scholarly journals Nuclear and cytoplasmic RNA exosomes and PELOTA1 prevent miRNA-induced secondary siRNA production in Arabidopsis

2021 ◽  
Author(s):  
Maria Louisa Vigh ◽  
Axel Thieffry ◽  
Laura Arribas-Hernández ◽  
Peter Brodersen
Keyword(s):  
Rna Silencing ◽  
Dwell Time ◽  
Release Factor ◽  
Subunit Dissociation ◽  
Ribosome Stalling ◽  
Mirna Targets ◽  
Cytoplasmic Rna ◽  
Nuclear Exosome ◽  
Secondary Sirna ◽  
Interfering Rna

Amplification of short interfering RNA (siRNAs) via RNA dependent RNA Polymerases (RdRPs) is of fundamental importance in RNA silencing. In plants, silencing by microRNAs (miRNAs) generally does not lead to engagement of RdRPs, in part thanks to an as yet poorly understood activity of the cytoplasmic exosome adaptor SKI2. Here, we show that mutation of the cytoplasmic exosome subunit RRP45B results in siRNA production very similar to what is observed in ski2 mutants. Furthermore, loss of the nuclear exosome adaptor HEN2 leads to secondary siRNA production from miRNA targets largely distinct from those producing siRNAs in ski2. Importantly, mutation of the Release Factor paralogue PELOTA1 required for subunit dissociation of stalled ribosomes causes siRNA production from miRNA targets overlapping with, but distinct from, those affected in ski2 and rrp45b mutants. We also show that miRNA-induced illicit secondary siRNA production correlates with miRNA levels rather than accumulation of stable 5'-cleavage fragments. We propose that stalled RNA-induced Silencing Complex (RISC) and ribosomes, but not stable target mRNA cleavage fragments released from RISC, trigger secondary siRNA production, and that the exosome limits siRNA amplification by reducing RISC dwell time on miRNA target mRNAs while PELOTA1 does so by reducing ribosome stalling.

scholarly journals Cymbidium Ringspot Virus Harnesses RNA Silencing To Control the Accumulation of Virus Parasite Satellite RNA

2008 ◽  
Vol 82 (23) ◽  
pp. 11851-11858 ◽  
Author(s):  
Vitantonio Pantaleo ◽  
József Burgyán
Keyword(s):  
Rna Silencing ◽  
Sequence Similarity ◽  
Helper Virus ◽  
Ringspot Virus ◽  
Silencing Suppressor ◽  
Short Interfering Rna ◽  
Satellite Rna ◽  
The Cost ◽  
Interfering Rna ◽  
Rna Replicon

ABSTRACT Cymbidium ringspot virus (CymRSV) satellite RNA (satRNA) is a parasitic subviral RNA replicon that replicates and accumulates at the cost of its helper virus. This 621-nucleotide (nt) satRNA species has no sequence similarity to the helper virus, except for a 51-nt-long region termed the helper-satellite homology (HSH) region, which is essential for satRNA replication. We show that the accumulation of satRNA strongly depends on temperature and on the presence of the helper virus p19 silencing suppressor protein, suggesting that RNA silencing plays a crucial role in satRNA accumulation. We also demonstrate that another member of the Tombusvirus genus, Carnation Italian ringspot virus (CIRV), supports satRNA accumulation at a higher level than CymRSV. Our results suggest that short interfering RNA (siRNA) derived from CymRSV targets satRNA more efficiently than siRNA from CIRV, possibly because of the higher sequence similarity between the HSH regions of the helper and CIRV satRNAs. RNA silencing sensor RNA carrying the putative satRNA target site in the HSH region was efficiently cleaved when transiently expressed in CymRSV-infected plants but not in CIRV-infected plants. Strikingly, replacing the CymRSV HSH box2 sequence with that of CIRV restores satRNA accumulation both at 24°C and in the absence of the p19 suppressor protein. These findings demonstrate the extraordinary adaptation of this virus to its host in terms of harnessing the antiviral silencing response of the plant to control the virus parasite satRNA.

scholarly journals Lack of pairing during meiosis triggers multigenerational transgene silencing in Caenorhabditis elegans

2015 ◽  
Vol 112 (20) ◽  
pp. E2667-E2676 ◽  
Author(s):  
Luciana E. Leopold ◽  
Bree N. Heestand ◽  
Soobin Seong ◽  
Ludmila Shtessel ◽  
Shawn Ahmed
Keyword(s):  
Caenorhabditis Elegans ◽  
Small Rna ◽  
Transgene Expression ◽  
Single Copy ◽  
Transgene Silencing ◽  
Meiotic Pairing ◽  
Homologous Chromosomes ◽  
Diverse Species ◽  
Secondary Sirna ◽  
Interfering Rna

Single-copy transgenes in Caenorhabditis elegans can be subjected to a potent, irreversible silencing process termed small RNA-induced epigenetic silencing (RNAe). RNAe is promoted by the Piwi Argonaute protein PRG-1 and associated Piwi-interacting RNAs (piRNAs), as well as by proteins that promote and respond to secondary small interfering RNA (siRNA) production. Here we define a related siRNA-mediated silencing process, termed “multigenerational RNAe,” which can occur for transgenes that are maintained in a hemizygous state for several generations. We found that transgenes that contain either GFP or mCherry epitope tags can be silenced via multigenerational RNAe, whereas a transgene that possesses GFP and a perfect piRNA target site can be rapidly and permanently silenced via RNAe. Although previous studies have shown that PRG-1 is typically dispensable for maintenance of RNAe, we found that both initiation and maintenance of multigenerational RNAe requires PRG-1 and the secondary siRNA biogenesis protein RDE-2. Although silencing via RNAe is irreversible, we found that transgene expression can be restored when hemizygous transgenes that were silenced via multigenerational RNAe become homozygous. Furthermore, multigenerational RNAe was accelerated when meiotic pairing of the chromosome possessing the transgene was abolished. We propose that persistent lack of pairing during meiosis elicits a reversible multigenerational silencing response, which can lead to permanent transgene silencing. Multigenerational RNAe may be broadly relevant to single-copy transgenes used in experimental biology and to shaping the epigenomic landscape of diverse species, where genomic polymorphisms between homologous chromosomes commonly result in unpaired DNA during meiosis.

scholarly journals PRKRA Localizes to Nuage Structures and the Ectoplasmic Specialization and Tubulobulbar Complexes in Rat and Mouse Testis

2014 ◽  
Vol 2014 ◽  
pp. 1-9
Author(s):  
Junya Suzuki ◽  
Sadaki Yokota
Keyword(s):  
Sertoli Cells ◽  
Rna Silencing ◽  
Binding Proteins ◽  
Spermatogenic Cells ◽  
P Bodies ◽  
Cytoplasmic Rna ◽  
Dsrna Binding ◽  
Chromatoid Bodies ◽  
Pachytene Spermatocytes ◽  
Ectoplasmic Specialization

The cytoplasmic RNA-induced silencing complex (RISC) contains dsRNA binding proteins, including PRKRA, TRBP, and Dicer. RISC localizes to P-bodies. The nuage of the spermatogenic cells has function similar to the P-bodies. We study whether PRKRA localizes to nuage of spermatogenic cells of rat and mouse. PRKRA localized to four types of nuage structures, including aggregates of 60–90 nm particles, irregularly-shaped perinuclear granules, and intermitochondrial cement of pachytene spermatocytes, and chromatoid bodies of round spermatids. In addition, PRKRA is associated with dense material surrounding tubulobulbar complexes and with the ectoplasmic specialization. The results suggest that PRKRA functions in the nuage as an element of RNA silencing system and plays unknown role in the ectoplasmic specialization and at the tubulobulbar complexes of Sertoli cells attaching the head of late spermatids.

scholarly journals Ribosome Recycling Factor and Release Factor 3 Action Promotes TnaC-Peptidyl-tRNA Dropoff and Relieves Ribosome Stalling during Tryptophan Induction of tna Operon Expression in Escherichia coli

2007 ◽  
Vol 189 (8) ◽  
pp. 3147-3155 ◽  
Author(s):  
Ming Gong ◽  
Luis R. Cruz-Vera ◽  
Charles Yanofsky
Keyword(s):  
Escherichia Coli ◽  
Growth Inhibition ◽  
Stop Codon ◽  
Elongation Factor ◽  
Initiation Factor ◽  
Release Factor ◽  
Ribosome Recycling Factor ◽  
Ribosome Stalling ◽  
Operon Expression

ABSTRACT Upon tryptophan induction of tna operon expression in Escherichia coli, the leader peptidyl-tRNA, TnaC- \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(tRNA_{2}^{Pro}\) \end{document} , resists cleavage, resulting in ribosome stalling at the tnaC stop codon. This stalled ribosome blocks Rho factor binding and action, preventing transcription termination in the tna operon's leader region. Plasmid-mediated overexpression of tnaC was previously shown to inhibit cell growth by reducing uncharged \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(tRNA_{2}^{Pro}\) \end{document}  availability. Which factors relieve ribosome stalling, facilitate TnaC- \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(tRNA_{2}^{Pro}\) \end{document}  cleavage, and relieve growth inhibition were addressed in the current study. In strains containing the chromosomal tna operon and lacking a tnaC plasmid, the overproduction of ribosome recycling factor (RRF) and release factor 3 (RF3) reduced tna operon expression. Their overproduction in vivo also increased the rate of cleavage of TnaC- \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(tRNA_{2}^{Pro}\) \end{document} , relieving the growth inhibition associated with plasmid-mediated tnaC overexpression. The overproduction of elongation factor G or initiation factor 3 did not have comparable effects, and tmRNA was incapable of attacking TnaC- \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(tRNA_{2}^{Pro}\) \end{document}  in stalled ribosome complexes. The stability of TnaC- \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(tRNA_{2}^{Pro}\) \end{document}  was increased appreciably in strains deficient in RRF and RF3 or deficient in peptidyl-tRNA hydrolase. These findings reveal the existence of a natural mechanism whereby an amino acid, tryptophan, binds to ribosomes that have just completed the synthesis of TnaC- \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(tRNA_{2}^{Pro}\) \end{document} . Bound tryptophan inhibits RF2-mediated cleavage of TnaC- \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(tRNA_{2}^{Pro}\) \end{document} , resulting in the stalling of the ribosome translating tnaC mRNA. This stalling results in increased transcription of the structural genes of the tna operon. RRF and RF3 then bind to this stalled ribosome complex and slowly release TnaC- \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(tRNA_{2}^{Pro}\) \end{document} . This release allows ribosome recycling and permits the cleavage of TnaC- \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(tRNA_{2}^{Pro}\) \end{document}  by peptidyl-tRNA hydrolase.

scholarly journals Aspergillus Mycoviruses Are Targets and Suppressors of RNA Silencing

2007 ◽  
Vol 7 (2) ◽  
pp. 350-357 ◽  
Author(s):  
T. M. Hammond ◽  
M. D. Andrewski ◽  
M. J. Roossinck ◽  
N. P. Keller
Keyword(s):  
Rna Silencing ◽  
Agaricus Bisporus ◽  
Defense Mechanism ◽  
Rna Virus ◽  
Physiological Changes ◽  
Button Mushroom ◽  
Diverse Range ◽  
The Third ◽  
Sphaeropsis Sapinea ◽  
Interfering Rna

ABSTRACT RNA silencing can function as a virus defense mechanism in a diverse range of eukaryotes, and many viruses are capable of suppressing the silencing machinery targeting them. However, the extent to which this occurs between fungal RNA silencing and mycoviruses is unclear. Here, three Aspergillus dsRNA mycoviruses were partially characterized, and their relationship to RNA silencing was investigated. Aspergillus virus 1816 is related to Agaricus bisporus white button mushroom virus 1 and suppresses RNA silencing through a mechanism that alters the level of small interfering RNA. Aspergillus virus 178 is related to RNA virus L1 of Gremmeniella abietina and does not appear to affect RNA silencing. The third virus investigated, Aspergillus virus 341, is distantly related to Sphaeropsis sapinea RNA virus 2. Detection of mycovirus-derived siRNA from this mycovirus demonstrates that it is targeted for degradation by the Aspergillus RNA silencing machinery. Thus, our results indicate that Aspergillus mycoviruses are both targets and suppressors of RNA silencing. In addition, they suggest that the morphological and physiological changes associated with some mycoviruses could be a result of their antagonistic relationship with RNA silencing.

scholarly journals MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs

2017 ◽  
Author(s):  
Saima Shahid ◽  
Gunjune Kim ◽  
Nathan R. Johnson ◽  
Eric Wafula ◽  
Feng Wang ◽  
...  
Keyword(s):  
Host Plants ◽  
Messenger Rnas ◽  
Host Gene Expression ◽  
Mrna Accumulation ◽  
Directional Movement ◽  
Plant Mirna ◽  
Cuscuta Campestris ◽  
Target Sites ◽  
Secondary Sirna ◽  
Interfering Rna

First paragraphDodders (Cuscuta spp.) are obligate parasitic plants that obtain water and nutrients from the stems of host plants via specialized feeding structures called haustoria. Dodder haustoria facilitate bi-directional movement of viruses, proteins, and mRNAs between host and parasite1, but the functional effects of these movements are not clear. Here we show that C. campestris haustoria accumulate high levels of many novel microRNAs (miRNAs) while parasitizing Arabidopsis thaliana hosts. Many of these miRNAs are 22 nts long, a usually rare size of plant miRNA associated with amplification of target silencing through secondary small interfering RNA (siRNA) production2. Several A. thaliana mRNAs are targeted by C. campestris 22 nt miRNAs during parasitism, resulting in mRNA cleavage, secondary siRNA production, and decreased mRNA accumulation levels. Hosts with mutations in two of the targets supported significantly higher growth of C. campestris. Homologs of target mRNAs from diverse plants also have predicted target sites to induced C. campestris miRNAs, and the same miRNAs are expressed and active against host targets when C. campestris parasitizes a different host, Nicotiana benthamiana. These data show that C. campestris miRNAs act as trans-species regulators of host gene expression, and suggest that they may act as virulence factors during parasitism.

scholarly journals RNA Silencing in the Management of Dyslipidemias

2021 ◽  
Vol 23 (11) ◽  
Author(s):  
Neil C. Henney ◽  
Maciej Banach ◽  
Peter E. Penson
Keyword(s):  
Rna Silencing ◽  
Scientific Basis ◽  
Pooled Analysis ◽  
Biological Molecules ◽  
Phase 3 ◽  
Alternative Approach ◽  
Cardiovascular Morbidity And Mortality ◽  
Patient Groups ◽  
Outcomes Study ◽  
Interfering Rna

Abstract Purpose of Review Remarkable reductions in cardiovascular morbidity and mortality have been achieved in recent decades through the widespread use of ‘small-molecule’ hypolipidaemic drugs such as statins and ezetimibe. An alternative approach is to perturb the production of proteins through ribonucleic acid (RNA) silencing, leading to long-lasting knock-down of specific biological molecules. This review describes the scientific basis of RNA silencing, and critically evaluates the evidence relating to inclisiran, a small interfering RNA against proprotein convertase subtilisin kexin 9 (PCSK9). Recent Findings Pooled analysis of three recent ORION trials has demonstrated that twice-yearly administration of inclisiran reduces LDL-C by 50% in a range of patient groups, with only mild adverse effects. Summary Inclisiran provides safe, effective and long-lasting reductions in PCSK9 and LDL-C. The results of the phase-3 ORION-4 outcomes study are eagerly awaited. Further promising RNA silencing technologies have the potential to improve the management of dyslipidaemia.

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