scholarly journals MicroRNA-independent roles of the RNase III enzymes Drosha and Dicer

Open Biology ◽  
2013 ◽  
Vol 3 (10) ◽  
pp. 130144 ◽  
Author(s):  
Timothy M. Johanson ◽  
Andrew M. Lew ◽  
Mark M. W. Chong
Keyword(s):  
Ribosomal Rna ◽  
Messenger Rnas ◽  
Small Interfering Rnas ◽  
Rnase Iii ◽  
Ribonuclease Iii ◽  
Stem Loop ◽  
Viral Rnas ◽  
Genome Regulation ◽  
Many Sources ◽  
Stem Cell Populations

The ribonuclease III enzymes Drosha and Dicer are renowned for their central roles in the biogenesis of microRNAs (miRNAs). For many years, this has overshadowed the true versatility and importance of these enzymes in the processing of other RNA substrates. For example, Drosha also recognizes and cleaves messenger RNAs (mRNAs), and potentially ribosomal RNA. The cleavage of mRNAs occurs via recognition of secondary stem-loop structures similar to miRNA precursors, and is an important mechanism of repressing gene expression, particularly in progenitor/stem cell populations. On the other hand, Dicer also has critical roles in genome regulation and surveillance. These include the production of endogenous small interfering RNAs from many sources, and the degradation of potentially harmful short interspersed element and viral RNAs. These findings have sparked a renewed interest in these enzymes, and their diverse functions in biology.

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.

scholarly journals METABOLISM OF RIBOSOMAL RNA IN MUTANTS OF ESCHERICHIA COLI DOUBLY DEFECTIVE IN RIBONUCLEASE III AND THE TRANSCRIPTION TERMINATION FACTOR RHO

Genetics ◽  
1978 ◽  
Vol 90 (1) ◽  
pp. 19-35
Author(s):  
David Apirion ◽  
Jeff Neil ◽  
Thong-Sung Ko ◽  
Ned Watson
Keyword(s):  
Ribosomal Rna ◽  
Temperature Sensitivity ◽  
Transcription Termination ◽  
Rnase Iii ◽  
Ribonuclease Iii ◽  
Rna Molecules ◽  
Transcription Termination Factor ◽  
Mutant Strains ◽  
Two Factors

ABSTRACT To determine if proteins RNase III and rho, both of which can determine the 3' ends of RNA molecules, can complement each other, double mutants defective in these two factors were constructed. In all cases (four rho mutations tested) the double mutants were viable at lower temperatures, but were unable to grow at higher temperatures at which both of the parental strains grew. Genetic analyses suggested that the combination of the rnc rho (RNase III-Rho-) mutations was necessary and probably sufficient to confer temperature sensitivity on carrier strains. Physiological studies showed that synthesis and maturation of rRNA, which is greatly affected by RNase III, as well as other RNAs, was indistinguishable in rnc rho strains as compared to rnc rho  + strains, thus suggesting that RNase III and rho do not complement one another in determining the 3' ends of RNA molecules. In rnc rho strains, however, the newly synthesized rRNA failed to accumulate. Thus, decay of rRNA could be the reason for the temperature sensitivity of the double mutant strains. These experiments suggest that RNase III and rho can both protect rRNA from degradation by cellular ribonucleases. They also point to the possibility that the nucleotide sequences involved in the determination of the 3' ends of RNA molecules by these two factors are not identical.

Current RNA-based Therapeutics in Clinical Trials

2019 ◽  
Vol 19 (3) ◽  
pp. 172-196 ◽  
Author(s):  
Ling-Yan Zhou ◽  
Zhou Qin ◽  
Yang-Hui Zhu ◽  
Zhi-Yao He ◽  
Ting Xu
Keyword(s):  
Clinical Trials ◽  
Rapid Development ◽  
Genetic Diseases ◽  
Three Dimensional ◽  
Therapeutic Effects ◽  
Messenger Rnas ◽  
Small Interfering Rnas ◽  
Rna Modifications ◽  
Guide Rna ◽  
Endogenous Genes

Long-term research on various types of RNAs has led to further understanding of diverse mechanisms, which eventually resulted in the rapid development of RNA-based therapeutics as powerful tools in clinical disease treatment. Some of the developing RNA drugs obey the antisense mechanisms including antisense oligonucleotides, small interfering RNAs, microRNAs, small activating RNAs, and ribozymes. These types of RNAs could be utilized to inhibit/activate gene expression or change splicing to provide functional proteins. In the meantime, some others based on different mechanisms like modified messenger RNAs could replace the dysfunctional endogenous genes to manage some genetic diseases, and aptamers with special three-dimensional structures could bind to specific targets in a high-affinity manner. In addition, the recent most popular CRISPR-Cas technology, consisting of a crucial single guide RNA, could edit DNA directly to generate therapeutic effects. The desired results from recent clinical trials indicated the great potential of RNA-based drugs in the treatment of various diseases, but further studies on improving delivery materials and RNA modifications are required for the novel RNA-based drugs to translate to the clinic. This review focused on the advances and clinical studies of current RNA-based therapeutics, analyzed their challenges and prospects.

scholarly journals Complex Regulation of the Organic Hydroperoxide Resistance Gene (ohr) from XanthomonasInvolves OhrR, a Novel Organic Peroxide-Inducible Negative Regulator, and Posttranscriptional Modifications

2001 ◽  
Vol 183 (15) ◽  
pp. 4405-4412 ◽  
Author(s):  
Rojana Sukchawalit ◽  
Suvit Loprasert ◽  
Sopapan Atichartpongkul ◽  
Skorn Mongkolsuk
Keyword(s):  
Secondary Structure ◽  
Organic Peroxide ◽  
Primer Extension ◽  
Negative Regulator ◽  
Rnase Iii ◽  
Stem Loop ◽  
Strong Activity ◽  
Reading Frame ◽  
Bicistronic Mrna

ABSTRACT Analysis of the sequence immediate upstream of ohrrevealed an open reading frame, designated ohrR, with the potential to encode a 17-kDa peptide with moderate amino acid sequence homology to the MarR family of negative regulators of gene expression. ohrR was transcribed as bicistronic mRNA with ohr, while ohr mRNA was found to be 95% monocistronic and 5% bicistronic with ohrR. Expression of both genes was induced by tert-butyl hydroperoxide (tBOOH) treatment. High-level expression ofohrR negatively regulated ohr expression. This repression could be overcome by tBOOH treatment. In vivo promoter analysis showed that the ohrR promoter (P1) has organic peroxide-inducible, strong activity, while the ohrpromoter (P2) has constitutive, weak activity. Only P1 is autoregulated by OhrR. ohr primer extension results revealed three major primer extension products corresponding to the 5′ ends ofohr mRNA, and their levels were strongly induced by tBOOH treatment. Sequence analysis of regions upstream of these sites showed no typical Xanthomonas promoter. Instead, the regions can form a stem-loop secondary structure with the 5′ ends ofohr mRNA located in the loop section. The secondary structure resembles the structure recognized and processed by RNase III enzyme. These findings suggest that the P1 promoter is responsible for tBOOH-induced expression of the ohrR-ohr operon. The bicistronic mRNA is then processed by RNase III-like enzymes to give high levels of ohr mRNA, while ohrR mRNA is rapidly degraded.

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 Unknown Areas of Activity of Human Ribonuclease Dicer: A Putative Deoxyribonuclease Activity

Molecules ◽  
2020 ◽  
Vol 25 (6) ◽  
pp. 1414 ◽  
Author(s):  
Marta Wojnicka ◽  
Agnieszka Szczepanska ◽  
Anna Kurzynska-Kokorniak
Keyword(s):  
Dnase Activity ◽  
Helicase Domain ◽  
Small Interfering Rnas ◽  
Rnase Iii ◽  
Domain Specific ◽  
Dsrna Binding ◽  
Small Regulatory Rnas ◽  
Paz Domain ◽  
Canonical Products ◽  
Truncated Variants

The Dicer ribonuclease plays a crucial role in the biogenesis of small regulatory RNAs (srRNAs) by processing long double-stranded RNAs and single-stranded hairpin RNA precursors into small interfering RNAs (siRNAs) and microRNAs (miRNAs), respectively. Dicer-generated srRNAs can control gene expression by targeting complementary transcripts and repressing their translation or inducing their cleavage. Human Dicer (hDicer) is a multidomain enzyme comprising a putative helicase domain, a DUF283 domain, platform, a PAZ domain, a connector helix, two RNase III domains (RNase IIIa and RNase IIIb) and a dsRNA-binding domain. Specific, ~20-base pair siRNA or miRNA duplexes with 2 nucleotide (nt) 3’-overhangs are generated by Dicer when an RNA substrate is anchored within the platform-PAZ-connector helix (PPC) region. However, increasing number of reports indicate that in the absence of the PAZ domain, binding of RNA substrates can occur by other Dicer domains. Interestingly, truncated variants of Dicer, lacking the PPC region, have been found to display a DNase activity. Inspired by these findings, we investigated how the lack of the PAZ domain, or the entire PPC region, would influence the cleavage activity of hDicer. Using immunopurified 3xFlag-hDicer produced in human cells and its two variants: one lacking the PAZ domain, and the other lacking the entire PPC region, we show that the PAZ domain deletion variants of hDicer are not able to process a pre-miRNA substrate, a dsRNA with 2-nt 3ʹ-overhangs, and a blunt-ended dsRNA. However, the PAZ deletion variants exhibit both RNase and DNase activity on short single-stranded RNA and DNAs, respectively. Collectively, our results indicate that when the PAZ domain is absent, other hDicer domains may contribute to substrate binding and in this case, non-canonical products can be generated.

scholarly journals Characterization of Aquifex aeolicus ribonuclease III and the reactivity epitopes of its pre-ribosomal RNA substrates

2010 ◽  
Vol 39 (7) ◽  
pp. 2756-2768 ◽  
Author(s):  
Zhongjie Shi ◽  
Rhonda H. Nicholson ◽  
Ritu Jaggi ◽  
Allen W. Nicholson
Keyword(s):  
Ribosomal Rna ◽  
Aquifex Aeolicus ◽  
Ribonuclease Iii

scholarly journals N6-methyladenosine modification of hepatitis B virus RNA differentially regulates the viral life cycle

2018 ◽  
Vol 115 (35) ◽  
pp. 8829-8834 ◽  
Author(s):  
Hasan Imam ◽  
Mohsin Khan ◽  
Nandan S. Gokhale ◽  
Alexa B. R. McIntyre ◽  
Geon-Woo Kim ◽  
...  
Keyword(s):  
Life Cycle ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Reverse Transcription ◽  
Mutational Analysis ◽  
Regulatory Function ◽  
Messenger Rnas ◽  
Stem Loop ◽  
B Virus ◽  
A Site

N6-methyladenosine (m6A) RNA methylation is the most abundant epitranscriptomic modification of eukaryotic messenger RNAs (mRNAs). Previous reports have found m6A on both cellular and viral transcripts and defined its role in regulating numerous biological processes, including viral infection. Here, we show that m6A and its associated machinery regulate the life cycle of hepatitis B virus (HBV). HBV is a DNA virus that completes its life cycle via an RNA intermediate, termed pregenomic RNA (pgRNA). Silencing of enzymes that catalyze the addition of m6A to RNA resulted in increased HBV protein expression, but overall reduced reverse transcription of the pgRNA. We mapped the m6A site in the HBV RNA and found that a conserved m6A consensus motif situated within the epsilon stem loop structure, is the site for m6A modification. The epsilon stem loop is located in the 3′ terminus of all HBV mRNAs and at both the 5′ and 3′ termini of the pgRNA. Mutational analysis of the identified m6A site in the 5′ epsilon stem loop of pgRNA revealed that m6A at this site is required for efficient reverse transcription of pgRNA, while m6A methylation of the 3′ epsilon stem loop results in destabilization of all HBV transcripts, suggesting that m6A has dual regulatory function for HBV RNA. Overall, this study reveals molecular insights into how m6A regulates HBV gene expression and reverse transcription, leading to an increased level of understanding of the HBV life cycle.

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