Koç, Ahmet
Loading...
Profile URL
Name Variants
Koc, Ahmet
Koç, A.
Koc, A.
Koç, A.
Koc, A.
Job Title
Email Address
Main Affiliation
04.03. Department of Molecular Biology and Genetics
Status
Former Staff
Website
ORCID ID
Scopus Author ID
Turkish CoHE Profile ID
Google Scholar ID
WoS Researcher ID
Sustainable Development Goals
1NO POVERTY
0
Research Products
2ZERO HUNGER
1
Research Products
3GOOD HEALTH AND WELL-BEING
4
Research Products
4QUALITY EDUCATION
0
Research Products
5GENDER EQUALITY
0
Research Products
6CLEAN WATER AND SANITATION
3
Research Products
7AFFORDABLE AND CLEAN ENERGY
2
Research Products
8DECENT WORK AND ECONOMIC GROWTH
0
Research Products
9INDUSTRY, INNOVATION AND INFRASTRUCTURE
4
Research Products
10REDUCED INEQUALITIES
0
Research Products
11SUSTAINABLE CITIES AND COMMUNITIES
0
Research Products
12RESPONSIBLE CONSUMPTION AND PRODUCTION
2
Research Products
13CLIMATE ACTION
2
Research Products
14LIFE BELOW WATER
0
Research Products
15LIFE ON LAND
0
Research Products
16PEACE, JUSTICE AND STRONG INSTITUTIONS
0
Research Products
17PARTNERSHIPS FOR THE GOALS
0
Research Products
Documents
80
Citations
2086
h-index
19
This researcher does not have a WoS ID.
Scholarly Output
48
Articles
31
Views / Downloads
45775/20524
Supervised MSc Theses
10
Supervised PhD Theses
3
WoS Citation Count
889
Scopus Citation Count
974
Patents
0
Projects
5
WoS Citations per Publication
18.52
Scopus Citations per Publication
20.29
Open Access Source
44
Supervised Theses
13
| Journal | Count |
|---|---|
| Biochemical and Biophysical Research Communications | 4 |
| Journal of Trace Elements in Medicine and Biology | 4 |
| Journal of Biological Chemistry | 3 |
| Biochemistry | 2 |
| PLoS ONE | 2 |
Current Page: 1 / 4
Scopus Quartile Distribution
Competency Cloud
48 results
Scholarly Output Search Results
Now showing 1 - 10 of 48
Article Citation - WoS: 7Citation - Scopus: 8Checkpoint Deficient Rad53-11 Yeast Cannot Accumulate Dntps in Response To Dna Damage(Elsevier Ltd., 2007) Koç, Ahmet; Merrill, Gary F.Deoxyribonucleotide pools are maintained at levels that support efficient and yet accurate DNA replication and repair. Rad53 is part of a protein kinase regulatory cascade that, conceptually, promotes dNTP accumulation in four ways: (1) it activates the transcription of ribonucleotide reductase subunits by inhibiting the Crt1 repressor; (2) it plays a role in relocalization of ribonucleotide reductase subunits RNR2 and RNR4 from nucleus to cytoplasm; (3) it antagonizes the action of Sml1, a protein that binds and inhibits ribonucleotide reductase; and (4) it blocks cell-cycle progression in response to DNA damage, thus preventing dNTP consumption through replication forks. Although several lines of evidence support the above modes of Rad53 action, an effect of a rad53 mutation on dNTP levels has not been directly demonstrated. In fact, in a previous study, a rad53-11 mutation did not result in lower dNTP levels in asynchronous cells or in synchronized cells that entered the S-phase in the presence of the RNR inhibitor hydroxyurea. These anomalies prompted us to investigate whether the rad53-11 mutation affected dNTP levels in cells exposed to a DNA-damaging dose of ethylmethyl sulfonate (EMS). Although dNTP levels increased by 2- to 3-fold in EMS treated wild-type cells, rad53-11 cells showed no such change. Thus, the results indicate that Rad53 checkpoint function is not required for dNTP pool maintenance in normally growing cells, but is required for dNTP pool expansion in cells exposed to DNA-damaging agents.Article Citation - WoS: 73Citation - Scopus: 78Functional Analysis of Free Methionine-R Reductase From Saccharomyces Cerevisiae(American Society for Biochemistry and Molecular Biology, 2009) Le, Dung Tien; Lee, Byung Cheon; Marino, Stefano M.; Zhang, Yan; Fomenko, Dmitri E.; Kaya, Alaattin; Hacıoğlu, Elise; Kwak, Geun-Hee; Koç, Ahmet; Kim, Hwa-Young; Gladyshev, Vadim N.Methionine sulfoxide reductases (Msrs) are oxidoreductases that catalyze thiol-dependent reduction of oxidized methionines. MsrA and MsrB are the best known Msrs that repair methionine S-sulfoxide (Met-S-SO) and methionine-R-sulfoxide (Met-R-SO) residues in proteins, respectively. In addition, an Escherichia coli enzyme specific for free Met-R-SO, designated fRMsr, was recently discovered. In this work, we carried out comparative genomic and experimental analyses to examine occurrence, evolution, and function of fRMsr. This protein is present in single copies and two mutually exclusive subtypes in about half of prokaryotes and unicellular eukaryotes but is missing in higher plants and animals. A Saccharomyces cerevisiae fRMsr homolog was found to reduce free Met-R-SO but not free Met-S-SO or dabsyl-Met-R-SO. fRMsr was responsible for growth of yeast cells on Met-R-SO, and the double fRMsr/MsrA mutant could not grow on a mixture of methionine sulfoxides. However, in the presence of methionine, even the triple fRMsr/MsrA/MsrB mutant was viable. In addition, fRMsr deletion strain showed an increased sensitivity to oxidative stress and a decreased life span, whereas overexpression of fRMsr conferred higher resistance to oxidants. Molecular modeling and cysteine residue targeting by thioredoxin pointed to Cys101 as catalytic and Cys125 as resolving residues in yeast fRMsr. These residues as well as a third Cys, resolving Cys91, clustered in the structure, and each was required for the catalytic activity of the enzyme. The data show that fRMsr is the main enzyme responsible for the reduction of free Met-R-SO in S. cerevisiae.Article Citation - WoS: 7Citation - Scopus: 7The Roles of Thiol Oxidoreductases in Yeast Replicative Aging(Elsevier Ltd., 2010) Hacıoğlu, Elise; Esmer, Işıl; Fomenko, Dmitri E.; Gladyshev, Vadim N.; Koç, AhmetThiol-based redox reactions are involved in the regulation of a variety of biological functions, such as protection against oxidative stress, signal transduction and protein folding. Some proteins involved in redox regulation have been shown to modulate life span in organisms from yeast to mammals. To assess the role of thiol oxidoreductases in aging on a genome-wide scale, we analyzed the replicative life span of yeast cells lacking known and candidate thiol oxidoreductases. The data suggest the role of several pathways in controlling yeast replicative life span, including thioredoxin reduction, protein folding and degradation, peroxide reduction, PIP3 signaling, and ATP synthesis. © 2010 Elsevier Ireland Ltd.Master Thesis Chacterization of Drug Resistance Mechanisms Against Antifungal Agent Voriconazole(Izmir Institute of Technology, 2015) Ercan, İlkcan; Koç, Ahmet; Koç, AhmetThe rapid progress in medicine provides an increase in both average life span but also increases number of patients who need intensive care throughout the world. The morbidity and mortality of systemic fungal infections have become a serious problem because of suppressed immunity due to chemotherapy or intentional use of suppressants after tissue/organ transplantations. Voriconazole (Vfend, Pfizer) is one of antifungal agent against these fungal infections as a derivative of fluconazole. However some fungi types gain resistance against this agent. In this project, we use budding yeast Saccharomyces cerevisiae as a model organism to identify the genes that cause resistance Voriconazole by performing a genome wide screening. MRS3 and TRI1 genes were determined as resistant genes against lethal dose of Voriconazole. Their overexpression exhibited resistance to Voriconazole and also Ketoconazole in cross-resistance test. According to real-time PCR results, both MRS3 and TRI genes showed overexpression in IC50 of Voriconazole treatment when compare with their untreated status. Microaaray analysis indicated the expression change of our resistant genes is not more than 2 fold. In addition to expression analysis, functional analysis such as membrane dynamics tests have salt (NaCl, LiCl) and cationic drug (HygB,spermine,TMA) tolerance, membrane potential, volume/size measurements and cytoplasmic pH values were analyzed to reveal the mechanisms of resistance. Our results showed that no linkage between Variconozole resistance provided by MSR3 and TRI1 genes and functional analyses mentioned above.Article Citation - WoS: 11Citation - Scopus: 14Proteomic Changes During Boron Tolerance in Barley (hordeum Vulgare) and the Role of Vacuolar Proton-Translocating Atpase Subunit E(Türkiye Klinikleri Journal of Medical Sciences, 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. The 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 differentially 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. These 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. These 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. © TÜBITAK.Article Citation - WoS: 4Citation - Scopus: 3Boron Stress Signal Is Transmitted Through the Tor Pathway(Elsevier, 2023) Uluışık, İrem; Koç, AhmetAlthough boron is an essential element for many organisms, an excess amount of it can cause toxicity, and the mechanism behind this toxicity is not yet fully understood. The Gcn4 transcription factor plays a crucial role in the boron stress response by directly activating the expression of the boron efflux pump Atr1. More than a dozen transcription factors and multiple cell signaling pathways have roles in regulating the Gcn4 transcription factor under various circumstances. However, it is unknown which pathways or factors mediate boron signaling to Gcn4. Using the yeast Saccharomyces cerevisiae as a model, we analyzed the factors that converge on the Gcn4 transcription factor to assess their possible roles in boron stress signaling. Our findings show that the GCN system is activated by uncharged tRNA stress in response to boron treatment and that GCN1, which plays a role in transferring uncharged tRNAs to Gcn2, is necessary for the kinase activity of Gcn2. The SNF and PKA pathways were not involved in mediating boron stress, even though they interact with Gcn4. Mutations in TOR pathway genes, such as GLN3 and TOR1, abolished Gcn4 and ATR1 activation in response to boric acid treatment. Therefore, our study suggests that the TOR pathway must be functional to form a proper response against boric acid stress.Conference Object Functional Characterization of Clinically Relevant Novel Mutations in Atp7b Gene Using the Saccharomyces Cerevisiae Model(Wiley, 2016) Şimşek Papur, Özlenen; Terzioğlu, Orhan; Koç, AhmetWilson disease is an autosomal recessive disorder of copper metabolism characterized as neurodegeneration and liver abnormalities. It is caused by defects in the ATP7B gene. ATP7B is responsible for the sequestration of Cu into secretory vesicles, and this function is exhibited by the orthologous Ccc2p in the yeast. We aimed to characterize clinically-relevant novel mutations of p.T788I, p.V1036I and p.R1038G-fsX8 in yeast lacking the CCC2 gene.Article Citation - WoS: 48Citation - Scopus: 52Boron Stress Activates the General Amino Acid Control Mechanism and Inhibits Protein Synthesis(Public Library of Science, 2011) Uluışık, İrem; Kaya, Alaattin; Fomenko, Dmitri E.; Karakaya, Hüseyin Çağlar; Carlson, Bradley A.; Gladyshev, Vadim N.; 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 eIF2α in a Gcn2 kinase dependent manner. The uncharged tRNA binding domain (HisRS) of Gcn2 is necessary for the phosphorylation of eIF2α 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.Doctoral Thesis Identification of Doxorubicin Drug Resistance Mechanisms by Using Genomic Techniques(Izmir Institute of Technology, 2015) Demir, Ayşe Banu; Koç, AhmetChemotherapy has been an important contributor for the treatment of cancer patients for a long time. The effectiveness of the therapies is influenced from the toxicity effects of the agents on normal cells and from the drug resistance. Therapeutic resistance is believed to cause the failure of the chemotherapy effectiveness in most cancer cases. Therefore, understanding the molecular mechanisms that underlie the drug resistance may contribute to increase the effectiveness of the chemotherapeutic treatment of cancer. Doxorubicin is a natural product that is widely used in treatment of various cancer types, yet many tumors have resistance against these agents. By using the budding yeast Saccharomyces cerevisiae as a model organism, we performed genome-wide screenings to identify the genes that cause resistance against this agent. Overexpression of CUE5, AKL1, CAN1, YHR177W and PDR5 genes have been identified to cause resistance against Doxorubicin at higher concentrations than the identified toxic level. Among these genes, only PDR5 overexpression was found to have cross-resistance to Cisplatin. Real-time PCR and microarray analysis for these genes were also performed. Upon 80μM Doxorubicin treatment for 2 hours, none of the CUE5, AKL1, CAN1, YHR177W and PDR5 genes showed expression changes compared to their correponding untreated wild-type status. Therefore, overexpression of these genes may not be a physiological response of yeast cells against Doxorubicin. Genome-wide microarray analysis showed changes in several cellular and biological functions upon Doxorubicin treatment. Identified genes mainly function in general stress response related events such as, filamentous growth, protein ubiquitination, autophagy, changes in membrane transportation and metabolic processes.Article Evidence for the Presence of a Second Electron Donor for the Cytoplasmic Thioredoxins in the Yeast Saccharomyces Cerevisiae(TUBITAK, 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.