FUNCTIONAL TRANSCRIPTOMICS TEAM


 

Head:
dr hab. Kamilla Bąkowska-Żywicka, prof. ICHB PAN

 

 


Staff:

dr Piotr Machtel,


 

PhD Students:

mgr Anna Mleczko,

mgr. inż. Klementyna Marciniak,

mgr inż. Piotr Pietras

mgr Anna Wasilewska

Anna Wasilewska

 
 

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Key words:

regulatory RNAs, noncoding RNAs, ribosome-associated noncoding RNAs (rancRNA), riboswitches

 

Research area:

The research profile of the Functional Transcriptomics Team includes the identification and characterization of molecular mechanisms of RNA-based gene expression regulation in model pro- and eukaryotic organisms, as a response to environmental changes.

Our research interest includes the following topics:

1)      identification, characterization and determination of the regulatory potential of small ribosome-associated noncoding RNAs (rancRNA) in Saccharomyces cerevisiae under various environmental conditions, with particular emphasis on heterogeneity of ribosomes,

2)      identification of riboswitches which regulate transcription and translation in model bacterium Bacillus subtilis,

3)      comprehensive characterization of changes in the transcriptional, translational and regulatory activity induced in response to antibiotic stress and culture in infectious conditions in the drug-resistant strain Staphylococcus aureus, with special emphasis on the therapeutic potential of regulatory RNAs.

 

Ongoing research projects:

1)      Changes in the ribosomal protein composition and in the ribosome-associated small noncoding RNAs in Saccharomyces cerevisiae as a response to environmental stress

NCN – Opus 14

2)      Designing a new method for direct identification and absolute quantification of premature transcription termination events, following the example of bacterial riboswitches

NCN – Preludium 12

3)      RNA regulatory networks as novel antimicrobial targets in multidrugs resistant bacteria (cooperation with Department of Computational Biology, Biology Faculty  UAM in Poznań)

NCN – Opus 13

 

Selected publications:

1)      Mleczko AM, Celichowski P, Bąkowska-Żywicka K. Transfer RNA-derived fragments target regulate ribosome-associated aminoacyl-transfer RNA synthetases. Biochim Biophys Acta Gene Regul Mech. 2018 Jun 6. pii: S1874-9399(17)30380-2. doi: 10.1016/j.bbagrm.2018.06.001

2)      Gebetsberger J, Wyss L, Mleczko AM, Reuther J, Polacek N. A tRNA-derived fragment competes with mRNA for ribosome binding and regulates translation during stress. RNA Biol. 2017 Oct 3;14(10):1364-1373. doi: 10.1080/15476286.2016.1257470

3)      Bąkowska-Żywicka K, Mleczko AM, Kasprzyk M, Machtel P, Żywicki M, Twardowski T. The widespread occurrence of tRNA-derived fragments in Saccharomyces cerevisiae. FEBS Open Bio. 2016 Oct 21;6(12):1186-1200. doi: 10.1002/2211-5463.12127

4)      Mleczko AM, Bąkowska-Żywicka K. When small RNAs become smaller: emerging functions of snoRNAs and their derivatives. Acta Biochim Pol. 2016;63(4):601-607. Epub 2016 Oct 26.

5)      Bąkowska-Żywicka K, Kasprzyk M, Twardowski T. tRNA-derived short RNAs bind to Saccharomyces cerevisiae ribosomes in a stress-dependent manner and inhibit protein synthesis in vitro. FEMS Yeast Res. 2016 Sep;16(6). pii: fow077

6)      Machtel P, Bąkowska-Żywicka K, Żywicki M. Emerging applications of riboswitches - from antibacterial targets to molecular tools. J Appl Genet. 2016 Nov;57(4):531-541

7)      Mleczko AM, Celichowski P, Bąkowska-Żywicka K. Ex-translational function of tRNAs and their fragments in cancer. Acta Biochim Pol. 2014;61(2):211-6

8)      Pircher A, Bakowska-Zywicka K, Schneider L, Zywicki M, Polacek N. An mRNA-derived noncoding RNA targets and regulates the ribosome. Mol Cell. 2014 Apr 10;54(1):147-155. doi: 10.1016/j.molcel.2014.02.024

9)      Zywicki M, Bakowska-Zywicka K, Polacek N. Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis. Nucleic Acids Res. 2012 May;40(9):4013-24. doi: 10.1093/nar/gks020