I'm a Teaching Assistant in laboratory practicals in Biochemistry I and Biochemistry III courses.

In my research, I focus on bacterial stress response mechanisms, especially linked to the inner membrane and the periplasm. I combine it with the research on recombinant protein production and biosensor construction. For more details, I recommend seeing my publication list.

A selection from Stockholm University publication database

• NrdR in Streptococcus and Listeria spp.: DNA Helix Phase Dependence of the Bacterial Ribonucleotide Reductase Repressor

  2025. Saher Shahid (et al.). Molecular Microbiology

  Article

  NrdR is a universal transcriptional repressor of bacterial genes coding for ribonucleotide reductases (RNRs), essential enzymes that provide DNA building blocks in all living cells. Despite its bacterial prevalence, the NrdR mechanism has been scarcely studied. We report the biochemical, biophysical, and bioinformatical characterization of NrdR and its binding sites from two major bacterial pathogens of the phylum Bacillota Listeria monocytogenes and Streptococcus pneumoniae. NrdR consists of a Zn-ribbon domain followed by an ATP-cone domain. We show that it forms tetramers that bind to DNA when loaded with ATP and dATP, but if loaded with only ATP, NrdR forms various oligomeric complexes unable to bind DNA. The DNA-binding site in L. monocytogenes is a pair of NrdR boxes separated by 15–16 bp, whereas in S. pneumoniae, the NrdR boxes are separated by unusually long spacers of 25–26 bp. This observation triggered a comprehensive binding study of four NrdRs from L. monocytogenes, S. pneumoniae, Escherichia coli, and Streptomyces coelicolor to a series of dsDNA fragments where the NrdR boxes were separated by 12–27 bp. The in vitro results were confirmed in vivo in E. coli and revealed that NrdR binds most efficiently when there is an integer number of DNA turns between the center of the two NrdR boxes. The study facilitates the prediction of NrdR binding sites in bacterial genomes and suggests that the NrdR mechanism is conserved throughout the bacterial domain. It sheds light on RNR regulation in Listeria and Streptococcus, and since NrdR does not occur in eukaryotes, opens a way to the development of novel antibiotics.

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• Improvement in mechanical properties of fungal-bacterial biocomposites as space construction material - transgenic microorganisms in mWALLd

  2023. Diana Pawlicki, Mateusz Balka.

  Conference

  Biocomposites have long stood as a promising alternative to current methods of structural development, and have proven by efforts of mWALLd to have even bigger potential for use in outer space. Aside from their advantageous factors in high radiation resistance, general shielding, the possibility of self-reparation and adaptable processing and build, as all materials, those too rise concerns, mainly relating to low mechanic rigidity. This paper serves as a study of modifications aiming at the reinforcement of the reliability of a fungal/bacterial composite as a structural material. On-site-produced polymers made from bacteria-produced hydrocarbons and their derivatives are likely to increase cohesion, while compression endurance could be achieved by the incorporation of native regolith as a scaffold for microbiological growth - included minerals allow microbial synthesis of complex compounds, serving further functions such as enabling biomineralisation or decreasing fracture vulnerability in combination with the organic fraction. The use of the recombinant expression in fungi and bacteria of elongated and branched morphology may lead to higher elasticity, as titin, CLPs (collagen-like proteins) and other fibrous proteins could be produced. Other complex biominerals could in turn provide greater stiffness and an additional increase in cohesion. Furthermore, bacterial cellulose production and biofilm-forming qualities of used bacteria such as the presence of pili and flagella could yield better mechanic rigidity. Additional reinforcement might be provided by fungal hyphae aerogel made from elastic and cohesive species, and genetic modification of the fungus.

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• Biosensor that Detects Stress Caused by Periplasmic Proteins

  2024. Alister James Cumming (et al.). ACS Synthetic Biology 13 (5), 1477-1491

  Article

  Escherichia coli is often used as a factory to produce recombinant proteins. In many cases, the recombinant protein needs disulfide bonds to fold and function correctly. These proteins are genetically fused to a signal peptide so that they are secreted to the oxidizing environment of the periplasm (where the enzymes required for disulfide bond formation exist). Currently, it is difficult to determine in vivo whether a recombinant protein is efficiently secreted from the cytoplasm and folded in the periplasm or if there is a bottleneck in one of these steps because cellular capacity has been exceeded. To address this problem, we have developed a biosensor that detects cellular stress caused by (1) inefficient secretion of proteins from the cytoplasm and (2) aggregation of proteins in the periplasm. We demonstrate how the fluorescence fingerprint obtained from the biosensor can be used to identify induction conditions that do not exceed the capacity of the cell and therefore do not cause cellular stress. These induction conditions result in more effective biomass and in some cases higher titers of soluble recombinant proteins.

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Show all publications by Mateusz Balka at Stockholm University