Ceren Alkım

ORCID: 0000-0002-5918-142X
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About
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Research Areas
  • Fungal and yeast genetics research
  • Microbial Metabolic Engineering and Bioproduction
  • Biofuel production and bioconversion
  • Enzyme Structure and Function
  • Glycosylation and Glycoproteins Research
  • Enzyme Catalysis and Immobilization
  • Amino Acid Enzymes and Metabolism
  • Fermentation and Sensory Analysis
  • Bacterial Genetics and Biotechnology
  • Photosynthetic Processes and Mechanisms
  • Microbial Natural Products and Biosynthesis
  • Polyamine Metabolism and Applications
  • Trace Elements in Health
  • Coffee research and impacts
  • Bioinformatics and Genomic Networks
  • Endoplasmic Reticulum Stress and Disease
  • Plant Micronutrient Interactions and Effects
  • Genetics, Aging, and Longevity in Model Organisms
  • GABA and Rice Research
  • DNA Repair Mechanisms
  • Diet, Metabolism, and Disease
  • Postharvest Quality and Shelf Life Management
  • Enzyme Production and Characterization
  • Pancreatic function and diabetes
  • Microfluidic and Capillary Electrophoresis Applications

Institut National des Sciences Appliquées de Toulouse
2020-2025

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2016-2025

Centre National de la Recherche Scientifique
2012-2025

Istanbul Technical University
2009-2023

Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés
2013-2020

Université de Toulouse
2012-2017

Université Toulouse III - Paul Sabatier
2013-2016

Institut National Polytechnique de Toulouse
2014

2-Phenylethanol is an aromatic compound commonly used in the food, cosmetic, and pharmaceutical industries. Due to increasing demand for natural products by consumers, production of this flavor microbial fermentation gaining interest, as a sustainable alternative chemical synthesis or expensive plant extraction, both processes relying on use fossil resources. However, drawback process high toxicity 2-phenylethanol producing microorganism. The aim study was obtain 2-phenylethanol-resistant...

10.3389/fmicb.2023.1148065 article EN cc-by Frontiers in Microbiology 2023-04-11

Oxidative stress is a major type observed in yeast bioprocesses, resulting decrease growth, viability, and productivity. Thus, robust strains with increased resistance to oxidative are highly demand by the industry. In addition, also associated aging age-related complex conditions such as cancer neurodegenerative diseases. Saccharomyces cerevisiae, model eukaryote, has been used study these eukaryotic processes. However, molecular mechanisms underlying responses unclear. this study, we have...

10.3389/fmicb.2022.822864 article EN cc-by Frontiers in Microbiology 2022-02-24

A synthetic pathway for (d)-xylose assimilation was stoichiometrically evaluated and implemented in Escherichia coli strains. The proceeds via isomerization of to (d)-xylulose, phosphorylation (d)-xylulose obtain (d)-xylulose-1-phosphate (X1P), aldolytic cleavage the latter yield glycolaldehyde DHAP. Stoichiometric analyses showed that this provides access ethylene glycol with a theoretical molar 1. Alternatively, both DHAP can be converted glycolic acid is 20% higher than exclusive...

10.1021/acssynbio.5b00103 article EN ACS Synthetic Biology 2015-07-17

Ethylene glycol (EG) is a bulk chemical that mainly used as an anti-freezing agent and raw material in the synthesis of plastics. Production commercial EG currently exclusively relies on using fossil resources. Biochemical production ethylene from renewable resources may be more sustainable.Herein, synthetic pathway described produces Escherichia coli through action (D)-xylose isomerase, (D)-xylulose-1-kinase, (D)-xylulose-1-phosphate aldolase, glycolaldehyde reductase. These reactions were...

10.1186/s12934-015-0312-7 article EN cc-by Microbial Cell Factories 2015-09-03

(L)-2,4-dihydroxybutyrate (DHB) is a versatile compound that can serve as precursor for the synthesis of methionine analog 2-hydroxy-4-(methylthio)butyrate and new advanced polymers. We previously implemented in Escherichia coli an artificial biosynthetic pathway aerobic production DHB from glucose, which relies on deamination (L)-homoserine followed by reduction 2-oxo-4-hydroxybutyrate (OHB) yields enzyme-bearing NADH-dependent OHB reductase activity. Under conditions, using NADPH cofactor...

10.3389/fbioe.2025.1504785 article EN cc-by Frontiers in Bioengineering and Biotechnology 2025-02-20

Increased exposure to nickel compounds and alloys due industrial development has resulted in pollution many pathological effects on human health. However, there is very limited information about response, transport, tolerance eukaryotes. To investigate resistance the model eukaryote Saccharomyces cerevisiae, evolutionary engineering by batch selection under gradually increasing stress levels was performed. Nickel hyper-resistant mutants that could resist up 5.3 mM NiCl2 , a lethal level for...

10.1111/1567-1364.12073 article EN FEMS Yeast Research 2013-08-31

Iron plays an essential role in all organisms and is involved the structure of many biomolecules. It also regulates Fenton reaction where highly reactive hydroxyl radicals occur. important for microbial biodiversity, health nutrition. Excessive iron levels can cause oxidative damage cells. Saccharomycescerevisiae evolved mechanisms to regulate its levels. To study stress resistance S. cerevisiae, evolutionary engineering was employed. The stress-resistant mutant "M8FE" analysed...

10.3390/microorganisms8010043 article EN cc-by Microorganisms 2019-12-24

Silver is a non-essential metal used in medical applications as an antimicrobial agent, but it also toxic for biological systems. To investigate the molecular basis of silver resistance yeast, we employed evolutionary engineering using successive batch cultures at gradually increased stress levels up to 0.25-mM AgNO3 29 populations and obtained highly silver-resistant genetically stable Saccharomyces cerevisiae strains. Cross-resistance analysis results indicated that mutants gained against...

10.1002/yea.3514 article EN Yeast 2020-07-21

Cobalt is an important metal ion with magnetic properties that widely used for several industrial applications. Overexposure to cobalt ions can be highly toxic the organisms because they usually overwhelm endogenous physiological system maintains their homeostasis causing (geno)toxic effects. To gain insight into mechanism of toxicity, we characterized at molecular and genetic levels a resistant CI25E Saccharomyces cerevisiae strain previously isolated by in vivo evolutionary engineering...

10.1039/c3mt00107e article EN Metallomics 2013-01-01

Salt-resistant yeast strains are highly demanded by industry due to the exposure of cells high concentrations salt, in various industrial bioprocesses. The aim this study was perform a physiological and transcriptomic analysis salt-resistant Saccharomyces cerevisiae (S. cerevisiae) mutant generated evolutionary engineering. NaCl-resistant S. were obtained ethyl methanesulfonate (EMS) mutagenesis followed successive batch cultivations presence gradually increasing NaCl concentrations, up 8.5%...

10.17305/bjbms.2017.2250 article EN Bosnian Journal of Basic Medical Sciences 2017-09-27

Glycolic acid (GA) is a two-carbon hydroxyacid with applications in the cosmetic, textile, and medical industry. Microbial GA production from all sugars can be achieved by engineering natural glyoxylate shunt. The synthetic (d)-xylulose-1 phosphate (X1P) pathway provides complementary route to produce (d)-xylose. simultaneous operation of X1P pathways increases theoretical yield xylose 20 %, which may strongly improve hemicellulosic hydrolysates.We herein describe construction an E. coli...

10.1186/s13068-016-0610-2 article EN cc-by Biotechnology for Biofuels 2016-09-20

In Saccharomyces cerevisiae, synthesis of T6P (trehalose 6-phosphate) is essential for growth on most fermentable carbon sources. the present study, metabolic response to glucose was analysed in mutants with different capacities accumulate T6P. A mutant carrying a deletion synthase encoding gene, TPS1, which had no measurable T6P, exhibited impaired ethanol production, showed diminished plasma membrane H⁺-ATPase activation, and became rapidly depleted nearly all adenine nucleotides were...

10.1042/bj20130587 article EN Biochemical Journal 2013-06-17

The meiotic developmental pathway in yeast enables both differentiation of vegetative cells into haploid spores that ensure long-term survival, and recombination the parental DNA to create genetic diversity. Despite importance proper metabolic regulation for supply building blocks energy, little is known about reprogramming central pathways meiotically differentiating during passage through successive stages.Metabolic budding was analysed by integrating information on genome-wide...

10.1186/s12915-014-0060-x article EN cc-by BMC Biology 2014-09-01

2,4-dihydroxybutyric acid (DHB) and 2-keto-4-hydroxybutyrate (OHB) are non-natural molecules obtained through synthetic pathways from renewable carbon source. As they structurally similar to lactate pyruvate respectively, could possibly interfere with the metabolic network of Escherichia coli. In fact, we showed that DHB can be easily oxidized by membrane associated L D-lactate dehydrogenases encoded lldD, dld ykgF into OHB, latter being cleaved formaldehyde several pyruvate-dependent...

10.1016/j.micres.2024.127888 article EN cc-by Microbiological Research 2024-08-31

The phosphoglucomutases (PGM) Pgm1, Pgm2, and Pgm3 of the yeast Saccharomyces cerevisiae were tested for their ability to interconvert ribose‐1‐phosphate ribose‐5‐phosphate. purified proteins studied in vitro with regard kinetic properties on glucose‐1‐phosphate ribose‐1‐phosphate. All enzymes active both substrates Pgm1 exhibiting only residual activity Pgm2 had almost equal ribose‐1‐phosphate, but a 2000 times higher preference when compared Pgm3. vivo function PGMs was characterized by...

10.1016/j.febslet.2012.09.042 article EN FEBS Letters 2012-10-24

10.1007/978-1-4939-0563-8_10 article EN Methods in molecular biology 2014-01-01

Abstract: The yeast Saccharomyces cerevisiae is a simple eukaryote and an excellent model organism for molecular biology. In this study, NaCl-resistant S. mutant obtained by inverse metabolic engineering was used as to investigate responses resistance behavior NaCl, LiCl, KCl, TMA, spermine sorbitol stresses., at physiological genetic levels. spot test results revealed that the showed higher LiCl NaCl. Gene expression analysis qRT-PCR ENA6 NHA1 genes of were induced in absence presence...

10.16883/jfpiu.54980 article EN Istanbul Journal of Pharmacy 2016-11-22

L-homoserine is a pivotal intermediate in the carbon and nitrogen metabolism of E. coli. However, this non-canonical amino acid cannot be used as source for growth. Furthermore, growth bacterium synthetic media potently inhibited by L-homoserine. To understand dual effect, an adapted laboratory evolution (ALE) was applied, which allowed isolation strain able to grow with was, at same time, desensitized inhibition acid. Sequencing evolved identified only four genomic modifications, including...

10.3389/fmicb.2022.1051425 article EN cc-by Frontiers in Microbiology 2022-12-13
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