scholarly journals Dual-level autoregulation of the E. coli DeaD RNA helicase via mRNA stability and Rho-dependent transcription termination

2020 ◽  
Author(s):  
Sandeep Ojha ◽  
Chaitanya Jain
Keyword(s):  
Mrna Stability ◽  
Transcription Termination ◽  
Rna Helicase ◽  
Feedback Mechanism ◽  
Helicase Activity ◽  
Coding Region ◽  
E Coli ◽  
Negative Feedback Mechanism ◽  
Dead Box ◽  
Rna Remodeling

ABSTRACTDEAD-box proteins (DBPs) are RNA remodeling factors associated with RNA helicase activity that are found in nearly all organisms. Despite extensive studies on the mechanisms used by DBPs to regulate RNA function, very little is known about how DBPs themselves are regulated. In this work, we have analyzed the expression and regulation of DeaD/CsdA, the largest of the DBPs in Escherichia coli (E. coli). We show that deaD transcription initiates 838 nts upstream of the start of the coding region. We have also found that DeaD is autoregulated through a negative feedback mechanism that operates both at the level of mRNA stability and Rho-dependent transcription termination, and this regulation is dependent upon the 5’ untranslated region (5’ UTR). These findings suggest that DeaD might be regulating the conformation of its own mRNA through its RNA helicase activity to facilitate ribonuclease and Rho access to its 5’UTR.

Fast Translation within the First 45 Codons Decreases mRNA Stability and Increases Premature Transcription Termination in E. coli

2019 ◽  
Vol 431 (6) ◽  
pp. 1088-1097 ◽  
Author(s):  
Steen Pedersen ◽  
Thilde Bagger Terkelsen ◽  
Mette Eriksen ◽  
Magnus Krarup Hauge ◽  
Casper Carstens Lund ◽  
...  
Keyword(s):  
Mrna Stability ◽  
Transcription Termination ◽  
E Coli

Modeling the Negative Feedback Mechanism in the Enzyme Carboxyltransferase

2011 ◽  
Author(s):  
Xiaoyu Cai ◽  
Marcio de Queiroz ◽  
Glen Meades ◽  
Grover Waldrop
Keyword(s):  
Fatty Acid ◽  
Negative Feedback ◽  
Acid Synthesis ◽  
Feedback Mechanism ◽  
Mass Action ◽  
Acetyl Coa Carboxylase ◽  
Acetyl Coa ◽  
Mass Action Kinetics ◽  
E Coli ◽  
Negative Feedback Mechanism

The enzyme acetyl-CoA carboxylase catalyzes the first committed step in fatty acid synthesis in all organisms. The E. coli form of the carboxyltransferase subunit was recently found to regulate its own activity and expression by binding its own mRNA. By binding acetyl-CoA or the mRNA encoding its own subunits, Carboxyltransferase is able to sense the metabolic state of the cell and attenuate its own translation and enzymatic activity using a negative feedback mechanism. In this paper, this network of interactions is modeled mathematically using mass action kinetics. Numerical simulations of the model show agreement with experimental results.

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 RNase R is associated in a functional complex with the RhpA DEAD-box RNA helicase in Helicobacter pylori

2021 ◽  
Author(s):  
Alejandro Tejada-Arranz ◽  
Rute G Matos ◽  
Yves Quentin ◽  
Maxime Bouilloux-Lafont ◽  
Eloïse Galtier ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Gene Expression Regulation ◽  
Rna Helicase ◽  
Minor Role ◽  
Helicase Activity ◽  
Rnase R ◽  
Dead Box ◽  
H Pylori

Abstract Ribonucleases are central players in post-transcriptional regulation, a major level of gene expression regulation in all cells. Here, we characterized the 3′-5′ exoribonuclease RNase R from the bacterial pathogen Helicobacter pylori. The ‘prototypical’ Escherichia coli RNase R displays both exoribonuclease and helicase activities, but whether this latter RNA unwinding function is a general feature of bacterial RNase R had not been addressed. We observed that H. pylori HpRNase R protein does not carry the domains responsible for helicase activity and accordingly the purified protein is unable to degrade in vitro RNA molecules with secondary structures. The lack of RNase R helicase domains is widespread among the Campylobacterota, which include Helicobacter and Campylobacter genera, and this loss occurred gradually during their evolution. An in vivo interaction between HpRNase R and RhpA, the sole DEAD-box RNA helicase of H. pylori was discovered. Purified RhpA facilitates the degradation of double stranded RNA by HpRNase R, showing that this complex is functional. HpRNase R has a minor role in 5S rRNA maturation and few targets in H. pylori, all included in the RhpA regulon. We concluded that during evolution, HpRNase R has co-opted the RhpA helicase to compensate for its lack of helicase activity.

A multigene locus containing the Manx and bobcat genes is required for development of chordate features in the ascidian tadpole larva

Development ◽  
1999 ◽  
Vol 126 (8) ◽  
pp. 1643-1653 ◽  
Author(s):  
B.J. Swalla ◽  
M.A. Just ◽  
E.L. Pederson ◽  
W.R. Jeffery
Keyword(s):  
Gene Locus ◽  
Single Copy ◽  
Rna Helicase ◽  
Untranslated Regions ◽  
Cdna Clones ◽  
Gene Complex ◽  
Coding Region ◽  
Dead Box ◽  
Dorsal Neural Tube ◽  
Alternatively Spliced

The Manx gene is required for the development of the tail and other chordate features in the ascidian tadpole larva. To determine the structure of the Manx gene, we isolated and sequenced genomic clones from the tailed ascidian Molgula oculata. The Manx gene contains 9 exons and encodes both major and minor Manx mRNAs, which differ in the length of their 5′ untranslated regions. The coding region of the single-copy bobcat gene, which encodes a DEAD-box RNA helicase, is embedded within the first Manx intron. The organization of the bobcat and Manx transcription units was determined by comparing genomic and cDNA clones. The Manx-bobcat gene locus has an unusual organization in which a non-coding first exon is alternatively spliced at the 5′ end of two different mRNAs. The bobcat and Manx genes are expressed coordinately during oogenesis and embryogenesis, but not during spermatogenesis, in which bobcat mRNA accumulates independently of Manx mRNA. Similar to Manx, zygotic bobcat transcripts accumulate in the embryonic primordia responsible for generating chordate features, including the dorsal neural tube and notochord, are downregulated during embryogenesis in the tailless species Molgula occulta and are upregulated in M. occulta X M. oculata hybrids, which restore these chordate features. Antisense experiments indicate that zygotic bobcat expression is required for development of the same suite of chordate features as Manx. The results show that the Manx-bobcat gene complex has a role in the development of chordate features in ascidian tadpole larvae.

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 Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination

Genetics ◽  
2019 ◽  
Vol 212 (1) ◽  
pp. 153-174 ◽  
Author(s):  
Yu-Hsuan Lai ◽  
Krishna Choudhary ◽  
Sara C. Cloutier ◽  
Zheng Xing ◽  
Sharon Aviran ◽  
...  
Keyword(s):  
Transcription Termination ◽  
Rna Helicase ◽  
Structural Remodeling ◽  
Dead Box ◽  
Genome Wide

scholarly journals Comprehensive Mechanism of Gene Silencing and Its Role in Plant Growth and Development

2021 ◽  
Vol 12 ◽  
Author(s):  
Ahmed H. El-Sappah ◽  
Kuan Yan ◽  
Qiulan Huang ◽  
Md. Monirul Islam ◽  
Quanzi Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Growth ◽  
Gene Silencing ◽  
Cell Fate ◽  
Crop Production ◽  
Molecular Mechanisms ◽  
Feedback Mechanism ◽  
Transcriptional Gene Silencing ◽  
Coding Region ◽  
Negative Feedback Mechanism

Gene silencing is a negative feedback mechanism that regulates gene expression to define cell fate and also regulates metabolism and gene expression throughout the life of an organism. In plants, gene silencing occurs via transcriptional gene silencing (TGS) and post-transcriptional gene silencing (PTGS). TGS obscures transcription via the methylation of 5′ untranslated region (5′UTR), whereas PTGS causes the methylation of a coding region to result in transcript degradation. In this review, we summarized the history and molecular mechanisms of gene silencing and underlined its specific role in plant growth and crop production.

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.

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