Controlling chromosome structure in starved bacteria

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DNA can be envisaged as a long piece of string and, just like string, if not carefully wound, DNA becomes a tangled mess. This presents a problem for living organisms because they have to package their string of DNA within the confines of a small compartment (the cell). Cells have evolved numerous mechanisms to package DNA and, for more complicated organisms (for example humans and plants) we have a reasonably good understanding of how these mechanisms work. However, our understanding of chromosome folding in bacteria (such as the familiar organisms E. coli and Salmonella) is less well developed. In our work we propose to identify mechanisms used by bacteria to organise their DNA. In particular we will pay attention to DNA organisation in starved bacteria. This is important because, in starved bacteria, the DNA string is packaged much more tightly than normal. It is believed that this is a protection mechanism to ensure that DNA is not damaged in the harsh environments bacteria may encounter when not growing in optimal conditions. For example, E. coli transferred to a chopping board from contaminated meat would employ such protection mechanisms until it encountered a more favourable environment (i.e. the gut of you or I). Our study will focus on a protein called Curved DNA Binding Protein A (CbpA) that binds to the DNA and is produced by E. coli cells only when they are starved. Our goals are to determine, exactly how CbpA structures DNA, which parts of the DNA are associated with CbpA, and how CbpA activity is regulated. Because CbpA is also produced by bacteria related to E. coli, such as Salmonella, our findings should also be applicable to these organisms.