Project Proposals for IMPRS 2014
This is the list of our currently available three PhD Projects. You can only apply for these three projects.
Please note: These positions are located in our partner institutions at the Universities of Cologne and Düsseldorf!
Synthetic microbes: Exploring the evolutionary and functional divergence of plant-derived triterpenes
Triterpenes belong to one of the largest classes of plant natural compounds, which contribute to protect plants from diseases and also serve as important drugs and anticancer agents for humans. The biosynthesis of triterpenes is not well understood and their function in plants remains largely unrecognized.
A diverse array of triterpenoid skeletons are synthesized via the isoprenoid pathway by enzymatic cyclization of 2,3-oxidosqualene. Oxidosqualene cyclases (OSCs) produce specific cyclization products, which are further modified by the cytochrome P450 monoxygenases (P450s) and subsequently by UDP-glucosyltransferases.
Within the CEPLAS consortium (http://ceplas.eu/en/research/research-area-d/) we have recently generated synthetic microbes, which express different triterpene pathway genes and are therefore able to produce various triterpene derivatives. In addition, the generation of microbes containing a promiscuous OSC that simultaneously produce more than 20 different triterpenes in combination with a promiscuous P450 enzyme is in progress. This will lead to a huge variety of compounds, which will be screened by the candidate in high throughput assays using human or murine hepatoma cell lines. These hepatoma cells contain bioactivity-responsive promoter cis-elements fused to green fluorescent protein (GFP) or luciferase (LUX) reporter constructs. GFP and LUX containing cell lines have been previously used in a screen to identify anticancerogenic compounds in chemical libraries and in screens to assess the bioactive potential of natural plant-derived products.
During the PhD studies, the function of the most potent and biologically active triterpenes and their derivatives will be addressed in more detail. In addition, co-cultivation assays of plants and triterpene-producing bacteria will be established to reveal the role of these compounds in plant-microbe interactions and possible in plant growth promotion. In addition, the effects of synthetic bacteria and triterpenes isolated from them on different plant traits, e.g. plant growth promotion and increased resistance against pathogens will be assessed.
Genome-scale transcriptional and metabolic regulatory networks involved in the plant response to phosphate starvation stress
Phosphate starvation stress affects plant architecture, metabolism, hormone balance and plant-microbe interactions. In this project, bioinformatics analysis of already available whole genome large scale RNA sequencing and metabolite profiling experiments will be used to predict the core regulatory system controlling activation and repression responses to phosphate starvation in different plant species. Network and flux balance analysis will reveal candidate genes and metabolites which can subsequently be validated in functional genomics and molecular physiological experiments. Ideal candidates have demonstrated experience in sequence and genome analyses, with at least some knowledge of primary short read analysis and genome/transcriptome annotation and of one major programming or scripting language.
C3-C4 intermediate species as models for early evolutionary steps on the path to C4 photosynthesis
C3-C4 intermediate plant species display lowered CO2 compensation points in comparison to C3 species. This is due to the operation of a primitive CO2 concentrating pump, which is based on a shift of photorespiratory GDC activity from leaf mesophyll to bundle sheath cells. C3-C4 intermediate species are therefore considered as naturally occurring evolutionary intermediates on the path from C3 to C4 photosynthesis. This project aims at identifying the key players of these first steps of C4 evolution by correlation of genetic, phenotypic, and physiological traits in a segregating mapping population of hybrids between C3 and C3-C4 intermediate Moricandia species (Brassicaceae).