Poster Presentation 39th Annual Lorne Genome Conference 2018

Genome-guided characterisation of evolved xylose metabolism in Saccharomyces cerevisiae (#142)

Richard J Edwards 1 2 , Asa Perez-Bercoff 1 , Gustave Severin 1 , Tonia L Russell 3 , Psyche Arcenal 4 , Anna Sophia Grobler 4 , Paul V Attfield 4 , Philip JL Bell 4
  1. School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
  2. NSW Systems Biology Initiative, University of New South Wales, Sydney, NSW, Australia
  3. Ramaciotti Centre for Genomics, University of New South Wales, Sydney, NSW, Australia
  4. Microbiogen Pty Ltd, Sydney, NSW, Australia

We have a unique opportunity to study the evolution of a new biochemical pathway in a sexually reproducing population. Microbiogen Pty Ltd have have successfully evolved a Saccharomyces cerevisiae (Baker’s yeast) strain ("MBG11a") that, unlike wild strains, grows efficiently on xylose as a sole carbon source (Attfield & Bell 2006). Using PacBio long reads, we have sequenced and assembled MBG11a and the founding yeast strains from which the xylose metabolism evolved. We are using a combination of comparative genomics, deep Illumina resequencing of the evolving population, RNA-Seq transcriptomics, and competition assays to identify genes involved in the evolution of this new metabolic activity.

Comparing our draft MBG11a assembly to the S288C yeast reference genome reveals over 115,000 variants, including over 14,000 coding changes across 3360 genes, plus has several large insertions and deletions (approx. 63 kb missing and 164 kb extra, excluding Ty element changes). To identify loci with important consequences for xylose utilisation, MBG11a was mated with a strain that could not grow on xylose or galactose. Haploid offspring were competed on glucose, galactose and xylose minimal media to identify MBG11a alleles increasing frequency under selection. Two candidate loci with unique protein-coding variants were identified in regions under significant positive selection on xylose minimal media. One showed classic signs of gene duplication followed by neofunctionalisation, while the other was identified as a master regulator of transcription. RNA-Seq analysis of MBG11a growing on xylose versus glucose highlighted two further candidate genes, previously shown to substitute for key xylose metabolic proteins.

Future work will focus on confirming whether the identified proteins are necessary and/or sufficient for S. cerevisiae to grow efficiently on xylose. Through "molecular palaeontology" on the evolving population, we will also trace how mutations have interacted with existing genetic variation to evolve this novel phenotype.

  1. Attfield P.V. & Bell P.J.L. (2006). Use of population genetics to derive non-recombinant Saccharomyces cerevisiae strains that grow using xylose as a sole carbon source. FEMS yeast Res. 6:862-868.