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

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.

Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum

“…Thirty-three of such genes were identified using SMURF software (http://www.tigr.org/software/) encoding for: 20 polyketide synthases (PKS), 10 nonribosomal peptide synthetases (NRPS), 2 hybrid NRPS-PKS enzymes and 1 dimethylallyltryptophan synthase (Supplementary Table 3 online). This is similar to the numbers found in Aspergilli 10,12,15,16 . The penicillin cluster is well known 17 , and the siderophore synthetases for ferrichrome (Pc13g05250) and triacetylfusarinine (Pc16g03850, Pc22g20400) were readily assigned by homology (Supplementary Table 4 online).…”

“…To generate the species tree, a total of 90 orthologous genes from P. chrysogenum, P. marneffei (GenBank ABAR00000000), T. stipitatus (GenBank ABAS00000000), A. niger 16 , A. nidulans 10 , A. oryzae 15 , A. fumigatus 12 , A. clavatus (GenBank AAKD00000000), A. terreus (Refseq NT_165925-NT_165951), Neosartorya fischeri (GenBank AAKE00000000) and Gibberella zeae (anamorph Fusarium graminearum) 49 were aligned at the amino acid level (Supplementary Table 22 online). To minimize the effect of incorrect or incongruent gene models, these proteins were chosen on the basis of having identical numbers of introns in each species and similar lengths (95% overlap).…”

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

“…The ER-associated protein degradation (ERAD) pathway of T. reesei seems to be more redundant than the secretory pathway in general, as two orthologs of the yeast DER1 and UFD1 genes are found. We found clear homologs of most of the other known ERAD components in T. reesei, despite an apparent lack of orthologs or little sequence similarity to yeast ERAD components in the Aspergillus niger genome 23 .…”

Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

“…Among the most widely utilised fungi in industrial and biological processes, A. niger has been called a cell factory (Pel et al 2007) to reflect its widespread adoption and impact. Because of its importance for both enzyme and organic acid production, multiple strains of A. niger have sequenced and analysed (Pel et al 2007).…”

“…Because of its importance for both enzyme and organic acid production, multiple strains of A. niger have sequenced and analysed (Pel et al 2007). The reference sequence data from these strains has been critical for development of ‘fast forward’ genetic approaches for association of genes with mutant phenotypes (Niu et al 2016a, 2016b).…”