Laboratory of Molecular Biology of Microorganisms


We study both basic cellular processes and mechanisms that enable bacteria to adapt to the environment, e.g. chromosome replication and the bacterial cell cycle, synthesis of secondary metabolites, response to stress, or resistance to antibiotics/active substances.

We mainly work with actinomycetes (the model strain is Streptomyces coelicolor A3(2)) and pathogenic Campylobacterales (Helicobacter pylori, Campylobacter jejuni, Arcobacter butzleri). We analyse them in the context of unique features for a given species and features common to various bacteria. We participate in interdisciplinary research involving innovative solutions in developing photodynamic therapies and the synthesis of biologically active nanoparticles.

In cooperation with the Wrocław University of Technology and the University of St. Andrew, we focus on developing and understanding the molecular mechanisms governing photoinactivation of pathogens and the exploration and understanding of new photosensitive compounds. The results of our research make it possible to describe hitherto unknown processes or mechanisms at the molecular level. However, the obtained results may be of practical importance in the future, as they concern essential physiological processes of pathogenic bacteria, synthesis of potential active substances (e.g. antibiotics) or bacterial resistance to treatment.

Laboratory Head

Anna Pawlik

Laboratory Head: Anna Pawlik, PhD, DSc (associate professor, 0000-0003-1824-1550)

Academic and Research Career:

  • Habilitation (biology), IIET PAS, Wrocław, Poland (2011)
  • Post-Doc. at Unité de Pathogénie Bactérienne des Muqueuses, Institute Pasteur, Paris, France (2004-2006)
  • PhD degree in biology, IIET PAS, Wrocław, Poland (2003)
  • M.Sc. degree in biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology (1999)

 Team management

  • Head of the Laboratory (since 2016)
  • PI in 7 research grants (2006-2023)
  • Supervisor of 6 PhD students (2012-2021)
  • Supervisor of >21 undergraduate/graduate students (2007-2021)

Scientific awards

  • The distinction of the Committee of Molecular Cell Biology of the Polish Academy of Sciences in the prof. K. Bassalik competition for the best Polish microbiological work (2015)
  • The special second prize awarded by the Director of the IIET PAS for the paper published in the journal with the highest impact factor (2010)
  • The scientific prize awarded by the Polish Academy of Sciences Medical Science Department for the coauthors of the series of publications concerning the basic steps of the bacterial cell cycle: replication and segregation of bacterial chromosomes (2007)
  • The Domestic Grant for Young Scientists funded by The Foundation for the Polish Science (2005)
Team

Secretary:

  • Anna Wysocka, MSc

Associate Professor:

Assistant Professors:

PhD Students:

Specialists and Technical Staff:

  • Jakub Muraszko, PhD (technician, 0000-0001-7232-0298)
  • Honorata Grzybowska (Labware & Media Kitchen)
Most important scientific achievements
  • Characterisation of the initiation of chromosome replication of the pathogenic bacterium Helicobacter pylori. We have demonstrated the unique features of this process: the unusual for G (-) bacteria bipartite structure of the region where replication begins (oriC), and topology-dependent interaction of the initiator DnaA protein with oriC.
  • Identification of hitherto unknown regulators of the pylori chromosome replication initiation process: HobA and HP1021. Both proteins regulate the formation of the replication initiation complex: HobA via interactions with DnaA, while HP1021 via interactions with oriC. We showed that HP1021 is a redox sensor protein.
  • Discovery of a previously unknown coloured secondary metabolite (coelimycin), a product of the ‘silent’ polyketide synthase Streptomyces coelicolor A3 (2) – a model species for genetic studies of actinomycetes. We described the key role of type II thioesterase in the functioning of the biosynthetic machinery of this compound.
Research methods
  • molecular microbiology
  • bacterial mutagenesis, in particular Streptomyces coelicolor, Helicobacter pylori, Campylobacter jejuni, Arcobacter butzleri
  • phenotypic analysis of mutants (e.g. growth curves, gene expression analysis using in vivo probes, RT-qPCR and western blotting, secondary metabolite production studies)
  • synthesis and purification of recombinant proteins
  • protein-protein and protein-DNA interactions (e.g., EMSA, footprinting, ChIP-PCR, protein crosslinking, affinity chromatography, gel filtration)
  • antibacterial activity of bioactive compounds
Key equipment
  • fully equipped molecular biology laboratories
  • class II biosafety laboratory
  • gas replacement culture system for anaerobic and microaerophilic bacteria
  • isotope laboratory (class III)
  • Typhoon FLA 9500 Imager versatile laser scanner for sensitive and quantitative measurements in a multiuser environment. (GE Healthcare)
  • Akta Purifier FPLC system (GE Healthcare)
  • Hitachi F-7000 fluorescence spectrophotometer
  • Hitachi U-29000 spectrophotometer
  • Clariostar multimode microplate reader with Atmospheric Unit Control ACU (BMGLabtech)
  • Sorvall MTX150 ultracentrifuge
  • Sorvall Lynx 6000 superspeed centrifuge
Most important projects (during the last 10 years)
  • The role of non-coding RNAs in Helicobacter pylori response to oxidative stress and the activity of the HP1021 regulon. National Science Centre, Preludium 21, (2023-2025) (PI Mateusz Noszka)
  • The role of HP1021-like orphan response regulators in physiology and virulence of selected pathogenic species of Epsilonproteobacteria. National Science Center OPUS17, (2020-2023) (PI Anna Pawlik)
  • Database for Scientific Information Supporting Innovative Therapies – BINWIT. Operational program: Digital Poland, Priority axis: II e-administration and open government, Action: 2.3 Digital accessibility and usability of public information, Secondary action: 2.3.1. Digital availability of public information from administrative and scientific sources. Contest number:  POPC.02.03.01-IP.01-00-006/17 (PI Krzysztof Pawlik)
  • Building bacterial orisome on bipartite origins – structural, functional and regulatory aspects of the process based on the analysis of the initiation of Helicobacter pylori chromosome replication. National Science Center Sonata Bis3 (2014-2020) (PI Anna Pawlik).
  • Initiation of chromosome replication in epsilonproteobacteria – identification and comparative analysis of the crucial factors. Foundation for Polish Science Parent-BRIDGE (grant for parents returning to research work POMOST) (2013-2015) (PI Anna Pawlik)
  • Replication and segregation mechanisms of bacterial chromosomes – identification of new antibiotic drug targets for Helicobacter pylori and Mycobacterium tuberculosis. The EIT+ research grant (2009-2014) (PI Jolanta Zakrzewska-Czerwińska)
Selected publications
  • Noszka M., Strzałka A., Muraszko J., Kolenda R,. Meng C., Ludwig C., Stingl K., Zawilak-Pawlik A. Profiling of the Helicobacter pylori redox switch HP1021 regulon using a multi-omics approach. Nat Commun. 2023 14(1):6715. https://pubmed.ncbi.nlm.nih.gov/37872172/
  • Piksa M., Fortuna W., Lian C., Gacka M., Samuel I.D.W., Matczyszyn K., Pawlik K.J. Treatment of antibiotic-resistant bacteria colonizing diabetic foot ulcers by OLED induced antimicrobial photodynamic therapy. Sci Rep. 2023 13(1):14087. https://pubmed.ncbi.nlm.nih.gov/37640720/
  • Piksa M, Lian C, Samuel IC, Pawlik K, Samuel ID, Matczyszyn K (2023) The role of the light source in antimicrobial photodynamic therapy. Chem Soc Rev 52(5):1697-1722. https://pubmed.ncbi.nlm.nih.gov/36779328/
  • Jaworski P., Zyla-Uklejewicz D., Nowaczyk-Cieszewska M., Donczew R., Mielke T., Weigel C., Zawilak-Pawlik A. (2021) Putative Cooperative ATP-DnaA Binding to Double-Stranded DnaA Box and Single-Stranded DnaA-Trio Motif upon Helicobacter pylori Replication Initiation Complex Assembly. Int J Mol Sci. 22(12):6643. https://pubmed.ncbi.nlm.nih.gov/34205762/
  • Szczepanowski P., Noszka M., Żyła-Uklejewicz D., Pikuła F., Nowaczyk-Cieszewska M., Krężel A., Stingl K., Zawilak-Pawlik A. (2021) HP1021 is a redox switch protein identified in Helicobacter pylori. Nucleic Acids Res. 49(12):6863-6879. https://pubmed.ncbi.nlm.nih.gov/34139017/
  • Bednarz B., Millan-Oropeza A., Kotowska M., Świat M., Quispe Haro J.J., Henry C., Pawlik K. (2021) Coelimycin Synthesis Activatory Proteins Are Key Regulators of Specialized Metabolism and Precursor Flux in Streptomyces coelicolor A3(2). Front Microbiol. 12:616050. doi: 10.3389/fmicb.2021.616050. https://pubmed.ncbi.nlm.nih.gov/33897632/
  • Nowaczyk-Cieszewska, M., Zyla-Uklejewicz, D., Noszka, M., Jaworski, P., Mielke, T., and Zawilak-Pawlik, A.M. (2020) The role of Helicobacter pylori DnaA domain I in orisome assembly on a bipartite origin of chromosome replication. Mol Microbiol 113: 338–355. https://pubmed.ncbi.nlm.nih.gov/31715026/
  • Bednarz, B., Kotowska, M., and Pawlik, K.J. (2019) Multi-level regulation of coelimycin synthesis in Streptomyces coelicolor A3(2). Appl Microbiol Biotechnol 103: 6423–6434. http://www.ncbi.nlm.nih.gov/pubmed/31250060
  • Kotowska, M., Świat, M., Zarȩba-Pasławska, J., Jaworski, P., and Pawlik, K. (2019) A GntR-Like Transcription Factor HypR Regulates Expression of Genes Associated With L-Hydroxyproline Utilization in Streptomyces coelicolor A3(2). Front Microbiol 10: 1451. http://www.ncbi.nlm.nih.gov/pubmed/31297104
  • Zawilak-Pawlik, A., Zarzecka, U., Żyła-Uklejewicz, D., Lach, J., Strapagiel, D., Tegtmeyer, N., et al. (2019) Establishment of serine protease htrA mutants in Helicobacter pylori is associated with secA mutations. Sci Rep 9: 11794. https://pubmed.ncbi.nlm.nih.gov/31409845/