Přehled

Doctoral study program: Life Sciences

Supervisor: Lukáš Žídek

Topic title : Structure and functions of proteins regulating bacterial transcription

Annotation:
The PhD project is a continuation of previous studies of the research group, in collaboration with the Libor Krasny of Institute of Microbiology, Academy of Sciences of The Czech Academy of Sciences. Krasny’s lab discovered several proteins of Gram-positive bacteria that play so far little understood roles in transcription regulation. The goal of the project is to combine structural biology approaches to establish relation between structure, biophysical properties, and function of these proteins and other poorly understood bacterial transcription factors. The particular aims include maping of transient interactions of the delta subunit with the RNA polymerase core of Bacillus subtilis, interplay between delta subunit and sigma factors, interactions of a recently discovered transcription factor MoaB2 with mycobacterial sigma factors and RNA polymerases. Cryo-electron microscopy will be used as a major tool to study structures of the proteins in complexes with RNA polymerase. A particular attention will be paid to dynamics of the proteins, that often contain large disordered regions, where cryo-EM data will be combined with results of NMR spectroscopy. As alternative methods, FRET (and potentially EPR in collaboration with V. Laguta) using advanced labelling techniques will be used. The project should result in publications in respected journals with the student being the (shared) first author.
Recommended literature:

Brezovská et al., J. Bacteriol. 2024, 122, 206
https://dx.doi.org/10.1128/jb.00066.24
Camacho-Zarco et al., Chem. Reviews. 2022, 122, 9331-9356
https://dx.doi.org/10.1021/acs.chemrev.1c01023
Kubáň et al., J. Am. Chem. Soc. 2019, 141, 16817-16828.
https://dx.doi.org/10.1021/jacs.9b07837

Research area:
infectious diseases
Keywords:
Bacterial RNA polymerase, transcritpion factors, protein dynamics, intrinsically disordered proteins, cryo-electron microscopy, NMR spectroscopy

Funding of the PhD candidate:
In the academic year 2026/27 the net income of the CEITEC PhD School student is expected to be at least CZK 29,400 (approx. EUR 1215)
GAČR grant 25-16037S (2025-2027, grant holder Lukáš Žídek)
Requirements for candidate:
Strong background in biophysics and/or physical chemistry, experience with electron microscopy or NMR spectroscopy is an advantage.
Information about the supervisor:
12 supervised students (9 defended, 3 currently supervised), more then 70 publications with > 2000 citations, 10 grants received

Start date: September 2026
Sign-up link: https://www.ceitec.eu/structure-and-functions-of-proteins-regulating-bacterial-transcription/t11446