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Pel, H. et al. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat. Biotechnol. 25, 221-231

Department of Biotechnology , Delft University of Technology, Delft, South Holland, Netherlands
Nature Biotechnology (Impact Factor: 39.08). 03/2007; 25(2):221-31. DOI: 10.1038/nbt1282
Source: PubMed

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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    • "In particular, Aspergillus niger (GRAS strain) is recognized as an important producer of enzymes and organic acids (Legiša and Mattey 2007). The complete genome sequences of A. niger CBS513.88 (Pel et al. 2007) and ATCC1015 (Andersen et al. 2011) have become available, and this has led to the identification of a large number of polyketide (PKS) and non-ribosomal peptide (NRPS) genes. Aspergillus niger thus has the potential to produce a number of secondary metabolites that have yet to be discovered and structurally elucidated (Ferracin et al. 2012). "
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    ABSTRACT: Genomic studies have shown that not only plants but also filamentous fungi contain type III polyketide synthases. To study the function of type III polyketide synthase (AnPKSIII) in Aspergillus niger, a deletion strain (delAnPKSIII) and an overexpression strain (oeAnPKSIII) were constructed in A. niger MA169.4, a derivative of the wild-type (WT) A. niger ATCC 9029 that produces large quantities of gluconic acid. Alterations in the metabolites were analyzed by HPLC when the extract of the overexpression strain was compared with extracts of the WT and deletion strains. Protocatechuic acid (PCA; 3,4-dihydroxybenzoic acid, 3.2 mg/l) was isolated and identified as the main product of AnPKSIII when inductively expressed in A. niger MA169.4. The molecular weight of PCA was 154.1 (m/z 153.1 [M-H](-)), was detected by ESI-MS in the negative ionization mode, and (1)H and (13)C NMR data confirmed its structure.
    Biotechnology Letters 07/2014; 36(11). DOI:10.1007/s10529-014-1609-z · 1.74 Impact Factor
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    • "The biosynthetic pathway for FBs has been described in Fusarium spp., and at least 15 key genes have been identified, occurring in a well-characterised cluster (Proctor et al. 2003). Whole-genome sequences of A. niger strains have been published (Baker 2006; Pel et al. 2007) and it was discovered that the genome contains gene sequences analogous to FB biosynthesis genes found in Fusarium spp. Subsequent research has demonstrated that some strains of A. niger can produce FB 2 and, to a lesser extent, FB 4 . "
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    ABSTRACT: Fumonisins (FBs), carcinogenic mycotoxins, are known to be typically produced by several phytopathogenic fungal species belonging to the genus Fusarium. F. proliferatum and F. verticillioides, two important pathogens of maize worldwide, are the most common species that produce fumonisins (FBs). The main FBs produced by these species are FB1, FB2 and FB3. Moreover, recently, fungal strains belonging to Aspergillus niger have been also reported to produce fumonisins (in particular, FB2 and FB4). In a survey on maize carried out in Central Italy, 17 maize kernel samples were collected at harvest and analyzed for FB1, FB2 and FB3, as well as fungal contamination, with a particular attention to the species producing FBs. All 17 samples were contaminated by F. verticillioides and/or F. proliferatum at a level ranging from 13% to 100% of kernels. However, 10 out of 17 samples were contaminated also by Aspergillus section Nigri with a range from 6% to 68% of kernels. There was a significant inverse logarithmic relationship between levels of Fusarium and Aspergillus contamination. All samples were contaminated by FBs; FB1 ranged from 0.09 to 30.2 μg/g, whereas FB2 ranged from 0.04 to 13.2 μg/g. The ratio of FB2/FB1 contamination in the maize samples was evaluated and the highest values occurred in samples contaminated with Aspergillus section Nigri. Thirty strains of Aspergillus section Nigri isolated from these samples were molecularly identified (based on sequences of 2 housekeeping genes) and analysed for their capability to produce FB2. Among the 30 strains isolated, 12 were identified as Aspergillus welwitschiae (syn A. awamori) and 18 as A. tubingensis. FB2 was produced by 5 out of 12 strains of A. welwitschiae within a range of 0.20-5 μg/g. This is the first report showing the capability of Aspergillus section Nigri from maize to produce FB2 and their possibility to contribute to FB accumulation in kernels.
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    • "List_of_sequenced_fungi_genomes) are available. Several fungi species are significant to industry and agriculture: the mold Aspergillus niger (Pel et al., 2007), the plant pathogen Magnaporthe oryzae (Dean et al., 2005), the entomopathogenic fungus Metarhizium anisopliae (Gao et al., 2011), and the " Chinese mushroom of immortality " Ganoderma lucidum (Chen et al., 2012). These large-scale functional and comparative genome analyses are now possible in a wide range of species (Soanes et al., 2008). "
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    ABSTRACT: Advances in genetic transformation techniques have made important contributions to molecular genetics. Various molecular tools and strategies have been developed for functional genomic analysis of filamentous fungi since the first DNA transformation was successfully achieved in Neurospora crassa in 1973. Increasing amounts of genomic data regarding filamentous fungi are continuously reported and large-scale functional studies have become common in a wide range of fungal species. In this review, various molecular tools used in filamentous fungi are compared and discussed, including methods for genetic transformation (e.g., protoplast transformation, electroporation, and microinjection), the construction of random mutant libraries (e.g., restriction enzyme mediated integration, transposon arrayed gene knockout, and Agrobacterium tumefaciens mediated transformation), and the analysis of gene function (e.g., RNA interference and transcription activator-like effector nucleases). We also focused on practical strategies that could enhance the efficiency of genetic manipulation in filamentous fungi, such as choosing a proper screening system and marker genes, assembling target-cassettes or vectors effectively, and transforming into strains that are deficient in the nonhomologous end joining pathway. In summary, we present an up-to-date review on the different molecular tools and latest strategies that have been successfully used in functional genomics in filamentous fungi.
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