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Foutz KR, Woloshuk CP, Payne GA. Cloning and assignment of linkage group loci to a karyotypic map of the filamentous fungusAspergillus flavus. Mycologia 2018. [DOI: 10.1080/00275514.1995.12026600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Kirk R. Foutz
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695-7616
| | - Charles P. Woloshuk
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Gary A. Payne
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695-7616
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Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJI, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R, Albermann K, Berka RM, Braus GH, Braus-Stromeyer SA, Corrochano LM, Dai Z, van Dijck PWM, Hofmann G, Lasure LL, Magnuson JK, Menke H, Meijer M, Meijer SL, Nielsen JB, Nielsen ML, van Ooyen AJJ, Pel HJ, Poulsen L, Samson RA, Stam H, Tsang A, van den Brink JM, Atkins A, Aerts A, Shapiro H, Pangilinan J, Salamov A, Lou Y, Lindquist E, Lucas S, Grimwood J, Grigoriev IV, Kubicek CP, Martinez D, van Peij NNME, Roubos JA, Nielsen J, Baker SE. Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Res 2011; 21:885-97. [PMID: 21543515 DOI: 10.1101/gr.112169.110] [Citation(s) in RCA: 279] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.
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Affiliation(s)
- Mikael R Andersen
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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4
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Cherry B, Bashkirova EV, Lopez de Leon A, Jin Q, Udagawa H, Takano H, Takagi S, Berka RM. ORIGINAL RESEARCH: Analysis of an Aspergillus niger glucoamylase strain pedigree using comparative genome hybridization & real-time quantitative polymerase chain reaction. Ind Biotechnol (New Rochelle N Y) 2009. [DOI: 10.1089/ind.2009.5.237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Barbara Cherry
- Novozymes, Inc., 1445 Drew Avenue, Davis, California, USA 95618
| | | | | | - Qiming Jin
- Novozymes, Inc., 1445 Drew Avenue, Davis, California, USA 95618
| | - Hiroaki Udagawa
- Novozymes, Inc., 1445 Drew Avenue, Davis, California, USA 95618
| | - Hiromi Takano
- Novozymes, Inc., 1445 Drew Avenue, Davis, California, USA 95618
| | - Shinobu Takagi
- Novozymes, Inc., 1445 Drew Avenue, Davis, California, USA 95618
| | - Randy M. Berka
- Novozymes, Inc., 1445 Drew Avenue, Davis, California, USA 95618
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Investigation of the physiological properties and synthesis of PUFAs from Thraustochytrids and its electrophoretic karyotypes. BIOTECHNOL BIOPROC E 2007. [DOI: 10.1007/bf02931091] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
Aspergillus niger is a filamentous ascomycete fungus that is ubiquitous in the environment and has been implicated in opportunistic infections of humans. In addition to its role as an opportunistic human pathogen, A. niger is economically important as a fermentation organism used for the production of citric acid. Industrial citric acid production by A. niger represents one of the most efficient, highest yield bioprocesses in use currently by industry. The genome size of A. niger is estimated to be between 35.5 and 38.5 megabases (Mb) divided among eight chromosomes/linkage groups that vary in size from 3.5-6.6 Mb. Currently, there are three independent A. niger genome projects, an indication of the economic importance of this organism. The rich amount of data resulting from these multiple A. niger genome sequences will be used for basic and applied research programs applicable to fermentation process development, morphology and pathogenicity.
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Affiliation(s)
- Scott E Baker
- Fungal Biotechnology Team, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
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van de Vondervoort PJI, Langeveld SMJ, Visser J, van Peij NNME, Pel HJ, van den Hondel CAMJJ, Ram AFJ. Identification of a mitotic recombination hotspot on chromosome III of the asexual fungus Aspergillus niger and its possible correlation with [corrected] elevated basal transcription. Curr Genet 2007; 52:107-14. [PMID: 17684745 PMCID: PMC2071955 DOI: 10.1007/s00294-007-0143-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 06/29/2007] [Accepted: 07/02/2007] [Indexed: 11/17/2022]
Abstract
Genetic recombination is an important tool in strain breeding in many organisms. We studied the possibilities of mitotic recombination in strain breeding of the asexual fungus Aspergillus niger. By identifying genes that complemented mapped auxotrophic mutations, the physical map was compared to the genetic map of chromosome III using the genome sequence. In a program to construct a chromosome III-specific marker strain by selecting mitotic crossing-over in diploids, a mitotic recombination hotspot was identified. Analysis of the mitotic recombination hotspot revealed some physical features, elevated basal transcription and a possible correlation with purine stretches.
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Affiliation(s)
- Peter J. I. van de Vondervoort
- Institute of Biology, Leiden University, Wassenaarseweg 64, 2333AL Leiden, The Netherlands
- DSM Food Specialties, Delft, P.O. Box 1, 2600MA Delft, The Netherlands
| | - Sandra M. J. Langeveld
- Institute of Biology, Leiden University, Wassenaarseweg 64, 2333AL Leiden, The Netherlands
| | - Jaap Visser
- FGT Consultancy, P.O Box 396, 6700AJ Wageningen, The Netherlands
| | | | - Herman J. Pel
- DSM Food Specialties, Delft, P.O. Box 1, 2600MA Delft, The Netherlands
| | | | - Arthur F. J. Ram
- Institute of Biology, Leiden University, Wassenaarseweg 64, 2333AL Leiden, The Netherlands
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Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JAE, van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EGJ, Debets AJM, Dekker P, van Dijck PWM, van Dijk A, Dijkhuizen L, Driessen AJM, d'Enfert C, Geysens S, Goosen C, Groot GSP, de Groot PWJ, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JPTW, van den Hondel CAMJJ, van der Heijden RTJM, van der Kaaij RM, Klis FM, Kools HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJEC, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NNME, Ram AFJ, Rinas U, Roubos JA, Sagt CMJ, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJJ, Wedler H, Wösten HAB, Zeng AP, van Ooyen AJJ, Visser J, Stam H. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol 2007; 25:221-31. [PMID: 17259976 DOI: 10.1038/nbt1282] [Citation(s) in RCA: 901] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Accepted: 11/27/2006] [Indexed: 11/09/2022]
Abstract
The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.
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Affiliation(s)
- Herman J Pel
- DSM Food Specialties, PO Box 1, 2600 MA Delft, The Netherlands
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Lukácsi G, Takó M, Nyilasi I. Pulsed-field gel electrophoresis: a versatile tool for analysis of fungal genomes. A review. Acta Microbiol Immunol Hung 2006; 53:95-104. [PMID: 16696553 DOI: 10.1556/amicr.53.2006.1.7] [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: 11/19/2022]
Abstract
The separation of chromosome-size DNA molecules by pulsed-field gel electrophoresis (PFGE) has become a well-established technique in recent years. Although it has very wide-ranging applications, it made a real breakthrough for fungal genome analysis. Because of the small size of fungal chromosomes, their investigation was not possible earlier. Different PFGE approaches allowed the separation of DNA molecules larger than 10 megabase pairs in size, and electrophoretic karyotypes for numerous previously genetically uncharacterized fungal species could be established. This review discusses the applicability of these electrophoretic karyotypes for the investigation of genome structure, for strain identification and for species delimitation.
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Affiliation(s)
- Gyöngyi Lukácsi
- Department of Microbiology, Faculty of Sciences, University of Szeged, P.O. Box 533, H-6701 Szeged, Hungary.
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Beadle J, Wright M, McNeely L, Bennett JW. Electrophoretic karyotype analysis in fungi. ADVANCES IN APPLIED MICROBIOLOGY 2004; 53:243-70. [PMID: 14696321 DOI: 10.1016/s0065-2164(03)53007-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The resolution of chromosomal-sized DNAs by PFGE has many applications that include karyotyping, strain identification of similar species, characterization of transformed strains, building of linkage maps, and preparation of DNA for genomic analysis. Successful electrophoretic separation of chromosomes is an empiric process in which the initial concentration of intact chromosome-sized DNA and the optimization of electrophoretic parameters are the most important experimental variables. Nonetheless, inherent attributes of the genome architecture of certain species may thwart success. When a karyotype contains numerous chromosomes of the same size and/or many large (greater than 8 Mb) chromosomes, no amount of manipulation of the electrophoretic parameters will resolve individual chromosome bands using present technology. Further, fungi display a surprising amount of intraspecific variation in both chromosome number and size, making it difficult to establish a standard "reference" karyotype for many species. Although PFGE is not a panacea for bringing genetics to species that lack classical genetic systems, it often does provide a way for developing a molecular linkage map in the absence of a formal genetic system. It is far faster than parasexual analysis in the discovery of linkage relationships. For genomics projects, DNA can be recovered from pulsed field gels and used to prepare chromosome-specific libraries. Where whole genome sequencing strategies are used, chromosomes separated by PFGE provide an anchor for sequencing data. Electrophoretic karyotypes can be probed with anonymous pieces of DNA from bacterial artificial chromosome (BAC) contigs, thereby facilitating the building of physical maps. In conclusion, despite its shortcomings, the PFGE technique underlies much of our current understanding of the physical nature of the fungal genome.
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Affiliation(s)
- J Beadle
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA
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Cervelatti EP, Ferreira-Nozawa MS, Aquino-Ferreira R, Fachin AL, Martinez-Rossi NM. Electrophoretic molecular karyotype of the dermatophyte Trichophyton rubrum. Genet Mol Biol 2004. [DOI: 10.1590/s1415-47572004000100016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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12
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Genomics of Economically Significant Aspergillus and Fusarium Species. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s1874-5334(04)80013-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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Swart K, Debets AJ, Bos CJ, Slakhorst M, Holub EF, Hoekstra RF. Genetic analysis in the asexual fungus Aspergillus niger. ACTA BIOLOGICA HUNGARICA 2002; 52:335-43. [PMID: 11426868 DOI: 10.1556/abiol.52.2001.2-3.18] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The genetics of A. niger has been developed since 1980. An overview is presented of the advances in developing methods and collecting data. Important tools have been a) the application of essentially different methods to isolate mutants, b) the adaptation to A. niger ofA. nidulans methodology for analysis of the parasexual cycle, c) the choice of marker genes, and in some cases the artificial introduction of such genes, to select homozygous segregants arising from mitotic recombination. With the use of parasexual recombination, a genetic linkage map of A. niger has been established. In total, 110 nuclear and 1 cytoplasmic (mitochondrial) markers are available. The application of A. niger genetics in applied research is illustrated by examples.
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Affiliation(s)
- K Swart
- Department of Plant Sciences, Wageningen University, The Netherlands.
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vanKuyk PA, de Groot MJ, Ruijter GJ, de Vries RP, Visser J. The Aspergillus niger D-xylulose kinase gene is co-expressed with genes encoding arabinan degrading enzymes, and is essential for growth on D-xylose and L-arabinose. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:5414-23. [PMID: 11606204 DOI: 10.1046/j.0014-2956.2001.02482.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Aspergillus niger D-xylulose kinase encoding gene has been cloned by complementation of a strain deficient in D-xylulose kinase activity. Expression of xkiA was observed in the presence of L-arabinose, L-arabitol and D-xylose. Expression of xkiA is not mediated by XLNR, the xylose-dependent positively-acting xylanolytic regulator. Although the expression of xkiA is subject to carbon catabolite repression, the wide domain regulator CREA is not directly involved. The A. niger D-xylulose kinase was purified to homogeneity, and the molecular mass determined using electrospray ionization mass spectrometry agreed with the calculated molecular mass of 62816.6 Da. The activity of XKIA is highly specific for D-xylulose. Kinetic parameters were determined as Km(D-xylulose) = 0.76 mM and Km(ATP) = 0.061 mM. Increased transcript levels of the genes encoding arabinan and xylan degrading enzymes, observed in the xylulose kinase deficient strain, correlate with increased accumulation of L-arabitol and xylitol, respectively. This result supports the suggestion that L-arabitol may be the specific low molecular mass inducer of the genes involved in arabinan degradation. It also suggests a possible role for xylitol in the induction of xylanolytic genes. Conversely, overproduction of XKIA did not reduce the size of the intracellular arabitol and xylitol pools, and therefore had no effect on expression of genes encoding xylan and arabinan degrading enzymes nor on the activity of the enzymes of the catabolic pathway.
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Affiliation(s)
- P A vanKuyk
- Molecular Genetics of Industrial Microorganisms, Wageningen University, Dreijenlaan 2, Wageningen, the Netherlands
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Abstract
Pulsed-field gel electrophoresis (PFGE) was originally developed as a technique for providing electrophoretic karyotypes of micro-organisms. Since then the technique has evolved and diversified in many new directions. This review traces the evolution of PFGE, summarizes our understanding of its theoretical basis, and provides a comprehensive description of the methodology. Established and novel applications are explored and the reader is provided with an extensive list of references.
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Affiliation(s)
- J Maule
- MRC Human Genetics Unit, Western General Hospital, Edinburgh, Scotland.
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van Peij NN, Visser J, de Graaff LH. Isolation and analysis of xlnR, encoding a transcriptional activator co-ordinating xylanolytic expression in Aspergillus niger. Mol Microbiol 1998; 27:131-42. [PMID: 9466262 DOI: 10.1046/j.1365-2958.1998.00666.x] [Citation(s) in RCA: 220] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Complementation by transformation of an Aspergillus niger mutant lacking xylanolytic activity led to the isolation of the xlnR gene. The xlnR gene encodes a polypeptide of 875 amino acids capable of forming a zinc binuclear cluster domain with similarity to the zinc clusters of the GAL4 superfamily of transcription factors. The XlnR-binding site 5'-GGCTAAA-3' was deduced after electrophoretic mobility shift assays, DNase I footprinting and comparison of various xylanolytic promoters. The importance of the second G within the presumed XlnR binding site 5'-GGCTAAA-3' was confirmed in vitro and in vivo. The 5'-GGCTAAA-3' consensus sequence is found within several xylanolytic promoters of various Aspergillus species and Penicillium chrysogenum. Therefore, this sequence may be an important and conserved cis-acting element in induction of xylanolytic genes in filamentous fungi. Our results indicate that XlnR is a transcriptional activator of the xylanolytic system in A. niger.
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MESH Headings
- Amino Acid Sequence
- Aspergillus niger/enzymology
- Aspergillus niger/genetics
- Aspergillus niger/metabolism
- Base Sequence
- Binding, Competitive
- Blotting, Northern
- Blotting, Southern
- Blotting, Western
- DNA Footprinting
- DNA, Fungal/chemistry
- Deoxyribonuclease I
- Electrophoresis, Polyacrylamide Gel
- Fungal Proteins
- Gene Expression Regulation, Enzymologic/physiology
- Gene Expression Regulation, Fungal/physiology
- Molecular Sequence Data
- Mutation
- Promoter Regions, Genetic/genetics
- Restriction Mapping
- Sequence Analysis, DNA
- Trans-Activators/genetics
- Transcription, Genetic
- Transformation, Genetic
- Xylan Endo-1,3-beta-Xylosidase
- Xylans/metabolism
- Xylosidases/chemistry
- Xylosidases/genetics
- Xylosidases/metabolism
- Zinc Fingers/genetics
- Zinc Fingers/physiology
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Affiliation(s)
- N N van Peij
- Section Molecular Genetics of Industrial Microorganisms, Wageningen Agricultural University, The Netherlands
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de Vries RP, Michelsen B, Poulsen CH, Kroon PA, van den Heuvel RH, Faulds CB, Williamson G, van den Hombergh JP, Visser J. The faeA genes from Aspergillus niger and Aspergillus tubingensis encode ferulic acid esterases involved in degradation of complex cell wall polysaccharides. Appl Environ Microbiol 1997; 63:4638-44. [PMID: 9406381 PMCID: PMC168785 DOI: 10.1128/aem.63.12.4638-4644.1997] [Citation(s) in RCA: 166] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We report the cloning and characterization of a gene encoding a ferulic acid esterase, faeA, from Aspergillus niger and Aspergillus tubingensis. The A. niger and A. tubingensis genes have a high degree of sequence identity and contain one conserved intron. The gene product, FAEA, was overexpressed in wild-type A. tubingensis and a protease-deficient A. niger mutant. Overexpression of both genes in wild-type A. tubingensis and an A. niger protease-deficient mutant showed that the A. tubingensis gene product is more sensitive to degradation than the equivalent gene product from A. niger. FAEA from A. niger was identical to A. niger FAE-III (C. B. Faulds and G. Williamson, Microbiology 140:779-787, 1994), as assessed by molecular mass, pH and temperature optima, pI, N-terminal sequence, and activity on methyl ferulate. The faeA gene was induced by growth on wheat arabinoxylan and sugar beet pectin, and its gene product (FAEA) released ferulic acid from wheat arabinoxylan. The rate of release was enhanced by the presence of a xylanase. FAEA also hydrolyzed smaller amounts of ferulic acid from sugar beet pectin, but the rate was hardly affected by addition of an endo-pectin lyase.
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Affiliation(s)
- R P de Vries
- Wageningen Agricultural University, The Netherlands
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18
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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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19
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Ruijter GJG, Vanhanen SA, Gielkens MMC, van de Vondervoort PJI, Visser J. Isolation of Aspergillus niger creA mutants and effects of the mutations on expression of arabinases and L-arabinose catabolic enzymes. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 9):2991-2998. [PMID: 9308182 DOI: 10.1099/00221287-143-9-2991] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Aspergillus niger mutants relieved of carbon repression were isolated from an areA parental strain by selection of colonies that exhibited improved growth on a combination of 4-aminobutanoic acid (GABA) and D-glucose. In addition to derepression of the utilization of GABA as a nitrogen source in the presence of D-glucose, three of the four mutants also showed derepression of L-alanine and L-proline utilization. Transformation of the mutants with the A. niger creA gene, encoding the repressor protein CREA, re-established the areA phenotype on GABA/D-glucose, identifying the mutations as creAd. The creA gene mapped on chromosome IV by linkage analysis and contour-clamped homogeneous electric field hybridization. The creA mutants obtained were used to study the involvement of CREA in repression by D-glucose of arabinases and L-arabinose catabolism in A. niger. In wild-type A. niger, alpha-L-arabinofuranosidase A, alpha-L-arabinofuranosidase B, endo-arabinase, L-arabinose reductase and L-arabitol dehydrogenase were induced on L-arabinose, but addition of D-glucose prevented this induction. Repression was relieved to varying degrees in the creA mutants, showing that biosynthesis of arabinases and L-arabinose catabolic enzymes is under control of CREA.
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Affiliation(s)
- George J G Ruijter
- Section Molecular Genetics of Industrial Microorganisms, Wageningen Agricultural University, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands
| | - Sipo A Vanhanen
- Section Molecular Genetics of Industrial Microorganisms, Wageningen Agricultural University, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands
| | - Marco M C Gielkens
- Section Molecular Genetics of Industrial Microorganisms, Wageningen Agricultural University, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands
| | - Peter J I van de Vondervoort
- Section Molecular Genetics of Industrial Microorganisms, Wageningen Agricultural University, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands
| | - Jaap Visser
- Section Molecular Genetics of Industrial Microorganisms, Wageningen Agricultural University, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands
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van den Hombergh JP, Sollewijn Gelpke MD, van de Vondervoort PJ, Buxton FP, Visser J. Disruption of three acid proteases in Aspergillus niger--effects on protease spectrum, intracellular proteolysis, and degradation of target proteins. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 247:605-13. [PMID: 9266703 DOI: 10.1111/j.1432-1033.1997.00605.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Three acid protease genes encoding two extracellular proteases (PEPA and PEPB) and one intracellular protease (PEPE) were disrupted in Aspergillus niger. Northern-blot analysis showed the absence of wild-type protease mRNAs in the disruptants while western-blot analysis proved the absence of the encoded proteases. Characterization of the residual proteolytic spectra in the disruptants indicated that the extracellular protease activity was reduced to 16% and 94% for the delta pepA and the delta pepB disruptants, repectively. In the delta pepE disruptant, the total intracellular proteolytic activity was reduced to 32%. Apart from the reduced intracellular pepstatin-inhibitable aspartyl protease activity, serine protease and serine carboxypeptidase activities were also significantly reduced in the delta pepE strain. This may indicate the presence of a cascade activation mechanism for several vacuolar proteases, triggered by the PEPE protein, similar to the situation in Saccharomyces cerevisiae. Disruption of a single protease gene had no effects on the transcription of other non-disrupted protease genes in A. niger. In supernatants of the disruptants, reduced degradation of a proteolytically very susceptible tester protein (PELB) was observed. By recombination, we also constructed delta pepA delta pepB, delta pepB delta pepE and delta pepA delta pepE double disruptants as well as a delta pepA delta pepB delta pepE triple disruptant, lacking all three acid protease activities. The in vitro residual PELB activity was the highest in the triple disruptant and the delta pepA delta pepB recombinant.
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Affiliation(s)
- J P van den Hombergh
- Section Molecular Genetics of Industrial Microorganisms, Wageningen Agricultural University, The Netherlands
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21
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van Peij NN, Brinkmann J, Vrsanská M, Visser J, de Graaff LH. beta-Xylosidase activity, encoded by xlnD, is essential for complete hydrolysis of xylan by Aspergillus niger but not for induction of the xylanolytic enzyme spectrum. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 245:164-73. [PMID: 9128738 DOI: 10.1111/j.1432-1033.1997.00164.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Two proteins exhibiting beta-D-xylosidase activity were identified upon fractionation and purification of a culture filtrate of an arabinoxylan-grown Aspergillus niger. A single band of 110 kDa by SDS/PAGE was obtained in both cases and these were active on xylo-oligosaccharides and on xylan. Partial xlnD cDNA clones were immunochemically identified and isolated from a lambda cDNA expression library. Sequence analysis showed that all cDNA clones correspond to a single gene. A genomic clone was isolated and overexpressed in A. niger and A. nidulans. The xlnD gene has an ORF of 2412 nucleotides, encodes a protein of 804 amino acids and contains a potential signal peptide of 26 amino acids. This results in a mature protein of 778 amino acids with a predicted molecular mass of 85 kDa and an isoelectric point of 4.5. The protein is N-glycosylated and contains 15 potential N-glycosylation sites. Sequence similarity is found with beta-D-glucosidases both of bacterial and fungal origin. Both beta-xylosidase proteins purified have high activity on the artificial substrate p-nitrophenyl beta-D-xylopyranoside (XylNp) and a side activity on p-nitrophenyl alpha-L-arabinofuranoside and p-nitrophenyl beta-D-glucopyranoside. A niger strains in which the xlnD gene was disrupted accumulate mainly xylobiose and xylotriose when grown on xylan and have no significant beta-xylosidase activity in the culture medium, indicating that this gene encodes the major extracellular beta-xylosidase.
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Affiliation(s)
- N N van Peij
- Section Molecular Genetics of Industrial Microorganisms, Wageningen Agricultural University, The Netherlands
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22
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van den Brink HJ, van Nistelrooy HJ, de Waard MA, van den Hondel CA, van Gorcom RF. Increased resistance to 14 alpha-demethylase inhibitors (DMIs) in Aspergillus niger by coexpression of the Penicillium italicum eburicol 14 alpha-demethylase (cyp51) and the A. niger cytochrome P450 reductase (cprA) genes. J Biotechnol 1996; 49:13-8. [PMID: 8879162 DOI: 10.1016/0168-1656(96)01403-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this paper we describe the effects of over-expression of the Penicillium italicum gene encoding eburicol 14 alpha-demethylase (cyp51), in Aspergillus niger strains with one or multiple copies of the gene encoding cytochrome P450 reductase (cprA), on the eburicol 14 alpha-demethylase activity. Eburicol 14 alpha-demethylase activity was determined by measuring the resistance of transformants against some eburicol 14 alpha-demethylase inhibitors (DMIs). DMIs are widely used as fungicides in crop protection and human and veterinarian health care. DMI resistance in a transformant overexpressing both CPR and CYP51 was increased 5-30-fold compared to DMI resistance in the wild type strain, depending on the test compound used. Resistance in this strain was approximately 2-5-fold increased compared to DMI resistance in a transformant that was overexpressing the cyp51 gene but had only the wild type copy of the cprA gene and approximately 3-12-fold increased compared to a strain overexpressing the cprA gene (and having only the wild type copy of the cyp51 gene). These results show the importance of CPR overexpression for increasing cytochrome P450 activities in filamentous fungi.
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Affiliation(s)
- H J van den Brink
- TNO Nutrition and Food Research Institute, Department of Molecular Genetics and Gene Technology, Rijswijk, The Netherlands.
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23
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van den Hombergh JP, MacCabe AP, van de Vondervoort PJ, Visser J. Regulation of acid phosphatases in an Aspergillus niger pacC disruption strain. MOLECULAR & GENERAL GENETICS : MGG 1996; 251:542-50. [PMID: 8709960 DOI: 10.1007/bf02173643] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
An Aspergillus niger strain has been constructed in which the pH-dependent regulatory gene, pacC, was disrupted. The pacC gene of A. niger, like that of A. nidulans, is involved in the regulation of acid phosphatase expression. Disruptants were identified by a reduction in acid phosphatase staining of colonies. Southern analysis demonstrated integration of the disruption plasmid at the pacC locus and Northern analysis showed that the disruption strain produced a truncated pacC mRNA of 2.2 kb (as compared to 2.8 kb in the wild type). The strain carrying the pacC disruption was used to assign the pacC gene to linkage group IV; this was confirmed by CHEF electrophoresis and Southern analysis. This strain further allowed us to determine which extracellular enzyme and transport systems are under the control of pacC in A. niger. Expression of the A. niger pacC wild-type gene and the truncated pacC gene showed that, in contrast to the auto-regulated wild-type expression, which was elevated only at alkaline pH, the truncated pacC gene was deregulated, as high-level expression occurred regardless of the pH of the culture medium. Analysis of the phosphatase spectrum by isoelectric focussing and enzyme activity staining both in the wild-type and the pacC disruptant showed that at least three acid phosphatases are regulated by the pacC. For the single alkaline phosphatase no pH regulation was observed.
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Affiliation(s)
- J P van den Hombergh
- Section Molecular Genetics of Industrial Microorganisms, Wageningen Agricultural University, The Netherlands
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24
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Gouka RJ, Punt PJ, Hessing JG, van den Hondel CA. Analysis of heterologous protein production in defined recombinant Aspergillus awamori strains. Appl Environ Microbiol 1996; 62:1951-7. [PMID: 8787393 PMCID: PMC167973 DOI: 10.1128/aem.62.6.1951-1957.1996] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A study was carried out to obtain more insight into the parameters that determine the secretion of heterologous proteins from filamentous fungi. A strategy was chosen in which the mRNA levels and protein levels of a number of heterologous genes of different origins were compared. All genes were under control of the Aspergillus awamori 1,4-beta-endoxylanase A (exlA) expression signals and were integrated in a single copy at the A. awamori pyrG locus. A Northern (RNA) analysis showed that large differences occurred in the steady-state mRNA levels obtained with the various genes; those levels varied from high values for genes of fungal origin (A. awamori 1,4-beta-endoxylanase A, Aspergillus niger glucoamylase, and Thermomyces lanuginosa lipase) to low values for genes of nonfungal origin (human interleukin 6 and Cyamopsis tetragonoloba [guar] alpha-galactosidase). With the C. tetragonoloba alpha-galactosidase wild-type gene full-length mRNA was even undetectable. Surprisingly, small amounts of full-length mRNA could be detected when a C. tetragonoloba alpha-galactosidase gene with an optimized Saccharomyces cerevisiae codon preference was expressed. In all cases except human interleukin 6, the protein levels corresponded to the amounts expected on basis of the mRNA levels. For human interleukin 6, very low protein levels were observed, whereas relatively high steady-state mRNA levels were obtained. Our data suggest that intracellular protein degradation is the most likely explanation for the low levels of secreted human interleukin 6.
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Affiliation(s)
- R J Gouka
- TNO Nutrition and Food Research Institute, Department of Molecular Genetics and Gene Technology, Rijswijk, The Netherlands
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25
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Glayzer DC, Roberts IN, Archer DB, Oliver RP. The isolation of Ant1, a transposable element from Aspergillus niger. MOLECULAR & GENERAL GENETICS : MGG 1995; 249:432-8. [PMID: 8552048 DOI: 10.1007/bf00287105] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A transposable element has been isolated from the industrially important fungus Aspergillus niger (strain N402). The element was identified as an insertion sequence within the coding region of the nitrate reductase gene. It had inserted at a TA site and appeared to have duplicated the target site upon insertion. The isolated element was found to be 4798 bp in length and contained 37-bp inverted, imperfect, terminal repeats (ITRs). The sequence of the central region of the element revealed an open reading frame (designated ORF1) which showed similarity, at the amino acid level, to the transposase of the Tc1/mariner class of DNA transposons. Another sequence within the central region of the element showed similarity to the 3' coding and downstream untranslated region of the amyA gene of A. niger. Sequence homology and structural features indicate that this element, which has been named Ant1 (A. niger transposon 1), is related to the Tc1/mariner group of DNA transposons. Ant1 is apparently present as a single copy in strain N402 of A. niger.
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Affiliation(s)
- D C Glayzer
- Norwich Molecular Plant Pathology Group, School of Biological Sciences, University of East Anglia, Norwich Research Park, UK
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26
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Abstract
The examination of fungal chromosomes by pulsed-field gel electrophoresis has revealed that length polymorphism is widespread in both sexual and asexual species. This review summarizes characteristics of fungal chromosome-length polymorphism and possible mitotic and meiotic mechanisms of chromosome length change. Most fungal chromosome-length polymorphisms are currently uncharacterized with respect to content and origin. However, it is clear that long tandem repeats, such as tracts of rRNA genes, are frequently variable in length and that other chromosomal rearrangements are suppressed during normal mitotic growth. Dispensable chromosomes and dispensable chromosome regions, which have been well documented for some fungi, also contribute to the variability of the fungal karyotype. For sexual species, meiotic recombination increases the overall karyotypic variability in a population while suppressing genetic translocations. The range of karyotypes observed in fungi indicates that many karyotypic changes may be genetically neutral, at least under some conditions. In addition, new linkage combinations of genes may also be advantageous in allowing adaptation of fungi to new environments.
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Affiliation(s)
- M E Zolan
- Department of Biology, Indiana University, Bloomington 47405, USA
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27
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van den Hombergh JP, van de Vondervoort PJ, van der Heijden NC, Visser J. New protease mutants in Aspergillus niger result in strongly reduced in vitro degradation of target proteins; genetical and biochemical characterization of seven complementation groups. Curr Genet 1995; 28:299-308. [PMID: 8590475 DOI: 10.1007/bf00326427] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Several mutants of Aspergillus niger, deficient in extracellular protease expression, have been isolated and characterized both genetically and biochemically. The mutant strains, obtained after in vivo UV-mutagenesis of conidiospores and selected by haloscreening on a new dual-substrate plate assay, belong to at least seven different complementation groups. These seven prt loci were assigned to linkage groups using master strains with marked chromosomes. One prt locus (prtC) could be assigned to linkage group I, three (prtB, prtE and prtG) to linkage group III, one (prtF) to linkage group V and the two remaining loci (prtA and prtD) to linkage group VIII. Extracellular proteolytic activities varied from 2 to 3% up to 80% of the protease activity of the parental strain. Assigning the different prt mutants to structural or regulatory genes is difficult since only one structural gene, pepA, has been mapped unambiguously on linkage group I but is not identical to prtC. All prt mutants except for prtC are likely to be regulatory mutants or else belong to a proteolytic cascade because residual activities showed that more proteolytic activities were affected simultaneously. Double mutants were constructed both by recombination and by a second round of mutagenesis. In both cases mutants with further reduced extracellular proteolytic activities were isolated. A sensitive in vitro degradation assay, based on the homologous pectin lyase B (PELB) protein to analyze proteolytic degradation in A. niger, was developed and used to show extremely reduced proteolytic PELB degradation in the culture media of some of these mutants.
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Affiliation(s)
- J P van den Hombergh
- Molecular Genetics of Industrial Microorganisms Agricultural University, HA Wageningen, The Netherlands
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28
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van den Brink HJ, van Zeijl CM, Brons JF, van den Hondel CA, van Gorcom RF. Cloning and characterization of the NADPH cytochrome P450 oxidoreductase gene from the filamentous fungus Aspergillus niger. DNA Cell Biol 1995; 14:719-29. [PMID: 7646819 DOI: 10.1089/dna.1995.14.719] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In this paper, we describe the cloning and molecular characterization of the Aspergillus niger cytochrome P450 reductase (CPR) gene, cprA. Attempts to clone the cprA gene by heterologous hybridization techniques were unsuccessful. Using the polymerase chain reaction (PCR) with degenerate primers based on conserved regions found in cpr genes from other organisms, we were able to isolate a fragment that contained part of the gene. With the aid of this fragment, a genomic fragment containing the entire coding region and 5' and 3' untranslated ends of the cprA gene was isolated and sequenced. The cprA gene was introduced in multiple copies in A. niger strain N402 using the amdS transformation system. One of the resulting transformants, AB2-2, showed a 14-fold increase in CPR activity, indicating that the cloned cprA gene is functional. We analyzed the induction of cprA gene expression by several generally used cytochrome P450 inducers but did not find any induction of cprA gene expression. However, A. niger cprA gene expression could be induced by benzoic acid, which is the substrate of the highly inducible A. niger cytochrome P450 gene, bphA (cyp53). On the basis of a comparison of the deduced protein sequence of the A. niger cprA gene with CPR proteins isolated from other organisms, the structure-function relationship of some conserved regions is discussed.
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Affiliation(s)
- H J van den Brink
- TNO Nutrition and Food Research Institute, Department of Molecular Genetics and Gene Technology, Rijswijk, The Netherlands
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29
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Verdoes JC, Punt PJ, van der Berg P, Debets F, Stouthamer AH, van den Hondel CA. Characterization of an efficient gene cloning strategy for Aspergillus niger based on an autonomously replicating plasmid: cloning of the nicB gene of A. niger. Gene 1994; 146:159-65. [PMID: 8076814 DOI: 10.1016/0378-1119(94)90288-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The development of an improved gene cloning strategy by complementation of mutant alleles in Aspergillus niger is described. The strategy is based on the use of a fungal autonomously replicating vector, pAB4-ARp1. This vector was constructed by the introduction of a previously described sequence involved in autonomous replication (AMA1), into a pyrG integrative vector, pAB4-1. With vector pAB4-ARp1, a 10-100-fold increase in transformation frequency was obtained, as compared to pAB4-1. Furthermore, the transformation frequency of a co-transformed plasmid is also increased using pAB4-ARp1. A. niger transformants containing pAB4-ARp1 are mitotically unstable. Co-transformed plasmids strictly co-segregated with the autonomously replicating vector, as a result of recombination between both vectors. The use of pAB4-ARp1 in gene cloning was demonstrated by the complementation of two linkage group-VII-specific A. niger mutants. Complementation of a lysF mutant was achieved by co-transformation of pAB4-ARp1 with total genomic A. niger DNA ('instant bank'). A nicB-deficient A. niger was complemented by co-transformation with pAB4-ARp1 and an A. niger cosmid library. The complementing DNA was re-isolated from a Nic+ transformant by transforming Escherichia coli with total genomic DNA of this transformant. Gene disruption and genetic analysis was carried out to prove that the previously unknown A. niger nicB gene had been cloned.
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Affiliation(s)
- J C Verdoes
- Department of Molecular Genetics and Gene Technology, TNO Nutrition and Food Research Institute, Rijswijk, The Netherlands
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30
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Punt PJ, Veldhuisen G, van den Hondel CA. Protein targeting and secretion in filamentous fungi. A progress report. Antonie Van Leeuwenhoek 1994; 65:211-6. [PMID: 7847888 DOI: 10.1007/bf00871949] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Although the application of filamentous fungi, such as Aspergillus niger for the production of extracellular proteins is well established for several decades, hardly any information is available about the molecular mechanisms of the process of protein secretion in these organisms. Two lines of research initiated towards a systematic analysis of the mechanism of protein targeting and secretion are presented in this paper. 1--To study routing and targeting of proteins in filamentous fungi the availability of a versatile reporter/carrier protein will be of considerable importance. Experiments towards the identification of such a protein are presented. 2--In analogy to the situation in Saccharomyces cerevisiae, the availability of defined (conditional) mutations in the secretion pathway will provide very important information about the organisation of the pathway. Therefore, based on results obtained in S. cerevisiae, the cloning of several fungal 'secretion' genes was started. The results of the cloning and characterisation of one of these genes is presented.
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Affiliation(s)
- P J Punt
- TNO Nutrition and Food Research Institute, Department of Molecular Genetics and Gene Technology, Rijswijk, The Netherlands
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