Supervisor: prof. Lukáš Žídek

Bacterial RNA polymerase (RNAP) is a key enzyme involved in gene expression and proved target of antibiotics. Although model RNAP of Gram-negative bacteria is well characterized, RNAP of other bacterial species differs substantially in subunit composition and regulation. In collaboration with Libor Krasny (Microbiology Institute of the Czech Academy of Sciences), we have recently characterized delta subunit and sigma-A factor of Bacillus subtilis. Topic of the thesis will be continuation of structural studies, namely investigation of dynamics and localization of the delta subunit in the holoenzyme, and structural characterization of proteins involved in non-canonical transcription initiation of RNAP of Mycobacterium smegmatis. The experimental approach will reflect the size and properties of the studied proteins. Cryo-electron microscopy will be the key technique of the holoenzyme studies, NMR spectroscopy will be applied to small a dynamic subunits. In particular, advanced NMR techniques developed in the group will facilitate studies of intrinsically disordered regions of the proteins.


1.    Zachrdla et al. Solution structure of domain 1.1 of the sigma(A) factor from Bacillus subtilis is preformed for binding to the RNA polymerase core. Journal of Biological Chemistry, 292 (2017) 11610-11617.

2. Kuban et al. Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase. J Am Chem Soc. 2019 Oct 10. doi: 10.1021/jacs.9b07837. [Epub ahead of print]

Keywords: RNA polymerase, transcription, bacteria, nuclear magnetic resonance

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