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García-Paz FDM, Del Moral S, Morales-Arrieta S, Ayala M, Treviño-Quintanilla LG, Olvera-Carranza C. Multidomain chimeric enzymes as a promising alternative for biocatalysts improvement: a minireview. Mol Biol Rep 2024; 51:410. [PMID: 38466518 DOI: 10.1007/s11033-024-09332-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024]
Abstract
Searching for new and better biocatalysts is an area of study in constant development. In nature, mechanisms generally occurring in evolution, such as genetic duplication, recombination, and natural selection processes, produce various enzymes with different architectures and properties. The recombination of genes that code proteins produces multidomain chimeric enzymes that contain two or more domains that sometimes enhance their catalytic properties. Protein engineering has mimicked this process to enhance catalytic activity and the global stability of enzymes, searching for new and better biocatalysts. Here, we present and discuss examples from both natural and synthetic multidomain chimeric enzymes and how additional domains heighten their stability and catalytic activity. Moreover, we also describe progress in developing new biocatalysts using synthetic fusion enzymes and revise some methodological strategies to improve their biological fitness.
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Affiliation(s)
- Flor de María García-Paz
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001 Col. Chamilpa CP 62210, Cuernavaca, Morelos, México
| | - Sandra Del Moral
- Investigador por México-CONAHCyT, Unidad de Investigación y Desarrollo en Alimentos, Tecnológico Nacional de México, Campus Veracruz. MA de Quevedo 2779, Col. Formando Hogar, CP 91960, Veracruz, Veracruz, México
| | - Sandra Morales-Arrieta
- Departamento de Biotecnología, Universidad Politécnica del Estado de Morelos, Boulevard Cuauhnáhuac No. 566 Col. Lomas del Texcal CP 62550, Jiutepec, Morelos, México
| | - Marcela Ayala
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001 Col. Chamilpa CP 62210, Cuernavaca, Morelos, México
| | - Luis Gerardo Treviño-Quintanilla
- Departamento de Biotecnología, Universidad Politécnica del Estado de Morelos, Boulevard Cuauhnáhuac No. 566 Col. Lomas del Texcal CP 62550, Jiutepec, Morelos, México
| | - Clarita Olvera-Carranza
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001 Col. Chamilpa CP 62210, Cuernavaca, Morelos, México.
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Chatterjee A, Puri S, Sharma PK, Deepa PR, Chowdhury S. Nature-inspired Enzyme engineering and sustainable catalysis: biochemical clues from the world of plants and extremophiles. Front Bioeng Biotechnol 2023; 11:1229300. [PMID: 37409164 PMCID: PMC10318364 DOI: 10.3389/fbioe.2023.1229300] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
The use of enzymes to accelerate chemical reactions for the synthesis of industrially important products is rapidly gaining popularity. Biocatalysis is an environment-friendly approach as it not only uses non-toxic, biodegradable, and renewable raw materials but also helps to reduce waste generation. In this context, enzymes from organisms living in extreme conditions (extremozymes) have been studied extensively and used in industries (food and pharmaceutical), agriculture, and molecular biology, as they are adapted to catalyze reactions withstanding harsh environmental conditions. Enzyme engineering plays a key role in integrating the structure-function insights from reference enzymes and their utilization for developing improvised catalysts. It helps to transform the enzymes to enhance their activity, stability, substrates-specificity, and substrate-versatility by suitably modifying enzyme structure, thereby creating new variants of the enzyme with improved physical and chemical properties. Here, we have illustrated the relatively less-tapped potentials of plant enzymes in general and their sub-class of extremozymes for industrial applications. Plants are exposed to a wide range of abiotic and biotic stresses due to their sessile nature, for which they have developed various mechanisms, including the production of stress-response enzymes. While extremozymes from microorganisms have been extensively studied, there are clear indications that plants and algae also produce extremophilic enzymes as their survival strategy, which may find industrial applications. Typical plant enzymes, such as ascorbate peroxidase, papain, carbonic anhydrase, glycoside hydrolases and others have been examined in this review with respect to their stress-tolerant features and further improvement via enzyme engineering. Some rare instances of plant-derived enzymes that point to greater exploration for industrial use have also been presented here. The overall implication is to utilize biochemical clues from the plant-based enzymes for robust, efficient, and substrate/reaction conditions-versatile scaffolds or reference leads for enzyme engineering.
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Affiliation(s)
| | | | | | - P. R. Deepa
- *Correspondence: P. R. Deepa, ; Shibasish Chowdhury,
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Ji S, Gavande PV, Choudhury B, Goyal A. Computational design and structure dynamics analysis of bifunctional chimera of endoxylanase from Clostridium thermocellum and xylosidase from Bacteroides ovatus. 3 Biotech 2023; 13:59. [PMID: 36714550 PMCID: PMC9877272 DOI: 10.1007/s13205-023-03482-6] [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: 08/27/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023] Open
Abstract
Development of chimeric enzymes by protein engineering can more efficiently contribute toward biomass conversion for bioenergy generation. Therefore, prior to experimental validation, a computational approach by modeling and molecular dynamic simulation can assess the structural and functional behavior of chimeric enzymes. In this study, a bifunctional chimera, CtXyn11A-BoGH43A comprising an efficient endoxylanase (CtXyn11A) from Clostridium thermocellum and xylosidase (BoGH43A) from Bacteroides ovatus was computationally designed and its binding and stability analysis with xylooligosaccharides were performed. The modeled chimera showed β-jellyroll fold for CtXyn11A and 5-bladed β-propeller fold for BoGH43A module. Stereo-chemical properties analyzed by Ramachandran plot showed 98.8% residues in allowed region, validating the modeled chimera. The catalytic residues identified by multiple sequence alignment were Glu94 and Glu184 for CtXyn11A and Asp229 and Glu384 for BoGH43A modules. CtXyn11A followed retaining-type, whereas BoGH43A enforced inverting-type of reaction mechanism during xylan hydrolysis as revealed by superposition and GH11 and GH43 familial analyses. Molecular docking studies showed binding energy, (ΔG) - 4.54 and - 4.18 kcal/mol for CtXyn11A and BoGH43A modules of chimera, respectively, with xylobiose, while - 3.94 and - 3.82 kcal/mol for CtXyn11A and BoGH43A modules of chimera, respectively, with xylotriose. MD simulation of CtXyn11A-BoGH43A complexed with xylobiose and xylotriose till 100 ns displayed stability by RMSD, compactness by R g and conformational stability by SASA analyses. The lowered values of RMSF in active-site residues, Glu94, Glu184, Asp229, Asp335 and Glu384 confirmed the efficient binding of chimera with xylobiose and xylotriose. These results were in agreement with the earlier experimental studies on CtXyn11A releasing xylooligosaccharides from xylan and BoGH43A releasing d-xylose from xylooligosaccharides and xylobiose. The chimera showed stronger affinity in terms of total short-range interaction energy; - 190 and - 121 kJ/mol for with xylobiose and xylotriose, respectively. The bifunctional chimera, CtXyn11A-BoGH43A showed stability and integrity with xylobiose and xylotriose. The designed chimera can be constructed and applied for efficient biomass conversion.
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Affiliation(s)
- Shyam Ji
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Parmeshwar Vitthal Gavande
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Bipasha Choudhury
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
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Li Y, Song W, Han X, Wang Y, Rao S, Zhang Q, Zhou J, Li J, Liu S, Du G. Recent progress in key lignocellulosic enzymes: Enzyme discovery, molecular modifications, production, and enzymatic biomass saccharification. BIORESOURCE TECHNOLOGY 2022; 363:127986. [PMID: 36126851 DOI: 10.1016/j.biortech.2022.127986] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 05/15/2023]
Abstract
Lignocellulose, the most prevalent biomass on earth, can be enzymatically converted into carbohydrates for bioethanol production and other uses. Among lignocellulosic enzymes, endoglucanase, xylanase, and laccase are the key enzymes, owing to their ability to disrupt the main structure of lignocellulose. Recently, new discovery methods have been established to obtain key lignocellulosic enzymes with excellent enzymatic properties. Molecular modification of enzymes to modulate their thermostability, catalytic activity, and substrate specificity has been performed with protein engineering technology. In addition, the enzyme expression has been effectively improved through expression element screening and host modification, as well as fermentation optimization. Immobilization of enzymes, use of surfactants, synergistic degradation, and optimization of reaction conditions have addressed the inefficiency of enzymatic saccharification. In this review, recent advances in key lignocellulosic enzymes are summarized, along with future prospects for the development of super-engineered strains and integrative technologies for enzymatic biomass saccharification.
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Affiliation(s)
- Yangyang Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Weiyan Song
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Xuyue Han
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Yachan Wang
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Shengqi Rao
- College of Food Science and Engineering, Yangzhou University, Yangzhou 214122, China
| | - Quan Zhang
- Dalian Research Institute of Petroleum and Petrochemicals, SINOPEC, Dalian 116000, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Song Liu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
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Martins M, Silva MF, Dinamarco TM, Goldbeck R. Novel bi-functional thermostable chimeric enzyme for feasible xylo-oligosaccharides production from agro-industrial wastes. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Gavande PV, Nath P, Kumar K, Ahmed N, Fontes CMGA, Goyal A. Highly efficient, processive and multifunctional recombinant endoglucanase RfGH5_4 from Ruminococcus flavefaciens FD-1 v3 for recycling lignocellulosic plant biomasses. Int J Biol Macromol 2022; 209:801-813. [PMID: 35421411 DOI: 10.1016/j.ijbiomac.2022.04.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/18/2022] [Accepted: 04/08/2022] [Indexed: 11/26/2022]
Abstract
Gene encoding endoglucanase, RfGH5_4 from R. flavefaciens FD-1 v3 was cloned, expressed in Escherichia coli BL21(DE3) cells and purified. RfGH5_4 showed molecular size 41 kDa and maximum activity at pH 5.5 and 55 °C. It was stable between pH 5.0-8.0, retaining 85% activity and between 5 °C-45 °C, retaining 75% activity, after 60 min. RfGH5_4 displayed maximum activity (U/mg) against barley β-D-glucan (665) followed by carboxymethyl cellulose (450), xyloglucan (343), konjac glucomannan (285), phosphoric acid swollen cellulose (86), beechwood xylan (21.7) and carob galactomannan (16), thereby displaying the multi-functionality. Catalytic efficiency (mL.mg-1 s-1) of RfGH5_4 against carboxymethyl cellulose (146) and konjac glucomannan (529) was significantly high. TLC and MALDI-TOF-MS analyses of RfGH5_4 treated hydrolysates of cellulosic and hemicellulosic polysaccharides displayed oligosaccharides of degree of polymerization (DP) between DP2-DP11. TLC, HPLC and Processivity-Index analyses revealed RfGH5_4 to be a processive endoglucanase as initially, for 30 min it hydrolysed cellulose to cellotetraose followed by persistent release of cellotriose and cellobiose. RfGH5_4 yielded sufficiently high Total Reducing Sugar (TRS, mg/g) from saccharification of alkali pre-treated sorghum (72), finger millet (62), sugarcane bagasse (38) and cotton (27) in a 48 h saccharification reaction. Thus, RfGH5_4 can be considered as a potential endoglucanase for renewable energy applications.
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Affiliation(s)
- Parmeshwar Vitthal Gavande
- Department of Biosciences and Bioengineering, Carbohydrate Enzyme Biotechnology Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Priyanka Nath
- Department of Biosciences and Bioengineering, Carbohydrate Enzyme Biotechnology Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Krishan Kumar
- Department of Biosciences and Bioengineering, Carbohydrate Enzyme Biotechnology Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Nazneen Ahmed
- Department of Biosciences and Bioengineering, Carbohydrate Enzyme Biotechnology Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Carlos M G A Fontes
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal; NZYTech - Genes & Enzymes, Estrada do Paço do Lumiar, Campus do Lumiar, Edifício, Lisbon, Portugal
| | - Arun Goyal
- Department of Biosciences and Bioengineering, Carbohydrate Enzyme Biotechnology Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
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Sharma A, Balda S, Capalash N, Sharma P. Engineering multifunctional enzymes for agro-biomass utilization. BIORESOURCE TECHNOLOGY 2022; 347:126706. [PMID: 35033642 DOI: 10.1016/j.biortech.2022.126706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Lignocellulosic biomass is a plentiful renewable resource that can be converted into a wide range of high-value-added industrial products. However, the complexity of its structural integrity is one of the major constraints and requires combinations of different fibrolytic enzymes for the cost-effective, industrially and environmentally feasible transformation. An interesting approach is constructing multifunctional enzymes, either in a single polypeptide or by joining multiple domains with linkers and performing diverse reactions simultaneously, in a single host. The production of such chimera proteins multiplies the advantages of different enzymatic reactions in a single setup, in lesser time, at lower production cost and with desirable and improved catalytic activities. This review embodies the various domain-tailoring and extracellular secretion strategies, possible solutions to their challenges, and efforts to experimentally connect different catalytic activities in a single host, as well as their applications.
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Affiliation(s)
- Aarjoo Sharma
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Sanjeev Balda
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Neena Capalash
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Prince Sharma
- Department of Microbiology, Panjab University, Chandigarh, India.
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Nath P, Goyal A. Structure and dynamics analysis of multi-domain putative β-1,4-glucosidase of family 3 glycoside hydrolase (PsGH3) from Pseudopedobacter saltans. J Mol Model 2021; 27:106. [PMID: 33694107 PMCID: PMC7945971 DOI: 10.1007/s00894-021-04721-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/01/2021] [Indexed: 11/30/2022]
Abstract
Structure and conformational behaviour of a putative β-1,4-glucosidase of glycoside hydrolase family 3 (PsGH3) from Pseudopedobacter saltans was predicted by using in-silico tools. PsGH3 modeled structure constructed using Phyre2 displayed multidomain architecture comprising an N-terminal (β/α)8-fold domain followed by (α/β)6-sandwich domain, PA14 domain, and a C-terminal domain resembling an immunoglobulin fold. Ramachandran plot displayed 99.3% of amino acids in the allowed region and 0.7% residues in the disallowed region. Multiple sequence alignment (MSA) and structure superposition of PsGH3 with other homologues from GH3 family revealed the conserved residues, Asp274 and Glu624 present in loops LA and LB, respectively originating from N-terminal domain act as catalytic residues. The volume and area calculated for PsGH3 displayed a deep active-site conformation comparable with its homologues, β-1,4-glucosidases (GH3) of Kluyveromyces marxianus and Streptomyces venezuelae. Molecular dynamic (MD) simulation of PsGH3 structure for 80 ns suggested stable and compact structure. Molecular docking studies revealed deeper active site conformation of PsGH3 that could house larger cellooligosaccharides up to 7° of polymerization (DP7). The amino acid residues, Ala86, Leu88, Cys275, Pro483, Phe493, Asn417, Asn491, Pro492, and Leu495 created a binding pocket near the catalytic cleft, crucial for ligand binding. MD simulation of PsGH3 in the presence of cellooligosaccharides, viz., cellobiose and celloheptaose showed stability in terms of RMSD, Rg, and SASA values till 80 ns. The calculation of average number of hydrogen bond (H-bond), interaction energy, and binding free energy confirmed the stronger binding affinity of the larger cellooligosaccharides such as celloheptaose in the binding cavity of PsGH3.
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Affiliation(s)
- Priyanka Nath
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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Mandeep, Liu H, Shukla P. Synthetic Biology and Biocomputational Approaches for Improving Microbial Endoglucanases toward Their Innovative Applications. ACS OMEGA 2021; 6:6055-6063. [PMID: 33718696 PMCID: PMC7948214 DOI: 10.1021/acsomega.0c05744] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/03/2021] [Indexed: 11/13/2023]
Abstract
Microbial endoglucanases belonging to the β-1-4 glycosyl hydrolase family are useful enzymes due to their vast industrial applications in pulp and paper industries and biorefinery. They convert lignocellulosic substrates to soluble sugars and help in the biodegradation process. Various biocomputational tools can be utilized to understand the catalytic activity, reaction kinetics, complexity of active sites, and chemical behavior of enzyme complexes in reactions. This might be helpful in increasing productivity and cost reduction in industries. The present review gives an overview of some interesting aspects of enzyme design, including computational techniques such as molecular dynamics simulation, homology modeling, mutational analysis, etc., toward enhancing the quality of these enzymes. Moreover, the review also covers the aspects of synthetic biology, which could be helpful in faster and reliable development of useful enzymes with desired characteristics and applications. Finally, the review also deciphers the utilization of endoglucanases in biodegradation and emphasizes the use of diversified protein engineering tools and the modification of metabolic pathways for enzyme engineering.
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Affiliation(s)
- Mandeep
- Enzyme
Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Hao Liu
- State
Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, China
| | - Pratyoosh Shukla
- Enzyme
Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
- School
of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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Glasgow E, Vander Meulen K, Kuch N, Fox BG. Multifunctional cellulases are potent, versatile tools for a renewable bioeconomy. Curr Opin Biotechnol 2021; 67:141-148. [PMID: 33550093 PMCID: PMC8366578 DOI: 10.1016/j.copbio.2020.12.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/09/2020] [Accepted: 12/28/2020] [Indexed: 11/21/2022]
Abstract
Enzyme performance is critical to the future bioeconomy based on renewable plant materials. Plant biomass can be efficiently hydrolyzed by multifunctional cellulases (MFCs) into sugars suitable for conversion into fuels and chemicals, and MFCs fall into three functional categories. Recent work revealed MFCs with broad substrate specificity, dual exo-activity/endo-activity on cellulose, and intramolecular synergy, among other novel characteristics. Binding modules and accessory catalytic domains amplify MFC and xylanase activity in a wide variety of ways, and processive endoglucanases achieve autosynergy on cellulose. Multidomain MFCs from Caldicellulosiruptor are heat-tolerant, adaptable to variable cellulose crystallinity, and may provide interchangeable scaffolds for recombinant design. Further studies of MFC properties and their reactivity with plant biomass are recommended for increasing biorefinery yields.
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Affiliation(s)
- Evan Glasgow
- Dept. of Biochemistry, University of Wisconsin - Madison, 433 Babcock Dr., Madison, WI, 53706, United States; Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, 1552 University Ave, Madison, WI, 53726, United States
| | - Kirk Vander Meulen
- Dept. of Biochemistry, University of Wisconsin - Madison, 433 Babcock Dr., Madison, WI, 53706, United States; Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, 1552 University Ave, Madison, WI, 53726, United States
| | - Nate Kuch
- Dept. of Biochemistry, University of Wisconsin - Madison, 433 Babcock Dr., Madison, WI, 53706, United States; Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, 1552 University Ave, Madison, WI, 53726, United States
| | - Brian G Fox
- Dept. of Biochemistry, University of Wisconsin - Madison, 433 Babcock Dr., Madison, WI, 53706, United States; Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, 1552 University Ave, Madison, WI, 53726, United States.
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Nath P, Maibam PD, Singh S, Rajulapati V, Goyal A. Sequential pretreatment of sugarcane bagasse by alkali and organosolv for improved delignification and cellulose saccharification by chimera and cellobiohydrolase for bioethanol production. 3 Biotech 2021; 11:59. [PMID: 33489678 DOI: 10.1007/s13205-020-02600-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/17/2020] [Indexed: 01/13/2023] Open
Abstract
Sequential pretreatments for sugarcane bagasse (scb) by NaOH followed by organosolv under mild conditions were evaluated for cellulose recovery and dilignification. The best-optimized sequential pretreatment of scb was obtained at 10% (w/v) of raw scb loading at 1% (w/v) NaOH (50 °C, 2 h) followed by treatment with organosolv (85%, v/v phosphoric acid, 50 °C, 1 h) with chilled acetone. This sequentially pretreated scb showed cellulose recovery, 66.1% (w/w) and delignification, 83.2% (w/w). NaOH or organosolv pretreated scb showed lower cellulose recovery 47.4% (w/w) or 54.5% (w/w) with lower delignification, 61% (w/w) or 56% (w/w), respectively. Pretreated solid residue of sequentially pretreated scb was enzymatically saccharified by chimera (β-glucosidase and endoglucanase, CtGH1-L1-CtGH5-F194A) and cellobiohydrolase (CtCBH5A) cloned from Clostridium thermocellum. Enzymatic hydrolysate of best sequentially pretreated scb gave total reducing sugar (TRS) yield, 230 mg/g and glucose yield, 137 mg/g pretreated scb. Only organosolv pretreated scb gave TRS yield, 112.5 mg/g and glucose yield, 72 mg/g of pretreated scb. Thus, sequentially pretreated scb resulted in 37% higher enzymatic digestibility than only orgnaosolv pretreated scb. Higher enzymatic digestibility was supported by higher crystallinity index CrI (45%) than those obtained with only organosolv pretreated (38%) or raw scb (25%). Field Emission Scanning Electron Microscope (FESEM) and Fourier-transform infrared (FT-IR) analyses showed enhanced cellulose exposure in sequentially pretreated scb. Preliminary investigation of bioethanol production at small scale by separate hydrolysis and fermentation (SHF) of enzymatic hydrolysate from best sequentially pretreated scb by Saccharomyces cerevisiae gave maximum ethanol yield of 0.42 g/g of glucose. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-020-02600-y.
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Affiliation(s)
- Priyanka Nath
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
- DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, Assam India
| | | | - Shweta Singh
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
- DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, Assam India
| | - Vikky Rajulapati
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
- Centre for Energy, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
- DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, Assam India
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12
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Kumar K, Singh S, Sharma K, Goyal A. Computational modeling and small-angle X-ray scattering based structure analysis and identifying ligand cleavage mechanism by processive endocellulase of family 9 glycoside hydrolase (HtGH9) from Hungateiclostridium thermocellum ATCC 27405. J Mol Graph Model 2020; 103:107808. [PMID: 33248343 DOI: 10.1016/j.jmgm.2020.107808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 11/16/2022]
Abstract
The cellulases of family 9 glycoside hydrolase with subtle difference in amino acid sequence have shown different types of catalytic activities such as endo-, exo- or processive endocellulase. However, the reason behind the different types of catalytic activities still unclear. In this study, the processive endocellulase, HtGH9 of family 9 GH from Hungateiclostridium thermocellum was modeled by homology modeling. The catalytic module (HtGH9t) of HtGH9 modeled structure displayed the (α/α)6 barrel topology and associated family 3 carbohydrate binding module (HtCBM3c) displayed β-sandwich fold. Ramachandran plot of HtGH9 modeled structure displayed all the amino acid residues in allowed region except Asn225 and Asp317. Secondary structure analysis of modeled HtGH9 showed the presence of 41.3% α-helices and 11.0% β-strands which was validated through circular dichroism analysis that showed the presence of 42.6% α-helices and 14.5% β-strands. Molecular Dynamic (MD) simulation of HtGH9 structure for 50 ns showed Root Mean Square Deviation (RMSD), 0.84 nm and radius of gyration (Rg) 3.1 nm. The Small-angle X-ray scattering of HtGH9 confirmed the monodisperse state. The radius of gyration for globular shape (Rg) was 5.50 ± 0.15 nm and for rod shape (Rc) by Guinier plot was 2.0 nm. The loop formed by amino acid residues, 264-276 towards one end of the catalytic site of HtGH9 forms a barrier, that blocks the non-reducing end of the cellulose chain causing the processive cleavage resulting in the release of cellotetraose. The position of the corresponding loop in cellulases of family 9 GH is responsible for different types of cleavage patterns.
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Affiliation(s)
- Krishan Kumar
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shubha Singh
- Division of Biological Sciences and Engineering, Netaji Subhas University of Technology, Delhi, 110078, India
| | - Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India; Laboratory of Small Molecules & Macro Molecular Crystallography, Department of Bioengineering, Indian Institute of Technology Gandhinagar, Gandhinagar, 382355, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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13
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Baklouti Z, Delattre C, Pierre G, Gardarin C, Abdelkafi S, Michaud P, Dubessay P. Biochemical Characterization of a Bifunctional Enzyme Constructed by the Fusion of a Glucuronan Lyase and a Chitinase from Trichoderma sp. Life (Basel) 2020; 10:life10100234. [PMID: 33049934 PMCID: PMC7601620 DOI: 10.3390/life10100234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 11/16/2022] Open
Abstract
Bifunctional enzymes created by the fusion of a glucuronan lyase (TrGL) and a chitinase (ThCHIT42) from Trichoderma sp. have been constructed with the aim to validate a proof of concept regarding the potential of the chimera lyase/hydrolase by analyzing the functionality and the efficiency of the chimeric constructions compared to parental enzymes. All the chimeric enzymes, including or nor linker (GGGGS), were shown functional with activities equivalent or higher to native enzymes. The velocity of glucuronan lyase was considerably increased for chimeras, and may involved structural modifications at the active site. The fusion has induced a slightly decrease of the thermostability of glucuronan lyase, without modifying its catalytic activity regarding pH variations ranging from 5 to 8. The biochemical properties of chitinase seemed to be more disparate between the different fusion constructions suggesting an impact of the linkers or structural interactions with the linked glucuronan lyase. The chimeric enzymes displayed a decreased stability to temperature and pH variations, compared to parental one. Overall, TrGL-ThCHIT42 offered the better compromise in terms of biochemical stability and enhanced activity, and could be a promising candidate for further experiments in the field of fungi Cell Wall-Degrading Enzymes (CWDEs).
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Affiliation(s)
- Zeineb Baklouti
- CNRS, SIGMA Clermont, Institut Pascal, Université Clermont-Auvergne, FS-63000 Clermont-Ferrand, France; (Z.B.); (C.D.); (G.P.); (C.G.); (P.M.)
- Département Génie Biologique, Université de Sfax, Unité de Biotechnologie des Algues, Ecole National d’Ingénieurs de Sfax, 3018 Sfax, Tunisia;
| | - Cédric Delattre
- CNRS, SIGMA Clermont, Institut Pascal, Université Clermont-Auvergne, FS-63000 Clermont-Ferrand, France; (Z.B.); (C.D.); (G.P.); (C.G.); (P.M.)
- Institut Universitaire de France (IUF), 1 rue Descartes, 75005 Paris, France
| | - Guillaume Pierre
- CNRS, SIGMA Clermont, Institut Pascal, Université Clermont-Auvergne, FS-63000 Clermont-Ferrand, France; (Z.B.); (C.D.); (G.P.); (C.G.); (P.M.)
| | - Christine Gardarin
- CNRS, SIGMA Clermont, Institut Pascal, Université Clermont-Auvergne, FS-63000 Clermont-Ferrand, France; (Z.B.); (C.D.); (G.P.); (C.G.); (P.M.)
| | - Slim Abdelkafi
- Département Génie Biologique, Université de Sfax, Unité de Biotechnologie des Algues, Ecole National d’Ingénieurs de Sfax, 3018 Sfax, Tunisia;
| | - Philippe Michaud
- CNRS, SIGMA Clermont, Institut Pascal, Université Clermont-Auvergne, FS-63000 Clermont-Ferrand, France; (Z.B.); (C.D.); (G.P.); (C.G.); (P.M.)
| | - Pascal Dubessay
- CNRS, SIGMA Clermont, Institut Pascal, Université Clermont-Auvergne, FS-63000 Clermont-Ferrand, France; (Z.B.); (C.D.); (G.P.); (C.G.); (P.M.)
- Correspondence:
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14
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Dadwal A, Sharma S, Satyanarayana T. Progress in Ameliorating Beneficial Characteristics of Microbial Cellulases by Genetic Engineering Approaches for Cellulose Saccharification. Front Microbiol 2020; 11:1387. [PMID: 32670240 PMCID: PMC7327088 DOI: 10.3389/fmicb.2020.01387] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/29/2020] [Indexed: 12/15/2022] Open
Abstract
Lignocellulosic biomass is a renewable and sustainable energy source. Cellulases are the enzymes that cleave β-1, 4-glycosidic linkages in cellulose to liberate sugars that can be fermented to ethanol, butanol, and other products. Low enzyme activity and yield, and thermostability are, however, some of the limitations posing hurdles in saccharification of lignocellulosic residues. Recent advancements in synthetic and systems biology have generated immense interest in metabolic and genetic engineering that has led to the development of sustainable technology for saccharification of lignocellulosics in the last couple of decades. There have been several attempts in applying genetic engineering in the production of a repertoire of cellulases at a low cost with a high biomass saccharification. A diverse range of cellulases are produced by different microbes, some of which are being engineered to evolve robust cellulases. This review summarizes various successful genetic engineering strategies employed for improving cellulase kinetics and cellulolytic efficiency.
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Affiliation(s)
- Anica Dadwal
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, New Delhi, India
| | - Shilpa Sharma
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, New Delhi, India
| | - Tulasi Satyanarayana
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, New Delhi, India
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15
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Nedumaran M, Singh S, Jamaldheen SB, Nath P, Moholkar VS, Goyal A. Assessment of combination of pretreatment of Sorghum durra stalk and production of chimeric enzyme (β-glucosidase and endo β-1,4 glucanase, CtGH1-L1- CtGH5-F194A) and cellobiohydrolase ( CtCBH5A) for saccharification to produce bioethanol. Prep Biochem Biotechnol 2020; 50:883-896. [PMID: 32425106 DOI: 10.1080/10826068.2020.1762214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Optimization of pretreatment and saccharification of Sorghum durra stalk (Sds) was carried out. The chimeric enzyme (CtGH1-L1-CtGH5-F194A) having β-glucosidase (CtGH1) and endo β-1,4 glucanase activity (CtGH5-F194A) and cellobiohydrolase (CtCBH5A) from Clostridium thermocellum were used for saccharification. Chimeric enzyme will save production cost of two enzymes, individually. Stage 2 pretreatment by 1% (w/v) NaOH assisted autoclaving + 1.5% (v/v) dilute H2SO4 assisted oven heating gave lower total sugar yield (366.6 mg/g of pretreated Sds) and total glucose yield (195 mg/g of pretreated Sds) in pretreated hydrolysate with highest crystallinity index 55.6% than the other stage 2 pretreatments. Optimized parameters for saccharification of above stage 2 pretreated biomass were 3% (w/v) biomass concentration, enzyme (chimera: cellobiohydrolase) ratio, 2:3 (U/g) of biomass, total enzyme loading (350 U/g of pretreated biomass), 24 h and 30 °C. Best stage 2 pretreated Sds under optimized enzyme saccharification conditions gave maximum total reducing sugar yield 417 mg/g and glucose yield 285 mg/g pretreated biomass in hydrolysate. Best stage 2 pretreated Sds showed significantly higher cellulose, 71.3% and lower lignin, 2.0% and hemicellulose, 12.2% (w/w) content suggesting the effectiveness of method. This hydrolysate upon SHF using Saccharomyces cerevisiae under unoptimized conditions produced ethanol yield, 0.12 g/g of glucose. Abbreviation: Ct-Clostridium thermocellum, Sds-Sorghum durra stalk, TRS-Total reducing sugar, HPLC-High performance liquid chromatography, RI-Refractive index, ADL-acid insoluble lignin, GYE-Glucose yeast extract, MGYP-Malt glucose yeast extract peptone, SHF-separate hydrolysis and fermentation, OD-Optical density, PVDF-Poly vinylidene fluoride, TS-total sugar, FESEM-Field emission scanning electron microscopy, XRD-X-ray diffraction, FTIR-Fourier transform infra-red spectroscopy and CrI-Crystallinity index.
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Affiliation(s)
- Mohanapriya Nedumaran
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Shweta Singh
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India.,DBT PAN-IIT Centre for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, India
| | - Sumitha Banu Jamaldheen
- DBT PAN-IIT Centre for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, India.,Centre for Energy, Indian Institute of Technology Guwahati, Guwahati, India
| | - Priyanka Nath
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India.,DBT PAN-IIT Centre for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, India
| | - Vijayanand Suryakant Moholkar
- Centre for Energy, Indian Institute of Technology Guwahati, Guwahati, India.,Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India.,DBT PAN-IIT Centre for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, India.,Centre for Energy, Indian Institute of Technology Guwahati, Guwahati, India
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16
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Nath P, Sharma K, Kumar K, Goyal A. Combined SAXS and computational approaches for structure determination and binding characteristics of Chimera (CtGH1-L1-CtGH5-F194A) generated by assembling β-glucosidase (CtGH1) and a mutant endoglucanase (CtGH5-F194A) from Clostridium thermocellum. Int J Biol Macromol 2020; 148:364-377. [PMID: 31945441 DOI: 10.1016/j.ijbiomac.2020.01.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 11/25/2022]
Abstract
Chimera (CtGH1-L1-CtGH5-F194A) developed by fusing β-glucosidase (CtGH1) at N-terminal and endoglucanase (CtGH5-F194A) at C-terminal was structurally characterized. Its secondary structure analysis by CD showed 38% α-helix, 9.3% β-sheets and 52.7% random coils corroborating with prediction. In-silico modeled structure of Chimera comprised two modules, CtGH1 and CtGH5-F194A displaying (α/β)8 fold. Ramachandran plot of Chimera showed 99.9% residues in allowed region. Binding interaction of Chimera with cello-oligosaccharides suggested active forms of CtGH1 and CtGH5-F194A and their involvement in catalysis. MD simulation of cellohexaose bound endoglucanase module of Chimera showed favourable flexibility in loops, LA with H-bond formation with Asn510 and in loop LC relocation of Tyr687 away from active site efficiently releasing the product after catalysis. Higher short range interaction energy of Chimera, -383 kJ/mol than the individual endoglucanase, 254 kJ/mol against cellohexaose suggested higher efficient catalysis by Chimera. β-Glucosidase module of Chimera showed fluctuations in outer loops suggesting conformational changes that might be contributing to improved hydrolysis. SAXS analysis of Chimera displayed monodispersed state. Guinier analysis of Chimera showed globular shape (Rg= 3.15 ± 0.10 nm). Kratky plot confirmed fully folded and flexible behaviour in solution. Gasbor modeled structure of Chimera displayed an elongated structure with two modules having shape similar to bean-bag contour.
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Affiliation(s)
- Priyanka Nath
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, India; DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, India
| | - Krishan Kumar
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, India; DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
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