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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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2
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Najavand S, Habibnejad M, Amani-Ghadim AR, Rahimizadeh P, Pazhang M. Optimized immobilization of endoglucanase Cel9A onto glutaraldehyde activated chitosan nanoparticles by response surface methodology: The study of kinetic behaviors. Biotechnol Prog 2020; 36:e2960. [PMID: 31925939 DOI: 10.1002/btpr.2960] [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: 08/28/2019] [Revised: 12/11/2019] [Accepted: 01/06/2020] [Indexed: 11/06/2022]
Abstract
Immobilization of enzyme onto nanoparticles such as chitosan can have biotechnological importance. In this study, chitosan nanoparticles (ChNPs) were prepared by Ionic gelation method and Endoglucanase Cel9A from Alicyclobacillus acidocaldariius (AaCel9A) immobilized on the nanoparticles. The FTIR results showed that the enzymes were immobilized on the ChNPs. The dynamic light scattering and scanning electron microscope (SEM) results illustrated that the AaCel9A-ChNPs approximately had 40 nm diameters. For optimizing enzyme immobilization, response surface methodology was employed using different variables (pH, enzyme immobilization time, and enzyme to ChNPs ratio [E/Cs]). The results showed that the high immobilization efficiency was achieved in pH 7, E/Cs of 0.4 in 2.63 hr. The enzyme activity results showed that, immobilization increased optimum pH for activity (from 6.5 to 7.5) and the enzyme Km (from 3.703 to 12.195 [mg/ml]), which make it suitable to use in some industries such as detergents.
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Affiliation(s)
- Saeed Najavand
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Mahdiyeh Habibnejad
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - A R Amani-Ghadim
- Department of Chemistry, Faculty of Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Parastou Rahimizadeh
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Mohammad Pazhang
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
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3
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Immobilization of endoglucanase Cel9A on chitosan nanoparticles leads to its stabilization against organic solvents: the use of polyols to improve the stability. 3 Biotech 2019; 9:269. [PMID: 31218180 DOI: 10.1007/s13205-019-1794-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/03/2019] [Indexed: 12/21/2022] Open
Abstract
The immobilization of enzymes improves their stability in non-conventional media such as organic solvents. In this work, the effects of solvents (DMSO, methanol, ethanol, and n-propanol) on the endoglucanase Cel9A activity and stability were studied. Then, the enzymes were stabilized by its immobilization on chitosan nanoparticles and also using polyols (sorbitol and glycerol) against organic solvents. The SEM results illustrated that the chitosan nanoparticles had about 40 nm diameter. The results indicated that the organic solvents, especially n-propanol, decreased the activity of the free and immobilized enzymes. The reduced activity of the immobilized enzyme was less than that of the free enzyme. Our studies about the enzymes' stability showed that the free and immobilized enzymes in hydrophobic solvents (with high log P) had the lowest stability compared to other solvents as we observed the half-life of the free enzyme in n-propanol solvent was 2.84 min, and the half-life of the immobilized enzyme was 4.98 min in n-propanol and ethanol solvents 4.50 min. Analysis of the combinatory effects of polyols (sorbitol and glycerol) and the solvents on the stability revealed that sorbitol and glycerol had the most stabilizing effect on the free enzyme in hydrophilic (DMSO) and hydrophobic (n-propanol) solvents, respectively. However, the stabilizing effects of polyols in the immobilized enzyme were independent of the solvents' hydrophobicity (or log P) due to the hydrophilic properties of chitosan nanoparticles. Therefore, one can conclude that the physiochemical properties of nanoparticles (such as hydrophilicity) influence the stabilizing effects of polyols on immobilized enzyme.
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Cui J, Mai G, Wang Z, Liu Q, Zhou Y, Ma Y, Liu C. Metagenomic Insights Into a Cellulose-Rich Niche Reveal Microbial Cooperation in Cellulose Degradation. Front Microbiol 2019; 10:618. [PMID: 30984144 PMCID: PMC6447707 DOI: 10.3389/fmicb.2019.00618] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 03/11/2019] [Indexed: 11/22/2022] Open
Abstract
Background Cellulose is the most abundant organic polymer mainly produced by plants in nature. It is insoluble and highly resistant to enzymatic hydrolysis. Cellulolytic microorganisms that are capable of producing a battery of related enzymes play an important role in recycling cellulose-rich plant biomass. Effective cellulose degradation by multiple synergic microorganisms has been observed within a defined microbial consortium in the lab culture. Metagenomic analysis may enable us to understand how microbes cooperate in cellulose degradation in a more complex microbial free-living ecosystem in nature. Results Here we investigated a typical cellulose-rich and alkaline niche where constituent microbes survive through inter-genera cooperation in cellulose utilization. The niche has been generated in an ancient paper-making plant, which has served as an isolated habitat for over 7 centuries. Combined amplicon-based sequencing of 16S rRNA genes and metagenomic sequencing, our analyses showed a microbial composition with 6 dominant genera including Cloacibacterium, Paludibacter, Exiguobacterium, Acetivibrio, Tolumonas, and Clostridium in this cellulose-rich niche; the composition is distinct from other cellulose-rich niches including a modern paper mill, bamboo soil, wild giant panda guts, and termite hindguts. In total, 11,676 genes of 96 glucoside hydrolase (GH) families, as well as 1,744 genes of carbohydrate transporters were identified, and modeling analysis of two representative genes suggested that these glucoside hydrolases likely evolved to adapt to alkaline environments. Further reconstruction of the microbial draft genomes by binning the assembled contigs predicted a mutualistic interaction between the dominant microbes regarding the cellulolytic process in the niche, with Paludibacter and Clostridium acting as helpers that produce endoglucanases, and Cloacibacterium, Exiguobacterium, Acetivibrio, and Tolumonas being beneficiaries that cross-feed on the cellodextrins by oligosaccharide uptake. Conclusion The analysis of the key genes involved in cellulose degradation and reconstruction of the microbial draft genomes by binning the assembled contigs predicted a mutualistic interaction based on public goods regarding the cellulolytic process in the niche, suggesting that in the studied microbial consortium, free-living bacteria likely survive on each other by acquisition and exchange of metabolites. Knowledge gained from this study will facilitate the design of complex microbial communities with a better performance in industrial bioprocesses.
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Affiliation(s)
- Jinming Cui
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Guoqin Mai
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zuowei Wang
- Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Quan Liu
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yan Zhou
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yingfei Ma
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chenli Liu
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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Foley MH, Déjean G, Hemsworth GR, Davies GJ, Brumer H, Koropatkin NM. A Cell-Surface GH9 Endo-Glucanase Coordinates with Surface Glycan-Binding Proteins to Mediate Xyloglucan Uptake in the Gut Symbiont Bacteroides ovatus. J Mol Biol 2019; 431:981-995. [PMID: 30668971 PMCID: PMC6478033 DOI: 10.1016/j.jmb.2019.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/14/2018] [Accepted: 01/04/2019] [Indexed: 01/07/2023]
Abstract
Dietary fiber is an important food source for members of the human gut microbiome. Members of the dominant Bacteroidetes phylum capture diverse polysaccharides via the action of multiple cell surface proteins encoded within polysaccharide utilization loci (PUL). The independent activities of PUL-encoded glycoside hydrolases (GHs) and surface glycan-binding proteins (SGBPs) for the harvest of various glycans have been studied in detail, but how these proteins work together to coordinate uptake is poorly understood. Here, we combine genetic and biochemical approaches to discern the interplay between the BoGH9 endoglucanase and the xyloglucan-binding proteins SGBP-A and SGBP-B from the Bacteroides ovatus xyloglucan utilization locus (XyGUL). The expression of BoGH9, a weakly active xyloglucanase in isolation, is required in a strain that expresses a non-binding version of SGBP-A (SGBP-A*). The crystal structure of the BoGH9 enzyme suggests the molecular basis for its robust activity on mixed-linkage β-glucan compared to xyloglucan. However, catalytically inactive site-directed mutants of BoGH9 fail to complement the deletion of the active BoGH9 in a SGBP-A* strain. We also find that SGBP-B is needed in an SGBP-A* background to support growth on xyloglucan, but that the non-binding SGBP-B* protein acts in a dominant negative manner to inhibit growth on xyloglucan. We postulate a model whereby the SGBP-A, SGBP-B, and BoGH9 work together at the cell surface, likely within a discrete complex, and that xyloglucan binding by SGBP-B and BoGH9 may facilitate the orientation of the xyloglucan for transfer across the outer membrane.
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Affiliation(s)
- Matthew H Foley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Guillaume Déjean
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Glyn R Hemsworth
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada; Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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de Araújo EA, de Oliveira Neto M, Polikarpov I. Biochemical characterization and low-resolution SAXS structure of two-domain endoglucanase BlCel9 from Bacillus licheniformis. Appl Microbiol Biotechnol 2018; 103:1275-1287. [PMID: 30547217 DOI: 10.1007/s00253-018-9508-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 10/03/2018] [Accepted: 11/07/2018] [Indexed: 12/16/2022]
Abstract
Lignocellulose feedstock constitutes the most abundant carbon source in the biosphere; however, its recalcitrance remains a challenge for microbial conversion into biofuel and bioproducts. Bacillus licheniformis is a microbial mesophilic bacterium capable of secreting a large number of glycoside hydrolase (GH) enzymes, including a glycoside hydrolase from GH family 9 (BlCel9). Here, we conducted biochemical and biophysical studies of recombinant BlCel9, and its low-resolution molecular shape was retrieved from small angle X-ray scattering (SAXS) data. BlCel9 is an endoglucanase exhibiting maximum catalytic efficiency at pH 7.0 and 60 °C. Furthermore, it retains 80% of catalytic activity within a broad range of pH values (5.5-8.5) and temperatures (up to 50 °C) for extended periods of time (over 48 h). It exhibits the highest hydrolytic activity against phosphoric acid swollen cellulose (PASC), followed by bacterial cellulose (BC), filter paper (FP), and to a lesser extent carboxymethylcellulose (CMC). The HPAEC-PAD analysis of the hydrolytic products demonstrated that the end product of the enzymatic hydrolysis is primarily cellobiose, and also small amounts of glucose, cellotriose, and cellotetraose are produced. SAXS data analysis revealed that the enzyme adopts a monomeric state in solution and has a molecular mass of 65.8 kDa as estimated from SAXS data. The BlCel9 has an elongated shape composed of an N-terminal family 3 carbohydrate-binding module (CBM3c) and a C-terminal GH9 catalytic domain joined together by 20 amino acid residue long linker peptides. The domains are closely juxtaposed in an extended conformation and form a relatively rigid structure in solution, indicating that the interactions between the CBM3c and GH9 catalytic domains might play a key role in cooperative cellulose biomass recognition and hydrolysis.
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Affiliation(s)
- Evandro Ares de Araújo
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970, Brazil
| | - Mário de Oliveira Neto
- Departmento de Física e Biofísica, Universidade Estadual Paulista "Júlio de Mesquita Filho", R. Prof. Dr. Antonio Celso Wagner Zanin 689, Jardim Sao Jose, Botucatu, SP, 18618-970, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970, Brazil.
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7
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Pazhang M, Younesi FS, Mehrnejad F, Najavand S, Tarinejad A, Haghi M, Rashno F, Khajeh K. Ig-like Domain in Endoglucanase Cel9A from Alicyclobacillus acidocaldarius Makes Dependent the Enzyme Stability on Calcium. Mol Biotechnol 2018; 60:698-711. [PMID: 30062637 DOI: 10.1007/s12033-018-0105-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Endoglucanase Cel9A from Alicyclobacillus acidocaldarius (AaCel9A) has an Ig-like domain and the enzyme stability is dependent to calcium. In this study the effect of calcium on the structure and stability of the wild-type enzyme and the truncated form (the wild-type enzyme without Ig-like domain, AaCel9AΔN) was investigated. Fluorescence quenching results indicated that calcium increased and decreased the rigidity of the wild-type and truncated enzymes, respectively. RMSF results indicated that AaCel9A has two flexible regions (regions A and B) and deleting the Ig-like domain increased the truncated enzyme stability by decreasing the flexibility of region B probably through increasing the hydrogen bonds. Calcium contact map analysis showed that deleting the Ig-like domain decreased the calcium contacting residues and their calcium binding affinities, especially, in region B which has a role in calcium binding site in AaCel9A. Metal depletion and activity recovering as well as stability results showed that the structure and stability of the wild-type and truncated enzymes are completely dependent on and independent of calcium, respectively. Finally, one can conclude that the deletion of Ig-like domain makes AaCel9AΔN independent of calcium via decreasing the flexibility of region B through increasing the hydrogen bonds. This suggests a new role for the Ig-like domain which makes AaCel9A structure dependent on calcium.
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Affiliation(s)
- Mohammad Pazhang
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran.
| | - Fereshteh S Younesi
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Saeed Najavand
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Alireza Tarinejad
- Department of Biotechnology, Faculty of Agriculture, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Mehrnaz Haghi
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Fatemeh Rashno
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
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8
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Ellinghaus TL, Pereira JH, McAndrew RP, Welner DH, DeGiovanni AM, Guenther JM, Tran HM, Feldman T, Simmons BA, Sale KL, Adams PD. Engineering glycoside hydrolase stability by the introduction of zinc binding. Acta Crystallogr D Struct Biol 2018; 74:702-710. [PMID: 29968680 PMCID: PMC6038386 DOI: 10.1107/s2059798318006678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/01/2018] [Indexed: 02/04/2023] Open
Abstract
The development of robust enzymes, in particular cellulases, is a key step in the success of biological routes to `second-generation' biofuels. The typical sources of the enzymes used to degrade biomass include mesophilic and thermophilic organisms. The endoglucanase J30 from glycoside hydrolase family 9 was originally identified through metagenomic analyses of compost-derived bacterial consortia. These studies, which were tailored to favor growth on targeted feedstocks, have already been shown to identify cellulases with considerable thermal tolerance. The amino-acid sequence of J30 shows comparably low identity to those of previously analyzed enzymes. As an enzyme that combines a well measurable activity with a relatively low optimal temperature (50°C) and a modest thermal tolerance, it offers the potential for structural optimization aimed at increased stability. Here, the crystal structure of wild-type J30 is presented along with that of a designed triple-mutant variant with improved characteristics for industrial applications. Through the introduction of a structural Zn2+ site, the thermal tolerance was increased by more than 10°C and was paralleled by an increase in the catalytic optimum temperature by more than 5°C.
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Affiliation(s)
- Thomas L. Ellinghaus
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jose H. Pereira
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ryan P. McAndrew
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ditte H. Welner
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Andy M. DeGiovanni
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joel M. Guenther
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Huu M. Tran
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Taya Feldman
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Blake A. Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kenneth L. Sale
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
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9
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Lee BD, Apel WA, Sheridan PP, DeVeaux LC. Glycoside hydrolase gene transcription by Alicyclobacillus acidocaldarius during growth on wheat arabinoxylan and monosaccharides: a proposed xylan hydrolysis mechanism. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:110. [PMID: 29686728 PMCID: PMC5901876 DOI: 10.1186/s13068-018-1110-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 04/06/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Metabolism of carbon bound in wheat arabinoxylan (WAX) polysaccharides by bacteria requires a number of glycoside hydrolases active toward different bonds between sugars and other molecules. Alicyclobacillus acidocaldarius is a Gram-positive thermoacidophilic bacterium capable of growth on a variety of mono-, di-, oligo-, and polysaccharides. Nineteen proposed glycoside hydrolases have been annotated in the A. acidocaldarius Type Strain ATCC27009/DSM 446 genome. Experiments were performed to understand the effect of monosaccharides on gene expression during growth on the polysaccharide, WAX. RESULTS Molecular analysis using high-density oligonucleotide microarrays was performed on A. acidocaldarius strain ATCC27009 when growing on WAX. When a culture growing exponentially at the expense of arabinoxylan saccharides was challenged with glucose or xylose, most glycoside hydrolases were downregulated. Interestingly, regulation was more intense when xylose was added to the culture than when glucose was added, showing a clear departure from classical carbon catabolite repression demonstrated by many Gram-positive bacteria. In silico analyses of the regulated glycoside hydrolases, along with the results from the microarray analyses, yielded a potential mechanism for arabinoxylan metabolism by A. acidocaldarius. Glycoside hydrolases expressed by this strain may have broad substrate specificity, and initial hydrolysis is catalyzed by an extracellular xylanase, while subsequent steps are likely performed inside the growing cell. CONCLUSIONS Glycoside hydrolases, for the most part, appear to be found in clusters, throughout the A. acidocaldarius genome. Not all of the glycoside hydrolase genes found at loci within these clusters were regulated during the experiment, indicating that a specific subset of the 19 glycoside hydrolase genes found in A. acidocaldarius were used during metabolism of WAX. While specific functions of the glycoside hydrolases were not tested as part of the research discussed, many of the glycoside hydrolases found in the A. acidocaldarius Type Strain appear to have a broader substrate range than that represented by the glycoside hydrolase family in which the enzymes were categorized.
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Affiliation(s)
- Brady D. Lee
- Biological Systems Department, Idaho National Laboratory, P. O. Box 1625, Idaho Falls, ID 83415 USA
- Department of Biological Sciences, Idaho State University, Campus Box 8007, Pocatello, ID 83209 USA
- Present Address: Pacific Northwest National Laboratory, Energy and Environment Directorate, Richland, WA USA
| | - William A. Apel
- Biological Systems Department, Idaho National Laboratory, P. O. Box 1625, Idaho Falls, ID 83415 USA
| | - Peter P. Sheridan
- Department of Biological Sciences, Idaho State University, Campus Box 8007, Pocatello, ID 83209 USA
| | - Linda C. DeVeaux
- Department of Biology, New Mexico Institute of Mining and Technology, 801 Leroy Pl, Socorro, NM 87801 USA
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Vita N, Ravachol J, Franche N, Borne R, Tardif C, Pagès S, Fierobe HP. Restoration of cellulase activity in the inactive cellulosomal protein Cel9V from Ruminiclostridium cellulolyticum. FEBS Lett 2017; 592:190-198. [PMID: 29282732 DOI: 10.1002/1873-3468.12957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 12/18/2017] [Accepted: 12/19/2017] [Indexed: 11/08/2022]
Abstract
Ruminiclostridium cellulolyticum produces extracellular cellulosomes which contain interalia numerous family-9 glycoside hydrolases, including the inactive Cel9V. The latter shares the same organization and 79% sequence identity with the active cellulase Cel9E. Nevertheless, two aromatic residues and a four-residue stretch putatively critical for the activity are missing in Cel9V. Introduction of one Trytophan and the four-residue stretch restored some weak activity in Cel9V, whereas the replacement of its catalytic domain by that of Cel9E generated a fully active cellulase. Altogether our data indicate that a series of mutations in the catalytic domain of Cel9V lead to an essentially inactive cellulase.
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Affiliation(s)
| | - Julie Ravachol
- Aix-Marseille Univ, CNRS, LCB UMR7283, France.,Waters SAS, 78056, Saint-Quentin-en-Yvelines, France
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11
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Lee BD, Apel WA, DeVeaux LC, Sheridan PP. Concurrent metabolism of pentose and hexose sugars by the polyextremophile Alicyclobacillus acidocaldarius. J Ind Microbiol Biotechnol 2017; 44:1443-1458. [PMID: 28776272 DOI: 10.1007/s10295-017-1968-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 07/18/2017] [Indexed: 11/24/2022]
Abstract
Alicyclobacillus acidocaldarius is a thermoacidophilic bacterium capable of growth on sugars from plant biomass. Carbon catabolite repression (CCR) allows bacteria to focus cellular resources on a sugar that provides efficient growth, but also allows sequential, rather than simultaneous use when more than one sugar is present. The A. acidocaldarius genome encodes all components of CCR, but transporters encoded are multifacilitator superfamily and ATP-binding cassette-type transporters, uncommon for CCR. Therefore, global transcriptome analysis of A. acidocaldarius grown on xylose or fructose was performed in chemostats, followed by attempted induction of CCR with glucose or arabinose. Alicyclobacillus acidocaldarius grew while simultaneously metabolizing xylose and glucose, xylose and arabinose, and fructose and glucose, indicating that CCR did not control carbon metabolism. Microarrays showed down-regulation of genes during growth on one sugar compared to two, and occurred primarily in genes encoding: (1) regulators; (2) enzymes for cell wall synthesis; and (3) sugar transporters.
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Affiliation(s)
- Brady D Lee
- Idaho National Laboratory, Biological Systems Department, Idaho Falls, ID, USA. .,Department of Biological Sciences, Idaho State University, Pocatello, ID, USA. .,Pacific Northwest National Laboratory, Energy and Environment Directorate, Richland, WA, USA.
| | - William A Apel
- Idaho National Laboratory, Biological Systems Department, Idaho Falls, ID, USA.,Aspenglow Associates, LLC, P. O. Box 12692, Jackson, WY, 83002, USA
| | - Linda C DeVeaux
- Department of Chemistry and Applied Biological Sciences, South Dakota School of Mines and Technology, Rapid City, SD, USA
| | - Peter P Sheridan
- Department of Biological Sciences, Idaho State University, Pocatello, ID, USA
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12
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Deleting the Ig-Like Domain of Alicyclobacillus acidocaldarius Endoglucanase Cel9A Causes a Simultaneous Increase in the Activity and Stability. Mol Biotechnol 2016; 58:12-21. [PMID: 26537871 DOI: 10.1007/s12033-015-9900-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Endoglucanase Cel9A from Alicyclobacillus acidocaldarius (AaCel9A) is a monomeric enzyme with 537 residues. This enzyme has an Ig-like domain in the N-terminus of the catalytic domain. In this study, the role of the Ig-like domain on the activity, stability, and structural rigidity of AaCel9A and the effect of calcium on enzyme activity and stability were examined by comparing a truncated enzyme with deletion of the Ig-like domain (AaCel9AΔN) to the wild-type enzyme. Our results showed that the deletion of the Ig-like domain increased the catalytic efficiency of the truncated enzyme up to threefold without any significant changes in the K m of the enzyme. Furthermore, pH and temperature optimum for activity were shifted from 6.5 to 7.5 and from 65 to 60 °C, respectively, by deletion of the Ig-like domain. The thermal stability and fluorescence quenching results indicated that the stability and rigidity of the truncated enzyme have been more than that of the wild-type enzyme. Calcium similarly increased the catalytic efficiency of the enzymes (up to 40 %) and remarkably raised the stability of the AaCel9A compared to the AaCel9AΔN. This shows that Ig-like domain has a role in the increase of the enzyme stability by calcium in the wild-type enzyme.
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13
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Polarity Alteration of a Calcium Site Induces a Hydrophobic Interaction Network and Enhances Cel9A Endoglucanase Thermostability. Appl Environ Microbiol 2016; 82:1662-1674. [PMID: 26729722 DOI: 10.1128/aem.03326-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 12/16/2015] [Indexed: 01/07/2023] Open
Abstract
Structural calcium sites control protein thermostability and activity by stabilizing native folds and changing local conformations. Alicyclobacillus acidocaldarius survives in thermal-acidic conditions and produces an endoglucanase Cel9A (AaCel9A) which contains a calcium-binding site (Ser465 to Val470) near the catalytic cleft. By superimposing the Ca(2+)-free and Ca(2+)-bounded conformations of the calcium site, we found that Ca(2+) induces hydrophobic interactions between the calcium site and its nearby region by driving a conformational change. The hydrophobic interactions at the high-B-factor region could be enhanced further by replacing the surrounding polar residues with hydrophobic residues to affect enzyme thermostability and activity. Therefore, the calcium-binding residue Asp468 (whose side chain directly ligates Ca(2+)), Asp469, and Asp471 of AaCel9A were separately replaced by alanine and valine. Mutants D468A and D468V showed increased activity compared with those of the wild type with 0 mM or 10 mM Ca(2+) added, whereas the Asp469 or Asp471 substitution resulted in decreased activity. The D468A crystal structure revealed that mutation D468A triggered a conformational change similar to that induced by Ca(2+) in the wild type and developed a hydrophobic interaction network between the calcium site and the neighboring hydrophobic region (Ala113 to Ala117). Mutations D468V and D468A increased 4.5°C and 5.9°C, respectively, in melting temperature, and enzyme half-life at 75°C increased approximately 13 times. Structural comparisons between AaCel9A and other endoglucanases of the GH9 family suggested that the stability of the regions corresponding to the AaCel9A calcium site plays an important role in GH9 endoglucanase catalysis at high temperature.
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14
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Weiss SC, Skerra A, Schiefner A. Structural Basis for the Interconversion of Maltodextrins by MalQ, the Amylomaltase of Escherichia coli. J Biol Chem 2015; 290:21352-64. [PMID: 26139606 DOI: 10.1074/jbc.m115.667337] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Indexed: 11/06/2022] Open
Abstract
Amylomaltase MalQ is essential for the metabolism of maltose and maltodextrins in Escherichia coli. It catalyzes transglycosylation/disproportionation reactions in which glycosyl or dextrinyl units are transferred among linear maltodextrins of various lengths. To elucidate the molecular basis of transglycosylation by MalQ, we have determined three crystal structures of this enzyme, i.e. the apo-form, its complex with maltose, and an inhibitor complex with the transition state analog acarviosine-glucose-acarbose, at resolutions down to 2.1 Å. MalQ represents the first example of a mesophilic bacterial amylomaltase with known structure and exhibits an N-terminal extension of about 140 residues, in contrast with previously described thermophilic enzymes. This moiety seems unique to amylomaltases from Enterobacteriaceae and folds into two distinct subdomains that associate with different parts of the catalytic core. Intriguingly, the three MalQ crystal structures appear to correspond to distinct states of this enzyme, revealing considerable conformational changes during the catalytic cycle. In particular, the inhibitor complex highlights the requirement of both a 3-OH group and a 4-OH group (or α1-4-glycosidic bond) at the acceptor subsite +1 for the catalytically competent orientation of the acid/base catalyst Glu-496. Using an HPLC-based MalQ enzyme assay, we could demonstrate that the equilibrium concentration of maltodextrin products depends on the length of the initial substrate; with increasing numbers of glycosidic bonds, less glucose is formed. Thus, both structural and enzymatic data are consistent with the extremely low hydrolysis rates observed for amylomaltases and underline the importance of MalQ for the metabolism of maltodextrins in E. coli.
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Affiliation(s)
- Simon C Weiss
- From the Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85350 Freising-Weihenstephan, Germany
| | - Arne Skerra
- From the Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85350 Freising-Weihenstephan, Germany
| | - André Schiefner
- From the Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85350 Freising-Weihenstephan, Germany
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Cobucci-Ponzano B, Strazzulli A, Iacono R, Masturzo G, Giglio R, Rossi M, Moracci M. Novel thermophilic hemicellulases for the conversion of lignocellulose for second generation biorefineries. Enzyme Microb Technol 2015. [PMID: 26215346 DOI: 10.1016/j.enzmictec.2015.06.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The biotransformation of lignocellulose biomasses into fermentable sugars is a very complex procedure including, as one of the most critical steps, the (hemi) cellulose hydrolysis by specific enzymatic cocktails. We explored here, the potential of stable glycoside hydrolases from thermophilic organisms, so far not used in commercial enzymatic preparations, for the conversion of glucuronoxylan, the major hemicellulose of several energy crops. Searches in the genomes of thermophilic bacteria led to the identification, efficient production, and detailed characterization of novel xylanase and α-glucuronidase from Alicyclobacillus acidocaldarius (GH10-XA and GH67-GA, respectively) and a α-glucuronidase from Caldicellulosiruptor saccharolyticus (GH67-GC). Remarkably, GH10-XA, if compared to other thermophilic xylanases from this family, coupled good specificity on beechwood xylan and the best stability at 65 °C (3.5 days). In addition, GH67-GC was the most stable α-glucuronidases from this family and the first able to hydrolyse both aldouronic acid and aryl-α-glucuronic acid substrates. These enzymes, led to the very efficient hydrolysis of beechwood xylan by using 7- to 9-fold less protein (concentrations <0.3 μM) and in much less reaction time (2h vs 12h) if compared to other known biotransformations catalyzed by thermophilic enzymes. In addition, remarkably, together with a thermophilic β-xylosidase, they catalyzed the production of xylose from the smart cooking pre-treated biomass of one of the most promising energy crops for second generation biorefineries. We demonstrated that search by the CAZy Data Bank of currently available genomes and detailed enzymatic characterization of recombinant enzymes allow the identification of glycoside hydrolases with novel and interesting properties and applications.
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Affiliation(s)
- Beatrice Cobucci-Ponzano
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy.
| | - Andrea Strazzulli
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy.
| | - Roberta Iacono
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy.
| | - Giuseppe Masturzo
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy.
| | - Rosa Giglio
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy.
| | - Mosè Rossi
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy.
| | - Marco Moracci
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy.
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16
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Okano H, Kanaya E, Ozaki M, Angkawidjaja C, Kanaya S. Structure, activity, and stability of metagenome-derived glycoside hydrolase family 9 endoglucanase with an N-terminal Ig-like domain. Protein Sci 2015; 24:408-19. [PMID: 25545469 DOI: 10.1002/pro.2632] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/22/2014] [Accepted: 12/22/2014] [Indexed: 11/07/2022]
Abstract
A metagenome-derived glycoside hydrolase family 9 enzyme with an N-terminal immunoglobulin-like (Ig-like) domain, leaf-branch compost (LC)-CelG, was characterized and its crystal structure was determined. LC-CelG did not hydrolyze p-nitrophenyl cellobioside but hydrolyzed CM-cellulose, indicating that it is endoglucanase. LC-CelG exhibited the highest activity at 70°C and >80% of the maximal activity at a broad pH range of 5-9. Its denaturation temperature was 81.4°C, indicating that LC-CelG is a thermostable enzyme. The structure of LC-CelG resembles those of CelD from Clostridium thermocellum (CtCelD), Cel9A from Alicyclobacillus acidocaldarius (AaCel9A), and cellobiohydrolase CbhA from C. thermocellum (CtCbhA), which show relatively low (29-31%) amino acid sequence identities to LC-CelG. Three acidic active site residues are conserved as Asp194, Asp197, and Glu558 in LC-CelG. Ten of the thirteen residues that form the substrate binding pocket of AaCel9A are conserved in LC-CelG. Removal of the Ig-like domain reduced the activity and stability of LC-CelG by 100-fold and 6.3°C, respectively. Removal of the Gln40- and Asp99-mediated interactions between the Ig-like and catalytic domains destabilized LC-CelG by 5.0°C without significantly affecting its activity. These results suggest that the Ig-like domain contributes to the stabilization of LC-CelG mainly due to the Gln40- and Asp99-mediated interactions. Because the LC-CelG derivative lacking the Ig-like domain accumulated in Escherichia coli cells mostly in an insoluble form and this derivative accumulated in a soluble form exhibited very weak activity, the Ig-like domain may be required to make the conformation of the active site functional and prevent aggregation of the catalytic domain.
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Affiliation(s)
- Hiroyuki Okano
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MWW, Kelly RM. Thermophilic lignocellulose deconstruction. FEMS Microbiol Rev 2014; 38:393-448. [DOI: 10.1111/1574-6976.12044] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 08/20/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022] Open
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Ravachol J, Borne R, Tardif C, de Philip P, Fierobe HP. Characterization of all family-9 glycoside hydrolases synthesized by the cellulosome-producing bacterium Clostridium cellulolyticum. J Biol Chem 2014; 289:7335-48. [PMID: 24451379 DOI: 10.1074/jbc.m113.545046] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The genome of Clostridium cellulolyticum encodes 13 GH9 enzymes that display seven distinct domain organizations. All but one contain a dockerin module and were formerly detected in the cellulosomes, but only three of them were previously studied (Cel9E, Cel9G, and Cel9M). In this study, the 10 uncharacterized GH9 enzymes were overproduced in Escherichia coli and purified, and their activity pattern was investigated in the free state or in cellulosome chimeras with key cellulosomal cellulases. The newly purified GH9 enzymes, including those that share similar organization, all exhibited distinct activity patterns, various binding capacities on cellulosic substrates, and different synergies with pivotal cellulases in mini-cellulosomes. Furthermore, one enzyme (Cel9X) was characterized as the first genuine endoxyloglucanase belonging to this family, with no activity on soluble and insoluble celluloses. Another GH9 enzyme (Cel9V), whose sequence is 78% identical to the cellulosomal cellulase Cel9E, was found inactive in the free and complexed states on all tested substrates. The sole noncellulosomal GH9 (Cel9W) is a cellulase displaying a broad substrate specificity, whose engineered form bearing a dockerin can act synergistically in minicomplexes. Finally, incorporation of all GH9 cellulases in trivalent cellulosome chimera containing Cel48F and Cel9G generated a mixture of heterogeneous mini-cellulosomes that exhibit more activity on crystalline cellulose than the best homogeneous tri-functional complex. Altogether, our data emphasize the importance of GH9 diversity in bacterial cellulosomes, confirm that Cel9G is the most synergistic GH9 with the major endoprocessive cellulase Cel48F, but also identify Cel9U as an important cellulosomal component during cellulose depolymerization.
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Affiliation(s)
- Julie Ravachol
- From the Aix-Marseille Université-CNRS, Laboratoire de Chimie Bactérienne UMR7283, Institut de Microbiologie de la Méditerranée, Marseille Cedex 20, France
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19
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Arimori T, Ito A, Nakazawa M, Ueda M, Tamada T. Crystal structure of endo-1,4-β-glucanase from Eisenia fetida. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:884-9. [PMID: 24121333 PMCID: PMC3795549 DOI: 10.1107/s0909049513021110] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/29/2013] [Indexed: 06/02/2023]
Abstract
The saccharification process is essential for bioethanol production from woody biomass including celluloses. Cold-adapted cellulase, which has sufficient activity at low temperature (<293 K), is capable of reducing heating costs during the saccharification process and is suitable for simultaneous saccharification and fermentation. Endo-1,4-β-glucanase from the earthworm Eisenia fetida (EF-EG2) belonging to glycoside hydrolase family 9 has been shown to have the highest activity at 313 K, and also retained a comparatively high activity at 283 K. The recombinant EF-EG2 was purified expressed in Pichia pastoris, and then grew needle-shaped crystals with dimensions of 0.02 × 0.02 × 1 mm. The crystals belonged to the space group P3221 with unit-cell parameters of a = b = 136 Å, c = 55.0 Å. The final model of EF-EG2, including 435 residues, two ions, seven crystallization reagents and 696 waters, was refined to a crystallographic R-factor of 14.7% (free R-factor of 16.8%) to 1.5 Å resolution. The overall structure of EF-EG2 has an (α/α)6 barrel fold which contains a putative active-site cleft and a negatively charged surface. This structural information helps us understand the catalytic and cold adaptation mechanisms of EF-EG2.
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Affiliation(s)
- Takao Arimori
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
| | - Akihiro Ito
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, Osaka 599-8531, Japan
| | - Masami Nakazawa
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, Osaka 599-8531, Japan
| | - Mitsuhiro Ueda
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, Osaka 599-8531, Japan
| | - Taro Tamada
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
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Blifernez-Klassen O, Klassen V, Doebbe A, Kersting K, Grimm P, Wobbe L, Kruse O. Cellulose degradation and assimilation by the unicellular phototrophic eukaryote Chlamydomonas reinhardtii. Nat Commun 2013; 3:1214. [PMID: 23169055 DOI: 10.1038/ncomms2210] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 10/15/2012] [Indexed: 12/29/2022] Open
Abstract
Plants convert sunlight to biomass, which is primarily composed of lignocellulose, the most abundant natural biopolymer and a potential feedstock for fuel and chemical production. Cellulose assimilation has so far only been described for heterotrophic organisms that rely on photosynthetically active primary producers of organic compounds. Among phototrophs, the unicellular green microalga Chlamydomonas reinhardtii is widely known as one of the best established model organisms. It occupies many habitats, including aquatic and soil ecosystems. This ubiquity underscores the versatile metabolic properties of this microorganism. Here we present yet another paradigm of adaptation for C. reinhardtii, highlighting its photoheterotrophic ability to utilize cellulose for growth in the absence of other carbon sources. When grown under CO(2)-limiting conditions in the light, secretion of endo-β-1,4-glucanases by the cell causes digestion of exogenous cellulose, followed by cellobiose uptake and assimilation. Phototrophic microbes like C. reinhardtii may thus serve as biocatalysts for cellulosic biofuel production.
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Affiliation(s)
- Olga Blifernez-Klassen
- Department of Biology, Algae Biotechnology and Bioenergy-Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
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Biochemical and mutational analyses of a multidomain cellulase/mannanase from Caldicellulosiruptor bescii. Appl Environ Microbiol 2012; 78:2230-40. [PMID: 22247178 DOI: 10.1128/aem.06814-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Thermophilic cellulases and hemicellulases are of significant interest to the biofuel industry due to their perceived advantages over their mesophilic counterparts. We describe here biochemical and mutational analyses of Caldicellulosiruptor bescii Cel9B/Man5A (CbCel9B/Man5A), a highly thermophilic enzyme. As one of the highly secreted proteins of C. bescii, the enzyme is likely to be critical to nutrient acquisition by the bacterium. CbCel9B/Man5A is a modular protein composed of three carbohydrate-binding modules flanked at the N terminus and the C terminus by a glycoside hydrolase family 9 (GH9) module and a GH5 module, respectively. Based on truncational analysis of the polypeptide, the cellulase and mannanase activities within CbCel9B/Man5A were assigned to the N- and C-terminal modules, respectively. CbCel9B/Man5A and its truncational mutants, in general, exhibited a pH optimum of ∼5.5 and a temperature optimum of 85°C. However, at this temperature, thermostability was very low. After 24 h of incubation at 75°C, the wild-type protein maintained 43% activity, whereas a truncated mutant, TM1, maintained 75% activity. The catalytic efficiency with phosphoric acid swollen cellulose as a substrate for the wild-type protein was 7.2 s(-1) ml/mg, and deleting the GH5 module led to a mutant (TM1) with a 2-fold increase in this kinetic parameter. Deletion of the GH9 module also increased the apparent k(cat) of the truncated mutant TM5 on several mannan-based substrates; however, a concomitant increase in the K(m) led to a decrease in the catalytic efficiencies on all substrates. These observations lead us to postulate that the two catalytic activities are coupled in the polypeptide.
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Moréra S, Vigouroux A, Stubbs KA. A potential fortuitous binding of inhibitors of an inverting family GH9 β-glycosidase derived from isofagomine. Org Biomol Chem 2011; 9:5945-7. [PMID: 21785782 DOI: 10.1039/c1ob05766a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using structural insight, the binding mode of isofagomine-derived inhibitors with family GH9 glycosidases is achieved via the study of Alicyclobacillus acidocaldarius (AaCel9A) endoglucanase. In contrast to what was observed in the first report using these compounds with inverting glycosidases from family GH6, these inhibitors do not adopt a distorted conformation in the active site.
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Affiliation(s)
- Solange Moréra
- Laboratoire d'Enzymologie et Biochimie Structurales (LEBS), CNRS, Avenue de la Terrasse, 91198, Gif-sur-Yvette, France.
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