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Kang Z, Wang T, Han X, Wang C, Zhang S, Yu H. Whole genome sequencing revealed the capability of Paenarthrobacter sp. KN0901 to simultaneously remove atrazine and corn straw at low temperatures: From gene identification to empirical validation. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134251. [PMID: 38640669 DOI: 10.1016/j.jhazmat.2024.134251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/21/2024]
Abstract
Corn planting is often associated with serious atrazine pollution and excessive corn straw amounts, causing severe threats to environmental and ecological security, as well as to green agricultural development. In this context, a Paenarthrobacter sp. KN0901 strain was applied to simultaneously remove atrazine and straw at low temperatures. The results of whole genome sequencing indicated that KN0901 encoded over nine straw biodegradation-related enzymes. In addition, 100 % and 27.3 % of atrazine and straw were simultaneously degraded by KN0901 following an incubation period of seven days at 15 ºC and 180 rpm in darkness. The KN0901 strain maintained high atrazine and straw biodegradation rates under temperature and pH ranges of 4-25 ºC and 5-9, respectively. The simultaneous atrazine and corn straw additions improved the microbial growth and biodegradation rates by increasing the functional gene expression level, cell viability, inner membrane permeability, and extracellular polymeric substance contents of KN0901. The hydroponic experiment results demonstrated the capability of the KN0901 strain to mitigate the toxicity of atrazine to soybeans in four days under the presence of corn straw. The present study provides a new perspective on the development of bioremediation approaches and their application to restore atrazine-polluted cornfields with large straw quantities, particularly in cold areas.
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Affiliation(s)
- Zhichao Kang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; College of Resources and Environment, University of Chinese Academy of Science, Beijing 101400, China
| | - Tianye Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Xuerong Han
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Chenxu Wang
- Institutional Center for Shared Technologies and Facilities of Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Shaoqing Zhang
- Institutional Center for Shared Technologies and Facilities of Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Hongwen Yu
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
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2
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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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3
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Liang Q, Yuan M, Xu L, Lio E, Zhang F, Mou H, Secundo F. Application of enzymes as a feed additive in aquaculture. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:208-221. [PMID: 37073222 PMCID: PMC10077164 DOI: 10.1007/s42995-022-00128-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 02/28/2022] [Indexed: 05/03/2023]
Abstract
Modern aquaculture must be sustainable in terms of energy consumption, raw materials used, and environmental impact, so alternatives are needed to replace fish feed with other raw materials. Enzyme use in the agri-food industry is based on their efficiency, safety, and protection of the environment, which aligns with the requirements of a resource-saving production system. Enzyme supplementation in fish feed can improve digestibility and absorption of both plant- and animal-derived ingredients, increasing the growth parameters of aquacultural animals. Herein we summarized the recent literature that reported the use of digestive enzymes (amylases, lipases, proteases, cellulases, and hemicellulases) and non-digestive enzymes (phytases, glucose oxidase, and lysozyme) in fish feed. In addition, we analyzed how critical steps of the pelleting process, including microencapsulation and immobilization, can interfere with enzyme activity in the final fish feed product. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00128-z.
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Affiliation(s)
- Qingping Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Mingxue Yuan
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Liping Xu
- College of Biology and Geography, Yili Normal University, Yining, 835000 China
| | - Elia Lio
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, CNR, Via Mario Bianco n. 9, 20131 Milan, Italy
| | - Fang Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Haijin Mou
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Francesco Secundo
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, CNR, Via Mario Bianco n. 9, 20131 Milan, Italy
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4
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Badhan A, Low KE, Jones DR, Xing X, Milani MRM, Polo RO, Klassen L, Venketachalam S, Hahn MG, Abbott DW, McAllister TA. Mechanistic insights into the digestion of complex dietary fibre by the rumen microbiota using combinatorial high-resolution glycomics and transcriptomic analyses. Comput Struct Biotechnol J 2022; 20:148-164. [PMID: 34976318 PMCID: PMC8702857 DOI: 10.1016/j.csbj.2021.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022] Open
Abstract
There is a knowledge gap regarding the factors that impede the ruminal digestion of plant cell walls or if rumen microbiota possess the functional activities to overcome these constraints. Innovative experimental methods were adopted to provide a high-resolution understanding of plant cell wall chemistries, identify higher-order structures that resist microbial digestion, and determine how they interact with the functional activities of the rumen microbiota. We characterized the total tract indigestible residue (TTIR) from cattle fed a low-quality straw diet using two comparative glycomic approaches: ELISA-based glycome profiling and total cell wall glycosidic linkage analysis. We successfully detected numerous and diverse cell wall glycan epitopes in barley straw (BS) and TTIR and determined their relative abundance pre- and post-total tract digestion. Of these, xyloglucans and heteroxylans were of higher abundance in TTIR. To determine if the rumen microbiota can further saccharify the residual plant polysaccharides within TTIR, rumen microbiota from cattle fed a diet containing BS were incubated with BS and TTIR ex vivo in batch cultures. Transcripts coding for carbohydrate-active enzymes (CAZymes) were identified and characterized for their contribution to cell wall digestion based on glycomic analyses, comparative gene expression profiles, and associated CAZyme families. High-resolution phylogenetic fingerprinting of these sequences encoded CAZymes with activities predicted to cleave the primary linkages within heteroxylan and arabinan. This experimental platform provides unprecedented precision in the understanding of forage structure and digestibility, which can be extended to other feed-host systems and inform next-generation solutions to improve the performance of ruminants fed low-quality forages.
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Key Words
- AB, arabinan
- ADF, acid detergent fibre
- AG, arabinogalactan
- AGP, arabinogalactan protein
- AIR, alcohol insoluble residue
- AO, ammonium oxalate
- AX, arabinoxylan
- BS, barley straw
- CAZyme, carbohydrate active enzyme
- CAZymes
- CE, carbohydrate esterase
- CH, chlorite
- DE, differentially expressed
- Dietary polysaccharides
- Differential gene expression
- ELISA, enzyme-linked immunosorbent assay
- FID, flame ionization detection GC, gas chromatography
- GH, glycosyl hydrolase
- Glycome profiling
- Glycoside hydrolase
- HG, homogalacturonan
- HPAEC-PAD, high performance anion exchange chromatography coupled with pulsed amperometric detection
- HX, heteroxylan
- Linkage analysis
- MS, mass spectrometry
- NDF, neutral detergent fibre
- Nutrient utilization
- PC, post-chlorite
- PL, polysaccharide lyase
- RG, rhamnogalacturonan
- Rumen microbiome
- SC, sodium carbonate
- TTIR, total tract indigestible residue
- Transcriptome
- XG, xyloglucan
- mAbs, monoclonal antibodies
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Affiliation(s)
- Ajay Badhan
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Kristin E Low
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Darryl R Jones
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Xiaohui Xing
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Mohammad Raza Marami Milani
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Rodrigo Ortega Polo
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Leeann Klassen
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Sivasankari Venketachalam
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Michael G Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Tim A McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
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Nath P, Goyal A. Structure and dynamics analysis of multi-domain putative β-1,4-glucosidase of family 3 glycoside hydrolase (PsGH3) from Pseudopedobacter saltans. J Mol Model 2021; 27:106. [PMID: 33694107 PMCID: PMC7945971 DOI: 10.1007/s00894-021-04721-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/01/2021] [Indexed: 11/30/2022]
Abstract
Structure and conformational behaviour of a putative β-1,4-glucosidase of glycoside hydrolase family 3 (PsGH3) from Pseudopedobacter saltans was predicted by using in-silico tools. PsGH3 modeled structure constructed using Phyre2 displayed multidomain architecture comprising an N-terminal (β/α)8-fold domain followed by (α/β)6-sandwich domain, PA14 domain, and a C-terminal domain resembling an immunoglobulin fold. Ramachandran plot displayed 99.3% of amino acids in the allowed region and 0.7% residues in the disallowed region. Multiple sequence alignment (MSA) and structure superposition of PsGH3 with other homologues from GH3 family revealed the conserved residues, Asp274 and Glu624 present in loops LA and LB, respectively originating from N-terminal domain act as catalytic residues. The volume and area calculated for PsGH3 displayed a deep active-site conformation comparable with its homologues, β-1,4-glucosidases (GH3) of Kluyveromyces marxianus and Streptomyces venezuelae. Molecular dynamic (MD) simulation of PsGH3 structure for 80 ns suggested stable and compact structure. Molecular docking studies revealed deeper active site conformation of PsGH3 that could house larger cellooligosaccharides up to 7° of polymerization (DP7). The amino acid residues, Ala86, Leu88, Cys275, Pro483, Phe493, Asn417, Asn491, Pro492, and Leu495 created a binding pocket near the catalytic cleft, crucial for ligand binding. MD simulation of PsGH3 in the presence of cellooligosaccharides, viz., cellobiose and celloheptaose showed stability in terms of RMSD, Rg, and SASA values till 80 ns. The calculation of average number of hydrogen bond (H-bond), interaction energy, and binding free energy confirmed the stronger binding affinity of the larger cellooligosaccharides such as celloheptaose in the binding cavity of PsGH3.
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Affiliation(s)
- Priyanka Nath
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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New thermostable endoglucanase from Spirochaeta thermophila and its mutants with altered substrate preferences. Appl Microbiol Biotechnol 2021; 105:1133-1145. [PMID: 33427929 DOI: 10.1007/s00253-020-11077-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/30/2020] [Accepted: 12/27/2020] [Indexed: 10/22/2022]
Abstract
Endoglucanases are key elements in several industrial applications, such as cellulosic biomass hydrolysis, cellulose fiber modification for the production paper and composite materials, and in nanocellulose production. In all of these applications, the desired function of the endoglucanase is to create nicks in the amorphous regions of the cellulose. However, endoglucanase can be diverted from its activity on the fibers by other substrates-soluble oligosaccharides. This issue was addressed in the current study using enzyme engineering and an enzyme evolution approach. To this end, a hypothetical endoglucanase from a thermostable bacterium Spirochaeta thermophila was for the first time cloned and characterized. The wild-type enzyme was used as a starting point for mutagenesis and molecular evolution toward a preference for the higher molecular weight substrates. The best of the evolved enzymes was more active than the wild-type enzyme toward high molecular weight substrate at temperatures below 45 °C (3-fold more active at 30 °C) and showed little or no activity with low molecular weight substrates. These findings can be instrumental in bioeconomy sectors, such as second-generation biofuels and biomaterials from lignocellulosic biomass. KEY POINTS: • A new thermostable endoglucanase was characterized. • The substrate specificity of this endoglucanase was changed by means of genetic engineering. • A mutant with a preference for long molecular weight substrate was obtained and proposed to be beneficial for cellulose fiber modification.
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7
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A steady-state approach for inhibition of heterogeneous enzyme reactions. Biochem J 2020; 477:1971-1982. [PMID: 32391552 DOI: 10.1042/bcj20200083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 02/02/2023]
Abstract
The kinetic theory of enzymes that modify insoluble substrates is still underdeveloped, despite the prevalence of this type of reaction both in vivo and industrial applications. Here, we present a steady-state kinetic approach to investigate inhibition occurring at the solid-liquid interface. We propose to conduct experiments under enzyme excess (E0 ≫ S0), i.e. the opposite limit compared with the conventional Michaelis-Menten framework. This inverse condition is practical for insoluble substrates and elucidates how the inhibitor reduces enzyme activity through binding to the substrate. We claim that this type of inhibition is common for interfacial enzyme reactions because substrate accessibility is low, and we show that it can be analyzed by experiments and rate equations that are analogous to the conventional approach, except that the roles of enzyme and substrate have been swapped. To illustrate the approach, we investigated the major cellulases from Trichoderma reesei (Cel6A and Cel7A) acting on insoluble cellulose. As model inhibitors, we used catalytically inactive variants of Cel6A and Cel7A. We made so-called inverse Michaelis-Menten curves at different concentrations of inhibitors and found that a new rate equation accounted well for the data. In most cases, we found a mixed type of surface-site inhibition mechanism, and this probably reflected that the inhibitor both competed with the enzyme for the productive binding-sites (competitive inhibition) and hampered the processive movement on the surface (uncompetitive inhibition). These results give new insights into the complex interplay of Cel7A and Cel6A on cellulose and the approach may be applicable to other heterogeneous enzyme reactions.
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Ghasemi S, Safaie N, Shahbazi S, Shams-Bakhsh M, Askari H. The Role of Cell Wall Degrading Enzymes in Antagonistic Traits of Trichoderma virens Against Rhizoctonia solani. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 18:e2333. [PMID: 34056015 PMCID: PMC8148636 DOI: 10.30498/ijb.2020.2333] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background: High antagonistic ability of different Trichoderma species against a diverse range of plant pathogenic fungi has led them to be used as a biological fungicide in agriculture. They can also promote plant growth, fertility, resistance to stress, and absorption of nutrients. They are also opportunistic and symbiotic pathogens, which can lead to the activation of plant defense mechanisms. Objectives: The aim of this present study was to investigate possible enhancement of lytic enzymes production and biocontrol activity of T. virens against Rhizoctonia solani through gamma radiation and to find the relationship between changes in lytic enzyme production and antagonistic activity of T. virens. Material and Methods: Dual culture conditions were used to evaluate the antagonistic effect of T. virens and its gamma mutants against R. solani. Then, their chitinase and cellulase activities were measured. For more detailed investigation of enzymes, densitometry pattern of the proteins was extracted from the T. virens wild-type and its mutants were obtained via SDS-polyacrylamide gel electrophoresis. Results: The mutant T.vi M8, T. virens wild-type and mutant T.vi M20 strains showed the maximum antagonistic effects
against the pathogen, respectively. Data showed that the mutant T. vi M8 reduced the growth of R. solani by 58 %.
The mutants revealed significantly different (p<0.05) protein contents, chitinase and cellulase production (mg.mL-1)
and activity (U.mL-1) compared to the wild-type strain. The highest extracellular protein production in the supernatant
of chitinase and cellulase TFM was observed for the T.vi M11 and T.vi M17 strains, respectively. The T.vi M12 and wild-type
strains secreted chitinase and cellulase significantly more than other strains did. Densitometry of SDS-PAGE gel bands
indicated that both the amount and diversity of chitinase related proteins in the selected mutant (T. vi M8) were far
higher than those of the wild-type. The diversity of molecular weight of proteins extracted from the T. virens
M8 (20 proteins or bands) was very high compared to the wild-type (10 proteins) and mutant T.vi M15 (2 proteins). Conclusions: Overall, there was a strong link between the diversity of various chitinase proteins and the antagonistic properties of the mutant M8.
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Affiliation(s)
- Soleiman Ghasemi
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Naser Safaie
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Samira Shahbazi
- Nuclear Science and Technology Research Institute (NSTRI), Atomic Energy organization of Iran (AEOI), Alborz, Iran
| | - Masoud Shams-Bakhsh
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Hamed Askari
- Nuclear Science and Technology Research Institute (NSTRI), Atomic Energy organization of Iran (AEOI), Alborz, Iran
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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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10
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Nath P, Sharma K, Kumar K, Goyal A. Combined SAXS and computational approaches for structure determination and binding characteristics of Chimera (CtGH1-L1-CtGH5-F194A) generated by assembling β-glucosidase (CtGH1) and a mutant endoglucanase (CtGH5-F194A) from Clostridium thermocellum. Int J Biol Macromol 2020; 148:364-377. [PMID: 31945441 DOI: 10.1016/j.ijbiomac.2020.01.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 11/25/2022]
Abstract
Chimera (CtGH1-L1-CtGH5-F194A) developed by fusing β-glucosidase (CtGH1) at N-terminal and endoglucanase (CtGH5-F194A) at C-terminal was structurally characterized. Its secondary structure analysis by CD showed 38% α-helix, 9.3% β-sheets and 52.7% random coils corroborating with prediction. In-silico modeled structure of Chimera comprised two modules, CtGH1 and CtGH5-F194A displaying (α/β)8 fold. Ramachandran plot of Chimera showed 99.9% residues in allowed region. Binding interaction of Chimera with cello-oligosaccharides suggested active forms of CtGH1 and CtGH5-F194A and their involvement in catalysis. MD simulation of cellohexaose bound endoglucanase module of Chimera showed favourable flexibility in loops, LA with H-bond formation with Asn510 and in loop LC relocation of Tyr687 away from active site efficiently releasing the product after catalysis. Higher short range interaction energy of Chimera, -383 kJ/mol than the individual endoglucanase, 254 kJ/mol against cellohexaose suggested higher efficient catalysis by Chimera. β-Glucosidase module of Chimera showed fluctuations in outer loops suggesting conformational changes that might be contributing to improved hydrolysis. SAXS analysis of Chimera displayed monodispersed state. Guinier analysis of Chimera showed globular shape (Rg= 3.15 ± 0.10 nm). Kratky plot confirmed fully folded and flexible behaviour in solution. Gasbor modeled structure of Chimera displayed an elongated structure with two modules having shape similar to bean-bag contour.
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Affiliation(s)
- Priyanka Nath
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, India; DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, India
| | - Krishan Kumar
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, India; DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
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11
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Sørlie M, Horn SJ, Vaaje-Kolstad G, Eijsink VG. Using chitosan to understand chitinases and the role of processivity in the degradation of recalcitrant polysaccharides. REACT FUNCT POLYM 2020. [DOI: 10.1016/j.reactfunctpolym.2020.104488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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Sun P, Frommhagen M, Kleine Haar M, van Erven G, Bakx EJ, van Berkel WJH, Kabel MA. Mass spectrometric fragmentation patterns discriminate C1- and C4-oxidised cello-oligosaccharides from their non-oxidised and reduced forms. Carbohydr Polym 2020; 234:115917. [PMID: 32070536 DOI: 10.1016/j.carbpol.2020.115917] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/13/2020] [Accepted: 01/24/2020] [Indexed: 11/26/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are powerful enzymes that degrade recalcitrant polysaccharides, such as cellulose. However, the identification of LPMO-generated C1- and/or C4-oxidised oligosaccharides is far from straightforward. In particular, their fragmentation patterns have not been well established when using mass spectrometry. Hence, we studied the fragmentation behaviours of non-, C1- and C4-oxidised cello-oligosaccharides, including their sodium borodeuteride-reduced forms, by using hydrophilic interaction chromatography and negative ion mode collision induced dissociation - mass spectrometry. Non-oxidised cello-oligosaccharides showed predominantly C- and A-type cleavages. In comparison, C4-oxidised ones underwent B-/Y- and X-cleavage close to the oxidised non-reducing end, while closer to the reducing end C-/Z- and A-fragmentation predominated. C1-oxidised cello-oligosaccharides showed extensively A-cleavage. Reduced oligosaccharides showed predominant glycosidic bond cleavage, both B-/Y- and C-/Z-, close to the non-reducing end. Our findings provide signature mass spectrometric fragmentation patterns to unambiguously elucidate the catalytic behaviour and classification of LPMOs.
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Affiliation(s)
- Peicheng Sun
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands.
| | - Matthias Frommhagen
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands.
| | - Maloe Kleine Haar
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands.
| | - Gijs van Erven
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands.
| | - Edwin J Bakx
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands.
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands.
| | - Mirjam A Kabel
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands.
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13
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Wang R, Xu D. Molecular dynamics investigations of oligosaccharides recognized by family 16 and 22 carbohydrate binding modules. Phys Chem Chem Phys 2019; 21:21485-21496. [PMID: 31535114 DOI: 10.1039/c9cp04673a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
As a non-catalytic domain, carbohydrate binding modules (CBMs) are often considered to play some key roles in the degradation and recognition of polysaccharides catalyzed by cellulases. In this work, we investigated the recognition dynamics of cello- or xylo-saccharides by two typical CBMs (CBM16-1 and CBM22-2), which are grouped into Type B CBMs. By combining extensive molecular dynamics, principle component analysis, and binding free energy calculations, we constructed several complex models of the two CBMs in both complex cello- and xylo-oligosaccharides. The corresponding substrate recognition affinity and critical residues having significant contributions were systematically investigated. The residues containing aromatic side chain groups were shown to contribute significantly to substrate binding. The calculated binding free energies were in fairly good agreement with the experimental measurements with the absolute mean error of 0.69 kcal mol-1. The overall electrostatic interactions were shown to have negative effects on substrate recognition. Further metadynamics simulations revealed the substrate dissociation process.
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Affiliation(s)
- Ruihan Wang
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China.
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China. and Research Center for Materials Genome Engineering, Sichuan University, Chengdu, Sichuan 610065, P. R. China
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14
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Jones DR, McLean R, Hobbs JK, Abbott DW. A surrogate structural platform informed by ancestral reconstruction and resurrection of a putative carbohydrate binding module hybrid illuminates the neofunctionalization of a pectate lyase. J Struct Biol 2019; 207:279-286. [PMID: 31200020 DOI: 10.1016/j.jsb.2019.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/30/2019] [Accepted: 06/10/2019] [Indexed: 12/16/2022]
Abstract
Yersinia enterocolitica is a pectinolytic zoonotic foodborne pathogen, the genome of which contains pectin-binding proteins and several different classes of pectinases, including polysaccharide lyases (PLs) and an exopolygalacturonase. These proteins operate within a coordinated pathway to completely saccharify homogalacturonan (HG). Polysaccharide lyase family 2 (PL2) is divided into two major subfamilies that are broadly-associated with contrasting 'endolytic' (PL2A) or 'exolytic' (PL2B) activities on HG. In the Y. enterocolitica genome, the PL2A gene is adjacent to an independent carbohydrate binding module from family 32 (YeCBM32), which possesses a N-terminal secretion tag and is known to specifically bind HG. Independent CBMs are rare in nature and, most commonly, are fused to enzymes in order to potentiate catalysis. The unconventional gene architecture of YePL2A and YeCBM32, therefore, may represent an ancestral relic of a fission event that decoupled PL2A from its cognate CBM. To provide further insight into the evolution of this pectinolytic locus and the molecular basis of HG depolymerisation within Y. enterocolitica, we have resurrected a YePL2A-YeCBM32 chimera and demonstrated that the extant PL2A digests HG more efficiently. In addition, we have engineered a tryptophan from the active site of the exolytic YePL2B into YePL2A (YePL2A-K291W) and demonstrated, using X-ray crystallography of substrate complexes, that it is a structural determinant of exo-activity within the PL2 family. In this manner, surrogate structural platforms may assist in the study of phylogenetic relationships informed by extant and resurrected sequences, and can be used to overcome challenging structural problems within carbohydrate active enzyme families.
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Affiliation(s)
- Darryl R Jones
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Richard McLean
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Joanne K Hobbs
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, British Columbia V8W 3P6, Canada
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada.
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15
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Nath P, Dhillon A, Kumar K, Sharma K, Jamaldheen SB, Moholkar VS, Goyal A. Development of bi-functional chimeric enzyme (CtGH1-L1-CtGH5-F194A) from endoglucanase (CtGH5) mutant F194A and β-1,4-glucosidase (CtGH1) from Clostridium thermocellum with enhanced activity and structural integrity. BIORESOURCE TECHNOLOGY 2019; 282:494-501. [PMID: 30897487 DOI: 10.1016/j.biortech.2019.03.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/08/2019] [Accepted: 03/09/2019] [Indexed: 06/09/2023]
Abstract
Site-directed mutagenesis of β-1,4-endoglucanase from family 5 glycoside hydrolase (CtGH5) from Clostridium thermocellum was performed to develop a mutant CtGH5-F194A that gave 40 U/mg specific activity against carboxymethyl cellulose, resulting 2-fold higher activity than wild-type CtGH5. CtGH5-F194A was fused with a β-1,4-glucosidase, CtGH1 from Clostridium thermocellum to develop a chimeric enzyme. The chimera (CtGH1-L1-CtGH5-F194A) expressed as a soluble protein using E. coli BL-21cells displaying 3- to 5-fold higher catalytic efficiency for endoglucanase and β-glucosidase activities. TLC analysis of hydrolysed product of CMC by chimera 1 revealed glucose as final product confirming both β-1,4-endoglucanase and β-1,4-glucosidase activities, while the products of CtGH5-F194A were cellobiose and cello-oligosaccharides. Protein melting studies of CtGH5-F194A showed melting temperature (Tm), 68 °C and of CtGH1, 79 °C, whereas, chimera showed 78 °C. The improved structural integrity, thermostability and enhanced bi-functional enzyme activities of chimera makes it potentially useful for industrial application in converting biomass to glucose and thus bioethanol.
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Affiliation(s)
- Priyanka Nath
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India; DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, India
| | - Arun Dhillon
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Krishan Kumar
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Sumitha Banu Jamaldheen
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India; Centre for Energy, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Vijayanand Suryakant Moholkar
- Centre for Energy, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India; Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India; DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, India; Centre for Energy, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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16
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Hamre AG, Kaupang A, Payne CM, Väljamäe P, Sørlie M. Thermodynamic Signatures of Substrate Binding for Three Thermobifida fusca Cellulases with Different Modes of Action. Biochemistry 2019; 58:1648-1659. [PMID: 30785271 DOI: 10.1021/acs.biochem.9b00014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzymatic breakdown of recalcitrant polysaccharides is achieved by synergistic enzyme cocktails of glycoside hydrolases (GHs) and accessory enzymes. Many GHs are processive, meaning that they stay bound to the substrate between subsequent catalytic interactions. Cellulases are GHs that catalyze the hydrolysis of cellulose [β-1,4-linked glucose (Glc)]. Here, we have determined the relative subsite binding affinity for a glucose moiety as well as the thermodynamic signatures for (Glc)6 binding to three of the seven cellulases produced by the bacterium Thermobifida fusca. TfCel48A is exo-processive, TfCel9A endo-processive, and TfCel5A endo-nonprocessive. Initial hydrolysis of (Glc)5 and (Glc)6 was performed in H218O enabling the incorporation of an 18O atom at the new reducing end anomeric carbon. A matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis of the products reveals the intensity ratios of otherwise identical 18O- and 16O-containing products to provide insight into how the substrate is placed during productive binding. The two processive cellulases have significant binding affinity in subsites where products dissociate during processive hydrolysis, aligned with a need to have a pushing potential to remove obstacles on the substrate. Moreover, we observed a correlation between processive ability and favorable binding free energy, as previously postulated. Upon ligand binding, the largest contribution to the binding free energy is desolvation for all three cellulases as determined by isothermal titration calorimetry. The two endo-active cellulases show a more favorable solvation entropy change compared to the exo-active cellulase, while the two processive cellulases have less favorable changes in binding enthalpy compared to the nonprocessive TfCel5A.
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Affiliation(s)
- Anne Grethe Hamre
- Department of Chemistry, Biotechnology and Food Science , Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås , Norway
| | - Anita Kaupang
- Department of Chemistry, Biotechnology and Food Science , Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås , Norway
| | - Christina M Payne
- Department of Chemical and Materials Engineering , University of Kentucky , 177 F. Paul Anderson Tower , Lexington , Kentucky 40506 , United States
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology , University of Tartu , 50090 Tartu , Estonia
| | - Morten Sørlie
- Department of Chemistry, Biotechnology and Food Science , Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås , Norway
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17
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Zhang F, Bunterngsook B, Li JX, Zhao XQ, Champreda V, Liu CG, Bai FW. Regulation and production of lignocellulolytic enzymes from Trichoderma reesei for biofuels production. ADVANCES IN BIOENERGY 2019. [DOI: 10.1016/bs.aibe.2019.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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Han F, Liu Y, E J, Guan S, Han W, Shan Y, Wang S, Zhang H. Effects of Tyr555 and Trp678 on the processivity of cellobiohydrolase A from Ruminiclostridium thermocellum: A simulation study. Biopolymers 2018; 109:e23238. [PMID: 30484856 DOI: 10.1002/bip.23238] [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] [Received: 07/31/2018] [Revised: 09/21/2018] [Accepted: 10/01/2018] [Indexed: 12/12/2022]
Abstract
Cellobiohydrolase A from Ruminiclostridium thermocellum (Cbh9A) is a processive exoglucanase from family 9 and is an important cellobiohydrolase that hydrolyzes cello-oligosaccharide into cellobiose. Residues Tyr555 and Trp678 considerably affect catalytic activity, but their mechanisms are still unknown. To investigate how the Tyr555 and Trp678 affect the processivity of Cbh9A, conventional molecular dynamics, steered molecular dynamics, and free energy calculation were performed to simulate the processive process of wild type (WT)-Cbh9A, Y555S mutant, and W678G mutant. Analysis of simulation results suggests that the binding free energies between the substrate and WT-Cbh9A are lower than those of Y555S and W678G mutants. The pull forces and energy barrier in Y555S and W678G mutants also reduced significantly during the steered molecular dynamics (SMD) simulation compared with that of the WT-Cbh9A. And the potential mean force calculations showed that the pulling energy barrier of Y555S and W678G mutants is much lower than that of WT-Cbh9A.
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Affiliation(s)
- Fei Han
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Ye Liu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Jingwen E
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Shanshan Guan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Yaming Shan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Hao Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
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19
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Lewin GR, Carlos C, Chevrette MG, Horn HA, McDonald BR, Stankey RJ, Fox BG, Currie CR. Evolution and Ecology of Actinobacteria and Their Bioenergy Applications. Annu Rev Microbiol 2017; 70:235-54. [PMID: 27607553 DOI: 10.1146/annurev-micro-102215-095748] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ancient phylum Actinobacteria is composed of phylogenetically and physiologically diverse bacteria that help Earth's ecosystems function. As free-living organisms and symbionts of herbivorous animals, Actinobacteria contribute to the global carbon cycle through the breakdown of plant biomass. In addition, they mediate community dynamics as producers of small molecules with diverse biological activities. Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make Actinobacteria a promising group for the bioenergy industry. Specifically, their enzymes can contribute to industrial-scale breakdown of cellulosic plant biomass into simple sugars that can then be converted into biofuels. Furthermore, harnessing their ability to biosynthesize a range of small molecules has potential for the production of specialty biofuels.
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Affiliation(s)
- Gina R Lewin
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Marc G Chevrette
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Heidi A Horn
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706;
| | - Bradon R McDonald
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Robert J Stankey
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Brian G Fox
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726.,Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
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20
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Kari J, Kont R, Borch K, Buskov S, Olsen JP, Cruyz-Bagger N, Väljamäe P, Westh P. Anomeric Selectivity and Product Profile of a Processive Cellulase. Biochemistry 2016; 56:167-178. [PMID: 28026938 DOI: 10.1021/acs.biochem.6b00636] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cellobiohydrolases (CBHs) make up an important group of enzymes for both natural carbon cycling and industrial deconstruction of lignocellulosic biomass. The consecutive hydrolysis of one cellulose strand relies on an intricate pattern of enzyme-substrate interactions in the long, tunnel-shaped binding site of the CBH. In this work, we have investigated the initial complexation mode with cellulose of the most thoroughly studied CBH, Cel7A from Hypocrea jecorina (HjCel7A). We found that HjCel7A predominantly produces glucose when it initiates a processive run on insoluble microcrystalline cellulose, confirming the validity of an even and odd product ratio as an estimate of processivity. Moreover, the glucose released from cellulose was predominantly α-glucose. A link between the initial binding mode of the enzyme and the reducing end configuration was investigated by inhibition studies with the two anomers of cellobiose. A clear preference for β-cellobiose in product binding site +2 was observed for HjCel7A, but not the homologous endoglucanase, HjCe7B. Possible relationships between this anomeric preference in the product site and the prevalence of odd-numbered initial-cut products are discussed, and a correlation between processivity and anomer selectivity is proposed.
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Affiliation(s)
- Jeppe Kari
- Research Unit for Functional Biomaterials, Roskilde University , Roskilde, Denmark
| | - Riin Kont
- Institute of Molecular and Cell Biology, University of Tartu , Tartu, Estonia
| | - Kim Borch
- Novozymes A/S , Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | - Steen Buskov
- Novozymes A/S , Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | - Johan Pelck Olsen
- Research Unit for Functional Biomaterials, Roskilde University , Roskilde, Denmark
| | | | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu , Tartu, Estonia
| | - Peter Westh
- Research Unit for Functional Biomaterials, Roskilde University , Roskilde, Denmark
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21
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Distribution of Herbivorous Fish Is Frozen by Low Temperature. Sci Rep 2016; 6:39600. [PMID: 28004804 PMCID: PMC5177937 DOI: 10.1038/srep39600] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/24/2016] [Indexed: 11/09/2022] Open
Abstract
The number of herbivores in populations of ectothermic vertebrates decreases with increasing latitude. At higher latitudes, fish consuming plant matter are exclusively omnivorous. We assess whether omnivorous fish readily shift to herbivory or whether animal prey is typically preferred. We address temperature as the key factor causing their absence at higher latitudes and discuss the potential poleward dispersion caused by climate changes. A controlled experiment illustrates that rudd (Scardinius erythrophthalmus) readily utilize plant matter at water temperatures above 20 °C and avoid its consumption below 20 °C. Field data support these results, showing that plant matter dominates rudd diets during the summer and is absent during the spring. Utilizing cellulose requires the enzyme cellulase, which is produced by microorganisms growing at temperatures of 15-42 °C. Water temperatures at higher latitudes do not reach 15 °C year-round; at our latitude of 50°N~150 days/year. Hence, the species richness of omnivorous fish decreases dramatically above 55° latitude. Our results provide support for the hypothesis that strict herbivorous specialists have developed only in the tropics. Temperatures below 15 °C, even for a short time period, inactivate cellulase and cause diet limitations for omnivorous fish. However, we may expect increases in herbivory at higher latitudes caused by climate change.
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22
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Karuna N, Jeoh T. The productive cellulase binding capacity of cellulosic substrates. Biotechnol Bioeng 2016; 114:533-542. [PMID: 27696345 DOI: 10.1002/bit.26193] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/12/2016] [Accepted: 09/26/2016] [Indexed: 01/18/2023]
Abstract
Cellulosic biomass is the most promising feedstock for renewable biofuel production; however, the mechanisms of the heterogeneous cellulose saccharification reaction are still unsolved. As cellulases need to bind isolated molecules of cellulose at the surface of insoluble cellulose fibrils or larger aggregated cellulose structures in order to hydrolyze glycosidic bonds, the "accessibility of cellulose to cellulases" is considered to be a reaction limiting property of cellulose. We have defined the accessibility of cellulose to cellulases as the productive binding capacity of cellulose, that is, the concentration of productive binding sites on cellulose that are accessible for binding and hydrolysis by cellulases. Productive cellulase binding to cellulose results in hydrolysis and can be quantified by measuring hydrolysis rates. In this study, we measured the productive Trichoderma reesei Cel7A (TrCel7A) binding capacity of five cellulosic substrates from different sources and processing histories. Swollen filter paper and bacterial cellulose had higher productive binding capacities of ∼6 µmol/g while filter paper, microcrystalline cellulose, and algal cellulose had lower productive binding capacities of ∼3 µmol/g. Swelling and regenerating filter paper using phosphoric acid increased the initial accessibility of the reducing ends to TrCel7A from 4 to 6 µmol/g. Moreover, this increase in initial productive binding capacity accounted in large part for the difference in the overall digestibility between filter paper and swollen filter paper. We further demonstrated that an understanding of how the productive binding capacity declines over the course of the hydrolysis reaction has the potential to predict overall saccharification time courses. Biotechnol. Bioeng. 2017;114: 533-542. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nardrapee Karuna
- Department of Biological and Agricultural Engineering, University of California, One Shields Ave., Davis 95616, California
| | - Tina Jeoh
- Department of Biological and Agricultural Engineering, University of California, One Shields Ave., Davis 95616, California
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23
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Sun X, Qian MD, Guan SS, Shan YM, Dong Y, Zhang H, Wang S, Han WW. Investigation of an "alternate water supply system" in enzymatic hydrolysis in the processive endocellulase Cel7A from Rasamsonia emersonii by molecular dynamics simulation. Biopolymers 2016; 107:46-60. [PMID: 27696356 DOI: 10.1002/bip.22991] [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] [Received: 07/20/2016] [Revised: 09/26/2016] [Accepted: 09/28/2016] [Indexed: 01/10/2023]
Abstract
Cel7A from Rasamsonia emersonii is one of the processive endocellulases classified under family 7 glycoside hydrolase. Molecular dynamics simulations were carried out to obtain the optimized sliding and hydrolyzing conformations, in which the reducing ends of sugar chains are located on different sites. Hydrogen bonds are investigated to clarify the interactions between protein and substrate in either conformation. Nine hydrogen bonding interactions are identified in the sliding conformation, and six similar interactions are also found correspondingly in the hydrolyzing conformation. In addition, four strong hydrophobic interactions are also determined. The domain cross-correlation map analysis shows movement correlation of protein including autocorrelation between residues. The root mean square fluctuations analysis represents the various flexibilities of different fragment in the two conformations. Comparing the two conformations reveals the water-supply mechanism of selective hydrolysis of cellulose in Cel7A. The mechanism can be described as follow. When the reducing end of substrate slides from the unhydrolyzing site (sliding conformation) to the hydrolyzing site (hydrolyzing conformation), His225 is pushed down and rotated, the rotation leads to the movement of Glu209 with the interstrand hydrogen bonding in β-sheet. It further makes Asp211 close to the hydrolysis center and provides a water molecule bounding on its carboxyl in the previous unhydrolyzing site. After the hydrolysis takes place and the product is excluded from the enzyme, the Asp211 comes back to its initial position. In summary, Asp211 acts as an elevator to transport outer water molecules into the hydrolysis site for every other glycosidic bond.
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Affiliation(s)
- Xun Sun
- Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, People's Republic of China
| | - Meng-Dan Qian
- Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, People's Republic of China
| | - Shan-Shan Guan
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, National Engineering Laboratory for AIDS Vaccine, College of Life Sciences, Jilin University, Changchun, 130012, People's Republic of China
| | - Ya-Ming Shan
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, National Engineering Laboratory for AIDS Vaccine, College of Life Sciences, Jilin University, Changchun, 130012, People's Republic of China
| | - Ying Dong
- Bethune pharmaceutical factory, Jilin University, Changchun, 130012, People's Republic of China
| | - Hao Zhang
- Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, People's Republic of China
| | - Song Wang
- Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, People's Republic of China
| | - Wei-Wei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, National Engineering Laboratory for AIDS Vaccine, College of Life Sciences, Jilin University, Changchun, 130012, People's Republic of China.,Department of Computer Science, C.S. Bond Life Sciences Center, University of Missouri Columbia, Missouri, 65211
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Functional and modular analyses of diverse endoglucanases from Ruminococcus albus 8, a specialist plant cell wall degrading bacterium. Sci Rep 2016; 6:29979. [PMID: 27439730 PMCID: PMC4954948 DOI: 10.1038/srep29979] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/24/2016] [Indexed: 11/09/2022] Open
Abstract
Ruminococcus albus 8 is a specialist plant cell wall degrading ruminal bacterium capable of utilizing hemicellulose and cellulose. Cellulose degradation requires a suite of enzymes including endoglucanases, exoglucanases, and β-glucosidases. The enzymes employed by R. albus 8 in degrading cellulose are yet to be completely elucidated. Through bioinformatic analysis of a draft genome sequence of R. albus 8, seventeen putatively cellulolytic genes were identified. The genes were heterologously expressed in E. coli, and purified to near homogeneity. On biochemical analysis with cellulosic substrates, seven of the gene products (Ra0185, Ra0259, Ra0325, Ra0903, Ra1831, Ra2461, and Ra2535) were identified as endoglucanases, releasing predominantly cellobiose and cellotriose. Each of the R. albus 8 endoglucanases, except for Ra0259 and Ra0325, bound to the model crystalline cellulose Avicel, confirming functional carbohydrate binding modules (CBMs). The polypeptides for Ra1831 and Ra2535 were found to contain distantly related homologs of CBM65. Mutational analysis of residues within the CBM65 of Ra1831 identified key residues required for binding. Phylogenetic analysis of the endoglucanases revealed three distinct subfamilies of glycoside hydrolase family 5 (GH5). Our results demonstrate that this fibrolytic bacterium uses diverse GH5 catalytic domains appended with different CBMs, including novel forms of CBM65, to degrade cellulose.
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Vasina DV, Pavlov AR, Koroleva OV. Extracellular proteins of Trametes hirsuta st. 072 induced by copper ions and a lignocellulose substrate. BMC Microbiol 2016; 16:106. [PMID: 27296712 PMCID: PMC4906887 DOI: 10.1186/s12866-016-0729-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 06/06/2016] [Indexed: 11/10/2022] Open
Abstract
Background Fungi are organisms with the highest natural capacity to degrade lignocellulose substrates, which is enabled by complex systems of extracellular enzymes, whose expression and secretion depend on the characteristics of substrates and the environment. Results This study reports a secretome analysis for white-rot basidiomycete Trametes hirsuta cultivated on a synthetic media and a lignocellulose substrate. We demonstrate that T. hirsuta st. 072 produces multiple extracellular ligninolytic, cellulolytic, hemicellulolytic, peroxide generating, and proteolytic enzymes, as well as cerato-platanins. In contrast to other white rot species described earlier, which mostly secreted glucanases and mannosidases in response to the presence of the lignocellulose substrate, T. hirsuta expressed a spectrum of extracellular cellulolytic enzymes containing predominantly cellobiases and xylanases. As proteomic analysis could not detect lignin peroxidase (LiP) among the secreted lignin degrading enzymes, we attributed the observed extracellular LiP - like activity to the expressed versatile peroxidase (VP). An accessory enzyme, glyoxal oxidase, was found among the proteins secreted in the media during submerged cultivation of T. hirsuta both in the presence and in the absence of copper. However, aryl-alcohol oxidase (AAO) was not identified, despite the presence of AAO enzymatic activity secreted by the fungus. The spectra of the expressed enzymes dramatically changed depending on the growth conditions. Transfer from submerged cultivation to surface cultivation with the lignocellulose substrate switched off expression of exo-β-1,3-glucanase and α-amylase and turned on secretion of endo-β-1,3-glucanase and a range of glycosidases. In addition, an aspartic peptidase started being expressed instead of family S53 protease. For the first time, we report production of cerato-platanin proteins by Trametes species. The secretion of cerato-platanins was observed only in response to contact with lignocellulose, thus indicating a specific role of these proteins in degradation of the lignocellulose substrates. Conclusions Our results suggest a sequential mechanism of natural substrate degradation by T. hirsuta, in which the fungus produces different sets of enzymes to digest all main components of the substrate during cultivation. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0729-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daria V Vasina
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave, Moscow, 119071, Russia.
| | - Andrey R Pavlov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave, Moscow, 119071, Russia
| | - Olga V Koroleva
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave, Moscow, 119071, Russia
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A Structurally Novel Chitinase from the Chitin-Degrading Hyperthermophilic Archaeon Thermococcus chitonophagus. Appl Environ Microbiol 2016; 82:3554-3562. [PMID: 27060120 DOI: 10.1128/aem.00319-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/03/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED A structurally novel chitinase, Tc-ChiD, was identified from the hyperthermophilic archaeon Thermococcus chitonophagus, which can grow on chitin as the sole organic carbon source. The gene encoding Tc-ChiD contains regions corresponding to a signal sequence, two chitin-binding domains, and a putative catalytic domain. This catalytic domain shows no similarity with previously characterized chitinases but resembles an uncharacterized protein found in the mesophilic anaerobic bacterium Clostridium botulinum Two recombinant Tc-ChiD proteins were produced in Escherichia coli, one without the signal sequence [Tc-ChiD(ΔS)] and the other corresponding only to the putative catalytic domain [Tc-ChiD(ΔBD)]. Enzyme assays using N-acetylglucosamine (GlcNAc) oligomers indicated that both proteins hydrolyze GlcNAc oligomers longer than (GlcNAc)4 Chitinase assays using colloidal chitin suggested that Tc-ChiD is an exo-type chitinase that releases (GlcNAc)2 or (GlcNAc)3 Analysis with GlcNAc oligomers modified with p-nitrophenol suggested that Tc-ChiD recognizes the reducing end of chitin chains. While Tc-ChiD(ΔBD) displayed a higher initial velocity than that of Tc-ChiD(ΔS), we found that the presence of the two chitin-binding domains significantly enhanced the thermostability of the catalytic domain. In T. chitonophagus, another chitinase ortholog that is similar to the Thermococcus kodakarensis chitinase ChiA is present and can degrade chitin from the nonreducing ends. Therefore, the presence of multiple chitinases in T. chitonophagus with different modes of cleavage may contribute to its unique ability to efficiently degrade chitin. IMPORTANCE A structurally novel chitinase, Tc-ChiD, was identified from Thermococcus chitonophagus, a hyperthermophilic archaeon. The protein contains a signal peptide for secretion, two chitin-binding domains, and a catalytic domain that shows no similarity with previously characterized chitinases. Tc-ChiD thus represents a new family of chitinases. Tc-ChiD is an exo-type chitinase that recognizes the reducing end of chitin chains and releases (GlcNAc)2 or (GlcNAc)3 As a thermostable chitinase that recognizes the reducing end of chitin chains was not previously known, Tc-ChiD may be useful in a wide range of enzyme-based technologies to degrade and utilize chitin.
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Chen M, Bu L, Alahuhta M, Brunecky R, Xu Q, Lunin VV, Brady JW, Crowley MF, Himmel ME, Bomble YJ. Strategies to reduce end-product inhibition in family 48 glycoside hydrolases. Proteins 2016; 84:295-304. [PMID: 26572060 DOI: 10.1002/prot.24965] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/02/2015] [Accepted: 11/06/2015] [Indexed: 11/07/2022]
Abstract
Family 48 cellobiohydrolases are some of the most abundant glycoside hydrolases in nature. They are able to degrade cellulosic biomass and therefore serve as good enzyme candidates for biofuel production. Family 48 cellulases hydrolyze cellulose chains via a processive mechanism, and produce end products composed primarily of cellobiose as well as other cellooligomers (dp ≤ 4). The challenge of utilizing cellulases in biofuel production lies in their extremely slow turnover rate. A factor contributing to the low enzyme activity is suggested to be product binding to enzyme and the resulting performance inhibition. In this study, we quantitatively evaluated the product inhibitory effect of four family 48 glycoside hydrolases using molecular dynamics simulations and product expulsion free-energy calculations. We also suggested a series of single mutants of the four family 48 glycoside hydrolases with theoretically reduced level of product inhibition. The theoretical calculations provide a guide for future experimental studies designed to produce mutant cellulases with enhanced activity.
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Affiliation(s)
- Mo Chen
- Department of Food Science, Cornell University, Ithaca, New York
| | - Lintao Bu
- National Renewable Energy Laboratory, Golden, Colorado
| | | | | | - Qi Xu
- National Renewable Energy Laboratory, Golden, Colorado
| | | | - John W Brady
- Department of Food Science, Cornell University, Ithaca, New York
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Deng K, Takasuka TE, Bianchetti CM, Bergeman LF, Adams PD, Northen TR, Fox BG. Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases. Front Bioeng Biotechnol 2015; 3:165. [PMID: 26579511 PMCID: PMC4621489 DOI: 10.3389/fbioe.2015.00165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/02/2015] [Indexed: 12/20/2022] Open
Abstract
Chemically synthesized nanostructure-initiator mass spectrometry (NIMS) probes derivatized with tetrasaccharides were used to study the reactivity of representative Clostridium thermocellum β-glucosidase, endoglucanases, and cellobiohydrolase. Diagnostic patterns for reactions of these different classes of enzymes were observed. Results show sequential removal of glucose by the β-glucosidase and a progressive increase in specificity of reaction from endoglucanases to cellobiohydrolase. Time-dependent reactions of these polysaccharide-selective enzymes were modeled by numerical integration, which provides a quantitative basis to make functional distinctions among a continuum of naturally evolved catalytic properties. Consequently, our method, which combines automated protein translation with high-sensitivity and time-dependent detection of multiple products, provides a new approach to annotate glycoside hydrolase phylogenetic trees with functional measurements.
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Affiliation(s)
- Kai Deng
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Taichi E Takasuka
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA
| | - Christopher M Bianchetti
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA ; Department of Chemistry, University of Wisconsin-Oshkosh , Oshkosh, WI , USA
| | - Lai F Bergeman
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA
| | - Paul D Adams
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA ; Department of Bioengineering, University of California Berkeley , Berkeley, CA , USA
| | - Trent R Northen
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Brian G Fox
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA ; Department of Biochemistry, University of Wisconsin-Madison , Madison, WI , USA
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29
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Hamid SBA, Islam MM, Das R. Cellulase biocatalysis: key influencing factors and mode of action. CELLULOSE 2015; 22:2157-2182. [DOI: 10.1007/s10570-015-0672-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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30
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Szydlowski L, Boschetti C, Crisp A, Barbosa E, Tunnacliffe A. Multiple horizontally acquired genes from fungal and prokaryotic donors encode cellulolytic enzymes in the bdelloid rotifer Adineta ricciae. Gene 2015; 566:125-37. [DOI: 10.1016/j.gene.2015.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 10/23/2022]
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31
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The directionality of processive enzymes acting on recalcitrant polysaccharides is reflected in the kinetic signatures of oligomer degradation. FEBS Lett 2015; 589:1807-12. [DOI: 10.1016/j.febslet.2015.05.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 04/17/2015] [Accepted: 05/20/2015] [Indexed: 11/18/2022]
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32
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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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33
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34
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Bornscheuer U, Buchholz K, Seibel J. Enzymatic degradation of (ligno)cellulose. Angew Chem Int Ed Engl 2014; 53:10876-93. [PMID: 25136976 DOI: 10.1002/anie.201309953] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Indexed: 11/06/2022]
Abstract
Glycoside-degrading enzymes play a dominant role in the biochemical conversion of cellulosic biomass into low-price biofuels and high-value-added chemicals. New insight into protein functions and substrate structures, the kinetics of recognition, and degradation events has resulted in a substantial improvement of our understanding of cellulose degradation.
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Affiliation(s)
- Uwe Bornscheuer
- Ernst-Moritz-Arndt-Universität Greifswald, Biotechnologie und Enzymkatalyse, Institut für Biochemie, Felix-Hausdorff-Strasse 4, 17487 Greifswald (Germany)
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35
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Shang BZ, Chu JW. Kinetic Modeling at Single-Molecule Resolution Elucidates the Mechanisms of Cellulase Synergy. ACS Catal 2014. [DOI: 10.1021/cs500126q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Barry Z. Shang
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Jhih-Wei Chu
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department
of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, ROC
- Institute
of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, ROC
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36
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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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37
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Zhang H, Zhang JL, Sun L, Niu XD, Wang S, Shan YM. Molecular dynamics simulation of the processive endocellulase Cel48F fromClostridium cellulolyticum: a novel “water-control mechanism” in enzymatic hydrolysis of cellulose. J Mol Recognit 2014; 27:438-47. [DOI: 10.1002/jmr.2364] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 01/14/2014] [Accepted: 01/28/2014] [Indexed: 11/05/2022]
Affiliation(s)
- Hao Zhang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry; Jilin University; Changchun 130023 China
| | - Ji-long Zhang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry; Jilin University; Changchun 130023 China
| | - Lu Sun
- Department of Pharmacy, China-Japan Union Hospital; Jilin University; Changchun 130033 China
| | - Xiao-di Niu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry; Jilin University; Changchun 130023 China
| | - Song Wang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry; Jilin University; Changchun 130023 China
| | - Ya-ming Shan
- College of Life Science; Jilin University; Changchun 130012 China
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38
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Biochemical properties and atomic resolution structure of a proteolytically processed β-mannanase from cellulolytic Streptomyces sp. SirexAA-E. PLoS One 2014; 9:e94166. [PMID: 24710170 PMCID: PMC3978015 DOI: 10.1371/journal.pone.0094166] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/11/2014] [Indexed: 01/07/2023] Open
Abstract
β-Mannanase SACTE_2347 from cellulolytic Streptomyces sp. SirexAA-E is abundantly secreted into the culture medium during growth on cellulosic materials. The enzyme is composed of domains from the glycoside hydrolase family 5 (GH5), fibronectin type-III (Fn3), and carbohydrate binding module family 2 (CBM2). After secretion, the enzyme is proteolyzed into three different, catalytically active variants with masses of 53, 42 and 34 kDa corresponding to the intact protein, loss of the CBM2 domain, or loss of both the Fn3 and CBM2 domains. The three variants had identical N-termini starting with Ala51, and the positions of specific proteolytic reactions in the linker sequences separating the three domains were identified. To conduct biochemical and structural characterizations, the natural proteolytic variants were reproduced by cloning and heterologously expressed in Escherichia coli. Each SACTE_2347 variant hydrolyzed only β-1,4 mannosidic linkages, and also reacted with pure mannans containing partial galactosyl- and/or glucosyl substitutions. Examination of the X-ray crystal structure of the GH5 domain of SACTE_2347 suggests that two loops adjacent to the active site channel, which have differences in position and length relative to other closely related mannanases, play a role in producing the observed substrate selectivity.
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39
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Chen M, Kostylev M, Bomble YJ, Crowley MF, Himmel ME, Wilson DB, Brady JW. Experimental and Modeling Studies of an Unusual Water-Filled Pore Structure with Possible Mechanistic Implications in Family 48 Cellulases. J Phys Chem B 2014; 118:2306-15. [DOI: 10.1021/jp408767j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mo Chen
- Department
of Food Science, Cornell University, Ithaca, New York 14853, United States
| | - Maxim Kostylev
- Department
of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States
| | - Yannick J. Bomble
- Biosciences
Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401-3393, United States
| | - Michael F. Crowley
- Biosciences
Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401-3393, United States
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401-3393, United States
| | - David B. Wilson
- Department
of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States
| | - John W. Brady
- Department
of Food Science, Cornell University, Ithaca, New York 14853, United States
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40
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Santos CR, Polo CC, Costa MCMF, Nascimento AFZ, Meza AN, Cota J, Hoffmam ZB, Honorato RV, Oliveira PSL, Goldman GH, Gilbert HJ, Prade RA, Ruller R, Squina FM, Wong DWS, Murakami MT. Mechanistic strategies for catalysis adopted by evolutionary distinct family 43 arabinanases. J Biol Chem 2014; 289:7362-73. [PMID: 24469445 DOI: 10.1074/jbc.m113.537167] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Arabinanases (ABNs, EC 3.2.1.99) are promising catalysts for environmentally friendly biomass conversion into energy and chemicals. These enzymes catalyze the hydrolysis of the α-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans releasing arabino-oligosaccharides and arabinose, the second most abundant pentose in nature. In this work, new findings about the molecular mechanisms governing activation, functional differentiation, and catalysis of GH43 ABNs are presented. Biophysical, mutational, and biochemical studies with the hyperthermostable two-domain endo-acting ABN from Thermotoga petrophila (TpABN) revealed how some GH43 ABNs are activated by calcium ions via hyperpolarization of the catalytically relevant histidine and the importance of the ancillary domain for catalysis and conformational stability. On the other hand, the two GH43 ABNs from rumen metagenome, ARN2 and ARN3, presented a calcium-independent mechanism in which sodium is the most likely substituent for calcium ions. The crystal structure of the two-domain endo-acting ARN2 showed that its ability to efficiently degrade branched substrates is due to a larger catalytic interface with higher accessibility than that observed in other ABNs with preference for linear arabinan. Moreover, crystallographic characterization of the single-domain exo-acting ARN3 indicated that its cleavage pattern producing arabinose is associated with the chemical recognition of the reducing end of the substrate imposed by steric impediments at the aglycone-binding site. By structure-guided rational design, ARN3 was converted into a classical endo enzyme, confirming the role of the extended Arg(203)-Ala(230) loop in determining its action mode. These results reveal novel molecular aspects concerning the functioning of GH43 ABNs and provide new strategies for arabinan degradation.
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41
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Navarro D, Rosso MN, Haon M, Olivé C, Bonnin E, Lesage-Meessen L, Chevret D, Coutinho PM, Henrissat B, Berrin JG. Fast solubilization of recalcitrant cellulosic biomass by the basidiomycete fungus Laetisaria arvalis involves successive secretion of oxidative and hydrolytic enzymes. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:143. [PMID: 25320637 PMCID: PMC4197297 DOI: 10.1186/s13068-014-0143-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/18/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND Enzymatic breakdown of lignocellulosic biomass is a known bottleneck for the production of high-value molecules and biofuels from renewable sources. Filamentous fungi are the predominant natural source of enzymes acting on lignocellulose. We describe the extraordinary cellulose-deconstructing capacity of the basidiomycete Laetisaria arvalis, a soil-inhabiting fungus. RESULTS The L. arvalis strain displayed the capacity to grow on wheat straw as the sole carbon source and to fully digest cellulose filter paper. The cellulolytic activity exhibited in the secretomes of L. arvalis was up to 7.5 times higher than that of a reference Trichoderma reesei industrial strain, resulting in a significant improvement of the glucose release from steam-exploded wheat straw. Global transcriptome and secretome analyses revealed that L. arvalis produces a unique repertoire of carbohydrate-active enzymes in the fungal taxa, including a complete set of enzymes acting on cellulose. Temporal analyses of secretomes indicated that the unusual degradation efficiency of L. arvalis relies on its early response to the carbon source, and on the finely tuned sequential secretion of several lytic polysaccharide monooxygenases and hydrolytic enzymes targeting cellulose. CONCLUSIONS The present study illustrates the adaptation of a litter-rot fungus to the rapid breakdown of recalcitrant plant biomass. The cellulolytic capabilities of this basidiomycete fungus result from the rapid, selective and successive secretion of oxidative and hydrolytic enzymes. These enzymes expressed at critical times during biomass degradation may inspire the design of improved enzyme cocktails for the conversion of plant cell wall resources into fermentable sugars.
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Affiliation(s)
- David Navarro
- />INRA, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
- />Aix-Marseille Université, Polytech Marseille, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
- />CIRM-CF, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
| | - Marie-Noëlle Rosso
- />INRA, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
- />Aix-Marseille Université, Polytech Marseille, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
| | - Mireille Haon
- />INRA, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
- />Aix-Marseille Université, Polytech Marseille, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
| | - Caroline Olivé
- />INRA, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
- />Aix-Marseille Université, Polytech Marseille, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
| | - Estelle Bonnin
- />INRA, Unité de Recherche Biopolymères, Interactions, Assemblages, 44316 Nantes, France
| | - Laurence Lesage-Meessen
- />INRA, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
- />Aix-Marseille Université, Polytech Marseille, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
| | - Didier Chevret
- />INRA, UMR1319 Micalis, Plateforme d’Analyse Protéomique de Paris Sud-Ouest, 78352 Jouy-en-Josas, France
| | - Pedro M Coutinho
- />CNRS, UMR7257 Architecture et Fonction des Macromolécules Biologiques, 13288 Marseille, France
- />Aix-Marseille Université, UMR7257 Architecture et Fonction des Macromolécules Biologiques, 13288 Marseille, France
| | - Bernard Henrissat
- />Aix-Marseille Université, UMR7257 Architecture et Fonction des Macromolécules Biologiques, 13288 Marseille, France
- />Department of Biological Sciences, King Abdulaziz University, Abdullah Sulayman, Jeddah, 22254 Saudi Arabia
| | - Jean-Guy Berrin
- />INRA, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
- />Aix-Marseille Université, Polytech Marseille, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
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42
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Xu L, Shen Y, Hou J, Peng B, Tang H, Bao X. Secretory pathway engineering enhances secretion of cellobiohydrolase I from Trichoderma reesei in Saccharomyces cerevisiae. J Biosci Bioeng 2014; 117:45-52. [DOI: 10.1016/j.jbiosc.2013.06.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 05/27/2013] [Accepted: 06/16/2013] [Indexed: 10/26/2022]
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Payne CM, Jiang W, Shirts MR, Himmel ME, Crowley MF, Beckham GT. Glycoside Hydrolase Processivity Is Directly Related to Oligosaccharide Binding Free Energy. J Am Chem Soc 2013; 135:18831-9. [DOI: 10.1021/ja407287f] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Wei Jiang
- Argonne
Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Michael R. Shirts
- Department
of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
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Wang J, Quirk A, Lipkowski J, Dutcher JR, Clarke AJ. Direct in situ observation of synergism between cellulolytic enzymes during the biodegradation of crystalline cellulose fibers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14997-5005. [PMID: 24195649 DOI: 10.1021/la403401c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
High-resolution atomic force microscopy (AFM) was used to image the real-time in situ degradation of crystalline by three types of T. reesei cellulolytic enzymes-TrCel6A, TrCel7A, and TrCel7B-and their mixtures. TrCel6A and TrCel7A are exo-acting cellobiohydrolases processing cellulose fibers from the nonreducing and reducing ends, respectively. TrCel7B is an endoglucanase that hydrolyzes amorphous cellulose within fibers. When acting alone on native cellulose fibers, each of the three enzymes is incapable of significant degradation. However, mixtures of two enzymes exhibited synergistic effects. The degradation effects of this synergism depended on the order in which the enzymes were added. Faster hydrolysis rates were observed when TrCel7A (exo) was added to fibers pretreated first with TrCel7B (endo) than when adding the enzymes in the opposite order. Endo-acting TrCel7B removed amorphous cellulose, softened and swelled the fibers, and exposed single microfibrils, facilitating the attack by the exo-acting enzymes. AFM images revealed that exo-acting enzymes processed the TrCel7B-pretreated fibers preferentially from one specific end (reducing or nonreducing). The most efficient (almost 100%) hydrolysis was observed with the mixture of the three enzymes. In this mixture, TrCel7B softened the fiber and TrCel6A and TrCel7A were directly observed to process it from the two opposing ends. This study provides high-resolution direct visualization of the nature of the synergistic relation between T. reesei exo- and endo-acting enzymes digesting native crystalline cellulose.
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Affiliation(s)
- Jingpeng Wang
- Department of Chemistry, ‡Department of Physics, and §Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario N1G 2W1, Canada
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45
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Kostylev M, Alahuhta M, Chen M, Brunecky R, Himmel ME, Lunin VV, Brady J, Wilson DB. Cel48A fromThermobifida fusca: Structure and site directed mutagenesis of key residues. Biotechnol Bioeng 2013; 111:664-73. [DOI: 10.1002/bit.25139] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 10/05/2013] [Accepted: 10/21/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Maxim Kostylev
- Department of Molecular Biology and Genetics; Cornell University; 458 Biotechnology Building Ithaca New York 14853
| | - Markus Alahuhta
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - Mo Chen
- Department of Food Science; Cornell University; Ithaca New York
| | - Roman Brunecky
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - Michael E. Himmel
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - Vladimir V. Lunin
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - John Brady
- Department of Food Science; Cornell University; Ithaca New York
| | - David B. Wilson
- Department of Molecular Biology and Genetics; Cornell University; 458 Biotechnology Building Ithaca New York 14853
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46
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A distinct model of synergism between a processive endocellulase (TfCel9A) and an exocellulase (TfCel48A) from Thermobifida fusca. Appl Environ Microbiol 2013; 80:339-44. [PMID: 24162578 DOI: 10.1128/aem.02706-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Lignocellulosic biomass is digested in nature by the synergistic activities of enzymes with complementary properties, and understanding synergistic interactions will improve the efficiency of industrial biomass use for sustainable fuels and chemicals. Cel9A and Cel48A from a model bacterium, Thermobifida fusca (TfCel9A and TfCel48A, respectively), are two cellulases with different properties and have previously been shown to synergize well with each other. TfCel9A is a processive endocellulase with relatively high activity on crystalline cellulose. TfCel48A is a reducing end-directed exocellulase with very low activity on crystalline cellulose. Neither enzyme fits its respective role in the classical synergism model of enzymatic cellulose digestion. Using the results of time course, endpoint, and sequential addition activity assays, we propose a model of synergistic cooperation between the two cellulases. TfCel9A is most effective on fresh bacterial cellulose with a presumably uniform surface at the molecular level. Its processive activity likely erodes the surface and thus reduces its own activity. TfCel48A is able to hydrolyze the TfCel9A-modified substrate efficiently and replenish the uniform surface required by TfCel9A, creating a feedback mechanism. The model of synergistic interactions is comparable to an earlier proposed model for Trichoderma reesei Cel7A and Cel7B, but the roles of endo- and exocellulases are reversed, a finding which suggests that bacteria and fungi may have evolved different approaches to efficient biomass degradation.
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47
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Improved cellobiose utilization in E. coli by including both hydrolysis and phosphorolysis mechanisms. Biotechnol Lett 2013; 36:301-7. [DOI: 10.1007/s10529-013-1355-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 09/13/2013] [Indexed: 10/26/2022]
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48
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Li Y, Peng X, Chen H. Comparative characterization of proteins secreted by Neurospora sitophila in solid-state and submerged fermentation. J Biosci Bioeng 2013; 116:493-8. [DOI: 10.1016/j.jbiosc.2013.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 03/05/2013] [Accepted: 04/01/2013] [Indexed: 10/26/2022]
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49
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Payne CM, Resch MG, Chen L, Crowley MF, Himmel ME, Taylor LE, Sandgren M, Ståhlberg J, Stals I, Tan Z, Beckham GT. Glycosylated linkers in multimodular lignocellulose-degrading enzymes dynamically bind to cellulose. Proc Natl Acad Sci U S A 2013; 110:14646-51. [PMID: 23959893 PMCID: PMC3767562 DOI: 10.1073/pnas.1309106110] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plant cell-wall polysaccharides represent a vast source of food in nature. To depolymerize polysaccharides to soluble sugars, many organisms use multifunctional enzyme mixtures consisting of glycoside hydrolases, lytic polysaccharide mono-oxygenases, polysaccharide lyases, and carbohydrate esterases, as well as accessory, redox-active enzymes for lignin depolymerization. Many of these enzymes that degrade lignocellulose are multimodular with carbohydrate-binding modules (CBMs) and catalytic domains connected by flexible, glycosylated linkers. These linkers have long been thought to simply serve as a tether between structured domains or to act in an inchworm-like fashion during catalytic action. To examine linker function, we performed molecular dynamics (MD) simulations of the Trichoderma reesei Family 6 and Family 7 cellobiohydrolases (TrCel6A and TrCel7A, respectively) bound to cellulose. During these simulations, the glycosylated linkers bind directly to cellulose, suggesting a previously unknown role in enzyme action. The prediction from the MD simulations was examined experimentally by measuring the binding affinity of the Cel7A CBM and the natively glycosylated Cel7A CBM-linker. On crystalline cellulose, the glycosylated linker enhances the binding affinity over the CBM alone by an order of magnitude. The MD simulations before and after binding of the linker also suggest that the bound linker may affect enzyme action due to significant damping in the enzyme fluctuations. Together, these results suggest that glycosylated linkers in carbohydrate-active enzymes, which are intrinsically disordered proteins in solution, aid in dynamic binding during the enzymatic deconstruction of plant cell walls.
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Affiliation(s)
- Christina M. Payne
- Biosciences Center and
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY 40506
| | | | - Liqun Chen
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80303
| | | | | | | | - Mats Sandgren
- Department of Molecular Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Molecular Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Ingeborg Stals
- Faculty of Applied Bioscience Engineering, University College Ghent, 9000 Ghent, Belgium
- Department of Biochemistry and Molecular Biology, Ghent University, 9000 Ghent, Belgium; and
| | - Zhongping Tan
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80303
| | - Gregg T. Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401
- Department of Chemical Engineering, Colorado School of Mines, Golden, CO 80401
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50
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Ghattyvenkatakrishna PK, Alekozai EM, Beckham GT, Schulz R, Crowley MF, Uberbacher EC, Cheng X. Initial recognition of a cellodextrin chain in the cellulose-binding tunnel may affect cellobiohydrolase directional specificity. Biophys J 2013; 104:904-12. [PMID: 23442969 DOI: 10.1016/j.bpj.2012.12.052] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/14/2012] [Accepted: 12/27/2012] [Indexed: 10/27/2022] Open
Abstract
Cellobiohydrolases processively hydrolyze glycosidic linkages in individual polymer chains of cellulose microfibrils, and typically exhibit specificity for either the reducing or nonreducing end of cellulose. Here, we conduct molecular dynamics simulations and free energy calculations to examine the initial binding of a cellulose chain into the catalytic tunnel of the reducing-end-specific Family 7 cellobiohydrolase (Cel7A) from Hypocrea jecorina. In unrestrained simulations, the cellulose diffuses into the tunnel from the -7 to the -5 positions, and the associated free energy profiles exhibit no barriers for initial processivity. The comparison of the free energy profiles for different cellulose chain orientations show a thermodynamic preference for the reducing end, suggesting that the preferential initial binding may affect the directional specificity of the enzyme by impeding nonproductive (nonreducing end) binding. Finally, the Trp-40 at the tunnel entrance is shown with free energy calculations to have a significant effect on initial chain complexation in Cel7A.
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