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Differential alteration of plant functions by homologous fungal candidate effectors

ABSTRACT: Rust fungi are plant pathogens that cause epidemics which threatens the production of many important plant species, such as wheat, soy, coffee and poplar. Melampsora larici-populina (Mlp) causes the poplar rust and encodes at least 1 184 candidate effectors (CEs), however their functions are poorly known. In this study, we analysed the transcriptome and metabolome of Arabidopsis constitutively expressing CEs of Mlp to discover processes targeted by these fungal proteins. For this purpose, we sequenced the transcriptome and used mass spectrometry to analyse the metabolome of Arabidopsis plants expressing one of 14 selected CEs and of a control line. We found 2 299 deregulated genes in at least one of the 14 transgenic lines. Among the down-regulated genes, the KEGG pathways MAPK signaling pathway and Plant-pathogen interaction were over-represented in six and five of the 14 transgenic lines, respectively. Moreover, the genes down-regulated across the fourteen transgenic lines are related to hormone response and defense. Regarding the metabolome, there were 680 metabolites deregulated across the 14 transgenic lines, with highly unsaturated and phenolic compounds and peptides enriched among down-regulated and up-regulated metabolites, respectively, in almost all transgenic lines. Interestingly, we found that some transgenic lines expressing CEs with no similarity in amino acid sequence had similar patterns of gene and metabolite deregulation, while plants expressing CEs from the same family deregulated different genes and metabolites. Taken together, our results indicate that the sequence of effectors may not be a good predictor of its impact in the plant.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE158410 | GEO | 2020/09/24

REPOSITORIES: GEO

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Differential alteration of plant functions by homologous fungal candidate effectors

Project description:<p>Rust fungi are plant pathogens that cause epidemics which threatens the production of many important plant species, such as wheat, soy, coffee and poplar. Melampsora larici-populina (Mlp) causes the poplar rust and encodes at least 1184 candidate effectors (CEs), however their functions are poorly known. In this study, we analysed the transcriptome and metabolome of Arabidopsis constitutively expressing CEs of Mlp to discover processes targeted by these fungal proteins. For this purpose, we sequenced the transcriptome and used mass spectrometry to analyse the metabolome of Arabidopsis plants expressing one of 14 selected CEs and of a control line. We found 2299 deregulated genes in at least one of the 14 transgenic lines. Among the down-regulated genes, the KEGG pathways “MAPK signaling pathway” and “Plant-pathogen interaction” were over-represented in six and five of the 14 transgenic lines, respectively. Moreover, the genes down-regulated across the fourteen transgenic lines are related to hormone response and defense. </p><p>Regarding the metabolome, there were 680 metabolites deregulated across the 14 transgenic lines, with highly unsaturated and phenolic compounds and peptides enriched among down-regulated and up-regulated metabolites, respectively, in almost all transgenic lines. Interestingly, we found that some transgenic lines expressing CEs with no similarity in amino acid sequence had similar patterns of gene and metabolite deregulation, while plants expressing CEs from the same family deregulated different genes and metabolites. Taken together, our results indicate that the sequence of effectors may not be a good predictor of its impact in the plant.</p>

2020-12-03 | MTBLS2096 | MetaboLights

Network analysis combining proteomics and metabolomics reveals new insights into early responses of Eucalyptus grandis during rust infection.

Project description:Eucalyptus rust is caused by the biotrophic fungus, Austropuccinia psidii, which affects commercial plantations of Eucalyptus, a major raw material for the pulp and paper industry in Brazil. Aiming to uncover the molecular mechanisms involved in rust resistance and susceptibility in Eucalyptus grandis, we used epifluorescence microscopy to follow the fungus development inside the leaves of two contrasting half-sibling genotypes (rust-resistance and rust-susceptible), to determine the time-course for comparative metabolomic and proteomic analyses in plantlets artificially inoculated with rust. Within 24 hours of complete fungal invasion, a total of 709 plant metabolites showed that the rust-resistant genotype suppressed many metabolites 6 hours after inoculation (hai), with responses being progressively induced after 12 hai. In contrast, the rust-susceptible genotype displayed an alternated metabolite response to infection, which culminated in a strong suppression at 24 hai. Multivariate analyses of genotypes and time points were used to select 16 differential metabolites chemically classified as flavonoids, benzenoids and other compounds. Applying the Weighted Gene Co-Expression Network Analysis (WGCNA), rust-resistant and rust-susceptible genotypes had, respectively, 871 and 852 proteins grouped into 14 and 13 modules, of which 10 and 7 protein modules were significantly correlated to the selected metabolites. Functional analyses revealed roles for oxidative-dependent responses leading to temporal activity of metabolites and proteins after 12 hai in rust-resistance, while the initial over-accumulation of metabolites and correlated proteins caused a lack of progressive response after 12 hai in rust-susceptible genotype. This study provides a brief understand on the temporal divergences of resistant and susceptible molecular responses of E. grandis plants to rust.

2021-09-09 | PXD021280 | Pride

Plant breeding involving genetic engineering does not result in unacceptable unintended effects in rice relative to conventional cross-breeding

Project description:Advancements in -omics techniques provide powerful tools to assess potential effects in composition of a plant at the RNA, protein and metabolite levels. These technologies can thus be deployed to assess whether genetic engineering causes changes in plants that go beyond the changes introduced by conventionally plant breeding. Here, we compare the extent of transcriptome and metabolome modification occurring in leaves of four GE rice lines expressing Bacillus thuringiensis (Bt) genes that developed by genetic engineering and seven rice lines developed by conventional cross-breeding. The results showed that both types of crop breeding methods can bring changes at transcriptomic and metabolic levels, but the differences were comparable between the two methods, and were less than those between conventional non-GE lines. Metabolome profiling analysis found several new metabolites in GE rice lines when compared to the closest non-GE parental lines, but these compounds were also found in several of the conventionally bred rice lines. Functional analyses suggest that the differentially expressed genes and metabolites caused by both genetic engineering and conventional cross-breeding do not involve detrimental metabolic pathways. The study successfully employed RNA-sequencing and HPLC-MS technology to assess the unintended changes in new rice varieties, and the results suggest that genetic engineering does not cause unintended effects that go beyond conventional cross-breeding in rice.

2020-10-01 | GSE152572 | GEO

Transcriptomic analysis of Medicago truncatula leaf after Asian soybean rust infection

Project description:To investigate the molecular mechanism of nonhost resistance of M. truncatula against soybean rust, we performed integrated tanscriptome and metabolome analyses using samples derived from M. truncatula leaves inoculated with soybean rust. To identify host signaling pathways triggered by soybean rust infection, we carried out microarray analysis to monitor the expression profiles associated with nonhost resistance including pre-invasive (12 hai) and apoplastic defense (24 hai) using Affymetrix GeneChip® Medicago Genome Array (Affymetrix).

2015-08-18 | E-MTAB-2911 | biostudies-arrayexpress

A multi-OMICs approach sheds light on the higher yield phenotype and enhanced abiotic stress tolerance in tobacco lines expressing the carrot lycopene β-cyclase1 gene

Project description:Here, we combine OMICs (RNAseq, proteomics, and metabolomics) approaches to advance our understanding of the broader effect of LCYB expression on the tobacco genome and metabolism. DcLCYB1 gene with accelerated development, increased carotenoid content, photosynthetic efficiency, and yield might be of general interest in crop species as a strategy to accelerate development and increase biomass production under field conditions. Upon DcLCYB1 expression, the tobacco genome (~2000 genes), proteome (~700 proteins), and metabolome (26 metabolites) showed a high number of changes in the genes involved in metabolic processes related to cell wall, lipids,glycolysis, and secondary metabolism. Gene and protein networks revealed clusters of interacting genes and proteins mainly involved in ribosome and RNA metabolism and translation. In addition, abiotic stress-related genes and proteins were mainly upregulated in the transgenic lines. This was well in line with an enhanced stress (high light, salt, and H2O2) tolerance response in all the transgenic lines compared with the wild type. Altogether, our results show an extended and coordinated response beyond the chloroplast (nucleus and cytosol) at the genome, proteome, and metabolome levels, supporting enhanced plant growth under normal and stress conditions. This final evidence completes the set of benefits conferred by the expression of the DcLCYB1 gene, making it a very promising bioengineering tool to generate super crops.

2021-09-10 | PXD023595 | Pride

Transcription profiling of Rpp2-resistant (PI230970) and susceptible (Embrapa-48) soybean cultivars to soybean rust from infection to symptom development

Project description:Expression profiling in Rpp2-resistant (PI230970) and susceptible (Embrapa-48) plant lines to soybean rust from infection to symptom development

2008-02-28 | E-TABM-230 | biostudies-arrayexpress

Early gestational maternal low-protein diet diminishes hepatic response to fasting in young adult male mice

Project description:Maternal low-protein (MLP) diet can lead to hepatic steatosis, which only develops with ageing. It is still unclear whether the young offspring show any signs of past exposure to prenatal adverse conditions. We hypothesized that early nutritional insult would first affect the dynamic responsiveness to nutritional challenges rather than the static state. We analyzed the transcriptome and metabolome profiles of the hepatic response to fasting/refeeding in young male mice offspring to identify changes induced by early gestational MLP diet. Restricted MLP exposure strictly to early gestation was achieved by the embryo transfer method. As a result, significant transcriptional differences between control and MLP pups were found only in the fasted state. The fasting-induced upregulation of genes for long-chain fatty acid metabolism and of stress response genes related to protein folding were significantly diminished in MLP pups. Gene Set Enrichment Analysis showed that peroxisome proliferator activated receptor  (PPAR)-mediated induction was impaired in fasted MLP pups. Lipid profiling showed that the hepatic signature of triacylglycerols was shifted to longer acyl-chains and higher saturation by the MLP diet. Taken together, early gestational MLP diet affected the hepatic dynamic response to nutritional stress in seemingly healthy young offspring, accompanied with partial deterioration of PPAR action.

2017-09-14 | GSE100313 | GEO

Transcription analysis by RNAseq of adult wheat after inoculation with Puccinia graminis f. sp. tritici

Project description:The RNA sequencing analysis was undertaken to investigate the transcriptomic changes in adult wheat inoculated with Puccinia graminis f. sp. tritici the causal agent of stem rust disease. The project firstly aims to compare gene expression in one susceptible wheat line with two wheat lines exhibiting adult plant resistance to the stem rust. Secondly, the project aims to examine the temporal changes in gene expression in wheat after inoculation. Wheat plants was grown until maturity under greenhouse conditions. Plants were inoculated with Puccinia graminis f. sp. tritici and the flag leaf sheath sampled for RNA sequencing. The project aims to give essential insight into the adult plant resistance response in wheat to Puccinia graminis f. sp. tritici inoculation.

2022-10-30 | E-MTAB-9681 | biostudies-arrayexpress

Lr1-mediated leaf rust resistance pathways of transgenic wheat lines

Project description:The wheat gene Lr1 imparts resistance to certain races of the leaf rust pathogen Puccinia triticina. However, the biological basis underlying the complex resistance mechanisms remains largely unknown. Gene expression profiling analyses using the Affymetrix GeneChipM-BM-. Wheat Genome Array were performed with six independent Lr1 transgenic lines sampled before inoculation (0h) and at 6 and 24 h after inoculation with the avirulent P. triticina race CCDS. For the 6 and 24 h time points, 3M-BM- 384 probe sets corresponding to 2M-BM- 978 transcripts were differentially expressed as compared to the plants before inoculation. Genes involved in defence signalling were triggered as early as 6 h post inoculation (HPI) and included COI1, the primary component of jasmonic acid signalling. By 24 HPI, a shift in plant cellular metabolism, namely carbon conservation, was notable. The enzymes of glycolysis and gluconeogenesis were down-regulated, however, enzymes linked to alternative carbon sequestration processes such as the glyoxylate cycle were up-regulated. Also at 24 HPI, various secondary signalling molecules belonging to the various hormone signalling pathways were triggered. These microarray data suggest that the Lr1 mediated leaf rust resistance is achieved by early onset of defence signalling followed by co-ordinated interplay of metabolism alteration and elicitation of defence responses. We used microarrays to detail the early gene expression events underlying Lr1-mediated resistance to Puccinia triticina pathogen in wheat. Three biological replicates with six independent Lr1 transgenic lines were used in this study to eliminate the possibility of false discovery of genes due to copy number variation or the position of insertion of the transgene Lr1. Early time points of 6 and 24 HPI were compared to 0 h (prior to inoculation) to capture the early signalling events involved in Lr1-mediated response to rust infection.

2012-09-14 | E-GEOD-32151 | biostudies-arrayexpress

Proteomics analysis of transgenic switchgrass overexpressing melatonin biosynthesis genes

Project description:To obtain better insight into the underlying mechanism of melatonin in switchgrass growth, flowering and defence, we performed proteomics analyses between transgenic lines overexpressing melatonin biosynthesis genes and transgenic control (expressing only the empty vector) plants.

2021-10-12 | PXD029065 | iProX

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