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Luo Z, Pan F, Zhu Y, Du S, Yan Y, Wang R, Li S, Xu H. Synergistic Improvement of 5-Aminolevulinic Acid Production with Synthetic Scaffolds and System Pathway Engineering. ACS Synth Biol 2022; 11:2766-2778. [PMID: 35939037 DOI: 10.1021/acssynbio.2c00157] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Engineered synthetic scaffolds to organize metabolic pathway enzymes and system pathway engineering to fine-tune metabolic fluxes play essential roles in microbial production. Here, we first obtained the most favorable combination of key enzymes for 5-aminolevulinic acid (5-ALA) synthesis through the C5 pathway by screening enzymes from different sources and optimizing their combination in different pathways. Second, we successfully constructed a multienzyme complex assembly system with PduA*, which spatially recruits the above three key enzymes for 5-ALA synthesis in a designable manner. By further optimizing the ratio of these key enzymes in synthetic scaffolds, the efficiency of 5-ALA synthesis through the C5 pathway was significantly improved. Then, the competitive metabolism pathway was fine-tuned by rationally designing different antisense RNAs, further significantly increasing 5-ALA titers. Furthermore, for efficient 5-ALA synthesis, obstacles of NADH and NADPH imbalances and feedback inhibition of the synthesis pathway were also overcome through engineering the NADPH regeneration pathway and transport pathway, respectively. Finally, combining these strategies with further fermentation optimization, we achieved a final 5-ALA titer of 11.4 g/L. These results highlight the importance of synthetic scaffolds and system pathway engineering to improve the microbial cell factory production performance.
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Affiliation(s)
- Zhengshan Luo
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Fei Pan
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Yifan Zhu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Shanshan Du
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Yifan Yan
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Rui Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Sha Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
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Hu Y, Li H, Ran Q, Liu J, Zhou S, Qiao Q, Song H, Peng F, Jiang Z. Effect of carbohydrate binding modules alterations on catalytic activity of glycoside hydrolase family 6 exoglucanase from Chaetomium thermophilum to cellulose. Int J Biol Macromol 2021; 191:222-229. [PMID: 34508724 DOI: 10.1016/j.ijbiomac.2021.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 12/31/2022]
Abstract
Exoglucanase (CBH) is the rate limiting enzyme in the process of cellulose degradation. The carbohydrate binding module (CBM) can improve the accessibility of cellulase to substrate, thereby promoting the enzymatic hydrolysis of cellulase. In this study, the influence of CBM on the properties of GH6 exoglucanase from Chaetomium thermophilum (CtCBH) is systematically explored from three perspectives: the fusion of exogenous CBM, the exogenous CBM replacement of its own CBM, and the deletion of its own CBM. The parental and reconstructed CtCBH presented the same optimum pH (6.0) and temperature (60 °C) for maximum activity. Fusion of exogenous CBM increased the binding capacity of CtCBH to Avicel by 8% and 9%, respectively, but it had no significant effect on its catalytic activity. The exogenous CBM replacement of its own CBM resulted in a 12% reduction in the binding ability of CtCBH to Avicel, and a 26% reduction in the catalytic activity of Avicel. The deletion of its own CBM significantly reduced the binding ability of CtCBH to Avicel by approximately 53%, but its catalytic activity was not obviously reduced. These observations suggest that binding ability of CBM is not necessary for the catalysis of CtCBH.
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Affiliation(s)
- Yanmei Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Industrial Biotechnology, School of Life Science, Hubei University, Wuhan 430062, PR China
| | - Huanan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Industrial Biotechnology, School of Life Science, Hubei University, Wuhan 430062, PR China
| | - Qiuping Ran
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Industrial Biotechnology, School of Life Science, Hubei University, Wuhan 430062, PR China
| | - Jiashu Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Industrial Biotechnology, School of Life Science, Hubei University, Wuhan 430062, PR China
| | - Shanna Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Industrial Biotechnology, School of Life Science, Hubei University, Wuhan 430062, PR China
| | - Qiming Qiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Industrial Biotechnology, School of Life Science, Hubei University, Wuhan 430062, PR China
| | - Huiting Song
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Science, Hubei University, Wuhan 430062, PR China
| | - Fang Peng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Science, Hubei University, Wuhan 430062, PR China
| | - Zhengbing Jiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Industrial Biotechnology, School of Life Science, Hubei University, Wuhan 430062, PR China.
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Biorefinery Gets Hot: Thermophilic Enzymes and Microorganisms for Second-Generation Bioethanol Production. Processes (Basel) 2021. [DOI: 10.3390/pr9091583] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
To mitigate the current global energy and the environmental crisis, biofuels such as bioethanol have progressively gained attention from both scientific and industrial perspectives. However, at present, commercialized bioethanol is mainly derived from edible crops, thus raising serious concerns given its competition with feed production. For this reason, lignocellulosic biomasses (LCBs) have been recognized as important alternatives for bioethanol production. Because LCBs supply is sustainable, abundant, widespread, and cheap, LCBs-derived bioethanol currently represents one of the most viable solutions to meet the global demand for liquid fuel. However, the cost-effective conversion of LCBs into ethanol remains a challenge and its implementation has been hampered by several bottlenecks that must still be tackled. Among other factors related to the challenging and variable nature of LCBs, we highlight: (i) energy-demanding pretreatments, (ii) expensive hydrolytic enzyme blends, and (iii) the need for microorganisms that can ferment mixed sugars. In this regard, thermophiles represent valuable tools to overcome some of these limitations. Thus, the aim of this review is to provide an overview of the state-of-the-art technologies involved, such as the use of thermophilic enzymes and microorganisms in industrial-relevant conditions, and to propose possible means to implement thermophiles into second-generation ethanol biorefineries that are already in operation.
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Zimmerling J, Oelschlägel M, Großmann C, Voitel M, Schlömann M, Tischler D. Biochemical Characterization of Phenylacetaldehyde Dehydrogenases from Styrene-degrading Soil Bacteria. Appl Biochem Biotechnol 2021; 193:650-667. [PMID: 33106986 PMCID: PMC7910268 DOI: 10.1007/s12010-020-03421-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 09/11/2020] [Indexed: 10/24/2022]
Abstract
Four phenylacetaldehyde dehydrogenases (designated as FeaB or StyD) originating from styrene-degrading soil bacteria were biochemically investigated. In this study, we focused on the Michaelis-Menten kinetics towards the presumed native substrate phenylacetaldehyde and the obviously preferred co-substrate NAD+. Furthermore, the substrate specificity on four substituted phenylacetaldehydes and the co-substrate preference were studied. Moreover, these enzymes were characterized with respect to their temperature as well as long-term stability. Since aldehyde dehydrogenases are known to show often dehydrogenase as well as esterase activity, we tested this capacity, too. Almost all results showed clearly different characteristics between the FeaB and StyD enzymes. Furthermore, FeaB from Sphingopyxis fribergensis Kp5.2 turned out to be the most active enzyme with an apparent specific activity of 17.8 ± 2.1 U mg-1. Compared with that, both StyDs showed only activities less than 0.2 U mg-1 except the overwhelming esterase activity of StyD-CWB2 (1.4 ± 0.1 U mg-1). The clustering of both FeaB and StyD enzymes with respect to their characteristics could also be mirrored in the phylogenetic analysis of twelve dehydrogenases originating from different soil bacteria.
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Affiliation(s)
- Juliane Zimmerling
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany.
| | - Michel Oelschlägel
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Carolin Großmann
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Matthias Voitel
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Michael Schlömann
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Dirk Tischler
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany.
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
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Enhanced Thermostability and Enzymatic Activity of Cel6A Variants from Thermobifida fusca by Empirical Domain Engineering (Short Title: Domain Engineering of Cel6A). BIOLOGY 2020; 9:biology9080214. [PMID: 32784797 PMCID: PMC7464639 DOI: 10.3390/biology9080214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/29/2020] [Accepted: 08/02/2020] [Indexed: 02/07/2023]
Abstract
Cellulases are a set of lignocellulolytic enzymes, capable of producing eco-friendly low-cost renewable bioethanol. However, low stability and hydrolytic activity limit their wide-scale applicability at the industrial scale. In this work, we report the domain engineering of endoglucanase (Cel6A) of Thermobifida fusca to improve their catalytic activity and thermal stability. Later, enzymatic activity and thermostability of the most efficient variant named as Cel6A.CBC was analyzed by molecular dynamics simulations. This variant demonstrated profound activity against soluble and insoluble cellulosic substrates like filter paper, alkali-treated bagasse, regenerated amorphous cellulose (RAC), and bacterial microcrystalline cellulose. The variant Cel6A.CBC showed the highest catalysis of carboxymethyl cellulose (CMC) and other related insoluble substrates at a pH of 6.0 and a temperature of 60 °C. Furthermore, a sound rationale was observed between experimental findings and molecular modeling of Cel6A.CBC which revealed thermostability of Cel6A.CBC at 26.85, 60.85, and 74.85 °C as well as structural flexibility at 126.85 °C. Therefore, a thermostable derivative of Cel6A engineered in the present work has enhanced biological performance and can be a useful construct for the mass production of bioethanol from plant biomass.
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Contreras F, Pramanik S, M. Rozhkova A, N. Zorov I, Korotkova O, P. Sinitsyn A, Schwaneberg U, D. Davari M. Engineering Robust Cellulases for Tailored Lignocellulosic Degradation Cocktails. Int J Mol Sci 2020; 21:E1589. [PMID: 32111065 PMCID: PMC7084875 DOI: 10.3390/ijms21051589] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/11/2022] Open
Abstract
Lignocellulosic biomass is a most promising feedstock in the production of second-generation biofuels. Efficient degradation of lignocellulosic biomass requires a synergistic action of several cellulases and hemicellulases. Cellulases depolymerize cellulose, the main polymer of the lignocellulosic biomass, to its building blocks. The production of cellulase cocktails has been widely explored, however, there are still some main challenges that enzymes need to overcome in order to develop a sustainable production of bioethanol. The main challenges include low activity, product inhibition, and the need to perform fine-tuning of a cellulase cocktail for each type of biomass. Protein engineering and directed evolution are powerful technologies to improve enzyme properties such as increased activity, decreased product inhibition, increased thermal stability, improved performance in non-conventional media, and pH stability, which will lead to a production of more efficient cocktails. In this review, we focus on recent advances in cellulase cocktail production, its current challenges, protein engineering as an efficient strategy to engineer cellulases, and our view on future prospects in the generation of tailored cellulases for biofuel production.
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Affiliation(s)
- Francisca Contreras
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Subrata Pramanik
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Aleksandra M. Rozhkova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan N. Zorov
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga Korotkova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Arkady P. Sinitsyn
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
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Yoav S, Stern J, Salama-Alber O, Frolow F, Anbar M, Karpol A, Hadar Y, Morag E, Bayer EA. Directed Evolution of Clostridium thermocellum β-Glucosidase A Towards Enhanced Thermostability. Int J Mol Sci 2019; 20:E4701. [PMID: 31547488 PMCID: PMC6801902 DOI: 10.3390/ijms20194701] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 12/27/2022] Open
Abstract
β-Glucosidases are key enzymes in the process of cellulose utilization. It is the last enzyme in the cellulose hydrolysis chain, which converts cellobiose to glucose. Since cellobiose is known to have a feedback inhibitory effect on a variety of cellulases, β-glucosidase can prevent this inhibition by hydrolyzing cellobiose to non-inhibitory glucose. While the optimal temperature of the Clostridium thermocellum cellulosome is 70 °C, C. thermocellum β-glucosidase A is almost inactive at such high temperatures. Thus, in the current study, a random mutagenesis directed evolutionary approach was conducted to produce a thermostable mutant with Kcat and Km, similar to those of the wild-type enzyme. The resultant mutant contained two mutations, A17S and K268N, but only the former was found to affect thermostability, whereby the inflection temperature (Ti) was increased by 6.4 °C. A17 is located near the central cavity of the native enzyme. Interestingly, multiple alignments revealed that position 17 is relatively conserved, whereby alanine is replaced only by serine. Upon the addition of the thermostable mutant to the C. thermocellum secretome for subsequent hydrolysis of microcrystalline cellulose at 70 °C, a higher soluble glucose yield (243%) was obtained compared to the activity of the secretome supplemented with the wild-type enzyme.
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Affiliation(s)
- Shahar Yoav
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, the Advanced School for Environmental Studies, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Johanna Stern
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Orly Salama-Alber
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Felix Frolow
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Michael Anbar
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Alon Karpol
- CelDezyner, 2 Bergman St, Tamar Science Park, Rehovot 7670504, Israel.
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, the Advanced School for Environmental Studies, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
| | - Ely Morag
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
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Affiliation(s)
- Ee Taek Hwang
- Center for Convergence Bioceramic Materials, Korea Institute of Ceramic Engineering & Technology, Cheongju-si, Chungcheongbuk-do 28160, Republic of Korea
| | - Seonbyul Lee
- Center for Convergence Bioceramic Materials, Korea Institute of Ceramic Engineering & Technology, Cheongju-si, Chungcheongbuk-do 28160, Republic of Korea
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Activity and Thermostability of GH5 Endoglucanase Chimeras from Mesophilic and Thermophilic Parents. Appl Environ Microbiol 2019; 85:AEM.02079-18. [PMID: 30552196 DOI: 10.1128/aem.02079-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/04/2018] [Indexed: 12/29/2022] Open
Abstract
Cellulases from glycoside hydrolase family 5 (GH5) are key endoglucanase enzymes in the degradation of diverse polysaccharide substrates and are used in industrial enzyme cocktails to break down biomass. The GH5 family shares a canonical (βα)8-barrel structure, where each (βα) module is essential for the enzyme's stability and activity. Despite their shared topology, the thermostability of GH5 endoglucanase enzymes can vary significantly, and highly thermostable variants are often sought for industrial applications. Based on the previously characterized thermophilic GH5 endoglucanase Egl5A from Talaromyces emersonii (TeEgl5A), which has an optimal temperature of 90°C, we created 10 hybrid enzymes with elements of the mesophilic endoglucanase Cel5 from Stegonsporium opalus (SoCel5) to determine which elements are responsible for enhanced thermostability. Five of the expressed hybrid enzymes exhibit enzyme activity. Two of these hybrids exhibited pronounced increases in the temperature optimum (10 and 20°C), the temperature at which the protein lost 50% of its activity (T 50) (15 and 19°C), and the melting temperature (Tm ) (16.5 and 22.9°C) and extended half-lives (t 1/2) (∼240- and 650-fold at 55°C) relative to the values for the mesophilic parent enzyme and demonstrated improved catalytic efficiency on selected substrates. The successful hybridization strategies were validated experimentally in another GH5 endoglucanase, Cel5 from Aspergillus niger (AnCel5), which demonstrated a similar increase in thermostability. Based on molecular dynamics (MD) simulations of both the SoCel5 and TeEgl5A parent enzymes and their hybrids, we hypothesize that improved hydrophobic packing of the interface between α2 and α3 is the primary mechanism by which the hybrid enzymes increase their thermostability relative to that of the mesophilic parent SoCel5.IMPORTANCE Thermal stability is an essential property of enzymes in many industrial biotechnological applications, as high temperatures improve bioreactor throughput. Many protein engineering approaches, such as rational design and directed evolution, have been employed to improve the thermal properties of mesophilic enzymes. Structure-based recombination has also been used to fuse TIM barrel fragments, and even fragments from unrelated folds, to generate new structures. However, little research has been done on GH5 endoglucanases. In this study, two GH5 endoglucanases exhibiting TIM barrel structure, SoCel5 and TeEgl5A, with different thermal properties, were hybridized to study the roles of different (βα) motifs. This work illustrates the role that structure-guided recombination can play in helping to identify sequence function relationships within GH5 enzymes by supplementing natural diversity with synthetic diversity.
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Disulfide bonds elimination of endoglucanase II from Trichoderma reesei by site-directed mutagenesis to improve enzyme activity and thermal stability: An experimental and theoretical approach. Int J Biol Macromol 2018; 120:1572-1580. [DOI: 10.1016/j.ijbiomac.2018.09.164] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 09/23/2018] [Accepted: 09/25/2018] [Indexed: 01/21/2023]
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Shi T, Han P, You C, Zhang YHPJ. An in vitro synthetic biology platform for emerging industrial biomanufacturing: Bottom-up pathway design. Synth Syst Biotechnol 2018; 3:186-195. [PMID: 30345404 PMCID: PMC6190512 DOI: 10.1016/j.synbio.2018.05.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 01/29/2023] Open
Abstract
Although most in vitro (cell-free) synthetic biology projects are usually used for the purposes of fundamental research or the formation of high-value products, in vitro synthetic biology platform, which can implement complicated biochemical reactions by the in vitro assembly of numerous enzymes and coenzymes, has been proposed for low-cost biomanufacturing of bioenergy, food, biochemicals, and nutraceuticals. In addition to the most important advantage-high product yield, in vitro synthetic biology platform features several other biomanufacturing advantages, such as fast reaction rate, easy product separation, open process control, broad reaction condition, tolerance to toxic substrates or products, and so on. In this article, we present the basic bottom-up design principles of in vitro synthetic pathway from basic building blocks-BioBricks (thermoenzymes and/or immobilized enzymes) to building modules (e.g., enzyme complexes or multiple enzymes as a module) with specific functions. With development in thermostable building blocks-BioBricks and modules, the in vitro synthetic biology platform would open a new biomanufacturing age for the cost-competitive production of biocommodities.
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Affiliation(s)
| | | | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Yi-Heng P. Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
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12
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Duan CJ, Huang MY, Pang H, Zhao J, Wu CX, Feng JX. Characterization of a novel theme C glycoside hydrolase family 9 cellulase and its CBM-chimeric enzymes. Appl Microbiol Biotechnol 2017; 101:5723-5737. [DOI: 10.1007/s00253-017-8320-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 04/09/2017] [Accepted: 04/29/2017] [Indexed: 01/27/2023]
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Walker JA, Pattathil S, Bergeman LF, Beebe ET, Deng K, Mirzai M, Northen TR, Hahn MG, Fox BG. Determination of glycoside hydrolase specificities during hydrolysis of plant cell walls using glycome profiling. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:31. [PMID: 28184246 PMCID: PMC5288845 DOI: 10.1186/s13068-017-0703-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/06/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND Glycoside hydrolases (GHs) are enzymes that hydrolyze polysaccharides into simple sugars. To better understand the specificity of enzyme hydrolysis within the complex matrix of polysaccharides found in the plant cell wall, we studied the reactions of individual enzymes using glycome profiling, where a comprehensive collection of cell wall glycan-directed monoclonal antibodies are used to detect polysaccharide epitopes remaining in the walls after enzyme treatment and quantitative nanostructure initiator mass spectrometry (oxime-NIMS) to determine soluble sugar products of their reactions. RESULTS Single, purified enzymes from the GH5_4, GH10, and GH11 families of glycoside hydrolases hydrolyzed hemicelluloses as evidenced by the loss of specific epitopes from the glycome profiles in enzyme-treated plant biomass. The glycome profiling data were further substantiated by oxime-NIMS, which identified hexose products from hydrolysis of cellulose, and pentose-only and mixed hexose-pentose products from the hydrolysis of hemicelluloses. The GH10 enzyme proved to be reactive with the broadest diversity of xylose-backbone polysaccharide epitopes, but was incapable of reacting with glucose-backbone polysaccharides. In contrast, the GH5 and GH11 enzymes studied here showed the ability to react with both glucose- and xylose-backbone polysaccharides. CONCLUSIONS The identification of enzyme specificity for a wide diversity of polysaccharide structures provided by glycome profiling, and the correlated identification of soluble oligosaccharide hydrolysis products provided by oxime-NIMS, offers a unique combination to understand the hydrolytic capabilities and constraints of individual enzymes as they interact with plant biomass.
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Affiliation(s)
- Johnnie A. Walker
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Sivakumar Pattathil
- US Department of Energy Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Lai F. Bergeman
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Emily T. Beebe
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Kai Deng
- US Department of Energy Joint Bioenergy Institute, Emeryville, CA 94608 USA
- Sandia National Laboratories, Livermore, CA 94551 USA
| | - Maryam Mirzai
- US Department of Energy Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Trent R. Northen
- US Department of Energy Joint Bioenergy Institute, Emeryville, CA 94608 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Michael G. Hahn
- US Department of Energy Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Brian G. Fox
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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14
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Boutard M, Ettwiller L, Cerisy T, Alberti A, Labadie K, Salanoubat M, Schildkraut I, Tolonen AC. Global repositioning of transcription start sites in a plant-fermenting bacterium. Nat Commun 2016; 7:13783. [PMID: 27982035 PMCID: PMC5171806 DOI: 10.1038/ncomms13783] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/01/2016] [Indexed: 01/03/2023] Open
Abstract
Bacteria respond to their environment by regulating mRNA synthesis, often by altering the genomic sites at which RNA polymerase initiates transcription. Here, we investigate genome-wide changes in transcription start site (TSS) usage by Clostridium phytofermentans, a model bacterium for fermentation of lignocellulosic biomass. We quantify expression of nearly 10,000 TSS at single base resolution by Capp-Switch sequencing, which combines capture of synthetically capped 5' mRNA fragments with template-switching reverse transcription. We find the locations and expression levels of TSS for hundreds of genes change during metabolism of different plant substrates. We show that TSS reveals riboswitches, non-coding RNA and novel transcription units. We identify sequence motifs associated with carbon source-specific TSS and use them for regulon discovery, implicating a LacI/GalR protein in control of pectin metabolism. We discuss how the high resolution and specificity of Capp-Switch enables study of condition-specific changes in transcription initiation in bacteria.
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Affiliation(s)
- Magali Boutard
- 1CEA, DRF, IG, Genoscope, Évry 91000, France.,CNRS-UMR8030, Évry 91000, France
| | | | - Tristan Cerisy
- 1CEA, DRF, IG, Genoscope, Évry 91000, France.,CNRS-UMR8030, Évry 91000, France.,Université Paris-Saclay, Évry 91000, France.,Université d'Évry, Évry 91000, France
| | | | | | - Marcel Salanoubat
- 1CEA, DRF, IG, Genoscope, Évry 91000, France.,CNRS-UMR8030, Évry 91000, France.,Université Paris-Saclay, Évry 91000, France.,Université d'Évry, Évry 91000, France
| | - Ira Schildkraut
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Andrew C Tolonen
- 1CEA, DRF, IG, Genoscope, Évry 91000, France.,CNRS-UMR8030, Évry 91000, France.,Université Paris-Saclay, Évry 91000, France.,Université d'Évry, Évry 91000, France
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15
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Polarity Alteration of a Calcium Site Induces a Hydrophobic Interaction Network and Enhances Cel9A Endoglucanase Thermostability. Appl Environ Microbiol 2016; 82:1662-1674. [PMID: 26729722 DOI: 10.1128/aem.03326-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 12/16/2015] [Indexed: 01/07/2023] Open
Abstract
Structural calcium sites control protein thermostability and activity by stabilizing native folds and changing local conformations. Alicyclobacillus acidocaldarius survives in thermal-acidic conditions and produces an endoglucanase Cel9A (AaCel9A) which contains a calcium-binding site (Ser465 to Val470) near the catalytic cleft. By superimposing the Ca(2+)-free and Ca(2+)-bounded conformations of the calcium site, we found that Ca(2+) induces hydrophobic interactions between the calcium site and its nearby region by driving a conformational change. The hydrophobic interactions at the high-B-factor region could be enhanced further by replacing the surrounding polar residues with hydrophobic residues to affect enzyme thermostability and activity. Therefore, the calcium-binding residue Asp468 (whose side chain directly ligates Ca(2+)), Asp469, and Asp471 of AaCel9A were separately replaced by alanine and valine. Mutants D468A and D468V showed increased activity compared with those of the wild type with 0 mM or 10 mM Ca(2+) added, whereas the Asp469 or Asp471 substitution resulted in decreased activity. The D468A crystal structure revealed that mutation D468A triggered a conformational change similar to that induced by Ca(2+) in the wild type and developed a hydrophobic interaction network between the calcium site and the neighboring hydrophobic region (Ala113 to Ala117). Mutations D468V and D468A increased 4.5°C and 5.9°C, respectively, in melting temperature, and enzyme half-life at 75°C increased approximately 13 times. Structural comparisons between AaCel9A and other endoglucanases of the GH9 family suggested that the stability of the regions corresponding to the AaCel9A calcium site plays an important role in GH9 endoglucanase catalysis at high temperature.
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16
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Karita S. Carbohydrate-Binding Modules in Plant Cell Wall-Degrading Enzymes. TRENDS GLYCOSCI GLYC 2016. [DOI: 10.4052/tigg.1403.1j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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18
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Zhang J, Shi H, Xu L, Zhu X, Li X. Site-Directed Mutagenesis of a Hyperthermophilic Endoglucanase Cel12B from Thermotoga maritima Based on Rational Design. PLoS One 2015. [PMID: 26218520 PMCID: PMC4517919 DOI: 10.1371/journal.pone.0133824] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
To meet the demand for the application of high activity and thermostable cellulases in the production of new-generation bioethanol from nongrain-cellulose sources, a hyperthermostable β-1,4-endoglucase Cel12B from Thermotoga maritima was selected for further modification by gene site-directed mutagenesis method in the present study, based on homology modeling and rational design. As a result, two recombinant enzymes showed significant improvement in enzyme activity by 77% and 87%, respectively, higher than the parental enzyme TmCel12B. Furthermore, the two mutants could retain 80% and 90.5% of their initial activity after incubation at 80°C for 8 h, while only 45% for 5 h to TmCel12B. The Km and Vmax of the two recombinant enzymes were 1.97±0.05 mM, 4.23±0.15 μmol·mg(-1)·min(-1) of TmCel12B-E225H-K207G-D37V, and 2.97±0.12 mM, 3.15±0.21 μmol·mg(-1)·min(-1) of TmCel12B-E225H-K207G, respectively, when using CMC-Na as the substrate. The roles of the mutation sites were also analyzed and evaluated in terms of electron density, hydrophobicity of the modeled protein structures. The recombinant enzymes may be used in the hydrolysis of cellulose at higher temperature in the future. It was concluded that the gene mutagenesis approach of a certain active residues may effectively improve the performance of cellulases for the industrial applications and contribute to the study the thermostable mechanism of thermophilic enzymes.
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Affiliation(s)
- Jinfeng Zhang
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- School of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
| | - Hao Shi
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
| | - Linyu Xu
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- School of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
| | - Xiaoyan Zhu
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- School of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- Jiangsu Key Laboratory for Biomass-based Energy and Enzyme Technology, Huaiyin Normal University, Huaian, Jiangsu 223300, P. R. China
| | - Xiangqian Li
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- School of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- * E-mail:
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19
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Petit E, Coppi MV, Hayes JC, Tolonen AC, Warnick T, Latouf WG, Amisano D, Biddle A, Mukherjee S, Ivanova N, Lykidis A, Land M, Hauser L, Kyrpides N, Henrissat B, Lau J, Schnell DJ, Church GM, Leschine SB, Blanchard JL. Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels. PLoS One 2015; 10:e0118285. [PMID: 26035711 PMCID: PMC4452783 DOI: 10.1371/journal.pone.0118285] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 01/12/2015] [Indexed: 11/18/2022] Open
Abstract
Clostridium phytofermentans was isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways. The objective of the present study was to understand the molecular mechanisms of biomass conversion to ethanol in a single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome during growth on plant carbohydrates. The saccharolytic versatility of C. phytofermentans is reflected in a diversity of genes encoding ATP-binding cassette sugar transporters and glycoside hydrolases, many of which may have been acquired through horizontal gene transfer. These genes are frequently organized as operons that may be controlled individually by the many transcriptional regulators identified in the genome. Preferential ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases and additional pathways maximizing ethanol yield. The genome also encodes three different proteinaceous bacterial microcompartments with the capacity to compartmentalize pathways that divert fermentation intermediates to various products. These characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels.
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Affiliation(s)
- Elsa Petit
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Maddalena V. Coppi
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - James C. Hayes
- Graduate Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Andrew C. Tolonen
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)-Genoscope, Unité Mixte de Recherche (UMR)-8030, National Center for Scientific Research (CNRS), Evry, France
| | - Thomas Warnick
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - William G. Latouf
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Danielle Amisano
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Amy Biddle
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Supratim Mukherjee
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Natalia Ivanova
- Department of Energy (DOE)- Joint Genome Institute, Genome Biology Program, Production Genomics Facility, Walnut Creek, California, United States of America
| | - Athanassios Lykidis
- Department of Energy (DOE)- Joint Genome Institute, Genome Biology Program, Production Genomics Facility, Walnut Creek, California, United States of America
| | - Miriam Land
- Oak Ridge National Laboratory (ORNL), Life Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Loren Hauser
- Oak Ridge National Laboratory (ORNL), Life Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Nikos Kyrpides
- Department of Energy (DOE)- Joint Genome Institute, Genome Biology Program, Production Genomics Facility, Walnut Creek, California, United States of America
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Unité mixte de recherche (UMR)-6098, National Center for Scientific Research (CNRS), and Universités d’Aix-Marseille I and II, Marseille, France
| | - Joanne Lau
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Danny J. Schnell
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Susan B. Leschine
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Jeffrey L. Blanchard
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Graduate Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
- Graduate Program in Organismal and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
- * E-mail:
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20
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Smith MR, Khera E, Wen F. Engineering Novel and Improved Biocatalysts by Cell Surface Display. Ind Eng Chem Res 2015; 54:4021-4032. [PMID: 29056821 PMCID: PMC5647830 DOI: 10.1021/ie504071f] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biocatalysts, especially enzymes, have the ability to catalyze reactions with high product selectivity, utilize a broad range of substrates, and maintain activity at low temperature and pressure. Therefore, they represent a renewable, environmentally friendly alternative to conventional catalysts. Most current industrial-scale chemical production processes using biocatalysts employ soluble enzymes or whole cells expressing intracellular enzymes. Cell surface display systems differ by presenting heterologous enzymes extracellularly, overcoming some of the limitations associated with enzyme purification and substrate transport. Additionally, coupled with directed evolution, cell surface display is a powerful platform for engineering enzymes with enhanced properties. In this review, we will introduce the molecular and cellular principles of cell surface display and discuss how it has been applied to engineer enzymes with improved properties as well as to develop surface-engineered microbes as whole-cell biocatalysts.
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Affiliation(s)
- Mason R. Smith
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Eshita Khera
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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21
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Chokhawala HA, Roche CM, Kim TW, Atreya ME, Vegesna N, Dana CM, Blanch HW, Clark DS. Mutagenesis of Trichoderma reesei endoglucanase I: impact of expression host on activity and stability at elevated temperatures. BMC Biotechnol 2015; 15:11. [PMID: 25879765 PMCID: PMC4347658 DOI: 10.1186/s12896-015-0118-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 01/28/2015] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Trichoderma reesei is a key cellulase source for economically saccharifying cellulosic biomass for the production of biofuels. Lignocellulose hydrolysis at temperatures above the optimum temperature of T. reesei cellulases (~50°C) could provide many significant advantages, including reduced viscosity at high-solids loadings, lower risk of microbial contamination during saccharification, greater compatibility with high-temperature biomass pretreatment, and faster rates of hydrolysis. These potential advantages motivate efforts to engineer T. reesei cellulases that can hydrolyze lignocellulose at temperatures ranging from 60-70°C. RESULTS A B-factor guided approach for improving thermostability was used to engineer variants of endoglucanase I (Cel7B) from T. reesei (TrEGI) that are able to hydrolyze cellulosic substrates more rapidly than the recombinant wild-type TrEGI at temperatures ranging from 50-70°C. When expressed in T. reesei, TrEGI variant G230A/D113S/D115T (G230A/D113S/D115T Tr_TrEGI) had a higher apparent melting temperature (3°C increase in Tm) and improved half-life at 60°C (t1/2 = 161 hr) than the recombinant (T. reesei host) wild-type TrEGI (t1/2 = 74 hr at 60°C, Tr_TrEGI). Furthermore, G230A/D113S/D115T Tr_TrEGI showed 2-fold improved activity compared to Tr_TrEGI at 65°C on solid cellulosic substrates, and was as efficient in hydrolyzing cellulose at 60°C as Tr_TrEGI was at 50°C. The activities and stabilities of the recombinant TrEGI enzymes followed similar trends but differed significantly in magnitude depending on the expression host (Escherichia coli cell-free, Saccharomyces cerevisiae, Neurospora crassa, or T. reesei). Compared to N.crassa-expressed TrEGI, S. cerevisiae-expressed TrEGI showed inferior activity and stability, which was attributed to the lack of cyclization of the N-terminal glutamine in Sc_TrEGI and not to differences in glycosylation. N-terminal pyroglutamate formation in TrEGI expressed in S. cerevisiae was found to be essential in elevating its activity and stability to levels similar to the T. reesei or N. crassa-expressed enzyme, highlighting the importance of this ubiquitous modification in GH7 enzymes. CONCLUSION Structure-guided evolution of T. reesei EGI was used to engineer enzymes with increased thermal stability and activity on solid cellulosic substrates. Production of TrEGI enzymes in four hosts highlighted the impact of the expression host and the role of N-terminal pyroglutamate formation on the activity and stability of TrEGI enzymes.
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Affiliation(s)
- Harshal A Chokhawala
- Energy Biosciences Institute, University of California, Berkeley, CA, 94720, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.
| | - Christine M Roche
- Energy Biosciences Institute, University of California, Berkeley, CA, 94720, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.
| | - Tae-Wan Kim
- Energy Biosciences Institute, University of California, Berkeley, CA, 94720, USA.
| | - Meera E Atreya
- Energy Biosciences Institute, University of California, Berkeley, CA, 94720, USA.
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
| | - Neeraja Vegesna
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, West Bengal, 721301, India.
| | - Craig M Dana
- Energy Biosciences Institute, University of California, Berkeley, CA, 94720, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.
| | - Harvey W Blanch
- Energy Biosciences Institute, University of California, Berkeley, CA, 94720, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.
| | - Douglas S Clark
- Energy Biosciences Institute, University of California, Berkeley, CA, 94720, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.
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22
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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23
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Walker JA, Takasuka TE, Deng K, Bianchetti CM, Udell HS, Prom BM, Kim H, Adams PD, Northen TR, Fox BG. Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:220. [PMID: 26697109 PMCID: PMC4687162 DOI: 10.1186/s13068-015-0402-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/30/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND Carbohydrate binding modules (CBMs) bind polysaccharides and help target glycoside hydrolases catalytic domains to their appropriate carbohydrate substrates. To better understand how CBMs can improve cellulolytic enzyme reactivity, representatives from each of the 18 families of CBM found in Ruminoclostridium thermocellum were fused to the multifunctional GH5 catalytic domain of CelE (Cthe_0797, CelEcc), which can hydrolyze numerous types of polysaccharides including cellulose, mannan, and xylan. Since CelE is a cellulosomal enzyme, none of these fusions to a CBM previously existed. RESULTS CelEcc_CBM fusions were assayed for their ability to hydrolyze cellulose, lichenan, xylan, and mannan. Several CelEcc_CBM fusions showed enhanced hydrolytic activity with different substrates relative to the fusion to CBM3a from the cellulosome scaffoldin, which has high affinity for binding to crystalline cellulose. Additional binding studies and quantitative catalysis studies using nanostructure-initiator mass spectrometry (NIMS) were carried out with the CBM3a, CBM6, CBM30, and CBM44 fusion enzymes. In general, and consistent with observations of others, enhanced enzyme reactivity was correlated with moderate binding affinity of the CBM. Numerical analysis of reaction time courses showed that CelEcc_CBM44, a combination of a multifunctional enzyme domain with a CBM having broad binding specificity, gave the fastest rates for hydrolysis of both the hexose and pentose fractions of ionic-liquid pretreated switchgrass. CONCLUSION We have shown that fusions of different CBMs to a single multifunctional GH5 catalytic domain can increase its rate of reaction with different pure polysaccharides and with pretreated biomass. This fusion approach, incorporating domains with broad specificity for binding and catalysis, provides a new avenue to improve reactivity of simple combinations of enzymes within the complexity of plant biomass.
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Affiliation(s)
- Johnnie A. Walker
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Taichi E. Takasuka
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Kai Deng
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Sandia National Laboratories, Livermore, CA 94551 USA
| | - Christopher M. Bianchetti
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Chemistry, University of Wisconsin-Oshkosh, Oshkosh, WI 54901 USA
| | - Hannah S. Udell
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Ben M. Prom
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Hyunkee Kim
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Paul D. Adams
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- />Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Trent R. Northen
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Brian G. Fox
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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24
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You C, Zhang YHP. Simple cloning and DNA assembly in Escherichia coli by prolonged overlap extension PCR. Methods Mol Biol 2014; 1116:183-92. [PMID: 24395365 DOI: 10.1007/978-1-62703-764-8_13] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We developed a simple method (Simple Cloning) for subcloning one, two, or three DNA fragments into any location of a targeted vector without the need for restriction enzyme, ligase, exonuclease, or recombinase. This cloning technology can be applied to a few common Escherichia coli hosts (e.g., BL21(DE3), DH5α, JM109, TOP10). The protocol includes three steps: (a) linear DNA fragments (i.e., the insert DNA and the vector backbone) with two overlap ends were generated by regular high-fidelity PCR, (b) the DNA multimers were generated based on these equimolar DNA templates by using prolonged overlap extension PCR (POE-PCR) without primers added, and (c) the POE-PCR product was transformed to E. coli strains directly. Because positive colony efficiencies are very high, it is not necessary to identify desired clones by using colony PCR. Simple Cloning provides a new cloning and DNA assembly method with great simplicity and flexibility.
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Affiliation(s)
- Chun You
- Biological Systems Engineering Department, Virginia Tech, Blacksburg, VA, USA
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26
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Bornscheuer U, Buchholz K, Seibel J. Enzymatic degradation of (ligno)cellulose. Angew Chem Int Ed Engl 2014; 53:10876-93. [PMID: 25136976 DOI: 10.1002/anie.201309953] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Indexed: 11/06/2022]
Abstract
Glycoside-degrading enzymes play a dominant role in the biochemical conversion of cellulosic biomass into low-price biofuels and high-value-added chemicals. New insight into protein functions and substrate structures, the kinetics of recognition, and degradation events has resulted in a substantial improvement of our understanding of cellulose degradation.
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Affiliation(s)
- Uwe Bornscheuer
- Ernst-Moritz-Arndt-Universität Greifswald, Biotechnologie und Enzymkatalyse, Institut für Biochemie, Felix-Hausdorff-Strasse 4, 17487 Greifswald (Germany)
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Kellermann SJ, Rentmeister A. Current Developments in Cellulase Engineering. CHEMBIOENG REVIEWS 2014. [DOI: 10.1002/cben.201300006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Huang GL, Anderson TD, Clubb RT. Engineering microbial surfaces to degrade lignocellulosic biomass. Bioengineered 2013; 5:96-106. [PMID: 24430239 PMCID: PMC4049913 DOI: 10.4161/bioe.27461] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Renewable lignocellulosic plant biomass is a promising feedstock from which to produce biofuels, chemicals, and materials. One approach to cost-effectively exploit this resource is to use consolidating bioprocessing (CBP) microbes that directly convert lignocellulose into valuable end products. Because many promising CBP-enabling microbes are non-cellulolytic, recent work has sought to engineer them to display multi-cellulase containing minicellulosomes that hydrolyze biomass more efficiently than isolated enzymes. In this review, we discuss progress in engineering the surfaces of the model microorganisms: Bacillus subtilis, Escherichia coli, and Saccharomyces cerevisiae. We compare the distinct approaches used to display cellulases and minicellulosomes, as well as their surface enzyme densities and cellulolytic activities. Thus far, minicellulosomes have only been grafted onto the surfaces of B. subtilis and S. cerevisiae, suggesting that the absence of an outer membrane in fungi and Gram-positive bacteria may make their surfaces better suited for displaying the elaborate multi-enzyme complexes needed to efficiently degrade lignocellulose.
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Affiliation(s)
- Grace L Huang
- Department of Chemistry and Biochemistry; University of California-Los Angeles; Los Angeles, CA USA; UCLA-DOE Institute of Genomics and Proteomics; University of California-Los Angeles; Los Angeles, CA USA
| | - Timothy D Anderson
- Department of Chemistry and Biochemistry; University of California-Los Angeles; Los Angeles, CA USA; UCLA-DOE Institute of Genomics and Proteomics; University of California-Los Angeles; Los Angeles, CA USA
| | - Robert T Clubb
- Department of Chemistry and Biochemistry; University of California-Los Angeles; Los Angeles, CA USA; UCLA-DOE Institute of Genomics and Proteomics; University of California-Los Angeles; Los Angeles, CA USA; Molecular Biology Institute; University of California-Los Angeles; Los Angeles, CA USA
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Chen Z, Pereira JH, Liu H, Tran HM, Hsu NSY, Dibble D, Singh S, Adams PD, Sapra R, Hadi MZ, Simmons BA, Sale KL. Improved activity of a thermophilic cellulase, Cel5A, from Thermotoga maritima on ionic liquid pretreated switchgrass. PLoS One 2013; 8:e79725. [PMID: 24244549 PMCID: PMC3828181 DOI: 10.1371/journal.pone.0079725] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 10/04/2013] [Indexed: 11/19/2022] Open
Abstract
Ionic liquid pretreatment of biomass has been shown to greatly reduce the recalcitrance of lignocellulosic biomass, resulting in improved sugar yields after enzymatic saccharification. However, even under these improved saccharification conditions the cost of enzymes still represents a significant proportion of the total cost of producing sugars and ultimately fuels from lignocellulosic biomass. Much of the high cost of enzymes is due to the low catalytic efficiency and stability of lignocellulolytic enzymes, especially cellulases, under conditions that include high temperatures and the presence of residual pretreatment chemicals, such as acids, organic solvents, bases, or ionic liquids. Improving the efficiency of the saccharification process on ionic liquid pretreated biomass will facilitate reduced enzyme loading and cost. Thermophilic cellulases have been shown to be stable and active in ionic liquids but their activity is typically at lower levels. Cel5A_Tma, a thermophilic endoglucanase from Thermotoga maritima, is highly active on cellulosic substrates and is stable in ionic liquid environments. Here, our motivation was to engineer mutants of Cel5A_Tma with higher activity on 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]) pretreated biomass. We developed a robotic platform to screen a random mutagenesis library of Cel5A_Tma. Twelve mutants with 25–42% improvement in specific activity on carboxymethyl cellulose and up to 30% improvement on ionic-liquid pretreated switchgrass were successfully isolated and characterized from a library of twenty thousand variants. Interestingly, most of the mutations in the improved variants are located distally to the active site on the protein surface and are not directly involved with substrate binding.
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Affiliation(s)
- Zhiwei Chen
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Jose H. Pereira
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Hanbin Liu
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Huu M. Tran
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Nathan S. Y. Hsu
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, United States of America
| | - Dean Dibble
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Seema Singh
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Paul D. Adams
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
| | - Rajat Sapra
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Masood Z. Hadi
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Blake A. Simmons
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Kenneth L. Sale
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
- * E-mail:
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Cunha ES, Hatem CL, Barrick D. Insertion of endocellulase catalytic domains into thermostable consensus ankyrin scaffolds: effects on stability and cellulolytic activity. Appl Environ Microbiol 2013; 79:6684-96. [PMID: 23974146 PMCID: PMC3811507 DOI: 10.1128/aem.02121-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/21/2013] [Indexed: 11/20/2022] Open
Abstract
Degradation of cellulose for biofuels production holds promise in solving important environmental and economic problems. However, the low activities (and thus high enzyme-to-substrate ratios needed) of hydrolytic cellulase enzymes, which convert cellulose into simple sugars, remain a major barrier. As a potential strategy to stabilize cellulases and enhance their activities, we have embedded cellulases of extremophiles into hyperstable α-helical consensus ankyrin domain scaffolds. We found the catalytic domains CelA (CA, GH8; Clostridium thermocellum) and Cel12A (C12A, GH12; Thermotoga maritima) to be stable in the context of the ankyrin scaffold and to be active against both soluble and insoluble substrates. The ankyrin repeats in each fusion are folded, although it appears that for the C12A catalytic domain (CD; where the N and C termini are distant in the crystal structure), the two flanking ankyrin domains are independent, whereas for CA (where termini are close), the flanking ankyrin domains stabilize each other. Although the activity of CA is unchanged in the context of the ankyrin scaffold, the activity of C12A is increased between 2- and 6-fold (for regenerated amorphous cellulose and carboxymethyl cellulose substrates) at high temperatures. For C12A, activity increases with the number of flanking ankyrin repeats. These results showed ankyrin arrays to be a promising scaffold for constructing designer cellulosomes, preserving or enhancing enzymatic activity and retaining thermostability. This modular architecture will make it possible to arrange multiple cellulase domains at a precise spacing within a single polypeptide, allowing us to search for spacings that may optimize reactivity toward the repetitive cellulose lattice.
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Affiliation(s)
- Eva S. Cunha
- Institute for Multiscale Modeling of Biological Interactions, Johns Hopkins University, Baltimore, Maryland, USA
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Christine L. Hatem
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Doug Barrick
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
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Ng IS, Chi X, Wu X, Bao Z, Lu Y, Chang JS, Ling X. Cloning and expression of Cel8A from Klebsiella pneumoniae in Escherichia coli and comparison to cel gene of Cellulomonas uda. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Reyes-Ortiz V, Heins RA, Cheng G, Kim EY, Vernon BC, Elandt RB, Adams PD, Sale KL, Hadi MZ, Simmons BA, Kent MS, Tullman-Ercek D. Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:93. [PMID: 23819686 PMCID: PMC3716932 DOI: 10.1186/1754-6834-6-93] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 06/18/2013] [Indexed: 05/03/2023]
Abstract
INTRODUCTION Cellulases are of great interest for application in biomass degradation, yet the molecular details of the mode of action of glycoside hydrolases during degradation of insoluble cellulose remain elusive. To further improve these enzymes for application at industrial conditions, it is critical to gain a better understanding of not only the details of the degradation process, but also the function of accessory modules. METHOD We fused a carbohydrate-binding module (CBM) from family 2a to two thermophilic endoglucanases. We then applied neutron reflectometry to determine the mechanism of the resulting enhancements. RESULTS Catalytic activity of the chimeric enzymes was enhanced up to three fold on insoluble cellulose substrates as compared to wild type. Importantly, we demonstrate that the wild type enzymes affect primarily the surface properties of an amorphous cellulose film, while the chimeras containing a CBM alter the bulk properties of the amorphous film. CONCLUSION Our findings suggest that the CBM improves the efficiency of these cellulases by enabling digestion within the bulk of the film.
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Affiliation(s)
- Vimalier Reyes-Ortiz
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Department of Bioengineering, University of California, Berkeley, CA 94720, US
| | - Richard A Heins
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Livermore, CA 94550, US
| | - Gang Cheng
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Livermore, CA 94550, US
| | - Edward Y Kim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, US
| | - Briana C Vernon
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Albuquerque, NM 87185, US
| | - Ryan B Elandt
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
| | - Paul D Adams
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Department of Bioengineering, University of California, Berkeley, CA 94720, US
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, US
| | - Kenneth L Sale
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Livermore, CA 94550, US
| | - Masood Z Hadi
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Livermore, CA 94550, US
| | - Blake A Simmons
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Livermore, CA 94550, US
| | - Michael S Kent
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Albuquerque, NM 87185, US
| | - Danielle Tullman-Ercek
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Department of Bioengineering, University of California, Berkeley, CA 94720, US
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, US
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, US
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Telke AA, Zhuang N, Ghatge SS, Lee SH, Ali Shah A, Khan H, Um Y, Shin HD, Chung YR, Lee KH, Kim SW. Engineering of family-5 glycoside hydrolase (Cel5A) from an uncultured bacterium for efficient hydrolysis of cellulosic substrates. PLoS One 2013; 8:e65727. [PMID: 23785445 PMCID: PMC3681849 DOI: 10.1371/journal.pone.0065727] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 04/27/2013] [Indexed: 01/29/2023] Open
Abstract
Cel5A, an endoglucanase, was derived from the metagenomic library of vermicompost. The deduced amino acid sequence of Cel5A shows high sequence homology with family-5 glycoside hydrolases, which contain a single catalytic domain but no distinct cellulose-binding domain. Random mutagenesis and cellulose-binding module (CBM) fusion approaches were successfully applied to obtain properties required for cellulose hydrolysis. After two rounds of error-prone PCR and screening of 3,000 mutants, amino acid substitutions were identified at various positions in thermotolerant mutants. The most heat-tolerant mutant, Cel5A_2R2, showed a 7-fold increase in thermostability. To enhance the affinity and hydrolytic activity of Cel5A on cellulose substrates, the family-6 CBM from Saccharophagus degradans was fused to the C-terminus of the Cel5A_2R2 mutant using overlap PCR. The Cel5A_2R2-CBM6 fusion protein showed 7-fold higher activity than the native Cel5A on Avicel and filter paper. Cellobiose was a major product obtained from the hydrolysis of cellulosic substrates by the fusion enzyme, which was identified by using thin layer chromatography analysis.
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Affiliation(s)
- Amar A. Telke
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Ningning Zhuang
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Sunil S. Ghatge
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Sook-Hee Lee
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Asad Ali Shah
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Haji Khan
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Youngsoon Um
- Center for Environmental Technology Research, KIST, Seoul, Republic of Korea
| | - Hyun-Dong Shin
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Young Ryun Chung
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Kon Ho Lee
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
- Department of Microbiology, School of Medicine, Gyeongsang National University, Jinju, Republic of Korea
- * E-mail: (SWK); (KHL)
| | - Seon-Won Kim
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
- * E-mail: (SWK); (KHL)
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Polysaccharide hydrolysis with engineered Escherichia coli for the production of biocommodities. ACTA ACUST UNITED AC 2013; 40:401-10. [DOI: 10.1007/s10295-013-1245-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 02/13/2013] [Indexed: 02/06/2023]
Abstract
Abstract
Escherichia coli can ferment a broad range of sugars, including pentoses, hexoses, uronic acids, and polyols. These features make E. coli a suitable microorganism for the development of biocatalysts to be used in the production of biocommodities and biofuels by metabolic engineering. E. coli cannot directly ferment polysaccharides because it does not produce and secrete the necessary saccharolytic enzymes; however, there are many genetic tools that can be used to confer this ability on this prokaryote. The construction of saccharolytic E. coli strains will reduce costs and simplify the production process because the saccharification and fermentation can be conducted in a single reactor with a reduced concentration or absence of additional external saccharolytic enzymes. Recent advances in metabolic engineering, surface display, and excretion of hydrolytic enzymes provide a framework for developing E. coli strains for the so-called consolidated bioprocessing. This review presents the different strategies toward the development of E. coli strains that have the ability to display and secrete saccharolytic enzymes to hydrolyze different sugar-polymeric substrates and reduce the loading of saccharolytic enzymes.
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Yang Y, Wu L, Lin Q, Yuan M, Xu D, Yu H, Hu Y, Duan J, Li X, He Z, Xue K, van Nostrand J, Wang S, Zhou J. Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland. GLOBAL CHANGE BIOLOGY 2013; 19:637-648. [PMID: 23504798 DOI: 10.1111/gcb.12065] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 10/11/2012] [Indexed: 06/01/2023]
Abstract
Microbes play key roles in various biogeochemical processes, including carbon (C) and nitrogen (N) cycling. However, changes of microbial community at the functional gene level by livestock grazing, which is a global land-use activity, remain unclear. Here we use a functional gene array, GeoChip 4.0, to examine the effects of free livestock grazing on the microbial community at an experimental site of Tibet, a region known to be very sensitive to anthropogenic perturbation and global warming. Our results showed that grazing changed microbial community functional structure, in addition to aboveground vegetation and soil geochemical properties. Further statistical tests showed that microbial community functional structures were closely correlated with environmental variables, and variations in microbial community functional structures were mainly controlled by aboveground vegetation, soil C/N ratio, and NH4 (+) -N. In-depth examination of N cycling genes showed that abundances of N mineralization and nitrification genes were increased at grazed sites, but denitrification and N-reduction genes were decreased, suggesting that functional potentials of relevant bioprocesses were changed. Meanwhile, abundances of genes involved in methane cycling, C fixation, and degradation were decreased, which might be caused by vegetation removal and hence decrease in litter accumulation at grazed sites. In contrast, abundances of virulence, stress, and antibiotics resistance genes were increased because of the presence of livestock. In conclusion, these results indicated that soil microbial community functional structure was very sensitive to the impact of livestock grazing and revealed microbial functional potentials in regulating soil N and C cycling, supporting the necessity to include microbial components in evaluating the consequence of land-use and/or climate changes.
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Affiliation(s)
- Yunfeng Yang
- School of Environment, Tsinghua University, Beijing, China.
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Processivity and enzymatic mode of a glycoside hydrolase family 5 endoglucanase from Volvariella volvacea. Appl Environ Microbiol 2012. [PMID: 23204424 DOI: 10.1128/aem.02725-12] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
EG1 is a modular glycoside hydrolase family 5 endoglucanase from Volvariella volvacea consisting of an N-terminal carbohydrate-binding module (CBM1) and a catalytic domain (CD). The ratios of soluble to insoluble reducing sugar produced from filter paper after 8 and 24 h of exposure to EG1 were 6.66 and 8.56, respectively, suggesting that it is a processive endoglucanase. Three derivatives of EG1 containing a core domain only or additional CBMs were constructed in order to evaluate the contribution of the CBM to the processivity and enzymatic mode of EG1 under stationary and agitated conditions. All four enzymatic forms exhibited the same mode of action on both soluble and insoluble cellulosic substrates with cellobiose as a main end product. An additional CBM fused at either the N or C terminus reduced specific activity toward soluble and insoluble celluloses under stationary reaction conditions. Deletion of the CBM significantly decreased enzyme processivity. Insertion of an additional CBM also resulted in a dramatic decrease in processivity in enzyme-substrate reaction mixtures incubated for 0.5 h, but this effect was reversed when reactions were allowed to proceed for longer periods (24 h). Further significant differences were observed in the substrate adsorption/desorption patterns of EG1 and enzyme derivatives equipped with an additional CBM under agitated reaction conditions. An additional family 1 CBM improved EG1 processivity on insoluble cellulose under highly agitated conditions. Our data indicate a strong link between high adsorption levels and low desorption levels in the processivity of EG1 and possibly other processive endoglucanses.
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Wang M, Si T, Zhao H. Biocatalyst development by directed evolution. BIORESOURCE TECHNOLOGY 2012; 115:117-25. [PMID: 22310212 PMCID: PMC3351540 DOI: 10.1016/j.biortech.2012.01.054] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 01/11/2012] [Accepted: 01/13/2012] [Indexed: 05/13/2023]
Abstract
Biocatalysis has emerged as a great addition to traditional chemical processes for production of bulk chemicals and pharmaceuticals. To overcome the limitations of naturally occurring enzymes, directed evolution has become the most important tool for improving critical traits of biocatalysts such as thermostability, activity, selectivity, and tolerance towards organic solvents for industrial applications. Recent advances in mutant library creation and high-throughput screening have greatly facilitated the engineering of novel and improved biocatalysts. This review provides an update of the recent developments in the use of directed evolution to engineer biocatalysts for practical applications.
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Affiliation(s)
- Meng Wang
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Tong Si
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Departments of Chemistry, Biochemistry, and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- To whom correspondence should be addressed. Phone: (217) 333-2631. Fax: (217) 333-5052.
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You C, Percival Zhang YH. Easy preparation of a large-size random gene mutagenesis library in Escherichia coli. Anal Biochem 2012; 428:7-12. [PMID: 22659340 DOI: 10.1016/j.ab.2012.05.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 05/21/2012] [Accepted: 05/22/2012] [Indexed: 11/17/2022]
Abstract
A simple and fast protocol for the preparation of a large-size mutant library for directed evolution in Escherichia coli was developed based on the DNA multimers generated by prolonged overlap extension polymerase chain reaction (POE-PCR). This protocol comprised the following: (i) a linear DNA mutant library was generated by error-prone PCR or shuffling, and a linear vector backbone was prepared by regular PCR; (ii) the DNA multimers were generated based on these two DNA templates by POE-PCR; and (iii) the one restriction enzyme-digested DNA multimers were ligated to circular plasmids, followed by transformation to E. coli. Because the ligation efficiency of one DNA fragment was several orders of magnitude higher than that of two DNA fragments for typical mutant library construction, it was very easy to generate a mutant library with a size of more than 10(7) protein mutants per 50 μl of the POE-PCR product. Via this method, four new fluorescent protein mutants were obtained based on monomeric cherry fluorescent protein. This new protocol was simple and fast because it did not require labor-intensive optimizations in restriction enzyme digestion and ligation, did not involve special plasmid design, and enabled constructing a large-size mutant library for directed enzyme evolution within 1 day.
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Affiliation(s)
- Chun You
- Biological Systems Engineering Department, Virginia Tech, Blacksburg, VA 24061, USA
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Mini-scaffoldin enhanced mini-cellulosome hydrolysis performance on low-accessibility cellulose (Avicel) more than on high-accessibility amorphous cellulose. Biochem Eng J 2012. [DOI: 10.1016/j.bej.2012.01.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Ye X, Zhang C, Zhang YHP. Engineering a large protein by combined rational and random approaches: stabilizing the Clostridium thermocellum cellobiose phosphorylase. MOLECULAR BIOSYSTEMS 2012; 8:1815-23. [DOI: 10.1039/c2mb05492b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Behrens GA, Hummel A, Padhi SK, Schätzle S, Bornscheuer UT. Discovery and Protein Engineering of Biocatalysts for Organic Synthesis. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100446] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Zhang YHP. Simpler Is Better: High-Yield and Potential Low-Cost Biofuels Production through Cell-Free Synthetic Pathway Biotransformation (SyPaB). ACS Catal 2011. [DOI: 10.1021/cs200218f] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Y.-H. Percival Zhang
- Biological Systems Engineering Department, Virginia Tech, 210-A Seitz Hall, Blacksburg, Virginia 24061, United States
- Institute for Critical Technology and Applied Science (ICTAS), Virginia Tech, Virginia 24061, United States
- DOE Bioenergy Science Center, Oak Ridge, Tennessee 37831, United States
- Gate Fuels Inc., 3107 Alice Dr., Blacksburg, Virginia 24060, United States
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One-step purification and immobilization of thermophilic polyphosphate glucokinase from Thermobifida fusca YX: glucose-6-phosphate generation without ATP. Appl Microbiol Biotechnol 2011; 93:1109-17. [PMID: 21766194 DOI: 10.1007/s00253-011-3458-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 06/17/2011] [Accepted: 06/19/2011] [Indexed: 10/18/2022]
Abstract
The discovery of stable and active polyphosphate glucokinase (PPGK, EC 2.7.1.63) would be vital to cascade enzyme biocatalysis that does not require a costly ATP input. An open reading frame Tfu_1811 from Thermobifida fusca YX encoding a putative PPGK was cloned and the recombinant protein fused with a family 3 cellulose-binding module (CBM-PPGK) was overexpressed in Escherichia coli. Mg²⁺ was an indispensible activator. This enzyme exhibited the highest activity in the presence of 4 mM Mg²⁺ at 55°C and pH 9.0. Under its suboptimal conditions (pH 7.5), the k (cat) and K(m) values of CBM-PPGK on glucose were 96.9 and 39.7 s⁻¹ as well as 0.77 and 0.45 mM at 37°C and 50°C respectively. The thermoinactivation of CBM-PPGK was independent of its mass concentration. Through one-step enzyme purification and immobilization on a high-capacity regenerated amorphous cellulose, immobilized CBM-PPGK had an approximately eightfold half lifetime enhancement (i.e., t(1/2) = 120 min) as compared to free enzyme at 50°C. To our limited knowledge, this enzyme was the first thermostable PPGK reported. Free PPGK and immobilized CBM-PPGK had total turnover number values of 126,000 and 961,000 mol product per mol enzyme, respectively, suggesting their great potential in glucose-6-phosphate generation based on low-cost polyphosphate.
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Zhang YHP. Substrate channeling and enzyme complexes for biotechnological applications. Biotechnol Adv 2011; 29:715-25. [PMID: 21672618 DOI: 10.1016/j.biotechadv.2011.05.020] [Citation(s) in RCA: 203] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 05/19/2011] [Accepted: 05/30/2011] [Indexed: 12/25/2022]
Abstract
Substrate channeling is a process of transferring the product of one enzyme to an adjacent cascade enzyme or cell without complete mixing with the bulk phase. Such phenomena can occur in vivo, in vitro, or ex vivo. Enzyme-enzyme or enzyme-cell complexes may be static or transient. In addition to enhanced reaction rates through substrate channeling in complexes, numerous potential benefits of such complexes are protection of unstable substrates, circumvention of unfavorable equilibrium and kinetics imposed, forestallment of substrate competition among different pathways, regulation of metabolic fluxes, mitigation of toxic metabolite inhibition, and so on. Here we review numerous examples of natural and synthetic complexes featuring substrate channeling. Constructing synthetic in vivo, in vitro or ex vivo complexes for substrate channeling would have great biotechnological potentials in metabolic engineering, multi-enzyme-mediated biocatalysis, and cell-free synthetic pathway biotransformation (SyPaB).
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Affiliation(s)
- Y-H Percival Zhang
- Biological Systems Engineering Department, 210-A Seitz Hall, Virginia Tech, Blacksburg, VA 24061, USA.
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47
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Fusion of a family 9 cellulose-binding module improves catalytic potential of Clostridium thermocellum cellodextrin phosphorylase on insoluble cellulose. Appl Microbiol Biotechnol 2011; 92:551-60. [DOI: 10.1007/s00253-011-3346-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 05/02/2011] [Accepted: 05/03/2011] [Indexed: 10/18/2022]
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48
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Cheng G, Liu Z, Murton JK, Jablin M, Dubey M, Majewski J, Halbert C, Browning J, Ankner J, Akgun B, Wang C, Esker AR, Sale KL, Simmons BA, Kent MS. Neutron Reflectometry and QCM-D Study of the Interaction of Cellulases with Films of Amorphous Cellulose. Biomacromolecules 2011; 12:2216-24. [DOI: 10.1021/bm200305u] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gang Cheng
- Joint BioEnergy Institute, Emeryville, California
- Sandia National Laboratories, Livermore, California and Albuquerque, New Mexico
| | - Zelin Liu
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
| | - Jaclyn K. Murton
- Sandia National Laboratories, Livermore, California and Albuquerque, New Mexico
| | - Michael Jablin
- Lujan Neutron Science Center, Los Alamos National Laboratories, Los Alamos, New Mexico
| | - Manish Dubey
- Lujan Neutron Science Center, Los Alamos National Laboratories, Los Alamos, New Mexico
| | - Jaroslaw Majewski
- Lujan Neutron Science Center, Los Alamos National Laboratories, Los Alamos, New Mexico
| | - Candice Halbert
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - James Browning
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - John Ankner
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Bulent Akgun
- National Institute of Standards and Technology, Gaithersburg, Maryland
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland
| | - Chao Wang
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
| | - Alan R. Esker
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
| | - Kenneth L. Sale
- Joint BioEnergy Institute, Emeryville, California
- Sandia National Laboratories, Livermore, California and Albuquerque, New Mexico
| | - Blake A. Simmons
- Joint BioEnergy Institute, Emeryville, California
- Sandia National Laboratories, Livermore, California and Albuquerque, New Mexico
| | - Michael S. Kent
- Joint BioEnergy Institute, Emeryville, California
- Sandia National Laboratories, Livermore, California and Albuquerque, New Mexico
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Zhang XZ, Sathitsuksanoh N, Zhu Z, Percival Zhang YH. One-step production of lactate from cellulose as the sole carbon source without any other organic nutrient by recombinant cellulolytic Bacillus subtilis. Metab Eng 2011; 13:364-72. [PMID: 21549854 DOI: 10.1016/j.ymben.2011.04.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 04/09/2011] [Accepted: 04/25/2011] [Indexed: 10/18/2022]
Abstract
Although intensive efforts have been made to create recombinant cellulolytic microorganisms, real recombinant cellulose-utilizing microorganisms that can produce sufficient secretory active cellulase, hydrolyze cellulose, and utilize released soluble sugars for supporting both cell growth and cellulase synthesis without any other organic nutrient (e.g., yeast extract, peptone, amino acids), are not available. Here we demonstrated that over-expression of Bacillus subtilis endoglucanase BsCel5 enabled B. subtilis to grow on solid cellulosic materials as the sole carbon source for the first time. Furthermore, two-round directed evolution was conducted to increase specific activity of BsCel5 on regenerated amorphous cellulose (RAC) and enhance its expression/secretion level in B. subtilis. To increase lactate yield, the alpha-acetolactate synthase gene (alsS) in the 2,3-butanediol pathway was knocked out. In the chemically defined minimal M9/RAC medium, B. subtilis XZ7(pBscel5-MT2C) strain (ΔalsS), which expressed a BsCel5 mutant MT2C, was able to hydrolyze RAC with cellulose digestibility of 74% and produced about 3.1g/L lactate with a yield of 60% of the theoretical maximum. When 0.1% (w/v) yeast extract was added in the M9/RAC medium, cellulose digestibility and lactate yield were enhanced to 92% and 63% of the theoretical maximum, respectively. The recombinant industrially safe cellulolytic B. subtilis would be a promising consolidated bioprocessing platform for low-cost production of biocommodities from cellulosic materials.
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Affiliation(s)
- Xiao-Zhou Zhang
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
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50
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Renewable Hydrogen Carrier — Carbohydrate: Constructing the Carbon-Neutral Carbohydrate Economy. ENERGIES 2011. [DOI: 10.3390/en4020254] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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