Pel, H. J. 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: 41.51). 03/2007; 25(2):221-31. DOI: 10.1038/nbt1282
Source: PubMed


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.
    Full-text · Article · Jul 2014 · Biotechnology Letters
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    • "Genes involved in sexual reproduction and the balance of sexuality and asexuality of Aspergillus spp. are given in Table S8 [74]–[76]. To identify genes involved in A. flavus sclerotia development, differentially expressed genes (DEGs) between the A. flavus mycelia and sclerotia cultures were detected. "
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    ABSTRACT: Aspergillus flavus has received much attention owing to its severe impact on agriculture and fermented products induced by aflatoxin. Sclerotia morphogenesis is an important process related to A. flavus reproduction and aflatoxin biosynthesis. In order to obtain an extensive transcriptome profile of A. flavus and provide a comprehensive understanding of these physiological processes, the isolated mRNA of A. flavus CA43 cultures was subjected to high-throughput strand-specific RNA sequencing (ssRNA-seq). Our ssRNA-seq data profiled widespread transcription across the A. flavus genome, quantified vast transcripts (73% of total genes) and annotated precise transcript structures, including untranslated regions, upstream open reading frames (ORFs), alternative splicing variants and novel transcripts. We propose natural antisense transcripts in A. flavus might regulate gene expression mainly on the post-transcriptional level. This regulation might be relevant to tune biological processes such as aflatoxin biosynthesis and sclerotia development. Gene Ontology annotation of differentially expressed genes between the mycelia and sclerotia cultures indicated sclerotia development was related closely to A. flavus reproduction. Additionally, we have established the transcriptional profile of aflatoxin biosynthesis and its regulation model. We identified potential genes linking sclerotia development and aflatoxin biosynthesis. These genes could be used as targets for controlled regulation of aflatoxigenic strains of A. flavus.
    Full-text · Article · May 2014 · PLoS ONE
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    • "Currently, a few hundreds of fungal genomes have been sequenced, including important human pathogens, plant pathogens and model organisms [14-20]. The genome of Industry-related fungi, like Aspergillus niger (which is widely used for the production of enzymes) and Trichoderma reesei (an industrial producer of plant biomass hydrolyzing enzymes), have also been sequenced [21,22]. Comparative genomic analyses of three thermophilic ascomycete species, Thermomyces lanuginosus [20], Thielavia terrestris and Myceliophthora thermophila suggest that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to be manipulated using classical and molecular genetics [23]. "
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    ABSTRACT: The zygomycete fungi like Rhizomucor miehei have been extensively exploited for the production of various enzymes. As a thermophilic fungus, R. miehei is capable of growing at temperatures that approach the upper limits for all eukaryotes. To date, over hundreds of fungal genomes are publicly available. However, Zygomycetes have been rarely investigated both genetically and genomically. Here, we report the genome of R. miehei CAU432 to explore the thermostable enzymatic repertoire of this fungus. The assembled genome size is 27.6-million-base (Mb) with 10,345 predicted protein-coding genes. Even being thermophilic, the G + C contents of fungal whole genome (43.8%) and coding genes (47.4%) are less than 50%. Phylogenetically, R. miehei is more closerly related to Phycomyces blakesleeanus than to Mucor circinelloides and Rhizopus oryzae. The genome of R. miehei harbors a large number of genes encoding secreted proteases, which is consistent with the characteristics of R. miehei being a rich producer of proteases. The transcriptome profile of R. miehei showed that the genes responsible for degrading starch, glucan, protein and lipid were highly expressed. The genome information of R. miehei will facilitate future studies to better understand the mechanisms of fungal thermophilic adaptation and the exploring of the potential of R. miehei in industrial-scale production of thermostable enzymes. Based on the existence of a large repertoire of amylolytic, proteolytic and lipolytic genes in the genome, R. miehei has potential in the production of a variety of such enzymes.
    Full-text · Article · Apr 2014 · BMC Genomics
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