Systems biology in fungi

Abstract

Systems Biology analyses both the components and the interactions of organisms to understand their organization and to predict behavior1,2. Currently, systems biology has a variety of applications using industrial organisms and in medical problems. This holistic approach involves a combination of modeling and omics analyses and was naturally more rapidly and easily applied to prokaryotic organisms. Nevertheless, fungal systems biology started as a discipline quite soon, especially driven by the accumulated knowledge in the yeast Sacharomyces cerevisiae that is, simultaneously, an eukaryotic model organism and a widely used industrial organism35. Within systems biology, integrated studies of metabolism (Metabolic Systems Biology) emerge for two main reasons: availability of data and importance of applications. Indeed, accumulated knowledge on metabolism is vast and allows creating reliable models that allows simulation of microorganism behavior in a variety of conditions. Also, metabolism is directly related to valuable end products and a variety of diseases have a metabolic origin6,7. Knowledge on metabolism of a given organism is easily applied to other organisms, using simple Bioinformatics tools such as Basic Local Alignment Tool (BLAST)8, while the same is not true for other functions such as transcription regulation and signaling. Therefore, it is easy to understand why a variety of metabolic models are available for organisms ranging from simple bacteria to filamentous fungi or even Homo sapiens9, while only a few regulatory or signaling models have been constructed10,11, and notably none for eukaryotes at a genome-scale. The general purpose of this chapter is detailing the state of the art of systems biology in fungi. Besides S. cerevisiae, several other fungi are being studied within metabolic systems biology which are important for industrial or pharmaceutical purposes. Several applications of models are also described throughout this chapter besides detailing the methodologies to build a genome-scale metabolic model for fungal species.