Chapter 24 : RNA Localization in Bacteria

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Spatial and temporal localization of macromolecules, including RNAs, reflects the compartmentalization of living cells and plays important roles in gene expression and regulation. In eukaryotic cells, physical separation between the transcription and translation machineries in the nucleus and cytoplasm, respectively, naturally results in the synthesis, processing, and translation of mRNA to be spatially disconnected. Both mRNA localization and localized translation can be important regulatory mechanisms underlying embryonic patterning, asymmetric cell division, epithelial polarity, cell migration, and neuronal morphogenesis ( ). RNAs can be transported in the eukaryotic cell in several ways, such as (i) vectorial movement of mRNA by direct coupling to motor proteins, (ii) transport of mRNA by hitchhiking on another cargo, (iii) random transport of mRNA-motor complexes and local enrichment of mRNAs at target sites, or (iv) diffusion and motor-driven cytoplasmic flows with subsequent localized anchorage of the mRNA ( ). Moreover, localized translation induction by phosphorylation and activation of translation initiation factors and their regulators in response to localized signals have been reported to impact gene regulation in eukaryotes ( ).

Citation: Fei J, Sharma C. 2019. RNA Localization in Bacteria, p 421-439. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0024-2018
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Figure 1

Methods to visualize bacterial RNAs. (A) smFISH and its application to imaging SgrS sRNA and its target mRNA . Images from diffraction-limited and super-resolution microscopes are shown for comparison. Adapted from reference . (B) Illustration of the FP reporter approaches with a FP-RBP and a corresponding RNA motif, using the MS2 system as an example, and its application to track mRNAs at the single-molecule level in live cells. Image adapted from reference . The scale bar in the image represents 1 μm. (C) The Spinach aptamer and its application to image mRNAs in live cells, in which a Spinach aptamer is fused to the RNA and with fluorescence detection upon addition of the organic ligand 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI). Image adapted from reference (licensed under a Creative Commons Attribution 4.0 International License [http://creativecommons.org/licenses/by/4.0/]).

Citation: Fei J, Sharma C. 2019. RNA Localization in Bacteria, p 421-439. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0024-2018
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Image of Figure 2
Figure 2

Diverse patterns of subcellular mRNA localization in bacteria. Schematic drawings of diverse mRNA localization patterns commonly reported in different bacteria. RNA molecules are shown in green, and the nucleoid in gray. (A) Distribution throughout the cytoplasm. (B) Localization at the site of transcription in the nucleoid. (C) Helical localization. (D) Enrichment at the inner membrane. (E) Localization at the cell poles and (F) septum.

Citation: Fei J, Sharma C. 2019. RNA Localization in Bacteria, p 421-439. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0024-2018
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Figure 3

Emerging mRNA imaging methods in eukaryotic systems. (A) In the HCR, binding of the primary probe initiates the alternating binding of two HCR probes, thereby amplifying the signal. (B) In the PCR, a cDNA is first generated from the RNA of interest. Padlock probes are hybridized to the cDNA and ligated to be circular DNAs. Fluorophore-labeled secondary probes are then hybridized to the products generated from rolling circle amplification of these circular DNA templates. (C) Schematic representation of the TRICK reporter construct. (D) Schematic representation of the SunTag construct. (E) Schematic representation of the TREAT reporter construct.

Citation: Fei J, Sharma C. 2019. RNA Localization in Bacteria, p 421-439. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0024-2018
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