RNA polymerase redistribution and increased gene dosage support growth in E. coli strains with a minimal number of ribosomal RNA operons

Abstract

ABSTRACTBacterial transcription by RNA polymerase (RNAP) is spatially organised. RNAPs transcribing highly expressed genes locate in the nucleoid periphery, and form clusters in rich media, with several studies linking RNAP clustering and transcription of ribosomal RNA (rrn). However, the nature of RNAP clusters and their association with rrn transcription remains unclear. Here we address these questions by using single-molecule tracking to monitor the subcellular distribution of mobile and immobile RNAP in strains with a heavily reduced number of chromosomal rrn operons (Δrrn strains). Strikingly, we find that the fraction of chromosome-associated RNAP (which is mainly engaged in transcription) is robust to deleting 5 or 6 of the 7 chromosomal rrn operons. Spatial analysis in Δrrn strains showed substantial RNAP redistribution during moderate growth, with clustering increasing at the cell end-caps, where the remaining rrn operons reside. These results support a model where RNAPs in Δrrn strains relocate to copies of the remaining rrn operons. We also show that Δrrn strains experience increased rrn gene dosage in rich media, minimising growth defects due to rrn deletions. Our study further links RNAP clusters and rrn transcription, and offers insight on how bacteria maintain growth in the presence of only 1-2 rrn operons.