DNA supercoiling and gene expression regulation: Mechanistic studies of a bacterial gene silencer and a 'boundary element'-like activity that modulates gene silencing activity

DNA supercoiling is known to play roles in transcriptional regulation. However, the molecular mechanism underlying the effect of DNA supercoiling on gene expression control remains largely unclear. The suppression of leu-500 mutation in Salmonella typhimurium topA mutant has been a paradigmatic phenomenon for demonstrating the importance of DNA supercoiling in the transcription initiation process. Toward studying the molecular mechanism that underlies the DNA supercoiling phenomenon, a sequential activation of genes in S. typhimurium ilvIH-leuO-leuABCD gene cluster was unraveled. Transcription-driven DNA supercoiling was found to play indispensable roles in the sequential gene activation. Transcription-driven DNA supercoiling appears to mediate through cis-elements found in the locus control regions (LCRs) of the gene cluster for exerting its effect in the expression regulation of genes in the gene cluster. A gene silencer and several LeuO binding sites were found in the LCRs. I have characterized a cis-spreading transcriptional repressive nucleoprotein structure mediated by the gene silencer and a "boundary element"-like activity mediated by the LeuO protein. A unique functional relationship between the two elements appears to be responsible for a sophisticated transcriptional repression-derepression process, which plays a crucial role in the control of expression of genes in the gene cluster. This finding is the molecular basis for future exploration of the effect of transcription-driven DNA supercoiling on control of gene expression.