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Significance In fast-growingEscherichia coli cells, RNA polymerase (RNAP) has been reported to form dense clusters, which were proposed to be active transcription centers for ribosomal RNA (rRNA) synthesis. Understanding how and why RNAP is spatially organized in bacterial cells could offer insights into the mechanism of transcription regulation in the native cellular environment. Using quantitative superresolution imaging coupled with genetic and biochemical analyses, we found that RNAP clusters were indeed active transcription centers engaged in rRNA synthesis under a rich media growth condition, but their formation was independent of rRNA transcription activity. Instead, the underlying nucleoid structure played a significant role in spatially organizing RNAP clusters. These results shed new light on the relationship between RNAP clusters and transcription activity.

Spatial organization of RNA polymerase and its relationship with transcription in Escherichia coli