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Garg P, Manoj N. Structure of an iminosugar complex of a glycoside hydrolase family 5 lichenase provides insights into the active site. Biochimie 2023; 204:69-77. [PMID: 36084911 DOI: 10.1016/j.biochi.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 05/23/2022] [Accepted: 09/01/2022] [Indexed: 01/12/2023]
Abstract
TmCel5B is a lichenase belonging to glycoside hydrolase family 5 subfamily 36 (GH5_36). To gain insights into the active site of this subfamily which contains multifunctional endoglycanases, we determined the crystal structure of TmCel5B in complex with an iminosugar, 1-deoxynojiromycin (DNJ). DNJ is bound to the -1 subsite, making a network of non-covalent interactions with the acid/base residue Glu139, the nucleophile Glu259, and with other residues that are conserved across the GH5 family. The catalytic site displayed a Glu-Arg-Glu triad of the catalytic glutamates that is unique to the GH5_36 subfamily. Structural comparison of active sites of GH5_36 homologs revealed divergent residues and loop regions that are likely molecular determinants of homolog-specific properties. Furthermore, a comparative analysis of the binding modes of iminocyclitol complexes of GH5 homologs revealed the structural basis of their binding to GH5 glycosidases, in which the subsite binding location, the interactions of the ligand with specific conserved residues, and the electrostatic interactions of the catalytic glutamates with the ring nitrogen, are crucial.
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Affiliation(s)
- Puneet Garg
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
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2
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Ishibashi Y. Functions and applications of glycolipid-hydrolyzing microbial glycosidases. Biosci Biotechnol Biochem 2022; 86:974-984. [PMID: 35675217 DOI: 10.1093/bbb/zbac089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/29/2022] [Indexed: 11/13/2022]
Abstract
Glycolipids are important components of cell membranes in several organisms. The major glycolipids in mammals are glycosphingolipids (GSLs), which are composed of ceramides. In mammals, GSLs are degraded stepwise from the non-reducing end of the oligosaccharides via exo-type glycosidases. However, endoglycoceramidase (EGCase), an endo-type glycosidase found in actinomycetes, is a unique enzyme that directly acts on the glycosidic linkage between oligosaccharides and ceramides to generate intact oligosaccharides and ceramides. Three molecular species of EGCase, namely EGCase I, EGCase II, and endogalactosylceramidase, have been identified based on their substrate specificity. EGCrP1 and EGCrP2, which are homologs of EGCase in pathogenic fungi, were identified as the first fungal glucosylceramide- and sterylglucoside-hydrolyzing glycosidases, respectively. These enzymes are promising targets for antifungal drugs against pathogenic fungi. This review describes the functions and properties of these microbial glycolipid-degrading enzymes, the molecular basis of their differential substrate specificity, and their applications.
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Affiliation(s)
- Yohei Ishibashi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, Japan
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3
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Ibarra-Laclette E, Venancio-Rodríguez CA, Vásquez-Aguilar AA, Alonso-Sánchez AG, Pérez-Torres CA, Villafán E, Ramírez-Barahona S, Galicia S, Sosa V, Rebollar EA, Lara C, González-Rodríguez A, Díaz-Fleisher F, Ornelas JF. Transcriptional Basis for Haustorium Formation and Host Establishment in Hemiparasitic Psittacanthus schiedeanus Mistletoes. Front Genet 2022; 13:929490. [PMID: 35769994 PMCID: PMC9235361 DOI: 10.3389/fgene.2022.929490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
The mistletoe Psittacanthus schiedeanus, a keystone species in interaction networks between plants, pollinators, and seed dispersers, infects a wide range of native and non-native tree species of commercial interest. Here, using RNA-seq methodology we assembled the whole circularized quadripartite structure of P. schiedeanus chloroplast genome and described changes in the gene expression of the nuclear genomes across time of experimentally inoculated seeds. Of the 140,467 assembled and annotated uniGenes, 2,000 were identified as differentially expressed (DEGs) and were classified in six distinct clusters according to their expression profiles. DEGs were also classified in enriched functional categories related to synthesis, signaling, homoeostasis, and response to auxin and jasmonic acid. Since many orthologs are involved in lateral or adventitious root formation in other plant species, we propose that in P. schiedeanus (and perhaps in other rootless mistletoe species), these genes participate in haustorium formation by complex regulatory networks here described. Lastly, and according to the structural similarities of P. schiedeanus enzymes with those that are involved in host cell wall degradation in fungi, we suggest that a similar enzymatic arsenal is secreted extracellularly and used by mistletoes species to easily parasitize and break through tissues of the host.
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Affiliation(s)
- Enrique Ibarra-Laclette
- Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | | | | | | | - Claudia-Anahí Pérez-Torres
- Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
- Investigador por Mexico-CONACyT en el Instituto de Ecología A.C. (INECOL), Xalapa, Mexico
| | - Emanuel Villafán
- Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de Mexico (UNAM), Ciudad de Mexico, Mexico
| | - Sonia Galicia
- Instituto de Ecología A.C. (INECOL), Red de Biología Evolutiva, Xalapa, Mexico
| | - Victoria Sosa
- Instituto de Ecología A.C. (INECOL), Red de Biología Evolutiva, Xalapa, Mexico
| | - Eria A. Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Mexico
| | - Carlos Lara
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Antonio González-Rodríguez
- Laboratorio de Genética de la Conservación, Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), UNAM, Morelia, Mexico
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4
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Barnsley KK, Ondrechen MJ. Enzyme active sites: Identification and prediction of function using computational chemistry. Curr Opin Struct Biol 2022; 74:102384. [DOI: 10.1016/j.sbi.2022.102384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/20/2022] [Accepted: 03/28/2022] [Indexed: 11/03/2022]
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5
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Iyengar SM, Barnsley KK, Xu R, Prystupa A, Ondrechen MJ. Electrostatic fingerprints of catalytically active amino acids in enzymes. Protein Sci 2022; 31:e4291. [PMID: 35481659 PMCID: PMC8994506 DOI: 10.1002/pro.4291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 11/06/2022]
Abstract
The computed electrostatic and proton transfer properties are studied for 20 enzymes that represent all six major enzyme commission classes and a variety of different folds. The properties of aspartate, glutamate, and lysine residues that have been previously experimentally determined to be catalytically active are reported. The catalytic aspartate and glutamate residues studied here are strongly coupled to at least one other aspartate or glutamate residue and often to multiple other carboxylate residues with intrinsic pKa differences less than 1 pH unit. Sometimes these catalytic acidic residues are also coupled to a histidine residue, such that the intrinsic pKa of the acidic residue is higher than that of the histidine. All catalytic lysine residues studied here are strongly coupled to tyrosine or cysteine residues, wherein the intrinsic pKa of the anion-forming residue is higher than that of the lysine. Some catalytic lysines are also coupled to other lysines with intrinsic pKa differences within 1 pH unit. Some evidence of the possible types of interactions that facilitate nucleophilicity is discussed. The interactions reported here provide important clues about how side chain functional groups that are weak Brønsted acids or bases for the free amino acid in solution can achieve catalytic potency and become strong acids, bases or nucleophiles in the enzymatic environment.
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Affiliation(s)
- Suhasini M. Iyengar
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Kelly K. Barnsley
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Rholee Xu
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Aleksandr Prystupa
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
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6
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Collet L, Vander Wauven C, Oudjama Y, Galleni M, Dutoit R. Highlighting the factors governing transglycosylation in the GH5_5 endo-1,4-β-glucanase RBcel1. Acta Crystallogr D Struct Biol 2022; 78:278-289. [PMID: 35234142 PMCID: PMC8900817 DOI: 10.1107/s2059798321013541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/22/2021] [Indexed: 11/11/2022] Open
Abstract
Transglycosylating glycoside hydrolases (GHs) offer great potential for the enzymatic synthesis of oligosaccharides. Although knowledge is progressing, there is no unique strategy to improve the transglycosylation yield. Obtaining efficient enzymatic tools for glycan synthesis with GHs remains dependent on an improved understanding of the molecular factors governing the balance between hydrolysis and transglycosylation. This enzymatic and structural study of RBcel1, a transglycosylase from the GH5_5 subfamily isolated from an uncultured bacterium, aims to unravel such factors. The size of the acceptor and donor sugars was found to be critical since transglycosylation is efficient with oligosaccharides at least the size of cellotetraose as the donor and cellotriose as the acceptor. The reaction pH is important in driving the balance between hydrolysis and transglycosylation: hydrolysis is favored at pH values below 8, while transglycosylation becomes the major reaction at basic pH. Solving the structures of two RBcel1 variants, RBcel1_E135Q and RBcel1_Y201F, in complex with ligands has brought to light some of the molecular factors behind transglycosylation. The structure of RBcel1_E135Q in complex with cellotriose allowed a +3 subsite to be defined, in accordance with the requirement for cellotriose as a transglycosylation acceptor. The structure of RBcel1_Y201F has been obtained with several transglycosylation intermediates, providing crystallographic evidence of transglycosylation. The catalytic cleft is filled with (i) donors ranging from cellotriose to cellohexaose in the negative subsites and (ii) cellobiose and cellotriose in the positive subsites. Such a structure is particularly relevant since it is the first structure of a GH5 enzyme in complex with transglycosylation products that has been obtained with neither of the catalytic glutamate residues modified.
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Affiliation(s)
- Laetitia Collet
- LABIRIS, 1 Avenue Emile Gryzon, 1070 Brussels, Belgium
- Center for Protein Engineering (CIP), Biological Macromolecules, University of Liège, 13 Allée du 6 Août, 4000 Liège, Belgium
| | | | | | - Moreno Galleni
- Center for Protein Engineering (CIP), Biological Macromolecules, University of Liège, 13 Allée du 6 Août, 4000 Liège, Belgium
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7
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Sadaqat B, Sha C, Rupani PF, Wang H, Zuo W, Shao W. Man/Cel5B, a Bifunctional Enzyme Having the Highest Mannanase Activity in the Hyperthermic Environment. Front Bioeng Biotechnol 2021; 9:637649. [PMID: 33796509 PMCID: PMC8007966 DOI: 10.3389/fbioe.2021.637649] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/25/2021] [Indexed: 01/07/2023] Open
Abstract
Thermotoga maritima (Tma) contains genes encoding various hyperthermophilic enzymes with great potential for industrial applications. The gene TM1752 in Tma genome has been annotated as cellulase gene encoding protein Cel5B. In this work, the gene TM1752 was cloned and expressed in Escherichia coli, and the recombinant enzyme was purified and characterized. Interestingly, the purified enzyme exhibited specific activities of 416 and 215 U/mg on substrates galactomannan and carboxy methyl cellulose, which is the highest among thermophilic mannanases. However, the putative enzyme did not show sequence homology with any of the previously reported mannanases; therefore, the enzyme Cel5B was identified as bifunctional mannanase and cellulase and renamed as Man/Cel5B. Man/Cel5B exhibited maximum activity at 85°C and pH 5.5. This enzyme retained more than 50% activity after 5 h of incubation at 85°C, and retained up to 80% activity after incubated for 1 h at pH 5–8. The Km and Vmax of Man/Cel5B were observed to be 4.5 mg/mL galactomannan and 769 U/mg, respectively. Thin layer chromatography depicted that locust bean gum could be efficiently degraded to mannobiose, mannotriose, and mannooligosaccharides by Man/Cel5B. These characteristics suggest that Man/Cel5B has attractive applications for future food, feed, and biofuel industries.
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Affiliation(s)
- Beenish Sadaqat
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Chong Sha
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Parveen Fatemeh Rupani
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Hongcheng Wang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Wanbing Zuo
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Weilan Shao
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
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8
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Zheng Y, Maruoka M, Nanatani K, Hidaka M, Abe N, Kaneko J, Sakai Y, Abe K, Yokota A, Yabe S. High cellulolytic potential of the Ktedonobacteria lineage revealed by genome-wide analysis of CAZymes. J Biosci Bioeng 2021; 131:622-630. [PMID: 33676867 DOI: 10.1016/j.jbiosc.2021.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/10/2021] [Accepted: 01/27/2021] [Indexed: 12/16/2022]
Abstract
Traditionally, filamentous fungi and actinomycetes are well-known cellulolytic microorganisms that have been utilized in the commercial production of cellulase enzyme cocktails for industrial-scale degradation of plant biomass. Noticeably, the Ktedonobacteria lineage (phylum Chloroflexi) with actinomycetes-like morphology was identified and exhibited diverse carbohydrate utilization or degradation abilities. In this study, we performed genome-wide profiling of carbohydrate-active enzymes (CAZymes) in the filamentous Ktedonobacteria lineage. Numerous CAZymes (153-290 CAZymes, representing 63-131 glycoside hydrolases (GHs) per genome), including complex mixtures of endo- and exo-cellulases, were predicted in 15 available Ktedonobacteria genomes. Of note, 4-28 CAZymes were predicted to be extracellular enzymes, whereas 3-29 CAZymes were appended with carbohydrate-binding modules (CBMs) that may promote their binding to insoluble carbohydrate substrates. This number far exceeded other Chloroflexi lineages and were comparable to the cellulolytic actinomycetes. Six multi-modular extracellular GHs were cloned from the thermophilic Thermosporothrix hazakensis SK20-1T strain and heterologously expressed. The putative endo-glucanases of ThazG5-1, ThazG9, and ThazG12 exhibited strong cellulolytic activity, whereas the putative exo-glucanases ThazG6 and ThazG48 formed weak but observable halos on carboxymethyl cellulose plates, indicating their potential biotechnological application. The purified recombinant ThazG12 had near-neutral pH (optimal 6.0), high thermostability (60°C), and broad specificity against soluble and insoluble polysaccharide substrates. It also represented described a novel thermostable bacterial β-1,4-glucanase in the GH12 family. Together, this research revealed the underestimated cellulolytic potential of the Ktedonobacteria lineage and highlighted its potential biotechnological utility as a promising microbial resource for the discovery of industrially useful cellulases.
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Affiliation(s)
- Yu Zheng
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan; Department of Microbial Biotechnology, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Mayumi Maruoka
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan; Department of Microbial Biotechnology, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Kei Nanatani
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Masafumi Hidaka
- Department of Molecular and Cell Biology, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Naoki Abe
- Department of Microbial Biotechnology, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Jun Kaneko
- Department of Microbial Biotechnology, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Yasuteru Sakai
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan; Hazaka Plant Research Center, Kennan Eisei Kogyo Co., Ltd., 44 Aza Inariyama, Oaza Ashitate, Murata-cho, Shibata-gun, Miyagi 989-1311, Japan
| | - Keietsu Abe
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan; Department of Microbial Biotechnology, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Akira Yokota
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan; Hazaka Plant Research Center, Kennan Eisei Kogyo Co., Ltd., 44 Aza Inariyama, Oaza Ashitate, Murata-cho, Shibata-gun, Miyagi 989-1311, Japan
| | - Shuhei Yabe
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan; Hazaka Plant Research Center, Kennan Eisei Kogyo Co., Ltd., 44 Aza Inariyama, Oaza Ashitate, Murata-cho, Shibata-gun, Miyagi 989-1311, Japan.
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9
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Summers SR, Alamdari S, Kraft CJ, Brunecky R, Pfaendtner J, Kaar JL. Substitution of distal and active site residues reduces product inhibition of E1 from Acidothermus Cellulolyticus. Protein Eng Des Sel 2021; 34:6476618. [PMID: 34935952 DOI: 10.1093/protein/gzab031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 09/22/2021] [Accepted: 11/13/2021] [Indexed: 11/14/2022] Open
Abstract
Cellulases are largely afflicted by inhibition from their reaction products, especially at high-substrate loading, which represents a major challenge for biomass processing. This challenge was overcome for endoglucanase 1 (E1) from Acidothermus cellulolyticus by identifying a large conformational change involving distal residues upon binding cellobiose. Having introduced alanine substitutions at each of these residues, we identified several mutations that reduced cellobiose inhibition of E1, including W212A, W213A, Q247A, W249A and F250A. One of the mutations (W212A) resulted in a 47-fold decrease in binding affinity of cellobiose as well as a 5-fold increase in the kcat. The mutation further increased E1 activity on Avicel and dilute-acid treated corn stover and enhanced its productivity at high-substrate loadings. These findings were corroborated by funnel metadynamics, which showed that the W212A substitution led to reduced affinity for cellobiose in the +1 and +2 binding sites due to rearrangement of key cellobiose-binding residues.
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Affiliation(s)
- Samantha R Summers
- Department of Chemical and Biological Engineering, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Sarah Alamdari
- Department of Chemical Engineering, University of Washington, 3781 Okanogan Lane NE, Seattle, WA 98195-1750, USA
| | - Casey J Kraft
- Department of Chemical and Biological Engineering, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Roman Brunecky
- Biosciences Center, National Renewable Energy Lab, 15013 Denver W Pkwy, Golden, CO 80401, USA
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, 3781 Okanogan Lane NE, Seattle, WA 98195-1750, USA
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80309, USA
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10
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Collet L, Vander Wauven C, Oudjama Y, Galleni M, Dutoit R. Glycoside hydrolase family 5: structural snapshots highlighting the involvement of two conserved residues in catalysis. Acta Crystallogr D Struct Biol 2021; 77:205-216. [PMID: 33559609 DOI: 10.1107/s2059798320015557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/24/2020] [Indexed: 11/10/2022] Open
Abstract
The ability of retaining glycoside hydrolases (GHs) to transglycosylate is inherent to the double-displacement mechanism. Studying reaction intermediates, such as the glycosyl-enzyme intermediate (GEI) and the Michaelis complex, could provide valuable information to better understand the molecular factors governing the catalytic mechanism. Here, the GEI structure of RBcel1, an endo-1,4-β-glucanase of the GH5 family endowed with transglycosylase activity, is reported. It is the first structure of a GH5 enzyme covalently bound to a natural oligosaccharide with the two catalytic glutamate residues present. The structure of the variant RBcel1_E135A in complex with cellotriose is also reported, allowing a description of the entire binding cleft of RBcel1. Taken together, the structures deliver different snapshots of the double-displacement mechanism. The structural analysis revealed a significant movement of the nucleophilic glutamate residue during the reaction. Enzymatic assays indicated that, as expected, the acid/base glutamate residue is crucial for the glycosylation step and partly contributes to deglycosylation. Moreover, a conserved tyrosine residue in the -1 subsite, Tyr201, plays a determinant role in both the glycosylation and deglycosylation steps, since the GEI was trapped in the RBcel1_Y201F variant. The approach used to obtain the GEI presented here could easily be transposed to other retaining GHs in clan GH-A.
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Affiliation(s)
| | | | | | - Moreno Galleni
- Center for Protein Engineering (CIP), Biological Macromolecules, University of Liège, 13 Allée du 6 Août, 4000 Liège, Belgium
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11
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Yuan Y, Zhang X, Zhang H, Wang W, Zhao X, Gao J, Zhou Y. Degradative GH5 β-1,3-1,4-glucanase PpBglu5A for glucan in Paenibacillus polymyxa KF-1. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Guerrero EB, de Villegas RMD, Soria MA, Santangelo MP, Campos E, Talia PM. Characterization of two GH5 endoglucanases from termite microbiome using synthetic metagenomics. Appl Microbiol Biotechnol 2020; 104:8351-8366. [DOI: 10.1007/s00253-020-10831-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
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13
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Li K, Qi H, Liu Q, Li T, Chen W, Li S, Piao HL, Yin H. Preparation and antitumor activity of selenium-modified glucomannan oligosaccharides. J Funct Foods 2020. [DOI: 10.1016/j.jff.2019.103731] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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14
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Crystallographic structure and molecular dynamics simulations of the major endoglucanase from Xanthomonas campestris pv. campestris shed light on its oligosaccharide products release pattern. Int J Biol Macromol 2019; 136:493-502. [PMID: 31216447 DOI: 10.1016/j.ijbiomac.2019.06.107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 06/09/2019] [Accepted: 06/15/2019] [Indexed: 12/23/2022]
Abstract
Cellulases are essential enzymatic components for the transformation of plant biomass into fuels, renewable materials and green chemicals. Here, we determined the crystal structure, pattern of hydrolysis products release, and conducted molecular dynamics simulations of the major endoglucanase from the Xanthomonas campestris pv. campestris (XccCel5A). XccCel5A has a TIM barrel fold with the catalytic site centrally placed in a binding groove surrounded by aromatic side chains. Molecular dynamics simulations show that productive position of the substrate is secured by a network of hydrogen bonds in the four main subsites, which differ in details from homologous structures. Capillary zone electrophoresis and computational studies reveal XccCel5A can act both as endoglucanase and licheninase, but there are preferable arrangements of substrate regarding β-1,3 and β-1,4 bonds within the binding cleft which are related to the enzymatic efficiency.
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15
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Dutoit R, Delsaute M, Collet L, Vander Wauven C, Van Elder D, Berlemont R, Richel A, Galleni M, Bauvois C. Crystal structure determination of Pseudomonas stutzeri A1501 endoglucanase Cel5A: the search for a molecular basis for glycosynthesis in GH5_5 enzymes. Acta Crystallogr D Struct Biol 2019; 75:605-615. [PMID: 31205022 DOI: 10.1107/s2059798319007113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/16/2019] [Indexed: 01/23/2023] Open
Abstract
The discovery of new glycoside hydrolases that can be utilized in the chemoenzymatic synthesis of carbohydrates has emerged as a promising approach for various biotechnological processes. In this study, recombinant Ps_Cel5A from Pseudomonas stutzeri A1501, a novel member of the GH5_5 subfamily, was expressed, purified and crystallized. Preliminary experiments confirmed the ability of Ps_Cel5A to catalyze transglycosylation with cellotriose as a substrate. The crystal structure revealed several structural determinants in and around the positive subsites, providing a molecular basis for a better understanding of the mechanisms that promote and favour synthesis rather than hydrolysis. In the positive subsites, two nonconserved positively charged residues (Arg178 and Lys216) were found to interact with cellobiose. This adaptation has also been reported for transglycosylating β-mannanases of the GH5_7 subfamily.
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Affiliation(s)
| | - Maud Delsaute
- InBioS - Center for Protein Engineering (CIP), Biological Macromolecules, University of Liège, 13 Allée du 6 Août, 4000 Liège, Belgium
| | | | | | - Dany Van Elder
- Laboratory of Microbiology, Université Libre de Bruxelles, 12 Rue des Professeurs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Renaud Berlemont
- Department of Biological Sciences, California State University Long Beach, 1250 Bellflower Boulevard, Long Beach, CA 90840-9502, USA
| | - Aurore Richel
- Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, 5030 Gembloux, Belgium
| | - Moreno Galleni
- InBioS - Center for Protein Engineering (CIP), Biological Macromolecules, University of Liège, 13 Allée du 6 Août, 4000 Liège, Belgium
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16
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Sahoo K, Sahoo RK, Gaur M, Subudhi E. Cellulolytic thermophilic microorganisms in white biotechnology: a review. Folia Microbiol (Praha) 2019; 65:25-43. [DOI: 10.1007/s12223-019-00710-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 04/15/2019] [Indexed: 10/26/2022]
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17
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Glasgow EM, Vander Meulen KA, Takasuka TE, Bianchetti CM, Bergeman LF, Deutsch S, Fox BG. Extent and Origins of Functional Diversity in a Subfamily of Glycoside Hydrolases. J Mol Biol 2019; 431:1217-1233. [PMID: 30685401 DOI: 10.1016/j.jmb.2019.01.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/19/2018] [Accepted: 01/16/2019] [Indexed: 12/16/2022]
Abstract
Some glycoside hydrolases have broad specificity for hydrolysis of glycosidic bonds, potentially increasing their functional utility and flexibility in physiological and industrial applications. To deepen the understanding of the structural and evolutionary driving forces underlying specificity patterns in glycoside hydrolase family 5, we quantitatively screened the activity of the catalytic core domains from subfamily 4 (GH5_4) and closely related enzymes on four substrates: lichenan, xylan, mannan, and xyloglucan. Phylogenetic analysis revealed that GH5_4 consists of three major clades, and one of these clades, referred to here as clade 3, displayed average specific activities of 4.2 and 1.2 U/mg on lichenan and xylan, approximately 1 order of magnitude larger than the average for active enzymes in clades 1 and 2. Enzymes in clade 3 also more consistently met assay detection thresholds for reaction with all four substrates. We also identified a subfamily-wide positive correlation between lichenase and xylanase activities, as well as a weaker relationship between lichenase and xyloglucanase. To connect these results to structural features, we used the structure of CelE from Hungateiclostridium thermocellum (PDB 4IM4) as an example clade 3 enzyme with activities on all four substrates. Comparison of the sequence and structure of this enzyme with others throughout GH5_4 and neighboring subfamilies reveals at least two residues (H149 and W203) that are linked to strong activity across the substrates. Placing GH5_4 in context with other related subfamilies, we highlight several possibilities for the ongoing evolutionary specialization of GH5_4 enzymes.
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Affiliation(s)
- Evan M Glasgow
- Great Lakes Bioenergy Research Center, Madison, WI 53706 USA; Department of Biochemistry, University of Wisconsin, Madison, WI 53706 USA
| | - Kirk A Vander Meulen
- Great Lakes Bioenergy Research Center, Madison, WI 53706 USA; Department of Biochemistry, University of Wisconsin, Madison, WI 53706 USA
| | - Taichi E Takasuka
- Great Lakes Bioenergy Research Center, Madison, WI 53706 USA; Department of Biochemistry, University of Wisconsin, Madison, WI 53706 USA; Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Christopher M Bianchetti
- Great Lakes Bioenergy Research Center, Madison, WI 53706 USA; Department of Biochemistry, University of Wisconsin, Madison, WI 53706 USA; Department of Chemistry, University of Wisconsin, Oshkosh, 54901 USA
| | - Lai F Bergeman
- Great Lakes Bioenergy Research Center, Madison, WI 53706 USA; Department of Biochemistry, University of Wisconsin, Madison, WI 53706 USA
| | | | - Brian G Fox
- Great Lakes Bioenergy Research Center, Madison, WI 53706 USA; Department of Biochemistry, University of Wisconsin, Madison, WI 53706 USA.
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18
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Abstract
Glycoside Hydrolase Family 7 cellobiohydrolases (GH7 CBHs) catalyze cellulose depolymerization in cellulolytic eukaryotes, making them key discovery and engineering targets. However, there remains a lack of robust structure–activity relationships for these industrially important cellulases. Here, we compare CBHs from Trichoderma reesei (TrCel7A) and Penicillium funiculosum (PfCel7A), which exhibit a multi-modular architecture consisting of catalytic domain (CD), carbohydrate-binding module, and linker. We show that PfCel7A exhibits 60% greater performance on biomass than TrCel7A. To understand the contribution of each domain to this improvement, we measure enzymatic activity for a library of CBH chimeras with swapped subdomains, demonstrating that the enhancement is mainly caused by PfCel7A CD. We solve the crystal structure of PfCel7A CD and use this information to create a second library of TrCel7A CD mutants, identifying a TrCel7A double mutant with near-equivalent activity to wild-type PfCel7A. Overall, these results reveal CBH regions that enable targeted activity improvements. Cellobiohydrolases (CBHs) are critical for natural and industrial biomass degradation but their structure–activity relationships are not fully understood. Here, the authors present the biochemical and structural characterization of two CBHs, identifying protein regions that confer enhanced CBH activity.
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Prajapati AS, Panchal KJ, Pawar VA, Noronha MJ, Patel DH, Subramanian RB. Review on Cellulase and Xylanase Engineering for Biofuel Production. Ind Biotechnol (New Rochelle N Y) 2018. [DOI: 10.1089/ind.2017.0027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Anil S. Prajapati
- P.G. Department of Biosciences, UGC-Centre of Advanced Studies, Satellite campus, Sardar Patel Maidan, Sardar Patel University, Gujarat, India
| | - Ketankumar J. Panchal
- P.G. Department of Biosciences, UGC-Centre of Advanced Studies, Satellite campus, Sardar Patel Maidan, Sardar Patel University, Gujarat, India
| | - Vishakha A. Pawar
- P.G. Department of Biosciences, UGC-Centre of Advanced Studies, Satellite campus, Sardar Patel Maidan, Sardar Patel University, Gujarat, India
| | - Monica J. Noronha
- P.G. Department of Biosciences, UGC-Centre of Advanced Studies, Satellite campus, Sardar Patel Maidan, Sardar Patel University, Gujarat, India
| | - Darshan H. Patel
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology Gujarat, India
| | - R. B. Subramanian
- P.G. Department of Biosciences, UGC-Centre of Advanced Studies, Satellite campus, Sardar Patel Maidan, Sardar Patel University, Gujarat, India
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20
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Angelov A, Pham VTT, Übelacker M, Brady S, Leis B, Pill N, Brolle J, Mechelke M, Moerch M, Henrissat B, Liebl W. A metagenome-derived thermostable β-glucanase with an unusual module architecture which defines the new glycoside hydrolase family GH148. Sci Rep 2017; 7:17306. [PMID: 29229913 PMCID: PMC5725463 DOI: 10.1038/s41598-017-16839-8] [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: 08/31/2017] [Accepted: 11/16/2017] [Indexed: 12/15/2022] Open
Abstract
The discovery of novel and robust enzymes for the breakdown of plant biomass bears tremendous potential for the development of sustainable production processes in the rapidly evolving new bioeconomy. By functional screening of a metagenomic library from a volcano soil sample a novel thermostable endo-β-glucanase (EngU) which is unusual with regard to its module architecture and cleavage specificity was identified. Various recombinant EngU variants were characterized. Assignment of EngU to an existing glycoside hydrolase (GH) family was not possible. Two regions of EngU showed weak sequence similarity to proteins of the GH clan GH-A, and acidic residues crucial for catalytic activity of EngU were identified by mutation. Unusual, a carbohydrate-binding module (CBM4) which displayed binding affinity for β-glucan, lichenin and carboxymethyl-cellulose was found as an insertion between these two regions. EngU hydrolyzed β-1,4 linkages in carboxymethyl-cellulose, but displayed its highest activity with mixed linkage (β-1,3-/β-1,4-) glucans such as barley β-glucan and lichenin, where in contrast to characterized lichenases cleavage occurred predominantly at the β-1,3 linkages of C4-substituted glucose residues. EngU and numerous related enzymes with previously unknown function represent a new GH family of biomass-degrading enzymes within the GH-A clan. The name assigned to the new GH family is GH148.
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Affiliation(s)
- Angel Angelov
- Department of Microbiology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Vu Thuy Trang Pham
- Department of Microbiology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Maria Übelacker
- Department of Microbiology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Silja Brady
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Göttingen, Germany
| | - Benedikt Leis
- Department of Microbiology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Nicole Pill
- Department of Microbiology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Judith Brolle
- Department of Microbiology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Matthias Mechelke
- Department of Microbiology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Matthias Moerch
- Department of Microbiology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Bernard Henrissat
- Architecture et Function des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Wolfgang Liebl
- Department of Microbiology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising-Weihenstephan, Germany.
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21
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Summers SR, Sprenger KG, Pfaendtner J, Marchant J, Summers MF, Kaar JL. Mechanism of Competitive Inhibition and Destabilization of Acidothermus cellulolyticus Endoglucanase 1 by Ionic Liquids. J Phys Chem B 2017; 121:10793-10803. [DOI: 10.1021/acs.jpcb.7b08435] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Samantha R. Summers
- Department of Chemical
and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - K. G. Sprenger
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jan Marchant
- Howard Hughes Medical Institute and Department
of Chemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Michael F. Summers
- Howard Hughes Medical Institute and Department
of Chemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Joel L. Kaar
- Department of Chemical
and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
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22
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Gupta P, Mishra AK, Vakhlu J. Cloning and characterization of thermo-alkalistable and surfactant stable endoglucanase from Puga hot spring metagenome of Ladakh (J&K). Int J Biol Macromol 2017; 103:870-877. [DOI: 10.1016/j.ijbiomac.2017.05.113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 11/28/2022]
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23
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Structural insights into the substrate specificity of a glycoside hydrolase family 5 lichenase from Caldicellulosiruptor sp. F32. Biochem J 2017; 474:3373-3389. [DOI: 10.1042/bcj20170328] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/15/2017] [Accepted: 08/23/2017] [Indexed: 01/12/2023]
Abstract
Glycoside hydrolase (GH) family 5 is one of the largest GH families with various GH activities including lichenase, but the structural basis of the GH5 lichenase activity is still unknown. A novel thermostable lichenase F32EG5 belonging to GH5 was identified from an extremely thermophilic bacterium Caldicellulosiruptor sp. F32. F32EG5 is a bi-functional cellulose and a lichenan-degrading enzyme, and exhibited a high activity on β-1,3-1,4-glucan but side activity on cellulose. Thin-layer chromatography and NMR analyses indicated that F32EG5 cleaved the β-1,4 linkage or the β-1,3 linkage while a 4-O-substitued glucose residue linked to a glucose residue through a β-1,3 linkage, which is completely different from extensively studied GH16 lichenase that catalyses strict endo-hydrolysis of the β-1,4-glycosidic linkage adjacent to a 3-O-substitued glucose residue in the mixed-linked β-glucans. The crystal structure of F32EG5 was determined to 2.8 Å resolution, and the crystal structure of the complex of F32EG5 E193Q mutant and cellotetraose was determined to 1.7 Å resolution, which revealed that the exit subsites of substrate-binding sites contribute to both thermostability and substrate specificity of F32EG5. The sugar chain showed a sharp bend in the complex structure, suggesting that a substrate cleft fitting to the bent sugar chains in lichenan is a common feature of GH5 lichenases. The mechanism of thermostability and substrate selectivity of F32EG5 was further demonstrated by molecular dynamics simulation and site-directed mutagenesis. These results provide biochemical and structural insights into thermostability and substrate selectivity of GH5 lichenases, which have potential in industrial processes.
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24
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Donohoe BS, Wei H, Mittal A, Shollenberger T, Lunin VV, Himmel ME, Brunecky R. Towards an Understanding of Enhanced Biomass Digestibility by In Planta Expression of a Family 5 Glycoside Hydrolase. Sci Rep 2017; 7:4389. [PMID: 28663545 PMCID: PMC5491509 DOI: 10.1038/s41598-017-04502-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 05/17/2017] [Indexed: 12/21/2022] Open
Abstract
In planta expression of a thermophilic endoglucanase (AcCel5A) reduces recalcitrance by creating voids and other irregularities in cell walls of Arabidopsis thaliana that increase enzyme accessibility without negative impacts on plant growth or cell wall composition. Our results suggest that cellulose β-1-4 linkages can be cut sparingly in the assembling wall and that these minimal changes, made at the proper time, have an impact on plant cell wall recalcitrance without negative effects on overall plant development.
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Affiliation(s)
- Bryon S Donohoe
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Ashutosh Mittal
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Todd Shollenberger
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Vladimir V Lunin
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Roman Brunecky
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States.
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25
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Improved transient production of a cellulase enzyme in detached sunflower leaves using plant hormones. BIOTECHNOL BIOPROC E 2017. [DOI: 10.1007/s12257-016-0410-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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26
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A novel pH-stable, endoglucanase (JqCel5A) isolated from a salt-lake microorganism, Jonesia quinghaiensis. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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28
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Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis. mBio 2016; 7:mBio.01106-16. [PMID: 27555310 PMCID: PMC4999548 DOI: 10.1128/mbio.01106-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Glycoside hydrolases (GHs) are key enzymes in the depolymerization of plant-derived cellulose, a process central to the global carbon cycle and the conversion of plant biomass to fuels and chemicals. A limited number of GH families hydrolyze crystalline cellulose, often by a processive mechanism along the cellulose chain. During cultivation of thermophilic cellulolytic microbial communities, substantial differences were observed in the crystalline cellulose saccharification activities of supernatants recovered from divergent lineages. Comparative community proteomics identified a set of cellulases from a population closely related to actinobacterium Thermobispora bispora that were highly abundant in the most active consortium. Among the cellulases from T. bispora, the abundance of a GH family 12 (GH12) protein correlated most closely with the changes in crystalline cellulose hydrolysis activity. This result was surprising since GH12 proteins have been predominantly characterized as enzymes active on soluble polysaccharide substrates. Heterologous expression and biochemical characterization of the suite of T. bispora hydrolytic cellulases confirmed that the GH12 protein possessed the highest activity on multiple crystalline cellulose substrates and demonstrated that it hydrolyzes cellulose chains by a predominantly random mechanism. This work suggests that the role of GH12 proteins in crystalline cellulose hydrolysis by cellulolytic microbes should be reconsidered. Cellulose is the most abundant organic polymer on earth, and its enzymatic hydrolysis is a key reaction in the global carbon cycle and the conversion of plant biomass to biofuels. The glycoside hydrolases that depolymerize crystalline cellulose have been primarily characterized from isolates. In this study, we demonstrate that adapting microbial consortia from compost to grow on crystalline cellulose generated communities whose soluble enzymes exhibit differential abilities to hydrolyze crystalline cellulose. Comparative proteomics of these communities identified a protein of glycoside hydrolase family 12 (GH12), a family of proteins previously observed to primarily hydrolyze soluble substrates, as a candidate that accounted for some of the differences in hydrolytic activities. Heterologous expression confirmed that the GH12 protein identified by proteomics was active on crystalline cellulose and hydrolyzed cellulose by a random mechanism, in contrast to most cellulases that act on the crystalline polymer in a processive mechanism.
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29
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Johnson LB, Snow CD. Molecular dynamics simulations of cellulase homologs in aqueous 1-ethyl-3-methylimidazolium chloride. J Biomol Struct Dyn 2016; 35:1990-2002. [DOI: 10.1080/07391102.2016.1204364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Lucas B. Johnson
- Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO 80523-1370, USA
| | - Christopher D. Snow
- Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO 80523-1370, USA
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30
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Lafond M, Sulzenbacher G, Freyd T, Henrissat B, Berrin JG, Garron ML. The Quaternary Structure of a Glycoside Hydrolase Dictates Specificity toward β-Glucans. J Biol Chem 2016; 291:7183-94. [PMID: 26755730 DOI: 10.1074/jbc.m115.695999] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Indexed: 02/05/2023] Open
Abstract
In the Carbohydrate-Active Enzyme (CAZy) database, glycoside hydrolase family 5 (GH5) is a large family with more than 6,000 sequences. Among the 51 described GH5 subfamilies, subfamily GH5_26 contains members that display either endo-β(1,4)-glucanase or β(1,3;1,4)-glucanase activities. In this study, we focused on the GH5_26 enzyme fromSaccharophagus degradans(SdGluc5_26A), a marine bacterium known for its capacity to degrade a wide diversity of complex polysaccharides.SdGluc5_26A displays lichenase activity toward β(1,3;1,4)-glucans with a side cellobiohydrolase activity toward β(1,4)-glucans. The three-dimensional structure ofSdGluc5_26A adopts a stable trimeric quaternary structure also observable in solution. The N-terminal region ofSdGluc5_26A protrudes into the active site of an adjacent monomer. To understand whether this occupation of the active site could influence its activity, we conducted a comprehensive enzymatic characterization ofSdGluc5_26A and of a mutant truncated at the N terminus. Ligand complex structures and kinetic analyses reveal that the N terminus governs the substrate specificity ofSdGluc5_26A. Its deletion opens the enzyme cleft at the -3 subsite and turns the enzyme into an endo-β(1,4)-glucanase. This study demonstrates that experimental approaches can reveal structure-function relationships out of reach of current bioinformatic predictions.
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Affiliation(s)
- Mickael Lafond
- From the Institut des Sciences Moléculaires de Marseille-BiosCiences, UMR7313 CNRS, Aix-Marseille University, Pôle de l'Etoile, 13284 Marseille, France, the INRA, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille University, Polytech'Marseille, F-13288 Marseille, France
| | - Gerlind Sulzenbacher
- the Architecture et Fonction des Macromolécules Biologiques, UMR7257 CNRS, Aix-Marseille University, F-13288 Marseille, France, the INRA, USC1408 Architecture et Fonction des Macromolécules Biologiques, F-13288 Marseille, France, and
| | - Thibaud Freyd
- the Architecture et Fonction des Macromolécules Biologiques, UMR7257 CNRS, Aix-Marseille University, F-13288 Marseille, France
| | - Bernard Henrissat
- the Architecture et Fonction des Macromolécules Biologiques, UMR7257 CNRS, Aix-Marseille University, F-13288 Marseille, France, the INRA, USC1408 Architecture et Fonction des Macromolécules Biologiques, F-13288 Marseille, France, and the Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jean-Guy Berrin
- the INRA, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille University, Polytech'Marseille, F-13288 Marseille, France,
| | - Marie-Line Garron
- the Architecture et Fonction des Macromolécules Biologiques, UMR7257 CNRS, Aix-Marseille University, F-13288 Marseille, France, the INRA, USC1408 Architecture et Fonction des Macromolécules Biologiques, F-13288 Marseille, France, and
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31
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Dhar H, Kasana RC, Dutt S, Gulati A. Cloning and expression of low temperature active endoglucanase EG5C from Paenibacillus sp. IHB B 3084. Int J Biol Macromol 2015; 81:259-66. [DOI: 10.1016/j.ijbiomac.2015.07.060] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 07/25/2015] [Accepted: 07/28/2015] [Indexed: 10/23/2022]
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32
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Dhar H, Kasana RC, Gulati A. Heterologous expression and characterization of detergent stable endoglucanase EG5B from Paenibacillus sp. IHB B 3084. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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33
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Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus. Sci Rep 2015; 5:11666. [PMID: 26133573 PMCID: PMC4488959 DOI: 10.1038/srep11666] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/27/2015] [Indexed: 11/24/2022] Open
Abstract
Previous gene-centric analysis of a cow rumen metagenome revealed the first potentially cellulolytic polysaccharide utilization locus, of which the main catalytic enzyme (AC2aCel5A) was identified as a glycoside hydrolase (GH) family 5 endo-cellulase. Here we present the 1.8 Å three-dimensional structure of AC2aCel5A, and characterization of its enzymatic activities. The enzyme possesses the archetypical (β/α)8-barrel found throughout the GH5 family, and contains the two strictly conserved catalytic glutamates located at the C-terminal ends of β-strands 4 and 7. The enzyme is active on insoluble cellulose and acts exclusively on linear β-(1,4)-linked glucans. Co-crystallization of a catalytically inactive mutant with substrate yielded a 2.4 Å structure showing cellotriose bound in the −3 to −1 subsites. Additional electron density was observed between Trp178 and Trp254, two residues that form a hydrophobic “clamp”, potentially interacting with sugars at the +1 and +2 subsites. The enzyme’s active-site cleft was narrower compared to the closest structural relatives, which in contrast to AC2aCel5A, are also active on xylans, mannans and/or xyloglucans. Interestingly, the structure and function of this enzyme seem adapted to less-substituted substrates such as cellulose, presumably due to the insufficient space to accommodate the side-chains of branched glucans in the active-site cleft.
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Watanabe T, Tani M, Ishibashi Y, Endo I, Okino N, Ito M. Ergosteryl-β-glucosidase (Egh1) involved in sterylglucoside catabolism and vacuole formation inSaccharomyces cerevisiae. Glycobiology 2015; 25:1079-89. [DOI: 10.1093/glycob/cwv045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/23/2015] [Indexed: 12/30/2022] Open
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Johnson LB, Gintner LP, Park S, Snow CD. Discriminating between stabilizing and destabilizing protein design mutations via recombination and simulation. Protein Eng Des Sel 2015; 28:259-67. [PMID: 26080450 DOI: 10.1093/protein/gzv030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/15/2015] [Indexed: 11/13/2022] Open
Abstract
Accuracy of current computational protein design (CPD) methods is limited by inherent approximations in energy potentials and sampling. These limitations are often used to qualitatively explain design failures; however, relatively few studies provide specific examples or quantitative details that can be used to improve future CPD methods. Expanding the design method to include a library of sequences provides data that is well suited for discriminating between stabilizing and destabilizing design elements. Using thermophilic endoglucanase E1 from Acidothermus cellulolyticus as a model enzyme, we computationally designed a sequence with 60 mutations. The design sequence was rationally divided into structural blocks and recombined with the wild-type sequence. Resulting chimeras were assessed for activity and thermostability. Surprisingly, unlike previous chimera libraries, regression analysis based on one- and two-body effects was not sufficient for predicting chimera stability. Analysis of molecular dynamics simulations proved helpful in distinguishing stabilizing and destabilizing mutations. Reverting to the wild-type amino acid at destabilized sites partially regained design stability, and introducing predicted stabilizing mutations in wild-type E1 significantly enhanced thermostability. The ability to isolate stabilizing and destabilizing elements in computational design offers an opportunity to interpret previous design failures and improve future CPD methods.
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Affiliation(s)
- Lucas B Johnson
- Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Lucas P Gintner
- Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Sehoo Park
- Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Christopher D Snow
- Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
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Jung SK, McDonald KA, Dandekar AM. Effect of leaf incubation temperature profiles onagrobacterium tumefaciens-mediated transient expression. Biotechnol Prog 2015; 31:783-90. [DOI: 10.1002/btpr.2077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 02/18/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Sang-Kyu Jung
- Dept. of Chemical Engineering and Materials Science; University of California; Davis CA 95616
| | - Karen A. McDonald
- Dept. of Chemical Engineering and Materials Science; University of California; Davis CA 95616
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Yang Y, Zhang L, Guo M, Sun J, Matsukawa S, Xie J, Wei D. Novel α-L-arabinofuranosidase from Cellulomonas fimi ATCC 484 and its substrate-specificity analysis with the aid of computer. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:3725-33. [PMID: 25797391 DOI: 10.1021/jf5059683] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In the process of gene mining for novel α-L-arabinofuranosidases (AFs), the gene Celf_3321 from Cellulomonas fimi ATCC 484 encodes an AF, termed as AbfCelf, with potent activity, 19.4 U/mg under the optimum condition, pH 6.0 and 40 °C. AbfCelf can hydrolyze α-1,5-linked oligosaccharides, sugar beet arabinan, linear 1,5-α-arabinan, and wheat flour arabinoxylan, which is partly different from some previously well-characterized GH 51 AFs. The traditional substrate-specificity analysis for AFs is labor-consuming and money costing, because the substrates include over 30 kinds of various 4-nitrophenol (PNP)-glycosides, oligosaccharides, and polysaccharides. Hence, a preliminary structure and mechanism based method was applied for substrate-specificity analysis. The binding energy (ΔG, kcal/mol) obtained by docking suggested the reaction possibility and coincided with the experimental results. AbfA crystal 1QW9 was used to test the rationality of docking method in simulating the interaction between enzyme and substrate, as well the credibility of the substrate-specificity analysis method in silico.
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Affiliation(s)
- Ying Yang
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Lujia Zhang
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Mingrong Guo
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Jiaqi Sun
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Shingo Matsukawa
- §Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Jingli Xie
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- ‡Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai 200237, People's Republic of China
| | - Dongzhi Wei
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- ‡Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai 200237, People's Republic of China
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Jung SK, Lindenmuth BE, McDonald KA, Hwang H, Bui MQN, Falk BW, Uratsu SL, Phu ML, Dandekar AM. Agrobacterium tumefaciens mediated transient expression of plant cell wall-degrading enzymes in detached sunflower leaves. Biotechnol Prog 2015; 30:905-15. [PMID: 25180328 DOI: 10.1002/btpr.1888] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
For biofuel applications, synthetic endoglucanase E1 and xylanase (Xyn10A) derived from Acidothermus cellulolyticus were transiently expressed in detached whole sunflower (Helianthus annuus L.) leaves using vacuum infiltration. Three different expression systems were tested, including the constitutive CaMV 35S-driven, CMVar (Cucumber mosaic virus advanced replicating), and TRBO (Tobacco mosaic virus RNA-Based Overexpression Vector) systems. For 6-day leaf incubations, codon-optimized E1 and xylanase driven by the CaMV 35S promoter were successfully expressed in sunflower leaves. The two viral expression vectors, CMVar and TRBO, were not successful although we found high expression in Nicotiana benthamiana leaves previously for other recombinant proteins. To further enhance transient expression, we demonstrated two novel methods: using the plant hormone methyl jasmonic acid in the agroinfiltration buffer and two-phase optimization of the leaf incubation temperature. When methyl jasmonic acid was added to Agrobacterium tumefaciens cell suspensions and infiltrated into plant leaves, the functional enzyme production increased 4.6-fold. Production also increased up to 4.2-fold when the leaf incubation temperature was elevated above the typical temperature, 20C, to 30C in the late incubation phase, presumably due to enhanced rate of protein synthesis in plant cells. Finally, we demonstrated co-expression of E1 and xylanase in detached sunflower leaves. To our knowledge, this is the first report of (co)expression of heterologous plant cell wall-degrading enzymes in sunflower.
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Dos Santos CR, Cordeiro RL, Wong DWS, Murakami MT. Structural basis for xyloglucan specificity and α-d-Xylp(1 → 6)-D-Glcp recognition at the -1 subsite within the GH5 family. Biochemistry 2015; 54:1930-42. [PMID: 25714929 DOI: 10.1021/acs.biochem.5b00011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
GH5 is one of the largest glycoside hydrolase families, comprising at least 20 distinct activities within a common structural scaffold. However, the molecular basis for the functional differentiation among GH5 members is still not fully understood, principally for xyloglucan specificity. In this work, we elucidated the crystal structures of two novel GH5 xyloglucanases (XEGs) retrieved from a rumen microflora metagenomic library, in the native state and in complex with xyloglucan-derived oligosaccharides. These results provided insights into the structural determinants that differentiate GH5 XEGs from parental cellulases and a new mode of action within the GH5 family related to structural adaptations in the -1 subsite. The oligosaccharide found in the XEG5A complex, permitted the mapping, for the first time, of the positive subsites of a GH5 XEG, revealing the importance of the pocket-like topology of the +1 subsite in conferring the ability of some GH5 enzymes to attack xyloglucan. Complementarily, the XEG5B complex covered the negative subsites, completing the subsite mapping of GH5 XEGs at high resolution. Interestingly, XEG5B is, to date, the only GH5 member able to cleave XXXG into XX and XG, and in the light of these results, we propose that a modification in the -1 subsite enables the accommodation of a xylosyl side chain at this position. The stereochemical compatibility of the -1 subsite with a xylosyl moiety was also reported for other structurally nonrelated XEGs belonging to the GH74 family, indicating it to be an essential attribute for this mode of action.
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Affiliation(s)
- Camila Ramos Dos Santos
- †Brazilian Biosciences National Laboratory, National Center of Research in Energy and Materials, Campinas, São Paulo 13083-970, Brazil
| | - Rosa Lorizolla Cordeiro
- †Brazilian Biosciences National Laboratory, National Center of Research in Energy and Materials, Campinas, São Paulo 13083-970, Brazil
| | - Dominic W S Wong
- ‡Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California 94710, United States
| | - Mário Tyago Murakami
- †Brazilian Biosciences National Laboratory, National Center of Research in Energy and Materials, Campinas, São Paulo 13083-970, Brazil
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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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Yuan SF, Wu TH, Lee HL, Hsieh HY, Lin WL, Yang B, Chang CK, Li Q, Gao J, Huang CH, Ho MC, Guo RT, Liang PH. Biochemical characterization and structural analysis of a bifunctional cellulase/xylanase from Clostridium thermocellum. J Biol Chem 2015; 290:5739-48. [PMID: 25575592 DOI: 10.1074/jbc.m114.604454] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We expressed an active form of CtCel5E (a bifunctional cellulase/xylanase from Clostridium thermocellum), performed biochemical characterization, and determined its apo- and ligand-bound crystal structures. From the structures, Asn-93, His-168, His-169, Asn-208, Trp-347, and Asn-349 were shown to provide hydrogen-bonding/hydrophobic interactions with both ligands. Compared with the structures of TmCel5A, a bifunctional cellulase/mannanase homolog from Thermotoga maritima, a flexible loop region in CtCel5E is the key for discriminating substrates. Moreover, site-directed mutagenesis data confirmed that His-168 is essential for xylanase activity, and His-169 is more important for xylanase activity, whereas Asn-93, Asn-208, Tyr-270, Trp-347, and Asn-349 are critical for both activities. In contrast, F267A improves enzyme activities.
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Affiliation(s)
| | - Tzu-Hui Wu
- the Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan and
| | - Hsiao-Lin Lee
- From the Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | | | - Wen-Ling Lin
- From the Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | | | - Chih-Kang Chang
- From the Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Qian Li
- the Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jian Gao
- the Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chun-Hsiang Huang
- the Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Meng-Chiao Ho
- the Institute of Biochemical Sciences, and From the Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan,
| | - Rey-Ting Guo
- the Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Po-Huang Liang
- the Institute of Biochemical Sciences, and From the Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan,
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Chung D, Young J, Cha M, Brunecky R, Bomble YJ, Himmel ME, Westpheling J. Expression of the Acidothermus cellulolyticus E1 endoglucanase in Caldicellulosiruptor bescii enhances its ability to deconstruct crystalline cellulose. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:113. [PMID: 26269712 PMCID: PMC4533959 DOI: 10.1186/s13068-015-0296-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 07/24/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND The Caldicellulosiruptor bescii genome encodes a potent set of carbohydrate-active enzymes (CAZymes), found primarily as multi-domain enzymes that exhibit high cellulolytic and hemicellulolytic activity on and allow utilization of a broad range of substrates, including plant biomass without conventional pretreatment. CelA, the most abundant cellulase in the C. bescii secretome, uniquely combines a GH9 endoglucanase and a GH48 exoglucanase in one protein. The most effective commercial enzyme cocktails used in vitro to pretreat biomass are derived from fungal cellulases (cellobiohydrolases, endoglucanases and a β-d-glucosidases) that act synergistically to release sugars for microbial conversion. The C. bescii genome contains six GH5 domains in five different open reading frames. Four exist in multi-domain proteins and two as single catalytic domains. E1 is a GH5 endoglucanase reported to have high specific activity and simple architecture and is active at the growth temperature of C. bescii. E1 is an endo-1,4-β-glucanase linked to a family 2 carbohydrate-binding module shown to bind primarily to cellulosic substrates. We tested if the addition of this protein to the C. bescii secretome would improve its cellulolytic activity. RESULTS In vitro analysis of E1 and CelA shows synergistic interaction. The E1 gene from Acidothermus cellulolyticus was cloned and expressed in C. bescii under the transcriptional control of the C. bescii S-layer promoter, and secretion was directed by the addition of the C. bescii CelA signal peptide sequence. The vector was integrated into the C. bescii chromosome at a site previously showing no detectable detrimental consequence. Increased activity of the secretome of the strain containing E1 was observed on both carboxymethylcellulose (CMC) and Avicel. Activity against CMC increased on average 10.8 % at 65 °C and 12.6 % at 75 °C. Activity against Avicel increased on average 17.5 % at 65 °C and 16.4 % at 75 °C. CONCLUSIONS Expression and secretion of E1 in C. bescii enhanced the cellulolytic ability of its secretome. These data agree with in vitro evidence that E1 acts synergistically with CelA to digest cellulose and offer the possibility of engineering additional enzymes for improved biomass deconstruction with the knowledge that C. bescii can express a gene from Acidothermus, and perhaps other heterologous genes, effectively.
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Affiliation(s)
- Daehwan Chung
- />Department of Genetics, University of Georgia, Athens, GA USA
- />Oak Ridge National Laboratory, The BioEnergy Science Center, Oak Ridge, TN USA
| | - Jenna Young
- />Department of Genetics, University of Georgia, Athens, GA USA
- />Oak Ridge National Laboratory, The BioEnergy Science Center, Oak Ridge, TN USA
| | - Minseok Cha
- />Department of Genetics, University of Georgia, Athens, GA USA
- />Oak Ridge National Laboratory, The BioEnergy Science Center, Oak Ridge, TN USA
| | - Roman Brunecky
- />National Renewable Energy Laboratory, Biosciences Center, Golden, CO USA
- />Oak Ridge National Laboratory, The BioEnergy Science Center, Oak Ridge, TN USA
| | - Yannick J Bomble
- />National Renewable Energy Laboratory, Biosciences Center, Golden, CO USA
- />Oak Ridge National Laboratory, The BioEnergy Science Center, Oak Ridge, TN USA
| | - Michael E Himmel
- />National Renewable Energy Laboratory, Biosciences Center, Golden, CO USA
- />Oak Ridge National Laboratory, The BioEnergy Science Center, Oak Ridge, TN USA
| | - Janet Westpheling
- />Department of Genetics, University of Georgia, Athens, GA USA
- />Oak Ridge National Laboratory, The BioEnergy Science Center, Oak Ridge, TN USA
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Brunecky R, Hobdey SE, Taylor LE, Tao L, Tucker MP, Himmel ME, Decker SR. High temperature pre-digestion of corn stover biomass for improved product yields. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:170. [PMID: 25489338 PMCID: PMC4258809 DOI: 10.1186/s13068-014-0170-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/14/2014] [Indexed: 05/23/2023]
Abstract
INTRODUCTION The efficient conversion of lignocellulosic feedstocks remains a key step in the commercialization of biofuels. One of the barriers to cost-effective conversion of lignocellulosic biomass to sugars remains the enzymatic saccharification process step. Here, we describe a novel hybrid processing approach comprising enzymatic pre-digestion with newly characterized hyperthermophilic enzyme cocktails followed by conventional saccharification with commercial enzyme preparations. Dilute acid pretreated corn stover was subjected to this new procedure to test its efficacy. Thermal tolerant enzymes from Acidothermus cellulolyticus and Caldicellulosiruptor bescii were used to pre-digest pretreated biomass at elevated temperatures prior to saccharification by the commercial cellulase formulation. RESULTS We report that pre-digestion of biomass with these enzymes at elevated temperatures prior to addition of the commercial cellulase formulation increased conversion rates and yields when compared to commercial cellulase formulation alone under low solids conditions. CONCLUSION Our results demonstrating improvements in rates and yields of conversion point the way forward for hybrid biomass conversion schemes utilizing catalytic amounts of hyperthermophilic enzymes.
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Affiliation(s)
- Roman Brunecky
- />Chemical Biosciences Center, National Renewable Energy Laboratory, 15013, Denver, West Parkway, Golden, CO 80401 USA
| | - Sarah E Hobdey
- />Chemical Biosciences Center, National Renewable Energy Laboratory, 15013, Denver, West Parkway, Golden, CO 80401 USA
| | - Larry E Taylor
- />Chemical Biosciences Center, National Renewable Energy Laboratory, 15013, Denver, West Parkway, Golden, CO 80401 USA
| | - Ling Tao
- />National Bioenergy Center, National Renewable Energy Laboratory, 15013, Denver, West Parkway, Golden, CO 80401 USA
| | - Melvin P Tucker
- />National Bioenergy Center, National Renewable Energy Laboratory, 15013, Denver, West Parkway, Golden, CO 80401 USA
| | - Michael E Himmel
- />Chemical Biosciences Center, National Renewable Energy Laboratory, 15013, Denver, West Parkway, Golden, CO 80401 USA
| | - Stephen R Decker
- />Chemical Biosciences Center, National Renewable Energy Laboratory, 15013, Denver, West Parkway, Golden, CO 80401 USA
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Watanabe T, Ito T, Goda HM, Ishibashi Y, Miyamoto T, Ikeda K, Taguchi R, Okino N, Ito M. Sterylglucoside catabolism in Cryptococcus neoformans with endoglycoceramidase-related protein 2 (EGCrP2), the first steryl-β-glucosidase identified in fungi. J Biol Chem 2014; 290:1005-19. [PMID: 25361768 DOI: 10.1074/jbc.m114.616300] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cryptococcosis is an infectious disease caused by pathogenic fungi, such as Cryptococcus neoformans and Cryptococcus gattii. The ceramide structure (methyl-d18:2/h18:0) of C. neoformans glucosylceramide (GlcCer) is characteristic and strongly related to its pathogenicity. We recently identified endoglycoceramidase-related protein 1 (EGCrP1) as a glucocerebrosidase in C. neoformans and showed that it was involved in the quality control of GlcCer by eliminating immature GlcCer during the synthesis of GlcCer (Ishibashi, Y., Ikeda, K., Sakaguchi, K., Okino, N., Taguchi, R., and Ito, M. (2012) Quality control of fungus-specific glucosylceramide in Cryptococcus neoformans by endoglycoceramidase-related protein 1 (EGCrP1). J. Biol. Chem. 287, 368-381). We herein identified and characterized EGCrP2, a homologue of EGCrP1, as the enzyme responsible for sterylglucoside catabolism in C. neoformans. In contrast to EGCrP1, which is specific to GlcCer, EGCrP2 hydrolyzed various β-glucosides, including GlcCer, cholesteryl-β-glucoside, ergosteryl-β-glucoside, sitosteryl-β-glucoside, and para-nitrophenyl-β-glucoside, but not α-glucosides or β-galactosides, under acidic conditions. Disruption of the EGCrP2 gene (egcrp2) resulted in the accumulation of a glycolipid, the structure of which was determined following purification to ergosteryl-3β-glucoside, a major sterylglucoside in fungi, by mass spectrometric and two-dimensional nuclear magnetic resonance analyses. This glycolipid accumulated in vacuoles and EGCrP2 was detected in vacuole-enriched fraction. These results indicated that EGCrP2 was involved in the catabolism of ergosteryl-β-glucoside in the vacuoles of C. neoformans. Distinct growth arrest, a dysfunction in cell budding, and an abnormal vacuole morphology were detected in the egcrp2-disrupted mutants, suggesting that EGCrP2 may be a promising target for anti-cryptococcal drugs. EGCrP2, classified into glycohydrolase family 5, is the first steryl-β-glucosidase identified as well as a missing link in sterylglucoside metabolism in fungi.
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Affiliation(s)
- Takashi Watanabe
- From the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Tomoharu Ito
- From the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Hatsumi M Goda
- From the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Yohei Ishibashi
- From the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Tomofumi Miyamoto
- the Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazutaka Ikeda
- the Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan, and
| | - Ryo Taguchi
- the Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, 1200 Matsumoto-cho, Kasugai-shi, Aichi 487-8501, Japan
| | - Nozomu Okino
- From the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Makoto Ito
- From the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan,
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Kim MK, An YJ, Song JM, Jeong CS, Kang MH, Kwon KK, Lee YH, Cha SS. Structure-based investigation into the functional roles of the extended loop and substrate-recognition sites in an endo-β-1,4-d-mannanase from the Antarctic springtail,Cryptopygus antarcticus. Proteins 2014; 82:3217-23. [DOI: 10.1002/prot.24655] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/15/2014] [Accepted: 07/21/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Min-Kyu Kim
- Marine Biotechnology Research Division; Korea Institute of Ocean Science and Technology; Ansan 426-744 Republic of Korea
| | - Young Jun An
- Marine Biotechnology Research Division; Korea Institute of Ocean Science and Technology; Ansan 426-744 Republic of Korea
| | - Jung Min Song
- Marine Ecosystem Research Division; Korea Institute of Ocean Science and Technology; Ansan 426-744 Republic of Korea
| | - Chang-Sook Jeong
- Marine Biotechnology Research Division; Korea Institute of Ocean Science and Technology; Ansan 426-744 Republic of Korea
| | - Mee Hye Kang
- Marine Ecosystem Research Division; Korea Institute of Ocean Science and Technology; Ansan 426-744 Republic of Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology Research Division; Korea Institute of Ocean Science and Technology; Ansan 426-744 Republic of Korea
| | - Youn-Ho Lee
- Marine Ecosystem Research Division; Korea Institute of Ocean Science and Technology; Ansan 426-744 Republic of Korea
| | - Sun-Shin Cha
- Marine Biotechnology Research Division; Korea Institute of Ocean Science and Technology; Ansan 426-744 Republic of Korea
- Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School; Korea Maritime and Ocean University; Pusan 606-791 Republic of Korea
- Department of Marine Biotechnology; University of Science and Technology; DaeJeon 305-333 Republic of Korea
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An Aspergillus nidulans β-mannanase with high transglycosylation capacity revealed through comparative studies within glycosidase family 5. Appl Microbiol Biotechnol 2014; 98:10091-104. [PMID: 24950755 PMCID: PMC4237917 DOI: 10.1007/s00253-014-5871-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 05/28/2014] [Accepted: 05/29/2014] [Indexed: 11/03/2022]
Abstract
β-Mannanases are involved in the conversion and modification of mannan-based saccharides. Using a retaining mechanism, they can, in addition to hydrolysis, also potentially perform transglycosylation reactions, synthesizing new glyco-conjugates. Transglycosylation has been reported for β-mannanases in GH5 and GH113. However, although they share the same fold and catalytic mechanism, there may be differences in the enzymes’ ability to perform transglycosylation. Three GH5 β-mannanases from Aspergillus nidulans, AnMan5A, AnMan5B and AnMan5C, which belong to subfamily GH5_7 were studied. Comparative studies, including the GH5_7 TrMan5A from Trichoderma reesei, showed some differences between the enzymes. All the enzymes could perform transglycosylation but AnMan5B stood out in generating comparably higher amounts of transglycosylation products when incubated with manno-oligosaccharides. In addition, AnMan5B did not use alcohols as acceptor, which was also different compared to the other three β-mannanases. In order to map the preferred binding of manno-oligosaccharides, incubations were performed in H218O. AnMan5B in contrary to the other enzymes did not generate any 18O-labelled products. This further supported the idea that AnMan5B potentially prefers to use saccharides as acceptor instead of water. A homology model of AnMan5B showed a non-conserved Trp located in subsite +2, not present in the other studied enzymes. Strong aglycone binding seems to be important for transglycosylation with saccharides. Depending on the application, it is important to select the right enzyme.
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Sammond DW, Yarbrough JM, Mansfield E, Bomble YJ, Hobdey SE, Decker SR, Taylor LE, Resch MG, Bozell JJ, Himmel ME, Vinzant TB, Crowley MF. Predicting enzyme adsorption to lignin films by calculating enzyme surface hydrophobicity. J Biol Chem 2014; 289:20960-9. [PMID: 24876380 DOI: 10.1074/jbc.m114.573642] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The inhibitory action of lignin on cellulase cocktails is a major challenge to the biological saccharification of plant cell wall polysaccharides. Although the mechanism remains unclear, hydrophobic interactions between enzymes and lignin are hypothesized to drive adsorption. Here we evaluate the role of hydrophobic interactions in enzyme-lignin binding. The hydrophobicity of the enzyme surface was quantified using an estimation of the clustering of nonpolar atoms, identifying potential interaction sites. The adsorption of enzymes to lignin surfaces, measured using the quartz crystal microbalance, correlates to the hydrophobic cluster scores. Further, these results suggest a minimum hydrophobic cluster size for a protein to preferentially adsorb to lignin. The impact of electrostatic contribution was ruled out by comparing the isoelectric point (pI) values to the adsorption of proteins to lignin surfaces. These results demonstrate the ability to predict enzyme-lignin adsorption and could potentially be used to design improved cellulase cocktails, thus lowering the overall cost of biofuel production.
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Affiliation(s)
| | | | - Elisabeth Mansfield
- the Applied Chemicals and Materials Division, National Institute for Standards and Technology, Boulder, Colorado 80305, and
| | | | | | | | | | - Michael G Resch
- From the Biosciences Center and National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Joseph J Bozell
- the Center for Renewable Carbon, Center for the Catalytic Conversion of Biomass (C3Bio), University of Tennessee, Knoxville, Tennessee 37917
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Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MWW, Kelly RM. Thermophilic lignocellulose deconstruction. FEMS Microbiol Rev 2014; 38:393-448. [DOI: 10.1111/1574-6976.12044] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 08/20/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022] Open
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49
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Wang K, Luo H, Bai Y, Shi P, Huang H, Xue X, Yao B. A thermophilic endo-1,4-β-glucanase from Talaromyces emersonii CBS394.64 with broad substrate specificity and great application potentials. Appl Microbiol Biotechnol 2014; 98:7051-60. [DOI: 10.1007/s00253-014-5680-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/05/2014] [Accepted: 03/09/2014] [Indexed: 10/25/2022]
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50
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Improving the specific activity of β-mannanase from Aspergillus niger BK01 by structure-based rational design. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:663-9. [DOI: 10.1016/j.bbapap.2014.01.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 12/24/2013] [Accepted: 01/22/2014] [Indexed: 11/20/2022]
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