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Herbaut M, Zoghlami A, Paës G. Dynamical assessment of fluorescent probes mobility in poplar cell walls reveals nanopores govern saccharification. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:271. [PMID: 30305844 PMCID: PMC6169017 DOI: 10.1186/s13068-018-1267-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/20/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND Improving lignocellulolytic enzymes' diffusion and accessibility to their substrate in the plant cell walls is recognised as a critical issue for optimising saccharification. Although many chemical features are considered as detrimental to saccharification, enzymes' dynamics within the cell walls remains poorly explored and understood. To address this issue, poplar fragments were submitted to hot water and ionic liquid pretreatments selected for their contrasted effects on both the structure and composition of lignocellulose. In addition to chemical composition and porosity analyses, the diffusion of polyethylene glycol probes of different sizes was measured at three different time points during the saccharification. RESULTS Probes' diffusion was mainly affected by probes size and pretreatments but only slightly by saccharification time. This means that, despite the removal of polysaccharides during saccharification, diffusion of probes was not improved since they became hindered by changes in lignin conformation, whose relative amount increased over time. Porosity measurements showed that probes' diffusion was highly correlated with the amount of pores having a diameter at least five times the size of the probes. Testing the relationship with saccharification demonstrated that accessibility of 1.3-1.7-nm radius probes measured by FRAP on non-hydrolysed samples was highly correlated with poplar digestibility together with the measurement of initial porosity on the range 5-20 nm. CONCLUSION Mobility measurements performed before hydrolysis can serve to explain and even predict saccharification with accuracy. The discrepancy observed between probes' size and pores' diameters to explain accessibility is likely due to biomass features such as lignin content and composition that prevent probes' diffusion through non-specific interactions probably leading to pores' entanglements.
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Affiliation(s)
- Mickaël Herbaut
- Fractionation of AgroResources and Environment (FARE) Laboratory, INRA, University of Reims Champagne-Ardenne, Reims, France
| | - Aya Zoghlami
- Fractionation of AgroResources and Environment (FARE) Laboratory, INRA, University of Reims Champagne-Ardenne, Reims, France
| | - Gabriel Paës
- Fractionation of AgroResources and Environment (FARE) Laboratory, INRA, University of Reims Champagne-Ardenne, Reims, France
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Samaei-Daryan S, Goliaei B, Ebrahim-Habibi A. Characterization of surface binding sites in glycoside hydrolases: A computational study. J Mol Recognit 2017; 30. [PMID: 28295743 DOI: 10.1002/jmr.2624] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 02/09/2017] [Accepted: 02/18/2017] [Indexed: 11/05/2022]
Abstract
Structural properties of carbohydrate surface binding sites (SBSs) were investigated with computational methods. Eighty-five SBSs of 44 enzymes in 119 Protein Data Bank (PDB) files were collected as a dataset. On the basis of SBSs shape, they were divided into 3 categories: flat surfaces, clefts, and cavities (types A, B, and C, respectively). Ligand varieties showed the correlation between shape of SBSs and ligands size. To reduce cut-off differences in each SBSs with different ligand size, molecular docking were performed. Molecular docking results were used to refine SBSs classification and binding sites cut-off. Docking results predicted putative ligands positions and displayed dependence of the ligands binding mode to the structural type of SBSs. Physicochemical properties of SBSs were calculated for all docking results with YASARA Structure. The results showed that all SBSs are hydrophilic, while their charges could vary and depended to ligand size and defined cut-off. Surface binding sites type B had highest average values of solvent accessible surface area. Analysis of interactions showed that hydrophobic interactions occur more than hydrogen bonds, which is related to the presence of aromatic residues and carbohydrates interactions.
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Affiliation(s)
| | - Bahram Goliaei
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Azadeh Ebrahim-Habibi
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.,Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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Paës G, Habrant A, Ossemond J, Chabbert B. Exploring accessibility of pretreated poplar cell walls by measuring dynamics of fluorescent probes. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:15. [PMID: 28101142 PMCID: PMC5237506 DOI: 10.1186/s13068-017-0704-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 01/06/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND The lignocellulosic cell wall network is resistant to enzymatic degradation due to the complex chemical and structural features. Pretreatments are thus commonly used to overcome natural recalcitrance of lignocellulose. Characterization of their impact on architecture requires combinatory approaches. However, the accessibility of the lignocellulosic cell walls still needs further insights to provide relevant information. RESULTS Poplar specimens were pretreated using different conditions. Chemical, spectral, microscopic and immunolabeling analysis revealed that poplar cell walls were more altered by sodium chlorite-acetic acid and hydrothermal pretreatments but weakly modified by soaking in aqueous ammonium. In order to evaluate the accessibility of the pretreated poplar samples, two fluorescent probes (rhodamine B-isothiocyanate-dextrans of 20 and 70 kDa) were selected, and their mobility was measured by using the fluorescence recovery after photobleaching (FRAP) technique in a full factorial experiment. The mobility of the probes was dependent on the pretreatment type, the cell wall localization (secondary cell wall and cell corner middle lamella) and the probe size. Overall, combinatory analysis of pretreated poplar samples showed that even the partial removal of hemicellulose contributed to facilitate the accessibility to the fluorescent probes. On the contrary, nearly complete removal of lignin was detrimental to accessibility due to the possible cellulose-hemicellulose collapse. CONCLUSIONS Evaluation of plant cell wall accessibility through FRAP measurement brings further insights into the impact of physicochemical pretreatments on lignocellulosic samples in combination with chemical and histochemical analysis. This technique thus represents a relevant approach to better understand the effect of pretreatments on lignocellulose architecture, while considering different limitations as non-specific interactions and enzyme efficiency.
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Affiliation(s)
- Gabriel Paës
- FARE laboratory, INRA, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | - Anouck Habrant
- FARE laboratory, INRA, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | - Jordane Ossemond
- FARE laboratory, INRA, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | - Brigitte Chabbert
- FARE laboratory, INRA, Université de Reims Champagne-Ardenne, 51100 Reims, France
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Lopez-Sanchez P, Schuster E, Wang D, Gidley MJ, Strom A. Diffusion of macromolecules in self-assembled cellulose/hemicellulose hydrogels. SOFT MATTER 2015; 11:4002-10. [PMID: 25898947 DOI: 10.1039/c5sm00103j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Cellulose hydrogels are extensively applied in many biotechnological fields and are also used as models for plant cell walls. We synthesised model cellulosic hydrogels containing hemicelluloses, as a biomimetic of plant cell walls, in order to study the role of hemicelluloses on their mass transport properties. Microbial cellulose is able to self-assemble into composites when hemicelluloses, such as xyloglucan and arabinoxylan, are present in the incubation media, leading to hydrogels with different nano and microstructures. We investigated the diffusivities of a series of fluorescently labelled dextrans, of different molecular weight, and proteins, including a plant pectin methyl esterase (PME), using fluorescence recovery after photobleaching (FRAP). The presence of xyloglucan, known to be able to crosslink cellulose fibres, confirmed by scanning electron microscopy (SEM) and (13)C NMR, reduced mobility of macromolecules of molecular weight higher than 10 kDa, reflected in lower diffusion coefficients. Furthermore PME diffusion was reduced in composites containing xyloglucan, despite the lack of a particular binding motif in PME for this polysaccharide, suggesting possible non-specific interactions between PME and this hemicellulose. In contrast, hydrogels containing arabinoxylan coating cellulose fibres showed enhanced diffusivity of the molecules studied. The different diffusivities were related to the architectural features found in the composites as a function of polysaccharide composition. Our results show the effect of model hemicelluloses in the mass transport properties of cellulose networks in highly hydrated environments relevant to understanding the role of hemicelluloses in the permeability of plant cell walls and aiding design of plant based materials with tailored properties.
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Affiliation(s)
- Patricia Lopez-Sanchez
- ARC Centre of Excellence in Plant Cell Walls, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, 4072, Australia. au
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Paës G. Fluorescent probes for exploring plant cell wall deconstruction: a review. Molecules 2014; 19:9380-402. [PMID: 24995923 PMCID: PMC6271034 DOI: 10.3390/molecules19079380] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/27/2014] [Accepted: 06/27/2014] [Indexed: 11/16/2022] Open
Abstract
Plant biomass is a potential resource of chemicals, new materials and biofuels that could reduce our dependency on fossil carbon, thus decreasing the greenhouse effect. However, due to its chemical and structural complexity, plant biomass is recalcitrant to green biological transformation by enzymes, preventing the establishment of integrated bio-refineries. In order to gain more knowledge in the architecture of plant cell wall to facilitate their deconstruction, many fluorescent probes bearing various fluorophores have been devised and used successfully to reveal the changes in structural motifs during plant biomass deconstruction, and the molecular interactions between enzymes and plant cell wall polymers. Fluorescent probes are thus relevant tools to explore plant cell wall deconstruction.
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Affiliation(s)
- Gabriel Paës
- INRA (French National Institute for Agricultural Research), UMR0614 Fractionation of AgroResources and Environment, 2 esplanade Roland-Garros, 51100 Reims, France.
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Paës G, Burr S, Saab MB, Molinari M, Aguié-Béghin V, Chabbert B. Modeling Progression of Fluorescent Probes in Bioinspired Lignocellulosic Assemblies. Biomacromolecules 2013; 14:2196-205. [DOI: 10.1021/bm400338b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Gabriel Paës
- INRA, UMR614 Fractionnement des AgroRessources
et Environnement, Reims,
France
- Université de Reims Champagne-Ardenne, UMR614 Fractionnement des
AgroRessources et Environnement, Reims, France
| | - Sally Burr
- INRA, UMR614 Fractionnement des AgroRessources
et Environnement, Reims,
France
- Université de Reims Champagne-Ardenne, UMR614 Fractionnement des
AgroRessources et Environnement, Reims, France
| | - Marie-Belle Saab
- INRA, UMR614 Fractionnement des AgroRessources
et Environnement, Reims,
France
- Université de Reims Champagne-Ardenne, UMR614 Fractionnement des
AgroRessources et Environnement, Reims, France
- Université de Reims Champagne-Ardenne, Laboratoire de Recherche
en Nanosciences LRN EA4682, Reims, France
| | - Michaël Molinari
- Université de Reims Champagne-Ardenne, Laboratoire de Recherche
en Nanosciences LRN EA4682, Reims, France
| | - Véronique Aguié-Béghin
- INRA, UMR614 Fractionnement des AgroRessources
et Environnement, Reims,
France
- Université de Reims Champagne-Ardenne, UMR614 Fractionnement des
AgroRessources et Environnement, Reims, France
| | - Brigitte Chabbert
- INRA, UMR614 Fractionnement des AgroRessources
et Environnement, Reims,
France
- Université de Reims Champagne-Ardenne, UMR614 Fractionnement des
AgroRessources et Environnement, Reims, France
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Heterogeneity in maize starch granule internal architecture deduced from diffusion of fluorescent dextran probes. Carbohydr Polym 2013; 93:365-73. [DOI: 10.1016/j.carbpol.2012.12.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 12/05/2012] [Accepted: 12/08/2012] [Indexed: 11/20/2022]
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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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Cuyvers S, Dornez E, Abou Hachem M, Svensson B, Hothorn M, Chory J, Delcour JA, Courtin CM. Isothermal titration calorimetry and surface plasmon resonance allow quantifying substrate binding to different binding sites of Bacillus subtilis xylanase. Anal Biochem 2011; 420:90-2. [PMID: 21964501 PMCID: PMC4854199 DOI: 10.1016/j.ab.2011.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/22/2011] [Accepted: 09/05/2011] [Indexed: 10/17/2022]
Abstract
Isothermal titration calorimetry and surface plasmon resonance were tested for their ability to study substrate binding to the active site (AS) and to the secondary binding site (SBS) of Bacillus subtilis xylanase A separately. To this end, three enzyme variants were compared. The first was a catalytically incompetent enzyme that allows substrate binding to both the AS and SBS. In the second enzyme, binding to the SBS was impaired by site-directed mutagenesis, whereas in the third enzyme, the AS was blocked using a covalent inhibitor. Both techniques were able to show that AS and SBS have a similar binding affinity.
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Affiliation(s)
- Sven Cuyvers
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre, Katholieke Universiteit Leuven, Leuven 3001, Belgium.
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Dornez E, Cuyvers S, Holopainen U, Nordlund E, Poutanen K, Delcour JA, Courtin CM. Inactive fluorescently labeled xylanase as a novel probe for microscopic analysis of arabinoxylan containing cereal cell walls. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:6369-75. [PMID: 21561164 DOI: 10.1021/jf200746g] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A new technique to visualize cereal cell walls by fluorescence microscopy was developed. The novel staining technique is based on an inactive fluorescently labeled xylanase binding to arabinoxylan (AX), an important polysaccharide in grain cell walls in terms of the technological and physiological functionalities of grain. The xylanase probe could stain AX in the seed coat, nucellar epidermis, aleurone layer, and starchy endosperm, but not the highly substituted AX of the pericarp layer. The advantage of this new staining technique over the existing immunolabeling techniques is that the staining procedure is clearly faster and less laborious, and uses a smaller probe that can easily be produced by marking a well characterized enzyme with a fluorescent label. In the future, the here proposed technology can be used to develop probes having specificity also for cell wall components other than AX and thus to study plant cell walls further through fluorescence microscopy.
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Affiliation(s)
- Emmie Dornez
- Laboratory of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven , Kasteelpark Arenberg 20-box 2463, B-3001 Leuven, Belgium
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The secondary substrate binding site of the Pseudoalteromonas haloplanktis GH8 xylanase is relevant for activity on insoluble but not soluble substrates. Appl Microbiol Biotechnol 2011; 92:539-49. [DOI: 10.1007/s00253-011-3343-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 04/18/2011] [Accepted: 04/18/2011] [Indexed: 10/18/2022]
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