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 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 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 Targets and Mechanisms of Geminivirus Silencing Suppressor Protein AC2

2021 ◽  
Vol 12 ◽  
Author(s):  
Karuppannan Veluthambi ◽  
Sukumaran Sunitha
Keyword(s):  
Gene Silencing ◽  
Defense Mechanism ◽  
Transcriptional Gene Silencing ◽  
Silencing Suppressor ◽  
Biotechnological Applications ◽  
Important Food ◽  
Dna Viruses ◽  
Post Transcriptional Gene Silencing ◽  
Transcriptional Activator Protein ◽  
Wide Range

Geminiviruses are plant DNA viruses that infect a wide range of plant species and cause significant losses to economically important food and fiber crops. The single-stranded geminiviral genome encodes a small number of proteins which act in an orchestrated manner to infect the host. The fewer proteins encoded by the virus are multifunctional, a mechanism uniquely evolved by the viruses to balance the genome-constraint. The host-mediated resistance against incoming virus includes post-transcriptional gene silencing, transcriptional gene silencing, and expression of defense responsive genes and other cellular regulatory genes. The pathogenicity property of a geminiviral protein is linked to its ability to suppress the host-mediated defense mechanism. This review discusses what is currently known about the targets and mechanism of the viral suppressor AC2/AL2/transcriptional activator protein (TrAP) and explore the biotechnological applications of AC2.

scholarly journals Two suppressors of RNA silencing encoded by cereal-infecting members of the family Luteoviridae

2012 ◽  
Vol 93 (8) ◽  
pp. 1825-1830 ◽  
Author(s):  
Yan Liu ◽  
Hao Zhai ◽  
Kun Zhao ◽  
Beilei Wu ◽  
Xifeng Wang
Keyword(s):  
Gene Silencing ◽  
Rna Silencing ◽  
Barley Yellow Dwarf Virus ◽  
Yellow Dwarf ◽  
Dwarf Virus ◽  
Transcriptional Gene Silencing ◽  
Post Transcriptional Gene Silencing ◽  
The Family ◽  
Cultivated Plant ◽  
Yellow Dwarf Virus

Several members of the family Luteoviridae are important pathogens of cultivated plant species of the family Gramineae. In this study, we explored RNA-silencing suppressors (RSSs) encoded by two cereal-infecting luteoviruses: barley yellow dwarf virus and wheat yellow dwarf virus (BYDV and WYDV, respectively). The P0 protein of WYDV-GPV (P0GPV) and the P6 protein of BYDV-GAV (P6GAV) displayed RSS activities when expressed in agro-infiltrated leaves of Nicotiana benthamiana, by their local ability to inhibit post-transcriptional gene silencing of GFP. Analysis of GFP, mRNA and GFP-specific small interfering RNA indicated that both P0GPV and P6GAV are suppressors of silencing that can restrain not only local but also systemic gene silencing. This is the first report of RSS activity of the P6 protein in a member of the genus Luteovirus.

scholarly journals Gene silencing by double stranded Ribonucleic acid (RNA)

2020 ◽  
Vol 5 (1) ◽  
pp. 41
Author(s):  
Hafiz Ghulam Muhu-Din Ahmed ◽  
Amna . ◽  
Shadab Shaukat ◽  
Iqra Kousar ◽  
Maria Rafiq ◽  
...  
Keyword(s):  
Rna Interference ◽  
Gene Silencing ◽  
Ribonucleic Acid ◽  
Rna Silencing ◽  
Defense Mechanism ◽  
Review Article ◽  
Transcriptional Gene Silencing ◽  
Post Transcriptional Gene Silencing ◽  
Silencing Pathways

Ribonucleic acid (RNA) silencing, RNA interference (RNAi) or post-transcriptional gene silencing takes place in a variety of eukaryotes and it was discovered firstly in the plants. The RNA silencing process is activated by a trigger from dsRNA predecessor. A very important step in the silencing pathways the conversion of dsRNA into small duplexes of RNA of the representative length and arrangement. Then these small dsRNA monitor RNA silencing by different mechanisms. Post transcriptional gene silencing mechanisms were initially identified as an anti-viral process that give protection to the organisms from the viruses or which inhibit the unsystematic incorporation of transposable components. The basic aim of this review article is to study the mechanism of gene silencing by dsRNA and the roles of certain proteins in cellular post transcriptional RNA silencing machinery and finally we also discuss the RNA silencing as an anti-viral defense mechanism in the plants. 

scholarly journals Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways inArabidopsis

RNA ◽  
2014 ◽  
Vol 20 (12) ◽  
pp. 1987-1999 ◽  
Author(s):  
Tadeusz Wroblewski ◽  
Marta Matvienko ◽  
Urszula Piskurewicz ◽  
Huaqin Xu ◽  
Belinda Martineau ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Small Rna ◽  
Inverted Repeat ◽  
Rna Silencing ◽  
Transcriptional Gene Silencing ◽  
Post Transcriptional Gene Silencing ◽  
Silencing Pathways

scholarly journals Interaction of dengue NS3 with human RNA silencing machinery through HSPA1A

2020 ◽  
Author(s):  
Pavan Kumar Kakumani ◽  
Rajgokul K. Shanmugam ◽  
Mahendran Chinnappan ◽  
Inderjeet Kaur ◽  
Arun P. Chopra ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Rna Silencing ◽  
Viral Suppression ◽  
Host Factors ◽  
Transcriptional Gene Silencing ◽  
Defence Mechanism ◽  
Expression Levels ◽  
Argonaute Proteins ◽  
Post Transcriptional Gene Silencing ◽  
Suppressor Of Rna Silencing

AbstractViruses encode multiple proteins that interact with different host factors to aid in their establishment inside the host. Viral Suppressor of RNA silencing (VSR) are one such class of proteins that have been shown to interact with components of host machinery involved in post transcriptional gene silencing, a known antiviral defence mechanism. In the present study, we showed that dengue NS3, a known VSR not only interacts with HSPA1A, a cellular chaperone, but also modulates its expression levels. Further, we revealed HSPA1A associated with host RNA silencing machinery through its interaction with Argonaute proteins; Ago1, Ago2 and co-localizes with them in the cytoplasm of the cell. Together, these results provide evidence for involvement of other host partners in mediating VSR function of dengue NS3 and aid in deeper understanding of mechanisms underlying viral suppression of RNA silencing.

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.

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