Every organisms in the tree of life faces the same challenge: the length of its DNA exceeds the volume of the cell it needs to fit in. Several strategies have evolved to solve this problem, one of... Show moreEvery organisms in the tree of life faces the same challenge: the length of its DNA exceeds the volume of the cell it needs to fit in. Several strategies have evolved to solve this problem, one of them being the expression of proteins that bind and organize the DNA. The best-known examples are the histone proteins of eukaryotes, but many other proteins have the same function. In this thesis I focused on bacterial and archaeal DNA organizing proteins, especially the ones that can bridge and/or wrap DNA. In bacteria, H-NS-like proteins have important functional and structural properties. The protein Rok from Bacillus subtilis is similar to H-NS in its DNA bridging behavior, but responds differently to environmental conditions. We propose that this is due to the different charge distribution. Archaea express histone proteins, like eukaryotes, but a more primitive version, reflective of their position in the tree of life. We investigated model archaeal histones and the effect of DNA sequence on hypernucleosome formation. Also, we looked at several other archaeal histones with different tails. A tail can have an effect on the DNA binding mode of the histone, switching from DNA wrapping to DNA bridging. Show less
The genetic information of all living organisms is contained in their DNA. Cells modify the degree of DNA compaction by epigenetics, which largely determines what genes are read out and which genes... Show moreThe genetic information of all living organisms is contained in their DNA. Cells modify the degree of DNA compaction by epigenetics, which largely determines what genes are read out and which genes are transcriptionally silent. Despite decades of research into this mechanism, there is no consensus on how cells realize the various degrees of DNA compaction in vivo. Eukaryotes, such as humans, compact their DNA into higher-order structures called compact chromatin fibers. We characterize these fibers through a combination of single-molecule force spectroscopy techniques like magnetic tweezers, and rigid base pair Monte Carlo simulations. We show that, for instance, the length and sequence of the linker DNA, the DNA between adjacent nucleosomes, control the mechanical properties of chromatin fibers. Our measurements suggest the formation of more than one higher-order fiber structure. A deeper understanding of the chromatin fiber and its compaction mechanism is important because the dysfunction of such regulation results in various medical conditions such as the epigenetic disorder type 1 diabetes, fragile X syndrome, or various cancers. Show less