1
|
Liu J, Shi J, Gao J, Shi R, Zhu J, Jensen MS, Li C, Yang J, Zhao S, Sun A, Sun D, Zhang Y, Liu C, Liu W. Functional studies on tandem carbohydrate-binding modules of a multimodular enzyme possessing two catalytic domains. Appl Environ Microbiol 2024:e0088824. [PMID: 38940565 DOI: 10.1128/aem.00888-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/09/2024] [Indexed: 06/29/2024] Open
Abstract
Although functional studies on carbohydrate-binding module (CBM) have been carried out extensively, the role of tandem CBMs in the enzyme containing multiple catalytic domains (CDs) is unclear. Here, we identified a multidomain enzyme (Lc25986) with a novel modular structure from lignocellulolytic bacterial consortium. It consists of a mannanase domain, two CBM65 domains (LcCBM65-1/LcCBM65-2), and an esterase domain. To investigate CBM function and domain interactions, full-length Lc25986 and its variants were constructed and used for enzymatic activity, binding, and bioinformatic analyses. The results showed that LcCBM65-1 and LcCBM65-2 both bind mannan and xyloglucan but not cellulose or β-1,3-1,4-glucan, which differs from the ligand specificity of reported CBM65s. Compared to LcCBM65-2, LcCBM65-1 showed a stronger ligand affinity and a preference for acetylation sites. Both CBM65s stimulated the enzymatic activities of their respective neighboring CDs against acetylated mannan, but did not contribute to the activities of the distal CDs. The time course of mannan hydrolysis indicated that the full-length Lc25986 was more effective in the complete degradation of mixed acetyl/non-acetyl substrates than the mixture of single-CD mutants. When acting on complex substrates, LcCBM65-1 not only improved the enzymatic activity of the mannanase domain, but also directed the esterase domain to the acetylated polysaccharides. LcCBM65-2 adopted a low affinity to reduce interference with the catalysis of the mannanase domain. These results demonstrate the importance of CBMs for the synergism between the two CDs of a multidomain enzyme and suggest that they contribute to the adequate degradation of complex substrates such as plant cell walls. IMPORTANCE Lignocellulolytic enzymes, particularly those of bacterial origin, often harbor multiple carbohydrate-binding modules (CBMs). However, the function of CBM multivalency remains poorly understood. This is especially true for enzymes that contain more than one catalytic domain (CD), as the interactions between CDs, CBMs, and CDs and CBMs can be complex. Our research demonstrates that homogeneous CBMs can have distinct functions in a multimodular enzyme. The tandem CBMs coordinate the CDs in catalytic conflict through their differences in binding affinity, ligand preference, and arrangement within the full-length enzyme. Additionally, although the synergism between mannanase and esterase is widely acknowledged, our study highlights the benefits of integrating the two enzymes into a single entity for the degradation of complex substrates. In summary, these findings enhance our understanding of the intra-synergism of a multimodular enzyme and emphasize the significance of multiple CBMs in this context.
Collapse
Affiliation(s)
- Jiawen Liu
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Jiani Shi
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Jiahui Gao
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Rui Shi
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Jingrong Zhu
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Marcus Sepo Jensen
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Chenchen Li
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Jing Yang
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Siyi Zhao
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Aofei Sun
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Di Sun
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Ying Zhang
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Cong Liu
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Weijie Liu
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| |
Collapse
|
2
|
Sadaqat B, Dar MA, Sha C, Abomohra A, Shao W, Yong YC. Thermophilic β-mannanases from bacteria: production, resources, structural features and bioengineering strategies. World J Microbiol Biotechnol 2024; 40:130. [PMID: 38460032 DOI: 10.1007/s11274-024-03912-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/29/2024] [Indexed: 03/11/2024]
Abstract
β-mannanases are pivotal enzymes that cleave the mannan backbone to release short chain mannooligosaccharides, which have tremendous biotechnological applications including food/feed, prebiotics and biofuel production. Due to the high temperature conditions in many industrial applications, thermophilic mannanases seem to have great potential to overcome the thermal impediments. Thus, structural analysis of thermostable β-mannanases is extremely important, as it could open up new avenues for genetic engineering, and protein engineering of these enzymes with enhanced properties and catalytic efficiencies. Under this scope, the present review provides a state-of-the-art discussion on the thermophilic β-mannanases from bacterial origin, their production, engineering and structural characterization. It covers broad insights into various molecular biology techniques such as gene mutagenesis, heterologous gene expression, and protein engineering, that are employed to improve the catalytic efficiency and thermostability of bacterial mannanases for potential industrial applications. Further, the bottlenecks associated with mannanase production and process optimization are also discussed. Finally, future research related to bioengineering of mannanases with novel protein expression systems for commercial applications are also elaborated.
Collapse
Affiliation(s)
- Beenish Sadaqat
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China
- Department of Biochemistry and Structural Biology, Lund University, Box 124, 22100, Lund, Sweden
| | - Mudasir A Dar
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China
| | - Chong Sha
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China
| | - Abdelfatah Abomohra
- Aquatic Ecophysiology and Phycology, Department of Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, 22609, Germany
| | - Weilan Shao
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China.
| | - Yang-Chun Yong
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China.
| |
Collapse
|
3
|
Eibinger M, Ganner T, Plank H, Nidetzky B. A Biological Nanomachine at Work: Watching the Cellulosome Degrade Crystalline Cellulose. ACS CENTRAL SCIENCE 2020; 6:739-746. [PMID: 32490190 PMCID: PMC7256933 DOI: 10.1021/acscentsci.0c00050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Indexed: 05/14/2023]
Abstract
The cellulosome is a supramolecular multienzymatic protein complex that functions as a biological nanomachine of cellulosic biomass degradation. How the megadalton-size cellulosome adapts to a solid substrate is central to its mechanism of action and is also key for its efficient use in bioconversion applications. We report time-lapse visualization of crystalline cellulose degradation by individual cellulosomes from Clostridium thermocellum by atomic force microscopy. Upon binding to cellulose, the cellulosomes switch to elongated, even filamentous shapes and morph these dynamically at below 1 min time scale according to requirements of the substrate surface under attack. Compared with noncomplexed cellulases that peel off material while sliding along crystalline cellulose surfaces, the cellulosomes remain bound locally for minutes and remove the material lying underneath. The consequent roughening up of the surface leads to an efficient deconstruction of cellulose nanocrystals both from the ends and through fissions within. Distinct modes of cellulose nanocrystal deconstruction by nature's major cellulase systems are thus revealed.
Collapse
Affiliation(s)
- Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Thomas Ganner
- Institute
for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Harald Plank
- Institute
for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
- Graz
Centre of Electron Microscopy, Steyrergasse 17, A-8010 Graz, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| |
Collapse
|
4
|
Sharma K, Fontes CMGA, Najmudin S, Goyal A. Small angle X-ray scattering based structure, modeling and molecular dynamics analyses of family 43 glycoside hydrolase α-L-arabinofuranosidase from Clostridium thermocellum. J Biomol Struct Dyn 2019; 39:209-218. [PMID: 31856699 DOI: 10.1080/07391102.2019.1707119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Enzymes that participate in the hydrolysis of complex carbohydrates display a modular architecture, although the significance of enzyme modularity to flexibility and catalytic efficacy is not fully understood. α-L-arabinofuranosidase from Clostridium thermocellum (CtAraf43) catalyzes the release of α-1,2-, α-1,3-, or α-1,5- linked L-arabinose from arabinose decorated polysaccharides. CtAraf43 comprises an N-terminal catalytic domain (CtAbf43A) connected with two family 6 carbohydrate-binding modules (CBMs), termed as CtCBM6A and CtCBM6B, through flexible linker peptides. Here, we modeled the structure of CtAraf43 revealing that the module, CtAbf43A displays a 5-fold β-propeller fold and the CBMs the typical jellyroll type β-sandwich folds. Ramachandran plot showed 98.5% residues in the favored region and 1.5% residues in the disallowed region. Molecular dynamics simulation analysis of CtAraf43 revealed significant flexibility that is more expressive in the C-terminal CtCBM6B module in terms of structure and orientation. Small angle X-ray scattering analysis of CtAraf43 revealed its elongated structure. CtAraf43 at 1.2 mg/mL demonstrated the monomeric nature and a multi-modular shaped molecular envelope in solution with a Dmax of 12 nm. However, at 4.7 mg/mL, CtAraf43 displayed a dimeric structure and elongated molecular envelope. Kratky plot analysis revealed the folded state of CtAraf43 with limited flexibility at both concentrations. The data revealed higher flexibility at the C-terminal of CtAraf43 suggesting a coordinated action of the N-terminal catalytic module CtAbf43A and the internal CtCBM6A.AbbreviationCBMsCarbohydrate Binding ModulesCtAraf43α-L-arabinofuranosidaseGHsGlycoside HydrolasesMDMolecular DynamicsRMSDRoot Mean Square DeviationRMSFRoot Mean Square FluctuationSAXSSmall angle X-ray scatteringCommunicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Carlos M G A Fontes
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - Shabir Najmudin
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| |
Collapse
|
5
|
Sharma K, Fontes CMGA, Najmudin S, Goyal A. Molecular organization and protein stability of the Clostridium thermocellum glucuronoxylan endo-β-1,4-xylanase of family 30 glycoside hydrolase in solution. J Struct Biol 2019; 206:335-344. [PMID: 30959107 DOI: 10.1016/j.jsb.2019.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 11/19/2022]
Abstract
Glucuronoxylan-β-1,4-xylanohydrolase from Clostridium thermocellum (CtXynGH30) hydrolyzes β-1,4-xylosidic linkages in 4-O-Methyl-D-glucuronoxylan. CtXynGH30 comprises an N-terminal catalytic domain, CtXyn30A, joined by a typical linker sequence to a family 6 carbohydrate-binding module, termed CtCBM6. ITC, mass spectrometric and enzyme activity analyses of CtXyn30A:CtCBM6 (1:1 M ratio), CtXyn30A and CtXynGH30 showed that the linker peptide plays a key role in connecting and orienting CtXyn30A and CtCBM6 modules resulting in the enhanced activity of CtXynGH30. To visualize the disposition of the two protein domains of CtXynGH30, SAXS analysis revealed that CtXynGH30 is monomeric and has a boot-shaped molecular envelope in solution with a Dmax of 18 nm and Rg of 3.6 nm. Kratky plot displayed the protein in a fully folded and flexible state. The ab initio derived dummy atom model of CtXynGH30 superposed well with the modelled structure.
Collapse
Affiliation(s)
- Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Carlos M G A Fontes
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Shabir Najmudin
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| |
Collapse
|
6
|
Wang Y, Cao X, Zhang R, Xiao L, Yuan T, Shi Q, Sun R. Evaluation of xylooligosaccharide production from residual hemicelluloses of dissolving pulp by acid and enzymatic hydrolysis. RSC Adv 2018; 8:35211-35217. [PMID: 35547053 PMCID: PMC9087475 DOI: 10.1039/c8ra07140c] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/09/2018] [Indexed: 11/21/2022] Open
Abstract
Xylooligosaccharides (XOS) are useful food and pharmaceutical additives, which can be produced from various xylans. However, the XOS prepared from lignocellulosic materials are difficult to purify due to the complexity of the degradation products. Thus, hemicelluloses with a high-purity will be the preferred feedstock for XOS production. In this work, acid hydrolysis and enzymatic hydrolysis were applied to prepare XOS from the residual hemicelluloses of the dissolving pulp. The results showed that the highest XOS yield (45.18%) obtained from the acid hydrolysis was achieved with 1% sulfuric acid at 120 °C for 60 min, and xylohexaose accounted for 47% of the XOS. For enzymatic hydrolysis, under optimal conditions, the highest XOS yield of 42.96% was observed, and xylobiose and xylotriose comprised 90.5% of the XOS. It is suggested that the distribution of the XOS could be controlled significantly according to the enzymatic or acid hydrolysis conditions used. The hemicelluloses extracted from dissolving pulp were applied to produce xylooligosaccharides (XOS) by acid and enzymatic hydrolysis.![]()
Collapse
Affiliation(s)
- Yuanyuan Wang
- Beijing Key Laboratory of Lignocellulosic Chemistry
- Beijing Forestry University
- Beijing
- China
| | - Xuefei Cao
- Beijing Key Laboratory of Lignocellulosic Chemistry
- Beijing Forestry University
- Beijing
- China
| | - Ruochen Zhang
- Beijing Key Laboratory of Lignocellulosic Chemistry
- Beijing Forestry University
- Beijing
- China
| | - Lin Xiao
- Shandong Longlive Bio-Technology Co., Ltd
- China
| | - Tongqi Yuan
- Beijing Key Laboratory of Lignocellulosic Chemistry
- Beijing Forestry University
- Beijing
- China
| | - Quentin Shi
- Jining Mingsheng New Materials Co., Ltd
- Xinglong Industrial Park
- Jining City
- China
| | - Runcang Sun
- Beijing Key Laboratory of Lignocellulosic Chemistry
- Beijing Forestry University
- Beijing
- China
| |
Collapse
|
7
|
Imran M, Pant P, Shanbhag YP, Sawant SV, Ghadi SC. Genome Sequence of Microbulbifer mangrovi DD-13 T Reveals Its Versatility to Degrade Multiple Polysaccharides. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:116-124. [PMID: 28161851 DOI: 10.1007/s10126-017-9737-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/12/2017] [Indexed: 06/06/2023]
Abstract
Microbulbifer mangrovi strain DD-13T is a novel-type species isolated from the mangroves of Goa, India. The draft genome sequence of strain DD-13 comprised 4,528,106 bp with G+C content of 57.15%. Out of 3479 open reading frames, functions for 3488 protein coding sequences were predicted on the basis of similarity with the cluster of orthologous groups. In addition to protein coding sequences, 34 tRNA genes and 3 rRNA genes were detected. Analysis of nucleotide sequence of predicted gene using a Carbohydrate-Active Enzymes (CAZymes) Analysis Toolkit indicates that strain DD-13 encodes a large set of CAZymes including 255 glycoside hydrolases, 76 carbohydrate esterases, 17 polysaccharide lyases, and 113 carbohydrate-binding modules (CBMs). Many genes from strain DD-13 were annotated as carbohydrases specific for degradation of agar, alginate, carrageenan, chitin, xylan, pullulan, cellulose, starch, β-glucan, pectin, etc. Some of polysaccharide-degrading genes were highly modular and were appended at least with one CBM indicating the versatility of strain DD-13 to degrade complex polysaccharides. The cell growth of strain DD-13 was validated using pure polysaccharides such as agarose or alginate as carbon source as well as by using red and brown seaweed powder as substrate. The homologous carbohydrase produced by strain DD-13 during growth degraded the polysaccharide, ensuring the production of metabolizable reducing sugars. Additionally, several other polysaccharides such as carrageenan, xylan, pullulan, pectin, starch, and carboxymethyl cellulose were also corroborated as growth substrate for strain DD-13 and were associated with concomitant production of homologous carbohydrase.
Collapse
Affiliation(s)
- Md Imran
- Department of Biotechnology, Goa University, Taleigao Plateau, Goa, 403206, India
| | - Poonam Pant
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Yogini P Shanbhag
- Department of Biotechnology, Goa University, Taleigao Plateau, Goa, 403206, India
| | - Samir V Sawant
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Sanjeev C Ghadi
- Department of Biotechnology, Goa University, Taleigao Plateau, Goa, 403206, India.
| |
Collapse
|
8
|
Biochemical characterization of extra- and intracellular endoxylanse from thermophilic bacterium Caldicellulosiruptor kronotskyensis. Sci Rep 2016; 6:21672. [PMID: 26899227 PMCID: PMC4761950 DOI: 10.1038/srep21672] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/28/2016] [Indexed: 01/25/2023] Open
Abstract
Caldicellulosiruptor kronotskyensis grows on lignocellulosic biomass by the catalysis of intrinsic glycoside hydrolase, and has potential application for consolidated bioprocessing. In current study, two predicted extra- (Xyn10A) and intracellular (Xyn10B) xylanase from C. kronotskyensis were comparatively characterized. Xyn10A and Xyn10B share GH10 catalytic domain with similarity of 41%, while the former contains two tandem N-terminus CBM22s. Xyn10A showed higher hydrolytic capability than Xyn10B on both beechwood xylan (BWX) and oat spelt xylan (OSX). Truncation mutation experiments revealed the importance of CBMs for hydrolytic activity, substrate binding and thermostability of Xyn10A.While the quantity of CBM was not directly related to bind and thermostability. Although CBM was considered to be crucial for substrate binding, Xyn10B and Xyn10A as well as truncations performed similar binding affinity to insoluble substrate OSX. Analysis of point mutation revealed similar key residues, Glu493, Glu601 and Trp658 for Xyn10A and Glu139, Glu247 and Trp305 for Xyn10B. Both Xyn10A and Xyn10B exhibited hydrolytic activity on the mechanical pretreated corncob. After pre-digested by Xyn10A or Xyn10B, the micropores inthe the mechanical pretreated corncob were observed, which enhanced the accessibility for cellulase. Compared with corncob hydrolyzed with cellulase alone, enhanced hydrolytic performance of was observed after pre-digestion by Xyn10A or Xyn10B.
Collapse
|
9
|
Ichikawa S, Yoshida M, Karita S, Kondo M, Goto M. Carbohydrate-binding modules influence substrate specificity of an endoglucanase from Clostridium thermocellum. Biosci Biotechnol Biochem 2016. [DOI: 10.1080/09168451.2015.1069696] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Abstract
Most cellulases contain carbohydrate-binding modules (CBMs) that largely contribute to their activity for insoluble substrates. Clostridium thermocellum Cel5E is an endoglucanase having xylanolytic activity. The Cel5E originally has a family 11 CBM preferentially binding to β-1,4- and β-1,3-1,4-mixed linkage glucans. In this study, we replaced the CBM with a different type of CBM, either a family 3 microcrystalline cellulose-directed CBM from Clostridium josui scaffoldin, or a family 6 xylan-directed CBM from Clostridium stercorarium xylanase 11A. Chimeric endoglucanases showed enhanced activity that was affected by CBM binding specificity. These chimeric enzymes could efficiently degrade milled lignocellulosic materials, such as corn hulls, because of heterologous components in the plant cell wall, indicating that diverse CBMs play roles in degradation of lignocellulosic materials.
Collapse
Affiliation(s)
- Shunsuke Ichikawa
- Graduate School of Regional Innovation Studies, Mie University, Tsu, Japan
| | - Mitsuki Yoshida
- Graduate School of Regional Innovation Studies, Mie University, Tsu, Japan
| | - Shuichi Karita
- Graduate School of Regional Innovation Studies, Mie University, Tsu, Japan
- Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Makoto Kondo
- Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Masakazu Goto
- Graduate School of Bioresources, Mie University, Tsu, Japan
| |
Collapse
|
10
|
Recombinant CBM-fusion technology - Applications overview. Biotechnol Adv 2015; 33:358-69. [PMID: 25689072 DOI: 10.1016/j.biotechadv.2015.02.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 02/04/2023]
Abstract
Carbohydrate-binding modules (CBMs) are small components of several enzymes, which present an independent fold and function, and specific carbohydrate-binding activity. Their major function is to bind the enzyme to the substrate enhancing its catalytic activity, especially in the case of insoluble substrates. The immense diversity of CBMs, together with their unique properties, has long raised their attention for many biotechnological applications. Recombinant DNA technology has been used for cloning and characterizing new CBMs. In addition, it has been employed to improve the purity and availability of many CBMs, but mainly, to construct bi-functional CBM-fused proteins for specific applications. This review presents a comprehensive summary of the uses of CBMs recombinantly produced from heterologous organisms, or by the original host, along with the latest advances. Emphasis is given particularly to the applications of recombinant CBM-fusions in: (a) modification of fibers, (b) production, purification and immobilization of recombinant proteins, (c) functionalization of biomaterials and (d) development of microarrays and probes.
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Qiao W, Tang S, Mi S, Jia X, Peng X, Han Y. Biochemical characterization of a novel thermostable GH11 xylanase with CBM6 domain from Caldicellulosiruptor kronotskyensis. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
13
|
Warner CD, Camci-Unal G, Pohl NLB, Ford C, Reilly PJ. Substrate Binding by the Catalytic Domain and Carbohydrate Binding Module ofRuminococcus flavefaciensFD-1 Xyloglucanase/Endoglucanase. Ind Eng Chem Res 2012. [DOI: 10.1021/ie202988a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
14
|
Abbott DW, Boraston AB. Quantitative approaches to the analysis of carbohydrate-binding module function. Methods Enzymol 2012; 510:211-31. [PMID: 22608728 DOI: 10.1016/b978-0-12-415931-0.00011-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Carbohydrate-binding modules (CBMs) are important components of carbohydrate-active enzymes. Their primary functions are to assist in substrate turnover by targeting appended catalytic modules to substrate and concentrating appended catalytic modules on the surface of substrate. Presented here are four well-established methodologies for investigating and quantifying the CBM-polysaccharide binding relationship. These methods include: (1) the solid state depletion assay, (2) affinity gel electrophoresis, (3) UV difference and fluorescence spectroscopy, and (4) isothermal titration calorimetry. In addition, entropy-driven CBM-crystalline cellulose binding events and differential approaches to calculating stoichiometry with polyvalent polysaccharide ligands are also discussed.
Collapse
Affiliation(s)
- D Wade Abbott
- Lethbridge Research Station, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | | |
Collapse
|
15
|
Yang H, Wang K, Song X, Xu F. Production of xylooligosaccharides by xylanase from Pichia stipitis based on xylan preparation from triploid Populas tomentosa. BIORESOURCE TECHNOLOGY 2011; 102:7171-7176. [PMID: 21565493 DOI: 10.1016/j.biortech.2011.03.110] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 03/31/2011] [Accepted: 03/31/2011] [Indexed: 05/30/2023]
Abstract
Xylooligosaccharides (XOS) with DP 2-4 are important synbiotics used as food ingredients based on its prebiotic characteristics. In this work, the production of XOS from lignocellulosic material was performed by combined chemical-enzymatic methods. Xylan was prepared from triploid Populas tomentosa, and bioconverted into XOS by crude xylanase solution obtained from Pichia stipitis. The effects of reaction time, temperature, enzyme dosage, and pH value on the production of XOS were fully evaluated. Under the optimal condition (25U g(-1) substrate, pH 5.4 and 50°C), 36.8% of the xylan preparation was converted to XOS, equivalent to 3.95 mg/mL of the hydrolyzate. Xylobiose, xylotriose and xylotetrose were analyzed to be the main products of the enzymatic hydrolyzate, which together accounted for over 95% of the released oligosaccharides. Meanwhile, the effect of sonication pretreatment on the conversion efficiency of the xylan preparation was also investigated.
Collapse
Affiliation(s)
- Haiyan Yang
- Institute of Biomass Chemistry and Technology, College of Material Science and Technology, Beijing Forestry University, Beijing, 100083, China
| | | | | | | |
Collapse
|
16
|
Montanier CY, Correia MAS, Flint JE, Zhu Y, Baslé A, McKee LS, Prates JAM, Polizzi SJ, Coutinho PM, Lewis RJ, Henrissat B, Fontes CMGA, Gilbert HJ. A novel, noncatalytic carbohydrate-binding module displays specificity for galactose-containing polysaccharides through calcium-mediated oligomerization. J Biol Chem 2011; 286:22499-509. [PMID: 21454512 PMCID: PMC3121395 DOI: 10.1074/jbc.m110.217372] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 03/14/2011] [Indexed: 01/25/2023] Open
Abstract
The enzymic degradation of plant cell walls plays a central role in the carbon cycle and is of increasing environmental and industrial significance. The catalytic modules of enzymes that catalyze this process are generally appended to noncatalytic carbohydrate-binding modules (CBMs). CBMs potentiate the rate of catalysis by bringing their cognate enzymes into intimate contact with the target substrate. A powerful plant cell wall-degrading system is the Clostridium thermocellum multienzyme complex, termed the "cellulosome." Here, we identify a novel CBM (CtCBM62) within the large C. thermocellum cellulosomal protein Cthe_2193 (defined as CtXyl5A), which establishes a new CBM family. Phylogenetic analysis of CBM62 members indicates that a circular permutation occurred within the family. CtCBM62 binds to d-galactose and l-arabinopyranose in either anomeric configuration. The crystal structures of CtCBM62, in complex with oligosaccharides containing α- and β-galactose residues, show that the ligand-binding site in the β-sandwich protein is located in the loops that connect the two β-sheets. Specificity is conferred through numerous interactions with the axial O4 of the target sugars, a feature that distinguishes galactose and arabinose from the other major sugars located in plant cell walls. CtCBM62 displays tighter affinity for multivalent ligands compared with molecules containing single galactose residues, which is associated with precipitation of these complex carbohydrates. These avidity effects, which confer the targeting of polysaccharides, are mediated by calcium-dependent oligomerization of the CBM.
Collapse
Affiliation(s)
- Cedric Y. Montanier
- the Institute for Cell and Molecular Biosciences, Newcastle University, Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Márcia A. S. Correia
- the Institute for Cell and Molecular Biosciences, Newcastle University, Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - James E. Flint
- the Institute for Cell and Molecular Biosciences, Newcastle University, Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Yanping Zhu
- From the Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- the Institute for Cell and Molecular Biosciences, Newcastle University, Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602-4712, and
| | - Arnaud Baslé
- the Institute for Cell and Molecular Biosciences, Newcastle University, Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Lauren S. McKee
- the Institute for Cell and Molecular Biosciences, Newcastle University, Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602-4712, and
| | - José A. M. Prates
- From the Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Samuel J. Polizzi
- the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229
| | - Pedro M. Coutinho
- the Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I and II, 163 Avenue de Luminy, 13288 Marseille, France
| | - Richard J. Lewis
- the Institute for Cell and Molecular Biosciences, Newcastle University, Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Bernard Henrissat
- the Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I and II, 163 Avenue de Luminy, 13288 Marseille, France
| | - Carlos M. G. A. Fontes
- From the Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Harry J. Gilbert
- the Institute for Cell and Molecular Biosciences, Newcastle University, Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602-4712, and
| |
Collapse
|
17
|
Dam P, Kataeva I, Yang SJ, Zhou F, Yin Y, Chou W, Poole FL, Westpheling J, Hettich R, Giannone R, Lewis DL, Kelly R, Gilbert HJ, Henrissat B, Xu Y, Adams MWW. Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725. Nucleic Acids Res 2011; 39:3240-54. [PMID: 21227922 PMCID: PMC3082886 DOI: 10.1093/nar/gkq1281] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Caldicellulosiruptor bescii DSM 6725 utilizes various polysaccharides and grows efficiently on untreated high-lignin grasses and hardwood at an optimum temperature of ∼80°C. It is a promising anaerobic bacterium for studying high-temperature biomass conversion. Its genome contains 2666 protein-coding sequences organized into 1209 operons. Expression of 2196 genes (83%) was confirmed experimentally. At least 322 genes appear to have been obtained by lateral gene transfer (LGT). Putative functions were assigned to 364 conserved/hypothetical protein (C/HP) genes. The genome contains 171 and 88 genes related to carbohydrate transport and utilization, respectively. Growth on cellulose led to the up-regulation of 32 carbohydrate-active (CAZy), 61 sugar transport, 25 transcription factor and 234 C/HP genes. Some C/HPs were overproduced on cellulose or xylan, suggesting their involvement in polysaccharide conversion. A unique feature of the genome is enrichment with genes encoding multi-modular, multi-functional CAZy proteins organized into one large cluster, the products of which are proposed to act synergistically on different components of plant cell walls and to aid the ability of C. bescii to convert plant biomass. The high duplication of CAZy domains coupled with the ability to acquire foreign genes by LGT may have allowed the bacterium to rapidly adapt to changing plant biomass-rich environments.
Collapse
Affiliation(s)
- Phuongan Dam
- Institute of Bioinformatics, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Hervé C, Rogowski A, Blake AW, Marcus SE, Gilbert HJ, Knox JP. Carbohydrate-binding modules promote the enzymatic deconstruction of intact plant cell walls by targeting and proximity effects. Proc Natl Acad Sci U S A 2010; 107:15293-8. [PMID: 20696902 PMCID: PMC2930570 DOI: 10.1073/pnas.1005732107] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cell wall degrading enzymes have a complex molecular architecture consisting of catalytic modules and noncatalytic carbohydrate-binding modules (CBMs). The function of CBMs in cell wall degrading processes is poorly understood. Here, we have evaluated the potential enzyme-targeting function of CBMs in the context of intact primary and secondary cell wall deconstruction. The capacity of a pectate lyase to degrade pectic homogalacturonan in primary cell walls was potentiated by cellulose-directed CBMs but not by xylan-directed CBMs. Conversely, the arabinofuranosidase-mediated removal of side chains from arabinoxylan in xylan-rich and cellulose-poor wheat grain endosperm cell walls was enhanced by a xylan-binding CBM but less so by a crystalline cellulose-specific module. The capacity of xylanases to degrade xylan in secondary cell walls was potentiated by both xylan- and cellulose-directed CBMs. These studies demonstrate that CBMs can potentiate the action of a cognate catalytic module toward polysaccharides in intact cell walls through the recognition of nonsubstrate polysaccharides. The targeting actions of CBMs therefore have strong proximity effects within cell wall structures, explaining why cellulose-directed CBMs are appended to many noncellulase cell wall hydrolases.
Collapse
Affiliation(s)
- Cécile Hervé
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Artur Rogowski
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HN, United Kingdom; and
| | - Anthony W. Blake
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Susan E. Marcus
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HN, United Kingdom; and
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602-4712
| | - J. Paul Knox
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| |
Collapse
|
20
|
Correia MAS, Abbott DW, Gloster TM, Fernandes VO, Prates JAM, Montanier C, Dumon C, Williamson MP, Tunnicliffe RB, Liu Z, Flint JE, Davies GJ, Henrissat B, Coutinho PM, Fontes CMGA, Gilbert HJ. Signature active site architectures illuminate the molecular basis for ligand specificity in family 35 carbohydrate binding module. Biochemistry 2010; 49:6193-205. [PMID: 20496884 DOI: 10.1021/bi1006139] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The deconstruction of the plant cell wall is an important biological process that is attracting considerable industrial interest, particularly in the bioenergy sector. Enzymes that attack the plant cell wall generally contain one or more noncatalytic carbohydrate binding modules (CBMs) that play an important targeting function. While CBMs that bind to the backbones of plant structural polysaccharides have been widely described, modules that recognize components of the vast array of decorations displayed on these polymers have been relatively unexplored. Here we show that a family 35 CBM member (CBM35), designated CtCBM35-Gal, binds to alpha-D-galactose (Gal) and, within the context of the plant cell wall, targets the alpha-1,6-Gal residues of galactomannan but not the beta-D-Gal residues in xyloglucan. The crystal structure of CtCBM35-Gal reveals a canonical beta-sandwich fold. Site-directed mutagenesis studies showed that the ligand is accommodated within the loops that connect the two beta-sheets. Although the ligand binding site of the CBM displays significant structural similarity with calcium-dependent CBM35s that target uronic acids, subtle differences in the conformation of conserved residues in the ligand binding site lead to the loss of metal binding and uronate recognition. A model is proposed in which the orientation of the pair of aromatic residues that interact with the two faces of the Gal pyranose ring plays a pivotal role in orientating the axial O4 atom of the ligand toward Asn140, which is invariant in CBM35. The ligand recognition site of exo-CBM35s (CBM35-Gal and the uronic acid binding CBM35s) appears to overlap with that of CBM35-Man, which binds to the internal regions of mannan, a beta-polymer of mannose. Using site-directed mutagenesis, we show that although there is conservation of several functional residues within the binding sites of endo- and exo-CBM35s, the endo-CBM does not utilize Asn113 (equivalent to Asn140 in CBM35-Gal) in mannan binding, despite the importance of the equivalent residue in ligand recognition across the CBM35 and CBM6 landscape. The data presented in this report are placed within a wider phylogenetic context for the CBM35 family.
Collapse
Affiliation(s)
- Márcia A S Correia
- CIISA, Faculdade de Medicina Veterinária, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Gilbert HJ. The biochemistry and structural biology of plant cell wall deconstruction. PLANT PHYSIOLOGY 2010; 153:444-55. [PMID: 20406913 PMCID: PMC2879781 DOI: 10.1104/pp.110.156646] [Citation(s) in RCA: 217] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 04/17/2010] [Indexed: 05/18/2023]
Affiliation(s)
- Harry J Gilbert
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA.
| |
Collapse
|
22
|
Correia MÃA, Pires VM, Gilbert HJ, Bolam DN, Fernandes VÃO, Alves VD, Prates JA, Ferreira LM, Fontes CM. Family 6 carbohydrate-binding modules display multiple β1,3-linked glucan-specific binding interfaces. FEMS Microbiol Lett 2009; 300:48-57. [DOI: 10.1111/j.1574-6968.2009.01764.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
23
|
Sunna A. Modular organisation and functional analysis of dissected modular β-mannanase CsMan26 from Caldicellulosiruptor Rt8B.4. Appl Microbiol Biotechnol 2009; 86:189-200. [DOI: 10.1007/s00253-009-2242-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 09/03/2009] [Accepted: 09/03/2009] [Indexed: 10/20/2022]
|
24
|
Kiyohara M, Sakaguchi K, Yamaguchi K, Araki T, Ito M. Characterization and application of carbohydrate-binding modules of beta-1,3-xylanase XYL4. J Biochem 2009; 146:633-41. [PMID: 19605459 DOI: 10.1093/jb/mvp108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
beta-1,3-Xylanase from Vibrio sp. strain AX-4 (XYL4) is a modular enzyme composed of an N-terminal catalytic module belonging to glycoside hydrolase family 26 and two putative carbohydrate-binding modules (CBMs) belonging to family 31 in the C-terminal region. To investigate the functions of these three modules, five deletion mutants lacking individual modules were constructed. The binding assay of these mutants showed that a repeating unit of the CBM was a non-catalytic beta-1,3-xylan-binding module, while the catalytic module per se was not likely to contribute to the binding activity when insoluble beta-1,3-xylan was used for the assay. The repeating CBMs were found to specifically bind to insoluble beta-1,3-xylan, but not to beta-1,4-xylan, Avicel, beta-1,4-mannan, curdlan, chitin or soluble glycol-beta-1,3-xylan. Both the enzyme and the binding activities for insoluble beta-1,3-xylan but not soluble glycol-beta-1,3-xylan were enhanced by NaCl in a concentration-dependent manner, indicating that the CBMs of XYL4 bound to beta-1,3-xylan through hydrophobic interaction. This property of the CBMs was successfully applied to the purification of a recombinant XYL4 from the cell extracts of Escherichia coli transformed with the xyl4 gene and the detection of beta-1,3-xylan-binding proteins including beta-1,3-xylanase from the extract of a turban shell, Turbo cornutus.
Collapse
Affiliation(s)
- Masashi Kiyohara
- Department of Bioscience, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 812-8581, Japan
| | | | | | | | | |
Collapse
|
25
|
Abou-hachem M, Olsson F, Williamson M, Linse S, Crennell S, Hreggvidsson G, Kristjansson J, Holst O, Nordberg Karlsson E. The Modular Organisation and Stability of a Thermostable Family 10 Xylanase. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/1024240310001614315] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
26
|
Connaris H, Crocker PR, Taylor GL. Enhancing the receptor affinity of the sialic acid-binding domain of Vibrio cholerae sialidase through multivalency. J Biol Chem 2009; 284:7339-51. [PMID: 19124471 DOI: 10.1074/jbc.m807398200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many glycoside hydrolases possess carbohydrate-binding modules (CBMs) that help target these enzymes to appropriate substrates and increase their catalytic efficiency. The Vibrio cholerae sialidase contains two CBMs, one of which is designated as a family CBM40 module and has been shown through structural and calorimetry studies to recognize the alpha-anomer of sialic acid with a KD of approximately 30 microM at 37 degrees C. The affinity of this V. cholerae CBM40 module for sialic acid is one of the highest reported for recognition of a monosaccharide by a CBM. As Nature often increases a weak substrate affinity through multivalency, we have explored the potential of developing reagents with an increased affinity for sialic acid receptors through linking CBM40 modules together. The V. cholerae CBM40 was subcloned and crystallized in the presence of sialyllactose confirming its ability to recognize sialic acid. Calorimetry revealed that this CBM40 demonstrated specificity to alpha(2,3)-, alpha(2,6)-, and alpha(2,8)-linked sialosides. Polypeptides containing up to four CBM40 modules in tandem were created to determine if an increase in affinity to sialic acid could be achieved through an avidity effect. Using SPR and a multivalent alpha(2,3)-sialyllactose ligand, we show that increasing the number of linked modules does increase the affinity for sialic acid. The four-CBM40 module protein has a 700- to 1500-fold increase in affinity compared with the single-CBM40 module. Varying the linker length of amino acids between each CBM40 module had little effect on the binding of these polypeptides. Finally, fluorescence-activated cell sorting analysis demonstrated that a green fluorescent protein fused to three CBM40 modules bound to subpopulations of human leukocytes. These studies lay the foundation for creating high affinity, multivalent CBMs that could have broad application in glycobiology.
Collapse
Affiliation(s)
- Helen Connaris
- Centre for Biomolecular Sciences, University of St. Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland, UK.
| | | | | |
Collapse
|
27
|
Weiner RM, Taylor LE, Henrissat B, Hauser L, Land M, Coutinho PM, Rancurel C, Saunders EH, Longmire AG, Zhang H, Bayer EA, Gilbert HJ, Larimer F, Zhulin IB, Ekborg NA, Lamed R, Richardson PM, Borovok I, Hutcheson S. Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T. PLoS Genet 2008; 4:e1000087. [PMID: 18516288 PMCID: PMC2386152 DOI: 10.1371/journal.pgen.1000087] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Accepted: 05/01/2008] [Indexed: 01/02/2023] Open
Abstract
The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40) is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment. A segment of the global marine carbon cycle that has been poorly characterized is the mineralization of complex polysaccharides to carbon dioxide, a greenhouse gas. It also remained a mystery whether prokaryotes mineralize plant/algal cell walls and woody material in the oceans via carbohydrase systems and, if so, which organisms are involved. We have analyzed the complete genome sequence of the marine bacterium Saccharophagus degradans to better ascertain the potential role of prokaryotes in marine carbon transformation. We discovered that S. degradans, which is related to a number of other newly discovered marine strains, has an unprecedented quantity and diversity of carbohydrases, including the first characterized marine cellulose system. In fact, extensive analysis of the S. degradans genome sequence and functional followup experiments identified an extensive collection of complete enzyme systems that degrade more than 10 complex polysaccharides. These include agar, alginate, and chitin, altogether representing an extraordinary range of catabolic capability. Genomic analyses further demonstrated that the carbohydrases are unusually modular; sequence comparisons revealed that many of the functional modules were acquired by lateral transfer. These results suggest that the prokaryotic contribution to marine carbon fluxes is substantial and cannot be ignored in predictions of climate change.
Collapse
Affiliation(s)
- Ronald M. Weiner
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
- Marine and Estuarine Environmental Sciences Program, University of Maryland, College Park, Maryland, United States of America
- * E-mail: (RMW); (SH)
| | - Larry E. Taylor
- Marine and Estuarine Environmental Sciences Program, University of Maryland, College Park, Maryland, United States of America
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, Marseille, France
| | - Loren Hauser
- Oak Ridge National Laboratory (ORNL), Life Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Miriam Land
- Oak Ridge National Laboratory (ORNL), Life Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Pedro M. Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, Marseille, France
| | - Corinne Rancurel
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, Marseille, France
| | - Elizabeth H. Saunders
- Joint Genome Institute, Group B-5 Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Atkinson G. Longmire
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Haitao Zhang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Edward A. Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne, United Kingdom
| | - Frank Larimer
- Oak Ridge National Laboratory (ORNL), Life Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Igor B. Zhulin
- Joint Institute for Computational Sciences, University of Tennessee–Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Nathan A. Ekborg
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Paul M. Richardson
- DOE Joint Genome Institute, Production Genomics Facility, Walnut Creek, California, United States of America
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Steven Hutcheson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
- * E-mail: (RMW); (SH)
| |
Collapse
|
28
|
Crystal Structure of a Cellulosomal Family 3 Carbohydrate Esterase from Clostridium thermocellum Provides Insights into the Mechanism of Substrate Recognition. J Mol Biol 2008; 379:64-72. [DOI: 10.1016/j.jmb.2008.03.037] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Revised: 03/03/2008] [Accepted: 03/12/2008] [Indexed: 11/23/2022]
|
29
|
Valdez HA, Busi MV, Wayllace NZ, Parisi G, Ugalde RA, Gomez-Casati DF. Role of the N-terminal starch-binding domains in the kinetic properties of starch synthase III from Arabidopsis thaliana. Biochemistry 2008; 47:3026-32. [PMID: 18260645 DOI: 10.1021/bi702418h] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Starch synthase III (SSIII), one of the SS isoforms involved in plant starch synthesis, has been reported to play a regulatory role in the synthesis of transient starch. SSIII from Arabidopsis thaliana contains 1025 amino acid residues and has an N-terminal transit peptide for chloroplast localization which is followed by three repeated starch-binding domains (SBDs; SSIII residues 22-591) and a C-terminal catalytic domain (residues 592-1025) similar to bacterial glycogen synthase. In this work, we constructed recombinant full-length and truncated isoforms of SSIII, lacking one, two, or three SBDs, and recombinant proteins, containing three, two, or one SBD, to investigate the role of these domains in enzyme activity. Results revealed that SSIII uses preferentially ADPGlc, although UDPGlc can also be used as a sugar donor substrate. When ADPGlc was used, the presence of the SBDs confers particular properties to each isoform, increasing the apparent affinity and the V max for the oligosaccharide acceptor substrate. However, no substantial changes in the kinetic parameters for glycogen were observed when UDPGlc was the donor substrate. Under glycogen saturating conditions, the presence of SBDs increases progressively the apparent affinity and V max for ADPGlc but not for UDPGlc. Adsorption assays showed that the N-terminal region of SSIII, containing three, two, or one SBD module have increased capacity to bind starch depending on the number of SBD modules, with the D23 protein (containing the second and third SBD module) being the one that makes the greatest contribution to binding. The results presented here suggest that the N-terminal SBDs have a regulatory role, showing a starch binding capacity and modulating the catalytic properties of SSIII.
Collapse
Affiliation(s)
- Hugo A Valdez
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), CONICET/UNSAM, Camino Circunvalación Km 6, 7130 Chascomús, Argentina
| | | | | | | | | | | |
Collapse
|
30
|
Nagy T, Tunnicliffe RB, Higgins LD, Walters C, Gilbert HJ, Williamson MP. Characterization of a double dockerin from the cellulosome of the anaerobic fungus Piromyces equi. J Mol Biol 2007; 373:612-22. [PMID: 17869267 DOI: 10.1016/j.jmb.2007.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Accepted: 08/01/2007] [Indexed: 10/22/2022]
Abstract
The assembly into supramolecular complexes of proteins having complementary activities is central to cellular function. One such complex of considerable biological and industrial significance is the plant cell wall-degrading apparatus of anaerobic microorganisms, termed the cellulosome. A central feature of bacterial cellulosomes is a large non-catalytic protein, the scaffoldin, which contains multiple cohesin domains. An array of digestive enzymes is incorporated into the cellulosome through the interaction of the dockerin domains, present in the catalytic subunits, with the cohesin domains that are present in the scaffoldin. By contrast, in anaerobic fungi, such as Piromyces equi, the dockerins of cellulosomal enzymes are often present in tandem copies; however, the identity of the cognate cohesin domains in these organisms is unclear, hindering further biotechnological development of the fungal cellulosome. Here, we characterise the solution structure and function of a double-dockerin construct from the P. equi endoglucanase Cel45A. We show that the two domains are connected by a flexible linker that is short enough to keep the binding sites of the two domains on adjacent surfaces, and allows the double-dockerin construct to bind more tightly to cellulosomes than a single domain and with greater coverage. The double dockerin binds to the GH3 beta-glucosidase component of the fungal cellulosome, which is thereby identified as a potential scaffoldin.
Collapse
Affiliation(s)
- Tibor Nagy
- Institute for Cell and Molecular Biosciences, The University of Newcastle upon Tyne, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | | | | | | | | | | |
Collapse
|
31
|
Guillén D, Santiago M, Linares L, Pérez R, Morlon J, Ruiz B, Sánchez S, Rodríguez-Sanoja R. Alpha-amylase starch binding domains: cooperative effects of binding to starch granules of multiple tandemly arranged domains. Appl Environ Microbiol 2007; 73:3833-7. [PMID: 17468268 PMCID: PMC1932744 DOI: 10.1128/aem.02628-06] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Lactobacillus amylovorus alpha-amylase starch binding domain (SBD) is a functional domain responsible for binding to insoluble starch. Structurally, this domain is dissimilar from other reported SBDs because it is composed of five identical tandem modules of 91 amino acids each. To understand adsorption phenomena specific to this SBD, the importance of their modular arrangement in relationship to binding ability was investigated. Peptides corresponding to one, two, three, four, or five modules were expressed as His-tagged proteins. Protein binding assays showed an increased capacity of adsorption as a function of the number of modules, suggesting that each unit of the SBD may act in an additive or synergic way to optimize binding to raw starch.
Collapse
Affiliation(s)
- D Guillén
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, UNAM, A.P. 70228, 04510 México D.F., Mexico
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Firouzabadi FN, Vincken JP, Ji Q, Suurs LCJM, Buléon A, Visser RGF. Accumulation of multiple-repeat starch-binding domains (SBD2-SBD5) does not reduce amylose content of potato starch granules. PLANTA 2007; 225:919-33. [PMID: 17039369 DOI: 10.1007/s00425-006-0411-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Accepted: 09/14/2006] [Indexed: 05/12/2023]
Abstract
This study investigates whether it is possible to produce an amylose-free potato starch by displacing the amylose enzyme, granule-bound starch synthase I (GBSSI), from the starch granule by engineered, high-affinity, multiple-repeat family 20 starch-binding domains (SBD2, SBD3, SBD4, and SBD5). The constructs were introduced in the amylose-containing potato cultivar (cv. Kardal), and the starches of the resulting transformants were compared with those of SBD2-expressing amylose-free (amf) potato clones. It is shown that a correctly sized protein accumulated in the starch granules of the various transformants. The amount of SBD accumulated in starch increased progressively from SBD to SBD3; however, it seemed as if less SBD4 and SBD5 was accumulated. A reduction in amylose content was not achieved in any of the transformants. However, it is shown that SBDn expression can affect physical processes underlying granule assembly, in both genetic potato backgrounds, without altering the primary structure of the constituent starch polymers and the granule melting temperature. Granule size distribution of the starches obtained from transgenic Kardal plants were similar to those from untransformed controls, irrespective of the amount of SBDn accumulated. In the amf background, granule size is severely affected. In both the Kardal and amf background, apparently normal oval-shaped starch granules were composed of multiple smaller ones, as evidenced from the many "Maltese crosses" within these granules. The results are discussed in terms of different binding modes of SBD.
Collapse
Affiliation(s)
- Farhad Nazarian Firouzabadi
- Graduate School Experimental Plant Sciences, Laboratory of Plant Breeding, Wageningen University, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | | | | | | | | | | |
Collapse
|
33
|
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.
Collapse
Affiliation(s)
- Alisdair B Boraston
- Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada.
| | | | | | | | | | | |
Collapse
|
34
|
Tunnicliffe RB, Bolam DN, Pell G, Gilbert HJ, Williamson MP. Structure of a mannan-specific family 35 carbohydrate-binding module: evidence for significant conformational changes upon ligand binding. J Mol Biol 2005; 347:287-96. [PMID: 15740741 DOI: 10.1016/j.jmb.2005.01.038] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Revised: 01/12/2005] [Accepted: 01/17/2005] [Indexed: 10/25/2022]
Abstract
Enzymes that digest plant cell wall polysaccharides generally contain non-catalytic, carbohydrate-binding modules (CBMs) that function by attaching the enzyme to the substrate, potentiating catalytic activity. Here, we present the first structure of a family 35 CBM, derived from the Cellvibrio japonicus beta-1,4-mannanase Man5C. The NMR structure has been determined for both the free protein and the protein bound to mannopentaose. The data show that the protein displays a typical beta-jelly-roll fold. Ligand binding is not located on the concave surface of the protein, as occurs in many CBMs that display the jelly-roll fold, but is formed by the loops that link the two beta-sheets of the protein, similar to family 6 CBMs. In contrast to the majority of CBMs, which are generally rigid proteins, CBM35 undergoes significant conformational change upon ligand binding. The curvature of the binding site and the narrow binding cleft are likely to be the main determinants of binding specificity. The predicted solvent exposure of O6 at several subsites provides an explanation for the observed accommodation of decorated mannans. Two of the key aromatic residues in Man5C-CBM35 that interact with mannopentaose are conserved in mannanase-derived CBM35s, which will guide specificity predictions based on the primary sequence of proteins in this CBM family.
Collapse
Affiliation(s)
- Richard B Tunnicliffe
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | | | | | | | | |
Collapse
|
35
|
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: 1434] [Impact Index Per Article: 75.5] [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.
Collapse
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
| |
Collapse
|
36
|
McCartney L, Gilbert HJ, Bolam DN, Boraston AB, Knox JP. Glycoside hydrolase carbohydrate-binding modules as molecular probes for the analysis of plant cell wall polymers. Anal Biochem 2004; 326:49-54. [PMID: 14769335 DOI: 10.1016/j.ab.2003.11.011] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2003] [Indexed: 11/27/2022]
Abstract
Novel molecular probes have been developed for the analysis and detection of polysaccharides in plant cell walls using carbohydrate-binding modules (CBMs) derived from modular glycoside hydrolases belonging to families 2a, 6, and 29. Recombinant forms of these proteins containing his-tags, in conjunction with anti-his-tag detection, provide a flexible system that utilizes CBMs as molecular probes in a range of applications. Assays for the rapid analysis of the binding of CBMs to polysaccharides and oligosaccharides using nitrocellulose-based CBM macroarrays and microtiter plate-based CBM capture and competitive-inhibition assays are described. We also demonstrate the use of CBMs with his-tags for the localization of their target ligands in planta. The generation of molecular probes from other families of CBMs will dramatically increase the repertoire of molecular probes available to determine the developmental and functional aspects of plant cell walls.
Collapse
Affiliation(s)
- Lesley McCartney
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
| | | | | | | | | |
Collapse
|
37
|
Roske Y, Sunna A, Pfeil W, Heinemann U. High-resolution crystal structures of Caldicellulosiruptor strain Rt8B.4 carbohydrate-binding module CBM27-1 and its complex with mannohexaose. J Mol Biol 2004; 340:543-54. [PMID: 15210353 DOI: 10.1016/j.jmb.2004.04.072] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Revised: 04/23/2004] [Accepted: 04/23/2004] [Indexed: 11/24/2022]
Abstract
Carbohydrate-binding modules (CBMs) are the most common non-catalytic modules associated with enzymes active in plant cell-wall hydrolysis. Despite the large number of putative CBMs being identified by amino acid sequence alignments, only few representatives have been experimentally shown to have a carbohydrate-binding function. Caldicellulosiruptor strain Rt8B.4 Man26 is a thermostable modular glycoside hydrolase beta-mannanase which contains two non-catalytic modules in tandem at its N terminus. These modules were recently shown to function primarily as beta-mannan-binding modules and have accordingly been classified as members of a novel family of CBMs, family 27. The N-terminal CBM27 (CsCBM27-1) of Man26 from Caldicellulosiruptor Rt8B.4 displays high-binding affinity towards mannohexaose with a Ka of 1 x 10(7) M(-1). Accordingly, the high-resolution crystal structures of CsCBM27-1 native and its mannohexaose complex were solved at 1.55 angstroms and 1.06 angstoms resolution, respectively. In the crystal, CsCBM27-1 shows the typical beta-sandwich jellyroll fold observed in other CBMs with a single metal ion bound, which was identified as calcium. The crystal structures reveal that the overall fold of CsCBM27-1 remains virtually unchanged upon sugar binding and that binding is mediated by three solvent-exposed tryptophan residues and few direct hydrogen bonds. Based on binding affinity and thermal unfolding experiments this structural calcium is shown to play a role in the thermal stability of CsCBM27-1 at high temperatures. The higher binding affinity of CsCBM27-1 to mannooligosaccharides when compared to other members of CBM family 27 might be explained by the different orientation of the residues forming the "aromatic platform" and by differences in the length of loops. Finally, evidence is presented, on the basis of fold similarities and the retention of the position of conserved motifs and a calcium ion, for the consolidation of related CBM families into a superfamily of CBMs.
Collapse
Affiliation(s)
- Yvette Roske
- Crystallography Group, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, D-13125 Berlin, Germany
| | | | | | | |
Collapse
|
38
|
Lammerts van Bueren A, Boraston AB. Binding Sub-site Dissection of a Carbohydrate-binding Module Reveals the Contribution of Entropy to Oligosaccharide Recognition at “Non-primary” Binding Subsites. J Mol Biol 2004; 340:869-79. [PMID: 15223327 DOI: 10.1016/j.jmb.2004.05.038] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2004] [Revised: 05/19/2004] [Accepted: 05/19/2004] [Indexed: 10/26/2022]
Abstract
The optimal ligands for many carbohydrate-binding proteins are often oligosaccharides comprising two, three, or more monosaccharide units. The binding affinity for these sugars is increased incrementally by contributions from binding subsites on the protein that accommodate the individual monosaccharide residues of the oligosaccharide. Here, we use CsCBM6-1, a xylan-specific type B carbohydrate-binding module (CBM) from Clostridium stercorarium falling into amino acid sequence family CBM6, as a model system to investigate the structural and thermodynamic contributions of binding subsites in this protein to carbohydrate recognition. The three-dimensional structures of uncomplexed CsCBM6-1 (at 1.8 A resolution) and bound to the oligosaccharides xylobiose, xylotriose, and xylotetraose (at 1.70 A, 1.89 A, and 1.69 A resolution, respectively) revealed the sequential occupation of four subsites within the binding site in the order of subsites 2, 3, 4 then 1. Overall, binding to all of the xylooligosaccharides tested was enthalpically favourable and entropically unfavourable, like most protein-carbohydrate interactions, with the primary subsites 2 and 3 providing the bulk of the free energy and enthalpy of binding. In contrast, the contributions to the changes in entropy of the non-primary subsites 1 and 4 to xylotriose and xylotetraose binding, respectively, were positive. This observation is remarkable, in that it shows that the 10-20-fold improvement in association constants for oligosaccharides longer than a disaccharide is facilitated by favourable entropic contributions from the non-primary binding subsites.
Collapse
Affiliation(s)
- Alicia Lammerts van Bueren
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 3055 STN CSC, Victoria, BC, Canada V8W 3P6
| | | |
Collapse
|
39
|
Bolam DN, Xie H, Pell G, Hogg D, Galbraith G, Henrissat B, Gilbert HJ. X4 modules represent a new family of carbohydrate-binding modules that display novel properties. J Biol Chem 2004; 279:22953-63. [PMID: 15004012 DOI: 10.1074/jbc.m313317200] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hydrolysis of the plant cell wall by microbial glycoside hydrolases and esterases is the primary mechanism by which stored organic carbon is utilized in the biosphere, and thus these enzymes are of considerable biological and industrial importance. Plant cell wall-degrading enzymes in general display a modular architecture comprising catalytic and non-catalytic modules. The X4 modules in glycoside hydrolases represent a large family of non-catalytic modules whose function is unknown. Here we show that the X4 modules from a Cellvibrio japonicus mannanase (Man5C) and arabinofuranosidase (Abf62A) bind to polysaccharides, and thus these proteins comprise a new family of carbohydrate-binding modules (CBMs), designated CBM35. The Man5C-CBM35 binds to galactomannan, insoluble amorphous mannan, glucomannan, and manno-oligosaccharides but does not interact with crystalline mannan, cellulose, cello-oligosaccharides, or other polysaccharides derived from the plant cell wall. Man5C-CBM35 also potentiates mannanase activity against insoluble amorphous mannan. Abf62A-CBM35 interacts with unsubstituted oat-spelt xylan but not substituted forms of the hemicellulose or xylo-oligosaccharides, and requires calcium for binding. This is in sharp contrast to other xylan-binding CBMs, which interact in a calcium-independent manner with both xylo-oligosaccharides and decorated xylans.
Collapse
Affiliation(s)
- David N Bolam
- School of Cell and Molecular Biosciences, University of Newcastle upon Tyne, The Agriculture Building, Newcastle upon Tyne NE1 7RU, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
40
|
Hogg D, Pell G, Dupree P, Goubet F, Martín-Orúe SM, Armand S, Gilbert HJ. The modular architecture of Cellvibrio japonicus mannanases in glycoside hydrolase families 5 and 26 points to differences in their role in mannan degradation. Biochem J 2003; 371:1027-43. [PMID: 12523937 PMCID: PMC1223318 DOI: 10.1042/bj20021860] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2002] [Revised: 12/18/2002] [Accepted: 01/10/2003] [Indexed: 11/17/2022]
Abstract
beta-1,4-Mannanases (mannanases), which hydrolyse mannans and glucomannans, are located in glycoside hydrolase families (GHs) 5 and 26. To investigate whether there are fundamental differences in the molecular architecture and biochemical properties of GH5 and GH26 mannanases, four genes encoding these enzymes were isolated from Cellvibrio japonicus and the encoded glycoside hydrolases were characterized. The four genes, man5A, man5B, man5C and man26B, encode the mannanases Man5A, Man5B, Man5C and Man26B, respectively. Man26B consists of an N-terminal signal peptide linked via an extended serine-rich region to a GH26 catalytic domain. Man5A, Man5B and Man5C contain GH5 catalytic domains and non-catalytic carbohydrate-binding modules (CBMs) belonging to families 2a, 5 and 10; Man5C in addition contains a module defined as X4 of unknown function. The family 10 and 2a CBMs bound to crystalline cellulose and ivory nut crystalline mannan, displaying very similar properties to the corresponding family 10 and 2a CBMs from Cellvibrio cellulases and xylanases. CBM5 bound weakly to these crystalline polysaccharides. The catalytic domains of Man5A, Man5B and Man26B hydrolysed galactomannan and glucomannan, but displayed no activity against crystalline mannan or cellulosic substrates. Although Man5C was less active against glucomannan and galactomannan than the other mannanases, it did attack crystalline ivory nut mannan. All the enzymes exhibited classic endo-activity producing a mixture of oligosaccharides during the initial phase of the reaction, although their mode of action against manno-oligosaccharides and glucomannan indicated differences in the topology of the respective substrate-binding sites. This report points to a different role for GH5 and GH26 mannanases from C. japonicus. We propose that as the GH5 enzymes contain CBMs that bind crystalline polysaccharides, these enzymes are likely to target mannans that are integral to the plant cell wall, while GH26 mannanases, which lack CBMs and rapidly release mannose from polysaccharides and oligosaccharides, target the storage polysaccharide galactomannan and manno-oligosaccharides.
Collapse
Affiliation(s)
- Deborah Hogg
- School of Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, UK
| | | | | | | | | | | | | |
Collapse
|
41
|
Boraston AB, Notenboom V, Warren RAJ, Kilburn DG, Rose DR, Davies G. Structure and ligand binding of carbohydrate-binding module CsCBM6-3 reveals similarities with fucose-specific lectins and "galactose-binding" domains. J Mol Biol 2003; 327:659-69. [PMID: 12634060 DOI: 10.1016/s0022-2836(03)00152-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Carbohydrate-binding polypeptides, including carbohydrate-binding modules (CBMs) from polysaccharidases, and lectins, are widespread in nature. Whilst CBMs are classically considered distinct from lectins, in that they are found appended to polysaccharide-degrading enzymes, this distinction is blurring. The crystal structure of CsCBM6-3, a "sequence-family 6" CBM in a xylanase from Clostridium stercorarium, at 2.3 A reveals a similar, all beta-sheet fold to that from MvX56, a module found in a family 33 glycoside hydrolase sialidase from Micromonospora viridifaciens, and the lectin AAA from Anguilla anguilla. Sequence analysis leads to the classification of MvX56 and AAA into a family distinct from that containing CsCBM6-3. Whilst these polypeptides are similar in structure they have quite different carbohydrate-binding specificities. AAA is known to bind fucose; CsCBM6-3 binds cellulose, xylan and other beta-glucans. Here we demonstrate that MvX56 binds galactose, lactose and sialic acid. Crystal structures of CsCBM6-3 in complex with xylotriose, cellobiose, and laminaribiose, 2.0 A, 1.35 A, and 1.0 A resolution, respectively, reveal that the binding site of CsCBM6-3 resides on the same polypeptide face as for MvX56 and AAA. Subtle differences in the ligand-binding surface give rise to the different specificities and biological activities, further blurring the distinction between classical lectins and CBMs.
Collapse
Affiliation(s)
- Alisdair B Boraston
- Department of Chemistry, The University of York, Heslington, York, YO10 5YW, UK
| | | | | | | | | | | |
Collapse
|
42
|
Boraston AB, Kwan E, Chiu P, Warren RAJ, Kilburn DG. Recognition and hydrolysis of noncrystalline cellulose. J Biol Chem 2003; 278:6120-7. [PMID: 12427734 DOI: 10.1074/jbc.m209554200] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellulase Cel5A from alkalophilic Bacillus sp. 1139 contains a family 17 carbohydrate-binding module (BspCBM17) and a family 28 CBM (BspCBM28) in tandem. The two modules have significantly similar amino acid sequences, but amino acid residues essential for binding are not conserved. BspCBM28 was obtained as a discrete polypeptide by engineering the cel5A gene. BspCBM17 could not be obtained as a discrete polypeptide, so a family 17 CBM from endoglucanase Cel5A of Clostridium cellulovorans, CcCBM17, was used to compare the binding characteristics of the two families of CBM. Both CcCBM17 and BspCBM28 recognized two classes of binding sites on amorphous cellulose: a high affinity site (K(a) approximately 1 x 10(6) M(-1)) and a low affinity site (K(a) approximately 2 x 10(4) M(-1)). They did not compete for binding to the high affinity sites, suggesting that they bound at different sites on the cellulose. A polypeptide, BspCBM17/CBM28, comprising the tandem CBMs from Cel5A, bound to amorphous cellulose with a significantly higher affinity than the sum of the affinities of CcCBM17 and BspCBM28, indicating cooperativity between the linked CBMs. Cel5A mutants were constructed that were defective in one or both of the CBMs. The mutants differed from the wild-type enzyme in the amounts and sizes of the soluble products produced from amorphous cellulose. This suggests that either the CBMs can modify the action of the catalytic module of Cel5A or that they target the enzyme to areas of the cellulose that differ in susceptibility to hydrolysis.
Collapse
Affiliation(s)
- Alisdair B Boraston
- Protein Engineering Network of Centres of Excellence, PENCE Inc., National Business Centre, Edmonton, Alberta T6G 2S2, Canada.
| | | | | | | | | |
Collapse
|
43
|
Chhabra SR, Kelly RM. Biochemical characterization of Thermotoga maritima endoglucanase Cel74 with and without a carbohydrate binding module (CBM). FEBS Lett 2002; 531:375-80. [PMID: 12417345 DOI: 10.1016/s0014-5793(02)03493-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The genome of the hyperthermophilic bacterium Thermotoga maritima (Tm) encodes at least eight glycoside hydrolases with putative signal peptides; the biochemical characteristics of seven of these have been reported previously. The eighth, Tm Cel74, is encoded by an open reading frame of 2124 bp corresponding to a polypeptide of 79 kDa with a signal peptide at the amino-terminus. The gene (lacking the signal peptide) encoding Tm Cel74 was expressed as a 77 kDa monomeric polypeptide in Escherichia coli and found to be optimally active at pH 6, 90 degrees C, with a melting temperature of approximately 105 degrees C. The cel74 gene was previously found to be induced during T. maritima growth on a variety of polysaccharides, including barley glucan, carboxymethyl cellulose (CMC), glucomannan, galactomannan and starch. However, while Tm Cel74 was most active towards barley glucan and to a lesser extent CMC, glucomannan and tamarind (xyloglucan), no activity was detected on other glycans, including galactomannan, laminarin and starch. Also, Tm Cel74 did not contain a carbohydrate binding module (CBM), versions of which have been identified in the amino acid sequences of other family 74 enzymes. As such, a CBM associated with a chitinase in another hyperthermophile, Pyrococcus furiosus, was used to create a fusion protein that was active on crystalline cellulose; Tm Cel74 lacked activity on this substrate. Based on the cleavage pattern determined for Tm Cel74 on glucan-based substrates, this enzyme likely initiates recruitment of carbohydrate carbon and energy sources by creating oligosaccharides that are transported into the cell for further processing.
Collapse
Affiliation(s)
- Swapnil R Chhabra
- Department of Chemical Engineering, North Carolina State University, Stinson Drive, Raleigh, NC 27695-7905, USA
| | | |
Collapse
|
44
|
Mitsumori M, Xu LM, Kajikawa H, Kurihara M. Properties of cellulose-binding modules in endoglucanase F from Fibrobacter succinogenes S85 by means of surface plasmon resonance. FEMS Microbiol Lett 2002; 214:277-81. [PMID: 12351243 DOI: 10.1111/j.1574-6968.2002.tb11359.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Properties of the recombinant proteins derived from Fibrobacter succinogenes endoglucanase F (EGF), AD2 and AD4, were characterized using surface plasmon resonance. Because AD2, which contains two reiterated regions, showed stronger affinity to immobilized carboxymethylcellulose (CMC) than did AD4, which contains only the first reiterated region, it has been assumed that the reiterated regions of EGF are cellulose-binding modules. While calcium enhanced the binding of AD2 to the immobilized CMC, it did not enhance the binding of AD4. Moreover, the results obtained from experiments using cellooligosaccharides showed that the binding sites of AD4 and AD2 span approximately four and nine glucosyl units, respectively.
Collapse
Affiliation(s)
- Makoto Mitsumori
- National Institute of Livestock and Grassland Science, Ikenodai 2, Kukizaki, Ibaraki 305-0901, Japan.
| | | | | | | |
Collapse
|