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.

Gene deletion of cytosolic ATP: citrate lyase leads to altered organic acid production in Aspergillus niger.

With the availability of the genome sequence of the filamentous fungus Aspergillus niger, the use of targeted genetic modifications has become feasible. This, together with the fact that A. niger is well established industrially, makes this fungus an attractive micro-organism for creating a cell factory platform for production of chemicals. Using molecular biology techniques, this study focused on metabolic engineering of A. niger to manipulate its organic acid production in the direction of succinic acid. The gene target for complete gene deletion was cytosolic ATP: citrate lyase (acl), which had previously been identified by using genome-scale stoichiometric metabolic model simulations. The acl gene was deleted using the bipartite gene-targeting method, and the mutant was characterized in batch cultivation. It was found that the succinic acid yield was increased threefold by deleting the acl gene. Additionally, the total amount of organic acids produced in the deletion strain was significantly increased. Genome-scale stoichiometric metabolic model predictions can be used for identifying gene targets. Deletion of the acl led to increased succinic acid production by A. niger.

Physiological characterisation of acuB deletion in Aspergillus niger.

The acuB gene of Aspergillus niger is an ortholog of facB in Aspergillus nidulans. Under carbon-repression conditions, facB is repressed, thereby preventing acetate metabolism when the repressing carbon source is present. Even though facB is reported to be repressed directly by CreA, it is believed that a basal level of FacB activity exists under glucose-repressive conditions. In the present study, the effect of deletion of acuB on the physiology of A. niger was assessed. Differences in organic acid and acetate production, enzyme activities and extracellular amino and non-amino organic acid production were determined under glucose-repressing and -derepressing conditions. Furthermore, consumption of alternative carbon sources (e.g. xylose, citrate, lactate and succinate) was investigated. It was shown that AcuB has pleiotropic effects on the physiology of A. niger. The results indicate that metabolic pathways that are not directly involved in acetate metabolism are influenced by acuB deletion. Clear differences in organic acid consumption and production were detected between the acuB and reference strain. However, the hypothesis that AcuB is responsible for basal AcuA activity necessary for activation of acetate metabolic pathways, even during growth on glucose, could not be confirmed. The experiments demonstrated that also when acuB was deleted, no acetate was formed. Therefore, AcuB cannot be the only activator of AcuA, and another control mechanism has to be available for activating AcuA.

Transient marker system for iterative gene targeting of a prototrophic fungus.

Auxotrophic microorganisms are often used for genetic engineering, because their biosynthetic deficiency can be complemented by the transforming DNA and allows selection for transformants that have become prototrophic. However, when complementation is obtained by ectopic expression this may lead to unpredictable side effects on the phenotype and, consequently, misinterpretation of experimental data. There are various ways to overcome the problem of auxotrophy, but the most reliable is to restore the function of the defective biosynthetic gene at the native genomic locus. This can be done by either sexual crossing or further genetic engineering. For fungal species lacking a perfect state or situations in which gene targeting is generally cumbersome we have developed a concept that allows transient disruption of pyrG. When the gene is in the disrupted state, multiple rounds of gene targeting can be performed with the strain. Once the desired genome engineering is completed, pyrG function can be rapidly returned to wild type by a simple selection scheme.

Persistent presentation of medically unexplained symptoms in general practice.

OBJECTIVES: To estimate the prevalence of persistent presentation of medically unexplained physical symptoms (MUPS) in general practice. To assess socio-demographic characteristics, health status and use of health services of patients who frequently present MUPS, compared with reference groups. DESIGN: One-year, nationwide, representative survey of morbidity in general practice in The Netherlands, including 400,000 enlisted patients in 104 general practices. RESULTS: Of all patients (age: 18 years and older), 2.45% who visited their GP at least once a year, presented at least 4 times in 1 year with symptoms which are commonly considered medically unexplained without getting a medical diagnosis during that period, that might explain the symptoms. These patients are significantly older, more often female, less educated, more frequently unemployed and more frequently from a non-Western origin than 'average' patients or patients with a medical diagnosis. CONCLUSION: Although 25-50% of all reasons for visit to a GP concern symptoms that are not medically explained, the frequent presentation of such symptoms is much more rare. Frequent attendance because of MUPS is most common among elderly women with a lower socio-economic status.

Coping styles and locus of control as predictors for psychological adjustment of adolescents with a chronic illness.

This study examines the way coping styles and locus of control contribute to the prediction of psychosocial adjustment in adolescents with a chronic illness. Psychosocial adjustment of 84 adolescents aged 13-16 years with a chronic illness was assessed with measures of social adjustment, global self-esteem and behavior problems. Linear regressions were performed with demographic factors (age and gender) and stress-processing factors (coping style and locus of control) as predictor variables. Results indicated that coping styles were related to most aspects of social adjustment. The coping styles 'seeking social support' and 'confrontation' were important predictors for positive social adjustment; the coping style 'depression' was a predictor for poor adjustment, viz, low social self-esteem and high social anxiety. Avoidance and locus of control were not strongly associated with psychosocial adjustment. Clinical implications of these findings were discussed in terms of preventive interventions for adolescents with a chronic illness.