Department of Biotransformation
DEPARTMENT HEAD
STAFF MEMBERS
PhD Students
- mgr Michał Bochynek | room: 2.21, Tel: +48 71375 7062
- mgr Dorota Misiorna | room: 2.21, Tel: +48 71375 7062
- mgr Liliana Cebula | room: 2.23, Tel: +48 71375 7976
CONTACT
- Head: dr hab. Dorota Dziadkowiec | room: 2.20, Tel: +48 71375 6238
- prof. dr hab. inż. Marcin Łukaszewicz | room: 2.19, Tel: +48 71375 6250
- dr hab. Anna Krasowska | room: 2.18, Tel: +48 71375 6426
- dr Sławomir Jabłoński | room: 2.21, Tel: +48 71375 7062
- dr Daria Derkacz | room: 2.23, Tel: +48 71375 7976
- mgr Filip Kot | room: 2.21, Tel: +48 71375 7062
RESEARCH TOPICS
Research conducted at the Department of Biotransformation is focused on several main areas, in three research teams
The role of homologous recombination mediators in DNA replication and repair and maintaining genome integrity
in Schizosaccharomyces pombe and Saccharomyces cerevisiae.
Homologous recombination is a very important mechanism that allows the exchange of genetic material between homologous sequences. It is involved in processes such as repair of double-strand DNA breaks, activation of stalled replication forks, and is important for maintaining the structure of telomeres and centromeres. Therefore, it plays a very important role in maintaining genome stability, crucial for prevention of cancer development in higher organisms.
We study two proteins in Schizosaccharomyces pombe, Rrp1 and Rrp2, that are involved in homologous recombination. They belong, together with the Saccharomyces cerevisiae paralog, Uls1, to a class of DNA-dependent translocases that connect two very important pathways of post-translational protein modifications– SUMOylation and ubiquitination, important for protein degradation, but also regulating their localisation, binding partners and activity.
We have shown that Uls1, as well as Rrp1 and Rrp2, is involved in the response to replication stress and regulate the choice of the repair pathway for damaged DNA. Uls1 and Rrp2 also play a role in stabilizing the structure of telomeres. Recently, we have shown that Rrp1 and Rrp2 modulate the balance between histone variants on chromatin, which is important for the proper functioning of the centromere. The functions of Uls1, Rrp1 and Rrp2 depend on the SUMO interaction motifs, the ATPase domain characteristic of translocases, and the RING domain characteristic of ubiquitin ligases, present in their structure.
We have shown directly, on a purified protein preparation, that Rrp1 regulates the activity of Rad51 recombinase, because it ubiquitylates it and removes it from double-stranded DNA.
We are currently investigating, using fluorescence microscopy and immunoprecipitation, the interactions of Rrp1 and Rrp2 proteins with other proteins involved in maintaining genome stability. We also examine, using mass spectrometry, which proteins are ubiquitylated and SUMOylated in a Rrp1- and Rrp2-dependent manner.
Principal investigator: dr hab. Dorota Dziadkowiec
PhD students:
Dorota Misiorna – SUMOylation and SUMO-dependent enzymes in response to replication stress in yeast. Co-supervisor: dr Karol Kramarz.
dr Gabriela Baranowska – The role of DNA-dependent translocases in maintaining genome stability in Schizosaccharomyces pombe. Completed in 2024.|
dr Jakub Muraszko – Rrp1 translocase as a regulator of Rad51 recombinase function in Schizosaccharomyces pombe. Completed in 2021.
dr Anna Barg–Wojas – The role of homologous recombination mediators in maintaining the integrity of Schizosaccharomyces pombe centromeres. Completed in 2019.
dr Karol Kramarz – The role of Rad5 orthologues in DNA repair in yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. Completed in 2016.
Latest publications:
Baranowska G., Misiorna D., Białek W., Kramarz K., Dziadkowiec D., PLoS One, 2024
Replication stress response in fission yeast differentially depends on maintaining proper levels of Srs2 helicase and Rrp1, Rrp2 DNA translocases.
Kramarz K., Dziadkowiec D., DNA Repair (Amst)., 2022
Rrp1, Rrp2 and Uls1 – Yeast SWI2/SNF2 DNA dependent translocases in genome stability maintenance.
Muraszko J., Kramarz K., Argunhan B., Ito K., Baranowska G., Kurokawa Y., Murayama Y., Tsubouchi H., Lambert S., Iwasaki H., Dziadkowiec D., Nucleic Acids Res., 2021
Rrp1 translocase and ubiquitin ligase activities restrict the genome destabilising effects of Rad51 in fission yeast.
Barg-Wojas A., Muraszko J., Kramarz K., Schirmeisen K., Baranowska G., Carr AM., Dziadkowiec D., J Cell Sci., 2020
Schizosaccharomyces pombe DNA translocases Rrp1 and Rrp2 have distinct roles at centromeres and telomeres that ensure genome stability.
Other publications
Regulation of Rad51 recombinase during DNA replication – the role of Srs2 in Schizosaccharomyces pombe.
Social behaviour of Myxococcus xanthus bacteria.
The role of Borrelia sp. virulence factors in the course of infection.
The research group of dr hab. Anna Krasowska, prof. UWr focuses on the analysis of the impact of changes in the cell membrane of the pathogenic fungus Candida albicans on its morphology, metabolism, virulence and multidrug resistance.
According to the fungal priority pathogens list (FPPL) which pose the greatest threat to public health, published in the report of the World Health Organization (WHO) from the end of 2022 (WHO fungal priority pathogens list to guide research, development and public health action), C. albicans are in the group of pathogens with the highest priority. The classification of this microorganism into the group of the most dangerous fungal pathogens is due to the frequent occurrence of infections worldwide, a high rate of deaths due to systemic mycoses (disseminated candidiasis) and the lack of effective antifungal therapies (occurrence of multidrug resistance of C. albicans).
Taking into account the above aspects, searching for new antibiotics and therapies that can effectively combat fungal infections is pivotal. The aim of most drugs used in medicine is the biosynthesis of ergosterol or directly this molecule present in the fungal cell membrane (respectively: azoles, polyenes). The above groups of drugs use one of the few differences between fungal cells (presence of ergosterol) and host cells (presence of cholesterol).
In our research group, we analyze the effect of these drugs on the lipid composition of cell membranes, the location and activity of membrane transporters responsible for the ejection of drugs from the fungal cell, and the expression of genes encoding key adhesins and invasins (proteins responsible for the first stages of fungal infection). We also have an extensive collection of strains with mutations in genes encoding enzymes of the ergosterol biosynthesis pathway (deletion of key genes, replacement of amino acids in the Erg11 protein sequence), which constitute a valuable model in studies on multidrug resistance of C. albicans.
In addition to antibiotics already used in medicine, we are also looking for compounds of natural origin that exhibit antifungal activity, which can be used in the treatment of infections separately or in parallel with conventional therapies. In our research team, we study the effect of such compounds on the survival and morphology of C. albicans cells, such as: capric acid, lactic acid or clove extracts.
The team’s latest projects concern the analysis of the role of sphingolipids in C. albicans resistance to antifungal drugs, virulence and inflammatory and cellular response of human cell lines. Sphingolipids are lipid molecules present next to ergosterol in the fungal cell membrane and are responsible for signal transduction, proper structure of the cell membrane, and the formation of microdomains. Recent studies indicate that sphingolipids also play a role in the occurrence of resistance to antifungal drugs, and modification of sphingolipid biosynthesis pathways can lead to an altered structure of the cell wall and, consequently, recognition of the pathogen by the immune system. In addition, C. albicans has the ability to mask PAMP molecules from the host’s immune system by modifying the structure of the cell wall (cell wall remodeling). In the project carried out by our team, we analyze the impact of changes in sphingolipid biosynthesis on the structure and composition of the membrane and cell wall, inflammatory and cellular response of human cell lines.
C. albicans is an opportunistic pathogen. This means that infections caused by it develop during host immunity deficiencies. For this reason, interactions between the fungus and the host organism in the context of the immune response are also interesting.
The project carried out by dr Daria Derkacz analyzes the impact of changes in β-glucan biosynthesis (a key PAMP molecule, pathogen-associated molecular pattern), present in the cell wall of the fungus C. albicans, on the inflammatory and cellular response of vaginal epithelial cell lines and gingival fibroblasts. It was found that the lack or increase in the amount of ergosterol in the fungal cell membrane causes a change in the structure of the cell wall, leading to the exposure of β-glucan and chitin on the cell surface. This may contribute to differences in the recognition of the pathogen by PRRs (pathogen recognition receptors) on host cells and, consequently, to an altered immune response.PhD thesis:
PhD thesis:
Liliana Cebula – „Changes in the structure of the Candida albicans plasma membrane and cell wall on the inflammatory and cellular immune response”. In progress (since 2024), Co-supervisor: dr Daria Derkacz.
dr Daria Derkacz – „The role of the Candida albicans plasma membrane and cell wall in the inflammatory response”. Defense 2024 – distinction.
dr Jakub Suchodolski – „The effect of ergosterol on the activity of the Cdr1 transporter and selected parameters of the plasma membrane in Candida albicans”. Defense 2020 – distinction.
dr Joanna Szczepaniak – „The effect of selected factors on the activity of Candida albicans ABC transporters”. Defense 2017 – distinction.
dr Anna Pawluk (Murzyn) – „The effect of Saccharomyces boulardii on the virulence factors of C. albicans”. Defense 2010 – distinction.
dr Ida Szmigiel – „Biotransformation of rapeseed meal using Bacillus subtilis”. Defense 2021 – distinction.
dr Damian Konkol – „Use of biotransformed rapeseed meal in poultry nutrition”. Defense 2022 – distinction.
Project NCN MINIATURA 8, 2024/08/X/N21/00702: “Isolation and determination of the structure of β-glucan obtained from the cell wall of Candida albicans strains with impaired ergosterol synthesis and assessment of the effect of β-glucan on the inflammatory and cellular response“, (2024-present).
Project manager: dr Daria Derkacz.
Project NCN OPUS 22, 2021/43/B/NZ1/00523: “The role of Candida albicans plasma membrane sphingolipids in a potentially new mechanism of drug resistance and inflammatory response“, (2022-present).
Project manager: dr hab. Anna Krasowska, prof. UWr.
Project NCN PRELUDIUM, 2017/25/N/NZ1/00050: “The role of fructose in multidrug resistance of Candida albicans“, (2018-2021).
Project manager: dr Jakub Suchodolski.
Project NCN OPUS 12, 2016/23/B/NZ1/01928: “Changes in drug resistance and virulence of Candida albicans in the presence of different carbon sources“, (2017-2021).
Project manager: dr hab. Anna Krasowska, prof. UWr.
Latest publications:
Derkacz D., Grzybowska M., Cebula L. and Krasowska A., (2023) Int. J. Mol. Sci, 24(24), 17499
Surfactin and capric acid affects the posaconazole susceptibility of Candida albicans strains with altered sterols and sphingolipids biosynthesis.
Sztafrowski D., Muraszko J., Jasiura A., Bryk P., Urbanek A.K. and Krasowska A., (2023), PloS OneThe alternating 50 Hz magnetic field depending on the hydrophobicity of the strain affects the viability, filamentation and sensitivity to drugs of Candida albicans.
Starosta R., de Almeida R.F.M., Suchodolski J., Derkacz D., Krasowska A., (2023), Journal of Inorganic Biochemistry
Anticandidal Cu(I) Complexes with Neocuproine and 1-(4-Methoxyphenyl)Piperazine Based Diphenylaminomethylphosphine: Is Cu-Diimine Moiety a Pharmacophore?
Derkacz D. and Krasowska A., (2023), Int. J. Mol. Sci., 24, 3966
Alterations in the level of ergosterol in Candida albicans’ plasma membrane correspond with changes in virulence and result in triggering diversed inflammatory response.
Urbanek A.K., Łapińska Z., Derkacz D. and Krasowska A., (2022) Pathogens, 11, 1289
The role of ERG11 point mutations in the resistance of Candida albicans to fluconazole in the presence of lactate.
Other Publications
1. The effect of selected plant extracts on Candida albicans.
2. Synergistic effect of posaconazole and capric acid on selected Candida albicans strains.
3. The effect of factors changing the Candida albicans cell wall on the survival of this fungus.
4. Synergistic activity of posaconazole with selected compounds against Candida albicans.
5. Analysis of the effect of caspofungin on the morphology of Candida albicans cells and the effect on the inflammatory response of human cell lines.
Isolation and Characterization of Biosurfactants
Some microorganisms—bacteria, yeasts, and fungi—produce surface-active compounds known as biosurfactants. These compounds vary in chemical structure, including low-molecular-weight types such as glycolipids, lipopeptides, and cyclic peptides, as well as high-molecular-weight types like lipopolysaccharides, biopolymer complexes, and lipoproteins.
In the Department of Biotransformation, several bacteria and fungi have been isolated from water and soil samples from Spitsbergen. These microorganisms belong to the group of psychrotolerants and do not grow at temperatures above 30°C. They exhibit a wide range of metabolic capabilities, including the secretion of biosurfactants into their environment.
The chemical structure of a biosurfactant, named pseudofactin, secreted by the Arctic strain Pseudomonas fluorescens BD5, has been identified. It is a lipopeptide that reduces surface tension from 72 mN/m to 31.5 mN/m at a concentration of 72 mg/L. The stability and emulsification index of pseudofactin are higher than those of Tween 20 and Triton X-100.
Additionally, pseudofactin has been found to exhibit anti-adhesive properties against uropathogenic microorganisms. The studied biosurfactant prevents microbial adhesion to glass, plastic, and silicone surfaces. Furthermore, it removes already-formed biofilms from these surfaces.
The research conducted at the Department of Biotransformation aims to identify new applications for biosurfactants and to develop efficient industrial-scale production technologies.
Bochynek M., et al. 2023 “Centrifugal partition chromatography as a potential method of isolation and purification of amphiphilic substances from a solid-state fermentation process”. Biomass Conv. Bioref. 13:16333.
Bochynek M., et al. 2023 “Formation and structural features of micelles formed by surfactin homologues”. Front. Bioeng. Biotechnol. 11:1211319.
Wójtowicz K., et al. 2021 “Surfactin cyclic lipopeptides change the plasma membrane composition and lateral organization in mammalian cells”. Biochimica et Biophysica Acta, 1863:183730.
Biniarz P., Henkel M., Hausmann R., Łukaszewicz M. 2020 “Development of a Bioprocess for the Production of Cyclic Lipopeptides Pseudofactins With Efficient Purification From Collected Foam”. Front Bioeng Biotechnol 8: 565619.
Biniarz P., Łukaszewicz M., Janek T. 2017 “Screening concepts, characterization and structural analysis of microbial-derived bioactive lipopeptides: a review”. Crit Rev Biotechnol 37(3):393–410.
Isolation, identification, and characterization of the biomedical properties of biosurfactants – PhD dissertation.
Biogas and Methanogenesis
The development of renewable energy sources is an urgent need of modern civilization. One such source is biogas, which is produced through the biological decomposition of organic matter under anaerobic conditions. The process of biogas production is complex and requires the cooperation of multiple microbial species. The Department of Biotransformation has a research facility for conducting methane fermentation under laboratory conditions, as well as equipment for basic analysis of raw materials used in biogas production.
Archaea play a crucial role in methane formation, which constitutes approximately 50% of biogas. These microorganisms are at the end of the anaerobic food chain and are essential for its stable functioning. Despite their significant role in anaerobic ecosystems, only about 170 species of archaea have been isolated to date, and many aspects of their function remain unexplored. However, available data indicate that the family of methanogenic archaea is highly diverse in terms of morphological structure, metabolic capabilities, and preferred environmental conditions.
The Department of Biotransformation has developed an online database (PhyMet 2) containing detailed descriptions of classified methanogenic archaea. This database serves as a valuable tool for collecting and analyzing data on microorganisms with potential industrial applications. One feature of archaea with possible industrial significance is the presence of extracellular structures known as archaella. In some species, such as Methanospirillum hungatei, archaella are responsible for active cell movement. Interestingly, genes encoding archaella proteins are also common in species that do not exhibit motility. In these cases, a possible function of archaella may be electrical conductivity, enabling electron exchange with the environment or other microorganisms.
The research on methanogenesis conducted at the Department of Biotransformation aims to enhance the industrial efficiency of biogas production and to deepen the understanding of molecular and cellular mechanisms essential for the functioning of methanogenic archaea.
Meserszmit M., et al. 2024 “Effect of mowing versus abandonment of mesic grasslands in Central Europe on biomass use for biogas production: Implications for semi-natural ecosystem conservation”. J Environ Manage 368:122132.
Burdukiewicz M., et al. 2018 “PhyMet 2 : a database and toolkit for phylogenetic and metabolic analyses of methanogens”. Environ Microbiol Rep 10(3):378–82.
Gaworski M., et al. 2017 “Enhancing biogas plant production using pig manure and corn silage by adding wheat straw processed with liquid hot water and steam explosion”. Biotechnology for Biofuels 10:259
Jabłoński S., et al. 2015 “Continuous mesophilic anaerobic digestion of manure and rape oilcake – Experimental and modelling study”. Waste Management 35:105
Jabłoński S., et al. 2014 “Mathematical modelling of methanogenic reactor start-up: Importance of volatile fatty acids degrading population”. Bioresource technology 174:74
Modelling of Anaerobic Digestion with ADM1 – PhD Dissertation by Sławomir Jabłoński
Identification of Methanogenic Archaea Potentially Capable of Extracellular Enzyme-Dependent Electron Uptake – Master’s Thesis
Analysis of Soluble Sugar Content and Biogas Production Potential in the Biomass of Selected Grass Species – Bachelor’s Thesis
Saccharomyces cerevisiae in Metabolomic Research
Yeasts of the Saccharomyces genus are a group of organisms important from both an industrial and scientific perspective. Saccharomyces cerevisiae are widely used in industry due to their ability to perform alcoholic fermentation. They produce alcohol for both food and technical purposes. Additionally, they serve as a source of various products, including higher alcohols (e.g. isobutanol), biomass used as animal feed, yeast extract, and prebiotic components such as β-glucan. S. cerevisiae is also one of the most commonly used organisms for heterologous protein production. Research is ongoing to develop specialized strains for specific applications, such as the fermentation of lignocellulosic biomass.
S. cerevisiae is a key model eukaryotic organism. Despite extensive research focused on this microorganism, many aspects of its biology remain unexplored. The function of approximately 10% of S. cerevisiae genes has yet to be determined, and its metabolic map still contains numerous gaps.
At the Department of Biotransformation, we conduct research aimed at developing technologies for the production of valuable compounds using yeast or their biomass, as well as expanding knowledge on the metabolism of S. cerevisiae. Our focus is particularly on the production of volatile aromatic compounds and the metabolism of hydrophobic amino acids. Our experiments are based on a collection of yeast strains originating from natural environments and those obtained through UV-induced mutagenesis.
In our research, we utilize ¹H-NMR techniques in collaboration with specialists from Wrocław University of Science and Technology and GC/MS chromatography in cooperation with Wrocław University of Environmental and Life Sciences.
Jabłoński S.J., Mielko-Niziałek K.A., Leszczyński P., Gasiński A., Kawa-Rygielska J., Młynarz P., et al. 2024 “Examination of internal metabolome and VOCs profile of brewery yeast and their mutants producing beer with improved aroma“. Sci Rep 14(1):14582.
Łukaszewicz M., Leszczyński P., Jabłoński S.J., Kawa-Rygielska J. 2024 “Potential applications of yeast biomass derived from small-scale breweries” Applied Sciences 14(6):2529.
Selection of Yeast Strains with Enhanced Aromatic Ester Production for the Brewing Industry – Master’s Thesis
Characterization of Selected Saccharomyces cerevisiae Strains for Industrial Applications – Master’s Thesis
