scholarly journals An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection

2021 ◽  
Author(s):  
Ganna Reshetnyak ◽  
Jonathan M. Jacobs ◽  
Florence Auguy ◽  
Coline Sciallano ◽  
Lisa Claude ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Stress Responses ◽  
Small Rnas ◽  
Early Stage ◽  
Kinase Domain ◽  
Transcriptional Gene Silencing ◽  
Small Interfering Rnas ◽  
Post Transcriptional Gene Silencing ◽  
Virulent Strains ◽  
Microbe Interactions

ABSTRACTNon-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant-microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20-22nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences often encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and some xisRNA loci coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not broadly suppress cis-genes expression on the basis of mRNA-seq data. Overall, our results identify a group of unusual sRNAs with a potential role in plant-microbe interactions.

scholarly journals An atypical class of non-coding small RNAs is produced in rice leaves upon bacterial infection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ganna Reshetnyak ◽  
Jonathan M. Jacobs ◽  
Florence Auguy ◽  
Coline Sciallano ◽  
Lisa Claude ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Stress Responses ◽  
Small Rnas ◽  
Early Stage ◽  
Kinase Domain ◽  
Transcriptional Gene Silencing ◽  
Small Interfering Rnas ◽  
Post Transcriptional Gene Silencing ◽  
Virulent Strains ◽  
Microbe Interactions

AbstractNon-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant–microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20–22 nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences, with about half of them encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and xisRNA loci predominantly coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not broadly suppress cis-genes expression on the basis of mRNA-seq data. Overall, our results identify a group of unusual sRNAs with a potential role in plant–microbe interactions.

scholarly journals Virus and Viroid-Derived Small RNAs as Modulators of Host Gene Expression: Molecular Insights Into Pathogenesis

2021 ◽  
Vol 11 ◽  
Author(s):  
S. V. Ramesh ◽  
Sneha Yogindran ◽  
Prabu Gnanasekaran ◽  
Supriya Chakraborty ◽  
Stephan Winter ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Small Rnas ◽  
Rna Silencing ◽  
Transcriptional Gene Silencing ◽  
Genomic Rnas ◽  
Post Transcriptional Gene Silencing ◽  
Viroid Infection ◽  
Wide Range ◽  
Associated Symptoms ◽  
Sequence Complementarity

Virus-derived siRNAs (vsiRNAs) generated by the host RNA silencing mechanism are effectors of plant’s defense response and act by targeting the viral RNA and DNA in post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) pathways, respectively. Contrarily, viral suppressors of RNA silencing (VSRs) compromise the host RNA silencing pathways and also cause disease-associated symptoms. In this backdrop, reports describing the modulation of plant gene(s) expression by vsiRNAs via sequence complementarity between viral small RNAs (sRNAs) and host mRNAs have emerged. In some cases, silencing of host mRNAs by vsiRNAs has been implicated to cause characteristic symptoms of the viral diseases. Similarly, viroid infection results in generation of sRNAs, originating from viroid genomic RNAs, that potentially target host mRNAs causing typical disease-associated symptoms. Pathogen-derived sRNAs have been demonstrated to have the propensity to target wide range of genes including host defense-related genes, genes involved in flowering and reproductive pathways. Recent evidence indicates that vsiRNAs inhibit host RNA silencing to promote viral infection by acting as decoy sRNAs. Nevertheless, it remains unclear if the silencing of host transcripts by viral genome-derived sRNAs are inadvertent effects due to fortuitous pairing between vsiRNA and host mRNA or the result of genuine counter-defense strategy employed by viruses to enhance its survival inside the plant cell. In this review, we analyze the instances of such cross reaction between pathogen-derived vsiRNAs and host mRNAs and discuss the molecular insights regarding the process of pathogenesis.

The long hand of the small RNAs reaches into several levels of gene regulation

2004 ◽  
Vol 82 (4) ◽  
pp. 472-481 ◽  
Author(s):  
Tony Nolan ◽  
Carlo Cogoni
Keyword(s):  
Gene Silencing ◽  
Small Rnas ◽  
Developmental Regulation ◽  
Transcriptional Gene Silencing ◽  
Rna Molecules ◽  
New Class ◽  
Post Transcriptional Gene Silencing ◽  
Wide Range ◽  
Cellular Defence ◽  
Genomic Organisation

Small RNA molecules such as siRNAs and miRNAs represent a new class of molecules that have been implicated in a wide range of diverse gene silencing phenomena. It is now becoming clear that these two similar molecules share several common features in both their biogenesis and their mechanism of action. Thus, the siRNA and miRNA pathways may have evolved from a common ancestral mechanism that has diverged to play important roles in developmental regulation, genomic organisation, and cellular defence against foreign nucleic acids.Key words: miRNA, siRNA, post-transcriptional gene silencing, RNAi, heterochromatin.

scholarly journals Comparison between the Repression Potency of siRNA Targeting the Coding Region and the 3′-Untranslated Region of mRNA

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Ching-Fang Lai ◽  
Chih-Ying Chen ◽  
Lo-Chun Au
Keyword(s):  
Gene Silencing ◽  
Thermodynamic Stability ◽  
Untranslated Region ◽  
Stop Codon ◽  
Secondary Structures ◽  
Transcriptional Gene Silencing ◽  
Small Interfering Rnas ◽  
Coding Region ◽  
Post Transcriptional Gene Silencing ◽  
Flanking Sequences

Small interfering RNAs (siRNAs) are applied for post-transcriptional gene silencing by binding target mRNA. A target coding region is usually chosen, although the3′-untranslated region (3′-UTR) can also be a target. This study elucidates whether the coding region or3′-UTR elicits higher repression. pFLuc and pRLuc are two reporter plasmids. A segment ofFLucgene was PCR-amplified and inserted behind the stop codon of theRLucgene of the pRLuc. Similarly, a segment ofRLucgene was inserted behind the stop codon ofFLuc. Two siFLuc and two siRLuc were siRNAs designed to target the central portions of these segments. Therefore, the siRNA encountered the same targets and flanking sequences. Results showed that the two siFLuc elicited higher repression when theFLucsegment resided in the coding region. Conversely, the two siRLuc showed higher repression when theRLucsegment was in the3′-UTR. These results indicate that both the coding region and the3′-UTR can be more effective targets. The thermodynamic stability of the secondary structures was analyzed. The siRNA elicited higher repression in the coding region when the target configuration was stable, and needed to be solved by translation. A siRNA may otherwise favor the target at3′-UTR.

The convergence of autophagy, small RNA and the stress response – implications for transgenerational epigenetic inheritance in plants

2014 ◽  
Vol 5 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Neil A. Youngson ◽  
Pin-Chun Lin ◽  
Shih-Shun Lin
Keyword(s):  
Stress Response ◽  
Viral Infection ◽  
Gene Silencing ◽  
Stress Responses ◽  
Epigenetic Inheritance ◽  
Transcriptional Gene Silencing ◽  
Transgenerational Epigenetic Inheritance ◽  
Protein Levels ◽  
Post Transcriptional Gene Silencing ◽  
Autophagic Degradation

AbstractRecent discoveries in eukaryotes have shown that autophagy-mediated degradation of DICER and ARGONAUTE (AGO), the proteins involved in post-transcriptional gene silencing (PTGS), can occur in response to viral infection and starvation. In plants, a virally encoded protein P0 specifically interacts with AGO1 and enhances degradation through autophagy, resulting in suppression of gene silencing. In HeLa cells, DICER and AGO2 protein levels decreased after nutrient starvation or after treatment to increase autophagy. Environmental exposures to viral infection and starvation have also recently been shown to sometimes not only induce a stress response in the exposed plant but also in their unexposed progeny. These, and other cases of inherited stress response in plants are thought to be facilitated through transgenerational epigenetic inheritance, and the mechanism involves the PTGS and transcriptional gene silencing (TGS) pathways. These recent discoveries suggest that the environmentally-induced autophagic degradation of the PTGS and TGS components may have significant effects on inherited stress responses.

scholarly journals The Diversity of Plant Small RNAs Silencing Mechanisms

2019 ◽  
Vol 73 (5) ◽  
pp. 362-367 ◽  
Author(s):  
Jens A. Schröder ◽  
Pauline E. Jullien
Keyword(s):  
Gene Regulation ◽  
Gene Silencing ◽  
Small Rna ◽  
Small Rnas ◽  
Genome Stability ◽  
Molecular Mechanisms ◽  
Transcriptional Gene Silencing ◽  
Regulation Mechanism ◽  
Regulatory Processes ◽  
Post Transcriptional Gene Silencing

Small RNAs gene regulation was first discovered about 20 years ago. It represents a conserve gene regulation mechanism across eukaryotes and is associated to key regulatory processes. In plants, small RNAs tightly regulate development, but also maintain genome stability and protect the plant against pathogens. Small RNA gene regulation in plants can be divided in two canonical pathways: Post-transcriptional Gene Silencing (PTGS) that results in transcript degradation and/or translational inhibition or Transcriptional Gene Silencing (TGS) that results in DNA methylation. In this review, we will focus on the model plant Arabidopsis thaliana. We will provide a brief overview of the molecular mechanisms involved in canonical small RNA pathways as well as introducing more atypical pathways recently discovered.

scholarly journals Exogenous miRNAs induce post-transcriptional gene silencing in plants

Nature Plants ◽  
2021 ◽  
Vol 7 (10) ◽  
pp. 1379-1388 ◽  
Author(s):  
Federico Betti ◽  
Maria Jose Ladera-Carmona ◽  
Daan A. Weits ◽  
Gianmarco Ferri ◽  
Sergio Iacopino ◽  
...  
Keyword(s):  
Small Rnas ◽  
Transcriptional Gene Silencing ◽  
Small Interfering Rnas ◽  
Rnai Machinery ◽  
Plant Communication ◽  
Signalling Molecules ◽  
Post Transcriptional Gene Silencing ◽  
Exogenous Rna ◽  
Micro Rnas ◽  
Living Organisms

AbstractPlants seem to take up exogenous RNA that was artificially designed to target specific genes, followed by activation of the RNA interference (RNAi) machinery. It is, however, not known whether plants use RNAs themselves as signalling molecules in plant-to-plant communication, other than evidence that an exchange of small RNAs occurs between parasitic plants and their hosts. Exogenous RNAs from the environment, if taken up by some living organisms, can indeed induce RNAi. This phenomenon has been observed in nematodes and insects, and host Arabidopsis cells secrete exosome-like extracellular vesicles to deliver plant small RNAs into Botrytis cinerea. Here we show that micro-RNAs (miRNAs) produced by plants act as signalling molecules affecting gene expression in other, nearby plants. Exogenous miRNAs, such as miR156 and miR399, trigger RNAi via a mechanism requiring both AGO1 and RDR6. This emphasizes that the production of secondary small interfering RNAs is required. This evidence highlights the existence of a mechanism in which miRNAs represent signalling molecules that enable communication between plants.

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.

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