Viral Silencing Suppressors and Plant Viruses

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Questions and Answers

What are the two types of gene silencing?

  • Transcriptional Gene Silencing (TGS) and Post-Transcriptional Gene Silencing (PTGS) (correct)
  • Transcriptional Gene Silencing (TGS) and Post-Translational Gene Silencing (PTGS)
  • Transcriptional Gene Silencing (TGS) and Post-Translational Gene Silencing (PTGS)

RNA silencing mechanisms are unique to plants and invertebrates.

False (B)

What are the three phases of RNA silencing?

  • Initiation Phase, Activation Phase, and Amplification Phase
  • Activation Phase, Effector Phase, and Amplification Phase
  • Initiation Phase, Effector Phase, and Amplification Phase (correct)

What type of enzyme processes dsRNA into short, 21-24 nt long, small RNA (sRNA) duplexes?

<p>Dicer</p> Signup and view all the answers

What enzyme stabilizes sRNA at the 3' end?

<p>HEN1</p> Signup and view all the answers

What protein exports sRNA from the nucleus?

<p>HASTY</p> Signup and view all the answers

What protein is involved in the silencing complex that induces slicing or translational repression of target RNAs for PTGS?

<p>Argonaute</p> Signup and view all the answers

What protein is involved in the RITS complex that causes histone and/or DNA methylation for TGS?

<p>Argonaute</p> Signup and view all the answers

Which of these are classes of small RNAs identified in plants?

<p>natural-antisense RNAs (nat-siRNAs) (A), repeat-associated siRNAs (ra-siRNAs) (B), microRNAs (miRNAs) (C), virus-activated siRNAs (vasiRNAs) (D), viral siRNAs (vsiRNAs) (E), trans-acting small interfering RNAs (ta-siRNAs) (F)</p> Signup and view all the answers

The production of viral siRNAs (vsiRNAs) is a hallmark of the antiviral silencing response.

<p>True (A)</p> Signup and view all the answers

Which DCL is mainly responsible for vsiRNA production from RNA virus infections?

<p>DCL4 (A)</p> Signup and view all the answers

What type of protein is involved in viral silencing suppression?

<p>Viral suppressor of RNA silencing (VSR)</p> Signup and view all the answers

Which of these mechanisms can be used to block the mounting of antiviral silencing?

<p>Dicer protein inhibition (A), AGO protein destabilization (B), dsRNA/siRNA-sequestration (C)</p> Signup and view all the answers

What is the name of the suppressor protein encoded by tombusviruses that sequesters siRNAs?

<p>P19</p> Signup and view all the answers

P19 sequesters both siRNAs and miRNAs.

<p>False (B)</p> Signup and view all the answers

The suppressor protein PO from poleroviruses possesses RNA binding activity.

<p>False (B)</p> Signup and view all the answers

PO enhances the degradation of multiple AGOS through the proteasome pathway.

<p>False (B)</p> Signup and view all the answers

What protein encoded by Sweet potato mild mottle ipomovirus (SPMMV) can directly interact with siRNA-loaded AGO1?

<p>P1</p> Signup and view all the answers

What kind of motifs are involved in the interaction of SPMMV P1 protein with AGO1?

<p>GW/WG motifs</p> Signup and view all the answers

What is the name of the TCV suppressor protein that can suppress silencing at multiple levels?

<p>p38</p> Signup and view all the answers

The p38 suppressor protein binds to both loaded and unloaded AGOs.

<p>False (B)</p> Signup and view all the answers

The p37 protein encoded by Pelargonium line pattern virus (PLPV) mainly acts by sequestering siRNAs.

<p>True (A)</p> Signup and view all the answers

What protein has the characteristic of binding ss-sRNAs but not dsRNA?

<p>AC4</p> Signup and view all the answers

What is the name of the protein encoded by Rice stripe virus that can suppress GFP silencing and also prevent long distance spread of silencing signal?

<p>NS3</p> Signup and view all the answers

What are the main functions of host RDRs (RDR1, RDR2, and RDR6)?

<p>RDRs are crucial for the amplification of RNA silencing and the spread of a systemic silencing signal.</p> Signup and view all the answers

What is the name of the protein in Tomato yellow leaf curl virus that directly interacts with SGS3 to block silencing amplification?

<p>V2</p> Signup and view all the answers

What is the name of the protein encoded by potexviruses that can inhibit RDR6/SGS3-dependent dsRNA synthesis?

<p>TGBp1</p> Signup and view all the answers

The suppressor protein 2b encoded by CMV can only prevent the spread of the silencing signal.

<p>False (B)</p> Signup and view all the answers

The 2b suppressor protein can also interact with AGO4.

<p>True (A)</p> Signup and view all the answers

What is the name of the host protein that interacts with potyviral HC-Pro?

<p>rgsCAM</p> Signup and view all the answers

RgsCAM can directly bind to HC-Pro and block its dsRNA binding activity.

<p>True (A)</p> Signup and view all the answers

It has been experimentally proven that the release of R-gene based defense is the cause of the inhibitory action of pathogen-encoded suppressors of silencing.

<p>False (B)</p> Signup and view all the answers

What is the name of the host hormone that is involved in local and systemic antiviral defense responses?

<p>Salicylic acid (SA)</p> Signup and view all the answers

What is the name of the viral suppressor that inhibits SA-induced gene expression through NPR1?

<p>CaMV P6 suppressor</p> Signup and view all the answers

Viral suppressors can be utilized as tools to unravel the molecular mechanisms of both antiviral and endogenous RNA silencing.

<p>True (A)</p> Signup and view all the answers

The use of viral suppressors can aid in the development of transgenic plants in biotechnology.

<p>True (A)</p> Signup and view all the answers

Why are viral suppressors important for the arms race between host and pathogen?

<p>Viral suppressors help to regulate multiple layers of the complex defense, counter-defense, and counter-counter-defense systems that are involved in host-pathogen interactions.</p> Signup and view all the answers

Viral suppressors are only effective against antiviral silencing and not against endogenous silencing.

<p>False (B)</p> Signup and view all the answers

Viral suppressors can only block one or a few steps in the RNA silencing pathway.

<p>False (B)</p> Signup and view all the answers

The suppressor protein PO from poleroviruses is more effective in suppressing silencing at a single cell level compared to siRNA binding proteins.

<p>False (B)</p> Signup and view all the answers

Suppression of antiviral silencing can be detrimental to host endogenous silencing.

<p>True (A)</p> Signup and view all the answers

Overexpression of VSRs can be a factor in the development of viral symptoms, however VSRs themselves may not be directly responsible for virus-induced symptoms in all cases.

<p>True (A)</p> Signup and view all the answers

Viral suppressors have the potential to be used to develop new plant breeding technologies through epigenetic modifications.

<p>True (A)</p> Signup and view all the answers

The use of natural host-virus pairs is an important approach in the future for furthering our understanding of viral silencing.

<p>True (A)</p> Signup and view all the answers

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Flashcards

RNA silencing

A fundamental genetic regulatory mechanism that controls gene expression by degrading mRNA or blocking translation. It plays a vital role in plant development, stress response, and defense against viral invaders.

RNA silencing initiation

A process that occurs in RNA silencing where dsRNA (double-stranded RNA) is processed into short, 21–24 nucleotides long, small RNA (sRNA) duplexes by a protein called Dicer.

Post-transcriptional gene silencing (PTGS)

A type of RNA silencing that acts at the post-transcriptional level, directly targeting mRNA molecules for degradation or blocking their translation.

Transcriptional gene silencing (TGS)

A type of RNA silencing that targets genes at the transcriptional level, causing changes in chromatin structure and gene silencing.

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Antiviral silencing

RNA silencing specific to viruses, targeting viral RNA to prevent their replication and spread throughout the plant.

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small interfering RNAs (siRNAs)

Short, double-stranded RNA molecules produced during RNA silencing. They are the key effectors of silencing, guiding the silencing machinery to target specific genes for degradation or repression.

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Dicer-like proteins (DCLs)

A family of enzymes with RNase III activity, responsible for processing dsRNA into siRNAs.

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DOUBLE-STRANDED RNA BINDING (DRB) proteins

Proteins that bind to dsRNA and are essential for Dicer activity, mediating the accurate production of siRNAs.

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microRNAs (miRNAs)

Short sequences of RNA (20–24 nucleotides) processed from longer, non-coding RNAs. They act as regulatory molecules, influencing gene expression by targeting mRNAs for silencing.

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Argonaute proteins (AGOs)

A family of proteins that bind to siRNAs and act as the effectors of RNA silencing. They guide the silencing machinery to target specific mRNAs for degradation or translational repression.

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RNA-Induced Silencing Complex (RISC)

A complex formed by an Argonaute protein loaded with a small RNA (like an siRNA or miRNA). It uses the guide siRNA or miRNA to recognize target mRNA molecules, silencing their expression by cleaving the RNA or blocking translation.

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RNA Induced Transcriptional Silencing complex (RITS)

A complex that acts in transcriptional gene silencing. It consists of an AGO protein bound to siRNA and interacts with chromatin, inducing methylation of specific DNA regions, leading to gene silencing.

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AGO1 and AGO2 proteins

Proteins that act as the main effectors in antiviral silencing by binding to viral siRNAs and targeting viral RNA. They play a central role in preventing viral replication and spread.

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HEN1 protein

An enzyme that adds a methyl group to the 3’ end of siRNAs. This methylation enhances siRNA stability and processing, contributing to a more robust antiviral response.

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HYL1/DRB1 protein

A protein that is crucial for the proper loading of siRNAs into AGO proteins. This loading process is essential for forming a functional RISC complex.

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RNA-dependent RNA polymerases (RDRs)

A class of enzymes that synthesize double-stranded RNA (dsRNA) from single-stranded RNA templates. They play a critical role in amplifying RNA silencing signals, generating more siRNAs.

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Viral suppressors of RNA silencing (VSRs)

Viral proteins encoded by viruses that interact with the plant's RNA silencing machinery to suppress its activity, thereby allowing viruses to evade the plant's immune response.

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VSRs blocking initiation of antiviral response

Viral proteins that target the Dicer-like proteins (DCLs), preventing them from processing dsRNA into siRNAs and thus blocking the initiation of RNA silencing

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VSRs sequestering siRNAs

Viral proteins that bind directly to siRNAs, sequestering them and preventing them from loading into AGO proteins to form a functional RISC complex.

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VSRs destabilizing AGO proteins

Viral proteins that interact with and destabilize Argonaute (AGO) proteins, preventing them from forming a functional RISC complex.

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VSRs directly targeting RISC components

Viral proteins that target specific components of the RISC complex, preventing it from carrying out its silencing functions, like cleaving target RNA.

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VSRs blocking RDR activity

Viral proteins that block the activity of RDRs, enzymes that amplify the silencing signal, thereby preventing a robust silencing response.

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VSRs targeting multiple silencing steps

Viral proteins that target multiple steps in the RNA silencing pathway, acting at various points to suppress its activity and allow viruses to evade the host's defenses.

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VSR interactions with host factors

A type of interaction between viral suppressor proteins (VSRs) and host factors, such as specific plant proteins that regulate signaling pathways or immune responses.

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Limitation of VSRs' suppressor strength

A mechanism where viruses evolve VSRs with varying strengths, balancing their ability to suppress the plant's immune response with the need to maintain their own viability.

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VSRs linking RNA-based and protein-based immunity

A dynamic interaction between viral suppressor proteins (VSRs) and the plant's RNA-mediated and protein-based immune systems. VSRs can manipulate both systems to promote viral infection.

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VSRs connecting antiviral silencing to hormone signaling

The ability of viral suppressor proteins (VSRs) to influence plant hormone signaling pathways, manipulating the plant's developmental responses to their advantage.

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VSRs as tools for studying silencing

Viral suppressors of RNA silencing (VSRs) can be utilized as tools to investigate the molecular mechanisms of RNA silencing, providing valuable insight into the process.

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VSRs as biotechnological and medical tools

Viral suppressors of RNA silencing (VSRs) have potential applications in molecular biology and biotechnology, such as developing new antiviral therapies or modifying gene expression in plants.

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Conclusions and perspectives on VSRs

Viral suppressor proteins (VSRs) serve as powerful tools for research and have possible diverse applications in biotechnology. The field offers abundant opportunities for further discoveries and breakthroughs.

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Study Notes

Viral Silencing Suppressors

  • RNA silencing is a gene inactivation process regulated by homology-dependent mechanisms, playing a vital role in antiviral defense in biological systems.
  • Viruses have evolved viral suppressors of RNA silencing to counteract host antiviral responses, enabling coexistence.
  • Viral suppressors of silencing (VSRs) can have other functions besides silencing suppression during viral infection, often in complex ways that are still not fully understood.
  • VSRs impact various steps of antiviral silencing in plants, including initiation, effector phase, and amplification.
  • Understanding VSRs is important for improving crop plants and for molecular biology/biotechnology applications.

Plant Viruses

  • Plant viruses, a significant class of pathogens, reduce crop yield and quality.
  • Different types of plant viruses (positive-sense, negative-sense, double-stranded RNA/DNA) utilize different replication strategies.
  • Viruses interact with plant host factors to manipulate biochemical events and molecular interactions crucial for virus replication and movement.
  • Viruses can spread within plants via plasmodesmata or vascular systems.
  • Host defenses against viruses include programmed hypersensitive reaction (HR), systemic acquired resistance (SAR), ubiquitin/26S proteasome system activation (UPS), and RNA silencing.

RNA Silencing Pathways

  • RNA silencing is fundamental for gene regulation in eukaryotes, influencing various biological processes.
  • It can operate at the transcriptional (TGS) or post-transcriptional (PTGS) levels.
  • RNAi pathways involve processing of double-stranded RNA (dsRNA) into small RNAs (sRNAs) by Dicer (DCL).
  • sRNAs bind Argonaute proteins, forming RISC (RNA-induced silencing complex) for targeted slicing, transcript repression or amplification of silencing responses .
  • sRNAs also bind RITS (RNA-induced transcriptional silencing) for histone/DNA methylation.

Antiviral Silencing Host Factors

  • Viral siRNAs (vsiRNAs) are a hallmark of antiviral silencing, produced from various viral dsRNA sources.
  • DCL proteins are crucial in the initiation phase processing viral dsRNA into vsiRNAs.
  • DCL4 is most critical for RNA virus response, with DCL2 having a supporting role.
  • DCL3 plays a minor role against RNA viruses and a more important role in defense against DNA viruses.
  • DCL1 is a positive regulator in vsiRNA production, applicable for both RNA and DNA viruses.

Actions of Viral Suppressors of RNA Silencing

  • VSRs employ various strategies to evade host silencing, including blocking initiation, arresting RISC assembly, or impairing silencing amplification.
  • Some VSRs bind dsRNAs to prevent RISC assembly.
  • VSRs can destabilize AGO proteins essential for RISC activity.
  • VSRs act on silencing amplification, suppressing RDR functions.
  • VSRs can modulate AGO protein levels and homeostasis through silencing pathways.

VSR Interactions with Host Factors

  • VSRs can modulate host factors that regulate silencing, affecting hormone signaling or general host defenses (e.g. influencing SA/JA pathways).
  • VSRs can interact with other silencing factors, forming complexes to regulate host functions.
  • VSRs can regulate the steps of the silencing pathway to their advantage/benefit.

Limitations of VSRs' Suppressor Strength

  • Some VSRs may selectively affect antiviral versus endogenous silencing pathways, impacting specific components or pathways in different ways.

VSRs as Tools

  • VSRs can be used in molecular research to unravel RNA silencing pathways (antiviral and endogenous).
  • VSRs have applications in biotechnology.
  • VSRs can be used in diagnostics especially in the detection of microRNAs.

Conclusions

  • VSRs play a major regulatory role in the complex interactions between host and pathogen, impacting various host defenses.

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