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Meng X, Miao Y, Liu Q, Ma L, Guo K, Liu D, Ran W, Shen Q. TgSWO from Trichoderma guizhouense NJAU4742 promotes growth in cucumber plants by modifying the root morphology and the cell wall architecture. Microb Cell Fact 2019; 18:148. [PMID: 31481065 PMCID: PMC6721366 DOI: 10.1186/s12934-019-1196-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 08/22/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Colonization of Trichoderma spp. is essential for exerting their beneficial functions on the plant. However, the interactions between Trichoderma spp. and plant roots are still not completely understood. The aim of this study was to investigate how TgSWO affect Trichoderma guizhouense to establish themselves in the plant rhizosphere and promote plant growth. In this study, we deeply analyzed the molecular mechanism by which the functional characterization of the TgSWO by expressing different functional region deletion proteins (FRDP) of TgSWO. RESULTS Root scanning analysis results showed that TgSWO could dramatically increase root density and promote growth. In addition, we also found that TgSWO could expand root cell walls, subsequently increase root colonization. Moreover, knockout of TgSWO mutants (KO) or overexpression of TgSWO mutants (OE) produced greatly reduced or increased the number of cucumber root, respectively. To clarify the molecular mechanism of TgSWO in plant-growth-promotion, we analyzed the ability of different FRDP to expand the root cell wall. The root cell wall architecture were considerably altered when treated by ΔCBD protein (the TgSWO gene of lacking in the CBD domain was cloned and heterologously expressed), in correlation with the present YoaJ domain of TgSWO. In contrast, neither the expansion of cell walls nor the increase of roots was detectable in ΔYoaJ protein. CONCLUSIONS Our results emphasize the YoaJ domain is the most critical functional area of TgSWO during the alteration of cell wall architecture. Simultaneously, the results obtained in this study also indicate that TgSWO might play a plant-growth-promotion role in the Trichoderma-plant interactions by targeting the root cell wall.
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Affiliation(s)
- Xiaohui Meng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Qiumei Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Lei Ma
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Kai Guo
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, Shandong, People's Republic of China
| | - Dongyang Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
| | - Wei Ran
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
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Hepler NK, Cosgrove DJ. Directed
in vitro
evolution of bacterial expansin BsEXLX1 for higher cellulose binding and its consequences for plant cell wall‐loosening activities. FEBS Lett 2019; 593:2545-2555. [DOI: 10.1002/1873-3468.13528] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Nathan K. Hepler
- Huck Institutes of the Life Sciences The Pennsylvania State University University Park PA USA
- Department of Biology The Pennsylvania State University University Park PA USA
| | - Daniel J. Cosgrove
- Huck Institutes of the Life Sciences The Pennsylvania State University University Park PA USA
- Department of Biology The Pennsylvania State University University Park PA USA
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Voutilainen S, Paananen A, Lille M, Linder MB. Modular protein architectures for pH-dependent interactions and switchable assembly of nanocellulose. Int J Biol Macromol 2019; 137:270-276. [PMID: 31260762 DOI: 10.1016/j.ijbiomac.2019.06.227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/17/2019] [Accepted: 06/28/2019] [Indexed: 11/27/2022]
Abstract
Protein engineering shows a wide range of possibilities for designing properties in novel materials. Following inspiration from natural systems we have studied how combinations or duplications of protein modules can be used to engineer their interactions and achieve functional properties. Here we used cellulose binding modules (CBM) coupled to spider silk N-terminal domains that dimerize in a pH-sensitive manner. We showed how the pH-sensitive switching into dimers affected cellulose binding affinity in relation to covalent coupling between CBMs. Finally, we showed how the pH-sensitive coupling could be used to assemble cellulose nanofibers in a dynamic pH-dependent way. The work shows how novel proteins can be designed by linking functional domains from widely different sources and thereby achieve new functions in the self-assembly of nanoscale materials.
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Affiliation(s)
- Sanni Voutilainen
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Box 16100, 00076, Aalto, Espoo, Finland; VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044 VTT Espoo, Finland
| | - Arja Paananen
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044 VTT Espoo, Finland
| | - Martina Lille
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044 VTT Espoo, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Box 16100, 00076, Aalto, Espoo, Finland.
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54
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Molecular Insights into FaEG1, a Strawberry Endoglucanase Enzyme Expressed during Strawberry Fruit Ripening. PLANTS 2019; 8:plants8060140. [PMID: 31141938 PMCID: PMC6631567 DOI: 10.3390/plants8060140] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/18/2019] [Accepted: 05/25/2019] [Indexed: 01/04/2023]
Abstract
The endo-β-1,4-glucanases (EGs) that belong to the glycosyl hydrolase family 9 (GH9) have roles in cell wall synthesis, remodeling and degradation. Previous studies have suggested that EGs may play a key role in the ripening of different fruits including strawberries. In this study, we used reverse-transcription quantitative polymerase chain reaction (RT-qPCR) assays to determine the transcript accumulation of an endo-β-1,4-glucanase (FaEG1) during fruit development in two different strawberry ‘Camarosa’ and ‘Monterey’ with contrasting softening ratios. Phylogenetic analyses suggest that FaEG1 belongs to the α group of the GH9 family with other proteins previously described with roles in elongation, abscission and ripening. Comparative modeling was used to obtain the FaEG1 structure. The model displays a α-barrel–type structure that is typical of the GH9 enzyme family, and comprises 12 α-helices, 2 310 helices and 6 β-sheets. The catalytic residues were oriented to the solvent in the middle of an open groove. Protein–ligand interactions were explored with cellulose and two xyloglucans as ligands; the results suggest that the FaEG1-cellulose and FaEG1-XXXGXXXG (the most abundant xyloglucan in strawberries) complexes were more stable complexes than XXFGXXFG. The cell wall degradation was observed by scanning electron microscopy (SEM). The data are congruent with the probable role of the FaEG1 protein in the dissembly of the cellulose-hemicellulose fraction during the ripening of strawberry fruit.
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55
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Purington E, Bousfield D, Gramlich WM. Fluorescent Dye Adsorption in Aqueous Suspension to Produce Tagged Cellulose Nanofibers for Visualization on Paper. CELLULOSE (LONDON, ENGLAND) 2019; 26:5117-5131. [PMID: 31130782 PMCID: PMC6532663 DOI: 10.1007/s10570-019-02439-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
Cellulose nanofibers (CNFs) have great potential to be a layer in packaging materials because of their good barrier properties. When paper is coated with CNFs, they are difficult to distinguish from the base sheet. This issue creates challenges when trying to determine where CNFs migrate relative to the paper fibers during coating and drying. A three- dimensional analysis is possible by using confocal laser scanning microscopy (CLSM) if CNFs can be tagged with fluorescently active groups. In this study, CNFs were fluorescently tagged through adsorption of fluorescent dyes such as fluorescein isothiocyanate (FITC) and thioflavin by mixing with CNFs in their native suspension followed by purification. The adsorbed dye remained attached during typical coating procedures, low pH values, and high ionic strengths, but not for high pH and in contact with acetone. CNFs were also covalently tagged with FITC following methods reported in the literature as a comparison to already established methods for tagging cellulose nanocrystals (CNCs). Images of never dried samples indicated that covalently tagging CNFs altered the state of the fines dispersion, while dye adsorption did not. Coatings of the adsorbed dye tagged CNFs on paper were successfully imaged by CLSM since the concentration of dye in the water phase was low enough to provide a good contrast between regions of CNFs and paper. With this method, the location and potential migration of CNFs coated on paper were successfully determined for the first time to the best of our knowledge. CNF based coatings with solids larger than 2.8% were found to have a distinct layer of CNFs at the paper surface with little CNFs penetrating into the paper structure, but lower solids result in significant penetration into the paper.
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Affiliation(s)
- Emilia Purington
- Department of Chemical and Biological Engineering, Paper Surface Science Program, University of Maine, Orono, ME 04469
| | - Douglas Bousfield
- Department of Chemical and Biological Engineering, Paper Surface Science Program, University of Maine, Orono, ME 04469
| | - William M Gramlich
- Department of Chemistry, Paper Surface Science Program, University of Maine, Orono, ME 04469
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Itoh T, Kimoto H. Bacterial Chitinase System as a Model of Chitin Biodegradation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1142:131-151. [PMID: 31102245 DOI: 10.1007/978-981-13-7318-3_7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chitin, a structural polysaccharide of β-1,4-linked N-acetyl-D-glucosamine residues, is the second most abundant natural biopolymer after cellulose. The metabolism of chitin affects the global carbon and nitrogen cycles, which are maintained by marine and soil-dwelling bacteria. The degradation products of chitin metabolism serve as important nutrient sources for the chitinolytic bacteria. Chitinolytic bacteria have elaborate enzymatic systems for the degradation of the recalcitrant chitin biopolymer. This chapter introduces chitin degradation and utilization systems of the chitinolytic bacteria. These bacteria secrete many chitin-degrading enzymes, including processive chitinases, endo-acting non-processive chitinases, lytic polysaccharide monooxygenases, and N-acetyl-hexosaminidases. Bacterial chitinases play a fundamental role in the degradation of chitin. Enzymatic properties, catalytic mechanisms, and three-dimensional structures of chitinases have been extensively studied by many scientists. These enzymes can be exploited to produce a range of chitin-derived products, e.g., biocontrol agents against many plant pathogenic fungi and insects. We introduce bacterial chitinases in terms of their reaction modes and structural features.
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Affiliation(s)
- Takafumi Itoh
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui, 910-1195, Japan.
| | - Hisashi Kimoto
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui, 910-1195, Japan
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57
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Valenzuela-Riffo F, Gaete-Eastman C, Stappung Y, Lizana R, Herrera R, Moya-León MA, Morales-Quintana L. Comparative in silico study of the differences in the structure and ligand interaction properties of three alpha-expansin proteins from Fragaria chiloensis fruit. J Biomol Struct Dyn 2018; 37:3245-3258. [PMID: 30175949 DOI: 10.1080/07391102.2018.1517610] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Expansins are cell wall proteins associated with several processes, including changes in the cell wall during ripening of fruit, which matches softening of the fruit. We have previously reported an increase in expression of specific expansins transcripts during softening of Fragaria chiloensis fruit. Here, we characterized three α-expansins. Their full-length sequences were obtained, and through qRT-PCR (real-time PCR) analyses, their transcript accumulation during softening of F. chiloensis fruit was confirmed. Interestingly, differential but overlapping expression patterns were observed. With the aim of elucidating their roles, 3D protein models were built using comparative modeling methodology. The models obtained were similar and displayed cellulose binding module(CBM ) with a β-sandwich structure, and a catalytic domain comparable to the catalytic core of protein of the family 45 glycosyl hydrolase. An open groove located at the central part of each expansin was described; however, the shape and size are different. Their protein-ligand interactions were evaluated, showing favorable binding affinity energies with xyloglucan, homogalacturonan, and cellulose, cellulose being the best ligand. However, small differences were observed between the protein-ligand conformations. Molecular mechanics-generalized Born-surface area (MM-GBSA) analyses indicate the major contribution of van der Waals forces and non-polar interactions. The data provide a dynamic view of interaction between expansins and cellulose as putative cell wall ligands at the molecular scale. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Felipe Valenzuela-Riffo
- a Functional genomics, biochemistry and plant physiology group , Instituto de Ciencias Biológicas , Universidad de Talca , Talca , Chile.,b Phytohormone Research Laboratory , Instituto de Ciencias Biológicas, Universidad de Talca , Talca , Chile
| | - Carlos Gaete-Eastman
- a Functional genomics, biochemistry and plant physiology group , Instituto de Ciencias Biológicas , Universidad de Talca , Talca , Chile
| | - Yazmina Stappung
- a Functional genomics, biochemistry and plant physiology group , Instituto de Ciencias Biológicas , Universidad de Talca , Talca , Chile
| | - Rodrigo Lizana
- a Functional genomics, biochemistry and plant physiology group , Instituto de Ciencias Biológicas , Universidad de Talca , Talca , Chile
| | - Raúl Herrera
- a Functional genomics, biochemistry and plant physiology group , Instituto de Ciencias Biológicas , Universidad de Talca , Talca , Chile
| | - María Alejandra Moya-León
- a Functional genomics, biochemistry and plant physiology group , Instituto de Ciencias Biológicas , Universidad de Talca , Talca , Chile
| | - Luis Morales-Quintana
- a Functional genomics, biochemistry and plant physiology group , Instituto de Ciencias Biológicas , Universidad de Talca , Talca , Chile.,c Multidisciplinary Agroindustry Research Laboratory , Carrera de Ingeniería en Informática, Universidad Autónoma de Chile , Talca , Chile.,d Instituto de Ciencias Biomédicas , Universidad Autónoma de Chile Sede Talca , Talca , del Maule , Chile
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58
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Armijos-Jaramillo V, Santander-Gordón D, Tejera E, Perez-Castillo Y. The dilemma of bacterial expansins evolution. The unusual case of Streptomyces acidiscabies and Kutzneria sp. 744. Commun Integr Biol 2018; 11:e1539612. [PMID: 30574264 PMCID: PMC6300095 DOI: 10.1080/19420889.2018.1539612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 10/13/2018] [Accepted: 10/18/2018] [Indexed: 11/16/2022] Open
Abstract
Expansins are a superfamily of proteins mainly present in plants that are also found in bacteria, fungi and amoebozoa. Expansin proteins bind the plant cells wall and relax the cellulose microfibrils without any enzymatic action. The evolution of this kind of proteins exposes a complex pattern of horizontal gene transferences that makes difficult to determine the precise origin of non-plant expansins. We performed a genome-wide search of inter-domain horizontal gene transfer events using Streptomyces species and found a plant-like expansin in the Streptomyces acidiscabies proteome. This finding leads us to study in deep the origin and the characteristics of this peculiar protein, also present in the species Kutzneria sp.744. Using phylogenetic analyses, we determine that indeed S. acidiscabies and Kutzneria sp.744 expansins are located inside the plants expansins A clade. Using secondary and tertiary structural information, we observed that the electrostatic potentials and the folding of expansins are similar, independently of the proteins' origin. Using all this information, we conclude that S. acidiscabies and Kutzneria sp.744 expansins have a plant origin but differ from plant and bacterial canonical expansins. This finding suggests that the experimental research around this kind of expansins can be promissory in the future.
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Affiliation(s)
- Vinicio Armijos-Jaramillo
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador
- Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | - Daniela Santander-Gordón
- Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
- Facultad de Ciencias Naturales y Ambientales, Universidad Internacional SEK, Quito, Ecuador
| | - Eduardo Tejera
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador
- Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | - Yunierkis Perez-Castillo
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador
- Ciencias Físicas y Matemáticas-Facultad de Formación General, Universidad de Las Américas, Quito, Ecuador
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Computational study of FaEXPA1, a strawberry alpha expansin protein, through molecular modeling and molecular dynamics simulation studies. Comput Biol Chem 2018; 76:79-86. [DOI: 10.1016/j.compbiolchem.2018.05.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 04/26/2018] [Accepted: 05/15/2018] [Indexed: 11/22/2022]
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Hurlburt NK, Chen LH, Stergiopoulos I, Fisher AJ. Structure of the Cladosporium fulvum Avr4 effector in complex with (GlcNAc)6 reveals the ligand-binding mechanism and uncouples its intrinsic function from recognition by the Cf-4 resistance protein. PLoS Pathog 2018; 14:e1007263. [PMID: 30148881 PMCID: PMC6128652 DOI: 10.1371/journal.ppat.1007263] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 09/07/2018] [Accepted: 08/07/2018] [Indexed: 11/18/2022] Open
Abstract
Effectors are microbial-derived secreted proteins with an essential function in modulating host immunity during infections. CfAvr4, an effector protein from the tomato pathogen Cladosporium fulvum and the founding member of a fungal effector family, promotes parasitism through binding fungal chitin and protecting it from chitinases. Binding of Avr4 to chitin is mediated by a carbohydrate-binding module of family 14 (CBM14), an abundant CBM across all domains of life. To date, the structural basis of chitin-binding by Avr4 effector proteins and of recognition by the cognate Cf-4 plant immune receptor are still poorly understood. Using X-ray crystallography, we solved the crystal structure of CfAvr4 in complex with chitohexaose [(GlcNAc)6] at 1.95Å resolution. This is the first co-crystal structure of a CBM14 protein together with its ligand that further reveals the molecular mechanism of (GlcNAc)6 binding by Avr4 effector proteins and CBM14 family members in general. The structure showed that two molecules of CfAvr4 interact through the ligand and form a three-dimensional molecular sandwich that encapsulates two (GlcNAc)6 molecules within the dimeric assembly. Contrary to previous assumptions made with other CBM14 members, the chitohexaose-binding domain (ChBD) extends to the entire length of CfAvr4 with the reducing end of (GlcNAc)6 positioned near the N-terminus and the non-reducing end at the C-terminus. Site-directed mutagenesis of residues interacting with (GlcNAc)6 enabled the elucidation of the precise topography and amino acid composition of Avr4’s ChBD and further showed that these residues do not individually mediate the recognition of CfAvr4 by the Cf-4 immune receptor. Instead, the studies highlighted the dependency of Cf-4-mediated recognition on CfAvr4’s stability and resistance against proteolysis in the leaf apoplast, and provided the evidence for structurally separating intrinsic function from immune receptor recognition in this effector family. Microbes mobilize an array of secreted effectors to manipulate their hosts during infections, whereas in response, hosts utilize cognate immune receptors to perceive effectors and mount a defense. To date, the structural basis of effector function and recognition by immune receptors are still poorly understood. Here we present the crystal structure in complex with chitohexaose of CfAvr4, a CBM14 lectin and the founding member of a fungal effector family that binds and protects chitin in fungal cell-walls from chitinases. This is the first structure of a CBM14 protein to be co-crystalized with its ligand that further reveals how Avr4 effectors function. Specifically, by leveraging structural and functional data, we elucidate the molecular basis for ligand-binding by CfAvr4 and show that two effector molecules are brought together through the ligand to form a sandwich structure that laminates two chitohexaose molecules within the dimeric assembly. We further show that recognition of CfAvr4 by the cognate Cf-4 immune receptor is not mediated through residues directly interacting with chitohexaose, thereby structurally uncoupling the ligand-binding function of Avr4 from recognition by Cf-4 and challenging early postulations that the broad recognition of Avr4 effectors by Cf-4 stems from perceiving residues implicated in binding their ligand.
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Affiliation(s)
- Nicholas K. Hurlburt
- Department of Chemistry, University of California, Davis, Davis, California, United States of America
| | - Li-Hung Chen
- Department of Plant Pathology, University of California, Davis, Davis, California, United States of America
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California, Davis, Davis, California, United States of America
- * E-mail: (IS); (AJF)
| | - Andrew J. Fisher
- Department of Chemistry, University of California, Davis, Davis, California, United States of America
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California, United States of America
- * E-mail: (IS); (AJF)
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61
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Song W, Zhao Y, Wu Y, Li Z, Lv H, Li S, Jiang Y, Song C, Wang F, Huang Y. Fabrication, characterization and biocompatibility of collagen/oxidized regenerated cellulose-Ca composite scaffold for carrying Schwann cells. Int J Biol Macromol 2018; 119:1195-1203. [PMID: 30110602 DOI: 10.1016/j.ijbiomac.2018.08.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 01/14/2023]
Abstract
Schwann cell (SC) is the primary structural and functional part of the peripheral nervous system, and it plays a key role in the repair and regeneration of peripheral nerve. In order to develop a suitable scaffold for SC nerve tissue engineering, three kinds of scaffolds, including pristine collagen, pure oxidized regenerated cellulose-Ca (ORCCa) and collagen/ORC-Ca composite scaffolds, have been fabricated for carrying SC in this study. SC is then seeded on the scaffolds to form SC-scaffold nerve tissue engineering composites and evaluate their biocompatibility. The chemical and physical structure of the scaffolds are investigated by FTIR, NMR and SEM. The wettability of the collagen/ORC-Ca composite scaffold is close to that of pristine collagen, and the tensile strength of the composite scaffold (0.58 MPa) is better than that of pristine collagen (0.36 MPa). Cytotoxicity, cell proliferation, cell adhesion and western blotting assays are conducted to evaluate the biocompatibility and properties of different scaffolds. The results show that the three scaffolds exhibit no toxicity, and the proliferation rate of SC on the collagen/ORC-Ca composite scaffold is significantly higher than that of the other scaffolds (p < 0.05). The number of the adhesion cells on the composite scaffold (244.67 ± 13.02) is much more than that in the pure ORC-Ca group (p < 0.01). Furthermore, the expression of N-Cadheri and PMP22 proteins in the collagen/ORC-Ca composite scaffold is significantly superior to the other two scaffolds (both p < 0.01). Therefore, it could be concluded that the collagen/ORC-Ca composite is a promising candidate as a scaffold for carrying SC to form nerve tissue engineering composites in order to assist the peripheral nervous in the repair and regeneration.
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Affiliation(s)
- Wenli Song
- Harbin Sport University, Harbin 150008, China
| | - Yuhua Zhao
- Harbin Sport University, Harbin 150008, China
| | - Yadong Wu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China.
| | - Zhipeng Li
- Harbin Sport University, Harbin 150008, China
| | - Hui Lv
- The First Affiliated Hospital of Harbin Medical University, Harbin 150007, China
| | - Siyu Li
- Harbin Medical University (Da Qing), Da Qing 163319, China
| | - Yue Jiang
- Harbin Medical University (Da Qing), Da Qing 163319, China
| | - Chun Song
- The First Affiliated Hospital of Harbin Medical University, Harbin 150007, China
| | - Fang Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Yudong Huang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
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62
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Tancos MA, Lowe‐Power TM, Peritore‐Galve FC, Tran TM, Allen C, Smart CD. Plant-like bacterial expansins play contrasting roles in two tomato vascular pathogens. MOLECULAR PLANT PATHOLOGY 2018; 19:1210-1221. [PMID: 28868644 PMCID: PMC5835177 DOI: 10.1111/mpp.12611] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/04/2017] [Accepted: 08/31/2017] [Indexed: 05/27/2023]
Abstract
Expansin proteins, which loosen plant cell walls, play critical roles in normal plant growth and development. The horizontal acquisition of functional plant-like expansin genes in numerous xylem-colonizing phytopathogenic bacteria suggests that bacterial expansins may also contribute to virulence. To investigate the role of bacterial expansins in plant diseases, we mutated the non-chimeric expansin genes (CmEXLX2 and RsEXLX) of two xylem-inhabiting bacterial pathogens, the Actinobacterium Clavibacter michiganensis ssp. michiganensis (Cmm) and the β-proteobacterium Ralstonia solanacearum (Rs), respectively. The Cmm ΔCmEXLX2 mutant caused increased symptom development on tomato, which was characterized by more rapid wilting, greater vascular necrosis and abundant atypical lesions on distant petioles. This increased disease severity correlated with larger in planta populations of the ΔCmEXLX2 mutant, even though the strains grew as well as the wild-type in vitro. Similarly, when inoculated onto tomato fruit, ΔCmEXLX2 caused significantly larger lesions with larger necrotic centres. In contrast, the Rs ΔRsEXLX mutant showed reduced virulence on tomato following root inoculation, but not following direct petiole inoculation, suggesting that the RsEXLX expansin contributes to early virulence at the root infection stage. Consistent with this finding, ΔRsEXLX attached to tomato seedling roots better than the wild-type Rs, which may prevent mutants from invading the plant's vasculature. These contrasting results demonstrate the diverse roles of non-chimeric bacterial expansins and highlight their importance in plant-bacterial interactions.
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Affiliation(s)
- Matthew A. Tancos
- Plant Pathology and Plant‐Microbe Biology Section, School of Integrative Plant SciencesCornell UniversityGenevaNY 14456USA
- Present address:
Foreign Disease‐Weed Science Research Unit, USDA‐ARSFort DetrickMD 21702USA
| | | | - F. Christopher Peritore‐Galve
- Plant Pathology and Plant‐Microbe Biology Section, School of Integrative Plant SciencesCornell UniversityGenevaNY 14456USA
| | - Tuan M. Tran
- Department of Plant PathologyUniversity of Wisconsin‐MadisonMadisonWI 53706USA
- Present address:
School of Biological SciencesNanyang Technological University639798Singapore
| | - Caitilyn Allen
- Department of Plant PathologyUniversity of Wisconsin‐MadisonMadisonWI 53706USA
| | - Christine D. Smart
- Plant Pathology and Plant‐Microbe Biology Section, School of Integrative Plant SciencesCornell UniversityGenevaNY 14456USA
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63
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Kobayashi H, Fukuoka A. Development of Solid Catalyst–Solid Substrate Reactions for Efficient Utilization of Biomass. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20170263] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hirokazu Kobayashi
- Institute for Catalysis, Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021
| | - Atsushi Fukuoka
- Institute for Catalysis, Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021
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64
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Santiago TR, Pereira VM, de Souza WR, Steindorff AS, Cunha BADB, Gaspar M, Fávaro LCL, Formighieri EF, Kobayashi AK, C. Molinari HB. Genome-wide identification, characterization and expression profile analysis of expansins gene family in sugarcane (Saccharum spp.). PLoS One 2018; 13:e0191081. [PMID: 29324804 PMCID: PMC5764346 DOI: 10.1371/journal.pone.0191081] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/26/2017] [Indexed: 01/03/2023] Open
Abstract
Expansins refer to a family of closely related non-enzymatic proteins found in the plant cell wall that are involved in the cell wall loosening. In addition, expansins appear to be involved in different physiological and environmental responses in plants such as leaf and stem initiation and growth, stomata opening and closing, reproduction, ripening and stress tolerance. Sugarcane (Saccharum spp.) is one of the main crops grown worldwide. Lignocellulosic biomass from sugarcane is one of the most promising raw materials for the ethanol industry. However, the efficient use of lignocellulosic biomass requires the optimization of several steps, including the access of some enzymes to the hemicellulosic matrix. The addition of expansins in an enzymatic cocktail or their genetic manipulation could drastically improve the saccharification process of feedstock biomass by weakening the hydrogen bonds between polysaccharides present in plant cell walls. In this study, the expansin gene family in sugarcane was identified and characterized by in silico analysis. Ninety two putative expansins in sugarcane (SacEXPs) were categorized in three subfamilies after phylogenetic analysis. The expression profile of some expansin genes in leaves of sugarcane in different developmental stages was also investigated. This study intended to provide suitable expansin targets for genetic manipulation of sugarcane aiming at biomass and yield improvement.
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Affiliation(s)
- Thaís R. Santiago
- Embrapa Agroenergia. Parque Estação Biológica, Av. W3 Norte (final), Asa Norte, Brasília, DF, Brazil
| | - Valquiria M. Pereira
- Embrapa Agroenergia. Parque Estação Biológica, Av. W3 Norte (final), Asa Norte, Brasília, DF, Brazil
| | - Wagner R. de Souza
- Embrapa Agroenergia. Parque Estação Biológica, Av. W3 Norte (final), Asa Norte, Brasília, DF, Brazil
| | - Andrei S. Steindorff
- Embrapa Agroenergia. Parque Estação Biológica, Av. W3 Norte (final), Asa Norte, Brasília, DF, Brazil
| | - Bárbara A. D. B. Cunha
- Embrapa Agroenergia. Parque Estação Biológica, Av. W3 Norte (final), Asa Norte, Brasília, DF, Brazil
| | - Marília Gaspar
- Instituto de Botânica, Núcleo de Pesquisa em Fisiologia e Bioquímica, São Paulo, SP, Brazil
| | - Léia C. L. Fávaro
- Embrapa Agroenergia. Parque Estação Biológica, Av. W3 Norte (final), Asa Norte, Brasília, DF, Brazil
| | - Eduardo F. Formighieri
- Embrapa Agroenergia. Parque Estação Biológica, Av. W3 Norte (final), Asa Norte, Brasília, DF, Brazil
| | - Adilson K. Kobayashi
- Embrapa Agroenergia. Parque Estação Biológica, Av. W3 Norte (final), Asa Norte, Brasília, DF, Brazil
| | - Hugo B. C. Molinari
- Embrapa Agroenergia. Parque Estação Biológica, Av. W3 Norte (final), Asa Norte, Brasília, DF, Brazil
- * E-mail:
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65
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Orłowski A, Artzi L, Cazade PA, Gunnoo M, Bayer EA, Thompson D. On the distinct binding modes of expansin and carbohydrate-binding module proteins on crystalline and nanofibrous cellulose: implications for cellulose degradation by designer cellulosomes. Phys Chem Chem Phys 2018. [DOI: 10.1039/c7cp07764e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Transformation of cellulose into monosaccharides can be achieved by hydrolysis of the cellulose chains, carried out by a special group of enzymes known as cellulases.
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Affiliation(s)
- Adam Orłowski
- Department of Physics
- Bernal Institute
- University of Limerick
- Ireland
| | - Lior Artzi
- Department of Biomolecular Sciences
- The Weizmann Institute of Science
- Rehovot
- Israel
| | | | | | - Edward A. Bayer
- Department of Biomolecular Sciences
- The Weizmann Institute of Science
- Rehovot
- Israel
| | - Damien Thompson
- Department of Physics
- Bernal Institute
- University of Limerick
- Ireland
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66
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Zheng Y, Wang X, Chen Y, Wagner E, Cosgrove DJ. Xyloglucan in the primary cell wall: assessment by FESEM, selective enzyme digestions and nanogold affinity tags. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:211-226. [PMID: 29160933 DOI: 10.1111/tpj.13778] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/02/2017] [Accepted: 11/06/2017] [Indexed: 05/02/2023]
Abstract
Xyloglucan has been hypothesized to bind extensively to cellulose microfibril surfaces and to tether microfibrils into a load-bearing network, thereby playing a central role in wall mechanics and growth, but this view is challenged by newer results. Here we combined high-resolution imaging by field emission scanning electron microscopy (FESEM) with nanogold affinity tags and selective endoglucanase treatments to assess the spatial location and conformation of xyloglucan in onion cell walls. FESEM imaging of xyloglucanase-digested cell walls revealed an altered microfibril organization but did not yield clear evidence of xyloglucan conformations. Backscattered electron detection provided excellent detection of nanogold affinity tags in the context of wall fibrillar organization. Labelling with xyloglucan-specific CBM76 conjugated with nanogold showed that xyloglucans were associated with fibril surfaces in both extended and coiled conformations, but tethered configurations were not observed. Labelling with nanogold-conjugated CBM3, which binds the hydrophobic surface of crystalline cellulose, was infrequent until the wall was predigested with xyloglucanase, whereupon microfibril labelling was extensive. When tamarind xyloglucan was allowed to bind to xyloglucan-depleted onion walls, CBM76 labelling gave positive evidence for xyloglucans in both extended and coiled conformations, yet xyloglucan chains were not directly visible by FESEM. These results indicate that an appreciable, but still small, surface of cellulose microfibrils in the onion wall is tightly bound with extended xyloglucan chains and that some of the xyloglucan has a coiled conformation.
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Affiliation(s)
- Yunzhen Zheng
- Center for Lignocellulose Structure and Formation, Penn State University, University Park, PA, 16802, USA
- Department of Biology, Penn State University, University Park, PA, 16802, USA
| | - Xuan Wang
- Center for Lignocellulose Structure and Formation, Penn State University, University Park, PA, 16802, USA
- Department of Biology, Penn State University, University Park, PA, 16802, USA
| | - Yuning Chen
- Department of Biology, Penn State University, University Park, PA, 16802, USA
| | - Edward Wagner
- Department of Biology, Penn State University, University Park, PA, 16802, USA
| | - Daniel J Cosgrove
- Center for Lignocellulose Structure and Formation, Penn State University, University Park, PA, 16802, USA
- Department of Biology, Penn State University, University Park, PA, 16802, USA
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67
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Cosgrove DJ. Diffuse Growth of Plant Cell Walls. PLANT PHYSIOLOGY 2018; 176:16-27. [PMID: 29138349 PMCID: PMC5761826 DOI: 10.1104/pp.17.01541] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/13/2017] [Indexed: 05/04/2023]
Abstract
Structural and functional roles of cellulose, xyloglucan, and pectins in cell wall enlargement are reappraised with insights from mechanics, atomic force microscopy, and other methods.
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Affiliation(s)
- Daniel J Cosgrove
- Department of Biology, Penn State University, University Park, Pennsylvania 16802
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68
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Affiliation(s)
- Daniel J. Cosgrove
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
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69
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Impact of Module-X2 and Carbohydrate Binding Module-3 on the catalytic activity of associated glycoside hydrolases towards plant biomass. Sci Rep 2017. [PMID: 28623337 PMCID: PMC5473887 DOI: 10.1038/s41598-017-03927-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Cellulolytic enzymes capable of hydrolyzing plant biomass are secreted by microbial cells specifically in response to the carbon substrate present in the environment. These enzymes consist of a catalytic domain, generally appended to one or more non-catalytic Carbohydrate Binding Module (CBM), which enhances their activity towards recalcitrant biomass. In the present study, the genome of a cellulolytic microbe Paenibacillus polymyxa A18 was annotated for the presence of CBMs and analyzed their expression in response to the plant biomass and model polysaccharides Avicel, CMC and xylan using quantitative PCR. A gene that encodes X2-CBM3 was found to be maximally induced in response to the biomass and crystalline substrate Avicel. Association of X2-CBM3 with xyloglucanase and endoglucanase led to up to 4.6-fold increase in activity towards insoluble substrates. In the substrate binding study, module X2 showed a higher affinity towards biomass and phosphoric acid swollen cellulose, whereas CBM3 showed a higher affinity towards Avicel. Further structural modeling of X2 also indicated its potential role in substrate binding. Our findings highlighted the role of module X2 along with CBM3 in assisting the enzyme catalysis of agricultural residue and paved the way to engineer glycoside hydrolases for superior activity.
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70
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Armenta S, Moreno-Mendieta S, Sánchez-Cuapio Z, Sánchez S, Rodríguez-Sanoja R. Advances in molecular engineering of carbohydrate-binding modules. Proteins 2017; 85:1602-1617. [PMID: 28547780 DOI: 10.1002/prot.25327] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/04/2017] [Accepted: 05/20/2017] [Indexed: 11/06/2022]
Abstract
Carbohydrate-binding modules (CBMs) are non-catalytic domains that are generally appended to carbohydrate-active enzymes. CBMs have a broadly conserved structure that allows recognition of a notable variety of carbohydrates, in both their soluble and insoluble forms, as well as in their alpha and beta conformations and with different types of bonds or substitutions. This versatility suggests a high functional plasticity that is not yet clearly understood, in spite of the important number of studies relating protein structure and function. Several studies have explored the flexibility of these systems by changing or improving their specificity toward substrates of interest. In this review, we examine the molecular strategies used to identify CBMs with novel or improved characteristics. The impact of the spatial arrangement of the functional amino acids of CBMs is discussed in terms of unexpected new functions that are not related to the original biological roles of the enzymes. Proteins 2017; 85:1602-1617. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Silvia Armenta
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Silvia Moreno-Mendieta
- CONACYT, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Zaira Sánchez-Cuapio
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
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71
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Continually emerging mechanistic complexity of the multi-enzyme cellulosome complex. Curr Opin Struct Biol 2017; 44:151-160. [DOI: 10.1016/j.sbi.2017.03.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/16/2017] [Accepted: 03/17/2017] [Indexed: 12/20/2022]
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72
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A single amino acid mutation affects elicitor and expansins-like activities of cerato-platanin, a non-catalytic fungal protein. PLoS One 2017; 12:e0178337. [PMID: 28542638 PMCID: PMC5444802 DOI: 10.1371/journal.pone.0178337] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 05/11/2017] [Indexed: 11/19/2022] Open
Abstract
Cerato-platanin (CP) is a non-catalytic, cysteine-rich protein, the first member of the cerato-platanin family. It is a single-domain protein with a double Ψ/β barrel domain resembling the D1 domain of plant and bacterial expansins. Similarly to expansins, CP shows a cell wall-loosening activity on cellulose and can be defined as an expanisin-like protein, in spite of the missing D2 domain, normally present in plant expansins. The weakening activity shown on cellulose may facilitate the CP-host interaction, corroborating the role of CP in eliciting plant defence response. Indeed, CP is an elicitor of primary defences acting as a Pathogen-Associated Molecular Patterns (PAMP). So far, structure-function relationship study has been mainly performed on the bacterial BsEXLX1 expansin, probably due to difficulties in expressing plant expansins in heterologous systems. Here, we report a subcloning and purification method of CP in the engineered E. coli SHuffle cells, which proved to be suitable to obtain the properly folded and biologically active protein. The method also enabled the production of the mutant D77A, rationally designed to be inactive. The wild-type and the mutated CP were characterized for cellulose weakening activity and for PAMP activity (i.e. induction of Reactive Oxygen Species synthesis and phytoalexins production). Our analysis reveals that the carboxyl group of D77 is crucial for expansin-like and PAMP activities, thus permitting to establish a correlation between the ability to weaken cellulose and the capacity to induce defence responses in plants. Our results enable the structural and functional characterization of a mono-domain eukaryotic expansin and identify the essential role of a specific aspartic residue in cellulose weakening.
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73
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Pires VMR, Pereira PMM, Brás JLA, Correia M, Cardoso V, Bule P, Alves VD, Najmudin S, Venditto I, Ferreira LMA, Romão MJ, Carvalho AL, Fontes CMGA, Prazeres DM. Stability and Ligand Promiscuity of Type A Carbohydrate-binding Modules Are Illustrated by the Structure of Spirochaeta thermophila StCBM64C. J Biol Chem 2017; 292:4847-4860. [PMID: 28179427 DOI: 10.1074/jbc.m116.767541] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/07/2017] [Indexed: 11/06/2022] Open
Abstract
Deconstruction of cellulose, the most abundant plant cell wall polysaccharide, requires the cooperative activity of a large repertoire of microbial enzymes. Modular cellulases contain non-catalytic type A carbohydrate-binding modules (CBMs) that specifically bind to the crystalline regions of cellulose, thus promoting enzyme efficacy through proximity and targeting effects. Although type A CBMs play a critical role in cellulose recycling, their mechanism of action remains poorly understood. Here we produced a library of recombinant CBMs representative of the known diversity of type A modules. The binding properties of 40 CBMs, in fusion with an N-terminal GFP domain, revealed that type A CBMs possess the ability to recognize different crystalline forms of cellulose and chitin over a wide range of temperatures, pH levels, and ionic strengths. A Spirochaeta thermophila CBM64, in particular, displayed plasticity in its capacity to bind both crystalline and soluble carbohydrates under a wide range of extreme conditions. The structure of S. thermophila StCBM64C revealed an untwisted, flat, carbohydrate-binding interface comprising the side chains of four tryptophan residues in a co-planar linear arrangement. Significantly, two highly conserved asparagine side chains, each one located between two tryptophan residues, are critical to insoluble and soluble glucan recognition but not to bind xyloglucan. Thus, CBM64 compact structure and its extended and versatile ligand interacting platform illustrate how type A CBMs target their appended plant cell wall-degrading enzymes to a diversity of recalcitrant carbohydrates under a wide range of environmental conditions.
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Affiliation(s)
- Virgínia M R Pires
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal
| | - Pedro M M Pereira
- the Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Joana L A Brás
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal.,NZYTech Genes Enzymes, 1649-038 Lisboa, Portugal, and
| | - Márcia Correia
- the UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Vânia Cardoso
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal.,NZYTech Genes Enzymes, 1649-038 Lisboa, Portugal, and
| | - Pedro Bule
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal
| | - Victor D Alves
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal
| | - Shabir Najmudin
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal
| | - Immacolata Venditto
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal
| | - Luís M A Ferreira
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal.,NZYTech Genes Enzymes, 1649-038 Lisboa, Portugal, and
| | - Maria João Romão
- the UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Luísa Carvalho
- the UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Carlos M G A Fontes
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal, .,NZYTech Genes Enzymes, 1649-038 Lisboa, Portugal, and
| | - Duarte Miguel Prazeres
- the Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal,
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74
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Catalytic Conversion of Structural Carbohydrates and Lignin to Chemicals. ADVANCES IN CATALYSIS 2017. [DOI: 10.1016/bs.acat.2017.09.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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75
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Wang T, Chen Y, Tabuchi A, Cosgrove DJ, Hong M. The Target of β-Expansin EXPB1 in Maize Cell Walls from Binding and Solid-State NMR Studies. PLANT PHYSIOLOGY 2016; 172:2107-2119. [PMID: 27729469 PMCID: PMC5129719 DOI: 10.1104/pp.16.01311] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/07/2016] [Indexed: 05/18/2023]
Abstract
The wall-loosening actions of β-expansins are known primarily from studies of EXPB1 extracted from maize (Zea mays) pollen. EXPB1 selectively loosens cell walls (CWs) of grasses, but its specific binding target is unknown. We characterized EXPB1 binding to sequentially extracted maize CWs, finding that the protein primarily binds glucuronoarabinoxylan (GAX), the major matrix polysaccharide in grass CWs. This binding is strongly reduced by salts, indicating that it is predominantly electrostatic in nature. For direct molecular evidence of EXPB1 binding, we conducted solid-state nuclear magnetic resonance experiments using paramagnetic relaxation enhancement (PRE), which is sensitive to distances between unpaired electrons and nuclei. By mixing 13C-enriched maize CWs with EXPB1 functionalized with a Mn2+ tag, we measured Mn2+-induced PRE Strong 1H and 13C PREs were observed for the carboxyls of GAX, followed by more moderate PREs for carboxyl groups in homogalacturonan and rhamnogalacturonan-I, indicating that EXPB1 preferentially binds GAX In contrast, no PRE was observed for cellulose, indicating very weak interaction of EXPB1 with cellulose. Dynamics experiments show that EXPB1 changes GAX mobility in a complex manner: the rigid fraction of GAX became more rigid upon EXPB1 binding while the dynamic fraction became more mobile. Combining these data with previous results, we propose that EXPB1 loosens grass CWs by disrupting noncovalent junctions between highly substituted GAX and GAX of low substitution, which binds cellulose. This study provides molecular evidence of β-expansin's target in grass CWs and demonstrates a new strategy for investigating ligand binding for proteins that are difficult to express heterologously.
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Affiliation(s)
- Tuo Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| | - Yuning Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| | - Akira Tabuchi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| | - Daniel J Cosgrove
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
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76
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Ding A, Marowa P, Kong Y. Genome-wide identification of the expansin gene family in tobacco (Nicotiana tabacum). Mol Genet Genomics 2016; 291:1891-907. [PMID: 27329217 DOI: 10.1007/s00438-016-1226-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/08/2016] [Indexed: 11/24/2022]
Abstract
Expansins are pH-dependent cell wall loosening proteins which form a large family in plants. They have been shown to be involved in various developmental processes and been implicated in enabling plants' ability to absorb nutrients from the soil as well as conferring biotic and abiotic stress resistances. It is therefore clear that they can be potential targets in genetic engineering for crop improvement. Tobacco (Nicotiana tabacum) is a major crop species as well as a model organism. Considering that only a few tobacco expansins have been studied, a genome-wide analysis of the tobacco expansin gene family is necessary. In this study, we identified 52 expansins in tobacco, which were classified into four subfamilies: 36 NtEXPAs, 6 NtEXPBs, 3 NtEXLAs and 7 NtEXLBs. Compared to other species, the NtEXLB subfamily size was relatively larger. Phylogenetic analysis showed that the 52 tobacco expansins were divided into 13 subgroups. Gene structure analysis revealed that genes within subfamilies/subgroups exhibited similar characteristics such as gene structure and protein motif arrangement. Whole-genome duplication and tandem duplication events may have played important roles in the expanding of tobacco expansins. Cis-Acting element analysis revealed that each expansin gene was regulated or several expansin genes were co-regulated by both internal and environmental factors. 35 of these genes were identified as being expressed according to a microarray analysis. In contrast to most NtEXPAs which had higher expression levels in young organs, NtEXLAs and NtEXLBs were preferentially expressed in mature or senescent tissues, suggesting that they might play different roles in different organs or at different developmental stages. As the first step towards genome-wide analysis of the tobacco expansin gene family, our work provides solid background information related to structure, evolution and expression as well as regulatory cis-acting elements of the tobacco expansins. This information will provide a strong foundation for cloning and functional exploration of expansin genes in tobacco.
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Affiliation(s)
- Anming Ding
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, Shandong, People's Republic of China
| | - Prince Marowa
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, Shandong, People's Republic of China
| | - Yingzhen Kong
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, Shandong, People's Republic of China.
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77
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Wang Q, Chen L, Lin H, Yu D, Shen Q, Wan L, Zhao Y. The binding, synergistic and structural characteristics of BsEXLX1 for loosening the main components of lignocellulose: Lignin, xylan, and cellulose. Enzyme Microb Technol 2016; 92:67-75. [DOI: 10.1016/j.enzmictec.2016.06.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 06/27/2016] [Accepted: 06/27/2016] [Indexed: 01/03/2023]
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78
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Campos BM, Liberato MV, Alvarez TM, Zanphorlin LM, Ematsu GC, Barud H, Polikarpov I, Ruller R, Gilbert HJ, Zeri ACDM, Squina FM. A Novel Carbohydrate-binding Module from Sugar Cane Soil Metagenome Featuring Unique Structural and Carbohydrate Affinity Properties. J Biol Chem 2016; 291:23734-23743. [PMID: 27621314 DOI: 10.1074/jbc.m116.744383] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Indexed: 11/06/2022] Open
Abstract
Carbohydrate-binding modules (CBMs) are appended to glycoside hydrolases and can contribute to the degradation of complex recalcitrant substrates such as the plant cell wall. For application in bioethanol production, novel enzymes with high catalytic activity against recalcitrant lignocellulosic material are being explored and developed. In this work, we report the functional and structural study of CBM_E1, which was discovered through a metagenomics approach and is the founding member of a novel CBM family, CBM81. CBM_E1, which is linked to an endoglucanase, displayed affinity for mixed linked β1,3-β1,4-glucans, xyloglucan, Avicel, and cellooligosaccharides. The crystal structure of CBM_E1 in complex with cellopentaose displayed a canonical β-sandwich fold comprising two β-sheets. The planar ligand binding site, observed in a parallel orientation with the β-strands, is a typical feature of type A CBMs, although the expected affinity for bacterial crystalline cellulose was not detected. Conversely, the binding to soluble glucans was enthalpically driven, which is typical of type B modules. These unique properties of CBM_E1 are at the interface between type A and type B CBMs.
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Affiliation(s)
| | | | | | | | | | - Hernane Barud
- the Centro Universitário de Araraquara-UNIARA, BioPolMat, CEP 14801-340, Araraquara-SP, Brazil
| | - Igor Polikarpov
- the Instituto de Física de São Carlos, Universidade de São Paulo, CEP 13566-590, São Carlos, São Paulo, Brazil
| | - Roberto Ruller
- the Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), and
| | - Harry J Gilbert
- the Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle-upon-Tyne NE 4HH, United Kingdom, and
| | - Ana Carolina de Mattos Zeri
- the Laboratório Nacional de Luz Sincrotron (LNLS), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, São Paulo, Brazil
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79
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Eibinger M, Sigl K, Sattelkow J, Ganner T, Ramoni J, Seiboth B, Plank H, Nidetzky B. Functional characterization of the native swollenin from Trichoderma reesei: study of its possible role as C1 factor of enzymatic lignocellulose conversion. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:178. [PMID: 27570542 PMCID: PMC5000517 DOI: 10.1186/s13068-016-0590-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/15/2016] [Indexed: 05/28/2023]
Abstract
BACKGROUND Through binding to cellulose, expansin-like proteins are thought to loosen the structural order of crystalline surface material, thus making it more accessible for degradation by hydrolytic enzymes. Swollenin SWO1 is the major expansin-like protein from the fungus Trichoderma reesei. Here, we have performed a detailed characterization of a recombinant native form of SWO1 with respect to its possible auxiliary role in the enzymatic saccharification of lignocellulosic substrates. RESULTS The swo1 gene was overexpressed in T. reesei QM9414 Δxyr1 mutant, featuring downregulated cellulase production, and the protein was purified from culture supernatant. SWO1 was N-glycosylated and its circular dichroism spectrum suggested a folded protein. Adsorption isotherms (25 °C, pH 5.0, 1.0 mg substrate/mL) revealed SWO1 to be 120- and 20-fold more specific for binding to birchwood xylan and kraft lignin, respectively, than for binding to Avicel PH-101. The SWO1 binding capacity on lignin (25 µmol/g) exceeded 12-fold that on Avicel PH-101 (2.1 µmol/g). On xylan, not only the binding capacity (22 µmol/g) but also the affinity of SWO1 (K d = 0.08 µM) was enhanced compared to Avicel PH-101 (K d = 0.89 µM). SWO1 caused rapid release of a tiny amount of reducing sugars (<1 % of total) from different substrates (Avicel PH-101, nanocrystalline cellulose, steam-pretreated wheat straw, barley β-glucan, cellotetraose) but did not promote continued saccharification. Atomic force microscopy revealed that amorphous cellulose films were not affected by SWO1. Also with AFM, binding of SWO1 to cellulose nanocrystallites was demonstrated at the single-molecule level, but adsorption did not affect this cellulose. SWO1 exhibited no synergy with T. reesei cellulases in the hydrolysis of the different celluloses. However, SWO1 boosted slightly (1.5-fold) the reducing sugar release from a native grass substrate. CONCLUSIONS SWO1 is a strongly glycosylated protein, which has implications for producing it in heterologous hosts. Although SWO1 binds to crystalline cellulose, its adsorption to xylan is much stronger. SWO1 is not an auxiliary factor of the enzymatic degradation of a variety of cellulosic substrates. Effect of SWO1 on sugar release from intact plant cell walls might be exploitable with certain (e.g., mildly pretreated) lignocellulosic feedstocks.
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Affiliation(s)
- Manuel Eibinger
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010 Graz, Austria
| | - Karin Sigl
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010 Graz, Austria
| | - Jürgen Sattelkow
- Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Thomas Ganner
- Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Jonas Ramoni
- Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstrasse 1A/166, 1060 Vienna, Austria
| | - Bernhard Seiboth
- Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstrasse 1A/166, 1060 Vienna, Austria
| | - Harald Plank
- Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
- Graz Centre for Electron Microscopy, Steyrergasse 17, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010 Graz, Austria
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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80
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Martinez-Anaya C. Understanding the structure and function of bacterial expansins: a prerequisite towards practical applications for the bioenergy and agricultural industries. Microb Biotechnol 2016; 9:727-736. [PMID: 27365165 PMCID: PMC5072189 DOI: 10.1111/1751-7915.12377] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/06/2016] [Accepted: 06/09/2016] [Indexed: 01/03/2023] Open
Abstract
Since the publication of a landmark article on the structure of EXLX1 from Bacillus subtilis in 2011, our knowledge of bacterial expansins has steadily increased and our view and understanding of these enigmatic proteins has advanced with relation to their structure, phylogenetic relationships and substrate interaction, although the molecular basis for their mechanism of action remains to be determined. Lignocellulosic material represents a source of fermentable sugars for the production of biofuels, and cell‐wall degrading activities are essential to efficiently release such sugars from their polymeric structures. Because expansins from fungi and bacteria seem to be required to properly colonize or cause disease to plant tissues, and because they share some characteristics with their plant counterparts for loosening the cell wall they have been seen as a promising tool to overcome the recalcitrance of these materials. However, microbial expansins activity is at best, very low compared with plant expansins activity. This revision analyses recent work on bacterial expansins structure, function and biological role, emphasizing our need to focus on their mechanism of action as a means to design better strategies for their use, in both in the energy and agricultural industries.
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Affiliation(s)
- Claudia Martinez-Anaya
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Chamilpa, Cuernavaca, 62210, Morelos, México.
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81
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Schiefner A, Angelov A, Liebl W, Skerra A. Structural basis for cellulose binding by the type A carbohydrate-binding module 64 of Spirochaeta thermophila. Proteins 2016; 84:855-8. [PMID: 26868291 DOI: 10.1002/prot.25010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 01/04/2016] [Accepted: 01/25/2016] [Indexed: 11/06/2022]
Abstract
Spirochaeta thermophila secretes seven glycoside hydrolases for plant biomass degradation that carry a carbohydrate-binding module 64 (CBM64) appended at the C-terminus. CBM64 adsorbs to various β1-4-linked pyranose substrates and shows high affinity for cellulose. We present the first crystal structure of a CBM64 at 1.2 Å resolution, which reveals a jelly-roll-like fold corresponding to a surface-binding type A CBM. Modeling of its interaction with cellulose indicates that CBM64 achieves association with the hydrophobic face of β-linked pyranose chains via a unique coplanar arrangement of four exposed tryptophan side chains. Proteins 2016; 84:855-858. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- André Schiefner
- Munich Center for Integrated Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising (Weihenstephan), Germany
| | - Angel Angelov
- Lehrstuhl Für Mikrobiologie, Technische Universität München, 85354 Freising (Weihenstephan), Germany
| | - Wolfgang Liebl
- Lehrstuhl Für Mikrobiologie, Technische Universität München, 85354 Freising (Weihenstephan), Germany
| | - Arne Skerra
- Munich Center for Integrated Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising (Weihenstephan), Germany
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82
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Li Y, Tu L, Pettolino FA, Ji S, Hao J, Yuan D, Deng F, Tan J, Hu H, Wang Q, Llewellyn DJ, Zhang X. GbEXPATR, a species-specific expansin, enhances cotton fibre elongation through cell wall restructuring. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:951-63. [PMID: 26269378 DOI: 10.1111/pbi.12450] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 05/08/2015] [Accepted: 05/26/2015] [Indexed: 05/18/2023]
Abstract
Cotton provides us the most important natural fibre. High fibre quality is the major goal of cotton breeding, and introducing genes conferring longer, finer and stronger fibre from Gossypium barbadense to Gossypium hirsutum is an important breeding strategy. We previously analysed the G. barbadense fibre development mechanism by gene expression profiling and found two homoeologous fibre-specific α-expansins from G. barbadense, GbEXPA2 and GbEXPATR. GbEXPA2 (from the DT genome) is a classical α-expansin, while its homoeolog, GbEXPATR (AT genome), encodes a truncated protein lacking the normal C-terminal polysaccharide-binding domain of other α-expansins and is specifically expressed in G. barbadense. Silencing EXPA in G. hirsutum induced shorter fibres with thicker cell walls. GbEXPA2 overexpression in G. hirsutum had no effect on mature fibre length, but produced fibres with a slightly thicker wall and increased crystalline cellulose content. Interestingly, GbEXPATR overexpression resulted in longer, finer and stronger fibres coupled with significantly thinner cell walls. The longer and thinner fibre was associated with lower expression of a number of secondary wall-associated genes, especially chitinase-like genes, and walls with lower cellulose levels but higher noncellulosic polysaccharides which advocated that a delay in the transition to secondary wall synthesis might be responsible for better fibre. In conclusion, we propose that α-expansins play a critical role in fibre development by loosening the cell wall; furthermore, a truncated form, GbEXPATR, has a more dramatic effect through reorganizing secondary wall synthesis and metabolism and should be a candidate gene for developing G. hirsutum cultivars with superior fibre quality.
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Affiliation(s)
- Yang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Filomena A Pettolino
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Plant Industry, Canberra, ACT, Australia
| | - Shengmei Ji
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Juan Hao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Fenglin Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jiafu Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Haiyan Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Danny J Llewellyn
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Plant Industry, Canberra, ACT, Australia
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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83
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Abstract
The growing cell wall in plants has conflicting requirements to be strong enough to withstand the high tensile forces generated by cell turgor pressure while selectively yielding to those forces to induce wall stress relaxation, leading to water uptake and polymer movements underlying cell wall expansion. In this article, I review emerging concepts of plant primary cell wall structure, the nature of wall extensibility and the action of expansins, family-9 and -12 endoglucanases, family-16 xyloglucan endotransglycosylase/hydrolase (XTH), and pectin methylesterases, and offer a critical assessment of their wall-loosening activity.
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Affiliation(s)
- Daniel J Cosgrove
- Department of Biology, 208 Mueller Lab, Pennsylvania State University, University Park, PA, USA
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84
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Crouch LI, Labourel A, Walton PH, Davies GJ, Gilbert HJ. The Contribution of Non-catalytic Carbohydrate Binding Modules to the Activity of Lytic Polysaccharide Monooxygenases. J Biol Chem 2016; 291:7439-49. [PMID: 26801613 PMCID: PMC4817175 DOI: 10.1074/jbc.m115.702365] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Indexed: 01/23/2023] Open
Abstract
Lignocellulosic biomass is a sustainable industrial substrate. Copper-dependent lytic polysaccharide monooxygenases (LPMOs) contribute to the degradation of lignocellulose and increase the efficiency of biofuel production. LPMOs can contain non-catalytic carbohydrate binding modules (CBMs), but their role in the activity of these enzymes is poorly understood. Here we explored the importance of CBMs in LPMO function. The family 2a CBMs of two monooxygenases,CfLPMO10 andTbLPMO10 fromCellulomonas fimiandThermobispora bispora, respectively, were deleted and/or replaced with CBMs from other proteins. The data showed that the CBMs could potentiate and, surprisingly, inhibit LPMO activity, and that these effects were both enzyme-specific and substrate-specific. Removing the natural CBM or introducingCtCBM3a, from theClostridium thermocellumcellulosome scaffoldin CipA, almost abolished the catalytic activity of the LPMOs against the cellulosic substrates. The deleterious effect of CBM removal likely reflects the importance of prolonged presentation of the enzyme on the surface of the substrate for efficient catalytic activity, as only LPMOs appended to CBMs bound tightly to cellulose. The negative impact ofCtCBM3a is in sharp contrast with the capacity of this binding module to potentiate the activity of a range of glycoside hydrolases including cellulases. The deletion of the endogenous CBM fromCfLPMO10 or the introduction of a family 10 CBM fromCellvibrio japonicusLPMO10B intoTbLPMO10 influenced the quantity of non-oxidized products generated, demonstrating that CBMs can modulate the mode of action of LPMOs. This study demonstrates that engineered LPMO-CBM hybrids can display enhanced industrially relevant oxygenations.
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Affiliation(s)
- Lucy I Crouch
- From the Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Newcastle upon Tyne NE2 4HH and
| | - Aurore Labourel
- From the Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Newcastle upon Tyne NE2 4HH and
| | - Paul H Walton
- the York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Gideon J Davies
- the York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Harry J Gilbert
- From the Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Newcastle upon Tyne NE2 4HH and
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85
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Identification of a novel family of carbohydrate-binding modules with broad ligand specificity. Sci Rep 2016; 6:19392. [PMID: 26765840 PMCID: PMC4725902 DOI: 10.1038/srep19392] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 11/03/2015] [Indexed: 11/13/2022] Open
Abstract
Most enzymes that act on carbohydrates include non-catalytic carbohydrate-binding modules (CBMs) that recognize and target carbohydrates. CBMs bring their appended catalytic modules into close proximity with the target substrate and increase the hydrolytic rate of enzymes acting on insoluble substrates. We previously identified a novel CBM (CBMC5614-1) at the C-terminus of endoglucanase C5614-1 from an uncultured microorganism present in buffalo rumen. In the present study, that the functional region of CBMC5614-1 involved in ligand binding was localized to 134 amino acids. Two representative homologs of CBMC5614-1, sharing the same ligand binding profile, targeted a range of β-linked polysaccharides that adopt very different conformations. Targeted substrates included soluble and insoluble cellulose, β-1,3/1,4-mixed linked glucans, xylan, and mannan. Mutagenesis revealed that three conserved aromatic residues (Trp-380, Tyr-411, and Trp-423) play an important role in ligand recognition and targeting. These results suggest that CBMC5614-1 and its homologs form a novel CBM family (CBM72) with a broad ligand-binding specificity. CBM72 members can provide new insight into CBM-ligand interactions and may have potential in protein engineering and biocatalysis.
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86
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Khazanov N, Iline-Vul T, Noy E, Goobes G, Senderowitz H. Design of Compact Biomimetic Cellulose Binding Peptides as Carriers for Cellulose Catalytic Degradation. J Phys Chem B 2016; 120:309-19. [DOI: 10.1021/acs.jpcb.5b11050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Netaly Khazanov
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Taly Iline-Vul
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Efrat Noy
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Gil Goobes
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
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87
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Silveira RL, Skaf MS. Molecular dynamics of the Bacillus subtilis expansin EXLX1: interaction with substrates and structural basis of the lack of activity of mutants. Phys Chem Chem Phys 2016; 18:3510-21. [DOI: 10.1039/c5cp06674c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Expansins are disruptive proteins that loosen growing plant cell walls and can enhance the enzymatic hydrolysis of cellulose.
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Affiliation(s)
| | - Munir S. Skaf
- Institute of Chemistry
- University of Campinas
- Campinas
- Brazil
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88
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Kutschera U, Wang ZY. Growth-limiting proteins in maize coleoptiles and the auxin-brassinosteroid hypothesis of mesocotyl elongation. PROTOPLASMA 2016; 253:3-14. [PMID: 25772679 PMCID: PMC6609159 DOI: 10.1007/s00709-015-0787-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/27/2015] [Indexed: 05/08/2023]
Abstract
The shoot of grass coleoptiles consists of the mesocotyl, the node, and the coleoptile (with enclosed primary leaf). Since the 1930s, it is known that auxin (indole-3-acetic acid, IAA), produced in the tip of the coleoptile, is the central regulator of turgor-driven organ growth. Fifty years ago, it was discovered that antibiotics that suppress protein biosynthesis, such as cycloheximide, inhibit auxin (IAA)-induced cell elongation in excised sections of coleoptiles and stems. Based on such inhibitor studies, the concept of "growth-limiting proteins (GLPs)" emerged that was subsequently elaborated and modified. Here, we summarize the history of this idea with reference to IAA-mediated shoot elongation in maize (Zea mays) seedlings and recent studies on the molecular mechanism underlying auxin action in Arabidopsis thaliana. In addition, the analysis of light-induced inhibition of shoot elongation in intact corn seedlings is discussed. We propose a concept to account for the GLP-mediated epidermal wall-loosening process in coleoptile segments and present a more general model of growth regulation in intact maize seedlings. Quantitative proteomic and genomic studies led to a refinement of the classic "GLP concept" to explain phytohormone-mediated cell elongation at the molecular level (i.e., the recently proposed theory of a "central growth regulation network," CGRN). Novel data show that mesocotyl elongation not only depends on auxin but also on brassinosteroids (BRs). However, the biochemical key processes that regulate the IAA/BR-mediated loosening of the expansion-limiting epidermal wall(s) have not yet been elucidated.
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Affiliation(s)
- Ulrich Kutschera
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
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89
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Characterization and expression analysis of the expansin gene NnEXPA1 in lotus Nelumbo nucifera. Biologia (Bratisl) 2016. [DOI: 10.1515/biolog-2016-0015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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90
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Yennawar NH, Fecko JA, Showalter SA, Bevilacqua PC. A High-Throughput Biological Calorimetry Core: Steps to Startup, Run, and Maintain a Multiuser Facility. Methods Enzymol 2015; 567:435-60. [PMID: 26794364 PMCID: PMC6474912 DOI: 10.1016/bs.mie.2015.07.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Many labs have conventional calorimeters where denaturation and binding experiments are setup and run one at a time. While these systems are highly informative to biopolymer folding and ligand interaction, they require considerable manual intervention for cleaning and setup. As such, the throughput for such setups is limited typically to a few runs a day. With a large number of experimental parameters to explore including different buffers, macromolecule concentrations, temperatures, ligands, mutants, controls, replicates, and instrument tests, the need for high-throughput automated calorimeters is on the rise. Lower sample volume requirements and reduced user intervention time compared to the manual instruments have improved turnover of calorimetry experiments in a high-throughput format where 25 or more runs can be conducted per day. The cost and efforts to maintain high-throughput equipment typically demands that these instruments be housed in a multiuser core facility. We describe here the steps taken to successfully start and run an automated biological calorimetry facility at Pennsylvania State University. Scientists from various departments at Penn State including Chemistry, Biochemistry and Molecular Biology, Bioengineering, Biology, Food Science, and Chemical Engineering are benefiting from this core facility. Samples studied include proteins, nucleic acids, sugars, lipids, synthetic polymers, small molecules, natural products, and virus capsids. This facility has led to higher throughput of data, which has been leveraged into grant support, attracting new faculty hire and has led to some exciting publications.
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Affiliation(s)
- Neela H Yennawar
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Julia A Fecko
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Scott A Showalter
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA; Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Philip C Bevilacqua
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA; Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA.
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91
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Leskinen T, Salas C, Kelley SS, Argyropoulos DS. Wood Extractives Promote Cellulase Activity on Cellulosic Substrates. Biomacromolecules 2015; 16:3226-34. [DOI: 10.1021/acs.biomac.5b00889] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Timo Leskinen
- Departments of Chemistry & Forest Biomaterials, North Carolina State University, Raleigh, North Carolina 27695-8005, United States
| | - Carlos Salas
- Departments of Chemistry & Forest Biomaterials, North Carolina State University, Raleigh, North Carolina 27695-8005, United States
| | - Stephen S. Kelley
- Departments of Chemistry & Forest Biomaterials, North Carolina State University, Raleigh, North Carolina 27695-8005, United States
| | - Dimitris S. Argyropoulos
- Departments of Chemistry & Forest Biomaterials, North Carolina State University, Raleigh, North Carolina 27695-8005, United States
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92
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Hernandez-Gomez MC, Rydahl MG, Rogowski A, Morland C, Cartmell A, Crouch L, Labourel A, Fontes CMGA, Willats WGT, Gilbert HJ, Knox JP. Recognition of xyloglucan by the crystalline cellulose-binding site of a family 3a carbohydrate-binding module. FEBS Lett 2015; 589:2297-303. [PMID: 26193423 DOI: 10.1016/j.febslet.2015.07.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/01/2015] [Accepted: 07/07/2015] [Indexed: 11/29/2022]
Abstract
Type A non-catalytic carbohydrate-binding modules (CBMs), exemplified by CtCBM3acipA, are widely believed to specifically target crystalline cellulose through entropic forces. Here we have tested the hypothesis that type A CBMs can also bind to xyloglucan (XG), a soluble β-1,4-glucan containing α-1,6-xylose side chains. CtCBM3acipA bound to xyloglucan in cell walls and arrayed on solid surfaces. Xyloglucan and cellulose were shown to bind to the same planar surface on CBM3acipA. A range of type A CBMs from different families were shown to bind to xyloglucan in solution with ligand binding driven by enthalpic changes. The nature of CBM-polysaccharide interactions is discussed.
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Affiliation(s)
| | - Maja G Rydahl
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Artur Rogowski
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Carl Morland
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Alan Cartmell
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Lucy Crouch
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Aurore Labourel
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Carlos M G A Fontes
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - William G T Willats
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
| | - J Paul Knox
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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93
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Cosgrove DJ. Plant expansins: diversity and interactions with plant cell walls. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:162-72. [PMID: 26057089 PMCID: PMC4532548 DOI: 10.1016/j.pbi.2015.05.014] [Citation(s) in RCA: 274] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/11/2015] [Accepted: 05/15/2015] [Indexed: 05/18/2023]
Abstract
Expansins were discovered two decades ago as cell wall proteins that mediate acid-induced growth by catalyzing loosening of plant cell walls without lysis of wall polymers. In the interim our understanding of expansins has gotten more complex through bioinformatic analysis of expansin distribution and evolution, as well as through expression analysis, dissection of the upstream transcription factors regulating expression, and identification of additional classes of expansin by sequence and structural similarities. Molecular analyses of expansins from bacteria have identified residues essential for wall loosening activity and clarified the bifunctional nature of expansin binding to complex cell walls. Transgenic modulation of expansin expression modifies growth and stress physiology of plants, but not always in predictable or even understandable ways.
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Affiliation(s)
- Daniel J Cosgrove
- Department of Biology, Penn State University, University Park, PA 16802, USA.
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94
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Research advances in expansins and expansion-like proteins involved in lignocellulose degradation. Biotechnol Lett 2015; 37:1541-51. [DOI: 10.1007/s10529-015-1842-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 04/29/2015] [Indexed: 12/12/2022]
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95
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Georgelis N, Nikolaidis N, Cosgrove DJ. Bacterial expansins and related proteins from the world of microbes. Appl Microbiol Biotechnol 2015; 99:3807-23. [PMID: 25833181 PMCID: PMC4427351 DOI: 10.1007/s00253-015-6534-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/05/2015] [Accepted: 03/09/2015] [Indexed: 12/31/2022]
Abstract
The discovery of microbial expansins emerged from studies of the mechanism of plant cell growth and the molecular basis of plant cell wall extensibility. Expansins are wall-loosening proteins that are universal in the plant kingdom and are also found in a small set of phylogenetically diverse bacteria, fungi, and other organisms, most of which colonize plant surfaces. They loosen plant cell walls without detectable lytic activity. Bacterial expansins have attracted considerable attention recently for their potential use in cellulosic biomass conversion for biofuel production, as a means to disaggregate cellulosic structures by nonlytic means ("amorphogenesis"). Evolutionary analysis indicates that microbial expansins originated by multiple horizontal gene transfers from plants. Crystallographic analysis of BsEXLX1, the expansin from Bacillus subtilis, shows that microbial expansins consist of two tightly packed domains: the N-terminal domain D1 has a double-ψ β-barrel fold similar to glycosyl hydrolase family-45 enzymes but lacks catalytic residues usually required for hydrolysis; the C-terminal domain D2 has a unique β-sandwich fold with three co-linear aromatic residues that bind β-1,4-glucans by hydrophobic interactions. Genetic deletion of expansin in Bacillus and Clavibacter cripples their ability to colonize plant tissues. We assess reports that expansin addition enhances cellulose breakdown by cellulase and compare expansins with distantly related proteins named swollenin, cerato-platanin, and loosenin. We end in a speculative vein about the biological roles of microbial expansins and their potential applications. Advances in this field will be aided by a deeper understanding of how these proteins modify cellulosic structures.
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Affiliation(s)
| | - Nikolas Nikolaidis
- Department of Biological Science, California State University, Fullerton, CA 92831, USA
| | - Daniel J. Cosgrove
- Department of Biology, Penn State University, University Park, PA 16802, USA
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96
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Gaete-Eastman C, Morales-Quintana L, Herrera R, Moya-León MA. In-silico analysis of the structure and binding site features of an α-expansin protein from mountain papaya fruit (VpEXPA2), through molecular modeling, docking, and dynamics simulation studies. J Mol Model 2015; 21:115. [PMID: 25863690 DOI: 10.1007/s00894-015-2656-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/16/2015] [Indexed: 11/25/2022]
Abstract
Fruit softening is associated to cell wall modifications produced by a set of hydrolytic enzymes and proteins. Expansins are proteins with no catalytic activity, which have been associated with several processes during plant growth and development. A role for expansins has been proposed during softening of fruits, and many fruit-specific expansins have been identified in a variety of species. A 3D model for VpEXPA2, an α-expansin involved in softening of Vasconcellea pubescens fruit, was built for the first time by comparative modeling strategy. The model was validated and refined by molecular dynamics simulation. The VpEXPA2 model shows a cellulose binding domain with a β-sandwich structure, and a catalytic domain with a similar structure to the catalytic core of endoglucanase V (EGV) from Humicola insolens, formed by six β-strands with interconnected loops. VpEXPA2 protein contains essential structural moieties related to the catalytic mechanism of EGV, such as the conserved HFD motif. Nevertheless, changes in the catalytic environment are observed in the protein model, influencing its mode of action. The lack of catalytic activity of this expansin and its preference for cellulose are discussed in light of the structural information obtained from the VpEXPA2 protein model, regarding the distance between critical amino acid residues. Finally, the VpEXPA2 model improves our understanding on the mechanism of action of α-expansins on plant cell walls during softening of V. pubescens fruit.
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Affiliation(s)
- Carlos Gaete-Eastman
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Casilla 747, Talca, Chile,
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97
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Blumer-Schuette SE, Alahuhta M, Conway JM, Lee LL, Zurawski JV, Giannone RJ, Hettich RL, Lunin VV, Himmel ME, Kelly RM. Discrete and structurally unique proteins (tāpirins) mediate attachment of extremely thermophilic Caldicellulosiruptor species to cellulose. J Biol Chem 2015; 290:10645-56. [PMID: 25720489 DOI: 10.1074/jbc.m115.641480] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Indexed: 11/06/2022] Open
Abstract
A variety of catalytic and noncatalytic protein domains are deployed by select microorganisms to deconstruct lignocellulose. These extracellular proteins are used to attach to, modify, and hydrolyze the complex polysaccharides present in plant cell walls. Cellulolytic enzymes, often containing carbohydrate-binding modules, are key to this process; however, these enzymes are not solely responsible for attachment. Few mechanisms of attachment have been discovered among bacteria that do not form large polypeptide structures, called cellulosomes, to deconstruct biomass. In this study, bioinformatics and proteomics analyses identified unique, discrete, hypothetical proteins ("tāpirins," origin from Māori: to join), not directly associated with cellulases, that mediate attachment to cellulose by species in the noncellulosomal, extremely thermophilic bacterial genus Caldicellulosiruptor. Two tāpirin genes are located directly downstream of a type IV pilus operon in strongly cellulolytic members of the genus, whereas homologs are absent from the weakly cellulolytic Caldicellulosiruptor species. Based on their amino acid sequence, tāpirins are specific to these extreme thermophiles. Tāpirins are also unusual in that they share no detectable protein domain signatures with known polysaccharide-binding proteins. Adsorption isotherm and trans vivo analyses demonstrated the carbohydrate-binding module-like affinity of the tāpirins for cellulose. Crystallization of a cellulose-binding truncation from one tāpirin indicated that these proteins form a long β-helix core with a shielded hydrophobic face. Furthermore, they are structurally unique and define a new class of polysaccharide adhesins. Strongly cellulolytic Caldicellulosiruptor species employ tāpirins to complement substrate-binding proteins from the ATP-binding cassette transporters and multidomain extracellular and S-layer-associated glycoside hydrolases to process the carbohydrate content of lignocellulose.
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Affiliation(s)
- Sara E Blumer-Schuette
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905
| | - Markus Alahuhta
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - Jonathan M Conway
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905
| | - Laura L Lee
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905
| | - Jeffrey V Zurawski
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905
| | - Richard J Giannone
- the Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Robert L Hettich
- the Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Vladimir V Lunin
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - Michael E Himmel
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - Robert M Kelly
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905,
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98
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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99
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Park YB, Cosgrove DJ. Xyloglucan and its Interactions with Other Components of the Growing Cell Wall. ACTA ACUST UNITED AC 2015; 56:180-94. [DOI: 10.1093/pcp/pcu204] [Citation(s) in RCA: 250] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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100
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Nishijima H, Nozaki K, Mizuno M, Arai T, Amano Y. Extra tyrosine in the carbohydrate-binding module of Irpex lacteus Xyn10B enhances its cellulose-binding ability. Biosci Biotechnol Biochem 2015; 79:738-46. [PMID: 25560084 DOI: 10.1080/09168451.2014.996203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The xylanase (Xyn10B) that strongly adsorbs on microcrystalline cellulose was isolated from Driselase. The Xyn10B contains a Carbohydrate-binding module family 1 (CBM1) (IrpCBMXyn10B) at N-terminus. The canonical essential aromatic residues required for cellulose binding were conserved in IrpCBMXyn10B; however, its adsorption ability was markedly higher than that typically observed for the CBM1 of an endoglucanase from Trametes hirsuta (ThCBMEG1). An analysis of the CBM-GFP fusion proteins revealed that the binding capacity to cellulose (7.8 μmol/g) and distribution coefficient (2.0 L/μmol) of IrpCBMXyn10B-GFP were twofold higher than those of ThCBMEG1-GFP (3.4 μmol/g and 1.2 L/μmol, respectively), used as a reference structure. Besides the canonical aromatic residues (W24-Y50-Y51) of typical CBM1-containing proteins, IrpCBMXyn10B had an additional aromatic residue (Y52). The mutation of Y52 to Ser (IrpCBMY52S-GFP) reduced these adsorption parameters to 4.4 μmol/g and 1.5 L/μmol, which were similar to those of ThCBMEG1-GFP. These results indicate that Y52 plays a crucial role in strong cellulose binding.
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Affiliation(s)
- Hiroto Nishijima
- a Department of Bioscience & Textile Technology, Interdisciplinary Graduate School of Science and Technology , Shinshu University , Nagano , Japan
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