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Nousi A, Molina GA, Schiano-di-Cola C, Sørensen TH, Borch K, Pedersen JN, Westh P, Marie R. Impact of Synergy Partner Cel7B on Cel7A Binding Rates: Insights from Single-Molecule Data. J Phys Chem B 2024; 128:635-647. [PMID: 38227769 PMCID: PMC10824242 DOI: 10.1021/acs.jpcb.3c05697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/02/2024] [Accepted: 01/05/2024] [Indexed: 01/18/2024]
Abstract
Enzymatic degradation of cellulosic biomass is a well-established route for the sustainable production of biofuels, chemicals, and materials. A strategy employed by nature and industry to achieve an efficient degradation of cellulose is that cellobiohydrolases (or exocellulases), such as Cel7A, work synergistically with endoglucanases, such as Cel7B, to achieve the complete degradation of cellulose. However, a complete mechanistic understanding of this exo-endo synergy is still lacking. Here, we used single-molecule fluorescence microscopy to quantify the binding kinetics of Cel7A on cellulose when it is acting alone on the cellulose fibrils and in the presence of its synergy partner, the endoglucanase Cel7B. To this end, we used a fluorescently tagged Cel7A and studied its binding in the presence of the unlabeled Cel7B. This provided the single-molecule data necessary for the estimation of the rate constants of association kON and dissociation kOFF of Cel7A for the substrate. We show that the presence of Cel7B does not impact the dissociation rate constant, kOFF. But, the association rate of Cel7A decreases by a factor of 2 when Cel7B is present at a molar proportion of 10:1. This ratio has previously been shown to lead to synergy. This decrease in association rate is observed in a wide range of total enzyme concentrations, from sub nM to μM concentrations. This decrease in kON is consistent with the formation of cellulase clusters recently observed by others using atomic force microscopy.
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Affiliation(s)
- Aimilia Nousi
- Department
of Health Technology, Technical University
of Denmark, 2800 Kongens Lyngby, Denmark
| | - Gustavo Avelar Molina
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | | | | | - Kim Borch
- Novozymes
A/S, Krogshøjvej
36, 2880 Bagsværd, Denmark
| | - Jonas N. Pedersen
- Department
of Health Technology, Technical University
of Denmark, 2800 Kongens Lyngby, Denmark
| | - Peter Westh
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Rodolphe Marie
- Department
of Health Technology, Technical University
of Denmark, 2800 Kongens Lyngby, Denmark
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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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3
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Donaldson L, Vaidya A. Visualising recalcitrance by colocalisation of cellulase, lignin and cellulose in pretreated pine biomass using fluorescence microscopy. Sci Rep 2017; 7:44386. [PMID: 28281670 PMCID: PMC5345003 DOI: 10.1038/srep44386] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/07/2017] [Indexed: 11/08/2022] Open
Abstract
Mapping the location of bound cellulase enzymes provides information on the micro-scale distribution of amenable and recalcitrant sites in pretreated woody biomass for biofuel applications. The interaction of a fluorescently labelled cellulase enzyme cocktail with steam-exploded pine (SEW) was quantified using confocal microscopy. The spatial distribution of Dylight labelled cellulase was quantified relative to lignin (autofluorescence) and cellulose (Congo red staining) by measuring their colocalisation using Pearson correlations. Correlations were greater in cellulose-rich secondary cell walls compared to lignin-rich middle lamella but with significant variations among individual biomass particles. The distribution of cellulose in the pretreated biomass accounted for 30% of the variation in the distribution of enzyme after correcting for the correlation between lignin and cellulose. For the first time, colocalisation analysis was able to quantify the spatial distribution of amenable and recalcitrant sites in relation to the histochemistry of cellulose and lignin. This study will contribute to understanding the role of pretreatment in enzymatic hydrolysis of recalcitrant softwood biomass.
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Affiliation(s)
- Lloyd Donaldson
- Scion, 49 Sala Street, Private Bag 3020, Rotorua 3010, New Zealand
| | - Alankar Vaidya
- Scion, 49 Sala Street, Private Bag 3020, Rotorua 3010, New Zealand
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Rose M, Babi M, Moran-Mirabal J. The Study of Cellulose Structure and Depolymerization Through Single-Molecule Methods. Ind Biotechnol (New Rochelle N Y) 2015. [DOI: 10.1089/ind.2014.0019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Markus Rose
- Department of Physics and Astronomy, McMaster University, Hamilton, Canada
| | - Mouhanad Babi
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Jose Moran-Mirabal
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
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Luterbacher JS, Moran-Mirabal JM, Burkholder EW, Walker LP. Modeling enzymatic hydrolysis of lignocellulosic substrates using confocal fluorescence microscopy I: Filter paper cellulose. Biotechnol Bioeng 2014; 112:21-31. [DOI: 10.1002/bit.25329] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/08/2014] [Accepted: 06/30/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Jeremy S. Luterbacher
- Department of Chemical and Biomolecular Engineering; Olin Hall; Cornell University; Ithaca New York
| | - Jose M. Moran-Mirabal
- Department of Chemistry and Chemical Biology; Arthur N. Bourns Science Building; McMaster University; Hamilton Ontario, Canada L8S4M1
| | - Eric W. Burkholder
- Department of Chemical and Biomolecular Engineering; Olin Hall; Cornell University; Ithaca New York
| | - Larry P. Walker
- Department of Biological and Environmental Engineering; Riley-Robb Hall; Cornell University; Ithaca New York 14850
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Yang D, Moran-Mirabal JM, Parlange JY, Walker LP. Investigation of the porous structure of cellulosic substrates through confocal laser scanning microscopy. Biotechnol Bioeng 2013; 110:2836-45. [PMID: 23737240 DOI: 10.1002/bit.24958] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 04/30/2013] [Accepted: 05/06/2013] [Indexed: 11/06/2022]
Abstract
At the most fundamental level, saccharification occurs when cell wall degrading enzymes (CWDEs) diffuse, bind to and react on readily accessible cellulose fibrils. Thus, the study of the diffusive behavior of solutes into and out of cellulosic substrates is important for understanding how biomass pore size distribution affects enzyme transport, binding, and catalysis. In this study, fluorescently labeled dextrans with molecular weights of 20, 70, and 150 kDa were used as probes to assess their diffusion into the porous structure of filter paper. Fluorescence microscopy with high numerical aperture objectives was used to generate high temporal and spatial resolution datasets of probe concentrations versus time. In addition, two diffusion models, including a simple transient diffusion and a pore grouping diffusion models, were developed. These models and the experimental datasets were used to investigate solute diffusion in macro- and micro-pores. Nonlinear least squares fitting of the datasets to the simple transient model yielded diffusion coefficient estimates that were inadequate for describing the initial fast diffusion and the later slow diffusion rates observed; on the other hand, nonlinear least squares fitting of the datasets to the pore grouping diffusion model yielded estimations of the micro-pore diffusion coefficient that described the inherently porous structure of plant-derived cellulose. In addition, modeling results show that on average 75% of the accessible pore volume is available for fast diffusion without any significant pore hindrance. The method developed can be applied to study the porous structure of plant-derived biomass and help assess the diffusion process for enzymes with known sizes.
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Affiliation(s)
- Dong Yang
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, 14853
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7
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Moran-Mirabal JM, Bolewski JC, Walker LP. Thermobifida fuscacellulases exhibit limited surface diffusion on bacterial micro-crystalline cellulose. Biotechnol Bioeng 2012; 110:47-56. [DOI: 10.1002/bit.24604] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 06/02/2012] [Accepted: 07/02/2012] [Indexed: 11/08/2022]
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8
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Luterbacher JS, Walker LP, Moran-Mirabal JM. Observing and modeling BMCC degradation by commercial cellulase cocktails with fluorescently labeled Trichoderma reseii Cel7A through confocal microscopy. Biotechnol Bioeng 2012; 110:108-17. [PMID: 22766843 DOI: 10.1002/bit.24597] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 06/14/2012] [Accepted: 06/20/2012] [Indexed: 11/07/2022]
Abstract
Understanding the depolymerization mechanisms of cellulosic substrates by cellulase cocktails is a critical step towards optimizing the production of monosaccharides from biomass. The Spezyme CP cellulase cocktail combined with the Novo 188 β-glucosidase blend was used to depolymerize bacterial microcrystalline cellulose (BMCC), which was immobilized on a glass surface. The enzyme mixture was supplemented with a small fraction of fluorescently labeled Trichoderma reseii Cel7A, which served as a reporter to track cellulase binding onto the physical structure of the cellulosic substrate. Both micro-scale imaging and bulk experiments were conducted. All reported experiments were conducted at 50 °C, the optimal temperature for maximum hydrolytic activity of the enzyme cocktail. BMCC structure was observed throughout degradation by labeling it with a fluorescent dye. This method allowed us to measure the binding of cellulases in situ and follow the temporal morphological changes of cellulose during its depolymerization by a commercial cellulase mixture. Three kinetic models were developed and fitted to fluorescence intensity data obtained through confocal microscopy: irreversible and reversible binding models, and an instantaneous binding model. The models were successfully used to predict the soluble sugar concentrations that were liberated from BMCC in bulk experiments. Comparing binding and kinetic parameters from models with different assumptions to previously reported constants in the literature led us to conclude that exposing new binding sites is an important rate-limiting step in the hydrolysis of crystalline cellulose.
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Affiliation(s)
- Jeremy S Luterbacher
- Department of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
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Paës G, Chabbert B. Characterization of Arabinoxylan/Cellulose Nanocrystals Gels to Investigate Fluorescent Probes Mobility in Bioinspired Models of Plant Secondary Cell Wall. Biomacromolecules 2011; 13:206-14. [DOI: 10.1021/bm201475a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gabriel Paës
- INRA, UMR614 Fractionnement des AgroRessources et Environnement, Reims, France
- University of Reims Champagne-Ardenne, UMR614 Fractionnement des AgroRessources
et Environnement, Reims, France
| | - Brigitte Chabbert
- INRA, UMR614 Fractionnement des AgroRessources et Environnement, Reims, France
- University of Reims Champagne-Ardenne, UMR614 Fractionnement des AgroRessources
et Environnement, Reims, France
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Kostylev M, Moran-Mirabal JM, Walker LP, Wilson DB. Determination of the molecular states of the processive endocellulase Thermobifida fusca Cel9A during crystalline cellulose depolymerization. Biotechnol Bioeng 2011; 109:295-9. [DOI: 10.1002/bit.23299] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 08/03/2011] [Accepted: 08/05/2011] [Indexed: 11/11/2022]
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11
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Moran-Mirabal JM, Bolewski JC, Walker LP. Reversibility and binding kinetics of Thermobifida fusca cellulases studied through fluorescence recovery after photobleaching microscopy. Biophys Chem 2011; 155:20-8. [PMID: 21396764 DOI: 10.1016/j.bpc.2011.02.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 02/14/2011] [Accepted: 02/14/2011] [Indexed: 11/26/2022]
Abstract
Cellulases are enzymes capable of depolymerizing cellulose. Understanding their interactions with cellulose can improve biomass saccharification and enzyme recycling in biofuel production. This paper presents a study on binding and binding reversibility of Thermobifida fusca cellulases Cel5A, Cel6B, and Cel9A bound onto Bacterial Microcrystalline Cellulose. Cellulase binding was assessed through fluorescence recovery after photobleaching (FRAP) at 23, 34, and 45 °C. It was found that cellulase binding is only partially reversible. For processive cellulases Cel6B and Cel9A, an increase in temperature resulted in a decrease of the fraction of cellulases reversibly bound, while for endocellulase Cel5A this fraction remained constant. Kinetic parameters were obtained by fitting the FRAP curves to a binding-dominated model. The unbinding rate constants obtained for all temperatures were highest for Cel5A and lowest for Cel9A. The results presented demonstrate the usefulness of FRAP to access the fast binding kinetics characteristic of cellulases operating at their optimal temperature.
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Affiliation(s)
- Jose M Moran-Mirabal
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA.
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