PhD in Structural Biology, Biophysics or Biochemistry at CEITEC/Masaryk University

Topic title:  Deciphering the Argonaute Loading Mechanisms in RNA-Silencing Pathways

Supervisor: prof. Mgr. Richard Štefl, Ph.D.


This PhD theme focuses on unraveling the intricate process of Argonaute protein loading by small RNAs, a critical step in gene regulation within RNA-silencing pathways, which are pivotal in both healthy and diseased states of animals and plants. Despite over two decades of research into the microRNA pathway and RNA interference, the precise mechanisms of miRNA strand selection and transfer to Argonaute proteins remain elusive. We propose the existence of two distinct mammalian Argonaute loading pathways, orchestrated by Dicer and heat shock protein chaperones, which both involve charged intrinsically disordered regions that have been overlooked in previous structural studies. The PhD project aims to dissect these mechanisms using electron cryomicroscopy (cryoEM). The objective is to elucidate the structures of critical complexes involving heat shock protein chaperone/co-chaperone-Argonaute-RNA and Dicer-Argonaute-RNA assemblies. By integrating cryoEM with functional analyses, the project aspires to establish the mechanistic principles of Argonaute loading. The findings of this PhD project will be instrumental in advancing RNA-based therapeutic applications and understanding one of the most crucial regulatory cellular processes.

Recommended literature:

Dicer structure and function: conserved and evolving features. Zapletal D, Kubicek, K, Svoboda P, Stefl R EMBO Reports (2023) 24:e57215 doi:10.15252/embr.202357215

microRNAs in action: biogenesis, function and regulation. Shang R, Lee S, Senavirathne G, Lai EC. Nat Rev Genet. 2023 doi:10.1038/s41576-023-00611-y.

Funding: Czech Science Foundation

Requirements on candidates: biochemistry/molecular biology

Keywords: gene silencing, small RNA, Argonaute, cryoEM, structures

Type of project: Structural biology studies of protein-protein, protein-ligand, protein-nucleic acids interaction using primarily NMR spectroscopy and SAXS in combination with a wide range of biophysical and biochemical techniques, such as fluorescence anisotropy (FA) and isothermal titration calorimetry (ITC) assays.

What do we want:

MSc in biochemistry/biophysics/biology
good computer skills (preferably Unix/Mac OSX)
basic knowledge of NMR/X-ray
eagerness to learn and share knowledge
motivated candidate able to cooperate in a team
English speaker

What do we offer:

modern laboratories
competitive projects = high risk, high gain
access to state-of-the-art instrument
stable funding of projects
access to literature
workshops and courses
travel money for conferences
competitive salary

Updated on 5th January 2024