Please refer to https://www.evolbio.mpg.de/3098366/group_microbialdyn and contact Jenna <email@example.com> for further information on the project.
Co-Supervisor Frederic Bertels (computational component)
https://www.evolbio.mpg.de/3178548/group-micromolevol, contact: firstname.lastname@example.org
The evolution of translation termination in bacteria
Translation - the process by which mRNA is decoded into proteins - is a central biological process performed by all organisms. Our research group uses bacteria to investigate the mechanisms by which such an ancient and important biological process can evolve in response to novel selection pressures.
The aim of this project is to investigate a specific aspect of bacterial translation: the evolution of translation termination by peptide release factors PrfA and PrfB in Pseudomonas fluorescens SBW25. Key questions include: What is the balance of PrfA and PrfB, and how does this correlate with STOP codon usage? How does altering the balance between PrfA and PrfB affect translation termination and fitness? Can an imbalance between PrfA and PrfB be compensated for by evolution?
The project is expected to involve a combination of computational work (with Frederic Bertels) and wet lab experiments (with Jenna Gallie). The computational component will require a comprehensive analysis of prf characteristics, and related STOP codon usage, in the Pseudomonas genus. The laboratory component is expected to involve a combination of genetic engineering (of prf and /or key STOP codons identified in the computational component), experimental evolution, and relevant biological assays (e.g., RNA-seq, YAMAT-seq, fitness assays).
While some experience in both programming and microbial genetics would be advantageous, we welcome applications from any interested and motivated candidates!
References for further reading
- Ayan GB, Park HJ, Gallie J. 2020. The birth of a bacterial tRNA gene. eLife 9:e57947. doi:10.7554/eLife.57947
- Rak R, Dahan O, Pilpel Y. 2018. Repertoires of tRNAs: The couplers of genomics and proteomics. Annu. Rev. Cell Dev. Biol. 34:239–264. doi:10.1146/annurev-cellbio-100617-062754
- Li C, Qian W, Maclean CJ, Zhang J. 2016. The fitness landscape of a tRNA gene. Science 352:837-840. doi:10.1126/science.aae0568