A DEAD-box RNA helicase in the Escherichia coli RNA degradosome

Nature ◽  
1996 ◽  
Vol 381 (6578) ◽  
pp. 169-172 ◽  
Author(s):  
Béatrice Py ◽  
Christopher F. Higgins ◽  
Henry M. Krisch ◽  
Agamemnon J. Carpousis
Keyword(s):  
Escherichia Coli ◽  
Rna Helicase ◽  
Dead Box ◽  
Rna Degradosome

The Escherichia coli RNA degradosome: structure, function and relationship to other ribonucleolytic multienyzme complexes

2002 ◽  
Vol 30 (2) ◽  
pp. 150-155 ◽  
Author(s):  
A. J. Carpousis
Keyword(s):  
Escherichia Coli ◽  
Rna Binding ◽  
Intrinsic Property ◽  
Rna Helicase ◽  
Rnase E ◽  
E Coli ◽  
Ribonucleolytic Activity ◽  
Dead Box ◽  
Rna Degradosome

mRNA instability is an intrinsic property that permits timely changes in gene expression by limiting the lifetime of a transcript. The RNase E of Escherichia coli is a single-strand-specific endonuclease involved in the processing of rRNA and the degradation of mRNA. A nucleolytic multienzyme complex now known as the RNA degradosome was discovered during the purification and characterization of RNase E. Two other components are a 3′ exoribonuclease (polynucleotide phosphorylase, PNPase) and a DEAD-box RNA helicase (RNA helicase B, RhlB). RNase E is a large multidomain protein with N-terminal ribonucleolytic activity, an RNA-binding domain and a C-terminal ‘scaffold’ that binds PNPase, enolase and RhlB. RhlB by itself has little activity but is strongly stimulated by its interaction with RNase E. RhlB in vitro can facilitate the degradation of structured RNA by PNPase. Since the discovery of the RNA degradosome in E. coli, related complexes have been described in other organisms.

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

2017 ◽  
Vol 199 (13) ◽  
Author(s):  
Angel A. Aguirre ◽  
Alexandre M. Vicente ◽  
Steven W. Hardwick ◽  
Daniela M. Alvelos ◽  
Ricardo R. Mazzon ◽  
...  
Keyword(s):  
Low Temperature ◽  
Caulobacter Crescentus ◽  
Immunoblot Analysis ◽  
Rna Helicase ◽  
Rnase E ◽  
Rna Helicases ◽  
Content Type ◽  
Dead Box ◽  
Rna Degradosome ◽  
The Dead

ABSTRACT 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.

scholarly journals The Sole DEAD-Box RNA Helicase of the Gastric PathogenHelicobacter pyloriIs Essential for Colonization

mBio ◽  
2018 ◽  
Vol 9 (2) ◽  
pp. e02071-17 ◽  
Author(s):  
Lamya El Mortaji ◽  
Sylvie Aubert ◽  
Eloïse Galtier ◽  
Christine Schmitt ◽  
Karine Anger ◽  
...  
Keyword(s):  
Mouse Model ◽  
Ribosome Biogenesis ◽  
Rna Helicase ◽  
Rna Decay ◽  
Dead Box ◽  
Major Player ◽  
Gastric Pathogen ◽  
Rna Degradosome ◽  
H Pylori

ABSTRACTPresent in every kingdom of life, generally in multiple copies, DEAD-box RNA helicases are specialized enzymes that unwind RNA secondary structures. They play major roles in mRNA decay, ribosome biogenesis, and adaptation to cold temperatures. Most bacteria have multiple DEAD-box helicases that present both specialized and partially redundant functions. By using phylogenomics, we revealed that theHelicobactergenus, including the major gastric pathogenH. pylori, is among the exceptions, as it encodes a sole DEAD-box RNA helicase. InH. pylori, this helicase, designated RhpA, forms a minimal RNA degradosome together with the essential RNase, RNase J, a major player in the control of RNA decay. Here, we usedH. pylorias a model organism with a sole DEAD-box helicase and investigated the role of this helicase inH. pyloriphysiology, ribosome assembly, and duringin vivocolonization. Our data showed that RhpA is dispensable for growth at 37°C but crucial at 33°C, suggesting an essential role of the helicase in cold adaptation. Moreover, we found that a ΔrhpAmutant was impaired in motility and deficient in colonization of the mouse model. RhpA is involved in the maturation of 16S rRNA at 37°C and is associated with translating ribosomes. At 33°C, RhpA is, in addition, recruited to individual ribosomal subunits. Finally, via its role in the RNA degradosome, RhpA directs the regulation of the expression of its partner, RNase J. RhpA is thus a multifunctional enzyme that, inH. pylori, plays a central role in gene regulation and in the control of virulence.IMPORTANCEWe present the results of our study on the role of RhpA, the sole DEAD-box RNA helicase encoded by the major gastric pathogenHelicobacter pylori. We observed that all theHelicobacterspecies possess such a sole helicase, in contrast to most free-living bacteria. RhpA is not essential for growth ofH. pyloriunder normal conditions. However, deletion ofrhpAleads to a motility defect and to total inhibition of the ability ofH. pylorito colonize a mouse model. We also demonstrated that this helicase encompasses most of the functions of its specialized orthologs described so far. We found that RhpA is a key element of the bacterial adaptation to colder temperatures and plays a minor role in ribosome biogenesis. Finally, RhpA regulates transcription of thernjgene encoding RNase J, its essential partner in the minimalH. pyloriRNA degradosome, and thus plays a crucial role in the control of RNA decay.

scholarly journals Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3' exonuclease and a DEAD-box RNA helicase

1999 ◽  
Vol 13 (19) ◽  
pp. 2594-2603 ◽  
Author(s):  
G. A. Coburn ◽  
X. Miao ◽  
D. J. Briant ◽  
G. A. Mackie
Keyword(s):  
Rna Helicase ◽  
Dead Box ◽  
Rna Degradosome

The DEAD-box RNA helicase SrmB is involved in the assembly of 50S ribosomal subunits in Escherichia coli

2003 ◽  
Vol 48 (5) ◽  
pp. 1253-1265 ◽  
Author(s):  
Julie Charollais ◽  
Delphine Pflieger ◽  
Joëlle Vinh ◽  
Marc Dreyfus ◽  
Isabelle Iost
Keyword(s):  
Escherichia Coli ◽  
Rna Helicase ◽  
Ribosomal Subunits ◽  
Dead Box ◽  
The Dead

Supramolecular membrane-associated assemblies of RNA metabolic proteins in Escherichia coli

2014 ◽  
Vol 458 (1) ◽  
pp. e1-e3 ◽  
Author(s):  
Philipp G. Hoch ◽  
Roland K. Hartmann
Keyword(s):  
Escherichia Coli ◽  
Rna Binding ◽  
De Novo ◽  
Rna Binding Proteins ◽  
Elongation Factor ◽  
Rna Degradation ◽  
Dead Box ◽  
Biochemical Journal ◽  
Rna Degradosome ◽  
Polymerase I

Controlled RNA degradation is known to be achieved via the exosome in Eukarya and Archaea, and the RNA degradosome in Bacteria. In this issue of the Biochemical Journal, Taghbalout et al. demonstrate in Escherichia coli that many additional proteins of the RNA degradation and processing network co-localize with the RNA degradosome in supramolecular structures. The latter appear as extended cytoplasmic membrane-associated assemblies that coil around the periphery of the cell when visualized by immunofluorescence microscopy. The co-localizing ensemble of RNA metabolic proteins includes RNaseE, PNPase (polynucleotide phosphorylase), the DEAD-box RNA helicase RhlB, the oligo-RNase Orn, RNases II and III, PAP I [poly(A) polymerase I], RppH (RNA pyrophosphohydrolase), proteins RraA and RraB that are negative regulators of RNaseE, and the RNA chaperone Hfq. Not all cellular RNA-binding proteins associate with these structures, as shown for EF-Tu (elongation factor Tu) and Rho helicase. Formation of the supramolecular architecture was shown to not be dependent on two other known cytoskeletal systems or on RNA de novo synthesis or nucleoid positioning within the cell. This novel dimension of compartmentalization in bacteria that lack classic cell compartments opens new perspectives on how RNA homoeostasis is achieved, organized and regulated in bacteria such as E. coli.

scholarly journals Both Enolase and the DEAD-Box RNA Helicase CrhB Can Form Complexes with RNase E in Anabaena sp. Strain PCC 7120

2020 ◽  
Vol 86 (13) ◽  
Author(s):  
Huaduo Yan ◽  
Xiuxiu Qin ◽  
Li Wang ◽  
Wenli Chen
Keyword(s):  
Rna Helicase ◽  
Rna Metabolism ◽  
Rnase E ◽  
Double Stranded Rna ◽  
Content Type ◽  
E Coli ◽  
Dead Box ◽  
Assembly Mechanism ◽  
Rna Degradosome ◽  
Pcc 7120

ABSTRACT At present, little is known about the RNA metabolism driven by the RNA degradosome in cyanobacteria. RNA helicase and enolase are the common components of the RNA degradosome in many bacteria. Here, we provide evidence that both enolase and the DEAD-box RNA helicase CrhB can interact with RNase E in Anabaena (Nostoc) sp. strain PCC 7120 (referred to here as PCC 7120). Furthermore, we found that the C-terminal domains of CrhB and AnaEno (enolase of PCC 7120) are required for the interaction, respectively. Moreover, their recognition motifs for AnaRne (RNase E of PCC 7120) turned out to be located in the N-terminal catalytic domain, which is obviously different from those identified previously in Proteobacteria. We also demonstrated in enzyme activity assays that CrhB can induce AnaRne to degrade double-stranded RNA with a 5′ tail. Furthermore, we investigated the localization of CrhB and AnaRne by green fluorescent protein (GFP) translation fusion in situ and found that they both localized in the center of the PCC 7120 cytoplasm. This localization pattern is also different from the membrane binding of RNase E and RhlB in Escherichia coli. Together with the previous identification of polynucleotide phosphorylase (PNPase) in PCC 7120, our results show that there is an RNA degradosome-like complex with a different assembly mechanism in cyanobacteria. IMPORTANCE In all domains of life, RNA turnover is important for gene regulation and quality control. The process of RNA metabolism is regulated by many RNA-processing enzymes and assistant proteins, where these proteins usually exist as complexes. However, there is little known about the RNA metabolism, as well as about the RNA degradation complex. In the present study, we described an RNA degradosome-like complex in cyanobacteria and revealed an assembly mechanism different from that of E. coli. Moreover, CrhB could help RNase E in Anabaena sp. strain PCC 7120 degrade double-stranded RNA with a 5′ tail. In addition, CrhB and AnaRne have similar cytoplasm localizations, in contrast to the membrane localization in E. coli.

scholarly journals An unusually long 5’UTR of ATP dependent cold shock DEAD-box RNA helicase gene csdA negatively regulates its own expression in Escherichia coli

2021 ◽  
Author(s):  
Soma Jana ◽  
Partha P. Datta
Keyword(s):  
Escherichia Coli ◽  
Cold Shock ◽  
Rna Helicase ◽  
Cold Shock Protein ◽  
Coding Region ◽  
Dead Box ◽  
Helicase Gene ◽  
Gfp Reporter ◽  
Gene Regulations

AbstractCold-shock DEAD-box protein A (CsdA) is an ATP dependant cold shock DEAD-box RNA helicase. It is a major cold shock protein needed for the cold adaptation in Escherichia coli. Although the CsdA has been studied at the protein level, further studies are necessary to understand its mechanisms of gene regulations. In this regard, we have constructed a promoter less vector with the ORF of a GFP reporter and found that the promoter of the csdA gene resides far upstream (more than 800 bases) of its coding region. Furthermore, our in vivo deletion experiment has confirmed the existence of this extraordinarily long 5’UTR. Our results show that it represses its own expression. In addition, the short peptide encoding (26 aa) yrbN gene resides within this 5’UTR as an operon with 8 overlapping nucleotides with the csdA coding region. Besides, we observed that the csdA gene expression may also occur along with immediate upstream (180 nucleotides) nlpI gene both at 37°C and 15°C and from the pnp gene (1173 nucleotides upstream) only during cold. In conclusion, csdA gene has operon feature like prokaryotes, in contrast, it also contains an extraordinarily long 5’UTR, found in eukaryotes.

scholarly journals A rice DEAD-box RNA helicase protein, OsRH17, suppresses 16S ribosomal RNA maturation in Escherichia coli

Gene ◽  
2015 ◽  
Vol 555 (2) ◽  
pp. 318-328 ◽  
Author(s):  
Jie Xu ◽  
Chaolei Liu ◽  
Meiru Li ◽  
Jiang Hu ◽  
Li Zhu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Ribosomal Rna ◽  
Rna Helicase ◽  
16S Ribosomal Rna ◽  
Dead Box ◽  
Rna Maturation
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