Insulation of ribosomal promoter activity by Fis, H-NS or a divergent promoter within the packed E. coli genome.

Abstract

Gene expression in bacterial cells is dependent on a genes position along the genome, mainly because of the effects of neighbouring genes expression, but also because of the local activity of nucleoid proteins, differing levels of DNA supercoiling and changes in gene copy number with growth rate and growth phase. This genome position dependence can be a source of specific regulation, however, in some cases it is necessary to have gene expression insulated from these local effects. Escherichia coli cells express ribosomal RNA from multiple operons found at different sites along the genome. The number of ribosomal operons varies in different strains and correlates with the maximal growth rate. rRNA promoters are under the regulation of Fis, H-NS, DNA supercoiling and ppGpp. These factors are known to result in growth phase and growth rate dependent regulation of gene expression. Here we show that the combined action of Fis and H-NS also provides insulation from the activity of both local and global regulatory factors. Furthermore, our results indicate that the presence of a divergently expressed gene can also act as an insulator revealing a DNA supercoiling gradient from the origin to the terminus. The organisation of ribosomal promoters therefore has been selected to allow for gene duplication independently of the influence of local genome organisation and neighbouring genes activity.