Michael Berger

• The process of transcription is intimately linked to the overall structure and superhelicity of DNA in the context of bacterial nucleoid. The structure of the nucleoid in Escherichia coli depends in part on the composition of nucleoid-associated proteins, which is changing with growth phase. In order to understand the influence of the nucleoid structure on gene expression, studies of genomic transcript profiles of mutants lacking nucleoid proteins have to be complemented by approaches revealing the mechanistic basis of nucleoid-shaping processes. In this study, the localization of RNA polymerase in several mutants of nucleoid-associated proteins was investigated and found to be dependent on the major nucleoid-associated protein HU. The HU mutant showed a spatial defect in coordinating gene expression. More specifically, genes located within a large region comprising OriC and bordered by the last ribosomal RNA genes on both arms of the chromosome were expressed stronger than in wild type. This defect is most easily explained by disturbances of effective DNA supercoiling - a variable modulating promoter activities - in the mutant lacking HU. This work proposes a holistic model explaining the HU-dependent spatial localization of RNAP and coordination of gene expression by means of gross DNA structures formed upon cooperative binding of HU, as opposed to the classical perspective emphasizing the rearrangements of interactions within a "digital" regulatory network. Defects in the transcriptional response of HU mutant to stress are easily accommodated in our general model. Moreover, this model proposes a novel autoregulatory mechanism implicating a self-organizing nucleoid structure in coordinating genomic transcription. By assuming the role of structural autoregulation of the entire bacterial genome in coordination of global transcription, this model may also provide insights into the mechanistic basis of cell differentiation in multicellular organisms.