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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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Moreno-Giménez E, Gandía M, Sáez Z, Manzanares P, Yenush L, Orzáez D, Marcos JF, Garrigues S. FungalBraid 2.0: expanding the synthetic biology toolbox for the biotechnological exploitation of filamentous fungi. Front Bioeng Biotechnol 2023; 11:1222812. [PMID: 37609115 PMCID: PMC10441238 DOI: 10.3389/fbioe.2023.1222812] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/12/2023] [Indexed: 08/24/2023] Open
Abstract
Fungal synthetic biology is a rapidly expanding field that aims to optimize the biotechnological exploitation of fungi through the generation of standard, ready-to-use genetic elements, and universal syntax and rules for contributory use by the fungal research community. Recently, an increasing number of synthetic biology toolkits have been developed and applied to filamentous fungi, which highlights the relevance of these organisms in the biotechnology field. The FungalBraid (FB) modular cloning platform enables interchangeability of DNA parts with the GoldenBraid (GB) platform, which is designed for plants, and other systems that are compatible with the standard Golden Gate cloning and syntax, and uses binary pCAMBIA-derived vectors to allow Agrobacterium tumefaciens-mediated transformation of a wide range of fungal species. In this study, we have expanded the original FB catalog by adding 27 new DNA parts that were functionally validated in vivo. Among these are the resistance selection markers for the antibiotics phleomycin and terbinafine, as well as the uridine-auxotrophic marker pyr4. We also used a normalized luciferase reporter system to validate several promoters, such as PpkiA, P7760, Pef1α, and PafpB constitutive promoters, and PglaA, PamyB, and PxlnA inducible promoters. Additionally, the recently developed dCas9-regulated GB_SynP synthetic promoter collection for orthogonal CRISPR activation (CRISPRa) in plants has been adapted in fungi through the FB system. In general, the expansion of the FB catalog is of great interest to the scientific community since it increases the number of possible modular and interchangeable DNA assemblies, exponentially increasing the possibilities of studying, developing, and exploiting filamentous fungi.
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Affiliation(s)
- Elena Moreno-Giménez
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universitat Politècnica de València (UPV), Valencia, Spain
| | - Mónica Gandía
- Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine Department. Faculty of Pharmacy. Universitat de València. Vicente Andrés Estellés s/n, Valencia, Spain
| | - Zara Sáez
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Paloma Manzanares
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Lynne Yenush
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universitat Politècnica de València (UPV), Valencia, Spain
| | - Diego Orzáez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universitat Politècnica de València (UPV), Valencia, Spain
| | - Jose F. Marcos
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Sandra Garrigues
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
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3
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Kun RS, Garrigues S, Di Falco M, Tsang A, de Vries RP. Blocking utilization of major plant biomass polysaccharides leads Aspergillus niger towards utilization of minor components. Microb Biotechnol 2021; 14:1683-1698. [PMID: 34114741 PMCID: PMC8313289 DOI: 10.1111/1751-7915.13835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 11/28/2022] Open
Abstract
Fungi produce a wide range of enzymes that allow them to grow on diverse plant biomass. Wheat bran is a low-cost substrate with high potential for biotechnological applications. It mainly contains cellulose and (arabino)xylan, as well as starch, proteins, lipids and lignin to a lesser extent. In this study, we dissected the regulatory network governing wheat bran degradation in Aspergillus niger to assess the relative contribution of the regulators to the utilization of this plant biomass substrate. Deletion of genes encoding transcription factors involved in (hemi-)cellulose utilization (XlnR, AraR, ClrA and ClrB) individually and in combination significantly reduced production of polysaccharide-degrading enzymes, but retained substantial growth on wheat bran. Proteomic analysis suggested the ability of A. niger to grow on other carbon components, such as starch, which was confirmed by the additional deletion of the amylolytic regulator AmyR. Growth was further reduced but not impaired, indicating that other minor components provide sufficient energy for residual growth, displaying the flexibility of A. niger, and likely other fungi, in carbon utilization. Better understanding of the complexity and flexibility of fungal regulatory networks will facilitate the generation of more efficient fungal cell factories that use plant biomass as a substrate.
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Affiliation(s)
- Roland S. Kun
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
| | - Sandra Garrigues
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
| | - Marcos Di Falco
- Centre for Structural and Functional GenomicsConcordia University7141 Sherbrooke Street WestMontrealQCH4B 1R6Canada
| | - Adrian Tsang
- Centre for Structural and Functional GenomicsConcordia University7141 Sherbrooke Street WestMontrealQCH4B 1R6Canada
| | - Ronald P. de Vries
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
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4
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Spatial induction of genes encoding secreted proteins in micro-colonies of Aspergillus niger. Sci Rep 2020; 10:1536. [PMID: 32001779 PMCID: PMC6992626 DOI: 10.1038/s41598-020-58535-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/13/2020] [Indexed: 11/21/2022] Open
Abstract
Aspergillus niger is used by the industry to produce enzymes and metabolites such as citric acid. In liquid cultures, it can grow as a dispersed mycelium or as micro-colonies with a width in the micrometer to millimeter range. Here, it was assessed whether expression of genes encoding secreted enzymes depends on mycelium morphology. To this end, expression of the reporter gene gfp from the promoters of the glucoamylase gene glaA, the feruloyl esterase gene faeA and the α-glucuronidase gene aguA was causally related to micro-colony size within a liquid shaken culture. Data could be fitted by hyperbolic functions, implying that the genes encoding these secreted proteins are expressed in a shell at the periphery of the micro-colony. The presence of such a shell was confirmed by confocal microscopy. Modelling predicted that the width of these zones was 13 to 156 µm depending on growth medium and micro-colony diameter. Together, data indicate that the highest productive micro-colonies are those colonies that have a radius ≤ the width of the peripheral expression zone.
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Reilly MC, Kim J, Lynn J, Simmons BA, Gladden JM, Magnuson JK, Baker SE. Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger. Appl Microbiol Biotechnol 2018; 102:1797-1807. [PMID: 29305699 PMCID: PMC5794824 DOI: 10.1007/s00253-017-8717-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 12/12/2022]
Abstract
Plant biomass, once reduced to its composite sugars, can be converted to fuel substitutes. One means of overcoming the recalcitrance of lignocellulose is pretreatment followed by enzymatic hydrolysis. However, currently available commercial enzyme cocktails are inhibited in the presence of residual pretreatment chemicals. Recent studies have identified a number of cellulolytic enzymes from bacteria that are tolerant to pretreatment chemicals such as ionic liquids. The challenge now is generation of these enzymes in copious amounts, an arena where fungal organisms such as Aspergillus niger have proven efficient. Fungal host strains still need to be engineered to increase production titers of heterologous protein over native enzymes, which has been a difficult task. Here, we developed a forward genetics screen coupled with whole-genome resequencing to identify specific lesions responsible for a protein hyper-production phenotype in A. niger. This strategy successfully identified novel targets, including a low-affinity glucose transporter, MstC, whose deletion significantly improved secretion of recombinant proteins driven by a glucoamylase promoter.
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Affiliation(s)
- Morgann C Reilly
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Joonhoon Kim
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jed Lynn
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Naval Medical Research Unit Dayton, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biomass Science and Conversion Technologies Department, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Jon K Magnuson
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Scott E Baker
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA. .,Biosystems Design and Simulation Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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6
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Gruben BS, Mäkelä MR, Kowalczyk JE, Zhou M, Benoit-Gelber I, De Vries RP. Expression-based clustering of CAZyme-encoding genes of Aspergillus niger. BMC Genomics 2017; 18:900. [PMID: 29169319 PMCID: PMC5701360 DOI: 10.1186/s12864-017-4164-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 10/05/2017] [Indexed: 11/29/2022] Open
Abstract
Background The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of plant biomass substrates. Which genes need to be activated in certain environmental conditions depends on the composition of the available substrate. Previous studies have demonstrated the involvement of a number of transcriptional regulators in plant biomass degradation and have identified sets of target genes for each regulator. In this study, a broad transcriptional analysis was performed of the A. niger genes encoding (putative) plant polysaccharide degrading enzymes. Microarray data focusing on the initial response of A. niger to the presence of plant biomass related carbon sources were analyzed of a wild-type strain N402 that was grown on a large range of carbon sources and of the regulatory mutant strains ΔxlnR, ΔaraR, ΔamyR, ΔrhaR and ΔgalX that were grown on their specific inducing compounds. Results The cluster analysis of the expression data revealed several groups of co-regulated genes, which goes beyond the traditionally described co-regulated gene sets. Additional putative target genes of the selected regulators were identified, based on their expression profile. Notably, in several cases the expression profile puts questions on the function assignment of uncharacterized genes that was based on homology searches, highlighting the need for more extensive biochemical studies into the substrate specificity of enzymes encoded by these non-characterized genes. The data also revealed sets of genes that were upregulated in the regulatory mutants, suggesting interaction between the regulatory systems and a therefore even more complex overall regulatory network than has been reported so far. Conclusions Expression profiling on a large number of substrates provides better insight in the complex regulatory systems that drive the conversion of plant biomass by fungi. In addition, the data provides additional evidence in favor of and against the similarity-based functions assigned to uncharacterized genes. Electronic supplementary material The online version of this article (10.1186/s12864-017-4164-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Birgit S Gruben
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Microbiology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Miia R Mäkelä
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Joanna E Kowalczyk
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Current affiliation: ATGM, Avans University of Applied Sciences, Lovensdijkstraat 61-63, 4818, AJ, Breda, The Netherlands
| | - Isabelle Benoit-Gelber
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Microbiology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Current affiliation: Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W, Montreal, QC, Canada
| | - Ronald P De Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. .,Microbiology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands. .,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.
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7
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Su X, Schmitz G, Zhang M, Mackie RI, Cann IKO. Heterologous gene expression in filamentous fungi. ADVANCES IN APPLIED MICROBIOLOGY 2016; 81:1-61. [PMID: 22958526 DOI: 10.1016/b978-0-12-394382-8.00001-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Filamentous fungi are critical to production of many commercial enzymes and organic compounds. Fungal-based systems have several advantages over bacterial-based systems for protein production because high-level secretion of enzymes is a common trait of their decomposer lifestyle. Furthermore, in the large-scale production of recombinant proteins of eukaryotic origin, the filamentous fungi become the vehicle of choice due to critical processes shared in gene expression with other eukaryotic organisms. The complexity and relative dearth of understanding of the physiology of filamentous fungi, compared to bacteria, have hindered rapid development of these organisms as highly efficient factories for the production of heterologous proteins. In this review, we highlight several of the known benefits and challenges in using filamentous fungi (particularly Aspergillus spp., Trichoderma reesei, and Neurospora crassa) for the production of proteins, especially heterologous, nonfungal enzymes. We review various techniques commonly employed in recombinant protein production in the filamentous fungi, including transformation methods, selection of gene regulatory elements such as promoters, protein secretion factors such as the signal peptide, and optimization of coding sequence. We provide insights into current models of host genomic defenses such as repeat-induced point mutation and quelling. Furthermore, we examine the regulatory effects of transcript sequences, including introns and untranslated regions, pre-mRNA (messenger RNA) processing, transcript transport, and mRNA stability. We anticipate that this review will become a resource for researchers who aim at advancing the use of these fascinating organisms as protein production factories, for both academic and industrial purposes, and also for scientists with general interest in the biology of the filamentous fungi.
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Affiliation(s)
- Xiaoyun Su
- Energy Biosciences Institute, University of Illinois, Urbana, IL, USA; Institute for Genomic Biology, University of Illinois, Urbana, IL, USA; Equal contribution
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8
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9
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Fernández FJ, Vega MC. Technologies to keep an eye on: alternative hosts for protein production in structural biology. Curr Opin Struct Biol 2013; 23:365-73. [DOI: 10.1016/j.sbi.2013.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/31/2013] [Accepted: 02/01/2013] [Indexed: 12/21/2022]
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10
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Tamayo-Ramos JA, Barends S, de Lange D, de Jel A, Verhaert R, de Graaff L. Enhanced production ofAspergillus nigerlaccase-like multicopper oxidases through mRNA optimization of the glucoamylase expression system. Biotechnol Bioeng 2012; 110:543-51. [DOI: 10.1002/bit.24723] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 08/14/2012] [Accepted: 08/17/2012] [Indexed: 02/03/2023]
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11
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Bleichrodt R, Vinck A, Krijgsheld P, van Leeuwen MR, Dijksterhuis J, Wösten HAB. Cytosolic streaming in vegetative mycelium and aerial structures of Aspergillus niger. Stud Mycol 2012; 74:31-46. [PMID: 23450745 PMCID: PMC3563289 DOI: 10.3114/sim0007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aspergillus niger forms aerial hyphae and conidiophores after a period of vegetative growth. The hyphae within the mycelium of A. niger are divided by septa. The central pore in these septa allows for cytoplasmic streaming. Here, we studied inter- and intra-compartmental streaming of the reporter protein GFP in A. niger. Expression of the gene encoding nuclear targeted GFP from the gpdA or glaA promoter resulted in strong fluorescence of nuclei within the vegetative hyphae and weak fluorescence in nuclei within the aerial structures. These data and nuclear run on experiments showed that gpdA and glaA are higher expressed in the vegetative mycelium when compared to aerial hyphae, conidiophores and conidia. Notably, gpdA or glaA driven expression of the gene encoding cytosolic GFP resulted in strongly fluorescent vegetative hyphae and aerial structures. Apparently, GFP streams from vegetative hyphae into aerial structures. This was confirmed by monitoring fluorescence of photo-activatable GFP (PA-GFP). In contrast, PA-GFP did not stream from aerial structures to vegetative hyphae. Streaming of PA-GFP within vegetative hyphae or within aerial structures of A. niger occurred at a rate of 10–15 μm s-1. Taken together, these results not only show that GFP streams from the vegetative mycelium to aerial structures but it also indicates that its encoding RNA is not streaming. Absence of RNA streaming would explain why distinct RNA profiles were found in aerial structures and the vegetative mycelium by nuclear run on analysis and micro-array analysis.
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Affiliation(s)
- R Bleichrodt
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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James ER, van Zyl WH, van Zyl PJ, Görgens JF. Recombinant hepatitis B surface antigen production in Aspergillus niger: evaluating the strategy of gene fusion to native glucoamylase. Appl Microbiol Biotechnol 2012; 96:385-94. [DOI: 10.1007/s00253-012-4191-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 05/15/2012] [Accepted: 05/16/2012] [Indexed: 10/28/2022]
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13
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Sharma R, Katoch M, Govindappa N, Srivastava PS, Sastry KN, Qazi GN. Evaluation of the catalase promoter for expressing the alkaline xylanase gene (alx) in Aspergillus niger. FEMS Microbiol Lett 2011; 327:33-40. [DOI: 10.1111/j.1574-6968.2011.02454.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 10/05/2011] [Accepted: 10/31/2011] [Indexed: 11/29/2022] Open
Affiliation(s)
- Ruchika Sharma
- Biotechnology Division; Indian Institute of Integrative Medicine (CSIR); Jammu; India
| | - Meenu Katoch
- Biotechnology Division; Indian Institute of Integrative Medicine (CSIR); Jammu; India
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Coleman JJ, Wasmann CC, Usami T, White GJ, Temporini ED, McCluskey K, VanEtten HD. Characterization of the gene encoding pisatin demethylase (FoPDA1) in Fusarium oxysporum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1482-91. [PMID: 22066900 DOI: 10.1094/mpmi-05-11-0119] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The pea pathogen Fusarium oxysporum f. sp. pisi is able to detoxify pisatin produced as a defense response by pea, and the gene encoding this detoxification mechanism, FoPDA1, was 82% identical to the cytochrome P450 pisatin demethylase PDA1 gene in Nectria haematococca. A survey of F. oxysporum f. sp. pisi isolates demonstrated that, as in N. haematococca, the PDA gene of F. oxysporum f. sp. pisi is generally located on a small chromosome. In N. haematococca, PDA1 is in a cluster of pea pathogenicity (PEP) genes. Homologs of these PEP genes also were found in the F. oxysporum f. sp. pisi isolates, and PEP1 and PEP5 were sometimes located on the same small chromosomes as the FoPDA1 homologs. Transforming FoPDA1 into a pda(?) F. oxysporum f. sp. lini isolate conferred pda activity and promoted pathogenicity on pea to some transformants. Different hybridization patterns of FoPDA1 were found in F. oxysporum f. sp. pisi but these did not correlate with the races of the fungus, suggesting that races within this forma specialis arose independently of FoPDA1. FoPDA1 also was present in the formae speciales lini, glycines, and dianthi of F. oxysporum but they had mutations resulting in nonfunctional proteins. However, an active FoPDA1 was present in F. oxysporum f. sp. phaseoli and it was virulent on pea. Despite their evolutionary distance, the amino acid sequences of FoPDA1 of F. oxysporum f. sp. pisi and F. oxysporum f. sp. phaseoli revealed only six amino acid differences, consistent with a horizontal gene transfer event accounting for the origin of these genes.
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Vinck A, de Bekker C, Ossin A, Ohm RA, de Vries RP, Wösten HAB. Heterogenic expression of genes encoding secreted proteins at the periphery of Aspergillus niger colonies. Environ Microbiol 2010; 13:216-225. [PMID: 20722697 DOI: 10.1111/j.1462-2920.2010.02322.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Colonization of a substrate by fungi starts with the invasion of exploring hyphae. These hyphae secrete enzymes that degrade the organic material into small molecules that can be taken up by the fungus to serve as nutrients. We previously showed that only part of the exploring hyphae of Aspergillus niger highly express the glucoamylase gene glaA. This was an unexpected finding since all exploring hyphae are exposed to the same environmental conditions. Using GFP as a reporter, we here demonstrate that the acid amylase gene aamA, the α-glucuronidase gene aguA, and the feruloyl esterase gene faeA of A. niger are also subject to heterogenic expression within the exploring mycelium. Coexpression studies using GFP and dTomato as reporters showed that hyphae that highly express one of these genes also highly express the other genes encoding secreted proteins. Moreover, these hyphae also highly express the amylolytic regulatory gene amyR, and the glyceraldehyde-3-phosphate dehydrogenase gene gpdA. In situ hybridization demonstrated that the high expressers are characterized by a high 18S rRNA content. Taken together, it is concluded that two subpopulations of hyphae can be distinguished within the exploring mycelium of A. niger. The experimental data indicate that these subpopulations differ in their transcriptional and translational activity.
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Affiliation(s)
- Arman Vinck
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Charissa de Bekker
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Adam Ossin
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Robin A Ohm
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ronald P de Vries
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Han A B Wösten
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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16
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Expression and export: recombinant protein production systems for Aspergillus. Appl Microbiol Biotechnol 2010; 87:1255-70. [DOI: 10.1007/s00253-010-2672-6] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 05/07/2010] [Accepted: 05/08/2010] [Indexed: 11/26/2022]
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Lu X, Sun J, Nimtz M, Wissing J, Zeng AP, Rinas U. The intra- and extracellular proteome of Aspergillus niger growing on defined medium with xylose or maltose as carbon substrate. Microb Cell Fact 2010; 9:23. [PMID: 20406453 PMCID: PMC2874515 DOI: 10.1186/1475-2859-9-23] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 04/20/2010] [Indexed: 12/03/2022] Open
Abstract
Background The filamentous fungus Aspergillus niger is well-known as a producer of primary metabolites and extracellular proteins. For example, glucoamylase is the most efficiently secreted protein of Aspergillus niger, thus the homologous glucoamylase (glaA) promoter as well as the glaA signal sequence are widely used for heterologous protein production. Xylose is known to strongly repress glaA expression while maltose is a potent inducer of glaA promoter controlled genes. For a more profound understanding of A. niger physiology, a comprehensive analysis of the intra- and extracellular proteome of Aspergillus niger AB1.13 growing on defined medium with xylose or maltose as carbon substrate was carried out using 2-D gel electrophoresis/Maldi-ToF and nano-HPLC MS/MS. Results The intracellular proteome of A. niger growing either on xylose or maltose in well-aerated controlled bioreactor cultures revealed striking similarities. In both cultures the most abundant intracellular protein was the TCA cycle enzyme malate-dehydrogenase. Moreover, the glycolytic enzymes fructose-bis-phosphate aldolase and glyceraldehyde-3-phosphate-dehydrogenase and the flavohemoglobin FhbA were identified as major proteins in both cultures. On the other hand, enzymes involved in the removal of reactive oxygen species, such as superoxide dismutase and peroxiredoxin, were present at elevated levels in the culture growing on maltose but only in minor amounts in the xylose culture. The composition of the extracellular proteome differed considerably depending on the carbon substrate. In the secretome of the xylose-grown culture, a variety of plant cell wall degrading enzymes were identified, mostly under the control of the xylanolytic transcriptional activator XlnR, with xylanase B and ferulic acid esterase as the most abundant ones. The secretome of the maltose-grown culture did not contain xylanolytic enzymes, instead high levels of catalases were found and glucoamylase (multiple spots) was identified as the most abundant extracellular protein. Surprisingly, the intracellular proteome of A. niger growing on xylose in bioreactor cultures differed more from a culture growing in shake flasks using the same medium than from the bioreactor culture growing on maltose. For example, in shake flask cultures with xylose as carbon source the most abundant intracellular proteins were not the glycolytic and the TCA cycle enzymes and the flavohemoglobin, but CipC, a protein of yet unknown function, superoxide dismutase and an NADPH dependent aldehyde reductase. Moreover, vacuolar proteases accumulated to higher and ER-resident chaperones and foldases to lower levels in shake flask compared to the bioreactor cultures. Conclusions The utilization of xylose or maltose was strongly affecting the composition of the secretome but of minor influence on the composition of the intracellular proteome. On the other hand, differences in culture conditions (pH control versus no pH control, aeration versus no aeration and stirring versus shaking) have a profound effect on the intracellular proteome. For example, lower levels of ER-resident chaperones and foldases and higher levels of vacuolar proteases render shake flask conditions less favorable for protein production compared to controlled bioreactor cultures.
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Affiliation(s)
- Xin Lu
- Helmholtz Center for Infection Research, Inhoffenstr, Braunschweig, Germany
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18
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A novel expression system for intracellular production and purification of recombinant affinity-tagged proteins in Aspergillus niger. Appl Microbiol Biotechnol 2009; 86:659-70. [DOI: 10.1007/s00253-009-2252-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Revised: 08/22/2009] [Accepted: 09/07/2009] [Indexed: 10/20/2022]
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19
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Kumar P, Satyanarayana T. Microbial glucoamylases: characteristics and applications. Crit Rev Biotechnol 2009; 29:225-55. [DOI: 10.1080/07388550903136076] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Vongsangnak W, Salazar M, Hansen K, Nielsen J. Genome-wide analysis of maltose utilization and regulation in aspergilli. MICROBIOLOGY-SGM 2009; 155:3893-3902. [PMID: 19696104 DOI: 10.1099/mic.0.031104-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Maltose utilization and regulation in aspergilli is of great importance for cellular physiology and industrial fermentation processes. In Aspergillus oryzae, maltose utilization requires a functional MAL locus, composed of three genes: MALR encoding a regulatory protein, MALT encoding maltose permease and MALS encoding maltase. Through a comparative genome and transcriptome analysis we show that the MAL regulon system is active in A. oryzae while it is not present in Aspergillus niger. In order to utilize maltose, A. niger requires a different regulatory system that involves the AmyR regulator for glucoamylase (glaA) induction. Analysis of reporter metabolites and subnetworks illustrates the major route of maltose transport and metabolism in A. oryzae. This demonstrates that overall metabolic responses of A. oryzae occur in terms of genes, enzymes and metabolites when the carbon source is altered. Although the knowledge of maltose transport and metabolism is far from being complete in Aspergillus spp., our study not only helps to understand the sugar preference in industrial fermentation processes, but also indicates how maltose affects gene expression and overall metabolism.
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Affiliation(s)
- Wanwipa Vongsangnak
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Margarita Salazar
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Kim Hansen
- Novozymes A/S, DK-2880 Bagsvaerd, Denmark
| | - Jens Nielsen
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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21
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Filamentous fungi for production of food additives and processing aids. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008. [PMID: 18253709 DOI: 10.1007/10_2007_094] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Filamentous fungi are metabolically versatile organisms with a very wide distribution in nature. They exist in association with other species, e.g. as lichens or mycorrhiza, as pathogens of animals and plants or as free-living species. Many are regarded as nature's primary degraders because they secrete a wide variety of hydrolytic enzymes that degrade waste organic materials. Many species produce secondary metabolites such as polyketides or peptides and an increasing range of fungal species is exploited commercially as sources of enzymes and metabolites for food or pharmaceutical applications. The recent availability of fungal genome sequences has provided a major opportunity to explore and further exploit fungi as sources of enzymes and metabolites. In this review chapter we focus on the use of fungi in the production of food additives but take a largely pre-genomic, albeit a mainly molecular, view of the topic.
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Study on the molecular basis of glucoamylase overproduction of a mutant strainAspergillus niger T21. SCIENCE IN CHINA. SERIES C, LIFE SCIENCES 2008; 44:287-93. [PMID: 18726408 DOI: 10.1007/bf02879335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2001] [Indexed: 10/22/2022]
Abstract
The molecular basis for increasing of the glucoamylase (GLA) production of anAspergillus niger mutant T21 was investigated. Northern blot analysis showed that the amount ofglaA specific mRNA ofA. niger T21 was about 20 times higher than that of its start strainA. niger AS 3.795. The twoglaA promoter fusions (PglaA)-uidAs were respectively introduced intoA. niger. Analysis of GUS activity of the transformants revealed that thePglaA activity of the strain T21 is about 3 times stronger than that of the strain AS 3.795. It is considered to be one of the reasons for the increase ofglaA transcriptional level in the strain T21. However, comparing with the 20 times increase in the amount of glaA mRNA the alteration oftrans regulation should be the most important reason for that. The results of deletion analysis of 5'-c/s region ofA. niger T21glaA gene indicated that the region from-408 to-513 bp upstream of ATG is responsible for the high level expression ofglaA.
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23
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Yuan XL, van der Kaaij RM, van den Hondel CAMJJ, Punt PJ, van der Maarel MJEC, Dijkhuizen L, Ram AFJ. Aspergillus niger genome-wide analysis reveals a large number of novel alpha-glucan acting enzymes with unexpected expression profiles. Mol Genet Genomics 2008; 279:545-61. [PMID: 18320228 PMCID: PMC2413074 DOI: 10.1007/s00438-008-0332-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 02/14/2008] [Indexed: 11/25/2022]
Abstract
The filamentous ascomycete Aspergillus niger is well known for its ability to produce a large variety of enzymes for the degradation of plant polysaccharide material. A major carbon and energy source for this soil fungus is starch, which can be degraded by the concerted action of α-amylase, glucoamylase and α-glucosidase enzymes, members of the glycoside hydrolase (GH) families 13, 15 and 31, respectively. In this study we have combined analysis of the genome sequence of A. niger CBS 513.88 with microarray experiments to identify novel enzymes from these families and to predict their physiological functions. We have identified 17 previously unknown family GH13, 15 and 31 enzymes in the A. niger genome, all of which have orthologues in other aspergilli. Only two of the newly identified enzymes, a putative α-glucosidase (AgdB) and an α-amylase (AmyC), were predicted to play a role in starch degradation. The expression of the majority of the genes identified was not induced by maltose as carbon source, and not dependent on the presence of AmyR, the transcriptional regulator for starch degrading enzymes. The possible physiological functions of the other predicted family GH13, GH15 and GH31 enzymes, including intracellular enzymes and cell wall associated proteins, in alternative α-glucan modifying processes are discussed.
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Affiliation(s)
- Xiao-Lian Yuan
- Clusius Laboratory, Molecular Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biology Leiden, Leiden University, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
- Microarray Department, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
| | - Rachel M. van der Kaaij
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
- Centre for Carbohydrate Bioprocessing, TNO, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
| | - Cees A. M. J. J. van den Hondel
- Clusius Laboratory, Molecular Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biology Leiden, Leiden University, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
| | - Peter J. Punt
- TNO Quality of Life, Business Unit Food and Biotechnology Innovations, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | - Marc J. E. C. van der Maarel
- Centre for Carbohydrate Bioprocessing, TNO, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
- TNO Quality of Life, Business Unit Food and Biotechnology Innovations, Rouaanstraat 27, 9723 CC Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
- Centre for Carbohydrate Bioprocessing, TNO, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
| | - Arthur F. J. Ram
- Clusius Laboratory, Molecular Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biology Leiden, Leiden University, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
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siRNA as a molecular tool for use in Aspergillus niger. Biotechnol Lett 2007; 30:885-90. [PMID: 18066687 DOI: 10.1007/s10529-007-9614-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Accepted: 11/15/2007] [Indexed: 10/22/2022]
Abstract
Gene silencing using siRNA has been examined in the industrially-important fungus, Aspergillus niger. Protoplasts of an A. niger strain containing a single genomic copy of the Escherichia coli uidA gene, encoding beta-glucuronidase (GUS), under control of the A. niger glaA promoter at the same genomic locus, were exposed to siRNA targeted against the uidA gene. Down-regulation of uidA mRNA and GUS activity by siRNA was observed in mycelia that developed from the protoplasts. The down-regulation was transient and was not carried over to conidiation. We concluded that gene silencing by siRNA provides a relatively quick method for analysis of gene function in A. niger.
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25
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Melzer G, Dalpiaz A, Grote A, Kucklick M, Göcke Y, Jonas R, Dersch P, Franco-Lara E, Nörtemann B, Hempel DC. Metabolic flux analysis using stoichiometric models for Aspergillus niger: comparison under glucoamylase-producing and non-producing conditions. J Biotechnol 2007; 132:405-17. [PMID: 17931730 DOI: 10.1016/j.jbiotec.2007.08.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 08/07/2007] [Accepted: 08/20/2007] [Indexed: 10/22/2022]
Abstract
Aspergillus niger AB1.13 cultures with glucoamylase production (with D-glucose as substrate) and without glucoamylase production (with D-xylose as substrate) were characterized by metabolic flux analysis. Two comprehensive metabolic models for d-glucose- as well as for D-xylose-consumption were used to quantify and compare the metabolic fluxes through the central pathways of carbon metabolism at different pH-values. The models consist of the most relevant metabolic pathways for A. niger including glycolysis, pentose-phosphate pathway, citrate cycle, energy metabolism and anaplerotic reactions comprising two intracellular compartments, the cytoplasm and mitochondrion. When D-xylose was used as the sole carbon source, the relative flux of the substrate through the oxidative pentose-phosphate pathway (PPP) via G6P-dehydrogenase was unaffected by the pH-value of the culture medium. About 30% of D-xylose consumed was routed through the oxidative PPP. In contrast, the flux of D-glucose (i.e., under glucoamylase-producing conditions) through the oxidative PPP was remarkably higher and, in addition was significantly affected by the pH-value of the culture medium (40% at pH 5.5, 56% at pH 3.7, respectively). Summarizing, the flux through the PPP under glucoamylase producing conditions was 30-90% higher than for non-producing conditions.
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Affiliation(s)
- Guido Melzer
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Gaussstr. 17, 38106 Braunschweig, Germany.
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26
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Bohle K, Jungebloud A, Göcke Y, Dalpiaz A, Cordes C, Horn H, Hempel DC. Selection of reference genes for normalisation of specific gene quantification data of Aspergillus niger. J Biotechnol 2007; 132:353-8. [PMID: 17868942 DOI: 10.1016/j.jbiotec.2007.08.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 06/27/2007] [Accepted: 08/01/2007] [Indexed: 11/28/2022]
Abstract
Aspergillus niger is a widely used expression host for homologous and heterologous protein production in biotechnological processes. In order to increase product yields, a thorough optimisation of these cultivation processes is necessary. Considering mRNA as the key molecule, which transports the genetic information between DNA and protein production side, the quantification of product specific gene expression provides useful information about product formation already on the level of transcription. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a powerful tool to obtain data about gene transcription. However, using this technique the choice of an appropriate reference system is a crucial aspect to provide optimal data normalisation. A prominent approach is the use of so called housekeeping genes as internal references. However, validation of the usability of these reference genes is the fundamental step before starting with qRT-PCR experiments. Adequate reference genes for A. niger have not been published so far. Therefore, 10 possible candidate genes from different functional classes were selected and their applicability as internal references validated. Transcript levels of these genes were compared in sets of 9, 41 and 19 samples from diverse cultivations of A. niger. Under the chosen experimental conditions, the genes act, sarA and cox5 have been identified as genes with the most stable gene expression. The three reference genes were used to normalise qRT-PCR data for glaA gene expression which showed a high correlation with glucoamylase production in continuous cultivations.
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Affiliation(s)
- K Bohle
- Technische Universität Braunschweig, Institute of Biochemical Engineering, Gaussstrasse 17, D-38106 Braunschweig, Germany.
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27
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Chen J, Zhang YQ, Zhao CQ, Li AN, Zhou QX, Li DC. Cloning of a gene encoding thermostable glucoamylase from Chaetomium thermophilum and its expression in Pichia pastoris. J Appl Microbiol 2007; 103:2277-84. [DOI: 10.1111/j.1365-2672.2007.03475.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Jungebloud A, Bohle K, Göcke Y, Cordes C, Horn H, Hempel DC. Quantification of product-specific gene expression in biopellets of Aspergillus niger with real-time PCR. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2006.05.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Vanden Wymelenberg A, Sabat G, Mozuch M, Kersten PJ, Cullen D, Blanchette RA. Structure, organization, and transcriptional regulation of a family of copper radical oxidase genes in the lignin-degrading basidiomycete Phanerochaete chrysosporium. Appl Environ Microbiol 2006; 72:4871-7. [PMID: 16820482 PMCID: PMC1489383 DOI: 10.1128/aem.00375-06] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The white rot basidiomycete Phanerochaete chrysosporium produces an array of nonspecific extracellular enzymes thought to be involved in lignin degradation, including lignin peroxidases, manganese peroxidases, and the H2O2-generating copper radical oxidase, glyoxal oxidase (GLX). Preliminary analysis of the P. chrysosporium draft genome had identified six sequences with significant similarity to GLX and designated cro1 through cro6. The predicted mature protein sequences diverge substantially from one another, but the residues coordinating copper and constituting the radical redox site are conserved. Transcript profiles, microscopic examination, and lignin analysis of inoculated thin wood sections are consistent with differential regulation as decay advances. The cro2-encoded protein was detected by liquid chromatography-tandem mass spectrometry in defined medium. The cro2 cDNA was successfully expressed in Aspergillus nidulans under the control of the A. niger glucoamylase promoter and secretion signal. The recombinant CRO2 protein had a substantially different substrate preference than GLX. The role of structurally and functionally diverse cro genes in lignocellulose degradation remains to be established.
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Affiliation(s)
- Amber Vanden Wymelenberg
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, Genetics and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USDA Forest Service, Forest Products Laboratory, Madison, Wisconsin 53726, Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Grzegorz Sabat
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, Genetics and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USDA Forest Service, Forest Products Laboratory, Madison, Wisconsin 53726, Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Michael Mozuch
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, Genetics and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USDA Forest Service, Forest Products Laboratory, Madison, Wisconsin 53726, Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Philip J. Kersten
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, Genetics and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USDA Forest Service, Forest Products Laboratory, Madison, Wisconsin 53726, Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Dan Cullen
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, Genetics and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USDA Forest Service, Forest Products Laboratory, Madison, Wisconsin 53726, Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
- Corresponding author. Mailing address: Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI 53726. Phone: (608) 231-9468. Fax: (608) 231-9262. E-mail:
| | - Robert A. Blanchette
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, Genetics and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USDA Forest Service, Forest Products Laboratory, Madison, Wisconsin 53726, Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
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Mander GJ, Wang H, Bodie E, Wagner J, Vienken K, Vinuesa C, Foster C, Leeder AC, Allen G, Hamill V, Janssen GG, Dunn-Coleman N, Karos M, Lemaire HG, Subkowski T, Bollschweiler C, Turner G, Nüsslein B, Fischer R. Use of laccase as a novel, versatile reporter system in filamentous fungi. Appl Environ Microbiol 2006; 72:5020-6. [PMID: 16820501 PMCID: PMC1489370 DOI: 10.1128/aem.00060-06] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Accepted: 05/02/2006] [Indexed: 11/20/2022] Open
Abstract
Laccases are copper-containing enzymes which oxidize phenolic substrates and transfer the electrons to oxygen. Many filamentous fungi contain several laccase-encoding genes, but their biological roles are mostly not well understood. The main interest in laccases in biotechnology is their potential to be used to detoxify phenolic substances. We report here on a novel application of laccases as a reporter system in fungi. We purified a laccase enzyme from the ligno-cellulolytic ascomycete Stachybotrys chartarum. It oxidized the artificial substrate 2,2'-azino-di-(3-ethylbenzthiazolinsulfonate) (ABTS). The corresponding gene was isolated and expressed in Aspergillus nidulans, Aspergillus niger, and Trichoderma reesei. Heterologously expressed laccase activity was monitored in colorimetric enzyme assays and on agar plates with ABTS as a substrate. The use of laccase as a reporter was shown in a genetic screen for the isolation of improved T. reesei cellulase production strains. In addition to the laccase from S. charatarum, we tested the application of three laccases from A. nidulans (LccB, LccC, and LccD) as reporters. Whereas LccC oxidized ABTS (Km = 0.3 mM), LccD did not react with ABTS but with DMA/ADBP (3,5-dimethylaniline/4-amino-2,6-dibromophenol). LccB reacted with DMA/ADBP and showed weak activity with ABTS. The different catalytic properties of LccC and LccD allow simultaneous use of these two laccases as reporters in one fungal strain.
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Affiliation(s)
- Gerd J Mander
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
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31
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Vinck A, Terlou M, Pestman WR, Martens EP, Ram AF, van den Hondel CAMJJ, Wösten HAB. Hyphal differentiation in the exploring mycelium of Aspergillus niger. Mol Microbiol 2006; 58:693-9. [PMID: 16238620 DOI: 10.1111/j.1365-2958.2005.04869.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Mycelial fungi play a central role in element cycling in nature by degrading dead organic material such as wood. Fungal colonization of a substrate starts with the invasion of exploring hyphae. These hyphae secrete enzymes that convert the organic material into small molecules that can be taken up by the fungus to serve as nutrients. Using green fluorescent protein (GFP) as a reporter, we show for the first time that exploring hyphae of Aspergillus niger differentiate with respect to enzyme secretion; some strongly express the glucoamylase gene glaA, while others hardly express it at all. When a cytoplasmic GFP was used, 27% of the exploring hyphae of a 5-day-old colony belonged to the low expressing hyphae. By fusing GFP to glucoamylase and by introducing an ER retention signal, this number increased to 50%. This difference is due to cytoplasmic streaming of the reporter in the former case, as was shown by using a photo-activatable GFP. Our findings indicate that a fungal mycelium is highly differentiated, especially when taking into account that hyphae in the exploration zone were exposed to the same nutritional conditions.
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Affiliation(s)
- Arman Vinck
- Institute of Biomembranes, Microbiology, University of Utrecht, Utrecht, the Netherlands
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32
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Rajoka MI, Yasmeen A. Induction, and production studies of a novel glucoamylase of Aspergillus niger. World J Microbiol Biotechnol 2005. [DOI: 10.1007/s11274-004-1766-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Storms R, Zheng Y, Li H, Sillaots S, Martinez-Perez A, Tsang A. Plasmid vectors for protein production, gene expression and molecular manipulations in Aspergillus niger. Plasmid 2004; 53:191-204. [PMID: 15848224 DOI: 10.1016/j.plasmid.2004.10.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2004] [Revised: 09/23/2004] [Accepted: 10/04/2004] [Indexed: 10/26/2022]
Abstract
We constructed three sets of plasmids for use in Aspergillus niger. These plasmids were assembled using various combinations of a series of modular DNA cassettes that included a selectable marker, pyrG, derived from Aspergillus nidulans; two promoter regions for directing protein expression; a cassette derived from the AMA1 replicator sequence to support autonomous replication; and a reporter gene based on the A. niger lacA gene. One set included integrating and autonomously replicating plasmids for the expression of homologous and heterologous proteins. The second was a set of autonomously replicating plasmids, with a secreted beta-galactosidase encoding reporter gene, for studying gene regulation events. The third set included pyrG-derived gene-blaster cassettes suitable for genome manipulation by targeted gene replacement.
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Affiliation(s)
- Reginald Storms
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Que., Canada H4B 1R6.
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34
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Khalaj V, Hey P, Smith L, Robson GD, Brookman J. TheAspergillus nigerannexin,anxC3.1is constitutively expressed and is not essential for protein secretion. FEMS Microbiol Lett 2004; 239:163-9. [PMID: 15451115 DOI: 10.1016/j.femsle.2004.08.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2004] [Accepted: 08/24/2004] [Indexed: 12/11/2022] Open
Abstract
An annexin, anxC3.1, was isolated and characterised from the industrially important filamentous fungus Aspergillus niger. anxC3.1 is a single copy gene encoding a 506 amino acid predicted protein which contains four annexin repeats. Disruption of the anxC3.1 gene did not lead to any visible changes in phenotype, nor in the levels of secreted protein, nor specifically in glucoamylase production, suggesting no major role in secretion. anxC3.1 expression was found to be unaltered under a variety of conditions such as increased secretion, altered nitrogen source, heat shock, and decreased Ca2+ levels, indicating that anxC3.1 is constitutively expressed. This is the first reported functional characterisation of a fungal annexin.
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Affiliation(s)
- Vahid Khalaj
- F2G Ltd., P.O. Box 1, Lankro Way, Eccles, Manchester M30 0BH, UK.
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35
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Mouyna I, Henry C, Doering TL, Latgé JP. Gene silencing with RNA interference in the human pathogenic fungus Aspergillus fumigatus. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09713.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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36
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Wallis GL, Swift RJ, Atterbury R, Trappe S, Rinas U, Hemming FW, Wiebe MG, Trinci AP, Peberdy JF. The effect of pH on glucoamylase production, glycosylation and chemostat evolution of Aspergillus niger. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1527:112-22. [PMID: 11479027 DOI: 10.1016/s0304-4165(01)00145-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effect of ambient pH on production and glycosylation of glucoamylase (GAM) and on the generation of a morphological mutant produced by Aspergillus niger strain B1 (a transformant containing an additional 20 copies of the homologous GAM glaA gene) was studied. We have shown that a change in the pH from 4 to 5.4 during continuous cultivation of the A. niger B1 strain instigates or accelerates the spontaneous generation of a morphological mutant (LB). This mutant strain produced approx. 50% less extracellular protein and GAM during both chemostat and batch cultivation compared to another strain with parental-type morphology (PS). The intracellular levels of GAM were also lower in the LB strain. In addition, cultivation of the original parent B1 strain in a batch-pulse bioreactor at pH 5.5 resulted in a 9-fold drop in GAM production and a 5-fold drop in extracellular protein compared to that obtained at pH 4. Glycosylation analysis of the glucoamylases purified from shake-flask cultivation showed that both principal forms of GAM secreted by the LB strain possessed enhanced galactosylation (2-fold), compared to those of the PS. Four diagnostic methods (immunostaining, mild methanolysis, mild acid hydrolysis and beta-galactofuranosidase digestion) provided evidence that the majority of this galactose was of the furanoic conformation. The GAMs produced during batch-pulse cultivation at pH 5.5 similarly showed an approx. 2-fold increase in galactofuranosylation compared to pH 4. Interestingly, in both cases the increased galactofuranosylation appears primarily restricted to the O-linked glycan component. Ambient pH therefore regulates both GAM production and influences its glycosylation.
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Affiliation(s)
- G L Wallis
- School of Biological, University of Nottingham, UK.
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37
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Zhao J, Chen YH, Kwan HS. Molecular cloning, characterization, and differential expression of a glucoamylase gene from the basidiomycetous fungus Lentinula edodes. Appl Environ Microbiol 2000; 66:2531-5. [PMID: 10831434 PMCID: PMC110576 DOI: 10.1128/aem.66.6.2531-2535.2000] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete nucleotide sequence of putative glucoamylase gene gla1 from the basidiomycetous fungus Lentinula edodes strain L54 is reported. The coding region of the genomic glucoamylase sequence, which is preceded by eukaryotic promoter elements CAAT and TATA, spans 2,076 bp. The gla1 gene sequence codes for a putative polypeptide of 571 amino acids and is interrupted by seven introns. The open reading frame sequence of the gla1 gene shows strong homology with those of other fungal glucoamylase genes and encodes a protein with an N-terminal catalytic domain and a C-terminal starch-binding domain. The similarity between the Gla1 protein and other fungal glucoamylases is from 45 to 61%, with the region of highest conservation found in catalytic domains and starch-binding domains. We compared the kinetics of glucoamylase activity and levels of gene expression in L. edodes strain L54 grown on different carbon sources (glucose, starch, cellulose, and potato extract) and in various developmental stages (mycelium growth, primordium appearance, and fruiting body formation). Quantitative reverse transcription PCR utilizing pairs of primers specific for gla1 gene expression shows that expression of gla1 was induced by starch and increased during the process of fruiting body formation, which indicates that glucoamylases may play an important role in the morphogenesis of the basidiomycetous fungus.
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MESH Headings
- Amino Acid Sequence
- Cloning, Molecular
- Culture Media
- Gene Expression Regulation, Fungal
- Genes, Fungal
- Genomic Library
- Glucan 1,4-alpha-Glucosidase/chemistry
- Glucan 1,4-alpha-Glucosidase/genetics
- Glucan 1,4-alpha-Glucosidase/metabolism
- Lentinula/enzymology
- Lentinula/genetics
- Lentinula/growth & development
- Molecular Sequence Data
- Promoter Regions, Genetic
- Reverse Transcriptase Polymerase Chain Reaction/methods
- Sequence Analysis, DNA
- Terminator Regions, Genetic
- Transcription, Genetic
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Affiliation(s)
- J Zhao
- Department of Biology, The Chinese University of Hong Kong, Shatin, N. T., Hong Kong SAR, People's Republic of China
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38
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MacKenzie DA, Jeenes DJ, Gou X, Archer DB. Molecular basis of glucoamylase overproduction by a mutagenised industrial strain of Aspergillus niger. Enzyme Microb Technol 2000; 26:193-200. [PMID: 10689077 DOI: 10.1016/s0141-0229(99)00145-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have compared a mutagenized strain of Aspergillus niger (S1), used industrially for glucoamylase production, and a related low glucoamylase-producing strain (S2) with a laboratory strain of A. niger (AB4.1). Our aim was to assess the properties of S1 in relation to the laboratory strain and to account at the molecular level for the basis of its glucoamylase overproduction. Both S1 and S2 have similar multiple copies of the glucoamylase-encoding gene (glaA) but only S1 has enhanced glaA transcript and glucoamylase levels compared to AB4.1 that has a single copy of the glaA gene. Glucoamylase production by S1 and AB4.1 was repressed by xylose and induced by starch but, in S2, remained unaffected by carbon source. S1 also secreted elevated levels of alpha-amylase relative to both S2 and AB4.1 but the production of alpha-glucosidase was low in all three strains. The gene encoding aspergillopepsin (pepA), an abundant secreted aspartyl protease, was present as a single copy in all strains but no aspergillopepsin could be detected by Western blotting in either S1 or S2 culture supernatants. We conclude that A. niger strain improvement by mutagenesis and screening for glucoamylase overproduction has led to glaA gene multiplication and an expression defect in the pepA gene.
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Affiliation(s)
- DA MacKenzie
- Division of Food Safety Science, Institute of Food Research, Norwich Research Park, Colney, Norwich, UK
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39
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Gordon CL, Khalaj V, Ram AFJ, Archer DB, Brookman JL, Trinci APJ, Jeenes DJ, Doonan JH, Wells B, Punt PJ, van den Hondel CAMJJ, Robson GD. Glucoamylase::green fluorescent protein fusions to monitor protein secretion in Aspergillus niger. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 2):415-426. [PMID: 10708380 DOI: 10.1099/00221287-146-2-415] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A glucoamylase::green fluorescent protein fusion (GLA::sGFP) was constructed which allows the green fluorescent protein to be used as an in vivo reporter of protein secretion in Aspergillus niger. Two secretory fusions were designed for secretion of GLA::sGFP which employed slightly different lengths of the glucoamylase protein (GLA499 and GLA514). Expression of GLA::sGFP revealed that fluorescence was localized in the hyphal cell walls and septa, and that fluorescence was most intense at hyphal apices. Extracellular GLA::sGFP was detectable by Western blotting only in the supernatant of young cultures grown in soya milk medium. In older cultures, acidification of the medium and induction of proteases were probably responsible for the loss of extracellular and cell wall fluorescence and the inability to detect GLA::sGFP by Western analysis. A strain containing the GLA::sGFP construct was subjected to UV mutagenesis and survivors screened for mutations in the general secretory pathway. Three mutants were isolated that were unable to form a halo on either starch or gelatin medium. All three mutants grew poorly compared to the parental strain. Fluorescence microscopy revealed that for two of the mutants, GLA::sGFP accumulated intracellularly with no evidence of wall fluorescence, whereas for the third mutant, wall fluorescence was observed with no evidence of intracellular accumulation. These results indicate that the GLA::sGFP fusion constructs can be used as convenient fluorescent markers to study the dynamics of protein secretion in vivo and as a tool in the isolation of mutants in the general secretory pathway.
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Affiliation(s)
- Caroline L Gordon
- School of Biological Sciences, Stopford Building, University of Manchester, Manchester M13 9PT, UK1
| | - Vahid Khalaj
- School of Biological Sciences, Stopford Building, University of Manchester, Manchester M13 9PT, UK1
| | - Arthur F J Ram
- Centre for Phytotechnology, Institute for Molecular Plant Sciences, Clusius Laboratory, Wassenaarseweg 64, 2333 Al Leiden, The Netherlands2
| | - David B Archer
- Department of Genetics and Microbiology, Institute of Food Research, Norwich Laboratory, Norwich Research Park, Colney, Norwich NR4 7UA, UK3
| | - Jayne L Brookman
- School of Biological Sciences, Stopford Building, University of Manchester, Manchester M13 9PT, UK1
| | - Anthony P J Trinci
- School of Biological Sciences, Stopford Building, University of Manchester, Manchester M13 9PT, UK1
| | - David J Jeenes
- Department of Genetics and Microbiology, Institute of Food Research, Norwich Laboratory, Norwich Research Park, Colney, Norwich NR4 7UA, UK3
| | - John H Doonan
- Department of Cell Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK5
| | - Brian Wells
- Department of Cell Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK5
| | - Peter J Punt
- TNO Nutrition and Food Research Institute, Department of Molecular Genetics and Gene Technology, Utrechtseweg 48, PO Box 360, 3700 AJ Zeist, The Netherlands4
| | - Cees A M J J van den Hondel
- TNO Nutrition and Food Research Institute, Department of Molecular Genetics and Gene Technology, Utrechtseweg 48, PO Box 360, 3700 AJ Zeist, The Netherlands4
| | - Geoffrey D Robson
- School of Biological Sciences, Stopford Building, University of Manchester, Manchester M13 9PT, UK1
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40
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Wallis GL, Swift RJ, Hemming FW, Trinci AP, Peberdy JF. Glucoamylase overexpression and secretion in Aspergillus niger: analysis of glycosylation. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1472:576-86. [PMID: 10564772 DOI: 10.1016/s0304-4165(99)00188-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We have studied the effects of overexpression and secretion of a homologous model glycoprotein, glucoamylase (GAM-1), on glycosylation in a single gene copy wild-type parent and multiple gene copy transformants of Aspergillus niger. In batch culture the B36 strain, which possess 80 additional copies of the GAM glaA gene, secreted about 5-8-fold more protein and GAM-1 than the parent strain (N402). A comparison of the glycosylation of GAM-1 secreted by the parent strain with that secreted by the multiple copy and hyper-secreting B36 strain showed that both the N-linked and O-linked glycan composition was very similar. Short oligomannose N-linked glycans were found (Man(7-8)GlcNAc(2)). O-Linked glycans were comprised of short (1-3 residues) oligosaccharide chains of mannose and galactose. Evidence is presented that this galactose is present in the novel galactofuranose conformation. This glycan composition of GAM-1 differed from that of a commercially available (A. niger) GAM source. Microsomes prepared from the mycelium showed a 2-3-fold co-ordinated increase in the activity of the dolichol phosphate:glycosyltransferases. Similar results were obtained from strains B1 (20 copies of glaA) and N402 when grown at a low dilution rate in a chemostat, although both the levels of GAM secretion and the activities of the dolichol phosphate:glycosyltransferases were lower than found in batch culture. These data suggest that A. niger is capable of secreting large amounts of a single glycoprotein combined with higher activity levels of the dolichol phosphate:glycosyltransferases without an increase in the heterogeneity of the glycan structures. Thus, from a biotechnological viewpoint, protein glycosylation may not be a bottleneck to enhanced glycoprotein production using A. niger.
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Affiliation(s)
- G L Wallis
- School of Biomedical Science (Biochemistry), The Medical School, Queens Medical Centre, The University of Nottingham, Nottingham, UK
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41
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Heterologous protein secretion and fungal morphology in chemostat cultures of a recombinant Aspergillus niger (B1-D). Enzyme Microb Technol 1999. [DOI: 10.1016/s0141-0229(98)00139-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Liu ZM, Kolattukudy PE. Early expression of the calmodulin gene, which precedes appressorium formation in Magnaporthe grisea, is inhibited by self-inhibitors and requires surface attachment. J Bacteriol 1999; 181:3571-7. [PMID: 10348871 PMCID: PMC93826 DOI: 10.1128/jb.181.11.3571-3577.1999] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fungal conidia contain chemicals that inhibit germination and appressorium formation until they are well dispersed in a favorable environment. Recently, such self-inhibitors were found to be present on the conidia of Magnaporthe grisea, and plant surface waxes were found to relieve this self-inhibition. To determine whether the self-inhibitors suppress the expression of early genes involved in the germination and differentiation of conidia, the calmodulin gene was chosen as a representative early gene, because it was found to be expressed early in Colletotrichum gloeosporioides and Colletotrichum trifolii differentiation. After calmodulin cDNA and genomic DNA from M. grisea were cloned, the promoter of the calmodulin gene was fused to a reporter gene, that for green fluorescent protein (GFP), and transformed into the M. grisea genome. Confocal microscopic examination and quantitation of expression of GFP green fluorescence showed (i) that the expression of the calmodulin gene decreased significantly when self-inhibition of M. grisea appressorium formation occurred because of high conidial density or addition of exogenous self-inhibitors and (ii) that the expression level of this gene was restored when self-inhibition was relieved by the addition of plant surface waxes. The increase in fluorescence correlated with the percentage of conidia that formed appressoria. The induction of calmodulin was also confirmed by RNA blotting. Concanavalin A inhibited surface attachment of conidia, GFP expression, and appressorium formation without affecting germination. The high correlation between GFP expression and appressorium formation strongly suggests that calmodulin gene expression and appressorium formation require surface attachment.
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MESH Headings
- Biological Factors/pharmacology
- Biological Factors/physiology
- Calmodulin/genetics
- Cell Adhesion/drug effects
- Cloning, Molecular
- Concanavalin A/pharmacology
- Cycloheximide/pharmacology
- Gene Expression Regulation, Fungal/drug effects
- Genes, Fungal/genetics
- Genes, Reporter
- Green Fluorescent Proteins
- Lipids/pharmacology
- Lipids/physiology
- Luminescent Proteins/genetics
- Luminescent Proteins/metabolism
- Magnaporthe/drug effects
- Magnaporthe/genetics
- Magnaporthe/growth & development
- Magnaporthe/physiology
- Microscopy, Confocal
- Molecular Sequence Data
- Plant Leaves/microbiology
- Plant Leaves/physiology
- Plant Lectins
- Promoter Regions, Genetic/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Analysis, DNA
- Spores, Fungal/physiology
- Waxes/pharmacology
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Affiliation(s)
- Z M Liu
- Departments of Biochemistry and Medical Biochemistry and Neurobiotechnology Center, The Ohio State University, Columbus, Ohio 43210, USA
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43
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Withers JM, Swift RJ, Wiebe MG, Robson GD, Punt PJ, van den Hondel CAMJJ, Trinci APJ. Optimization and stability of glucoamylase production by recombinant strains ofAspergillus niger in chemostat culture. Biotechnol Bioeng 1998. [DOI: 10.1002/(sici)1097-0290(19980820)59:4<407::aid-bit3>3.0.co;2-k] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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44
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Abstract
Enzymes from filamentous fungi are already widely exploited, but new applications for known enzymes and new enzymic activities continue to be found. In addition, enzymes from less amenable non-fungal sources require heterologous production and fungi are being used as the production hosts. In each case there is a need to improve production and to ensure quality of product. While conventional, mutagenesis-based, strain improvement methods will continue to be applied to enzyme production from filamentous fungi the application of recombinant DNA techniques is beginning to reveal important information on the molecular basis of fungal enzyme production and this knowledge is now being applied both in the laboratory and commercially. We review the current state of knowledge on the molecular basis of enzyme production by filamentous fungi. We focus on transcriptional and post-transcriptional regulation of protein production, the transit of proteins through the secretory pathway and the structure of the proteins produced including glycosylation.
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Affiliation(s)
- D B Archer
- Genetics and Microbiology Department, Institute of Food Research, Norwich, UK
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45
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Zaldivar-Aguero J, Badino Jr. A, Vilaça P, Facciotti M, Schmidell W. INFLUENCE OF PHOSPHATE CONCENTRATIONS ON GLUCOAMYLASE PRODUCTION BY Aspergillus awamori IN SUBMERGED CULTURE. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 1997. [DOI: 10.1590/s0104-66321997000400014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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46
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van Gemeren IA, Punt PJ, Drint-Kuyvenhoven A, Broekhuijsen MP, van't Hoog A, Beijersbergen A, Verrips CT, van den Hondel CA. The ER chaperone encoding bipA gene of black Aspergilli is induced by heat shock and unfolded proteins. Gene 1997; 198:43-52. [PMID: 9370263 DOI: 10.1016/s0378-1119(97)00290-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We describe the cloning and characterisation of the BiP gene homologues of the filamentous fungi Aspergillus niger and Aspergillus awamori. The BiP genes of these black Aspergilli encode an identical protein of 672 amino acids, which has a high homology with the BiP protein from Saccharomyces cerevisiae and contains a putative signal sequence of 38 amino acids. The DNA sequences of the Aspergillus BiP genes diverge in particular in the three intronic sequences and the 5'- and 3'- noncoding regions. Sequences resembling Heat Shock Elements (HSE) and Unfolded Protein Response (UPR) elements, as found in the yeast KAR2 promoter, are present in the 5' non-transcribed regions of both genes. The expression of the A. niger bipA gene is increased by heat shock and tunicamycin treatment.
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Affiliation(s)
- I A van Gemeren
- Department of Molecular and Cellular Biology, University of Utrecht, The Netherlands
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47
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Nakamura A, Nishimura I, Yokoyama A, Lee DG, Hidaka M, Masaki H, Kimura A, Chiba S, Uozumi T. Cloning and sequencing of an alpha-glucosidase gene from Aspergillus niger and its expression in A. nidulans. J Biotechnol 1997; 53:75-84. [PMID: 9165762 DOI: 10.1016/s0168-1656(97)01664-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have cloned an extracellular alpha-glucosidase gene from Aspergillus niger with oligonucleotide probes synthesized on the basis of the determined peptide sequences. The nucleotide sequence revealed an open reading frame of 985 amino acids split with three introns, and the deduced amino acid sequence was nearly identical to that of the alpha-glucosidase previously determined. The cloned gene was introduced into Aspergillus nidulans, and its expression in the transformants was shown to be regulated by the carbon sources in the medium, suggesting that a common regulatory expression system is shared by these two species as is the case of other starch-degrading enzymes of Aspergillus species.
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Affiliation(s)
- A Nakamura
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Japan
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48
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MacKenzie DA, Spencer JA, Le Gal-Coëffet MF, Archer DB. Efficient production from Aspergillus niger of a heterologous protein and an individual protein domain, heavy isotope-labelled, for structure-function analysis. J Biotechnol 1996; 46:85-93. [PMID: 8672288 DOI: 10.1016/0168-1656(95)00179-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Aspergillus niger has been used successfully to secrete proteins labelled with 13C and/or 15N to a specific activity of > 99% for high resolution NMR analysis. In the case of a heterologous protein, hen egg-white lysozyme, 15N single-labelled and 13C, 15N double-labelled forms were secreted at yields of 100-200 mg l-1 by optimising the type of carbon source used and the ratio of carbon to nitrogen. Another protein, the glucoamylase starch-binding domain from A. niger, was also produced as the 15N single-labelled form at 20-40 mg l-1.
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Affiliation(s)
- D A MacKenzie
- Institute of Food Research, Norwich Research Park, Colney, UK
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49
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Kersten PJ, Witek C, vanden Wymelenberg A, Cullen D. Phanerochaete chrysosporium glyoxal oxidase is encoded by two allelic variants: structure, genomic organization, and heterologous expression of glx1 and glx2. J Bacteriol 1995; 177:6106-10. [PMID: 7592374 PMCID: PMC177449 DOI: 10.1128/jb.177.21.6106-6110.1995] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A cDNA clone (glx-2c) encoding glyoxal oxidase (GLOX) was isolated from a Phanerochaete chrysosporium lambda gt11 library, and its nucleotide sequence was shown to be distinct from that of the previously described clone glx-1c (P. J. Kersten and D. Cullen, Proc. Natl. Acad. Sci. USA 90:7411-7413, 1993). Genomic clones corresponding to both cDNAs were also isolated and sequenced. overall nucleotide sequence identity was 98%, and the predicted proteins differed by a single residue: Lys-308<==>Thr-308. Analyses of parental dikaryotic strain BKM-F-1767 and homokaryotic progeny firmly established allelism for these structural variants. Southern blots of pulsed-field gels localized the GLOX gene (glx) to a dimorphic chromosome separate from the peroxidase and cellobiohydrolase genes of P. chrysosporium. Controlled expression of active GLOX was obtained from Aspergillus nidulans transformants when glx-1c was fused to the promoter and secretion signal of the A. niger glucoamylase gene. The GLOX isozyme corresponding to glx-2c was also efficiently secreted by A. nidulans following site-specific mutagenesis of the expression vector at codon 308 of glx-1c.
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Affiliation(s)
- P J Kersten
- Forest Products Laboratory, U.S. Department of Agriculture Forest Service, Madison, Wisconsin, USA
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Ventura L, González-Candelas L, Pérez-González JA, Ramón D. Molecular cloning and transcriptional analysis of the Aspergillus terreus gla1 gene encoding a glucoamylase. Appl Environ Microbiol 1995; 61:399-402. [PMID: 7534054 PMCID: PMC167299 DOI: 10.1128/aem.61.1.399-402.1995] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The Aspergillus terreus gla1 gene, coding for a glucoamylase, has been cloned by heterologous hybridization. The gene is interrupted by four introns and encodes a protein with an N-terminal catalytic domain and a C-terminal starch-binding domain. The expression of the gene is induced by starch and maltose and repressed by glucose.
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Affiliation(s)
- L Ventura
- Departamento de Biotecnología, Consejo Superior de Investigaciones Científicas, Valencia, Spain
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