Yazar "Karakaya, Hüseyin Çağlar" seçeneğine göre listele
Listeleniyor 1 - 9 / 9
Sayfa Başına Sonuç
Sıralama seçenekleri
Öğe Absence of superoxide dismutase activity causes nuclear DNA fragmentation during the aging process(Biochemical and Biophysical Research Communications, 2014) Muid, Khandaker Ashfaqul; Karakaya, Hüseyin Çağlar; Koç, AhmetSuperoxide dismutases (SOD) serve as an important antioxidant defense mechanism in aerobic organisms, and deletion of these genes shortens the replicative life span in the budding yeast Saccharomyces cerevisiae. Even though involvement of superoxide dismutase enzymes in ROS scavenging and the aging process has been studied extensively in different organisms, analyses of DNA damages has not been performed for replicatively old superoxide dismutase deficient cells. In this study, we investigated the roles of SOD1, SOD2 and CCS1 genes in preserving genomic integrity in replicatively old yeast cells using the single cell comet assay. We observed that extend of DNA damage was not significantly different among the young cells of wild type, sod1D and sod2D strains. However, ccs1D mutants showed a 60% higher amount of DNA damage in the young stage compared to that of the wild type cells. The aging process increased the DNA damage rates 3-fold in the wild type and more than 5-fold in sod1D, sod2D, and ccs1D mutant cells. Furthermore, ROS levels of these strains showed a similar pattern to their DNA damage contents. Thus, our results confirm that cells accumulate DNA damages during the aging process and reveal that superoxide dismutase enzymes play a substantial role in preserving the genomic integrity in this process.Öğe Boron stress activates the general amino acid control mechanism and ınhibits protein synthesis(PLoS ONE, 2011) Uluışık, İrem; Kaya, Alaattin; Dima, Fomenko; Karakaya, Hüseyin Çağlar; Brad, Carlson; Vadim, Gladyshev; Koç, AhmetBoron is an essential micronutrient for plants, and it is beneficial for animals. However, at high concentrations boron is toxic to cells although the mechanism of this toxicity is not known. Atr1 has recently been identified as a boron efflux pump whose expression is upregulated in response to boron treatment. Here, we found that the expression of ATR1 is associated with expression of genes involved in amino acid biosynthesis. These mechanisms are strictly controlled by the transcription factor Gcn4 in response to boron treatment. Further analyses have shown that boron impaired protein synthesis by promoting phosphorylation of eIF2a in a Gcn2 kinase dependent manner. The uncharged tRNA binding domain (HisRS) of Gcn2 is necessary for the phosphorylation of eIF2a in the presence of boron. We postulate that boron exerts its toxic effect through activation of the general amino acid control system and inhibition of protein synthesis. Since the general amino acid control pathway is conserved among eukaryotes, this mechanism of boron toxicity may be of general importance.Öğe Characterization of two genes encoding metal tolerance proteins from Beta vulgaris subspecies maritima that confers manganese tolerance in yeast(BioMetals, 2013) Bozdağ, Gönensin Ozan; Erbasol, Isil; Koç, Ahmet; Pedas, Pai; Karakaya, Hüseyin ÇağlarManganese (Mn2?) is an essential micronutrient in plants. However increased Mn2? levels are toxic to plant cells. Metal tolerance proteins (MTPs), member of cation diffusion facilitator protein (CDF) family, have important roles in metal homeostatis in different plant species and catalyse efflux of excess metal ions. In this study, we identified and characterized two MTP genes from Beta vulgaris spp. maritima (B. v. ssp. maritima). Overexpression of these two genes provided Mn tolerance in yeast cells. Sequence analyses displayed BmMTP10 and BmMTP11as members of the Mn-CDF family. Functional analyses of these proteins indicated that they are specific to Mn2? with a role in reducing excess cellular Mn2? levels when expressed in yeast. GFP-fusion constructs of both proteins localized to the Golgi apparatus as a punctuated pattern. Finally, Q-RT-PCR results showed that BmMTP10 expression was induced threefold in response to the excess Mn2? treatment. On the other hand BmMTP11 expression was not affected in response to excess Mn2? levels. Thus, our results suggest that the BmMTP10 and BmMTP11 proteins from B. v. ssp. maritima have non-redundant functions in terms of Mn2? detoxification with a similar in planta localization and function as the Arabidopsis Mn-CDF homolog AtMTP11 and this conservation shows the evolutionary importance of these vesicular proteins in heavy metal homeostatis among plant species.Öğe Evidence for the presence of a second electron donor for cytoplasmic thioredoxins in the yeast s cerevisiae(T Journal Biol, 2006) Koç, Ahmet; Karakaya, Hüseyin Çağlar; Ünlü, Ercan SelçukIn yeast, the cytoplasmic thioredoxin system is composed of NADPH, thioredoxin reductase-1 (TRR1) and 2 thioredoxin genes (TRX1, TRX2). In this study, using yeast knockout mutants for TRR1, TRX1 and TRX2 genes, the role of the thioredoxin system in methionine sulfoxide reduction was investigated. Cells lacking both TRX1 and TRX2 genes simultaneously were not able to reduce methionine sulfoxides to methionine; however, mutants missing the TRR1 gene were able to reduce methionine sulfoxides to methionine, which showed that electrons could be transferred from NADPH to thioredoxins in the absence of TRR1. Similar results were observed for 3-phosphoadenosine 5-phosphosulfate reduction in the inorganic sulfate assimilation pathway. Results from both assays suggested that yeast cells have additional cytoplasmic thioredoxin reductase activity that could compensate for methionine sulfoxide reduction and sulfate assimilation in the absence of TRR1. This report also constitutes the first evidence that thioredoxins are the in vivo electron donors for methionine sulfoxide reductases in yeast.Öğe Genome wide identification of genes that play a role in boron stress response in yeast(Genomics, 2011) Uluışık, İrem; Kaya, Alaattin; Avşar, Kadir; Karakaya, Hüseyin ÇağlarBoron is an essential micronutrient for plants and it is either necessary or beneficial for animals. Studies identified only few genes related to boron metabolism thus far and details of how boron is imported into cells and used in cell metabolism are largely unknown. In order to identify genes that play roles in boron metabolism, we screened the entire set of yeast haploid deletion mutants and identified 6 mutants that were resistant to toxic levels of boron, and 21 mutants that were highly sensitive to boron treatment. Furthermore, we performed a proteomic approach to identify additional proteins that are significantly up-regulated by boron treatment. Our results revealed many genes and pathways related to boron stress response and suggest a possible link between boron toxicity and translational control.Öğe Identification of a novel system for boron transport: atr1 ıs a main Boron exporter in yeast_(Molecular and Cellular Biology, 2009) Kaya, Alaattin; Karakaya, Hüseyin Çağlar; Fomenko, Dmitri E.; Gladyshev, Vadim N.; Koç, AhmetBoron is a micronutrient in plants and animals, but its specific roles in cellular processes are not known. To understand boron transport and functions, we screened a yeast genomic DNA library for genes that confer resistance to the element in Saccharomyces cerevisiae. Thirty boron-resistant transformants were isolated, and they all contained the ATR1 (YML116w) gene. Atr1 is a multidrug resistance transport protein belonging to the major facilitator superfamily. C-terminal green fluorescent protein-tagged Atr1 localized to the cell membrane and vacuole, and ATR1 gene expression was upregulated by boron and several stress conditions. We found that atr1 mutants were highly sensitive to boron treatment, whereas cells overexpressing ATR1 were boron resistant. In addition, atr1 cells accumulated boron, whereas ATR1-overexpressing cells had low intracellular levels of the element. Furthermore, atr1 cells showed stronger boron-dependent phenotypes than mutants deficient in genes previously reported to be implicated in boron metabolism. ATR1 is widely distributed in bacteria, archaea, and lower eukaryotes. Our data suggest that Atr1 functions as a boron efflux pump and is required for boron tolerance.Öğe Living donor liver transplantation for hepatocellular carcinoma(Transplantation Proceedings, 2012) Işık, Burak; İnce, Volkan; Karakaya, Hüseyin Çağlar; Kayaalp, Cüneyt; Yılmaz, SezaiBackground. Liver transplantation is a widely accepted modality in the treatment of hepatocellular carcinoma (HCC). In our center, patients with HCC limited to the liver without macrovascular invasion are accepted as candidates for living donor liver transplantation (LDLT). The aim of this study was to describe the patient characteristics and outcomes at a single institution to analyze the impact of our criteria on the survival of HCC patients. Patients and Methods. We reviewed the medical records of all HCC (n 105) patients who underwent liver transplantation in our institution. We excluded deaths in the early postoperative period and deceased donor liver transplantation (DDLT) patients, leaving 74 subjects (65 males and 9 female). Their median age was 53 years (range, 19–69). Univariate Kaplan-Meier and multivariate Cox proportional hazards models were used to analyze overall and disease-free survivals. Results. Thirty-two (43%) patients were within the Milan criteria, and 42 (57%) exceeded them. One- and 2-year overall survival rates for patients within versus exceeding the Milan criteria were 72% versus 68% and 61% versus 58%, respectively. One- and 2-year disease-free survival rates for patients within versus exceeding the Milan criteria were 72% versus 68% and 60% versus 55%, respectively (P .05). Tumor recurrence rates for patients within versus exceeding the Milan criteria were 0% versus 36%, respectively (P .0002). Alpha-fetoprotein level was the only predictor of overall survival; alphafetoprotein level and tumor differentiation were predictors of disease-free survival. Conclusion. Although higher recurrence rates have been observed among patients exceeding the Milan criteria, LDLT is the only treatment option for the patients in countries with limited sources of cadaveric organs. As a general principle, we believe that the use of cadaveric donor liver grafts is not suitable for patients who exceed these criteria.Öğe Proteomic changes during boron tolerance in barley Hordeum vulgare and role of vacuolar proton translocatingATPase subunit E(İnönü Üniversitesi, 2011) Atik, Ahmet Emin; Bozdağ, Gönensin Ozan; Akıncı, Ersin; Kaya, Alaattin; Koç, Ahmet; Yalçın, Talat; Karakaya, Hüseyin ÇağlarBoron is an essential micronutrient for plants and animals; however, it can be toxic when present at high concentrations. Th e purpose of this study was to understand the mechanisms of boron tolerance in the Turkish barley (Hordeum vulgare) Anadolu cultivar. For this purpose, 2-dimensional electrophoresis (2-DE) was used to screen diff erentially expressed proteins for both control and boron-stressed Anadolu barley genotypes. Seven proteins were revealed by 2-DE: 1) ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo large chain), 2) TLP5, a thaumatin-like protein, 3) PR5, a basic pathogenesis-related protein, 4) a RNase S-like protein, 5) a PSI type III chlorophyll a/b-binding protein, 6) a light-harvesting complex I LHC I, and 7) the vacuolar proton-translocating ATPase subunit E protein. Th ese were found to be upregulated in response to boron treatment. Even though the protein encoded by the V-ATPase subunit E gene was overexpressed, its transcript level was downregulated by boron treatment. Heterologous expression of the barley V-ATPase subunit E gene in yeast provided boron resistance to yeast cells. Th ese results indicated that the V-ATPase subunit E gene was functional and conferred tolerance to toxic boron levels in yeast and might play a role in the overall boron tolerance of barley.Öğe Roles of ATR1 paralogs YMR279c and YOR378w in boron stress tolerance(Biochemical and Biophysical Research Communications, 2011) Bozdağ, Gönensin Ozan; Uluışık, İrem; Gülce, Sıla Gülcüler; Karakaya, Hüseyin Çağlar; Koç, AhmetBoron is a necessary nutrient for plants and animals, however excess of it causes toxicity. Previously, Atr1 and Arabidopsis Bor1 homolog were identified as the boron efflux pump in yeast, which lower the cytosolic boron concentration and help cells to survive in the presence of toxic amount of boron. In this study, we analyzed ATR1 paralogs, YMR279c and YOR378w, to understand whether they participate in boron stress tolerance in yeast. Even though these genes share homology with ATR1, neither their deletion rendered cells boron sensitive nor their expression was significantly upregulated by boron treatment. However, expression of YMR279, but not YOR378w, from the constitutive GAPDH promoter on a high copy plasmid provided remarkable boron resistance by decreasing intracellular boron levels. Thus our results suggest the presence of a third boron exporter, YMR279c, which functions similar to ATR1 and provides boron resistance in yeast.
