RNA localization in prokaryotes: Where, when, how, and why

Abstract

Only recently has it been recognized that the transcriptome of bacteria and archaea can be spatiotemporally regulated. All types of prokaryotic transcripts—rRNAs, tRNAs, mRNAs, and regulatory RNAs—may acquire specific localization and these patterns can be temporally regulated. In some cases bacterial RNAs reside in the vicinity of the transcription site, but in many others, transcripts show distinct localizations to the cytoplasm, the inner membrane, or the pole of rod‐shaped species. This localization, which often overlaps with that of the encoded proteins, can be achieved either in a translation‐dependent or translation‐independent fashion. The latter implies that RNAs carry sequence‐level features that determine their final localization with the aid of RNA‐targeting factors. Localization of transcripts regulates their posttranscriptional fate by affecting their degradation and processing, translation efficiency, sRNA‐mediated regulation, and/or propensity to undergo RNA modifications. By facilitating complex assembly and liquid–liquid phase separation, RNA localization is not only a consequence but also a driver of subcellular spatiotemporal complexity. We foresee that in the coming years the study of RNA localization in prokaryotes will produce important novel insights regarding the fundamental understanding of membrane‐less subcellular organization and lead to practical outputs with biotechnological and therapeutic implications. This article is categorized under: RNA Export and Localization > RNA Localization Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Protein‐RNA Interactions: Functional Implications

Wisdom of the crowds: A suggested polygenic plan for small-RNA-mediated regulation in bacteria

“…In recent years it has become apparent that bacteria have adopted complex mechanisms for specific localization of macromolecules ( Irastortza-Olaziregi and Amster-Choder, 2020 ; Rudner and Losick, 2010 ). Notably, enrichment of sRNAs before and, significantly more, after stress is confined to the cell poles ( Kannaiah et al., 2019 ).…”

Liquid–Liquid Phase Separation by Intrinsically Disordered Protein Regions of Viruses: Roles in Viral Life Cycle and Control of Virus–Host Interactions

“…In Escherichia coli, clusters of RNA polymerase (RNAP) are formed via LLPS, as cells enter the log phase in nutrient-rich media, and the transcription antitermination factor NusA forms droplets in vitro and in vivo, suggesting that this protein might nucleate formation of RNAP clusters [231]. It was also pointed out that all types of prokaryotic transcripts, such as mRNAs, rRNAs, tRNAs, and regulatory RNAs, may show distinct localizations within the cytoplasm, or the inner membrane, or the pole of rod-shaped species, with such subcellular spatiotemporal complexity and specific compartmentalization being driven by LLPS mediated by RNA-binding proteins [232].…”

In vivotargets ofSalmonellaFinO include a FinP-like small RNA controlling copy number of a cohabitating plasmid

“…Intracellular localization might also play a role, as there is increasing evidence for spatial control of gene expression in bacteria ( 66 , 67 ). For example, will ProQ expressed from plasmid pSLT show the same target profile as when made from its native chromosomal gene?…”