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Paul M, Mohapatra S, Kumar Das Mohapatra P, Thatoi H. Microbial cellulases - An update towards its surface chemistry, genetic engineering and recovery for its biotechnological potential. BIORESOURCE TECHNOLOGY 2021; 340:125710. [PMID: 34365301 DOI: 10.1016/j.biortech.2021.125710] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The inherent resistance of lignocellulosic biomass makes it impervious for industrially important enzymes such as cellulases to hydrolyze cellulose. Further, the competitive absorption behavior of lignin and hemicellulose for cellulases, due to their electron-rich surfaces augments the inappropriate utilization of these enzymes. Hence, modification of the surface charge of the cellulases to reduce its non-specific binding to lignin and enhance its affinity for cellulose is an urgent necessity. Further, maintaining the stability of cellulases by the preservation of their secondary structures using immobilization techniques will also play an integral role in its industrial production. In silico approaches for increasing the catalytic activity of cellulase enzymes is also significant along with a range of substrate specificity. In addition, enhanced productivity of cellulases by tailoring the related genes through the process of genetic engineering and higher cellulase recovery after saccharification seems to be promising areas for efficient and large-scale enzyme production concepts.
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Affiliation(s)
- Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada 757003, Odisha, India
| | - Sonali Mohapatra
- Department of Biotechnology, College of Engineering & Technology, Bhubaneswar 751003, Odisha, India
| | - Pradeep Kumar Das Mohapatra
- Department of Microbiology, Raiganj University, Raiganj - 733134, Uttar Dinajpur, West Bengal, India; PAKB Environment Conservation Centre, Raiganj University, Raiganj - 733134, Uttar Dinajpur, West Bengal, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada 757003, Odisha, India.
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2
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Understanding the conformational change and inhibition of hyperthermophilic GH10 xylanase in ionic liquid. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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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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Manna B, Ghosh A. Structure and dynamics of ionic liquid tolerant hyperthermophilic endoglucanase Cel12A from Rhodothermus marinus. RSC Adv 2020; 10:7933-7947. [PMID: 35492170 PMCID: PMC9049953 DOI: 10.1039/c9ra09612d] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/04/2020] [Indexed: 12/25/2022] Open
Abstract
Economic deconstruction of lignocellulose remains a challenge due to the complex architecture of cellulose, hemicellulose, and lignin. Advancements in pretreatment processes have introduced ionic liquids (ILs) as promising non-derivatizing solvents for reducing biomass recalcitrance and for promoting enzymatic hydrolysis. However, available commercial cellulases are destabilized or inactivated even in low concentration of residual ILs. Thus, a molecular understanding of IL-enzyme interactions is crucial for developing IL-tolerant enzymes with high catalytic activity. In this study, molecular insight behind the IL tolerance of hyperthermophilic endoglucanase Cel12A from Rhodothermus marinus (RmCel12A) has been investigated in 20%, 40%, and 60% 1-ethyl-3-methylimidazolium acetate (EmimAc) through molecular dynamic simulations at 368 K. Though the enzyme retained its stability in all EmimAc concentrations, the activity was affected due to the loss of essential dynamic motions. A protein structure network was constructed using the snapshots of protein structures from the simulation trajectories and the hub properties of residues R20, Y59, W68, W197, E203, and F220 were found to be lost in 60% EmimAc. Emim cations were observed to intrude the active site tunnel and interact with more number of catalytic residues with higher cumulative fractional occupancy in 60% EmimAc than in 20% or 40% EmimAc. Some non-catalytic residues have also been identified at the active site, which can be probable mutation targets for improving the IL tolerance. Our findings reveal the molecular understanding behind the origin of activity loss of RmCel12A and proposed insights for the further improvement of IL sensitivity. Understanding the behavior of ionic liquid tolerant hyperthermophilic endoglucanase Cel12A from Rhodothermus marinus in different concentrations of EmimAc.![]()
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Affiliation(s)
- Bharat Manna
- School of Energy Science and Engineering
- Indian Institute of Technology Kharagpur
- Kharagpur 721302
- India
| | - Amit Ghosh
- School of Energy Science and Engineering
- Indian Institute of Technology Kharagpur
- Kharagpur 721302
- India
- P.K. Sinha Centre for Bioenergy and Renewables
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Ghanbari-Ardestani S, Khojasteh-Band S, Zaboli M, Hassani Z, Mortezavi M, Mahani M, Torkzadeh-Mahani M. The effect of different percentages of triethanolammonium butyrate ionic liquid on the structure and activity of urate oxidase: Molecular docking, molecular dynamics simulation, and experimental study. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111318] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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6
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Oleson KR, Sprenger KG, Pfaendtner J, Schwartz DT. Inhibition of the Exoglucanase Cel7A by a Douglas-Fir-Condensed Tannin. J Phys Chem B 2018; 122:8665-8674. [PMID: 30111095 DOI: 10.1021/acs.jpcb.8b05850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Douglas-fir forestry residues are a potential feedstock for saccharification-based biofuels, and condensed tannins are expected to make up ∼3% of the dry mass of this feedstock. Condensed tannins are well-known for their ability to interact with proteins and can bind and inhibit cellulase enzymes used in saccharification. In this study, we use molecular docking and classical molecular dynamics simulations to investigate how a characterized condensed tannin from Douglas-fir bark binds to the exoglucanase Cel7A from Trichoderma reesei. Through looking at the "occupancy" and "residency" of specific amino acid residue-tannin interactions, we find that the binding sites are characterized by many simultaneous tannin-enzyme interactions with the strongest occurring on the catalytic module as opposed to the carbohydrate-binding module. The simulations indicate that tannin inhibition can result from binding at or near the catalytic tunnel's entrance and exit. The analyzed tannin further prefers to bind to loops around the catalytic region and has affinity for aromatic and charged amino acid residues. These insights provide direction for the rational design of tannin-resistant cellulases.
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Affiliation(s)
- Karl R Oleson
- Dept. of Chemical Engineering , University of Washington , Box 351750, Seattle , Washington 98198-1750 , United States
| | - Kayla G Sprenger
- Dept. of Chemical Engineering , University of Washington , Box 351750, Seattle , Washington 98198-1750 , United States.,Institute for Medical Engineering and Science , Massachusetts Institute of Technology , E25-352, Cambridge , Massachusetts 02139 , United States
| | - Jim Pfaendtner
- Dept. of Chemical Engineering , University of Washington , Box 351750, Seattle , Washington 98198-1750 , United States
| | - Daniel T Schwartz
- Dept. of Chemical Engineering , University of Washington , Box 351750, Seattle , Washington 98198-1750 , United States
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Lim GS, Klähn M. On the Stability of Proteins Solvated in Imidazolium-Based Ionic Liquids Studied with Replica Exchange Molecular Dynamics. J Phys Chem B 2018; 122:9274-9288. [DOI: 10.1021/acs.jpcb.8b06452] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Geraldine S. Lim
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16, Connexis, Singapore 138632, Republic of Singapore
| | - Marco Klähn
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, 1 Pesek Road, Jurong Island, Singapore 627833, Republic of Singapore
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Janati-Fard F, Housaindokht MR, Monhemi H, Esmaeili AA, Nakhaei Pour A. The influence of two imidazolium-based ionic liquids on the structure and activity of glucose oxidase: Experimental and theoretical studies. Int J Biol Macromol 2018; 114:656-665. [DOI: 10.1016/j.ijbiomac.2018.03.083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/27/2018] [Accepted: 03/17/2018] [Indexed: 01/27/2023]
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Sprenger KG, Plaks JG, Kaar JL, Pfaendtner J. Elucidating sequence and solvent specific design targets to protect and stabilize enzymes for biocatalysis in ionic liquids. Phys Chem Chem Phys 2018. [PMID: 28650512 DOI: 10.1039/c7cp03013d] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
For many different frameworks, the structure, function, and dynamics of an enzyme is largely determined by the nature of its interactions with the surrounding host environment, thus a molecular level understanding of enzyme/host interactions is essential to the design of new processes and applications. Ionic liquid (IL) solvents are a popular class of solvents in which to study enzyme behavior, yet it is still not possible to predict how a given enzyme will behave in a given IL solvent. Furthermore, a dearth of experimental data with which to evaluate simulation force fields has prevented the full integration of experimental and computational techniques to gain a complete picture of enzyme/IL interactions. Utilizing recently published crystallographic data of an enzyme in complex with an IL, this study aims to validate the use of current molecular force fields for studying enzyme/IL interactions, and to provide new mechanistic insight into enzyme stabilization in IL solvents. Classical molecular dynamics (MD) simulations have been performed on both the folded and unfolded state of Bacillus subtilis lipase A and a quadruple-mutant version of lipase A, in solutions of aqueous 1-butyl-3-methylimidazolium chloride. Results show classical MD simulations can predict the preferred surface binding locations of IL cations as well as reductions in IL anion binding to mutated surface residues with high accuracy. The results also point to a mechanistic difference between IL binding to the folded and unfolded state of an enzyme, which we call the "counter-ion effect". These findings could have important implications for future rational design efforts to stabilize enzymes in non-conventional media.
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Affiliation(s)
- K G Sprenger
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98105, USA.
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Tanghe M, Danneels B, Last M, Beerens K, Stals I, Desmet T. Disulfide bridges as essential elements for the thermostability of lytic polysaccharide monooxygenase LPMO10C from Streptomyces coelicolor. Protein Eng Des Sel 2017; 30:401-408. [PMID: 28338903 DOI: 10.1093/protein/gzx014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/20/2017] [Indexed: 12/17/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are crucial components of cellulase mixtures but their stability has not yet been studied in detail, let alone been engineered for industrial applications. In this work, we have evaluated the importance of disulfide bridges for the thermodynamic stability of Streptomyces coelicolor LPMO10C. Interestingly, this enzyme was found to retain 34% of its activity after 2-h incubation at 80°C while its apparent melting temperature (Tm) is only 51°C. When its three disulfide bridges were broken, however, irreversible unfolding occurred and no residual activity could be detected after a similar heat treatment. Based on these findings, additional disulfide bridges were introduced, as predicted by computational tools (MOdelling of DIsulfide bridges in Proteins (MODiP) and Disulfide by Design (DbD)) and using the most flexible positions in the structure as target sites. Four out of 16 variants displayed an improvement in Tm, ranging from 2 to 9°C. Combining the positive mutations yielded additional improvements (up to 19°C) but aberrant unfolding patterns became apparent in some cases, resulting in a diminished capacity for heat resistance. Nonetheless, the best variant, a combination of A143C-P183C and S73C-A115C, displayed a 12°C increase in Tm and was able to retain and was able to retain no less than 60% of its activity after heat treatment.
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Affiliation(s)
- Magali Tanghe
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Barbara Danneels
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Matthias Last
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Koen Beerens
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Ingeborg Stals
- Industrial Catalysis and Adsorption Technology (INCAT), Faculty of Engineering and Architecture, Ghent University, Valentin Vaerwyckweg 1, B-9000 Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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Borrell KL, Cancglin C, Stinger BL, DeFrates KG, Caputo GA, Wu C, Vaden TD. An Experimental and Molecular Dynamics Study of Red Fluorescent Protein mCherry in Novel Aqueous Amino Acid Ionic Liquids. J Phys Chem B 2017; 121:4823-4832. [PMID: 28425717 DOI: 10.1021/acs.jpcb.7b03582] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The search for biocompatible ionic liquids (ILs) with novel biochemical and biomedical applications has recently gained greater attention. In this report, we characterize the effects of two novel amino acid-based aqueous ILs composed of tetramethylguanidinium (TMG) and amino acids on the structure and stability of a widely used red fluorescent protein (mCherry). Our experimental data shows that while the aspartic acid-based IL (TMGAsp) has effects similar to previously studied conventional ILs (BMIBF4, EMIAc, and TMGAc), the alanine-based IL (TMGAla) has a much stronger destabilization effect on the protein structure. Addition of 0.30 M TMGAla to mCherry decreases the unfolding temperature from 83 to 60 °C. Even at 25 °C, TMGAla results in a blue shift of the mCherry absorbance and fluorescence peaks and an increased Stokes shift. Molecular dynamics simulations show that the chromophore conformation and its interaction with mCherry with TMGAla are changed relative to those with TMGAsp or in the absence of ILs. Protein-ILs contact analysis indicates that the mCherry-Asp interactions are hydrophilic but the (fewer) mCherry-Ala interactions are more hydrophobic and may modulate the TMG interaction with the protein. Hence, the anion hydrophobicity may explain the special TMGAla destabilization of mCherry.
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Affiliation(s)
- Kelsey L Borrell
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Christine Cancglin
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Brittany L Stinger
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Kelsey G DeFrates
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Gregory A Caputo
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Chun Wu
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Timothy D Vaden
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
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13
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Jaeger VW, Pfaendtner J. Destabilization of Human Serum Albumin by Ionic Liquids Studied Using Enhanced Molecular Dynamics Simulations. J Phys Chem B 2016; 120:12079-12087. [DOI: 10.1021/acs.jpcb.6b09410] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Vance W. Jaeger
- Department of Chemical Engineering, University of Washington, 105 Benson Hall, Box 351750, Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, 105 Benson Hall, Box 351750, Seattle, Washington 98195, United States
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Johnson LB, Snow CD. Molecular dynamics simulations of cellulase homologs in aqueous 1-ethyl-3-methylimidazolium chloride. J Biomol Struct Dyn 2016; 35:1990-2002. [DOI: 10.1080/07391102.2016.1204364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Lucas B. Johnson
- Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO 80523-1370, USA
| | - Christopher D. Snow
- Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO 80523-1370, USA
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