Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Comparative RNA-Seq of Cupriavidus necator H16, formerly Ralstonia eutropha H16, grown in minimal media with 3-hydroxypropionic acid (3-HP) or fructose as sole carbon source.

ABSTRACT: 3-hydroxypropionic acid (3-HP) is a promising platform chemical with various industrial applications. Several metabolic routes to produce 3-HP from organic substrates such as sugars or glycerol have been implemented in yeast, enterobacterial species and other microorganisms. In this work, we investigated 3-HP metabolism of the well-studied ‘Knallgas bacterium’ Cupriavidus necator, a potential C1-chassis for the production of 3-HP and other fatty acid derivatives from CO2 and H2. When testing C. necator for its tolerance towards 3-HP, it was noted that it could utilise the compound as the sole source of carbon and energy.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Cupriavidus necator H16

SUBMITTER: Frederik Walter

PROVIDER: E-MTAB-7701 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Grape powdery mildew (PM), caused by the biotrophic ascomycete Erysiphe necator, is a devastating fungal disease that affects most Vitis vinifera cultivars. We have previously identified a panel of V. vinifera accessions from Central Asia with partial resistance to PM that possess a Ren1-like local haplotype. In this study we show that in addition to the typical Ren1-associated late post-penetration resistance, these accessions display a range of different levels of disease development suggesting that alternative alleles or additional genes contribute to determining the outcome of the interaction with the pathogen. To identify potential Ren1-dependent transcriptional responses and functions associated with the different levels of resistance, we sequenced and analyzed the transcriptomes of these Central Asian accessions at two time-points of PM infection. Transcriptomes were compared to identify constitutive differences and PM-inducible responses that may underlie their disease resistant phenotype. Responses to E. necator in all resistant accessions were characterized by an early up-regulation of 13 genes, most encoding putative defense functions, and a late down-regulation of 32 genes, enriched in transcriptional regulators and protein kinases. Potential Ren1-dependent responses included a hotspot of co-regulated genes on chromosome 18. We also identified 81 genes whose expression levels and dynamics correlated with the phenotypic differences between the most resistant accessions ?Karadzhandahal?, DVIT3351.27, and O34-16 and the other genotypes. This study provides a first exploration of the functions associated with varying levels of partial resistance to PM in V. vinifera accessions that can be exploited as sources of genetic resistance in grape breeding programs. Eight varieties (7 resistant to powdery mildew, 2 of which are V. vinifera spp. sylvestris, 5 of which are V. vinifera spp. sativa) are infected with powdery mildew (E. necator) at two timepoints (1 dpi and 5 dpi) with three replicates for each timepoint for each condition (uninfected vs. infected), for a total of 96 samples

Project description:Infection by the pathogen grape powdery mildew (Erysiphe necator) causes changes in the transcriptome of its susceptible host Vitis vinifera. Infection triggers the host to synthesize the signaling molecule salicylic acid (SA) which regulates the expression of a broad range of defense-related plant genes. In addition, it is hypothesized that E. necator directly modulates gene expression in V. vinifera via the haustorial complex. This microarray experiment was designed to dissect host transcriptome changes triggered directly by E. necator infection and indirectly through the SA response. We accomplished this by conducting two separate global leaf transcriptome analyses using the Vitis Affymetrix GeneChip platform: in one, we compared the leaves with fully established PM colonies to healthy reference leaves, in another, we compared healthy leaves with artificially elevated SA levels to healthy reference leaves. Overlaying host transcriptome changes from these two experiments enabled us to glean out V. vinifera genes that modulate their expression in response E. necator in an SA-independent manner. We characterized gene expression profiles in (1) healthy reference leaves, (2) leaves with well-established by E. necator colonies, and (3) healthy leaves in which SA levels were artificially elevated by the presence of methyl salicylate (15 µM) in the atmosphere. Treatments (1) and (2) differed only in the presence E. necator infection, whereas treatments (1) and (3) differed only in SA levels. Consequently, statistical comparisons were made only between signal intensities from treatments (1) and (2) and from treatments (1) and (3). Each treatment was done in three biological repeats, that is, each experiment was repeated three times in 14-day intervals with dedicated biological material (plants were used in a single replicate and not reused in another repeat or treatment). Each biological replicate consisted of 10 potted vines. For RNA extraction, two young leaves were harvested from each of the 10 vines and pooled into a single sample.

Dataset Information

Comparative RNA-Seq of Cupriavidus necator H16, formerly Ralstonia eutropha H16, grown in minimal media with 3-hydroxypropionic acid (3-HP) or fructose as sole carbon source.

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