Ontology highlight
ABSTRACT:
PROVIDER: PRJNA387702 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5591370_1.fastq.gz | Fastqsanger.gz | |||
| SRR5591370_2.fastq.gz | Fastqsanger.gz | |||
| SRR5591380_1.fastq.gz | Fastqsanger.gz | |||
| SRR5591380_2.fastq.gz | Fastqsanger.gz | |||
| SRR5591371_1.fastq.gz | Fastqsanger.gz |
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Project description:Virus infection induces activation and suppression of global gene expression in the host. Profiling gene expression changes in the host may provide insights into the molecular mechanisms that underlie host physiological and phenotypic responses to virus infection. In this study, the Arabidopsis Affymetrix ATH1 whole genome array was used to assess global gene expression changes in Arabidopsis thaliana plants infected with Plum pox virus (PPV). To identify early genes in response to PPV infection, an Arabidopsis synchronized single-cell transformation system was developed. Arabidopsis protoplasts were transfected with a PPV infectious clone, PPV-SK68 and global gene expression changes in the transfected protoplasts were profiled. Experiment Overall Design: For PPV infection in Arabdiopsis leaves, eight independent hybridizations were performed using total RNA isolated from three independent biological replicates of the virus-infected or mock-inoculated control samples. Experiment Overall Design: For PPV infection in Arabidopsis protoplasts, 24 gene chips in total were used to hybridize with RNA isolated from protoplasts transfected with PPV infectious clone and PPV deletion mutant.
2008-11-07 | E-GEOD-11217 | biostudies-arrayexpress
Project description:Virus infection induces activation and suppression of global gene expression in the host. Profiling gene expression changes in the host may provide insights into the molecular mechanisms that underlie host physiological and phenotypic responses to virus infection. In this study, the Arabidopsis Affymetrix ATH1 whole genome array was used to assess global gene expression changes in Arabidopsis thaliana plants infected with Plum pox virus (PPV). To identify early genes in response to PPV infection, an Arabidopsis synchronized single-cell transformation system was developed. Arabidopsis protoplasts were transfected with a PPV infectious clone, PPV-SK68 and global gene expression changes in the transfected protoplasts were profiled. Keywords: Time course and cell type comparison
2008-11-04 | GSE11217 | GEO
Project description:Phosphorylation and O-GlcNAcylation are widespread post-translational modifications (PTMs) often sharing protein targets. Numerous studies have reported phosphorylation of plant virus proteins. In plants, research on O-GlcNAcylation lags behind regarding other eukaryotes and information about O-GlcNAcylated plant viral proteins is extremely scarce. The potyvirus Plum pox virus (PPV) causes sharka disease in Prunus trees, and also infects a wide range of experimental hosts. Capsid protein (CP) from virions of the PPV-R isolate purified from herbaceous plants can be extensively modified by O-GlcNAcylation and phosphorylation. In this study, a combination of proteomics and biochemical approaches has been employed to broaden knowledge of PPV CP PTMs. CP proved to be modified regardless it is assembled or not in mature particles. PTMs of CP occur in the natural host Prunus persica, similar to what happens in herbaceous plants. Additionally, we observe O-GlcNAcylation and phosphorylation are general features of different PPV strains, suggesting that roles of these modifications are part of overall strategies deployed during plant-virus interactions. Interestingly, phosphorylation at a casein kinase II motif conserved among potyviral CPs exhibits strain specificity in PPV; however, it does not display the critical role attributed to same modification in the CP of another potyvirus, Potato virus A.
2020-05-27 | PXD017780 | Pride
Project description:Plum pox virus (PPV) causes the serious sharka disease in Prunus trees. Peach [P. persica (L.) Batsch] trees are severely affected by PPV and no definitive source of genetic resistance has been identified at this moment. Previous results showed, however, that PPV-resistant ‘Garrigues’ almond [P. dulcis (Mill.) D.A. Webb] was able to transfer its resistance to ‘GF305’ peach through grafting, preventing these trees from PPV infection and reducing symptomatology and viral load in PPV-infected plants. A recent study tried to identify genes responsible for this effect by studying mRNA expression through RNAseq data in peach and almond plants, before and after grafting, and before and after PPV infection. In this work, we used the same peach and almond samples, but focused the high-throughput analyses on small RNAs (sRNAs) expression. We studied massive sequencing data and found an interesting pattern of sRNAs overexpression linked to antiviral defense genes that suggested activation of these genes followed by downregulation to basal levels. We also discovered that ‘Garrigues’ almond plants were infected by different plant viruses that were transferred to peach plants. The large amounts of viral sRNAs found in grafted peaches indicated a strong RNA silencing antiviral response and led us to postulate that these plant viruses could be collaborating by cross-protection in the observed ‘Garrigues’ effect.
2022-11-02 | GSE188935 | GEO
Project description:Transcriptomes of wild-type Nicotiana benthamiana plants inoculated with plum pox virus (PPV) or the P1Pro clone, a PPV deletion mutant that lacks the self-cleavage inhibitory domain of the P1 leader protease; in addition, N. benthamiana nahG-expressing plants inoculated with P1Pro were analyzed to identify genes whose expression is altered by P1Pro infections but does not depend on salicylic acid signaling.
2020-07-30 | GSE146746 | GEO
Project description:Plum pox virus (PPV, family Potyviridae) is one of the most important viral pathogens of Prunus spp. causing considerable damage to stone-fruit industry worldwide each year. Among the PPV strains identified so far, only PPV-C and PPV-CR are able to infect cherries under natural conditions. Herein, we evaluated the impact of strains differing by the pathogenic potential on herbaceous host Nicotiana benthamiana. At first glance, a faster accumulation of PPV capsid protein was noticed by semi-quantitative DAS-ELISA on tobacco leaves infected by PPV-CR (the RU-30sc isolate) in contrast to PPV-C (BY-101 isolate). This result was correlated perfectly with observed phenotypic symptoms. To assess the host response to infection more deeply, a comprehensive proteomic profiling was performed using reverse phase UHPLC followed by label-free mass spectrometry quantification. Thirty-one unique plant proteins were identified as significantly altered due to the infection. Precise evaluation of particular amount shifts of identified proteins in relation to infection has revealed that the aggressive PPV-CR isolate has a stronger influence on the abundance of photosynthesis-related proteins, mainly from Calvin cycle, as the mild PPV-C. This observation was accompanied by a significant reduction of photosynthetic pigments extracted from the leaves of PPV-CR infected plants. Shifts in the abundance of remaining identified proteins, indicates activation of repair mechanism, stimulation of photosynthetic capacity, and modifications in amino acid and carbohydrate metabolism to affect plant growth and initiate energy formation via gluconeogenesis. Furthermore, we speculate that accumulation of H2O2, in PPV-CR infected leaves may activate glutathione synthesis, which plays a crucial role in further plant defense and development.
2018-08-13 | PXD010018 | Pride
Project description:Phosphorylation and O-GlcNAcylation are two widespread post-translational modifications (PTM) often affecting the same eukaryotic target protein. Plum pox virus (PPV) is a member of the genus Potyvirus that infects a wide range of plant species. O-GlcNAcylation of the capsid protein (CP) of PPV has been extensively studied, and some evidence about CP phosphorylation has been additionally reported. Here, we made use of proteomics analyses to demonstrate that PPV CP is phosphorylated in vivo at its N-terminal region. In contrast with the classical “Yin-Yang” mechanism that applies to some mammalian proteins, PPV CP phosphorylation affects residues different from the O-GlcNAcylated ones (serines Ser-25, Ser-81, Ser-101 and Ser-118). Our findings show that PPV CP can be concurrently phosphorylated and O-GlcNAcylated at nearby residues. However, an analysis using a differential proteomics strategy based on iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) showed a significant enhancement of phosphorylation at Ser-25 in virions recovered from O-GlcNAcylation-deficient plants, which uncovers the existence of some cross-talk between O-GlcNAcylation and phosphorylation in PPV-CP. Whereas precluding phosphorylation at the four identified phosphotarget sites only had a limited impact in viral infection, mimicking phosphorylation prevents PPV infection in Prunus persica and weakens infection in Nicotiana benthamiana and other herbaceous hosts, favouring the emergence of potentially compensatory second mutations. We postulate that the joint action of phosphorylation and O-GlcNAcylation in the N-terminal region of CP allows a fine-tuning of the protein stability, providing the fair amount of CP required in each step of viral infection.
2022-03-03 | PXD006159 | Pride
Project description:Objectives: Our work focuses on the responses of Solanaceous plants to viruses that cause economically important diseases in tree fruits. Using mock inoculated leaf tissue as a reference, we plan to compare the gene expression profiles of Nicotiana Benthamiana plants infected with one of three viruses; Plum Pox Potyvirus (PPV), Tomato Ringspot Nepovirus (ToRSV), and Prunus Nectrotic Ringspot Nepovirus (PNRSV). Our goals are as follows: (1) Identify genes that are induced/repressed in response to individual viruses. (2) Identify genes that are induced/repressed in response to all 3 viruses. (3) Compare results to existing potato array data to look for similarities in responses to other pathogens. Experimental Design: Nicotiana benthamiana plants were inoculated with one of three viruses: PPV, ToRSV, or PNRSV. 3 week old plants were inoculated by rubbing virus infected plant sap onto leaves dusted with carborundum. Control plants were mock inoculated using sap from healthy plants. All plants were maintained in a growth chamber at 22C for 18 days. 8 plants were inoculated with each virus or mock inoculated. This experiment was repeated twice. 4 biological replicates derived from 2 virus infected plants from each replica experiment (4 plants) are to be used for hybridizations. RNA from all mock inoculated plants was similarly pooled to create 4 biological replicates. Each replicate control will serve as a universal reference sample that is to be hybridized pair wise with each of the three virus infected samples. RNA extraction: After 18 days, un-inoculated leaves displaying clear symptoms were harvested and immediately frozen in liquid N2. Total RNA was purified using Trizol according to TIGRs listed protocol. RNA was subsequently treated with Turbo DNA-free RNase (Ambion cat#1907). Finally, total RNA was further purified on RNeasy columns (Qiagen) according to manufacturer’s instructions and quantified using a Nanodrop spectrophotometer. Keywords: Reference design 23 hybs total
2007-09-01 | E-GEOD-8256 | biostudies-arrayexpress
Project description:Hypersensitive response-related programmed cell death (PCD) has been extensively analyzed in various plant–virus interactions. However, little is known about changes in gene expression associated with cell death caused by compatible viruses. The synergistic interaction of Potato virus X (PVX) with Plum pox virus (PPV) results in increased symptoms that lead to systemic necrosis (SN) in Nicotiana benthamiana. Here, we performed three transcriptome comparisons in response to i) a PVX recombinant virus expressing the helper component-proteinase (HC-Pro) gene from PPV that leads to SN, ii) a systemic incompatible interaction conferred by the Tobacco mosaic virus (TMV)-resistance gene N (SHR), and iii) the depletion of the PBE subunit of the proteasome that leads to PCD by virus induced gene silencing (VIGS Prot), at early and late stages of infection. Our analysis indicated that the SN response was clustered with SHR by the similarity of their overall gene expression profiles. However, the expression profiles of defence-related and hormone-responsive genes in response to SN were more closely related to the response to VIGS Prot than to that elicited by SHR. This suggests the potential contribution of proteasome dysfunction to the increase in pathogenicity observed in PVX-potyvirus infections
2012-02-02 | GSE34841 | GEO
Project description:In this study we used a translating ribosome affinity purification strategy to identify phloem and non-phloem associated translatomes in Prunus domesitca L during PPV infection. Three different promoter:His6FLAG-RPL18 lines were used. These included two phloem specific promoters (pSUC2 and pSULTR2;2) as well as the more ubiquitously expressed cauliflower mosaic virus 35S promoter (p35S). Immunopurification of ribosome-mRNA complexes was accomplished by the method described in Reynoso et al. (Plant Functional Genomics: Methods and Protocols, 185-207; 2015). The dataset includes samples from plum leaves taken at 2, 4, 6, and 12 weeks post cold induced dormancy.
2019-07-30 | GSE131832 | GEO