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Alonso Baez L, Bacete L. Cell wall dynamics: novel tools and research questions. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6448-6467. [PMID: 37539735 PMCID: PMC10662238 DOI: 10.1093/jxb/erad310] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 08/02/2023] [Indexed: 08/05/2023]
Abstract
Years ago, a classic textbook would define plant cell walls based on passive features. For instance, a sort of plant exoskeleton of invariable polysaccharide composition, and probably painted in green. However, currently, this view has been expanded to consider plant cell walls as active, heterogeneous, and dynamic structures with a high degree of complexity. However, what do we mean when we refer to a cell wall as a dynamic structure? How can we investigate the different implications of this dynamism? While the first question has been the subject of several recent publications, defining the ideal strategies and tools needed to address the second question has proven to be challenging due to the myriad of techniques available. In this review, we will describe the capacities of several methodologies to study cell wall composition, structure, and other aspects developed or optimized in recent years. Keeping in mind cell wall dynamism and plasticity, the advantages of performing long-term non-invasive live-imaging methods will be emphasized. We specifically focus on techniques developed for Arabidopsis thaliana primary cell walls, but the techniques could be applied to both secondary cell walls and other plant species. We believe this toolset will help researchers in expanding knowledge of these dynamic/evolving structures.
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Affiliation(s)
- Luis Alonso Baez
- Institute for Biology, Faculty of Natural Sciences, Norwegian University of Science and Technology, 5 Høgskoleringen, Trondheim, 7491, Norway
| | - Laura Bacete
- Institute for Biology, Faculty of Natural Sciences, Norwegian University of Science and Technology, 5 Høgskoleringen, Trondheim, 7491, Norway
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
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Badruna L, Burlat V, Montanier CY. CBMs as Probes to Explore Plant Cell Wall Heterogeneity Using Immunocytochemistry. Methods Mol Biol 2023; 2657:163-179. [PMID: 37149530 DOI: 10.1007/978-1-0716-3151-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Immunocytochemistry is a widely used technique to localize antigen within intact tissues. Plant cell walls are complex matrixes of highly decorated polysaccharides and the large number of CBM families displaying specific substrate recognition reflects this complexity. The accessibility of large proteins, such as antibodies, to their cell wall epitopes may be sometimes difficult due to steric hindrance problems. Due to their smaller size, CBMs are interesting alternative probes. The aim of this chapter is to describe the use of CBM as probes to explore complex polysaccharide topochemistry in muro and to quantify enzymatic deconstruction.
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Affiliation(s)
- Louise Badruna
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Vincent Burlat
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UT3, INP-ENSAT, Auzeville-Tolosane, France
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Khatri V, Meddeb-Mouelhi F, Adjallé K, Barnabé S, Beauregard M. Determination of optimal biomass pretreatment strategies for biofuel production: investigation of relationships between surface-exposed polysaccharides and their enzymatic conversion using carbohydrate-binding modules. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:144. [PMID: 29796085 PMCID: PMC5960114 DOI: 10.1186/s13068-018-1145-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/09/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Pretreatment of lignocellulosic biomass (LCB) is a key step for its efficient bioconversion into ethanol. Determining the best pretreatment and its parameters requires monitoring its impacts on the biomass material. Here, we used fluorescent protein-tagged carbohydrate-binding modules method (FTCM)-depletion assay to study the relationship between surface-exposed polysaccharides and enzymatic hydrolysis of LCB. RESULTS Our results indicated that alkali extrusion pretreatment led to the highest hydrolysis rates for alfalfa stover, cattail stems and flax shives, despite its lower lignin removal efficiency compared to alkali pretreatment. Corn crop residues were more sensitive to alkali pretreatments, leading to higher hydrolysis rates. A clear relationship was consistently observed between total surface-exposed cellulose detected by the FTCM-depletion assay and biomass enzymatic hydrolysis. Comparison of bioconversion yield and total composition analysis (by NREL/TP-510-42618) of LCB prior to or after pretreatments did not show any close relationship. Lignin removal efficiency and total cellulose content (by NREL/TP-510-42618) led to an unreliable prediction of enzymatic polysaccharide hydrolysis. CONCLUSIONS Fluorescent protein-tagged carbohydrate-binding modules method (FTCM)-depletion assay provided direct evidence that cellulose exposure is the key determinant of hydrolysis yield. The clear and robust relationships that were observed between the cellulose accessibility by FTCM probes and enzymatic hydrolysis rates change could be evolved into a powerful prediction tool that might help develop optimal biomass pretreatment strategies for biofuel production.
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Affiliation(s)
- Vinay Khatri
- Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada
- PROTEO, Université Laval, Québec, QC G1V 4G2 Canada
| | - Fatma Meddeb-Mouelhi
- Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada
- PROTEO, Université Laval, Québec, QC G1V 4G2 Canada
| | - Kokou Adjallé
- Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada
| | - Simon Barnabé
- Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada
| | - Marc Beauregard
- Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada
- PROTEO, Université Laval, Québec, QC G1V 4G2 Canada
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Khatri V, Hébert-Ouellet Y, Meddeb-Mouelhi F, Beauregard M. Specific tracking of xylan using fluorescent-tagged carbohydrate-binding module 15 as molecular probe. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:74. [PMID: 27019671 PMCID: PMC4807533 DOI: 10.1186/s13068-016-0486-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/14/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Xylan has been identified as a physical barrier which limits cellulose accessibility by covering the outer surface of fibers and interfibrillar space. Therefore, tracking xylan is a prerequisite for understanding and optimizing lignocellulosic biomass processes. RESULTS In this study, we developed a novel xylan tracking approach using a two-domain probe called OC15 which consists of a fusion of Cellvibrio japonicus carbohydrate-binding domain 15 with the fluorescent protein mOrange2. The new probe specifically binds to xylan with an affinity similar to that of CBM15. The sensitivity of the OC15-xylan detection approach was compared to that of standard methods such as X-ray photoelectron spectroscopy (XPS) and chemical composition analysis (NREL/TP-510-42618). All three approaches were used to analyze the variations of xylan content of kraft pulp fibers. XPS, which allows for surface analysis of fibers, did not clearly indicate changes in xylan content. Chemical composition analysis responded to the changes in xylan content, but did not give any specific information related to the fibers surface. Interestingly, only the OC15 probe enabled the highly sensitive detection of xylan variations at the surface of kraft pulp fibers. At variance with the other methods, the OC15 probe can be used in a high throughput format. CONCLUSIONS We developed a rapid and high throughput approach for the detection of changes in xylan exposure at the surface of paper fibers. The introduction of this method into the lignocellulosic biomass-based industries should revolutionize the understanding and optimization of most wood biomass processes.
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Affiliation(s)
- Vinay Khatri
- />Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada
- />PROTEO, Université Laval, Quebec, QC G1V 4G2 Canada
| | - Yannick Hébert-Ouellet
- />Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada
- />PROTEO, Université Laval, Quebec, QC G1V 4G2 Canada
| | - Fatma Meddeb-Mouelhi
- />Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada
- />PROTEO, Université Laval, Quebec, QC G1V 4G2 Canada
- />Buckman North America, Vaudreuil-Dorion, QC J7V 5V5 Canada
| | - Marc Beauregard
- />Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada
- />PROTEO, Université Laval, Quebec, QC G1V 4G2 Canada
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Ohlin M, von Schantz L, Schrader TE, Ostermann A, Logan DT, Fisher SZ. Crystallization, neutron data collection, initial structure refinement and analysis of a xyloglucan heptamer bound to an engineered carbohydrate-binding module from xylanase. Acta Crystallogr F Struct Biol Commun 2015; 71:1072-7. [PMID: 26249702 PMCID: PMC4528944 DOI: 10.1107/s2053230x15011383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/11/2015] [Indexed: 11/10/2022] Open
Abstract
Carbohydrate-binding modules (CBMs) are discrete parts of carbohydrate-hydrolyzing enzymes that bind specific types of carbohydrates. Ultra high-resolution X-ray crystallographic studies of CBMs have helped to decipher the basis for specificity in carbohydrate-protein interactions. However, additional studies are needed to better understand which structural determinants confer which carbohydrate-binding properties. To address these issues, neutron crystallographic studies were initiated on one experimentally engineered CBM derived from a xylanase, X-2 L110F, a protein that is able to bind several different plant carbohydrates such as xylan, β-glucan and xyloglucan. This protein evolved from a CBM present in xylanase Xyn10A of Rhodothermus marinus. The protein was complexed with a branched xyloglucan heptasaccharide. Large single crystals of hydrogenous protein (∼1.6 mm(3)) were grown at room temperature and subjected to H/D exchange. Both neutron and X-ray diffraction data sets were collected to 1.6 Å resolution. Joint neutron and X-ray refinement using phenix.refine showed significant density for residues involved in carbohydrate binding and revealed the details of a hydrogen-bonded water network around the binding site. This is the first report of a neutron structure of a CBM and will add to the understanding of protein-carbohydrate binding interactions.
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Affiliation(s)
- Mats Ohlin
- Department of Immunotechnology, Lund University, Medicon Village, Building 406, 223 81 Lund, Sweden
| | - Laura von Schantz
- Department of Immunotechnology, Lund University, Medicon Village, Building 406, 223 81 Lund, Sweden
| | - Tobias E. Schrader
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Derek T. Logan
- Department of Chemistry, Lund University, PO Box 124, 221 00 Lund, Sweden
| | - S. Zoë Fisher
- Scientific Activities Division, European Spallation Source, Tunavägen 24, 221 00 Lund, Sweden
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Tsai AY, Goacher RE, Master ER. Detecting changes in arabidopsis cell wall composition using time‐of‐flight secondary ion mass spectrometry. SURF INTERFACE ANAL 2015. [DOI: 10.1002/sia.5756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Alex Yi‐Lin Tsai
- Department of Cell & Systems BiologyUniversity of Toronto Toronto ON Canada
| | - Robyn E. Goacher
- Department of Biochemistry, Chemistry and PhysicsNiagara University Lewiston NY USA
- Department of Chemical Engineering & Applied ChemistryUniversity of Toronto Toronto ON Canada
| | - Emma R. Master
- Department of Cell & Systems BiologyUniversity of Toronto Toronto ON Canada
- Department of Chemical Engineering & Applied ChemistryUniversity of Toronto Toronto ON Canada
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Application of X-ray and neutron small angle scattering techniques to study the hierarchical structure of plant cell walls: a review. Carbohydr Polym 2015; 125:120-34. [PMID: 25857967 DOI: 10.1016/j.carbpol.2015.02.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 11/23/2022]
Abstract
Plant cell walls present an extremely complex structure of hierarchically assembled cellulose microfibrils embedded in a multi-component matrix. The biosynthesis process determines the mechanism of cellulose crystallisation and assembly, as well as the interaction of cellulose with other cell wall components. Thus, a knowledge of cellulose microfibril and bundle architecture, and the structural role of matrix components, is crucial for understanding cell wall functional and technological roles. Small angle scattering techniques, combined with complementary methods, provide an efficient approach to characterise plant cell walls, covering a broad and relevant size range while minimising experimental artefacts derived from sample treatment. Given the system complexity, approaches such as component extraction and the use of plant cell wall analogues are typically employed to enable the interpretation of experimental results. This review summarises the current research status on the characterisation of the hierarchical structure of plant cell walls using small angle scattering techniques.
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