Biology subjects

Öztürk, M. A.

Publications and source records attributed to Öztürk, M. A..

3 recordsLinked to original sources

bioRxiv2025

Chromosome segregation in Escherichia coli involves DNA binding by the MinC-MinD complex

The Escherichia coli Min system, composed of the proteins MinC, MinD, and MinE, is crucial for directing septum formation at mid-cell. MinD has also been shown to bind DNA in a non-sequence-specific manner and to tether plasmid DNA to liposomes. A role for the Min system in chromosome segregation has been proposed, whereby repeated, transient membrane-tethering events mediated by MinD could help prevent backward movements of the duplicated chromosomes once entropic forces weaken. However, the contribution of the other Min proteins to DNA binding has remained unclear. Here, we demonstrate that DNA binding is strongly enhanced when MinD and MinC form a complex, while MinE and FtsZ (at high concentrations) interfere with this binding. We reveal a critical role for the linker connecting MinCs N- and C-terminal domains in both DNA binding and inhibition of FtsZ polymerization. E. coli strains expressing MinC linker variants from the native locus, in combination with the alpha subunit of HU tagged with GFP, display chromosomes that appear more spread throughout the cell. This phenotype could reflect reduced compaction, chromosome segregation defects, or a combination of both. These findings suggest a previously unrecognized role for the MinC linker in DNA binding and provide new insights into a potential physiological role of MinCD-DNA bnding in chromosome organization and/or dynamics.

microbiology↗

bioRxiv2023

Int&in: a machine learning-based web server for split site identification in inteins

Inteins are proteins that excise themselves out of host proteins and ligate the flanking polypeptides in an auto-catalytic process called protein splicing. They are gaining momentum in synthetic biology for their ability to post-translationally modify proteins of interest. In nature, inteins are either contiguous or split, in which case the two intein fragments must first form a complex for the splicing to occur. So far, heuristic methods have been employed whenever a new split site in an intein had to be identified. To make the process of split site identification in inteins faster, easier and less costly, we developed Int&in, a web server that uses a gaussian Naive Bayes machine learning model to predict active and inactive split sites with high accuracy. The model was trained on a data set generated by us and validated using a large diverse data set from the literature, resulting in an accuracy of 0.76. Int&in will facilitate the engineering of novel split inteins for applications in biotechnology and synthetic biology.

synthetic biology↗

bioRxiv2020

C-terminal eYFP fusion impairs Escherichia coli MinE function

The Escherichia coli Min system plays an important role in the proper placement of the septum ring (Z-ring) at mid-cell during cell division. MinE forms a pole-to-pole spatial oscillator together with the membrane-bound ATPase MinD, which results in MinD having a concentration gradient with maxima at the poles and minimum at mid-cell. MinC, the direct inhibitor of the Z-ring initiator protein FtsZ, forms a complex with MinD at the membrane, thus mirroring MinD polar gradients. Therefore, MinC-mediated FtsZ inhibition occurs away from mid-cell. The existence of the oscillations was revealed by performing time-lapse microscopy with fluorescently-labeled Min proteins. These fusion proteins have been since then widely used to study properties of the Min system. Here we show that, despite permitting oscillations to occur in a range of protein concentrations, the enhanced yellow fluorescent protein (eYFP) C-terminally fused to MinE impairs its function. Combining in vivo, in vitro and in silico approaches, we demonstrate that the eYFP compromises MinE ability to displace MinC from MinD, to stimulate MinD ATPase activity and to directly bind to the membrane. Moreover, we reveal that MinE-eYFP is prone to aggregation. Taken together, our results indicate that this fusion is functionally impaired and should be used with caution in cell biological studies.

microbiology↗