RNA Localization in Bacteria

Abstract

Diverse mechanisms and functions of post-transcriptional regulation by small regulatory RNAs (sRNAs) and RNA binding proteins (RBPs) have been described in bacteria. In contrast, little is known about the spatial organization of RNAs in bacterial cells. In eukaryotes, subcellular localization and transport of RNAs play important roles in diverse physiological processes, such as embryonic patterning, asymmetric cell division, epithelial polarity, and neuronal plasticity. It is now clear that bacterial RNAs also can accumulate at distinct sites in the cell. However, due the small size of bacterial cells, localized RNA and translation are more challenging to study in bacterial cells, and the underlying molecular mechanisms of transcript localization are less understood. Here we review the emerging examples of RNAs localized to specific subcellular locations in bacteria, with indications that subcellular localization of transcripts might be important for regulatory processes. Diverse mechanisms for bacterial RNA localization have been suggested, including close association to their genomic site of transcription, or to the localizations of their protein products in translation-dependent or independent processes. We also provide an overview of the state-of-the-art of technologies to visualize and track bacterial RNAs, ranging from hybridization-based approaches in fixed cells to in vivo imaging approaches using fluorescent protein reporters and/or RNA aptamers in single living bacterial cells. We conclude with a discussion of open questions in the field and ongoing technological developments regarding RNA imaging in eukaryotic systems that might likewise provide novel insights into RNA localization in bacteria.

Kinetic model of small RNA-mediated regulation suggests that a small RNA can regulate co-transcriptionally

“…In order to co-transcriptionally regulate chromosomally encoded targets, sRNAs should be able to diffuse into the nucleoid region, which normally has a higher diffusion barrier. A previous report demonstrated that sRNAs have unbiased distribution between the nucleoid and cytoplasm using a few plasmid-encoded sRNAs as examples (69,70). Here, using single-molecule localization microscopy (SMLM), we confirmed the unbiased localization for these two sRNAs under our experimental conditions (Figure 7).…”

Formation of synthetic RNA protein granules using engineered phage-coat-protein -RNA complexes

“…Subsequently, the brightest spots (top 10%) in the field of view were tracked using the algorithm developed by Sbalazarini and Koumoutsakos (Sbalzarini and Koumoutsakos, 2005). A typical field of view usually contained dozens of cells, a portion of which were not fluorescent while others presented distinct bright speckles, localized at the cell poles as expected from literature (Fei and Sharma, 2018).…”

mRNA localization is linked to translation regulation in theCaenorhabditis elegansgerm lineage

“…Diverse examples of transcript-specific mRNA localization have been described across the tree of life ranging from bacteria (Fei and Sharma, 2018) to humans (Khalil et al, 2018). Although early discoveries of localized mRNAs were thought to represent exceptional cases, recent advances in mRNA proximity labeling suggest that mRNA localization may be more widespread than previously thought (Fazal et al, 2019;Taliaferro, 2019).…”