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Yamaguchi S, Sunagawa N, Samejima M, Igarashi K. Thermotolerance Mechanism of Fungal GH6 Cellobiohydrolase. Part I. Characterization of Thermotolerant Mutant from the Basidiomycete Phanerochaete chrysosporium. J Appl Glycosci (1999) 2024; 71:55-62. [PMID: 38863951 PMCID: PMC11163330 DOI: 10.5458/jag.jag.jag-2023_0017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/14/2024] [Indexed: 06/13/2024] Open
Abstract
Cellobiohydrolase (CBH), belonging to glycoside hydrolase family 6 (GH6), plays an essential role in cellulose saccharification, but its low thermotolerance presents a challenge in improving the reaction efficiency. Based on a report that chimeric CBH II (GH6) engineered to remove non-disulfide-bonded free Cys shows increased thermotolerance, we previously mutated the two free Cys residues to Ser in GH6 CBH from the basidiomycete Phanerochaete chrysosporium (PcCel6A) and obtained a thermotolerant double mutant, C240S/C393S (Yamaguchi et al., J. Appl. Glycosci. 2020; 67: 79-86). Here, characterization of the double mutant revealed that its activity towards both amorphous and crystalline cellulose was higher than that of the wild-type enzyme at elevated temperature, suggesting that the catalytic domain is the major contributor to the increased thermotolerance. To investigate the role of each free Cys residue, we prepared both single mutants, C240S and C393S, of the catalytic domain of PcCel6A and examined their residual activity at high temperature and the temperature-dependent changes of folding by means of circular dichroism measurements and thermal shift assay. The results indicate that the C393S mutation is the main contributor to both the increased thermotolerance of C240S/C393S and the increased activity of the catalytic domain at high temperature.
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Affiliation(s)
- Sora Yamaguchi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
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2
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Yamaguchi S, Sunagawa N, Samejima M, Igarashi K. Thermotolerance Mechanism of Fungal GH6 Cellobiohydrolase. Part II. Structural Analysis of Thermotolerant Mutant from the Basidiomycete Phanerochaete chrysosporium. J Appl Glycosci (1999) 2024; 71:63-72. [PMID: 38863950 PMCID: PMC11163327 DOI: 10.5458/jag.jag.jag-2023_0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/04/2024] [Indexed: 06/13/2024] Open
Abstract
Glycoside hydrolase family 6 cellobiohydrolase (GH6 CBH) is a group of cellulases capable of hydrolyzing crystalline cellulose. However, the synergistic reaction of GH6 CBH with other cellulases is hindered by its relatively low thermotolerance. We previously obtained a thermotolerant double mutant, C240S/C393S, of GH6 CBH from the basidiomycete Phanerochaete chrysosporium (PcCel6A) by replacing the two free cysteine (Cys) residues, C240 and C393, with serine (Yamaguchi et al., J Appl Glycosci. 2020; 67;79-86). In the accompanying paper (Part I; Yamaguchi et al., J Appl Glycosci. 2024; 71: 55-62), we measured the temperature dependence of the activity and folding of C240S/C393S and its single mutants, C240S and C393S, and found that replacement of C393 was the major contributor to the increased thermotolerance of C240S/C393S. Here, in order to investigate the mechanism involved, we crystallized the wild-type and the mutant enzymes and compared their X-ray crystal structures. The overall structures of the wild-type and the three mutant enzymes were similar. However, C240S/C393S had the lowest relative B-factor at both the N-terminal loop (residues 172-177) and the C-terminal loop (residues 390-425). This result suggests that reduced structural fluctuation of the substrate-enclosing loops, possibly due to stronger hydrogen bonding involving C393, could account for the increased thermotolerance of C240S/C393S.
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Affiliation(s)
- Sora Yamaguchi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
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3
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Brunecky R, Knott BC, Subramanian V, Linger JG, Beckham GT, Amore A, Taylor LE, Vander Wall TA, Lunin VV, Zheng F, Garrido M, Schuster L, Fulk EM, Farmer S, Himmel ME, Decker SR. Engineering of glycoside hydrolase family 7 cellobiohydrolases directed by natural diversity screening. J Biol Chem 2024; 300:105749. [PMID: 38354778 PMCID: PMC10943489 DOI: 10.1016/j.jbc.2024.105749] [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: 11/16/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
Protein engineering and screening of processive fungal cellobiohydrolases (CBHs) remain challenging due to limited expression hosts, synergy-dependency, and recalcitrant substrates. In particular, glycoside hydrolase family 7 (GH7) CBHs are critically important for the bioeconomy and typically difficult to engineer. Here, we target the discovery of highly active natural GH7 CBHs and engineering of variants with improved activity. Using experimentally assayed activities of genome mined CBHs, we applied sequence and structural alignments to top performers to identify key point mutations linked to improved activity. From ∼1500 known GH7 sequences, an evolutionarily diverse subset of 57 GH7 CBH genes was expressed in Trichoderma reesei and screened using a multiplexed activity screening assay. Ten catalytically enhanced natural variants were identified, produced, purified, and tested for efficacy using industrially relevant conditions and substrates. Three key amino acids in CBHs with performance comparable or superior to Penicillium funiculosum Cel7A were identified and combinatorially engineered into P. funiculosum cel7a, expressed in T. reesei, and assayed on lignocellulosic biomass. The top performer generated using this combined approach of natural diversity genome mining, experimental assays, and computational modeling produced a 41% increase in conversion extent over native P. funiculosum Cel7A, a 55% increase over the current industrial standard T. reesei Cel7A, and 10% improvement over Aspergillus oryzae Cel7C, the best natural GH7 CBH previously identified in our laboratory.
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Affiliation(s)
- Roman Brunecky
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Brandon C Knott
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Venkataramanan Subramanian
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Jeffrey G Linger
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Gregg T Beckham
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Antonella Amore
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Larry E Taylor
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Todd A Vander Wall
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Vladimir V Lunin
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Fei Zheng
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Mercedes Garrido
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Logan Schuster
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Emily M Fulk
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Samuel Farmer
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Michael E Himmel
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA.
| | - Stephen R Decker
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA.
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4
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Senthilkumar S, Mahesh S, Jaisankar S, Yennamalli RM. Surface exposed and charged residues drive thermostability in fungi. Proteins 2023. [PMID: 37909647 DOI: 10.1002/prot.26623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 11/03/2023]
Abstract
Fungi, though mesophilic, include thermophilic and thermostable species, as well. The thermostability of proteins observed in these fungi is most likely to be attributed to several molecular factors, such as the presence of salt bridges and hydrogen bond interactions between side chains. These factors cannot be generalized for all fungi. Factors impacting thermostability can guide how fungal thermophilic proteins gain thermostability. We curated a dataset of proteins for 14 thermophilic fungi and their evolutionarily closer mesophiles. Additionally, the proteome of Chaetomium thermophilum and its evolutionarily related mesophile Chaetomium globosum was analyzed. Using eggNOG, we categorized the proteomes into clusters of orthologous groups (COGs). While the individual count of proteins is over-represented in mesophiles (for COGs S, G, L, and Q), there are certain features that are significantly enriched in thermophiles (such as charged residues, exposed residues, polar residues, etc.). Since fungi are known to be cellulolytic and chitinolytic by nature, we selected 37 existing carbohydrate-active enzymes (CAZyme) families in Eurotiales, Mucorales, and Sordariales. We looked at closely similar sequences and their modeled structures for further comparison. Comparing solvent accessibilities of thermophilic and mesophilic proteins, exposed and intermediate residues are observed higher in thermophiles whereas buried residues are observed higher in mesophiles. For specific five CAZYme families (GH7, GH11, GH18, GH45, and CBM1) we looked at position-specific substitutions between thermophiles and mesophiles. We also found that there are relatively more intramolecular interactions in thermophiles compared to mesophiles. Thus, we found factors such as surface exposed residues and charged residues that are highly likely to impart thermostability in fungi, and this study sets the stage for further studies in the area of fungal thermostability.
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Affiliation(s)
- Shricharan Senthilkumar
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Sankar Mahesh
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Subachandran Jaisankar
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Ragothaman M Yennamalli
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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5
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Jiang F, Bian J, Liu H, Li S, Bai X, Zheng L, Jin S, Liu Z, Yang GY, Hong L. Creatinase: Using Increased Entropy to Improve the Activity and Thermostability. J Phys Chem B 2023; 127:2671-2682. [PMID: 36926920 DOI: 10.1021/acs.jpcb.2c08062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Improving protein thermostability in mutagenesis-based enzyme engineering was often achieved by enhancing interresidue interactions via mutation to increase the enthalpy penalty of unfolding. However, this approach may trade off the functional activity due to the loss of structural flexibility of the biomolecule. Here, by performing X-ray crystallography, enzymatic kinetic experiments, neutron scattering, and thermodynamical measurements, we compared the structures, catalytic behaviors, dynamics, and thermostability between a wild-type creatinase and its four-point mutant. We found that the mutant is an entropy-driven thermostable protein with higher structural flexibility, i.e., higher conformational entropy, in the folded state compared to the wild type. The increased conformational entropy of the mutant in the folded state can reduce the entropy gain during unfolding and thus renders it greater thermostability. Moreover, the increased structural flexibility, particularly around the catalytic site, can broaden the mutant's working temperature range and considerably improve its activity at ambient conditions, which is crucial for its application in diagnosing kidney diseases. Complementary all-atom molecular dynamics simulations indicated that the four mutations replaced several of the strong interresidue interactions (electrostatic interactions and hydrogen bonds) with weak hydrophobic interactions. These substitutions not only release the structural flexibility to promote the thermostability and enzymatic activity of the protein but they also preserve the protein structure from collapsing. Our findings may pave a route for the entropy-driven strategy to design proteins with high thermostability and activity.
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Affiliation(s)
- Fan Jiang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiahao Bian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Liu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Song Li
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lirong Zheng
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sha Jin
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhuo Liu
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
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6
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Kumar S, Duggineni VK, Singhania V, Misra SP, Deshpande PA. Unravelling and Quantifying the Biophysical– Biochemical Descriptors Governing Protein Thermostability by Machine Learning. ADVANCED THEORY AND SIMULATIONS 2023. [DOI: 10.1002/adts.202200703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Shashi Kumar
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur 721302 India
| | - Vinay Kumar Duggineni
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur 721302 India
| | - Vibhuti Singhania
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur 721302 India
| | - Swayam Prabha Misra
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur 721302 India
| | - Parag A. Deshpande
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur 721302 India
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7
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Dodda SR, Hossain M, Jain P, Aikat K, Mukhopadhyay SS. Comparative Biochemical and Structural Properties of an Industrially Important Biocatalyst Cellobiohydrolase Cel7A from Thermophilic Aspergillus fumigatus. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822050064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Metagenomic mining and structure-function studies of a hyper-thermostable cellobiohydrolase from hot spring sediment. Commun Biol 2022; 5:247. [PMID: 35318423 PMCID: PMC8940973 DOI: 10.1038/s42003-022-03195-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/25/2022] [Indexed: 11/09/2022] Open
Abstract
Enzymatic breakdown is an attractive cellulose utilisation method with a low environmental load. Its high temperature operation could promote saccharification and lower contamination risk. Here we report a hyper-thermostable cellobiohydrolase (CBH), named HmCel6A and its variant HmCel6A-3SNP that were isolated metagenomically from hot spring sediments and expressed in Escherichia coli. They are classified into glycoside hydrolases family 6 (GH6). HmCel6A-3SNP had three amino acid replacements to HmCel6A (P88S/L230F/F414S) and the optimum temperature at 95 °C, while HmCel6A did it at 75 °C. Crystal structure showed conserved features among GH6, a (β/α)8-barrel core and catalytic residues, and resembles TfCel6B, a bacterial CBH II of Thermobifida fusca, that had optimum temperature at 60 °C. From structure-function studies, we discuss unique structural features that allow the enzyme to reach its high thermostability level, such as abundance of hydrophobic and charge-charge interactions, characteristic metal bindings and disulphide bonds. Moreover, structure and surface plasmon resonance analysis with oligosaccharides suggested that the contribution of an additional tryptophan located at the tunnel entrance could aid in substrate recognition and thermostability. These results may help to design efficient enzymes and saccharification methods for cellulose working at high temperatures. Bacteria from hot springs are known for highly thermostable enzymes, which may have industrial potential. Here, a unique thermostable cellobiohydrolase is reported that can breakdown cellulose at temperature up to 95 degrees Celsius.
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9
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Pan Q, Nguyen TB, Ascher DB, Pires DEV. Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures. Brief Bioinform 2022; 23:bbac025. [PMID: 35189634 PMCID: PMC9155634 DOI: 10.1093/bib/bbac025] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 01/13/2022] [Accepted: 01/30/2022] [Indexed: 12/26/2022] Open
Abstract
Changes in protein sequence can have dramatic effects on how proteins fold, their stability and dynamics. Over the last 20 years, pioneering methods have been developed to try to estimate the effects of missense mutations on protein stability, leveraging growing availability of protein 3D structures. These, however, have been developed and validated using experimentally derived structures and biophysical measurements. A large proportion of protein structures remain to be experimentally elucidated and, while many studies have based their conclusions on predictions made using homology models, there has been no systematic evaluation of the reliability of these tools in the absence of experimental structural data. We have, therefore, systematically investigated the performance and robustness of ten widely used structural methods when presented with homology models built using templates at a range of sequence identity levels (from 15% to 95%) and contrasted performance with sequence-based tools, as a baseline. We found there is indeed performance deterioration on homology models built using templates with sequence identity below 40%, where sequence-based tools might become preferable. This was most marked for mutations in solvent exposed residues and stabilizing mutations. As structure prediction tools improve, the reliability of these predictors is expected to follow, however we strongly suggest that these factors should be taken into consideration when interpreting results from structure-based predictors of mutation effects on protein stability.
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Affiliation(s)
- Qisheng Pan
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, Queensland 4072, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3052, Australia
| | - Thanh Binh Nguyen
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, Queensland 4072, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3052, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, Queensland 4072, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3052, Australia
- Department of Biochemistry, University of Cambridge, 80 Tennis Ct Rd, Cambridge CB2 1GA, UK
| | - Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, Queensland 4072, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3052, Australia
- School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria 3053, Australia
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10
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Fungal cellulases: protein engineering and post-translational modifications. Appl Microbiol Biotechnol 2021; 106:1-24. [PMID: 34889986 DOI: 10.1007/s00253-021-11723-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 12/18/2022]
Abstract
Enzymatic degradation of lignocelluloses into fermentable sugars to produce biofuels and other biomaterials is critical for environmentally sustainable development and energy resource supply. However, there are problems in enzymatic cellulose hydrolysis, such as the complex cellulase composition, low degradation efficiency, high production cost, and post-translational modifications (PTMs), all of which are closely related to specific characteristics of cellulases that remain unclear. These problems hinder the practical application of cellulases. Due to the rapid development of computer technology in recent years, computer-aided protein engineering is being widely used, which also brings new opportunities for the development of cellulases. Especially in recent years, a large number of studies have reported on the application of computer-aided protein engineering in the development of cellulases; however, these articles have not been systematically reviewed. This article focused on the aspect of protein engineering and PTMs of fungal cellulases. In this manuscript, the latest literatures and the distribution of potential sites of cellulases for engineering have been systematically summarized, which provide reference for further improvement of cellulase properties. KEY POINTS: •Rational design based on virtual mutagenesis can improve cellulase properties. •Modifying protein side chains and glycans helps obtain superior cellulases. •N-terminal glutamine-pyroglutamate conversion stabilizes fungal cellulases.
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11
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Arya PS, Yagnik SM, Rajput KN, Panchal RR, Raval VH. Understanding the Basis of Occurrence, Biosynthesis, and Implications of Thermostable Alkaline Proteases. Appl Biochem Biotechnol 2021; 193:4113-4150. [PMID: 34648116 DOI: 10.1007/s12010-021-03701-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/04/2021] [Indexed: 12/29/2022]
Abstract
The group of hydrolytic enzymes synonymously known as proteases is predominantly most favored for the class of industrial enzymes. The present work focuses on the thermostable nature of these proteolytic enzymes that occur naturally among mesophilic and thermophilic microbes. The broad thermo-active feature (40-80 °C), ease of cultivation, maintenance, and bulk production are the key features associated with these enzymes. Detailing of contemporary production technologies, and controllable operational parameters including the purification strategies, are the key features that justify their industrial dominance as biocatalysts. In addition, the rigorous research inputs by protein engineering and enzyme immobilization studies add up to the thermo-catalytic features and application capabilities of these enzymes. The work summarizes key features of microbial proteases that make them numero-uno for laundry, biomaterials, waste management, food and feed, tannery, and medical as well as pharmaceutical industries. The quest for novel and/or designed and engineered thermostable protease from unexplored sources is highly stimulating and will address the ever-increasing industrial demands.
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Affiliation(s)
- Prashant S Arya
- Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Shivani M Yagnik
- Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Kiransinh N Rajput
- Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Rakeshkumar R Panchal
- Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Vikram H Raval
- Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India.
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12
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Enhanced Thermostability of Pseudomonas nitroreducens Isoeugenol Monooxygenase by the Combinatorial Strategy of Surface Residue Replacement and Consensus Mutagenesis. Catalysts 2021. [DOI: 10.3390/catal11101199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Vanillin has many applications in industries. Isoeugenol monooxygenase (IEM) can catalyze the oxidation of isoeugenol to vanillin in the presence of oxygen under mild conditions. However, the low thermal stability of IEM limits its practical application in the biosynthesis of natural vanillin. Herein, two rational strategies were combined to improve the thermostability of IEM from Pseudomonas nitroreducens Jin1. Two variants (K83R and K95R) with better thermostability and one mutant (G398A) with higher activity were identified from twenty candidates based on the Surface Residue Replacement method. According to the Consensus Mutagenesis method, one mutant (I352R) with better thermostability and another mutant (L273F) with higher activity were also identified from nine candidates. After combinatorial mutation, a triple mutant K83R/K95R/L273F with the best thermostability and catalytic efficiency was generated. Compared with the wild-type IEM, the thermal inactivation half-lives (t1/2) of K83R/K95R/L273F at 25 °C, 30 °C, and 35 °C increased 2.9-fold, 11.9-fold, and 24.7-fold, respectively. Simultaneously, it also exhibited a 4.8-fold increase in kcat, leading to a 1.2-fold increase in catalytic efficiency (kcat/Km). When the whole cell of K83R/K95R/L273F was applied to the biotransformation of isoeugenol on preparative scale, the vanillin concentration reached 240.1 mM with space-time yield of 109.6 g/L/d, and vanillin was achieved in 77.6% isolated yield and >99% purity.
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Pramanik S, Semenova MV, M Rozhkova A, Zorov IN, Korotkova O, Sinitsyn AP, Davari MD. An engineered cellobiohydrolase I for sustainable degradation of lignocellulosic biomass. Biotechnol Bioeng 2021; 118:4014-4027. [PMID: 34196389 DOI: 10.1002/bit.27877] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/29/2021] [Accepted: 06/20/2021] [Indexed: 11/11/2022]
Abstract
This study provides computational-assisted engineering of the cellobiohydrolase I (CBH-I) from Penicillium verruculosum with simultaneous enhanced thermostability and tolerance in ionic liquids, deep eutectic solvent, and concentrated seawater without affecting its wild-type activity. Engineered triple variant CBH-I R1 (A65R-G415R-S181F) showed 2.48-fold higher thermostability in terms of relative activity at 65°C after 1 h of incubation when compared with CBH-I wild type. CBH-I R1 exhibited 1.87-fold, 1.36-fold, and 1.57-fold higher specific activities compared with CBH-I wild type in [Bmim]Cl (50 g/L), [Ch]Cl (50 g/L), and two-fold concentrated seawater, respectively. In the multicellulases mixture, CBH-I R1 showed higher hydrolytic efficiency to hydrolyze aspen wood compared with CBH-I wild type in the buffer, [Bmim]Cl (50 g/L), and two-fold concentrated seawater, respectively. Structural analysis revealed a molecular basis for the higher stability of the CBH-I structure in which A65R and G415R substitutions form salt bridges (D64 … R65, E411 … R415) and S181F forms π-π interaction (Y155 … F181), leading to stabilize surface-exposed flexible α-helixes and loop in the multidomain β-jelly roll fold structure, respectively. In conclusion, the variant CBH-I R1 could enable efficient lignocellulosic biomass degradation as a cost-effective alternative for the sustainable production of biofuels and value-added chemicals.
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Affiliation(s)
- Subrata Pramanik
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Margarita V Semenova
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Aleksandra M Rozhkova
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Ivan N Zorov
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia.,Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Olga Korotkova
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Arkady P Sinitsyn
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia.,Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
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14
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Rozhkova AM, Kislitsin VY. CRISPR/Cas Genome Editing in Filamentous Fungi. BIOCHEMISTRY (MOSCOW) 2021; 86:S120-S139. [PMID: 33827404 DOI: 10.1134/s0006297921140091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The review describes the CRISPR/CAS system and its adaptation for the genome editing in filamentous fungi commonly used for production of enzyme complexes, enzymes, secondary metabolites, and other compounds used in industrial biotechnology and agriculture. In the second part of this review, examples of the CRISPR/CAS technology application for improving properties of the industrial strains of fungi from the Trichoderma, Aspergillus, Penicillium, and other genera are presented. Particular attention is given to the efficiency of genome editing, as well as system optimization for specific industrial producers.
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Affiliation(s)
- Aleksandra M Rozhkova
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Valeriy Yu Kislitsin
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia
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15
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Yang G, Yang D, Wang X, Cao W. A novel thermostable cellulase-producing Bacillus licheniformis A5 acts synergistically with Bacillus subtilis B2 to improve degradation of Chinese distillers' grains. BIORESOURCE TECHNOLOGY 2021; 325:124729. [PMID: 33493746 DOI: 10.1016/j.biortech.2021.124729] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
Lack of effective degradation approaches of Chinese distillers' grains (CDGs) produced by Chinese liquor industry results in environmental pollution and economic waste. Cellulase activity was characterized at different temperatures to find thermostable cellulase-producing bacteria, and microbial co-culture method was used to improve the degradation of CDGs. Incubation of endoglucanase produced by Bacillus licheniformis A5 at 80 °C for 120 min showed 82% residual enzyme activity. Notably, enzyme activity increased by 30%-70% after co-culturing Bacillus licheniformis A5 and Bacillus subtilis B2. The two strains increased degradation rate of CDGs by 70% compared with optimized results of Bacillus subtilis B2 culture alone, and increased the reducing sugar content to 16.6 mg/mL. In addition, 2% ethanol increased degradation rate of CDGs by 15% in co-culture. The findings of this study imply that Bacillus licheniformis A5 acts synergistically with Bacillus subtilis B2 to improve degradation of CDGs.
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Affiliation(s)
- Gang Yang
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
| | - Diqin Yang
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
| | - Xiaodan Wang
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
| | - Wentao Cao
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China.
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16
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Molecular engineering to improve lignocellulosic biomass based applications using filamentous fungi. ADVANCES IN APPLIED MICROBIOLOGY 2020; 114:73-109. [PMID: 33934853 DOI: 10.1016/bs.aambs.2020.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Lignocellulosic biomass is an abundant and renewable resource, and its utilization has become the focus of research and biotechnology applications as a very promising raw material for the production of value-added compounds. Filamentous fungi play an important role in the production of various lignocellulolytic enzymes, while some of them have also been used for the production of important metabolites. However, wild type strains have limited efficiency in enzyme production or metabolic conversion, and therefore many efforts have been made to engineer improved strains. Examples of this are the manipulation of transcriptional regulators and/or promoters of enzyme-encoding genes to increase gene expression, and protein engineering to improve the biochemical characteristics of specific enzymes. This review provides and overview of the applications of filamentous fungi in lignocellulosic biomass based processes and the development and current status of various molecular engineering strategies to improve these processes.
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17
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Yamaguchi S, Sunagawa N, Tachioka M, Igarashi K, Samejima M. Thermostable Mutants of Glycoside Hydrolase Family 6 Cellobiohydrolase from the Basidiomycete Phanerochaete chrysosporium. J Appl Glycosci (1999) 2020; 67:79-86. [PMID: 34354533 PMCID: PMC8132074 DOI: 10.5458/jag.jag.jag-2020_0004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 06/09/2020] [Indexed: 11/24/2022] Open
Abstract
Thermal inactivation of saccharifying enzymes is a crucial issue for the efficient utilization of cellulosic biomass as a renewable resource. Cellobiohydrolases (CBHs) are a kind of cellulase. In general, CBHs belonging to glycoside hydrolase (GH) family 6 (Cel6) act synergistically with CBHs of GH family 7 (Cel7) and other carbohydrate-active enzymes during the degradation of cellulosic biomass. However, while the catalytic rate of enzymes generally becomes faster at higher temperatures, Cel6 CBHs are inactivated at lower temperatures than Cel7 CBHs, and this represents a limiting factor for industrial utilization. In this study, we produced a series of mutants of the glycoside hydrolase family 6 cellobiohydrolase Pc Cel6A from the fungus Phanerochaete chrysosporium , and compared their thermal stability. Eight mutants from a random mutagenesis library and one rationally designed mutant were selected as candidate thermostable mutants and produced by heterologous expression in the yeast Pichia pastoris . Comparison of the hydrolytic activities at 50 and 60 °C indicated that the thermal stability of Pc Cel6A is influenced by the number and position of cysteine residues that are not involved in disulfide bonds.
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Affiliation(s)
- Sora Yamaguchi
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Naoki Sunagawa
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Mikako Tachioka
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo.,2 Deep-Sea Nanoscience Research Group, Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology
| | - Kiyohiko Igarashi
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo.,3 VTT Technical Research Centre of Finland
| | - Masahiro Samejima
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo.,4 Faculty of Engineering, Shinshu University
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18
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Protease—A Versatile and Ecofriendly Biocatalyst with Multi-Industrial Applications: An Updated Review. Catal Letters 2020. [DOI: 10.1007/s10562-020-03316-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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19
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Huang P, Chu SKS, Frizzo HN, Connolly MP, Caster RW, Siegel JB. Evaluating Protein Engineering Thermostability Prediction Tools Using an Independently Generated Dataset. ACS OMEGA 2020; 5:6487-6493. [PMID: 32258884 PMCID: PMC7114132 DOI: 10.1021/acsomega.9b04105] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/06/2020] [Indexed: 05/04/2023]
Abstract
Engineering proteins to enhance thermal stability is a widely utilized approach for creating industrially relevant biocatalysts. The development of new experimental datasets and computational tools to guide these engineering efforts remains an active area of research. Thus, to complement the previously reported measures of T 50 and kinetic constants, we are reporting an expansion of our previously published dataset of mutants for β-glucosidase to include both measures of T M and ΔΔG. For a set of 51 mutants, we found that T 50 and T M are moderately correlated, with a Pearson correlation coefficient and Spearman's rank coefficient of 0.58 and 0.47, respectively, indicating that the two methods capture different physical features. The performance of predicted stability using nine computational tools was also evaluated on the dataset of 51 mutants, none of which are found to be strong predictors of the observed changes in T 50, T M, or ΔΔG. Furthermore, the ability of the nine algorithms to predict the production of isolatable soluble protein was examined, which revealed that Rosetta ΔΔG, FoldX, DeepDDG, PoPMuSiC, and SDM were capable of predicting if a mutant could be produced and isolated as a soluble protein. These results further highlight the need for new algorithms for predicting modest, yet important, changes in thermal stability as well as a new utility for current algorithms for prescreening designs for the production of mutants that maintain fold and soluble production properties.
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Affiliation(s)
- Peishan Huang
- Biophysics
Graduate Group, University of California, Davis 95616, California, United States
| | - Simon K. S. Chu
- Biophysics
Graduate Group, University of California, Davis 95616, California, United States
| | - Henrique N. Frizzo
- Genome
Center, University of California, Davis 95616, California, United States
| | - Morgan P. Connolly
- Microbiology
Graduate Group, University of California, Davis 95616, California, United States
| | - Ryan W. Caster
- Genome
Center, University of California, Davis 95616, California, United States
| | - Justin B. Siegel
- Genome
Center, University of California, Davis 95616, California, United States
- Department
of Biochemistry & Molecular Medicine, University of California, Davis 95616, California, United States
- Department
of Chemistry, University of California, Davis 95616, California, United States
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20
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Ali M, Ishqi HM, Husain Q. Enzyme engineering: Reshaping the biocatalytic functions. Biotechnol Bioeng 2020; 117:1877-1894. [DOI: 10.1002/bit.27329] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/13/2020] [Accepted: 03/09/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Misha Ali
- Department of Biochemistry, Faculty of Life SciencesAligarh Muslim University Aligarh Uttar Pradesh India
| | | | - Qayyum Husain
- Department of Biochemistry, Faculty of Life SciencesAligarh Muslim University Aligarh Uttar Pradesh India
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21
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Contreras F, Pramanik S, M. Rozhkova A, N. Zorov I, Korotkova O, P. Sinitsyn A, Schwaneberg U, D. Davari M. Engineering Robust Cellulases for Tailored Lignocellulosic Degradation Cocktails. Int J Mol Sci 2020; 21:E1589. [PMID: 32111065 PMCID: PMC7084875 DOI: 10.3390/ijms21051589] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/11/2022] Open
Abstract
Lignocellulosic biomass is a most promising feedstock in the production of second-generation biofuels. Efficient degradation of lignocellulosic biomass requires a synergistic action of several cellulases and hemicellulases. Cellulases depolymerize cellulose, the main polymer of the lignocellulosic biomass, to its building blocks. The production of cellulase cocktails has been widely explored, however, there are still some main challenges that enzymes need to overcome in order to develop a sustainable production of bioethanol. The main challenges include low activity, product inhibition, and the need to perform fine-tuning of a cellulase cocktail for each type of biomass. Protein engineering and directed evolution are powerful technologies to improve enzyme properties such as increased activity, decreased product inhibition, increased thermal stability, improved performance in non-conventional media, and pH stability, which will lead to a production of more efficient cocktails. In this review, we focus on recent advances in cellulase cocktail production, its current challenges, protein engineering as an efficient strategy to engineer cellulases, and our view on future prospects in the generation of tailored cellulases for biofuel production.
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Affiliation(s)
- Francisca Contreras
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Subrata Pramanik
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Aleksandra M. Rozhkova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan N. Zorov
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga Korotkova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Arkady P. Sinitsyn
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
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22
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Minges H, Schnepel C, Böttcher D, Weiß MS, Sproß J, Bornscheuer UT, Sewald N. Targeted Enzyme Engineering Unveiled Unexpected Patterns of Halogenase Stabilization. ChemCatChem 2019. [DOI: 10.1002/cctc.201901827] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Hannah Minges
- Organic and Bioorganic Chemistry Department of ChemistryBielefeld University Universitätsstraße 25 33615 Bielefeld Germany
| | - Christian Schnepel
- Organic and Bioorganic Chemistry Department of ChemistryBielefeld University Universitätsstraße 25 33615 Bielefeld Germany
| | - Dominique Böttcher
- Institute of Biochemistry Department of Biotechnology and Enzyme CatalysisGreifswald University Felix-Hausdorff-Str.4 17489 Greifswald Germany
| | - Martin S. Weiß
- Institute of Biochemistry Department of Biotechnology and Enzyme CatalysisGreifswald University Felix-Hausdorff-Str.4 17489 Greifswald Germany
| | - Jens Sproß
- Industrial Organic Chemistry and Biotechnology Department of ChemistryBielefeld University Universitätsstraße 25 33615 Bielefeld Germany
| | - Uwe T. Bornscheuer
- Institute of Biochemistry Department of Biotechnology and Enzyme CatalysisGreifswald University Felix-Hausdorff-Str.4 17489 Greifswald Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry Department of ChemistryBielefeld University Universitätsstraße 25 33615 Bielefeld Germany
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23
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J B, M M B, Chanda K. Evolutionary approaches in protein engineering towards biomaterial construction. RSC Adv 2019; 9:34720-34734. [PMID: 35530663 PMCID: PMC9074691 DOI: 10.1039/c9ra06807d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/01/2019] [Indexed: 11/29/2022] Open
Abstract
The tailoring of proteins for specific applications by evolutionary methods is a highly active area of research. Rational design and directed evolution are the two main strategies to reengineer proteins or create chimeric structures. Rational engineering is often limited by insufficient knowledge about proteins' structure-function relationships; directed evolution overcomes this restriction but poses challenges in the screening of candidates. A combination of these protein engineering approaches will allow us to create protein variants with a wide range of desired properties. Herein, we focus on the application of these approaches towards the generation of protein biomaterials that are known for biodegradability, biocompatibility and biofunctionality, from combinations of natural, synthetic, or engineered proteins and protein domains. Potential applications depend on the enhancement of biofunctional, mechanical, or other desired properties. Examples include scaffolds for tissue engineering, thermostable enzymes for industrial biocatalysis, and other therapeutic applications.
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Affiliation(s)
- Brindha J
- Department of Chemistry, School of Advanced Science, Vellore Institute of Technology, Chennai Campus Vandalur-Kelambakkam Road Chennai-600 127 Tamil Nadu India
| | - Balamurali M M
- Department of Chemistry, School of Advanced Science, Vellore Institute of Technology, Chennai Campus Vandalur-Kelambakkam Road Chennai-600 127 Tamil Nadu India
| | - Kaushik Chanda
- Department of Chemistry, School of Advanced Science, Vellore Institute of Technology Vellore-632014 Tamil Nadu India
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24
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Yoav S, Stern J, Salama-Alber O, Frolow F, Anbar M, Karpol A, Hadar Y, Morag E, Bayer EA. Directed Evolution of Clostridium thermocellum β-Glucosidase A Towards Enhanced Thermostability. Int J Mol Sci 2019; 20:E4701. [PMID: 31547488 PMCID: PMC6801902 DOI: 10.3390/ijms20194701] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 12/27/2022] Open
Abstract
β-Glucosidases are key enzymes in the process of cellulose utilization. It is the last enzyme in the cellulose hydrolysis chain, which converts cellobiose to glucose. Since cellobiose is known to have a feedback inhibitory effect on a variety of cellulases, β-glucosidase can prevent this inhibition by hydrolyzing cellobiose to non-inhibitory glucose. While the optimal temperature of the Clostridium thermocellum cellulosome is 70 °C, C. thermocellum β-glucosidase A is almost inactive at such high temperatures. Thus, in the current study, a random mutagenesis directed evolutionary approach was conducted to produce a thermostable mutant with Kcat and Km, similar to those of the wild-type enzyme. The resultant mutant contained two mutations, A17S and K268N, but only the former was found to affect thermostability, whereby the inflection temperature (Ti) was increased by 6.4 °C. A17 is located near the central cavity of the native enzyme. Interestingly, multiple alignments revealed that position 17 is relatively conserved, whereby alanine is replaced only by serine. Upon the addition of the thermostable mutant to the C. thermocellum secretome for subsequent hydrolysis of microcrystalline cellulose at 70 °C, a higher soluble glucose yield (243%) was obtained compared to the activity of the secretome supplemented with the wild-type enzyme.
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Affiliation(s)
- Shahar Yoav
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, the Advanced School for Environmental Studies, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Johanna Stern
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Orly Salama-Alber
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Felix Frolow
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Michael Anbar
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Alon Karpol
- CelDezyner, 2 Bergman St, Tamar Science Park, Rehovot 7670504, Israel.
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, the Advanced School for Environmental Studies, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
| | - Ely Morag
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
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25
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Ribeiro LF, Amarelle V, Alves LDF, Viana de Siqueira GM, Lovate GL, Borelli TC, Guazzaroni ME. Genetically Engineered Proteins to Improve Biomass Conversion: New Advances and Challenges for Tailoring Biocatalysts. Molecules 2019; 24:molecules24162879. [PMID: 31398877 PMCID: PMC6719137 DOI: 10.3390/molecules24162879] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/30/2019] [Accepted: 08/06/2019] [Indexed: 01/02/2023] Open
Abstract
Protein engineering emerged as a powerful approach to generate more robust and efficient biocatalysts for bio-based economy applications, an alternative to ecologically toxic chemistries that rely on petroleum. On the quest for environmentally friendly technologies, sustainable and low-cost resources such as lignocellulosic plant-derived biomass are being used for the production of biofuels and fine chemicals. Since most of the enzymes used in the biorefinery industry act in suboptimal conditions, modification of their catalytic properties through protein rational design and in vitro evolution techniques allows the improvement of enzymatic parameters such as specificity, activity, efficiency, secretability, and stability, leading to better yields in the production lines. This review focuses on the current application of protein engineering techniques for improving the catalytic performance of enzymes used to break down lignocellulosic polymers. We discuss the use of both classical and modern methods reported in the literature in the last five years that allowed the boosting of biocatalysts for biomass degradation.
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Affiliation(s)
- Lucas Ferreira Ribeiro
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, Brazil.
| | - Vanesa Amarelle
- Department of Microbial Biochemistry and Genomics, Biological Research Institute Clemente Estable, Montevideo, PC 11600, Uruguay
| | - Luana de Fátima Alves
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | | | - Gabriel Lencioni Lovate
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Tiago Cabral Borelli
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, Brazil
| | - María-Eugenia Guazzaroni
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, Brazil.
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26
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A biochemical comparison of fungal GH6 cellobiohydrolases. Biochem J 2019; 476:2157-2172. [DOI: 10.1042/bcj20190185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/14/2019] [Accepted: 07/16/2019] [Indexed: 02/02/2023]
Abstract
AbstractCellobiohydrolases (CBHs) from glycoside hydrolase family 6 (GH6) make up an important part of the secretome in many cellulolytic fungi. They are also of technical interest, particularly because they are part of the enzyme cocktails that are used for the industrial breakdown of lignocellulosic biomass. Nevertheless, functional studies of GH6 CBHs are scarce and focused on a few model enzymes. To elucidate functional breadth among GH6 CBHs, we conducted a comparative biochemical study of seven GH6 CBHs originating from fungi living in different habitats, in addition to one enzyme variant. The enzyme sequences were investigated by phylogenetic analyses to ensure that they were not closely related phylogenetically. The selected enzymes were all heterologously expressed in Aspergillus oryzae, purified and thoroughly characterized biochemically. This approach allowed direct comparisons of functional data, and the results revealed substantial variability. For example, the adsorption capacity on cellulose spanned two orders of magnitude and kinetic parameters, derived from two independent steady-state methods also varied significantly. While the different functional parameters covered wide ranges, they were not independent since they changed in parallel between two poles. One pole was characterized by strong substrate interactions, high adsorption capacity and low turnover number while the other showed weak substrate interactions, poor adsorption and high turnover. The investigated enzymes essentially defined a continuum between these two opposites, and this scaling of functional parameters raises interesting questions regarding functional plasticity and evolution of GH6 CBHs.
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27
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Xu X, Fan C, Song L, Li J, Chen Y, Zhang Y, Liu B, Zhang W. A Novel CreA-Mediated Regulation Mechanism of Cellulase Expression in the Thermophilic Fungus Humicola insolens. Int J Mol Sci 2019; 20:ijms20153693. [PMID: 31357701 PMCID: PMC6696435 DOI: 10.3390/ijms20153693] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 12/24/2022] Open
Abstract
The thermophilic fungus Humicola insolens produces cellulolytic enzymes that are of great scientific and commercial interest; however, few reports have focused on its cellulase expression regulation mechanism. In this study, we constructed a creA gene (carbon catabolite repressor gene) disruption mutant strain of H. insolens that exhibited a reduced radial growth rate and stouter hyphae compared to the wild-type (WT) strain. The creA disruption mutant also expressed elevated pNPCase (cellobiohydrolase activities), pNPGase (β-glucosidase activities), and xylanase levels in non-inducing fermentation with glucose. Unlike other fungi, the H. insolenscreA disruption mutant displayed lower FPase (filter paper activity), CMCase (carboxymethyl cellulose activity), pNPCase, and pNPGase activity than observed in the WT strain when fermentation was induced using Avicel, whereas its xylanase activity was higher than that of the parental strain. These results indicate that CreA acts as a crucial regulator of hyphal growth and is part of a unique cellulase expression regulation mechanism in H. insolens. These findings provide a new perspective to improve the understanding of carbon catabolite repression regulation mechanisms in cellulase expression, and enrich the knowledge of metabolism diversity and molecular regulation of carbon metabolism in thermophilic fungi.
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Affiliation(s)
- Xinxin Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing 100081, China
| | - Chao Fan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing 100081, China
| | - Liya Song
- Beijing Key Lab of Plant Resource Research and Development, Beijing Technology and Business University, No.11 Fucheng Road, Haidian District, Beijing 100048, China
| | - Jinyang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing 100081, China
| | - Yuan Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing 100081, China
| | - Yuhong Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing 100081, China
| | - Bo Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing 100081, China.
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing 100081, China.
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Chen C, Su L, Xu F, Xia Y, Wu J. Improved Thermostability of Maltooligosyltrehalose Synthase from Arthrobacter ramosus by Directed Evolution and Site-Directed Mutagenesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5587-5595. [PMID: 31016980 DOI: 10.1021/acs.jafc.9b01123] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Maltooligosyltrehalose synthase (MTSase) is a key enzyme in trehalose production. MTSase from Arthrobacter ramosus has poor thermostability, limiting its industrial use. In this study, mutant G415P was obtained by directed evolution and S361R/S444E was subsequently generated based on a structure analysis of the region around G415. The t1/2 of G415P and S361R/S444E at 60 °C increased by 3.0- and 3.2-fold, respectively, compared with the wild-type enzyme. A triple mutant (G415P/S361R/S444E) was obtained through a combination of the above mutants, and its t1/2 significantly increased by 19.7-fold. Kinetic and thermodynamic stability results showed that the T50 and Tm values of the triple mutant increased by 7.1 and 7.3 °C, respectively, compared with those of the wild-type enzyme. When the triple mutant was used in trehalose production, the yield reached 71.6%, higher than the 70.3% achieved with the wild-type. Thus, the mutant has a potential application for industrial trehalose production.
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Ashraf NM, Krishnagopal A, Hussain A, Kastner D, Sayed AMM, Mok YK, Swaminathan K, Zeeshan N. Engineering of serine protease for improved thermostability and catalytic activity using rational design. Int J Biol Macromol 2019; 126:229-237. [DOI: 10.1016/j.ijbiomac.2018.12.218] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/15/2018] [Accepted: 12/22/2018] [Indexed: 10/27/2022]
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30
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Cai LN, Xu SN, Lu T, Lin DQ, Yao SJ. Directed expression of halophilic and acidophilic β-glucosidases by introducing homologous constitutive expression cassettes in marine Aspergillus niger. J Biotechnol 2019; 292:12-22. [DOI: 10.1016/j.jbiotec.2018.12.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/18/2018] [Accepted: 12/29/2018] [Indexed: 01/31/2023]
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31
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Han B, Hou Y, Jiang T, Lv B, Zhao L, Feng X, Li C. Computation-Aided Rational Deletion of C-Terminal Region Improved the Stability, Activity, and Expression Level of GH2 β-Glucuronidase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:11380-11389. [PMID: 30296070 DOI: 10.1021/acs.jafc.8b03449] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this study, computation-aided design on the basis of structural analysis was employed to rationally identify a highly dynamic C-terminal region that regulates the stability, expression level, and activity of a GH2 fungal glucuronidase from Aspergillus oryzae Li-3 (PGUS). Then, four mutants with a precisely truncated C-terminal region in different lengths were constructed; among them, mutant D591-604 with a 3.8-fold increase in half-life at 65 °C and a 6.8 kJ/mol increase in Gibbs free energy showed obviously improved kinetic and thermodynamic stability in comparison to PGUS. Mutants D590-604 and D591-604 both showed approximately 2.4-fold increases in the catalytic efficiency kcat/ Km and 1.8-fold increases in the expression level. Additionally, the expression level of PGUS was doubled through a C-terminal region swap with bacterial GUS from E. coli (EGUS). Finally, the robust PGUS mutants D590-604 and D591-604 were applied in the preparation of glycyrrhetinic acid with 4.0- and 4.4-fold increases in concentration through glycyrrhizin hydrolysis by a fed-batch process.
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Affiliation(s)
- Beijia Han
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Yuhui Hou
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Tian Jiang
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Bo Lv
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Lina Zhao
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety , Institute of High Energy Physics, Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Xudong Feng
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Chun Li
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
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Sutiono S, Carsten J, Sieber V. Structure-Guided Engineering of α-Keto Acid Decarboxylase for the Production of Higher Alcohols at Elevated Temperature. CHEMSUSCHEM 2018; 11:3335-3344. [PMID: 29953730 DOI: 10.1002/cssc.201800944] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/15/2018] [Indexed: 06/08/2023]
Abstract
Branched-chain keto acid decarboxylases (KDCs) are a class of enzymes that catalyze the decarboxylation of α-keto acids. They are key enzymes for production of higher alcohols in vivo and in vitro. However, the two most active KDCs (KivD and KdcA) have only moderate thermostability (<55 °C), which hinders the production of alcohols at high temperatures. Herein, structure-guided engineering toward improved thermostability of KdcA is outlined. Strategies such as stabilization of the catalytic center, surface engineering, and optimization of dimer interactions were applied. With seven amino acid substitutions, variant 7M.D showed an increase of the temperature at which 50 % of activity remains after one-hour incubation T1h50 by 14.8 °C without compromising its substrate specificity. 7M.D exhibited greater than 400-fold improvement of half-life at 70 °C and greater than 600-fold increase in process stability in the presence of 4 % isobutanol at 50 °C. 7M.D is more promising for the production of higher alcohols in thermophiles (>65 °C) and in cell-free applications.
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Affiliation(s)
- Samuel Sutiono
- Chair of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Jörg Carsten
- Catalytic Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, 85748, Garching, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
- Catalytic Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, 85748, Garching, Germany
- Straubing Branch BioCat, Fraunhofer IGB, Schulgasse 11a, 94315, Straubing, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Copper Road, St., Lucia, 4072, Australia
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Shi T, Han P, You C, Zhang YHPJ. An in vitro synthetic biology platform for emerging industrial biomanufacturing: Bottom-up pathway design. Synth Syst Biotechnol 2018; 3:186-195. [PMID: 30345404 PMCID: PMC6190512 DOI: 10.1016/j.synbio.2018.05.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 01/29/2023] Open
Abstract
Although most in vitro (cell-free) synthetic biology projects are usually used for the purposes of fundamental research or the formation of high-value products, in vitro synthetic biology platform, which can implement complicated biochemical reactions by the in vitro assembly of numerous enzymes and coenzymes, has been proposed for low-cost biomanufacturing of bioenergy, food, biochemicals, and nutraceuticals. In addition to the most important advantage-high product yield, in vitro synthetic biology platform features several other biomanufacturing advantages, such as fast reaction rate, easy product separation, open process control, broad reaction condition, tolerance to toxic substrates or products, and so on. In this article, we present the basic bottom-up design principles of in vitro synthetic pathway from basic building blocks-BioBricks (thermoenzymes and/or immobilized enzymes) to building modules (e.g., enzyme complexes or multiple enzymes as a module) with specific functions. With development in thermostable building blocks-BioBricks and modules, the in vitro synthetic biology platform would open a new biomanufacturing age for the cost-competitive production of biocommodities.
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Affiliation(s)
| | | | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Yi-Heng P. Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
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Escuder-Rodríguez JJ, DeCastro ME, Cerdán ME, Rodríguez-Belmonte E, Becerra M, González-Siso MI. Cellulases from Thermophiles Found by Metagenomics. Microorganisms 2018; 6:microorganisms6030066. [PMID: 29996513 PMCID: PMC6165527 DOI: 10.3390/microorganisms6030066] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 01/05/2023] Open
Abstract
Cellulases are a heterogeneous group of enzymes that synergistically catalyze the hydrolysis of cellulose, the major component of plant biomass. Such reaction has biotechnological applications in a broad spectrum of industries, where they can provide a more sustainable model of production. As a prerequisite for their implementation, these enzymes need to be able to operate in the conditions the industrial process requires. Thus, cellulases retrieved from extremophiles, and more specifically those of thermophiles, are likely to be more appropriate for industrial needs in which high temperatures are involved. Metagenomics, the study of genes and gene products from the whole community genomic DNA present in an environmental sample, is a powerful tool for bioprospecting in search of novel enzymes. In this review, we describe the cellulolytic systems, we summarize their biotechnological applications, and we discuss the strategies adopted in the field of metagenomics for the discovery of new cellulases, focusing on those of thermophilic microorganisms.
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Affiliation(s)
- Juan-José Escuder-Rodríguez
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - María-Eugenia DeCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - María-Esperanza Cerdán
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - Esther Rodríguez-Belmonte
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - Manuel Becerra
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
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35
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Menon BRK, Latham J, Dunstan MS, Brandenburger E, Klemstein U, Leys D, Karthikeyan C, Greaney MF, Shepherd SA, Micklefield J. Structure and biocatalytic scope of thermophilic flavin-dependent halogenase and flavin reductase enzymes. Org Biomol Chem 2018; 14:9354-9361. [PMID: 27714222 DOI: 10.1039/c6ob01861k] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Flavin-dependent halogenase (Fl-Hal) enzymes have been shown to halogenate a range of synthetic as well as natural aromatic compounds. The exquisite regioselectively of Fl-Hal enzymes can provide halogenated building blocks which are inaccessible using standard halogenation chemistries. Consequently, Fl-Hal are potentially useful biocatalysts for the chemoenzymatic synthesis of pharmaceuticals and other valuable products, which are derived from haloaromatic precursors. However, the application of Fl-Hal enzymes, in vitro, has been hampered by their poor catalytic activity and lack of stability. To overcome these issues, we identified a thermophilic tryptophan halogenase (Th-Hal), which has significantly improved catalytic activity and stability, compared with other Fl-Hal characterised to date. When used in combination with a thermostable flavin reductase, Th-Hal can efficiently halogenate a number of aromatic substrates. X-ray crystal structures of Th-Hal, and the reductase partner (Th-Fre), provide insights into the factors that contribute to enzyme stability, which could guide the discovery and engineering of more robust and productive halogenase biocatalysts.
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Affiliation(s)
- Binuraj R K Menon
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Jonathan Latham
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Mark S Dunstan
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Eileen Brandenburger
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Ulrike Klemstein
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - David Leys
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Chinnan Karthikeyan
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Michael F Greaney
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Sarah A Shepherd
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Jason Micklefield
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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Abstract
Glycoside Hydrolase Family 7 cellobiohydrolases (GH7 CBHs) catalyze cellulose depolymerization in cellulolytic eukaryotes, making them key discovery and engineering targets. However, there remains a lack of robust structure–activity relationships for these industrially important cellulases. Here, we compare CBHs from Trichoderma reesei (TrCel7A) and Penicillium funiculosum (PfCel7A), which exhibit a multi-modular architecture consisting of catalytic domain (CD), carbohydrate-binding module, and linker. We show that PfCel7A exhibits 60% greater performance on biomass than TrCel7A. To understand the contribution of each domain to this improvement, we measure enzymatic activity for a library of CBH chimeras with swapped subdomains, demonstrating that the enhancement is mainly caused by PfCel7A CD. We solve the crystal structure of PfCel7A CD and use this information to create a second library of TrCel7A CD mutants, identifying a TrCel7A double mutant with near-equivalent activity to wild-type PfCel7A. Overall, these results reveal CBH regions that enable targeted activity improvements. Cellobiohydrolases (CBHs) are critical for natural and industrial biomass degradation but their structure–activity relationships are not fully understood. Here, the authors present the biochemical and structural characterization of two CBHs, identifying protein regions that confer enhanced CBH activity.
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Saab-Rincón G, Alwaseem H, Guzmán-Luna V, Olvera L, Fasan R. Stabilization of the Reductase Domain in the Catalytically Self-Sufficient Cytochrome P450 BM3 by Consensus-Guided Mutagenesis. Chembiochem 2018; 19:622-632. [PMID: 29276819 PMCID: PMC5941085 DOI: 10.1002/cbic.201700546] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Indexed: 11/07/2022]
Abstract
The multidomain, catalytically self-sufficient cytochrome P450 BM-3 from Bacillus megaterium (P450BM3 ) constitutes a versatile enzyme for the oxyfunctionalization of organic molecules and natural products. However, the limited stability of the diflavin reductase domain limits the utility of this enzyme for synthetic applications. In this work, a consensus-guided mutagenesis approach was applied to enhance the thermal stability of the reductase domain of P450BM3 . Upon phylogenetic analysis of a set of distantly related P450s (>38 % identity), a total of 14 amino acid substitutions were identified and evaluated in terms of their stabilizing effects relative to the wild-type reductase domain. Recombination of the six most stabilizing mutations generated two thermostable variants featuring up to tenfold longer half-lives at 50 °C and increased catalytic performance at elevated temperatures. Further characterization of the engineered P450BM3 variants indicated that the introduced mutations increased the thermal stability of the FAD-binding domain and that the optimal temperature (Topt ) of the enzyme had shifted from 25 to 40 °C. This work demonstrates the effectiveness of consensus mutagenesis for enhancing the stability of the reductase component of a multidomain P450. The stabilized P450BM3 variants developed here could potentially provide more robust scaffolds for the engineering of oxidation biocatalysts.
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Affiliation(s)
- Gloria Saab-Rincón
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, 62250, Cuernavaca, Mor., México
| | - Hanan Alwaseem
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, NY, 14627, USA
| | - Valeria Guzmán-Luna
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, 62250, Cuernavaca, Mor., México
| | - Leticia Olvera
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, 62250, Cuernavaca, Mor., México
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, NY, 14627, USA
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Huang R, Chen H, Zhou W, Ma C, Zhang YHP. Engineering a thermostable highly active glucose 6-phosphate dehydrogenase and its application to hydrogen production in vitro. Appl Microbiol Biotechnol 2018; 102:3203-3215. [DOI: 10.1007/s00253-018-8798-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/16/2018] [Accepted: 01/18/2018] [Indexed: 10/17/2022]
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Engineering the conserved and noncatalytic residues of a thermostable β-1,4-endoglucanase to improve specific activity and thermostability. Sci Rep 2018; 8:2954. [PMID: 29440674 PMCID: PMC5811441 DOI: 10.1038/s41598-018-21246-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/01/2018] [Indexed: 12/18/2022] Open
Abstract
Endoglucanases are increasingly applied in agricultural and industrial applications as a key biocatalyst for cellulose biodegradation. However, the low performance in extreme conditions seriously challenges the enzyme’s commercial utilization. To obtain endoglucanases with substantially improved activity and thermostability, structure-based rational design was carried out based on the Chaetomium thermophilum β-1,4-endoglucanase CTendo45. In this study, five mutant enzymes were constructed by substitution of conserved and noncatalytic residues using site-directed mutagenesis. Mutants were constitutively expressed in Pichia pastoris, purified, and ultimately tested for enzymatic characteristics. Two single mutants, Y30F and Y173F, increased the enzyme’s specific activity 1.35- and 1.87-fold using carboxymethylcellulose sodium (CMC-Na) as a substrate, respectively. Furthermore, CTendo45 and mutants exhibited higher activity towards β-D-glucan than that of CMC-Na, and activities of Y173F and Y30F were also increased obviously against β-D-glucan. In addition, Y173F significantly improved the enzyme’s heat resistance at 80 °C and 90 °C. More interestingly, the double mutant Y30F/Y173F obtained considerably higher stability at elevated temperatures but failed to inherit the increased catalytic efficiency of its single mutant counterparts. This work gives an initial insight into the biological function of conserved and noncatalytic residues of thermostable endoglucanases and proposes a feasible path for the improvement of enzyme redesign proposals.
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40
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Joseph G, Wang L. Production of Biofuels from Biomass by Fungi. Fungal Biol 2018. [DOI: 10.1007/978-3-319-90379-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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41
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Seppälä S, Wilken SE, Knop D, Solomon KV, O’Malley MA. The importance of sourcing enzymes from non-conventional fungi for metabolic engineering and biomass breakdown. Metab Eng 2017; 44:45-59. [DOI: 10.1016/j.ymben.2017.09.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/16/2017] [Accepted: 09/16/2017] [Indexed: 10/18/2022]
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42
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Improved thermostability of a metagenomic glucose-tolerant β-glycosidase based on its X-ray crystal structure. Appl Microbiol Biotechnol 2017; 101:8353-8363. [DOI: 10.1007/s00253-017-8525-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/08/2017] [Accepted: 09/07/2017] [Indexed: 12/29/2022]
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Latham J, Brandenburger E, Shepherd SA, Menon BRK, Micklefield J. Development of Halogenase Enzymes for Use in Synthesis. Chem Rev 2017; 118:232-269. [PMID: 28466644 DOI: 10.1021/acs.chemrev.7b00032] [Citation(s) in RCA: 207] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature has evolved halogenase enzymes to regioselectively halogenate a diverse range of biosynthetic precursors, with the halogens introduced often having a profound effect on the biological activity of the resulting natural products. Synthetic endeavors to create non-natural bioactive small molecules for pharmaceutical and agrochemical applications have also arrived at a similar conclusion: halogens can dramatically improve the properties of organic molecules for selective modulation of biological targets in vivo. Consequently, a high proportion of pharmaceuticals and agrochemicals on the market today possess halogens. Halogenated organic compounds are also common intermediates in synthesis and are particularly valuable in metal-catalyzed cross-coupling reactions. Despite the potential utility of organohalogens, traditional nonenzymatic halogenation chemistry utilizes deleterious reagents and often lacks regiocontrol. Reliable, facile, and cleaner methods for the regioselective halogenation of organic compounds are therefore essential in the development of economical and environmentally friendly industrial processes. A potential avenue toward such methods is the use of halogenase enzymes, responsible for the biosynthesis of halogenated natural products, as biocatalysts. This Review will discuss advances in developing halogenases for biocatalysis, potential untapped sources of such biocatalysts and how further optimization of these enzymes is required to achieve the goal of industrial scale biohalogenation.
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Affiliation(s)
- Jonathan Latham
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Eileen Brandenburger
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sarah A Shepherd
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Binuraj R K Menon
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jason Micklefield
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
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Soh LMJ, Mak WS, Lin PP, Mi L, Chen FYH, Damoiseaux R, Siegel JB, Liao JC. Engineering a Thermostable Keto Acid Decarboxylase Using Directed Evolution and Computationally Directed Protein Design. ACS Synth Biol 2017; 6:610-618. [PMID: 28052191 DOI: 10.1021/acssynbio.6b00240] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Keto acid decarboxylase (Kdc) is a key enzyme in producing keto acid derived higher alcohols, like isobutanol. The most active Kdc's are found in mesophiles; the only reported Kdc activity in thermophiles is 2 orders of magnitude less active. Therefore, the thermostability of mesophilic Kdc limits isobutanol production temperature. Here, we report development of a thermostable 2-ketoisovalerate decarboxylase (Kivd) with 10.5-fold increased residual activity after 1h preincubation at 60 °C. Starting with mesophilic Lactococcus lactis Kivd, a library was generated using random mutagenesis and approximately 8,000 independent variants were screened. The top single-mutation variants were recombined. To further improve thermostability, 16 designs built using Rosetta Comparative Modeling were screened and the most active was recombined to form our best variant, LLM4. Compared to wild-type Kivd, a 13 °C increase in melting temperature and over 4-fold increase in half-life at 60 °C were observed. LLM4 will be useful for keto acid derived alcohol production in lignocellulosic thermophiles.
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Affiliation(s)
| | - Wai Shun Mak
- Department of Chemistry, Biochemistry & Molecular Medicine, and the Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | | | | | | | - Robert Damoiseaux
- California NanoSystems Institute, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Justin B. Siegel
- Department of Chemistry, Biochemistry & Molecular Medicine, and the Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - James C. Liao
- UCLA-DOE Institute of Genomics and Proteomics, 420 Westwood Plaza, Los Angeles, California 90095, United States
- Academia Sinica, 128 Academia
Road, Section 2, Nankang, Taipei 115, Taiwan, R.O.C
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Jiang X, Li W, Chen G, Wang L. Dynamic Perturbation of the Active Site Determines Reversible Thermal Inactivation in Glycoside Hydrolase Family 12. J Chem Inf Model 2017; 57:288-297. [DOI: 10.1021/acs.jcim.6b00692] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xukai Jiang
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
| | - Wen Li
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
| | - Guanjun Chen
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
| | - Lushan Wang
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
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Harrington LB, Jha RK, Kern TL, Schmidt EN, Canales GM, Finney KB, Koppisch AT, Strauss CEM, Fox DT. Rapid Thermostabilization of Bacillus thuringiensis Serovar Konkukian 97-27 Dehydroshikimate Dehydratase through a Structure-Based Enzyme Design and Whole Cell Activity Assay. ACS Synth Biol 2017; 6:120-129. [PMID: 27548779 DOI: 10.1021/acssynbio.6b00159] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thermostabilization of an enzyme with complete retention of catalytic efficiency was demonstrated on recombinant 3-dehydroshikimate dehydratase (DHSase or wtAsbF) from Bacillus thuringiensis serovar konkukian 97-27 (hereafter, B. thuringiensis 97-27). The wtAsbF is relatively unstable at 37 °C, in vitro (t1/237 = 15 min), in the absence of divalent metal. We adopted a structure-based design to identify stabilizing mutations and created a combinatorial library based upon predicted mutations at specific locations on the enzyme surface. A diversified asbF library (∼2000 variants) was expressed in E. coli harboring a green fluorescent protein (GFP) reporter system linked to the product of wtAsbF activity (3,4-dihydroxybenzoate, DHB). Mutations detrimental to DHSase function were rapidly eliminated using a high throughput fluorescence activated cell sorting (FACS) approach. After a single sorting round and heat screen at 50 °C, a triple AsbF mutant (Mut1), T61N, H135Y, and H257P, was isolated and characterized. The half-life of Mut1 at 37 °C was >10-fold higher than the wtAsbF (t1/237 = 169 min). Further, the second-order rate constants for both wtAsbF and Mut1 were approximately equal (9.9 × 105 M-1 s-1, 7.8 × 105 M-1 s-1, respectively), thus demonstrating protein thermostability did not come at the expense of enzyme thermophilicity. In addition, in vivo overexpression of Mut1 in E. coli resulted in a ∼60-fold increase in functional enzyme when compared to the wild-type enzyme under the identical expression conditions. Finally, overexpression of the thermostable AsbF resulted in an approximate 80-120% increase in DHB accumulation in the media relative to the wild-type enzyme.
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Affiliation(s)
- Lucas B. Harrington
- Bioscience
Division, Los Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, New Mexico 87545, United States
| | - Ramesh K. Jha
- Bioscience
Division, Los Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, New Mexico 87545, United States
| | - Theresa L. Kern
- Bioscience
Division, Los Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, New Mexico 87545, United States
| | - Emily N. Schmidt
- Bioscience
Division, Los Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, New Mexico 87545, United States
| | - Gustavo M. Canales
- Department
of Chemistry, Northern Arizona University, P.O. Box 5698, Flagstaff, Arizona 86001, United States
| | - Kellan B. Finney
- Department
of Chemistry, Northern Arizona University, P.O. Box 5698, Flagstaff, Arizona 86001, United States
| | - Andrew T. Koppisch
- Department
of Chemistry, Northern Arizona University, P.O. Box 5698, Flagstaff, Arizona 86001, United States
| | - Charlie E. M. Strauss
- Bioscience
Division, Los Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, New Mexico 87545, United States
| | - David T. Fox
- Chemistry
Division, Los Alamos National Laboratory, P.O. Box 1663, MS E554, Los Alamos, New Mexico 87545, United States
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Gusakov AV, Dotsenko AS, Rozhkova AM, Sinitsyn AP. N-Linked glycans are an important component of the processive machinery of cellobiohydrolases. Biochimie 2017; 132:102-108. [DOI: 10.1016/j.biochi.2016.11.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/10/2016] [Indexed: 02/02/2023]
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48
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Kubicek CP, Kubicek EM. Enzymatic deconstruction of plant biomass by fungal enzymes. Curr Opin Chem Biol 2016; 35:51-57. [DOI: 10.1016/j.cbpa.2016.08.028] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
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Tachioka M, Sugimoto N, Nakamura A, Sunagawa N, Ishida T, Uchiyama T, Igarashi K, Samejima M. Development of simple random mutagenesis protocol for the protein expression system in Pichia pastoris. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:199. [PMID: 27660653 PMCID: PMC5028916 DOI: 10.1186/s13068-016-0613-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/07/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Random mutagenesis is a powerful technique to obtain mutant proteins with different properties from the wild-type molecule. Error-prone PCR is often employed for random mutagenesis in bacterial protein expression systems, but has rarely been used in the methylotrophic yeast Pichia pastoris system, despite its significant advantages, mainly because large (μg-level) amounts of plasmids are required for transformation. RESULTS We developed a quick and easy technique for random mutagenesis in P. pastoris by sequential Phi29 DNA polymerase-based amplification methods, error-prone rolling circle amplification (RCA) and multiple displacement amplification (MDA). The methodology was validated by applying it for random mutation of the gene encoding cellulase from the basidiomycete Phanerochaete chrysosporium (PcCel6A), a key enzyme in degradation of cellulosic biomass. In the error-prone RCA step, the concentrations of manganese ion (Mn(2+)) and cellulase gene-containing plasmid were varied, and the products obtained under each condition were subjected to the second MDA step in the absence of Mn(2+). The maximum error rate was 2.6 mutations/kb, as evaluated from the results of large-scale sequencing. Several μg of MDA products was transformed by electroporation into Pichia cells, and the activities of extracellularly expressed PcCel6A mutants towards crystalline and amorphous celluloses were compared with those of wild-type enzyme to identify key amino acid residues affecting degradation of crystalline cellulose. CONCLUSIONS We present a rapid and convenient random mutagenesis method that does not require laborious steps such as ligation, cloning, and synthesis of specific primers. This method was successfully applied to the protein expression system in P. pastoris.
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Affiliation(s)
- Mikako Tachioka
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Naohisa Sugimoto
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
- Biomaterial in Tokyo Co., Ltd., Fukuoka Lab, Ōnojō, Fukuoka 816-0905 Japan
| | - Akihiko Nakamura
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
- Institute for Molecular Science, National Institute of Natural Sciences, Okazaki, 444-8787 Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Takuya Ishida
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Taku Uchiyama
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
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Eibinger M, Sigl K, Sattelkow J, Ganner T, Ramoni J, Seiboth B, Plank H, Nidetzky B. Functional characterization of the native swollenin from Trichoderma reesei: study of its possible role as C1 factor of enzymatic lignocellulose conversion. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:178. [PMID: 27570542 PMCID: PMC5000517 DOI: 10.1186/s13068-016-0590-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/15/2016] [Indexed: 05/28/2023]
Abstract
BACKGROUND Through binding to cellulose, expansin-like proteins are thought to loosen the structural order of crystalline surface material, thus making it more accessible for degradation by hydrolytic enzymes. Swollenin SWO1 is the major expansin-like protein from the fungus Trichoderma reesei. Here, we have performed a detailed characterization of a recombinant native form of SWO1 with respect to its possible auxiliary role in the enzymatic saccharification of lignocellulosic substrates. RESULTS The swo1 gene was overexpressed in T. reesei QM9414 Δxyr1 mutant, featuring downregulated cellulase production, and the protein was purified from culture supernatant. SWO1 was N-glycosylated and its circular dichroism spectrum suggested a folded protein. Adsorption isotherms (25 °C, pH 5.0, 1.0 mg substrate/mL) revealed SWO1 to be 120- and 20-fold more specific for binding to birchwood xylan and kraft lignin, respectively, than for binding to Avicel PH-101. The SWO1 binding capacity on lignin (25 µmol/g) exceeded 12-fold that on Avicel PH-101 (2.1 µmol/g). On xylan, not only the binding capacity (22 µmol/g) but also the affinity of SWO1 (K d = 0.08 µM) was enhanced compared to Avicel PH-101 (K d = 0.89 µM). SWO1 caused rapid release of a tiny amount of reducing sugars (<1 % of total) from different substrates (Avicel PH-101, nanocrystalline cellulose, steam-pretreated wheat straw, barley β-glucan, cellotetraose) but did not promote continued saccharification. Atomic force microscopy revealed that amorphous cellulose films were not affected by SWO1. Also with AFM, binding of SWO1 to cellulose nanocrystallites was demonstrated at the single-molecule level, but adsorption did not affect this cellulose. SWO1 exhibited no synergy with T. reesei cellulases in the hydrolysis of the different celluloses. However, SWO1 boosted slightly (1.5-fold) the reducing sugar release from a native grass substrate. CONCLUSIONS SWO1 is a strongly glycosylated protein, which has implications for producing it in heterologous hosts. Although SWO1 binds to crystalline cellulose, its adsorption to xylan is much stronger. SWO1 is not an auxiliary factor of the enzymatic degradation of a variety of cellulosic substrates. Effect of SWO1 on sugar release from intact plant cell walls might be exploitable with certain (e.g., mildly pretreated) lignocellulosic feedstocks.
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Affiliation(s)
- Manuel Eibinger
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010 Graz, Austria
| | - Karin Sigl
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010 Graz, Austria
| | - Jürgen Sattelkow
- Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Thomas Ganner
- Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Jonas Ramoni
- Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstrasse 1A/166, 1060 Vienna, Austria
| | - Bernhard Seiboth
- Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstrasse 1A/166, 1060 Vienna, Austria
| | - Harald Plank
- Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
- Graz Centre for Electron Microscopy, Steyrergasse 17, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010 Graz, Austria
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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