COIL-seq: Dissecting Cyanobacterial Chromosome Dynamics

• Applicants: Professorin Dr. Ilka Maria Axmann; Professor Dr. Peter Florian Stadler
• Subject Area: Bioinformatics and Theoretical Biology ; Metabolism, Biochemistry and Genetics of Microorganisms ; Structural Biology ; Cell Biology
• Term: from 2015 to 2019
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 282947395

There is mounting evidence that changes in nucleoid structure (the bacterial chromosome) are intimately related to global changes in gene expression programs and underlie a homeostatic feedback system of growth control in response to nutrient supply. Unlike eukaryotic and archaeal chromatin bacterial DNA is not packaged into nucleosomes but organized by active negative supercoiling by ATP-dependent gyrase, a major target of antibiotics, and nucleoid-associated proteins (NAP). Among known NAP only the HU protein is conserved in most if not all bacterial genomes. Bacterial DNA structure is thus organized fundamentally different but the data is very scarce, lacking far behind the myriad of experimental and theoretical analyses of eukaryotic nucleosome structure and dynamics. Our approach to change this is conceptually and methodologically highly similar to a very recent study by Teves & Henikoff (Nat Struct Mol Biol 2014) on the effects of transcription-induced torsional strain on nucleosomes in Drosophila; but here applied to gauge bacterial genome dynamics instead.Recently, strong evidence has accumulated that this cell-wide homeostatic feedback system of DNA supercoiling is capable of autonomous oscillatory behaviour in cyanobacteria and forms an integral part of the cyanobacterial circadian clock. Some polyploid cyanobacterial species, where DNA replication is coupled to growth but uncoupled from cell division, feature an unusually pronounced ~11.5 bp sequence signature of DNA structure. Both of these observations make cyanobacteria ideal candidates to investigate relations between bacterial DNA sequence and structure in a dynamic natural context (diurnal transcription and replication). We therefore propose to comparatively investigate the chromosomal dynamics in two cyanobacterial species: Synechocystis sp. PCC 6803, polyploid with a pronounced ~11.5 bp signature, and multiple copies of the circadian clock proteins vs. another species with exactly opposite properties, the marine Prochlorococcus MED4.We plan to map the diurnal dynamics of both, the local torsional strain and binding of the HU protein by deep sequencing. The main questions we want to answer are: What is the relation of torsional strain (negative and positive supercoiling) to HU binding? Is either of the two related in the pronounced ~11.5 bp signature in the polyploid species? Can we relate local dynamics of DNA torsion to supercoiling-dependent circadian gene regulation?

• DFG Programme: Research Grants