Our lab is focused on studying of gram positive, soil living, multicellular bacteria of the genus Streptomyces. They undergo complex life cycle, which include spore germination, substrate mycelium formation, vegetative hyphae formation and sporulation. Streptomycetes are very important producers of wide variety of biological active compounds, such as antibiotics, antifungal (nystatin), antiviral, antitumoral, anticancer agents (doxorubicin), immunosupressants (rapamycin), siderophores (deferoxamine), pigments, volatiles (geosmin) (Hopwood, 2007; Bentley et al., 2002). They are also involved in decomposing the insoluble remains of other organisms such as lignocellulose and chitin, that makes them central organisms in carbon recycling (Bentley et al., 2002). They are widely used as a model organism of a complex developmental life cycle among prokaryotes.
We study regulation of gene expression of their life cycle, especially on the transcriptional level that is represented by sigma factors, as a major transcriptional regulators and on the post-transriptional level represented by small non-coding RNAs.
We are also interested in the life stage spore germination that appears after the dormancy state and it is not yet fully understood in Streptomyces. During spore germination cells awake its metabolism and start to form vegetative mycelium.
We collaborate with Laboratory of Bioinformatics of dr. Vohradský at the Institute of Microbiology of the ASCR (http://sun2.biomed.cas.cz/mbu/proteom/ ). They provide bioinformatical support for measured data gained from our experiments. They simulate and predict regulatory processes in the cells, identify and predict functions of sigma factors, small regulatory RNAs etc.

Research Interests

• Small non-coding RNAs in Streptomyces
• Sigma factors in Streptomyces
• Role of the 6S RNA in Streptomyces
• Systems biology of the spore germination in Streptomyces

Bobek J. (2016) Novel bioactive compounds produced by Actinomycetales through the mixed cultivation techniques (pdf)

Cihak M. (Master student) (2016) midterm report on sec. metabolism during germination [in Czech] (pdf)

Setinova D. (PhD student) (2016) asRNAs manuscript to be submitted (pdf)

Smidova K. (PhD student) (2016) submitted SigQ manuscript (pdf)

Setinova D, Novotna K, Vohradsky J, Bobek J. (2015) Cis-antisense RNAs in Streptomyces, to be submitted (pdf)

Head
Jan Bobek, Ph.D.
Email: jan.bobek@lf1.cuni.cz


PhD students
Klára Šmídová (Novotná)
Studied Biochemistry at the Institute of Chemical Technology in Prague. She is focused on studying of sigma factors in Streptomyces, mapping their binding sites on DNA and clarifying their function.
Email: klara.novotna@lf1.cuni.cz

Dita Šetinová
Studied Clinical Bioanalytics at the Institute of Chemical Technology in Prague and Process Engineering at the Czech Technical University in Prague. She is specialized in studying of RNA-mediated regulation in Streptomyces. Email: dita.setinova@lf1.cuni.cz

The GiardiaLab research group focuses on cell and molecular biology of a parasitic protist Giardia intestinalis. It was established in 2020 thanks to the institutional support of Charles University PRIMUS 20/MED/008.

Group leader: RNDr. Pavla Tůmová, Ph.D., (pavla.tumova@lf1.cuni.cz, tel. +420 224 968 465).

Website: https://giardialab.lf1.cuni.cz/