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Heng S, Sutheeworapong S, Wangnai C, Champreda V, Kosugi A, Ratanakhanokchai K, Tachaapaikoon C, Ceballos RM. Hydrolysis of ionic liquid-treated substrate with an Iocasia fonsfrigidae strain SP3-1 endoglucanase. Appl Microbiol Biotechnol 2024; 108:63. [PMID: 38189956 PMCID: PMC10774164 DOI: 10.1007/s00253-023-12918-1] [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: 07/26/2023] [Revised: 12/04/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024]
Abstract
Recently, we reported the discovery of a novel endoglucanase of the glycoside hydrolase family 12 (GH12), designated IfCelS12A, from the haloalkaliphilic anaerobic bacterium Iocasia fonsfrigidae strain SP3-1, which was isolated from a hypersaline pond in the Samut Sakhon province of Thailand (ca. 2017). IfCelS12A exhibits high substrate specificity on carboxymethyl cellulose and amorphous cellulose but low substrate specificity on b-1,3;1,4-glucan. Unlike some endoglucanases of the GH12 family, IfCelS12A does not exhibit hydrolytic activity on crystalline cellulose (i.e., Avicel™). High-Pressure Liquid Chromatography (HPLC) and Thin Layer Chromatography (TLC) analyses of products resulting from IfCelS12-mediated hydrolysis indicate mode of action for this enzyme. Notably, IfCelS12A preferentially hydrolyzes cellotetraoses, cellopentaoses, and cellohexaoses with negligible activity on cellobiose or cellotriose. Kinetic analysis with cellopentaose and barely b-D-glucan as cellulosic substrates were conducted. On cellopentaose, IfCelS12A demonstrates a 16-fold increase in activity (KM = 0.27 mM; kcat = 0.36 s-1; kcat/KM = 1.34 mM-1 s-1) compared to the enzymatic hydrolysis of barley b-D-glucan (KM: 0.04 mM, kcat: 0.51 s-1, kcat/KM = 0.08 mM-1 s-1). Moreover, IfCelS12A enzymatic efficacy is stable in hypersaline sodium chlorids (NaCl) solutions (up to 10% NaCl). Specifically, IfCel12A retains notable activity after 24 h at 2M NaCl (10% saline solution). IfCelS12A used as a cocktail component with other cellulolytic enzymes and in conjunction with mobile sequestration platform technology offers additional options for deconstruction of ionic liquid-pretreated cellulosic feedstock. KEY POINTS: • IfCelS12A from an anaerobic alkaliphile Iocasia fronsfrigidae shows salt tolerance • IfCelS12A in cocktails with other enzymes efficiently degrades cellulosic biomass • IfCelS12A used with mobile enzyme sequestration platforms enhances hydrolysis.
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Affiliation(s)
- Sobroney Heng
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
- Department of Molecular and Cell Biology, University of California, Merced, CA, 95343, USA
| | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Laboratory, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chinnapong Wangnai
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road Klong Luang, Pathumthani, 12120, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
| | - Ruben Michael Ceballos
- Department of Molecular and Cell Biology, University of California, Merced, CA, 95343, USA.
- Quantitative Systems Biology Program, University of California, Merced, CA, 95343, USA.
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Tayi L, Nathawat R, Kumar S, Maku RV, Patel HK, Sankaranarayanan R, Sonti RV. Mutational analysis of predicted active site residues of an exoglucanase secreted by Xanthomonas oryzae pv. oryzae to determine their role in catalysis and in virulence on rice. Enzyme Microb Technol 2024; 174:110372. [PMID: 38104475 DOI: 10.1016/j.enzmictec.2023.110372] [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: 10/11/2023] [Revised: 12/04/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight disease in rice. As a part of its virulence repertoire, Xoo secretes a cell wall degrading enzyme Cellobiosidase (CbsA), which is a critical virulence factor and also a determinant of tissue specificity. CbsA protein is made up of an N-terminal catalytic domain and a C-terminal fibronectin type III domain. According to the CAZy classification, the catalytic domain of CbsA protein belongs to the glycosyl hydrolase-6 (GH6) family that performs acid-base catalysis. However, the identity of the catalytic acid and the catalytic base of CbsA is not known. Based on the available structural and biochemical data, we identified putative catalytic residues and probed them by site-directed mutagenesis. Intriguingly, the biochemical analysis showed that none of the mutations abolishes the catalytic activity of CbsA, an observation that is contrary to other GH6 family members. All the mutants exhibited altered enzymatic activity and caused significant virulence deficiency in Xoo emphasising the requirement of specific exoglucanase activity of wild-type CbsA for virulence on rice. Our study highlights the need for further studies and the detailed characterisation of bacterial exoglucanases.
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Affiliation(s)
- Lavanya Tayi
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500007, India
| | - Rajkanwar Nathawat
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500007, India
| | - Sushil Kumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500007, India
| | - Roshan V Maku
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500007, India
| | - Hitendra Kumar Patel
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500007, India
| | - Rajan Sankaranarayanan
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500007, India.
| | - Ramesh V Sonti
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500007, India.
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Ashcroft E, Munoz-Munoz J. A review of the principles and biotechnological applications of glycoside hydrolases from extreme environments. Int J Biol Macromol 2024; 259:129227. [PMID: 38185295 DOI: 10.1016/j.ijbiomac.2024.129227] [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: 07/28/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
It is apparent that Biocatalysts are shaping the future by providing a more sustainable approach to established chemical processes. Industrial processes rely heavily on the use of toxic compounds and high energy or pH reactions, factors that both contributes to the worsening climate crisis. Enzymes found in bacterial systems and other microorganisms, from the glaciers of the Arctic to the sandy deserts of Abu Dhabi, provide key tools and understanding as to how we can progress in the biotechnology sector. These extremophilic bacteria harness the adaptive enzymes capable of withstanding harsh reaction conditions in terms of stability and reactivity. Carbohydrate-active enzymes, including glycoside hydrolases or carbohydrate esterases, are extremely beneficial for the presence and future of biocatalysis. Their involvement in the industry spans from laundry detergents to paper and pulp treatment by degrading oligo/polysaccharides into their monomeric products in almost all detrimental environments. This includes exceedingly high temperatures, pHs or even in the absence of water. In this review, we discuss the structure and function of different glycoside hydrolases from extremophiles, and how they can be applied to industrial-scale reactions to replace the use of harsh chemicals, reduce waste, or decrease energy consumption.
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Affiliation(s)
- Ellie Ashcroft
- Microbial Enzymology Lab, Department of Applied Sciences, Ellison Building A, Northumbria University, Newcastle Upon Tyne NE1 8ST, United Kingdom.
| | - Jose Munoz-Munoz
- Microbial Enzymology Lab, Department of Applied Sciences, Ellison Building A, Northumbria University, Newcastle Upon Tyne NE1 8ST, United Kingdom.
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Tsudome M, Tachioka M, Miyazaki M, Uchimura K, Tsuda M, Takaki Y, Deguchi S. An ultrasensitive nanofiber-based assay for enzymatic hydrolysis and deep-sea microbial degradation of cellulose. iScience 2022; 25:104732. [PMID: 36039358 PMCID: PMC9418596 DOI: 10.1016/j.isci.2022.104732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/10/2022] [Accepted: 07/02/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mikiko Tsudome
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Mikako Tachioka
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Masayuki Miyazaki
- SUGAR Program, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Kohsuke Uchimura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Miwako Tsuda
- SUGAR Program, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yoshihiro Takaki
- SUGAR Program, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Shigeru Deguchi
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Corresponding author
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Metagenomic mining and structure-function studies of a hyper-thermostable cellobiohydrolase from hot spring sediment. Commun Biol 2022; 5:247. [PMID: 35318423 PMCID: PMC8940973 DOI: 10.1038/s42003-022-03195-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/25/2022] [Indexed: 11/09/2022] Open
Abstract
Enzymatic breakdown is an attractive cellulose utilisation method with a low environmental load. Its high temperature operation could promote saccharification and lower contamination risk. Here we report a hyper-thermostable cellobiohydrolase (CBH), named HmCel6A and its variant HmCel6A-3SNP that were isolated metagenomically from hot spring sediments and expressed in Escherichia coli. They are classified into glycoside hydrolases family 6 (GH6). HmCel6A-3SNP had three amino acid replacements to HmCel6A (P88S/L230F/F414S) and the optimum temperature at 95 °C, while HmCel6A did it at 75 °C. Crystal structure showed conserved features among GH6, a (β/α)8-barrel core and catalytic residues, and resembles TfCel6B, a bacterial CBH II of Thermobifida fusca, that had optimum temperature at 60 °C. From structure-function studies, we discuss unique structural features that allow the enzyme to reach its high thermostability level, such as abundance of hydrophobic and charge-charge interactions, characteristic metal bindings and disulphide bonds. Moreover, structure and surface plasmon resonance analysis with oligosaccharides suggested that the contribution of an additional tryptophan located at the tunnel entrance could aid in substrate recognition and thermostability. These results may help to design efficient enzymes and saccharification methods for cellulose working at high temperatures. Bacteria from hot springs are known for highly thermostable enzymes, which may have industrial potential. Here, a unique thermostable cellobiohydrolase is reported that can breakdown cellulose at temperature up to 95 degrees Celsius.
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Zheng Y, Maruoka M, Nanatani K, Hidaka M, Abe N, Kaneko J, Sakai Y, Abe K, Yokota A, Yabe S. High cellulolytic potential of the Ktedonobacteria lineage revealed by genome-wide analysis of CAZymes. J Biosci Bioeng 2021; 131:622-630. [PMID: 33676867 DOI: 10.1016/j.jbiosc.2021.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/10/2021] [Accepted: 01/27/2021] [Indexed: 12/16/2022]
Abstract
Traditionally, filamentous fungi and actinomycetes are well-known cellulolytic microorganisms that have been utilized in the commercial production of cellulase enzyme cocktails for industrial-scale degradation of plant biomass. Noticeably, the Ktedonobacteria lineage (phylum Chloroflexi) with actinomycetes-like morphology was identified and exhibited diverse carbohydrate utilization or degradation abilities. In this study, we performed genome-wide profiling of carbohydrate-active enzymes (CAZymes) in the filamentous Ktedonobacteria lineage. Numerous CAZymes (153-290 CAZymes, representing 63-131 glycoside hydrolases (GHs) per genome), including complex mixtures of endo- and exo-cellulases, were predicted in 15 available Ktedonobacteria genomes. Of note, 4-28 CAZymes were predicted to be extracellular enzymes, whereas 3-29 CAZymes were appended with carbohydrate-binding modules (CBMs) that may promote their binding to insoluble carbohydrate substrates. This number far exceeded other Chloroflexi lineages and were comparable to the cellulolytic actinomycetes. Six multi-modular extracellular GHs were cloned from the thermophilic Thermosporothrix hazakensis SK20-1T strain and heterologously expressed. The putative endo-glucanases of ThazG5-1, ThazG9, and ThazG12 exhibited strong cellulolytic activity, whereas the putative exo-glucanases ThazG6 and ThazG48 formed weak but observable halos on carboxymethyl cellulose plates, indicating their potential biotechnological application. The purified recombinant ThazG12 had near-neutral pH (optimal 6.0), high thermostability (60°C), and broad specificity against soluble and insoluble polysaccharide substrates. It also represented described a novel thermostable bacterial β-1,4-glucanase in the GH12 family. Together, this research revealed the underestimated cellulolytic potential of the Ktedonobacteria lineage and highlighted its potential biotechnological utility as a promising microbial resource for the discovery of industrially useful cellulases.
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Affiliation(s)
- Yu Zheng
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan; Department of Microbial Biotechnology, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Mayumi Maruoka
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan; Department of Microbial Biotechnology, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Kei Nanatani
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Masafumi Hidaka
- Department of Molecular and Cell Biology, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Naoki Abe
- Department of Microbial Biotechnology, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Jun Kaneko
- Department of Microbial Biotechnology, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Yasuteru Sakai
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan; Hazaka Plant Research Center, Kennan Eisei Kogyo Co., Ltd., 44 Aza Inariyama, Oaza Ashitate, Murata-cho, Shibata-gun, Miyagi 989-1311, Japan
| | - Keietsu Abe
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan; Department of Microbial Biotechnology, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Akira Yokota
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan; Hazaka Plant Research Center, Kennan Eisei Kogyo Co., Ltd., 44 Aza Inariyama, Oaza Ashitate, Murata-cho, Shibata-gun, Miyagi 989-1311, Japan
| | - Shuhei Yabe
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan; Hazaka Plant Research Center, Kennan Eisei Kogyo Co., Ltd., 44 Aza Inariyama, Oaza Ashitate, Murata-cho, Shibata-gun, Miyagi 989-1311, Japan.
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Nakamura A, Ishiwata D, Visootsat A, Uchiyama T, Mizutani K, Kaneko S, Murata T, Igarashi K, Iino R. Domain architecture divergence leads to functional divergence in binding and catalytic domains of bacterial and fungal cellobiohydrolases. J Biol Chem 2020; 295:14606-14617. [PMID: 32816991 PMCID: PMC7586223 DOI: 10.1074/jbc.ra120.014792] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/15/2020] [Indexed: 01/09/2023] Open
Abstract
Cellobiohydrolases directly convert crystalline cellulose into cellobiose and are of biotechnological interest to achieve efficient biomass utilization. As a result, much research in the field has focused on identifying cellobiohydrolases that are very fast. Cellobiohydrolase A from the bacterium Cellulomonas fimi (CfCel6B) and cellobiohydrolase II from the fungus Trichoderma reesei (TrCel6A) have similar catalytic domains (CDs) and show similar hydrolytic activity. However, TrCel6A and CfCel6B have different cellulose-binding domains (CBDs) and linkers: TrCel6A has a glycosylated peptide linker, whereas CfCel6B's linker consists of three fibronectin type 3 domains. We previously found that TrCel6A's linker plays an important role in increasing the binding rate constant to crystalline cellulose. However, it was not clear whether CfCel6B's linker has similar function. Here we analyze kinetic parameters of CfCel6B using single-molecule fluorescence imaging to compare CfCel6B and TrCel6A. We find that CBD is important for initial binding of CfCel6B, but the contribution of the linker to the binding rate constant or to the dissociation rate constant is minor. The crystal structure of the CfCel6B CD showed longer loops at the entrance and exit of the substrate-binding tunnel compared with TrCel6A CD, which results in higher processivity. Furthermore, CfCel6B CD showed not only fast surface diffusion but also slow processive movement, which is not observed in TrCel6A CD. Combined with the results of a phylogenetic tree analysis, we propose that bacterial cellobiohydrolases are designed to degrade crystalline cellulose using high-affinity CBD and high-processivity CD.
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Affiliation(s)
- Akihiko Nakamura
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, Shizuoka, Shizuoka, Japan.
| | - Daiki Ishiwata
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Akasit Visootsat
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Taku Uchiyama
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Kenji Mizutani
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, Japan
| | - Satoshi Kaneko
- Department of Subtropical Biochemistry and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Ryota Iino
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.
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8
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Abstract
Some cellulases exhibit “processivity”: the ability to degrade crystalline cellulose through successive hydrolytic catalytic reactions without the release of the enzyme from the substrate surface. We previously observed the movement of fungal processive cellulases by high-speed atomic force microscopy, and here, we use the same technique to directly observe the processive movement of bacterial cellobiohydrolases settling a long-standing controversy. Although fungal and bacterial processive cellulases have completely different protein folds, they have evolved to acquire processivity through the same strategy of adding subsites to extend the substrate-binding site and forming a tunnel-like active site by increasing the number of loops covering the active site. This represents an example of protein-level convergent evolution to acquire the same functions from different ancestors. Cellulose is the most abundant biomass on Earth, and many microorganisms depend on it as a source of energy. It consists mainly of crystalline and amorphous regions, and natural degradation of the crystalline part is highly dependent on the degree of processivity of the degrading enzymes (i.e., the extent of continuous hydrolysis without detachment from the substrate cellulose). Here, we report high-speed atomic force microscopic (HS-AFM) observations of the movement of four types of cellulases derived from the cellulolytic bacteria Cellulomonas fimi on various insoluble cellulose substrates. The HS-AFM images clearly demonstrated that two of them (CfCel6B and CfCel48A) slide on crystalline cellulose. The direction of processive movement of CfCel6B is from the nonreducing to the reducing end of the substrate, which is opposite that of processive cellulase Cel7A of the fungus Trichoderma reesei (TrCel7A), whose movement was first observed by this technique, while CfCel48A moves in the same direction as TrCel7A. When CfCel6B and TrCel7A were mixed on the same substrate, “traffic accidents” were observed, in which the two cellulases blocked each other’s progress. The processivity of CfCel6B was similar to those of fungal family 7 cellulases but considerably higher than those of fungal family 6 cellulases. The results indicate that bacteria utilize family 6 cellulases as high-processivity enzymes for efficient degradation of crystalline cellulose, whereas family 7 enzymes have the same function in fungi. This is consistent with the idea of convergent evolution of processive cellulases in fungi and bacteria to achieve similar functionality using different protein foldings.
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Huang HC, Qi LH, Chen YC, Tsai LC. Crystal structures of the GH6 Orpinomyces sp. Y102 CelC7 enzyme with exo and endo activity and its complex with cellobiose. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:1138-1147. [PMID: 31793907 DOI: 10.1107/s2059798319013597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/04/2019] [Indexed: 11/10/2022]
Abstract
The catalytic domain (residues 128-449) of the Orpinomyces sp. Y102 CelC7 enzyme (Orp CelC7) exhibits cellobiohydrolase and cellotriohydrolase activities. Crystal structures of Orp CelC7 and its cellobiose-bound complex have been solved at resolutions of 1.80 and 2.78 Å, respectively. Cellobiose occupies subsites +1 and +2 within the active site of Orp CelC7 and forms hydrogen bonds to two key residues: Asp248 and Asp409. Furthermore, its substrate-binding sites have both tunnel-like and open-cleft conformations, suggesting that the glycoside hydrolase family 6 (GH6) Orp CelC7 enzyme may perform enzymatic hydrolysis in the same way as endoglucanases and cellobiohydrolases. LC-MS/MS analysis revealed cellobiose (major) and cellotriose (minor) to be the respective products of endo and exo activity of the GH6 Orp CelC7.
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Affiliation(s)
- Hsiao Chuan Huang
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei, Taiwan
| | - Liu Hong Qi
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei, Taiwan
| | - Yo Chia Chen
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Li Chu Tsai
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei, Taiwan
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Mosina NL, Schubert WD, Cowan DA. Characterization and homology modelling of a novel multi-modular and multi-functional Paenibacillus mucilaginosus glycoside hydrolase. Extremophiles 2019; 23:681-686. [PMID: 31372752 DOI: 10.1007/s00792-019-01121-8] [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: 06/06/2019] [Accepted: 07/21/2019] [Indexed: 10/26/2022]
Abstract
Glycoside hydrolases, particularly cellulases, xylanases and mannanases, are essential for the depolymerisation of lignocellulosic substrates in various industrial bio-processes. In the present study, a novel glycoside hydrolase from Paenibacillus mucilaginosus (PmGH) was expressed in E. coli, purified and characterised. Functional analysis indicated that PmGH is a 130 kDa thermophilic multi-modular and multi-functional enzyme, comprising a GH5, a GH6 and two CBM3 domains and exhibiting cellulase, mannanase and xylanase activities. The enzyme displayed optimum hydrolytic activities at pH 6 and 60 °C and moderate thermostability. Homology modelling of the full-length protein highlighted the structural and functional novelty of native PmGH, with no close structural homologs identified. However, homology modelling of the individual GH5, GH6 and the two CBM3 domains yielded excellent models based on related structures from the Protein Data Bank. The catalytic GH5 and GH6 domains displayed a (β/α)8 and a distorted seven stranded (β/α) fold, respectively. The distinct homology at the domain level but low homology of the full-length protein suggests that this protein evolved by exogenous gene acquisition and recombination.
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Affiliation(s)
- Ntsoaki Leticia Mosina
- Department Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa
| | - Wolf-Dieter Schubert
- Department Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa
| | - Don A Cowan
- Department Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa.
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Hefferon KL, Cantero‐Tubilla B, Brady J, Wilson D. Aromatic residues surrounding the active site tunnel of TfCel48A influence activity, processivity, and synergistic interactions with other cellulases. Biotechnol Bioeng 2019; 116:2463-2472. [DOI: 10.1002/bit.27086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/29/2019] [Accepted: 06/02/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Kathleen L. Hefferon
- Department of Cellular and Molecular GeneticsCornell University Ithaca New York
- Department of Food Science and TechnologyCornell University Ithaca New York
| | - Borja Cantero‐Tubilla
- Robert Frederick Smith School of Chemical and Biomolecular EngineeringCornell University Ithaca New York
| | - John Brady
- Department of Food Science and TechnologyCornell University Ithaca New York
| | - David Wilson
- Department of Cellular and Molecular GeneticsCornell University Ithaca New York
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12
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Tomazini A, Lal S, Munir R, Stott M, Henrissat B, Polikarpov I, Sparling R, Levin DB. Analysis of carbohydrate-active enzymes in Thermogemmatispora sp. strain T81 reveals carbohydrate degradation ability. Can J Microbiol 2018; 64:992-1003. [PMID: 30338698 DOI: 10.1139/cjm-2018-0336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The phylum Chloroflexi is phylogenetically diverse and is a deeply branching lineage of bacteria that express a broad spectrum of physiological and metabolic capabilities. Members of the order Ktedonobacteriales, including the families Ktedonobacteriaceae, Thermosporotrichaceae, and Thermogemmatisporaceae, all have flexible aerobic metabolisms capable of utilizing a wide range of carbohydrates. A number of species within these families are considered cellulolytic and are capable of using cellulose as a sole carbon and energy source. In contrast, Ktedonobacter racemifer, the type strain of the order, does not appear to possess this cellulolytic phenotype. In this study, we confirmed the ability of Thermogemmatispora sp. strain T81 to hydrolyze cellulose, determined the whole-genome sequence of Thermogemmatispora sp. T81, and using comparative bioinformatics analyses, identified genes encoding putative carbohydrate-active enzymes (CAZymes) in the Thermogemmatispora sp. T81, Thermogemmatispora onikobensis, and Ktedonobacter racemifer genomes. Analyses of the Thermogemmatispora sp. T81 genome identified 64 CAZyme gene sequences belonging to 57 glycoside hydrolase families. The genome of Thermogemmatispora sp. T81 encodes 19 genes for putative extracellular CAZymes, similar to the number of putative extracellular CAZymes identified in T. onikobensis (17) and K. racemifer (17), despite K. racemifer not possessing a cellulolytic phenotype. These results suggest that these members of the order Ktedonobacteriales may use a broader range of carbohydrate polymers than currently described.
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Affiliation(s)
- Atilio Tomazini
- a São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil
| | - Sadhana Lal
- b Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Riffat Munir
- b Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Matthew Stott
- c School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Bernard Henrissat
- d Architecture et fonction des macromolécules biologiques (AFMB), CNRS-INRA, Aix-Marseille Université, Marseille, France USC1408
| | - Igor Polikarpov
- a São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil
| | - Richard Sparling
- e Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - David B Levin
- b Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
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13
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Characterization of truncated endo-β-1,4-glucanases from a compost metagenomic library and their saccharification potentials. Int J Biol Macromol 2018; 115:554-562. [DOI: 10.1016/j.ijbiomac.2018.04.102] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 11/23/2022]
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14
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Genomically Defined Paenibacillus polymyxa ND24 for Efficient Cellulase Production Utilizing Sugarcane Bagasse as a Substrate. Appl Biochem Biotechnol 2018; 187:266-281. [PMID: 29926286 DOI: 10.1007/s12010-018-2820-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/11/2018] [Indexed: 12/29/2022]
Abstract
Cellulolytic bacteria from cattle rumen with ability to hydrolyze cellulose rich biomass were explored. The study selected Paenibacillus polymyxa ND24 from 847 isolates as the most potent strain, which can efficiently produce cellulase by utilizing sugarcane bagasse, rice straw, corn starch, CMC, and avicel as a sole carbon source. On annotation of P. polymyxa ND24 genome, 116 members of glycoside hydrolase (GH) family from CAZy clusters were identified and the presence of 10 potential cellulases was validated using protein folding information. Cellulase production was further demonstrated at lab-scale 5-L bioreactor exhibiting maximum endoglucanase activity up to 0.72 U/mL when cultivated in the medium containing bagasse (2% w/v) after 72 h. The bagasse hydrolysate so produced was further utilized for efficient biogas production. The presence of diverse hydrolytic enzymes and formidable cellulase activity supports the use of P. polymyxa ND24 for cost-effective bioprocessing of cellulosic biomass.
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15
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Tayi L, Kumar S, Nathawat R, Haque AS, Maku RV, Patel HK, Sankaranarayanan R, Sonti RV. A mutation in an exoglucanase of Xanthomonas oryzae pv. oryzae, which confers an endo mode of activity, affects bacterial virulence, but not the induction of immune responses, in rice. MOLECULAR PLANT PATHOLOGY 2018; 19:1364-1376. [PMID: 28976110 PMCID: PMC6638110 DOI: 10.1111/mpp.12620] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/16/2017] [Accepted: 09/29/2017] [Indexed: 05/08/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight, a serious disease of rice. Xoo secretes a repertoire of cell wall-degrading enzymes, including cellulases, xylanases and pectinases, to degrade various polysaccharide components of the rice cell wall. A secreted Xoo cellulase, CbsA, is not only a key virulence factor of Xoo, but is also a potent inducer of innate immune responses of rice. In this study, we solved the crystal structure of the catalytic domain of the CbsA protein to a resolution of 1.86 Å. The core structure of CbsA shows a central distorted TIM barrel made up of eight β strands with N- and C-terminal loops enclosing the active site, which is a characteristic structural feature of an exoglucanase. The aspartic acid at the 131st position of CbsA was predicted to be important for catalysis and was therefore mutated to alanine to study its role in the catalysis and biological functions of CbsA. Intriguingly, the D131A CbsA mutant protein displayed the enzymatic activity of a typical endoglucanase. D131A CbsA was as proficient as wild-type (Wt) CbsA in inducing rice immune responses, but was deficient in virulence-promoting activity. This indicates that the specific exoglucanase activity of the Wt CbsA protein is required for this protein to promote the growth of Xoo in rice.
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Affiliation(s)
- Lavanya Tayi
- CSIR‐Centre for Cellular and Molecular BiologyHyderabad 500007India
- Present address:
Centre for Plant Molecular BiologyOsmania UniversityHyderabad 500007India
| | - Sushil Kumar
- CSIR‐Centre for Cellular and Molecular BiologyHyderabad 500007India
- Present address:
Institute of Life SciencesNalco SquareBhuvaneshwar 751023India
| | | | - Asfarul S. Haque
- CSIR‐Centre for Cellular and Molecular BiologyHyderabad 500007India
- Present address:
Department of BiochemistryMcGill UniversityMontréalQC H3G 0B1Canada
| | - Roshan V. Maku
- CSIR‐Centre for Cellular and Molecular BiologyHyderabad 500007India
| | | | | | - Ramesh V. Sonti
- CSIR‐Centre for Cellular and Molecular BiologyHyderabad 500007India
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16
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Discovery and characterization of a thermostable two-domain GH6 endoglucanase from a compost metagenome. PLoS One 2018; 13:e0197862. [PMID: 29795644 PMCID: PMC5968413 DOI: 10.1371/journal.pone.0197862] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/09/2018] [Indexed: 11/19/2022] Open
Abstract
Enzymatic depolymerization of recalcitrant polysaccharides plays a key role in accessing the renewable energy stored within lignocellulosic biomass, and natural biodiversities may be explored to discover microbial enzymes that have evolved to conquer this task in various environments. Here, a metagenome from a thermophilic microbial community was mined to yield a novel, thermostable cellulase, named mgCel6A, with activity on an industrial cellulosic substrate (sulfite-pulped Norway spruce) and a glucomannanase side activity. The enzyme consists of a glycoside hydrolase family 6 catalytic domain (GH6) and a family 2 carbohydrate binding module (CBM2) that are connected by a linker rich in prolines and threonines. MgCel6A exhibited maximum activity at 85°C and pH 5.0 on carboxymethyl cellulose (CMC), but in prolonged incubations with the industrial substrate, the highest yields were obtained at 60°C, pH 6.0. Differential scanning calorimetry (DSC) indicated a Tm(app) of 76°C. Both functional data and the crystal structure, solved at 1.88 Å resolution, indicate that mgCel6A is an endoglucanase. Comparative studies with a truncated variant of the enzyme showed that the CBM increases substrate binding, while not affecting thermal stability. Importantly, at higher substrate concentrations the full-length enzyme was outperformed by the catalytic domain alone, underpinning previous suggestions that CBMs may be less useful in high-consistency bioprocessing.
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17
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Burgin T, Ståhlberg J, Mayes HB. Advantages of a distant cellulase catalytic base. J Biol Chem 2018; 293:4680-4687. [PMID: 29321205 PMCID: PMC5880141 DOI: 10.1074/jbc.ra117.001186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/02/2018] [Indexed: 11/06/2022] Open
Abstract
The inverting glycoside hydrolase Trichoderma reesei (Hypocrea jecorina) Cel6A is a promising candidate for protein engineering for more economical production of biofuels. Until recently, its catalytic mechanism had been uncertain: The best candidate residue to serve as a catalytic base, Asp-175, is farther from the glycosidic cleavage site than in other glycoside hydrolase enzymes. Recent unbiased transition path sampling simulations revealed the hydrolytic mechanism for this more distant base, employing a water wire; however, it is not clear why the enzyme employs a more distant catalytic base, a highly conserved feature among homologs across different kingdoms. In this work, we describe molecular dynamics simulations designed to uncover how a base with a longer side chain, as in a D175E mutant, affects procession and active site alignment in the Michaelis complex. We show that the hydrogen bond network is tuned to the shorter aspartate side chain, and that a longer glutamate side chain inhibits procession as well as being less likely to adopt a catalytically productive conformation. Furthermore, we draw comparisons between the active site in Trichoderma reesei Cel6A and another inverting, processive cellulase to deduce the contribution of the water wire to the overall enzyme function, revealing that the more distant catalytic base enhances product release. Our results can inform efforts in the study and design of enzymes by demonstrating how counterintuitive sacrifices in chemical reactivity can have worthwhile benefits for other steps in the catalytic cycle.
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Affiliation(s)
- Tucker Burgin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, 48109
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Heather B Mayes
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, 48109.
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18
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Payal D, Prateek K, Munendra K, Renu S, Monisha KK. Purification and molecular characterization of chitinases from soil actinomycetes. ACTA ACUST UNITED AC 2017. [DOI: 10.5897/ajmr2017.8612] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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19
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Impact of Module-X2 and Carbohydrate Binding Module-3 on the catalytic activity of associated glycoside hydrolases towards plant biomass. Sci Rep 2017. [PMID: 28623337 PMCID: PMC5473887 DOI: 10.1038/s41598-017-03927-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Cellulolytic enzymes capable of hydrolyzing plant biomass are secreted by microbial cells specifically in response to the carbon substrate present in the environment. These enzymes consist of a catalytic domain, generally appended to one or more non-catalytic Carbohydrate Binding Module (CBM), which enhances their activity towards recalcitrant biomass. In the present study, the genome of a cellulolytic microbe Paenibacillus polymyxa A18 was annotated for the presence of CBMs and analyzed their expression in response to the plant biomass and model polysaccharides Avicel, CMC and xylan using quantitative PCR. A gene that encodes X2-CBM3 was found to be maximally induced in response to the biomass and crystalline substrate Avicel. Association of X2-CBM3 with xyloglucanase and endoglucanase led to up to 4.6-fold increase in activity towards insoluble substrates. In the substrate binding study, module X2 showed a higher affinity towards biomass and phosphoric acid swollen cellulose, whereas CBM3 showed a higher affinity towards Avicel. Further structural modeling of X2 also indicated its potential role in substrate binding. Our findings highlighted the role of module X2 along with CBM3 in assisting the enzyme catalysis of agricultural residue and paved the way to engineer glycoside hydrolases for superior activity.
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20
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A bacterial GH6 cellobiohydrolase with a novel modular structure. Appl Microbiol Biotechnol 2017; 101:2943-2952. [PMID: 28120014 DOI: 10.1007/s00253-017-8129-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/19/2016] [Accepted: 12/28/2016] [Indexed: 02/01/2023]
Abstract
Cel6D from Paenibacillus barcinonensis is a modular cellobiohydrolase with a novel molecular architecture among glycosyl hydrolases of family 6. It contains an N-terminal catalytic domain (family 6 of glycosyl hydrolases (GH6)), followed by a fibronectin III-like domain repeat (Fn31,2) and a C-terminal family 3b cellulose-binding domain (CBM3b). The enzyme has been identified and purified showing catalytic activity on cellulosic substrates and cellodextrins, with a marked preference for phosphoric acid swollen cellulose (PASC). Analysis of mode of action of Cel6D shows that it releases cellobiose as the only hydrolysis product from cellulose. Kinetic parameters were determined on PASC showing a K m of 68.73 mg/ml and a V max of 1.73 U/mg. A series of truncated derivatives of Cel6D have been constructed and characterized. Deletion of CBM3b caused a notable reduction in hydrolytic activity, while deletion of the Fn3 domain abolished activity, as the isolated GH6 domain was not active on any of the substrates tested. Mutant enzymes Cel6D-D146A and Cel6D-D97A were constructed in the residues corresponding to the putative acid catalyst and to the network for the nucleophilic attack. The lack of activity of the mutant enzymes indicates the important role of these residues in catalysis. Analysis of cooperative activity of Cel6D with cellulases from the same producing P. barcinonensis strain reveals high synergistic activity with processive endoglucanase Cel9B on hydrolysis of crystalline substrates. The characterized cellobiohydrolase can be a good contribution for depolymerization of cellulosic substrates and for the deconstruction of native cellulose.
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21
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Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels. Appl Microbiol Biotechnol 2017; 101:2603-2618. [PMID: 28078400 DOI: 10.1007/s00253-017-8091-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022]
Abstract
Recently, several endophytic fungi have been demonstrated to produce volatile organic compounds (VOCs) with properties similar to fossil fuels, called "mycodiesel," while growing on lignocellulosic plant and agricultural residues. The fact that endophytes are plant symbionts suggests that some may be able to produce lignocellulolytic enzymes, making them capable of both deconstructing lignocellulose and converting it into mycodiesel, two properties that indicate that these strains may be useful consolidated bioprocessing (CBP) hosts for the biofuel production. In this study, four endophytes Hypoxylon sp. CI4A, Hypoxylon sp. EC38, Hypoxylon sp. CO27, and Daldinia eschscholzii EC12 were selected and evaluated for their CBP potential. Analysis of their genomes indicates that these endophytes have a rich reservoir of biomass-deconstructing carbohydrate-active enzymes (CAZys), which includes enzymes active on both polysaccharides and lignin, as well as terpene synthases (TPSs), enzymes that may produce fuel-like molecules, suggesting that they do indeed have CBP potential. GC-MS analyses of their VOCs when grown on four representative lignocellulosic feedstocks revealed that these endophytes produce a wide spectrum of hydrocarbons, the majority of which are monoterpenes and sesquiterpenes, including some known biofuel candidates. Analysis of their cellulase activity when grown under the same conditions revealed that these endophytes actively produce endoglucanases, exoglucanases, and β-glucosidases. The richness of CAZymes as well as terpene synthases identified in these four endophytic fungi suggests that they are great candidates to pursue for development into platform CBP organisms.
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22
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Baramee S, Teeravivattanakit T, Phitsuwan P, Waeonukul R, Pason P, Tachaapaikoon C, Kosugi A, Sakka K, Ratanakhanokchai K. A novel GH6 cellobiohydrolase from Paenibacillus curdlanolyticus B-6 and its synergistic action on cellulose degradation. Appl Microbiol Biotechnol 2016; 101:1175-1188. [PMID: 27743043 DOI: 10.1007/s00253-016-7895-8] [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: 08/14/2016] [Revised: 09/12/2016] [Accepted: 09/25/2016] [Indexed: 11/30/2022]
Abstract
We recently discovered a novel glycoside hydrolase family 6 (GH6) cellobiohydrolase from Paenibacillus curdlanolyticus B-6 (PcCel6A), which is rarely found in bacteria. This enzyme is a true exo-type cellobiohydrolase which exhibits high substrate specificity on amorphous cellulose and low substrate specificity on crystalline cellulose, while this showed no activity on substitution substrates, carboxymethyl cellulose and xylan, distinct from all other known GH6 cellobiohydrolases. Product profiles, HPLC analysis of the hydrolysis products and a schematic drawing of the substrate-binding subsites catalysing cellooligosaccharides can explain the new mode of action of this enzyme which prefers to hydrolyse cellopentaose. PcCel6A was not inhibited by glucose or cellobiose at concentrations up to 300 and 100 mM, respectively. A good synergistic effect for glucose production was found when PcCel6A acted together with processive endoglucanase Cel9R from Clostridium thermocellum and β-glucosidase CglT from Thermoanaerobacter brockii. These properties of PcCel6A make it a suitable candidate for industrial application in the cellulose degradation process.
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Affiliation(s)
- Sirilak Baramee
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Thitiporn Teeravivattanakit
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Paripok Phitsuwan
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, 305-8686, Japan
| | - Kazuo Sakka
- Graduated School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
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23
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Luo Z, Dauter Z. Detection of twinning in macromolecular crystallography. Z KRIST-CRYST MATER 2016. [DOI: 10.1515/zkri-2016-1946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The merohedrally or pseudo-merohedrally twinned crystals cannot be identified during diffraction pattern inspection at the stage of data collection. Several methods for identifying twinning and estimating the twin fraction are suitable for macromolecular crystals, and all are based on the statistical properties of the measured diffraction intensities. They can be based on either the overall statistical properties of the measured reflection intensities or on the comparison of reflection intensities related by the twinning operation. The application of various tests for identification of twinning and estimation of twinning fraction is discussed, with examples of diffraction data from the Protein Data Bank. Twinning makes the solution of crystal structures more difficult, but once initially solved, the atomic models can be properly refined by the existing programs.
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Affiliation(s)
- Zhipu Luo
- Argonne National Laboratory, Synchrotron Radiation Research Section, National Cancer Institute, Argonne, Illinois 60439, United States of America
| | - Zbigniew Dauter
- Argonne National Laboratory, Synchrotron Radiation Research Section, National Cancer Institute, Argonne, Illinois 60439, United States of America
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24
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Mayes HB, Knott BC, Crowley MF, Broadbelt LJ, Ståhlberg J, Beckham GT. Who's on base? Revealing the catalytic mechanism of inverting family 6 glycoside hydrolases. Chem Sci 2016; 7:5955-5968. [PMID: 30155195 PMCID: PMC6091422 DOI: 10.1039/c6sc00571c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/29/2016] [Indexed: 12/16/2022] Open
Abstract
In several important classes of inverting carbohydrate-active enzymes, the identity of the catalytic base remains elusive, including in family 6 Glycoside Hydrolase (GH6) enzymes, which are key components of cellulase cocktails for cellulose depolymerization. Despite many structural and kinetic studies with both wild-type and mutant enzymes, especially on the Trichoderma reesei (Hypocrea jecorina) GH6 cellulase (TrCel6A), the catalytic base in the single displacement inverting mechanism has not been definitively identified in the GH6 family. Here, we employ transition path sampling to gain insight into the catalytic mechanism, which provides unbiased atomic-level understanding of key order parameters involved in cleaving the strong glycosidic bond. Our hybrid quantum mechanics and molecular mechanics (QM/MM) simulations reveal a network of hydrogen bonding that aligns two active site water molecules that play key roles in hydrolysis: one water molecule drives the reaction by nucleophilic attack on the substrate and a second shuttles a proton to the putative base (D175) via a short water wire. We also investigated the case where the putative base is mutated to an alanine, an enzyme that is experimentally still partially active. The simulations predict that proton hopping along a water wire via a Grotthuss mechanism provides a mechanism of catalytic rescue. Further simulations reveal that substrate processive motion is 'driven' by strong electrostatic interactions with the protein at the product sites and that the -1 sugar adopts a 2SO ring configuration as it reaches its binding site. This work thus elucidates previously elusive steps in the processive catalytic mechanism of this important class of enzymes.
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Affiliation(s)
- Heather B Mayes
- Department of Chemical and Biological Engineering , Northwestern University , Evanston , IL 60208 , USA
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
| | - Brandon C Knott
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
| | - Michael F Crowley
- Biosciences Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA
| | - Linda J Broadbelt
- Department of Chemical and Biological Engineering , Northwestern University , Evanston , IL 60208 , USA
| | - Jerry Ståhlberg
- Department of Chemistry and Biotechnology , Swedish University of Agricultural Sciences , SE-75007 , Uppsala , Sweden .
| | - Gregg T Beckham
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
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25
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Genetic Enhancement of Saccharomyces cerevisiae for First and Second Generation Ethanol Production. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1201/b19347-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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26
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Tegl G, Öhlknecht C, Vielnascher R, Rollett A, Hofinger-Horvath A, Kosma P, Guebitz GM. Cellobiohydrolases Produce Different Oligosaccharides from Chitosan. Biomacromolecules 2016; 17:2284-92. [DOI: 10.1021/acs.biomac.6b00547] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gregor Tegl
- Institute
of Environmental Biotechnology, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Straße 20, 3430 Tulln an der Donau, Austria
| | - Christoph Öhlknecht
- Institute
of Environmental Biotechnology, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Straße 20, 3430 Tulln an der Donau, Austria
| | - Robert Vielnascher
- Institute
of Environmental Biotechnology, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Straße 20, 3430 Tulln an der Donau, Austria
| | - Alexandra Rollett
- Institute
of Environmental Biotechnology, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Straße 20, 3430 Tulln an der Donau, Austria
| | - Andreas Hofinger-Horvath
- Department
of Chemistry, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Wien, Austria
| | - Paul Kosma
- Department
of Chemistry, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Wien, Austria
| | - Georg M. Guebitz
- Institute
of Environmental Biotechnology, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Straße 20, 3430 Tulln an der Donau, Austria
- ACIB − Austrian Centre of Industrial Biotechnology, Konrad Lorenz Straße 20, 3430 Tulln, Austria
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27
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Ligand-binding specificity and promiscuity of the main lignocellulolytic enzyme families as revealed by active-site architecture analysis. Sci Rep 2016; 6:23605. [PMID: 27009476 PMCID: PMC4806347 DOI: 10.1038/srep23605] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/09/2016] [Indexed: 02/02/2023] Open
Abstract
Biomass can be converted into sugars by a series of lignocellulolytic enzymes, which belong to the glycoside hydrolase (GH) families summarized in CAZy databases. Here, using a structural bioinformatics method, we analyzed the active site architecture of the main lignocellulolytic enzyme families. The aromatic amino acids Trp/Tyr and polar amino acids Glu/Asp/Asn/Gln/Arg occurred at higher frequencies in the active site architecture than in the whole enzyme structure. And the number of potential subsites was significantly different among different families. In the cellulase and xylanase families, the conserved amino acids in the active site architecture were mostly found at the −2 to +1 subsites, while in β-glucosidase they were mainly concentrated at the −1 subsite. Families with more conserved binding amino acid residues displayed strong selectivity for their ligands, while those with fewer conserved binding amino acid residues often exhibited promiscuity when recognizing ligands. Enzymes with different activities also tended to bind different hydroxyl oxygen atoms on the ligand. These results may help us to better understand the common and unique structural bases of enzyme-ligand recognition from different families and provide a theoretical basis for the functional evolution and rational design of major lignocellulolytic enzymes.
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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Towards a molecular-level theory of carbohydrate processivity in glycoside hydrolases. Curr Opin Biotechnol 2014; 27:96-106. [DOI: 10.1016/j.copbio.2013.12.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 12/04/2013] [Indexed: 10/25/2022]
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Wu M, Bu L, Vuong TV, Wilson DB, Crowley MF, Sandgren M, Ståhlberg J, Beckham GT, Hansson H. Loop motions important to product expulsion in the Thermobifida fusca glycoside hydrolase family 6 cellobiohydrolase from structural and computational studies. J Biol Chem 2013; 288:33107-17. [PMID: 24085303 DOI: 10.1074/jbc.m113.502765] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellobiohydrolases (CBHs) are typically major components of natural enzyme cocktails for biomass degradation. Their active sites are enclosed in a tunnel, enabling processive hydrolysis of cellulose chains. Glycoside hydrolase Family 6 (GH6) CBHs act from nonreducing ends by an inverting mechanism and are present in many cellulolytic fungi and bacteria. The bacterial Thermobifida fusca Cel6B (TfuCel6B) exhibits a longer and more enclosed active site tunnel than its fungal counterparts. Here, we determine the structures of two TfuCel6B mutants co-crystallized with cellobiose, D274A (catalytic acid), and the double mutant D226A/S232A, which targets the putative catalytic base and a conserved serine that binds the nucleophilic water. The ligand binding and the structure of the active site are retained when compared with the wild type structure, supporting the hypothesis that these residues are directly involved in catalysis. One structure exhibits crystallographic waters that enable construction of a model of the α-anomer product after hydrolysis. Interestingly, the product sites of TfuCel6B are completely enclosed by an "exit loop" not present in fungal GH6 CBHs and by an extended "bottom loop". From the structures, we hypothesize that either of the loops enclosing the product subsites in the TfuCel6B active site tunnel must open substantially for product release. With simulation, we demonstrate that both loops can readily open to allow product release with equal probability in solution or when the enzyme is engaged on cellulose. Overall, this study reveals new structural details of GH6 CBHs likely important for functional differences among enzymes from this important family.
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Affiliation(s)
- Miao Wu
- From the Department of Molecular Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
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