1
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Pfeiffer S, Swoboda I. Problems Encountered Using Fungal Extracts as Test Solutions for Fungal Allergy Diagnosis. J Fungi (Basel) 2023; 9:957. [PMID: 37888213 PMCID: PMC10607634 DOI: 10.3390/jof9100957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/28/2023] Open
Abstract
Fungal allergy is a worldwide public health burden, and problems associated with a reliable allergy diagnosis are far from being solved. Especially, the lack of high-quality standardized fungal extracts contributes to the underdiagnosis of fungal allergy. Compared to the manufacturing processes of extracts from other allergen sources, the processes used to manufacture extracts from fungi show the highest variability. The reasons for the high variability are manifold as the starting material, the growth conditions, the protein extraction methods, and the storage conditions all have an influence on the presence and quantity of individual allergens. Despite the vast variety of studies that have analyzed the impact of the different production steps on the allergenicity of fungal allergen extracts, much remains unknown. This review points to the need for further research in the field of fungal allergology, for standardization and for generally accepted guidelines on the preparation of fungal allergen extracts. In particular, the standardization of fungal extracts has been and will continue to be difficult, but it will be crucial for improving allergy diagnosis and therapy.
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Affiliation(s)
| | - Ines Swoboda
- The Molecular Biotechnology Section, Department Applied Life Sciences, FH Campus Wien, University of Applied Sciences, 1100 Vienna, Austria;
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2
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Li J, Chroumpi T, Garrigues S, Kun RS, Meng J, Salazar-Cerezo S, Aguilar-Pontes MV, Zhang Y, Tejomurthula S, Lipzen A, Ng V, Clendinen CS, Tolić N, Grigoriev IV, Tsang A, Mäkelä MR, Snel B, Peng M, de Vries RP. The Sugar Metabolic Model of Aspergillus niger Can Only Be Reliably Transferred to Fungi of Its Phylum. J Fungi (Basel) 2022; 8:jof8121315. [PMID: 36547648 PMCID: PMC9781776 DOI: 10.3390/jof8121315] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Fungi play a critical role in the global carbon cycle by degrading plant polysaccharides to small sugars and metabolizing them as carbon and energy sources. We mapped the well-established sugar metabolic network of Aspergillus niger to five taxonomically distant species (Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium and Dichomitus squalens) using an orthology-based approach. The diversity of sugar metabolism correlates well with the taxonomic distance of the fungi. The pathways are highly conserved between the three studied Eurotiomycetes (A. niger, A. nidulans, P. subrubescens). A higher level of diversity was observed between the T. reesei and A. niger, and even more so for the two Basidiomycetes. These results were confirmed by integrative analysis of transcriptome, proteome and metabolome, as well as growth profiles of the fungi growing on the corresponding sugars. In conclusion, the establishment of sugar pathway models in different fungi revealed the diversity of fungal sugar conversion and provided a valuable resource for the community, which would facilitate rational metabolic engineering of these fungi as microbial cell factories.
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Affiliation(s)
- Jiajia Li
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Tania Chroumpi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Roland S. Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jiali Meng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Sonia Salazar-Cerezo
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | | | - Yu Zhang
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Sravanthi Tejomurthula
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Anna Lipzen
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Vivian Ng
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Chaevien S. Clendinen
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Nikola Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Igor V. Grigoriev
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94598, USA
| | - Adrian Tsang
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada
| | - Miia R. Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Correspondence:
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3
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Alternative transcription start sites of the enolase-encoding gene enoA are stringently used in glycolytic/gluconeogenic conditions in Aspergillus oryzae. Curr Genet 2020; 66:729-747. [PMID: 32072240 DOI: 10.1007/s00294-020-01053-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/24/2019] [Accepted: 01/07/2020] [Indexed: 10/25/2022]
Abstract
Gene expression using alternative transcription start sites (TSSs) is an important transcriptional regulatory mechanism for environmental responses in eukaryotes. Here, we identify two alternative TSSs in the enolase-encoding gene (enoA) in Aspergillus oryzae, an industrially important filamentous fungus. TSS use in enoA is strictly dependent on the difference in glycolytic and gluconeogenic carbon sources. Transcription from the upstream TSS (uTSS) or downstream TSS (dTSS) predominantly occurs under gluconeogenic or glycolytic conditions, respectively. In addition to enoA, most glycolytic genes involved in reversible reactions possess alternative TSSs. The fbaA gene, which encodes fructose-bisphosphate aldolase, also shows stringent alternative TSS selection, similar to enoA. Alignment of promoter sequences of enolase-encoding genes in Aspergillus predicted two conserved regions that contain a putative cis-element required for enoA transcription from each TSS. However, uTSS-mediated transcription of the acuN gene, an enoA ortholog in Aspergillus nidulans, is not strictly dependent on carbon source, unlike enoA. Furthermore, enoA transcript levels in glycolytic conditions are higher than in gluconeogenic conditions. Conversely, acuN is more highly transcribed in gluconeogenic conditions. This suggests that the stringent usage of alternative TSSs and higher transcription in glycolytic conditions in enoA may reflect that the A. oryzae evolutionary genetic background was domesticated by exclusive growth in starch-rich environments. These findings provide novel insights into the complexity and diversity of transcriptional regulation of glycolytic/gluconeogenic genes among Aspergilli.
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4
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Nguyen DX, Sakaguchi T, Nakazawa T, Sakamoto M, Honda Y. A 14-bp stretch plays a critical role in regulating gene expression from β1-tubulin promoters of basidiomycetes. Curr Genet 2019; 66:217-228. [DOI: 10.1007/s00294-019-01014-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/27/2019] [Accepted: 07/03/2019] [Indexed: 11/25/2022]
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5
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Green BJ, Nayak AP, Lemons AR, Rittenour WR, Hettick JM, Beezhold DH. Production of a Chaetomium globosum enolase monoclonal antibody. Monoclon Antib Immunodiagn Immunother 2016; 33:428-37. [PMID: 25495488 DOI: 10.1089/mab.2014.0042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Chaetomium globosum is a hydrophilic fungal species and a contaminant of water-damaged building materials in North America. Methods to detect Chaetomium species include subjective identification of ascospores, viable culture, or molecular-based detection methods. In this study, we describe the production and initial characterization of a monoclonal antibody (MAb) for C. globosum enolase. MAb 1C7, a murine IgG1 isotype MAb, was produced and reacted with recombinant C. globosum enolase (rCgEno) in an enzyme-linked immunosorbent assay and with a putative C. globosum enolase in a Western blot. Epitope mapping showed MAb 1C7 specific reactivity to an enolase decapeptide, LTYEELANLY, that is highly conserved within the fungal class Sordariomycetes. Cross-reactivity studies showed MAb 1C7 reactivity to C. atrobrunneum but not C. indicum. MAb 1C7 did not react with enolase from Aspergillus fumigatus, which is divergent in only two amino acids within this epitope. The results of this study suggest potential utility of MAb 1C7 in Western blot applications for the detection of Chaetomium and other Sordariomycetes species.
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Affiliation(s)
- Brett J Green
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health , Centers for Disease Control and Prevention, Morgantown, West Virginia
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6
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Zhao G, Yao Y, Hao G, Fang D, Yin B, Cao X, Chen W. Gene regulation in Aspergillus oryzae promotes hyphal growth and flavor formation in soy sauce koji. RSC Adv 2015. [DOI: 10.1039/c4ra16819d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Aspergillus oryzae100-8 and the parental strainA. oryzae3.042 are used in soy sauce fermentation in China.
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Affiliation(s)
- Guozhong Zhao
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Yunping Yao
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Guangfei Hao
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Dongsheng Fang
- Yangzhou University Healthy Source Dairy Co. Ltd
- Yangzhou 225004
- P. R. China
| | - Boxing Yin
- Yangzhou University Healthy Source Dairy Co. Ltd
- Yangzhou 225004
- P. R. China
| | - Xiaohong Cao
- Key Laboratory of Food Nutrition and Safety (Tianjin University of Science & Technology)
- Ministry of Education
- Tianjin 300457
- China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
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7
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Isolation and Expression of Enolase Gene in Fusarium oxysporum f. sp. lycopersici. Appl Biochem Biotechnol 2014; 175:902-8. [DOI: 10.1007/s12010-014-1338-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/15/2014] [Indexed: 10/24/2022]
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8
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Highly efficient biodiesel production by a whole-cell biocatalyst employing a system with high lipase expression in Aspergillus oryzae. Appl Microbiol Biotechnol 2011; 90:1171-7. [DOI: 10.1007/s00253-011-3186-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 02/09/2011] [Accepted: 02/12/2011] [Indexed: 10/18/2022]
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9
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Expression of ribonuclease A and ribonuclease N1 in the filamentous fungus Neurospora crassa. Appl Microbiol Biotechnol 2009; 85:1041-9. [PMID: 19662399 DOI: 10.1007/s00253-009-2161-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2007] [Revised: 07/20/2009] [Accepted: 07/20/2009] [Indexed: 10/20/2022]
Abstract
In this study, we investigated the ability of the fungus Neurospora crassa to produce and secrete two ribonucleases: the heterologous bovine RNase A and the endogenous RNase N(1). A set of expression vectors was constructed, each consisting of an RNase A open reading frame under the control of a specific promoter and each with a specific terminator. N. crassa transformants were analyzed at the transcriptional and protein levels. Irrespective of the promoter used, all transformants showed an RNase A-specific transcript in northern hybridization, but transcriptional strengths differed significantly. The strongest transcription was detected in transformants under the control of the cfp promoter. Western blot analysis and ELISA assays of selected transformants showed an effective secretion up to 356 ng/mL of recombinant RNase A protein. However, the highest ribonuclease activity could be detected in transformants carrying the endogenous RNase N(1) under the control of the ccg1 promoter. Expression and secretion of RNase N(1) thus represent an alternative to recombinant expression of RNase A protein. In conclusion, we have created a viable expression system for expression of homologous and heterologous proteins in N. crassa.
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10
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Hynes MJ, Szewczyk E, Murray SL, Suzuki Y, Davis MA, Sealy-Lewis HM. Transcriptional control of gluconeogenesis in Aspergillus nidulans. Genetics 2007; 176:139-50. [PMID: 17339216 PMCID: PMC1893031 DOI: 10.1534/genetics.107.070904] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2007] [Accepted: 02/16/2007] [Indexed: 11/18/2022] Open
Abstract
Aspergillus nidulans can utilize carbon sources that result in the production of TCA cycle intermediates, thereby requiring gluconeogenesis. We have cloned the acuG gene encoding fructose-1,6 bisphosphatase and found that expression of this gene is regulated by carbon catabolite repression as well as by induction by a TCA cycle intermediate similar to the induction of the previously studied acuF gene encoding phosphoenolpyruvate carboxykinase. The acuN356 mutation results in loss of growth on gluconeogenic carbon sources. Cloning of acuN has shown that it encodes enolase, an enzyme involved in both glycolysis and gluconeogenesis. The acuN356 mutation is a translocation with a breakpoint in the 5' untranslated region resulting in loss of expression in response to gluconeogenic but not glycolytic carbon sources. Mutations in the acuK and acuM genes affect growth on carbon sources requiring gluconeogenesis and result in loss of induction of the acuF, acuN, and acuG genes by sources of TCA cycle intermediates. Isolation and sequencing of these genes has shown that they encode proteins with similar but distinct Zn(2) Cys(6) DNA-binding domains, suggesting a direct role in transcriptional control of gluconeogenic genes. These genes are conserved in other filamentous ascomycetes, indicating their significance for the regulation of carbon source utilization.
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Affiliation(s)
- Michael J Hynes
- Department of Genetics, University of Melbourne, Victoria, Australia.
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11
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Koda A, Bogaki T, Minetoki T, Hirotsune M. 5′ Untranslated region of the Hsp12 gene contributes to efficient translation in Aspergillus oryzae. Appl Microbiol Biotechnol 2006; 70:333-6. [PMID: 16059686 DOI: 10.1007/s00253-005-0083-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Revised: 06/03/2005] [Accepted: 06/28/2005] [Indexed: 10/25/2022]
Abstract
We describe a 5' untranslated region (5'UTR) that dramatically increases the expression level of an exogenous gene in Aspergillus oryzae. Using a series of 5'UTR::GUS (uidA) fusion constructs, we analyzed the translation efficiency of chimeric mRNAs with different 5'UTRs at different temperatures. We found that the 5'UTR of a heat-shock protein gene, Hsp12, greatly enhanced the translation efficiency of the chimeric GUS mRNA at normal temperature (30 degrees C). Moreover, at high temperature (37 degrees C), the translation efficiency of the mRNA containing the Hsp12 5'UTR was far superior to that of mRNAs containing nonheat-shock 5'UTRs, resulting in much more efficient expression of GUS protein (about 20-fold higher GUS activity compared to the control construct). This 5'UTR can be used in combination with various strong promoters to enhance the expression of foreign proteins in A. oryzae.
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Affiliation(s)
- Akio Koda
- General Research Laboratory, Ozeki Corp., 4-9, Imazu, Dezaike-cho, Nishinomiya-shi, Hyogo, 663-8227, Japan.
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12
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Tsuboi H, Koda A, Toda T, Minetoki T, Hirotsune M, Machida M. Improvement of the Aspergillus oryzae enolase promoter (P-enoA) by the introduction of cis-element repeats. Biosci Biotechnol Biochem 2005; 69:206-8. [PMID: 15665487 DOI: 10.1271/bbb.69.206] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We constructed a protein expression vector with an improved enoA promoter that harbored 12 tandem repeats of the cis-acting element (region III) of Aspergillus oryzae. The improved promoter yielded reporter beta-glucuronidase (GUS) activity approximately 30-fold of the original promoter. Northern blot analysis confirmed that GUS expression was increased at the transcriptional level. The transformant harboring seven copies of the novel vector showed more than 100,000 U/mg GUS protein, which was approximately 30% of all the cell-free soluble proteins.
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Affiliation(s)
- Hirokazu Tsuboi
- General Research Laboratory, Ozeki Corporation, Hyogo, Japan.
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13
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Ishikawa E, Sakai T, Ikemura H, Matsumoto K, Abe H. Identification, cloning, and characterization of a Sporobolomyces singularis β-galactosidase-like enzyme involved in galacto-oligosaccharide production. J Biosci Bioeng 2005; 99:331-9. [PMID: 16233798 DOI: 10.1263/jbb.99.331] [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: 12/22/2004] [Accepted: 01/25/2005] [Indexed: 11/17/2022]
Abstract
Sporobolomyces singularis can be used as a biocatalyst in galacto-oligosaccharide production. We isolated 2-deoxy-D-glucose-resistant mutants of S. singularis ATCC 24193 and recovered a mutant that showed 10-fold higher beta-galactosidase-like activity than the parent strain and which was insensitive to catabolite repression. Thereafter, the beta-galactosidase-like enzyme was purified from the mutant and revealed to be a glycoprotein with both beta-glucosidase- and beta-galactosidase-like activity, the Michaelis-Menten constants of which for o-nitrophenyl-beta-D-galactopyranoside and p-nitrophenyl-beta-D-glucopyranoside were 5.40 and 1.96 mM, respectively, and the maximum velocities were 3.07 and 2.30 micromol/min per mg of protein, respectively. Its molecular mass was estimated to be 73.9 kDa by sodium dodecyl sulfate polyacrylamide gel electrophoresis and 146 kDa by gel filtration, suggesting that it has a homodimeric structure. We sequenced the N-terminus and internal peptides of this protein and isolated both a cDNA and a gene with degenerate primers. The gene, named bg l A, has 18 introns and 19 exons and encodes a polypeptide of 594 amino acids. The Bg l A protein was approximately 35% identical and 50% similar to plant beta-glucosidases belonging to family 1 glycosyl hydrolases, but with a unique 110-amino-acid sequence at the N-terminus. The beta-galactosidase-like enzyme (i.e., Bg l A protein) in S. singularis is a beta-glucosidase with high transgalactosidase activity.
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Affiliation(s)
- Eiji Ishikawa
- Yakult Central Institute for Microbiological Research, 1796 Yaho, Kunitachi-shi, Tokyo 186-8650, Japan.
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14
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Koda A, Minetoki T, Ozeki K, Hirotsune M. Translation efficiency mediated by the 5' untranslated region greatly affects protein production in Aspergillus oryzae. Appl Microbiol Biotechnol 2005; 66:291-6. [PMID: 15309336 DOI: 10.1007/s00253-004-1681-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate that the 5' untranslated region (5'UTR) plays an important role in determining translation efficiency in Aspergillus oryzae, using a model beta-glucuronidase (GUS) expression system. Alterations in the 5' UTR resulted in an increase in GUS activity of up to eight-fold, without affecting mRNA levels. Moreover, using the most effective 5'UTR construct, we could achieve remarkable intracellular overproduction of GUS protein; and the GUS level reached more than 50% of the total soluble protein. This is the first experimental evidence indicating the feasibility of improving recombinant protein yield by promoting translation initiation in filamentous fungi.
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Affiliation(s)
- Akio Koda
- General Research Laboratory, Ozeki Corporation, 4-9, Imazu, Dezaike-cho, Nishinomiya-shi, Hyogo, 663-8227, Japan.
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15
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te Biesebeke R, van Biezen N, de Vos WM, van den Hondel CAMJJ, Punt PJ. Different control mechanisms regulate glucoamylase and protease gene transcription in Aspergillus oryzae in solid-state and submerged fermentation. Appl Microbiol Biotechnol 2004; 67:75-82. [PMID: 15800731 DOI: 10.1007/s00253-004-1807-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2004] [Revised: 10/04/2004] [Accepted: 10/19/2004] [Indexed: 11/28/2022]
Abstract
Solid-state fermentation (SSF) with Aspergillus oryzae results in high levels of secreted protein. However, control mechanisms of gene expression in SSF have been only poorly studied. In this study we show that both glucoamylase (glaB) and protease (alpA, nptB) genes are highly expressed during surface cultivation on wheat-based solid medium, and even higher during cultivation on wheat kernels. In wheat-based liquid medium, low levels of gene expression are observed. Typical SSF cultivation conditions, such as low water activity and the formation of aerial hyphae, did not contribute to the high-level gene expression on wheat-based solid medium. Analysis of wheat-based solid and liquid cultivations showed differences in carbon and nitrogen utilisation and external pH. The results presented show that the difference in regulation of transcription of the alpA and nptB genes in wheat-based liquid and solid medium could be pH dependent, involving a pH-dependent transcription regulator. The results obtained suggest that the difference in regulation of transcription of the glaB gene in wheat-based liquid and solid medium is caused by a difference in carbohydrate degradation and consumption under the different culture conditions.
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Affiliation(s)
- R te Biesebeke
- TNO Nutrition and Food Research Institute, Utrechtseweg 48, 3700 AJ Zeist, The Netherlands.
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16
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Polidori E, Saltarelli R, Ceccaroli P, Buffalini M, Pierleoni R, Palma F, Bonfante P, Stocchi V. Enolase from the ectomycorrhizal fungus Tuber borchii Vittad.: biochemical characterization, molecular cloning, and localization. Fungal Genet Biol 2004; 41:157-67. [PMID: 14732262 DOI: 10.1016/j.fgb.2003.10.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enolase from Tuber borchii mycelium was purified to electrophoretical homogeneity using an anion-exchange and a gel permeation chromatography. Furthermore, the corresponding gene (eno-1) was cloned and characterized. The purified enzyme showed a higher affinity for 2-PGA (0.26 mM) with respect to PEP; the stability and activity of enolase were dependent of the divalent cation Mg2+. T. borchii eno-1 has an ORF of 1323 bp coding for a putative protein of 440 amino acids and Southern blotting analysis revealed that the gene is present as a single copy in T. borchii. The enzymatic activity and the mRNA expression level evaluated in mycelia grown either in different carbon sources, in pyruvate or during starvation were the same in all the conditions tested, while biochemical and Northern blotting analyses performed with mycelia at different days of growth showed T. borchii eno-1 regulation in response to the growth phase. Finally, Western blotting analysis demonstrated that enolase is localized only in the cytosolic fraction confirming its important role in glycolysis.
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MESH Headings
- Amino Acid Sequence
- Ascomycota/enzymology
- Ascomycota/genetics
- Ascomycota/growth & development
- Ascomycota/metabolism
- Base Sequence
- Chromatography, Gel
- Chromatography, Ion Exchange
- Cloning, Molecular
- Coenzymes/analysis
- DNA, Fungal/chemistry
- DNA, Fungal/isolation & purification
- Gene Expression Regulation, Fungal
- Genes, Fungal/genetics
- Genes, Fungal/physiology
- Glyceric Acids/metabolism
- Introns/genetics
- Magnesium/metabolism
- Molecular Sequence Data
- Molecular Weight
- Phosphoenolpyruvate/metabolism
- Phosphopyruvate Hydratase/genetics
- Phosphopyruvate Hydratase/isolation & purification
- Phosphopyruvate Hydratase/physiology
- Promoter Regions, Genetic
- RNA 3' Polyadenylation Signals/genetics
- Sequence Analysis, DNA
- Substrate Specificity/physiology
- Transcription Initiation Site
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Affiliation(s)
- Emanuela Polidori
- Istituto di Chimica Biologica Giorgio Fornaini, Università degli Studi di Urbino Carlo Bo, Via A. Saffi, 2, 61029 Urbino (PU), Italy
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17
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Kunihiro S, Kawanishi Y, Sano M, Naito K, Matsuura Y, Tateno Y, Gojobori T, Yamagata Y, Abe K, Machida M. A polymerase chain reaction-based method for cloning novel members of a gene family using a combination of degenerate and inhibitory primers. Gene 2002; 289:177-84. [PMID: 12036596 DOI: 10.1016/s0378-1119(02)00547-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We have developed a novel method for cloning gene family members by using a polymerase chain reaction technique. The method is based on the amplification of a broad range of homologous genes in combination with the specific inhibition of already cloned genes. To accomplish this, we designed degenerate primers to highly conserved regions among the gene family members, and inhibitory primers to the divergent region at the 3'-margin of each degenerate primer. The 5'-end of the inhibitory primer, the 3'-end of which was aminated, had 3-4 bases overlapping the 3'-end of the degenerate primer. The potential of this method was demonstrated by the successful cloning of a novel member of the yeast MKC7/YAP3 gene family homologue from a filamentous fungus, Aspergillus oryzae, by inhibiting amplification of an already cloned homologue, opsB.
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Affiliation(s)
- Sumiko Kunihiro
- Institute of Molecular and Cell Biology, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
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Gao XD, Nishikawa A, Dean N. Identification of a conserved motif in the yeast golgi GDP-mannose transporter required for binding to nucleotide sugar. J Biol Chem 2001; 276:4424-32. [PMID: 11067855 DOI: 10.1074/jbc.m009114200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glycoproteins and lipids in the Golgi complex are modified by the addition of sugars. In the yeast Saccharomyces cerevisiae, these terminal Golgi carbohydrate modifications primarily involve mannose additions that utilize GDP-mannose as the substrate. The transport of GDP-mannose from its site of synthesis in the cytosol into the lumen of the Golgi is mediated by the VRG4 gene product, a nucleotide sugar transporter that is a member of a large family of related membrane proteins. Loss of VRG4 function leads to lethality, but several viable vrg4 mutants were isolated whose GDP-mannose transport activity was reduced but not obliterated. Mutations in these alleles mapped to a region of the Vrg4 protein that is highly conserved among other GDP-mannose transporters but not other types of nucleotide sugar transporters. Here, we present evidence that suggest an involvement of this region of the protein in binding GDP-mannose. Most of the mutations that were introduced within this conserved domain, spanning amino acids 280-291 of Vrg4p, lead to lethality, and none interfere with Vrg4 protein stability, localization, or dimer formation. The null phenotype of these mutant vrg4 alleles can be complemented by their overexpression. Vesicles prepared from vrg4 mutant strains were reduced in luminal GDP-mannose transport activity, but this effect could be suppressed by increasing the concentration of GDP-mannose in vitro. Thus, either an increased substrate concentration, in vitro, or an increased Vrg4 protein concentration, in vivo, can suppress these vrg4 mutant phenotypes. Vrg4 proteins with alterations in this region were reduced in binding to guanosine 5'-[gamma-(32)P]triphosphate gamma-azidoanilide, a photoaffinity substrate analogue whose binding to Vrg4-HAp was specifically inhibited by GDP-mannose. Taken together, these data are consistent with the model that amino acids in this region of the yeast GDP-mannose transporter mediate the recognition of or binding to nucleotide sugar prior to its transport into the Golgi.
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Affiliation(s)
- X D Gao
- Department of Biochemistry, Institute for Cell and Developmental Biology, State University of New York, Stony Brook, New York 11794-5215, USA
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19
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Current progress in the analysis of transcriptional regulation in the industrially valuable microorganismAspergillus oryzae. BIOTECHNOL BIOPROC E 2000. [DOI: 10.1007/bf02942182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Nakajima K, Chang YC, Suzuki T, Jigami Y, Machida M. Molecular cloning and characterization of rpbA encoding RNA polymerase II largest subunit from a filamentous fungus, Aspergillus oryzae. Biosci Biotechnol Biochem 2000; 64:641-6. [PMID: 10803973 DOI: 10.1271/bbb.64.641] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have cloned rpbA encoding the RNA polymerase II largest subunit (polIIL) from a filamentous fungus, Aspergillus oryzae. The rpbA product included eight highly conserved regions and the carboxyl-terminal domain (CTD). A. oryzae polIIL CTD with 184 amino acids was composed of 25 CTD consensus repeats, which was a similar number to those of lower eukaryotes. The amino acids in each repeat of A. oryzae polIIL, however, conformed less to the CTD consensus than those of polIILs from other lower eukaryotes.
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Affiliation(s)
- K Nakajima
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
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21
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Cloning, sequencing, and expression of the gene encoding enolase from Cunninghamella elegans. ACTA ACUST UNITED AC 2000. [DOI: 10.1017/s0953756299001112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Machida M, Yamazaki S, Kunihiro S, Tanaka T, Kushida N, Jinnno K, Haikawa Y, Yamazaki J, Yamamoto S, Sekine M, Oguchi A, Nagai Y, Sakai M, Aoki K, Ogura K, Kudoh Y, Kikuchi H, Zhang MQ, Yanagida M. A 38 kb segment containing the cdc2 gene from the left arm of fission yeast chromosome II: sequence analysis and characterization of the genomic DNA and cDNAs encoded on the segment. Yeast 2000; 16:71-80. [PMID: 10620777 DOI: 10.1002/(sici)1097-0061(20000115)16:1<71::aid-yea505>3.0.co;2-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A genomic 38 kbp segment on the c1750 cosmid clone containing the cdc2 gene, located in the left arm of chromosome II from Schizosaccharomyces pombe, was sequenced. The segment was found to have five previously known genes, pht1, cdc2, his3, act1 and mei4. Among 11 coding sequences (CDSs) predicted by the gene finding software INTRON.PLOT., four CDSs, pi007, pi010, pi014 and pi016, had considerable similarity to 40S ribosomal protein, glycosyltransferase, cdc2-related protein kinase and alpha-1, 2-mannosyltransferase, respectively. Another unusually huge open reading frame (ORF) (pi011), consisting of 2233 amino acids, existed, having significant homology to alpha-amylase, granule-bound glycogen synthase and the Sz. pombe YS 1110 clone product at the N-terminal, middle and C-terminal regions, respectively. All the predicted 11 CDSs were experimentally analysed by RACE PCR. The sequencing of the RACE products revealed that there were two small overlaps at the 3' untranslated regions (UTRs) between pi004 and pi005 (17 bp) and between pi007 and pi008 (2 bp). The distances between 5' end of the 5'UTR and the putative translation initiation codon varied from 10 to 302 nucleotides (nt) among the nine CDSs successfully analysed by 5'-RACE. The expression level of each CDS on this clone was determined. Among the 16 genes on this clone, the previously determined genes, pht1, cdc2, his3 and act1, were found to be most highly expressed. Finally, cDNAs of all the newly identified genes were detected by RACE, proving the actual expression of these genes. The nucleotide sequence has been submitted to the EMBL database under Accession No. AB004534.
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Affiliation(s)
- M Machida
- Molecular Biology Department, National Institute of Bioscience and Human Technology, Higashi 1-1, Tsukuba, Ibaraki 305-8566, Japan.
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Honda M, Minetoki T, Gomi K, Machida M. Rapid detection of homologously integrated DNA fragments and accurate quantitation of their copy number in transgenic Aspergillus oryzae by PCR. J Biosci Bioeng 2000. [DOI: 10.1016/s1389-1723(01)80046-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Kormanec J, Lempel'ov A, Nov Kov R, Re Uchov B, Hom Rov D. Expression of the Streptomyces aureofaciens glyceraldehyde-3-phosphate dehydrogenase gene (gap) is developmentally regulated and induced by glucose. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 11):3555-3561. [PMID: 9387234 DOI: 10.1099/00221287-143-11-3555] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In previous experiments, the Streptomyces aureofaciens gap gene encoding glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was identified. To investigate expression of the gene, S1 nuclease mapping and Northern blot hybridization were performed using RNA prepared from S. aureofaciens cultivated under various conditions. These studies suggested monocistronic organization and developmental regulation of the gene. A single promoter, gap-P, was identified upstream of the gap coding region. In cultures grown on solid medium in the absence of glucose, its transcription was induced at the time of aerial mycelium formation. In addition, gap transcription was also induced in substrate mycelium by glucose. A promoter-bearing DNA fragment was inserted into two promoter-probe vectors, to give expression patterns consistent with the results of direct RNA analysis.
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Affiliation(s)
- J Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, 842 51 Bratislava, Slovak Republic
| | - A Lempel'ov
- Institute of Molecular Biology, Slovak Academy of Sciences, 842 51 Bratislava, Slovak Republic
| | - R Nov Kov
- Institute of Molecular Biology, Slovak Academy of Sciences, 842 51 Bratislava, Slovak Republic
| | - B Re Uchov
- Institute of Molecular Biology, Slovak Academy of Sciences, 842 51 Bratislava, Slovak Republic
| | - D Hom Rov
- Institute of Molecular Biology, Slovak Academy of Sciences, 842 51 Bratislava, Slovak Republic
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