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Zhang Y, Liu C, Yang M, Ou Z, Lin Y, Zhao F, Han S. Characterization and application of a novel xylanase from Halolactibacillus miurensis in wholewheat bread making. Front Bioeng Biotechnol 2022; 10:1018476. [PMID: 36177175 PMCID: PMC9513849 DOI: 10.3389/fbioe.2022.1018476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 08/26/2022] [Indexed: 11/13/2022] Open
Abstract
The presence of arabinoxylan in wholewheat flour affects its quality significantly. Here, an efficient arabinoxylan hydrolytic enzyme, Hmxyn, from Halolactibacillus miurensis was identified and heterologously expressed in pichia pastoris. Moreover, its relevant properties, including potential application in the wholewheat bread were evaluated. Recombinant Hmxyn exhibited maximal activity at 45°C and pH 6.5, and was stable at mid-range temperature (<55°C) and pH (5.5–8.0) conditions. Hmxyn had a clear hydrolysis effect on wheat arabinoxylan in dough and caused the degradation of the water-unextractable arabinoxylan, which increased the content of wheat soluble arabinoxylan of dough. The fermentation characteristics results and microstructure analysis revealed that Hmxyn improved the organizational structure and air holding capacity of fermented dough, thus promoting the dough expansion. Baking experiments further showed that Hmxyn significantly increased specific volume- and texture-linked properties of wholewheat breads. This study indicates the application potential of Hmxyn in the preparation of wholewheat bread.
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Affiliation(s)
- Yaping Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Chun Liu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Manli Yang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zuyun Ou
- Dongguan Huamei Food Co. Ltd., Dongguan, China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Fengguang Zhao
- School of Light Industry and Engineering, South China University of Technology, Guangzhou, China
- *Correspondence: Fengguang Zhao, ; Shuangyan Han,
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- *Correspondence: Fengguang Zhao, ; Shuangyan Han,
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Chai S, Zhu Z, Tian E, Xiao M, Wang Y, Zou G, Zhou Z. Building a Versatile Protein Production Platform Using Engineered Trichoderma reesei. ACS Synth Biol 2022; 11:486-496. [PMID: 34928572 DOI: 10.1021/acssynbio.1c00570] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Trichoderma reesei has an extremely high capacity for synthesizing and secreting proteins, thus exhibiting promise as an expression platform for heterologous proteins. However, T. reesei secretes large amounts of native proteins, which hinders its widespread application for heterologous protein production. Here, we designed and built a series of T. reesei chassis using an iterative gene deletion approach based on an efficient genome editing system. Donor DNAs with specially designed construct facilitated screening of positive deletion strains without ectopic insertion. Finally, marker-free T. reesei chassis with lower rates of native protein secretion and low levels of extracellular protease activity were constructed after 11 consecutive rounds of gene deletion. Higher production levels of three heterologous proteins─a bacterial xylanase XYL7, a fungal immunomodulatory protein LZ8, and the human serum albumin HSA─were achieved with these chassis using the cbh1 promoter. It is possible that diverse high-value proteins might be produced at a high yield using this engineered platform.
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Affiliation(s)
- Shunxing Chai
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19(A) Yuquan Rd, Beijing 100049, China
| | - Zhihua Zhu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19(A) Yuquan Rd, Beijing 100049, China
| | - Ernuo Tian
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| | - Meili Xiao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19(A) Yuquan Rd, Beijing 100049, China
| | - Yan Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| | - Gen Zou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Rd, Shanghai 201403, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
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Singh A, Schermann G, Reislöhner S, Kellner N, Hurt E, Brunner M. Global Transcriptome Characterization and Assembly of the Thermophilic Ascomycete Chaetomium thermophilum. Genes (Basel) 2021; 12:1549. [PMID: 34680944 PMCID: PMC8535861 DOI: 10.3390/genes12101549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 12/30/2022] Open
Abstract
A correct genome annotation is fundamental for research in the field of molecular and structural biology. The annotation of the reference genome of Chaetomium thermophilum has been reported previously, but it is essentially limited to open reading frames (ORFs) of protein coding genes and contains only a few noncoding transcripts. In this study, we identified and annotated full-length transcripts of C. thermophilum by deep RNA sequencing. We annotated 7044 coding genes and 4567 noncoding genes. Astonishingly, 23% of the coding genes are alternatively spliced. We identified 679 novel coding genes as well as 2878 novel noncoding genes and corrected the structural organization of more than 50% of the previously annotated genes. Furthermore, we substantially extended the Gene Ontology (GO) and Enzyme Commission (EC) lists, which provide comprehensive search tools for potential industrial applications and basic research. The identified novel transcripts and improved annotation will help to understand the gene regulatory landscape in C. thermophilum. The analysis pipeline developed here can be used to build transcriptome assemblies and identify coding and noncoding RNAs of other species.
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Affiliation(s)
| | | | | | | | | | - Michael Brunner
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany; (A.S.); (G.S.); (S.R.); (N.K.); (E.H.)
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Abdel-Azeem AM, Abu-Elsaoud AM, Abo Nahas HH, Abdel-Azeem MA, Balbool BA, Mousa MK, Ali NH, Darwish AMG. Biodiversity and Industrial Applications of Genus Chaetomium. Fungal Biol 2021. [DOI: 10.1007/978-3-030-67561-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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5
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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.
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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.
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Han C, Yang R, Sun Y, Liu M, Zhou L, Li D. Identification and Characterization of a Novel Hyperthermostable Bifunctional Cellobiohydrolase- Xylanase Enzyme for Synergistic Effect With Commercial Cellulase on Pretreated Wheat Straw Degradation. Front Bioeng Biotechnol 2020; 8:296. [PMID: 32328483 PMCID: PMC7160368 DOI: 10.3389/fbioe.2020.00296] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/20/2020] [Indexed: 12/19/2022] Open
Abstract
The novel cellobiohydrolase gene ctcel7 was identified from Chaetomium thermophilum, and its recombinant protein CtCel7, a member of glycoside hydrolase family 7, was heterologously expressed in Pichia pastoris and biochemically characterized. Compared with commercial hydrolases, purified CtCel7 exhibited superior bifunctional cellobiohydrolase and xylanase activities against microcrystalline cellulose and xylan, respectively, under optimal conditions of 60°C and pH 4.0. Moreover, CtCel7 displayed remarkable thermostability with over 90% residual activity after heat (60°C) treatment for 180 min. CtCel7 was insensitive to most detected cations and reagents and preferentially cleaved the β-1,4-glycosidic bond to generate oligosaccharides through the continuous saccharification of lignocellulosic substrates, which are crucial for various practical applications. Notably, the hydrolysis effect of a commercial cellulase cocktail on pretreated wheat straw was substantively improved by its combination with CtCel7. Taken together, these excellent properties distinguish CtCel7 as a robust candidate for the biotechnological production of biofuels and biobased chemicals.
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Affiliation(s)
- Chao Han
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Ruirui Yang
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Yanxu Sun
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Mengyu Liu
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Lifan Zhou
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Duochuan Li
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
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Abdel-Azeem AM, El-Mansy SA, Abo Nahas HAH, Mousa MK, Gandal HE, Hamdy SE, El-Ansary MM, Abdel-Azeem MA. Thermophilic Chaetomium in Biotechnology. Fungal Biol 2020. [DOI: 10.1007/978-3-030-31612-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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9
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Novel genetic tools that enable highly pure protein production in Trichoderma reesei. Sci Rep 2019; 9:5032. [PMID: 30902998 PMCID: PMC6430808 DOI: 10.1038/s41598-019-41573-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 03/08/2019] [Indexed: 01/31/2023] Open
Abstract
Trichoderma reesei is an established protein production host with high natural capacity to secrete enzymes. The lack of efficient genome engineering approaches and absence of robust constitutive gene expression systems limits exploitation of this organism in some protein production applications. Here we report engineering of T. reesei for high-level production of highly enriched lipase B of Candida antarctica (calB) using glucose as a carbon source. Multiplexed CRISPR/Cas9 in combination with the use of our recently established synthetic expression system (SES) enabled accelerated construction of strains, which produced high amounts of highly pure calB. Using SES, calB production levels in cellulase-inducing medium were comparable to the levels obtained by using the commonly employed inducible cbh1 promoter, where a wide spectrum of native enzymes were co-produced. Due to highly constitutive expression provided by the SES, it was possible to carry out the production in cellulase-repressing glucose medium leading to around 4 grams per liter of fully functional calB and simultaneous elimination of unwanted background enzymes.
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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.
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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.
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Hua C, Li W, Han W, Wang Q, Bi P, Han C, Zhu L. Characterization of a novel thermostable GH7 endoglucanase from Chaetomium thermophilum capable of xylan hydrolysis. Int J Biol Macromol 2018; 117:342-349. [DOI: 10.1016/j.ijbiomac.2018.05.189] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/01/2018] [Accepted: 05/25/2018] [Indexed: 01/19/2023]
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12
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Expression of catalytically efficient xylanases from thermophilic fungus Malbranchea cinnamomea for synergistically enhancing hydrolysis of lignocellulosics. Int J Biol Macromol 2018; 108:185-192. [DOI: 10.1016/j.ijbiomac.2017.11.131] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 11/20/2017] [Accepted: 11/20/2017] [Indexed: 01/20/2023]
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13
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Gagoski D, Shi Z, Nielsen LK, Vickers CE, Mahler S, Speight R, Johnston WA, Alexandrov K. Cell-free pipeline for discovery of thermotolerant xylanases and endo -1,4-β-glucanases. J Biotechnol 2017; 259:191-198. [DOI: 10.1016/j.jbiotec.2017.07.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/04/2017] [Accepted: 07/12/2017] [Indexed: 11/29/2022]
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Shida Y, Furukawa T, Ogasawara W. Deciphering the molecular mechanisms behind cellulase production in Trichoderma reesei, the hyper-cellulolytic filamentous fungus. Biosci Biotechnol Biochem 2016; 80:1712-29. [DOI: 10.1080/09168451.2016.1171701] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Abstract
The filamentous fungus Trichoderma reesei is a potent cellulase producer and the best-studied cellulolytic fungus. A lot of investigations not only on glycoside hydrolases produced by T. reesei, but also on the machinery controlling gene expression of these enzyme have made this fungus a model organism for cellulolytic fungi. We have investigated the T. reesei strain including mutants developed in Japan in detail to understand the molecular mechanisms that control the cellulase gene expression, the biochemical and morphological aspects that could favor this phenotype, and have attempted to generate novel strains that may be appropriate for industrial use. Subsequently, we developed recombinant strains by combination of these insights and the heterologous-efficient saccharifing enzymes. Resulting enzyme preparations were highly effective for saccharification of various biomass. In this review, we present some of the salient findings from the recent biochemical, morphological, and molecular analyses of this remarkable cellulase hyper-producing fungus.
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Affiliation(s)
- Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Takanori Furukawa
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
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Fungal Biotechnology for Industrial Enzyme Production: Focus on (Hemi)cellulase Production Strategies, Advances and Challenges. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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16
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Extractive Fermentation of Xylanase from Aspergillus tamarii URM 4634 in a Bioreactor. Appl Biochem Biotechnol 2014; 173:1652-66. [DOI: 10.1007/s12010-014-0953-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 05/06/2014] [Indexed: 10/25/2022]
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Liu L, Yang H, Shin HD, Chen RR, Li J, Du G, Chen J. How to achieve high-level expression of microbial enzymes: strategies and perspectives. Bioengineered 2013; 4:212-23. [PMID: 23686280 DOI: 10.4161/bioe.24761] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Microbial enzymes have been used in a large number of fields, such as chemical, agricultural and biopharmaceutical industries. The enzyme production rate and yield are the main factors to consider when choosing the appropriate expression system for the production of recombinant proteins. Recombinant enzymes have been expressed in bacteria (e.g., Escherichia coli, Bacillus and lactic acid bacteria), filamentous fungi (e.g., Aspergillus) and yeasts (e.g., Pichia pastoris). The favorable and very advantageous characteristics of these species have resulted in an increasing number of biotechnological applications. Bacterial hosts (e.g., E. coli) can be used to quickly and easily overexpress recombinant enzymes; however, bacterial systems cannot express very large proteins and proteins that require post-translational modifications. The main bacterial expression hosts, with the exception of lactic acid bacteria and filamentous fungi, can produce several toxins which are not compatible with the expression of recombinant enzymes in food and drugs. However, due to the multiplicity of the physiological impacts arising from high-level expression of genes encoding the enzymes and expression hosts, the goal of overproduction can hardly be achieved, and therefore, the yield of recombinant enzymes is limited. In this review, the recent strategies used for the high-level expression of microbial enzymes in the hosts mentioned above are summarized and the prospects are also discussed. We hope this review will contribute to the development of the enzyme-related research field.
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Affiliation(s)
- Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
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18
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van Noort V, Bradatsch B, Arumugam M, Amlacher S, Bange G, Creevey C, Falk S, Mende DR, Sinning I, Hurt E, Bork P. Consistent mutational paths predict eukaryotic thermostability. BMC Evol Biol 2013; 13:7. [PMID: 23305080 PMCID: PMC3546890 DOI: 10.1186/1471-2148-13-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 01/07/2013] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Proteomes of thermophilic prokaryotes have been instrumental in structural biology and successfully exploited in biotechnology, however many proteins required for eukaryotic cell function are absent from bacteria or archaea. With Chaetomium thermophilum, Thielavia terrestris and Thielavia heterothallica three genome sequences of thermophilic eukaryotes have been published. RESULTS Studying the genomes and proteomes of these thermophilic fungi, we found common strategies of thermal adaptation across the different kingdoms of Life, including amino acid biases and a reduced genome size. A phylogenetics-guided comparison of thermophilic proteomes with those of other, mesophilic Sordariomycetes revealed consistent amino acid substitutions associated to thermophily that were also present in an independent lineage of thermophilic fungi. The most consistent pattern is the substitution of lysine by arginine, which we could find in almost all lineages but has not been extensively used in protein stability engineering. By exploiting mutational paths towards the thermophiles, we could predict particular amino acid residues in individual proteins that contribute to thermostability and validated some of them experimentally. By determining the three-dimensional structure of an exemplar protein from C. thermophilum (Arx1), we could also characterise the molecular consequences of some of these mutations. CONCLUSIONS The comparative analysis of these three genomes not only enhances our understanding of the evolution of thermophily, but also provides new ways to engineer protein stability.
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Affiliation(s)
- Vera van Noort
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
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19
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Production of recombinant proteins by filamentous fungi. Biotechnol Adv 2012; 30:1119-39. [DOI: 10.1016/j.biotechadv.2011.09.012] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 08/30/2011] [Accepted: 09/15/2011] [Indexed: 11/17/2022]
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20
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Andrioli WJ, Damásio ARL, Silva TM, da Silva VB, Maller A, Nanayakkara NPD, Silva CHTP, Polizeli MLTM, Bastos JK. Endo-xylanase GH11 activation by the fungal metabolite eugenitin. Biotechnol Lett 2012; 34:1487-92. [PMID: 22481300 DOI: 10.1007/s10529-012-0918-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 03/21/2012] [Indexed: 10/28/2022]
Abstract
Eugenitin, a chromone derivative and a metabolite of the endophyte Mycoleptodiscus indicus, at 5 mM activated a recombinant GH11 endo-xylanase by 40 %. The in silico prediction of ligand-binding sites on the three-dimensional structure of the endo-xylanase revealed that eugenitin interacts mainly by a hydrogen bond with a serine residue and a stacking interaction of the heterocyclic aromatic ring system with a tryptophan residue. Eugenitin improved the GH11 endo-xylanase activity on different substrates, modified the optimal pH and temperature activities and slightly affected the kinetic parameters of the enzyme.
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Affiliation(s)
- Willian J Andrioli
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14040-903, Brazil.
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21
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Paës G, Berrin JG, Beaugrand J. GH11 xylanases: Structure/function/properties relationships and applications. Biotechnol Adv 2011; 30:564-92. [PMID: 22067746 DOI: 10.1016/j.biotechadv.2011.10.003] [Citation(s) in RCA: 281] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/06/2011] [Accepted: 10/13/2011] [Indexed: 01/02/2023]
Abstract
For technical, environmental and economical reasons, industrial demands for process-fitted enzymes have evolved drastically in the last decade. Therefore, continuous efforts are made in order to get insights into enzyme structure/function relationships to create improved biocatalysts. Xylanases are hemicellulolytic enzymes, which are responsible for the degradation of the heteroxylans constituting the lignocellulosic plant cell wall. Due to their variety, xylanases have been classified in glycoside hydrolase families GH5, GH8, GH10, GH11, GH30 and GH43 in the CAZy database. In this review, we focus on GH11 family, which is one of the best characterized GH families with bacterial and fungal members considered as true xylanases compared to the other families because of their high substrate specificity. Based on an exhaustive analysis of the sequences and 3D structures available so far, in relation with biochemical properties, we assess biochemical aspects of GH11 xylanases: structure, catalytic machinery, focus on their "thumb" loop of major importance in catalytic efficiency and substrate selectivity, inhibition, stability to pH and temperature. GH11 xylanases have for a long time been used as biotechnological tools in various industrial applications and represent in addition promising candidates for future other uses.
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Affiliation(s)
- Gabriel Paës
- INRA, UMR614 FARE, 2 esplanade Roland-Garros, F-51686 Reims, France.
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Characterisation of a thermostable xylanase from Chaetomium sp. and its application in Chinese steamed bread. Food Chem 2010. [DOI: 10.1016/j.foodchem.2009.10.038] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Ghaffar A, Khan SA, Mukhtar Z, Rajoka MI, Latif F. Heterologous expression of a gene for thermostable xylanase from Chaetomium thermophilum in Pichia pastoris GS115. Mol Biol Rep 2010; 38:3227-33. [DOI: 10.1007/s11033-010-9996-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 02/07/2010] [Indexed: 11/27/2022]
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Molecular cloning of fungal xylanases: an overview. Appl Microbiol Biotechnol 2009; 84:19-35. [PMID: 19568746 DOI: 10.1007/s00253-009-2079-4] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 06/05/2009] [Accepted: 06/05/2009] [Indexed: 10/20/2022]
Abstract
Xylanases have received great attention in the development of environment-friendly technologies in the paper and pulp industry. Their use could greatly improve the overall lignocellulosic materials for the generation of liquid fuels and chemicals. Fungi are widely used as xylanase producers and are generally considered as more potent producers of xylanases than bacteria and yeasts. Large-scale production of xylanases is facilitated with the advent of genetic engineering. Recent breakthroughs in genomics have helped to overcome the problems such as limited enzyme availability, substrate scope, and operational stability. Genes encoding xylanases have been cloned in homologous and heterologous hosts with the objectives of overproducing the enzyme and altering its properties to suit commercial applications. Owing to the industrial importance of xylanases, a significant number of studies are reported on cloning and expression of the enzymes during the last few years. We, therefore, have reviewed recent knowledge regarding cloning of fungal xylanase genes into various hosts for heterologous production. This will bring an insight into the current status of cloning and expression of the fungal xylanases for industrial applications.
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Rahman Z, Shida Y, Furukawa T, Suzuki Y, Okada H, Ogasawara W, Morikawa Y. Evaluation and characterization of Trichoderma reesei cellulase and xylanase promoters. Appl Microbiol Biotechnol 2009; 82:899-908. [DOI: 10.1007/s00253-008-1841-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 12/18/2008] [Accepted: 12/19/2008] [Indexed: 11/30/2022]
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