51
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Fu B, Brown C, Mäler L. Expression and Purification of DGD2, a Chloroplast Outer Membrane-Associated Glycosyltransferase for Galactolipid Synthesis. Biochemistry 2020; 59:999-1009. [PMID: 32067450 DOI: 10.1021/acs.biochem.0c00028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Galactolipids are characteristic lipids of the photosynthetic membranes. They are highly enriched in the chloroplast and are present in photosystem structures. There are two major types of galactolipids, i.e., monogalactosyldiacylglycerol and digalactosyldiacylglycerol (DGDG) in chloroplastic membranes, which amount to ∼50 and ∼20 mol % of the total chloroplast lipids, respectively. Under phosphate-limiting conditions, the amount of DGDG increases dramatically for rescuing phosphate from phospholipids. In Arabidopsis thaliana, the gene digalactosyldiacylglycerol synthase 2 (DGD2) encodes a membrane-associated glycosyltransferase. The gene expression is highly responsive to phosphate starvation and is significantly upregulated in this case. To understand the molecular mechanism of DGD2, we established a protocol for DGD2 expression and purification in an Escherichia coli-based system. The work involved optimization of the expression condition and the purification protocol and a careful selection of buffer additives. It was found that a removal of around 70 C-terminal residues was necessary to produce a homogeneous monomeric protein sample with high purity, which was highly active. The purified sample was characterized by an activity assay for enzyme kinetics in which a range of membrane mimetics with different lipid compositions were used. The results demonstrate that DGD2 activity is stimulated by the presence of negatively charged lipids, which highlight the importance of the membrane environment in modulating the enzyme's activity. The study also paves way for future biophysical and structural studies of the enzyme.
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Affiliation(s)
- Biao Fu
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Christian Brown
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Department of Chemistry, University of Umeå, SE-901 87 Umeå, Sweden
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52
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Røjel N, Kari J, Sørensen TH, Badino SF, Morth JP, Schaller K, Cavaleiro AM, Borch K, Westh P. Substrate binding in the processive cellulase Cel7A: Transition state of complexation and roles of conserved tryptophan residues. J Biol Chem 2020; 295:1454-1463. [PMID: 31848226 PMCID: PMC7008363 DOI: 10.1074/jbc.ra119.011420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/17/2019] [Indexed: 11/06/2022] Open
Abstract
Cellobiohydrolases effectively degrade cellulose and are of biotechnological interest because they can convert lignocellulosic biomass to fermentable sugars. Here, we implemented a fluorescence-based method for real-time measurements of complexation and decomplexation of the processive cellulase Cel7A and its insoluble substrate, cellulose. The method enabled detailed kinetic and thermodynamic analyses of ligand binding in a heterogeneous system. We studied WT Cel7A and several variants in which one or two of four highly conserved Trp residues in the binding tunnel had been replaced with Ala. WT Cel7A had on/off-rate constants of 1 × 105 m-1 s-1 and 5 × 10-3 s-1, respectively, reflecting the slow dynamics of a solid, polymeric ligand. Especially the off-rate constant was many orders of magnitude lower than typical values for small, soluble ligands. Binding rate and strength both were typically lower for the Trp variants, but effects of the substitutions were moderate and sometimes negligible. Hence, we propose that lowering the activation barrier for complexation is not a major driving force for the high conservation of the Trp residues. Using so-called Φ-factor analysis, we analyzed the kinetic and thermodynamic results for the variants. The results of this analysis suggested a transition state for complexation and decomplexation in which the reducing end of the ligand is close to the tunnel entrance (near Trp-40), whereas the rest of the binding tunnel is empty. We propose that this structure defines the highest free-energy barrier of the overall catalytic cycle and hence governs the turnover rate of this industrially important enzyme.
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Affiliation(s)
- Nanna Røjel
- Institut for Naturvidenskab og Miljo, Roskilde University, DK-4000 Roskilde, Denmark
| | - Jeppe Kari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | | | - Silke F Badino
- Institut for Naturvidenskab og Miljo, Roskilde University, DK-4000 Roskilde, Denmark
| | - J Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Kay Schaller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | | | - Kim Borch
- Novozymes A/S, DK-2800 Kgs. Lyngby Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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53
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Selective pressure on an interfacial enzyme: Functional roles of a highly conserved asparagine residue in a cellulase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140359. [PMID: 31911207 DOI: 10.1016/j.bbapap.2019.140359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/18/2019] [Accepted: 12/25/2019] [Indexed: 11/24/2022]
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54
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Kołaczkowski BM, Schaller KS, Sørensen TH, Peters GHJ, Jensen K, Krogh KBRM, Westh P. Removal of N-linked glycans in cellobiohydrolase Cel7A from Trichoderma reesei reveals higher activity and binding affinity on crystalline cellulose. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:136. [PMID: 32782472 PMCID: PMC7412794 DOI: 10.1186/s13068-020-01779-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/29/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Cellobiohydrolase from glycoside hydrolase family 7 is a major component of commercial enzymatic mixtures for lignocellulosic biomass degradation. For many years, Trichoderma reesei Cel7A (TrCel7A) has served as a model to understand structure-function relationships of processive cellobiohydrolases. The architecture of TrCel7A includes an N-glycosylated catalytic domain, which is connected to a carbohydrate-binding module through a flexible, O-glycosylated linker. Depending on the fungal expression host, glycosylation can vary not only in glycoforms, but also in site occupancy, leading to a complex pattern of glycans, which can affect the enzyme's stability and kinetics. RESULTS Two expression hosts, Aspergillus oryzae and Trichoderma reesei, were utilized to successfully express wild-types TrCel7A (WT Ao and WT Tr ) and the triple N-glycosylation site deficient mutants TrCel7A N45Q, N270Q, N384Q (ΔN-glyc Ao and ΔN-glyc Tr ). Also, we expressed single N-glycosylation site deficient mutants TrCel7A (N45Q Ao , N270Q Ao , N384Q Ao ). The TrCel7A enzymes were studied by steady-state kinetics under both substrate- and enzyme-saturating conditions using different cellulosic substrates. The Michaelis constant (K M ) was consistently found to be lowered for the variants with reduced N-glycosylation content, and for the triple deficient mutants, it was less than half of the WTs' value on some substrates. The ability of the enzyme to combine productively with sites on the cellulose surface followed a similar pattern on all tested substrates. Thus, site density (number of sites per gram cellulose) was 30-60% higher for the single deficient variants compared to the WT, and about twofold larger for the triple deficient enzyme. Molecular dynamic simulation of the N-glycan mutants TrCel7A revealed higher number of contacts between CD and cellulose crystal upon removal of glycans at position N45 and N384. CONCLUSIONS The kinetic changes of TrCel7A imposed by removal of N-linked glycans reflected modifications of substrate accessibility. The presence of N-glycans with extended structures increased K M and decreased attack site density of TrCel7A likely due to steric hindrance effect and distance between the enzyme and the cellulose surface, preventing the enzyme from achieving optimal conformation. This knowledge could be applied to modify enzyme glycosylation to engineer enzyme with higher activity on the insoluble substrates.
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Affiliation(s)
| | - Kay S. Schaller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, 2800 Kgs. Lyngby, Denmark
| | | | - Günther H. J. Peters
- Department of Chemistry, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Kenneth Jensen
- Novozymes A/S, Biologiens Vej 2, 2800 Kgs. Lyngby, Denmark
| | | | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, 2800 Kgs. Lyngby, Denmark
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55
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Mudinoor AR, Goodwin PM, Rao RU, Karuna N, Hitomi A, Nill J, Jeoh T. Interfacial molecular interactions of cellobiohydrolase Cel7A and its variants on cellulose. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:10. [PMID: 31988662 PMCID: PMC6969433 DOI: 10.1186/s13068-020-1649-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/02/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Molecular-scale mechanisms of the enzymatic breakdown of cellulosic biomass into fermentable sugars are still poorly understood, with a need for independent measurements of enzyme kinetic parameters. We measured binding times of cellobiohydrolase Trichoderma reesei Cel7A (Cel7A) on celluloses using wild-type Cel7A (WTintact), the catalytically deficient mutant Cel7A E212Q (E212Qintact) and their proteolytically isolated catalytic domains (CD) (WTcore and E212Qcore, respectively). The binding time distributions were obtained from time-resolved, super-resolution images of fluorescently labeled enzymes on cellulose obtained with total internal reflection fluorescence microscopy. RESULTS Binding of WTintact and E212Qintact on the recalcitrant algal cellulose (AC) showed two bound populations: ~ 85% bound with shorter residence times of < 15 s while ~ 15% were effectively immobilized. The similarity between binding times of the WT and E212Q suggests that the single point mutation in the enzyme active site does not affect the thermodynamics of binding of this enzyme. The isolated catalytic domains, WTcore and E212Qcore, exhibited three binding populations on AC: ~ 75% bound with short residence times of ~ 15 s (similar to the intact enzymes), ~ 20% bound for < 100 s and ~ 5% that were effectively immobilized. CONCLUSIONS Cel7A binding to cellulose is driven by the interactions between the catalytic domain and cellulose. The cellulose-binding module (CBM) and linker increase the affinity of Cel7A to cellulose likely by facilitating recognition and complexation at the substrate interface. The increased affinity of Cel7A to cellulose by the CBM and linker comes at the cost of increasing the population of immobilized enzyme on cellulose. The residence time (or inversely the dissociation rates) of Cel7A on cellulose is not catalysis limited.
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Affiliation(s)
- Akshata R. Mudinoor
- Biological and Agricultural Engineering, University of California, Davis, One Shields Ave., Davis, CA 95616 USA
| | - Peter M. Goodwin
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Raghavendra U. Rao
- Gracenote, Inc., 2000 Powell Street, Suite 1500, Emeryville, CA 94608 USA
| | - Nardrapee Karuna
- Biological and Agricultural Engineering, University of California, Davis, One Shields Ave., Davis, CA 95616 USA
- Biotechnology, Faculty of Engineering and Industrial Technology, Silpakorn University, Nakhon Pathom, 73000 Thailand
| | - Alex Hitomi
- Biological and Agricultural Engineering, University of California, Davis, One Shields Ave., Davis, CA 95616 USA
| | - Jennifer Nill
- Chemical Engineering, University of California, Davis, One Shields Ave., Davis, CA 95616 USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Tina Jeoh
- Biological and Agricultural Engineering, University of California, Davis, One Shields Ave., Davis, CA 95616 USA
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56
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Røjel N, Kari J, Sørensen TH, Borch K, Westh P. pH profiles of cellulases depend on the substrate and architecture of the binding region. Biotechnol Bioeng 2019; 117:382-391. [PMID: 31631319 DOI: 10.1002/bit.27206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/09/2019] [Accepted: 10/13/2019] [Indexed: 01/06/2023]
Abstract
Understanding the pH effect of cellulolytic enzymes is of great technological importance. In this study, we have examined the influence of pH on activity and stability for central cellulases (Cel7A, Cel7B, Cel6A from Trichoderma reesei, and Cel7A from Rasamsonia emersonii). We systematically changed pH from 2 to 7, temperature from 20°C to 70°C, and used both soluble (4-nitrophenyl β- d-lactopyranoside [pNPL]) and insoluble (Avicel) substrates at different concentrations. Collective interpretation of these data provided new insights. An unusual tolerance to acidic conditions was observed for both investigated Cel7As, but only on real insoluble cellulose. In contrast, pH profiles on pNPL were bell-shaped with a strong loss of activity both above and below the optimal pH for all four enzymes. On a practical level, these observations call for the caution of the common practice of using soluble substrates for the general characterization of pH effects on cellulase activity. Kinetic modeling of the experimental data suggested that the nucleophile of Cel7A experiences a strong downward shift in pKa upon complexation with an insoluble substrate. This shift was less pronounced for Cel7B, Cel6A, and for Cel7A acting on the soluble substrate, and we hypothesize that these differences are related to the accessibility of water to the binding region of the Michaelis complex.
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Affiliation(s)
- Nanna Røjel
- Department of Science and Environment (INM), Roskilde University, Roskilde, Denmark.,Present address: Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, DK-2800, Kgs. Lyngby, Denmark
| | - Jeppe Kari
- Department of Science and Environment (INM), Roskilde University, Roskilde, Denmark.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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57
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Schiano‐di‐Cola C, Kołaczkowski B, Sørensen TH, Christensen SJ, Cavaleiro AM, Windahl MS, Borch K, Morth JP, Westh P. Structural and biochemical characterization of a family 7 highly thermostable endoglucanase from the fungusRasamsonia emersonii. FEBS J 2019; 287:2577-2596. [DOI: 10.1111/febs.15151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/01/2019] [Accepted: 11/20/2019] [Indexed: 01/21/2023]
Affiliation(s)
| | | | - Trine Holst Sørensen
- Department of Science and Environment Roskilde University Denmark
- Novozymes A/S Lyngby Denmark
| | | | | | - Michael Skovbo Windahl
- Department of Science and Environment Roskilde University Denmark
- Novozymes A/S Lyngby Denmark
| | | | - Jens Preben Morth
- Department of Biotechnology and Biomedicine Technical University of Denmark Lyngby Denmark
| | - Peter Westh
- Department of Science and Environment Roskilde University Denmark
- Department of Biotechnology and Biomedicine Technical University of Denmark Lyngby Denmark
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58
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Kari J, Christensen SJ, Andersen M, Baiget SS, Borch K, Westh P. A practical approach to steady-state kinetic analysis of cellulases acting on their natural insoluble substrate. Anal Biochem 2019; 586:113411. [PMID: 31520594 DOI: 10.1016/j.ab.2019.113411] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 10/26/2022]
Abstract
Measurement of steady-state rates (vSS) is straightforward in standard enzymology with soluble substrate, and it has been instrumental for comparative biochemical analyses within this area. For insoluble substrate, however, experimental values of vss remain controversial, and this has strongly limited the amount and quality of comparative analyses for cellulases and other enzymes that act on the surface of an insoluble substrate. In the current work, we have measured progress curves over a wide range of conditions for two cellulases, TrCel6A and TrCel7A from Trichoderma reesei, acting on their natural, insoluble substrate, cellulose. Based on this, we consider practical compromises for the determination of experimental vSS values, and propose a basic protocol that provides representative reaction rates and is experimentally simple so that larger groups of enzymes and conditions can be readily assayed with standard laboratory equipment. We surmise that the suggested experimental approach can be useful in comparative biochemical studies of cellulases; an area that remains poorly developed.
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Affiliation(s)
- Jeppe Kari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800, Kgs. Lyngby, Denmark
| | - Stefan Jarl Christensen
- Department of Science and Environment, Roskilde University, Universitetsvej, Build. 28.C, DK-4000, Roskilde, Denmark
| | - Morten Andersen
- Department of Science and Environment, Roskilde University, Universitetsvej, Build. 28.C, DK-4000, Roskilde, Denmark
| | | | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880, Bagsværd, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800, Kgs. Lyngby, Denmark.
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59
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Zhang Y, Zeng X, Jiang X, Chen H, Long Z. Ce-based UiO-66 metal-organic frameworks as a new redox catalyst for atomic spectrometric determination of Se(VI) and colorimetric sensing of Hg(II). Microchem J 2019. [DOI: 10.1016/j.microc.2019.103967] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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60
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A biochemical comparison of fungal GH6 cellobiohydrolases. Biochem J 2019; 476:2157-2172. [DOI: 10.1042/bcj20190185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/14/2019] [Accepted: 07/16/2019] [Indexed: 02/02/2023]
Abstract
AbstractCellobiohydrolases (CBHs) from glycoside hydrolase family 6 (GH6) make up an important part of the secretome in many cellulolytic fungi. They are also of technical interest, particularly because they are part of the enzyme cocktails that are used for the industrial breakdown of lignocellulosic biomass. Nevertheless, functional studies of GH6 CBHs are scarce and focused on a few model enzymes. To elucidate functional breadth among GH6 CBHs, we conducted a comparative biochemical study of seven GH6 CBHs originating from fungi living in different habitats, in addition to one enzyme variant. The enzyme sequences were investigated by phylogenetic analyses to ensure that they were not closely related phylogenetically. The selected enzymes were all heterologously expressed in Aspergillus oryzae, purified and thoroughly characterized biochemically. This approach allowed direct comparisons of functional data, and the results revealed substantial variability. For example, the adsorption capacity on cellulose spanned two orders of magnitude and kinetic parameters, derived from two independent steady-state methods also varied significantly. While the different functional parameters covered wide ranges, they were not independent since they changed in parallel between two poles. One pole was characterized by strong substrate interactions, high adsorption capacity and low turnover number while the other showed weak substrate interactions, poor adsorption and high turnover. The investigated enzymes essentially defined a continuum between these two opposites, and this scaling of functional parameters raises interesting questions regarding functional plasticity and evolution of GH6 CBHs.
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61
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Algar WR, Jeen T, Massey M, Peveler WJ, Asselin J. Small Surface, Big Effects, and Big Challenges: Toward Understanding Enzymatic Activity at the Inorganic Nanoparticle-Substrate Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:7067-7091. [PMID: 30415548 DOI: 10.1021/acs.langmuir.8b02733] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Enzymes are important biomarkers for molecular diagnostics and targets for the action of drugs. In turn, inorganic nanoparticles (NPs) are of interest as materials for biological assays, biosensors, cellular and in vivo imaging probes, and vectors for drug delivery and theranostics. So how does an enzyme interact with a NP, and what are the outcomes of multivalent conjugation of its substrate to a NP? This invited feature article addresses the current state of the art in answering this question. Using gold nanoparticles (Au NPs) and semiconductor quantum dots (QDs) as illustrative materials, we discuss aspects of enzyme structure-function and the properties of NP interfaces and surface chemistry that determine enzyme-NP interactions. These aspects render the substrate-on-NP configurations far more complex and heterogeneous than the conventional turnover of discrete substrate molecules in bulk solution. Special attention is also given to the limitations of a standard kinetic analysis of the enzymatic turnover of these configurations, the need for a well-defined model of turnover, and whether a "hopping" model can account for behaviors such as the apparent acceleration of enzyme activity. A detailed and predictive understanding of how enzymes turn over multivalent NP-substrate conjugates will require a convergence of many concepts and tools from biochemistry, materials, and interface science. In turn, this understanding will help to enable rational, optimized, and value-added designs of NP bioconjugates for biomedical and clinical applications.
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Affiliation(s)
- W Russ Algar
- Department of Chemistry , University of British Columbia , 2036 Main Mall , Vancouver , British Columbia V6T 1Z1 , Canada
| | - Tiffany Jeen
- Department of Chemistry , University of British Columbia , 2036 Main Mall , Vancouver , British Columbia V6T 1Z1 , Canada
| | - Melissa Massey
- Department of Chemistry , University of British Columbia , 2036 Main Mall , Vancouver , British Columbia V6T 1Z1 , Canada
| | - William J Peveler
- Department of Chemistry , University of British Columbia , 2036 Main Mall , Vancouver , British Columbia V6T 1Z1 , Canada
- Division of Biomedical Engineering, School of Engineering , University of Glasgow , Glasgow G12 8LT , United Kingdom
| | - Jérémie Asselin
- Department of Chemistry , University of British Columbia , 2036 Main Mall , Vancouver , British Columbia V6T 1Z1 , Canada
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62
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Kont R, Pihlajaniemi V, Borisova AS, Aro N, Marjamaa K, Loogen J, Büchs J, Eijsink VGH, Kruus K, Väljamäe P. The liquid fraction from hydrothermal pretreatment of wheat straw provides lytic polysaccharide monooxygenases with both electrons and H 2O 2 co-substrate. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:235. [PMID: 31624497 PMCID: PMC6781412 DOI: 10.1186/s13068-019-1578-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/24/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Enzyme-aided valorization of lignocellulose represents a green and sustainable alternative to the traditional chemical industry. The recently discovered lytic polysaccharide monooxygenases (LPMOs) are important components of the state-of-the art enzyme cocktails for cellulose conversion. Yet, these monocopper enzymes are poorly characterized in terms of their kinetics, as exemplified by the growing evidence for that H2O2 may be a more efficient co-substrate for LPMOs than O2. LPMOs need external electron donors and one key question of relevance for bioprocess development is whether the required reducing power may be provided by the lignocellulosic substrate. RESULTS Here, we show that the liquid fraction (LF) resulting from hydrothermal pretreatment of wheat straw supports LPMO activity on both chitin and cellulose. The initial, transient activity burst of the LPMO reaction was caused by the H2O2 present in the LF before addition of LPMO, while the steady-state rate of LPMO reaction was limited by the LPMO-independent production of H2O2 in the LF. H2O2 is an intermediate of LF oxidation as evidenced by a slow H2O2 accumulation in LF, despite high H2O2 production rates. This H2O2 scavenging ability of LF is important since high concentrations of H2O2 may lead to irreversible inactivation of LPMOs. CONCLUSIONS Our results support the growing understanding that fine-tuned control over the rates of H2O2 production and consumption in different, enzymatic and non-enzymatic reactions is essential for harnessing the full catalytic potential of LPMOs in lignocellulose valorization.
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Affiliation(s)
- Riin Kont
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | | | - Nina Aro
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Kaisa Marjamaa
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Judith Loogen
- Department of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Aachen, Germany
| | - Jochen Büchs
- Department of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Aachen, Germany
| | | | - Kristiina Kruus
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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63
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The role of enzyme adsorption in the enzymatic degradation of an aliphatic polyester. Enzyme Microb Technol 2019; 120:110-116. [DOI: 10.1016/j.enzmictec.2018.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 10/10/2018] [Accepted: 10/12/2018] [Indexed: 11/19/2022]
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64
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Schiano-di-Cola C, Røjel N, Jensen K, Kari J, Sørensen TH, Borch K, Westh P. Systematic deletions in the cellobiohydrolase (CBH) Cel7A from the fungus Trichoderma reesei reveal flexible loops critical for CBH activity. J Biol Chem 2018; 294:1807-1815. [PMID: 30538133 DOI: 10.1074/jbc.ra118.006699] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/08/2018] [Indexed: 11/06/2022] Open
Abstract
Glycoside hydrolase family 7 (GH7) cellulases are some of the most efficient degraders of cellulose, making them particularly relevant for industries seeking to produce renewable fuels from lignocellulosic biomass. The secretome of the cellulolytic model fungus Trichoderma reesei contains two GH7s, termed TrCel7A and TrCel7B. Despite having high structural and sequence similarities, the two enzymes are functionally quite different. TrCel7A is an exolytic, processive cellobiohydrolase (CBH), with high activity on crystalline cellulose, whereas TrCel7B is an endoglucanase (EG) with a preference for more amorphous cellulose. At the structural level, these functional differences are usually ascribed to the flexible loops that cover the substrate-binding areas. TrCel7A has an extensive tunnel created by eight peripheral loops, and the absence of four of these loops in TrCel7B makes its catalytic domain a more open cleft. To investigate the structure-function relationships of these loops, here we produced and kinetically characterized several variants in which four loops unique to TrCel7A were individually deleted to resemble the arrangement in the TrCel7B structure. Analysis of a range of kinetic parameters consistently indicated that the B2 loop, covering the substrate-binding subsites -3 and -4 in TrCel7A, was a key determinant for the difference in CBH- or EG-like behavior between TrCel7A and TrCel7B. Conversely, the B3 and B4 loops, located closer to the catalytic site in TrCel7A, were less important for these activities. We surmise that these results could be useful both in further mechanistic investigations and for guiding engineering efforts of this industrially important enzyme family.
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Affiliation(s)
- Corinna Schiano-di-Cola
- From the Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, DK-4000 Roskilde, Denmark
| | - Nanna Røjel
- From the Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, DK-4000 Roskilde, Denmark
| | - Kenneth Jensen
- Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsværd, Denmark, and
| | - Jeppe Kari
- From the Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, DK-4000 Roskilde, Denmark
| | - Trine Holst Sørensen
- From the Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, DK-4000 Roskilde, Denmark
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsværd, Denmark, and
| | - Peter Westh
- the Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, DK-2800 Kgs. Lyngby, Denmark
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65
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Kuusk S, Kont R, Kuusk P, Heering A, Sørlie M, Bissaro B, Eijsink VGH, Väljamäe P. Kinetic insights into the role of the reductant in H 2O 2-driven degradation of chitin by a bacterial lytic polysaccharide monooxygenase. J Biol Chem 2018; 294:1516-1528. [PMID: 30514757 DOI: 10.1074/jbc.ra118.006196] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/23/2018] [Indexed: 12/13/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are monocopper enzymes that catalyze oxidative cleavage of glycosidic bonds in polysaccharides in the presence of an external electron donor (reductant). In the classical O2-driven monooxygenase reaction, the reductant is needed in stoichiometric amounts. In a recently discovered, more efficient H2O2-driven reaction, the reductant would be needed only for the initial reduction (priming) of the LPMO to its catalytically active Cu(I) form. However, the influence of the reductant on reducing the LPMO or on H2O2 production in the reaction remains undefined. Here, we conducted a detailed kinetic characterization to investigate how the reductant affects H2O2-driven degradation of 14C-labeled chitin by a bacterial LPMO, SmLPMO10A (formerly CBP21). Sensitive detection of 14C-labeled products and careful experimental set-ups enabled discrimination between the effects of the reductant on LPMO priming and other effects, in particular enzyme-independent production of H2O2 through reactions with O2 When supplied with H2O2, SmLPMO10A catalyzed 18 oxidative cleavages per molecule of ascorbic acid, suggesting a "priming reduction" reaction. The dependence of initial rates of chitin degradation on reductant concentration followed hyperbolic saturation kinetics, and differences between the reductants were manifested in large variations in their half-saturating concentrations (K mR app). Theoretical analyses revealed that K mR app decreases with a decreasing rate of polysaccharide-independent LPMO reoxidation (by either O2 or H2O2). We conclude that the efficiency of LPMO priming depends on the relative contributions of reductant reactivity, on the LPMO's polysaccharide monooxygenase/peroxygenase and reductant oxidase/peroxidase activities, and on reaction conditions, such as O2, H2O2, and polysaccharide concentrations.
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Affiliation(s)
- Silja Kuusk
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Riin Kont
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Piret Kuusk
- Institute of Molecular and Physics, University of Tartu, 51010 Tartu, Estonia
| | - Agnes Heering
- Institute of Molecular and Chemistry, University of Tartu, 51010 Tartu, Estonia
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia.
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66
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Christensen SJ, Kari J, Badino SF, Borch K, Westh P. Rate‐limiting step and substrate accessibility of cellobiohydrolase Cel6A from
Trichoderma reesei. FEBS J 2018; 285:4482-4493. [DOI: 10.1111/febs.14668] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 09/11/2018] [Accepted: 09/28/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Stefan J. Christensen
- Research Unit for Functional Biomaterials Department of Science and Environment Roskilde University Denmark
| | - Jeppe Kari
- Research Unit for Functional Biomaterials Department of Science and Environment Roskilde University Denmark
| | - Silke F. Badino
- Research Unit for Functional Biomaterials Department of Science and Environment Roskilde University Denmark
| | | | - Peter Westh
- Research Unit for Functional Biomaterials Department of Science and Environment Roskilde University Denmark
- Department of Biotechnology and Biomedicine Technical University of Denmark Lyngby Denmark
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67
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Michaelis–Menten equation for degradation of insoluble substrate. Math Biosci 2018; 296:93-97. [DOI: 10.1016/j.mbs.2017.11.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 11/20/2017] [Accepted: 11/28/2017] [Indexed: 02/01/2023]
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68
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Badino SF, Kari J, Christensen SJ, Borch K, Westh P. Direct kinetic comparison of the two cellobiohydrolases Cel6A and Cel7A from Hypocrea jecorina. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1739-1745. [DOI: 10.1016/j.bbapap.2017.08.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/25/2017] [Accepted: 08/14/2017] [Indexed: 01/17/2023]
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69
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Kuusk S, Bissaro B, Kuusk P, Forsberg Z, Eijsink VGH, Sørlie M, Väljamäe P. Kinetics of H 2O 2-driven degradation of chitin by a bacterial lytic polysaccharide monooxygenase. J Biol Chem 2017; 293:523-531. [PMID: 29138240 DOI: 10.1074/jbc.m117.817593] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/31/2017] [Indexed: 11/06/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) catalyze the oxidative cleavage of glycosidic bonds in recalcitrant polysaccharides, such as cellulose and chitin, and are of interest in biotechnological utilization of these abundant biomaterials. It has recently been shown that LPMOs can use H2O2, instead of O2, as a cosubstrate. This peroxygenase-like reaction by a monocopper enzyme is unprecedented in nature and opens new avenues in chemistry and enzymology. Here, we provide the first detailed kinetic characterization of chitin degradation by the bacterial LPMO chitin-binding protein CBP21 using H2O2 as cosubstrate. The use of 14C-labeled chitin provided convenient and sensitive detection of the released soluble products, which enabled detailed kinetic measurements. The kcat for chitin oxidation found here (5.6 s-1) is more than an order of magnitude higher than previously reported (apparent) rate constants for reactions containing O2 but no added H2O2 The kcat/Km for H2O2-driven degradation of chitin was on the order of 106 m-1 s-1, indicating that LPMOs have catalytic efficiencies similar to those of peroxygenases. Of note, H2O2 also inactivated CBP21, but the second-order rate constant for inactivation was about 3 orders of magnitude lower than that for catalysis. In light of the observed CBP21 inactivation at higher H2O2 levels, we conclude that controlled generation of H2O2in situ seems most optimal for fueling LPMO-catalyzed oxidation of polysaccharides.
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Affiliation(s)
- Silja Kuusk
- From the Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway, and
| | - Piret Kuusk
- Institute of Physics, University of Tartu, 50411 Tartu, Estonia
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway, and
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway, and
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway, and
| | - Priit Väljamäe
- From the Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia,
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70
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Khrenova MG, Kots ED, Varfolomeev SD, Lushchekina SV, Nemukhin AV. Three Faces of N-Acetylaspartate: Activator, Substrate, and Inhibitor of Human Aspartoacylase. J Phys Chem B 2017; 121:9389-9397. [DOI: 10.1021/acs.jpcb.7b08759] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria G. Khrenova
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Ekaterina D. Kots
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Sergey D. Varfolomeev
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Sofya V. Lushchekina
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexander V. Nemukhin
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
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