1
|
Zhao Y, Zhang B, Gu H, Xu T, Chen Q, Li J, Zhou P, Guan X, He L, Liang Y, Zhang K, Liu S, Shi K. A mutant GH3 family β-glucosidase from Oenococcus oeni exhibits superior adaptation to wine stresses and potential for improving wine aroma and phenolic profiles. Food Microbiol 2024; 119:104458. [PMID: 38225057 DOI: 10.1016/j.fm.2023.104458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/17/2024]
Abstract
In this study, we conducted a comprehensive investigation into a GH3 family β-glucosidase (BGL) from the wild-type strain of Oenococcus oeni and its mutated counterpart from the acid-tolerant mutant strain. Our analysis revealed the mutant BGL's remarkable capacity to adapt to wine-related stress conditions, including heightened tolerance to low pH, elevated ethanol concentrations, and metal ions. Additionally, the mutant BGL exhibited superior hydrolytic activity towards various substrates. Through de novo modeling, we identified specific amino acid mutations responsible for its resilience to low pH and high ethanol environments. In simulated wine conditions, the mutant BGL outperformed both wild-type and commercial BGLs, efficiently releasing terpene and phenolic aglycones from glycosides in wine grapes. These findings not only expand our understanding of O. oeni BGLs but also highlight their potential in enhancing wine production. The mutant BGL's enhanced adaptation to wine stress conditions opens promising avenue for improving wine quality and flavor.
Collapse
Affiliation(s)
- Yuzhu Zhao
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China
| | - Biying Zhang
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China
| | - Huawei Gu
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China
| | - Tongxin Xu
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiling Chen
- College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Jin Li
- COFCO GreatWall Wine, Penglai, Shandong, China
| | | | - Xueqiang Guan
- Shandong Academy of Grape / Shandong Technology Innovation Center of Wine Grape and Wine, Jinan, Shandong, China
| | - Ling He
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanying Liang
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China
| | - Kekun Zhang
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuwen Liu
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China.
| | - Kan Shi
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China.
| |
Collapse
|
2
|
Hasan WANBW, Nezhad NG, Yaacob MA, Salleh AB, Rahman RNZRA, Leow TC. Shifting the pH profiles of Staphylococcus epidermidis lipase (SEL) and Staphylococcus hyicus lipase (SHL) through generating chimeric lipases by DNA shuffling strategy. World J Microbiol Biotechnol 2024; 40:106. [PMID: 38386107 DOI: 10.1007/s11274-024-03927-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Enzymes are often required to function in a particular reaction condition by the industrial procedure. In order to identify critical residues affecting the optimum pH of Staphylococcal lipases, chimeric lipases from homologous lipases were generated via a DNA shuffling strategy. Chimeric 1 included mutations of G166S, K212E, T243A, H271Y. Chimeric 2 consisted of substitutions of K212E, T243A, H271Y. Chimeric 3 contained substitutions of K212E, R359L. From the screening results, the pH profiles for chimeric 1 and 2 lipases were shifted from pH 7 to 6. While the pH of chimeric 3 was shifted to 8. It seems the mutation of K212E in chimeric 1 and 2 decreased the pH to 6 by changing the electrostatic potential surface. Furthermore, chimeric 3 showed 10 ˚C improvement in the optimum temperature due to the rigidification of the catalytic loop through the hydrophobic interaction network. Moreover, the substrate specificity of chimeric 1 and 2 was increased towards the longer carbon length chains due to the mutation of T243A adjacent to the lid region through increasing the flexibility of the lid. Current study illustrated that directed evolution successfully modified lipase properties including optimum pH, temperature and substrate specificity through mutations, especially near catalytic and lid regions.
Collapse
Affiliation(s)
- Wan Atiqah Najiah Binti Wan Hasan
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Mohd Adilin Yaacob
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Abu Bakar Salleh
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abdul Rahman
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia.
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia.
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia.
| |
Collapse
|
3
|
Fernández-López MG, Batista-García RA, Aréchiga-Carvajal ET. Alkaliphilic/Alkali-Tolerant Fungi: Molecular, Biochemical, and Biotechnological Aspects. J Fungi (Basel) 2023; 9:652. [PMID: 37367588 DOI: 10.3390/jof9060652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 06/28/2023] Open
Abstract
Biotechnologist interest in extremophile microorganisms has increased in recent years. Alkaliphilic and alkali-tolerant fungi that resist alkaline pH are among these. Alkaline environments, both terrestrial and aquatic, can be created by nature or by human activities. Aspergillus nidulans and Saccharomyces cerevisiae are the two eukaryotic organisms whose pH-dependent gene regulation has received the most study. In both biological models, the PacC transcription factor activates the Pal/Rim pathway through two successive proteolytic mechanisms. PacC is a repressor of acid-expressed genes and an activator of alkaline-expressed genes when it is in an active state. It appears, however, that these are not the only mechanisms associated with pH adaptations in alkali-tolerant fungi. These fungi produce enzymes that are resistant to harsh conditions, i.e., alkaline pH, and can be used in technological processes, such as in the textile, paper, detergent, food, pharmaceutical, and leather tanning industries, as well as in bioremediation of pollutants. Consequently, it is essential to understand how these fungi maintain intracellular homeostasis and the signaling pathways that activate the physiological mechanisms of alkali resistance in fungi.
Collapse
Affiliation(s)
- Maikel Gilberto Fernández-López
- Unidad de Manipulación Genética, Laboratorio de Micología y Fitopatología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66451, Mexico
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
| | - Elva Teresa Aréchiga-Carvajal
- Unidad de Manipulación Genética, Laboratorio de Micología y Fitopatología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66451, Mexico
| |
Collapse
|
4
|
Gomes M, Rondelez Y, Leibler L. Lessons from Biomass Valorization for Improving Plastic-Recycling Enzymes. Annu Rev Chem Biomol Eng 2022; 13:457-479. [PMID: 35378043 DOI: 10.1146/annurev-chembioeng-092120-091054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Synthetic polymers such as plastics exhibit numerous advantageous properties that have made them essential components of our daily lives, with plastic production doubling every 15 years. The relatively low cost of petroleum-based polymers encourages their single use and overconsumption. Synthetic plastics are recalcitrant to biodegradation, and mismanagement of plastic waste leads to their accumulation in the ecosystem, resulting in a disastrous environmental footprint. Enzymes capable of depolymerizing plastics have been reported recently that may provide a starting point for eco-friendly plastic recycling routes. However, some questions remain about the mechanisms by which enzymes can digest insoluble solid substrates. We review the characterization and engineering of plastic-eating enzymes and provide some comparisons with the field of lignocellulosic biomass valorization. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Margarida Gomes
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
| | - Yannick Rondelez
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
| | - Ludwik Leibler
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
| |
Collapse
|
5
|
Enhanced acidic resistance ability and catalytic properties of Bacillus 1,3-1,4-β-glucanases by sequence alignment and surface charge engineering. Int J Biol Macromol 2021; 192:426-434. [PMID: 34627850 DOI: 10.1016/j.ijbiomac.2021.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/13/2021] [Accepted: 10/02/2021] [Indexed: 11/24/2022]
Abstract
High stability at acidic environment is required for 1,3-1,4-β-glucanase to function in biofuel, brewing and animal feed industries. In this study, a mesophilic β-glucanase from Bacillus terquilensis CGX 5-1 was rationally engineered through sequence alignment and surface charge engineering to improve its acidic resistance ability. Nineteen singly-site variants were constructed and Q1E, I133L and V134A variants showed better acidic stability without the compromise of catalytic property and thermostability. Furthermore, four multi-site variants were constructed and one double-site variant Q1E/I133L with better stability at acidic environment and higher catalytic property was obtained. The fluorescence spectroscopy and structural analysis showed that more surface negative charge, decreased exposure degree of residue No.1, shifted side chain direction of residue No.133 and the lower total and folding free energy might be the reason for the improvement of acidic stability of Q1E/I133L variant. The obtained Q1E/I133L variant has potential applications in industries.
Collapse
|
6
|
Sinitsyn AP, Sinitsyna OA. Bioconversion of Renewable Plant Biomass. Second-Generation Biofuels: Raw Materials, Biomass Pretreatment, Enzymes, Processes, and Cost Analysis. BIOCHEMISTRY (MOSCOW) 2021; 86:S166-S195. [PMID: 33827407 DOI: 10.1134/s0006297921140121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review discusses various aspects of renewable plant biomass conversion and production of the second-generation biofuels, including the types of plant biomass, its composition and reaction ability in the enzymatic hydrolysis, and various pretreatment methods for increasing the biomass reactivity. Conversion of plant biomass into sugars requires the use of a complex of enzymes, the composition of which should be adapted to the biomass type and the pretreatment method. The efficiency of enzymatic hydrolysis can be increased by optimizing the composition of the enzymatic complex and by increasing the catalytic activity and operational stability of its constituent enzymes. The availability of active enzyme producers also plays an important role. Examples of practical implementation and scaling of processes for the production of second-generation biofuels are presented together with the cost analysis of bioethanol production.
Collapse
Affiliation(s)
- Arkadij P Sinitsyn
- Bakh Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia. .,Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Olga A Sinitsyna
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| |
Collapse
|
7
|
Ecological Genomics and Evolution of Trichoderma reesei. Methods Mol Biol 2021; 2234:1-21. [PMID: 33165775 DOI: 10.1007/978-1-0716-1048-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) is an efficient industrial cell factory for the production of cellulolytic enzymes used for biofuel and other applications. Therefore, researches addressing T. reesei are relatively advanced compared to other Trichoderma spp. because of the significant bulk of available knowledge, multiple genomic data, and gene manipulation techniques. However, the established role of T. reesei in industry has resulted in a frequently biased understanding of the biology of this fungus. Thus, the recent studies unexpectedly show that the superior cellulolytic activity of T. reesei and other Trichoderma species evolved due to multiple lateral gene transfer events, while the innate ability to parasitize other fungi (mycoparasitism) was maintained in the genus, including T. reesei. In this chapter, we will follow the concept of ecological genomics and describe the ecology, distribution, and evolution of T. reesei, as well as critically discuss several common misconceptions that originate from the success of this species in applied sciences and industry.
Collapse
|
8
|
Chettri D, Verma AK, Verma AK. Innovations in CAZyme gene diversity and its modification for biorefinery applications. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 28:e00525. [PMID: 32963975 PMCID: PMC7490808 DOI: 10.1016/j.btre.2020.e00525] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/04/2020] [Accepted: 08/30/2020] [Indexed: 02/07/2023]
Abstract
For sustainable growth, concept of biorefineries as recourse to the "fossil derived" energy source is important. Here, the Carbohydrate Active enZymes (CAZymes) play decisive role in generation of biofuels and related sugar-based products utilizing lignocellulose as a carbon source. Given their industrial significance, extensive studies on the evolution of CAZymes have been carried out. Various bacterial and fungal organisms have been scrutinized for the development of CAZymes, where advance techniques for strain enhancement such as CRISPR and analysis of specific expression systems have been deployed. Specific Omic-based techniques along with protein engineering have been adopted to unearth novel CAZymes and improve applicability of existing enzymes. In-Silico computational research and functional annotation of new CAZymes to synergy experiments are being carried out to devise cocktails of enzymes for use in biorefineries. Thus, with the establishment of these technologies, increased diversity of CAZymes with broad span of functions and applications is seen.
Collapse
|
9
|
Molecular engineering to improve lignocellulosic biomass based applications using filamentous fungi. ADVANCES IN APPLIED MICROBIOLOGY 2020; 114:73-109. [PMID: 33934853 DOI: 10.1016/bs.aambs.2020.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Lignocellulosic biomass is an abundant and renewable resource, and its utilization has become the focus of research and biotechnology applications as a very promising raw material for the production of value-added compounds. Filamentous fungi play an important role in the production of various lignocellulolytic enzymes, while some of them have also been used for the production of important metabolites. However, wild type strains have limited efficiency in enzyme production or metabolic conversion, and therefore many efforts have been made to engineer improved strains. Examples of this are the manipulation of transcriptional regulators and/or promoters of enzyme-encoding genes to increase gene expression, and protein engineering to improve the biochemical characteristics of specific enzymes. This review provides and overview of the applications of filamentous fungi in lignocellulosic biomass based processes and the development and current status of various molecular engineering strategies to improve these processes.
Collapse
|
10
|
Basit A, Tajwar R, Sadaf S, Zhang Y, Akhtar MW. Improvement in activity of cellulase Cel12A of Thermotoga neapolitana by error prone PCR. J Biotechnol 2019; 306:118-124. [DOI: 10.1016/j.jbiotec.2019.09.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 11/15/2022]
|
11
|
Tuning the pH profile of β-glucuronidase by rational site-directed mutagenesis for efficient transformation of glycyrrhizin. Appl Microbiol Biotechnol 2019; 103:4813-4823. [PMID: 31055652 DOI: 10.1007/s00253-019-09790-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/16/2019] [Accepted: 03/20/2019] [Indexed: 02/05/2023]
Abstract
In this study, we aimed to shift the optimal pH of acidic β-glucuronidase from Aspergillus oryzae Li-3 (PGUS) to the neutral region by site-directed mutagenesis, thus allowing high efficient biotransformation of glycyrrhizin (GL) into glycyrrhetinic acid (GA) under higher pH where the solubility of GL could be greatly enhanced. Based on PGUS structure analysis, five critical aspartic acid and glutamic acid residues were replaced with arginine on the surface to generate a variant 5Rs with optimal pH shifting from 4.5 to 6.5. The catalytic efficiency (kcat /Km) value of 5Rs at pH 6.5 was 10.7-fold higher than that of PGUS wild-type at pH 6.5, even 1.4-fold higher than that of wild-type at pH 4.5. Molecular dynamics simulation was performed to explore the molecular mechanism for the shifted pH profile and enhanced pH stability of 5Rs.
Collapse
|
12
|
de Paula RG, Antoniêto ACC, Ribeiro LFC, Srivastava N, O'Donovan A, Mishra PK, Gupta VK, Silva RN. Engineered microbial host selection for value-added bioproducts from lignocellulose. Biotechnol Adv 2019; 37:107347. [PMID: 30771467 DOI: 10.1016/j.biotechadv.2019.02.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/27/2019] [Accepted: 02/08/2019] [Indexed: 12/12/2022]
Abstract
Lignocellulose is a rich and sustainable globally available carbon source and is considered a prominent alternative raw material for producing biofuels and valuable chemical compounds. Enzymatic hydrolysis is one of the crucial steps of lignocellulose degradation. Cellulolytic and hemicellulolytic enzyme mixes produced by different microorganisms including filamentous fungi, yeasts and bacteria, are used to degrade the biomass to liberate monosaccharides and other compounds for fermentation or conversion to value-added products. During biomass pretreatment and degradation, toxic compounds are produced, and undesirable carbon catabolic repression (CCR) can occur. In order to solve this problem, microbial metabolic pathways and transcription factors involved have been investigated along with the application of protein engineering to optimize the biorefinery platform. Engineered Microorganisms have been used to produce specific enzymes to breakdown biomass polymers and metabolize sugars to produce ethanol as well other biochemical compounds. Protein engineering strategies have been used for modifying lignocellulolytic enzymes to overcome enzymatic limitations and improving both their production and functionality. Furthermore, promoters and transcription factors, which are key proteins in this process, are modified to promote microbial gene expression that allows a maximum performance of the hydrolytic enzymes for lignocellulosic degradation. The present review will present a critical discussion and highlight the aspects of the use of microorganisms to convert lignocellulose into value-added bioproduct as well combat the bottlenecks to make the biorefinery platform from lignocellulose attractive to the market.
Collapse
Affiliation(s)
- Renato Graciano de Paula
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Liliane Fraga Costa Ribeiro
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Neha Srivastava
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, U.P, India
| | - Anthonia O'Donovan
- School of Science and Computing, Galway-Mayo Institute of Technology, Galway, Ireland
| | - P K Mishra
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, U.P, India
| | - Vijai K Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia.
| | - Roberto N Silva
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
| |
Collapse
|
13
|
Kwan DH. Structure-Guided Directed Evolution of Glycosidases: A Case Study in Engineering a Blood Group Antigen-Cleaving Enzyme. Methods Enzymol 2018; 597:25-53. [PMID: 28935105 DOI: 10.1016/bs.mie.2017.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Directed evolution is an incredibly powerful strategy for engineering enzyme function. Applying this approach to glycosidases offers enormous potential for the development of highly specialized tools in chemical glycobiology. Performing enzyme directed evolution requires the generation, by random mutagenesis, of mutant libraries from which large numbers of variant enzymes must be screened in high-throughput assays. A structure-guided "semirational" method for library creation allows researchers to target specific amino acid positions for mutagenesis, concentrating mutations where they might be most effective in order to produce mutant libraries of a manageable size, minimizing screening effort while maximizing the chances of finding improved mutants. Well-designed assays, which may use specially prepared substrates, enable efficient screening of these mutant libraries. This chapter will detail general methods in the structure-guided directed evolution of glycosidases, which have previously been employed in engineering a blood group antigen-cleaving enzyme.
Collapse
Affiliation(s)
- David H Kwan
- Centre for Applied Synthetic Biology, Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec, Canada.
| |
Collapse
|
14
|
Wei Y, Zhang SH. Abiostress resistance and cellulose degradation abilities of haloalkaliphilic fungi: applications for saline-alkaline remediation. Extremophiles 2017; 22:155-164. [PMID: 29290045 DOI: 10.1007/s00792-017-0986-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 12/08/2017] [Indexed: 01/02/2023]
Abstract
Soda saline-alkaline lands are significantly harmful to agriculture; thus, effective strategies to remediate such soil are urgently needed. Multiple negative factors exist in the community structure of saline-alkaline fields, among which the lack of fungal species diversity remains the most prominent problem. The haloalkaliphilic fungi are a unique group of extremophiles that grow optimally under conditions of extreme salinity and alkalinity; these fungi, which buffer salinity and alkalinity by absorbing and/or constraining salt ions, produce organic acids and/or macromolecules, secrete macromolecules such as cellulose degradation enzymes, and provide biomass that is beneficial for soil health. Considering that haloalkaliphilic fungi are a valuable genetic resource of resistance and degradation genes, these fungi are expected to be applied in biotechnology. Aspergillus glaucus exhibits high resistance to a variety of stressors and the ability to degrade crop straw; and it is a practical genetic tool that can be used to identify and validate genes involved in abiotic stress resistance and cellulose decomposition genes. This review will focus on the following aspects: isolation of extreme haloalkaliphilic fungi, fungal genes involved in salt and alkalinity resistance, macromolecule degrading enzymes, applications for genetic improvement of haloalkaliphilic fungi, and application of haloalkaliphilic fungi in saline-alkali soil mycoremediation.
Collapse
Affiliation(s)
- Yi Wei
- College of Plant Sciences, Jilin University, Changchun, 130062, People's Republic of China
| | - Shi-Hong Zhang
- College of Plant Sciences, Jilin University, Changchun, 130062, People's Republic of China.
| |
Collapse
|
15
|
Ben Hmad I, Gargouri A. Neutral and alkaline cellulases: Production, engineering, and applications. J Basic Microbiol 2017; 57:653-658. [PMID: 28503798 DOI: 10.1002/jobm.201700111] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 01/08/2023]
Abstract
Neutral and alkaline cellulases from microorganisms constitute a major group of the industrial enzymes and find applications in various industries. Screening is the important ways to get novel cellulases. Most fungal cellulases have acidic pH optima, except some fungi like Humicola insolens species. However, new applications require the use of neutral and alkaline cellulases in food, brewery and wine, animal feed, textile and laundry, pulp and paper industries, agriculture as well in scientific research purposes. Indeed, the demand for these enzymes is growing more rapidly than ever before, and becomes the driving force for research on engineering the cellulolytic enzymes. Here, we present an overview of the biotechnological research for neutral and alkaline cellulases.
Collapse
Affiliation(s)
- Ines Ben Hmad
- Laboratory of Molecular Biology of Eukaryotes, Centre of Biotechnology of Sfax CBS/University of Sfax, Sfax, Tunisia
| | - Ali Gargouri
- Laboratory of Molecular Biology of Eukaryotes, Centre of Biotechnology of Sfax CBS/University of Sfax, Sfax, Tunisia
| |
Collapse
|
16
|
Applications of Haloalkaliphilic Fungi in Mycoremediation of Saline-Alkali Soil. Fungal Biol 2017. [DOI: 10.1007/978-3-319-68957-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
17
|
Mao S, Gao P, Lu Z, Lu F, Zhang C, Zhao H, Bie X. Engineering of a thermostable β-1,3-1,4-glucanase from Bacillus altitudinis YC-9 to improve its catalytic efficiency. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:109-115. [PMID: 25546703 DOI: 10.1002/jsfa.7066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 12/21/2014] [Accepted: 12/21/2014] [Indexed: 06/04/2023]
Abstract
BACKGROUND Error-prone polymerase chain reaction (PCR) is frequently used in directed evolution of enzymes to modify their quality. In this study, error-prone PCR was used to improve the catalytic efficiency of β-1,3-1,4-glucanase from Bacillus altitudinis YC-9. RESULTS By screening, the mutant Glu-3060 with higher activity was selected among 5000 transformants. After induction with isopropyl β-D-1-thiogalactopyranoside (IPTG), the activity of the mutant Glu-3060 reached 474.6 U mL(-1), resulting in a 48.6% increment of the parent enzyme activity. Research on the characterization of the mutated enzyme showed the optimal pH of the mutated enzyme to be 5.0, which is lower than the parent enzyme, but thermal stability was almost the same between them. Sequence analysis of the mutated enzyme revealed that three amino acids were changed compared with the parent enzyme, including K142N, Q203L and N214D. CONCLUSION The three-dimensional structure predicted by SWISS-MODEL of the mutated enzyme Glu-3060 showed that the substitution of three amino acids had an effect on the catalytic activity, stability and optimal pH of the enzyme, through changing the charge properties or electron density, forming secondary keys, the acidity of the amino acids and the side chain group. The sum effects of all the factors were increased activity of the mutated enzyme and decreased optimal pH, while the same thermostability was maintained, thereby increasing the suitability of the enzyme for industrial use.
Collapse
Affiliation(s)
- Shurui Mao
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, Nanjing 210095, People's Republic of China
- China Tobacco Jiangsu Industrial Co., Ltd., Nanjing 210000, People's Republic of China
| | - Peng Gao
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, Nanjing 210095, People's Republic of China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, Nanjing 210095, People's Republic of China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, Nanjing 210095, People's Republic of China
| | - Chong Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, Nanjing 210095, People's Republic of China
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, Nanjing 210095, People's Republic of China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, Nanjing 210095, People's Republic of China
| |
Collapse
|
18
|
Guan W, Shi S, Tu M, Lee YY. Acetone-butanol-ethanol production from Kraft paper mill sludge by simultaneous saccharification and fermentation. BIORESOURCE TECHNOLOGY 2016; 200:713-721. [PMID: 26562687 DOI: 10.1016/j.biortech.2015.10.102] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/30/2015] [Accepted: 10/31/2015] [Indexed: 06/05/2023]
Abstract
Paper mill sludge (PS), a solid waste from pulp and paper industry, was investigated as a feedstock for acetone-butanol-ethanol (ABE) production by simultaneous saccharification and fermentation (SSF). ABE fermentation of paper sludge by Clostridium acetobutylicum required partial removal of ash in PS to enhance its enzymatic digestibility. Enzymatic hydrolysis was found to be a rate-limiting step in the SSF. A total of 16.4-18.0g/L of ABE solvents were produced in the SSF of de-ashed PS with solid loading of 6.3-7.4% and enzyme loading of 10-15FPU/g-glucan, and the final solvent yield reached 0.27g/g sugars. No pretreatment and pH control were needed in ABE fermentation of paper sludge, which makes it an attractive feedstock for butanol production. The results suggested utilization of paper sludge should not only consider the benefits of buffering effect of CaCO3 in fermentation, but also take into account its inhibitory effect on enzymatic hydrolysis.
Collapse
Affiliation(s)
- Wenjian Guan
- Department of Chemical Engineering, Auburn University, 212 Ross Hall, Auburn, AL 36849, United States
| | - Suan Shi
- Department of Chemical Engineering, Auburn University, 212 Ross Hall, Auburn, AL 36849, United States
| | - Maobing Tu
- Department of Biomedical, Chemical and Environmental Engineering, University of Cincinnati, 2901 Woodside Drive, Cincinnati, OH 45221, United States; Forest Products Laboratory and Center for Bioenergy and Bioproducts, Auburn University, 520 Devall Drive, Auburn, AL 36849, United States.
| | - Yoon Y Lee
- Department of Chemical Engineering, Auburn University, 212 Ross Hall, Auburn, AL 36849, United States
| |
Collapse
|
19
|
Larue K, Melgar M, Martin VJJ. Directed evolution of a fungal β-glucosidase in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:52. [PMID: 26949413 PMCID: PMC4778352 DOI: 10.1186/s13068-016-0470-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/22/2016] [Indexed: 05/13/2023]
Abstract
BACKGROUND β-glucosidases (BGLs) catalyze the hydrolysis of soluble cellodextrins to glucose and are a critical component of cellulase systems. In order to engineer Saccharomyces cerevisiae for the production of ethanol from cellulosic biomass, a BGL tailored to industrial bioconversions is needed. RESULTS We applied a directed evolution strategy to a glycosyl hydrolase family 3 (GH3) BGL from Aspergillus niger (BGL1) by expressing a library of mutated bgl1 genes in S. cerevisiae and used a two-step functional screen to identify improved enzymes. Twelve BGL variants that supported growth of S. cerevisiae on cellobiose and showed increased activity on the synthetic substrate p-nitrophenyl-β-D-glucopyranoside were identified and characterized. By performing kinetic experiments, we found that a Tyr → Cys substitution at position 305 of BGL1 dramatically reduced transglycosidation activity that causes inhibition of the hydrolytic reaction at high substrate concentrations. Targeted mutagenesis demonstrated that the position 305 residue is critical in GH3 BGLs and likely determines the extent to which transglycosidation reactions occur. We also found that a substitution at Gln(140) reduced the inhibitory effect of glucose and could be combined with the Y305C substitution to produce a BGL with decreased sensitivity to both the product and substrate. Using the crystal structure of a GH3 BGL from A. aculeatus, we mapped a group of beneficial mutations to the β/α domain of the molecule and postulate that this region modulates activity through subunit interactions. Six BGL variants were identified with substitutions in the MFα pre-sequence that was used to mediate secretion of the protein. Substitutions at Pro(21) or Val(22) of the MFα pre-sequence could produce up to a twofold increase in supernatant hydrolase activity and provides evidence that expression and/or secretion was an additional factor limiting hydrolytic activity. CONCLUSIONS Using directed evolution on BGL1, we identified a key residue that controls hydrolytic and transglycosidation reactions in GH3 BGLs. We also found that several beneficial mutations could be combined and increased the hydrolytic activity for both synthetic and natural substrates.
Collapse
Affiliation(s)
- Kane Larue
- Department of Biology, Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke West, Montreal, QC H4B 1R6 Canada
| | - Mindy Melgar
- Department of Biology, Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke West, Montreal, QC H4B 1R6 Canada
| | - Vincent J. J. Martin
- Department of Biology, Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke West, Montreal, QC H4B 1R6 Canada
| |
Collapse
|
20
|
Hansen GH, Lübeck M, Frisvad JC, Lübeck PS, Andersen B. Production of cellulolytic enzymes from ascomycetes: Comparison of solid state and submerged fermentation. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.05.017] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
21
|
Expression of Heterologous Cellulases in Thermotoga sp. Strain RQ2. BIOMED RESEARCH INTERNATIONAL 2015; 2015:304523. [PMID: 26273605 PMCID: PMC4529897 DOI: 10.1155/2015/304523] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 01/21/2015] [Accepted: 02/06/2015] [Indexed: 11/18/2022]
Abstract
The ability of Thermotoga spp. to degrade cellulose is limited due to a lack of exoglucanases. To address this deficiency, cellulase genes Csac_1076 (celA) and Csac_1078 (celB) from Caldicellulosiruptor saccharolyticus were cloned into T. sp. strain RQ2 for heterologous overexpression. Coding regions of Csac_1076 and Csac_1078 were fused to the signal peptide of TM1840 (amyA) and TM0070 (xynB), resulting in three chimeric enzymes, namely, TM1840-Csac_1078, TM0070-Csac_1078, and TM0070-Csac_1076, which were carried by Thermotoga-E. coli shuttle vectors pHX02, pHX04, and pHX07, respectively. All three recombinant enzymes were successfully expressed in E. coli DH5α and T. sp. strain RQ2, rendering the hosts with increased endo- and/or exoglucanase activities. In E. coli, the recombinant enzymes were mainly bound to the bacterial cells, whereas in T. sp. strain RQ2, about half of the enzyme activities were observed in the culture supernatants. However, the cellulase activities were lost in T. sp. strain RQ2 after three consecutive transfers. Nevertheless, this is the first time heterologous genes bigger than 1 kb (up to 5.3 kb in this study) have ever been expressed in Thermotoga, demonstrating the feasibility of using engineered Thermotoga spp. for efficient cellulose utilization.
Collapse
|
22
|
Flannelly DF, Aoki TG, Aristilde L. Short-time dynamics of pH-dependent conformation and substrate binding in the active site of beta-glucosidases: A computational study. J Struct Biol 2015; 191:352-64. [PMID: 26160737 DOI: 10.1016/j.jsb.2015.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 06/17/2015] [Accepted: 07/03/2015] [Indexed: 12/25/2022]
Abstract
The complete degradation of cellulose to glucose is essential to carbon turnover in terrestrial ecosystems and to engineered biofuel production. A rate-limiting step in this pathway is catalyzed by beta-glucosidase (BG) enzymes, which convert cellulobiose into two glucose molecules. The activity of these enzymes has been shown to vary with solution pH. However, it is not well understood how pH influences the enzyme conformation required for catalytic action on the substrate. A structural understanding of this pH effect is important for predicting shifts in BG activity in bioreactors and environmental matrices, in addition to informing targeted protein engineering. Here we applied molecular dynamics simulations to explore conformational and substrate binding dynamics in two well-characterized BGs of bacterial (Clostridium cellulovorans) and fungal (Trichoderma reesei) origins as a function of pH. The enzymes were simulated in an explicit solvated environment, with NaCl as electrolytes, at their prominent ionization states obtained at pH 5, 6, 7, and 7.5. Our findings indicated that pH-dependent changes in the ionization states of non-catalytic residues localized outside of the immediate active site led to pH-dependent disruption of the active site conformation. This disruption interferes with favorable H-bonding interactions with catalytic residues required to initiate catalysis on the substrate. We also identified specific non-catalytic residues that are involved in stabilizing the substrate at the optimal pH for enzyme activity. The simulations further revealed the dynamics of water-bridging interactions both outside and inside the substrate binding cleft during structural changes in the enzyme-substrate complex. These findings provide new structural insights into the pH-dependent substrate binding specificity in BGs.
Collapse
Affiliation(s)
- David F Flannelly
- The Institute for Comparative and Environmental Toxicology, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Thalia G Aoki
- Department of Biological and Environmental Engineering, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Ludmilla Aristilde
- The Institute for Comparative and Environmental Toxicology, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, USA; Department of Biological and Environmental Engineering, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
23
|
Pei H, Guo X, Yang W, Lv J, Chen Y, Cao Y. Directed evolution of a β-1,3-1,4-glucanase fromBacillus subtilisMA139 for improving thermal stability and other characteristics. J Basic Microbiol 2015; 55:869-78. [DOI: 10.1002/jobm.201400664] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 02/22/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Honglei Pei
- National Key Laboratory of Animal Nutrition; China Agricultural University; Beijing PR China
| | - Xiaojing Guo
- National Key Laboratory of Animal Nutrition; China Agricultural University; Beijing PR China
| | - Wenhan Yang
- National Key Laboratory of Animal Nutrition; China Agricultural University; Beijing PR China
| | - Junnan Lv
- National Key Laboratory of Animal Nutrition; China Agricultural University; Beijing PR China
| | - Yiqun Chen
- National Key Laboratory of Animal Nutrition; China Agricultural University; Beijing PR China
| | - Yunhe Cao
- National Key Laboratory of Animal Nutrition; China Agricultural University; Beijing PR China
| |
Collapse
|
24
|
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
| |
Collapse
|
25
|
Malinowska KH, Verdorfer T, Meinhold A, Milles LF, Funk V, Gaub HE, Nash MA. Redox-initiated hydrogel system for detection and real-time imaging of cellulolytic enzyme activity. CHEMSUSCHEM 2014; 7:2825-2831. [PMID: 25116339 DOI: 10.1002/cssc.201402428] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/12/2014] [Indexed: 06/03/2023]
Abstract
Understanding the process of biomass degradation by cellulolytic enzymes is of urgent importance for biofuel and chemical production. Optimizing pretreatment conditions and improving enzyme formulations both require assays to quantify saccharification products on solid substrates. Typically, such assays are performed using freely diffusing fluorophores or dyes that measure reducing polysaccharide chain ends. These methods have thus far not allowed spatial localization of hydrolysis activity to specific substrate locations with identifiable morphological features. Here we describe a hydrogel reagent signaling (HyReS) system that amplifies saccharification products and initiates crosslinking of a hydrogel that localizes to locations of cellulose hydrolysis, allowing for imaging of the degradation process in real time. Optical detection of the gel in a rapid parallel format on synthetic and natural pretreated solid substrates was used to quantify activity of T. emersonii and T. reesei enzyme cocktails. When combined with total internal reflection fluorescence microscopy and AFM imaging, the reagent system provided a means to visualize enzyme activity in real-time with high spatial resolution (<2 μm). These results demonstrate the versatility of the HyReS system in detecting cellulolytic enzyme activity and suggest new opportunities in real-time chemical imaging of biomass depolymerization.
Collapse
Affiliation(s)
- Klara H Malinowska
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, Amalienstrasse 54, 80799 Munich (Germany)
| | | | | | | | | | | | | |
Collapse
|
26
|
Tang B, Zhang Y, Yang Y, Song Z, Li X. Expression and functional analysis of a glycoside hydrolase family 45 endoglucanase from Rhizopus stolonifer. World J Microbiol Biotechnol 2014; 30:2943-52. [PMID: 25164957 DOI: 10.1007/s11274-014-1722-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 08/11/2014] [Indexed: 11/29/2022]
Abstract
A novel endoglucanase gene was cloned from Rhizopus stolonifer and expressed in Escherichia coli, the gene product EG II (45 kDa) was assigned to Glycoside Hydrolase Family 45 (GH45), and its specific activity on phosphoric acid-swollen cellulose (PASC) was 48 IU/mg. To solve the problem of substrate accumulation in the cellulose hydrolysis and enhance the catalytic efficiency of endoglucanase, the eg2 gene was modified by site directed mutagenesis. Mutations generated by overlapping PCR have been proven to increase its catalytic activity on carboxymenthyl cellulose, microcrystalline cellulose (Avicel) and PASC, among which the mutant EG II-E containing all 6 mutations (N39S, V136D, T251G, D255G, P256S and E260D) peaked 121 IU/mg on PASC. The bioinformatic analysis showed that 2 key catalytic residues (D136 and D260) moved closer with the opening of a loop after mutagenesis, and a tunnel was formed by structural transformation. This structure was conducive for the substrate to access the active centre, and D136 played an indispensable role in the substrate recognition.
Collapse
Affiliation(s)
- Bin Tang
- College of Biochemical Engineering, Anhui Polytechnic University, Wuhu, 241000, China,
| | | | | | | | | |
Collapse
|
27
|
Suplatov D, Panin N, Kirilin E, Shcherbakova T, Kudryavtsev P, Svedas V. Computational design of a pH stable enzyme: understanding molecular mechanism of penicillin acylase's adaptation to alkaline conditions. PLoS One 2014; 9:e100643. [PMID: 24959852 PMCID: PMC4069103 DOI: 10.1371/journal.pone.0100643] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 05/29/2014] [Indexed: 01/12/2023] Open
Abstract
Protein stability provides advantageous development of novel properties and can be crucial in affording tolerance to mutations that introduce functionally preferential phenotypes. Consequently, understanding the determining factors for protein stability is important for the study of structure-function relationship and design of novel protein functions. Thermal stability has been extensively studied in connection with practical application of biocatalysts. However, little work has been done to explore the mechanism of pH-dependent inactivation. In this study, bioinformatic analysis of the Ntn-hydrolase superfamily was performed to identify functionally important subfamily-specific positions in protein structures. Furthermore, the involvement of these positions in pH-induced inactivation was studied. The conformational mobility of penicillin acylase in Escherichia coli was analyzed through molecular modeling in neutral and alkaline conditions. Two functionally important subfamily-specific residues, Gluβ482 and Aspβ484, were found. Ionization of these residues at alkaline pH promoted the collapse of a buried network of stabilizing interactions that consequently disrupted the functional protein conformation. The subfamily-specific position Aspβ484 was selected as a hotspot for mutation to engineer enzyme variant tolerant to alkaline medium. The corresponding Dβ484N mutant was produced and showed 9-fold increase in stability at alkaline conditions. Bioinformatic analysis of subfamily-specific positions can be further explored to study mechanisms of protein inactivation and to design more stable variants for the engineering of homologous Ntn-hydrolases with improved catalytic properties.
Collapse
Affiliation(s)
- Dmitry Suplatov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Moscow, Russia
| | - Nikolay Panin
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Moscow, Russia
| | - Evgeny Kirilin
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Moscow, Russia
| | - Tatyana Shcherbakova
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Moscow, Russia
| | - Pavel Kudryavtsev
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Moscow, Russia
| | - Vytas Svedas
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Moscow, Russia
| |
Collapse
|
28
|
Granum DM, Schutt TC, Maupin CM. Computational Evaluation of the Dynamic Fluctuations of Peripheral Loops Enclosing the Catalytic Tunnel of a Family 7 Cellobiohydrolase. J Phys Chem B 2014; 118:5340-9. [DOI: 10.1021/jp5011555] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David M. Granum
- Chemical
and Biological Engineering
Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - Timothy C. Schutt
- Chemical
and Biological Engineering
Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - C. Mark Maupin
- Chemical
and Biological Engineering
Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| |
Collapse
|
29
|
Molecular analysis of hyperthermophilic endoglucanase Cel12B from Thermotoga maritima and the properties of its functional residues. BMC STRUCTURAL BIOLOGY 2014; 14:8. [PMID: 24529187 PMCID: PMC3936955 DOI: 10.1186/1472-6807-14-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 02/13/2014] [Indexed: 12/30/2022]
Abstract
Background Although many hyperthermophilic endoglucanases have been reported from archaea and bacteria, a complete survey and classification of all sequences in these species from disparate evolutionary groups, and the relationship between their molecular structures and functions are lacking. The completion of several high-quality gene or genome sequencing projects provided us with the unique opportunity to make a complete assessment and thorough comparative analysis of the hyperthermophilic endoglucanases encoded in archaea and bacteria. Results Structure alignment of the 19 hyperthermophilic endoglucanases from archaea and bacteria which grow above 80°C revealed that Gly30, Pro63, Pro83, Trp115, Glu131, Met133, Trp135, Trp175, Gly227 and Glu229 are conserved amino acid residues. In addition, the average percentage composition of residues cysteine and histidine of 19 endoglucanases is only 0.28 and 0.74 while it is high in thermophilic or mesophilic one. It can be inferred from the nodes that there is a close relationship among the 19 protein from hyperthermophilic bacteria and archaea based on phylogenetic analysis. Among these conserved amino acid residues, as far as Cel12B concerned, two Glu residues might be the catalytic nucleophile and proton donor, Gly30, Pro63, Pro83 and Gly227 residues might be necessary to the thermostability of protein, and Trp115, Met133, Trp135, Trp175 residues is related to the binding of substrate. Site-directed mutagenesis results reveal that Pro63 and Pro83 contribute to the thermostability of Cel12B and Met133 is confirmed to have role in enhancing the binding of substrate. Conclusions The conserved acids have been shown great importance to maintain the structure, thermostability, as well as the similarity of the enzymatic properties of those proteins. We have made clear the function of these conserved amino acid residues in Cel12B protein, which is helpful in analyzing other undetailed molecular structure and transforming them with site directed mutagenesis, as well as providing the theoretical basis for degrading cellulose from woody and herbaceous plants.
Collapse
|
30
|
Granum DM, Vyas S, Sambasivarao SV, Maupin CM. Computational Evaluations of Charge Coupling and Hydrogen Bonding in the Active Site of a Family 7 Cellobiohydrolase. J Phys Chem B 2014; 118:434-48. [DOI: 10.1021/jp408536s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David M. Granum
- Chemical and Biological Engineering Department and ‡Chemistry and Geochemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - Shubham Vyas
- Chemical and Biological Engineering Department and ‡Chemistry and Geochemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - Somisetti V. Sambasivarao
- Chemical and Biological Engineering Department and ‡Chemistry and Geochemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - C. Mark Maupin
- Chemical and Biological Engineering Department and ‡Chemistry and Geochemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| |
Collapse
|
31
|
Characterization and High Level Expression of Acidic Endoglucanase in Pichia pastoris. Appl Biochem Biotechnol 2013; 172:2253-65. [DOI: 10.1007/s12010-013-0672-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 12/03/2013] [Indexed: 10/25/2022]
|
32
|
Liu G, Qin Y, Li Z, Qu Y. Development of highly efficient, low-cost lignocellulolytic enzyme systems in the post-genomic era. Biotechnol Adv 2013; 31:962-75. [PMID: 23507038 DOI: 10.1016/j.biotechadv.2013.03.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 03/09/2013] [Accepted: 03/10/2013] [Indexed: 11/19/2022]
Abstract
The current high cost of lignocellulolytic enzymes is a major bottleneck in the economic bioconversion of lignocellulosic biomass to fuels and chemicals. Fungal lignocellulolytic enzyme systems are secreted at high levels, making them the most promising starting points for further development of highly efficient lignocellulolytic enzyme systems. In this paper, recent advances in improvement of fungal lignocellulolytic enzyme systems are reviewed, with an emphasis on the achievements made using genomic approaches. A general strategy for lignocellulolytic enzyme system development is proposed, including the improvement of the hydrolysis efficiencies and productivities of current enzyme systems. The applications of genomic, transcriptomic and proteomic analysis methods in examining the composition of native enzyme systems, discovery of novel enzymes and synergistic proteins from natural sources, and understanding of regulatory mechanisms for lignocellulolytic enzyme biosynthesis are summarized. By combining systems biology and synthetic biology tools, engineered fungal strains are expected to produce high levels of optimized lignocellulolytic enzyme systems.
Collapse
Affiliation(s)
- Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | | | | | | |
Collapse
|
33
|
Li CH, Wang HR, Yan TR. Cloning, purification, and characterization of a heat- and alkaline-stable endoglucanase B from Aspergillus niger BCRC31494. Molecules 2012; 17:9774-89. [PMID: 22893022 PMCID: PMC6269021 DOI: 10.3390/molecules17089774] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 08/09/2012] [Accepted: 08/10/2012] [Indexed: 11/29/2022] Open
Abstract
Endoglucanase B (EGLB) derived from Aspergillus niger BCRC31494 has been used in the food fermentation industry because of its thermal and alkaline tolerance. It was cloned and expressed in Pichia pastoris. According to sequence analysis, the gene open reading frame comprises 1,217 bp with five introns (GenBank GQ292753). According to sequence and protein domain analyses, EGLB was assigned to glycosyl hydrolase family 5 of the cellulase superfamily. Several binding sites were found in the promoter region. The purified recombinant enzyme was induced by 0.5% methanol, and it exhibited optimal activity at 70 °C and pH 4. EGLB was stable for 3 h at temperatures below 60 °C, with more than 90% of its activity remaining. The enzyme was specific for substrates with β-1,3 and β-1,4 linkages. In Lineweaver-Burk plot analysis, the Km and Vmax values of EGLB for β-D-glucan were 134 mg/mL and 4.68 U/min/mg, respectively. The enzyme activity was increased by 1.86-fold by Co2+ and by 2-fold by Triton X-100 and Tween 80. These favorable properties make EGLB a potential candidate for use in laundry and textile industrial applications.
Collapse
Affiliation(s)
| | | | - Tsong-Rong Yan
- Author to whom correspondence should be addressed; ; Tel.: +886-2-2182-2928 (ext. 6300); Fax: +886-2-2585-4735
| |
Collapse
|
34
|
Verma D, Satyanarayana T. Molecular approaches for ameliorating microbial xylanases. BIORESOURCE TECHNOLOGY 2012; 117:360-367. [PMID: 22595098 DOI: 10.1016/j.biortech.2012.04.034] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 04/09/2012] [Accepted: 04/11/2012] [Indexed: 05/31/2023]
Abstract
In industrial processes, chemical catalysis is being replaced by enzyme catalysis, since the latter is environmentally benign, non-persistent and cost effective. Microbial xylanases have significant applications in textile, baking, food and feed industries, and in paper and pulp industries for reducing the chlorine requirement. The hazardous chlorine required for bleaching can be reduced up to 25-30% by including an enzymatic step in the pulp bleaching process. The paper pulp bleaching requires xylanases that are active at alkaline pH and elevated temperatures. The enzymes from the cultured microbes do not perform optimally in the paper industry due to their inadequate stability under the process conditions of high temperature and alkaline pH. This review, therefore, deals with the rationale of molecular approaches such as protein engineering for designing xylanases with improved characteristics to suit the process conditions in industries, and prospects and problems.
Collapse
Affiliation(s)
- Digvijay Verma
- Department of Microbiology, University of Delhi South Campus, New Delhi 110 021, India
| | | |
Collapse
|
35
|
Jung YR, Shin HY, Yoo HY, Um Y, Kim SW. Production of cellulases and β-glucosidase in Trichoderma reesei mutated by proton beam irradiation. KOREAN J CHEM ENG 2012. [DOI: 10.1007/s11814-011-0272-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
36
|
Directed evolution and structural prediction of cellobiohydrolase II from the thermophilic fungus Chaetomium thermophilum. Appl Microbiol Biotechnol 2012; 95:1469-78. [PMID: 22215071 DOI: 10.1007/s00253-011-3799-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 11/23/2011] [Accepted: 11/26/2011] [Indexed: 10/14/2022]
Abstract
Cellulases can be engineered with enhanced properties for broad use in scientific and industrial applications. In this study, the wild-type cbh2 gene of the thermophilic fungus Chaetomium thermophilum encoding cellobiohydrolase II (CBHII) was mutagenized through in vitro directed evolution. The resulting Pichia pastoris yeast library was screened, and two transformants were selected for enhanced CBHII activities that were not attributed to increased gene copy numbers. The optimum fermentation times of the two mutant transformants were shortened to 4-5 days after methanol induction compared to 6 days for the wild-type. The optimum reaction temperature (60 °C) and pH level (5 or 6) of the mutant CBHII proteins, designated CBHIIX16 and CBHIIX305, were higher than those of wild-type CBHII (50 °C and pH 4). Kept at 80 °C for 1 h, CBHIIX16 and CBHIIX305 retained >50% of their activities, while the wild-type CBHII lost all activity. Sequence analysis of CBHIIX16 and CBHIIX305 revealed that they contained five and six mutated amino acids, respectively. Structural modeling confirmed the presence of carbohydrate binding type-1 and catalytic domains, where the hydrogen bond numbers between the 227th and 203rd amino acids were increased, which perhaps contributed to the elevated enzyme stability. Therefore, the two CBHII mutants selected for increased enzymatic activities also demonstrated elevated optimum reaction temperature and pH levels and enhanced thermal stability. These properties may be beneficial in practical applications for CBHII.
Collapse
|
37
|
Cellulolytic Enzyme Production and Enzymatic Hydrolysis for Second-Generation Bioethanol Production. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012; 128:1-24. [DOI: 10.1007/10_2011_131] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
38
|
|
39
|
Liang C, Fioroni M, Rodríguez-Ropero F, Xue Y, Schwaneberg U, Ma Y. Directed evolution of a thermophilic endoglucanase (Cel5A) into highly active Cel5A variants with an expanded temperature profile. J Biotechnol 2011; 154:46-53. [PMID: 21501637 DOI: 10.1016/j.jbiotec.2011.03.025] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 03/03/2011] [Accepted: 03/29/2011] [Indexed: 10/18/2022]
Abstract
Cel5A is a highly active endoglucanase from Thermoanaerobacter tengcongensis MB4, displaying an optimal temperature range between 75 and 80°C. After three rounds of error-prone PCR and screening of 4700 mutants, five variants of Cel5A with improved activities were identified by Congo Red based screening method. Compared with the wild type, the best variants 3F6 and C3-13 display 135±6% and 193±8% of the wild type specific activity for the substrate carboxymethyl cellulose (CMC), besides improvements in the relative expression level in Escherichia coli system. Remarkable are especially the improvements in activities at reduced temperatures (50% of maximum activity at 50°C and about 45°C respectively, while 65°C for the wild type). Molecular Dynamics simulations performed on the 3F6 and C3-13 variants show a decreased number of intra-Cel5A hydrogen bonds compared to the wild type, implying a more flexible protein skeleton which correlates well to the higher catalytic activity at lower temperatures. To investigate functions of each individual amino acid position site-directed (saturation) mutagenesis were generated and screened. Amino acid positions Val249 and Ile321 were found to be crucial for improving activity and residue Ile13 (encoded by rare codon AUA) yields an improved expression level in E. coli.
Collapse
Affiliation(s)
- Chaoning Liang
- State Key Laboratory of Microbial Resource, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | | | | | | | | | | |
Collapse
|
40
|
Willis JD, Oppert B, Oppert C, Klingeman WE, Jurat-Fuentes JL. Identification, cloning, and expression of a GHF9 cellulase from Tribolium castaneum (Coleoptera: Tenebrionidae). JOURNAL OF INSECT PHYSIOLOGY 2011; 57:300-306. [PMID: 21126522 DOI: 10.1016/j.jinsphys.2010.11.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 11/23/2010] [Accepted: 11/23/2010] [Indexed: 05/28/2023]
Abstract
The availability of sequenced insect genomes has allowed for discovery and functional characterization of novel genes and proteins. We report use of the Tribolium castaneum (Herbst) (red flour beetle) genome to identify, clone, express, and characterize a novel endo-β-1,4-glucanase we named TcEG1 (T. castaneum endoglucanase 1). Sequence analysis of a full-length TcEG1 cDNA clone (1356bp) revealed sequence homology to enzymes in glycosyl hydrolase family 9 (GHF9), and verified presence of a change (Gly for Ser) in the conserved catalytic domain for GHF9 cellulases. This TcEG1 cDNA clone was predicted to encode a 49.5kDa protein with a calculated pI of 5.39. Heterologous expression of TcEG1 in Drosophila S2 cell cultures resulted in secretion of a 51-kDa protein, as determined by Western blotting. The expressed protein was used to characterize TcEG1 enzymatic activity against two cellulose substrates to determine its specificity and stability. Our data support that TcEG1 as a novel endo-β-1,4-glucanase, the first functional characterization of a cellulase enzyme derived from an insect genome with potential applications in the biofuel industry due to its high relative activity at alkaline pH.
Collapse
Affiliation(s)
- Jonathan D Willis
- Department of Entomology and Plant Pathology, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, TN 37996-4560, USA
| | | | | | | | | |
Collapse
|
41
|
Cockburn DW, Clarke AJ. Modulating the pH-activity profile of cellulase A from Cellulomonas fimi by replacement of surface residues. Protein Eng Des Sel 2011; 24:429-37. [DOI: 10.1093/protein/gzr004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
42
|
An alkali-halotolerant cellulase from Bacillus flexus isolated from green seaweed Ulva lactuca. Carbohydr Polym 2011. [DOI: 10.1016/j.carbpol.2010.08.069] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
43
|
Anbar M, Lamed R, Bayer E. Thermostability Enhancement of Clostridium thermocellum Cellulosomal Endoglucanase Cel8A by a Single Glycine Substitution. ChemCatChem 2010. [DOI: 10.1002/cctc.201000112] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
44
|
Engineering of Clostridium phytofermentans Endoglucanase Cel5A for improved thermostability. Appl Environ Microbiol 2010; 76:4914-7. [PMID: 20511418 DOI: 10.1128/aem.00958-10] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A family 5 glycoside hydrolase from Clostridium phytofermentans was cloned and engineered through a cellulase cell surface display system in Escherichia coli. The presence of cell surface anchoring, a cellulose binding module, or a His tag greatly influenced the activities of wild-type and mutant enzymes on soluble and solid cellulosic substrates, suggesting the high complexity of cellulase engineering. The best mutant had 92%, 36%, and 46% longer half-lives at 60 degrees C on carboxymethyl cellulose, regenerated amorphous cellulose, and Avicel, respectively.
Collapse
|
45
|
Cockburn DW, Vandenende C, Clarke AJ. Modulating the pH−Activity Profile of Cellulase by Substitution: Replacing the General Base Catalyst Aspartate with Cysteinesulfinate in Cellulase A from Cellulomonas fimi. Biochemistry 2010; 49:2042-50. [DOI: 10.1021/bi1000596] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Darrell W. Cockburn
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Chris Vandenende
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Anthony J. Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| |
Collapse
|
46
|
Liu W, Hong J, Bevan DR, Zhang YHP. Fast identification of thermostable beta-glucosidase mutants on cellobiose by a novel combinatorial selection/screening approach. Biotechnol Bioeng 2009; 103:1087-94. [PMID: 19388085 DOI: 10.1002/bit.22340] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Engineering costly cellulases on natural cellulosic substrates is of importance for emerging biomass-based biorefineries. Directed enzyme evolution is becoming a popular tool, but identification of desired mutants from a large mutant library remains challenging sometimes. In this work, we demonstrated a novel combinatorial selection/screening strategy for finding thermostable beta-glucosidase on its natural substrate-cellobiose. First, selection was conducted through complementation of beta-glucosidase for non-cellobiose-utilizing Escherichia coli so that only the cells expressing active beta-glucosidase can grow on a M9 synthetic medium with cellobiose as the sole carbon source (selection plate). Second, the clones on the selection plates were duplicated by using nylon membranes. After heat treatment, the nylon membranes were overlaid on M9/cellobiose screening plates so that remaining activities of thermostable beta-glucosidase mutants hydrolyzed cellobiose on the screening plates to glucose. Third, the growth of an indicator E. coli strain that can utilize glucose but not cellobiose on the screening plates helped detect the thermostable beta-glucosidase mutants on the selection plates. Several thermostable mutants were identified from a random mutant library of the Paenibacillus polymyxa beta-glucosidase. The most thermostable mutant A17S had an 11-fold increase in the half-life of thermoinactivation at 50 degrees C.
Collapse
Affiliation(s)
- Wenjin Liu
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, 210-A Seitz Hall, Blacksburg, Virginia 24061, USA
| | | | | | | |
Collapse
|
47
|
Qin Y, Wei X, Song X, Qu Y. The role of the site 342 in catalytic efficiency and pH optima of endoglucanase II fromTrichoderma reeseias probed by saturation mutagenesis. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420802249299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
48
|
Stephens DE, Singh S, Permaul K. Error-prone PCR of a fungal xylanase for improvement of its alkaline and thermal stability. FEMS Microbiol Lett 2009; 293:42-7. [PMID: 19220468 DOI: 10.1111/j.1574-6968.2009.01519.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Random mutagenesis was used to improve the alkaline and thermal stability of the xylanase (XynA) from Thermomyces lanuginosus. Error-prone PCR reactions were carried out; the PCR products were cloned into Escherichia coli and a library of 960 clones was selected on xylan-containing agar plates. The crude filtrates of positive xylanase producers were screened at 80 degrees C and tested separately at pH 10 for alkaline tolerance. The native XynA lost 80% activity after 90 min at 80 degrees C and lost 70% activity at pH 10. Conversely, the most thermostable variant, G41, retained 75% activity after 90 min at 80 degrees C and the best alkali-stable variant, G53, retained 93% activity at pH 10. Sequence analysis revealed four amino acid substitutions in G41 and a single substitution in G53. These variants, therefore, have improved thermal and alkaline stability and are ideal candidates for DNA shuffling experiments to produce a robust xylanase for industrial application.
Collapse
Affiliation(s)
- Dawn Elizabeth Stephens
- Department of Biotechnology and Food Technology, ML Sultan Campus, Durban University of Technology, Durban, South Africa
| | | | | |
Collapse
|
49
|
Improved catalytic efficiency of endo-beta-1,4-glucanase from Bacillus subtilis BME-15 by directed evolution. Appl Microbiol Biotechnol 2008; 82:671-9. [PMID: 19050861 DOI: 10.1007/s00253-008-1789-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 11/06/2008] [Accepted: 11/06/2008] [Indexed: 10/21/2022]
Abstract
Bacillus subtilis endo-beta-1,4-glucanase (Cel5A) hydrolyzes cellulose by cleavage of the internal bonds in the glucose chains, producing new ends randomly. Using directed evolution techniques of error-prone polymerase chain reaction (PCR) and DNA shuffling, several Cel5A variants with improved catalytic activity had been screened from the mutant library, which contained 71,000 colonies. Compared with the wild-type enzyme, the variants (M44-11, S75 and S78) showed 2.03 to 2.68-fold increased activities toward sodium carboxymethyl cellulose (CMC), while the M44-11 also exhibited a wider pH tolerance and higher thermostability. Structural models of M44-11, S75, S78, and WT proteins revealed that most of the substitutions were not located in the strictly conserved regions, except the mutation V255A of S75, which was closed to the nucleophile Glu257 in the catalytic center of the enzyme. Moreover, V74A and D272G of M44-11, which were not located in the substrate binding sites and the catalytic center, might result in improved stability and catalytic activity. These results provided useful references for directed evolution of the enzymes that belonged to the glycoside hydrolase family 5 (GH5).
Collapse
|
50
|
Nakazawa H, Okada K, Kobayashi R, Kubota T, Onodera T, Ochiai N, Omata N, Ogasawara W, Okada H, Morikawa Y. Characterization of the catalytic domains of Trichoderma reesei endoglucanase I, II, and III, expressed in Escherichia coli. Appl Microbiol Biotechnol 2008; 81:681-9. [DOI: 10.1007/s00253-008-1667-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 08/11/2008] [Accepted: 08/12/2008] [Indexed: 11/30/2022]
|