Master Thesis Defense: Tuğçe Altınuşak
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Tuğçe Altınuşak
Biological Sciences and Bioengineering, M.Sc. Thesis, 2014 

Thesis Jury
Assist Prof.  Erdal Toprak (Thesis Supervisor), Assoc. Prof. Batu Erman, Prof. Dr. Canan Atılgan

Date &Time: January,13rd, 2014 – 11:00

Place: Fens L063 

Keywords: Antibiotic Resistance, Trimethoprim, Trimethoprim Resistance, DHFR, Mutation, Protein Evolution, Morbidostat, Sequencing, SCA, FIS, f statistic


Understanding the molecular basis of antibiotic resistance is of great importance since antibiotic resistance is an ever growing public health problem. Pathogenic bacteria can accumulate resistance against antibiotics via horizontal gene transfer and spontaneous mutations. One of the most prevalent resistance mechanisms is increased antibiotic tolerance as a result of spontaneous mutations on the enzymes that are targeted by antibiotic molecules. Here, in this study, we investigated how ecological factors influence genetic trajectories that lead to antibiotic resistance. In a custom made continuous culture device that we call the Morbidostat, we evolved several wild type Escherichia coli populations against trimethoprim where six of these populations were continuously diluted with a mild dilution factor (~ 0.3 hour-1) and remaining seven populations were continuously diluted with a strong dilution factor (~ 0.6 hour-1). At the end of four weeks, all of the populations evolved to similar levels of trimethoprim resistance in a stepwise manner by accumulating three or four mutations on the promoter and coding regions of DHFR gene. The first mutation was almost always on the promoter region and the following first amino acid replacement on the protein was chosen from the sector regions we predicted by Statistical Coupling Analysis (SCA). Strikingly, evolutionary trajectories of  the populations that evolved under strong dilution were far from predictability and population structures were highly heterogeneous. Prolonged clonal interference was abundantly observed in the populations evolving under strong dilution. Our results suggest that evolution of resistance highly depend on fitness constraints imposed by ecological factors.