A cis-spreading nucleoprotein filament is responsible for the gene silencing activity found in the promoter relay mechanism

Transcription-generated DNA supercoiling plays a decisive role in a promoter relay mechanism for the coordinated expression of genes in the Salmonella typhimurium ilvIH-leuO-leuABCD gene cluster. A similar mechanism also operates to control expression of the genes in the Escherichia coli ilvIH-leuO-leuABCD gene cluster. However, the mechanism underlying the DNA supercoiling effect remained elusive. A bacterial gene silencer AT8 was found to be important for the repression state of the leuO gene as part of the promoter relay mechanism. In this communication, we demonstrated that the gene silencer AT8 is a nucleation site for recruiting histone-like nucleoid structuring protein to form a cis-spreading nucleoprotein filament that is responsible for silencing of the leuO gene. With a DNA geometric similarity rather than a DNA sequence specificity, the E. coli gene silencer EAT6 was capable of replacing the histone-like nucleoid structuring protein nucleation function of the S. typhimurium gene silencer AT8 for the leuO gene silencing. The interchangeability between DNA geometrical elements for supporting the silencing activity in the region is consistent with a previous finding that a neighboring transcription activity determines the outcome of the gene silencing activity. The geometric requirement, which was revealed for this silencing activity, explains the decisive role of transcription-generated DNA supercoiling found in the promoter relay mechanism.