Project description:We report the banana transcriptome profile in response to two distinct growth-promoting rhizobacteria, Bacillus amyloliquefaciens and Pseudomonas fluorescens. The goal of our study is to identify plant genes differentially regulated by rhizobacteria-plant interaction along time. At the same time, we show that despite these two rhizobacteria regulate distinct sets of genes, the same functional categories has been over-represented, such as transcription factor activity, response to stress and metabolic processes.
Project description:Purpose: The goal of this study is to demonstrate the global expression profile of Arabidopsis wild type and PRR mutant plants in response to PTI- and ETI-eliciting strains of Pseudomonas syringae pv tomato (Pst) bacterium. Methods: Four-week-old Arabidopsis plant leaves were infiltrated with sterile water (Mock) or different Pst strains and harvested at 3h or 6h after infiltration for RNA extraction and deep sequencing by Illumina. Raw data were cleaned up and trimmed and reads were mapped to Arabidopsis genome. Gene expression levels were calculated using the TPM method (Transcripts per Kb of exon model per Million mapped reads). Results and Conclusions: This study showed that Pst DC3000 D36E and D36E(avrRpt2) strains both induced significant gene expression changes (with changes of more than 3000 and 7000 genes respectively) in Col-0 plant, and D36E(avrRpt2) strain induced stronger expression changes globally. Furthermore, many genes are differentially regulated in the PRR mutant plants in response to D36E inoculation compared with wild type plant; however, D36E(avrRpt2) inoculation induced very similar expression patterns in two genotypes, suggesting that ETI can largely restore PTI-associated gene expression in the PRR mutant plant. In addition, we also found that ETI can largely induce the expression levels of many key PTI signaling components.
Project description:we investigated three Bacillus strains (HT1, HT2, and HT3) isolated from the soybean root microbiome for their potential plant growth-promoting and biocontrol activities. Bacillus-HT1 and HT2 significantly enhanced soybean seed germination, while Bacillus-HT3 promoted leaf area expansion, indicating strain-specific developmental effects. To elucidate the molecular basis of these effects, we conducted shotgun proteomic profiling of soybean leaves. The analysis revealed significant modulation of proteins involved in key biological processes, including amino acid metabolism, biosynthesis of cellular nitrogen and aromatic compounds, and cellular component organization and biogenesis. Notably, proteins such as anthranilate synthase and proteasome subunit alpha type were differentially expressed, suggesting the activation of growth- and defense-related pathways. These findings provide mechanistic insights into how specific Bacillus strains modulate soybean development at the molecular level and highlight their potential for use as bio-inoculants to enhance crop productivity and resilience under stress conditions.
Project description:We used RNA-seq to profile E. coli K-12 MG1655 strains subjected to adaptive laboratory evolution after knockout of endogenous glucose-6-phosphate isomerase (pgi) and subsequent expression of heterologous version of the pgi gene from Pseudomonas aeruginosa and Bacillus megaterium.
Project description:We introduced the GAME1i construct into the indeterminate M82 cultivar by crossing, obtaining plants that displayed a phenotype of severe growth retardation, deformed leaves and abortion of flower buds . In addition, leaves of these plants exhibited dark necrotic spots resembling symptoms typically seen after infection of tomato by pathogenic bacteria like Xanthamonas campestris pv. vesicatoria (Xcv) or Pseudomonas syringae pv. tomato (Pst) . As no other tomato lines grown in the same greenhouse at the same time showed similar disease-like symptoms, we hypothesized that silencing GAME1 might mimic induction of disease symptoms in the absence of a pathogen. Indeed, we were able to isolate neither Xcv nor Pst (or other putative pathogens) from GAME1i leaves that displayed necrotic spots. Microarray analysis was performed to examine if the transgene, and possibly, the corresponding changes in the metabolic profile, induced the plant response system at the transcriptional level.
Project description:We used three different strains of Pseudomonas syringae pv tomato DC3000 to investigate systemic responses to infection in Arabidopsis and the development of SAR. Wildtype DC3000, the hrpA mutant and DC3000 carrying the avirulence gene avrRpm1 were syringe infiltrated into 4-week-old plants at a concentration of 10e8 cfu/ml. At least 5 leaves per plant were infiltrated and at least 10 plants were pooled for each sample. Systemic, uninfected tissue was then harvested at 8, 12 and 21h after inoculation. Three independent experiments were carried out to give three biological replicates for each timepoint.
Project description:We sought to compare and contrast plant host and bacterial transcriptional changes during compatible infections that cause disease (albeit within different symptoms). We investigated the infection by the two Pseudomonas syringae sensu lato strains P. syringae pv. syringae B728a (Psy) and P. amygdali pv. tabaci 11528 (Pta) of Nicotiana benthamiana at an early time point post inoculation to understand how a plant host responds to two related bacteria with different infection strategies. Plant and bacterial transcriptomes were analyzed prior to and five hours post inoculation.
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.
Project description:We acquired the largest bacterial proteomic resource, covering 303 species, 119 genera, and five phyla. The proteome coverage is, on average, over 50%. Additionally, we acquired further datasets for bacterial identification algorithm validation: i) 303 species at a 30-minute gradient (38 samples per day throughput), ii) 303 species at a 10-minute gradient (80 samples per day throughput), iii) reproducibility dataset, iv) genus-specific Pseudomonas spp. dataset (94 Pseudomonas spp. strains), v) genus-specific Bacillus spp. dataset (28 Bacillus cereus s.l. strains), vi) food routine dataset (60 dairy product isolates), and vii) clinical routine dataset (570 clinical isolates).