scholarly journals RNA helicase–regulated processing of the Synechocystis rimO–crhR operon results in differential cistron expression and accumulation of two sRNAs

2020 ◽  
Vol 295 (19) ◽  
pp. 6372-6386 ◽  
Author(s):  
Albert Remus R. Rosana ◽  
Denise S. Whitford ◽  
Anzhela Migur ◽  
Claudia Steglich ◽  
Sonya L. Kujat-Choy ◽  
...  
Keyword(s):  
Small Rnas ◽  
Rna Helicase ◽  
Rnase E ◽  
Gene Encoding ◽  
Modeling And Analysis ◽  
Dead Box ◽  
Bacterial Rna ◽  
Additional Processing ◽  
Operon Expression

The arrangement of functionally-related genes in operons is a fundamental element of how genetic information is organized in prokaryotes. This organization ensures coordinated gene expression by co-transcription. Often, however, alternative genetic responses to specific stress conditions demand the discoordination of operon expression. During cold temperature stress, accumulation of the gene encoding the sole Asp–Glu–Ala–Asp (DEAD)-box RNA helicase in Synechocystis sp. PCC 6803, crhR (slr0083), increases 15-fold. Here, we show that crhR is expressed from a dicistronic operon with the methylthiotransferase rimO/miaB (slr0082) gene, followed by rapid processing of the operon transcript into two monocistronic mRNAs. This cleavage event is required for and results in destabilization of the rimO transcript. Results from secondary structure modeling and analysis of RNase E cleavage of the rimO–crhR transcript in vitro suggested that CrhR plays a role in enhancing the rate of the processing in an auto-regulatory manner. Moreover, two putative small RNAs are generated from additional processing, degradation, or both of the rimO transcript. These results suggest a role for the bacterial RNA helicase CrhR in RNase E-dependent mRNA processing in Synechocystis and expand the known range of organisms possessing small RNAs derived from processing of mRNA transcripts.

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.

The multiple lives of DEAD-box RNA helicase DP103/DDX20/Gemin3

2018 ◽  
Vol 46 (2) ◽  
pp. 329-341 ◽  
Author(s):  
Frank Curmi ◽  
Ruben J. Cauchi
Keyword(s):  
Rna Binding ◽  
Muscular Atrophy ◽  
Essential Gene ◽  
Rna Helicase ◽  
Survival Motor Neuron ◽  
In Vivo Studies ◽  
Critical Function ◽  
Dead Box ◽  
Small Nuclear Ribonucleoprotein

Gemin3, also known as DDX20 or DP103, is a DEAD-box RNA helicase which is involved in more than one cellular process. Though RNA unwinding has been determined in vitro, it is surprisingly not required for all of its activities in cellular metabolism. Gemin3 is an essential gene, present in Amoeba and Metazoa. The highly conserved N-terminus hosts the helicase core, formed of the helicase- and DEAD-domains, which, based on crystal structure determination, have key roles in RNA binding. The C-terminus of Gemin3 is highly divergent between species and serves as the interaction site for several accessory factors that could recruit Gemin3 to its target substrates and/or modulate its function. This review article focuses on the known roles of Gemin3, first as a core member of the survival motor neuron (SMN) complex, in small nuclear ribonucleoprotein biogenesis. Although mechanistic details are lacking, a critical function for Gemin3 in this pathway is supported by numerous in vitro and in vivo studies. Gene expression activities of Gemin3 are next underscored, mainly messenger ribonucleoprotein trafficking, gene silencing via microRNA processing, and transcriptional regulation. The involvement of Gemin3 in abnormal cell signal transduction pathways involving p53 and NF-κB is also highlighted. Finally, the clinical implications of Gemin3 deregulation are discussed including links to spinal muscular atrophy, poliomyelitis, amyotrophic lateral sclerosis, and cancer. Impressive progress made over the past two decades since the discovery of Gemin3 bodes well for further work that refines the mechanism(s) underpinning its multiple activities.

A yeast gene encoding a putative RNA helicase of the “DEAD”-box family

Yeast ◽  
1993 ◽  
Vol 9 (4) ◽  
pp. 429-432 ◽  
Author(s):  
Sabine Strahl-Bolsinger ◽  
Widmar Tanner
Keyword(s):  
Rna Helicase ◽  
Yeast Gene ◽  
Gene Encoding ◽  
Dead Box ◽  
The Dead

Phosphorylation of threonine 204 of DEAD-box RNA helicase DDX3 by cyclin B/cdc2 in vitro

2007 ◽  
Vol 356 (3) ◽  
pp. 668-673 ◽  
Author(s):  
Takeshi Sekiguchi ◽  
Yoshiko Kurihara ◽  
Junko Fukumura
Keyword(s):  
Rna Helicase ◽  
Cyclin B ◽  
Dead Box

scholarly journals The DEAD-box RNA helicase 5 positively regulates the replication of porcine reproductive and respiratory syndrome virus by interacting with viral Nsp9 in vitro

2015 ◽  
Vol 195 ◽  
pp. 217-224 ◽  
Author(s):  
Shuangcheng Zhao ◽  
Xinna Ge ◽  
Xiaolong Wang ◽  
Aijing Liu ◽  
Xin Guo ◽  
...  
Keyword(s):  
Rna Helicase ◽  
Respiratory Syndrome Virus ◽  
Dead Box ◽  
The Dead

scholarly journals The DEAD box RNA helicase Ddx39a is essential for myocyte and lens development in zebrafish

2017 ◽  
Author(s):  
Linlin Zhang ◽  
Beibei Li ◽  
Yuxi Yang ◽  
Ian C. Scott ◽  
Xin Lou
Keyword(s):  
Heart Development ◽  
Rna Helicase ◽  
Lens Fiber ◽  
Rna Helicases ◽  
Gene Encoding ◽  
Animal Development ◽  
Fiber Cells ◽  
Dead Box ◽  
The Dead ◽  
Almost All

AbstractRNA helicases from the DEAD-box family are found in almost all organisms and have important roles in RNA metabolism including RNA synthesis, processing and degradation. The function and mechanism of action of most of these helicases in animal development and human disease are largely unexplored. In a zebrafish mutagenesis screen to identify genes essential for heart development we identified a zebrafish mutant, which disrupts the gene encoding the RNA helicase DEAD-box 39a (ddx39a).Homozygous ddx39a mutant embryos exhibit profound cardiac and trunk muscle dystrophy, along with lens abnormalities caused by abrupt terminal differentiation of cardiomyocyte, myoblast and lens fiber cells. Further investigation indicated that loss of ddx39a hindered mRNA splicing of members of the kmt2 gene family, leading to mis-regulation of structural gene expression in cardiomyocyte, myoblast and lens fiber cells. Taken together, these results show that Ddx39a plays an essential role in establishment of proper epigenetic status during cell differentiation.

scholarly journals Regulation of Alternative Splicing by the ATP-Dependent DEAD-Box RNA Helicase p72

2002 ◽  
Vol 22 (16) ◽  
pp. 5698-5707 ◽  
Author(s):  
Arnd Hönig ◽  
Didier Auboeuf ◽  
Marjorie M. Parker ◽  
Bert W. O'Malley ◽  
Susan M. Berget
Keyword(s):  
Alternative Splicing ◽  
Rna Splicing ◽  
Globin Gene ◽  
Rna Helicase ◽  
Close Relative ◽  
Rna Helicases ◽  
Enhancer Element ◽  
Dead Box ◽  
Precursor Rna

ABSTRACT Although a number of ATP-dependent RNA helicases are important for constitutive RNA splicing, no helicases have been implicated in alternative RNA splicing. Here, we show that the abundant DEAD-box RNA helicase p72, but not its close relative p68, affects the splicing of alternative exons containing AC-rich exon enhancer elements. The effect of p72 was tested by using mini-genes that undergo different types of alternative splicing. When the concentration of p72 was increased in transient transfections, the inclusion of enhancer-containing CD44 alternative exons v4 and v5 increased using a mini-gene that contained these exons and their flanking introns inserted into a β-globin gene. Other types of alternative splicing were not impacted by altering p72 concentrations. Mutation of the p72 helicase ATP-binding site or deletion of the carboxy-terminal region of the protein reduced the ability of the transfected protein to affect CD44 variable exon splicing. Use of in vitro extracts overexpressing p72 indicated that p72 becomes associated with complexes containing precursor RNA. Helicases have been implicated both in altering RNA-RNA interactions and in remodeling RNA-protein complexes. CD44 exon v4 contains a potential internal secondary structure element that base pairs the 5′ splice site with a region inside the exon located between enhancer elements. Mutations that destroyed this complementarity modestly increased inclusion in the absence of p72 but still responded to increasing p72 concentration like the wild-type exon, suggesting that p72 might have effects on protein-RNA interactions. In agreement with this hypothesis, p72 was not able to restore the inclusion of an exon mutated for its major enhancer element. Our results suggest that RNA helicases may be important alternative splicing regulatory factors.

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