Do you want to join us?

A position for PhD student

The doctoral research project is focused on the biology of regulatory RNAs and assisting proteins in bacteria. The project in the OPUS program of National Science Centre.

Description of the projects. Noncoding RNA (sRNA) enable bacteria to adapt to changing environmental conditions, they participate in the regulation of cellular metabolism and in the interactions with the host organisms during infection, and they also control bacterial virulence. The correct functioning of sRNAs is dependent on RNA-binding proteins. In Gram-positive bacteria this role is performed by such chaperone proteins as Hfq [1-3], and FinO-domain proteins [4, 5]. On the other hand, much less is known about proteins that perform this role in Gram-positive bacteria. Recent studies showed that this role may be played by KH-domain proteins, named KhpA and KhpB, which are present in many Gram-positive bacteria [6]. In several species, including Streptococcus pneumoniae, it was discovered that these proteins recognize, and strongly bind numerous RNA molecules, as well as participate in the regulation of cellular division. The aim of the studies in this project is to learn how KhpA and KhpB proteins recognize RNA molecules and what is the contribution of these interactions to the regulation of gene expression in S. pneumoniae bacteria. Since these proteins participate in the regulation of the cell division, the research planned in the project may also lead to conclusions regarding this important process.

The research tasks of the PhD student will be focused on explaining how KhpA and KhpB proteins recognize regulatory RNAs. The methods used will include genetic engineering to obtain the studied proteins and their mutants, the methods for examining the interactions of proteins with RNAs using fluorescently labeled molecules, and the methods to study these interactions in bacterial cells with the use of RNA-seq.

PhD studies: take place in the PhD School of AMU in the Section of natural Sciences. Information on the recruitment procedures is available on the webpage: http://snp.home.amu.edu.pl/

How to apply?

The application should be sent to mol@amu.edu.pl by June 2, 2024. The application should include a cover letter, scientific CV, and diplomas of completion of BSc and MSc studies, or the planned date of defense of the MSc thesis. The planned competition outcome date is June 10, 2024. The status of doctoral student at the doctoral school from October 2024 is required.

The application should include a declaration of consent to the processing of personal data.

If you have any questions, please contact me at the following e-mail address: mol@amu.edu.pl.

Literature

1. Małecka E.M., Stróżecka J., Sobańska D. and Olejniczak M. “Structure of bacterial regulatory RNAs determines their performance in competition for the chaperone protein Hfq.” Biochemistry (2015), 54, 1157-70
   PubMed
2. Wróblewska Z, Olejniczak M. “Hfq assists small RNAs in binding to the coding sequence of ompD mRNA and in rearranging its structure”, RNA (2016), 22(7):979-94
   PubMed
3. Kwiatkowska J, Wroblewska Z, Johnson KA, Olejniczak M. „The binding of Class II sRNA MgrR to two different sites on matchmaker protein Hfq enables efficient competition for Hfq and annealing to regulated mRNAs.”, RNA (2018), 24(12):1761-1784
   PubMed
4. Olejniczak M, Storz G. “ProQ/FinO-domain proteins: Another ubiquitous family of RNA matchmakers?” Molecular Microbiology. (2017), 104(6):905-915.
   PubMed
5. Ewa M. Stein, Joanna Kwiatkowska, Maciej M. Basczok, Chandra M. Gravel, Katherine E. Berry, Mikołaj Olejniczak „Determinants of RNA recognition by the FinO domain of the Escherichia coli ProQ protein”, Nucleic Acids Research (2020),
   PubMed
6. Olejniczak M., Jiang X, Basczok MM, Storz G. KH domain proteins: Another family of bacterial RNA matchmakers? Molecular Microbiology 117(1):10-19 (2022)
   https://pubmed.ncbi.nlm.nih.gov/34748246