Genome scale metabolic modeling of the riboflavin overproducer Ashbya gossypii

Abstract

Ashbya gossypii is a filamentous fungus that naturally overproduces riboflavin, or vitamin B2. Advances in genetic and metabolic engineering of A. gossypii have permitted the switch from industrial chemical synthesis to the current biotechnological production of this vitamin. Additionally, A. gossypii is a model organism with one of the smallest eukaryote genomes being phylogenetically close to Saccharomyces cerevisiae. It has therefore been used to study evolutionary aspects of bakers' yeast. We here reconstructed the first genome scale metabolic model of A. gossypii, iRL766. The model was validated by biomass growth, riboflavin production and substrate utilization predictions. Gene essentiality analysis of the A. gossypii model in comparison with the S. cerevisiae model demonstrated how the whole-genome duplication event that separates the two species has led to an even spread of paralogs among all metabolic pathways. Additionally, iRL766 was used to integrate transcriptomics data from two different growth stages of A. gossypii, comparing exponential growth to riboflavin production stages. Both reporter metabolite analysis and in silico identification of transcriptionally regulated enzymes demonstrated the important involvement of beta-oxidation and the glyoxylate cycle in riboflavin production.

Ashbya gossypii beyond industrial riboflavin production: A historical perspective and emerging biotechnological applications

“…In this context, the A. gossypii genome was re-annotated(Gomes et al, 2014) and its reaction set compiled to create a genome scale metabolic model (GSMM) able to simulate the cell behaviour, being now this model in its experimental validation phase(Gomes et al, personal communication). Other GSMM for A. gossypii was already published (iRL766) and successfully validated by predictions and comparisons for three experimental parameters: biomass growth, riboflavin production and substrate utilization(Ledesma-Amaro et al, 2014b).…”

Microbial biotechnology for the synthesis of (pro)vitamins, biopigments and antioxidants: challenges and opportunities

“…A striking example is the production by fermentation of vitamin B 2 using Ashbya gossypii . The productivity of the initial industrial strains developed by classical mutagenesis techniques has been greatly improved by a combination of metabolic engineering, comparative genome and transcriptome analysis and genome metabolic modelling approaches (Karos et al ., 2004; Ledesma‐Amaro et al ., 2014, 2015). The success of this strain improvement programme allowed the replacement at industrial level of the vitamin B 2 chemical process by the currently used based on microbial fermentation.…”

RAVEN 2.0: a versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

“…In addition to facilitating the analysis and visualization of existing GEMs, RAVEN particularly aimed to assist semi-automated draft model reconstruction, utilizing existing template GEMs and the KEGG database [10]. Since publication, RAVEN has been used in GEMs reconstruction for a wide variety of organisms, ranging from bacteria [11], archaea [12] to human gut microbiome [13], eukaryotic microalgae [14], parasites [15][16][17], and fungi [18], as well as various human tissues [19,20] and generic mammalians models with complex metabolism [21,22]. As such, the RAVEN toolbox has functioned as one of the two major MATLABbased packages for constraint-based metabolic modelling, together with the COBRA Toolbox [23][24][25].…”