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Arentshorst M, Kooloth Valappil P, Mózsik L, Regensburg-Tuïnk TJG, Seekles SJ, Tjallinks G, Fraaije MW, Visser J, Ram AFJ. A CRISPR/Cas9-based multicopy integration system for protein production in Aspergillus niger. FEBS J 2023; 290:5127-5140. [PMID: 37335926 DOI: 10.1111/febs.16891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/25/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023]
Abstract
The filamentous fungus Aspergillus niger is well known for its high protein secretion capacity and a preferred host for homologous and heterologous protein production. To improve the protein production capacity of A. niger even further, a set of dedicated protein production strains was made containing up to 10 glucoamylase landing sites (GLSs) at predetermined sites in the genome. These GLSs replace genes encoding enzymes abundantly present or encoding unwanted functions. Each GLS contains the promotor and terminator region of the glucoamylase gene (glaA), one of the highest expressed genes in A. niger. Integrating multiple gene copies, often realized by random integration, is known to boost protein production yields. In our approach the GLSs allow for rapid targeted gene replacement using CRISPR/Cas9-mediated genome editing. By introducing the same or different unique DNA sequences (dubbed KORE sequences) in each GLS and designing Cas9-compatible single guide RNAs, one is able to select at which GLS integration of a target gene occurs. In this way a set of identical strains with different copy numbers of the gene of interest can be easily and rapidly made to compare protein production levels. As an illustration of its potential, we successfully used the expression platform to generate multicopy A. niger strains producing the Penicillium expansum PatE::6xHis protein catalysing the final step in patulin biosynthesis. The A. niger strain expressing 10 copies of the patE::6xHis expression cassette produced about 70 μg·mL-1 PatE protein in the culture medium with a purity just under 90%.
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Affiliation(s)
- Mark Arentshorst
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Prajeesh Kooloth Valappil
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - László Mózsik
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Tonny J G Regensburg-Tuïnk
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Sjoerd J Seekles
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Gwen Tjallinks
- Molecular Enzymology, University of Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology, University of Groningen, The Netherlands
| | - Jaap Visser
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Arthur F J Ram
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
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Effect of Glucose on Endo-xylanase and β-xylosidase Production by Fungi Isolated in Indonesia. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.1.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xylanases are widely produced by fungi, and the production of polysaccharide-degrading enzymes, in general, are usually subjected to carbon catabolite repression. In this work, the ability of several Indonesian indigenous fungi to produce endo-xylanase and β-xylosidase and their responses to glucose as a repressor were determined. Ten fungi were grown in a liquid medium supplemented with glucose as the repressor (0, 1%, 3%, and 5%), and the endo-xylanase and β-xylosidase productions were assayed. Aspergillus aculeatus FIG1 and A. oryzae KKB4 produced 3.85 and 0.70 U/mL of endo-xylanase, respectively, compared with other strains (0.22 U/mL or less). Trichoderma asperellum PK1J2, T. virens MLT2J2, A. aculeatus FIG1, T. asperellum MLT5J1, A. oryzae KKB4, and T. asperellum MLT3J2 produced 0.021–0.065 U/mL of β-xylosidase, whereas the other strains produced 0.013 U/mL or less of β-xylosidase. Adding 1% glucose to the growth medium can partially repress endo-xylanase production in A. aculeatus FIG1, T. asperellum PK1J2, and T. virens MLT4J1 and completely repress other strains. By adding 1% glucose, strains FIG1, PK1J2, and MLT4J1 suffered almost complete repression of β-xylosidase production, although such strains exhibited partial repression of endo-xylanase production. β-Xylosidase produced by the other strains showed complete repression by adding 1% glucose, except for A. aculeatus FIG1, A. tamarii FNCC 6151, and T. asperellum MLT1J1, which showed partial repression. Therefore, adding 3% glucose to the growth medium can result in complete repression of endo-xylanase and β-xylosidase productions in all strains examined.
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Solid-state fermentation enhances inulinase and invertase production by Aspergillus brasiliensis. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Takenaka S, Ogawa C, Uemura M, Umeki T, Kimura Y, Yokota S, Doi M. Identification and characterization of extracellular enzymes secreted by Aspergillus spp. involved in lipolysis and lipid-antioxidation during katsuobushi fermentation and ripening. Int J Food Microbiol 2021; 353:109299. [PMID: 34153828 DOI: 10.1016/j.ijfoodmicro.2021.109299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/17/2021] [Accepted: 06/05/2021] [Indexed: 10/21/2022]
Abstract
A mild-flavored soup stock made from katsuobushi is an important element of traditional Japanese cuisine and is the basic seasoning responsible for the taste. Fermented and ripened katsuobushi, known as karebushi, is manufactured by simmering skipjack tuna that is then smoke-dried, fermented, and ripened in a repeated molding process by five dominant Aspergillus species. Here, our aim was to characterize and identify the lipolytic enzymes secreted by the dominant Aspergillus species, especially A. chevalieri and A. pseudoglaucus, which are involved in hydrolyzing lipids during the molding process. The crude enzyme preparations from the five Aspergillus spp. cultivated on katsuobushi solid medium hydrolyzed triglycerides in fish oil, and more saturated and unsaturated fatty acids (C16:0, C16:1, C18:0, C18:1) were produced than major polyunsaturated fatty acids (C20:5, C22:6). On the basis of ion exchange chromatograms, the composition of the lipolytic enzymes was different in the five species. There was at least one active fraction with high hydrolytic activity toward fish oil in four of the Aspergillus spp., but not A. sydowii; the lipolytic enzyme secreted by A. sydowii had quite high activity toward the artificial substrate p-nitrophenyl butyrate, but low activity toward the natural oil. The lipolytic fractions from A. chevalieri and A. pseudoglaucus were further purified by hydrophobic interaction chromatography then gel-filtration chromatography; LC-MS-MS Mascot analysis identified a variety of lipolytic enzymes, including cutinase, esterase, phospholipase, and carboxyl esterase in the lipolytic fractions from these species. The identified enzymes had 30%-70% identity to previously reported or manually annotated lipases or esterases from taxa other than Aspergillus. The different lipolytic enzymes likely acted on triglycerides in the katsuobushi fish oil. Furthermore, catalase B and Cu/Zn superoxide dismutase, which limit oxidative damage of lipids, were also identified. These antioxidant enzymes may prevent lipid oxidation and rancidity as the lipolytic enzymes hydrolyze lipids during the long fermentation and ripening process. Umami and richness tastes tended to increase in extracts from culture of protease- and peptidase-producing A. sydowii. Our results will aid in the selection and application of desirable strains of Aspergillus species as starter cultures to improve the storage and quality of fermented and ripened karebushi.
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Affiliation(s)
- Shinji Takenaka
- Division of Agrobioscience, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.
| | - Chiaki Ogawa
- Division of Agrobioscience, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Mariko Uemura
- Division of Agrobioscience, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Tomoya Umeki
- Division of Agrobioscience, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Yukihiro Kimura
- Division of Agrobioscience, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Satoko Yokota
- Marutomo Co., Ltd., 1696 Kominato, Iyo, Ehime 799-3192, Japan
| | - Mikiharu Doi
- Marutomo Co., Ltd., 1696 Kominato, Iyo, Ehime 799-3192, Japan
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Salgado-Bautista D, Volke-Sepúlveda T, Figueroa-Martínez F, Carrasco-Navarro U, Chagolla-López A, Favela-Torres E. Solid-state fermentation increases secretome complexity in Aspergillus brasiliensis. Fungal Biol 2020; 124:723-734. [PMID: 32690254 DOI: 10.1016/j.funbio.2020.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 04/19/2020] [Accepted: 04/25/2020] [Indexed: 02/06/2023]
Abstract
Aspergillus is used for the industrial production of enzymes and organic acids, mainly by submerged fermentation (SmF). However, solid-state fermentation (SSF) offers several advantages over SmF. Although differences related to lower catabolite repression and substrate inhibition, as well as higher extracellular enzyme production in SSF compared to SmF have been shown, the mechanisms undelaying such differences are still unknown. To explain some differences among SSF and SmF, the secretome of Aspergillus brasiliensis obtained from cultures in a homogeneous physiological state with high glucose concentrations was analyzed. Of the regulated proteins produced by SmF, 74% were downregulated by increasing the glucose concentration, whereas all those produced by SSF were upregulated. The most abundant and upregulated protein found in SSF was the transaldolase, which could perform a moonlighting function in fungal adhesion to the solid support. This study evidenced that SSF: (i) improves the kinetic parameters in relation to SmF, (ii) prevents the catabolite repression, (iii) increases the branching level of hyphae and oxidative metabolism, as well as the concentration and diversity of secreted proteins, and (iv) favors the secretion of typically intracellular proteins that could be involved in fungal adhesion. All these differences can be related to the fact that molds are more specialized to growth in solid materials because they mimic their natural habitat.
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Affiliation(s)
- Daniel Salgado-Bautista
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, 09340, Ciudad de México, Mexico.
| | - Tania Volke-Sepúlveda
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, 09340, Ciudad de México, Mexico.
| | - Francisco Figueroa-Martínez
- CONACyT Research Fellow, Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, 09340, Ciudad de México, Mexico.
| | - Ulises Carrasco-Navarro
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, 09340, Ciudad de México, Mexico.
| | - Alicia Chagolla-López
- Laboratorio de Proteómica- Cinvestav Unidad Irapuato, Km 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, 36824, Guanajuato, Mexico.
| | - Ernesto Favela-Torres
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, 09340, Ciudad de México, Mexico.
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Aleem B, Rashid MH, Zeb N, Saqib A, Ihsan A, Iqbal M, Ali H. Random mutagenesis of super Koji (Aspergillus oryzae): improvement in production and thermal stability of α-amylases for maltose syrup production. BMC Microbiol 2018; 18:200. [PMID: 30486793 PMCID: PMC6264608 DOI: 10.1186/s12866-018-1345-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 11/16/2018] [Indexed: 01/26/2023] Open
Abstract
Background Alpha-amylases hydrolyze 1,4 α-glycosidic bonds of starch and produce malto-oligosaccharides. It is an important enzyme generally applied in textile, food and brewing industries. Enhancement in thermal stability and productivity of enzymes are the two most sought after properties for industrial use. The Aspergillus oryzae (Koji) has Generally Recognized as Safe (GRAS) status and safe for use in food industry. Hence, Koji strain’s development for the screening of potent mutants, hyper producer of thermostable α-amylases, with desired attributes is the need of the time. Results A process has been developed to improve super Koji (A. oryzae cmc1) strain through γ-rays treatment. The doses i.e. 0.60, 0.80, 1.00, 1.20 & 1.40 KGy gave more than 3.0 log kill. Initially, 52 Koji mutants resistant to 1% (w/v) Triton X-100 were selected. 2nd screening was based on α-amylases hyper production and 23 mutants were sorted out by measuring clearing zones index (CI). Afterwards nine potent mutants, resistant to 2-deoxy D-glucose, were screened based on CI. These were further analyzed for thermal stability and productivity of α-amylase under submerged conditions. The mutants’ M-80(10), M-100(6) & M-120(5) gave about four fold increases in α-amylases productivity. The half life of M-100(6) α-amylase at 55 °C was 52 min and was highest among the mutants. Liquid Chromatography-Mass Spectrometry (LC-MS) analysis confirmed that mutants did not produce aflatoxins. Field Emission Scanning Electron Microscopy (FESEM) of Koji mycelia depicted that exposure to gamma rays increased rigidity of the mycelium. The potent Koji mutant M-100(6) was grown on soluble starch in 10L fermenter and produced 40.0 IU ml-1 of α-amylases with specific activity of 2461 IU mg-1 protein. Growth kinetic parameters were: μ = Specific growth rate= 0.069 h-1, td = Biomass doubling time= 10.0 h, Yp/x = Product yield coefficient with respect to cell mass = 482 U g-1; qp= Specific rate of product formation= 33.29 U g-1 h-1. Conclusion It was concluded that the developed five step screening process has great potential to generate potent mutants for the hyper production of thermostable enzymes through γ-rays mediated physical mutagenesis. The developed thermostable α-amylases of super Koji mutantM-100(6) has immense potential for application in saccharification process for maltose syrup production. Moreover, the developed five step strain’s development process may be used for the simultaneous improvement in productivity and thermal stability of other microbial enzymes. Electronic supplementary material The online version of this article (10.1186/s12866-018-1345-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bushra Aleem
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P. O. Box 577, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamaabd, Pakistan
| | - Muhammad Hamid Rashid
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P. O. Box 577, Faisalabad, Pakistan. .,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamaabd, Pakistan.
| | - Neelam Zeb
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P. O. Box 577, Faisalabad, Pakistan
| | - Anam Saqib
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P. O. Box 577, Faisalabad, Pakistan
| | - Ayesha Ihsan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P. O. Box 577, Faisalabad, Pakistan
| | - Mazhar Iqbal
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P. O. Box 577, Faisalabad, Pakistan
| | - Hazrat Ali
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P. O. Box 577, Faisalabad, Pakistan
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