In Conversation with Dr Rich Edwards, CI on 2016 ARC Linkage Grant


Dr Rich Edwards, Professor Marc Wilkins and A/Professor Mark Tanaka are the BABS academics on a new $325k ARC Linking Project grant awarded in in partnership with Dr Paul Attfield and Dr Phillip Bell from Microbiogen Pty Ltd.

While the project's official title is "Elucidating the Genetic Basis of Newly Evolved Metabolic Functions in Yeast", Rich translates this for the non-science audience as:

How do they do that? Understanding Complex Trait Evolution in Yeast

Q: What are industry connection grants and who have you partnered with?

Previously called Research Connections, the Australian Government Innovation Connections Grant scheme provides matched funding for small/medium businesses to collaborate with university research groups. Projects can be up to $100k over 12 months. I partnered with Microbiogen Pty Ltd, a local company that specialises in breeding, evolving and engineering strains of Saccharomyces cerevisiae (Baker’s yeast) for industrial applications.

Q: How did you start collaborating with Microbiogen?
As with many industrial-academic collaborations, this one was born of serendipity. Microbiogen’s Director of Research, Dr Philip Bell, gave a research presentation in 2014 as part of the seminar program for our Faculty of Science neighbour, the School of Biological, Earth and Environmental Sciences. Phil presented research carried out by Microgen wherein a complex mixed population of yeast had evolved over 15 years to do something that wild yeast is normally unable to do: grow efficiently on xylose, an important sugar in second-generation biofuel production.

After the seminar, we got chatting and it became clear that they would benefit from some bioinformatics expertise. I visited them at their premises in Lane Cove to discuss possibilities, and over the next few months we put together the Research Connections proposal.

Q: What is the project aimed at doing?
While modest in scale, we had three main aims. First, we wanted to sequence the genome of Microbiogen’s highly adapted xylose utiliser. This would enable us to establish how it was different from wild-type yeasts that lack this ability. 

The timing dovetailed beautifully with the arrival of the new PacBio single molecule real time long-read sequencing machine at the Ramaciotti Centre for Genomics, located in our School, and we were their first customer for this technology.

Second, we wanted to get some clues regarding which variants were important. We are currently doing this by mating the xylose strain with a wild-type yeast and analysing which genetic variants increase in frequency in response to selection on xylose.

Third, we want to take a peek at the evolutionary process itself. For this, we have sequenced some of the ancestral yeast strains from Phil’s original experiment and are mapping sequence data from the evolving population back onto these strains.

Q: What outcomes can you see developing from the grant?
The PacBio sequencing has been fantastic and we have produced a complete genome for Microbiogen, which we are now in the process of annotating. The ultimate goal is to pinpoint the key genetic variants for xylose metabolism, which will allow Microbiogen to patent their strains. Most importantly, the Research Connections grant was a pilot study that provided a solid foundation for a larger collaborative application under the ARC Linkage Program. Happily, this project has just been funded.