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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; 90:e0088824. [PMID: 38940565 PMCID: PMC11267928 DOI: 10.1128/aem.00888-24] [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: 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.
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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
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2
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You Y, Kong H, Li C, Gu Z, Ban X, Li Z. Carbohydrate binding modules: Compact yet potent accessories in the specific substrate binding and performance evolution of carbohydrate-active enzymes. Biotechnol Adv 2024; 73:108365. [PMID: 38677391 DOI: 10.1016/j.biotechadv.2024.108365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
Carbohydrate binding modules (CBMs) are independent non-catalytic domains widely found in carbohydrate-active enzymes (CAZymes), and they play an essential role in the substrate binding process of CAZymes by guiding the appended catalytic modules to the target substrates. Owing to their precise recognition and selective affinity for different substrates, CBMs have received increasing research attention over the past few decades. To date, CBMs from different origins have formed a large number of families that show a variety of substrate types, structural features, and ligand recognition mechanisms. Moreover, through the modification of specific sites of CBMs and the fusion of heterologous CBMs with catalytic domains, improved enzymatic properties and catalytic patterns of numerous CAZymes have been achieved. Based on cutting-edge technologies in computational biology, gene editing, and protein engineering, CBMs as auxiliary components have become portable and efficient tools for the evolution and application of CAZymes. With the aim to provide a theoretical reference for the functional research, rational design, and targeted utilization of novel CBMs in the future, we systematically reviewed the function-related characteristics and potentials of CAZyme-derived CBMs in this review, including substrate recognition and binding mechanisms, non-catalytic contributions to enzyme performances, module modifications, and innovative applications in various fields.
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Affiliation(s)
- Yuxian You
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Haocun Kong
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Caiming Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaofeng Ban
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China.
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3
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Hackl M, Power Z, Chundawat SPS. Oriented display of cello-oligosaccharides for pull-down binding assays to distinguish binding preferences of glycan binding proteins. Carbohydr Res 2023; 534:108943. [PMID: 37783054 DOI: 10.1016/j.carres.2023.108943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 10/04/2023]
Abstract
The production of biofuels from lignocellulosic biomass using carbohydrate-active enzymes like cellulases is key to a sustainable energy production. Understanding the adsorption mechanism of cellulases and associated binding domain proteins down to the molecular level details will help in the rational design of improved cellulases. In nature, carbohydrate-binding modules (CBMs) from families 17 and 28 often appear in tandem appended to the C-terminus of several endocellulases. Both CBMs are known to bind to the amorphous regions of cellulose non-competitively and show similar binding affinity towards soluble cello-oligosaccharides. Based on the available crystal structures, these CBMs may display a uni-directional binding preference towards cello-oligosaccharides (based on how the oligosaccharide was bound within the CBM binding cleft). However, molecular dynamics (MD) simulations have indicated no such clear preference. Considering that most soluble oligosaccharides are not always an ideal substrate surrogate to study the binding of CBMs to the native cell wall or cell surface displayed glycans, it is critical to use alternative reagents or substrates. To better understand the binding of type B CBMs towards smaller cello-oligosaccharides, we have developed a simple solid-state depletion or pull-down binding assay. Here, we specifically orient azido-labeled carbohydrates from the reducing end to alkyne-labeled micron-sized bead surfaces, using click chemistry, to mimic insoluble cell wall surface-displayed glycans. Our results reveal that both family 17 and 28 CBMs displayed a similar binding affinity towards cellohexaose-modified beads, but not cellopentaose-modified beads, which helps rationalize previously reported crystal structure and MD data. This may indicate a preferred uni-directional binding of specific CBMs and could explain their co-evolution as tandem constructs appended to endocellulases to increase amorphous cellulose substrate targeting efficiency. Overall, our proposed workflow can be easily translated to measure the affinity of glycan-binding proteins to click-chemistry based immobilized surface-displayed carbohydrates or antigens.
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Affiliation(s)
- Markus Hackl
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Zachary Power
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Shishir P S Chundawat
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
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4
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Huang Z, Ni G, Dai L, Zhang W, Feng S, Wang F. Biochemical Characterization of Novel GH6 Endoglucanase from Myxococcus sp. B6-1 and Its Effects on Agricultural Straws Saccharification. Foods 2023; 12:2517. [PMID: 37444255 DOI: 10.3390/foods12132517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/21/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Cellulase has been widely used in many industrial fields, such as feed and food industry, because it can hydrolyze cellulose to oligosaccharides with a lower degree of polymerization. Endo-β-1,4-glucanase is a critical speed-limiting cellulase in the saccharification process. In this study, endo-β-1,4-glucanase gene (CelA257) from Myxococcus sp. B6-1 was cloned and expressed in Escherichia coli. CelA257 contained carbohydrate-binding module (CBM) 4-9 and glycosyl hydrolase (GH) family 6 domain that shares 54.7% identity with endoglucanase from Streptomyces halstedii. The recombinant enzyme exhibited optimal activity at pH 6.5 and 50 °C and was stable over a broad pH (6-9.5) range and temperature < 50 °C. CelA257 exhibited broad substrate specificity to barley β-glucan, lichenin, CMC, chitosan, laminarin, avicel, and phosphoric acid swollen cellulose (PASC). CelA257 degraded both cellotetrose (G4) and cellppentaose (G5) to cellobiose (G2) and cellotriose (G3). Adding CelA257 increased the release of reducing sugars in crop straw powers, including wheat straw (0.18 mg/mL), rape straw (0.42 mg/mL), rice straw (0.16 mg/mL), peanut straw (0.16 mg/mL), and corn straw (0.61 mg/mL). This study provides a potential additive in biomass saccharification applications.
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Affiliation(s)
- Zhen Huang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Guorong Ni
- College of Land Resources and Environment, Jiangxi Agriculture University, Nanchang 330045, China
| | - Longhua Dai
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Weiqi Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Siting Feng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Fei Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
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5
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Native structure of mosquito salivary protein uncovers domains relevant to pathogen transmission. Nat Commun 2023; 14:899. [PMID: 36797290 PMCID: PMC9935623 DOI: 10.1038/s41467-023-36577-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/07/2023] [Indexed: 02/18/2023] Open
Abstract
Female mosquitoes inject saliva into vertebrate hosts during blood feeding. This process transmits mosquito-borne human pathogens that collectively cause ~1,000,000 deaths/year. Among the most abundant and conserved proteins secreted by female salivary glands is a high-molecular weight protein called salivary gland surface protein 1 (SGS1) that facilitates pathogen transmission, but its mechanism remains elusive. Here, we determine the native structure of SGS1 by the cryoID approach, showing that the 3364 amino-acid protein has a Tc toxin-like Rhs/YD shell, four receptor domains, and a set of C-terminal daisy-chained helices. These helices are partially shielded inside the Rhs/YD shell and poised to transform into predicted transmembrane helices. This transformation, and the numerous receptor domains on the surface of SGS1, are likely key in facilitating sporozoite/arbovirus invasion into the salivary glands and manipulating the host's immune response.
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6
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Thakur K, Shlain MA, Marianski M, Braunschweig AB. Regiochemical Effects on the Carbohydrate Binding and Selectivity of Flexible Synthetic Carbohydrate Receptors with Indole and Quinoline Heterocyclic Groups. European J Org Chem 2021; 2021:5262-5274. [PMID: 35694139 PMCID: PMC9186342 DOI: 10.1002/ejoc.202100763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Indexed: 08/07/2023]
Abstract
Synthetic carbohydrate receptors (SCRs) that bind cell-surface carbohydrates could be used for disease detection, drug-delivery, and therapeutics, or for the site-selective modification of complex carbohydrates but their potential has not been realized because of remaining challenges associated with binding affinity and substrate selectivity. We have reported recently a series of flexible SCRs based upon a biaryl core with four pendant heterocyclic groups that bind glycans selectively through noncovalent interactions. Here we continue to explore the role of heterocycles on substrate selectivity by expanding our library to include a series of indole and quinoline heterocycles that vary in their regiochemistry of attachment to the biaryl core. The binding of these SCRs to a series of biologically-relevant carbohydrates was studied by 1H NMR titrations in CD2Cl2 and density-functional theory calculations. We find SCR030, SCR034 and SCR037 are selective, SCR031, SCR032, and SCR039 are strong binders, and SCR033, SCR035, SCR036, and SCR038 are promiscuous and bind weakly. Computational analysis reveals the importance of C-H⋯π and H-bonding interactions in defining the binding properties of these new receptors. By combining these data with those obtained from our previous studies on this class of flexible SCRs, we develop a series of design rules that account for the binding of all SCRs of this class and anticipate the binding of future, not-yet imagined tetrapodal SCRs.
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Affiliation(s)
- Khushabu Thakur
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York 85 St Nicholas Terrace, New York, NY 10031 (USA)
- Department of Chemistry and Biochemistry, Hunter College 695 Park Ave, New York, NY 10065 (USA)
| | - Milan A Shlain
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York 85 St Nicholas Terrace, New York, NY 10031 (USA)
- Department of Chemistry and Biochemistry, Hunter College 695 Park Ave, New York, NY 10065 (USA)
| | - Mateusz Marianski
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York 85 St Nicholas Terrace, New York, NY 10031 (USA)
- Department of Chemistry and Biochemistry, Hunter College 695 Park Ave, New York, NY 10065 (USA)
- The PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 5 Ave, New York, NY 10016 (USA)
- The PhD Program in Biochemistry, The Graduate Center of the City University of New York, 365 5 Ave, New York, NY 10016 (USA)
| | - Adam B Braunschweig
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York 85 St Nicholas Terrace, New York, NY 10031 (USA)
- Department of Chemistry and Biochemistry, Hunter College 695 Park Ave, New York, NY 10065 (USA)
- The PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 5 Ave, New York, NY 10016 (USA)
- The PhD Program in Biochemistry, The Graduate Center of the City University of New York, 365 5 Ave, New York, NY 10016 (USA)
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7
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Abstract
Cellulosomes are elaborate multienzyme complexes capable of efficiently deconstructing lignocellulosic substrates, produced by cellulolytic anaerobic microorganisms, colonizing a large variety of ecological niches. These macromolecular structures have a modular architecture and are composed of two main elements: the cohesin-bearing scaffoldins, which are non-catalytic structural proteins, and the various dockerin-bearing enzymes that tenaciously bind to the scaffoldins. Cellulosome assembly is mediated by strong and highly specific interactions between the cohesin modules, present in the scaffoldins, and the dockerin modules, present in the catalytic units. Cellulosomal architecture and composition varies between species and can even change within the same organism. These differences seem to be largely influenced by external factors, including the nature of the available carbon-source. Even though cellulosome producing organisms are relatively few, the development of new genomic and proteomic technologies has allowed the identification of cellulosomal components in many archea, bacteria and even some primitive eukaryotes. This reflects the importance of this cellulolytic strategy and suggests that cohesin-dockerin interactions could be involved in other non-cellulolytic processes. Due to their building-block nature and highly cellulolytic capabilities, cellulosomes hold many potential biotechnological applications, such as the conversion of lignocellulosic biomass in the production of biofuels or the development of affinity based technologies.
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Affiliation(s)
- Victor D Alves
- CIISA, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477, Lisbon, Portugal
| | - Carlos M G A Fontes
- CIISA, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477, Lisbon, Portugal
| | - Pedro Bule
- CIISA, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477, Lisbon, Portugal.
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8
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Tan YZ, Zhang L, Rodrigues J, Zheng RB, Giacometti SI, Rosário AL, Kloss B, Dandey VP, Wei H, Brunton R, Raczkowski AM, Athayde D, Catalão MJ, Pimentel M, Clarke OB, Lowary TL, Archer M, Niederweis M, Potter CS, Carragher B, Mancia F. Cryo-EM Structures and Regulation of Arabinofuranosyltransferase AftD from Mycobacteria. Mol Cell 2020; 78:683-699.e11. [PMID: 32386575 PMCID: PMC7263364 DOI: 10.1016/j.molcel.2020.04.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/21/2020] [Accepted: 04/13/2020] [Indexed: 01/21/2023]
Abstract
Mycobacterium tuberculosis causes tuberculosis, a disease that kills over 1 million people each year. Its cell envelope is a common antibiotic target and has a unique structure due, in part, to two lipidated polysaccharides-arabinogalactan and lipoarabinomannan. Arabinofuranosyltransferase D (AftD) is an essential enzyme involved in assembling these glycolipids. We present the 2.9-Å resolution structure of M. abscessus AftD, determined by single-particle cryo-electron microscopy. AftD has a conserved GT-C glycosyltransferase fold and three carbohydrate-binding modules. Glycan array analysis shows that AftD binds complex arabinose glycans. Additionally, AftD is non-covalently complexed with an acyl carrier protein (ACP). 3.4- and 3.5-Å structures of a mutant with impaired ACP binding reveal a conformational change, suggesting that ACP may regulate AftD function. Mutagenesis experiments using a conditional knockout constructed in M. smegmatis confirm the essentiality of the putative active site and the ACP binding for AftD function.
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Affiliation(s)
- Yong Zi Tan
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA; National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Lei Zhang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - José Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | | | - Sabrina I Giacometti
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Ana L Rosário
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Brian Kloss
- Center on Membrane Protein Production and Analysis, New York Structural Biology Center, New York, NY 10027, USA
| | - Venkata P Dandey
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Hui Wei
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Richard Brunton
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Ashleigh M Raczkowski
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Diogo Athayde
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Maria João Catalão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Madalena Pimentel
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA; Department of Anesthesiology, Columbia University, New York, NY 10032, USA
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, #128 Nangang, Taipei 11529, Taiwan
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Clinton S Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.
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Krishnan B, Srivastava SS, Sankeshi V, Garg R, Srivastava S, Sankaranarayanan R, Sharma Y. βγ-Crystallination Endows a Novel Bacterial Glycoside Hydrolase 64 with Ca 2+-Dependent Activity Modulation. J Bacteriol 2019; 201:e00392-19. [PMID: 31527113 PMCID: PMC6832075 DOI: 10.1128/jb.00392-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 09/05/2019] [Indexed: 01/10/2023] Open
Abstract
The prokaryotic βγ-crystallins are a large group of uncharacterized domains with Ca2+-binding motifs. We have observed that a vast number of these domains are found appended to other domains, in particular, the carbohydrate-active enzyme (CAZy) domains. To elucidate the functional significance of these prospective Ca2+ sensors in bacteria and this widespread domain association, we have studied one typical example from Clostridium beijerinckii, a bacterium known for its ability to produce acetone, butanol, and ethanol through fermentation of several carbohydrates. This novel glycoside hydrolase of family 64 (GH64), which we named glucanallin, is composed of a βγ-crystallin domain, a GH64 domain, and a carbohydrate-binding module 56 (CBM56). The substrates of GH64, β-1,3-glucans, are the targets for industrial biofuel production due to their plenitude. We have examined the Ca2+-binding properties of this protein, assayed its enzymatic activity, and analyzed the structural features of the β-1,3-glucanase domain through its high-resolution crystal structure. The reaction products resulting from the enzyme reaction of glucanallin reinforce the mixed nature of GH64 enzymes, in contrast to the prevailing notion of them being an exotype. Upon disabling Ca2+ binding and comparing different domain combinations, we demonstrate that the βγ-crystallin domain in glucanallin acts as a Ca2+ sensor and enhances the glycolytic activity of glucanallin through Ca2+ binding. We also compare the structural peculiarities of this new member of the GH64 family to two previously studied members.IMPORTANCE We have biochemically and structurally characterized a novel glucanase from the less studied GH64 family in a bacterium significant for fermentation of carbohydrates into biofuels. This enzyme displays a peculiar property of being distally modulated by Ca2+ via assistance from a neighboring βγ-crystallin domain, likely through changes in the domain interface. In addition, this enzyme is found to be optimized for functioning in an acidic environment, which is in line with the possibility of its involvement in biofuel production. Multiple occurrences of a similar domain architecture suggest that such a "βγ-crystallination"-mediated Ca2+ sensitivity may be widespread among bacterial proteins.
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Affiliation(s)
- Bal Krishnan
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Indian Institute of Science Education and Research Berhampur, Odisha, India
| | | | - Venu Sankeshi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Rupsi Garg
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - Yogendra Sharma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Indian Institute of Science Education and Research Berhampur, Odisha, India
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10
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Kognole AA, Payne CM. Cellulose-specific Type B carbohydrate binding modules: understanding oligomeric and non-crystalline substrate recognition mechanisms. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:319. [PMID: 30519283 PMCID: PMC6267901 DOI: 10.1186/s13068-018-1321-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 11/22/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND Effective enzymatic degradation of crystalline polysaccharides requires a synergistic cocktail of hydrolytic enzymes tailored to the wide-ranging degree of substrate crystallinity. To accomplish this type of targeted carbohydrate recognition, nature produces multi-modular enzymes, having at least one catalytic domain appended to one or more carbohydrate binding modules (CBMs). The Type B CBM categorization encompasses several families (i.e., protein folds) of CBMs that are generally thought to selectively bind oligomeric polysaccharides; however, a subset of cellulose-specific CBM families (17 and 28) appear to bind non-crystalline cellulose more tightly than oligomers and in a manner that discriminates between surface topology. RESULTS To provide insight into this unexplained phenomenon, we investigated the molecular-level origins of oligomeric and non-crystalline carbohydrate recognition in cellulose-specific Type B CBMs using molecular dynamics (MD) simulation and free energy calculations. Examining two CBMs from three different families (4, 17, and 28), we describe how protein-ligand dynamics contribute to observed variations in binding affinity of oligomers within the same CBM family. Comparisons across the three CBM families identified factors leading to modified functionality prohibiting competitive binding, despite similarity in sequence and specificity. Using free energy perturbation with Hamiltonian replica exchange MD, we also examined the hypothesis that the open topology of the binding grooves in families 17 and 28 necessitates tight binding of an oligomer, while the more confined family 4 binding groove does not require the same degree of tight binding. Finally, we elucidated the mechanisms of non-crystalline carbohydrate recognition by modeling CBMs complexed with a partially decrystallized cellulose substrate. Molecular simulation provided structural and dynamic data for direct comparison to oligomeric modes of carbohydrate recognition, and umbrella sampling MD was used to determine ligand binding free energy. Comparing both protein-carbohydrate interactions and ligand binding free energies, which were in good agreement with experimental values, we confirmed the hypothesis that family 17 and 28 CBMs bind non-crystalline cellulose and oligomers with different affinities (i.e., high and low). CONCLUSIONS Our study provides an unprecedented level of insight into the complex solid and soluble carbohydrate substrate recognition mechanisms of Type B CBMs, the findings of which hold considerable promise for enhancing lignocellulosic biomass conversion technology and development of plant cell wall probes.
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Affiliation(s)
- Abhishek A. Kognole
- Department of Chemical and Materials Engineering, University of Kentucky, 177 F Paul Anderson Tower, Lexington, KY 40506 USA
| | - Christina M. Payne
- Department of Chemical and Materials Engineering, University of Kentucky, 177 F Paul Anderson Tower, Lexington, KY 40506 USA
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11
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Сarbohydrate binding module CBM28 of endoglucanase Cel5D from Caldicellulosiruptor bescii recognizes crystalline cellulose. Int J Biol Macromol 2018; 107:305-311. [DOI: 10.1016/j.ijbiomac.2017.08.165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 08/29/2017] [Accepted: 08/29/2017] [Indexed: 11/23/2022]
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12
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Tyufekchiev M, Duan P, Schmidt-Rohr K, Granados Focil S, Timko MT, Emmert MH. Cellulase-Inspired Solid Acids for Cellulose Hydrolysis: Structural Explanations for High Catalytic Activity. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04117] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
| | - Pu Duan
- Department
of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Klaus Schmidt-Rohr
- Department
of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Sergio Granados Focil
- Gustaf
H. Carlson School of Chemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, United States
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13
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Singh S, Hinkley T, Nugen SR, Talbert JN. Fusion of carbohydrate binding module to mutant alkaline phosphatase for immobilization on cellulose. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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14
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Functional analysis of arabinofuranosidases and a xylanase of Corynebacterium alkanolyticum for arabinoxylan utilization in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2017; 101:5019-5032. [DOI: 10.1007/s00253-017-8280-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/22/2017] [Accepted: 03/29/2017] [Indexed: 11/27/2022]
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15
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Pires VMR, Pereira PMM, Brás JLA, Correia M, Cardoso V, Bule P, Alves VD, Najmudin S, Venditto I, Ferreira LMA, Romão MJ, Carvalho AL, Fontes CMGA, Prazeres DM. Stability and Ligand Promiscuity of Type A Carbohydrate-binding Modules Are Illustrated by the Structure of Spirochaeta thermophila StCBM64C. J Biol Chem 2017; 292:4847-4860. [PMID: 28179427 DOI: 10.1074/jbc.m116.767541] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/07/2017] [Indexed: 11/06/2022] Open
Abstract
Deconstruction of cellulose, the most abundant plant cell wall polysaccharide, requires the cooperative activity of a large repertoire of microbial enzymes. Modular cellulases contain non-catalytic type A carbohydrate-binding modules (CBMs) that specifically bind to the crystalline regions of cellulose, thus promoting enzyme efficacy through proximity and targeting effects. Although type A CBMs play a critical role in cellulose recycling, their mechanism of action remains poorly understood. Here we produced a library of recombinant CBMs representative of the known diversity of type A modules. The binding properties of 40 CBMs, in fusion with an N-terminal GFP domain, revealed that type A CBMs possess the ability to recognize different crystalline forms of cellulose and chitin over a wide range of temperatures, pH levels, and ionic strengths. A Spirochaeta thermophila CBM64, in particular, displayed plasticity in its capacity to bind both crystalline and soluble carbohydrates under a wide range of extreme conditions. The structure of S. thermophila StCBM64C revealed an untwisted, flat, carbohydrate-binding interface comprising the side chains of four tryptophan residues in a co-planar linear arrangement. Significantly, two highly conserved asparagine side chains, each one located between two tryptophan residues, are critical to insoluble and soluble glucan recognition but not to bind xyloglucan. Thus, CBM64 compact structure and its extended and versatile ligand interacting platform illustrate how type A CBMs target their appended plant cell wall-degrading enzymes to a diversity of recalcitrant carbohydrates under a wide range of environmental conditions.
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Affiliation(s)
- Virgínia M R Pires
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal
| | - Pedro M M Pereira
- the Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Joana L A Brás
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal.,NZYTech Genes Enzymes, 1649-038 Lisboa, Portugal, and
| | - Márcia Correia
- the UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Vânia Cardoso
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal.,NZYTech Genes Enzymes, 1649-038 Lisboa, Portugal, and
| | - Pedro Bule
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal
| | - Victor D Alves
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal
| | - Shabir Najmudin
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal
| | - Immacolata Venditto
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal
| | - Luís M A Ferreira
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal.,NZYTech Genes Enzymes, 1649-038 Lisboa, Portugal, and
| | - Maria João Romão
- the UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Luísa Carvalho
- the UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Carlos M G A Fontes
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal, .,NZYTech Genes Enzymes, 1649-038 Lisboa, Portugal, and
| | - Duarte Miguel Prazeres
- the Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal,
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16
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Franche N, Tardif C, Ravachol J, Harchouni S, Ferdinand PH, Borne R, Fierobe HP, Perret S. Cel5I, a SLH-Containing Glycoside Hydrolase: Characterization and Investigation on Its Role in Ruminiclostridium cellulolyticum. PLoS One 2016; 11:e0160812. [PMID: 27501457 PMCID: PMC4976890 DOI: 10.1371/journal.pone.0160812] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/25/2016] [Indexed: 11/19/2022] Open
Abstract
Ruminiclostridium cellulolyticum (Clostridium cellulolyticum) is a mesophilic cellulolytic anaerobic bacterium that produces a multi-enzymatic system composed of cellulosomes and non-cellulosomal enzymes to degrade plant cell wall polysaccharides. We characterized one of the non-cellulosomal enzymes, Cel5I, composed of a Family-5 Glycoside Hydrolase catalytic module (GH5), a tandem of Family-17 and -28 Carbohydrate Binding Modules (CBM), and three S-layer homologous (SLH) modules, where the latter are expected to anchor the protein on the cell surface. Cel5I is the only putative endoglucanase targeting the cell surface as well as the only putative protein in R. cellulolyticum containing CBM17 and/or CBM28 modules. We characterized different recombinant structural variants from Cel5I. We showed that Cel5I has an affinity for insoluble cellulosic substrates through its CBMs, that it is the most active endoglucanase on crystalline cellulose of R. cellulolyticum characterized to date and mostly localized in the cell envelope of R. cellulolyticum. Its role in vivo was analyzed using a R. cellulolyticum cel5I mutant strain. Absence of Cel5I in the cell envelope did not lead to a significant variation of the phenotype compared to the wild type strain. Neither in terms of cell binding to cellulose, nor for its growth on crystalline cellulose, thus indicating that the protein has a rather subtle role in tested conditions. Cel5I might be more important in a natural environment, at low concentration of degradable glucose polymers, where its role might be to generate higher concentration of short cellodextrins close to the cell surface, facilitating their uptake or for signalization purpose.
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Affiliation(s)
| | | | | | | | | | - Romain Borne
- Aix Marseille Univ, CNRS, LCB, Marseille, France
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17
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Das SN, Wagenknecht M, Nareddy PK, Bhuvanachandra B, Niddana R, Balamurugan R, Swamy MJ, Moerschbacher BM, Podile AR. Amino Groups of Chitosan Are Crucial for Binding to a Family 32 Carbohydrate Binding Module of a Chitosanase from Paenibacillus elgii. J Biol Chem 2016; 291:18977-90. [PMID: 27405759 DOI: 10.1074/jbc.m116.721332] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Indexed: 11/06/2022] Open
Abstract
We report here the role and mechanism of specificity of a family 32 carbohydrate binding module (CBM32) of a glycoside hydrolase family 8 chitosanase from Paenibacillus elgii (PeCsn). Both the activity and mode of action of PeCsn toward soluble chitosan polymers were not different with/without the CBM32 domain of P. elgii (PeCBM32). The decreased activity of PeCsn without PeCBM32 on chitosan powder suggested that PeCBM32 increases the relative concentration of enzyme on the substrate and thereby enhanced enzymatic activity. PeCBM32 specifically bound to polymeric and oligomeric chitosan and showed very weak binding to chitin and cellulose. In isothermal titration calorimetry, the binding stoichiometry of 2 and 1 for glucosamine monosaccharide (GlcN) and disaccharide (GlcN)2, respectively, was indicative of two binding sites in PeCBM32. A three-dimensional model-guided site-directed mutagenesis and the use of defined disaccharides varying in the pattern of acetylation suggested that the amino groups of chitosan and the polar residues Glu-16 and Glu-38 of PeCBM32 play a crucial role for the observed binding. The specificity of CBM32 has been further elucidated by a generated fusion protein PeCBM32-eGFP that binds to the chitosan exposing endophytic infection structures of Puccinia graminis f. sp. tritici Phylogenetic analysis showed that CBM32s appended to chitosanases are highly conserved across different chitosanase families suggesting their role in chitosan recognition and degradation. We have identified and characterized a chitosan-specific CBM32 useful for in situ staining of chitosans in the fungal cell wall during plant-fungus interaction.
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Affiliation(s)
| | - Martin Wagenknecht
- the Institute of Plant Biology and Biotechnology, Westphalian Wilhelms-University of Münster, 48143 Münster, Germany
| | | | | | - Ramana Niddana
- School of Chemistry, University of Hyderabad, 500046-Hyderabad, India and
| | | | - Musti J Swamy
- School of Chemistry, University of Hyderabad, 500046-Hyderabad, India and
| | - Bruno M Moerschbacher
- the Institute of Plant Biology and Biotechnology, Westphalian Wilhelms-University of Münster, 48143 Münster, Germany
| | - Appa Rao Podile
- From the Department of Plant Sciences, School of Life Sciences,
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18
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Abstract
The enzyme-catalysed degradation of oligo and polysaccharides is of considerable interest in many fields ranging from the fundamental–understanding the intrinsic chemical beauty–through to the applied, including diverse practical applications in medicine and biotechnology. Carbohydrates are the most stereochemically-complex biopolymer, and myriad different natural polysaccharides have led to evolution of multifaceted enzyme consortia for their degradation. The glycosidic bonds that link sugar monomers are among the most chemically-stable, yet enzymatically-labile, bonds in the biosphere. That glycoside hydrolases can achieve a rate enhancement (kcat/kuncat) >1017-fold provides testament to their remarkable proficiency and the sophistication of their catalysis reaction mechanisms. The last two decades have seen significant advances in the discovery of new glycosidase sequences, sequence-based classification into families and clans, 3D structures and reaction mechanisms, providing new insights into enzymatic catalysis. New impetus to these studies has been provided by the challenges inherent in plant and microbial polysaccharide degradation, both in the context of environmentally-sustainable routes to foods and biofuels, and increasingly in human nutrition. Study of the reaction mechanism of glycoside hydrolases has also inspired the development of enzyme inhibitors, both as mechanistic probes and increasingly as therapeutic agents. We are on the cusp of a new era where we are learning how to dovetail powerful computational techniques with structural and kinetic data to provide an unprecedented view of conformational details of enzyme action.
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19
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Kundu S, Sharma R. In silico Identification and Taxonomic Distribution of Plant Class C GH9 Endoglucanases. FRONTIERS IN PLANT SCIENCE 2016; 7:1185. [PMID: 27570528 PMCID: PMC4981690 DOI: 10.3389/fpls.2016.01185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/22/2016] [Indexed: 05/08/2023]
Abstract
The glycoside hydrolase 9 superfamily, mainly comprising the endoglucanases, is represented in all three domains of life. The current division of GH9 enzymes, into three subclasses, namely A, B, and C, is centered on parameters derived from sequence information alone. However, this classification is ambiguous, and is limited by the paralogous ancestry of classes B and C endoglucanases, and paucity of biochemical and structural data. Here, we extend this classification schema to putative GH9 endoglucanases present in green plants, with an emphasis on identifying novel members of the class C subset. These enzymes cleave the β(1 → 4) linkage between non-terminal adjacent D-glucopyranose residues, in both, amorphous and crystalline regions of cellulose. We utilized non redundant plant GH9 enzymes with characterized molecular data, as the training set to construct Hidden Markov Models (HMMs) and train an Artificial Neural Network (ANN). The parameters that were used for predicting dominant enzyme function, were derived from this training set, and subsequently refined on 147 sequences with available expression data. Our knowledge-based approach, can ascribe differential endoglucanase activity (A, B, or C) to a query sequence with high confidence, and was used to construct a local repository of class C GH9 endoglucanases (GH9C = 241) from 32 sequenced green plants.
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Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, Dr. Baba Saheb Ambedkar Medical College & HospitalNew Delhi, India
- Mathematical and Computational Biology, Information Technology Research Academy, Media Lab AsiaNew Delhi, India
- School of Computational and Integrative Sciences, Jawaharlal Nehru UniversityNew Delhi, India
- *Correspondence: Siddhartha Kundu
| | - Rita Sharma
- School of Computational and Integrative Sciences, Jawaharlal Nehru UniversityNew Delhi, India
- Rita Sharma
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20
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Hidayat BJ, Weisskopf C, Felby C, Johansen KS, Thygesen LG. The binding of cellulase variants to dislocations: a semi-quantitative analysis based on CLSM (confocal laser scanning microscopy) images. AMB Express 2015; 5:76. [PMID: 26626331 PMCID: PMC4666858 DOI: 10.1186/s13568-015-0165-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/21/2015] [Indexed: 11/23/2022] Open
Abstract
Binding of enzymes to the substrate is the first step in enzymatic hydrolysis of lignocellulose, a key process within biorefining. During this process elongated plant cells such as fibers and tracheids have been found to break into segments at irregular cell wall regions known as dislocations or slip planes. Here we study whether cellulases bind to dislocations to a higher extent than to the surrounding cell wall. The binding of fluorescently labelled cellobiohydrolases and endoglucanases to filter paper fibers was investigated using confocal laser scanning microscopy and a ratiometric method was developed to assess and quantify the abundance of the binding of cellulases to dislocations as compared to the surrounding cell wall. Only Humicola insolens EGV was found to have stronger binding preference to dislocations than to the surrounding cell wall, while no difference in binding affinity was seen for any of the other cellulose variants included in the study (H. insolens EGV variants, Trichoderma reesei CBHI, CBHII and EGII). This result favours the hypothesis that fibers break at dislocations during the initial phase of hydrolysis mostly due to mechanical failure rather than as a result of faster degradation at these locations.
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21
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Wallenstein MD, Burns RG. Ecology of Extracellular Enzyme Activities and Organic Matter Degradation in Soil: A Complex Community-Driven Process. SSSA BOOK SERIES 2015. [DOI: 10.2136/sssabookser9.c2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
| | - Richard G. Burns
- School of Agriculture and Food Sciences; University of Queensland; Brisbane Australia
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22
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Venditto I, Najmudin S, Luís AS, Ferreira LMA, Sakka K, Knox JP, Gilbert HJ, Fontes CMGA. Family 46 Carbohydrate-binding Modules Contribute to the Enzymatic Hydrolysis of Xyloglucan and β-1,3-1,4-Glucans through Distinct Mechanisms. J Biol Chem 2015; 290:10572-86. [PMID: 25713075 PMCID: PMC4409224 DOI: 10.1074/jbc.m115.637827] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 02/05/2015] [Indexed: 11/06/2022] Open
Abstract
Structural carbohydrates comprise an extraordinary source of energy that remains poorly utilized by the biofuel sector as enzymes have restricted access to their substrates within the intricacy of plant cell walls. Carbohydrate active enzymes (CAZYmes) that target recalcitrant polysaccharides are modular enzymes containing noncatalytic carbohydrate-binding modules (CBMs) that direct enzymes to their cognate substrate, thus potentiating catalysis. In general, CBMs are functionally and structurally autonomous from their associated catalytic domains from which they are separated through flexible linker sequences. Here, we show that a C-terminal CBM46 derived from BhCel5B, a Bacillus halodurans endoglucanase, does not interact with β-glucans independently but, uniquely, acts cooperatively with the catalytic domain of the enzyme in substrate recognition. The structure of BhCBM46 revealed a β-sandwich fold that abuts onto the region of the substrate binding cleft upstream of the active site. BhCBM46 as a discrete entity is unable to bind to β-glucans. Removal of BhCBM46 from BhCel5B, however, abrogates binding to β-1,3-1,4-glucans while substantially decreasing the affinity for decorated β-1,4-glucan homopolymers such as xyloglucan. The CBM46 was shown to contribute to xyloglucan hydrolysis only in the context of intact plant cell walls, but it potentiates enzymatic activity against purified β-1,3-1,4-glucans in solution or within the cell wall. This report reveals the mechanism by which a CBM can promote enzyme activity through direct interaction with the substrate or by targeting regions of the plant cell wall where the target glucan is abundant.
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Affiliation(s)
- Immacolata Venditto
- From the Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Shabir Najmudin
- From the Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Ana S Luís
- the Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Luís M A Ferreira
- From the Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Kazuo Sakka
- the Graduate School of Bioresources, Mie University, Tsu 514-8507, Japan, and
| | - J Paul Knox
- the Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Harry J Gilbert
- the Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom,
| | - Carlos M G A Fontes
- From the Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal,
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23
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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.
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24
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Kim IJ, Lee HJ, Choi IG, Kim KH. Synergistic proteins for the enhanced enzymatic hydrolysis of cellulose by cellulase. Appl Microbiol Biotechnol 2014; 98:8469-80. [PMID: 25129610 DOI: 10.1007/s00253-014-6001-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 07/28/2014] [Accepted: 07/29/2014] [Indexed: 01/09/2023]
Abstract
Reducing the enzyme loadings for enzymatic saccharification of lignocellulose is required for economically feasible production of biofuels and biochemicals. One strategy is addition of small amounts of synergistic proteins to cellulase mixtures. Synergistic proteins increase the activity of cellulase without causing significant hydrolysis of cellulose. Synergistic proteins exert their activity by inducing structural modifications in cellulose. Recently, synergistic proteins from various biological sources, including bacteria, fungi, and plants, were identified based on genomic data, and their synergistic activities were investigated. Currently, an up-to-date overview of several aspects of synergistic proteins, such as their functions, action mechanisms and synergistic activity, are important for future industrial application. In this review, we summarize the current state of research on four synergistic proteins: carbohydrate-binding modules, plant expansins, expansin-like proteins, and Auxiliary Activity family 9 (formerly GH61) proteins. This review provides critical information to aid in promoting research on the development of efficient and industrially feasible synergistic proteins.
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Affiliation(s)
- In Jung Kim
- Department of Biotechnology, Korea University Graduate School, Seoul, 136-713, Republic of Korea
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25
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Characterization of Family 17 and Family 28 Carbohydrate-Binding Modules fromClostridium josuiCel5A. Biosci Biotechnol Biochem 2014; 73:1028-32. [DOI: 10.1271/bbb.80802] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Synergism of glycoside hydrolase secretomes from two thermophilic bacteria cocultivated on lignocellulose. Appl Environ Microbiol 2014; 80:2592-601. [PMID: 24532065 DOI: 10.1128/aem.00295-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two cellulolytic thermophilic bacterial strains, CS-3-2 and CS-4-4, were isolated from decayed cornstalk by the addition of growth-supporting factors to the medium. According to 16S rRNA gene-sequencing results, these strains belonged to the genus Clostridium and showed 98.87% and 98.86% identity with Clostridium stercorarium subsp. leptospartum ATCC 35414(T) and Clostridium cellulosi AS 1.1777(T), respectively. The endoglucanase and exoglucanase activities of strain CS-4-4 were approximately 3 to 5 times those of strain CS-3-2, whereas the β-glucosidase activity of strain CS-3-2 was 18 times higher than that of strain CS-4-4. The xylanase activity of strain CS-3-2 was 9 times that of strain CS-4-4, whereas the β-xylosidase activity of strain CS-4-4 was 27 times that of strain CS-3-2. The enzyme activities in spent cultures following cocultivation of the two strains with cornstalk as the substrate were much greater than those in pure cultures or an artificial mixture of samples, indicating synergism of glycoside hydrolase secretomes between the two strains. Quantitative measurement of the two strains in the cocultivation system indicated that strain CS-3-2 grew robustly during the initial stages, whereas strain CS-4-4 dominated the system in the late-exponential phase. Liquid chromatography-tandem mass spectrometry analysis of protein bands appearing in the native zymograms showed that ORF3880 and ORF3883 from strain CS-4-4 played key roles in the lignocellulose degradation process. Both these open reading frames (ORFs) exhibited endoglucanase and xylanase activities, but ORF3880 showed tighter adhesion to insoluble substrates at 4, 25, and 60°C owing to its five carbohydrate-binding modules (CBMs).
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Ghatge SS, Telke AA, Kang SH, Arulalapperumal V, Lee KW, Govindwar SP, Um Y, Oh DB, Shin HD, Kim SW. Characterization of modular bifunctional processive endoglucanase Cel5 from Hahella chejuensis KCTC 2396. Appl Microbiol Biotechnol 2013; 98:4421-35. [PMID: 24343767 DOI: 10.1007/s00253-013-5446-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 11/28/2013] [Accepted: 11/28/2013] [Indexed: 11/29/2022]
Abstract
Cel5 from marine Hahella chejuensis is composed of glycoside hydrolase family-5 (GH5) catalytic domain (CD) and two carbohydrate binding modules (CBM6-2). The enzyme was expressed in Escherichia coli and purified to homogeneity. The optimum endoglucanase and xylanase activities of recombinant Cel5 were observed at 65 °C, pH 6.5 and 55 °C, pH 5.5, respectively. It exhibited K m of 1.8 and 7.1 mg/ml for carboxymethyl cellulose and birchwood xylan, respectively. The addition of Ca(2+) greatly improved thermostability and endoglucanase activity of Cel5. The Cel5 retained 90 % of its endoglucanase activity after 24 h incubation in presence of 5 M concentration of NaCl. Recombinant Cel5 showed production of cellobiose after hydrolysis of cellulosic substrates (soluble/insoluble) and methylglucuronic acid substituted xylooligosaccharides after hydrolysis of glucuronoxylans by endo-wise cleavage. These results indicated that Cel5 as bifunctional enzyme having both processive endoglucanase and xylanase activities. The multidomain structure of Cel5 is clearly distinguished from the GH5 bifunctional glycoside hydrolases characterized to date, which are single domain enzymes. Sequence analysis and homology modeling suggested presence of two conserved binding sites with different substrate specificities in CBM6-2 and a single catalytic site in CD. Residues Glu132 and Glu219 were identified as key catalytic amino acids by sequence alignment and further verified by using site directed mutagenesis. CBM6-2 plays vital role in catalytic activity and thermostability of Cel5. The bifunctional activities and multiple substrate specificities of Cel5 can be utilized for efficient hydrolysis of cellulose and hemicellulose into soluble sugars.
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Affiliation(s)
- Sunil Subhash Ghatge
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Gyeongnam, Republic of Korea
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Gutelius D, Hokeness K, Logan SM, Reid CW. Functional analysis of SleC from Clostridium difficile: an essential lytic transglycosylase involved in spore germination. MICROBIOLOGY-SGM 2013; 160:209-216. [PMID: 24140647 DOI: 10.1099/mic.0.072454-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Clostridium difficile is the most common cause of enteric disease and presents a major burden on healthcare systems globally due in part to the observed rapid rise in antibiotic resistance. The ability of C. difficile to form endospores is a key feature in the organism's pathogenesis and transmission, and contributes greatly to its resilient nature. Endospores are highly resistant to disinfection, allowing them to persist on hospital surfaces. In order for the organism to cause disease, the spores must germinate and revert to a vegetative form. While spore germination in Bacillus spp. is well understood, very little is known about this process in Clostridia. Here we report the characterization of SleC (CD0551) from C. difficile 630. Bioinformatic analysis of SleC indicated a multi-domained protein possessing a peptidoglycan-binding (PGB) domain, a SpoIID/LytB domain and an undefined N-terminal region. We have confirmed that SleC is an exo-acting lytic transglycosylase with the catalytic activity localized to the N-terminal region. Additionally, we have shown that both the N-terminal catalytic domain and the C-terminal PGB domain require muramyl-δ-lactam for substrate binding. As with carbohydrate-binding modules from cellulases and xylanases, the PGB domain may be responsible for increasing the processivity of SleC by concentrating the enzyme at the surface of the substrate.
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Affiliation(s)
- Danielle Gutelius
- Department of Science and Technology, Bryant University, Smithfield, RI 02917, USA
| | - Kirsten Hokeness
- Department of Science and Technology, Bryant University, Smithfield, RI 02917, USA
| | - Susan M Logan
- National Research Council - Human Health Therapeutics Portfolio, Ottawa, ON K1A 0R6, Canada
| | - Christopher W Reid
- Department of Science and Technology, Bryant University, Smithfield, RI 02917, USA
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Zhang X, Zhang Z, Wang F, Wang Y, Song Q, Xu J. Lignosulfonate-based heterogeneous sulfonic acid catalyst for hydrolyzing glycosidic bonds of polysaccharides. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcata.2013.05.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Shinya S, Ohnuma T, Yamashiro R, Kimoto H, Kusaoke H, Anbazhagan P, Juffer AH, Fukamizo T. The first identification of carbohydrate binding modules specific to chitosan. J Biol Chem 2013; 288:30042-30053. [PMID: 23986450 DOI: 10.1074/jbc.m113.503243] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two carbohydrate binding modules (DD1 and DD2) belonging to CBM32 are located at the C terminus of a chitosanase from Paenibacillus sp. IK-5. We produced three proteins, DD1, DD2, and tandem DD1/DD2 (DD1+DD2), and characterized their binding ability. Transition temperature of thermal unfolding (Tm) of each protein was elevated by the addition of cello-, laminari-, chitin-, or chitosan-hexamer (GlcN)6. The Tm elevation (ΔTm) in DD1 was the highest (10.3 °C) upon the addition of (GlcN)6 and was markedly higher than that in DD2 (1.0 °C). A synergistic effect was observed (ΔTm = 13.6 °C), when (GlcN)6 was added to DD1+DD2. From isothermal titration calorimetry experiments, affinities to DD1 were not clearly dependent upon chain length of (GlcN)n; ΔGr° values were -7.8 (n = 6), -7.6 (n = 5), -7.6 (n = 4), -7.6 (n = 3), and -7.1 (n = 2) kcal/mol, and the value was not obtained for GlcN due to the lowest affinity. DD2 bound (GlcN)n with the lower affinities (ΔGr° = -5.0 (n = 3) ~ -5.2 (n = 6) kcal/mol). Isothermal titration calorimetry profiles obtained for DD1+DD2 exhibited a better fit when the two-site model was used for analysis and provided greater affinities to (GlcN)6 for individual DD1 and DD2 sites (ΔGr° = -8.6 and -6.4 kcal/mol, respectively). From NMR titration experiments, (GlcN)n (n = 2~6) were found to bind to loops extruded from the core β-sandwich of individual DD1 and DD2, and the interaction sites were similar to each other. Taken together, DD1+DD2 is specific to chitosan, and individual modules synergistically interact with at least two GlcN units, facilitating chitosan hydrolysis.
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Affiliation(s)
- Shoko Shinya
- From the Department of Advanced Bioscience, Kinki University, Nara 631-8505 Japan
| | - Takayuki Ohnuma
- From the Department of Advanced Bioscience, Kinki University, Nara 631-8505 Japan
| | - Reina Yamashiro
- From the Department of Advanced Bioscience, Kinki University, Nara 631-8505 Japan
| | - Hisashi Kimoto
- Department of Bioscience, Fukui Prefectural University, Fukui 910-1195
| | - Hideo Kusaoke
- Department of Environmental and Biotechnological Frontier Engineering, Fukui University of Technology, Fukui 910-8505, Japan, and
| | - Padmanabhan Anbazhagan
- Biocenter Oulu and Department of Biochemistry, University of Oulu, Oulu, FI-90014 Finland
| | - André H Juffer
- Biocenter Oulu and Department of Biochemistry, University of Oulu, Oulu, FI-90014 Finland
| | - Tamo Fukamizo
- From the Department of Advanced Bioscience, Kinki University, Nara 631-8505 Japan,.
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Reyes-Ortiz V, Heins RA, Cheng G, Kim EY, Vernon BC, Elandt RB, Adams PD, Sale KL, Hadi MZ, Simmons BA, Kent MS, Tullman-Ercek D. Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:93. [PMID: 23819686 PMCID: PMC3716932 DOI: 10.1186/1754-6834-6-93] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 06/18/2013] [Indexed: 05/03/2023]
Abstract
INTRODUCTION Cellulases are of great interest for application in biomass degradation, yet the molecular details of the mode of action of glycoside hydrolases during degradation of insoluble cellulose remain elusive. To further improve these enzymes for application at industrial conditions, it is critical to gain a better understanding of not only the details of the degradation process, but also the function of accessory modules. METHOD We fused a carbohydrate-binding module (CBM) from family 2a to two thermophilic endoglucanases. We then applied neutron reflectometry to determine the mechanism of the resulting enhancements. RESULTS Catalytic activity of the chimeric enzymes was enhanced up to three fold on insoluble cellulose substrates as compared to wild type. Importantly, we demonstrate that the wild type enzymes affect primarily the surface properties of an amorphous cellulose film, while the chimeras containing a CBM alter the bulk properties of the amorphous film. CONCLUSION Our findings suggest that the CBM improves the efficiency of these cellulases by enabling digestion within the bulk of the film.
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Affiliation(s)
- Vimalier Reyes-Ortiz
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Department of Bioengineering, University of California, Berkeley, CA 94720, US
| | - Richard A Heins
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Livermore, CA 94550, US
| | - Gang Cheng
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Livermore, CA 94550, US
| | - Edward Y Kim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, US
| | - Briana C Vernon
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Albuquerque, NM 87185, US
| | - Ryan B Elandt
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
| | - Paul D Adams
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Department of Bioengineering, University of California, Berkeley, CA 94720, US
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, US
| | - Kenneth L Sale
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Livermore, CA 94550, US
| | - Masood Z Hadi
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Livermore, CA 94550, US
| | - Blake A Simmons
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Livermore, CA 94550, US
| | - Michael S Kent
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Albuquerque, NM 87185, US
| | - Danielle Tullman-Ercek
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Department of Bioengineering, University of California, Berkeley, CA 94720, US
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, US
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, US
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A single-molecule analysis reveals morphological targets for cellulase synergy. Nat Chem Biol 2013; 9:356-61. [DOI: 10.1038/nchembio.1227] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 02/28/2013] [Indexed: 11/08/2022]
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Luís AS, Venditto I, Temple MJ, Rogowski A, Baslé A, Xue J, Knox JP, Prates JAM, Ferreira LMA, Fontes CMGA, Najmudin S, Gilbert HJ. Understanding how noncatalytic carbohydrate binding modules can display specificity for xyloglucan. J Biol Chem 2012; 288:4799-809. [PMID: 23229556 PMCID: PMC3576085 DOI: 10.1074/jbc.m112.432781] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Plant biomass is central to the carbon cycle and to environmentally sustainable industries exemplified by the biofuel sector. Plant cell wall degrading enzymes generally contain noncatalytic carbohydrate binding modules (CBMs) that fulfil a targeting function, which enhances catalysis. CBMs that bind β-glucan chains often display broad specificity recognizing β1,4-glucans (cellulose), β1,3-β1,4-mixed linked glucans and xyloglucan, a β1,4-glucan decorated with α1,6-xylose residues, by targeting structures common to the three polysaccharides. Thus, CBMs that recognize xyloglucan target the β1,4-glucan backbone and only accommodate the xylose decorations. Here we show that two closely related CBMs, CBM65A and CBM65B, derived from EcCel5A, a Eubacterium cellulosolvens endoglucanase, bind to a range of β-glucans but, uniquely, display significant preference for xyloglucan. The structures of the two CBMs reveal a β-sandwich fold. The ligand binding site comprises the β-sheet that forms the concave surface of the proteins. Binding to the backbone chains of β-glucans is mediated primarily by five aromatic residues that also make hydrophobic interactions with the xylose side chains of xyloglucan, conferring the distinctive specificity of the CBMs for the decorated polysaccharide. Significantly, and in contrast to other CBMs that recognize β-glucans, CBM65A utilizes different polar residues to bind cellulose and mixed linked glucans. Thus, Gln106 is central to cellulose recognition, but is not required for binding to mixed linked glucans. This report reveals the mechanism by which β-glucan-specific CBMs can distinguish between linear and mixed linked glucans, and show how these CBMs can exploit an extensive hydrophobic platform to target the side chains of decorated β-glucans.
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Affiliation(s)
- Ana S Luís
- CIISA, Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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Kim IJ, Ko HJ, Kim TW, Choi IG, Kim KH. Characteristics of the binding of a bacterial expansin (BsEXLX1) to microcrystalline cellulose. Biotechnol Bioeng 2012; 110:401-7. [DOI: 10.1002/bit.24719] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 07/13/2012] [Accepted: 08/13/2012] [Indexed: 11/08/2022]
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35
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Ruel K, Nishiyama Y, Joseleau JP. Crystalline and amorphous cellulose in the secondary walls of Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 193-194:48-61. [PMID: 22794918 DOI: 10.1016/j.plantsci.2012.05.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 05/09/2012] [Accepted: 05/11/2012] [Indexed: 06/01/2023]
Abstract
In the cell walls of higher plants, cellulose chains are present in crystalline microfibril, with an amorphous part at the surface, or present as amorphous material. To assess the distribution and relative occurrence of the two forms of cellulose in the inflorescence stem of Arabidopsis, we used two carbohydrate-binding modules, CBM3a and CBM28, specific for crystalline and amorphous cellulose, respectively, with immunogold detection in TEM. The binding of the two CBMs displayed specific patterns suggesting that the synthesis of cellulose leads to variable nanodomains of cellulose structures according to cell type. In developing cell walls, only CBM3a bound significantly to the incipient primary walls, indicating that at the onset of its deposition cellulose is in a crystalline structure. As the secondary wall develops, the labeling with both CBMs becomes more intense. The variation of the labeling pattern by CBM3a between transverse and longitudinal sections appeared related to microfibril orientation and differed between fibers and vessels. Although the two CBMs do not allow the description of the complete status of cellulose microstructures, they revealed the dynamics of the deposition of crystalline and amorphous forms of cellulose during wall formation and between cell types adapting cellulose microstructures to the cell function.
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Affiliation(s)
- Katia Ruel
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS UPR 5301), BP 53 38041 Grenoble CEDEX 9, France
| | - Yoshiharu Nishiyama
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS UPR 5301), BP 53 38041 Grenoble CEDEX 9, France
| | - Jean-Paul Joseleau
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS UPR 5301), BP 53 38041 Grenoble CEDEX 9, France.
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36
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Structural basis for entropy-driven cellulose binding by a type-A cellulose-binding module (CBM) and bacterial expansin. Proc Natl Acad Sci U S A 2012; 109:14830-5. [PMID: 22927418 DOI: 10.1073/pnas.1213200109] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Components of modular cellulases, type-A cellulose-binding modules (CBMs) bind to crystalline cellulose and enhance enzyme effectiveness, but structural details of the interaction are uncertain. We analyzed cellulose binding by EXLX1, a bacterial expansin with ability to loosen plant cell walls and whose domain D2 has type-A CBM characteristics. EXLX1 strongly binds to crystalline cellulose via D2, whereas its affinity for soluble cellooligosaccharides is weak. Calorimetry indicated cellulose binding was largely entropically driven. We solved the crystal structures of EXLX1 complexed with cellulose-like oligosaccharides to find that EXLX1 binds the ligands through hydrophobic interactions of three linearly arranged aromatic residues in D2. The crystal structures revealed a unique form of ligand-mediated dimerization, with the oligosaccharide sandwiched between two D2 domains in opposite polarity. This report clarifies the molecular target of expansin and the specific molecular interactions of a type-A CBM with cellulose.
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37
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Analysis of crystallinity changes in cellulose II polymers using carbohydrate-binding modules. Carbohydr Polym 2012; 89:213-21. [DOI: 10.1016/j.carbpol.2012.02.073] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 02/27/2012] [Accepted: 02/29/2012] [Indexed: 11/20/2022]
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38
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Caparrós C, Lant N, Smets J, Cavaco-Paulo A. Effects of adsorption properties and mechanical agitation of two detergent cellulases towards cotton cellulose. BIOCATAL BIOTRANSFOR 2012. [DOI: 10.3109/10242422.2012.666840] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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39
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Fox JM, Levine SE, Clark DS, Blanch HW. Initial- and Processive-Cut Products Reveal Cellobiohydrolase Rate Limitations and the Role of Companion Enzymes. Biochemistry 2011; 51:442-52. [DOI: 10.1021/bi2011543] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jerome M. Fox
- Energy Biosciences Institute and ‡Department of
Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Seth E. Levine
- Energy Biosciences Institute and ‡Department of
Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Douglas S. Clark
- Energy Biosciences Institute and ‡Department of
Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Harvey W. Blanch
- Energy Biosciences Institute and ‡Department of
Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
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40
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Caparrós C, López C, Torrell M, Lant N, Smets J, Cavaco-Paulo A. Treatment of cotton with an alkaline Bacillus spp cellulase: Activity towards crystalline cellulose. Biotechnol J 2011; 7:275-83. [DOI: 10.1002/biot.201000352] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 07/21/2011] [Accepted: 09/22/2011] [Indexed: 11/07/2022]
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41
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Brás JLA, Cartmell A, Carvalho ALM, Verzé G, Bayer EA, Vazana Y, Correia MAS, Prates JAM, Ratnaparkhe S, Boraston AB, Romão MJ, Fontes CMGA, Gilbert HJ. Structural insights into a unique cellulase fold and mechanism of cellulose hydrolysis. Proc Natl Acad Sci U S A 2011; 108:5237-42. [PMID: 21393568 PMCID: PMC3069175 DOI: 10.1073/pnas.1015006108] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Clostridium thermocellum is a well-characterized cellulose-degrading microorganism. The genome sequence of C. thermocellum encodes a number of proteins that contain type I dockerin domains, which implies that they are components of the cellulose-degrading apparatus, but display no significant sequence similarity to known plant cell wall-degrading enzymes. Here, we report the biochemical properties and crystal structure of one of these proteins, designated CtCel124. The protein was shown to be an endo-acting cellulase that displays a single displacement mechanism and acts in synergy with Cel48S, the major cellulosomal exo-cellulase. The crystal structure of CtCel124 in complex with two cellotriose molecules, determined to 1.5 Å, displays a superhelical fold in which a constellation of α-helices encircle a central helix that houses the catalytic apparatus. The catalytic acid, Glu96, is located at the C-terminus of the central helix, but there is no candidate catalytic base. The substrate-binding cleft can be divided into two discrete topographical domains in which the bound cellotriose molecules display twisted and linear conformations, respectively, suggesting that the enzyme may target the interface between crystalline and disordered regions of cellulose.
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Affiliation(s)
- Joana L. A. Brás
- Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Alan Cartmell
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602-4712
| | - Ana Luísa M. Carvalho
- Rede de Química e Tecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Genny Verzé
- Rede de Química e Tecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Biocrystallography Laboratory, Department of Biotechnology, University of Verona, 37129 Verona, Italy
| | - Edward A. Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100 Israel; and
| | - Yael Vazana
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100 Israel; and
| | - Márcia A. S. Correia
- Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - José A. M. Prates
- Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Supriya Ratnaparkhe
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602-4712
| | - Alisdair B. Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6
| | - Maria J. Romão
- Rede de Química e Tecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Carlos M. G. A. Fontes
- Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Harry J. Gilbert
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602-4712
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Georgelis N, Tabuchi A, Nikolaidis N, Cosgrove DJ. Structure-function analysis of the bacterial expansin EXLX1. J Biol Chem 2011; 286:16814-23. [PMID: 21454649 DOI: 10.1074/jbc.m111.225037] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We made use of EXLX1, an expansin from Bacillus subtilis, to investigate protein features essential for its plant cell wall binding and wall loosening activities. We found that the two expansin domains, D1 and D2, need to be linked for wall extension activity and that D2 mediates EXLX1 binding to whole cell walls and to cellulose via distinct residues on the D2 surface. Binding to cellulose is mediated by three aromatic residues arranged linearly on the putative binding surface that spans D1 and D2. Mutation of these three residues to alanine eliminated cellulose binding and concomitantly eliminated wall loosening activity measured either by cell wall extension or by weakening of filter paper but hardly affected binding to whole cell walls, which is mediated by basic residues located on other D2 surfaces. Mutation of these basic residues to glutamine reduced cell wall binding but not wall loosening activities. We propose domain D2 as the founding member of a new carbohydrate binding module family, CBM63, but its function in expansin activity apparently goes beyond simply anchoring D1 to the wall. Several polar residues on the putative binding surface of domain D1 are also important for activity, most notably Asp82, whose mutation to alanine or asparagine completely eliminated wall loosening activity. The functional insights based on this bacterial expansin may be extrapolated to the interactions of plant expansins with cell walls.
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Affiliation(s)
- Nikolaos Georgelis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Montanier C, Flint JE, Bolam DN, Xie H, Liu Z, Rogowski A, Weiner DP, Ratnaparkhe S, Nurizzo D, Roberts SM, Turkenburg JP, Davies GJ, Gilbert HJ. Circular permutation provides an evolutionary link between two families of calcium-dependent carbohydrate binding modules. J Biol Chem 2010; 285:31742-54. [PMID: 20659893 PMCID: PMC2951246 DOI: 10.1074/jbc.m110.142133] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 07/13/2010] [Indexed: 11/06/2022] Open
Abstract
The microbial deconstruction of the plant cell wall is a critical biological process, which also provides important substrates for environmentally sustainable industries. Enzymes that hydrolyze the plant cell wall generally contain non-catalytic carbohydrate binding modules (CBMs) that contribute to plant cell wall degradation. Here we report the biochemical properties and crystal structure of a family of CBMs (CBM60) that are located in xylanases. Uniquely, the proteins display broad ligand specificity, targeting xylans, galactans, and cellulose. Some of the CBM60s display enhanced affinity for their ligands through avidity effects mediated by protein dimerization. The crystal structure of vCBM60, displays a β-sandwich with the ligand binding site comprising a broad cleft formed by the loops connecting the two β-sheets. Ligand recognition at site 1 is, exclusively, through hydrophobic interactions, whereas binding at site 2 is conferred by polar interactions between a protein-bound calcium and the O2 and O3 of the sugar. The observation, that ligand recognition at site 2 requires only a β-linked sugar that contains equatorial hydroxyls at C2 and C3, explains the broad ligand specificity displayed by vCBM60. The ligand-binding apparatus of vCBM60 displays remarkable structural conservation with a family 36 CBM (CBM36); however, the residues that contribute to carbohydrate recognition are derived from different regions of the two proteins. Three-dimensional structure-based sequence alignments reveal that CBM36 and CBM60 are related by circular permutation. The biological and evolutionary significance of the mechanism of ligand recognition displayed by family 60 CBMs is discussed.
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Affiliation(s)
- Cedric Montanier
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - James E. Flint
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - David N. Bolam
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Hefang Xie
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Ziyuan Liu
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Artur Rogowski
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | | | - Supriya Ratnaparkhe
- the Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia 30602-4712
| | - Didier Nurizzo
- the European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, F-38043 Grenoble Cedex, France
| | - Shirley M. Roberts
- the York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom, and
| | - Johan P. Turkenburg
- the York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom, and
| | - Gideon J. Davies
- the York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom, and
| | - Harry J. Gilbert
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- the Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia 30602-4712
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Santos CR, Squina FM, Navarro AM, Ruller R, Prade R, Murakami MT. Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of the catalytic domain of a hyperthermostable endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1078-81. [PMID: 20823531 DOI: 10.1107/s1744309110029131] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 07/21/2010] [Indexed: 05/26/2023]
Abstract
Endo-1,4-beta-D-mannanases play key roles in seed germination and fruit ripening and have recently received much attention owing to their potential applications in the food, detergent and kraft pulp industries. In order to delineate their structural determinants for specificity and stability, X-ray crystallographic investigations combined with detailed functional studies are being performed. In this work, crystals of the catalytic domain of a hyperthermostable endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 were obtained from three different conditions, resulting in two crystalline forms. Crystals from conditions with phosphate or citrate salts as precipitant (CryP) belonged to space group P2(1)2(1)2(1), with unit-cell parameters a=58.76, b=87.99, c=97.34 A, while a crystal from a condition with ethanol as precipitant (CryE) belonged to space group I2(1)2(1)2(1), with unit-cell parameters a=91.03, b=89.97, c=97.89 A. CryP and CryE diffracted to resolutions of 1.40 and 1.45 A, respectively.
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Affiliation(s)
- Camila Ramos Santos
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, 13083-970 Campinas-SP, Brazil
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Engineering of Clostridium phytofermentans Endoglucanase Cel5A for improved thermostability. Appl Environ Microbiol 2010; 76:4914-7. [PMID: 20511418 DOI: 10.1128/aem.00958-10] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A family 5 glycoside hydrolase from Clostridium phytofermentans was cloned and engineered through a cellulase cell surface display system in Escherichia coli. The presence of cell surface anchoring, a cellulose binding module, or a His tag greatly influenced the activities of wild-type and mutant enzymes on soluble and solid cellulosic substrates, suggesting the high complexity of cellulase engineering. The best mutant had 92%, 36%, and 46% longer half-lives at 60 degrees C on carboxymethyl cellulose, regenerated amorphous cellulose, and Avicel, respectively.
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Levine SE, Fox JM, Blanch HW, Clark DS. A mechanistic model of the enzymatic hydrolysis of cellulose. Biotechnol Bioeng 2010; 107:37-51. [DOI: 10.1002/bit.22789] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Family 17 and 28 carbohydrate-binding modules discriminated different cell-wall sites in sweet potato roots. Biosci Biotechnol Biochem 2010; 74:802-5. [PMID: 20378993 DOI: 10.1271/bbb.90845] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Endoglucanase Cel5A from Clostridium josui contains a family 17 carbohydrate-binding module (CBM) (CjCBM17) and a family 28 CBM (CjCBM28) in tandem. These two CBMs bound to non-crystalline cellulose and beta-1,3-1,4-glucan. Our results indicate that the CBMs recognized different components on the cell wall of a sweet potato root. The root was cut into longitudinal sections. We used CjCBM17 and CjCBM28 fused to two different fluorescent proteins to visualize differential recognition of the plant cell wall. When they were microscopically observed, CjCBM28-fused cyan fluorescent protein (CFP) differentially bound to the root cap, but CjCBM17-fused blue fluorescent protein (BFP) did not. CjCBM17-BFP bound to the central part or the root apical meristem. These results suggest that CjCBM17 and CjCBM28 recognize different sites of the cell wall and that the cell-wall components and the polysaccharides configuration in the cell wall differ between tissues.
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Kawakubo T, Karita S, Araki Y, Watanabe S, Oyadomari M, Takada R, Tanaka F, Abe K, Watanabe T, Honda Y, Watanabe T. Analysis of exposed cellulose surfaces in pretreated wood biomass using carbohydrate-binding module (CBM)-cyan fluorescent protein (CFP). Biotechnol Bioeng 2010; 105:499-508. [PMID: 19777599 DOI: 10.1002/bit.22550] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In enzymatic saccharification of lignocellulosics, the access of the enzymes to exposed cellulose surfaces is a key initial step in triggering hydrolysis. However, knowledge of the structure-hydrolyzability relationship of the pretreated biomass is still limited. Here we used fluorescent-labeled recombinant carbohydrate-binding modules (CBMs) from Clostridium josui as specific markers for crystalline cellulose (CjCBM3) and non-crystalline cellulose (CjCBM28) to analyze the complex surfaces of wood tissues pretreated with NaOH, NaOH-Na(2)S (kraft pulping), hydrothermolysis, ball-milling, and organosolvolysis. Japanese cedar wood, one of the most recalcitrant softwood species was selected for the analysis. The binding analysis clarified the linear dependency of the exposure of crystalline and non-crystalline cellulose surfaces for enzymatic saccharification yield by the organosolv and kraft delignification processes. Ball-milling for 5-30 min increased saccharification yield up to 77%, but adsorption by the CjCBM-cyan fluorescent proteins (CFPs) was below 5%. Adsorption of CjCBM-CFPs on the hydrothermolysis pulp were less than half of those for organosolvolysis pulp, in coincidence with low saccharification yields. For all the pretreated wood, crystallinity index was not directly correlated with the overall saccharification yield. Fluorescent microscopy revealed that CjCBM3-CFP and CjCBM28-CFP were site-specifically adsorbed on external fibrous structures and ruptured or distorted fiber surfaces. The assay system with CBM-CFPs is a powerful measure to estimate the initiation sites of hydrolysis and saccharification yields from chemically delignified wood pulps.
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Affiliation(s)
- Takeshi Kawakubo
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Japan
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Tsukimoto K, Takada R, Araki Y, Suzuki K, Karita S, Wakagi T, Shoun H, Watanabe T, Fushinobu S. Recognition of cellooligosaccharides by a family 28 carbohydrate-binding module. FEBS Lett 2010; 584:1205-11. [DOI: 10.1016/j.febslet.2010.02.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 02/08/2010] [Accepted: 02/10/2010] [Indexed: 11/28/2022]
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50
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Carbohydrate-binding domains: multiplicity of biological roles. Appl Microbiol Biotechnol 2009; 85:1241-9. [DOI: 10.1007/s00253-009-2331-y] [Citation(s) in RCA: 253] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2009] [Revised: 10/23/2009] [Accepted: 10/24/2009] [Indexed: 10/20/2022]
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