Abstract
The group of filamentous fungi contains important species used in industrial biotechnology for acid, antibiotics and enzyme production. Their unique lifestyle turns these organisms into a valuable genetic reservoir of new natural products and biomass degrading enzymes that has not been used to full capacity. One of the major bottlenecks in the development of new strains into viable industrial hosts is the alteration of the metabolism towards optimal production. Genome-scale models promise a reduction in the time needed for metabolic engineering by predicting the most potent targets in silico before testing them in vivo. The increasing availability of high quality models and molecular biological tools for manipulating filamentous fungi renders the model-guided engineering of these fungal factories possible with comprehensive metabolic networks. A typical fungal model contains on average 1138 unique metabolic reactions and 1050 ORFs, making them a vast knowledge-base of fungal metabolism. In the present review we focus on the current state as well as potential future applications of genome-scale models in filamentous fungi.
Highlights
Filamentous fungi have been used for decades in industrial biotechnology exploiting their ability to utilize various sources of nutrients and tolerating adverse growth conditions
In the present review we focus on the current state as well as potential future applications of genome-scale models in filamentous fungi
The availability of genome sequence information provides the opportunity to expand the scope of metabolic engineering to the whole metabolism transforming the field towards systems biotechnology
Summary
Filamentous fungi have been used for decades in industrial biotechnology exploiting their ability to utilize various sources of nutrients and tolerating adverse growth conditions. The availability of these genomes enabled early reconstruction of the metabolic networks of several species in the groups of viruses (Edwards and Palsson 1999), bacteria (Edwards and Palsson 2000), and yeast (Forster et al 2003) on the genome scale These initial drafts have been continuously updated and curated over time, extending the scope and biochemical information contained (Orth et al 2011; Osterlund et al 2012). The complementary approach aims at establishing genomescale reconstructions (semi-)automatically based on sequence comparisons and gene assignments, enabling the prediction of genome-scale networks for less covered species While these models generally move towards a larger number of genes and reactions included as models are progressively improved, a qualitative comparison with respect to the numbers of reactions and genes included in the resulting models of these different strategies is not directly possible. This use and the synergism between genome-scale models and omics technologies have been reviewed by Hyduke et al (2013)
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