The complete karyotype of Aspergilius niger: the use of introduced electrophoretic mobility variation of chromosomes for gene assignment studies

Verdoes, J.C.; Calil, M.R.; Punt, Peter J.; Debets, Fons; Swart, K.; Stouthamer, A. H.; Hondel, Cees A. M. J. J. van den

doi:10.1007/bf00280189

Cited by 42 publications

(20 citation statements)

References 26 publications

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“…3. The large translocation/inversion event of ChrIII and ChrVII explains the discrepancies in chromosome size reported by Pel et al (2007) between strain N400 (Verdoes et al 1994) and calculated sizes of ChrIII and ChrVII for CBS 513.88. This fact and that the breakpoints are within two otherwise intact genes indicate that the event occurred after the branching of strains N400 and NRRL 3122, possibly in the mutagenesis of the predecessor of CBS 513.88.…”

Section: Discussionmentioning

confidence: 92%

“…By way of comparison, 48,798 ESTs (97.6%) showed hits to the assembly. Orientation of the chromosome arms was based on eight available telomere sequences, the supercontig orientation proposed by Pel et al (2007), and research on linkage groups in A. niger Debets et al 1989Debets et al , 1990aSwart et al 1992;Verdoes et al 1994). …”

Section: Methods Atcc 1015 Genome Assemblymentioning

confidence: 99%

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Comparative genomics of citric-acid-producingAspergillus nigerATCC 1015 versus enzyme-producing CBS 513.88

Andersen

Salazar²,

Schaap³

et al. 2011

Genome Res.

315

268

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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 wholegenome 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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Section: Discussionmentioning

confidence: 92%

Section: Methods Atcc 1015 Genome Assemblymentioning

confidence: 99%

Comparative genomics of citric-acid-producingAspergillus nigerATCC 1015 versus enzyme-producing CBS 513.88

Andersen

Salazar²,

Schaap³

et al. 2011

Genome Res.

315

268

View full text Add to dashboard Cite

show abstract

“…niger genetic and physical map. The genetic location of cloned genes was established using pulsed field electrophoresis followed by Southern blot analysis 15 . Parasexual analysis 14 was used to determine the genetic location of cpcA by linkage of the phleomycin resistance to hisD4.…”

Section: Methodsmentioning

confidence: 99%

“…Four putative oxalate/formate antiporters for formate transport were found (Supplementary Table 12). The eight linkage groups were numbered in the order of which new markers were characterized and were later shown to corrrespond to chromosomes I to VIII 15 Protein secretion in A. niger For reasons unknown, A. niger is a far more effective natural secretor of proteins than the well-studied yeast S. cerevisiae 31 . In eukaryotes protein secretion involves transport via endoplasmatic reticulum (ER), Golgi apparatus and vesicles to the cell membrane ( Fig.…”

Section: Central Metabolism and Organic Acid Productionmentioning

confidence: 99%

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

et al. 2007

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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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“…A. nidulans urgB expression also appears to be regulated in A. niger as expression is high in glucose and ammonium-containing medium whereas expression is low in medium lacking both glucose and ammonium and also in the presence of protein. Verdoes et al (1994) it was known that in A. niger the pepA gene is located on linkage group 1. In pulsed field electrophoresis-Southern experiments, the A. niger pepB, and pepE genes have been allocated to linkage groups I1 and IV, respectively (van den Hombergh, J. P. T. Allocation o f p e p A to linkage group I was concluded from the 3.4% recombination frequency between thefwnA6 and the argB' marker Allocation of peps to linkage group I1 was concluded from the 5.0% recombination frequency between the goxC17 and the argB+ marker.…”

Section: Resultsmentioning

confidence: 99%

Disruption of Three Acid Proteases in Aspergillus Niger— Effects on Protease Spectrum, Intracellular Proteolysis, and Degradation of Target Proteins

Hombergh¹,

Gelpke²,

Vondervoort³

et al. 1997

European Journal of Biochemistry

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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 ApepA and the ApepB disruptants, repectively. In the ApepE 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 ApepE 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 ApepAApepB, ApepBApepE and ApepAApepE double disruptants as well as a ApepAApepBApepE triple disruptant, lacking all three acid protease activities. The in vitro residual PELB activity was the highest in the triple disruptant and the ApepAApepB recombinant.Keywords: Aspergillus ; protease ; disruption ; cascade activation ; proteolytic degradation.Aspergillus niger produces a broad spectrum of proteases, both specific and non-specific, which is recognized to be one of the major reasons for the low protein expression yields that are frequently observed, especially when producing heterologous proteins. The genetics of proteolytic degradation in Aspergilli is very complex due the involvement of many regulatory factors in protease expression. Cohen (1972Cohen ( , 1973 showed in a series of pioneering studies that in A. niduluns extracellular proteases were repressed by low-molecular-mass sources of carbon, nitrogen, and sulphur. and van den Hombergh et al. (1994) have recently shown that in A. niger both pathway-specific induction by proteins and wide domain regulatory mechanisms (carbon catabolite repression, nitrogen metabolite repression, and pH regulation) are involved in the overall regulation of extracellular proteases. Several intracellular

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The complete karyotype of Aspergilius niger: the use of introduced electrophoretic mobility variation of chromosomes for gene assignment studies

Cited by 42 publications

References 26 publications

Comparative genomics of citric-acid-producingAspergillus nigerATCC 1015 versus enzyme-producing CBS 513.88

Comparative genomics of citric-acid-producingAspergillus nigerATCC 1015 versus enzyme-producing CBS 513.88

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

Disruption of Three Acid Proteases in Aspergillus Niger— Effects on Protease Spectrum, Intracellular Proteolysis, and Degradation of Target Proteins

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