RNaseE and RNA Helicase B Play Central Roles in the Cytoskeletal Organization of the RNA Degradosome

Taghbalout, Aziz; Rothfield, Lawrence

doi:10.1074/jbc.m709118200

Cited by 48 publications

(58 citation statements)

References 35 publications

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“…3G). This pattern was reminiscent of many helical patterns present in bacterial cells (20,(22)(23)(24)(25)(26)(27)(28). Note, however, that these RNArelated patterns were more diffuse than most helical patterns revealed by protein labeling.…”

Section: Estimation Of Number Of Egfp Molecules Per Cell After Rna Inmentioning

confidence: 84%

“…These structures are independent of the MreB and MinD cytoskeletal structures and may play important roles in cell growth, division, and chromosome segregation. They may also serve to compartmentalize RNA processing and RNA degradation (27,28). It is tempting to speculate that the RNA network that we are revealing may be related to the same structures.…”

Section: Discussionmentioning

confidence: 98%

“…This finding raises many intriguing questions about RNA localization and processing in bacteria. Recent studies showed that RNase E and RNA helicase, two components of the bacterial degradosome, form helical filamentous structures that coil around the length of the cell (27,28). These structures are independent of the MreB and MinD cytoskeletal structures and may play important roles in cell growth, division, and chromosome segregation.…”

Section: Discussionmentioning

confidence: 99%

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Spatiotemporal patterns and transcription kinetics of induced RNA in single bacterial cells

Valencia-Burton

Shah

Sutin

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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Bacteria have a complex internal organization with specific localization of many proteins and DNA, which dynamically move during the cell cycle and in response to changing environmental stimuli. Much less is known, however, about the localization and movements of RNA molecules. By modifying our previous RNA labeling system, we monitor the expression and localization of a model RNA transcript in live Escherichia coli cells. Our results reveal that the target RNA is not evenly distributed within the cell and localizes laterally along the long cell axis, in a pattern suggesting the existence of ordered helical RNA structures reminiscent of known bacterial cytoskeletal cellular elements.espite their relatively small dimensions, bacterial cells show a remarkable, rich internal subcellular organization that has captured the interest of researchers over the past decade (1-4). Many cytoplasmic and membrane proteins, particularly those involved in cell division, DNA replication, and chromosome segregation, have specific subcellular localizations that can change quickly over time in response to cell cycle progression, motility, and environmental cues. This dynamic and organized behavior is also true for bacterial chromosomal DNA. The use of GFP fusions and in situ fluorescence hybridization (FISH) have shown that every chromosomal locus has a defined subcellular address and is replicated and segregated into the new cell as part of an active and directed process (4, 5). Bacterial plasmids, both low and high copy, also have specific cellular addresses and segregate in a fashion that is unique for a given plasmid (6-8).Little is known, however, about RNA dynamics in bacteria. With the advent of new methods to label RNA in live cells, the transcription kinetics, localization, and movement of RNA in the bacterium Escherichia coli has begun to be discerned only recently (9-13).To understand RNA dynamics in live cells better, it would be useful to develop RNA labeling methods that would allow direct visualization and real-time quantitation of RNAs with low background levels. We recently reported a system based on protein complementation that uses binding of a split and inactive protein complex to a short interacting sequence on a target RNA. The marker protein re-associates and becomes fluorescent only upon binding to RNA (13), which makes this approach more desirable than alternative techniques relying on expression of full-size fluorescent proteins. Briefly, the method consists of fusing the Nterminal fragment of EGFP to the N-terminal domain of an RNA-binding protein, the eukaryotic initiation factor 4A (eIF4A), via a polypeptide linker. Similarly, the C-terminal fragment of EGFP is fused to the C-terminal domain of eIF4A. The target RNA is tagged at the 3Ј end with an aptamer sequence known to bind eIF4A with high affinity (14) (Fig. 1A). Expression of the labeling components in E. coli cells generates a fluorescent signal only in the presence of the target RNA, caused by the reassociation of the two EGFP fragments and forma...

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Section: Estimation Of Number Of Egfp Molecules Per Cell After Rna Inmentioning

confidence: 84%

Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Spatiotemporal patterns and transcription kinetics of induced RNA in single bacterial cells

Valencia-Burton

Shah

Sutin

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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“…Using similar techniques, Shih et al then reported that MreB (and three other proteins) formed extended helices in Escherichia coli as well (27). Numerous publications have since claimed that MreB and various other proteins polymerize into extended helices that encircle diverse rod-shaped bacteria (5,8,15,22,30,31,36). Data supporting these claims include fluorescence microscopy of both cells harboring fluorescent protein fusions and wild-type cells probed with fluorescently labeled antibodies.…”

mentioning

confidence: 84%

The Helical MreB Cytoskeleton in Escherichia coli MC1000/pLE7 Is an Artifact of the N-Terminal Yellow Fluorescent Protein Tag

2012

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Based on fluorescence microscopy, the actin homolog MreB has been thought to form extended helices surrounding the cytoplasm of rod-shaped bacterial cells. The presence of these and other putative helices has come to dominate models of bacterial cell shape regulation, chromosome segregation, polarity, and motility. Here we use electron cryotomography to show that MreB does in fact form extended helices and filaments in Escherichia coli when yellow fluorescent protein (YFP) is fused to its N terminus but native (untagged) MreB expressed to the same levels does not. In contrast, mCherry fused to an internal loop (MreB-RFP SW ) does not induce helices. The helices are therefore an artifact of the placement of the fluorescent protein tag. YFP-MreB helices were also clearly distinguishable from the punctate, "patchy" localization patterns of MreB-RFP SW , even by standard light microscopy. The many interpretations in the literature of such punctate patterns as helices should therefore be reconsidered.

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“…RNase E and other degradosome components are associated with the inner surface of the cell (110), interact with the bacterial cytoskeleton (111,112) and the inner membrane (113). RNase Y has a transmembrane domain at its N-terminus and has been localized at the membrane in vivo (81).…”

Section: Multiprotein Complexes and Cellular Localizationmentioning

confidence: 99%

mRNA degradation and maturation in prokaryotes: the global players

Laalami

Putzer

2011

BioMolecular Concepts

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The degradation of messenger RNA is of universal importance for controlling gene expression. It directly affects protein synthesis by modulating the amount of mRNA available for translation. Regulation of mRNA decay provides an efficient means to produce just the proteins needed and to rapidly alter patterns of protein synthesis. In bacteria, the half-lives of individual mRNAs can differ by as much as two orders of magnitude, ranging from seconds to an hour. Most of what we know today about the diverse mechanisms of mRNA decay and maturation in prokaryotes comes from studies of the two model organisms Escherichia coli and Bacillus subtilis. Their evolutionary distance provided a large picture of potential pathways and enzymes involved in mRNA turnover. Among them are three ribonucleases, two of which have been discovered only recently, which have a truly general role in the initiating events of mRNA degradation: RNase E, RNase J and RNase Y. Their enzymatic characteristics probably determine the strategies of mRNA metabolism in the organism in which they are present. These ribonucleases are coded, alone or in various combinations, in all prokaryotic genomes, thus reflecting how mRNA turnover has been adapted to different ecological niches throughout evolution.

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RNaseE and RNA Helicase B Play Central Roles in the Cytoskeletal Organization of the RNA Degradosome

Cited by 48 publications

References 35 publications

Spatiotemporal patterns and transcription kinetics of induced RNA in single bacterial cells

Spatiotemporal patterns and transcription kinetics of induced RNA in single bacterial cells

The Helical MreB Cytoskeleton in Escherichia coli MC1000/pLE7 Is an Artifact of the N-Terminal Yellow Fluorescent Protein Tag

mRNA degradation and maturation in prokaryotes: the global players

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