Biology subjects

Bartosik, A. A.

Publications and source records attributed to Bartosik, A. A..

5 recordsLinked to original sources

bioRxiv2026

Genome-wide CRISPRi-seq maps essential-gene contributions to aminoglycoside susceptibility in Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic ESKAPE pathogen whose multiple intrinsic and acquired antibiotic resistance mechanisms restrict treatment options. Essential genes offer potential antimicrobial targets, but their vulnerability to partial inhibition and contribution to antibiotic susceptibility remain incompletely characterized. Here, we developed a rhamnose-inducible CRISPR interference (CRISPRi) platform and an 83,078-guide library for genome-wide screening in PAO1, with mismatch guides enabling graded repression. Fitness profiling in antibiotic-free Mueller-Hinton medium identified 743 genes whose repression reduced competitive fitness and revealed sequence features associated with guide performance. Combining full-match and mismatch-guide responses revealed substantial variation in essential-gene fitness effects across predicted repression strengths, while comparison of fitness profiles between Mueller-Hinton medium and fetal bovine serum identified condition-dependent effects alongside a conserved fitness landscape. Under aminoglycoside exposure, we identified 118 recurrent sensitizing and 120 recurrent protective gene knockdowns, including many targeting essential and fitness-associated functions. Growth and killing assays with individual strains confirmed that CRISPRi targeting of atpI, accC, secA and ftsZ enhanced tobramycin activity. Finally, transcriptome analysis of these knockdowns confirmed target silencing, captured polar effects on neighboring genes and revealed distinct but overlapping transcriptional responses. Together, these findings quantify the variable fitness costs of essential-gene repression and identify candidate targets for potentiating aminoglycoside activity. IMPORTANCE Essential bacterial genes are difficult to study because their complete disruption prevents growth. Yet knowing that a gene is essential does not reveal how strongly its activity must be reduced to impair growth. Here, we developed a method to examine how reduced gene expression affects fitness across the genome of Pseudomonas aeruginosa, a major cause of difficult-to-treat infections. This approach identified essential functions particularly vulnerable to partial depletion and mapped how gene repression alters aminoglycoside susceptibility. Repressing selected genes impaired growth and disproportionately increased killing by tobramycin. These tools and datasets provide a resource for prioritizing candidate antibacterial targets and investigating whether partial inhibition of essential functions can enhance the activity of existing antibiotics.

microbiology↗

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↗

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↗

bioRxiv2018

Pseudomonas aeruginosa partitioning protein ParB acts as a nucleoid-associated protein binding to multiple copies of a parS-related motif.

ParA and ParB homologs are involved in accurate chromosome segregation in bacteria. ParBs participate in separation of ori domains by binding to specific parS sites, mainly localized close to oriC. In Pseudomonas aeruginosa neither a lack of parB gene nor modification of ten parSs is lethal. Remarkably, such mutants show not only defects in chromosome segregation but also growth retardation and motility dysfunctions. Moreover, a lack of parB alters expression of over one thousand genes, suggesting that ParB could interact with the chromosome outside its canonical parS targets.\n\nIndeed, DNA immunoprecipitation with anti-ParB antibodies followed by deep sequencing (ChIP-seq) revealed 420 enriched regions in WT PAO1161 strain and around 1000 in a ParB-overproducing strain and in various parS mutants. Vast majority of the ParB-enriched loci contained a heptanucleotide motif corresponding to one arm of the parS palindrome. All previously postulated parS sites with the exception of parS5 interacted with ParB in vivo. Whereas the ParB binding to the four parS sites closest to oriC, parS1-4, is involved in chromosome segregation, its genome-wide interactions with hundreds of parS half-sites could affect chromosome topology, compaction and gene expression classifying P. aeruginosa ParB as a Nucleoid Associated Protein (NAP).

molecular biology↗

bioRxiv2017

Increased ParB level affects expression of stress response, adaptation and virulence operons and potentiates repression of promoters adjacent to the high affinity binding sites parS3 and parS4 in Pseudomonas aeruginosa

Similarly to its homologs in other bacteria, Pseudomonas aeruginosa partitioning protein ParB facilitates segregation of newly replicated chromosomes. Lack of ParB is not lethal but results in increased frequency of anucleate cells production, longer division time, cell elongation, altered colony morphology and defective swarming and swimming motility. Unlike in other bacteria, inactivation of parB leads to major changes of the transcriptome, suggesting that, directly or indirectly, ParB plays a role in regulation of gene expression in this organism.\n\nParB overproduction affects growth rate, cell division and motility in a similar way as ParB deficiency. To identify primary ParB targets, here we analysed the impact of a slight increase in ParB level on P. aeruginosa transcriptome. ParB excess, which does not cause changes in growth rate and chromosome segregation, significantly alters the expression of 176 loci. Most notably, the mRNA level of genes adjacent to high affinity ParB binding sites parS1-4 close to oriC is reduced. Conversely, in cells lacking either parB or functional parS sequences the orfs adjacent to parS3 and parS4 are upregulated, indicating that direct ParB-parS3/parS4 interactions repress the transcription in this region. In addition, increased ParB level brings about repression or activation of numerous genes including several transcriptional regulators involved in SOS response, virulence and adaptation. Overall, our data support the role of partitioning protein ParB as a transcriptional regulator in Pseudomonas aeruginosa.

microbiology↗