Spatial organization and dynamics of RNase E and ribosomes in<i>Caulobacter crescentus</i>

Bayas, Camille; Wang, Jiarui; Lee, Marissa K.; Schrader, Jared M.; Shapiro, Lucy; Moerner, W. E.

doi:10.1073/pnas.1721648115

Cited by 72 publications

(69 citation statements)

References 55 publications

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“…For example, inner-membrane bound ribosomes in E. coli that are actively engaged in translation (89) might play a role in specific translation of inner membrane proteins. In C. crescentus and another alpha-proteobacterium Sinorhizobium meliloti , ribosomes are detected throughout the cell including the nucleoid region (64, 90), which is different from the ribosome/nucleoid segregation observed in E. coli and B. subtilis (82, 84) . Hereby, it was suggested that, mRNA-bound ribosomal subunits show limited mobility in C. crescentus due to the observed limited dispersion of their mRNA targets from their site of transcription (64, 90, 91).…”

Section: Localized Mrna Translation and Degradationmentioning

confidence: 76%

“…Hereby, the localization of RNase E clusters was found to correlate with two subcellular chromosomal positions that encode the highly expressed rRNA genes, indicating that RNase E mediated rRNA processing occurs at the site of rRNA synthesis (90). Although mediated by apparently different mechanisms compared to E. coli , the association of RNase E with DNA in C. crescentus also indicates that there is spatially organized mRNA decay in this organism.…”

Section: Localized Mrna Translation and Degradationmentioning

confidence: 90%

“…Interestingly, RNase E shows a patchy localization pattern in C. crescentus and the clustered localization of this enzyme is determined by the location of DNA, independent of its mRNA substrates (64, 90). Hereby, the localization of RNase E clusters was found to correlate with two subcellular chromosomal positions that encode the highly expressed rRNA genes, indicating that RNase E mediated rRNA processing occurs at the site of rRNA synthesis (90).…”

Section: Localized Mrna Translation and Degradationmentioning

confidence: 99%

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RNA Localization in Bacteria

Fei

Sharma

2018

Microbiol Spectr

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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.

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Section: Localized Mrna Translation and Degradationmentioning

confidence: 76%

Section: Localized Mrna Translation and Degradationmentioning

confidence: 90%

Section: Localized Mrna Translation and Degradationmentioning

confidence: 99%

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RNA Localization in Bacteria

Fei

Sharma

2018

Microbiol Spectr

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“…It has been demonstrated that ExM is compatible with conventional antibodies [21,25,34] and RNA fluorescence in situ hybridization [20], therefore μExM is readily adaptable to image nanometer-scale ultrastructures in bacterial cells that are under the diffraction limit of optical imaging. Subcellular organization in bacterial cells is a field of active discovery [35], but has been so far accessible only through specialized super-resolution equipment [22,36,37]. μExM should open up new applications and provide technical convenience in this research area.…”

Section: Discussionmentioning

confidence: 99%

Mechanically Resolved Imaging of Bacteria using Expansion Microscopy

Lim

Khariton

Lane

et al. 2019

Preprint

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18Imaging dense and diverse microbial communities has broad applications in basic microbiology 19 and medicine, but remains a grand challenge due to the fact that many species adopt similar 20 morphologies. While prior studies have relied on techniques involving spectral labeling, we have 21 developed an expansion microscopy method (µExM) in which cells are physically expanded 22 prior imaging and their expansion patterns depend on the structural and mechanical properties of 23 their cell walls, which vary across species and conditions. We use this phenomenon as a 24 quantitative and sensitive phenotypic imaging contrast orthogonal to spectral separation in order 25 to resolve bacterial cells of different species or in distinct physiological states. Focusing on host- 26 microbe interactions that are difficult to quantify through fluorescence alone, we demonstrate the 27 ability of µExM to distinguish species within a dense community through in vivo imaging of a 28 model gut microbiota, and to sensitively detect cell-envelope damage caused by antibiotics or 29 previously unrecognized cell-to-cell phenotypic heterogeneity among pathogenic bacteria as they 30 infect macrophages. 32Imaging of heterogeneous bacterial populations has broad applications in understanding the 33 complex microbiota that exist on and within our bodies, as well as complex host-microbial 34 interfaces, yet remains a significant challenge due to the lack of suitable tools for distinguishing 35 species and identifying altered physiological states [1][2][3]. Analyses to date have mostly relied on 36 spectral separation using fluorescence in situ hybridization (FISH) with probes designed to target 37 16S RNA sequences specific to certain taxa [4], or genetically engineered microbes that express 38 distinct fluorescent proteins [5]. However, these methods are generally insensitive to 39 physiological changes in bacterial cells that are often modulated by host environments and 40 believed to be critical for the growth and spatial organizations of microbes [6,7]. 42The bacterial cell wall is a macromolecule responsible for shape determination in virtually all 43 bacteria. Although little is known about the molecular architecture of the cell wall in most non-44 model organisms, its dimensions can vary widely, with the wall typically thick (tens of 45 nanometers [8,9]) in Gram-positive species and thin (~2-4 nm) in Gram-negative species [10], 46 and their rigidity can vary across ~10-100 MPa for Young's modulus [11,12]. The cell wall also 47 has various biochemical compositions [13] and exhibit distinct spatial patterns of cross-linking 48 density [14], molecular organization [15,16], thickness [8,9], and stiffness [11,12], all of which 49 depend on species and cell physiology. Thus, cell wall mechanics can potentially provide a 50 contrast that is orthogonal to spectral separation in distinguishing species and even cellular 51 physiological states. However, while cell-wall structure and mechanics have been measured by 52 e...

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“…Over the last decade there has been an explosion of research demonstrating the importance of selfassembling, liquid phase separated domains in both eukaryotic cells [1][2][3][4][5][6][7][8] and bacteria [9,10]. These droplets of RNA and protein, commonly referred to as 'membraneless organelles,' take advantage of liquid-liquid phase separation to achieve intracellular compartmentalization while enabling rapid exchange of their contents with the surroundings.…”

Section: Introductionmentioning

confidence: 99%

Phase separation: Bridging polymer physics and biology

Perry

2019

Current Opinion in Colloid & Interface Science

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Significant parallels exist between the phase separation behavior of polymers in solution and the types of biomolecular condensates, or 'membraneless organelles,' that are of increasing interest in living systems. Liquid-liquid phase separation allows for compartmentalization and the sequestration of materials, and can be harnessed as a sensitive strategy for responding to small changes in the environment. Here, I review many of the parallels and synergies between ongoing efforts to study and take advantage of phase separation in living vs. synthetic materials.

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Spatial organization and dynamics of RNase E and ribosomes inCaulobacter crescentus

Cited by 72 publications

References 55 publications

RNA Localization in Bacteria

RNA Localization in Bacteria

Mechanically Resolved Imaging of Bacteria using Expansion Microscopy

Phase separation: Bridging polymer physics and biology

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