Quantitative transcriptional changes associated with chlorosis severity in mosaic leaves of tobacco plants infected with the Cucumber mosaic virus
Ontology highlight
ABSTRACT:
ORGANISM(S): Nicotiana tabacum
PROVIDER: GSE47410 | GEO | 2013/09/15
SECONDARY ACCESSION(S): PRJNA205533
REPOSITORIES: GEO
Similar Datasets
Project description:In this study, we compared transcriptomes in chlorotic tissues infected with wild type CMV or two CP mutants (129A and 129Q) with diverse chlorosis severity. Differentially expressed genes analysis showed that the CMV inoculation appeared to have similar effects on transcriptional expression profiles of the symptomatic chlorotic tissues and only the magnitude of expression differed among CMVs. Gene ontology analysis with biological process and cellular component terms revealed that many nuclear genes related to abiotic stress responses, including cadmium, heat, cold, and salt, were up-regulated while chloroplast- and photosynthesis-related genes (CPRGs) were down-regulated in the chlorotic tissues. Interestingly, down-regulation level of CPRGs was correlated with the chlorosis severity. The expression difference genes (DEGs) between mock-inoculated healthy tissues and CMV-inoculated chlorotic tissues in mosaic leaves of tobacco plants were examined by the comparison on one-colour microarray data. Three biological replicates per each treatment were used in this experiment.
2013-09-15 | E-GEOD-47410 | biostudies-arrayexpress
Project description:Cucumber mosaic virus (CMV) causes mosaic disease in inoculated tobacco plants. Coat protein (CP) is one of the major virulence determinants of CMV, and an amino acid substitution at residue 129 in CP alters the severity of chlorosis, such as pale green chlorosis and white chlorosis, in symptomatic tissues of mosaic leaves of infected tobacco. In this study, we compared the transcriptomes of chlorotic tissues infected with the wild-type pepo strain of CMV and two strains carrying CP mutants with diverse chlorosis severity. Differential gene expression analysis showed that CMV inoculation appeared to have similar effects on the transcriptional expression profiles of the symptomatic chlorotic tissues, and only the magnitude of expression differed among the different CMVs. Gene ontology analysis with biological process and cellular component terms revealed that many nuclear genes related to abiotic stress responses, including responses to cadmium, heat, cold and salt, were up-regulated, whereas chloroplast- and photosynthesis-related genes (CPRGs) were down-regulated, in the chlorotic tissues. Interestingly, the level of CPRG down-regulation was correlated with the severity of chlorosis. These results indicate that CP mutation governs the repression level and mRNA accumulation of CPRGs, which are closely associated with the induction of chlorosis.
| S-EPMC6638806 | biostudies-literature
Project description:A pseudometallophyte Arabidopsis halleri is frequently found to be infected with cucumber mosaic virus (CMV) in its natural habitat. The purpose of this study is to elucidate the effect of CMV infection on its natural hosts. The CMV(Ho) strain isolated from A. halleri was inoculated into clonal A. halleri plants that were obtained from runners of mother plants, and the pathosystem consisting of CMV(Ho) and its natural host A. halleri was established.In low heavy metal environment, the CMV(Ho) infection caused growth retardation in the above-ground part (stems and leaves) of host plants, and thereby conferred strong drought tolerance on host plants. On the other hand, in high heavy metal environment, which simulates a natural habitat for A halleri, the CMV(Ho) infection did not cause any symptoms to host plants and conferred mild drought tolerance. And the result of transcriptome analysis suggests that CMV(Ho) is recognized as a symbiont rather than a pathogen by its host plant. These results indicate a resilient mutualistic interaction between CMV(Ho) and its natural host A. halleri to adapt to an environmental change.
2022-03-05 | GSE197739 | GEO
Project description:We constructed two independent small RNA libraries from leaves of mock and Cucumber mosaic virus (CMV) infected tomatoes, respectively, and sequenced with a high-throughput Illumina Solexa system. Based on sequence analysis and hairpin structure prediction, a total of 50 known miRNAs (32 families) and 568 potentially candidate miRNAs (PC-miRNAs) were firstly identified in tomato, with 12 known miRNAs and 154 PC-miRNAs supported by both the 3p and 5p strands. Comparative analysis revealed 79 miRNAs (including 15 novel tomato miRNAs) and 40 PC-miRNAs were differentially expressed between the two libraries. Among these virus responsive miRNAs, expression patters of some novel tomato miRNAs and PC-miRNAs in mock and in CMV-Fny infected tomatoes were further validated by qRT-PCR. Moreover, we revealed 563 potential targets for 66 tomato miRNAs by the recently developed degradome sequencing approach, including 124 targets for 7 new tomato miRNAs and 97 targets for 24 PC-miRNAs. Target annotation for the newly identified miRNA and PC-miRNAs indicated that they were involved in multiple biological processes, including transcriptional regulation and virus resistance. Gene ontology analysis of these target transcripts demonstrated that stress response- and photosynthesis-related genes were most affected in CMV-Fny infected tomatoes. Examination of small RNAs and their targets in mock and CMV-Fny infected tomatoes.
2014-10-20 | E-GEOD-56974 | biostudies-arrayexpress
Project description:We constructed two independent small RNA libraries from leaves of mock and Cucumber mosaic virus (CMV) infected tomatoes, respectively, and sequenced with a high-throughput Illumina Solexa system. Based on sequence analysis and hairpin structure prediction, a total of 50 known miRNAs (32 families) and 568 potentially candidate miRNAs (PC-miRNAs) were firstly identified in tomato, with 12 known miRNAs and 154 PC-miRNAs supported by both the 3p and 5p strands. Comparative analysis revealed 79 miRNAs (including 15 novel tomato miRNAs) and 40 PC-miRNAs were differentially expressed between the two libraries. Among these virus responsive miRNAs, expression patters of some novel tomato miRNAs and PC-miRNAs in mock and in CMV-Fny infected tomatoes were further validated by qRT-PCR. Moreover, we revealed 563 potential targets for 66 tomato miRNAs by the recently developed degradome sequencing approach, including 124 targets for 7 new tomato miRNAs and 97 targets for 24 PC-miRNAs. Target annotation for the newly identified miRNA and PC-miRNAs indicated that they were involved in multiple biological processes, including transcriptional regulation and virus resistance. Gene ontology analysis of these target transcripts demonstrated that stress response- and photosynthesis-related genes were most affected in CMV-Fny infected tomatoes.
2014-10-20 | GSE56974 | GEO
Project description:Plant viruses are a major threat for a wide range of host species, causing substantial losses in agriculture. Particularly, Cucumber mosaic virus (CMV) evokes severe symptoms, thus dramatically limiting yield. Activation of plant immunity is associated with changes in the gene expression and consequently, cellular proteome to ensure virus resistance. Proteomics proved to be an extremely valuable tool for discovering multiple targets for the rational design of plant protection strategies. Herein, we studied two cultivars of cucumber (Cucumis sativus) resistant ´Heliana´ and susceptible ´Vanda´. Plant cotyledons were mechanically inoculated with CMV isolate PK1, and systemic leaves were harvested at 33 days post-inoculation. Upon protein extraction and filter-aided sample preparations, peptides were profiled by ultrahigh-performance liquid chromatography and comprehensively quantified by ion mobility enhanced mass spectrometry. From 1,516 reproducibly quantified proteins using label-free approach, 133 were differentially abundant among genotypes or treatments by strict statistic and effect size criteria. Pigments and hydrogen peroxide measurements corroborated proteomic findings. Advanced bioinformatics revealed a modular network of affected host proteins. Direct comparison of both genotypes in the uninfected state highlighted more abundant photosynthetic and development-related proteins in resistant cucumber cultivar. Long-term CMV infection showed worse preservation of energy processes and less robust translation in susceptible cultivar versus resistant genotype. Contrary, susceptible cultivar had numerous more abundant stress and defense-related proteins. We proposed promising targets for functional validation in transgenic lines a step toward durable virus resistance in cucurbits and other crops.
2020-01-09 | PXD015088 | Pride
Project description:RNA silencing has an important role mediating sequence-specific virus resistance. Here, we analyzed in detail the interference of Cucumber Mosaic Virus (CMV) with the RNA silencing machinery of Arabidopsis thaliana. We detected that CMV infection induced the production of viral small interfering RNAs (vsiRNAs) that account for a significant part of the sRNome affecting the levels of other sRNA classes. Furthermore, we analyzed the incorporation of vsiRNAs into the main ARGONAUTE (AGO) proteins with a described antiviral role and the viral RNA silencing suppressor (VRS) 2b, by combining protein immunoprecipitation with sRNA high-throughput sequencing. vsiRNAs accumulated to high levels in AGO2, followed by AGO1, AGO5 and AGO7. Interestingly, vsiRNAs represented a significant percentage of AGO-loaded sRNAs and displaced other endogenous sRNAs. As a countermeasure, the VSR 2b loaded vsiRNAs and mRNA-derived siRNAs, which affected the expression of the genes they derived from. Additionally, we analyzed how vsiRNAs incorporated into the endogenous RNA silencing pathways by exploring their target mRNAs using parallel analysis of RNA end (PARE) sequencing. This strategy allowed us to identify 61 genes with degradome data supporting their vsiRNA-mediated cleavage. This work exemplifies the complex relationship of RNA viruses with the endogenous RNA silencing machinery and the multiple aspects of virus resistance and virulence that this interaction induces.
2021-12-01 | GSE169677 | GEO
Project description:Cyanobacteria that do not fix nitrogen adapt to prolonged periods of nitrogen deprivation in a chlorotic state where cell growth and metabolism is arrested. Upon nutrient availability, the cells return back to vegetative growth within 2-3 days. This resuscitation process is highly orchestrated and relies on the stepwise re-installation and activation of essential cellular structures and functions. We investigate transition into chlorosis and return to vegetative life as a simple model of a cellular developmental process that represents a fundamental survival strategy in biology. In the present study, we describe the process through quantitative proteomics and phosphoproteomics analysis of long-term nitrogen-starved Synechocystis sp. PCC 6803 cells during different time points of resuscitation. Intriguingly, substantial O phosphorylation of proteins involved in photosynthesis was detected in the chlorotic state, including hyperphosphorylation of the remaining phycobiliproteins. We provide evidence that hyperphosphorylation of the terminal rod linker CpcD increases the lifespan of phycobiliproteins during chlorosis.
2018-06-28 | PXD008027 | Pride
Project description:Background: Congenital cytomegalovirus (cCMV) is a common intrauterine infection, leading to neurodevelopmental disabilities. Early prognostic assessment of the severity of cCMV has remained an ongoing challenge. We aimed to identify amniotic fluid biomarkers of the severity of cCMV-related fetal brain injury. Methods: Global proteome analysis was performed in mid-gestation amniotic fluid samples, comparing fetuses with severe cCMV to asymptomatic CMV-infected fetuses (the discovery cohort). The levels of selected differentially-excreted proteins were further determined by specific immunoassays, and evaluated in an independent validation cohort, including clinically-blinded amniotic fluid of CMV-infected fetuses from unrelated centers. Findings: Proteome analysis identified 29 amniotic fluid proteins with distinct abundance in fetuses with severe-, compared to asymptomatic, cCMV. Pathway analysis of the differentially-excreted proteins revealed enriched pathways of inflammatory response, cellular compromise, immunological disease, organismal injury, and neurological disease, underlining a link between excessive inflammation at the maternal-fetal interface and the development of cCMV-related fetal brain damage. Importantly, the levels of two of these proteins, chemerin and galectin-3-binding protein (Gal-3BP), selected for validation, demonstrated 88.2% sensitivity (each), 100-96.2% specificity, 100-93.8% positive predictive value, and 92.9-92.6% negative predictive value, with 0.98-0.97 area under the curve (for chemerin - Gal-3BP, respectively) in differentiating 17 fetuses with severe cCMV from 26 asymptomatic CMV-infected fetuses. Interpretation: These results identify the immunomodulatory proteins chemerin and Gal-3BP as new highly predictive amniotic fluid biomarkers of cCMV severity, which could guide early prognostic stratification and potential personalized treatment of cCMV-infected fetuses. Funding: Israel Science Foundation; Research Fund of the Hadassah Medical Organization
2022-05-25 | PXD029105 | Pride
Project description:Cucumber mosaic virus (CMV), which is vectored by aphids, has a tripartite RNA genome encoding five proteins. In tobacco (Nicotiana tabacum), a subgroup IA CMV strain, Fny-CMV, increases plant susceptibility to aphid infestation but a viral mutant unable to express the 2b protein (Fny-CMV?2b) induces aphid resistance. We hypothesized that in tobacco, one or more of the four other Fny-CMV gene products (the 1a or 2a replication proteins, the movement protein, or the coat protein) are potential aphid resistance elicitors, whilst the 2b protein counteracts induction of aphid resistance. Mutation of the Fny-CMV 2b protein indicated that inhibition of virus-induced resistance to aphids (Myzus persicae) depends on amino acid sequences known to control nucleus-to-cytoplasm shuttling. LS-CMV (subgroup II) also increased susceptibility to aphid infestation but the LS-CMV?2b mutant did not induce aphid resistance. Using reassortant viruses comprising different combinations of LS and Fny genomic RNAs, we showed that Fny-CMV RNA 1 but not LS-CMV RNA 1 conditions aphid resistance in tobacco, suggesting that the Fny-CMV 1a protein triggers resistance. However, the 2b proteins of both strains suppress aphid resistance, suggesting that the ability of 2b proteins to inhibit aphid resistance is conserved among divergent CMV strains.
| S-EPMC6988427 | biostudies-literature