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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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2
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Lu Z, Kvammen A, Li H, Hao M, Inman AR, Bulone V, McKee LS. A polysaccharide utilization locus from Chitinophaga pinensis simultaneously targets chitin and β-glucans found in fungal cell walls. mSphere 2023; 8:e0024423. [PMID: 37493618 PMCID: PMC10449523 DOI: 10.1128/msphere.00244-23] [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: 05/04/2023] [Accepted: 06/06/2023] [Indexed: 07/27/2023] Open
Abstract
In nature, complex carbohydrates are rarely found as pure isolated polysaccharides. Instead, bacteria in competitive environments are presented with glycans embedded in heterogeneous matrices such as plant or microbial cell walls. Members of the Bacteroidota phylum thrive in such ecosystems because they are efficient at extracting nutrients from complex substrates, secreting consortia of synergistic enzymes to release metabolizable sugars. Carbohydrate-binding modules (CBMs) are used to target enzymes to substrates, enhancing reaction rate and product release. Additionally, genome organizational tools like polysaccharide utilization loci (PULs) ensure that the appropriate set of enzymes is produced when needed. In this study, we show that the soil bacterium Chitinophaga pinensis uses a PUL and several CBMs to coordinate the activities of enzymes targeting two distinct polysaccharides found in fungal cell walls. We describe the enzymatic activities and carbohydrate-binding behaviors of components of the fungal cell wall utilization locus (FCWUL), which uses multiple chitinases and one β-1,3-glucanase to hydrolyze two different substrates. Unusually, one of the chitinases is appended to a β-glucan-binding CBM, implying targeting to a bulk cell wall substrate rather than to the specific polysaccharide being hydrolyzed. Based on our characterization of the PUL's outer membrane sensor protein, we suggest that the FCWUL is activated by β-1,3-glucans, even though most of its enzymes are chitin-degrading. Our data showcase the complexity of polysaccharide deconstruction in nature and highlight an elegant solution for how multiple different glycans can be accessed using one enzymatic cascade. IMPORTANCE We report that the genome of the soil bacterium Chitinophaga pinensis encodes three multi-modular carbohydrate-active enzymes that work together to hydrolyze the major polysaccharide components found in fungal cell walls (FCWs). The enzymes are all encoded by one polysaccharide utilization locus and are co-expressed, potentially induced in the presence of β-1,3-glucans. We present biochemical characterization of each enzyme, including the appended carbohydrate-binding modules that likely tether the enzymes to a FCW substrate. Finally, we propose a model for how this so-called fungal cell wall utilization locus might enable C. pinensis to metabolize both chitin and β-1,3-glucans found in complex biomass in the soil.
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Affiliation(s)
- Zijia Lu
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Alma Kvammen
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - He Li
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mengshu Hao
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Annie R. Inman
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Vincent Bulone
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Lauren S. McKee
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, Stockholm, Sweden
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3
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Morais MAB, Paiva JH, Murakami MT. Molecular plasticity of CBM3 ancillary domain leads to conformational changes in the cellulose binding interface. Biochem Biophys Res Commun 2023; 645:71-78. [PMID: 36680939 DOI: 10.1016/j.bbrc.2023.01.020] [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: 12/03/2022] [Revised: 12/14/2022] [Accepted: 01/10/2023] [Indexed: 01/12/2023]
Abstract
Carbohydrate-binding modules (CBMs) constitute independently folded domains typically associated with carbohydrate-active enzymes (CAZymes). These modules are considered to have a rigid structure without notable conformational changes upon ligand binding, exhibiting a complementary topography in relation to the target carbohydrate. Herein, the high-resolution SAD-solved structure of a CBM from family 3 (BsCBM3) that binds to crystalline cellulose is reported in two crystalline forms. This module showed molecular plasticity with structural differences detected between the two crystalline forms and high RMSD values when compared to NMR ensemble of models. Pronounced structural variances were observed in the cellulose binding interface between NMR and XTAL structures, which were corroborated by molecular dynamics simulations. These findings support that family 3 CBMs targeting to cellulose are rather structurally dynamic modules than rigid entities, suggesting a potential role of conformational changes in polysaccharide recognition and modulation of enzyme activity.
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Affiliation(s)
- Mariana Abrahão Bueno Morais
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Joice Helena Paiva
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Mário Tyago Murakami
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.
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4
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Lu Z, Rämgård C, Ergenlioğlu İ, Sandin L, Hammar H, Andersson H, King K, Inman AR, Hao M, Bulone V, McKee LS. Multiple enzymatic approaches to hydrolysis of fungal β-glucans by the soil bacterium Chitinophaga pinensis. FEBS J 2023. [PMID: 36610032 DOI: 10.1111/febs.16720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/26/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
The genome of the soil Bacteroidota Chitinophaga pinensis encodes a large number of glycoside hydrolases (GHs) with noteworthy features and potentially novel functions. Several are predicted to be active on polysaccharide components of fungal and oomycete cell walls, such as chitin, β-1,3-glucan and β-1,6-glucan. While several fungal β-1,6-glucanase enzymes are known, relatively few bacterial examples have been characterised to date. We have previously demonstrated that C. pinensis shows strong growth using β-1,6-glucan as the sole carbon source, with the efficient release of oligosaccharides from the polymer. We here characterise the capacity of the C. pinensis secretome to hydrolyse the β-1,6-glucan pustulan and describe three distinct enzymes encoded by its genome, all of which show different levels of β-1,6-glucanase activity and which are classified into different GH families. Our data show that C. pinensis has multiple tools to deconstruct pustulan, allowing the species' broad utility of this substrate, with potential implications for bacterial biocontrol of pathogens via cell wall disruption. Oligosaccharides derived from fungal β-1,6-glucans are valuable in biomedical research and drug synthesis, and these enzymes could be useful tools for releasing such molecules from microbial biomass, an underexploited source of complex carbohydrates.
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Affiliation(s)
- Zijia Lu
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Carl Rämgård
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - İrem Ergenlioğlu
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Lova Sandin
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Hugo Hammar
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Helena Andersson
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Katharine King
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Annie R Inman
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Mengshu Hao
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.,College of Medicine & Public Health, Flinders University, Adelaide, SA, Australia
| | - Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.,Wallenberg Wood Science Centre, Stockholm, Sweden
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5
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Acoustic force spectroscopy reveals subtle differences in cellulose unbinding behavior of carbohydrate-binding modules. Proc Natl Acad Sci U S A 2022; 119:e2117467119. [PMID: 36215467 PMCID: PMC9586272 DOI: 10.1073/pnas.2117467119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein adsorption to solid carbohydrate interfaces is critical to many biological processes, particularly in biomass deconstruction. To engineer more-efficient enzymes for biomass deconstruction into sugars, it is necessary to characterize the complex protein-carbohydrate interfacial interactions. A carbohydrate-binding module (CBM) is often associated with microbial surface-tethered cellulosomes or secreted cellulase enzymes to enhance substrate accessibility. However, it is not well known how CBMs recognize, bind, and dissociate from polysaccharides to facilitate efficient cellulolytic activity, due to the lack of mechanistic understanding and a suitable toolkit to study CBM-substrate interactions. Our work outlines a general approach to study the unbinding behavior of CBMs from polysaccharide surfaces using a highly multiplexed single-molecule force spectroscopy assay. Here, we apply acoustic force spectroscopy (AFS) to probe a Clostridium thermocellum cellulosomal scaffoldin protein (CBM3a) and measure its dissociation from nanocellulose surfaces at physiologically relevant, low force loading rates. An automated microfluidic setup and method for uniform deposition of insoluble polysaccharides on the AFS chip surfaces are demonstrated. The rupture forces of wild-type CBM3a, and its Y67A mutant, unbinding from nanocellulose surfaces suggests distinct multimodal CBM binding conformations, with structural mechanisms further explored using molecular dynamics simulations. Applying classical dynamic force spectroscopy theory, the single-molecule unbinding rate at zero force is extrapolated and found to agree with bulk equilibrium unbinding rates estimated independently using quartz crystal microbalance with dissipation monitoring. However, our results also highlight critical limitations of applying classical theory to explain the highly multivalent binding interactions for cellulose-CBM bond rupture forces exceeding 15 pN.
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6
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Alonzo LF, Hinkley TC, Miller A, Calderon R, Garing S, Williford J, Clute-Reinig N, Spencer E, Friend M, Madan D, Dinh VTT, Bell D, Weigl BH, Nugen SR, Nichols KP, Le Ny ALM. A microfluidic device and instrument prototypes for the detection of Escherichia coli in water samples using a phage-based bioluminescence assay. LAB ON A CHIP 2022; 22:2155-2164. [PMID: 35521688 DOI: 10.1039/d1lc00888a] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Current quantification methods of Escherichia coli (E. coli) contamination in water samples involve long incubation, laboratory equipment and facilities, or complex processes that require specialized training for accurate operation and interpretation. To address these limitations, we have developed a microfluidic device and portable instrument prototypes capable of performing a rapid and highly sensitive bacteriophage-based assay to detect E. coli cells with detection limit comparable to traditional methods in a fraction of the time. The microfluidic device combines membrane filtration and selective enrichment using T7-NanoLuc-CBM, a genetically engineered bacteriophage, to identify 4.1 E. coli CFU in 100 mL of drinking water within 5.5 hours. The microfluidic device was designed and tested to process up to 100 mL of real-world drinking water samples with turbidities below 10 NTU. Prototypes of custom instrumentation, compatible with our valveless microfluidic device and capable of performing all of the assay's units of operation with minimal user intervention, demonstrated similar assay performance to that obtained on the benchtop assay. This research is the first step towards a faster, portable, and semi-automated, phage-based microfluidic platform for improved in-field water quality monitoring in low-resource settings.
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Affiliation(s)
- Luis F Alonzo
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA 98007, USA
| | - Troy C Hinkley
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA 98007, USA
| | - Andrew Miller
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA 98007, USA
| | - Ryan Calderon
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA 98007, USA
| | - Spencer Garing
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA 98007, USA
| | - John Williford
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA 98007, USA
| | - Nick Clute-Reinig
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA 98007, USA
| | - Ethan Spencer
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA 98007, USA
| | - Michael Friend
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA 98007, USA
| | - Damian Madan
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA 98007, USA
| | - Van T T Dinh
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA 98007, USA
| | - David Bell
- Independent Consultant, Issaquah, WA 98027, USA
| | - Bernhard H Weigl
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA 98007, USA
| | - Sam R Nugen
- Department of Food Science, Cornell University, Ithaca, NY 14850, USA
| | - Kevin P Nichols
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA 98007, USA
| | - Anne-Laure M Le Ny
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA 98007, USA
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7
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Alonzo LF, Jain P, Hinkley T, Clute-Reinig N, Garing S, Spencer E, Dinh VTT, Bell D, Nugen S, Nichols KP, Le Ny ALM. Rapid, sensitive, and low-cost detection of Escherichia coli bacteria in contaminated water samples using a phage-based assay. Sci Rep 2022; 12:7741. [PMID: 35562180 PMCID: PMC9095594 DOI: 10.1038/s41598-022-11468-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/18/2022] [Indexed: 11/29/2022] Open
Abstract
Inadequate drinking water quality is among the major causes of preventable mortality, predominantly in young children. Identifying contaminated water sources remains a significant challenge, especially where resources are limited. The current methods for measuring Escherichia coli (E. coli), the WHO preferred indicator for measuring fecal contamination of water, involve overnight incubation and require specialized training. In 2016, UNICEF released a Target Product Profile (TPP) to incentivize product innovations to detect low levels of viable E. coli in water samples in the field in less than 6 h. Driven by this challenge, we developed a phage-based assay to detect and semi-quantify E. coli. We formulated a phage cocktail containing a total of 8 phages selected against an extensive bacterial strain library and recombined with the sensitive NanoLuc luciferase reporter. The assay was optimized to be processed in a microfluidic chip designed in-house and was tested against locally sourced sewage samples and on drinking water sources in Nairobi, Kenya. With this assay, combined with the microfluidic chip platform, we propose a complete automated solution to detect and semi-quantify E. coli at less than 10 MPN/100 mL in 5.5 h by minimally trained personnel.
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Affiliation(s)
- Luis F Alonzo
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA, 98007, USA
- Global Health Labs, 14360 Eastgate Way, Bellevue, WA, 98007, USA
| | - Paras Jain
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA, 98007, USA
- Cell Therapy and Cell Engineering Facility, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Troy Hinkley
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA, 98007, USA
| | - Nick Clute-Reinig
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA, 98007, USA
| | - Spencer Garing
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA, 98007, USA
- Global Health Labs, 14360 Eastgate Way, Bellevue, WA, 98007, USA
| | - Ethan Spencer
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA, 98007, USA
- Global Health Labs, 14360 Eastgate Way, Bellevue, WA, 98007, USA
| | - Van T T Dinh
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA, 98007, USA
| | - David Bell
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA, 98007, USA
- Cell Therapy and Cell Engineering Facility, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sam Nugen
- Independent Consultant, Issaquah, WA, 98027, USA
| | - Kevin P Nichols
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA, 98007, USA
| | - Anne-Laure M Le Ny
- Intellectual Ventures Laboratory, 14360 SE Eastgate Way, Bellevue, WA, 98007, USA.
- Global Health Labs, 14360 Eastgate Way, Bellevue, WA, 98007, USA.
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8
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Perrot T, Pauly M, Ramírez V. Emerging Roles of β-Glucanases in Plant Development and Adaptative Responses. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11091119. [PMID: 35567119 PMCID: PMC9099982 DOI: 10.3390/plants11091119] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 05/04/2023]
Abstract
Plant β-glucanases are enzymes involved in the synthesis, remodelling and turnover of cell wall components during multiple physiological processes. Based on the type of the glycoside bond they cleave, plant β-glucanases have been grouped into three categories: (i) β-1,4-glucanases degrade cellulose and other polysaccharides containing 1,4-glycosidic bonds to remodel and disassemble the wall during cell growth. (ii) β-1,3-glucanases are responsible for the mobilization of callose, governing the symplastic trafficking through plasmodesmata. (iii) β-1,3-1,4-glucanases degrade mixed linkage glucan, a transient wall polysaccharide found in cereals, which is broken down to obtain energy during rapid seedling growth. In addition to their roles in the turnover of self-glucan structures, plant β-glucanases are crucial in regulating the outcome in symbiotic and hostile plant-microbe interactions by degrading non-self glucan structures. Plants use these enzymes to hydrolyse β-glucans found in the walls of microbes, not only by contributing to a local antimicrobial defence barrier, but also by generating signalling glucans triggering the activation of global responses. As a counterpart, microbes developed strategies to hijack plant β-glucanases to their advantage to successfully colonize plant tissues. This review outlines our current understanding on plant β-glucanases, with a particular focus on the latest advances on their roles in adaptative responses.
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Liberato MV, Campos BM, Tomazetto G, Crouch LI, Garcia W, Zeri ACDM, Bolam DN, Squina FM. Unique properties of a Dictyostelium discoideum carbohydrate-binding module expand our understanding of CBM-ligand interactions. J Biol Chem 2022; 298:101891. [PMID: 35378128 PMCID: PMC9079177 DOI: 10.1016/j.jbc.2022.101891] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/23/2022] [Accepted: 03/26/2022] [Indexed: 12/04/2022] Open
Abstract
Deciphering how enzymes interact, modify, and recognize carbohydrates has long been a topic of interest in academic, pharmaceutical, and industrial research. Carbohydrate-binding modules (CBMs) are noncatalytic globular protein domains attached to carbohydrate-active enzymes that strengthen enzyme affinity to substrates and increase enzymatic efficiency via targeting and proximity effects. CBMs are considered auspicious for various biotechnological purposes in textile, food, and feed industries, representing valuable tools in basic science research and biomedicine. Here, we present the first crystallographic structure of a CBM8 family member (CBM8), DdCBM8, from the slime mold Dictyostelium discoideum, which was identified attached to an endo-β-1,4-glucanase (glycoside hydrolase family 9). We show that the planar carbohydrate-binding site of DdCBM8, composed of aromatic residues, is similar to type A CBMs that are specific for crystalline (multichain) polysaccharides. Accordingly, pull-down assays indicated that DdCBM8 was able to bind insoluble forms of cellulose. However, affinity gel electrophoresis demonstrated that DdCBM8 also bound to soluble (single chain) polysaccharides, especially glucomannan, similar to type B CBMs, although it had no apparent affinity for oligosaccharides. Therefore, the structural characteristics and broad specificity of DdCBM8 represent exceptions to the canonical CBM classification. In addition, mutational analysis identified specific amino acid residues involved in ligand recognition, which are conserved throughout the CBM8 family. This advancement in the structural and functional characterization of CBMs contributes to our understanding of carbohydrate-active enzymes and protein–carbohydrate interactions, pushing forward protein engineering strategies and enhancing the potential biotechnological applications of glycoside hydrolase accessory modules.
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Affiliation(s)
- Marcelo Vizona Liberato
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, SP, Brazil
| | - Bruna Medeia Campos
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Geizecler Tomazetto
- Department of Biological and Chemical Engineering (BCE), Aarhus University, Aarhus, Denmark
| | - Lucy Isobel Crouch
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | - Ana Carolina de Mattos Zeri
- Laboratório Nacional de Luz Sincrotron (LNLS), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - David Nichol Bolam
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle, United Kingdom
| | - Fabio Marcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, SP, Brazil.
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10
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Kim S, Bae G, Shin M, Kang E, Park TY, Choi YS, Cha HJ. Oriented in situ immobilization of a functional tyrosinase on microcrystalline cellulose effectively incorporates DOPA residues in bioengineered mussel adhesive protein. Biotechnol J 2021; 16:e2100216. [PMID: 34536060 DOI: 10.1002/biot.202100216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/12/2021] [Accepted: 09/15/2021] [Indexed: 11/09/2022]
Abstract
BACKGROUND Catechol-containing polymers such as mussel adhesive proteins (MAPs) are attractive as biocompatible adhesive biomaterials, and the catecholic amino acid 3,4-dihydroxyphenyl-L-alanine (DOPA) is considered a key molecule in underwater mussel adhesion. Tyrosinases can specifically convert tyrosine to DOPA without any cofactors. However, their catalytic properties still need to be adjusted to minimize unwanted DOPA oxidation via their diphenolase activity and catechol instability at neutral and basic pH values in the reaction products. METHODS AND RESULTS In this work, we constructed a novel functional tyrosinase, mTyr-CNK_CBM, by fusion of mTyr-CNK with a cellulose-binding motif (CBM) for oriented in situ immobilization on microcrystalline cellulose via the C-terminal CBM without any additional purification steps. mTyr-CNK_CBM showed optimal catalytic activity at pH 4.5-6.5 and room temperature and had a high monophenolase/diphenolase activity ratio (Vmax mono/Vmax di = 2.08 at pH 6 and 25°C). mTyr-CNK_CBM exhibited 2.17-fold higher (as a unimmobilized free enzyme) and similarly high (upon immobilization) in vitro DOPA modification of a bioengineered MAP compared to a commercially available mushroom tyrosinase. Moreover, the immobilized mTyr-CNK_CBM showed long-term storability and improved reusability. CONCLUSIONS These results clearly demonstrate a strong potential for practical use of immobilized mTyr-CNK_CBM as a monophenol monooxygenase in preparing biocompatible DOPA-tethered biomaterials and other catechol-containing polymers.
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Affiliation(s)
- Suhyeok Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Gaeun Bae
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Mincheol Shin
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Eungsu Kang
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Tae Yoon Park
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Yoo Seong Choi
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Hyung Joon Cha
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Republic of Korea
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11
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Nemmaru B, Ramirez N, Farino CJ, Yarbrough JM, Kravchenko N, Chundawat SPS. Reduced type-A carbohydrate-binding module interactions to cellulose I leads to improved endocellulase activity. Biotechnol Bioeng 2020; 118:1141-1151. [PMID: 33245142 DOI: 10.1002/bit.27637] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/12/2020] [Accepted: 11/15/2020] [Indexed: 12/24/2022]
Abstract
Dissociation of nonproductively bound cellulolytic enzymes from cellulose is hypothesized to be a key rate-limiting factor impeding cost-effective biomass conversion to fermentable sugars. However, the role of carbohydrate-binding modules (CBMs) in enabling nonproductive enzyme binding is not well understood. Here, we examine the subtle interplay of CBM binding and cellulose hydrolysis activity for three models type-A CBMs (Families 1, 3a, and 64) tethered to multifunctional endoglucanase (CelE) on two distinct cellulose allomorphs (i.e., cellulose I and III). We generated a small library of mutant CBMs with varying cellulose affinity, as determined by equilibrium binding assays, followed by monitoring cellulose hydrolysis activity of CelE-CBM fusion constructs. Finally, kinetic binding assays using quartz crystal microbalance with dissipation were employed to measure CBM adsorption and desorption rate constants k on and k off , respectively, towards nanocrystalline cellulose derived from both allomorphs. Overall, our results indicate that reduced CBM equilibrium binding affinity towards cellulose I alone, resulting from increased desorption rates ( k off ) and reduced effective adsorption rates ( nk on ), is correlated to overall improved endocellulase activity. Future studies could employ similar approaches to unravel the role of CBMs in nonproductive enzyme binding and develop improved cellulolytic enzymes for industrial applications.
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Affiliation(s)
| | - Nicholas Ramirez
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Cindy J Farino
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - John M Yarbrough
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Nicholas Kravchenko
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Shishir P S Chundawat
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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12
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Aïssa K, Karaaslan MA, Renneckar S, Saddler JN. Functionalizing Cellulose Nanocrystals with Click Modifiable Carbohydrate-Binding Modules. Biomacromolecules 2019; 20:3087-3093. [DOI: 10.1021/acs.biomac.9b00646] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kevin Aïssa
- Forest Products, Biotechnology and Bioenergy Group, Department of Wood Science, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, Canada
- Advanced Renewable Materials Lab, Department of Wood Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Muzaffer A. Karaaslan
- Forest Products, Biotechnology and Bioenergy Group, Department of Wood Science, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, Canada
- Advanced Renewable Materials Lab, Department of Wood Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott Renneckar
- Forest Products, Biotechnology and Bioenergy Group, Department of Wood Science, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, Canada
- Advanced Renewable Materials Lab, Department of Wood Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jack N. Saddler
- Forest Products, Biotechnology and Bioenergy Group, Department of Wood Science, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, Canada
- Advanced Renewable Materials Lab, Department of Wood Science, University of British Columbia, Vancouver, British Columbia, Canada
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13
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Hinkley TC, Garing S, Singh S, Le Ny ALM, Nichols KP, Peters JE, Talbert JN, Nugen SR. Reporter bacteriophage T7 NLC utilizes a novel NanoLuc::CBM fusion for the ultrasensitive detection of Escherichia coli in water. Analyst 2019; 143:4074-4082. [PMID: 30069563 DOI: 10.1039/c8an00781k] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Rapid detection of bacteria responsible for foodborne diseases is a growing necessity for public health. Reporter bacteriophages (phages) are robust biorecognition elements uniquely suited for the rapid and sensitive detection of bacterial species. The advantages of phages include their host specificity, ability to distinguish viable and non-viable cells, low cost, and ease of genetic engineering. Upon infection with reporter phages, target bacteria express reporter enzymes encoded within the phage genome. In this study, the T7 coliphage was genetically engineered to express the newly developed luceriferase, NanoLuc (NLuc), as an indicator of bacterial contamination. While several genetic approaches were employed to optimize reporter enzyme expression, the novel achievement of this work was the successful fusion of the NanoLuc reporter to a carbohydrate binding module (CBM) with specificity to crystalline cellulose. This novel chimeric reporter (nluc::cbm) bestows the specific and irreversible immobilization of NanoLuc onto a low-cost, widely available crystalline cellulosic substrate. We have shown the possibility of detecting the immobilized fusion protein in a filter plate which resulted from a single CFU of E. coli. We then demonstrated that microcrystalline cellulose can be used to concentrate the fusion reporter from 100 mL water samples allowing a limit of detection of <10 CFU mL-1E. coli in 3 hours. Therefore, we conclude that our phage-based detection assay displays significant aptitude as a proof-of-concept drinking water diagnostic assay for the low-cost, rapid and sensitive detection of E. coli. Additional improvements in the capture efficiency of the phage-based fusion reporter should allow a limit of detection of <10 CFU per 100 mL.
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Affiliation(s)
- T C Hinkley
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
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14
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Pulkkinen EM, Hinkley TC, Nugen SR. Utilizing in vitro DNA assembly to engineer a synthetic T7 Nanoluc reporter phage for Escherichia coli detection. Integr Biol (Camb) 2019; 11:63-68. [PMID: 30927414 DOI: 10.1093/intbio/zyz005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 01/18/2019] [Accepted: 01/31/2019] [Indexed: 02/06/2023]
Abstract
Bacteria have major role in regulating human health and disease, therefore, there is a continuing need to develop new detection methods and therapeutics to combat them. Bacteriophages can be used to infect specific bacteria, which make them good candidates for detecting and editing bacterial populations. However, creating phage-based detection assays is somewhat limited by the difficulties in the engineering of phages. We present here a synthetic biology strategy to engineer phages using a simple in vitro method. We used this method to insert a NanoLuc luciferase expression cassette into the T7 phage, in order to construct the NRGp6 reporter phage. The synthetic NRGp6 phage was used to efficiently detect low concentrations of Escherichia coli from liquid culture. We envision that our approach will benefit synthetic biologists for constructing different kinds of engineered phages, and enable new approaches for phage-based therapeutics and diagnostics.
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Affiliation(s)
- Elsi M Pulkkinen
- Department of Food Science, Cornell University, Ithaca, NY, USA
- Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Troy C Hinkley
- Department of Food Science, Cornell University, Ithaca, NY, USA
| | - Sam R Nugen
- Department of Food Science, Cornell University, Ithaca, NY, USA
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15
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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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16
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Hinkley TC, Singh S, Garing S, Le Ny ALM, Nichols KP, Peters JE, Talbert JN, Nugen SR. A phage-based assay for the rapid, quantitative, and single CFU visualization of E. coli (ECOR #13) in drinking water. Sci Rep 2018; 8:14630. [PMID: 30279488 PMCID: PMC6168599 DOI: 10.1038/s41598-018-33097-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/21/2018] [Indexed: 01/06/2023] Open
Abstract
Drinking water standards in the United States mandate a zero tolerance of generic E. coli in 100 mL of water. The presence of E. coli in drinking water indicates that favorable environmental conditions exist that could have resulted in pathogen contamination. Therefore, the rapid and specific enumeration of E. coli in contaminated drinking water is critical to mitigate significant risks to public health. To meet this challenge, we developed a bacteriophage-based membrane filtration assay that employs novel fusion reporter enzymes to fully quantify E. coli in less than half the time required for traditional enrichment assays. A luciferase and an alkaline phosphatase, both specifically engineered for increased enzymatic activity, were selected as reporter probes due to their strong signal, small size, and low background. The genes for the reporter enzymes were fused to genes for carbohydrate binding modules specific to cellulose. These constructs were then inserted into the E. coli-specific phage T7 which were used to infect E. coli trapped on a cellulose filter. During the infection, the reporters were expressed and released from the bacterial cells following the lytic infection cycle. The binding modules facilitated the immobilization of the reporter probes on the cellulose filter in proximity to the lysed cells. Following substrate addition, the location and quantification of E. coli cells could then be determined visually or using bioluminescence imaging for the alkaline phosphatase and luciferase reporters, respectively. As a result, a detection assay capable of quantitatively detecting E. coli in drinking water with similar results to established methods, but less than half the assay time was developed.
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Affiliation(s)
- Troy C Hinkley
- Department of Food Science, Cornell University, Ithaca, NY, 14853, United States
| | - Sangita Singh
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, 50011, United States
| | - Spencer Garing
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA, 98007, United States
| | - Anne-Laure M Le Ny
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA, 98007, United States
| | - Kevin P Nichols
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA, 98007, United States
| | - Joseph E Peters
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, United States
| | - Joey N Talbert
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, 50011, United States
| | - Sam R Nugen
- Department of Food Science, Cornell University, Ithaca, NY, 14853, United States.
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17
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Kundu S, Sharma R. Origin, evolution, and divergence of plant class C GH9 endoglucanases. BMC Evol Biol 2018; 18:79. [PMID: 29848310 PMCID: PMC5977491 DOI: 10.1186/s12862-018-1185-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 04/18/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glycoside hydrolases of the GH9 family encode cellulases that predominantly function as endoglucanases and have wide applications in the food, paper, pharmaceutical, and biofuel industries. The partitioning of plant GH9 endoglucanases, into classes A, B, and C, is based on the differential presence of transmembrane, signal peptide, and the carbohydrate binding module (CBM49). There is considerable debate on the distribution and the functions of these enzymes which may vary in different organisms. In light of these findings we examined the origin, emergence, and subsequent divergence of plant GH9 endoglucanases, with an emphasis on elucidating the role of CBM49 in the digestion of crystalline cellulose by class C members. RESULTS Since, the digestion of crystalline cellulose mandates the presence of a well-defined set of aromatic and polar amino acids and/or an attributable domain that can mediate this conversion, we hypothesize a vertical mode of transfer of genes that could favour the emergence of class C like GH9 endoglucanase activity in land plants from potentially ancestral non plant taxa. We demonstrated the concomitant occurrence of a GH9 domain with CBM49 and other homologous carbohydrate binding modules, in putative endoglucanase sequences from several non-plant taxa. In the absence of comparable full length CBMs, we have characterized several low strength patterns that could approximate the CBM49, thereby, extending support for digestion of crystalline cellulose to other segments of the protein. We also provide data suggestive of the ancestral role of putative class C GH9 endoglucanases in land plants, which includes detailed phylogenetics and the presence and subsequent loss of CBM49, transmembrane, and signal peptide regions in certain populations of early land plants. These findings suggest that classes A and B of modern vascular land plants may have emerged by diverging directly from CBM49 encompassing putative class C enzymes. CONCLUSION Our detailed phylogenetic and bioinformatics analysis of putative GH9 endoglucanase sequences across major taxa suggests that plant class C enzymes, despite their recent discovery, could function as the last common ancestor of classes A and B. Additionally, research into their ability to digest or inter-convert crystalline and amorphous forms of cellulose could make them lucrative candidates for engineering biofuel feedstock.
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Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, Government of NCT of Delhi, Dr. Baba Saheb Ambedkar Medical College & Hospital, New Delhi, 110085, India. .,Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Rita Sharma
- Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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18
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Meier KK, Jones SM, Kaper T, Hansson H, Koetsier MJ, Karkehabadi S, Solomon EI, Sandgren M, Kelemen B. Oxygen Activation by Cu LPMOs in Recalcitrant Carbohydrate Polysaccharide Conversion to Monomer Sugars. Chem Rev 2018; 118:2593-2635. [PMID: 29155571 PMCID: PMC5982588 DOI: 10.1021/acs.chemrev.7b00421] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Natural carbohydrate polymers such as starch, cellulose, and chitin provide renewable alternatives to fossil fuels as a source for fuels and materials. As such, there is considerable interest in their conversion for industrial purposes, which is evidenced by the established and emerging markets for products derived from these natural polymers. In many cases, this is achieved via industrial processes that use enzymes to break down carbohydrates to monomer sugars. One of the major challenges facing large-scale industrial applications utilizing natural carbohydrate polymers is rooted in the fact that naturally occurring forms of starch, cellulose, and chitin can have tightly packed organizations of polymer chains with low hydration levels, giving rise to crystalline structures that are highly recalcitrant to enzymatic degradation. The topic of this review is oxidative cleavage of carbohydrate polymers by lytic polysaccharide mono-oxygenases (LPMOs). LPMOs are copper-dependent enzymes (EC 1.14.99.53-56) that, with glycoside hydrolases, participate in the degradation of recalcitrant carbohydrate polymers. Their activity and structural underpinnings provide insights into biological mechanisms of polysaccharide degradation.
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Affiliation(s)
- Katlyn K. Meier
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Stephen M. Jones
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Thijs Kaper
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, California 94304, United States
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Martijn J. Koetsier
- DuPont Industrial Biosciences, Netherlands, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
| | - Saeid Karkehabadi
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Bradley Kelemen
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, California 94304, United States
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19
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Dreßen A, Hilberath T, Mackfeld U, Rudat J, Pohl M. Phenylalanine ammonia lyase from Arabidopsis thaliana ( At PAL2): A potent MIO-enzyme for the synthesis of non-canonical aromatic alpha-amino acids. J Biotechnol 2017; 258:158-166. [DOI: 10.1016/j.jbiotec.2017.04.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/28/2017] [Accepted: 04/28/2017] [Indexed: 11/15/2022]
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20
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Hettle A, Fillo A, Abe K, Massel P, Pluvinage B, Langelaan DN, Smith SP, Boraston AB. Properties of a family 56 carbohydrate-binding module and its role in the recognition and hydrolysis of β-1,3-glucan. J Biol Chem 2017; 292:16955-16968. [PMID: 28827308 DOI: 10.1074/jbc.m117.806711] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/11/2017] [Indexed: 11/06/2022] Open
Abstract
BH0236 from Bacillus halodurans is a multimodular β-1,3-glucanase comprising an N-terminal family 81 glycoside hydrolase catalytic module, an internal family 6 carbohydrate-binding module (CBM) that binds the nonreducing end of β-1,3-glucan chains, and an uncharacterized C-terminal module classified into CBM family 56. Here, we determined that this latter CBM, BhCBM56, bound the soluble β-1,3-glucan laminarin with a dissociation constant (Kd ) of ∼26 μm and displayed higher affinity for insoluble β-1,3-glucans with Kd values of ∼2-10 μm but lacked affinity for β-1,3-glucooligosaccharides. The X-ray crystal structure of BhCBM56 and NMR-derived chemical shift mapping of the binding site revealed a β-sandwich fold, with the face of one β-sheet possessing the β-1,3-glucan-binding surface. On the basis of the functional and structural properties of BhCBM56, we propose that it binds a quaternary polysaccharide structure, most likely the triple helix adopted by polymerized β-1,3-glucans. Consistent with the BhCBM56 and BhCBM6/56 binding profiles, deletion of the CBM56 from BH0236 decreased activity of the enzyme on the insoluble β-1,3-glucan curdlan but not on soluble laminarin; additional deletion of the CBM6 also did not affect laminarin degradation but further decreased curdlan hydrolysis. The pseudo-atomic solution structure of BH0236 determined by small-angle X-ray scattering revealed structural insights into the nature of avid binding by the BhCBM6/56 pair and how the orientation of the active site in the catalytic module factors into recognition and degradation of β-1,3-glucans. Our findings reinforce the notion that catalytic modules and their cognate CBMs have complementary specificities, including targeting of polysaccharide quaternary structure.
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Affiliation(s)
- Andrew Hettle
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
| | - Alexander Fillo
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
| | - Kento Abe
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
| | - Patricia Massel
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
| | - Benjamin Pluvinage
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
| | - David N Langelaan
- the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Steven P Smith
- the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Alisdair B Boraston
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
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21
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Keadtidumrongkul P, Suttangkakul A, Pinmanee P, Pattana K, Kittiwongwattana C, Apisitwanich S, Vuttipongchaikij S. Growth modulation effects of CBM2a under the control of AtEXP4 and CaMV35S promoters in Arabidopsis thaliana, Nicotiana tabacum and Eucalyptus camaldulensis. Transgenic Res 2017; 26:447-463. [PMID: 28349287 DOI: 10.1007/s11248-017-0015-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 03/21/2017] [Indexed: 11/29/2022]
Abstract
The expression of cell-wall-targeted Carbohydrate Binding Modules (CBMs) can alter cell wall properties and modulate growth and development in plants such as tobacco and potato. CBM2a identified in xylanase 10A from Cellulomonas fimi is of particular interest for its ability to bind crystalline cellulose. However, its potential for promoting plant growth has not been explored. In this work, we tested the ability of CBM2a to promote growth when expressed using both CaMV35S and a vascular tissue-specific promoter derived from Arabidopsis expansin4 (AtEXP4) in three plant species: Arabidopsis, Nicotiana tabacum and Eucalyptus camaldulensis. In Arabidopsis, the expression of AtEXP4pro:CBM2a showed trends for growth promoting effects including the increase of root and hypocotyl lengths and the enlargements of the vascular xylem area, fiber cells and vessel cells. However, in N. tabacum, the expression of CBM2a under the control of either CaMV35S or AtEXP4 promoter resulted in subtle changes in the plant growth, and the thickness of secondary xylem and vessel and fiber cell sizes were generally reduced in the transgenic lines with AtEXP4pro:CBM2a. In Eucalyptus, while transgenics expressing CaMV35S:CBM2a showed very subtle changes compared to wild type, those transgenics with AtEXP4pro:CBM2a showed increases in plant height, enlargement of xylem areas and xylem fiber and vessel cells. These data provide comparative effects of expressing CBM2a protein in different plant species, and this finding can be applied for plant biomass improvement.
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Affiliation(s)
- Pornthep Keadtidumrongkul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, Bangkok, 10900, Thailand
| | - Phitsanu Pinmanee
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
| | - Kanokwan Pattana
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
| | - Chokchai Kittiwongwattana
- Department of Biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Chalongkrung Road, Ladkrabang, Bangkok, 10520, Thailand
| | - Somsak Apisitwanich
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, Bangkok, 10900, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand.
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, Bangkok, 10900, Thailand.
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22
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Ezeilo UR, Zakaria II, Huyop F, Wahab RA. Enzymatic breakdown of lignocellulosic biomass: the role of glycosyl hydrolases and lytic polysaccharide monooxygenases. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1330124] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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23
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Yang JK, Xiong W, Chen FY, Xu L, Han ZG. Aromatic amino acids in the cellulose binding domain of Penicillium crustosum endoglucanase EGL1 differentially contribute to the cellulose affinity of the enzyme. PLoS One 2017; 12:e0176444. [PMID: 28475645 PMCID: PMC5419506 DOI: 10.1371/journal.pone.0176444] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/10/2017] [Indexed: 11/29/2022] Open
Abstract
The cellulose binding domain (CBD) of cellulase binding to cellulosic materials is the initiation of a synergistic action on the enzymatic hydrolysis of the most abundant renewable biomass resources in nature. The binding of the CBD domain to cellulosic substrates generally relies on the interaction between the aromatic amino acids structurally located on the flat face of the CBD domain and the glucose rings of cellulose. In this study, we found the CBD domain of a newly cloned Penicillium crustosum endoglucanase EGL1, which was phylogenetically related to Aspergillus, Fusarium and Rhizopus, and divergent from the well-characterized Trichoderma reeseis cellulase CBD domain, contain two conserved aromatic amino acid-rich regions, Y451-Y452 and Y477-Y478-Y479, among which three amino acids Y451, Y477, and Y478 structurally sited on a flat face of this domain. Cellulose binding assays with green fluorescence protein as the marker, adsorption isotherm assays and an isothermal titration calorimetry assays revealed that although these three amino acids participated in this process, the Y451-Y452 appears to contribute more to the cellulose binding than Y477-Y478-Y479. Further glycine scanning mutagenesis and structural modelling revealed that the binding between CBD domain and cellulosic materials might be multi-amino-acids that participated in this process. The flexible poly-glucose molecule could contact Y451, Y477, and Y478 which form the contacting flat face of CBD domain as the typical model, some other amino acids in or outside the flat face might also participate in the interaction. Thus, it is possible that the conserved Y451-Y452 of CBD might have a higher chance of contacting the cellulosic substrates, contributing more to the affinity of CBD than the other amino acids.
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Affiliation(s)
- Jiang-Ke Yang
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
- * E-mail:
| | - Wei Xiong
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Fang-Yuan Chen
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Li Xu
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Zheng-Gang Han
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
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Han GH, Seong W, Fu Y, Yoon PK, Kim SK, Yeom SJ, Lee DH, Lee SG. Leucine zipper-mediated targeting of multi-enzyme cascade reactions to inclusion bodies in Escherichia coli for enhanced production of 1-butanol. Metab Eng 2016; 40:41-49. [PMID: 28038953 DOI: 10.1016/j.ymben.2016.12.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/19/2016] [Accepted: 12/26/2016] [Indexed: 10/20/2022]
Abstract
Metabolons in nature have evolved to facilitate more efficient catalysis of multistep reactions through the co-localization of functionally related enzymes to cellular organelles or membrane structures. To mimic the natural metabolon architecture, we present a novel artificial metabolon that was created by targeting multi-enzyme cascade reactions onto inclusion body (IB) in Escherichia coli. The utility of this system was examined by co-localizing four heterologous enzymes of the 1-butanol pathway onto an IB that was formed in E. coli through overexpression of the cellulose binding domain (CBD) of Cellulomonas fimi exoglucanase. To target the 1-butanol pathway enzymes to the CBD IB, we utilized a peptide-peptide interaction between leucine zipper (LZ) peptides. We genetically fused the LZ peptide to the N-termini of four heterologous genes involved in the synthetic 1-butanol pathway, whereas an antiparallel LZ peptide was fused to the CBD gene. The in vivo activity of the CBD IB-based metabolon was examined through the determination of 1-butanol synthesis using E. coli transformed with two plasmids containing the LZ-fused CBD and LZ-fused 1-butanol pathway genes, respectively. In vivo synthesis of 1-butanol using the engineered E. coli yielded 1.98g/L of 1-butanol from glucose, representing a 1.5-fold increase over that obtained from E. coli expressing the LZ-fused 1-butanol pathway genes alone. In an attempt to examine the in vitro 1-butanol productivity, we reconstituted CBD IB-based metabolon using CBD IB and individual enzymes of 1-butanol pathway. The 1-butanol productivity of in vitro reconstituted CBD IB-based metabolon using acetoacetyl-CoA as the starting material was 2.29mg/L/h, 7.9-fold higher than that obtained from metabolon-free enzymes of 1-butanol pathway. Therefore, this novel CBD-based artificial metabolon may prove useful in metabolic engineering both in vivo and in vitro for the efficient production of desired products.
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Affiliation(s)
- Gui Hwan Han
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Wonjae Seong
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Yaoyao Fu
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Paul K Yoon
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Seong Keun Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Soo-Jin Yeom
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon 34113, Republic of Korea.
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon 34113, Republic of Korea.
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25
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Characterization of a Cellulomonas fimi exoglucanase/xylanase-endoglucanase gene fusion which improves microbial degradation of cellulosic biomass. Enzyme Microb Technol 2016; 93-94:113-121. [DOI: 10.1016/j.enzmictec.2016.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 11/17/2022]
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26
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Campos BM, Liberato MV, Alvarez TM, Zanphorlin LM, Ematsu GC, Barud H, Polikarpov I, Ruller R, Gilbert HJ, Zeri ACDM, Squina FM. A Novel Carbohydrate-binding Module from Sugar Cane Soil Metagenome Featuring Unique Structural and Carbohydrate Affinity Properties. J Biol Chem 2016; 291:23734-23743. [PMID: 27621314 DOI: 10.1074/jbc.m116.744383] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Indexed: 11/06/2022] Open
Abstract
Carbohydrate-binding modules (CBMs) are appended to glycoside hydrolases and can contribute to the degradation of complex recalcitrant substrates such as the plant cell wall. For application in bioethanol production, novel enzymes with high catalytic activity against recalcitrant lignocellulosic material are being explored and developed. In this work, we report the functional and structural study of CBM_E1, which was discovered through a metagenomics approach and is the founding member of a novel CBM family, CBM81. CBM_E1, which is linked to an endoglucanase, displayed affinity for mixed linked β1,3-β1,4-glucans, xyloglucan, Avicel, and cellooligosaccharides. The crystal structure of CBM_E1 in complex with cellopentaose displayed a canonical β-sandwich fold comprising two β-sheets. The planar ligand binding site, observed in a parallel orientation with the β-strands, is a typical feature of type A CBMs, although the expected affinity for bacterial crystalline cellulose was not detected. Conversely, the binding to soluble glucans was enthalpically driven, which is typical of type B modules. These unique properties of CBM_E1 are at the interface between type A and type B CBMs.
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Affiliation(s)
| | | | | | | | | | - Hernane Barud
- the Centro Universitário de Araraquara-UNIARA, BioPolMat, CEP 14801-340, Araraquara-SP, Brazil
| | - Igor Polikarpov
- the Instituto de Física de São Carlos, Universidade de São Paulo, CEP 13566-590, São Carlos, São Paulo, Brazil
| | - Roberto Ruller
- the Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), and
| | - Harry J Gilbert
- the Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle-upon-Tyne NE 4HH, United Kingdom, and
| | - Ana Carolina de Mattos Zeri
- the Laboratório Nacional de Luz Sincrotron (LNLS), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, São Paulo, Brazil
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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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28
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Højgaard C, Kofoed C, Espersen R, Johansson KE, Villa M, Willemoës M, Lindorff-Larsen K, Teilum K, Winther JR. A Soluble, Folded Protein without Charged Amino Acid Residues. Biochemistry 2016; 55:3949-56. [PMID: 27307139 DOI: 10.1021/acs.biochem.6b00269] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Charges are considered an integral part of protein structure and function, enhancing solubility and providing specificity in molecular interactions. We wished to investigate whether charged amino acids are indeed required for protein biogenesis and whether a protein completely free of titratable side chains can maintain solubility, stability, and function. As a model, we used a cellulose-binding domain from Cellulomonas fimi, which, among proteins of more than 100 amino acids, presently is the least charged in the Protein Data Bank, with a total of only four titratable residues. We find that the protein shows a surprising resilience toward extremes of pH, demonstrating stability and function (cellulose binding) in the pH range from 2 to 11. To ask whether the four charged residues present were required for these properties of this protein, we altered them to nontitratable ones. Remarkably, this chargeless protein is produced reasonably well in Escherichia coli, retains its stable three-dimensional structure, and is still capable of strong cellulose binding. To further deprive this protein of charges, we removed the N-terminal charge by acetylation and studied the protein at pH 2, where the C-terminus is effectively protonated. Under these conditions, the protein retains its function and proved to be both soluble and have a reversible folding-unfolding transition. To the best of our knowledge, this is the first time a soluble, functional protein with no titratable side chains has been produced.
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Affiliation(s)
- Casper Højgaard
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Christian Kofoed
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Roall Espersen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Kristoffer Enøe Johansson
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Mara Villa
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Martin Willemoës
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Kaare Teilum
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Jakob R Winther
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
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29
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Abouhmad A, Mamo G, Dishisha T, Amin MA, Hatti-Kaul R. T4 lysozyme fused with cellulose-binding module for antimicrobial cellulosic wound dressing materials. J Appl Microbiol 2016; 121:115-25. [PMID: 27028513 DOI: 10.1111/jam.13146] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 03/13/2016] [Accepted: 03/23/2016] [Indexed: 12/19/2022]
Abstract
AIMS Bacterial infection is a major challenge in wound care. Antimicrobial wound dressings are of great value for treating wound infections. Endolysins are evolving as a new class of antimicrobials with multiple applications. This study describes the production and evaluation of T4 lysozyme (T4Lyz), product of gene e of the T4 bacteriophage, fused with Cellulose Binding Module (CBM) for facile immobilization to cellulosic wound dressing. METHODS AND RESULTS Genes encoding T4Lyz-CBM and T4Lyz were cloned and expressed in Escherichia coli and the enzymes were purified by cation exchange chromatography. While the CBM tag did not alter the optimum pH and stability features of T4Lyz, the lytic activity of the fusion protein was lowered. The bactericidal activity of T4Lyz-CBM, determined by viable count plating assay after 1 h incubation with Micrococcus lysodeikticus was 97·5% with 10 μg ml(-1) , and 99·96% and 95% for E. coli and Pseudomonas mendocina, respectively, with 200 μg ml(-1) enzyme. T4Lyz-CBM was immobilized to wound dressing gauze with a capacity of 5·5 μg mg(-1) matrix, whereas the unmodified T4Lyz did not exhibit any binding. The immobilized protein retained its bactericidal activity against Gram-positive and Gram-negative bacteria. Both free and immobilized T4Lyz-CBM, after heat denaturation, retained their bactericidal activities against Gram-negative bacteria only. The immobilized enzyme exhibited higher stability than the free enzyme when stored in dry form or in the presence of polyol stabilizers. CONCLUSION Tagging T4Lyz with CBM provides a facile, irreversible binding to cellulosic wound dressing while retaining its activity. This approach may be suitable even for other antimicrobial enzymes and -peptides. SIGNIFICANCE AND IMPACT OF THE STUDY The spread of antibiotic resistance requires innovative strategies for discovery and development of effective antimicrobial alternatives. This report presents a novel strategy for producing antimicrobial wound dressing materials.
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Affiliation(s)
- A Abouhmad
- Division of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, Lund, Sweden.,Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
| | - G Mamo
- Division of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - T Dishisha
- Division of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, Lund, Sweden.,Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - M A Amin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - R Hatti-Kaul
- Division of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
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30
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Crouch LI, Labourel A, Walton PH, Davies GJ, Gilbert HJ. The Contribution of Non-catalytic Carbohydrate Binding Modules to the Activity of Lytic Polysaccharide Monooxygenases. J Biol Chem 2016; 291:7439-49. [PMID: 26801613 PMCID: PMC4817175 DOI: 10.1074/jbc.m115.702365] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Indexed: 01/23/2023] Open
Abstract
Lignocellulosic biomass is a sustainable industrial substrate. Copper-dependent lytic polysaccharide monooxygenases (LPMOs) contribute to the degradation of lignocellulose and increase the efficiency of biofuel production. LPMOs can contain non-catalytic carbohydrate binding modules (CBMs), but their role in the activity of these enzymes is poorly understood. Here we explored the importance of CBMs in LPMO function. The family 2a CBMs of two monooxygenases,CfLPMO10 andTbLPMO10 fromCellulomonas fimiandThermobispora bispora, respectively, were deleted and/or replaced with CBMs from other proteins. The data showed that the CBMs could potentiate and, surprisingly, inhibit LPMO activity, and that these effects were both enzyme-specific and substrate-specific. Removing the natural CBM or introducingCtCBM3a, from theClostridium thermocellumcellulosome scaffoldin CipA, almost abolished the catalytic activity of the LPMOs against the cellulosic substrates. The deleterious effect of CBM removal likely reflects the importance of prolonged presentation of the enzyme on the surface of the substrate for efficient catalytic activity, as only LPMOs appended to CBMs bound tightly to cellulose. The negative impact ofCtCBM3a is in sharp contrast with the capacity of this binding module to potentiate the activity of a range of glycoside hydrolases including cellulases. The deletion of the endogenous CBM fromCfLPMO10 or the introduction of a family 10 CBM fromCellvibrio japonicusLPMO10B intoTbLPMO10 influenced the quantity of non-oxidized products generated, demonstrating that CBMs can modulate the mode of action of LPMOs. This study demonstrates that engineered LPMO-CBM hybrids can display enhanced industrially relevant oxygenations.
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Affiliation(s)
- Lucy I Crouch
- From the Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Newcastle upon Tyne NE2 4HH and
| | - Aurore Labourel
- From the Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Newcastle upon Tyne NE2 4HH and
| | - Paul H Walton
- the York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Gideon J Davies
- the York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Harry J Gilbert
- From the Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Newcastle upon Tyne NE2 4HH and
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31
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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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Nishijima H, Nozaki K, Mizuno M, Arai T, Amano Y. Extra tyrosine in the carbohydrate-binding module of Irpex lacteus Xyn10B enhances its cellulose-binding ability. Biosci Biotechnol Biochem 2015; 79:738-46. [PMID: 25560084 DOI: 10.1080/09168451.2014.996203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The xylanase (Xyn10B) that strongly adsorbs on microcrystalline cellulose was isolated from Driselase. The Xyn10B contains a Carbohydrate-binding module family 1 (CBM1) (IrpCBMXyn10B) at N-terminus. The canonical essential aromatic residues required for cellulose binding were conserved in IrpCBMXyn10B; however, its adsorption ability was markedly higher than that typically observed for the CBM1 of an endoglucanase from Trametes hirsuta (ThCBMEG1). An analysis of the CBM-GFP fusion proteins revealed that the binding capacity to cellulose (7.8 μmol/g) and distribution coefficient (2.0 L/μmol) of IrpCBMXyn10B-GFP were twofold higher than those of ThCBMEG1-GFP (3.4 μmol/g and 1.2 L/μmol, respectively), used as a reference structure. Besides the canonical aromatic residues (W24-Y50-Y51) of typical CBM1-containing proteins, IrpCBMXyn10B had an additional aromatic residue (Y52). The mutation of Y52 to Ser (IrpCBMY52S-GFP) reduced these adsorption parameters to 4.4 μmol/g and 1.5 L/μmol, which were similar to those of ThCBMEG1-GFP. These results indicate that Y52 plays a crucial role in strong cellulose binding.
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Affiliation(s)
- Hiroto Nishijima
- a Department of Bioscience & Textile Technology, Interdisciplinary Graduate School of Science and Technology , Shinshu University , Nagano , Japan
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33
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von Schantz L, Håkansson M, Logan DT, Nordberg-Karlsson E, Ohlin M. Carbohydrate binding module recognition of xyloglucan defined by polar contacts with branching xyloses and CH-Π interactions. Proteins 2014; 82:3466-75. [PMID: 25302425 DOI: 10.1002/prot.24700] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 09/03/2014] [Accepted: 09/19/2014] [Indexed: 12/13/2022]
Abstract
Engineering of novel carbohydrate-binding proteins that can be utilized in various biochemical and biotechnical applications would benefit from a deeper understanding of the biochemical interactions that determine protein-carbohydrate specificity. In an effort to understand further the basis for specificity we present the crystal structure of the multi-specific carbohydrate-binding module (CBM) X-2 L110F bound to a branched oligomer of xyloglucan (XXXG). X-2 L110F is an engineered CBM that can recognize xyloglucan, xylans and β-glucans. The structural observations of the present study compared with previously reported structures of X-2 L110F in complex with linear oligomers, show that the π-surface of a phenylalanine, F110, allows for interactions with hydrogen atoms on both linear (xylopentaose and cellopentaose) and branched ligands (XXXG). Furthermore, X-2 L110F is shown to have a relatively flexible binding cleft, as illustrated in binding to XXXG. This branched ligand requires a set of reorientations of protein side chains Q72, N31, and R142, although these residues have previously been determined as important for binding to xylose oligomers by mediating polar contacts. The loss of these polar contacts is compensated for in binding to XXXG by polar interactions mediated by other protein residues, T74, R115, and Y149, which interact mainly with the branching xyloses of the xyloglucan oligomer. Taken together, the present study illustrates in structural detail how CH-π interactions can influence binding specificity and that flexibility is a key feature for the multi-specificity displayed by X-2 L110F, allowing for the accommodation of branched ligands.
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Affiliation(s)
- Laura von Schantz
- Department of Immunotechnology, Lund University, Medicon Village, SE-223 81 Lund, Sweden
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34
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Fuenzalida JP, Weikert T, Hoffmann S, Vila-Sanjurjo C, Moerschbacher BM, Goycoolea FM, Kolkenbrock S. Affinity protein-based FRET tools for cellular tracking of chitosan nanoparticles and determination of the polymer degree of acetylation. Biomacromolecules 2014; 15:2532-9. [PMID: 24835451 DOI: 10.1021/bm500394v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chitosan (CS) is a family of linear polysaccharides with diverse applications in medicine, agriculture, and industry. Its bioactive properties are determined by parameters such as the degree of acetylation (DA), but current techniques to measure the DA are laborious and require large amounts of substrate and sophisticated equipment. It is also challenging to monitor the fate of chitosan-based nanoparticles (CS-NPs) in vitro because current tools cannot measure their enzymatic or chemical degradation. We have developed a method based on the Förster resonance energy transfer (FRET) that occurs between two independent fluorescent proteins fused to a CS-binding domain, who interact with CS polymers or CS-NPs. We used this approach to calibrate a simple and rapid analytical method that can determine the DA of CS substrates. We showed unequivocally that FRET occurs on the surface of CS-NPs and that the FRET signal is quenched by enzymatic degradation of the CS substrate. Finally, we provide in vitro proof-of-concept that these approaches can be used to label CS-NPs and colocalize them following their interactions with mammalian cells.
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Affiliation(s)
- J P Fuenzalida
- IBBP, Westfälische Wilhelms-Universität Münster Schlossgarten 3, 48149, Münster, Germany
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Choi SL, Lee SJ, Yeom SJ, Kim HJ, Rhee YH, Jung HC, Lee SG. Controlled localization of functionally active proteins to inclusion bodies using leucine zippers. PLoS One 2014; 9:e97093. [PMID: 24897378 PMCID: PMC4045587 DOI: 10.1371/journal.pone.0097093] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 04/14/2014] [Indexed: 11/23/2022] Open
Abstract
Inclusion bodies (IBs) are typically non-functional particles of aggregated proteins. However, some proteins in fusion with amyloid-like peptides, viral coat proteins, and cellulose binding domains (CBDs) generate IB particles retaining the original functions in cells. Here, we attempted to generate CBD IBs displaying functional leucine zipper proteins (LZs) as bait for localizing cytosolic proteins in E. coli. When a red fluorescent protein was tested as a target protein, microscopic observations showed that the IBs red-fluoresced strongly. When different LZ pairs with KDs of 8–1,000 µM were tested as the bait and prey, the localization of the red fluorescence appeared to change following the affinities between the LZs, as observed by fluorescence imaging and flow cytometry. This result proposed that LZ-tagged CBD IBs can be applied as an in vivo matrix to entrap cytosolic proteins in E. coli while maintaining their original activities. In addition, easy detection of localization to IBs provides a unique platform for the engineering and analyses of protein-protein interactions in E. coli.
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Affiliation(s)
- Su-Lim Choi
- Biochemicals and Synthetic Biology Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
- Department of Bioscience and Biotechnology, Chungnam National University, Yuseong-gu, Daejeon, Korea
| | - Sang Jun Lee
- Infection and Immunity Biology Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
- Korea University of Science and Technology, Yuseong-gu, Daejeon, Korea
| | - Soo-Jin Yeom
- Biochemicals and Synthetic Biology Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
| | - Hyun Ju Kim
- Infection and Immunity Biology Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
- Korea University of Science and Technology, Yuseong-gu, Daejeon, Korea
| | - Young Ha Rhee
- Department of Bioscience and Biotechnology, Chungnam National University, Yuseong-gu, Daejeon, Korea
| | - Heung-Chae Jung
- Biochemicals and Synthetic Biology Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
| | - Seung-Goo Lee
- Biochemicals and Synthetic Biology Research Center, KRIBB, Yuseong-gu, Daejeon, Korea
- Korea University of Science and Technology, Yuseong-gu, Daejeon, Korea
- * E-mail:
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Lim S, Chundawat SP, Fox BG. Expression, purification and characterization of a functional carbohydrate-binding module from Streptomyces sp. SirexAA-E. Protein Expr Purif 2014; 98:1-9. [DOI: 10.1016/j.pep.2014.02.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/23/2014] [Accepted: 02/25/2014] [Indexed: 11/25/2022]
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Bianchetti CM, Brumm P, Smith RW, Dyer K, Hura GL, Rutkoski TJ, Phillips GN. Structure, dynamics, and specificity of endoglucanase D from Clostridium cellulovorans. J Mol Biol 2013; 425:4267-85. [PMID: 23751954 PMCID: PMC4039632 DOI: 10.1016/j.jmb.2013.05.030] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 05/22/2013] [Accepted: 05/30/2013] [Indexed: 11/17/2022]
Abstract
The enzymatic degradation of cellulose is a critical step in the biological conversion of plant biomass into an abundant renewable energy source. An understanding of the structural and dynamic features that cellulases utilize to bind a single strand of crystalline cellulose and hydrolyze the β-1,4-glycosidic bonds of cellulose to produce fermentable sugars would greatly facilitate the engineering of improved cellulases for the large-scale conversion of plant biomass. Endoglucanase D (EngD) from Clostridium cellulovorans is a modular enzyme comprising an N-terminal catalytic domain and a C-terminal carbohydrate-binding module, which is attached via a flexible linker. Here, we present the 2.1-Å-resolution crystal structures of full-length EngD with and without cellotriose bound, solution small-angle X-ray scattering (SAXS) studies of the full-length enzyme, the characterization of the active cleft glucose binding subsites, and substrate specificity of EngD on soluble and insoluble polymeric carbohydrates. SAXS data support a model in which the linker is flexible, allowing EngD to adopt an extended conformation in solution. The cellotriose-bound EngD structure revealed an extended active-site cleft that contains seven glucose-binding subsites, but unlike the majority of structurally determined endocellulases, the active-site cleft of EngD is partially enclosed by Trp162 and Tyr232. EngD variants, which lack Trp162, showed a significant reduction in activity and an alteration in the distribution of cellohexaose degradation products, suggesting that Trp162 plays a direct role in substrate binding.
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Affiliation(s)
- Christopher M. Bianchetti
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706, USA
| | - Phillip Brumm
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706, USA
- Lucigen Corporation and C5-6 Technologies, Madison WI 53562, USA
| | - Robert W. Smith
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706, USA
| | - Kevin Dyer
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Greg L. Hura
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Thomas J. Rutkoski
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706, USA
| | - George N. Phillips
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706, USA
- Department of Biochemistry and Cell Biology Rice University, Houston, TX 77005
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Ahmed S, Luís AS, Brás JLA, Fontes CMGA, Goyal A. Functional and structural characterization of family 6 carbohydrate-binding module (CtCBM6A) of Clostridium thermocellum α-L-arabinofuranosidase. BIOCHEMISTRY (MOSCOW) 2013; 78:1272-9. [DOI: 10.1134/s0006297913110072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Zhang M, Wang B, Xu B. Measurements of single molecular affinity interactions between carbohydrate-binding modules and crystalline cellulose fibrils. Phys Chem Chem Phys 2013; 15:6508-15. [PMID: 23532050 DOI: 10.1039/c3cp51072g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Combining atomic force microscopy (AFM) recognition imaging and single molecule dynamic force spectroscopy (SMDFS), we studied the single molecule affinity interactions between the carbohydrate-binding module (CBM) and plant cell wall cellulose using the CBM3a (from Clostridium thermocellum) and CBM2a (from Cellvibrio japonicus) functionalized AFM tips. The binding efficiencies of the CBMs to the cellulose were determined by the binding areas on the crystalline cellulose fibrils surface using the recognition imaging. Several dynamic and kinetic parameters, such as the reconstructed free energy change, energy barrier and bond lifetime constant, were also obtained based on the measured single molecule unbinding forces, which are used to illuminate the affinity of the CBMs binding to the natural and single cellulose surface from a totally different aspect. It was found that CBM3a has a little higher binding efficiency and affinity than CBM2a to both natural and extracted cellulose surfaces and both the CBMs have higher affinities to the natural cell wall cellulose compared to the extracted single cellulose. The in-depth understanding of the binding mechanisms of the CBM-cellulose interactions of this study may pave the way for more efficient plant cell wall degradation and eventually facilitate biofuel production.
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Affiliation(s)
- Mengmeng Zhang
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, GA 30602, USA
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40
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Engineering chimeric thermostable GH7 cellobiohydrolases in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2013; 98:2991-3001. [DOI: 10.1007/s00253-013-5177-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/29/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
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Liu L, Shang-Guan K, Zhang B, Liu X, Yan M, Zhang L, Shi Y, Zhang M, Qian Q, Li J, Zhou Y. Brittle Culm1, a COBRA-like protein, functions in cellulose assembly through binding cellulose microfibrils. PLoS Genet 2013; 9:e1003704. [PMID: 23990797 PMCID: PMC3749933 DOI: 10.1371/journal.pgen.1003704] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 06/22/2013] [Indexed: 11/30/2022] Open
Abstract
Cellulose represents the most abundant biopolymer in nature and has great economic importance. Cellulose chains pack laterally into crystalline forms, stacking into a complicated crystallographic structure. However, the mechanism of cellulose crystallization is poorly understood. Here, via functional characterization, we report that Brittle Culm1 (BC1), a COBRA-like protein in rice, modifies cellulose crystallinity. BC1 was demonstrated to be a glycosylphosphatidylinositol (GPI) anchored protein and can be released into cell walls by removal of the GPI anchor. BC1 possesses a carbohydrate-binding module (CBM) at its N-terminus. In vitro binding assays showed that this CBM interacts specifically with crystalline cellulose, and several aromatic residues in this domain are essential for binding. It was further demonstrated that cell wall-localized BC1 via the CBM and GPI anchor is one functional form of BC1. X-ray diffraction (XRD) assays revealed that mutations in BC1 and knockdown of BC1 expression decrease the crystallite width of cellulose; overexpression of BC1 and the CBM-mutated BC1s caused varied crystallinity with results that were consistent with the in vitro binding assay. Moreover, interaction between the CBM and cellulose microfibrils was largely repressed when the cell wall residues were pre-stained with two cellulose dyes. Treating wild-type and bc1 seedlings with the dyes resulted in insensitive root growth responses in bc1 plants. Combined with the evidence that BC1 and three secondary wall cellulose synthases (CESAs) function in different steps of cellulose production as revealed by genetic analysis, we conclude that BC1 modulates cellulose assembly by interacting with cellulose and affecting microfibril crystallinity. Cellulose is an important natural resource with great economic value. Plant cellulose packs laterally into a complicated crystallographic structure, which determines cellulose quality and commercial uses. However, the mechanism of cellulose crystallization is poorly understood. Here we report that Brittle Culm1 (BC1), a COBRA-like (COBL) protein of rice, modifies cellulose crystallinity. Although previous studies have indicated the involvement of COB and COBL proteins in cellulose biosynthesis, the underlying molecular basis for this remains elusive. We demonstrate that BC1 localizes to the cell-wall and functions in a process that is distinct from that of the three secondary wall cellulose synthases (CESAs). A carbohydrate-binding module (CBM) at the N-terminus of BC1 interacts specifically with crystalline cellulose and regulates microfibril crystallite size. We conclude that BC1 modulates cellulose structure by binding to cellulose and affecting microfibril crystallinity. These findings provide new insights into the mechanism of cellulose assembly and further our understanding of the roles of COB and COBLs in cell wall biogenesis.
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Affiliation(s)
- Lifeng Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Keke Shang-Guan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Baocai Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiangling Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Meixian Yan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Lanjun Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yanyun Shi
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mu Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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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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Kim HD, Choi SL, Kim H, Sohn JH, Lee SG. Enzyme-linked assay of cellulose-binding domain functions from Cellulomonas fimi on multi-well microtiter plate. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-013-0242-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Guo J, Catchmark JM. Binding Specificity and Thermodynamics of Cellulose-Binding Modules from Trichoderma reesei Cel7A and Cel6A. Biomacromolecules 2013; 14:1268-77. [DOI: 10.1021/bm300810t] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Jing Guo
- Intercollege
Graduate Degree Program in Plant Biology, §Department of Agricultural and Biological
Engineering, ‡Center for NanoCellulosics, The Pennsylvania State University, University Park, Pennsylvania 16802,
United States
| | - Jeffrey M. Catchmark
- Intercollege
Graduate Degree Program in Plant Biology, §Department of Agricultural and Biological
Engineering, ‡Center for NanoCellulosics, The Pennsylvania State University, University Park, Pennsylvania 16802,
United States
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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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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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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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50
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Gourlay K, Arantes V, Saddler JN. Use of substructure-specific carbohydrate binding modules to track changes in cellulose accessibility and surface morphology during the amorphogenesis step of enzymatic hydrolysis. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:51. [PMID: 22828270 PMCID: PMC3432595 DOI: 10.1186/1754-6834-5-51] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 07/02/2012] [Indexed: 05/05/2023]
Abstract
BACKGROUND Cellulose amorphogenesis, described as the non-hydrolytic "opening up" or disruption of a cellulosic substrate, is becoming increasingly recognized as one of the key steps in the enzymatic deconstruction of cellulosic biomass when used as a feedstock for fuels and chemicals production. Although this process is thought to play a major role in facilitating hydrolysis, the lack of quantitative techniques capable of accurately describing the molecular-level changes occurring in the substrate during amorphogenesis has hindered our understanding of this process. RESULTS In this work, techniques for measuring changes in cellulose accessibility are reviewed and a new quantitative assay method is described. Carbohydrate binding modules (CBMs) with specific affinities for crystalline (CBM2a) or amorphous (CBM44) cellulose were used to track specific changes in the surface morphology of cotton fibres during amorphogenesis. The extents of phosphoric acid-induced and Swollenin-induced changes to cellulose accessibility were successfully quantified using this technique. CONCLUSIONS The adsorption of substructure-specific CBMs can be used to accurately quantify the extent of changes to cellulose accessibility induced by non-hydrolytic disruptive proteins. The technique provided a quick, accurate and quantitative measure of the accessibility of cellulosic substrates. Expanding the range of CBMs used for adsorption studies to include those specific for such compounds as xylan or mannan should also allow for the accurate quantitative tracking of the accessibility of these and other polymers within the lignocellulosic biomass matrix.
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Affiliation(s)
- Keith Gourlay
- Forest Products Biotechnology/Bioenergy Group, Department of Wood Science, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Valdeir Arantes
- Forest Products Biotechnology/Bioenergy Group, Department of Wood Science, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jack N Saddler
- Forest Products Biotechnology/Bioenergy Group, Department of Wood Science, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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