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Pinku Sarmah

Unravelling the role of mRNA targeting pathways and exploring its discrete localization

Principal investigator: Prof. Dr. Hans-Georg Koch

Institut für Biochemie und Molekularbiologie
Stefan-Meier-Str. 17
79104 Freiburg

Phone: +49 (0) 761-203-5290
pinku.sarmah@biochemie.uni-freiburg.de

Abstract

The spatial and temporal coordination of protein trafficking is essential in all cells and particularly important for aggregation-prone membrane proteins. Decades of research have revealed that bacterial membrane proteins are targeted and inserted into the membrane primarily co-translationally by the signal recognition particle (SRP). However, there is an alternative targeting system that exists in both prokaryotes and eukaryotes in which the mRNA is first targeted to the membrane and only then translation and insertion occurs. Our study is focused on the mRNA targeting machineries and on exploring the subcellular localization of membrane protein transcripts. However, various evidences have already suggested that the mRNAs are localized at its respective sites where its encoded protein products functions. But certain observations and conclusions in the field of mRNA localization are still controversial and the mechanism underlying observed examples of subcellular localized transcripts to be further explored. Investigating the exact localization of protein molecules inside a cell is the first step toward better understanding of the link between spatial organization and functionality. But the translation independent mechanism for transporting mRNAs to the cell pole or membranes still remains a big mystery. Since bacterial cells are small in size and cannot be compartmentalized, localized mRNA and translation have become more challenging to study in bacterial cells. At the same time, it is still unclear about the underlying molecular mechanisms of transcripts localization. We are applying the MS2 mRNA tagging technology to understand the bacterial mRNA localization in vivo by using a 3D single-particle tracking approach. Unravelling the underlying molecular mechanism of mRNA targeting will help exploring the relative contribution of mRNA and protein targeting pathways in the spatio-temporal organization of the bacterial cell.

Methods

  • In vitro synthesis
  • 3D-single particle tracking imaging, Confocal
  • Site directed mutagenesis
  • Cloning
  • Pull down assay