Fungal food spoilage often starts with a contamination with spores. Experimental data strongly indicate the existence of subpopulations of spores with different levels of resistance to preservation... Show moreFungal food spoilage often starts with a contamination with spores. Experimental data strongly indicate the existence of subpopulations of spores with different levels of resistance to preservation methods. In this thesis, the extent of this heterogeneity and the underlying mechanisms using fungal model systems is studied. The role of the genetic background, environmental conditions and the developmental state of the spores were studied, using quantitative imaging, genome and RNA/protein sequencing as well as functional gene analysis. The role of transcription factors in weak acid stress resistance of Aspergillus niger is described. Next, heat resistance of fungal spores of three food spoilage species was quantified and compared. The genomes of Aspergillus niger strains were sequenced and compared revealing the existence of a possible sexual cycle. Melanin of fungal spores impacts UV-C resistance, but not heat resistance and a functional CRISPR/Cas9 genome editing system for Paecilomyces variotii and Penicillium roqueforti is described. Older spores are more heat resistant than younger spores, which can be contributed to differences in compatible solute composition. Additionally, a high cultivation temperature results in fungal spores with high heat resistance, possibly due to heat shock proteins. Show less
Autopaghy is an intracellular degradation system which targets cytosolic components to lytic compartments for degradation and recycling of the building blocks of the cell. The process is highly... Show moreAutopaghy is an intracellular degradation system which targets cytosolic components to lytic compartments for degradation and recycling of the building blocks of the cell. The process is highly induced by carbon starvation conditions. In this thesis, different roles of autophagy in the filamentous fungus Aspergillus niger were studied, focusing on its role during carbon starvation, endoplasmic reticulum (ER) stress and unconventional protein secretion. Show less
Aspergillus niger is an important industrial producer of organic acids and enzymes producing large amounts of spent fungal biomass. In the European Research Area Industrial Biotechnology (ERA-IB)... Show moreAspergillus niger is an important industrial producer of organic acids and enzymes producing large amounts of spent fungal biomass. In the European Research Area Industrial Biotechnology (ERA-IB) funded project, we effectively aimed to improve the composition of post-fermentation fungal biomass for extraction of the value-added product chitosan as a derivative of cell wall chitin (FunChi). As chitin/chitosan is not encountered in plant or human tissue, it often acts as an elicitor to plant and animal immune responses in order to fight off possible impending fungal infections. The application of both chitin and chitosan oligomers have been shown to prime plants against infection. This thesis discusses the identification of genes that are important for chitin deposition in the cell wall of A. niger. In addition, the work described here also investigates the genes that facilitate chitin cross-linking to the cell wall. The relevance of all findings are discussed in relation to both the improvement of chitin extraction from post-fermentation biomass and to the integrity of the fungal cell wall. Show less
Pectin is a plant cell wall polysaccharide made of mainly D-galacturonic acid (GA) subunits. The potency of the filamentous fungus Aspergillus niger to naturally secrete high amounts of pectinases... Show morePectin is a plant cell wall polysaccharide made of mainly D-galacturonic acid (GA) subunits. The potency of the filamentous fungus Aspergillus niger to naturally secrete high amounts of pectinases to degrade pectin has been utilized for the industrial production of pectinases. Industrially produced pectinases by A. niger are subsequently used mainly in the food industry, and for the hydrolysis of plant biomass to produce renewable energy. In this thesis, the key players in the transcriptional regulatory system of pectinases in A. niger, such as the transcriptional activator GaaR, the repressor GaaX and the physiological inducer 2-keto-3-deoxy-L-galactonate, are discovered. Several approaches to exploit this system for increased or constitutive expression of the genes encoding pectinases are also presented, such as overexpression and constitutive activation of gaaR, accumulation of 2-keto-3-deoxy-L-galactonate, and deletion of gaaX or creA, the main transcriptional repressor involved in CCR. Show less
This study investigated carbon starvation in the filamentous fungus Aspergillus niger during submerged cultivation in bioreactor batch cultures. The work described in this thesis can be discussed... Show moreThis study investigated carbon starvation in the filamentous fungus Aspergillus niger during submerged cultivation in bioreactor batch cultures. The work described in this thesis can be discussed as follows: (I) Establishment of computational resources for omics data analysis and interpretation in chapters 2 and 3; (II) Cultivation of A. niger, data generation, analysis and interpretation in chapter 4; (III) Investigation of a candidate pathway with strong transcriptional induction during carbon starvation by molecular genetic approaches in chapter 5. Show less
Aspergillus niger produces a wide variety of carbohydrate hydrolytic enzymes which have potential applications in the baking, starch, textile, food and feed industries. The goal of this thesis is... Show moreAspergillus niger produces a wide variety of carbohydrate hydrolytic enzymes which have potential applications in the baking, starch, textile, food and feed industries. The goal of this thesis is to unravel the molecular mechanisms of starch and inulin modifying network of A. niger, in order to improve the enzyme production and substrate utilization as well as to find novel enzyme activities. The research described in this thesis shows how we identify genes which encode enzymes involved in starch and inulin catabolism, how they are transcriptionally regulated, as well as how the expressed enzymes react to the carbon sources and what are their physiological roles in A. niger. Important findings are outlined as follows. We have identified inulin pathway activator InuR. The activation of InuR is thought to be triggered by the pathway inducer, sucrose or its derivative, but not previously known fructose. The activated InuR induces the expression of genes encoding inulin modifying enzymes and related sugar transporters in inulin metabolism. In addition, using the tightly regulated inuE promoter combined with racA(G12V) and GFP reporter genes, we set up a novel screening method for isolation of mutants involved in inulin signaling pathway. Show less
