Spatial organization shapes the turnover of a bacterial transcriptome

Abstract

Spatial organization of the transcriptome has emerged as a powerful means for regulating the post-transcriptional fate of RNA in eukaryotes; however, whether prokaryotes use RNA spatial organization as a mechanism for post-transcriptional regulation remains unclear. Here we used super-resolution microscopy to image the E. coli transcriptome and observed a genome-wide spatial organization of RNA: mRNAs encoding inner-membrane proteins are enriched at the membrane, whereas mRNAs encoding outer-membrane, cytoplasmic and periplasmic proteins are distributed throughout the cytoplasm. Membrane enrichment is caused by co-translational insertion of signal peptides recognized by the signal-recognition particle. Time-resolved RNA-sequencing revealed that degradation rates of inner-membrane-protein mRNAs are on average greater that those of the other mRNAs and that this selective destabilization of inner-membrane-protein mRNAs is abolished by dissociating the RNA degradosome from the membrane. Together, these results demonstrate that the bacterial transcriptome is spatially organized and suggest that this organization shapes the post-transcriptional dynamics of mRNAs.DOI: http://dx.doi.org/10.7554/eLife.13065.001

Spatial organization and dynamics of RNase E and ribosomes inCaulobacter crescentus

“…It has been shown to be membraneassociated in E. coli and B. subtilis, [3][4][5][6] but deployed throughout the nucleoid in Caulobacter. 10 Previous studies of ribosome localization in E. coli 24,25 and B. subtilis 12 revealed enrichment at the cell poles, where they are excluded from the nucleoid, while similar studies in Caulobacter revealed no apparent separation of ribosomes and the nucleoid.…”

“…10 In sharp contrast to RNase E sequestration to the inner membrane in E. coli, 4,5 RNase E in Caulobacter was observed to cluster along the central axis of the cell and nucleoid ( Fig. 3a- clustering metric from the integral between the two curves ( Fig.…”

“…[3][4][5][6] One proposed rationale behind the observed membrane association is to physically separate transcription within the nucleoid from RNA degradation, thus providing an inherent time delay between transcript synthesis and the onset of transcript decay, avoiding a futile cycle. Caulobacter crescentus (Caulobacter) is an alpha-proteobacterium widely studied as a model system for asymmetric cell division.…”

RNA Localization in Bacteria

“…Similarly, FISH analysis revealed distinct, uneven patterns of localization and specific foci at one or both poles for the dinitrogenase reductase-encoding nifH transcripts of Klebsiella oxytoca and Azotobacter vinelandii with specific foci at one or both poles in K. oxytoca (69) . One intriguing hypothesis is that mRNAs can be targeted to the subcellular domains where their encoded protein products are required (cytoplasm, poles or inner-membrane) (65, 70, 71). For example, while the cat mRNA, encoding the cytoplasmic chloramphenicol acetyltransferase, was observed in a helix-like pattern in the cytoplasm of E. coli , the mRNA of lacY , encoding the membrane-bound lactose permease, was preferentially detected near the cytoplasmic membrane (65).…”

“…While most studies have mainly looked at localization of only a single or small set of mRNAs, recently Zhuang and co-workers investigated the spatial organization of mRNAs in E. coli on the transcriptome scale (70). They designed complex FISH probe sets to visualize defined sets of mRNAs, categorized by the subcellular localizations of their encoded proteins, allowing examination of about 27% of all E. coli mRNAs.…”