Ribosome profiling to reveal how temperature affects protein synthesis in diatoms

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Diatoms are important microalgae with high biotechnological potential. Several aspects of diatom physiology including the silica frustule, lipid storage and photosynthesis are being applied to biotechnology. Areas of interest include nanotechnology, drug delivery, biofuels, solar capture and bioactive compounds. Given the ecological importance of diatoms and their applications for biotechnology, several different genetic tools have recently been developed in the Mock lab for the model diatom Thalassiosira pseudonana such as genome editing by CRISPR/Cas9 and ribosome profiling. The application of both tools in this project will enable the PhD student to obtain fundamental insights into how temperature affects translation in the model diatom Thalassiosira pseudonana. Since there are no data available yet on how temperature regulates protein synthesis in any algae on a mechanistic level, we suggest to apply ribosome profiling to provide fundamental insights into if and how temperature affects a) the location of translation start sites, b) the density of ribosomes on messenger RNAs and c) the speed of translating ribosomes. Furthermore, the role of codon usage and its impact on tRNA evolution in relation to the recently discovered tRNA-derived small non-coding RNAs for protein synthesis in diatoms will be investigated using the genome editing tool CRISPR/Cas in combination with ribosome profiling. We aim to modify the genetic code in T. pseudonana in order to obtain first insights into codon usage, tRNA expression and the role of tRNA-derived non-coding RNAs. Data from this project will lay the foundation for synthetic biology with diatoms as translation underpins the synthesis of various different enzymes and materials (e.g. silica) used in algal biotechnology.