1
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DeChellis A, Nemmaru B, Sammond D, Douglass J, Patil N, Reste O, Chundawat SPS. Supercharging carbohydrate-binding module alone enhances endocellulase thermostability, binding, and activity on cellulosic biomass. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.09.557007. [PMID: 37745483 PMCID: PMC10515785 DOI: 10.1101/2023.09.09.557007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Lignocellulosic biomass recalcitrance to enzymatic degradation necessitates high enzyme loadings incurring large processing costs for industrial-scale biofuels or biochemicals production. Manipulating surface charge interactions to minimize non-productive interactions between cellulolytic enzymes and plant cell wall components (e.g., lignin or cellulose) via protein supercharging has been hypothesized to improve biomass biodegradability, but with limited demonstrated success to date. Here we characterize the effect of introducing non-natural enzyme surface mutations and net charge on cellulosic biomass hydrolysis activity by designing a library of supercharged family-5 endoglucanase Cel5A and its native family-2a carbohydrate binding module (CBM) originally belonging to an industrially relevant thermophilic microbe Thermobifida fusca . A combinatorial library of 33 mutant constructs containing different CBM and Cel5A designs spanning a net charge range of -52 to 37 was computationally designed using Rosetta macromolecular modelling software. Activity for all mutants was rapidly characterized as soluble cell lysates and promising mutants (containing mutations either on the CBM, Cel5A catalytic domain, or both CBM and Cel5A domains) were then purified and systematically characterized. Surprisingly, often endocellulases with mutations on the CBM domain alone resulted in improved activity on cellulosic biomass, with three top-performing supercharged CBM mutants exhibiting between 2-5-fold increase in activity, compared to native enzyme, on both pretreated biomass enriched in lignin (i.e., corn stover) and isolated crystalline/amorphous cellulose. Furthermore, we were able to clearly demonstrate that endocellulase net charge can be selectively fine-tuned using protein supercharging protocol for targeting distinct substrates and maximizing biocatalytic activity. Additionally, several supercharged CBM containing endocellulases exhibited a 5-10 °C increase in optimal hydrolysis temperature, compared to native enzyme, which enabled further increase in hydrolytic yield at higher operational reaction temperatures. This study demonstrates the first successful implementation of enzyme supercharging of cellulolytic enzymes to increase hydrolytic activity towards complex lignocellulosic biomass derived substrates.
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2
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Mu Y, Meng F, Ju X, Li L. Inactivation and process intensification of β-glucosidase in biomass utilization. Appl Microbiol Biotechnol 2023; 107:3191-3204. [PMID: 37058231 DOI: 10.1007/s00253-023-12483-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/07/2023] [Accepted: 03/12/2023] [Indexed: 04/15/2023]
Abstract
Lignocellulosic biomass has emerged as a promising environmental resource. Enzyme catalysis, as one of the most environmentally friendly and efficient tools among various treatments, is used for the conversion of biomass into chemicals and fuels. Cellulase is a complex enzyme composed of β-glucosidase (BGL), endo-β-1,4-glucanase (EG), and exo-β-1,4-glucanase (CBH), which synergistically hydrolyzes cellulose into monosaccharides. BGL, which further deconstructs cellobiose and short-chain cellooligosaccharides obtained by EG and CBH catalysis into glucose, is the most sensitive component of the synergistic enzyme system constituted by the three enzymes and is highly susceptible to inactivation by external conditions, becoming the rate-limiting component in biomass conversion. This paper firstly introduces the source and catalytic mechanism of BGL used in the process of biomass resource utilization. The focus is on the review of various factors affecting BGL activity during hydrolysis, including competitive adsorption of lignin, gas-liquid interface inactivation, thermal inactivation, and solvent effect. And the methods to improve BGL inactivation are proposed from two aspects-substrate initiation and enzyme initiation. In particular, the screening, modification, and alteration of the enzyme molecules themselves are discussed with emphasis. This review can provide novel ideas for studies of BGL inactivation mechanism, containment of inactivation, and activity enhancement. KEY POINTS: • Factors affecting β-glucosidase inactivation are described. • Process intensification is presented in terms of substrate and enzyme. • Solvent selection, protein engineering, and immobilization remain topics of interest.
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Affiliation(s)
- Yinghui Mu
- School of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China
| | - Fanjin Meng
- School of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China
| | - Xin Ju
- School of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China
| | - Liangzhi Li
- School of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China.
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3
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Hazeena SH, Shurpali NJ, Siljanen H, Lappalainen R, Anoop P, Adarsh VP, Sindhu R, Pandey A, Binod P. Bioprocess development of 2, 3-butanediol production using agro-industrial residues. Bioprocess Biosyst Eng 2022; 45:1527-1537. [PMID: 35960335 PMCID: PMC9399043 DOI: 10.1007/s00449-022-02761-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/18/2022] [Indexed: 11/26/2022]
Abstract
The valorization of agricultural and industrial wastes for fuel and chemical production benefits environmental sustainability. 2, 3-Butanediol (2,3-BDO) is a value-added platform chemical covering many industrial applications. Since the global market is increasing drastically, production rates have to increase. In order to replace the current petroleum-based 2,3-BDO production, renewable feedstock's ability has been studied for the past few decades. This study aims to find an improved bioprocess for producing 2,3-BDO from agricultural and industrial residues, consequently resulting in a low CO2 emission bioprocess. For this, screening of 13 different biomass samples for hydrolyzable sugars has been done. Alkali pretreatment has been performed with the processed biomass and enzyme hydrolysis performed using commercial cellulase. Among all biomass hydrolysate oat hull and spruce bark biomass could produce the maximum amount of total reducing sugars. Later oat hull and spruce bark biomass with maximum hydrolyzable sugars have been selected for submerged fermentation studies using Enterobacter cloacae SG1. After fermentation, 37.59 and 26.74 g/L of 2,3-BDO was obtained with oat hull and spruce bark biomass, respectively. The compositional analysis of each step of biomass processing has been performed and changes in each component have been evaluated. The compositional analysis has revealed that biomass composition has changed significantly after pretreatment and hydrolysis leading to a remarkable release of sugars which can be utilized by bacteria for 2,3-BDO production. The results have been found to be promising, showing the potential of waste biomass residues as a low-cost raw material for 2,3-BDO production and thus a new lead in an efficient waste management approach for less CO2 emission.
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Affiliation(s)
- Sulfath Hakkim Hazeena
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Narasinha J Shurpali
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio campus, Kuopio, Finland.
- Natural Resources Institute Finland (Luke), Halolantie 31 A, 71750, Maaninka, FI, Finland.
| | - Henri Siljanen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio campus, Kuopio, Finland
| | - Reijo Lappalainen
- Biomaterials Technology, Dept. of Applied Physics & SIB-Labs, University of Eastern Finland (Kuopio Campus), Yliopistonranta 1 F, 70211, Kuopio, FI, Finland
| | - Puthiyamdam Anoop
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695019, Kerala, India
| | - Velayudhanpillai Prasannakumari Adarsh
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695019, Kerala, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695019, Kerala, India
| | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, 226 001, India
- Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, 248 007, Dehradun, India
- Centre for Energy and Environmental Sustainability, Lucknow, 226 029, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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4
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Guo R, Sinha NJ, Misra R, Tang Y, Langenstein M, Kim K, Fagan JA, Kloxin CJ, Jensen G, Pochan DJ, Saven JG. Computational Design of Homotetrameric Peptide Bundle Variants Spanning a Wide Range of Charge States. Biomacromolecules 2022; 23:1652-1661. [PMID: 35312288 DOI: 10.1021/acs.biomac.1c01539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the ability to design their sequences and structures, peptides can be engineered to realize a wide variety of functionalities and structures. Herein, computational design was used to identify a set of 17 peptides having a wide range of putative charge states but the same tetrameric coiled-coil bundle structure. Calculations were performed to identify suitable locations for ionizable residues (D, E, K, and R) at the bundle's exterior sites, while interior hydrophobic interactions were retained. The designed bundle structures spanned putative charge states of -32 to +32 in units of electron charge. The peptides were experimentally investigated using spectroscopic and scattering techniques. Thermal stabilities of the bundles were investigated using circular dichroism. Molecular dynamics simulations assessed structural fluctuations within the bundles. The cylindrical peptide bundles, 4 nm long by 2 nm in diameter, were covalently linked to form rigid, micron-scale polymers and characterized using transmission electron microscopy. The designed suite of sequences provides a set of readily realized nanometer-scale structures of tunable charge that can also be polymerized to yield rigid-rod polyelectrolytes.
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Affiliation(s)
- Rui Guo
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Nairiti J Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,NIST Center for Neutron Research (NCNR), National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Rajkumar Misra
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Yao Tang
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Matthew Langenstein
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Kyunghee Kim
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffrey A Fagan
- Materials Science and Engineering Division, National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Grethe Jensen
- NIST Center for Neutron Research (NCNR), National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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5
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Bulos JA, Guo R, Wang Z, DeLessio MA, Saven JG, Dmochowski IJ. Design of a Superpositively Charged Enzyme: Human Carbonic Anhydrase II Variant with Ferritin Encapsulation and Immobilization. Biochemistry 2021; 60:3596-3609. [PMID: 34757723 DOI: 10.1021/acs.biochem.1c00515] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Supercharged proteins exhibit high solubility and other desirable properties, but no engineered superpositively charged enzymes have previously been made. Superpositively charged variants of proteins such as green fluorescent protein have been efficiently encapsulated within Archaeoglobus fulgidus thermophilic ferritin (AfFtn). Encapsulation by supramolecular ferritin can yield systems with a variety of sequestered cargo. To advance applications in enzymology and green chemistry, we sought a general method for supercharging an enzyme that retains activity and is compatible with AfFtn encapsulation. The zinc metalloenzyme human carbonic anhydrase II (hCAII) is an attractive encapsulation target based on its hydrolytic activity and physiologic conversion of carbon dioxide to bicarbonate. A computationally designed variant of hCAII contains positively charged residues substituted at 19 sites on the protein's surface, resulting in a shift of the putative net charge from -1 to +21. This designed hCAII(+21) exhibits encapsulation within AfFtn without the need for fusion partners or additional reagents. The hCAII(+21) variant retains esterase activity comparable to the wild type and spontaneously templates the assembly of AfFtn 24mers around itself. The AfFtn-hCAII(+21) host-guest complex exhibits both greater activity and thermal stability when compared to hCAII(+21). Upon immobilization on a solid support, AfFtn-hCAII(+21) retains enzymatic activity and exhibits an enhancement of activity at elevated temperatures.
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Affiliation(s)
- Joshua A Bulos
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rui Guo
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zhiheng Wang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Maegan A DeLessio
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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6
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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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7
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Zhou Z, Ju X, Chen J, Wang R, Zhong Y, Li L. Charge-oriented strategies of tunable substrate affinity based on cellulase and biomass for improving in situ saccharification: A review. BIORESOURCE TECHNOLOGY 2021; 319:124159. [PMID: 33010717 DOI: 10.1016/j.biortech.2020.124159] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
The intrinsic recalcitrance of lignocellulosic biomass makes it resistant to enzymatic hydrolysis. The electron-rich surface of the lignin and cellulose-alike structure of hemicellulose competitively absorb the cellulase. Thus, modifying the surface charge on biomass components to alter cellulase affinity is an urgent requisite. Developing charge tunable cellulase will alter substrate affinity. Also, charge-based immobilization generates controllable substrate affinity. Within immobilized cellulase involved in situ biomass saccharification, charge effects made a crucial contribution. In addition to affecting the interaction between immobilized cellulase and biomass, charge exerts an impact on cellulase to immobilize the materials, further investigation is essential. This study aims to review the charge effects on the cellulase affinity in biomass saccharification, strategies of charge tunable cellulase, and immobilized cellulase, thereby explaining the role of electrostatic interaction. In terms of electrostatic behavior, the pathways and plans to improve in situ biomass saccharification seem to be promising.
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Affiliation(s)
- Zheng Zhou
- College of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Xin Ju
- College of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Jiajia Chen
- College of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Rong Wang
- College of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Yuqing Zhong
- College of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Liangzhi Li
- College of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou 215009, PR China.
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8
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Nemmaru B, Ramirez N, Farino CJ, Yarbrough JM, Kravchenko N, Chundawat SPS. Reduced type-A carbohydrate-binding module interactions to cellulose I leads to improved endocellulase activity. Biotechnol Bioeng 2020; 118:1141-1151. [PMID: 33245142 DOI: 10.1002/bit.27637] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/12/2020] [Accepted: 11/15/2020] [Indexed: 12/24/2022]
Abstract
Dissociation of nonproductively bound cellulolytic enzymes from cellulose is hypothesized to be a key rate-limiting factor impeding cost-effective biomass conversion to fermentable sugars. However, the role of carbohydrate-binding modules (CBMs) in enabling nonproductive enzyme binding is not well understood. Here, we examine the subtle interplay of CBM binding and cellulose hydrolysis activity for three models type-A CBMs (Families 1, 3a, and 64) tethered to multifunctional endoglucanase (CelE) on two distinct cellulose allomorphs (i.e., cellulose I and III). We generated a small library of mutant CBMs with varying cellulose affinity, as determined by equilibrium binding assays, followed by monitoring cellulose hydrolysis activity of CelE-CBM fusion constructs. Finally, kinetic binding assays using quartz crystal microbalance with dissipation were employed to measure CBM adsorption and desorption rate constants k on and k off , respectively, towards nanocrystalline cellulose derived from both allomorphs. Overall, our results indicate that reduced CBM equilibrium binding affinity towards cellulose I alone, resulting from increased desorption rates ( k off ) and reduced effective adsorption rates ( nk on ), is correlated to overall improved endocellulase activity. Future studies could employ similar approaches to unravel the role of CBMs in nonproductive enzyme binding and develop improved cellulolytic enzymes for industrial applications.
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Affiliation(s)
| | - Nicholas Ramirez
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Cindy J Farino
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - John M Yarbrough
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Nicholas Kravchenko
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Shishir P S Chundawat
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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9
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Li Y, Guan X, Chaffey PK, Ruan Y, Ma B, Shang S, Himmel ME, Beckham GT, Long H, Tan Z. Carbohydrate-binding module O-mannosylation alters binding selectivity to cellulose and lignin. Chem Sci 2020; 11:9262-9271. [PMID: 34123172 PMCID: PMC8163390 DOI: 10.1039/d0sc01812k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Improved understanding of the effect of protein glycosylation is expected to provide the foundation for the design of protein glycoengineering strategies. In this study, we examine the impact of O-glycosylation on the binding selectivity of a model Family 1 carbohydrate-binding module (CBM), which has been shown to be one of the primary sub-domains responsible for non-productive lignin binding in multi-modular cellulases. Specifically, we examine the relationship between glycan structure and the binding specificity of the CBM to cellulose and lignin substrates. We find that the glycosylation pattern of the CBM exhibits a strong influence on the binding affinity and the selectivity between both cellulose and lignin. In addition, the large set of binding data collected allows us to examine the relationship between binding affinity and the correlation in motion between pairs of glycosylation sites. Our results suggest that glycoforms displaying highly correlated motion in their glycosylation sites tend to bind cellulose with high affinity and lignin with low affinity. Taken together, this work helps lay the groundwork for future exploitation of glycoengineering as a tool to improve the performance of industrial enzymes. Improved understanding of the effect of protein glycosylation is expected to provide the foundation for the design of protein glycoengineering strategies.![]()
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Affiliation(s)
- Yaohao Li
- Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College Beijing 100050 China .,Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder CO 80303 USA
| | - Xiaoyang Guan
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder CO 80303 USA
| | - Patrick K Chaffey
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder CO 80303 USA
| | - Yuan Ruan
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder CO 80303 USA
| | - Bo Ma
- Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College Beijing 100050 China
| | - Shiying Shang
- School of Pharmaceutical Sciences, Tsinghua University Beijing 100084 China
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory Golden CO 80401 USA
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory Golden CO 80401 USA
| | - Hai Long
- Computational Science Center, National Renewable Energy Laboratory Golden CO 80401 USA
| | - Zhongping Tan
- Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College Beijing 100050 China
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10
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Fülöp L, Ecker J. An overview of biomass conversion: exploring new opportunities. PeerJ 2020; 8:e9586. [PMID: 32765969 PMCID: PMC7382363 DOI: 10.7717/peerj.9586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/30/2020] [Indexed: 12/28/2022] Open
Abstract
Recycling biomass is indispensable these days not only because fossil energy sources are gradually depleted, but also because pollution of the environment, caused by the increasing use of energy, must be reduced. This article intends to overview the results of plant biomass processing methods that are currently in use. Our aim was also to review published methods that are not currently in use. It is intended to explore the possibilities of new methods and enzymes to be used in biomass recycling. The results of this overview are perplexing in almost every area. Advances have been made in the pre-treatment of biomass and in the diversity and applications of the enzymes utilized. Based on molecular modeling, very little progress has been made in the modification of existing enzymes for altered function and adaptation for the environmental conditions during the processing of biomass. There are hardly any publications in which molecular modeling techniques are used to improve enzyme function and to adapt enzymes to various environmental conditions. Our view is that using modern computational, biochemical, and biotechnological methods would enable the purposeful design of enzymes that are more efficient and suitable for biomass processing.
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Affiliation(s)
- László Fülöp
- Department of Chemistry, Szent István University, Gödöllő, Hungary
| | - János Ecker
- Department of Chemistry, Szent István University, Gödöllő, Hungary
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11
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Suzuki Y, Okamura-Abe Y, Nakamura M, Otsuka Y, Araki T, Otsuka H, Navarro RR, Kamimura N, Masai E, Katayama Y. Development of the production of 2-pyrone-4,6-dicarboxylic acid from lignin extracts, which are industrially formed as by-products, as raw materials. J Biosci Bioeng 2020; 130:71-75. [DOI: 10.1016/j.jbiosc.2020.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/07/2020] [Accepted: 02/01/2020] [Indexed: 10/24/2022]
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12
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Torres AF, Xu X, Nikiforidis CV, Bitter JH, Trindade LM. Exploring the Treasure of Plant Molecules With Integrated Biorefineries. FRONTIERS IN PLANT SCIENCE 2019; 10:478. [PMID: 31040858 PMCID: PMC6476976 DOI: 10.3389/fpls.2019.00478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Despite significant progress toward the commercialization of biobased products, today's biorefineries are far from achieving their intended goal of total biomass valorization and effective product diversification. The problem is conceptual. Modern biorefineries were built around well-optimized, cost-effective chemical synthesis routes, like those used in petroleum refineries for the synthesis of fuels, plastics, and solvents. However, these were designed for the conversion of fossil resources and are far from optimal for the processing of biomass, which has unique chemical characteristics. Accordingly, existing biomass commodities were never intended for modern biorefineries as they were bred to meet the needs of conventional agriculture. In this perspective paper, we propose a new path toward the design of efficient biorefineries, which capitalizes on a cross-disciplinary synergy between plant, physical, and catalysis science. In our view, the best opportunity to advance profitable and sustainable biorefineries requires the parallel development of novel feedstocks, conversion protocols and synthesis routes specifically tailored for total biomass valorization. Above all, we believe that plant biologists and process technologists can jointly explore the natural diversity of plants to synchronously develop both, biobased crops with designer chemistries and compatible conversion protocols that enable maximal biomass valorization with minimum input utilization. By building biorefineries from the bottom-up (i.e., starting with the crop), the envisioned partnership promises to develop cost-effective, biomass-dedicated routes which can be effectively scaled-up to deliver profitable and resource-use efficient biorefineries.
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Affiliation(s)
- Andres F. Torres
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
- Biobased Chemistry and Technology, Wageningen University, Wageningen, Netherlands
- Graduate School Experimental Plant Sciences, Wageningen University, Wageningen, Netherlands
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Xuan Xu
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | | | - Johannes H. Bitter
- Biobased Chemistry and Technology, Wageningen University, Wageningen, Netherlands
| | - Luisa M. Trindade
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
- Graduate School Experimental Plant Sciences, Wageningen University, Wageningen, Netherlands
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13
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Zheng C, Li Z, Yang H, Zhang T, Niu H, Liu D, Wang J, Ying H. Computation-aided rational design of a halophilic choline kinase for cytidine diphosphate choline production in high-salt condition. J Biotechnol 2018; 290:59-66. [PMID: 30445133 DOI: 10.1016/j.jbiotec.2018.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 10/27/2022]
Abstract
Biocatalysis has become the main approach to produce cytidine diphosphate choline (CDP-choline), which has been applied for treatment of acute craniocerebral injury and consciousness after brain surgery. However, salt accumulates with the production and inhibits enzyme activity, and eventually reduces yield and product accumulation rate. Our work provided a possible solution to this problem by applying a computational designed halophilic choline kinase. The halotolerant CKI (choline kinase) was designed following a unique strategy considering the most variable residue positions on the protein surface among target enzymes from different sources. The basic and neutral surface residues were replaced with acidic ones. This approach was enlightened by features of natural halophilic enzymes. Mutants in the work represented higher catalytic activities and IC50 (inhibit activity by 50%) at high salt concentrations (over 1200 mM). Furthermore, when the mutant was used in fed-batch production, the CDP-choline accumulation rate doubled comparing with process using wild-type CKI at acetate concentration of over 700 mM. The maximum titer was 151 ± 3.2 mM, the productivity was 5.8 ± 0.1 mM·L-1 h-1, and molar yield to CMP and utilization efficiency of energy were 85.3 and 63.5%. The idea of computational design in our work can also be applied to modify other enzymes in industry, and sheds light on alleviating effect of salt accumulation during industrial manufacturing process.
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Affiliation(s)
- Cheng Zheng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 211816, China; National Engineering Technique Research Center for Biotechnology, Nanjing, 211816, China
| | - Zhenjian Li
- National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China
| | - Haifeng Yang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China; Jiangsu Industrial Technology Research Institute, Nanjing, China
| | - Tianyi Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 211816, China; National Engineering Technique Research Center for Biotechnology, Nanjing, 211816, China
| | - Huanqing Niu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 211816, China; National Engineering Technique Research Center for Biotechnology, Nanjing, 211816, China; Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing, 211816, China
| | - Dong Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 211816, China; National Engineering Technique Research Center for Biotechnology, Nanjing, 211816, China
| | - Junzhi Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 211816, China; National Engineering Technique Research Center for Biotechnology, Nanjing, 211816, China; Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing, 211816, China; Jiangsu Industrial Technology Research Institute, Nanjing, China.
| | - Hanjie Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 211816, China; National Engineering Technique Research Center for Biotechnology, Nanjing, 211816, China; Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing, 211816, China.
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14
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Grisham DR, Nanda V. Hydrodynamic radius coincides with the slip plane position in the electrokinetic behavior of lysozyme. Proteins 2018; 86:515-523. [PMID: 29383755 DOI: 10.1002/prot.25469] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/19/2018] [Accepted: 01/23/2018] [Indexed: 02/01/2023]
Abstract
The zeta potential (ζ) is the effective charge energy of a solvated protein, describing the magnitude of electrostatic interactions in solution. It is commonly used in the assessment of adsorption processes and dispersion stability. Predicting ζ from molecular structure would be useful to the structure-based molecular design of drugs, proteins, and other molecules that hold charge-dependent function while remaining suspended in solution. One challenge in predicting ζ is identifying the location of the slip plane (XSP ), a distance from the protein surface where ζ is theoretically defined. This study tests the hypothesis that the XSP can be estimated by the Stokes-Einstein hydrodynamic radius (Rh ), using globular hen egg white lysozyme as a model system. Although the XSP and Rh differ in their theoretical definitions, with the XSP being the position of the ζ during electrokinetic phenomena (e.g., electrophoresis) and the Rh being a radius pertaining to the edge of solvation during diffusion, they both represent the point where water and ions no longer adhere to a molecule. This work identifies the limited range of ionic strengths in which the XSP can be determined using diffusivity measurements and the Stokes-Einstein equation. In addition, a computational protocol is developed for determining the ζ from a protein crystal structure. At low ionic strengths, a hyperdiffusivity regime exists, requiring direct measurement of electrophoretic mobility to determine ζ. This work, therefore, supports a basic tenant of EDL theory that the electric double layer during diffusion and electrophoresis are equivalent in the Stokes-Einstein regime.
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Affiliation(s)
- Daniel R Grisham
- Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey
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15
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Althuri A, Gujjala LKS, Banerjee R. Partially consolidated bioprocessing of mixed lignocellulosic feedstocks for ethanol production. BIORESOURCE TECHNOLOGY 2017; 245:530-539. [PMID: 28898853 DOI: 10.1016/j.biortech.2017.08.140] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
Rapid urbanization and industrialization have accelerated the energy demand which cannot be met by decreasing fossil fuels thereby substantiate the need for lignocellulosic ethanol. The present study is one such attempt towards bioethanol production in an eco-friendly manner using enzymes in which a mixture of lignocellulosic biomass namely, Ricinus communis, Saccharum officinarum (tops) and Saccharum spontaneum were taken as a substrate. The mixed biomass was processed through partially consolidated bioprocessing (PCBP) approach which involves a non-isothermal simultaneous pretreatment and saccharification step where a concoction of laccase (Pleurotus djamor) and holocellulase (Trichoderma reseei RUT C30) was used followed by co-fermentation within the same reactor. The process parameters influencing PCBP were optimized using feed-forward ANN model which resulted in a maximum ethanol concentration of 7.86% (v/v) (62.01g/L) at pentose to hexose strain ratio of 0.696 (v/v), substrate loading of 27.54% (w/v) and incubation time of 21.96h.
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Affiliation(s)
- Avanthi Althuri
- Advanced Technology Development Centre, Indian Institute of Technology, Kharagpur 721 302, India
| | | | - Rintu Banerjee
- Agricultural & Food Engineering Department, Indian Institute of Technology, Kharagpur 721 302, India; Advanced Technology Development Centre, Indian Institute of Technology, Kharagpur 721 302, India.
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16
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Lu X, Wang C, Li X, Zhao J. Temperature and pH influence adsorption of cellobiohydrolase onto lignin by changing the protein properties. BIORESOURCE TECHNOLOGY 2017; 245:819-825. [PMID: 28926914 DOI: 10.1016/j.biortech.2017.08.139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 05/03/2023]
Abstract
Non-productive adsorption of cellulase onto lignin restricted the movement of cellulase and also hindered the cellulase recycling in bioconversion of lignocellulose. In this study, effect of temperature and pH on adsorption and desorption of cellobiohydrolase (CBH) on lignin and its possible mechanism were discussed. It found that pH value and temperature influenced the adsorption and desorption behaviors of CBH on lignin. Different thermodynamic models suggested that the action between lignin and CBH was physical action. More CBH was adsorbed onto lignin, but lower initial adsorption velocity was detected at 50°C comparing with 4°C. Elevating pH value could improve desorption of cellulase from lignin. The changes of hydrophobicity and electric potential on protein surface may partially explain the impact of environmental conditions on the adsorption and desorption behaviors of CBH on lignin, and comparing to electrical interaction, the hydrophobicity may be the dominating factor influencing the behaviors.
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Affiliation(s)
- Xianqin Lu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100, China
| | - Can Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100, China
| | - Xuezhi Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100, China
| | - Jian Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100, China.
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