Abstract

Water is crucial for life as we know it. High salinity, drought and freezing all lead to decreased water activity and thus disturb the functioning of biological systems. In addition to this, ions of inorganic salts are directly toxic to the cells. Halophilic/halotolerant and psychrophilic/psychrotolerant fungi have evolved specialized molecular mechanisms for avoiding and managing these detrimental effects. Due to their excellent adaptability many of these fungi have great biotechnological potential, due to two reasons in particular: 1) Hypersaline, arid and polar environments are very specific and promote competition for the scarce resources, and are thus promising sources of novel and unique antibacterial, antifungal and/or antialgal compounds. 2) Enzymes from psychrophiles and halophiles are functional at low temperatures and high salinity and therefore interesting for sustainable cleantech biotechnological applications, such as degradation of macro-algae in cold Arctic, marine, hypersaline waters and snow and ice algae covering the surface of glaciers and ice sheets.

Different life strategies of extremophilic fungi will be exemplified by five representative species: Aureobasidium pullulans, Hortaea werneckii, A. subglaciale, Penicillium sp. nov. and Articulospora sp. nov., which inhabit hypersaline waters of salterns around the world, Arctic glaciers and black Greenland ice sheet, respectively. Environmental data and information on their molecular mechanisms of adaptations combined with the knowledge produced by their genome sequencing will be presented for Aureobasidium pullulans, A. subglaciale and Hortaea werneckii, while Penicillium sp. nov. and Articulospora sp. nov. will be presented in the context of environmental data related to their recent discovery in the Greenland ice in association with the non-cultivable black ice algae. In the analysis of the genomes and transcriptomes we focussed on (i) the presence and characteristics of genes involved in stress tolerance, (ii) the presence of biotechnologically important genes, in particular enzymes relevant for decomposition of abundant algal biomass.Introduction

Abstract

Abstract

Wood-degrading white-rot basidiomycetes are exclusively found on wood in nature, where they play a significant role in the degradation of all polymeric components of wood cell walls, including both polysaccharides and the extremely recalcitrant aromatic polymer lignin. The increasing number of fungal genome sequences has revealed that white-rot basidiomycete genomes typically possess a wider repertoire of genes predicted to encode diverse plant cell wall modifying enzymes compared to ascomycete fungi. Therefore, wood-degrading white-rot fungi have a high potential as a source of industrially interesting enzymes or enzyme sets. The white-rot fungus Dichomitus squalens is an efficient wood degrader, which is commonly found in the northern regions of Europe, Asia and North America. When grown on different wood and non-woody plant biomasses, D. squalens upregulates specific sets of genes and secretes the corresponding enzymes matching the composition of the different substrates. The ability of D. squalens to respond to the various plant biomass types, including those that do not exist in its natural habitat, makes it an ideal species to study modification and degradation of plant biomass. Four genome sequenced D. squalens strains providing the best coverage of a filamentous basidiomycete species to date together with recently established genetic transformation system further facilitate the use of this species to understand basidiomycete gene function and development of improved strains for biotechnological applications. We have also detected differences between mono- and dikaryotic strains of D. squalens to grow on and degrade plant biomass. To study this in more detail, we grew four dikaryotic and three monokaryotic strains of D. squalens on spruce wood sticks and analysed the cultures after two and four weeks for their transcriptome, proteome and metabolome. Highlights from this study will also be presented.

Abstract

For many fungi, plant biomass is the predominant carbon source, but also a highly challenging substrate due to its complex and variable composition. It consists mainly of polymers, of which the polysaccharides are the major carbon sources used by fungi. Secreted enzymes degrade these polymeric compounds to mono- and small oligomers that are taken up by the fungal cell.

Filamentous fungi typically contain between 120 and 350 genes in their genome that encode plant biomass degrading enzymes. Therefore it is important that the genes expressed by a fungus encode those enzymes that match the composition of the prevailing substrate. For this fungi have evolved an intricate regulatory system that responds to the various mono- and disaccharides that are released from plant biomass. This system does not consist of a set of independent regulators, but rather of a network in which links between the individual regulators exist not only with respect to their target genes, but also by influencing each other’s expression level.

In this presentation the current knowledge on regulation of plant biomass degradation from several well-studied ascomycete fungi will be compared and linked, to provide an overall view of this highly complex process. The recent identification of the L-arabinose responsive regulatory systems in eurotiomycetes and sordariomycetes, which are a clear example of parallel evolution, will also be discussed, as well as the regulatory differences between species.

Abstract

The reduction of unwanted endogenous proteases has already been an important target for strain improvement of fungal host strains used in protein production for many years. Targeted deletion of specific proteases has been used extensively for this purpose. Surprisingly, only very little is known about regulatory circuits that specifically control fungal protease production. The only protease-specific regulator gene discovered to date is the prtT gene from Aspergillus niger, which encodes a canonical Zn2-Cys6 activator protein (Punt et al., 2008) involved in the expression of a wide range of protease genes. Interestingly, homologues of prtT are only found in Aspergillus species, whereas no prtT homologue is present in Trichoderma reesei. We aimed to discover a similar protease master switch in our research. T. reesei mutants with strongly reduced overall protease levels and strongly reduced expression of a number of protease genes were obtained using a biological screen for the selection of protease-deficient mutants (Braaksma et al., 2008). Genome sequencing of a number of these strains followed by SNP analysis revealed that several of these mutants carried mutant alleles from a single gene, which we termed pea1 for protease-expression-affected. Disruption of this gene in both T. reesei and Fusarium sp. confirmed the role of pea1 in protease gene expression. Intriguingly, the encoded protein does not show any similarity to known regulatory proteins, indicating that a completely new regulatory circuit may be governing protease gene expression in T. reesei, which opens the way to further research in this area.