j.1742-4658.2005.04625.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cellobiohydrolase Pc_Cel7D is the major cellulase produced by the white-rot fungus Phanerochaete chrysosporium, constituting approximately 10% of the total secreted protein in liquid culture on cellulose. The enzyme is classified into family 7 of the glycoside hydrolases and, like other family members, catalyses cellulose hydrolysis with net retention of the anomeric carbon configuration. Previous work described the apo structure of the enzyme. Here we investigate the binding of the product, cellobiose, and several inhibitors, i.e. lactose, cellobioimidazole, Tris/HCl, calcium and a thio-linked substrate analogue, methyl 4-S-beta-cellobiosyl-4-thio-beta-cellobioside (GG-S-GG). The three disaccharides bind in the glucosyl-binding subsites +1 and +2, close to the exit of the cellulose-binding tunnel/cleft. Pc_Cel7D binds to lactose more strongly than cellobiose, while the opposite is true for the homologous Trichoderma reesei cellobiohydrolase Tr_Cel7A. Although both sugars bind Pc_Cel7D in a similar fashion, the different preferences can be explained by varying interactions with nearby loops. Cellobioimidazole is bound at a slightly different position, displaced approximately 2 A toward the catalytic centre. Thus the Pc_Cel7D complexes provide evidence for two binding modes of the reducing-end cellobiosyl moiety; this conclusion is confirmed by comparison with other available structures. The combined results suggest that hydrolysis of the glycosyl-enzyme intermediate may not require the prior release of the cellobiose product from the enzyme. Further, the structure obtained in the presence of both GG-S-GG and cellobiose revealed electron density for Tris at the catalytic centre. Inhibition experiments confirm that both Tris and calcium are effective inhibitors at the conditions used for crystallization.
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Affiliation(s)
- Wimal Ubhayasekera
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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39
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Gruno M, Väljamäe P, Pettersson G, Johansson G. Inhibition of the Trichoderma reesei cellulases by cellobiose is strongly dependent on the nature of the substrate. Biotechnol Bioeng 2005; 86:503-11. [PMID: 15129433 DOI: 10.1002/bit.10838] [Citation(s) in RCA: 201] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The inhibition effect of cellobiose on the initial stage of hydrolysis when cellobiohydrolase Cel 7A and endoglucanases Cel 7B, Cel 5A, and Cel 12A from Trichoderma reesei were acting on bacterial cellulose and amorphous cellulose that were [(3)H]- labeled at the reducing end was quantified. The apparent competitive inhibition constant (K(i)) for Cel 7A on [(3)H]-bacterial cellulose was found to be 1.6 +/- 0.5 mM, 100-fold higher than that for Cel 7A acting on low-molecular-weight model substrates. The hydrolysis of [(3)H]-amorphous cellulose by endoglucanases was even less affected by cellobiose inhibition with apparent K(i) values of 11 +/- 3 mM and 34 +/- 6 mM for Cel 7B and Cel 5A, respectively. Contrary to the case for the other enzymes studied, the release of radioactive label by Cel 12A was stimulated by cellobiose, possibly due to a more pronounced transglycosylating activity. Theoretical analysis of the inhibition of Cel 7A by cellobiose predicted an inhibition analogous to that of mixed type with two limiting cases, competitive inhibition if the prevalent enzyme-substrate complex without inhibitor is productive and conventional mixed type when the prevalent enzyme-substrate complex is nonproductive.
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Affiliation(s)
- Marju Gruno
- Institute of Molecular and Cell Biology, University of Tartu, Vanemuise 46-138, Tartu 51010, Estonia
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40
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De Vriendt K, Sandra K, Desmet T, Nerinckx W, Van Beeumen J, Devreese B. Evaluation of automated nano-electrospray mass spectrometry in the determination of non-covalent protein-ligand complexes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2004; 18:3061-7. [PMID: 15543530 DOI: 10.1002/rcm.1728] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The use of electrospray ionization mass spectrometry (ESI-MS) for studying non-covalent interactions between macromolecules and ligands is well established. ESI-MS can be a useful tool for the determination of dissociation constants between molecules in the gas phase. We validate this method by studying the binding of the catalytic domain of cellobiohydrolase I (CBH I) from Trichoderma reesei to the disaccharide inhibitor cellobiose. The method was further applied to study two newly synthesized cellobiose derivatives (m-iodobenzyl 2-deoxy-2-azido-beta-cellobioside and p-benzyloxybenzyl beta-cellobioside). In a titration experiment, peak areas of different charge states of the free enzyme and the complex were summed in order to determine the dissociation constant. For cellobiose and m-iodobenzyl 2-deoxy-2-azido-beta-cellobioside, the calculated values are in good agreement with those reported from either displacement titration or equilibrium binding experiments in solution. Due to non-specific binding, the dissociation constant of p-benzyloxybenzyl beta-cellobioside does not correspond with the solution-based value. Our results indicate the need for careful interpretation of data sets when using nanoESI to study non-covalent interactions.
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Affiliation(s)
- Kris De Vriendt
- Laboratory of Protein Biochemistry and Protein Engineering, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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41
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Comparison of domains function between cellobiohydrolase I and endoglucanase I from Trichoderma pseudokoningii S-38 by limited proteolysis. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1381-1177(03)00070-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Tuohy MG, Walsh DJ, Murray PG, Claeyssens M, Cuffe MM, Savage AV, Coughlan MP. Kinetic parameters and mode of action of the cellobiohydrolases produced by Talaromyces emersonii. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1596:366-80. [PMID: 12007616 DOI: 10.1016/s0167-4838(01)00308-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Three forms of cellobiohydrolase (EC 3.2.1.91), CBH IA, CBH IB and CBH II, were isolated to apparent homogeneity from culture filtrates of the aerobic fungus Talaromyces emersonii. The three enzymes are single sub-unit glycoproteins, and unlike most other fungal cellobiohydrolases are characterised by noteworthy thermostability. The kinetic properties and mode of action of each enzyme against polymeric and small soluble oligomeric substrates were investigated in detail. CBH IA, CBH IB and CBH II catalyse the hydrolysis of microcrystalline cellulose, albeit to varying extents. Hydrolysis of a soluble cellulose derivative (CMC) and barley 1,3;1,4-beta-D-glucan was not observed. Cellobiose (G2) is the main reaction product released by CBH IA, CBH IB, and CBH II from microcrystalline cellulose. All three CBHs are competitively inhibited by G2; inhibition constant values (K(i)) of 2.5 and 0.18 mM were obtained for CBH IA and CBH IB, respectively (4-nitrophenyl-beta-cellobioside as substrate), while a K(i) of 0.16 mM was determined for CBH II (2-chloro-4-nitrophenyl-beta-cellotrioside as substrate). Bond cleavage patterns were determined for each CBH on 4-methylumbelliferyl derivatives of beta-cellobioside and beta-cellotrioside (MeUmbG(n)). While the Tal. emersonii CBHs share certain properties with their counterparts from Trichoderma reesei, Humicola insolens and other fungal sources, distinct differences were noted.
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Affiliation(s)
- Maria G Tuohy
- Department of Biochemistry, National University of Ireland, Galway, Ireland.
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43
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Cortez JM, Ellis J, Bishop DP. Cellulase finishing of woven, cotton fabrics in jet and winch machines. J Biotechnol 2001; 89:239-45. [PMID: 11500218 DOI: 10.1016/s0168-1656(01)00307-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Some authors have reported that as the applied agitation rate increases, the apparent activity of the endoglucanases from Trichoderma reesei towards cotton cellulose increases more markedly than does the apparent activity of the cellobiohydrolases. This suggests that the quality of cellulase finishing effects on cellulosic textiles may be machine-type dependent. The present work using total crude, endoglucanase-rich and cellobiohydrolase-rich cellulases from T. reesei confirmed that the final properties of woven, cotton fabrics treated under realistic processing conditions in a jet machine, were measurably and perceivably different from those of the same fabrics, treated using the same processing conditions of temperature, time, pH, enzyme concentration and fabric to liquor ratio, but in a winch machine. The results are interpreted in terms of the effects of agitation rate on the adsorption-desorption behaviour of the T. reesei endoglucanases and cellobiohydrolases.
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Affiliation(s)
- J M Cortez
- Department of Textile Design and Production, De Montfort University, The Gateway, LE1 9BH, Leicester, UK.
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44
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Isolation and Characterisation of a Major Cellobiohydrolase (S8) and a Major Endoglucanase (S11) Subunit from the Cellulosome of Clostridium thermocellum. Anaerobe 2001. [DOI: 10.1006/anae.2001.0374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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45
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Becker D, Braet C, Brumer H, Claeyssens M, Divne C, Fagerström BR, Harris M, Jones TA, Kleywegt GJ, Koivula A, Mahdi S, Piens K, Sinnott ML, Ståhlberg J, Teeri TT, Underwood M, Wohlfahrt G. Engineering of a glycosidase Family 7 cellobiohydrolase to more alkaline pH optimum: the pH behaviour of Trichoderma reesei Cel7A and its E223S/ A224H/L225V/T226A/D262G mutant. Biochem J 2001; 356:19-30. [PMID: 11336632 PMCID: PMC1221808 DOI: 10.1042/0264-6021:3560019] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The crystal structures of Family 7 glycohydrolases suggest that a histidine residue near the acid/base catalyst could account for the higher pH optimum of the Humicola insolens endoglucanase Cel7B, than the corresponding Trichoderma reesei enzymes. Modelling studies indicated that introduction of histidine at the homologous position in T. reesei Cel7A (Ala(224)) required additional changes to accommodate the bulkier histidine side chain. X-ray crystallography of the catalytic domain of the E223S/A224H/L225V/T226A/D262G mutant reveals that major differences from the wild-type are confined to the mutations themselves. The introduced histidine residue is in plane with its counterpart in H. insolens Cel7B, but is 1.0 A (=0.1 nm) closer to the acid/base Glu(217) residue, with a 3.1 A contact between N(epsilon2) and O(epsilon1). The pH variation of k(cat)/K(m) for 3,4-dinitrophenyl lactoside hydrolysis was accurately bell-shaped for both wild-type and mutant, with pK(1) shifting from 2.22+/-0.03 in the wild-type to 3.19+/-0.03 in the mutant, and pK(2) shifting from 5.99+/-0.02 to 6.78+/-0.02. With this poor substrate, the ionizations probably represent those of the free enzyme. The relative k(cat) for 2-chloro-4-nitrophenyl lactoside showed similar behaviour. The shift in the mutant pH optimum was associated with lower k(cat)/K(m) values for both lactosides and cellobiosides, and a marginally lower stability. However, k(cat) values for cellobiosides are higher for the mutant. This we attribute to reduced non-productive binding in the +1 and +2 subsites; inhibition by cellobiose is certainly relieved in the mutant. The weaker binding of cellobiose is due to the loss of two water-mediated hydrogen bonds.
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Affiliation(s)
- D Becker
- Department of Paper Science, University of Manchester Institute of Science and Technology, P.O. Box 88, Sackville Street, Manchester M60 lQD, UK
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46
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Ståhlberg J, Henriksson H, Divne C, Isaksson R, Pettersson G, Johansson G, Jones TA. Structural basis for enantiomer binding and separation of a common beta-blocker: crystal structure of cellobiohydrolase Cel7A with bound (S)-propranolol at 1.9 A resolution. J Mol Biol 2001; 305:79-93. [PMID: 11114249 DOI: 10.1006/jmbi.2000.4237] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cellobiohydrolase Cel7A (previously called CBH 1), the major cellulase produced by the mould fungus Trichoderma reesei, has been successfully exploited as a chiral selector for separation of stereo-isomers of some important pharmaceutical compounds, e.g. adrenergic beta-blockers. Previous investigations, including experiments with catalytically deficient mutants of Cel7A, point unanimously to the active site as being responsible for discrimination of enantiomers. In this work the structural basis for enantioselectivity of basic drugs by Cel7A has been studied by X-ray crystallography. The catalytic domain of Cel7A was co-crystallised with the (S)-enantiomer of a common beta-blocker, propranolol, at pH 7, and the structure of the complex was determined and refined at 1. 9 A resolution. Indeed, (S)-propranolol binds at the active site, in glucosyl-binding subsites -1/+1. The catalytic residues Glu212 and Glu217 make tight salt links with the secondary amino group of (S)-propranolol. The oxygen atom attached to the chiral centre of (S)-propranolol forms hydrogen bonds to the nucleophile Glu212 O(epsilon1) and to Gln175 N(epsilon2), whereas the aromatic naphthyl moiety stacks with the indole ring of Trp376 in site +1. The bidentate charge interaction with the catalytic glutamate residues is apparently crucial, since no enantioselectivity has been obtained with the catalytically deficient mutants E212Q and E217Q. Activity inhibition experiments with wild-type Cel7A were performed in conditions close to those used for crystallisation. Competitive inhibition constants for (R)- and (S)-propranolol were determined at 220 microM and 44 microM, respectively, corresponding to binding free energies of 20 kJ/mol and 24 kJ/mol, respectively. The K(i) value for (R)-propranolol was 57-fold lower than the highest concentration, 12.5 mM, used in co-crystallisation experiments. Still several attempts to obtain a complex with the (R)-enantiomer have failed. By using cellobiose as a selective competing ligand, the retention of the enantiomers of propranolol on the chiral stationary phase (CSP) based on Cel7A mutant D214N were resolved into enantioselective and non- selective binding. The enantioselective binding was weaker for both enantiomers on D214N-CSP than on wild-type-CSP.
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Affiliation(s)
- J Ståhlberg
- Department of Molecular Biology, University of Uppsala, Uppsala, SE-751 24, Sweden
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Henriksson H, Pettersson G, Johansson G. Discrimination between enantioselective and non-selective binding sites on cellobiohydrolase-based stationary phases by site specific competing ligands. J Chromatogr A 1999; 857:107-15. [PMID: 10536829 DOI: 10.1016/s0021-9673(99)00776-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A systematic study was performed to investigate the influence of cellobiose or lactose on the enantioselective retention behaviour of some beta-blockers in liquid chromatography using Cellobiohydrolase (CHB) I from Trichoderma reesei or Cellobiohydrolase 58 from Phanerochaete chrysosporium immobilized on silica as stationary phases. The results revealed that the retention could be described by the function [equation; see text] where the observed capacity factor corresponds to the sum of an enantioselective mode being influenced by a site specific competing ligand (competitor) and a non-selective mode unaffected by the competitor. A non-constrained non-linear least-square regression gave in all cases virtually identical nondisplacable capacity factors (k'ns) for both enantiomers of the same drug. The experimental capacity factors (k'(x,C)) of the enantiomers all show a close fit to the adapted function. The Kd values calculated for the competitor were also virtually identical for each pair of enantiomers and were in accordance with Ki data determined for the competitors in classical enzyme kinetics experiments, demonstrating that one unique site; namely, the catalytic site, was responsible for the enantioselective binding. Similar results were obtained with the resolution of rac-alprenolol and rac-metoprolol on CBH I phase.
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Affiliation(s)
- H Henriksson
- Department of Biochemistry, Uppsala University, Biomedical Centre, Sweden
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Harjunpää V, Helin J, Koivula A, Siika-aho M, Drakenberg T. A comparative study of two retaining enzymes of Trichoderma reesei: transglycosylation of oligosaccharides catalysed by the cellobiohydrolase I, Cel7A, and the beta-mannanase, Man5A. FEBS Lett 1999; 443:149-53. [PMID: 9989594 DOI: 10.1016/s0014-5793(98)01692-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
HPLC, MALDI-TOF MS and NMR spectroscopy were used to investigate the hydrolysis of cello- and mannooligosaccharides by Cel7A and Man5A from Trichoderma reesei. The experimental progress curves were analysed by fitting the numerically integrated kinetic equations, which provided cleavage patterns for oligosaccharides. This data evaluation procedure accounts for product inhibition and avoids the initial slope approximation. In addition, a transglycosylation step had to be included in the model to reproduce the experimental progress curves. For the hydrolysis of manno-oligosaccharides, Man4-6, by Man5A no mannose was detected at the beginning of the reaction showing that only the internal linkages are hydrolysed. For cellotriose and cellotetraose hydrolysis by Cel7A, the main product is cellobiose and glucose is released from the non-reducing end of the substrate. Intermediary products longer than the substrates were detected by MALDI-TOF MS when oligosaccharides (Glc4-6 or Man4-6) were hydrolysed by either Cel7A or Man5A. Interestingly, two distinct transglycosylation pathways could be observed. Cel7A produced intermediates that are one unit longer than the substrate, whereas Man5A produced intermediates that are two units longer than the substrate.
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Henriksson G, Nutt A, Henriksson H, Pettersson B, Ståhlberg J, Johansson G, Pettersson G. Endoglucanase 28 (Cel12A), a new Phanerochaete chrysosporium cellulase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 259:88-95. [PMID: 9914479 DOI: 10.1046/j.1432-1327.1999.00011.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A 28-kDa endoglucanase was isolated from the culture filtrate of Phanerochaete chrysosporium strain K3 and named EG 28. It degrades carboxymethylated cellulose and amorphous cellulose, and to a lesser degree xylan and mannan but not microcrystalline cellulose (Avicel). EG 28 is unusual among cellulases from aerobic fungi, in that it appears to lack a cellulose-binding domain and does not bind to crystalline cellulose. The enzyme is efficient at releasing short fibres from filter paper and mechanical pulp, and acts synergistically with cellobiohydrolases. Its mode of degrading filter paper appears to be different to that of endoglucanase I from Trichoderma reesei. Furthermore, EG 28 releases colour from stained cellulose beads faster than any other enzyme tested. Peptide mapping suggests that it is not a fragment of another known endoglucanases from P. chrysosporium and peptide sequences indicate that it belongs to family 12 of the glycosyl hydrolases. EG 28 is glycosylated. The biological function of the enzyme is discussed, and it is hypothesized that it is homologous to EG III in Trichoderma reesei and the role of the enzyme is to make the cellulose in wood more accessible to other cellulases.
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Affiliation(s)
- G Henriksson
- Department of Pulp and Paper Technique and Chemistry, Royal Institute of Technology, Stockholm, Sweden.
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