Biology subjects

Modrzejewska, M.

Publications and source records attributed to Modrzejewska, M..

4 recordsLinked to original sources

bioRxiv2021

The LysR-type transcriptional regulator BsrA (PA2121) controls vital metabolic pathways in Pseudomonas aeruginosa

Pseudomonas aeruginosa, a facultative human pathogen causing nosocomial infections, has complex regulatory systems involving many transcriptional regulators. LTTR (LysR-Type Transcriptional Regulator) family proteins are involved in the regulation of various processes including stress responses, motility, virulence and amino acid metabolism. The aim of this study was to characterize the LysR-type protein BsrA (PA2121), previously described as a negative regulator of biofilm formation in P. aeruginosa. Genome wide identification of BsrA binding sites using ChIP-seq revealed 765 BsrA-bound regions in the P. aeruginosa PAO1161 genome, including 367 sites in intergenic regions. The motif T-N11-A was identified within sequences bound by BsrA. Transcriptomic analysis showed altered expression of 157 genes in response to BsrA excess, of which 35 had a BsrA binding site within their promoter regions, suggesting a direct influence of BsrA on the transcription of these genes. BsrA-repressed loci included genes encoding proteins engaged in key metabolic pathways such as the tricarboxylic acid cycle. The panel of loci possibly directly activated by BsrA, included genes involved in pili/fimbriae assembly as well as secretion and transport systems. In addition, DNA pull-down and regulatory analyses showed the involvement of PA2551, PA3398 and PA5189 in regulation of bsrA expression, indicating that this gene is part of an intricate regulatory network. Taken together, these findings reveal the existence of a BsrA regulon, which performs important functions in P. aeruginosa. IMPORTANCEThis study shows that BsrA, a LysR-type transcriptional regulator from P. aeruginosa, previously identified as a repressor of biofilm synthesis, is part of an intricate global regulatory network. BsrA acts directly and/or indirectly as the repressor and/or activator of genes from vital metabolic pathways (e.g. pyruvate, acetate, tricarboxylic acid cycle), and is involved in control of transport functions and the formation of surface appendages. Expression of the bsrA gene is increased in the presence of antibiotics, which suggests its induction in response to stress, possibly reflecting the need to redirect metabolism under stressful conditions. This is particularly relevant for the treatment of infections caused by P. aeruginosa. In summary, the findings of this study demonstrate that the BsrA regulator performs important roles in carbon metabolism, biofilm formation and antibiotic resistance in P. aeruginosa.

molecular biology↗

bioRxiv2020

An IDH-independent mechanism of DNA hypermethylation upon VHL inactivation in cancer

Hypermethylation of tumor suppressors and other aberrations of DNA methylation in tumors play a significant role in cancer progression. DNA methylation can be affected by various environmental conditions including hypoxia. The response to hypoxia is mainly achieved through activation of the transcription program associated with HIF1a transcription factor. VHL inactivation by genetic or epigenetic events, which also induces aberrant activation of HIF1a, is the most common driver event for renal cancer. With whole-genome bisulfite sequencing and LC-MS, we demonstrated that VHL inactivation induced global genome hypermethylation in human kidney cancer cells under normoxic conditions. This effect was reverted by exogenous expression of wild-type VHL. We show that global genome hypermethylation in VHL mutants can be explained by transcriptional changes in MDH and L2HGDH genes that cause the accumulation of 2-hydroxyglutarate--a metabolite that inhibits DNA demethylation by Tet enzymes. Unlike the known cases of DNA hypermethylation in cancer, 2-hydroxyglutarate was accumulated in IDH wild type cells. Key pointsO_LIInactivation of VHL gene leads to genome hypermethylation in kidney cancer cells. The DNA methylation phenotype can be rescued by endogenous expression of wild-type VHL. C_LIO_LIDNA hypermethylation can be attributed to the accumulation of a Tet inhibitor 2-hydroxyglutarate C_LIO_LIThe accumulation of 2-hydroxyglutarate in IDH wild-type cells is explained by gene expression changes in key metabolic enzymes (malate dehydrogenase MDH and 2-hydroxyglutrarate dehydrogenase L2HGDH). C_LI

cancer biology↗

bioRxiv2018

Genome sequence of Pseudomonas aeruginosa PAO1161, a PAO1 derivative with the ICEFP2 integrative and conjugative element

Pseudomonas aeruginosa is a common cause of nosocomial infections, especially in patients with cystic fibrosis and burn wounds. An attenuated PAO1 strain and its derivatives are widely used to study the biology of this bacterium, however recent studies indicated an ongoing evolution of the laboratory strains, highlighted by changes in the genomes of PAO1 sublines and derivatives used in different laboratories worldwide.\n\nHere we have sequenced the genome of Pseudomonas aeruginosa PAO1161 strain, a leu-, RifR, restriction-modification defective PAO1 derivative. This strain is described as the host of IncP-8 plasmid FP2, conferring the resistance to mercury and used in the past for preparation of genetic map of the P. aeruginosa chromosome. Comparison of PAO1161 genome sequence with PAO1-UW reference genome revealed an inversion of the large genome segment between rrnA and rrnB rRNA operons and more than 100 nucleotide polymorphisms and short insertions-deletions, many of which were also found within the recently re-sequenced PAO1 sublines. The PAO1161 specific sequence variants include E108K mutation in PA3792 (leuA), which we showed is responsible for leucine auxotrophy, H531L in PA4270 (rpoB), likely conferring rifampicin resistance, as well as nonsense mutations in PA2735 encoding a DNA methyltransferase as well as a putative OLD family endonuclease PA1939. Additionally, PAO1161 genome poses a 12 kb RPG42 prophage and a 108 kbp insertion within tRNA-Lys, encompassing a putative mercury resistance and showing similarity to PAPI-1 like integrative conjugative elements (ICE). Our data indicate that the ICE can excise from the bacterial chromosome and can be transferred to Pseudomonas putida cells where it integrates in the genome at three specific sites and confers the cells with mercury resistance. Overall this data provide insight into the genome variation between P. aeruginosa laboratory strains. Moreover, this data indicate that the FP2 element for years described as a IncP-8 plasmid is an integrative conjugative element.

microbiology↗

bioRxiv2017

Distinct Pattern Of Epigenetic DNA Modification In Leukocytes From Patients With Colorectal Carcinoma And Individuals With Precancerous Conditions, Benign Adenoma And Inflammatory Bowel Disease; A Link To Oxidative Stress

A characteristic feature of malignant cells, including colorectal cancer cells, is a profound decrease in level of 5-hydroxymethylcytosine, product of 5-methylcytosine oxidation by TET enzymes. This study included four groups of subjects: healthy controls, and patients with inflammatory bowel disease (IBD), benign polyps and colorectal cancer. Patients from all groups presented with significantly lower levels of 5-methylcytosine and 5-hydroxymethylcytosine than the controls. A similar tendency was also observed for 5-hydroxymethyluracil level. Patients with IBD showed the highest levels of 5-formylcytosine and 8-oxo-7,8-dihydro-2-deoxyguanosine of all study subjects, and individuals with colorectal cancer presented with the lowest concentrations of vitamin C and A. Expressions of TET1 and TET2 turned out to be the highest in IBD group. To the best of our knowledge, this is the first study to show that healthy subjects, individuals with precancerous conditions and colorectal cancerpatients present with distinct specific patterns of epigenetic modifications in leukocyte DNA.

cancer biology↗