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Kholousi Adab F, Mehdi Yaghoobi M, Gharechahi J. Enhanced crystalline cellulose degradation by a novel metagenome-derived cellulase enzyme. Sci Rep 2024; 14:8560. [PMID: 38609443 PMCID: PMC11014956 DOI: 10.1038/s41598-024-59256-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
Metagenomics has revolutionized access to genomic information of microorganisms inhabiting the gut of herbivorous animals, circumventing the need for their isolation and cultivation. Exploring these microorganisms for novel hydrolytic enzymes becomes unattainable without utilizing metagenome sequencing. In this study, we harnessed a suite of bioinformatic analyses to discover a novel cellulase-degrading enzyme from the camel rumen metagenome. Among the protein-coding sequences containing cellulase-encoding domains, we identified and subsequently cloned and purified a promising candidate cellulase enzyme, Celcm05-2, to a state of homogeneity. The enzyme belonged to GH5 subfamily 4 and exhibited robust enzymatic activity under acidic pH conditions. It maintained hydrolytic activity under various environmental conditions, including the presence of metal ions, non-ionic surfactant Triton X-100, organic solvents, and varying temperatures. With an optimal temperature of 40 °C, Celcm05-2 showcased remarkable efficiency when deployed on crystalline cellulose (> 3.6 IU/mL), specifically Avicel, thereby positioning it as an attractive candidate for a myriad of biotechnological applications spanning biofuel production, paper and pulp processing, and textile manufacturing. Efficient biodegradation of waste paper pulp residues and the evidence of biopolishing suggested that Celcm05-2 can be used in the bioprocessing of cellulosic craft fabrics in the textile industry. Our findings suggest that the camel rumen microbiome can be mined for novel cellulase enzymes that can find potential applications across diverse biotechnological processes.
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Affiliation(s)
- Faezeh Kholousi Adab
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Mohammad Mehdi Yaghoobi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
| | - Javad Gharechahi
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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2
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Han X, Ding N, Ban X, Gu Z, Cheng L, Hong Y, Li C, Li Z. Fusion of maltooligosaccharide-forming amylases from two origins for the improvement of maltopentaose synthesis. Food Res Int 2021; 150:110735. [PMID: 34865754 DOI: 10.1016/j.foodres.2021.110735] [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: 02/17/2021] [Revised: 09/02/2021] [Accepted: 09/25/2021] [Indexed: 01/10/2023]
Abstract
Maltopentaose-forming amylases are promising enzymes for their ability to hydrolyze starch and produce functional maltooligosaccharides. Two maltopentaose-forming amylase genes from Bacillus megaterium (BmMFA) and Saccharophagus degradans (SdMFA) were expressed heterologously and their characteristics were analyzed. BmMFA has substantial thermostability and SdMFA owns superior product specificity. The carbohydrate-binding module of SdMFA was fused with BmMFA and the fused protein showed ideal enzymatic properties and displayed potential for industrial production of maltopentaose. Under the optimized conditions, the final product containing 47.41% maltopentaose was obtained with a conversion rate of 92.67% from starch. This study provides a novel strategy for the directed modification of MFAses through protein fusion approach.
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Affiliation(s)
- Xu Han
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Ning Ding
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Xiaofeng Ban
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, PR China
| | - Li Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, PR China
| | - Yan Hong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, PR China
| | - Caiming Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, PR China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, PR China.
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3
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Thakur K, Shlain MA, Marianski M, Braunschweig AB. Regiochemical Effects on the Carbohydrate Binding and Selectivity of Flexible Synthetic Carbohydrate Receptors with Indole and Quinoline Heterocyclic Groups. European J Org Chem 2021; 2021:5262-5274. [PMID: 35694139 PMCID: PMC9186342 DOI: 10.1002/ejoc.202100763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Indexed: 08/07/2023]
Abstract
Synthetic carbohydrate receptors (SCRs) that bind cell-surface carbohydrates could be used for disease detection, drug-delivery, and therapeutics, or for the site-selective modification of complex carbohydrates but their potential has not been realized because of remaining challenges associated with binding affinity and substrate selectivity. We have reported recently a series of flexible SCRs based upon a biaryl core with four pendant heterocyclic groups that bind glycans selectively through noncovalent interactions. Here we continue to explore the role of heterocycles on substrate selectivity by expanding our library to include a series of indole and quinoline heterocycles that vary in their regiochemistry of attachment to the biaryl core. The binding of these SCRs to a series of biologically-relevant carbohydrates was studied by 1H NMR titrations in CD2Cl2 and density-functional theory calculations. We find SCR030, SCR034 and SCR037 are selective, SCR031, SCR032, and SCR039 are strong binders, and SCR033, SCR035, SCR036, and SCR038 are promiscuous and bind weakly. Computational analysis reveals the importance of C-H⋯π and H-bonding interactions in defining the binding properties of these new receptors. By combining these data with those obtained from our previous studies on this class of flexible SCRs, we develop a series of design rules that account for the binding of all SCRs of this class and anticipate the binding of future, not-yet imagined tetrapodal SCRs.
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Affiliation(s)
- Khushabu Thakur
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York 85 St Nicholas Terrace, New York, NY 10031 (USA)
- Department of Chemistry and Biochemistry, Hunter College 695 Park Ave, New York, NY 10065 (USA)
| | - Milan A Shlain
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York 85 St Nicholas Terrace, New York, NY 10031 (USA)
- Department of Chemistry and Biochemistry, Hunter College 695 Park Ave, New York, NY 10065 (USA)
| | - Mateusz Marianski
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York 85 St Nicholas Terrace, New York, NY 10031 (USA)
- Department of Chemistry and Biochemistry, Hunter College 695 Park Ave, New York, NY 10065 (USA)
- The PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 5 Ave, New York, NY 10016 (USA)
- The PhD Program in Biochemistry, The Graduate Center of the City University of New York, 365 5 Ave, New York, NY 10016 (USA)
| | - Adam B Braunschweig
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York 85 St Nicholas Terrace, New York, NY 10031 (USA)
- Department of Chemistry and Biochemistry, Hunter College 695 Park Ave, New York, NY 10065 (USA)
- The PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 5 Ave, New York, NY 10016 (USA)
- The PhD Program in Biochemistry, The Graduate Center of the City University of New York, 365 5 Ave, New York, NY 10016 (USA)
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4
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Møller MS, El Bouaballati S, Henrissat B, Svensson B. Functional diversity of three tandem C-terminal carbohydrate-binding modules of a β-mannanase. J Biol Chem 2021; 296:100638. [PMID: 33838183 PMCID: PMC8121702 DOI: 10.1016/j.jbc.2021.100638] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 03/29/2021] [Accepted: 04/05/2021] [Indexed: 11/16/2022] Open
Abstract
Carbohydrate active enzymes, such as those involved in plant cell wall and storage polysaccharide biosynthesis and deconstruction, often contain repeating noncatalytic carbohydrate-binding modules (CBMs) to compensate for low-affinity binding typical of protein–carbohydrate interactions. The bacterium Saccharophagus degradans produces an endo-β-mannanase of glycoside hydrolase family 5 subfamily 8 with three phylogenetically distinct family 10 CBMs located C-terminally from the catalytic domain (SdGH5_8-CBM10x3). However, the functional roles and cooperativity of these CBM domains in polysaccharide binding are not clear. To learn more, we studied the full-length enzyme, three stepwise CBM family 10 (CBM10) truncations, and GFP fusions of the individual CBM10s and all three domains together by pull-down assays, affinity gel electrophoresis, and activity assays. Only the C-terminal CBM10-3 was found to bind strongly to microcrystalline cellulose (dissociation constant, Kd = 1.48 μM). CBM10-3 and CBM10-2 bound galactomannan with similar affinity (Kd = 0.2–0.4 mg/ml), but CBM10-1 had 20-fold lower affinity for this substrate. CBM10 truncations barely affected specific activity on carob galactomannan and konjac glucomannan. Full-length SdGH5_8-CBM10x3 was twofold more active on the highly galactose-decorated viscous guar gum galactomannan and crystalline ivory nut mannan at high enzyme concentrations, but the specific activity was fourfold to ninefold reduced at low enzyme and substrate concentrations compared with the enzyme lacking CBM10-2 and CBM10-3. Comparison of activity and binding data for the different enzyme forms indicates unproductive and productive polysaccharide binding to occur. We conclude that the C-terminal-most CBM10-3 secures firm binding, with contribution from CBM10-2, which with CBM10-1 also provides spatial flexibility.
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Affiliation(s)
- Marie Sofie Møller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
| | - Souad El Bouaballati
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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5
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Madland E, Crasson O, Vandevenne M, Sørlie M, Aachmann FL. NMR and Fluorescence Spectroscopies Reveal the Preorganized Binding Site in Family 14 Carbohydrate-Binding Module from Human Chitotriosidase. ACS OMEGA 2019; 4:21975-21984. [PMID: 31891077 PMCID: PMC6933781 DOI: 10.1021/acsomega.9b03043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/26/2019] [Indexed: 05/02/2023]
Abstract
Carbohydrate-binding modules (CBM) play important roles in targeting and increasing the concentration of carbohydrate active enzymes on their substrates. Using NMR to get the solution structure of CBM14, we can gain insight into secondary structure elements and intramolecular interactions with our assigned nuclear overhauser effect peaks. This reveals that two conserved aromatic residues (Phe437 and Phe456) make up the hydrophobic core of the CBM. These residues are also responsible for connecting the two β-sheets together, by being part of β2 and β4, respectively, and together with disulfide bridges, they create CBM14's characteristic "hevein-like" fold. Most CBMs rely on aromatic residues for substrate binding; however, CBM14 contains just a single tryptophan (Trp465) that together with Asn466 enables substrate binding. Interestingly, an alanine mutation of a single residue (Leu454) located behind Trp465 renders the CBM incapable of binding. Fluorescence spectroscopy performed on this mutant reveals a significant blue shift, as well as a minor blue shift for its neighbor Val455. The reduction in steric hindrance causes the tryptophan to be buried into the hydrophobic core of the structure and therefore suggests a preorganized binding site for this CBM. Our results show that both Trp465 and Asn466 are affected when CBM14 interacts with both (GlcNAc)3 and β-chitin, that the binding interactions are weak, and that CBM14 displays a slightly higher affinity toward β-chitin.
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Affiliation(s)
- Eva Madland
- Department
of Biotechnology and Food Science, Norwegian Biopolymer Laboratory
(NOBIPOL), NTNU Norwegian University of
Science and Technology, Trondheim 7491, Norway
| | - Oscar Crasson
- InBioS—Center
for Protein Engineering, Institut de Chimie B6a, Université de Liège, Sart-Tilman, Liège 4000, Belgium
| | - Maryléne Vandevenne
- InBioS—Center
for Protein Engineering, Institut de Chimie B6a, Université de Liège, Sart-Tilman, Liège 4000, Belgium
| | - Morten Sørlie
- Department
of Chemistry, Biotechnology and Food Science, NMBU Norwegian University of Life Sciences, Ås 1430, Norway
| | - Finn L. Aachmann
- Department
of Biotechnology and Food Science, Norwegian Biopolymer Laboratory
(NOBIPOL), NTNU Norwegian University of
Science and Technology, Trondheim 7491, Norway
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6
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Huang HC, Qi LH, Chen YC, Tsai LC. Crystal structures of the GH6 Orpinomyces sp. Y102 CelC7 enzyme with exo and endo activity and its complex with cellobiose. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:1138-1147. [PMID: 31793907 DOI: 10.1107/s2059798319013597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/04/2019] [Indexed: 11/10/2022]
Abstract
The catalytic domain (residues 128-449) of the Orpinomyces sp. Y102 CelC7 enzyme (Orp CelC7) exhibits cellobiohydrolase and cellotriohydrolase activities. Crystal structures of Orp CelC7 and its cellobiose-bound complex have been solved at resolutions of 1.80 and 2.78 Å, respectively. Cellobiose occupies subsites +1 and +2 within the active site of Orp CelC7 and forms hydrogen bonds to two key residues: Asp248 and Asp409. Furthermore, its substrate-binding sites have both tunnel-like and open-cleft conformations, suggesting that the glycoside hydrolase family 6 (GH6) Orp CelC7 enzyme may perform enzymatic hydrolysis in the same way as endoglucanases and cellobiohydrolases. LC-MS/MS analysis revealed cellobiose (major) and cellotriose (minor) to be the respective products of endo and exo activity of the GH6 Orp CelC7.
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Affiliation(s)
- Hsiao Chuan Huang
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei, Taiwan
| | - Liu Hong Qi
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei, Taiwan
| | - Yo Chia Chen
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Li Chu Tsai
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei, Taiwan
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7
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Voiniciuc C, Pauly M, Usadel B. Monitoring Polysaccharide Dynamics in the Plant Cell Wall. PLANT PHYSIOLOGY 2018; 176:2590-2600. [PMID: 29487120 PMCID: PMC5884611 DOI: 10.1104/pp.17.01776] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/07/2018] [Indexed: 05/18/2023]
Abstract
New technologies reveal the deposition and remodeling of plant cell wall polysaccharides and their impact on plant development.
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Affiliation(s)
- Cătălin Voiniciuc
- Institute for Plant Cell Biology and Biotechnology and Cluster of Excellence on Plant Sciences, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Markus Pauly
- Institute for Plant Cell Biology and Biotechnology and Cluster of Excellence on Plant Sciences, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Björn Usadel
- Institute for Biology I, BioSC, RWTH Aachen University, 52074 Aachen, Germany
- Forschungszentum Jülich, IBG-2 Plant Sciences, 52428 Juelich, Germany
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8
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Liu S, Ding S. Replacement of carbohydrate binding modules improves acetyl xylan esterase activity and its synergistic hydrolysis of different substrates with xylanase. BMC Biotechnol 2016; 16:73. [PMID: 27770795 PMCID: PMC5075172 DOI: 10.1186/s12896-016-0305-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/13/2016] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Acetylation of the xylan backbone was a major obstacle to enzymatic decomposition. Removal of acetyl groups by acetyl xylan esterases (AXEs) is essential for completely enzymatic hydrolysis of xylan. Appended carbohydrate binding modules (CBMs) can promote the enzymatic deconstruction of plant cell walls by targeting and proximity effects. Fungal acetyl xylan esterases are strictly appended to cellulose-specific CBM1. It is still unclear whether xylan-specific CBMs have a greater advantage than CBM1 in potentiating the activity of fungal deacetylating enzymes and its synergistic hydrolysis of different substrates with xylanase. RESULTS Three recombinant AXE1s fused with different xylan-specific CBMs, together with wild-type AXE1 with CBM1 and CBM1-deleted mutant AXE1dC, were constructed in this study. The optimal temperature and pH of recombinant AXE1s was 50 °C and 8.0 (except AXE1dC-CBM6), respectively. Cellulose-specific CBM1 in AXE1 obviously contributed to its catalytic action against substrates compared with AXE1dC. However, replacement of CBM1 with xylan-specific CBM4-2 significantly enhanced AXE1 thermostability and catalytic activity against soluble substrate 4-methylumbelliferyl acetate. Whereas replacements with xylan-specific CBM6 and CBM22-2 were more effective in enzymatic release of acetic acid from destarched wheat bran, NaClO2-treated wheat straw, and water-insoluble wheat arabinoxylan compared to AXE1. Moreover, replacement with CBM6 and CBM22-2 also resulted in higher degree releases of reducing sugar and acetic acid from different substrates when simultaneous hydrolysis with xylanase. A good linear relationship exists between the acetic acid and reducing sugar release. CONCLUSIONS Our findings suggested that the replacement with CBM6 and CBM22-2 not only significantly improved the catalysis efficiency of AXE1, but also increased its synergistic hydrolysis of different substrates with xylanase, indicating the significance of targeting effect in AXE1 catalysis mediated by xylan-specific CBMs.
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Affiliation(s)
- Shiping Liu
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Shaojun Ding
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
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9
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Das SN, Wagenknecht M, Nareddy PK, Bhuvanachandra B, Niddana R, Balamurugan R, Swamy MJ, Moerschbacher BM, Podile AR. Amino Groups of Chitosan Are Crucial for Binding to a Family 32 Carbohydrate Binding Module of a Chitosanase from Paenibacillus elgii. J Biol Chem 2016; 291:18977-90. [PMID: 27405759 DOI: 10.1074/jbc.m116.721332] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Indexed: 11/06/2022] Open
Abstract
We report here the role and mechanism of specificity of a family 32 carbohydrate binding module (CBM32) of a glycoside hydrolase family 8 chitosanase from Paenibacillus elgii (PeCsn). Both the activity and mode of action of PeCsn toward soluble chitosan polymers were not different with/without the CBM32 domain of P. elgii (PeCBM32). The decreased activity of PeCsn without PeCBM32 on chitosan powder suggested that PeCBM32 increases the relative concentration of enzyme on the substrate and thereby enhanced enzymatic activity. PeCBM32 specifically bound to polymeric and oligomeric chitosan and showed very weak binding to chitin and cellulose. In isothermal titration calorimetry, the binding stoichiometry of 2 and 1 for glucosamine monosaccharide (GlcN) and disaccharide (GlcN)2, respectively, was indicative of two binding sites in PeCBM32. A three-dimensional model-guided site-directed mutagenesis and the use of defined disaccharides varying in the pattern of acetylation suggested that the amino groups of chitosan and the polar residues Glu-16 and Glu-38 of PeCBM32 play a crucial role for the observed binding. The specificity of CBM32 has been further elucidated by a generated fusion protein PeCBM32-eGFP that binds to the chitosan exposing endophytic infection structures of Puccinia graminis f. sp. tritici Phylogenetic analysis showed that CBM32s appended to chitosanases are highly conserved across different chitosanase families suggesting their role in chitosan recognition and degradation. We have identified and characterized a chitosan-specific CBM32 useful for in situ staining of chitosans in the fungal cell wall during plant-fungus interaction.
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Affiliation(s)
| | - Martin Wagenknecht
- the Institute of Plant Biology and Biotechnology, Westphalian Wilhelms-University of Münster, 48143 Münster, Germany
| | | | | | - Ramana Niddana
- School of Chemistry, University of Hyderabad, 500046-Hyderabad, India and
| | | | - Musti J Swamy
- School of Chemistry, University of Hyderabad, 500046-Hyderabad, India and
| | - Bruno M Moerschbacher
- the Institute of Plant Biology and Biotechnology, Westphalian Wilhelms-University of Münster, 48143 Münster, Germany
| | - Appa Rao Podile
- From the Department of Plant Sciences, School of Life Sciences,
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10
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Gardner JG. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus. World J Microbiol Biotechnol 2016; 32:121. [PMID: 27263016 DOI: 10.1007/s11274-016-2068-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 04/07/2016] [Indexed: 01/10/2023]
Abstract
Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. This review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkable ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications.
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Affiliation(s)
- Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA.
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11
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Crouch LI, Labourel A, Walton PH, Davies GJ, Gilbert HJ. The Contribution of Non-catalytic Carbohydrate Binding Modules to the Activity of Lytic Polysaccharide Monooxygenases. J Biol Chem 2016; 291:7439-49. [PMID: 26801613 PMCID: PMC4817175 DOI: 10.1074/jbc.m115.702365] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Indexed: 01/23/2023] Open
Abstract
Lignocellulosic biomass is a sustainable industrial substrate. Copper-dependent lytic polysaccharide monooxygenases (LPMOs) contribute to the degradation of lignocellulose and increase the efficiency of biofuel production. LPMOs can contain non-catalytic carbohydrate binding modules (CBMs), but their role in the activity of these enzymes is poorly understood. Here we explored the importance of CBMs in LPMO function. The family 2a CBMs of two monooxygenases,CfLPMO10 andTbLPMO10 fromCellulomonas fimiandThermobispora bispora, respectively, were deleted and/or replaced with CBMs from other proteins. The data showed that the CBMs could potentiate and, surprisingly, inhibit LPMO activity, and that these effects were both enzyme-specific and substrate-specific. Removing the natural CBM or introducingCtCBM3a, from theClostridium thermocellumcellulosome scaffoldin CipA, almost abolished the catalytic activity of the LPMOs against the cellulosic substrates. The deleterious effect of CBM removal likely reflects the importance of prolonged presentation of the enzyme on the surface of the substrate for efficient catalytic activity, as only LPMOs appended to CBMs bound tightly to cellulose. The negative impact ofCtCBM3a is in sharp contrast with the capacity of this binding module to potentiate the activity of a range of glycoside hydrolases including cellulases. The deletion of the endogenous CBM fromCfLPMO10 or the introduction of a family 10 CBM fromCellvibrio japonicusLPMO10B intoTbLPMO10 influenced the quantity of non-oxidized products generated, demonstrating that CBMs can modulate the mode of action of LPMOs. This study demonstrates that engineered LPMO-CBM hybrids can display enhanced industrially relevant oxygenations.
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Affiliation(s)
- Lucy I Crouch
- From the Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Newcastle upon Tyne NE2 4HH and
| | - Aurore Labourel
- From the Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Newcastle upon Tyne NE2 4HH and
| | - Paul H Walton
- the York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Gideon J Davies
- the York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Harry J Gilbert
- From the Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Newcastle upon Tyne NE2 4HH and
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12
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Expression and characteristics of a Ca2+-dependent endoglucanase from Cytophaga hutchinsonii. Appl Microbiol Biotechnol 2015; 99:9617-23. [DOI: 10.1007/s00253-015-6746-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/27/2015] [Accepted: 05/29/2015] [Indexed: 10/23/2022]
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13
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Walker JA, Takasuka TE, Deng K, Bianchetti CM, Udell HS, Prom BM, Kim H, Adams PD, Northen TR, Fox BG. Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:220. [PMID: 26697109 PMCID: PMC4687162 DOI: 10.1186/s13068-015-0402-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/30/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND Carbohydrate binding modules (CBMs) bind polysaccharides and help target glycoside hydrolases catalytic domains to their appropriate carbohydrate substrates. To better understand how CBMs can improve cellulolytic enzyme reactivity, representatives from each of the 18 families of CBM found in Ruminoclostridium thermocellum were fused to the multifunctional GH5 catalytic domain of CelE (Cthe_0797, CelEcc), which can hydrolyze numerous types of polysaccharides including cellulose, mannan, and xylan. Since CelE is a cellulosomal enzyme, none of these fusions to a CBM previously existed. RESULTS CelEcc_CBM fusions were assayed for their ability to hydrolyze cellulose, lichenan, xylan, and mannan. Several CelEcc_CBM fusions showed enhanced hydrolytic activity with different substrates relative to the fusion to CBM3a from the cellulosome scaffoldin, which has high affinity for binding to crystalline cellulose. Additional binding studies and quantitative catalysis studies using nanostructure-initiator mass spectrometry (NIMS) were carried out with the CBM3a, CBM6, CBM30, and CBM44 fusion enzymes. In general, and consistent with observations of others, enhanced enzyme reactivity was correlated with moderate binding affinity of the CBM. Numerical analysis of reaction time courses showed that CelEcc_CBM44, a combination of a multifunctional enzyme domain with a CBM having broad binding specificity, gave the fastest rates for hydrolysis of both the hexose and pentose fractions of ionic-liquid pretreated switchgrass. CONCLUSION We have shown that fusions of different CBMs to a single multifunctional GH5 catalytic domain can increase its rate of reaction with different pure polysaccharides and with pretreated biomass. This fusion approach, incorporating domains with broad specificity for binding and catalysis, provides a new avenue to improve reactivity of simple combinations of enzymes within the complexity of plant biomass.
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Affiliation(s)
- Johnnie A. Walker
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Taichi E. Takasuka
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Kai Deng
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Sandia National Laboratories, Livermore, CA 94551 USA
| | - Christopher M. Bianchetti
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Chemistry, University of Wisconsin-Oshkosh, Oshkosh, WI 54901 USA
| | - Hannah S. Udell
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Ben M. Prom
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Hyunkee Kim
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Paul D. Adams
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- />Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Trent R. Northen
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Brian G. Fox
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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14
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Zhang X, Rogowski A, Zhao L, Hahn MG, Avci U, Knox JP, Gilbert HJ. Understanding how the complex molecular architecture of mannan-degrading hydrolases contributes to plant cell wall degradation. J Biol Chem 2014; 289:2002-12. [PMID: 24297170 PMCID: PMC3900950 DOI: 10.1074/jbc.m113.527770] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 11/25/2013] [Indexed: 12/16/2022] Open
Abstract
Microbial degradation of plant cell walls is a central component of the carbon cycle and is of increasing importance in environmentally significant industries. Plant cell wall-degrading enzymes have a complex molecular architecture consisting of catalytic modules and, frequently, multiple non-catalytic carbohydrate binding modules (CBMs). It is currently unclear whether the specificities of the CBMs or the topology of the catalytic modules are the primary drivers for the specificity of these enzymes against plant cell walls. Here, we have evaluated the relationship between CBM specificity and their capacity to enhance the activity of GH5 and GH26 mannanases and CE2 esterases against intact plant cell walls. The data show that cellulose and mannan binding CBMs have the greatest impact on the removal of mannan from tobacco and Physcomitrella cell walls, respectively. Although the action of the GH5 mannanase was independent of the context of mannan in tobacco cell walls, a significant proportion of the polysaccharide was inaccessible to the GH26 enzyme. The recalcitrant mannan, however, was fully accessible to the GH26 mannanase appended to a cellulose binding CBM. Although CE2 esterases display similar specificities against acetylated substrates in vitro, only CjCE2C was active against acetylated mannan in Physcomitrella. Appending a mannan binding CBM27 to CjCE2C potentiated its activity against Physcomitrella walls, whereas a xylan binding CBM reduced the capacity of esterases to deacetylate xylan in tobacco walls. This work provides insight into the biological significance for the complex array of hydrolytic enzymes expressed by plant cell wall-degrading microorganisms.
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Affiliation(s)
- Xiaoyang Zhang
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle-upon-Tyne, NE 4HH, United Kingdom
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, and
| | - Artur Rogowski
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle-upon-Tyne, NE 4HH, United Kingdom
| | - Lei Zhao
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, and
| | - Michael G. Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, and
| | - Utku Avci
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, and
| | - J. Paul Knox
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Harry J. Gilbert
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle-upon-Tyne, NE 4HH, United Kingdom
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, and
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15
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Yadav MK, Chuck RS, Park CY. Composition of Artificial Tear Solution AffectsIn Vitro Pseudomonas aeruginosaBiofilm Formation on Silicone Hydrogel Lens. J Ocul Pharmacol Ther 2013; 29:591-4. [DOI: 10.1089/jop.2012.0078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Mukesh Kumar Yadav
- Department of Ophthalmology, Ilsan Hospital, Dongguk University, Koyang, Kyunggido, South Korea
| | - Roy S. Chuck
- Department of Ophthalmology and Visual Sciences, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York
| | - Choul Yong Park
- Department of Ophthalmology, Ilsan Hospital, Dongguk University, Koyang, Kyunggido, South Korea
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16
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Kim HD, Choi SL, Kim H, Sohn JH, Lee SG. Enzyme-linked assay of cellulose-binding domain functions from Cellulomonas fimi on multi-well microtiter plate. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-013-0242-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Fujimoto Z, Jackson A, Michikawa M, Maehara T, Momma M, Henrissat B, Gilbert HJ, Kaneko S. The structure of a Streptomyces avermitilis α-L-rhamnosidase reveals a novel carbohydrate-binding module CBM67 within the six-domain arrangement. J Biol Chem 2013; 288:12376-85. [PMID: 23486481 DOI: 10.1074/jbc.m113.460097] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
α-L-rhamnosidases hydrolyze α-linked L-rhamnosides from oligosaccharides or polysaccharides. We determined the crystal structure of the glycoside hydrolase family 78 Streptomyces avermitilis α-L-rhamnosidase (SaRha78A) in its free and L-rhamnose complexed forms, which revealed the presence of six domains N, D, E, F, A, and C. In the ligand complex, L-rhamnose was bound in the proposed active site of the catalytic module, revealing the likely catalytic mechanism of SaRha78A. Glu(636) is predicted to donate protons to the glycosidic oxygen, and Glu(895) is the likely catalytic general base, activating the nucleophilic water, indicating that the enzyme operates through an inverting mechanism. Replacement of Glu(636) and Glu(895) resulted in significant loss of α-rhamnosidase activity. Domain D also bound L-rhamnose in a calcium-dependent manner, with a KD of 135 μm. Domain D is thus a non-catalytic carbohydrate binding module (designated SaCBM67). Mutagenesis and structural data identified the amino acids in SaCBM67 that target the features of L-rhamnose that distinguishes it from the other major sugars present in plant cell walls. Inactivation of SaCBM67 caused a substantial reduction in the activity of SaRha78A against the polysaccharide composite gum arabic, but not against aryl rhamnosides, indicating that SaCBM67 contributes to enzyme function against insoluble substrates.
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Affiliation(s)
- Zui Fujimoto
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan.
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18
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Zhang J, Moilanen U, Tang M, Viikari L. The carbohydrate-binding module of xylanase from Nonomuraea flexuosa decreases its non-productive adsorption on lignin. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:18. [PMID: 23363927 PMCID: PMC3577619 DOI: 10.1186/1754-6834-6-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 01/21/2013] [Indexed: 05/08/2023]
Abstract
BACKGROUND The enzymatic hydrolysis step converting lignocellulosic materials into fermentable sugars is recognized as one of the major limiting steps in biomass-to-ethanol process due to the low efficiency of enzymes and their cost. Xylanases have been found to be important in the improvement of the hydrolysis of cellulose due to the close interaction of cellulose and xylan. In this work, the effects of carbohydrate-binding module (CBM family II) of the xylanase 11 from Nonomuraea flexuosa (Nf Xyn11) on the adsorption and hydrolytic efficiency toward isolated xylan and lignocellulosic materials were investigated. RESULTS The intact family 11 xylanase of N. flexuosa clearly adsorbed on wheat straw and lignin, following the Langmuir-type isotherm. The presence of the CBM in the xylanase increased the adsorption and hydrolytic efficiency on insoluble oat spelt xylan. But the presence of the CBM did not increase adsorption on pretreated wheat straw or isolated lignin. On the contrary, the CBM decreased the adsorption of the core protein to lignin containing substrates, indicating that the CBM of N. flexuosa xylanase did not contribute to the non-productive adsorption. CONCLUSION The CBM of the N. flexuosa xylanase was shown to be a xylan-binding module, which had low affinity on cellulose. The CBM of the N. flexuosa xylanase reduced the non-specific adsorption of the core protein to lignin and showed potential for improving the hydrolysis of lignocellulosic materials to platform sugars.
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Affiliation(s)
- Junhua Zhang
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, China
| | - Ulla Moilanen
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 27, Helsinki, Finland
| | - Ming Tang
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, China
| | - Liisa Viikari
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 27, Helsinki, Finland
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19
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How nature can exploit nonspecific catalytic and carbohydrate binding modules to create enzymatic specificity. Proc Natl Acad Sci U S A 2012; 109:20889-94. [PMID: 23213210 DOI: 10.1073/pnas.1212034109] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Noncatalytic carbohydrate binding modules (CBMs) are components of glycoside hydrolases that attack generally inaccessible substrates. CBMs mediate a two- to fivefold elevation in the activity of endo-acting enzymes, likely through increasing the concentration of the appended enzymes in the vicinity of the substrate. The function of CBMs appended to exo-acting glycoside hydrolases is unclear because their typical endo-binding mode would not fulfill a targeting role. Here we show that the Bacillus subtilis exo-acting β-fructosidase SacC, which specifically hydrolyses levan, contains the founding member of CBM family 66 (CBM66). The SacC-derived CBM66 (BsCBM66) targets the terminal fructosides of the major fructans found in nature. The crystal structure of BsCBM66 in complex with ligands reveals extensive interactions with the terminal fructose moiety (Fru-3) of levantriose but only limited hydrophobic contacts with Fru-2, explaining why the CBM displays broad specificity. Removal of BsCBM66 from SacC results in a ~100-fold reduction in activity against levan. The truncated enzyme functions as a nonspecific β-fructosidase displaying similar activity against β-2,1- and β-2,6-linked fructans and their respective fructooligosaccharides. Conversely, appending BsCBM66 to BT3082, a nonspecific β-fructosidase from Bacteroides thetaiotaomicron, confers exolevanase activity on the enzyme. We propose that BsCBM66 confers specificity for levan, a branched fructan, through an "avidity" mechanism in which the CBM and the catalytic module target the termini of different branches of the same polysaccharide molecule. This report identifies a unique mechanism by which CBMs modulate enzyme function, and shows how specificity can be tailored by integrating nonspecific catalytic and binding modules into a single enzyme.
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20
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Pourramezan Z, Ghezelbash GR, Romani B, Ziaei S, Hedayatkhah A. Screening and identification of newly isolated cellulose-degrading bacteria from the gut of xylophagous termite Microcerotermes diversus (Silvestri). Microbiology (Reading) 2012. [DOI: 10.1134/s0026261712060124] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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21
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Stephen P, Cheng KC, Lyu PC. Crystal structure of circular permuted RoCBM21 (CP90): dimerisation and proximity of binding sites. PLoS One 2012; 7:e50488. [PMID: 23226294 PMCID: PMC3511584 DOI: 10.1371/journal.pone.0050488] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Accepted: 10/22/2012] [Indexed: 11/20/2022] Open
Abstract
Glucoamylases, containing starch-binding domains (SBD), have a wide range of scientific and industrial applications. Random mutagenesis and DNA shuffling of the gene encoding a starch-binding domain have resulted in only minor improvements in the affinities of the corresponding protein to their ligands, whereas circular permutation of the RoCBM21 substantially improved its binding affinity and selectivity towards longer-chain carbohydrates. For the study reported herein, we used a standard soluble ligand (amylose EX-I) to characterize the functional and structural aspects of circularly permuted RoCBM21 (CP90). Site-directed mutagenesis and the analysis of crystal structure reveal the dimerisation and an altered binding path, which may be responsible for improved affinity and altered selectivity of this newly created starch-binding domain. The functional and structural characterization of CP90 suggests that it has significant potential in industrial applications.
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Affiliation(s)
- Preyesh Stephen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Kuo-Chang Cheng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Medical Sciences, National Tsing Hua University, Hsinchu, Taiwan
- Graduate Institute of Molecular Systems Biomedicine, China Medical University, Taichung, Taiwan
- * E-mail:
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22
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Jiang TY, Ci YP, Chou WI, Lee YC, Sun YJ, Chou WY, Li KM, Chang MDT. Two unique ligand-binding clamps of Rhizopus oryzae starch binding domain for helical structure disruption of amylose. PLoS One 2012; 7:e41131. [PMID: 22815939 PMCID: PMC3398936 DOI: 10.1371/journal.pone.0041131] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 06/17/2012] [Indexed: 11/30/2022] Open
Abstract
The N-terminal starch binding domain of Rhizopus oryzae glucoamylase (RoSBD) has a high binding affinity for raw starch. RoSBD has two ligand-binding sites, each containing a ligand-binding clamp: a polyN clamp residing near binding site I is unique in that it is expressed in only three members of carbohydrate binding module family 21 (CBM21) members, and a Y32/F58 clamp located at binding site II is conserved in several CBMs. Here we characterized different roles of these sites in the binding of insoluble and soluble starches using an amylose-iodine complex assay, atomic force microscopy, isothermal titration calorimetry, site-directed mutagenesis, and structural bioinformatics. RoSBD induced the release of iodine from the amylose helical cavity and disrupted the helical structure of amylose type III, thereby significantly diminishing the thickness and length of the amylose type III fibrils. A point mutation in the critical ligand-binding residues of sites I and II, however, reduced both the binding affinity and amylose helix disruption. This is the first molecular model for structure disruption of the amylose helix by a non-hydrolytic CBM21 member. RoSBD apparently twists the helical amylose strands apart to expose more ligand surface for further SBD binding. Repeating the process triggers the relaxation and unwinding of amylose helices to generate thinner and shorter amylose fibrils, which are more susceptible to hydrolysis by glucoamylase. This model aids in understanding the natural roles of CBMs in protein-glycan interactions and contributes to potential molecular engineering of CBMs.
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Affiliation(s)
- Ting-Ying Jiang
- Institute of Molecular and Cellular Biology and Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Yuan-Pei Ci
- Institute of Molecular and Cellular Biology and Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Wei-I Chou
- Institute of Molecular and Cellular Biology and Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- Simpson Biotech Company, Ltd., Taoyuan County, Taiwan, Republic of China
| | - Yuan-Chuan Lee
- Institute of Molecular and Cellular Biology and Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Yuh-Ju Sun
- Institute of Bioinformatics and Structural Biology and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Wei-Yao Chou
- Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Kun-Mou Li
- Institute of Bioinformatics and Structural Biology and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Margaret Dah-Tsyr Chang
- Institute of Molecular and Cellular Biology and Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- * E-mail:
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23
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Production and characterization of a bacteriocin from ruminal bacterium Ruminococcus albus 7. Biosci Biotechnol Biochem 2012; 76:34-41. [PMID: 22232237 DOI: 10.1271/bbb.110348] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The characteristics of a bacteriocin from Ruminococcus albus 7 and its potential as an antibiotic alternative were examined in this study. The addition of 3 µM 3-phenylpropanoic acid (PPA) and 0.2% Tween 80 to the culturing medium improved bacteriocin production by 2.5-fold. Native polyacrylamide gel electrophoresis of the antagonistically active gel filtration fraction established that the molecular weight of the R. albus 7 bacteriocin was approximately 36 kDa. The bacteriocin was sensitive to pepsin, protease, and pancreatin, and was inactivated by heating at 65 °C for 1 h. Simulating in vitro avian digestion decreased the antagonistic activity by 74.7%, but the addition of 1% bovin serum albumin restored 13% of the lost antagonistic activity. Following ion-exchange purification, the bacteriocin had sufficient antagonistic activity against five tested pathogenic strains, but the addition of a protectant is necessary for utilization of bacteriocin of R. albus 7 as an antibiotic alternative in animal feed.
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Liu D, Zhang R, Yang X, Xu Y, Tang Z, Tian W, Shen Q. Expression, purification and characterization of two thermostable endoglucanases cloned from a lignocellulosic decomposing fungi Aspergillus fumigatus Z5 isolated from compost. Protein Expr Purif 2011; 79:176-86. [DOI: 10.1016/j.pep.2011.06.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 06/08/2011] [Accepted: 06/09/2011] [Indexed: 11/27/2022]
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CBM3d, a novel subfamily of family 3 carbohydrate-binding modules identified in Cel48A exoglucanase of Cellulosilyticum ruminicola. J Bacteriol 2011; 193:5199-206. [PMID: 21803997 DOI: 10.1128/jb.05227-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previously, we found that exoglucanase Cel48A from Cellulosilyticum ruminicola H1 bound intensively to Avicel; however, no known carbohydrate-binding module (CBM) was observed in the protein. Bioinformatics suggested that a C-terminal fragment of 127 amino acids, named the Cellulosilyticum-specific paralogous module (CPM), could function in binding. CPM-appended proteins are all putative (hemi)cellulases from Cellulosilyticum spp. In the present work, we demonstrated that Cel48A without the CPM retained only exoglucanase activity and lost the Avicel-binding ability, while the isolated CPM exhibited a high affinity for Avicel. In addition, the CPM bound to chitin, but not to soluble polysaccharides, making it a type A CBM, which binds only insoluble polysaccharides. Phylogenetic analysis clustered the CPM and its homologs as a separate branch that was distantly related to CBM subfamilies 3a (28% identity), 3b (24% identity), and 3c (21% identity). Sequence alignment revealed distinct secondary structures of the new CBM 3 group, in particular, a conserved Pro66-Trp67 insert preceding strand β4', a deletion preceding strand β6, and incomplete strands β8 and β9. An alanine scan for six aromatic and three nonaromatic amino acid residues (D66, P66, and R111) by site-directed mutagenesis determined that Phe62, Pro66, Trp67, Tyr68, Arg111, and Trp117 were the functional residues for binding. Among them, Phe62, Pro66, and Trp67 were the newly determined key sites in the CPM for binding. Three-dimensional homolog modeling revealed two types of substrate-binding sites, planar and groove, in the CPM. Thus, a new subfamily, CBM family 3d, is proposed.
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26
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Sukharnikov LO, Cantwell BJ, Podar M, Zhulin IB. Cellulases: ambiguous nonhomologous enzymes in a genomic perspective. Trends Biotechnol 2011; 29:473-9. [PMID: 21683463 DOI: 10.1016/j.tibtech.2011.04.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 04/19/2011] [Accepted: 04/22/2011] [Indexed: 01/30/2023]
Abstract
The key material for bioethanol production is cellulose, which is one of the main components of the plant cell wall. Enzymatic depolymerization of cellulose is an essential step in bioethanol production, and can be accomplished by fungal and bacterial cellulases. Most of the biochemically characterized bacterial cellulases come from only a few cellulose-degrading bacteria, thus limiting our knowledge of a range of cellulolytic activities that exist in nature. The recent explosion of genomic data offers a unique opportunity to search for novel cellulolytic activities; however, the absence of clear understanding of structural and functional features that are important for reliable computational identification of cellulases precludes their exploration in the genomic datasets. Here, we explore the diversity of cellulases and propose a genomic approach to overcome this bottleneck.
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Affiliation(s)
- Leonid O Sukharnikov
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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27
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Brás JLA, Cartmell A, Carvalho ALM, Verzé G, Bayer EA, Vazana Y, Correia MAS, Prates JAM, Ratnaparkhe S, Boraston AB, Romão MJ, Fontes CMGA, Gilbert HJ. Structural insights into a unique cellulase fold and mechanism of cellulose hydrolysis. Proc Natl Acad Sci U S A 2011; 108:5237-42. [PMID: 21393568 PMCID: PMC3069175 DOI: 10.1073/pnas.1015006108] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Clostridium thermocellum is a well-characterized cellulose-degrading microorganism. The genome sequence of C. thermocellum encodes a number of proteins that contain type I dockerin domains, which implies that they are components of the cellulose-degrading apparatus, but display no significant sequence similarity to known plant cell wall-degrading enzymes. Here, we report the biochemical properties and crystal structure of one of these proteins, designated CtCel124. The protein was shown to be an endo-acting cellulase that displays a single displacement mechanism and acts in synergy with Cel48S, the major cellulosomal exo-cellulase. The crystal structure of CtCel124 in complex with two cellotriose molecules, determined to 1.5 Å, displays a superhelical fold in which a constellation of α-helices encircle a central helix that houses the catalytic apparatus. The catalytic acid, Glu96, is located at the C-terminus of the central helix, but there is no candidate catalytic base. The substrate-binding cleft can be divided into two discrete topographical domains in which the bound cellotriose molecules display twisted and linear conformations, respectively, suggesting that the enzyme may target the interface between crystalline and disordered regions of cellulose.
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Affiliation(s)
- Joana L. A. Brás
- Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Alan Cartmell
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602-4712
| | - Ana Luísa M. Carvalho
- Rede de Química e Tecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Genny Verzé
- Rede de Química e Tecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Biocrystallography Laboratory, Department of Biotechnology, University of Verona, 37129 Verona, Italy
| | - Edward A. Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100 Israel; and
| | - Yael Vazana
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100 Israel; and
| | - Márcia A. S. Correia
- Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - José A. M. Prates
- Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Supriya Ratnaparkhe
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602-4712
| | - Alisdair B. Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6
| | - Maria J. Romão
- Rede de Química e Tecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Carlos M. G. A. Fontes
- Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Harry J. Gilbert
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602-4712
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Georgelis N, Tabuchi A, Nikolaidis N, Cosgrove DJ. Structure-function analysis of the bacterial expansin EXLX1. J Biol Chem 2011; 286:16814-23. [PMID: 21454649 DOI: 10.1074/jbc.m111.225037] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We made use of EXLX1, an expansin from Bacillus subtilis, to investigate protein features essential for its plant cell wall binding and wall loosening activities. We found that the two expansin domains, D1 and D2, need to be linked for wall extension activity and that D2 mediates EXLX1 binding to whole cell walls and to cellulose via distinct residues on the D2 surface. Binding to cellulose is mediated by three aromatic residues arranged linearly on the putative binding surface that spans D1 and D2. Mutation of these three residues to alanine eliminated cellulose binding and concomitantly eliminated wall loosening activity measured either by cell wall extension or by weakening of filter paper but hardly affected binding to whole cell walls, which is mediated by basic residues located on other D2 surfaces. Mutation of these basic residues to glutamine reduced cell wall binding but not wall loosening activities. We propose domain D2 as the founding member of a new carbohydrate binding module family, CBM63, but its function in expansin activity apparently goes beyond simply anchoring D1 to the wall. Several polar residues on the putative binding surface of domain D1 are also important for activity, most notably Asp82, whose mutation to alanine or asparagine completely eliminated wall loosening activity. The functional insights based on this bacterial expansin may be extrapolated to the interactions of plant expansins with cell walls.
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Affiliation(s)
- Nikolaos Georgelis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Montanier C, Flint JE, Bolam DN, Xie H, Liu Z, Rogowski A, Weiner DP, Ratnaparkhe S, Nurizzo D, Roberts SM, Turkenburg JP, Davies GJ, Gilbert HJ. Circular permutation provides an evolutionary link between two families of calcium-dependent carbohydrate binding modules. J Biol Chem 2010; 285:31742-54. [PMID: 20659893 PMCID: PMC2951246 DOI: 10.1074/jbc.m110.142133] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 07/13/2010] [Indexed: 11/06/2022] Open
Abstract
The microbial deconstruction of the plant cell wall is a critical biological process, which also provides important substrates for environmentally sustainable industries. Enzymes that hydrolyze the plant cell wall generally contain non-catalytic carbohydrate binding modules (CBMs) that contribute to plant cell wall degradation. Here we report the biochemical properties and crystal structure of a family of CBMs (CBM60) that are located in xylanases. Uniquely, the proteins display broad ligand specificity, targeting xylans, galactans, and cellulose. Some of the CBM60s display enhanced affinity for their ligands through avidity effects mediated by protein dimerization. The crystal structure of vCBM60, displays a β-sandwich with the ligand binding site comprising a broad cleft formed by the loops connecting the two β-sheets. Ligand recognition at site 1 is, exclusively, through hydrophobic interactions, whereas binding at site 2 is conferred by polar interactions between a protein-bound calcium and the O2 and O3 of the sugar. The observation, that ligand recognition at site 2 requires only a β-linked sugar that contains equatorial hydroxyls at C2 and C3, explains the broad ligand specificity displayed by vCBM60. The ligand-binding apparatus of vCBM60 displays remarkable structural conservation with a family 36 CBM (CBM36); however, the residues that contribute to carbohydrate recognition are derived from different regions of the two proteins. Three-dimensional structure-based sequence alignments reveal that CBM36 and CBM60 are related by circular permutation. The biological and evolutionary significance of the mechanism of ligand recognition displayed by family 60 CBMs is discussed.
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Affiliation(s)
- Cedric Montanier
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - James E. Flint
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - David N. Bolam
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Hefang Xie
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Ziyuan Liu
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Artur Rogowski
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | | | - Supriya Ratnaparkhe
- the Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia 30602-4712
| | - Didier Nurizzo
- the European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, F-38043 Grenoble Cedex, France
| | - Shirley M. Roberts
- the York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom, and
| | - Johan P. Turkenburg
- the York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom, and
| | - Gideon J. Davies
- the York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom, and
| | - Harry J. Gilbert
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- the Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia 30602-4712
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31
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Beloqui A, Nechitaylo TY, López-Cortés N, Ghazi A, Guazzaroni ME, Polaina J, Strittmatter AW, Reva O, Waliczek A, Yakimov MM, Golyshina OV, Ferrer M, Golyshin PN. Diversity of glycosyl hydrolases from cellulose-depleting communities enriched from casts of two earthworm species. Appl Environ Microbiol 2010; 76:5934-46. [PMID: 20622123 PMCID: PMC2935051 DOI: 10.1128/aem.00902-10] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 07/01/2010] [Indexed: 11/20/2022] Open
Abstract
The guts and casts of earthworms contain microbial assemblages that process large amounts of organic polymeric substrates from plant litter and soil; however, the enzymatic potential of these microbial communities remains largely unexplored. In the present work, we retrieved carbohydrate-modifying enzymes through the activity screening of metagenomic fosmid libraries from cellulose-depleting microbial communities established with the fresh casts of two earthworm species, Aporrectodea caliginosa and Lumbricus terrestris, as inocula. Eight glycosyl hydrolases (GHs) from the A. caliginosa-derived community were multidomain endo-beta-glucanases, beta-glucosidases, beta-cellobiohydrolases, beta-galactosidase, and beta-xylosidases of known GH families. In contrast, two GHs derived from the L. terrestris microbiome had no similarity to any known GHs and represented two novel families of beta-galactosidases/alpha-arabinopyranosidases. Members of these families were annotated in public databases as conserved hypothetical proteins, with one being structurally related to isomerases/dehydratases. This study provides insight into their biochemistry, domain structures, and active-site architecture. The two communities were similar in bacterial composition but significantly different with regard to their eukaryotic inhabitants. Further sequence analysis of fosmids and plasmids bearing the GH-encoding genes, along with oligonucleotide usage pattern analysis, suggested that those apparently originated from Gammaproteobacteria (pseudomonads and Cellvibrio-like organisms), Betaproteobacteria (Comamonadaceae), and Alphaproteobacteria (Rhizobiales).
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Affiliation(s)
- Ana Beloqui
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Taras Y. Nechitaylo
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Nieves López-Cortés
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Azam Ghazi
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - María-Eugenia Guazzaroni
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Julio Polaina
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Axel W. Strittmatter
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Oleg Reva
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Agnes Waliczek
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Michail M. Yakimov
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Olga V. Golyshina
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Manuel Ferrer
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
| | - Peter N. Golyshin
- CSIC, Institute of Catalysis, 28049 Madrid, Spain, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany, CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain, Eurofins MWG Operon, 85560 Ebersberg, Germany, Department of Biochemistry, University of Pretoria, 0002 Pretoria, South Africa, Istituto per l'Ambiente Marino Costiero, CNR, Messina 98122, Italy, School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom, Centre for Integrated Research in the Rural Environment (CRRE), Aberystwyth University-Bangor University Partnership, Aberystwyth, Ceredigion SY23 3BF, United Kingdom
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Engineering of Clostridium phytofermentans Endoglucanase Cel5A for improved thermostability. Appl Environ Microbiol 2010; 76:4914-7. [PMID: 20511418 DOI: 10.1128/aem.00958-10] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A family 5 glycoside hydrolase from Clostridium phytofermentans was cloned and engineered through a cellulase cell surface display system in Escherichia coli. The presence of cell surface anchoring, a cellulose binding module, or a His tag greatly influenced the activities of wild-type and mutant enzymes on soluble and solid cellulosic substrates, suggesting the high complexity of cellulase engineering. The best mutant had 92%, 36%, and 46% longer half-lives at 60 degrees C on carboxymethyl cellulose, regenerated amorphous cellulose, and Avicel, respectively.
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33
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Montanier C, Money VA, Pires VMR, Flint JE, Pinheiro BA, Goyal A, Prates JAM, Izumi A, Stålbrand H, Morland C, Cartmell A, Kolenova K, Topakas E, Dodson EJ, Bolam DN, Davies GJ, Fontes CMGA, Gilbert HJ. The active site of a carbohydrate esterase displays divergent catalytic and noncatalytic binding functions. PLoS Biol 2009; 7:e71. [PMID: 19338387 PMCID: PMC2661963 DOI: 10.1371/journal.pbio.1000071] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 02/17/2009] [Indexed: 11/19/2022] Open
Abstract
Multifunctional proteins, which play a critical role in many biological processes, have typically evolved through the recruitment of different domains that have the required functional diversity. Thus the different activities displayed by these proteins are mediated by spatially distinct domains, consistent with the specific chemical requirements of each activity. Indeed, current evolutionary theory argues that the colocalization of diverse activities within an enzyme is likely to be a rare event, because it would compromise the existing activity of the protein. In contrast to this view, a potential example of multifunctional recruitment into a single protein domain is provided by CtCel5C-CE2, which contains an N-terminal module that displays cellulase activity and a C-terminal module, CtCE2, which exhibits a noncatalytic cellulose-binding function but also shares sequence identity with the CE2 family of esterases. Here we show that, unlike other CE2 members, the CtCE2 domain displays divergent catalytic esterase and noncatalytic carbohydrate binding functions. Intriguingly, these diverse activities are housed within the same site on the protein. Thus, a critical component of the active site of CtCE2, the catalytic Ser-His dyad, in harness with inserted aromatic residues, confers noncatalytic binding to cellulose whilst the active site of the domain retains its esterase activity. CtCE2 catalyses deacetylation of noncellulosic plant structural polysaccharides to deprotect these substrates for attack by other enzymes. Yet it also acts as a cellulose-binding domain, which promotes the activity of the appended cellulase on recalcitrant substrates. The CE2 family encapsulates the requirement for multiple activities by biocatalysts that attack challenging macromolecular substrates, including the grafting of a second, powerful and discrete noncatalytic binding functionality into the active site of an enzyme. This article provides a rare example of “gene sharing,” where the introduction of a second functionality into the active site of an enzyme does not compromise the original activity of the biocatalyst. Proteins that display multiple activities have typically evolved through the recruitment of different domains, each of which has a specific function. Thus, in a multifunctional protein, the different activities are mediated by spatially distinct domains such that a single domain can provide the specific chemical requirements for one activity. Indeed, current evolutionary theory argues that the colocalization of diverse activities within a single-domain enzyme is likely to be a rare event, as it would compromise the existing activity of the protein when a new function evolves. Nonetheless, a potential example of multifunctional recruitment into a single protein domain is provided by an enzyme that contains a cellulase enzyme module and a discrete noncatalytic cellulose-binding module. In this article, we show that the cellulose-binding module displays esterase activity and that these diverse activities are housed within the same site on the protein. Structural analysis of the enzyme reveals that its catalytic residues also contribute to the noncatalytic cellulose-binding function. This report provides a rare example of “gene sharing,” whereby the introduction of a second functionality into the active site of an enzyme does not compromise the original activity of the catalyst. The active of site of an esterase enzyme has acquired a noncatalytic carbohydrate-binding function without compromising its catalytic activity, providing support for the "gene sharing" model of protein diversification.
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Affiliation(s)
- Cedric Montanier
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne, United Kingdom
| | - Victoria A Money
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, United Kingdom
| | - Virginia M. R Pires
- CIISA - Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, Lisboa, Portugal
| | - James E Flint
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne, United Kingdom
| | - Benedita A Pinheiro
- CIISA - Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, Lisboa, Portugal
| | - Arun Goyal
- CIISA - Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, Lisboa, Portugal
| | - José A. M Prates
- CIISA - Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, Lisboa, Portugal
| | - Atsushi Izumi
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, United Kingdom
| | - Henrik Stålbrand
- Department of Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - Carl Morland
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne, United Kingdom
| | - Alan Cartmell
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne, United Kingdom
| | - Katarina Kolenova
- Department of Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - Evangelos Topakas
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne, United Kingdom
| | - Eleanor J Dodson
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, United Kingdom
| | - David N Bolam
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne, United Kingdom
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, United Kingdom
- * To whom correspondence should be addressed. E-mail: (GJD); (HJG)
| | - Carlos M. G. A Fontes
- CIISA - Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, Lisboa, Portugal
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne, United Kingdom
- * To whom correspondence should be addressed. E-mail: (GJD); (HJG)
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34
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A Novel Endoglucanase (Cel9P) From a Marine Bacterium Paenibacillus sp. BME-14. Appl Biochem Biotechnol 2009; 160:1627-36. [DOI: 10.1007/s12010-009-8648-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2009] [Accepted: 04/12/2009] [Indexed: 11/27/2022]
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35
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Michel G, Barbeyron T, Kloareg B, Czjzek M. The family 6 carbohydrate-binding modules have coevolved with their appended catalytic modules toward similar substrate specificity. Glycobiology 2009; 19:615-23. [PMID: 19240276 DOI: 10.1093/glycob/cwp028] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The survey of carbohydrate active enzymes in genomic data uncovered the modular architecture of most of these proteins. Many of the additional modules associated with catalytic modules tightly bind carbohydrates. The primary role of these carbohydrate-binding modules (CBMs) is to enhance the enzymatic activity of the ensemble by bringing their appended catalytic module(s) in intimate contact with their substrates. Biochemical and biophysical approaches have unraveled the subtle interplay of the modules and the structural basis for their ligand specificities, but little attention has been paid to the evolutionary mechanisms leading to the appearance of modular architecture in carbohydrate active enzymes. Focusing on the promiscuous family CBM6 modules, we investigated the evolution of substrate specificities in parallel to that of their respectively appended catalytic modules. An extensive phylogenetic analysis of family CBM6 modules indicates that these noncatalytic modules have diverged into clades which coincide with their substrate selectivity. These data as well as the remarkable congruence of the phylogenetic trees inferred from CBM6s on the one hand and their associated catalytic modules on the other hand show that CBM6s and their associated glycoside hydrolases have coevolved to acquire the same substrate specificity. We also propose an evolutionary scenario explaining the emergence of the modular agarases, by which existent alpha-agarases acquired their agar-binding CBM6 module through a lateral transfer from pre-existing beta-agarases. Altogether, this observed coevolution between CBM6s and their catalytic modules will facilitate the prediction of the substrate specificity of uncharacterized CBM6 modules present in genomic data.
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Affiliation(s)
- Gurvan Michel
- UPMC University Paris 06, 3CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique de Roscoff, Roscoff, Bretagne, France.
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36
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Evidence that family 35 carbohydrate binding modules display conserved specificity but divergent function. Proc Natl Acad Sci U S A 2009; 106:3065-70. [PMID: 19218457 PMCID: PMC2651348 DOI: 10.1073/pnas.0808972106] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymes that hydrolyze complex carbohydrates play important roles in numerous biological processes that result in the maintenance of marine and terrestrial life. These enzymes often contain noncatalytic carbohydrate binding modules (CBMs) that have important substrate-targeting functions. In general, there is a tight correlation between the ligands recognized by bacterial CBMs and the substrate specificity of the appended catalytic modules. Through high-resolution structural studies, we demonstrate that the architecture of the ligand binding sites of 4 distinct family 35 CBMs (CBM35s), appended to 3 plant cell wall hydrolases and the exo-beta-D-glucosaminidase CsxA, which contributes to the detoxification and metabolism of an antibacterial fungal polysaccharide, is highly conserved and imparts specificity for glucuronic acid and/or Delta4,5-anhydrogalaturonic acid (Delta4,5-GalA). Delta4,5-GalA is released from pectin by the action of pectate lyases and as such acts as a signature molecule for plant cell wall degradation. Thus, the CBM35s appended to the 3 plant cell wall hydrolases, rather than targeting the substrates of the cognate catalytic modules, direct their appended enzymes to regions of the plant that are being actively degraded. Significantly, the CBM35 component of CsxA anchors the enzyme to the bacterial cell wall via its capacity to bind uronic acid sugars. This latter observation reveals an unusual mechanism for bacterial cell wall enzyme attachment. This report shows that the biological role of CBM35s is not dictated solely by their carbohydrate specificities but also by the context of their target ligands.
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Crystal structures of the starch-binding domain from Rhizopus oryzae glucoamylase reveal a polysaccharide-binding path. Biochem J 2008; 416:27-36. [DOI: 10.1042/bj20080580] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
GA (glucoamylase) hydrolyses starch and polysaccharides to β-D-glucose. RoGA (Rhizopus oryzae GA) consists of two functional domains, an N-terminal SBD (starch-binding domain) and a C-terminal catalytic domain, which are connected by an O-glycosylated linker. In the present study, the crystal structures of the SBD from RoGA (RoGACBM21) and the complexes with β-cyclodextrin (SBD–βCD) and maltoheptaose (SBD–G7) were determined. Two carbohydrate binding sites, I (Trp47) and II (Tyr32), were resolved and their binding was co-operative. Besides the hydrophobic interaction, two unique polyN loops comprising consecutive asparagine residues also participate in the sugar binding. A conformational change in Tyr32 was observed between unliganded and liganded SBDs. To elucidate the mechanism of polysaccharide binding, a number of mutants were constructed and characterized by a quantitative binding isotherm and Scatchard analysis. A possible binding path for long-chain polysaccharides in RoGACBM21 was proposed.
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38
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Emami K, Topakas E, Nagy T, Henshaw J, Jackson KA, Nelson KE, Mongodin EF, Murray JW, Lewis RJ, Gilbert HJ. Regulation of the xylan-degrading apparatus of Cellvibrio japonicus by a novel two-component system. J Biol Chem 2008; 284:1086-96. [PMID: 18922794 DOI: 10.1074/jbc.m805100200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The microbial degradation of lignocellulose biomass is not only an important biological process but is of increasing industrial significance in the bioenergy sector. The mechanism by which the plant cell wall, an insoluble composite structure, activates the extensive repertoire of microbial hydrolytic enzymes required to catalyze its degradation is poorly understood. Here we have used a transposon mutagenesis strategy to identify a genetic locus, consisting of two genes that modulate the expression of xylan side chain-degrading enzymes in the saprophytic bacterium Cellvibrio japonicus. Significantly, the locus encodes a two-component signaling system, designated AbfS (sensor histidine kinase) and AbfR (response regulator). The AbfR/S two-component system is required to activate the expression of the suite of enzymes that remove the numerous side chains from xylan, but not the xylanases that hydrolyze the beta1,4-linked xylose polymeric backbone of this polysaccharide. Studies on the recombinant sensor domain of AbfS (AbfS(SD)) showed that it bound to decorated xylans and arabinoxylo-oligosaccharides, but not to undecorated xylo-oligosaccharides or other plant structural polysaccharides/oligosaccharides. The crystal structure of AbfS(SD) was determined to a resolution of 2.6A(.) The overall fold of AbfS(SD) is that of a classical Per Arndt Sim domain with a central antiparallel four-stranded beta-sheet flanked by alpha-helices. Our data expand the number of molecules known to bind to the sensor domain of two-component histidine kinases to include complex carbohydrates. The biological rationale for a regulatory system that induces enzymes that remove the side chains of xylan, but not the hydrolases that cleave the backbone of the polysaccharide, is discussed.
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Affiliation(s)
- Kaveh Emami
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Framlington Place, Newcastle-upon-Tyne, NE2 4HH, United Kingdom
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CelAB, a multifunctional cellulase encoded by Teredinibacter turnerae T7902T, a culturable symbiont isolated from the wood-boring marine bivalve Lyrodus pedicellatus. Appl Environ Microbiol 2007; 73:7785-8. [PMID: 17933945 DOI: 10.1128/aem.00876-07] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterized a multifunctional cellulase (CelAB) encoded by the endosymbiont Teredinibacter turnerae T7902(T). CelAB contains two catalytic and two carbohydrate-binding domains, each separated by polyserine linker regions. CelAB binds cellulose and chitin, degrades multiple complex polysaccharides, and displays two catalytic activities, cellobiohydrolase (EC 3.2.1.91) and beta-1,4(3) endoglucanase (EC 3.2.1.4).
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40
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Ludwiczek ML, Heller M, Kantner T, McIntosh LP. A secondary xylan-binding site enhances the catalytic activity of a single-domain family 11 glycoside hydrolase. J Mol Biol 2007; 373:337-54. [PMID: 17822716 DOI: 10.1016/j.jmb.2007.07.057] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Accepted: 07/24/2007] [Indexed: 11/20/2022]
Abstract
Bacillus circulans xylanase (BcX) is a single-domain family 11 glycoside hydrolase. Using NMR-monitored titrations, we discovered that an inactive variant of this enzyme, E78Q-BcX, bound xylooligosaccharides not only within its pronounced active site (AS) cleft, but also at a distal surface region. Chemical shift perturbation mapping and affinity electrophoresis, combined with mutational studies, identified the xylan-specific secondary binding site (SBS) as a shallow groove lined by Asn, Ser, and Thr residues and with a Trp at one end. The AS and SBS bound short xylooligosaccharides with similar dissociation constants in the millimolar range. However, the on and off-rates to the SBS were at least tenfold faster than those of kon approximately 3x10(5) M(-1) s(-1) and koff approximately 1000 s(-1) measured for xylotetraose to the AS of E78Q-BcX. Consistent with their structural differences, this suggests that a conformational change in the enzyme and/or the substrate is required for association to and dissociation from the deep AS, but not the shallow SBS. In contrast to the independent binding of small xylooligosaccharides, high-affinity binding of soluble and insoluble xylan, as well as xylododecaose, occurred cooperatively to the two sites. This was evidenced by an approximately 100-fold increase in relative Kd values for these ligands upon mutation of the SBS. The SBS also enhances the activity of BcX towards soluble and insoluble xylan through a significant reduction in the Michaelis KM values for these polymeric substrates. This study provides an unexpected example of how a single domain family 11 xylanase overcomes the lack of a carbohydrate-binding module through the use of a secondary binding site to enhance substrate specificity and affinity.
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Affiliation(s)
- Martin L Ludwiczek
- Department of Biochemistry and Molecular Biology, Department of Chemistry, The Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
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41
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Poon DKY, Withers SG, McIntosh LP. Direct demonstration of the flexibility of the glycosylated proline-threonine linker in the Cellulomonas fimi Xylanase Cex through NMR spectroscopic analysis. J Biol Chem 2006; 282:2091-100. [PMID: 17121820 DOI: 10.1074/jbc.m609670200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The modular xylanase Cex (or CfXyn10A) from Cellulomonas fimi consists of an N-terminal catalytic domain and a C-terminal cellulose-binding domain, joined by a glycosylated proline-threonine (PT) linker. To characterize the conformation and dynamics of the Cex linker and the consequences of its modification, we have used NMR spectroscopy to study full-length Cex in its nonglycosylated ( approximately 47 kDa) and glycosylated ( approximately 51 kDa) forms. The PT linker lacks any predominant structure in either form as indicated by random coil amide chemical shifts. Furthermore, heteronuclear (1)H-(15)N nuclear Overhauser effect relaxation measurements demonstrate that the linker is flexible on the ns-to-ps time scale and that glycosylation partially dampens this flexibility. The catalytic and cellulose-binding domains also exhibit identical amide chemical shifts whether in isolation or in the context of either unmodified or glycosylated full-length Cex. Therefore, there are no noncovalent interactions between the two domains of Cex or between either domain and the linker. This conclusion is supported by the distinct (15)N relaxation properties of the two domains, as well as their differential alignment within a magnetic field by Pf1 phage particles. These data demonstrate that the PT linker is a flexible tether, joining the structurally independent catalytic and cellulose-binding domains of Cex in an ensemble of conformations; however, more extended forms may predominate because of restrictions imparted by the alternating proline residues. This supports the postulate that the binding-domain anchors Cex to the surface of cellulose, whereas the linker provides flexibility for the catalytic domain to hydrolyze nearby hemicellulose (xylan) chains.
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Affiliation(s)
- David K Y Poon
- Department of Biochemistry and Molecular Biology, The Protein Engineering Network of Centres of Excellence, and The Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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42
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Pason P, Kyu KL, Ratanakhanokchai K. Paenibacillus curdlanolyticus strain B-6 xylanolytic-cellulolytic enzyme system that degrades insoluble polysaccharides. Appl Environ Microbiol 2006; 72:2483-90. [PMID: 16597947 PMCID: PMC1448999 DOI: 10.1128/aem.72.4.2483-2490.2006] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A facultatively anaerobic bacterium, Paenibacillus curdlanolyticus B-6, isolated from an anaerobic digester produces an extracellular xylanolytic-cellulolytic enzyme system containing xylanase, beta-xylosidase, arabinofuranosidase, acetyl esterase, mannanase, carboxymethyl cellulase (CMCase), avicelase, cellobiohydrolase, beta-glucosidase, amylase, and chitinase when grown on xylan under aerobic conditions. During growth on xylan, the bacterial cells were found to adhere to xylan from the early exponential growth phase to the late stationary growth phase. Scanning electron microscopic analysis revealed the adhesion of cells to xylan. The crude enzyme preparation was found to be capable of binding to insoluble xylan and Avicel. The xylanolytic-cellulolytic enzyme system efficiently hydrolyzed insoluble xylan, Avicel, and corn hulls to soluble sugars that were exclusively xylose and glucose. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of a crude enzyme preparation exhibited at least 17 proteins, and zymograms revealed multiple xylanases and cellulases containing 12 xylanases and 9 CMCases. The cellulose-binding proteins, which are mainly in a multienzyme complex, were isolated from the crude enzyme preparation by affinity purification on cellulose. This showed nine proteins by SDS-PAGE and eight xylanases and six CMCases on zymograms. Sephacryl S-300 gel filtration showed that the cellulose-binding proteins consisted of two multienzyme complexes with molecular masses of 1,450 and 400 kDa. The results indicated that the xylanolytic-cellulolytic enzyme system of this bacterium exists as multienzyme complexes.
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Affiliation(s)
- Patthra Pason
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
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43
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Chou WI, Pai TW, Liu SH, Hsiung BK, Chang MT. The family 21 carbohydrate-binding module of glucoamylase from Rhizopus oryzae consists of two sites playing distinct roles in ligand binding. Biochem J 2006; 396:469-77. [PMID: 16509822 PMCID: PMC1482813 DOI: 10.1042/bj20051982] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The starch-hydrolysing enzyme GA (glucoamylase) from Rhizopus oryzae is a commonly used glycoside hydrolase in industry. It consists of a C-terminal catalytic domain and an N-terminal starch-binding domain, which belong to the CBM21 (carbohydrate-binding module, family 21). In the present study, a molecular model of CBM21 from R. oryzae GA (RoGACBM21) was constructed according to PSSC (progressive secondary structure correlation), modified structure-based sequence alignment, and site-directed mutagenesis was used to identify and characterize potential ligand-binding sites. Our model suggests that RoGACBM21 contains two ligand-binding sites, with Tyr32 and Tyr67 grouped into site I, and Trp47, Tyr83 and Tyr93 grouped into site II. The involvement of these aromatic residues has been validated using chemical modification, UV difference spectroscopy studies, and both qualitative and quantitative binding assays on a series of RoGACBM21 mutants. Our results further reveal that binding sites I and II play distinct roles in ligand binding, the former not only is involved in binding insoluble starch, but also facilitates the binding of RoGACBM21 to long-chain soluble polysaccharides, whereas the latter serves as the major binding site mediating the binding of both soluble polysaccharide and insoluble ligands. In the present study we have for the first time demonstrated that the key ligand-binding residues of RoGACBM21 can be identified and characterized by a combination of novel bioinformatics methodologies in the absence of resolved three-dimensional structural information.
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Affiliation(s)
- Wei-I Chou
- *Institute of Molecular and Cellular Biology, Department of Life Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, Taiwan 30013, Republic of China
| | - Tun-Wen Pai
- †Department of Computer Science, National Taiwan Ocean University, No. 2, Pei Ning Rd, Keelung, Taiwan 20224, Republic of China
| | - Shi-Hwei Liu
- *Institute of Molecular and Cellular Biology, Department of Life Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, Taiwan 30013, Republic of China
| | - Bor-Kai Hsiung
- *Institute of Molecular and Cellular Biology, Department of Life Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, Taiwan 30013, Republic of China
| | - Margaret D.-T. Chang
- *Institute of Molecular and Cellular Biology, Department of Life Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, Taiwan 30013, Republic of China
- To whom correspondence should be addressed (email )
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44
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Shoseyov O, Shani Z, Levy I. Carbohydrate binding modules: biochemical properties and novel applications. Microbiol Mol Biol Rev 2006; 70:283-95. [PMID: 16760304 PMCID: PMC1489539 DOI: 10.1128/mmbr.00028-05] [Citation(s) in RCA: 351] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polysaccharide-degrading microorganisms express a repertoire of hydrolytic enzymes that act in synergy on plant cell wall and other natural polysaccharides to elicit the degradation of often-recalcitrant substrates. These enzymes, particularly those that hydrolyze cellulose and hemicellulose, have a complex molecular architecture comprising discrete modules which are normally joined by relatively unstructured linker sequences. This structure is typically comprised of a catalytic module and one or more carbohydrate binding modules (CBMs) that bind to the polysaccharide. CBMs, by bringing the biocatalyst into intimate and prolonged association with its substrate, allow and promote catalysis. Based on their properties, CBMs are grouped into 43 families that display substantial variation in substrate specificity, along with other properties that make them a gold mine for biotechnologists who seek natural molecular "Velcro" for diverse and unusual applications. In this article, we review recent progress in the field of CBMs and provide an up-to-date summary of the latest developments in CBM applications.
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Affiliation(s)
- Oded Shoseyov
- The Institute of Plant Science and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 76100, Israel.
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45
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McCartney L, Blake AW, Flint J, Bolam DN, Boraston AB, Gilbert HJ, Knox JP. Differential recognition of plant cell walls by microbial xylan-specific carbohydrate-binding modules. Proc Natl Acad Sci U S A 2006; 103:4765-70. [PMID: 16537424 PMCID: PMC1450244 DOI: 10.1073/pnas.0508887103] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2005] [Indexed: 11/18/2022] Open
Abstract
Glycoside hydrolases that degrade plant cell walls have complex molecular architectures in which one or more catalytic modules are appended to noncatalytic carbohydrate-binding modules (CBMs). CBMs promote binding to polysaccharides and potentiate enzymic hydrolysis. Although there are diverse sequence-based families of xylan-binding CBMs, these modules, in general, recognize both decorated and unsubstituted forms of the target polysaccharide, and thus the evolutionary rationale for this diversity is unclear. Using immunohistochemistry to interrogate the specificity of six xylan-binding CBMs for their target polysaccharides in cell walls has revealed considerable differences in the recognition of plant materials between these protein modules. Family 2b and 15 CBMs bind to xylan in secondary cell walls in a range of dicotyledon species, whereas family 4, 6, and 22 CBMs display a more limited capability to bind to secondary cell walls. A family 35 CBM, which displays more restricted ligand specificity against purified xylans than the other five protein modules, reveals a highly distinctive binding pattern to plant material including the recognition of primary cell walls of certain dicotyledons, a feature shared with CBM15. Differences in the specificity of the CBMs toward walls of wheat grain and maize coleoptiles were also evident. The variation in CBM specificity for ligands located in plant cell walls provides a biological rationale for the repertoire of structurally distinct xylan-binding CBMs present in nature, and points to the utility of these modules in probing the molecular architecture of cell walls.
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Affiliation(s)
- Lesley McCartney
- *Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Anthony W. Blake
- *Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - James Flint
- Institute for Cell and Molecular Biosciences, University of Newcastle-upon-Tyne, Newcastle-upon-Tyne NE2 4HH, United Kingdom; and
| | - David N. Bolam
- Institute for Cell and Molecular Biosciences, University of Newcastle-upon-Tyne, Newcastle-upon-Tyne NE2 4HH, United Kingdom; and
| | - Alisdair B. Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, University of Newcastle-upon-Tyne, Newcastle-upon-Tyne NE2 4HH, United Kingdom; and
| | - J. Paul Knox
- *Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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46
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Boraston AB, Healey M, Klassen J, Ficko-Blean E, Lammerts van Bueren A, Law V. A structural and functional analysis of alpha-glucan recognition by family 25 and 26 carbohydrate-binding modules reveals a conserved mode of starch recognition. J Biol Chem 2005; 281:587-98. [PMID: 16230347 DOI: 10.1074/jbc.m509958200] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Starch-hydrolyzing enzymes lacking alpha-glucan-specific carbohydrate-binding modules (CBMs) typically have lowered activity on granular starch relative to their counterparts with CBMs. Thus, consideration of starch recognition by CBMs is a key factor in understanding granular starch hydrolysis. To this end, we have dissected the modular structure of the maltohexaose-forming amylase from Bacillus halodurans (C-125). This five-module protein comprises an N-terminal family 13 catalytic module followed in order by two modules of unknown function, a family 26 CBM (BhCBM26), and a family 25 CBM (BhCBM25). Here we present a comprehensive structure-function analysis of starch and alpha-glucooligosaccharide recognition by BhCBM25 and BhCBM26 using UV methods, isothermal titration calorimetry, and x-ray crystallography. The results reveal that the two CBMs bind alpha-glucooligosaccharides, particularly those containing alpha-1,6 linkages, with different affinities but have similar abilities to bind granular starch. Notably, these CBMs appear to recognize the same binding sites in granular starch. The enhanced affinity of the tandem CBMs for granular starch is suggested to be the main biological advantage for this enzyme to contain two CBMs. Structural studies of the native and ligand-bound forms of BhCBM25 and BhCBM26 show a structurally conserved mode of ligand recognition but through non-sequence-conserved residues. Comparison of these CBM structures with other starch-specific CBM structures reveals a generally conserved mode of starch recognition.
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Affiliation(s)
- Alisdair B Boraston
- Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada.
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47
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Taylor EJ, Goyal A, Guerreiro CIPD, Prates JAM, Money VA, Ferry N, Morland C, Planas A, Macdonald JA, Stick RV, Gilbert HJ, Fontes CMGA, Davies GJ. How Family 26 Glycoside Hydrolases Orchestrate Catalysis on Different Polysaccharides. J Biol Chem 2005; 280:32761-7. [PMID: 15987675 DOI: 10.1074/jbc.m506580200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
One of the most intriguing features of the 90 glycoside hydrolase families (GHs) is the range of specificities displayed by different members of the same family, whereas the catalytic apparatus and mechanism are often invariant. Family GH26 predominantly comprises beta-1,4 mannanases; however, a bifunctional Clostridium thermocellum GH26 member (hereafter CtLic26A) displays a markedly different specificity. We show that CtLic26A is a lichenase, specific for mixed (Glcbeta1,4Glcbeta1,4Glcbeta1,3)n oligo- and polysaccharides, and displays no activity on manno-configured substrates or beta-1,4-linked homopolymers of glucose or xylose. The three-dimensional structure of the native form of CtLic26A has been solved at 1.50-A resolution, revealing a characteristic (beta/alpha)8 barrel with Glu-109 and Glu-222 acting as the catalytic acid/base and nucleophile in a double-displacement mechanism. The complex with the competitive inhibitor, Glc-beta-1,3-isofagomine (Ki 1 microm), at 1.60 A sheds light on substrate recognition in the -2 and -1 subsites and illuminates why the enzyme is specific for lichenan-based substrates. Hydrolysis of beta-mannosides by GH26 members is thought to proceed through transition states in the B2,5 (boat) conformation in which structural distinction of glucosides versus mannosides reflects not the configuration at C2 but the recognition of the pseudoaxial O3 of the B2,5 conformation. We suggest a different conformational itinerary for the GH26 enzymes active on gluco-configured substrates.
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Affiliation(s)
- Edward J Taylor
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5YW, United Kingdom
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48
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Varrot A, Leydier S, Pell G, Macdonald JM, Stick RV, Henrissat B, Gilbert HJ, Davies GJ. Mycobacterium tuberculosis Strains Possess Functional Cellulases. J Biol Chem 2005; 280:20181-4. [PMID: 15824123 DOI: 10.1074/jbc.c500142200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The genomes of various Mycobacterium tuberculosis strains encode proteins that do not appear to play a role in the growth or survival of the bacterium in its mammalian host, including some implicated in plant cell wall breakdown. Here we show that M. tuberculosis H37Rv does indeed possess a functional cellulase. The x-ray crystal structure of this enzyme, in ligand complex forms, from 1.9 to 1.1A resolution, reveals a highly conserved substrate-binding cleft, which affords similar, and unusual, distortion of the substrate at the catalytic center. The endoglucanase activity, together with the existence of a putative membrane-associated crystalline polysaccharide-binding protein, may reflect the ancestral soil origin of the Mycobacterium or hint at a previously unconsidered environmental niche.
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Affiliation(s)
- Annabelle Varrot
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, Y010 5YW, United Kingdom
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49
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Boraston A, Bolam D, Gilbert H, Davies G. Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem J 2005; 382:769-81. [PMID: 15214846 PMCID: PMC1133952 DOI: 10.1042/bj20040892] [Citation(s) in RCA: 1438] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2004] [Revised: 06/15/2004] [Accepted: 06/23/2004] [Indexed: 11/17/2022]
Abstract
The enzymic degradation of insoluble polysaccharides is one of the most important reactions on earth. Despite this, glycoside hydrolases attack such polysaccharides relatively inefficiently as their target glycosidic bonds are often inaccessible to the active site of the appropriate enzymes. In order to overcome these problems, many of the glycoside hydrolases that utilize insoluble substrates are modular, comprising catalytic modules appended to one or more non-catalytic CBMs (carbohydrate-binding modules). CBMs promote the association of the enzyme with the substrate. In view of the central role that CBMs play in the enzymic hydrolysis of plant structural and storage polysaccharides, the ligand specificity displayed by these protein modules and the mechanism by which they recognize their target carbohydrates have received considerable attention since their discovery almost 20 years ago. In the last few years, CBM research has harnessed structural, functional and bioinformatic approaches to elucidate the molecular determinants that drive CBM-carbohydrate recognition. The present review summarizes the impact structural biology has had on our understanding of the mechanisms by which CBMs bind to their target ligands.
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Affiliation(s)
- Alisdair B. Boraston
- *Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, BC, Canada V8W 3P6
- To whom correspondence should be addressed (email )
| | - David N. Bolam
- †School of Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, U.K
| | - Harry J. Gilbert
- †School of Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, U.K
| | - Gideon J. Davies
- ‡Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, U.K
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50
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Jamal-Talabani S, Boraston AB, Turkenburg JP, Tarbouriech N, Ducros VMA, Davies GJ. Ab Initio Structure Determination and Functional Characterization Of CBM36. Structure 2004; 12:1177-87. [PMID: 15242594 DOI: 10.1016/j.str.2004.04.022] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2004] [Revised: 04/15/2004] [Accepted: 04/18/2004] [Indexed: 11/16/2022]
Abstract
The enzymatic degradation of polysaccharides harnesses multimodular enzymes whose carbohydrate binding modules (CBM) target the catalytic domain onto the recalcitrant substrate. Here we report the ab initio structure determination and subsequent refinement, at 0.8 A resolution, of the CBM36 domain of the Paenibacillus polymyxa xylanase 43A. Affinity electrophoresis, isothermal titration calorimetry, and UV difference spectroscopy demonstrate that CBM36 is a novel Ca(2+)-dependent xylan binding domain. The 3D structure of CBM36 in complex with xylotriose and Ca(2+), at 1.5 A resolution, displays significant conformational changes compared to the native structure and reveals the molecular basis for its unique Ca(2+)-dependent binding of xylooligosaccharides through coordination of the O2 and O3 hydroxyls. CBM36 is one of an emerging spectrum of carbohydrate binding modules that increasingly find applications in industry and display great potential for mapping the "glyco-architecture" of plant cells.
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Affiliation(s)
- Sheelan Jamal-Talabani
- Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, United Kingdom
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