1 Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark2 Department of Systems Biology, Technical University of Denmark3 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark4 Department of Biotechnology, Technical University of Denmark
The recent dawn of the new biological mindset called systems biology has put forth a new way of analyzing and understanding biology. Carried by the notion that no element of a cell is an island, systems biology takes a holistic approach, and attempts to understand life as systems that have co-evolved and not as a haphazardly compiled list of parts. This has been made possible by the socalled genomic revolution — the sequencing of the genomic DNA of a rapidly increasing number of organisms — and the “omic” tecniques following in the wake of the genome projects: metabolomic, proteomic, and transcriptomic to mention a few. The recent publication of the genome sequences of several filamentous fungi of the Aspergillus species (Aspergilli), has, along with the accumulation of years of reductionist studies, been a catalyst for the application of systems biology to this interesting group of fungi. Among the genome sequenced Aspergilli are a known human pathogen (Aspergillus fumigatus), a model organism for cellular mechanisms (Aspergillus nidulans) and two industrial workhorses (Aspergillus niger and Aspergillus oryzae). In the presented work, new analytical and computational tools have been designed and a systems biology approach has been applied to a wide range of issues. These tools include the compilation of data from literature on A. niger enzymes to form a re-constructed metabolic network and model of metabolism, allowing assessment of the industrial production potential of metabolites from this fungus. Based on the network, a map of metabolism has been drawn in the notation of biochemistry text books and a web server built that allows the analysis of genome-scale data for a number of Aspergillus species. Further efforts have produced a tri-Aspergillus species Affymetrix DNA microarray for expression analysis of the predicted genes of A. nidulans, A. niger and A. oryzae, and a case study of an advanced application of this chip identified a regulatory response conserved through evolution. In an application of the tools, a multi-disciplinary comparison of two genome sequenced strains of A. niger was conducted using sequence analysis, exo-metabolomics, transcriptomics and classical genetics. With a special focus on the traits making one strain a high-yield citric acid producer and the other an efficient glucoamylase producer, a surprising number of co-enhancing factors were found on multiple levels of cellular metabolism. Transcriptome profiling coupled with metabolic modeling further allowed the charting of the genome-wide regulation of A. niger in response to ambient pH in the context of organic acid production and a plausible explanation for the evolution of the capabilities to be a high-yield producer of citric acid. Furthermore, a detailed transcriptome profiling of all of the genes of A. niger predicted to code for extracellular enzymes was made using a new literature-based graphical tool for analysis of the degradation targets of the enzymes. In conclusion, the versatility of a systems biology approach to understanding Aspergillus physiology has been demonstrated through a number of studies with results relevant to biotechnological processes.