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

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 116; no. 40; pp. 20115 - 20123
• Main Authors: Weng, Xiaoli, Bohrer, Christopher H., Bettridge, Kelsey, Lagda, Arvin Cesar, Cagliero, Cedric, Jin, Ding Jun, Xiao, Jie
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 01-10-2019
• Series: PNAS Plus
• Subjects: Bacillus subtilis; Bacteria; Biological Sciences; Cluster Analysis; Clusters; DNA-directed RNA polymerase; DNA-Directed RNA Polymerases - genetics; DNA-Directed RNA Polymerases - metabolism; E coli; Escherichia coli; Escherichia coli - genetics; Escherichia coli - metabolism; Gene Expression Regulation, Bacterial; Growth conditions; In Situ Hybridization, Fluorescence; Morphology; Physical Sciences; PNAS Plus; Ribonucleic acid; RNA; RNA polymerase; RNA, Ribosomal - genetics; RNA, Ribosomal, 16S - genetics; rRNA; Supercoiling; Synthesis; Transcription; Transcription Factors - genetics; Transcription, Genetic; transcription factories; transcription regulation; RNA polymerase; spatial organization; superresolution
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1903968116

Recent studies have shown that RNA polymerase (RNAP) is organized into distinct clusters in Escherichia coli and Bacillus subtilis cells. Spatially organized molecular components in prokaryotic systems imply compartmentalization without the use of membranes, which may offer insights into unique functions and regulations. It has been proposed that the formation of RNAP clusters is driven by active ribosomal RNA (rRNA) transcription and that RNAP clusters function as factories for highly efficient transcription. In this work, we examined these hypotheses by investigating the spatial organization and transcription activity of RNAP in E. coli cells using quantitative superresolution imaging coupled with genetic and biochemical assays. We observed that RNAP formed distinct clusters that were engaged in active rRNA synthesis under a rich medium growth condition. Surprisingly, a large fraction of RNAP clusters persisted in the absence of high rRNA transcription activities or when the housekeeping σ70 was sequestered, and was only significantly diminished when all RNA transcription was inhibited globally. In contrast, the cellular distribution of RNAP closely followed the morphology of the underlying nucleoid under all conditions tested irrespective of the corresponding transcription activity, and RNAP redistributed into dispersed, smaller clusters when the supercoiling state of the nucleoid was perturbed. These results suggest that RNAP was organized into active transcription centers under the rich medium growth condition; its spatial arrangement at the cellular level, however, was not dependent on rRNA synthesis activity and was likely organized by the underlying nucleoid.