The evolution of eukaryotic gene order: Following the birth, life and death of a eukaryotic gene cluster

Project Background

How are eukaryotic genomes organised? How are they evolving? How are genes ordered along chromosomes? Does gene order matter for sustainable applications? These are the questions at the heart of this PhD project that combines experimental evolution, genomics, chromatin genetics and biotechnology to improve our fundamental understanding of eukaryotic genome evolution and to expand the design principles in synthetic biology.

In our project, you will study the real-time evolution of metabolic pathway genes in yeasts. Fungi and yeast produce a vast variety of metabolites (or natural products). These complex molecules have important ecological functions in the interaction between microbes and the environment.

In addition to their ecological functions, natural products are major sources of pharmaceuticals and other high-value compounds. The repertoire of natural products found in fungi and yeasts is highly diverse, each species and even strain having its own pool of molecules to cope with the demands of its environmental niche. The genes for the synthesis of large numbers of natural products are rapidly evolving and physically co-localised in so called 'gene clusters'. But how these clusters come about and evolve so rapidly is entirely unknown?

Project Aims and Methods

Here, we propose to follow the real-time evolution of the pulcherriminic acid gene cluster as model system to study the evolution of gene order in eukaryotes. This cluster is present in distantly related yeasts and provides host species with growth advantages under iron-limiting conditions and in competition with other microbes. Pulcherriminic acid has recently become of interest to the biotech industry as a biocontrol agent.

The project will be divided into three subprojects:

(i) A large-scale phylo-genomic analysis of the distribution of pulcherriminic acid genes across microbial genomes. Here, we will apply a comprehensive bioinformatic analysis to evaluate natural evolution of this cluster with a particular focus on the origin of genes, the distribution of transposable elements, the possibility of horizontal gene-transfer and the frequency of gene loss.

(ii) An experimental evolution approach to optimise pulcherriminic acid production in Metschnikowia pulcherrima and to analyse gene cluster organisation over time. M. pulcherrima is a natural high-producer of pulcherriminic acid and the associated cluster of biosynthesis genes has recently been identified in DH's lab as part of ongoing work to use the yeast in industrial applications.

To mimic different selection pressures, we will grow M. pulcherrima under high and low iron growth conditions and in co-cultivation with Escherichia coli for multiple yeast generations. We will then analyse pulcherriminic acid production under standard conditions and monitor the genomic organisation of pulcherriminic acid biosynthesis genes.

(iii) An experimental evolution approach to study the birth and structural trajectory of a gene cluster. Here, we will employ Saccharomyces cerevisiae, a yeast that is not producing pulcherriminic acid, as model system. We will introduce pulcherriminic acid biosynthesis genes into the genome of S. cerevisiae as clustered genes, as non-clustered genes and as partly clustered genes.

We will use different strain backgrounds with mutations in key recombination, DNA repair and gene regulatory pathways. Using initial fitness assessment as a guide we will evolve each strain for multiple generations in selective and non-selective conditions and analyse the genomic organisation of our target genes.

Altogether, the proposed project will provide an interdisciplinary research experience to the student and contribute to our fundamental understanding of genome evolution.

In this project, the prospective student will actively participate in the design of the project and is encouraged to bring in their own research ideas.