Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Metabolic and transcriptional response of Arabidopsis thaliana wildtype and mutants to Phytophtora infestans

ABSTRACT: The oomycete P. infestans is the causal agent of late blight, the most devastating potato disease. In contrast to potato, A. thaliana is able to successfully prevent colonization of the pathogen due to a multi-layered nonhost resistance. Several mutants have been isolated which are impaired in penetration resistance. A mutation in the gene PEN2, which encodes for an enzyme involved in indole glucosinolate metabolism (Bednarek et al. (2009)), results in the loss of penetration resistance against P. infestans (Lipka et al. (2005)). Despite its ability to penetrate epidermal cells of pen2 mutant plants, P. infestans is still not able to colonize these plants. Additional mutants were isolated by Kopischke et al. (2013) which show enhanced defense responses upon infection with P. infestans: pen2erp1 and pen2erp2, and backcrossed mutants erp140 and erp2D. We used six different plant lines, the wildtype-like gl1, and the five different mutants (pen2, pen2erp1, pen2erp2, erp2D, erp140). The plants were either infected with P. infestans spores or treated with water as control, and harvested 6h and 12h after treatment. The experiment was repeated three times with different P. infestans cultures, resulting in biological triplicates, for an overall of 6 x 2 x 2 x 3 = 72 samples. A metabolomics data set from the same set of samples has been submitted to MetaboLights database at EMBL-EBI (http://www.ebi.ac.uk/metabolights/index) under accession number MTBLS18 .

INSTRUMENT(S): 418 [Affymetrix]

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Steffen Neumann

PROVIDER: E-MTAB-3287 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Impaired sterol ester synthesis alters the response of Arabidopsis thaliana to Phytophthora infestans.

Kopischke Michaela M Westphal Lore L Schneeberger Korbinian K Clark Richard R Ossowski Stephan S Wewer Vera V Fuchs René R Landtag Jörn J Hause Gerd G Dörmann Peter P Lipka Volker V Weigel Detlef D Schulze-Lefert Paul P Scheel Dierk D Rosahl Sabine S

The Plant journal : for cell and molecular biology 20121212 3

Non-host resistance of Arabidopsis thaliana against Phytophthora infestans, the causal agent of late blight disease of potato, depends on efficient extracellular pre- and post-invasive resistance responses. Pre-invasive resistance against P. infestans requires the myrosinase PEN2. To identify additional genes involved in non-host resistance to P. infestans, a genetic screen was performed by re-mutagenesis of pen2 plants. Fourteen independent mutants were isolated that displayed an enhanced respo ...[more]

PMID: 23072470

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Project description:To gain novel molecular insights into quantitative late blight resistance, we performed a high-resolution quantitative analysis of gene expression using potato cultivars with contrasting SNP alleles at the StAOS2 locus associated with maturity corrected resistance (MCR). SuperSAGE samples were generated from uninfected and infected plants of the selected genotypes under controlled environmental conditions. Genotypes were pooled to reduce the influence of the genetic background on the transcriptome. Nine SuperSAGE samples were prepared from artificially inoculated plants in a growth chamber using total RNA of the pooled 14, 6 and 9 genotypes in groups A1, A2 and B2, respectively, at three infection time points T0, T1 and T2. Combining the tag counts of both NlaIII and DpnII libraries resulted in 1.1 to 6.2 million tags per sample. Of total 266361 unique tags (unitags), 52.6% matched to the potato genome sequence when up to three mismatches per 26 base pairs were allowed, and 23.3% matched without mismatch. Fifteen pair wise comparisons were performed between the nine SuperSAGE samples to identify transcripts that were differentially expressed in response to infection (six comparisons) or between three genotype pools at the infection time points T0, T1 and T2 (nine comparisons). The number of unitags per comparison ranged from 127 000 to 182 000 (average 158 000). Between 2100 and 11800 tags were differentially expressed in pair wise comparisons, depending on arbitrary cut-off p-values for a significant difference. The highest number of differences was observed for the comparison between genotype pools A1 and A2 one day after infection (A1-T1 vs A2-T1), and the lowest between genotype pools A2 and B2 two days after infection (B2-T2 vs A2-T2). The number of differences in response to infection and between genotype pools even before infection (T0) was in the same order of magnitude. Based on the annotations in the DFCI potato gene index, in the potato genome and in few cases by BLASTX searches against the protein database at NCBI, transcripts that showed reproducible differential expression over the infection time course or between genotype pools A1, A2 and B2 were grouped in 16 functional categories, with overlaps between categories. Genes with genotype dependent, constitutive differential expression provide excellent targets for developing novel diagnostic markers for breeding cultivars with improved quantitative resistance to late blight and possibly other biotic and abiotic stresses. Relevant in this respect appear, besides numerous genes of unknown or ill-defined function, genes with known function involved in stress responses, photosynthesis, protein biosynthesis, protein degradation via the 26S proteasome, transport of proteins, lipids, ions and other small molecules, cell wall structure and many others. Eighteen SuperSAGE libraries were constructed based on nine leaf samples from one infection experiment. For each time point (T0, T1 and T2) one leaflet each of 14, 6 and 9 SL genotypes in genotypic groups A1, A2 and B2, respectively, were pooled. Frozen pooled leaf tissue was powdered in a CryoMill. SuperSAGE libraries were generated at GenXPro GmbH (Frankfurt, Germany) essentially as described (Matsumura et al. 2010). To prevent amplification biases the TrueQuant technology was applied as described by B. Rotter (Patent application Nr. WO2009152928). Besides NlaIII (recognition site: 5M-bM-^@M-^Y-CATG-3M-bM-^@M-^Y), DpnII (recognition site: 5M-bM-^@M-^Y-GATC-3M-bM-^@M-^Y) was used as second anchoring enzyme, to capture transcripts without a NlaIII site. Therefore, the 26 bp tags carry either CATG or GATC at their 5M-bM-^@M-^Y end. The libraries were pooled and sequenced by Solexa/Illumina technology (Illumina, Inc., USA).

Dataset Information

Metabolic and transcriptional response of Arabidopsis thaliana wildtype and mutants to Phytophtora infestans

Publications

Impaired sterol ester synthesis alters the response of Arabidopsis thaliana to Phytophthora infestans.

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