Person: ARĞA, KAZIM YALÇIN
Loading...
Email Address
Birth Date
Research Projects
Organizational Units
Job Title
Last Name
ARĞA
First Name
KAZIM YALÇIN
Name
6 results
Search Results
Now showing 1 - 6 of 6
Publication Metadata only Genome reprogramming in Saccharomyces cerevisiae upon nonylphenol exposure(AMER PHYSIOLOGICAL SOC, 2017) MERTOĞLU, BÜLENT; Bereketoglu, Ceyhun; Arga, Kazim Yalcin; Eraslan, Serpil; Mertoglu, BulentBioaccumulative environmental estrogen, nonylphenol (NP; 4-nonylphenol), is widely used as a nonionic surfactant and can affect human health. Since genomes of Saccharomyces cerevisiae and higher eukaryotes share many structural and functional similarities, we investigated subcellular effects of NP on S.cerevisiae BY4742 cells by analyzing genome-wide transcriptional profiles. We examined effects of low (1 mg/l; <15% cell number reduction) and high (5 mg/l; > 65% cell number reduction) inhibitory concentration exposures for 120 or 180 min. After 120 and 180 min of 1 mg/l NP exposure, 187 (63 downregulated, 124 upregulated) and 103 genes (56 downregulated, 47 upregulated), respectively, were differentially expressed. Similarly, 678 (168 repressed, 510 induced) and 688 genes (215 repressed, 473 induced) were differentially expressed in cells exposed to 5 mg/l NP for 120 and 180 min, respectively. Only 15 downregulated and 63 upregulated genes were common between low and high NP inhibitory concentration exposure for 120 min, whereas 16 downregulated and 31 upregulated genes were common after the 180-min exposure. Several processes/pathways were prominently affected by either low or high inhibitory concentration exposure, while certain processes were affected by both inhibitory concentrations, including ion transport, response to chemicals, transmembrane transport, cellular amino acids, and carbohydrate metabolism. While minimal expression changes were observed with low inhibitory concentration exposure, 5 mg/l NP treatment induced substantial expression changes in genes involved in oxidative phosphorylation, cell wall biogenesis, ribosomal biogenesis, and RNA processing, and encoding heat shock proteins and ubiquitin-conjugating enzymes. Collectively, these results provide considerable information on effects of NP at the molecular level.Publication Metadata only Transcriptomic analysis displays the effect of (-)-roemerine on the motility and nutrient uptake in Escherichia coli(SPRINGER, 2017) SARIYAR AKBULUT, BERNA; Ayyildiz, Dilara; Arga, Kazim Yalcin; Avci, Fatma Gizem; Altinisik, Fatma Ece; Gurer, Caglayan; Toplan, Gizem Gulsoy; Kazan, Dilek; Wozny, Katharina; Bruegger, Britta; Mertoglu, Bulent; Akbulut, Berna SariyarAmong the different families of plant alkaloids, (-)-roemerine, an aporphine type, was recently shown to possess significant antibacterial activity in Escherichia coli. Based on the increasing demand for antibacterials with novel mechanisms of action, the present work investigates the potential of the plant-derived alkaloid (-)-roemerine as an antibacterial in E. coli cells using microarray technology. Analysis of the genome-wide transcriptional reprogramming in cells after 60 min treatment with 100 mu g/mL (-)-roemerine showed significant changes in the expression of 241 genes (p value < 0.05 and fold change > 2). Expression of selected genes was confirmed by qPCR. Differentially expressed genes were classified into functional categories to map biological processes and molecular pathways involved. Cellular activities with roles in carbohydrate transport and metabolism, energy production and conversion, lipid transport and metabolism, amino acid transport and metabolism, two-component signaling systems, and cell motility (in particular, the flagellar organization and motility) were among metabolic processes altered in the presence of (-)-roemerine. The down-regulation of the outer membrane proteins probably led to a decrease in carbohydrate uptake rate, which in turn results in nutrient limitation. Consequently, energy metabolism is slowed down. Interestingly, the majority of the expressional alterations were found in the flagellar system. This suggested reduction in motility and loss in the ability to form biofilms, thus affecting protection of E. coli against host cell defense mechanisms. In summary, our findings suggest that the antimicrobial action of (-)-roemerine in E. coli is linked to disturbances in motility and nutrient uptake.Publication Metadata only Investigating the toxic effects of nonylphenol on Saccharomyces cerevisiae(2016-07-06) BEREKETOĞLU, CEYHUN; ARĞA, KAZIM YALÇIN; MERTOĞLU, BÜLENT; BEREKETOĞLU C., ARĞA K. Y., MERTOĞLU B.Publication Metadata only Investigating the toxic effects of nonylphenol on Saccharomyces cerevisiae(ELSEVIER SCIENCE BV, 2016) MERTOĞLU, BÜLENT; Bereketoglu, Ceyhun; Arga, Kazim Yalcin; Mertoglu, BulentPublication Metadata only Analysis of transcriptional profiles of Saccharomyces cerevisiae exposed to bisphenol A(SPRINGER, 2017) MERTOĞLU, BÜLENT; Bereketoglu, Ceyhun; Arga, Kazim Yalcin; Eraslan, Serpil; Mertoglu, BulentBisphenol A (BPA), an endocrine disrupting chemical, is used as a monomer in the production of epoxy resins and polycarbonates, and as a plasticizer in polyvinyl chloride. As such, it is produced in large quantities worldwide and continuously leaches into the environment. To capture the genome reprogramming in eukaryotic cells under BPA exposure, here, we used Saccharomyces cerevisiae as model organism and analyzed the genome-wide transcriptional profiles of S. cerevisiae BY4742 in response to BPA, focusing on two exposure scenarios: (1) exposure to a low inhibition concentration (50 mg/L; resulting in < 10 % inhibition in cell number) and (2) a high inhibition concentration (300 mg/L; resulting in > 70 % inhibition in cell number). Based on the transcriptional profiling analyses, 81 genes were repressed and 104 genes were induced in response to 50 mg/L BPA. Meanwhile, 378 genes were downregulated and 606 genes were significantly upregulated upon exposure to 300 mg/L BPA. While similar processes were affected by exposure to distinct BPA concentrations, including mitochondrial processes, nucleobase-containing small molecule metabolic processes, transcription from the RNA polymerase II promoter, and mitosis and associated processes, the number and magnitude of differentially expressed genes differ between low and high inhibition concentration treatments. For example, exposure to 300 mg/L BPA resulted in severe changes in the expression levels of several genes involved in oxidative phosphorylation, the tricarboxylic acid cycle, ribosomal activity, replication, and chemical responses. Conversely, only slight changes were observed in the expression of genes involved in these processes in cells exposed to 50 mg/L BPA. These results demonstrate that yeast cells respond to BPA in a concentration-dependent manner at the transcriptional level via different genes and provide insight into the molecular mechanisms underlying the modes of action of BPA.Publication Metadata only Transcriptional analysis of nonylphenol on saccharomyces cerevisiae using DNA microarray(2016-06-16) BEREKETOĞLU, CEYHUN; ARĞA, KAZIM YALÇIN; MERTOĞLU, BÜLENT; BEREKETOĞLU C., ARĞA K. Y., Eraslan S., MERTOĞLU B.