scholarly journals RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis

2019 ◽  
Author(s):  
Heike Lange ◽  
Simon Y. A. Ndecky ◽  
Carlos Gomez-Diaz ◽  
David Pflieger ◽  
Nicolas Butel ◽  
...  
Keyword(s):  
Domain Architecture ◽  
Transcriptional Gene Silencing ◽  
Functional Link ◽  
Interacting Protein ◽  
Post Transcriptional Gene Silencing ◽  
Evolutionarily Conserved ◽  
Rna Quality Control ◽  
Rna Exosome ◽  
And Function ◽  
Similar Domain

AbstractThe RNA exosome is a key 3’-5’ exoribonuclease with an evolutionarily conserved structure and function. Its cytosolic functions require the co-factors SKI7 and the Ski complex. Here we demonstrate by co-purification experiments that the ARM repeat protein RESURRECTION1 (RST1) and RST1 INTERACTING PROTEIN (RIPR) connect the cytosolic Arabidopsis RNA exosome to the Ski complex. rst1 and ripr mutants accumulate RNA quality control siRNAs (rqc-siRNAs) produced by the post-transcriptional gene silencing (PTGS) machinery when mRNA degradation is compromised. The small RNA populations observed in rst1 and ripr mutants are also detected in mutants lacking the RRP45B/CER7 core exosome subunit. Thus, molecular and genetic evidence supports a physical and functional link between RST1, RIPR and the RNA exosome. Our data reveal the existence of additional cytosolic exosome co-factors besides the known SKI subunits. RST1 is not restricted to plants, as homologues with a similar domain architecture but unknown function exist in animals, including humans.

scholarly journals MicroRNAs in Cardiac Autophagy: Small Molecules and Big Role

Cells ◽  
2018 ◽  
Vol 7 (8) ◽  
pp. 104 ◽  
Author(s):  
Teng Sun ◽  
Meng-Yang Li ◽  
Pei-Feng Li ◽  
Ji-Min Cao
Keyword(s):  
Cardiac Fibrosis ◽  
Heart Diseases ◽  
Critical Role ◽  
Transcriptional Gene Silencing ◽  
Close Link ◽  
Post Transcriptional Gene Silencing ◽  
Evolutionarily Conserved ◽  
Cardiac Disorders ◽  
Cellular Components

Autophagy, which is an evolutionarily conserved process according to the lysosomal degradation of cellular components, plays a critical role in maintaining cell homeostasis. Autophagy and mitochondria autophagy (mitophagy) contribute to the preservation of cardiac homeostasis in physiological settings. However, impaired or excessive autophagy is related to a variety of diseases. Recently, a close link between autophagy and cardiac disorders, including myocardial infarction, cardiac hypertrophy, cardiomyopathy, cardiac fibrosis, and heart failure, has been demonstrated. MicroRNAs (miRNAs) are a class of small non-coding RNAs with a length of approximately 21–22 nucleotides (nt), which are distributed widely in viruses, plants, protists, and animals. They function in mediating the post-transcriptional gene silencing. A growing number of studies have demonstrated that miRNAs regulate cardiac autophagy by suppressing the expression of autophagy-related genes in a targeted manner, which are involved in the pathogenesis of heart diseases. This review summarizes the role of microRNAs in cardiac autophagy and related cardiac disorders. Furthermore, we mainly focused on the autophagy regulation pathways, which consisted of miRNAs and their targeted genes.

scholarly journals FIERY1 promotes microRNA accumulation by suppressing rRNA-derived small interfering RNAs in Arabidopsis

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Chenjiang You ◽  
Wenrong He ◽  
Runlai Hang ◽  
Cuiju Zhang ◽  
Xiaofeng Cao ◽  
...  
Keyword(s):  
Rna Degradation ◽  
Transcriptional Gene Silencing ◽  
Rrna Processing ◽  
Small Interfering Rnas ◽  
Post Transcriptional Gene Silencing ◽  
Processing Defects ◽  
And Function ◽  
Mirna Abundance ◽  
Unknown Link

Abstract Plant microRNAs (miRNAs) associate with ARGONAUTE1 (AGO1) to direct post-transcriptional gene silencing and regulate numerous biological processes. Although AGO1 predominantly binds miRNAs in vivo, it also associates with endogenous small interfering RNAs (siRNAs). It is unclear whether the miRNA/siRNA balance affects miRNA activities. Here we report that FIERY1 (FRY1), which is involved in 5′−3′ RNA degradation, regulates miRNA abundance and function by suppressing the biogenesis of ribosomal RNA-derived siRNAs (risiRNAs). In mutants of FRY1 and the nuclear 5′−3′ exonuclease genes XRN2 and XRN3, we find that a large number of 21-nt risiRNAs are generated through an endogenous siRNA biogenesis pathway. The production of risiRNAs correlates with pre-rRNA processing defects in these mutants. We also show that these risiRNAs are loaded into AGO1, causing reduced loading of miRNAs. This study reveals a previously unknown link between rRNA processing and miRNA accumulation.

scholarly journals MicroRNAs in the skin: role in development, homoeostasis and regeneration

2017 ◽  
Vol 131 (15) ◽  
pp. 1923-1940 ◽  
Author(s):  
Steven Horsburgh ◽  
Nicola Fullard ◽  
Mathilde Roger ◽  
Abbie Degnan ◽  
Stephen Todryk ◽  
...  
Keyword(s):  
Therapeutic Interventions ◽  
Transcriptional Gene Silencing ◽  
Biological Functions ◽  
Vast Number ◽  
Regulate Gene Expression ◽  
Post Transcriptional Gene Silencing ◽  
Non Coding Rnas ◽  
And Function ◽  
Molecular Signals

The skin is the largest organ of the integumentary system and possesses a vast number of functions. Due to the distinct layers of the skin and the variety of cells which populate each, a tightly regulated network of molecular signals control development and regeneration, whether due to programmed cell termination or injury. MicroRNAs (miRs) are a relatively recent discovery; they are a class of small non-coding RNAs which possess a multitude of biological functions due to their ability to regulate gene expression via post-transcriptional gene silencing. Of interest, is that a plethora of data demonstrates that a number of miRs are highly expressed within the skin, and are evidently key regulators of numerous vital processes to maintain non-aberrant functioning. Recently, miRs have been targeted as therapeutic interventions due to the ability of synthetic ‘antagomiRs’ to down-regulate abnormal miR expression, thereby potentiating wound healing and attenuating fibrotic processes which can contribute to disease such as systemic sclerosis (SSc). This review will provide an introduction to the structure and function of the skin and miR biogenesis, before summarizing the literature pertaining to the role of miRs. Finally, miR therapies will also be discussed, highlighting important future areas of research.

scholarly journals Distinct expression, localization and function of two Rab7 proteins encoded by paralogous genes in a free-living model eukaryote.

2011 ◽  
Vol 58 (4) ◽  
Author(s):  
Magdalena Osińska ◽  
Jolanta Wiejak ◽  
Emilia Wypych ◽  
Henryk Bilski ◽  
Rafał Bartosiewicz ◽  
...  
Keyword(s):  
Membrane Trafficking ◽  
Pcr Analysis ◽  
Transcriptional Gene Silencing ◽  
Post Translational Modification ◽  
Paralogous Genes ◽  
Post Transcriptional Gene Silencing ◽  
2D Gel ◽  
And Function ◽  
Microtubular Structures ◽  
Confocal And Electron Microscopy

Rab7 GTPases are involved in membrane trafficking in the late endosomal/lysosomal pathway. In Paramecium octaurelia Rab7a and Rab7b are encoded by paralogous genes. Antipeptide antibodies generated against divergent C-termini recognize Rab7a of 22.5 kDa and Rab7b of 25 kDa, respectively. In 2D gel electrophoresis two immunoreactive spots were identified for Rab7b at pI about 6.34 and about 6.18 and only one spot for Rab7a of pI about 6.34 suggesting post-translational modification of Rab7b. Mass spectrometry revealed eight identical phosphorylated residues in the both proteins. ProQ Emerald staining and ConA overlay of immunoprecipitated Rab7b indicated its putative glycosylation that was further supported by a faster electrophoretic mobility of this protein upon deglycosylation. Such a post-translational modification and substitution of Ala(140) in Rab7a for Ser(140) in Rab7b may result in distinct targeting to the oral apparatus where Rab7b associates with the microtubular structures as revealed by STED confocal and electron microscopy. Rab7a was mapped to phagosomal compartment. Absolute qReal-Time PCR analysis revealed that expression of Rab7a was 2.6-fold higher than that of Rab7b. Upon latex internalization it was further 2-fold increased for Rab7a and only slightly for Rab7b. Post-transcriptional gene silencing of rab7a suppressed phagosome formation by 70 % and impaired their acidification. Ultrastructural analysis with double immunogold labeling revealed that this effect was due to the lack of V-ATPase recruitment to phagolysosomes. No significant phenotype changes were noticed in cells upon rab7b silencing. In conclusion, Rab7b acquired a new function, whereas Rab7a can be assigned to the phagolysosomal pathway.

scholarly journals In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs

2015 ◽  
Author(s):  
Angel Emilio Martínez de Alba ◽  
Ana Moreno ◽  
Marc Gabriel ◽  
Allison C Mallory ◽  
Aurélie Christ ◽  
...  
Keyword(s):  
Quality Control ◽  
Rna Polymerase ◽  
Gene Silencing ◽  
Transcriptional Gene Silencing ◽  
Small Interfering Rnas ◽  
Rna Dependent Rna Polymerase ◽  
P Bodies ◽  
New Class ◽  
Post Transcriptional Gene Silencing ◽  
Rna Quality Control

Cytoplasmic degradation of endogenous RNAs is an integral part of RNA quality control (RQC) and often relies on the removal of the 5’ cap structure and their subsequent 5’ to 3’ degradation in cytoplasmic processing (P-)bodies. In parallel, many eukaryotes degrade exogenous and selected endogenous RNAs through post-transcriptional gene silencing (PTGS). In plants, PTGS depends on small interfering (si)RNAs produced after the conversion of single-stranded RNAs to doublestranded RNAs by the cellular RNA DEPENDENT RNA POLYMERASE 6 (RDR6) in cytoplasmic siRNA-bodies. PTGS and RQC compete for transgene-derived RNAs, but it is unknown whether this competition also occurs for endogenous transcripts. We show that the lethality of decapping mutants is suppressed by impairing RDR6 activity. We establish that upon decapping impairment hundreds of endogenous mRNAs give rise to a new class of rqc-siRNAs, that over-accumulate when RQC processes are impaired, a subset of which depending on RDR6 for their production. We observe that P- and siRNA-bodies often are dynamically juxtaposed, potentially allowing for crosstalk of the two machineries. Our results suggest that the decapping of endogenous RNA limits their entry into the PTGS pathway. We anticipate that the rqc-siRNAs identified in decapping mutants represent a subset of a larger ensemble of endogenous siRNAs.

scholarly journals Functional dissection of the ARGONAUTE7 promoter

2018 ◽  
Author(s):  
J. Steen Hoyer ◽  
Jose L. Pruneda-Paz ◽  
Ghislain Breton ◽  
Mariah A. Hassert ◽  
Emily E. Holcomb ◽  
...  
Keyword(s):  
Binding Sites ◽  
Rna Silencing ◽  
Leaf Shape ◽  
Effector Proteins ◽  
Transcriptional Gene Silencing ◽  
Antiviral Defense ◽  
Post Transcriptional Gene Silencing ◽  
And Function ◽  
Central Effector ◽  
Ranked List

AbstractARGONAUTES are the central effector proteins of RNA silencing which bind target transcripts in a small RNA-guided manner. Arabidopsis thaliana has ten ARGONAUTE (AGO) genes, with specialized roles in RNA-directed DNA methylation, post-transcriptional gene silencing, and antiviral defense. To better understand specialization among AGO genes at the level of transcriptional regulation we tested a library of 1497 transcription factors for binding to the promoters of AGO1, AGO10, and AGO7 using yeast 1-hybrid assays. A ranked list of candidate DNA-binding TFs revealed binding of the AGO7 promoter by a number of proteins in two families: the miR156-regulated SPL family and the miR319-regulated TCP family, both of which have roles in developmental timing and leaf morphology. Possible functions for SPL and TCP binding are unclear: we showed that these binding sites are not required for the polar expression pattern of AGO7, nor for the function of AGO7 in leaf shape. Normal AGO7 transcription levels and function appear to depend instead on an adjacent 124-bp region. Progress in understanding the structure of this promoter may aid efforts to understand how the conserved AGO7-triggered TAS3 pathway functions in timing and polarity.

scholarly journals RNA uridylation and decay in plants

2018 ◽  
Vol 373 (1762) ◽  
pp. 20180163 ◽  
Author(s):  
Caroline de Almeida ◽  
Hélène Scheer ◽  
Anthony Gobert ◽  
Veronica Fileccia ◽  
Federico Martinelli ◽  
...  
Keyword(s):  
Rna Degradation ◽  
Flowering Plant ◽  
Future Research ◽  
Transcriptional Gene Silencing ◽  
Messenger Rnas ◽  
Plant Infection ◽  
Post Transcriptional Gene Silencing ◽  
Key Points ◽  
History Of ◽  
And Function

RNA uridylation consists of the untemplated addition of uridines at the 3′ extremity of an RNA molecule. RNA uridylation is catalysed by terminal uridylyltransferases (TUTases), which form a subgroup of the terminal nucleotidyltransferase family, to which poly(A) polymerases also belong. The key role of RNA uridylation is to regulate RNA degradation in a variety of eukaryotes, including fission yeast, plants and animals. In plants, RNA uridylation has been mostly studied in two model species, the green algaeChlamydomonas reinhardtiiand the flowering plantArabidopsis thaliana. Plant TUTases target a variety of RNA substrates, differing in size and function. These RNA substrates include microRNAs (miRNAs), small interfering silencing RNAs (siRNAs), ribosomal RNAs (rRNAs), messenger RNAs (mRNAs) and mRNA fragments generated during post-transcriptional gene silencing. Viral RNAs can also get uridylated during plant infection. We describe here the evolutionary history of plant TUTases and we summarize the diverse molecular functions of uridylation during RNA degradation processes in plants. We also outline key points of future research.This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.

scholarly journals Identification and Functional Analysis of Apoptotic Protease Activating Factor-1 (Apaf-1) from Spodoptera litura

Insects ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 64
Author(s):  
Haihao Ma ◽  
Xiumei Yan ◽  
Lin Yan ◽  
Jingyan Zhao ◽  
Jiping Song ◽  
...  
Keyword(s):  
Spodoptera Litura ◽  
Actinomycin D ◽  
Titration Calorimetry ◽  
Apoptosis Pathway ◽  
Downstream Effector ◽  
Lepidopteran Insects ◽  
Evolutionarily Conserved ◽  
Effector Caspases ◽  
And Function

Apoptotic protease activating factor-1 (Apaf-1) is an adaptor molecule, essential for activating initiator caspase and downstream effector caspases, which directly cause apoptosis. In fruit flies, nematodes, and mammals, Apaf-1 has been extensively studied. However, the structure and function of Apaf-1 in Lepidoptera remain unclear. This study identified a novel Apaf-1 from Spodoptera litura, named Sl-Apaf-1. Sl-Apaf-1 contains three domains: a CARD domain, as well as NOD and WD motifs, and is very similar to mammalian Apaf-1. Interference of Sl-apaf-1 expression in SL-1 cells blocked apoptosis induced by actinomycin D. Overexpression of Sl-apaf-1 significantly enhances apoptosis induced by actinomycin D in Sf9/SL-1/U2OS cells, suggesting that the function of Sl-Apaf-1 is evolutionarily conserved. Furthermore, Sl-Apaf-1 could interact with Sl-caspase-5 (a homologue of mammalian caspase-9) and yielded a binding affinity of 1.37 × 106 M–1 according isothermal titration calorimetry assay. Initiator caspase (procaspase-5) of S. litura could be activated by Sl-Apaf-1 (without WD motif) in vitro, and the activated Sl-caspase-5 could cleave Sl-procaspase-1 (a homologue of caspase-3 in mammals), which directly caused apoptosis. This study demonstrates the key role of Sl-Apaf-1 in the apoptosis pathway, suggesting that the apoptosis pathway in Lepidopteran insects and mammals is conserved.

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