Multiple cellular compartments engagement in Nicotiana benthamiana-peanut stunt virus-satRNA interactions revealed by systems biology approach
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PROVIDER: PRJNA526723 | ENA |
REPOSITORIES: ENA
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Project description:Virus infection is a process resulting in numerous molecular, cellular, and physiological changes, a wide range of which can be analyzed due to development of many high-throughput techniques. Plant RNA viruses are known to replicate in the cytoplasm; however, the roles of chloroplasts and other cellular structures in the viral replication cycle and in plant antiviral defense have been recently emphasized. Therefore, the aim of this study was to analyze the small RNAs, transcripts, proteins, and phosphoproteins affected during peanut stunt virus strain P (PSV-P)–Nicotiana benthamiana interactions with or without satellite RNA (satRNA) in the context of their cellular localization or functional connections with particular cellular compartments to elucidate the compartments most affected during pathogenesis at the early stages of infection. Moreover, the processes associated with particular cell compartments were determined. The ‘omic’ results were subjected to comparative data analyses. Transcriptomic and small RNA (sRNA)–seq data were obtained to provide new insights into PSV-P–satRNA–plant interactions, whereas previously obtained proteomic and phosphoproteomic data were used to broaden the analysis to terms associated with cellular compartments affected by virus infection. Based on the collected results, infection with PSV-P contributed to changes in the abundance of transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and the cytosol, and the most affected processes were photosynthesis, translation, transcription, and mRNA splicing. Furthermore, sRNA-seq and phosphoproteomic analyses indicated that kinase regulation resulted in decreases in phosphorylation levels. The kinases were associated with the membrane, cytoplasm, and nucleus components.
2021-05-27 | GSE128200 | GEO
Project description:Key messagePSV infection changed the abundance of host plant's transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and cytosol, affecting photosynthesis, translation, transcription, and splicing. Virus infection is a process resulting in numerous molecular, cellular, and physiological changes, a wide range of which can be analyzed due to development of many high-throughput techniques. Plant RNA viruses are known to replicate in the cytoplasm; however, the roles of chloroplasts and other cellular structures in the viral replication cycle and in plant antiviral defense have been recently emphasized. Therefore, the aim of this study was to analyze the small RNAs, transcripts, proteins, and phosphoproteins affected during peanut stunt virus strain P (PSV-P)-Nicotiana benthamiana interactions with or without satellite RNA (satRNA) in the context of their cellular localization or functional connections with particular cellular compartments to elucidate the compartments most affected during pathogenesis at the early stages of infection. Moreover, the processes associated with particular cell compartments were determined. The 'omic' results were subjected to comparative data analyses. Transcriptomic and small RNA (sRNA)-seq data were obtained to provide new insights into PSV-P-satRNA-plant interactions, whereas previously obtained proteomic and phosphoproteomic data were used to broaden the analysis to terms associated with cellular compartments affected by virus infection. Based on the collected results, infection with PSV-P contributed to changes in the abundance of transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and the cytosol, and the most affected processes were photosynthesis, translation, transcription, and mRNA splicing. Furthermore, sRNA-seq and phosphoproteomic analyses indicated that kinase regulation resulted in decreases in phosphorylation levels. The kinases were associated with the membrane, cytoplasm, and nucleus components.
| S-EPMC8233301 | biostudies-literature
Project description:Peanut stunt virus (PSV) of Cucumovirus genus is serious vegetables and legume pathogen. Some PSV strains are associated with satellite RNA (satRNA). SatRNAs are dependent on their helper virus and their presence usually attenuates the severity of the disease symptoms induced by the virus. However, the final outcome of satRNA pathogenesis modification depends on the satRNA sequence, virus strain and external conditions. In this study we elucidated the plant response to PSV-G strain which occurs in natural conditions without satRNA. However, it was found that it might easily acquire satRNA which causes exacerbation of pathogenesis in Nicotiana benthamiana. In order to study plant response to PSV infection and to explain mechanisms underlying symptoms exacerbation caused by satRNA we did transcriptome profiling of N. benthamiana challenged by PSV with/ without satRNA using species-specific microarrays.
2017-09-20 | GSE104026 | GEO
Project description:Peanut stunt virus (PSV) belongs to cucumoviruses which infect many agriculturally important plants. Certain PSV strains contain a small RNA molecule, referred to as satellite RNA (satRNA), which has a propensity to modulate pathogenesis process.Plant viruses with ssRNA genomes are known to replicate in cytoplasm, however, they utilize other cellular structures to their life cycle as well. Among them the role of chloroplast is recently particularly underlined. Here, we tried to indicate the host factors associated with various cellular structures, the levels of which are changed during virus infection. To this end we did transcriptome profiling of N. benthamiana challenged by PSV-P with/ without satRNA using species-specific microarrays.
2019-06-22 | GSE133124 | GEO
Project description:Signaling in host plants is an integral part of a successful infection by pathogenic RNA viruses. Therefore, identifying early signaling events in host plants that play an important role in establishing the infection process will help our understanding of the disease process. In this context, phosphorylation constitutes one of the most important post-translational protein modifications, regulating many cellular processes. In this study, we aimed to identify the processes affected by peanut stunt virus (PSV) and its satellite RNA (satRNA) infection in Nicotiana benthamiana at the early stage of pathogenesis. To achieve this, we performed proteome and phosphoproteome analyses on plants treated with PSV and its satRNA. The analysis of the number of differentially phosphorylated proteins showed strong down-regulation in phosphorylation in virus-treated plants (without satRNA). Moreover, the proteome analysis revealed more down-regulated proteins in PSV+satRNA-treated plants, which indicated a complex dependence between proteins and their modifications. Apart from changes in photosynthesis and carbon metabolism usually observed in virus-infected plants, alterations in proteins involved in RNA synthesis, transport, and turnover were observed. This is the first community resource on the proteome and phosphoproteome of cucumovirus and its satRNA infection in N. benthamiana constituting a valuable data set for future studies.
2018-10-25 | PXD010675 | Pride
Project description:The presence of satellite RNA exacerbates symptoms and transcriptomic response of Nicotiana benthamiana during peanut stunt virus infection
| PRJNA407984 | ENA
Project description:Rice ragged stunt virus (RRSV) is the causal agent of rice ragged stunt disease which causes severe loss of rice yield in Asia countries. In this study, we have analyzed the relationship between symptom and host gene responses by RRSV infection. Comparison between RRSV and mock infected rice. Biological replicates: 3 control, 3 infected, independently grown and harvested. 1 samples derived from 5 plants grown under same conditons
2012-12-01 | E-GEOD-34265 | biostudies-arrayexpress
Project description:Rice ragged stunt virus (RRSV) is the causal agent of rice ragged stunt disease which causes severe loss of rice yield in Asia countries. In this study, we have analyzed the relationship between symptom and host gene responses by RRSV infection.
2012-12-01 | GSE34265 | GEO
Project description:Maize bushy stunt phytoplasma overview
| PRJNA35673 | ENA
Project description:Peanut stunt virus (PSV) is a widespread disease infecting legumes. The PSV strains are classified into four subgroups and some are defined by the association of satellite RNAs (satRNAs). In the case of PSV, the presence of satRNAs alters the symptoms of disease in infected plants. In this study, we elucidated the plant response to PSV-G strain, which occurs in natural conditions without satRNA. However, it was found that it might easily acquire satRNA, which exacerbated pathogenesis in Nicotiana benthamiana. To explain the mechanisms underlying PSV infection and symptoms exacerbation caused by satRNA, we carried out transcriptome profiling of N. benthamiana challenged by PSV-G and satRNA using species-specific microarrays. Co-infection of plants with PSV-G + satRNA increased the number of identified differentially expressed genes (DEGs) compared with the number identified in PSV-G-infected plants. In both treatments, the majority of up-regulated DEGs were engaged in translation, ribosome biogenesis, RNA metabolism, and response to stimuli, while the down-regulated DEGs were required for photosynthesis. The presence of satRNA in PSV-G-infected plants caused different trends in expression of DEGs associated with phosphorylation, ATP binding, and plasma membrane.
| S-EPMC6165542 | biostudies-literature