Modelling the Segregation Mechanism of low copy number Plasmid pB171

Often low copy number plasmids in bacterial cells exhibit active mechanisms to ensure stable inheritance. In this master thesis we investigate several models that aim to explain the equidistant positioning of pB171 plasmids in E. coli. In this system a walker type ATPase, ParA, forms filamentous structures on the nucleoid. Plasmids with attached ParB, a DNA binding protein, follow the retractive movement of ParA. We show that a polymer pulling model in which the plasmid detachment rate depends critically on the plasmid bound ParB levels can generate partitioning. Furthermore a recently proposed biased diffusion model in which the plasmid diffusion is influenced by the dynamic ParA concentration can direct motion towards mid cell. However the necessity of a high plasmid diffusion constant renders it unlikely to be the actual mechanism used by bacteria. A slight variation of this idea where diffusing oligomers pull on plasmids encounters the same problems as a biased diffusion model....Show moreOften low copy number plasmids in bacterial cells exhibit active mechanisms to ensure stable inheritance. In this master thesis we investigate several models that aim to explain the equidistant positioning of pB171 plasmids in E. coli. In this system a walker type ATPase, ParA, forms filamentous structures on the nucleoid. Plasmids with attached ParB, a DNA binding protein, follow the retractive movement of ParA. We show that a polymer pulling model in which the plasmid detachment rate depends critically on the plasmid bound ParB levels can generate partitioning. Furthermore a recently proposed biased diffusion model in which the plasmid diffusion is influenced by the dynamic ParA concentration can direct motion towards mid cell. However the necessity of a high plasmid diffusion constant renders it unlikely to be the actual mechanism used by bacteria. A slight variation of this idea where diffusing oligomers pull on plasmids encounters the same problems as a biased diffusion model. The influence of polymer drag which depends on the length of the filament can be beneficial though it seems unlikely to be the sole mechanism to partition plasmids. Finally, in our favoured model we show that ParA polymers can position plasmids equidistantly with the assumption that ParA subunits bind along the filament and slide to the tip end, thereby influencing the polymerization rate critically.Show less

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Modelling the Segregation Mechanism of low copy number Plasmid pB171