scholarly journals The Functional Cycle of Rnt1p: Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase III

Structure ◽  
2017 ◽  
Vol 25 (2) ◽  
pp. 353-363 ◽  
Author(s):  
He Song ◽  
Xianyang Fang ◽  
Lan Jin ◽  
Gary X. Shaw ◽  
Yun-Xing Wang ◽  
...  
Keyword(s):  
Rna Processing ◽  
Rnase Iii ◽  
Double Stranded Rna

Heterodimer-based analysis of subunit and domain contributions to double-stranded RNA processing by Escherichia coli RNase III in vitro

2008 ◽  
Vol 410 (1) ◽  
pp. 39-48 ◽  
Author(s):  
Wenzhao Meng ◽  
Allen W. Nicholson
Keyword(s):  
Escherichia Coli ◽  
Rna Processing ◽  
Metal Ion ◽  
Catalytic Site ◽  
Ion Concentration ◽  
Hill Coefficient ◽  
Rnase Iii ◽  
Double Stranded Rna ◽  
Catalytic Sites ◽  
Scissile Bond

Members of the RNase III family are the primary cellular agents of dsRNA (double-stranded RNA) processing. Bacterial RNases III function as homodimers and contain two dsRBDs (dsRNA-binding domains) and two catalytic sites. The potential for functional cross-talk between the catalytic sites and the requirement for both dsRBDs for processing activity are not known. It is shown that an Escherichia coli RNase III heterodimer that contains a single functional wt (wild-type) catalytic site and an inactive catalytic site (RNase III[E117A/wt]) cleaves a substrate with a single scissile bond with a kcat value that is one-half that of wt RNase III, but exhibits an unaltered Km. Moreover, RNase III[E117A/wt] cleavage of a substrate containing two scissile bonds generates singly cleaved intermediates that are only slowly cleaved at the remaining phosphodiester linkage, and in a manner that is sensitive to excess unlabelled substrate. These results demonstrate the equal probability, during a single binding event, of placement of a scissile bond in a functional or nonfunctional catalytic site of the heterodimer and reveal a requirement for substrate dissociation and rebinding for cleavage of both phosphodiester linkages by the mutant heterodimer. The rate of phosphodiester hydrolysis by RNase III[E117A/wt] has the same dependence on Mg2+ ion concentration as that of the wt enzyme, and exhibits a Hill coefficient (h) of 2.0±0.1, indicating that the metal ion dependence essentially reflects a single catalytic site that employs a two-Mg2+-ion mechanism. Whereas an E. coli RNase III mutant that lacks both dsRBDs is inactive, a heterodimer that contains a single dsRBD exhibits significant catalytic activity. These findings support a reaction pathway involving the largely independent action of the dsRBDs and the catalytic sites in substrate recognition and cleavage respectively.

scholarly journals Endoribonuclease-mediated control of hns mRNA stability constitutes a key regulatory pathway for Salmonella Typhimurium pathogenicity island 1 expression

2021 ◽  
Vol 17 (2) ◽  
pp. e1009263 ◽  
Author(s):  
Minho Lee ◽  
Minkyung Ryu ◽  
Minju Joo ◽  
Young-Jin Seo ◽  
Jaejin Lee ◽  
...  
Keyword(s):  
Rna Processing ◽  
Mrna Stability ◽  
Type Iii Secretion ◽  
Transcriptional Repression ◽  
Environmental Changes ◽  
Pathogenicity Island ◽  
Cleavage Sites ◽  
Regulatory Pathway ◽  
Rnase Iii ◽  
Rnase G

Bacteria utilize endoribonuclease-mediated RNA processing and decay to rapidly adapt to environmental changes. Here, we report that the modulation of hns mRNA stability by the endoribonuclease RNase G plays a key role in Salmonella Typhimurium pathogenicity. We found that RNase G determines the half-life of hns mRNA by cleaving its 5′ untranslated region and that altering its cleavage sites by genome editing stabilizes hns mRNA, thus decreasing S. Typhimurium virulence in mice. Under anaerobic conditions, the FNR-mediated transcriptional repression of rnc encoding RNase III, which degrades rng mRNA, and simultaneous induction of rng transcription resulted in rapid hns mRNA degradation, leading to the derepression of genes involved in the Salmonella pathogenicity island 1 (SPI-1) type III secretion system (T3SS). Together, our findings show that RNase III and RNase G levels-mediated control of hns mRNA abundance acts as a regulatory pathway upstream of a complex feed-forward loop for SPI-1 expression.

7S RNA, containing 5S ribosomal RNA and the termination stem, is a specific substrate for the two RNA processing enzymes RNase III and RNase E

Biochemistry ◽  
1984 ◽  
Vol 23 (13) ◽  
pp. 2952-2957 ◽  
Author(s):  
Jozsef Szeberenyi ◽  
Monoj K. Roy ◽  
Hemant C. Vaidya ◽  
David Apirion
Keyword(s):  
Ribosomal Rna ◽  
Rna Processing ◽  
Specific Substrate ◽  
Rnase E ◽  
Rnase Iii ◽  
5S Ribosomal Rna ◽  
Processing Enzymes

scholarly journals Human REXO2 controls short mitochondrial RNAs generated by mtRNA processing and decay machinery to prevent accumulation of double-stranded RNA

2020 ◽  
Vol 48 (10) ◽  
pp. 5572-5590 ◽  
Author(s):  
Maciej Szewczyk ◽  
Deepshikha Malik ◽  
Lukasz S Borowski ◽  
Sylwia D Czarnomska ◽  
Anna V Kotrys ◽  
...  
Keyword(s):  
Rna Processing ◽  
Mitochondrial Rna ◽  
Sequence Specificity ◽  
Dual Roles ◽  
Double Stranded Rna ◽  
Mitochondrial Homeostasis ◽  
Short Rnas ◽  
Mitochondrial Functions ◽  
Steady State Levels ◽  
Primary Substrate

Abstract RNA decay is a key element of mitochondrial RNA metabolism. To date, the only well-documented machinery that plays a role in mtRNA decay in humans is the complex of polynucleotide phosphorylase (PNPase) and SUV3 helicase, forming the degradosome. REXO2, a homolog of prokaryotic oligoribonucleases present in humans both in mitochondria and the cytoplasm, was earlier shown to be crucial for maintaining mitochondrial homeostasis, but its function in mitochondria has not been fully elucidated. In the present study, we created a cellular model that enables the clear dissection of mitochondrial and non-mitochondrial functions of human REXO2. We identified a novel mitochondrial short RNA, referred to as ncH2, that massively accumulated upon REXO2 silencing. ncH2 degradation occurred independently of the mitochondrial degradosome, strongly supporting the hypothesis that ncH2 is a primary substrate of REXO2. We also investigated the global impact of REXO2 depletion on mtRNA, revealing the importance of the protein for maintaining low steady-state levels of mitochondrial antisense transcripts and double-stranded RNA. Our detailed biochemical and structural studies provide evidence of sequence specificity of the REXO2 oligoribonuclease. We postulate that REXO2 plays dual roles in human mitochondria, ‘scavenging’ nanoRNAs that are produced by the degradosome and clearing short RNAs that are generated by RNA processing.

scholarly journals A stepwise model for double-stranded RNA processing by ribonuclease III

2007 ◽  
Vol 67 (1) ◽  
pp. 143-154 ◽  
Author(s):  
Jianhua Gan ◽  
Gary Shaw ◽  
Joseph E. Tropea ◽  
David S. Waugh ◽  
Donald L. Court ◽  
...  
Keyword(s):  
Rna Processing ◽  
Ribonuclease Iii ◽  
Double Stranded Rna

scholarly journals The Evolutionary Significance of RNAi in the Fungal Kingdom

2020 ◽  
Vol 21 (24) ◽  
pp. 9348
Author(s):  
Carlos Lax ◽  
Ghizlane Tahiri ◽  
José Alberto Patiño-Medina ◽  
José T. Cánovas-Márquez ◽  
José A. Pérez-Ruiz ◽  
...  
Keyword(s):  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Genome Integrity ◽  
Evolutionary Significance ◽  
Messenger Rnas ◽  
Small Interfering Rnas ◽  
Rnase Iii ◽  
Double Stranded Rna ◽  
Main Component ◽  
Fungal Kingdom

RNA interference (RNAi) was discovered at the end of last millennium, changing the way scientists understood regulation of gene expression. Within the following two decades, a variety of different RNAi mechanisms were found in eukaryotes, reflecting the evolutive diversity that RNAi entails. The essential silencing mechanism consists of an RNase III enzyme called Dicer that cleaves double-stranded RNA (dsRNA) generating small interfering RNAs (siRNAs), a hallmark of RNAi. These siRNAs are loaded into the RNA-induced silencing complex (RISC) triggering the cleavage of complementary messenger RNAs by the Argonaute protein, the main component of the complex. Consequently, the expression of target genes is silenced. This mechanism has been thoroughly studied in fungi due to their proximity to the animal phylum and the conservation of the RNAi mechanism from lower to higher eukaryotes. However, the role and even the presence of RNAi differ across the fungal kingdom, as it has evolved adapting to the particularities and needs of each species. Fungi have exploited RNAi to regulate a variety of cell activities as different as defense against exogenous and potentially harmful DNA, genome integrity, development, drug tolerance, or virulence. This pathway has offered versatility to fungi through evolution, favoring the enormous diversity this kingdom comprises.

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