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Wei L, Zhu J, Zhao D, Pei Y, Guo L, Guo J, Guo Z, Cui H, Li Y, Gao J. Microbial fungicides can positively affect aubergine photosynthetic properties, soil enzyme activity and microbial community structure. PeerJ 2024; 12:e17620. [PMID: 38952982 PMCID: PMC11216198 DOI: 10.7717/peerj.17620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/31/2024] [Indexed: 07/03/2024] Open
Abstract
Background This study examined the effects of microbial agents on the enzyme activity, microbial community construction and potential functions of inter-root soil of aubergine (Fragaria × ananassa Duch.). This study also sought to clarify the adaptability of inter-root microorganisms to environmental factors to provide a theoretical basis for the stability of the microbiology of inter-root soil of aubergine and for the ecological preservation of farmland soil. Methods Eggplant inter-root soils treated with Bacillus subtilis (QZ_T1), Bacillus subtilis (QZ_T2), Bacillus amyloliquefaciens (QZ_T3), Verticillium thuringiensis (QZ_T4) and Verticillium purpureum (QZ_T5) were used to analyse the effects of different microbial agents on the inter-root soils of aubergine compared to the untreated control group (QZ_CK). The effects of different microbial agents on the characteristics and functions of inter-root soil microbial communities were analysed using 16S rRNA and ITS (internal transcribed spacer region) high-throughput sequencing techniques. Results The bacterial diversity index and fungal diversity index of the aubergine inter-root soil increased significantly with the application of microbial fungicides; gas exchange parameters and soil enzyme activities also increased. The structural and functional composition of the bacterial and fungal communities in the aubergine inter-root soil changed after fungicide treatment compared to the control, with a decrease in the abundance of phytopathogenic fungi and an increase in the abundance of beneficial fungi in the soil. Enhancement of key community functions, reduction of pathogenic fungi, modulation of environmental factors and improved functional stability of microbial communities were important factors contributing to the microbial stability of fungicide-treated aubergine inter-root soils.
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Affiliation(s)
- Longxue Wei
- Dezhou Institute of Agricultural Science, Dezhou, Shandong, China
| | - Jinying Zhu
- Dezhou Institute of Agricultural Science, Dezhou, Shandong, China
| | - Dongbo Zhao
- Dezhou Institute of Agricultural Science, Dezhou, Shandong, China
| | - Yanting Pei
- Dezhou Institute of Agricultural Science, Dezhou, Shandong, China
| | - Lianghai Guo
- Dezhou Institute of Agricultural Science, Dezhou, Shandong, China
| | - Jianjun Guo
- Dezhou Institute of Agricultural Science, Dezhou, Shandong, China
| | - Zhihui Guo
- Dezhou Institute of Agricultural Science, Dezhou, Shandong, China
| | - Huini Cui
- Dezhou Institute of Agricultural Science, Dezhou, Shandong, China
| | - Yongjun Li
- Dezhou Institute of Agricultural Science, Dezhou, Shandong, China
| | - Jiansheng Gao
- Dezhou Institute of Agricultural Science, Dezhou, Shandong, China
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Yamaguchi S, Sunagawa N, Samejima M, Igarashi K. Thermotolerance Mechanism of Fungal GH6 Cellobiohydrolase. Part II. Structural Analysis of Thermotolerant Mutant from the Basidiomycete Phanerochaete chrysosporium. J Appl Glycosci (1999) 2024; 71:63-72. [PMID: 38863950 PMCID: PMC11163327 DOI: 10.5458/jag.jag.jag-2023_0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/04/2024] [Indexed: 06/13/2024] Open
Abstract
Glycoside hydrolase family 6 cellobiohydrolase (GH6 CBH) is a group of cellulases capable of hydrolyzing crystalline cellulose. However, the synergistic reaction of GH6 CBH with other cellulases is hindered by its relatively low thermotolerance. We previously obtained a thermotolerant double mutant, C240S/C393S, of GH6 CBH from the basidiomycete Phanerochaete chrysosporium (PcCel6A) by replacing the two free cysteine (Cys) residues, C240 and C393, with serine (Yamaguchi et al., J Appl Glycosci. 2020; 67;79-86). In the accompanying paper (Part I; Yamaguchi et al., J Appl Glycosci. 2024; 71: 55-62), we measured the temperature dependence of the activity and folding of C240S/C393S and its single mutants, C240S and C393S, and found that replacement of C393 was the major contributor to the increased thermotolerance of C240S/C393S. Here, in order to investigate the mechanism involved, we crystallized the wild-type and the mutant enzymes and compared their X-ray crystal structures. The overall structures of the wild-type and the three mutant enzymes were similar. However, C240S/C393S had the lowest relative B-factor at both the N-terminal loop (residues 172-177) and the C-terminal loop (residues 390-425). This result suggests that reduced structural fluctuation of the substrate-enclosing loops, possibly due to stronger hydrogen bonding involving C393, could account for the increased thermotolerance of C240S/C393S.
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Affiliation(s)
- Sora Yamaguchi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
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Mayr SA, Rennhofer H, Gille L, Schwaiger N, Nyanhongo GS, Weiss R, Guebitz GM. Effect of Salts on Laccase-Catalyzed Polymerization of Lignosulfonate. CHEMSUSCHEM 2024:e202301134. [PMID: 38456224 DOI: 10.1002/cssc.202301134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 03/09/2024]
Abstract
Enzymatic polymerization of lignosulfonate (LS) has a high potential for various applications ranging from coatings to adhesives. Here, the effect of different ions in low concentrations on enzymatic polymerization of LS was investigated, including salt solutions consisting of mono- and dicarboxylic acids, sulfate, phosphate and chloride with sodium as counter ion. LS polymerization was followed by viscometry and size exclusion (SEC) chromatography. Interestingly, there was only a small effect of ions on the activity of the laccase on standard substrate ABTS, while the effect on polymerization of LS was substantially different. The presence of acetate led to a 39 % higher degree of polymerization (DP) for LS. Small angle X-ray scattering (SAXS) revealed that the structure of the enzyme was largely unaffected by the ions, while the determination of the zeta potential showed that those ions conveying higher negative surface charges onto LS particles showed lower DPs, than those not affecting the surface charge. Further, electron paramagnetic resonance (EPR) spectroscopy showed 5-times higher intensity in phenoxyl radicals for the monovalent ions compared to the divalent ones. It was concluded that the DPs of LS could be tuned in the presence of certain ions, by facilitating the interaction between the laccase substrate-binding site and the LS molecules.
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Affiliation(s)
- Sebastian A Mayr
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology, IFA-Tulln, Institute of Environmental Biotechnology, Konrad Lorenz-Strasse 20, 3430, Tulln an der Donau, Austria
| | - Harald Rennhofer
- University of Natural Resources and Life Sciences, Vienna, Department of Material Science and Process Engineering, Institute of Physics and Material Science, Peter-Jordan-Strasse 82, 1190, Vienna, Austria
| | - Lars Gille
- University of Veterinary Medicine, Vienna, Department of Biomedical Sciences, Institute of Pharmacology and Toxicology, Veterinärplatz 1, 1210, Vienna, Austria
| | | | - Gibson S Nyanhongo
- University of Johannesburg, Department of Biotechnology and Food Technology, Faculty of Science, Corner Siemert and Louisa, Doornfontein 2028, John Orr Building, Johannesburg, South Africa
| | - Renate Weiss
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology, IFA-Tulln, Institute of Environmental Biotechnology, Konrad Lorenz-Strasse 20, 3430, Tulln an der Donau, Austria
| | - Georg M Guebitz
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology, IFA-Tulln, Institute of Environmental Biotechnology, Konrad Lorenz-Strasse 20, 3430, Tulln an der Donau, Austria
- Austrian Centre for Industrial Biotechnology (ACIB), Konrad Lorenz Strasse 20, 3430, Tulln, Austria
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Gu S, Wu T, Zhao J, Sun T, Zhao Z, Zhang L, Li J, Tian C. Rewiring metabolic flux to simultaneously improve malate production and eliminate by-product succinate accumulation by Myceliophthora thermophila. Microb Biotechnol 2024; 17:e14410. [PMID: 38298109 PMCID: PMC10884987 DOI: 10.1111/1751-7915.14410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/07/2023] [Accepted: 01/05/2024] [Indexed: 02/02/2024] Open
Abstract
Although a high titre of malic acid is achieved by filamentous fungi, by-product succinic acid accumulation leads to a low yield of malic acid and is unfavourable for downstream processing. Herein, we conducted a series of metabolic rewiring strategies in a previously constructed Myceliophthora thermophila to successfully improve malate production and abolish succinic acid accumulation. First, a pyruvate carboxylase CgPYC variant with increased activity was obtained using a high-throughput system and introduced to improve malic acid synthesis. Subsequently, shifting metabolic flux to malate synthesis from mitochondrial metabolism by deleing mitochondrial carriers of pyruvate and malate, led to a 53.7% reduction in succinic acid accumulation. The acceleration of importing cytosolic succinic acid into the mitochondria for consumption further decreased succinic acid formation by 53.3%, to 2.12 g/L. Finally, the importer of succinic acid was discovered and used to eliminate by-product accumulation. In total, malic acid production was increased by 26.5%, relative to the start strain JG424, to 85.23 g/L and 89.02 g/L on glucose and Avicel, respectively, in the flasks. In a 5-L fermenter, the titre of malic acid reached 182.7 g/L using glucose and 115.8 g/L using raw corncob, without any by-product accumulation. This study would accelerate the industrial production of biobased malic acid from renewable plant biomass.
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Affiliation(s)
- Shuying Gu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Taju Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
- School of Life Science, Bengbu Medical CollegeBengbuChina
| | - Junqi Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Tao Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Zhen Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Lu Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Jingen Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Chaoguang Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
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Li J, Wang Y, Yang K, Wang X, Wang Y, Zhang H, Huang H, Su X, Yao B, Luo H, Qin X. Development of an efficient protein expression system in the thermophilic fungus Myceliophthora thermophila. Microb Cell Fact 2023; 22:236. [PMID: 37974259 PMCID: PMC10652509 DOI: 10.1186/s12934-023-02245-5] [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: 07/07/2023] [Accepted: 11/05/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Thermophilic fungus Myceliophthora thermophila has been widely used in industrial applications due to its ability to produce various enzymes. However, the lack of an efficient protein expression system has limited its biotechnological applications. RESULTS In this study, using a laccase gene reporting system, we developed an efficient protein expression system in M. thermophila through the selection of strong constitutive promoters, 5'UTRs and signal peptides. The expression of the laccase was confirmed by enzyme activity assays. The results showed that the Mtpdc promoter (Ppdc) was able to drive high-level expression of the target protein in M. thermophila. Manipulation of the 5'UTR also has significant effects on protein expression and secretion. The best 5'UTR (NCA-7d) was identified. The transformant containing the laccase gene under the Mtpdc promoter, NCA-7d 5'UTR and its own signal peptide with the highest laccase activity (1708 U/L) was obtained. In addition, the expression system was stable and could be used for the production of various proteins, including homologous proteins like MtCbh-1, MtGh5-1, MtLPMO9B, and MtEpl1, as well as a glucoamylase from Trichoderma reesei. CONCLUSIONS An efficient protein expression system was established in M. thermophila for the production of various proteins. This study provides a valuable tool for protein production in M. thermophila and expands its potential for biotechnological applications.
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Affiliation(s)
- Jinyang Li
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Yidi Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Kun Yang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Honglian Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China.
| | - Xing Qin
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China.
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Zhu Z, Zhang M, Liu D, Liu D, Sun T, Yang Y, Dong J, Zhai H, Sun W, Liu Q, Tian C. Development of the thermophilic fungus Myceliophthora thermophila into glucoamylase hyperproduction system via the metabolic engineering using improved AsCas12a variants. Microb Cell Fact 2023; 22:150. [PMID: 37568174 PMCID: PMC10416393 DOI: 10.1186/s12934-023-02149-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/13/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND Glucoamylase is an important enzyme for starch saccharification in the food and biofuel industries and mainly produced from mesophilic fungi such as Aspergillus and Rhizopus species. Enzymes produced from thermophilic fungi can save the fermentation energy and reduce costs as compared to the fermentation system using mesophiles. Thermophilic fungus Myceliophthora thermophila is industrially deployed fungus to produce enzymes and biobased chemicals from biomass during optimal growth at 45 °C. This study aimed to construct the M. thermophila platform for glucoamylase hyper-production by broadening genomic targeting range of the AsCas12a variants, identifying key candidate genes and strain engineering. RESULTS In this study, to increase the genome targeting range, we upgraded the CRISPR-Cas12a-mediated technique by engineering two AsCas12a variants carrying the mutations S542R/K607R and S542R/K548V/N552R. Using the engineered AsCas12a variants, we deleted identified key factors involved in the glucoamylase expression and secretion in M. thermophila, including Mtstk-12, Mtap3m, Mtdsc-1 and Mtsah-2. Deletion of four targets led to more than 1.87- and 1.85-fold higher levels of secretion and glucoamylases activity compared to wild-type strain MtWT. Transcript level of the major amylolytic genes showed significantly increased in deletion mutants. The glucoamylase hyper-production strain MtGM12 was generated from our previously strain MtYM6 via genetically engineering these targets Mtstk-12, Mtap3m, Mtdsc-1 and Mtsah-2 and overexpressing Mtamy1 and Mtpga3. Total secreted protein and activities of amylolytic enzymes in the MtGM12 were about 35.6-fold and 51.9‒55.5-fold higher than in MtWT. Transcriptional profiling analyses revealed that the amylolytic gene expression levels were significantly up-regulated in the MtGM12 than in MtWT. More interestingly, the MtGM12 showed predominantly short and highly bulging hyphae with proliferation of rough ER and abundant mitochondria, secretion vesicles and vacuoles when culturing on starch. CONCLUSIONS Our results showed that these AsCas12a variants worked well for gene deletions in M. thermophila. We successfully constructed the glucoamylase hyper-production strain of M. thermophila by the rational redesigning and engineering the transcriptional regulatory and secretion pathway. This targeted engineering strategy will be very helpful to improve industrial fungal strains and promote the morphology engineering for enhanced enzyme production.
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Affiliation(s)
- Zhijian Zhu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Manyu Zhang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Dandan Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Defei Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Tao Sun
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Yujing Yang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Jiacheng Dong
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Huanhuan Zhai
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Wenliang Sun
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Qian Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
| | - Chaoguang Tian
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
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Zhao Z, Gu S, Liu D, Liu D, Chen B, Li J, Tian C. The putative methyltransferase LaeA regulates mycelium growth and cellulase production in Myceliophthora thermophila. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:58. [PMID: 37013645 PMCID: PMC10071736 DOI: 10.1186/s13068-023-02313-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023]
Abstract
BACKGROUND Filamentous fungi with the ability to use complex carbon sources has been developed as platforms for biochemicals production. Myceliophthora thermophila has been developed as the cell factory to produce lignocellulolytic enzymes and plant biomass-based biofuels and biochemicals in biorefinery. However, low fungal growth rate and cellulose utilization efficiency are significant barriers to the satisfactory yield and productivity of target products, which needs our further exploration and improvement. RESULTS In this study, we comprehensively explored the roles of the putative methyltransferase LaeA in regulating mycelium growth, sugar consumption, and cellulases expression. Deletion of laeA in thermophile fungus Myceliophthora thermophila enhanced mycelium growth and glucose consumption significantly. Further exploration of LaeA regulatory network indicated that multiple growth regulatory factors (GRF) Cre-1, Grf-1, Grf-2, and Grf-3, which act as negative repressors of carbon metabolism, were regulated by LaeA in this fungus. We also determined that phosphoenolpyruvate carboxykinase (PCK) is the core node of the metabolic network related to fungal vegetative growth, of which enhancement partially contributed to the elevated sugar consumption and fungal growth of mutant ΔlaeA. Noteworthily, LaeA participated in regulating the expression of cellulase genes and their transcription regulator. ΔlaeA exhibited 30.6% and 5.5% increases in the peak values of extracellular protein and endo-glucanase activity, respectively, as compared to the WT strain. Furthermore, the global histone methylation assays indicated that LaeA is associated with modulating H3K9 methylation levels. The normal function of LaeA on regulating fungal physiology is dependent on methyltransferase activity. CONCLUSIONS The research presented in this study clarified the function and elucidated the regulatory network of LaeA in the regulation of fungal growth and cellulase production, which will significantly deepen our understanding about the regulation mechanism of LaeA in filamentous fungi and provides the new strategy for improvement the fermentation properties of industrial fungal strain by metabolic engineering.
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Affiliation(s)
- Zhen Zhao
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuying Gu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Defei Liu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Dandan Liu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Bingchen Chen
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Jingen Li
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
| | - Chaoguang Tian
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
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8
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Gu S, Zhao Z, Xue F, Liu D, Liu Q, Li J, Tian C. The arabinose transporter MtLat-1 is involved in hemicellulase repression as a pentose transceptor in Myceliophthora thermophila. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:51. [PMID: 36966330 PMCID: PMC10040116 DOI: 10.1186/s13068-023-02305-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Filamentous fungi possess an array of secreted enzymes to depolymerize the structural polysaccharide components of plant biomass. Sugar transporters play an essential role in nutrient uptake and sensing of extracellular signal molecules to inhibit or trigger the induction of lignocellulolytic enzymes. However, the identities and functions of transceptors associated with the induction of hemicellulase genes remain elusive. RESULTS In this study, we reveal that the L-arabinose transporter MtLat-1 is associated with repression of hemicellulase gene expression in the filamentous fungus Myceliophthora thermophila. The absence of Mtlat-1 caused a decrease in L-arabinose uptake and consumption rates. However, mycelium growth, protein production, and hemicellulolytic activities were markedly increased in a ΔMtlat-1 mutant compared with the wild-type (WT) when grown on arabinan. Comparative transcriptomic analysis showed a different expression profile in the ΔMtlat-1 strain from that in the WT in response to arabinan, and demonstrated that MtLat-1 was involved in the repression of the main hemicellulase-encoding genes. A point mutation that abolished the L-arabinose transport activity of MtLat-1 did not impact the repression of hemicellulase gene expression when the mutant protein was expressed in the ΔMtlat-1 strain. Thus, the involvement of MtLat-1 in the expression of hemicellulase genes is independent of its transport activity. The data suggested that MtLat-1 is a transceptor that senses and transduces the molecular signal, resulting in downstream repression of hemicellulolytic gene expression. MtAra-1 protein directly regulated the expression of Mtlat-1 by binding to its promoter region. Transcriptomic profiling indicated that the transcription factor MtAra-1 also plays an important role in expression of arabinanolytic enzyme genes and L-arabinose catabolism. CONCLUSIONS M. thermophila MtLat-1 functions as a transceptor that is involved in L-arabinose transport and signal transduction associated with suppression of the expression of hemicellulolytic enzyme-encoding genes. The data presented in this study add to the models of the regulation of hemicellulases in filamentous fungi.
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Affiliation(s)
- Shuying Gu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhen Zhao
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Fanglei Xue
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Defei Liu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Qian Liu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Jingen Li
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Chaoguang Tian
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
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9
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Ghattavi S, Homaei A. Marine enzymes: Classification and application in various industries. Int J Biol Macromol 2023; 230:123136. [PMID: 36621739 DOI: 10.1016/j.ijbiomac.2023.123136] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/23/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023]
Abstract
Oceans are regarded as a plentiful and sustainable source of biological compounds. Enzymes are a group of marine biomaterials that have recently drawn more attention because they are produced in harsh environmental conditions such as high salinity, extensive pH, a wide temperature range, and high pressure. Hence, marine-derived enzymes are capable of exhibiting remarkable properties due to their unique composition. In this review, we overviewed and discussed characteristics of marine enzymes as well as the sources of marine enzymes, ranging from primitive organisms to vertebrates, and presented the importance, advantages, and challenges of using marine enzymes with a summary of their applications in a variety of industries. Current biotechnological advancements need the study of novel marine enzymes that could be applied in a variety of ways. Resources of marine enzyme can benefit greatly for biotechnological applications duo to their biocompatible, ecofriendly and high effectiveness. It is beneficial to use the unique characteristics offered by marine enzymes to either develop new processes and products or improve existing ones. As a result, marine-derived enzymes have promising potential and are an excellent candidate for a variety of biotechnology applications and a future rise in the use of marine enzymes is to be anticipated.
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Affiliation(s)
- Saba Ghattavi
- Fisheries Department, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran.
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10
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Daddaoua A, Álvarez C, Oggerin M, Rodriguez N, Duque E, Amils R, Armengaud J, Segura A, Ramos JL. Rio Tinto as a niche for acidophilus enzymes of industrial relevance. Microb Biotechnol 2023; 16:1069-1086. [PMID: 36748404 PMCID: PMC10128141 DOI: 10.1111/1751-7915.14192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/06/2022] [Indexed: 02/08/2023] Open
Abstract
Lignocellulosic residues are amongst the most abundant waste products on Earth. Therefore, there is an increasing interest in the utilization of these residues for bioethanol production and for biorefineries to produce compounds of industrial interest. Enzymes that breakdown cellulose and hemicellulose into oligomers and monosaccharides are required in these processes and cellulolytic enzymes with optimum activity at a low pH area are desirable for industrial processes. Here, we explore the fungal biodiversity of Rıo Tinto, the largest acidic ecosystem on Earth, as far as the secretion of cellulolytic enzymes is concerned. Using colorimetric and industrial substrates, we show that a high proportion of the fungi present in this extremophilic environment secrete a wide range of enzymes that are able to hydrolyze cellulose and hemicellulose at acidic pH (4.5-5). Shotgun proteomic analysis of the secretomes of some of these fungi has identified different cellulases and hemicellulolytic enzymes as well as a number of auxiliary enzymes. Supplementation of pre-industrial cocktails from Myceliophtora with Rio Tinto secretomes increased the amount of monosaccharides released from corn stover or sugar cane straw. We conclude that the Rio Tinto fungi display a good variety of hydrolytic enzymes with high industrial potential.
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Affiliation(s)
- Abdelali Daddaoua
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Consolación Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis (CSIC-US), Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, CIC Cartuja, Seville, Spain
| | - Monika Oggerin
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Nuria Rodriguez
- Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Spain
| | - Estrella Duque
- Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.,Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Spain
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - Ana Segura
- Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
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11
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Allegretti C, Bellinetto E, D’Arrigo P, Ferro M, Griffini G, Rossato LAM, Ruffini E, Schiavi L, Serra S, Strini A, Turri S. Fractionation of Raw and Parboiled Rice Husks with Deep Eutectic Solvents and Characterization of the Extracted Lignins towards a Circular Economy Perspective. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248879. [PMID: 36558011 PMCID: PMC9785053 DOI: 10.3390/molecules27248879] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
In the present work, rice husks (RHs), which, worldwide, represent one of the most abundant agricultural wastes in terms of their quantity, have been treated and fractionated in order to allow for their complete valorization. RHs coming from the raw and parboiled rice production have been submitted at first to a hydrothermal pretreatment followed by a deep eutectic solvent fractionation, allowing for the separation of the different components by means of an environmentally friendly process. The lignins obtained from raw and parboiled RHs have been thoroughly characterized and showed similar physico-chemical characteristics, indicating that the parboiling process does not introduce obvious lignin alterations. In addition, a preliminary evaluation of the potentiality of such lignin fractions as precursors of cement water reducers has provided encouraging results. A fermentation-based optional preprocess has also been investigated. However, both raw and parboiled RHs demonstrated a poor performance as a microbiological growth substrate, even in submerged fermentation using cellulose-degrading fungi. The described methodology appears to be a promising strategy for the valorization of these important waste biomasses coming from the rice industry towards a circular economy perspective.
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Affiliation(s)
- Chiara Allegretti
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, p.zza L. da Vinci 32, 20133 Milano, Italy
| | - Emanuela Bellinetto
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, p.zza L. da Vinci 32, 20133 Milano, Italy
| | - Paola D’Arrigo
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, p.zza L. da Vinci 32, 20133 Milano, Italy
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, Consiglio Nazionale delle Ricerche (SCITEC-CNR), Via Luigi Mancinelli 7, 20131 Milano, Italy
- Correspondence: (P.D.); (S.S.); Tel.: +39-2-23993075 (P.D.); +39-2-23993076 (S.S.)
| | - Monica Ferro
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, p.zza L. da Vinci 32, 20133 Milano, Italy
| | - Gianmarco Griffini
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, p.zza L. da Vinci 32, 20133 Milano, Italy
| | - Letizia Anna Maria Rossato
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, p.zza L. da Vinci 32, 20133 Milano, Italy
| | - Eleonora Ruffini
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, p.zza L. da Vinci 32, 20133 Milano, Italy
| | - Luca Schiavi
- Istituto per le Tecnologie della Costruzione, Consiglio Nazionale delle Ricerche (ITC-CNR), Via Lombardia 49, 20098 San Giuliano Milanese, Italy
| | - Stefano Serra
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, Consiglio Nazionale delle Ricerche (SCITEC-CNR), Via Luigi Mancinelli 7, 20131 Milano, Italy
- Correspondence: (P.D.); (S.S.); Tel.: +39-2-23993075 (P.D.); +39-2-23993076 (S.S.)
| | - Alberto Strini
- Istituto per le Tecnologie della Costruzione, Consiglio Nazionale delle Ricerche (ITC-CNR), Via Lombardia 49, 20098 San Giuliano Milanese, Italy
| | - Stefano Turri
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, p.zza L. da Vinci 32, 20133 Milano, Italy
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12
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Qin X, Zou J, Yang K, Li J, Wang X, Tu T, Wang Y, Yao B, Huang H, Luo H. Deciphering the efficient cellulose degradation by the thermophilic fungus Myceliophthora thermophila focused on the synergistic action of glycoside hydrolases and lytic polysaccharide monooxygenases. BIORESOURCE TECHNOLOGY 2022; 364:128027. [PMID: 36174898 DOI: 10.1016/j.biortech.2022.128027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
The thermophilic fungus Myceliophthora thermophila as an efficient decomposer secretes various glycoside hydrolases and auxiliary oxidation enzymes to deconstruct cellulose. However, the core enzymes critical for efficient cellulose degradation and their interactions with other cellulolytic enzymes remain unclear. Herein, the transcriptomic analysis of M. thermophila grown on Avicel exhibited that cellulases from GH5_5, GH6 and GH7, and lytic polysaccharide monooxygenases (LPMOs) from AA9 contributed to cellulose degradation. Moreover, the peptide mass fingerprinting analysis of major extracellular proteins and corresponding gene-knockout strains studies revealed that MtCel7A and MtCel5A were the core cellulolytic enzymes. Furthermore, synergistic experiments found that hydrolytic efficiencies of MtCel7A and MtCel5A were both improved by mixture C1/C4 oxidizing MtLPMO9H, but inhibited by C1 oxidizing MtLPMO9E and C4 oxidizing MtLPMO9J respectively. These results demonstrated the potential application of C1/C4 oxidizing LPMOs for future designing novel cellulolytic enzyme cocktails on the efficient conversion of cellulose into biofuels and biochemicals.
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Affiliation(s)
- Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiahuan Zou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Kun Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jinyang Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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13
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MtTRC-1, a Novel Transcription Factor, Regulates Cellulase Production via Directly Modulating the Genes Expression of the Mthac-1 and Mtcbh-1 in Myceliophthora thermophila. Appl Environ Microbiol 2022; 88:e0126322. [PMID: 36165620 PMCID: PMC9552611 DOI: 10.1128/aem.01263-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The thermophilic fungus Myceliophthora thermophila has been used to produce industrial enzymes and biobased chemicals. In saprotrophic fungi, the mechanisms regulating cellulase production have been studied, which revealed the involvement of multiple transcription factors. However, in M. thermophila, the transcription factors influencing cellulase gene expression and secretion remain largely unknown. In this study, we identified and characterized a novel cellulase regulator (MtTRC-1) in M. thermophila through a combination of functional genomics and genetic analyses. Deletion of Mttrc-1 resulted in significantly decreased cellulase production and activities. Transcriptome analysis revealed downregulation of not only the encoding genes of main cellulases but also the transcriptional regulator MtHAC-1 of UPR pathway after disruption of MtTRC-1 under cellulolytic induction conditions. Herein, we also characterized the ortholog of the yeast HAC1p in M. thermophila. We show that Mthac-1 mRNA undergoes an endoplasmic reticulum (ER) stress-induced splicing by removing a 23-nucleotide (nt) intron. Notably, the protein secretion on cellulose was dramatically impaired by the deletion of MtHAC-1. Moreover, the colonial growth on various carbon sources was defective in the absence of MtHAC-1. Electrophoretic mobility shift assays and chromatin immunoprecipitation assays verified MtTRC-1 regulates the transcription of Mthac-1 and the major cellulase gene Mtcbh-1 by binding directly to the promoters in vitro and in vivo. Furthermore, DNase I footprinting assays identified the putative consensus binding site (5′-GNG/C-3′). These results revealed the importance of MtTRC-1 for positively regulating cellulase production. This finding has clarified the complex regulatory pathways involved in cellulolytic enzyme production. IMPORTANCE In the present study, we characterized a novel regulator MtTRC-1 in M. thermophila, which regulated cellulase production through direct transcriptional regulation of the Mthac-1 and Mtcbh-1 genes. Our data demonstrated that MtHAC-1 is a key factor for the cellulase secretion capacity of M. thermophila. Our data indicate that this thermophilic fungus regulates cellulase production through a multilevels network, in which the protein secretory pathway is modulated by MtHAC-1-dependent UPR pathway and the cellulase gene expression is directly regulated in parallel by transcription factors. The conservation of Mttrc1 in filamentous fungi suggests this mechanism may be exploited to engineer filamentous fungal cell factories capable of producing proteins on an industrial scale.
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14
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Development of an Efficient C-to-T Base-Editing System and Its Application to Cellulase Transcription Factor Precise Engineering in Thermophilic Fungus Myceliophthora thermophila. Microbiol Spectr 2022; 10:e0232121. [PMID: 35608343 PMCID: PMC9241923 DOI: 10.1128/spectrum.02321-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Myceliophthora thermophila is a thermophilic fungus with great potential in biorefineries and biotechnology. The base editor is an upgraded version of the clustered regularly interspaced short palindromic repeats (CRISPR)-dependent genome-editing tool that introduces precise point mutations without causing DNA double-strand breaks (DSBs) and has been used in various organisms but rarely in filamentous fungi, especially thermophilic filamentous fungi. Here, for the first time, we constructed three cytosine base editors (CBEs) in M. thermophila, namely, evolved apolipoprotein B mRNA-editing enzyme catalytic subunit 1 (APOBEC1) cytosine base editor 4 max (Mtevo-BE4max), bacteriophage Mu Gam protein cytosine base editor 4 max (MtGAM-BE4max), and evolved CDA1 deaminase cytosine base editor (Mtevo-CDA1), and efficiently inactivated genes by precisely converting three codons (CAA, CAG, and CGA) into stop codons without DSB formation. The Mtevo-CDA1 editor with up to 92.6% editing efficiency is a more suitable tool for cytosine base editing in thermophilic fungi. To investigate the function of each motif of the cellulase transcription factor M. thermophila CLR-2 (MtCLR-2), we used the Mtevo-CDA1 editor. The fungal-specific motif of MtCLR-2 was found to be strongly involved in cellulase secretion, conidium formation, hyphal branching, and colony formation. Mutation of the fungus-specific motif caused significant defects in these characteristics. Thus, we developed an efficient thermophilic fungus-compatible base-editing system that could also be used for genetic engineering in other relevant filamentous fungi. IMPORTANCE A CRISPR/Cas-based base-editing approach has been developed to introduce point mutations without inducing double-strand breaks (DSBs) and attracted substantial academic and industrial interest. Our study developed the deaminase-cytosine base-editing system to efficiently edit three target genes, amdS, cre-1, and the essential cellulase regulator gene Mtclr-2, in Myceliophthora thermophila. A variety of point mutations in the target loci of the DNA-binding domain and fungus-specific motif of M. thermophila CLR-2 (MtCLR-2) were successfully generated via our base editor Mtevo-CDA1 to elucidate its function. Here, we show that the DNA-binding domain of MtCLR-2 is important for the fungal response to cellulose conditions, while its fungus-specific motif is involved in fungal growth. These findings indicate that our base editor can be an effective tool for elucidating the functions of motifs of target genes in filamentous fungi and for metabolic engineering in the field of synthetic biology.
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15
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Delangiz N, Aliyar S, Pashapoor N, Nobaharan K, Asgari Lajayer B, Rodríguez-Couto S. Can polymer-degrading microorganisms solve the bottleneck of plastics' environmental challenges? CHEMOSPHERE 2022; 294:133709. [PMID: 35074325 DOI: 10.1016/j.chemosphere.2022.133709] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/27/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Increasing world population and industrial activities have enhanced anthropogenic pollution, plastic pollution being especially alarming. So, plastics should be recycled and/or make them biodegradable. Chemical and physical remediating methods are usually energy consuming and costly. In addition, they are not ecofriendly and usually produce toxic byproducts. Bioremediation is a proper option as it is cost-efficient and environmentally friendly. Plastic production and consumption are increasing daily, and, as a consequence, more microorganisms are exposed to these nonbiodegradable polymers. Therefore, investigating new efficient microorganisms and increasing the knowledge about their biology can pave the way for efficient and feasible plastic bioremediation processes. In this sense, omics, systems biology and bioinformatics are three important fields to analyze the biodegradation pathways in microorganisms. Based on the above-mentioned technologies, researchers can engineer microorganisms with specific desired properties to make bioremediation more efficient.
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Affiliation(s)
- Nasser Delangiz
- Department of Plant Biotechnology and Breeding, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
| | - Sajad Aliyar
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Neda Pashapoor
- Department of Soil Science, Faculty of Agriculture, Urmia University, Urmia, Iran
| | | | - Behnam Asgari Lajayer
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
| | - Susana Rodríguez-Couto
- Department of Separation Science, LUT School of Engineering Science, LUT University, Sammonkatu 12, FI-50130 Mikkeli, Finland
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16
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Liu D, Xu Z, Li J, Liu Q, Yuan Q, Guo Y, Ma H, Tian C. Reconstruction and analysis of genome-scale metabolic model for thermophilic fungus Myceliophthora thermophila. Biotechnol Bioeng 2022; 119:1926-1937. [PMID: 35257374 DOI: 10.1002/bit.28080] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/24/2022] [Accepted: 03/03/2022] [Indexed: 11/11/2022]
Abstract
Myceliophthora thermophila, a thermophilic fungus that can degrade and utilize all major polysaccharides in plant biomass, has great potential in biotechnological industries. Here, the first manually curated genome-scale metabolic model iDL1450 for M. thermophila was reconstructed using an auto-generating pipeline with thorough manual curation. The model contains 1450 genes, 2592 reactions and 1784 unique metabolites. High accuracy was shown in predictions related to carbon and nitrogen source utilization based on data obtained from Biolog experiments. Besides, metabolism profiles were analyzed using iDL1450 integrated with transcriptomics data of M. thermophila at various growth temperatures. The refined model provides new insights into thermophilic fungi metabolism and sheds light on model-driven strain design to improve biotechnological applications of this thermophilic lignocellulosic fungus. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Defei Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Zixiang Xu
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Qianqian Yuan
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yanmei Guo
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Hongwu Ma
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
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17
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Naeem M, Manzoor S, Abid MUH, Tareen MBK, Asad M, Mushtaq S, Ehsan N, Amna D, Xu B, Hazafa A. Fungal Proteases as Emerging Biocatalysts to Meet the Current Challenges and Recent Developments in Biomedical Therapies: An Updated Review. J Fungi (Basel) 2022; 8:jof8020109. [PMID: 35205863 PMCID: PMC8875690 DOI: 10.3390/jof8020109] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 02/07/2023] Open
Abstract
With the increasing world population, demand for industrialization has also increased to fulfill humans' living standards. Fungi are considered a source of essential constituents to produce the biocatalytic enzymes, including amylases, proteases, lipases, and cellulases that contain broad-spectrum industrial and emerging applications. The present review discussed the origin, nature, mechanism of action, emerging aspects of genetic engineering for designing novel proteases, genome editing of fungal strains through CRISPR technology, present challenges and future recommendations of fungal proteases. The emerging evidence revealed that fungal proteases show a protective role to many environmental exposures and discovered that an imbalance of protease inhibitors and proteases in the epithelial barriers leads to the protection of chronic eosinophilic airway inflammation. Moreover, mitoproteases recently were found to execute intense proteolytic processes that are crucial for mitochondrial integrity and homeostasis function, including mitochondrial biogenesis, protein synthesis, and apoptosis. The emerging evidence revealed that CRISPR/Cas9 technology had been successfully developed in various filamentous fungi and higher fungi for editing of specific genes. In addition to medical importance, fungal proteases are extensively used in different industries such as foods to prepare butter, fruits, juices, and cheese, and to increase their shelf life. It is concluded that hydrolysis of proteins in industries is one of the most significant applications of fungal enzymes that led to massive usage of proteomics.
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Affiliation(s)
- Muhammad Naeem
- College of Life Science, Hebei Normal University, Shijiazhuang 050025, China;
| | - Saba Manzoor
- Department of Zoology, University of Sialkot, Sialkot 51310, Pakistan;
| | | | | | - Mirza Asad
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - Sajida Mushtaq
- Department of Zoology, Government College Women University, Sialkot 51040, Pakistan;
| | - Nazia Ehsan
- Department of Zoology, Wildlife and Fisheries, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - Dua Amna
- Institute of Food Science & Nutrition, Bahauddin Zakariya University, Multan 60800, Pakistan;
| | - Baojun Xu
- Food Science and Technology Program, Beijing Normal University-Hong Kong Baptist University (BNU-HKBU) United International College, Zhuhai 519087, China
- Correspondence: (B.X.); (A.H.)
| | - Abu Hazafa
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
- Correspondence: (B.X.); (A.H.)
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18
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Keresztes G, Baer M, Alfenito MR, Verwoerd TC, Kovalchuk A, Wiebe MG, Andersen TK, Saloheimo M, Tchelet R, Kensinger R, Grødeland G, Emalfarb M. The Highly Productive Thermothelomyces heterothallica C1 Expression System as a Host for Rapid Development of Influenza Vaccines. Vaccines (Basel) 2022; 10:vaccines10020148. [PMID: 35214607 PMCID: PMC8877961 DOI: 10.3390/vaccines10020148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 01/27/2023] Open
Abstract
(1) Influenza viruses constantly change and evade prior immune responses, forcing seasonal re-vaccinations with updated vaccines. Current FDA-approved vaccine manufacturing technologies are too slow and/or expensive to quickly adapt to mid-season changes in the virus or to the emergence of pandemic strains. Therefore, cost-effective vaccine technologies that can quickly adapt to newly emerged strains are desirable. (2) The filamentous fungal host Thermothelomyces heterothallica C1 (C1, formerly Myceliophthora thermophila) offers a highly efficient and cost-effective alternative to reliably produce immunogens of vaccine quality at large scale. (3) We showed the utility of the C1 system expressing hemagglutinin (HA) and a HA fusion protein from different H1N1 influenza A virus strains. Mice vaccinated with the C1-derived HA proteins elicited anti-HA immune responses similar, or stronger than mice vaccinated with HA products derived from prototypical expression systems. A challenge study demonstrated that vaccinated mice were protected against the aggressive homologous viral challenge. (4) The C1 expression system is proposed as part of a set of protein expression systems for plug-and-play vaccine manufacturing platforms. Upon the emergence of pathogens of concern these platforms could serve as a quick solution for producing enough vaccines for immunizing the world population in a much shorter time and more affordably than is possible with current platforms.
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Affiliation(s)
- Gabor Keresztes
- Dyadic International Inc., 140 Intracoastal Pointe Drive, Suite 404, Jupiter, FL 33477, USA; (G.K.); (T.C.V.); (R.T.)
| | - Mark Baer
- EnGen Bio LLC, 61 Avondale Ave., Redwood City, CA 94062, USA; (M.B.); (M.R.A.)
| | - Mark R. Alfenito
- EnGen Bio LLC, 61 Avondale Ave., Redwood City, CA 94062, USA; (M.B.); (M.R.A.)
| | - Theo C. Verwoerd
- Dyadic International Inc., 140 Intracoastal Pointe Drive, Suite 404, Jupiter, FL 33477, USA; (G.K.); (T.C.V.); (R.T.)
| | - Andriy Kovalchuk
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044 Espoo, Finland; (A.K.); (M.G.W.); (M.S.)
| | - Marilyn G. Wiebe
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044 Espoo, Finland; (A.K.); (M.G.W.); (M.S.)
| | - Tor Kristian Andersen
- Institute of Clinical Medicine, University of Oslo, 0027 Oslo, Norway; (T.K.A.); (G.G.)
| | - Markku Saloheimo
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044 Espoo, Finland; (A.K.); (M.G.W.); (M.S.)
| | - Ronen Tchelet
- Dyadic International Inc., 140 Intracoastal Pointe Drive, Suite 404, Jupiter, FL 33477, USA; (G.K.); (T.C.V.); (R.T.)
| | - Richard Kensinger
- Sanofi Pasteur, 1541 Ave. Marcel Mérieux, 69280 Marcy l’Etoile, France;
| | - Gunnveig Grødeland
- Institute of Clinical Medicine, University of Oslo, 0027 Oslo, Norway; (T.K.A.); (G.G.)
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0027 Oslo, Norway
| | - Mark Emalfarb
- Dyadic International Inc., 140 Intracoastal Pointe Drive, Suite 404, Jupiter, FL 33477, USA; (G.K.); (T.C.V.); (R.T.)
- Correspondence:
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19
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Gu S, Zhao Z, Yao Y, Li J, Tian C. Designing and Constructing a Novel Artificial Pathway for Malonic Acid Production Biologically. Front Bioeng Biotechnol 2022; 9:820507. [PMID: 35127677 PMCID: PMC8807515 DOI: 10.3389/fbioe.2021.820507] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/14/2021] [Indexed: 11/13/2022] Open
Abstract
Malonic acid is used as a common component of many products and processes in the pharmaceutical and cosmetic industries. Here, we designed a novel artificial synthetic pathway of malonic acid, in which oxaloacetate, an intermediate of cytoplasmic reductive tricarboxylic acid (rTCA) pathway, is converted to malonic semialdehyde and then to malonic acid, sequentially catalyzed by a-keto decarboxylase and malonic semialdehyde dehydrogenase. After the systematic screening, we discovered the enzyme oxaloacetate decarboxylase Mdc, catalyzing the first step of the artificially designed pathway in vitro. Then, this synthetic pathway was functionally constructed in cellulolytic thermophilic fungus Myceliophthora thermophila. After enhancement of glucose uptake, the titer of malonic acid achieved 42.5 mg/L. This study presents a novel biological pathway for producing malonic acid from renewable resources in the future.
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Affiliation(s)
- Shuying Gu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhen Zhao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yonghong Yao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- *Correspondence: Jingen Li, ; Chaoguang Tian,
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- *Correspondence: Jingen Li, ; Chaoguang Tian,
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20
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Hofrichter M, Kellner H, Herzog R, Karich A, Kiebist J, Scheibner K, Ullrich R. Peroxide-Mediated Oxygenation of Organic Compounds by Fungal Peroxygenases. Antioxidants (Basel) 2022; 11:163. [PMID: 35052667 PMCID: PMC8772875 DOI: 10.3390/antiox11010163] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/03/2022] Open
Abstract
Unspecific peroxygenases (UPOs), whose sequences can be found in the genomes of thousands of filamentous fungi, many yeasts and certain fungus-like protists, are fascinating biocatalysts that transfer peroxide-borne oxygen (from H2O2 or R-OOH) with high efficiency to a wide range of organic substrates, including less or unactivated carbons and heteroatoms. A twice-proline-flanked cysteine (PCP motif) typically ligates the heme that forms the heart of the active site of UPOs and enables various types of relevant oxygenation reactions (hydroxylation, epoxidation, subsequent dealkylations, deacylation, or aromatization) together with less specific one-electron oxidations (e.g., phenoxy radical formation). In consequence, the substrate portfolio of a UPO enzyme always combines prototypical monooxygenase and peroxidase activities. Here, we briefly review nearly 20 years of peroxygenase research, considering basic mechanistic, molecular, phylogenetic, and biotechnological aspects.
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Affiliation(s)
- Martin Hofrichter
- Department of Bio- and Environmental Sciences, TU Dresden-International Institute Zittau, Markt 23, 02763 Zittau, Germany; (H.K.); (R.H.); (A.K.); (R.U.)
| | - Harald Kellner
- Department of Bio- and Environmental Sciences, TU Dresden-International Institute Zittau, Markt 23, 02763 Zittau, Germany; (H.K.); (R.H.); (A.K.); (R.U.)
| | - Robert Herzog
- Department of Bio- and Environmental Sciences, TU Dresden-International Institute Zittau, Markt 23, 02763 Zittau, Germany; (H.K.); (R.H.); (A.K.); (R.U.)
| | - Alexander Karich
- Department of Bio- and Environmental Sciences, TU Dresden-International Institute Zittau, Markt 23, 02763 Zittau, Germany; (H.K.); (R.H.); (A.K.); (R.U.)
| | - Jan Kiebist
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany; (J.K.); (K.S.)
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Am Mühlenberg 13, 14476 Potsdam-Golm, Germany
| | - Katrin Scheibner
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany; (J.K.); (K.S.)
| | - René Ullrich
- Department of Bio- and Environmental Sciences, TU Dresden-International Institute Zittau, Markt 23, 02763 Zittau, Germany; (H.K.); (R.H.); (A.K.); (R.U.)
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21
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Pragya, Sharma KK, Kumar A, Singh D, Kumar V, Singh B. Immobilized phytases: an overview of different strategies, support material, and their applications in improving food and feed nutrition. Crit Rev Food Sci Nutr 2021; 63:5465-5487. [PMID: 34965785 DOI: 10.1080/10408398.2021.2020719] [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] [Indexed: 10/19/2022]
Abstract
Phytases are the most widely used food and feed enzymes, which aid in nutritional improvement by reducing anti-nutritional factor. Despite the benefits, enzymes usage in the industry is restricted by several factors such as their short life-span and poor reusability, which result in high costs for large-scale utilization at commercial scale. Furthermore, under pelleting conditions such as high temperatures, pH, and other factors, the enzyme becomes inactive due to lesser stability. Immobilization of phytases has been suggested as a way to overcome these limitations with improved performance. Matrices used to immobilize phytases include inorganic (Hydroxypatite, zeolite, and silica), organic (Polyacrylamide, epoxy resins, alginate, chitosan, and starch agar), soluble matrix (Polyvinyl alcohol), and nanomaterials including nanoparticles, nanofibers, nanotubes. Several surface analysis methods, including thermal gravimetric analysis (TGA), differential scanning calorimetry (DSC), and FTIR analysis, have been used to characterize immobilized phytase. Immobilized phytases have been used in a broad range of biotechnological applications such as animal feed, biodegradation of food phytates, preparations of myo-inositol phosphates, and sulfoxidation by vanadate-substituted peroxidase. This article provides information on different matrices used for phytase immobilization from the last two decades, including the process of immobilization and support material, surface analysis techniques, and multifarious biotechnological applications of the immobilized phytases.
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Affiliation(s)
- Pragya
- Laboratory of Bioprocess Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Anil Kumar
- Department of Botany, Pt. N.R.S. Govt. College, Rohtak, India
| | - Davender Singh
- Department of Physics, RPS Degree College, Mahendergarh, India
| | - Vijay Kumar
- Department of Botany, Shivaji College, University of Delhi, New Delhi, India
| | - Bijender Singh
- Laboratory of Bioprocess Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- Department of Biotechnology, Central University of Haryana, Jant-Pali, India
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22
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Yang YJ, Liu Y, Liu DD, Guo WZ, Wang LX, Wang XJ, Lv HX, Yang Y, Liu Q, Tian CG. Development of a flow cytometry-based plating-free system for strain engineering in industrial fungi. Appl Microbiol Biotechnol 2021; 106:713-727. [PMID: 34921331 DOI: 10.1007/s00253-021-11733-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 01/02/2023]
Abstract
Recent technical advances regarding filamentous fungi have accelerated the engineering of fungal-based production and benefited basic science. However, challenges still remain and limit the speed of fungal applications. For example, high-throughput technologies tailored to filamentous fungi are not yet commonly available for genetic modification. The currently used fungal genetic manipulations are time-consuming and laborious. Here, we developed a flow cytometry-based plating-free system to directly screen and isolate the transformed protoplasts in industrial fungi Myceliophthora thermophila and Aspergillus niger. This system combines genetic engineering via the 2A peptide and the CRISPR-Cas9 system, strain screening by flow cytometry, and direct sorting of colonies for deep-well-plate incubation and phenotypic analysis while avoiding culturing transformed protoplasts in plates, colony picking, conidiation, and cultivation. As a proof of concept, we successfully applied this system to generate the glucoamylase-hyperproducing strains MtYM6 and AnLM3 in M. thermophila and A. niger, respectively. Notably, the protein secretion level and enzyme activities in MtYM6 were 17.3- and 25.1-fold higher than in the host strain. Overall, these findings suggest that the flow cytometry-based plating-free system can be a convenient and efficient tool for strain engineering in fungal biotechnology. We expect this system to facilitate improvements of filamentous fungal strains for industrial applications. KEY POINTS: • Development of a flow cytometry-based plating-free (FCPF) system is presented. • Application of FCPF system in M. thermophila and A. niger for glucoamylase platform. • Hyper-produced strains MtYM6 and AnLM3 for glucoamylase production are generated.
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Affiliation(s)
- Yu-Jing Yang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Yin Liu
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Dan-Dan Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wen-Zhu Guo
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Li-Xian Wang
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Xing-Ji Wang
- Longda Biotechnology Inc, 276400, Linyi, Shandong, China
| | - He-Xin Lv
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yang Yang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
| | - Chao-Guang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
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23
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Mayr SA, Subagia R, Weiss R, Schwaiger N, Weber HK, Leitner J, Ribitsch D, Nyanhongo GS, Guebitz GM. Oxidation of Various Kraft Lignins with a Bacterial Laccase Enzyme. Int J Mol Sci 2021; 22:ijms222313161. [PMID: 34884966 PMCID: PMC8658217 DOI: 10.3390/ijms222313161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 01/26/2023] Open
Abstract
Modification of kraft lignin (KL), traditionally uses harsh and energy-demanding physical and chemical processes. In this study, the potential of the bacterial laccase CotA (spore coating protein A) for oxidation of KL under mild conditions was assessed. Thereby, the efficiency of CotA to oxidize both softwood and hardwood KL of varying purity at alkaline conditions was examined. For the respective type of wood, the highest oxidation activity by CotA was determined for the medium ash content softwood KL (MA_S) and the medium ash content hardwood KL (MA_H), respectively. By an up to 95% decrease in fluorescence and up to 65% in phenol content coupling of the structural lignin units was indicated. These results correlated with an increase in viscosity and molecular weight, which increased nearly 2 and 20-fold for MA_H and about 1.3 and 6.0-fold for MA_S, respectively. Thus, this study confirms that the CotA laccase can oxidize a variety of KL at alkaline conditions, while the origin and purity of KL were found to have a major impact on the efficiency of oxidation. Under the herein tested conditions, it was observed that the MA_H KL showed the highest susceptibility to CotA oxidation when compared to the other hardwood KLs and the softwood KLs. Therefore, this could be a viable method to produce sustainable resins and adhesives.
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Affiliation(s)
- Sebastian A. Mayr
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences (BOKU), Konrad Lorenz Strasse 20, 3430 Tulln, Austria; (S.A.M.); (D.R.); (G.S.N.); (G.M.G.)
| | - Raditya Subagia
- Austrian Centre for Industrial Biotechnology (ACIB), Konrad Lorenz Strasse 20, 3430 Tulln, Austria;
| | - Renate Weiss
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences (BOKU), Konrad Lorenz Strasse 20, 3430 Tulln, Austria; (S.A.M.); (D.R.); (G.S.N.); (G.M.G.)
- Correspondence: ; Tel.: +43-1-47654-97486
| | - Nikolaus Schwaiger
- Sappi Paper Holding GmbH, Brucker Strasse 21, 8101 Gratkorn, Austria; (N.S.); (H.K.W.)
| | - Hedda K. Weber
- Sappi Paper Holding GmbH, Brucker Strasse 21, 8101 Gratkorn, Austria; (N.S.); (H.K.W.)
| | | | - Doris Ribitsch
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences (BOKU), Konrad Lorenz Strasse 20, 3430 Tulln, Austria; (S.A.M.); (D.R.); (G.S.N.); (G.M.G.)
- Austrian Centre for Industrial Biotechnology (ACIB), Konrad Lorenz Strasse 20, 3430 Tulln, Austria;
| | - Gibson S. Nyanhongo
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences (BOKU), Konrad Lorenz Strasse 20, 3430 Tulln, Austria; (S.A.M.); (D.R.); (G.S.N.); (G.M.G.)
- Austrian Centre for Industrial Biotechnology (ACIB), Konrad Lorenz Strasse 20, 3430 Tulln, Austria;
| | - Georg M. Guebitz
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences (BOKU), Konrad Lorenz Strasse 20, 3430 Tulln, Austria; (S.A.M.); (D.R.); (G.S.N.); (G.M.G.)
- Austrian Centre for Industrial Biotechnology (ACIB), Konrad Lorenz Strasse 20, 3430 Tulln, Austria;
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24
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Li J, Chen B, Gu S, Zhao Z, Liu Q, Sun T, Zhang Y, Wu T, Liu D, Sun W, Tian C. Coordination of consolidated bioprocessing technology and carbon dioxide fixation to produce malic acid directly from plant biomass in Myceliophthora thermophila. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:186. [PMID: 34556173 PMCID: PMC8461902 DOI: 10.1186/s13068-021-02042-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Consolidated bioprocessing (CBP) technique is a promising strategy for biorefinery construction, producing bulk chemicals directly from plant biomass without extra hydrolysis steps. Fixing and channeling CO2 into carbon metabolism for increased carbon efficiency in producing value-added compounds is another strategy for cost-effective bio-manufacturing. It has not been reported whether these two strategies can be combined in one microbial platform. RESULTS In this study, using the cellulolytic thermophilic fungus Myceliophthora thermophila, we designed and constructed a novel biorefinery system DMCC (Direct microbial conversion of biomass with CO2 fixation) through incorporating two CO2 fixation modules, PYC module and Calvin-Benson-Bassham (CBB) pathway. Harboring the both modules, the average rate of fixing and channeling 13CO2 into malic acid in strain CP51 achieved 44.4, 90.7, and 80.7 mg/L/h, on xylose, glucose, and cellulose, respectively. The corresponding titers of malic acid were up to 42.1, 70.4, and 70.1 g/L, respectively, representing the increases of 40%, 10%, and 7%, respectively, compared to the parental strain possessing only PYC module. The DMCC system was further improved by enhancing the pentose uptake ability. Using raw plant biomass as the feedstock, yield of malic acid produced by the DMCC system was up to 0.53 g/g, with 13C content of 0.44 mol/mol malic acid, suggesting DMCC system can produce 1 t of malic acid from 1.89 t of biomass and fix 0.14 t CO2 accordingly. CONCLUSIONS This study designed and constructed a novel biorefinery system named DMCC, which can convert raw plant biomass and CO2 into organic acid efficiently, presenting a promising strategy for cost-effective production of value-added compounds in biorefinery. The DMCC system is one of great options for realization of carbon neutral economy.
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Affiliation(s)
- Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Bingchen Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shuying Gu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhen Zhao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Tao Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Yongli Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Taju Wu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Defei Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Wenliang Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
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25
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Mayr SA, Schwaiger N, Weber HK, Kovač J, Guebitz GM, Nyanhongo GS. Enzyme Catalyzed Copolymerization of Lignosulfonates for Hydrophobic Coatings. Front Bioeng Biotechnol 2021; 9:697310. [PMID: 34336809 PMCID: PMC8317694 DOI: 10.3389/fbioe.2021.697310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
Enzymatic polymerization of lignin can generate a variety of value-added products concomitantly replacing fossil-based resources. In line with this approach, a laccase from the thermophilic fungus Myceliophthora thermophila (MtL) was used to couple a hydrophobicity enhancing fluorophenol (FP) molecule, namely 4-[4-(trifluoromethyl)phenoxy]phenol (4,4-F3MPP), as a model substrate onto lignosulfonate (LS). During the coupling reaction changes in fluorescence, phenol content, viscosity and molecular weight (size exclusion chromatography; SEC) were monitored. The effects of enzymatic coupling of FP onto LS on hydrophobicity were investigated by the means of water contact angle (WCA) measurement and determination of swelling capacity. Full polymerization of LS resulting in the production of water-insoluble polymers was achieved at a pH of 7 and 33°C. Incorporation of 2% (w/v) of FP led to an increase in WCA by 59.2% while the swelling capacity showed a decrease by 216.8%. Further, Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) analysis indicated successful covalent coupling of the FP molecule onto LS by an emerging peak at 1,320 cm–1 in the FTIR spectrum and the evidence of Fluor in the XPS spectrum. This study shows the ability of laccase to mediate the tailoring of LS properties to produce functional polymers.
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Affiliation(s)
- Sebastian A Mayr
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Tulln, Austria
| | | | | | - Janez Kovač
- Department of Surface Engineering, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Georg M Guebitz
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Tulln, Austria.,Austrian Centre of Industrial Biotechnology, Tulln, Austria
| | - Gibson S Nyanhongo
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Tulln, Austria.,Austrian Centre of Industrial Biotechnology, Tulln, Austria
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26
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Singh B, Bala A, Anu, Alokika, Kumar V, Singh D. Biochemical properties of cellulolytic and xylanolytic enzymes from Sporotrichum thermophile and their utility in bioethanol production using rice straw. Prep Biochem Biotechnol 2021; 52:197-209. [PMID: 34010094 DOI: 10.1080/10826068.2021.1925911] [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: 10/21/2022]
Abstract
Production of cellulolytic and xylanolytic enzymes by Sporotrichum thermophile was enhanced using response surface methodology in solid-state fermentation (SSF) using wheat straw and cotton oil cake. Cellulolytic and xylanolytic enzymes were partially purified by ammonium sulfate precipitation followed by ion exchange and gel filtration chromatographic techniques. Xylanase of S. thermophile is neutral xylanase displaying optimal activity at 60 °C with Km and Vmax values of 0.2 mg/mL and 238.05 µmole/min, respectively. All cellulases produced by the thermophilic mold showed optimal activity at pH 5.0 and 60 °C with Km values of 0.312 mg/mL, 0.113 mg/mL, and 0.285 mM for carboxymethyl cellulase (CMCase), filter paper cellulase (FPase), and β-glucosidase, respectively and while Vmax values were 181.81, 138.88, and 66.67 µmole/min, respectively. The presence of various metal ions (Ca2+ and Co2+), chemical reagent (glutaraldehyde), and surfactants (Tween 80 and Triton X-100) significantly improved the activities of all enzymes. All the enzymes showed high storage stability under low temperature (-20 and 4 °C) conditions. Cellulolytic and xylanolytic enzymes resulted in enhanced liberation of reducing sugars (356.34 mg/g) by hydrolyzing both cellulosic and hemicellulosic fractions of ammonia-pretreated rice straw as compared to other pretreatment methods used in the study. Fermentation of enzymatic hydrolysate resulted in the formation of 28.88 and 27.18 g/L of bioethanol in separate hydrolysis and fermentation (SHF) process by Saccharomyces cerevisiae and Pichia stipitis, respectively. Therefore, cellulolytic and xylanolytic enzymes of S. thermophile exhibited ideal properties of biocatalysts useful in the saccharification of cellulosic and hemicellulosic fractions of rice straw for the production of bioethanol.
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Affiliation(s)
- Bijender Singh
- Laboratory of Bioprocess Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, India.,Department of Biotechnology, Central University of Haryana, Mahendergarh, India
| | - Anju Bala
- Laboratory of Bioprocess Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Anu
- Laboratory of Bioprocess Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Alokika
- Laboratory of Bioprocess Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Vinod Kumar
- Department of Chemistry, Central University of Haryana, Mahendergarh, India
| | - Davender Singh
- Department of Physics, RPS Degree College, Mahendergarh, India
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27
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Wang H, Sun T, Zhao Z, Gu S, Liu Q, Wu T, Wang D, Tian C, Li J. Transcriptional Profiling of Myceliophthora thermophila on Galactose and Metabolic Engineering for Improved Galactose Utilization. Front Microbiol 2021; 12:664011. [PMID: 33995328 PMCID: PMC8113861 DOI: 10.3389/fmicb.2021.664011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/19/2021] [Indexed: 11/13/2022] Open
Abstract
Efficient biological conversion of all sugars from lignocellulosic biomass is necessary for the cost-effective production of biofuels and commodity chemicals. Galactose is one of the most abundant sugar in many hemicelluloses, and it will be important to capture this carbon for an efficient bioconversion process of plant biomass. Thermophilic fungus Myceliophthora thermophila has been used as a cell factory to produce biochemicals directly from renewable polysaccharides. In this study, we draw out the two native galactose utilization pathways, including the Leloir pathway and oxido-reductive pathway, and identify the significance and contribution of them, through transcriptional profiling analysis of M. thermophila and its mutants on galactose. We find that galactokinase was necessary for galactose transporter expression, and disruption of galK resulted in decreased galactose utilization. Through metabolic engineering, both galactokinase deletion and galactose transporter overexpression can activate internal the oxido-reductive pathway and improve the consumption rate of galactose. Finally, the heterologous galactose-degradation pathway, De Ley–Doudoroff (DLD) pathway, was successfully integrated into M. thermophila, and the consumption rate of galactose in the engineered strain was increased by 57%. Our study focuses on metabolic engineering for accelerating galactose utilization in a thermophilic fungus that will be beneficial for the rational design of fungal strains to produce biofuels and biochemicals from a variety of feedstocks with abundant galactose.
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Affiliation(s)
- Hanyu Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Tao Sun
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhen Zhao
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Shuying Gu
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Qian Liu
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Taju Wu
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Depei Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Chaoguang Tian
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jingen Li
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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28
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Improved strategies to efficiently isolate thermophilic, thermotolerant, and heat-resistant fungi from compost and soil. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01674-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractThermophilic, thermotolerant and heat-resistant fungi developed different physiological traits, enabling them to sustain or even flourish under elevated temperatures, which are life-hostile for most other eukaryotes. With the growing demand of heat-stable molecules in biotechnology and industry, the awareness of heat-adapted fungi as a promising source of respective enzymes and biomolecules is still increasing. The aim of this study was to test two different strategies for the efficient isolation and identification of distinctly heat-adapted fungi from easily accessible substrates and locations. Eight compost piles and ten soil sites were sampled in combination with different culture-dependent approaches to describe suitable strategies for the isolation and selection of thermophilous fungi. Additionally, an approach with a heat-shock treatment, but without elevated temperature incubation led to the isolation of heat-resistant mesophilic species. The cultures were identified based on morphology, DNA barcodes, and microsatellite fingerprinting. In total, 191 obtained isolates were assigned to 31 fungal species, from which half are truly thermophilic or thermotolerant, while the other half are heat-resistant fungi. A numerous amount of heat-adapted fungi was isolated from both compost and soil samples, indicating the suitability of the used approaches and that the richness and availability of those organisms in such environments are substantially high.
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29
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Wichgers Schreur PJ, Tacken M, Gutjahr B, Keller M, van Keulen L, Kant J, van de Water S, Lin Y, Eiden M, Rissmann M, von Arnim F, König R, Brix A, Charreyre C, Audonnet JC, Groschup MH, Kortekaas J. Vaccine Efficacy of Self-Assembled Multimeric Protein Scaffold Particles Displaying the Glycoprotein Gn Head Domain of Rift Valley Fever Virus. Vaccines (Basel) 2021; 9:vaccines9030301. [PMID: 33806789 PMCID: PMC8005036 DOI: 10.3390/vaccines9030301] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/18/2021] [Accepted: 03/20/2021] [Indexed: 02/06/2023] Open
Abstract
Compared to free antigens, antigens immobilized on scaffolds, such as nanoparticles, generally show improved immunogenicity. Conventionally, antigens are conjugated to scaffolds through genetic fusion or chemical conjugation, which may result in impaired assembly or heterogeneous binding and orientation of the antigens. By combining two emerging technologies-i.e., self-assembling multimeric protein scaffold particles (MPSPs) and bacterial superglue-these shortcomings can be overcome and antigens can be bound on particles in their native conformation. In the present work, we assessed whether this technology could improve the immunogenicity of a candidate subunit vaccine against the zoonotic Rift Valley fever virus (RVFV). For this, the head domain of glycoprotein Gn, a known target of neutralizing antibodies, was coupled on various MPSPs to further assess immunogenicity and efficacy in vivo. The results showed that the Gn head domain, when bound to the lumazine synthase-based MPSP, reduced mortality in a lethal mouse model and protected lambs, the most susceptible RVFV target animals, from viremia and clinical signs after immunization. Furthermore, the same subunit coupled to two other MPSPs (Geobacillus stearothermophilus E2 or a modified KDPG Aldolase) provided full protection in lambs as well.
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Affiliation(s)
- Paul J. Wichgers Schreur
- Department of Virology, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands; (M.T.); (L.v.K.); (J.K.); (S.v.d.W.); (Y.L.); (J.K.)
- Correspondence:
| | - Mirriam Tacken
- Department of Virology, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands; (M.T.); (L.v.K.); (J.K.); (S.v.d.W.); (Y.L.); (J.K.)
| | - Benjamin Gutjahr
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (B.G.); (M.K.); (M.E.); (M.R.); (F.v.A.); (R.K.); (M.H.G.)
| | - Markus Keller
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (B.G.); (M.K.); (M.E.); (M.R.); (F.v.A.); (R.K.); (M.H.G.)
| | - Lucien van Keulen
- Department of Virology, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands; (M.T.); (L.v.K.); (J.K.); (S.v.d.W.); (Y.L.); (J.K.)
| | - Jet Kant
- Department of Virology, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands; (M.T.); (L.v.K.); (J.K.); (S.v.d.W.); (Y.L.); (J.K.)
| | - Sandra van de Water
- Department of Virology, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands; (M.T.); (L.v.K.); (J.K.); (S.v.d.W.); (Y.L.); (J.K.)
| | - Yanyin Lin
- Department of Virology, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands; (M.T.); (L.v.K.); (J.K.); (S.v.d.W.); (Y.L.); (J.K.)
| | - Martin Eiden
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (B.G.); (M.K.); (M.E.); (M.R.); (F.v.A.); (R.K.); (M.H.G.)
| | - Melanie Rissmann
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (B.G.); (M.K.); (M.E.); (M.R.); (F.v.A.); (R.K.); (M.H.G.)
| | - Felicitas von Arnim
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (B.G.); (M.K.); (M.E.); (M.R.); (F.v.A.); (R.K.); (M.H.G.)
| | - Rebecca König
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (B.G.); (M.K.); (M.E.); (M.R.); (F.v.A.); (R.K.); (M.H.G.)
| | - Alexander Brix
- Boehringer Ingelheim Veterinary Research Center GmbH & Co. KG, 30559 Hannover, Germany;
| | | | | | - Martin H. Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (B.G.); (M.K.); (M.E.); (M.R.); (F.v.A.); (R.K.); (M.H.G.)
| | - Jeroen Kortekaas
- Department of Virology, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands; (M.T.); (L.v.K.); (J.K.); (S.v.d.W.); (Y.L.); (J.K.)
- Laboratory of Virology, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
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30
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Arntzen MØ, Bengtsson O, Várnai A, Delogu F, Mathiesen G, Eijsink VGH. Quantitative comparison of the biomass-degrading enzyme repertoires of five filamentous fungi. Sci Rep 2020; 10:20267. [PMID: 33219291 PMCID: PMC7679414 DOI: 10.1038/s41598-020-75217-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 10/07/2020] [Indexed: 12/26/2022] Open
Abstract
The efficiency of microorganisms to degrade lignified plants is of great importance in the Earth's carbon cycle, but also in industrial biorefinery processes, such as for biofuel production. Here, we present a large-scale proteomics approach to investigate and compare the enzymatic response of five filamentous fungi when grown on five very different substrates: grass (sugarcane bagasse), hardwood (birch), softwood (spruce), cellulose and glucose. The five fungi included the ascomycetes Aspergillus terreus, Trichoderma reesei, Myceliophthora thermophila, Neurospora crassa and the white-rot basidiomycete Phanerochaete chrysosporium, all expressing a diverse repertoire of enzymes. In this study, we present comparable quantitative protein abundance values across five species and five diverse substrates. The results allow for direct comparison of fungal adaptation to the different substrates, give indications as to the substrate specificity of individual carbohydrate-active enzymes (CAZymes), and reveal proteins of unknown function that are co-expressed with CAZymes. Based on the results, we present a quantitative comparison of 34 lytic polysaccharide monooxygenases (LPMOs), which are crucial enzymes in biomass deconstruction.
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Affiliation(s)
- Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Ås, Norway.
| | - Oskar Bengtsson
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Ås, Norway
| | - Francesco Delogu
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Ås, Norway
| | - Geir Mathiesen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Ås, Norway
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31
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Grieco MAB, Haon M, Grisel S, de Oliveira-Carvalho AL, Magalhães AV, Zingali RB, Pereira N, Berrin JG. Evaluation of the Enzymatic Arsenal Secreted by Myceliophthora thermophila During Growth on Sugarcane Bagasse With a Focus on LPMOs. Front Bioeng Biotechnol 2020; 8:1028. [PMID: 32984289 PMCID: PMC7477043 DOI: 10.3389/fbioe.2020.01028] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/06/2020] [Indexed: 01/08/2023] Open
Abstract
The high demand for energy and the increase of the greenhouse effect propel the necessity to develop new technologies to efficiently deconstruct the lignocellulosic materials into sugars monomers. Sugarcane bagasse is a rich polysaccharide residue from sugar and alcohol industries. The thermophilic fungus Myceliophthora thermophila (syn. Sporotrichum thermophilum) is an interesting model to study the enzymatic degradation of biomass. The genome of M. thermophila encodes an extensive repertoire of cellulolytic enzymes including 23 lytic polysaccharide monooxygenases (LPMOs) from the Auxiliary Activity family 9 (AA9), which are known to oxidatively cleave the β-1,4 bonds and boost the cellulose conversion in a biorefinery context. To achieve a deeper understanding of the enzymatic capabilities of M. thermophila on sugarcane bagasse, we pretreated this lignocellulosic residue with different methods leading to solids with various cellulose/hemicellulose/lignin proportions and grew M. thermophila on these substrates. The secreted proteins were analyzed using proteomics taking advantage of two mass spectrometry methodologies. This approach unraveled the secretion of many CAZymes belonging to the Glycosyl Hydrolase (GH) and AA classes including several LPMOs that may contribute to the biomass degradation observed during fungal growth. Two AA9 LPMOs, called MtLPMO9B and MtLPMO9H, were selected from secretomic data and enzymatically characterized. Although MtLPMO9B and MtLPMO9H were both active on cellulose, they differed in terms of optimum temperatures and regioselectivity releasing either C1 or C1-C4 oxidized oligosaccharides, respectively. LPMO activities were also measured on sugarcane bagasse substrates with different levels of complexity. The boosting effect of these LPMOs on bagasse sugarcane saccharification by a Trichoderma reesei commercial cocktail was also observed. The partially delignified bagasse was the best substrate considering the oxidized oligosaccharides released and the acid treated bagasse was the best one in terms of saccharification boost.
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Affiliation(s)
- Maria Angela B Grieco
- Laboratório de Desenvolvimento de Bioprocessos, Departamento de Engenharia Bioquímica, Escola de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,INRAE, Faculté des Sciences de Luminy, Aix Marseille Université, UMR 1163 Biodiversité et Biotechnologie Fongiques, Polytech Marseille, Marseille, France
| | - Mireille Haon
- INRAE, Faculté des Sciences de Luminy, Aix Marseille Université, UMR 1163 Biodiversité et Biotechnologie Fongiques, Polytech Marseille, Marseille, France
| | - Sacha Grisel
- INRAE, Faculté des Sciences de Luminy, Aix Marseille Université, UMR 1163 Biodiversité et Biotechnologie Fongiques, Polytech Marseille, Marseille, France
| | - Ana Lucia de Oliveira-Carvalho
- Unidade de Espectrometria de Massas e Proteômica, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Augusto Vieira Magalhães
- Unidade de Espectrometria de Massas e Proteômica, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Russolina B Zingali
- Unidade de Espectrometria de Massas e Proteômica, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nei Pereira
- Laboratório de Desenvolvimento de Bioprocessos, Departamento de Engenharia Bioquímica, Escola de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jean-Guy Berrin
- INRAE, Faculté des Sciences de Luminy, Aix Marseille Université, UMR 1163 Biodiversité et Biotechnologie Fongiques, Polytech Marseille, Marseille, France
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32
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Kadowaki MAS, Higasi PMR, de Godoy MO, de Araújo EA, Godoy AS, Prade RA, Polikarpov I. Enzymatic versatility and thermostability of a new aryl-alcohol oxidase from Thermothelomyces thermophilus M77. Biochim Biophys Acta Gen Subj 2020; 1864:129681. [PMID: 32653619 DOI: 10.1016/j.bbagen.2020.129681] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/14/2020] [Accepted: 06/30/2020] [Indexed: 01/23/2023]
Abstract
Background Fungal aryl-alcohol oxidases (AAOx) are extracellular flavoenzymes that belong to glucose-methanol-choline oxidoreductase family and are responsible for the selective conversion of primary aromatic alcohols into aldehydes and aromatic aldehydes to their corresponding acids, with concomitant production of hydrogen peroxide (H2O2) as by-product. The H2O2 can be provided to lignin degradation pathway, a biotechnological property explored in biofuel production. In the thermophilic fungus Thermothelomyces thermophilus (formerly Myceliophthora thermophila), just one AAOx was identified in the exo-proteome. Methods The glycosylated and non-refolded crystal structure of an AAOx from T. thermophilus at 2.6 Å resolution was elucidated by X-ray crystallography combined with small-angle X-ray scattering (SAXS) studies. Moreover, biochemical analyses were carried out to shed light on enzyme substrate specificity and thermostability. Results This flavoenzyme harbors a flavin adenine dinucleotide as a cofactor and is able to oxidize aromatic substrates and 5-HMF. Our results also show that the enzyme has similar oxidation rates for bulky or simple aromatic substrates such as cinnamyl and veratryl alcohols. Moreover, the crystal structure of MtAAOx reveals an open active site, which might explain observed specificity of the enzyme. Conclusions MtAAOx shows previously undescribed structural differences such as a fully accessible catalytic tunnel, heavy glycosylation and Ca2+ binding site providing evidences for thermostability and activity of the enzymes from AA3_2 subfamily. General significance Structural and biochemical analyses of MtAAOx could be important for comprehension of aryl-alcohol oxidases structure-function relationships and provide additional molecular tools to be used in future biotechnological applications.
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Affiliation(s)
- Marco Antonio Seiki Kadowaki
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil.
| | - Paula Miwa Rabelo Higasi
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil
| | - Mariana Ortiz de Godoy
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil
| | - Evandro Ares de Araújo
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil
| | - Andre Schutzer Godoy
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil
| | - Rolf Alexander Prade
- Departments of Microbiology & Molecular Genetics and Biochemistry & Molecular Biology, Oklahoma State University, OK, USA
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil.
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33
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Li F, Liu Q, Li X, Zhang C, Li J, Sun W, Liu D, Xiao D, Tian C. Construction of a new thermophilic fungus Myceliophthora thermophila platform for enzyme production using a versatile 2A peptide strategy combined with efficient CRISPR-Cas9 system. Biotechnol Lett 2020; 42:1181-1191. [PMID: 32253539 DOI: 10.1007/s10529-020-02882-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 03/31/2020] [Indexed: 12/26/2022]
Abstract
OBJECTIVE To construct a new thermophilic platform for glucoamylase production through 2A peptide strategy combined with CRISPR-Cas9 system using Myceliophthora thermophila as host, thermophilic filamentous fungus with industrial attractiveness to produce enzymes and chemicals from biomass. RESULTS We adapted the viral 2A peptide approach for M. thermophila and constructed a bicistronic vector for co-expressing two heterologous genes MhglaA and egfp. We obtained positive transformants OE-MhglaA-gfp overexpressing MhGlaA-9 ×His-2A-eGFP through convenient fluorescence screening, western blotting and RT-qPCR. We purified and characterized the recombinant MhGlaA, which exhibited stability in a broader pH range of 3.0-9.0 and thermostable stability at 65 °C, suggesting its potential industrial application. Furthermore, to improve glucoamylase secretion, we genetically engineered the obtained strain OE-MhglaA-gfp through our efficient CRISPR/Cas9 system and generated the quintuple mutant OE-MhglaA-gfpOE-amyRΔalp-1Δres-1Δcre-1, in which protein productivity and amylase activity were increased by approximately 12.0- and 8.2-fold compared with WT. CONCLUSIONS The 2A peptide approach worked well in M. thermophila and can be used to heterologously co-express two different proteins, and thus in combination with efficient CRISPR-Cas system will accelerate establishing hyper-secretion platforms for biotechnological applications.
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Affiliation(s)
- Fangya Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Xiaolin Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chenyang Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Wenliang Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Dandan Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Dongguang Xiao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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34
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Liu Q, Zhang Y, Li F, Li J, Sun W, Tian C. Upgrading of efficient and scalable CRISPR-Cas-mediated technology for genetic engineering in thermophilic fungus Myceliophthora thermophila. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:293. [PMID: 31890021 PMCID: PMC6927189 DOI: 10.1186/s13068-019-1637-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/12/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND Thermophilic filamentous fungus Myceliophthora thermophila has great capacity for biomass degradation and is an attractive system for direct production of enzymes and chemicals from plant biomass. Its industrial importance inspired us to develop genome editing tools to speed up the genetic engineering of this fungus. First-generation CRISPR-Cas9 technology was developed in 2017 and, since then, some progress has been made in thermophilic fungi genetic engineering, but a number of limitations remain. They include the need for complex independent expression cassettes for targeting multiplex genomic loci and the limited number of available selectable marker genes. RESULTS In this study, we developed an Acidaminococcus sp. Cas12a-based CRISPR system for efficient multiplex genome editing, using a single-array approach in M. thermophila. These CRISPR-Cas12a cassettes worked well for simultaneous multiple gene deletions/insertions. We also developed a new simple approach for marker recycling that relied on the novel cleavage activity of the CRISPR-Cas12a system to make DNA breaks in selected markers. We demonstrated its performance by targeting nine genes involved in the cellulase production pathway in M. thermophila via three transformation rounds, using two selectable markers neo and bar. We obtained the nonuple mutant M9 in which protein productivity and lignocellulase activity were 9.0- and 18.5-fold higher than in the wild type. We conducted a parallel investigation using our transient CRISPR-Cas9 system and found the two technologies were complementary. Together we called them CRISPR-Cas-assisted marker recycling technology (Camr technology). CONCLUSIONS Our study described new approaches (Camr technology) that allow easy and efficient marker recycling and iterative stacking of traits in the same thermophilic fungus strain either, using the newly established CRISPR-Cas12a system or the established CRISPR-Cas9 system. This Camr technology will be a versatile and efficient tool for engineering, theoretically, an unlimited number of genes in fungi. We expect this advance to accelerate biotechnology-oriented engineering processes in fungi.
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Affiliation(s)
- Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Yongli Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Fangya Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Wenliang Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
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35
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Improving cellulases production by Myceliophthora thermophila through disruption of protease genes. Biotechnol Lett 2019; 42:219-229. [DOI: 10.1007/s10529-019-02777-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/26/2019] [Indexed: 02/07/2023]
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Li J, Gu S, Zhao Z, Chen B, Liu Q, Sun T, Sun W, Tian C. Dissecting cellobiose metabolic pathway and its application in biorefinery through consolidated bioprocessing in Myceliophthora thermophila. Fungal Biol Biotechnol 2019; 6:21. [PMID: 31754437 PMCID: PMC6852783 DOI: 10.1186/s40694-019-0083-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/04/2019] [Indexed: 02/08/2023] Open
Abstract
Background Lignocellulosic biomass has long been recognized as a potential sustainable source for industrial applications. The costs associated with conversion of plant biomass to fermentable sugar represent a significant barrier to the production of cost-competitive biochemicals. Consolidated bioprocessing (CBP) is considered a potential breakthrough for achieving cost-efficient production of biomass-based fuels and commodity chemicals. During the degradation of cellulose, cellobiose (major end-product of cellulase activity) is catabolized by hydrolytic and phosphorolytic pathways in cellulolytic organisms. However, the details of the two intracellular cellobiose metabolism pathways in cellulolytic fungi remain to be uncovered. Results Using the engineered malic acid production fungal strain JG207, we demonstrated that the hydrolytic pathway by β-glucosidase and the phosphorolytic pathway by phosphorylase are both used for intracellular cellobiose metabolism in Myceliophthora thermophila, and the yield of malic acid can benefit from the energy advantages of phosphorolytic cleavage. There were obvious differences in regulation of the two cellobiose catabolic pathways depending on whether M. thermophila JG207 was grown on cellobiose or Avicel. Disruption of Mtcpp in strain JG207 led to decreased production of malic acid under cellobiose conditions, while expression levels of all three intracellular β-glucosidase genes were significantly up-regulated to rescue the impairment of the phosphorolytic pathway under Avicel conditions. When the flux of the hydrolytic pathway was reduced, we found that β-glucosidase encoded by bgl1 was the dominant enzyme in the hydrolytic pathway and deletion of bgl1 resulted in significant enhancement of protein secretion but reduction of malate production. Combining comprehensive manipulation of both cellobiose utilization pathways and enhancement of cellobiose uptake by overexpression of a cellobiose transporter, the final strain JG412Δbgl2Δbgl3 produced up to 101.2 g/L and 77.4 g/L malic acid from cellobiose and Avicel, respectively, which corresponded to respective yields of 1.35 g/g and 1.03 g/g, representing significant improvement over the starting strain JG207. Conclusions This is the first report of detailed investigation of intracellular cellobiose catabolism in cellulolytic fungus M. thermophila. These results provide insights that can be applied to industrial fungi for production of biofuels and biochemicals from cellobiose and cellulose.
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Affiliation(s)
- Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Shuying Gu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Zhen Zhao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Bingchen Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Tao Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Wenliang Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
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Sadaf A, Sinha R, Khare SK. Proteomic profiling of Sporotrichum thermophile under the effect of ionic liquids: manifestation of an oxidative stress response. 3 Biotech 2019; 9:240. [PMID: 31168433 PMCID: PMC6542886 DOI: 10.1007/s13205-019-1771-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/18/2019] [Indexed: 01/24/2023] Open
Abstract
Sporotrichum thermophile, a known producer of industrial enzymes exhibited stability in the presence of ionic liquids (ILs).The study reports, for the first time, the stress response of S. thermophile upon exposure to ILs. In vitro assay showed increased anti-oxidative enzyme levels indicating ROS-mediated oxidative stress by ILs. The proteomic profile and identification of differential proteins confirmed the fungal adaptations by (i) increased expression of glycolytic enzymes and ATP synthases (ii) downregulation of TCA cycle and protein synthesis machinery components (iii) expression of HSP70 and catalase/peroxidase. These changes are indicative of metabolic regulation of many important pathways and how ILs can be used to manipulate protein behavior.
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Affiliation(s)
- Ayesha Sadaf
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi, 110016 India
| | - Rajeshwari Sinha
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi, 110016 India
| | - Sunil K. Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi, 110016 India
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Dahiya S, Singh B. Enhanced endoxylanase production by Myceliophthora thermophila with applicability in saccharification of agricultural substrates. 3 Biotech 2019; 9:214. [PMID: 31114738 DOI: 10.1007/s13205-019-1750-4] [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: 03/01/2019] [Accepted: 05/08/2019] [Indexed: 11/25/2022] Open
Abstract
The production of enzymes by solid-state fermentation is an interesting process and currently used worldwide as it can be carried out in solid matrix in absence of free water. In present study, Myceliophthora thermophila BJTLRMDU3 produced high titres of endoxylanase (890.55 U/g DR, dry residue) using 5 g rice straw at pH 7.0 and at 45 °C with 1:7 (w/v) solid-to-moisture ratio with inoculum rate of 12 × 106 spores/ml after 4 days in solid-state fermentation. High enzyme titre was produced after moistening the rice straw with solution containing ammonium sulphate (0.4%), K2HPO4 (1.0%), MgSO4·7H2O (0.3%), FeSO4·7H2O (0.03%) and CaCl2 (0.03%). Addition of sucrose (2% w/v) and ammonium nitrate (2% w/v) further enhanced the endoxylanase production. A high endoxylanase production was achieved at water activity (a W) of 0.95 (1639.80 U/g DR) that declined drastically below this value. Among different surfactants, Tween 20 (3% v/v) enhanced the secretion of endoxylanase (2047.91 U/g DR). Furthermore, on optimization of K2HPO4 concentration, it was found that 0.5% K2HPO4 improved (2191.28 U/g DR) endoxylanase production and overall 4.35-folds increase in production of endoxylanase was achieved after optimization of culture conditions. The enzyme has potential to liberate monomeric (xylose) as well as oligomeric (xylotiose, xylotetrose, and xylopantose) sugars from xylan. On saccharification of rice straw and corncob with endoxylanase, maximum yield of reducing sugars was 135.61 and 132.61 mg/g of substrate recorded after 48, and 36 h, respectively.
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Affiliation(s)
- Seema Dahiya
- 1Laboratory of Bioprocess Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Bijender Singh
- 1Laboratory of Bioprocess Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
- 2Department of Biotechnology, School of Interdisciplinary and Applied Life Sciences, Central University of Haryana, Jant-Pali, Mahendergarh, Haryana 123031 India
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Liu Q, Li J, Gao R, Li J, Ma G, Tian C. CLR-4, a novel conserved transcription factor for cellulase gene expression in ascomycete fungi. Mol Microbiol 2018; 111:373-394. [DOI: 10.1111/mmi.14160] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
| | - Ranran Gao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
| | - Jinyang Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
| | - Guoli Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
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40
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Ni J, Wu YT, Tao F, Peng Y, Xu P. A Coenzyme-Free Biocatalyst for the Value-Added Utilization of Lignin-Derived Aromatics. J Am Chem Soc 2018; 140:16001-16005. [DOI: 10.1021/jacs.8b08177] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jun Ni
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Yu-Tong Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Yuan Peng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
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41
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Characterization of a cutinase from Myceliophthora thermophila and its application in polyester hydrolysis and deinking process. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.11.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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42
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Gu S, Li J, Chen B, Sun T, Liu Q, Xiao D, Tian C. Metabolic engineering of the thermophilic filamentous fungus Myceliophthora thermophila to produce fumaric acid. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:323. [PMID: 30534201 PMCID: PMC6278111 DOI: 10.1186/s13068-018-1319-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/22/2018] [Indexed: 05/16/2023]
Abstract
BACKGROUND Fumaric acid is widely used in food and pharmaceutical industries and is recognized as a versatile industrial chemical feedstock. Increasing concerns about energy and environmental problems have resulted in a focus on fumaric acid production by microbial fermentation via bioconversion of renewable feedstocks. Filamentous fungi are the predominant microorganisms used to produce organic acids, including fumaric acid, and most studies to date have focused on Rhizopus species. Thermophilic filamentous fungi have many advantages for the production of compounds by industrial fermentation. However, no previous studies have focused on fumaric acid production by thermophilic fungi. RESULTS We explored the feasibility of producing fumarate by metabolically engineering Myceliophthora thermophila using the CRISPR/Cas9 system. Screening of fumarases suggested that the fumarase from Candida krusei was the most suitable for efficient production of fumaric acid in M. thermophila. Introducing the C. krusei fumarase into M. thermophila increased the titer of fumaric acid by threefold. To further increase fumarate production, the intracellular fumarate digestion pathway was disrupted. After deletion of the two fumarate reductase and the mitochondrial fumarase genes of M. thermophila, the resulting strain exhibited a 2.33-fold increase in fumarate titer. Increasing the pool size of malate, the precursor of fumaric acid, significantly increased the final fumaric acid titer. Finally, disruption of the malate-aspartate shuttle increased the intracellular malate content by 2.16-fold and extracellular fumaric acid titer by 42%, compared with that of the parental strain. The strategic metabolic engineering of multiple genes resulted in a final strain that could produce up to 17 g/L fumaric acid from glucose in a fed-batch fermentation process. CONCLUSIONS This is the first metabolic engineering study on the production of fumaric acid by the thermophilic filamentous fungus M. thermophila. This cellulolytic fungal platform provides a promising method for the sustainable and efficient-cost production of fumaric acid from lignocellulose-derived carbon sources in the future.
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Affiliation(s)
- Shuying Gu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Bingchen Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Tao Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Dongguang Xiao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
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Baker G, Girvan HM, Matthews S, McLean KJ, Golovanova M, Waltham TN, Rigby SEJ, Nelson DR, Blankley RT, Munro AW. Expression, Purification, and Biochemical Characterization of the Flavocytochrome P450 CYP505A30 from Myceliophthora thermophila. ACS OMEGA 2017; 2:4705-4724. [PMID: 30023729 PMCID: PMC6044835 DOI: 10.1021/acsomega.7b00450] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 05/26/2017] [Indexed: 05/21/2023]
Abstract
The cytochrome P450/P450 reductase fusion enzyme CYP505A30 from the thermophilic fungus Myceliophthora thermophila and its heme (P450) domain were expressed in Escherichia coli and purified using affinity, ion exchange, and size exclusion chromatography. CYP505A30 binds straight chain fatty acids (from ∼C10 to C20), with highest affinity for tridecanoic acid (KD = 2.7 μM). Reduced nicotinamide adenine dinucleotide phosphate is the preferred reductant for CYP505A30 (KM = 3.1 μM compared to 330 μM for reduced nicotinamide adenine dinucleotide in cytochrome c reduction). Electron paramagnetic resonance confirmed cysteine thiolate coordination of heme iron in CYP505A30 and its heme domain. Redox potentiometry revealed an unusually positive midpoint potential for reduction of the flavin adenine dinucleotide and flavin mononucleotide cofactors (E0' ∼ -118 mV), and a large increase in the CYP505A30 heme domain FeIII/FeII redox couple (ca. 230 mV) on binding arachidonic acid substrate. This switch brings the ferric heme iron potential into the same range as that of the reductase flavins. Multiangle laser light scattering analysis revealed CYP505A30's ability to dimerize, whereas the heme domain is monomeric. These data suggest CYP505A30 may function catalytically as a dimer (as described for Bacillus megaterium P450 BM3), and that binding interactions between CYP505A30 heme domains are not required for dimer formation. CYP505A30 catalyzed hydroxylation of straight chain fatty acids at the ω-1 to ω-3 positions, with a strong preference for ω-1 over ω-3 hydroxylation in the oxidation of dodecanoic and tetradecanoic acids (88 vs 2% products and 63 vs 9% products, respectively). CYP505A30 has important structural and catalytic similarities to P450 BM3 but distinct regioselectivity of lipid substrate oxidation with potential biotechnological applications.
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Affiliation(s)
- George
J. Baker
- Centre
for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Hazel M. Girvan
- Centre
for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Sarah Matthews
- Centre
for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Kirsty J. McLean
- Centre
for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Marina Golovanova
- Centre
for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Timothy N. Waltham
- Centre
for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Stephen E. J. Rigby
- Centre
for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - David R. Nelson
- Department
of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Richard T. Blankley
- Agilent
Technologies U.K. Ltd., Lakeside, Cheadle Royal Business Park, Stockport, Cheshire SK8 3GR, U.K.
| | - Andrew W. Munro
- Centre
for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- E-mail: . Phone: 0044-161-306-5151
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Concomitant production of cellulase and xylanase by thermophilic mould Sporotrichum thermophile in solid state fermentation and their applicability in bread making. World J Microbiol Biotechnol 2017; 33:109. [DOI: 10.1007/s11274-017-2278-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 04/26/2017] [Indexed: 10/19/2022]
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Liu Q, Gao R, Li J, Lin L, Zhao J, Sun W, Tian C. Development of a genome-editing CRISPR/Cas9 system in thermophilic fungal Myceliophthora species and its application to hyper-cellulase production strain engineering. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:1. [PMID: 28053662 PMCID: PMC5209885 DOI: 10.1186/s13068-016-0693-9] [Citation(s) in RCA: 240] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 12/20/2016] [Indexed: 05/02/2023]
Abstract
BACKGROUND Over the past 3 years, the CRISPR/Cas9 system has revolutionized the field of genome engineering. However, its application has not yet been validated in thermophilic fungi. Myceliophthora thermophila, an important thermophilic biomass-degrading fungus, has attracted industrial interest for the production of efficient thermostable enzymes. Genetic manipulation of Myceliophthora is crucial for metabolic engineering and to unravel the mechanism of lignocellulose deconstruction. The lack of a powerful, versatile genome-editing tool has impeded the broader exploitation of M. thermophila in biotechnology. RESULTS In this study, a CRISPR/Cas9 system for efficient multiplexed genome engineering was successfully developed in the thermophilic species M. thermophila and M. heterothallica. This CRISPR/Cas9 system could efficiently mutate the imported amdS gene in the genome via NHEJ-mediated events. As a proof of principle, the genes of the cellulase production pathway, including cre-1, res-1, gh1-1, and alp-1, were chosen as editing targets. Simultaneous multigene disruptions of up to four of these different loci were accomplished with neomycin selection marker integration via a single transformation using the CRISPR/Cas9 system. Using this genome-engineering tool, multiple strains exhibiting pronounced hyper-cellulase production were generated, in which the extracellular secreted protein and lignocellulase activities were significantly increased (up to 5- and 13-fold, respectively) compared with the parental strain. CONCLUSIONS A genome-wide engineering system for thermophilic fungi was established based on CRISPR/Cas9. Successful expansion of this system without modification to M. heterothallica indicates it has wide adaptability and flexibility for use in other Myceliophthora species. This system could greatly accelerate strain engineering of thermophilic fungi for production of industrial enzymes, such as cellulases as shown in this study and possibly bio-based fuels and chemicals in the future.
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Affiliation(s)
- Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Ranran Gao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Liangcai Lin
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Junqi Zhao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Wenliang Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
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Kou F, Zhao J, Liu J, Shen J, Ye Q, Zheng P, Li Z, Sun J, Ma Y. Characterization of a new lysine decarboxylase from Aliivibrio salmonicida for cadaverine production at alkaline pH. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.11.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Xu J, Li J, Lin L, Liu Q, Sun W, Huang B, Tian C. Development of genetic tools for Myceliophthora thermophila. BMC Biotechnol 2015; 15:35. [PMID: 26013561 PMCID: PMC4446196 DOI: 10.1186/s12896-015-0165-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 05/15/2015] [Indexed: 11/12/2022] Open
Abstract
Background The thermophilic filamentous fungus Myceliophthora thermophila has many suitable characteristics for industrial biotechnology and could be a promising new chassis system for synthetic biology, particularly the ATCC 42464 strain, whose genome was sequenced in 2011. However, metabolic engineering of this strain using genetic approaches has not been reported owing to a lack of genetic tools for this organism. Results In the present study, we developed a high efficiency Agrobacterium tumefaciens mediated transformation system for M. thermophila, including an approach for targeted gene deletion using green fluorescence protein (GFP) as a marker for selection. Up to 145 transformants per 105 conidia were obtained in one transformation plate. Moreover, a ku70 deletion mutant was constructed in the ATCC 42464 background using the tools developed in present study and subsequently characterized. The ku70 deletion construct was designed using resistance to phosphinothricin as the selection marker. Additionally, a GFP-encoding cassette was incorporated that allowed for the selection of site-specific (no fluorescence) or ectopic (fluorescence) integration of the ku70 construct. Transformants with ectopically integrated ku70 deletion constructs were therefore identified using the fluorescent signal of GFP. PCR and Southern blotting analyses of non-fluorescent putative ku70 deletion transformants revealed all 11 tested transformants to be correct deletions. The deletion frequency in a pool of 116 transformants analyzed was 58 %. Moreover, the homologous rate improved about 3 folds under ku70 mutant using the pyrG as a test gene to disrupt in M. thermophila. Conclusions We successfully developed an efficient transformation and target gene disruption approach for M. thermophila ATCC 42464 mediated by A. tumefaciens. The tools and the ku70 deletion strain developed here should advance the development of M. thermophila as an industrial host through metabolic engineering and accelerate the elucidation of the mechanism of rapid cellulose degradation in this thermophilic fungus.
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Affiliation(s)
- Jing Xu
- College of Life Sciences, Hubei University, Wuhan, 430062, China. .,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Liangcai Lin
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Wenliang Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Bangquan Huang
- College of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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