The Escherichia coli PAIusp is a small pathogenicity island encoding usp, for the uropathogenic specific protein (Usp), a genotoxin and three associated downstream imu1-3 genes that protect the producer against its own toxin. Bioinformatic analysis revealed the presence of the PAIusp also in publically available Salmonella bongori and Salmonella enterica subps. salamae genome sequences. PAIusp is in all examined sequences integrated within the aroP-pdhR chromosomal intergenic region. The focus of this work was identification of the usp promoter and regulatory elements controlling its activity. We show that, in both E. coli and S. bongori, the divergent TyrR regulated P3 promoter of the aroP gene, encoding an aromatic amino acid membrane transporter, drives usp transcription while H-NS acts antagonistically repressing expression. Our results show that the horizontally acquired PAIusp has integrated into the TyrR regulatory network and that environmental factors such as aromatic amino acids, temperature and urea induce usp expression.
COBISS.SI-ID: 5318991
Cells employ specific and nonspecific mechanisms to protect their genome integrity against exogenous and endogenous factors. The clbS gene is part of the polyketide synthase machinery (pks genomic island) encoding colibactin, a genotoxin implicated in promoting colorectal cancer. The pks is found among the Enterobacteriaceae, in particular Escherichia coli strains of the B2 phylogenetic group. Several resistance mechanisms protect toxin producers against toxicity of their products. ClbS, a cyclopropane hydrolase, was shown to confer colibactin resistance by opening its electrophilic cyclopropane ring. Here we report that ClbS sustained viability and enabled growth also of E. coli expressing another genotoxin, the Usp nuclease. The recA::gfp reporter system showed that ClbS protects against Usp induced DNA damage. To elucidate the mechanism of ClbS mediated protection, we studied the DNA binding ability of the ClbS protein. We show that ClbS directly interacts with single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), whereas ssDNA seems to be the preferred substrate. Thus, the ClbS DNA-binding characteristics may serve bacteria to protect their genomes against DNA degradation.
COBISS.SI-ID: 5079119
The achievement describes the genome sequencing of all known strains of the fungus Wallemia ichtyophaga, which is the most salt-resistant fungus known. Wallemia ichthyophaga is also a close relative of Wallemia mellicola, which is frequently found as part of the intestinal microbiota and according to some studies it is one of the key microbiota determinants of the allergic reactions of the host. The population genomics of W. mellicola was also published in the co-authorship of the programme group members (COBISS.SI-ID 5103695). Population genomics of fungi is mostly limited to medically relevant species, which makes the here described study one of the rare examples of the population genomics of environmental fungi. Similar research was done for Hortaea werneckii (Capnodiales, Ascomycota), an extremely halotolerant organism that occupies natural and man-made hypersaline environments and has been extensively studied as a model of halotolerance in eukaryotes for over two decades. Although it is typically saprobic, H. werneckii can also act as a coloniser on human skin and cause tinea nigra on the hands and soles of the feet. Discovery of numerous genotypes on ribosomal DNA sequences and associated sequencing problems of household genes assigned heterozygous genome of many H. werneckii strains, which is very rare situation in fungi. This was confirmed by the analysis of whole genome sequences (COBISS.SI-ID 4704847), which additionally showed substantial reticulation within the phylogenetic history of the strains. The study presents an important new view on the genetic structure of a fungal population that can act both as saprobe and human pathogen.
COBISS.SI-ID: 5158479
The efficiency of the bacteriocin ColE7, bacterial conjugation-based "kill" - "anti-kill" antimicrobial system, was assessed using real-time PCR, flow cytometry and bioluminescence. The ColE7 antimicrobial system consists of the genetically modified Escherichia coli strain Nissle 1917 harbouring a conjugative plasmid (derivative of the F-plasmid) encoding the ColE7 activity gene ("kill" gene, as ColE7 is a DNase) and a chromosomally encoded ColE7 immunity gene ("anti-kill" gene). On the basis of traJ gene expression in the killer donor cells, our results showed that the efficiency of the here studied antimicrobial system against target E. coli was higher at 4 than at 24 h. Flow cytometry was used to indirectly estimate DNase activity of the antimicrobial system, as lysis of target E. coli cells in the conjugative mixture with the killer donor strain led to reduction in cell cytosol fluorescence. According to a lux assay, E. coli TG1 (pXen lux+ Apr ) with constitutive luminescence were killed already after 2 h of treatment. Target sensor E. coli C600 with DNA damage SOS-inducible luminescence showed significantly lower SOS induction 6 and 24 h following treatment with the killer donor strain. Our results thus showed that bioluminescent techniques are quick and suitable for estimation of the ColE7 bacterial conjugation-based antimicrobial system antibacterial activity.
COBISS.SI-ID: 4688463
The published work extends the phenotypic characterization of a bacterial culture collection obtained from white, yellow, grey or pink microbial cave wall colonies that are common in the caves of Slovenian Karst. We have determined antibiotic resistance to 22 natural and synthetic antibiotics in 69 isolates from the microbial mats. Thirty-eight isolates (52%) were resistant to 1-5 antibiotics; another 27 isolates (37%) were resistant to 6-10 antibiotics; and 7 isolates (0.1%) were resistant to 11-17 antibiotics. According to the research objectives of our research program, the ability to synthesize antimicrobial compounds was tested also tested. We screened for production of antimicrobial compounds by growing cave isolates on five different media and overlaying individual cultures with ten Gram-positive and Gram negative multidrug resistant isolates. Out of 78 isolates tested, 15.3% showed antimicrobial activity against Escherichia coli DH5, 15.3% against extended-spectrum ß-lactamase producing Escherichia coli, 3.8% against Salmonella enterica serovar Typhimurium TL747, 9% against Klebsiella pneumoniae ATCC BAA-1706, 9% against carbapenem-resistant Klebsiella pneumoniae ATCC BAA-1705, 7.7% against Bacillus cereus, 20.5% against Bacillus subtilis, 9% against Listeria monocytogenes, 19.2% against methicillin-resistant Staphylococcus aureus, and 20.5% against methicillin resistant Staphylococcus pseudointermedius. Results showed the potential of cave microbes to suppress the growth of multi-resistant pathogens, and, a relatively high resistance to antibiotics.
COBISS.SI-ID: 5309263