Thesis supervisor: Éva Csősz
Location of studies (in Hungarian): University of Debrecen Abbreviation of location of studies: DEAOK
Description of the research topic:
The increasing need for a sustainable climate and ecosystem friendly economy demands the development of biobased alternatives to the petrochemical industry. ‘Cell factories’, in which organisms convert renewable biomass into various biochemicals and biomaterials that would otherwise be derived from fossil fuels or harsh chemistry, can be the solution. Currently cell factories are typically based on commonly used microorganisms such as E. coli, which are limited to low temperatures. This prevents cost-effective bioconversions, which in turn hampers industrial-scale viability in competition with fossil fuels. Industry focus is therefore shifting towards the use of thermophilic prokaryotes (bacteria and archaea) that operate at high temperatures, enabling more efficient production processes, for example by combining fermentation with high temperature biomass pretreatment and by lowering contamination risks. However, we know very little about the proteome of thermophiles and about their cellular protein machinery.
Thermal Proteome Profiling will be used to examine the adaptation of the proteome of some selected thermophile species to temperature changes. In order to do so, extensive optimization is required. First is the optimization of the sample preparation protocols for thermophilic species (extreme > 65ºC and moderate >45ºC), including adjusted temperature ranges, as well as optimization of the digestion protocols for each of the analyzed thermophile species. Following extensive optimization, the optimized protocols will be used for the analysis of at least five thermophile species.
The PhD student will need to optimize the protocols for sample preparation, TMT labeling and mass spectrometry analysis and apply these protocols for the examination of thermophiles. The PhD student will be part of the PROHITS Marie Sklodowska Curie Action (https://prohits.eu/) involving 10 PhD students offering extensive networking, secondments and hands-on courses on proteomics, data analysis and soft skills.
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