Maria Victoria Aguilar Pontes is interested in genetics, in metabolic pathways, in bioinformatics. And she also likes the idea of applied research. In her case the combination of all these interests led to research on the metabolism of Aspergillus niger and not, for example to human research. ‘I don’t like human research, I don’t like to work with human data. Besides that: I really like fungi, they look beautiful, you don’t have to feed them every day and you don’t have to feel guilty if you kill them. What I want to do in my research is to improve industrial processes by using fungal enzymes while studying A. niger primary metabolism as a whole.

Maria Victoria choose Aspergillus niger to work with because it is one of the best studied filamentous fungi and considered ‘an industrial workhorse’ due to its ability as producer of citric acid and plant biomass degrading enzymes.

In collaboration with Denmark Technical University (PhD student Julian Brandl), she expanded the knowledge of A. niger metabolism to three different strains (ATCC 1015, CBS 513.88 and NRRL 3) through orthology, extending the coverage of the existing model of A. niger metabolism by 940 reactions, 777 metabolites and 454 genes and thus developed the best validated genome scale model on A. niger to date.

A special focus of her work was carbon metabolism, for which she manually curated the carbon catabolic reconstructed network of A. niger NRRL 3 based on the gold-standard genome, literature, orthology and experimental data. The network comprised 329 enzymes assigned to 274 enzymatic reactions associated to 149 literature references. This network has proven essential to identify and experimentally characterize unknown enzymes involved in different reactions of metabolism.

The research of Maria Victoria is an example of systems biology. Cellular metabolism is more complex than we often think. It is not enough to do many experiments in the lab in a petri dish, what you really want to know is how it works in a more general context, in the cell itself, in natural conditions. ‘Listing genes, proteins and reactions is not sufficient to understand the complexity of the organism (or cell) They need to be assembled into a network where genes, reactions, regulatory elements and their interactions can be examined as one entity, rather than as parts of a cell or organism.’

And that is what this elaborate, thorough and beautiful thesis is about. The research was done with simple sugars, but also with more natural substrates, showing how Aspergillus niger is able to release and transport into the cell plant-biomass derived sugars in a largely sequential manner. How this sequence is regulated is not reflected in the catabolic genes however. So a full explanation of the sequential uptake observed in the cultures cannot be given. The research points to sugar transport as a possible explanation here.

In her thesis Maria Victoria also shows that genome content can be used to predict metabolic abilities of other species. However, this works best with closely related species.

‘It is very important to do a large screening before you enter the lab, you need a good model to predict the best candidates’. This thesis is an important step in improving industrial processes by better understanding ¬†A. niger carbon metabolism and using bioinformatics tools to make it manageable.