Comparative analysis of RNA interference and pattern-triggered immunity induced by dsRNA in response to virus infection
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ABSTRACT:
PROVIDER: PRJNA1068016 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27697244_1.fastq.gz | Fastqsanger.gz | |||
| SRR27697244_2.fastq.gz | Fastqsanger.gz | |||
| SRR27697245_1.fastq.gz | Fastqsanger.gz | |||
| SRR27697245_2.fastq.gz | Fastqsanger.gz | |||
| SRR27697246_1.fastq.gz | Fastqsanger.gz |
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Project description:The main goal of this study was to compare the differential efficiency of the antiviral activity triggered by externally delivered virus-specific and nonspecific dsRNAs in plants. RNAi mediated by virus-specific dsRNA is the main antiviral defense mechanism in plants, but nonspecific dsRNA-triggered responses have been documented to play a role in antiviral defense. Using PVX as a model, we have determined that co-inoculation with either virus-specific or nonspecific dsRNA reduced virus accumulation in both inoculated and systemic leaves although at different extent. While the administration of dsRNA specific for the targeted virus induced a potent RNAi-based antiviral response that resulted in highly effective control of viral disease, the degree of interference with PVX-GFP infection afforded by nonspecific dsRNA (PTI) was limited. To identify early biological processes and pathways associated with dsRNA-based immunity, we conducted a global transcriptome RNAseq assay from N. benthamiana leaves inoculated with four different treatments, i.e., dsGFP alone (dsG), PVX-GFP combined with dsGFP (dsG_VG), wild-type (Wt) PVX combined with dsGFP (dsG_V) and bacterial nucleic acid extracts not expressing dsRNA as a control (Ctr). KEGG analysis of differentially expressed genes showed a significant enrichment of terms related to plant-pathogen signaling pathways (KEGG terms Plant-pathogen interaction and MAPK signaling) in all the three treatments with dsRNA. Our results further indicate that the transcriptomic response triggered by dsRNA alone includes canonical immune pathways or genes known to be involved in defense responses, i.e., Ca+2 signaling, ethylene signaling, MAPK signaling, WRKY transcription factors, PR transcriptional factors, NBS-LRR resistance genes, EDS1, and LRR receptor-like kinases, many of which are typical of antimicrobial PTI . Moreover, the transcriptomic response to the homologous combination (dsGFP plus PVX-GFP) had a greater overrepresentation of genes involved in plant-pathogen signaling pathways than the heterologous combination (dsGFP plus Wt PVX), highlighting a quantitative difference between RNAi and PTI immune responses.
2024-02-12 | GSE253964 | GEO
Project description:tRNA-seq of Arabidopsis leaves during pattern-triggered immunity
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Project description:Plants deploy cell surface and intracellular leucine rich-repeat domain (LRR) immune receptors to detect pathogens. LRR receptor kinases (LRR-RKs) and LRR receptor proteins (LRR-RPs) recognise microbe-derived molecules to elicit pattern-triggered immunity (PTI), whereas nucleotide-binding LRR (NLR) proteins detect microbial effectors inside cells to confer effector-triggered immunity (ETI). Although PTI and ETI are initiated in different host cell compartments, they rely on the transcriptional activation of similar sets of genes, suggesting pathway convergence upstream of nuclear events. We report that PTI triggered by Arabidopsis LRR-RP (RLP23) requires signalling-competent dimers of the lipase-like proteins EDS1 and PAD4, and ADR1-family helper NLRs, which are all components of ETI. The cell surface LRR-RK SOBIR1 links RLP23 with EDS1, PAD4 and ADR1 proteins, suggesting formation of constitutive supramolecular complexes containing PTI receptors and transducers at the inner side of the plasma membrane.
2021-07-05 | PXD026120 | Pride
Project description:In this work we developed and exploited a spray-induced gene silencing (SIGS)-based approach to deliver double-stranded RNA (dsRNA), which was found to protect potato against potato virus Y (PVY) infection. Given that dsRNA can act as a defence-inducing signal that can trigger sequence-specific RNA interference (RNAi) and non-specific pattern-triggered immunity (PTI), we suspected that these two pathways may be invoked via exogeneous application of dsRNA, which may account for the alterations in PVY susceptibility in dsRNA-treated potato plants. Therefore, we tested the impact of exogenously applied PVY-derived dsRNA on both these layers of defence (RNAi and PTI) and explored its effect on accumulation of a homologous virus (PVY) and an unrelated virus (potato virus X, PVX). Here, we show that application of PVY dsRNA in potato plants induced accumulation of both small interfering RNAs (siRNAs), a hallmark of RNAi, and some PTI-related gene transcripts such as WRKY29 (WRKY transcription factor 29; molecular marker of PTI), RbohD (respiratory burst oxidase homolog D), EDS5 (enhanced disease susceptibility 5), SERK3 (somatic embryogenesis receptor kinase 3) encoding brassinosteroid-insensitive 1-associated receptor kinase 1 (BAK1), and PR-1b (pathogenesis-related gene 1b). With respect to virus infections, PVY dsRNA suppressed only PVY replication but did not exhibit any effect on PVX infection in spite of the induction of PTI-like effects in the presence of PVX. Given that RNAi-mediated antiviral immunity acts as the major virus resistance mechanism in plants, it can be suggested that dsRNA-based PTI alone may not be strong enough to suppress virus infection. In addition to RNAi- and PTI-inducing activities, we also showed that PVY-specific dsRNA is able to upregulate production of a key enzyme involved in poly(ADP-ribose) metabolism, namely poly(ADP-ribose) glycohydrolase (PARG), which is regarded as a positive regulator of biotic stress responses. These findings offer insights for future development of innovative approaches which could integrate dsRNA-induced RNAi, PTI and modulation of poly(ADP-ribose) metabolism in a co-ordinated manner, to ensure a high level of crop protection.
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Project description:During pattern-triggered immunity (PTI), the first line of active defense against infection in plants, the translatome undergoes rapid reprogamming. To understand how defense proteins are selectively translated, we conducted a genetic screen for regulators of PTI using a translational reporter. We identified a mutant of RNA helicase 12 (RH12) showing compromised reporter translation and pathogen resistance. RH12 is a homolog of yeast DEAD-box Helicase Homolog 1, which targets mRNAs with low codon optimality for decay. Therefore, we sequenced the Arabidopsis tRNAome to determine codon optimality during PTI. We discovered a PTI-associated reduction in overall codon optimality of the transcriptome, and found that the decay of transcripts with reduced optimality is mediated by interaction with RH12. Our results demonstrate the first example of codon optimality-associated decay as part of an adaptive response in which the dynamics of both the tRNAome and the transcriptome facilitate rapid changes in translational output during PTI.
2023-04-02 | GSE171411 | GEO
Project description:The apoplast is a critical interface in plant-pathogen interactions particularly in the context of pattern-triggered immunity (PTI), which is initiated by recognition of microbe-associated molecular patterns (PAMPs). Our study characterizes the proteomic profile of the Arabidopsis apoplast during PTI induced by flg22, a 22 amino acid bacterial flagellin epitope, to elucidate the output of PTI. Apoplastic washing fluid (AWF) was extracted with minimal cytoplasmic contamination for LC-MS/MS analysis. We observed consistent identification of PTI enriched and depleted peptides across replicates with limited correlation between total protein abundance and transcript abundance. We observed topological bias in peptide recovery of receptor-like kinases with peptides predominantly recovered from their ectodomains. Notably, tetraspanin 8, an exosome marker, was enriched in PTI samples. We additionally confirmed increased concentrations of exosomes during PTI. This study enhances our understanding of the proteomic changes in the apoplast during plant immune responses and lays the groundwork for future investigations into the molecular mechanisms of plant defense under recognition of pathogen patterns.
2025-02-11 | PXD060654 | Pride
Project description:Genome-wide identification of transcribed enhancer candidates during pattern triggered immunity in Arabidopsis
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Project description:Seedlings of Arabidopsis wild type and ATE1/2 double knock-out mutants were treated with flagellin 22 peptide to elicit pathogen-triggered immunity (PTI) responses. Leaves were harvested and proteome composition assessed.
2024-07-25 | PXD046263 | Pride
Project description:RNA interference (RNAi) is a gene-silencing mechanism triggered by the cytosolic entry of double-stranded RNAs (dsRNAs). Many animal cells internalize extracellular dsRNAs via endocytosis for RNAi induction. However, it is not clear how the endocytosed dsRNAs are translocated into the cytosol across the endo/lysosomal membrane. Herein, we show that in Drosophila S2 cells, endocytosed dsRNAs induce lysosomal membrane permeabilization (LMP) that allows cytosolic dsRNA translocation. LMP mediated by dsRNAs requires the lysosomal Cl−/H+ antiporter ClC-b/DmOstm1. In clc-b or dmostm1 knockout S2 cells, extracellular dsRNAs are endocytosed and reach the lysosomes normally but fail to enter the cytosol. Pharmacological induction of LMP restores extracellular dsRNA-directed RNAi in clc-b or dmostm1-knockout cells. Furthermore, clc-b or dmostm1 mutant flies are defective in extracellular dsRNA-directed RNAi and its associated antiviral immunity. Therefore, endocytosed dsRNAs have an intrinsic ability to induce ClC-b/DmOstm1-dependent LMP that allows cytosolic dsRNA translocation for RNAi responses in Drosophila cells.
2024-07-07 | GSE244523 | GEO
Project description:Plants have evolved a two-layered immune system that mainly includes pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) against pathogen attack. PTI and ETI signaling are functionally linked, but also distinct due to specific perceived ligands and activation modes. Unraveling how PTI and ETI coordinate the immune responses against pathogens is crucial for understanding the regulatory mechanisms in plant immunity. To better understand the protein profiling and phosphorylation events during PTI and ETI, we employed integrated whole proteome and phosphoproteome analyses in the tomato-Pst pathosystem with different Pst DC3000 mutants that allow dissection of different layers of immune responses. A total of 225 proteins and 79 phosphopeptides were differentially regulated in tomato leaves during immune responses. Our proteomics results indicate that some overlapping immune responses are triggered by both PTI and ETI-inducing treatment, and ETI response is more robust than PTI response for most proteins. The change patterns of protein abundance and phosphorylation revealed some key regulators involved in Ca2+ signaling, mitogen-activated protein kinase cascades, and reversible protein phosphorylation, ROS and redox homeostasis, direct defense, transcription machinery and protein turnover, cell wall remodeling, hormone biosynthesis, as well as immune molecule accumulation, are modulated during PTI and/or ETI, suggesting their common or specific roles in plant immune responses. However, NAC domain protein and lipid particle serine esterase, two PTI-specific genes from previous transcriptomic work, have not been detected as differentially regulated in our proteomic analysis, and they were proved to be not PTI-specific inducible and therefore cannot be used as PTI-reporters through “overlapping circle” pattern assay. These results provide insights into the fine-tuned regulatory mechanisms between PTI and ETI in-Pst pathosystem, which will springboard further investigations into the sophisticated mechanisms in plant immunity.
2021-11-25 | PXD028240 | Pride