Project description: This project aims to identify the genetic basis behind colonial variants, in Fusarium venenatum which arise via spontaneous mutations during myco-protein fermentations. To do this bioinformatics approaches will be used in combination with lab based techniques to identify and characterise Fusarium venenatum C variant. Firstly putative genes causal of C variant will be identified by repeated sampling and sequencing of C variant isolates. SNPs and structural variants will be called against a F.venenatum A3/5 reference genome using pipeline such as SAMTOOLS and SVABA. Genes thought to be causal to C variant will be selected for disruption, with the expectation that putative mutants will confer a loss of function within the gene of which they are contained. Gene editing tools such as CRISPR Cas-9 will be used to disrupt putative mutant genes in order to validate and further characterise the mechanism of C variant growth. Secondly a function will be assigned to candidate genes by studying work done in other species such as Saccharomyces and Aspergillus sp. Finally mechanisms of alleviating C variant emergence during fermentation will be explored by running benchtop fermenters and applying known interventions such as pH oscillations and nutrient limitation to them, as these have been reported to reduce the emergence of C variant in culture conditions.
This project is comprised of three work packages:
- Determine the genetic basis of C variant through repeated sampling and sequencing of distinct C variant isolates
- Validate the genetic mechanism of colonial variant production
- Develop and test hypotheses for C variant amelioration
Principal Investigator: Richard Harrison
Student: John Connell