Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88.

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.

Yarrowia lipolytica: safety assessment of an oleaginous yeast with a great industrial potential.

Yarrowia lipolytica has been developed as a production host for a large variety of biotechnological applications. Efficacy and safety studies have demonstrated the safe use of Yarrowia-derived products containing significant proportions of Yarrowia biomass (as for DuPont's eicosapentaenoic acid-rich oil) or with the yeast itself as the final product (as for British Petroleum's single-cell protein product). The natural occurrence of the species in food, particularly cheese, other dairy products and meat, is a further argument supporting its safety. The species causes rare opportunistic infections in severely immunocompromised or otherwise seriously ill people with other underlying diseases or conditions. The infections can be treated effectively by the use of regular antifungal drugs, and in some cases even disappeared spontaneously. Based on our assessment, we conclude that Y. lipolytica is a "safe-to-use" organism.

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

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.

On the safety of a new generation of DSM Aspergillus niger enzyme production strains.

Consumers safety of enzyme preparations is determined by three variables: the producing organism, the raw materials used in the production, and the production process itself. The latter one is embedded in current Good Manufacturing Practice (cGMP) and Hazard Analysis of Critical Control Points (HACCP); therefore the safety focus can be directed to raw materials and the producing organism. In this paper, we describe the use of novel genetically modified strains of Aspergillus niger-made by a design and build strategy-from a lineage of classically improved strains with a history of safe use in enzyme production. The specifics of the host strain allow for integration and over-expression of any gene of interest at a targeted integration site implying that the rest of the host genome is not affected by this integration. Furthermore due to the fact that the newly integrated gene copies are put under the genetic regulation of the host's own glucoamylase promoter, the recipe of the production process of any new production strain can be kept constant with respect to the raw materials composition. Consequently the safety of a new enzyme product from these novel genetically modified strains is determined by the background of the production organism. The use of a strain with a history of safe use and targeted integration according to the concept described above has consequences for the safety studies on the final product. If a known enzymatic activity is over-expressed the safety of a new enzyme preparation is covered by the results of the safety studies performed for other strains from this specific Aspergillus niger strain lineage. In this paper an overview is given on the available toxicity tests with these strains. We conclude that for new enzyme products produced with strains from this lineage using the design and build technology no new sub-acute/chronic oral toxicity studies are needed. This also has the benefit that no longer test animals are needed to demonstrate the safety of products produced by these strains.