Ribosome profiling to reveal how temperature affects protein synthesis in diatoms

硅藻是一种重要的微藻，具有很高的生物技术潜力。硅藻生理学的几个方面，包括硅锥体、脂肪储存和光合作用，正被应用于生物技术。感兴趣的领域包括纳米技术、药物输送、生物燃料、太阳能捕获和生物活性化合物。鉴于硅藻的生态重要性及其在生物技术中的应用，模拟实验室最近为模式硅藻假性海链藻开发了几种不同的遗传工具，例如使用CRISPR/Cas9进行基因组编辑和核糖体分析。在这个项目中，这两个工具的应用将使博士生能够获得关于温度如何影响硅藻模型中的平移的基本见解。由于目前还没有关于温度如何在机制水平上调节任何藻类中蛋白质合成的数据，我们建议应用核糖体图谱来提供基本的见解，以了解温度是否以及如何影响a)翻译起点的位置，b)信使RNA上的核糖体密度，以及c)核糖体翻译的速度。此外，将使用基因组编辑工具CRISPR/Cas与核糖体图谱相结合，研究密码子的使用及其对tRNA进化的影响，这与最近发现的tRNA衍生的用于硅藻蛋白质合成的非编码小RNA有关。我们的目标是修改假性毛滴虫的遗传密码，以获得对密码子使用、tRNA表达和tRNA衍生的非编码RNA的作用的初步见解。该项目的数据将为硅藻合成生物学奠定基础，因为硅藻是合成各种不同的酶和用于藻类生物技术的材料(例如二氧化硅)的基础。

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.