Segregation of protein aggregates in Escherichia coli

Abstract

Not long ago it was believed that symmetrically dividing bacteria didn't age, but fairly recently this belief has been challenged, as the development of microscopy techniques has allowed more detailed study of these organisms. The discovery of bacterial ageing has made it possible to study fundamental ageing related mechanisms in organisms where they can be observed on a molecular level with relative ease. As a result, the accumulation of misfolded proteins, corrupted end products of gene expression, has been identified to be the main ageing factor in Escherichia coli. This accumulation is also associated with many diseases in higher organisms, including humans. Studying the basic concepts related to ageing could thus potentially provide clues to develop methods of managing these diseases in the future, as well as improve our general understanding of ageing and it's evolutionary origin. The research this thesis is a part of takes a look at the effect of different types of stress on protein production and the mechanisms that cells use to cope with corrupted proteins. The main focus here is on the robustness of one of the mechanism the cells use to mitigate protein damage, which is the segregation, retention and eventual asymmetric inheritance of unwanted protein aggregates. The nucleoid, a denser region containing the genetic material of the cell, has been recently identified to have an instrumental role in this mechanism in Escherichia coli cells. Here we study the effects of stress, which alters the size of this region on the robustness of this mechanism. Some related results are also presented regarding the effects of stress on gene expression dynamics. The segregation and retention mechanisms are studied here using time lapse microscopy measurements to observe the relative movement of the nucleoids and unwanted protein aggregates within individual cells. In addition to presenting the results, this thesis focuses on the statistical and image analysis methods used during the project, as the majority of the work done for this thesis was done on this part. These methods are introduced in chapter 3 of the thesis. After that, we present the results which show that changes in the relative size of the nucleoid within the cell do cause significant changes in the spatial distribution and dynamics of the aggregates. Based on our observations, we conclude that even though the segregation and retention mechanisms are fairly robust to these changes, they are not completely immune. Additionally, we show that the functioning of these mechanisms seems to be optimized with moderate nucleoid sizes, whereas significant increases or decreases in nucleoid size lead to diminished functionality.