SNIC
SUPR
SNIC SUPR
Investigation of synergistic effects among lignocellulosic inhibitors on Saccharomyces cerevisiae using evolutionary engineering combined with DNA and RNA sequencing - Computing
Dnr:

SNIC 2018/8-25

Type:

SNAC Small

Principal Investigator:

Maurizio Bettiga

Affiliation:

Chalmers tekniska högskola

Start Date:

2018-05-02

End Date:

2019-08-01

Primary Classification:

20999: Other Industrial Biotechnology

Allocation

Abstract

The aim of the project is to identify certain cell responses when S. cerevisiae is grown in the presence of multiple inhibitory compounds. S. cerevisiae 113-7D was evolved in continuous cultivation, in a turbidostat. Two turbidostat experiments were performed. In the first one S. cerevisiae was firstly cultivated in the presence of acetic acid (inhibitor A) for a period of ~30 days. After this period Vanillin (inhibitor B) was added and the experiment continued for 30 more days. In the second turbidostat S. cerevisiae was cultivated with Vanillin in the beginning (30 days) and then acetic acid was added (30 more days). After all different stages of the experiment, chemostats have been performed and RNA samples for RNA sequencing have been obtained. Thus, these RNAs, are samples from evolved populations (not strains) at different stages of the project. In principle and according to the set up of the experiments, the differences/characteristics leading to a better performan ce of cells should increase their frequency in the population over time, and thus they should be dominant or at least visible. The comparative analysis of these RNAs should help us identify cell responses (difference in gene expression levels) to each of the inhibitors (cell responce to acetic acid and cell response to vanillin) and most important, differences in gene expression levels that are unique only in the case that both inhibitors were present. In addition, five different S. cerevisiae populations which were obtained after different stages of the experiments will go through a comparative analysis based on DNA sequencing. The aim of the analysis is to identify unique and/or common mutations among these populations obtained at different stages of the experiments. As the DNA samples are taken from populations and not S. cerevisiae strains, an approach similar to metagenomics should probably be followed. It is however expected due to the experimental set up that key mutations will be present to a large extent (they will have a high frequency) in the evolved populations.