Laboratory of Gene Expression

Team

Dr hab. Agata L Starosta – head of laboratory | agata.starosta@umcs.pl | tel. +48 81 537 7790
Dr Olga Chrobak – Post Doc | olga.chrobak@umcs.pl | tel. +48 81 537 7785
Dr Magdalena Suchora - Post Doc | magdalena.suchora@umcs.pl | tel. +48 81 537 7785
Mgr Przemysław Latoch – PhD student | przemyslaw.latoch@umcs.pl | tel. +48 81 537 7785
Mgr Natalia Kopik – PhD student | tel. +48 81 537 7785

Laboratory of Gene Expression

We study protein biosynthesis in bacteria, especially the involvement of translational apparatus in the regulation of protein biosynthesis and putative factors which may determine specialization of the bacterial ribosomes.

Hierarchical managing of the genetic information stored in DNA lays at the basis of every living cell – DNA is a blueprint that codes for all cellular functions, while RNA stores executive commands. Transcription is the process in which the information stored in DNA is rewritten into RNA. The information from RNA is then translated into protein sequences in the process of protein biosynthesis (translation). At the heart of translation lies the ribosome. Thus, the ribosome transforms genetic information into proteins, which are the basis of all life as we know it.

Ribosomes, sometimes called molecular nanomachines, are at the centre of our group’s attention. Historically, ribosomes were perceived as homogeneous macromolecules carrying a constant set of ribosomal RNAs and proteins. Consequently, ribosomes were not considered to actively participate in the regulatory role of gene expression, and regulation was associated with features of mRNA. Recently specialized ribosomes hypothesis was proposed, significantly expanding the function of translational machinery, proposing new roles for ribosomal particle in regulating fundamental aspects of cell metabolism, namely the gene expression. The hypothesis assumes the existence of a subpopulation of ribosomes carrying unique properties (for example unique rRNA modifications, alternative ribosomal proteins, binding of small molecules in the active centre) allowing fast and precise response to environmental stimuli throughout selectivity for distinct mRNAs. It was proposed that the ribosome functional heterogeneity may represent immediate implementation of information about environmental changes, providing the cell with "fast-track reaction'' system, but also may serve as a hub for signal integration at the post-transcriptional level, related to usage of a specific pool of mRNAs.

Disturbances of the translational machinery lead to many different metabolic disorders. In case of human health, these can manifest themselves in the form of so called ribosomopathies – diseases affecting various organs including heart or spleen. In bacterial cells however, translation is a validated drug target for antibiotic action. In the era of increasing antibiotic resistance it is crucial to find new metabolic targets for novel antimicrobials. We believe that specialised ribosomes can serve as a new antibiotic target, allowing for development of new, targeted inhibitors of bacterial translation.

In the project we focus on the sporulation process in B. subtilis bacteria as a model to study regulation of gene expression at the translational level . B. subtilis is by far the best-understood endospore forming bacterium. Spores can remain dormant for a very long period of time (probably centuries or more) before germinating, are resistant to most forms of disinfection, can survive very high and low temperatures, radiation and harsh chemicals. Infections with sporulating pathogenic bacteria are relevant and problematic in hospital environments, agriculture and food industry. Examples of the pathogenic sporulating bacteria include Bacillus anthracis used as a bioweapon or Clostridium difficile, a causing agent of a serious life-threatening condition of the gastrointestinal system, pseudomembranous colitis. Although B. subtilis is their close relative, it is not pathogenic which makes it a perfect model organism.

Our group is interested in the life cycle of B. subtilis, especially the process of sporulation and the role specialised ribosomes play in it. We hope to identify factors affecting ribosomal heterogeneity as it could potentially lead to designing novel drugs that would target translation in a more selective way. As shown in previous studies, such approach based on deactivation of specific pathways of protein biosynthesis would result in accumulation of toxic proteins in bacterial cell and as a consequence – death of the bacterial cell.

In our research we employ knock-out mutants of B. subtilis constructed basing on the classical recombination methods using antibiotic resistance cassettes, as well as knock-down mutants constructed using the CRISPRi-Cas9 system. Moreover, we utilise next generation sequencing of transcriptomes (RNA-seq) and translatomes (Ribo-seq), as well as mass spectrometry based proteome analyses. The results of our experiments will be further verified in vitro by e.g. toe-printing

Grants in realisation:

1) 'Translation regulation in spore-forming bacterium – Specialized ribosomes in Bacillus subtilis'
First TEAM 03/2017, Fundacja na Rzecz Nauki Polskiej, 2M zł

2) 'Ribosome specialization in Bacillus subtilis'
EMBO Installation Grant 2017, European Molecular Biology Organization, 50k EURO/yr (3–5 yrs)

Laboratory equipment

The laboratory is suited for work with genetically modified microorganisms (GMM).
The laboratory is equipped with standard microbiological and molecular biology equipment.

Types of analyses

We are highly experienced in the mode-of-action analyses of antibiotics, including in vivo and in vitro screens, antibiotic purification and studying antibiotic molecular mechanisms of action.

We are practised in nucleic acid research including extraction and purification of nucleic acids from different materials and sample preparation for next-generation sequencing.


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