Spatiotemporal organization of the E. coli transcriptome: novel insights into regulation

RNA localization in eukaryotes is emerging as a mechanism to regulate transcripts fate. In contrast, until recently bacterial RNAs were not assumed to have distinct localization patterns. We previously demonstrated that E. coli mRNAs may localize to where their products localize in a translation-independent manner*. These findings challenged the extent of transcription-translation coupling*, but the scope of RNA localization in bacteria remained unknown.

To monitor the localization of all mRNAs and sRNAs in E. coli, we developed a protocol, termed Rloc-seq, which assigns sub-cellular localization data to each transcript between the membrane, cytoplasm and poles*. Our results reveal asymmetric distribution of RNAs on a transcriptome-wide scale, which significantly correlates with proteome localization. Notably, we found that translation-independent RNA localization is prevalent in bacteria.

The poles are emerging as regulation hubs, enriched with stress-related mRNAs and sRNAs, the latter becoming further enriched upon stress, depending on their chaperone Hfq, thus providing a spatiotemporal-based mechanism for sRNA-mediated regulation.

The dramatic polar enrichment with most sRNAs upon stress supports a polygenic plan for sRNA activity, i.e., the sRNAs assemble to orchestrate cell adaptation to stresses. This plan explains the subtle effect of deleting single sRNA genes. Our preliminary results support this model and suggest that sRNA exert their effects cooperatively.

^*Nevo-Dinur, Nussbaum-Shochat, Ben-Yehuda and Amster-Choder. Translation-independent localization of mRNA in E. coli. Science (2011).

^*Adler. 2011: Signaling breakthroughs of the year. Science Signaling (2012)

^*Kannaiah, Livny and Amster-Choder. Spatiotemporal organization of the E. coli transcriptome: Translation-independence and engagement in regulation. Molecular Cell (2019)