Molecular recognition of RhlB and RNase D in the Caulobacter crescentus RNA degradosome

Voss, Jarrod E.; Luisi, Ben F.; Hardwick, Steven W.

doi:10.1093/nar/gku1134

Cited by 34 publications

(32 citation statements)

References 31 publications

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“…RhlB was shown to bind to the S1 and sensor domain at the amino-terminal domain of C. crescentus RNase E (40). Our results showed that RhlB is not displaced from the degradosome by the presence of RhlE, and the absence of RhlB does not increase the amounts of RhlE associated with the assembly (Fig.…”

Section: Discussionmentioning

confidence: 99%

Association of the Cold Shock DEAD-Box RNA Helicase RhlE to the RNA Degradosome in Caulobacter crescentus

et al. 2017

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In diverse bacterial lineages, multienzyme assemblies have evolved that are central elements of RNA metabolism and RNA-mediated regulation. The aquatic Gram-negative bacterium Caulobacter crescentus, which has been a model system for studying the bacterial cell cycle, has an RNA degradosome assembly that is formed by the endoribonuclease RNase E and includes the DEAD-box RNA helicase RhlB. Immunoprecipitations of extracts from cells expressing an epitope-tagged RNase E reveal that RhlE, another member of the DEAD-box helicase family, associates with the degradosome at temperatures below those optimum for growth. Phenotype analyses of rhlE, rhlB, and rhlE rhlB mutant strains show that RhlE is important for cell fitness at low temperature and its role may not be substituted by RhlB. Transcriptional and translational fusions of rhlE to the lacZ reporter gene and immunoblot analysis of an epitope-tagged RhlE indicate that its expression is induced upon temperature decrease, mainly through posttranscriptional regulation. RNase E pulldown assays show that other proteins, including the transcription termination factor Rho, a second DEAD-box RNA helicase, and ribosomal protein S1, also associate with the degradosome at low temperature. The results suggest that the RNA degradosome assembly can be remodeled with environmental change to alter its repertoire of helicases and other accessory proteins.IMPORTANCE DEAD-box RNA helicases are often present in the RNA degradosome complex, helping unwind secondary structures to facilitate degradation. Caulobacter crescentus is an interesting organism to investigate degradosome remodeling with change in temperature, because it thrives in freshwater bodies and withstands low temperature. In this study, we show that at low temperature, the cold-induced DEAD-box RNA helicase RhlE is recruited to the RNA degradosome, along with other helicases and the Rho protein. RhlE is essential for bacterial fitness at low temperature, and its function may not be complemented by RhlB, although RhlE is able to complement for rhlB loss. These results suggest that RhlE has a specific role in the degradosome at low temperature, potentially improving adaptation to this condition.

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Section: Discussionmentioning

confidence: 99%

Association of the Cold Shock DEAD-Box RNA Helicase RhlE to the RNA Degradosome in Caulobacter crescentus

et al. 2017

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“…Other components include the exoribonuclease polynucleotide phosphorylase, a DEAD-box RNA helicase RhlB, the Krebs cycle enzyme aconitase, and the exoribonuclease RNase D. 2,17 To study the motional dynamics of RNase E, we performed 3D SPT in live Caulobacter cells using a strain…”

Section: Rnase Ementioning

confidence: 99%

Spatial organization and dynamics of RNase E and ribosomes inCaulobacter crescentus

Bayas

Wang

Lee

et al. 2017

Preprint

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We report the dynamic spatial organization of Caulobacter crescentus RNase E (RNA degradosome) and ribosomal protein L1 (ribosome) using 3D single particle tracking and super-resolution microscopy. RNase E formed clusters along the central axis of the cell, while weak clusters of ribosomal protein L1 were deployed throughout the cytoplasm. These results contrast with RNase E and ribosome distribution in E. coli, where RNase E colocalizes with the cytoplasmic membrane and ribosomes accumulate in polar nucleoid-free zones. For both RNase E and ribosomes in Caulobacter, we observed a decrease in confinement and clustering upon transcription inhibition and subsequent depletion of nascent RNA, suggesting that RNA substrate availability for processing, degradation, and translation facilitates confinement and clustering. Moreover, RNase E cluster positions correlate with the subcellular location of chromosomal loci of two highly transcribed ribosomal RNA genes, suggesting that RNase E's function in ribosomal RNA processing occurs at the site of rRNA synthesis. Thus, components of the RNA degradosome and ribosome assembly are spatiotemporally organized in Caulobacter, with chromosomal readout serving as the template for this organization.. CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/228122 doi: bioRxiv preprint first posted online Dec. 3, 2017; In bacteria, the RNA degradosome mediates the majority of messenger RNA (mRNA) turnover and ribosomal RNA (rRNA) and transfer RNA (tRNA) maturation. 1 The RNA degradosome assembles on the C-terminal scaffold region of the RNase E endoribonuclease.2 RNase E in Escherichia coli (E. coli) and RNase Y, the RNase E homolog in Bacillus subtilis (B. subtilis),both associate with the cell membrane through a membrane-binding helix. [3][4][5][6] One proposed rationale behind the observed membrane association is to physically separate transcription within the nucleoid from RNA degradation, thus providing an inherent time delay between transcript synthesis and the onset of transcript decay, avoiding a futile cycle. Caulobacter crescentus (Caulobacter) is an alpha-proteobacterium widely studied as a model system for asymmetric cell division. Unlike E. coli or B. subtilis, Caulobacter contains a pole-tethered chromosome that fills the cytoplasm. 7-9 Surprisingly, Caulobacter RNase E does not have a membrane targeting sequence and is not membrane-associated. 2, 10 Furthermore, diffraction-limited (DL) images of RNase E exhibited a patchy localization throughout the cell, with RNase E directly or indirectly associating with DNA. 10Fluorescently labeled ribosomal proteins S2 and L1, proxies for ribosomes in E. coli and B. subtilis, respectively, were found enriched at the cell poles, spatially excluded from the nucleoid on the hundreds of nanometer scale. 11,12 Similar fluorescence imaging studies in Caulobacter revealed no apparent separation of ribosome...

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“…C. In the absence of precise mapping, these cartoons depict interactions with the noncatalytic region, although as indicated in text, it has recently been shown that the DEAD ‐box RNA helicase interacts with the catalytic domain of C. crenscentus RN ase E (Voss et al ., ). For each type of enzyme, the taxonomic distribution is indicated.…”

Section: Distribution and Classification Of Rnase E Homologsmentioning

confidence: 99%

“…RNase D in E. coli is involved in 3′ end processing of tRNA and rRNA. The DEAD‐box RNA helicase has been shown to interact with the region of the catalytic site containing the RP‐rich insertion (Voss et al ., ). This is a novel finding since DEAD‐box RNA helicase interactions characterized in type I enzymes have been mapped to the noncatalytic region of RNase E. Other differences include the observation that Cc ‐RNase E levels vary during the cell cycle (Hardwick et al ., ) and that Cc ‐RNase E localizes to the nucleoid (Montero Llopis et al ., ).…”

Section: Type II Enzymesmentioning

confidence: 99%

RNA degradosomes in bacteria and chloroplasts: classification, distribution and evolution of RNase E homologs

Ait-Bara

Carpousis

2015

Molecular Microbiology

108

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SummaryRibonuclease E (RNase E) of Escherichia coli, which is the founding member of a widespread family of proteins in bacteria and chloroplasts, is a fascinating enzyme that still has not revealed all its secrets. RNase E is an essential single-strand specific endoribonuclease that is involved in the processing and degradation of nearly every transcript in E. coli. A striking enzymatic property is a preference for substrates with a 5′ monophosphate end although recent work explains how RNase E can overcome the protection afforded by the 5′ triphosphate end of a primary transcript. Other features of E. coli RNase E include its interaction with enzymes involved in RNA degradation to form the multienzyme RNA degradosome and its localization to the inner cytoplasmic membrane. The N-terminal catalytic core of the RNase E protomer associates to form a tetrameric holoenzyme. Each RNase E protomer has a large C-terminal intrinsically disordered (ID) noncatalytic region that contains sites for interactions with protein components of the RNA degradosome as well as RNA and phospholipid bilayers. In this review, RNase E homologs have been classified into five types based on their primary structure. A recent analysis has shown that type I RNase E in the γ-proteobacteria forms an orthologous group of proteins that has been inherited vertically. The RNase E catalytic core and a large ID noncatalytic region containing an RNA binding motif and a membrane targeting sequence are universally conserved features of these orthologs. Although the ID noncatalytic region has low composition and sequence complexity, it is possible to map microdomains, which are short linear motifs that are sites of interaction with protein and other ligands. Throughout bacteria, the composition of the multienzyme RNA degradosome varies with species, but interactions with exoribonucleases (PNPase, RNase R), glycolytic enzymes (enolase, aconitase) and RNA helicases (DEAD-box proteins, Rho) are common. Plasticity in RNA degradosome composition is due to rapid evolution of RNase E microdomains. Characterization of the RNase E-PNPase interaction in α-proteobacteria, γ-proteobacteria and cyanobacteria suggests that it arose independently several times during evolution, thus conferring an advantage in control and coordination of RNA processing and degradation.

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Molecular recognition of RhlB and RNase D in the Caulobacter crescentus RNA degradosome

Cited by 34 publications

References 31 publications

Association of the Cold Shock DEAD-Box RNA Helicase RhlE to the RNA Degradosome in Caulobacter crescentus

Association of the Cold Shock DEAD-Box RNA Helicase RhlE to the RNA Degradosome in Caulobacter crescentus

Spatial organization and dynamics of RNase E and ribosomes inCaulobacter crescentus

RNA degradosomes in bacteria and chloroplasts: classification, distribution and evolution of RNase E homologs

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