Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae

Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), gives rise to devastating crop losses in rice. Disease resistant rice cultivars are the most economical way to combat the disease. The TP309 cultivar is susceptible to infection by Xoo strain PXO99. A transgenic variety, TP309_Xa21, expresses the pattern recognition receptor Xa21, and is resistant. PXO99△raxST, a strain lacking the raxST gene, is able to overcome Xa21-mediated immunity. We used a single extraction solvent to demonstrate comprehensive metabolomics and transcriptomics profiling under sample limited conditions, and analyze the molecular responses of two rice lines challenged with either PXO99 or PXO99△raxST. LC–TOF raw data file filtering resulted in better within group reproducibility of replicate samples for statistical analyses. Accurate mass match compound identification with molecular formula generation (MFG) ranking of 355 masses was achieved with the METLIN database. GC–TOF analysis yielded an additional 441 compounds after BinBase database processing, of which 154 were structurally identified by retention index/MS library matching. Multivariate statistics revealed that the susceptible and resistant genotypes possess distinct profiles. Although few mRNA and metabolite differences were detected in PXO99 challenged TP309 compared to mock, many differential changes occurred in the Xa21-mediated response to PXO99 and PXO99△raxST. Acetophenone, xanthophylls, fatty acids, alkaloids, glutathione, carbohydrate and lipid biosynthetic pathways were affected. Significant transcriptional induction of several pathogenesis related genes in Xa21 challenged strains, as well as differential changes to GAD, PAL, ICL1 and Glutathione-S-transferase transcripts indicated limited correlation with metabolite changes under single time point global profiling conditions.

• Publication year

  2010

• Venue

  Metabolomics

• Publication date

  2010-05-27

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1007/s11306-010-0218-7PMID 20676379PMCID 2899020
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• Multivariate statistics separated susceptible and resistant rice genotypes into distinct profiles, and Xa21-mediated immunity produced broad molecular responses to PXO99 and PXO99△raxST.

  Confidence 0.94

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• LC-TOF raw data file filtering improved replicate within-group reproducibility, and METLIN plus GC-TOF/BinBase workflows enabled broad compound identification, including 355 accurate-mass matches and 441 additional GC-TOF compounds with 154 structurally identified.

  Confidence 0.95

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• A single extraction solvent supported combined metabolomic and transcriptomic profiling under sample-limited conditions.

  Confidence 0.96

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review

• binbase database

  database

  A metabolite annotation resource used to process GC-TOF data and match compounds by retention index and library spectra.

  Aliases: BinBase

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• gc-tof analysis

  measurement method

  Gas chromatography time-of-flight mass spectrometry used to detect additional metabolites.

  Aliases: GC-TOF, gas chromatography time-of-flight analysis

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• lc-tof raw data file filtering

  method

  A preprocessing step applied to LC-TOF raw files before statistical comparison of replicate samples.

  Aliases: LC-TOF filtering, liquid chromatography time-of-flight filtering

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• metabolomics and transcriptomics profiling

  profiling approach

  Parallel measurement of metabolites and mRNA abundance from the same rice samples.

  Aliases: integrated metabolomics/transcriptomics profiling

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• metlin database

  database

  A reference metabolite database used for accurate-mass matching and molecular formula ranking.

  Aliases: METLIN

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• multivariate statistics

  analysis method

  Statistical methods that compare many metabolite and transcript variables jointly across sample groups.

  Aliases: multivariate analysis

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• single extraction solvent

  method

  A one-solvent extraction workflow used to obtain material for both metabolite and transcript measurements from limited rice samples.

  Aliases: single-solvent extraction

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• xa21-mediated immunity

  biological process

  The rice resistance response triggered by the Xa21 pattern-recognition receptor.

  Aliases: Xa21 resistance, Xa21-mediated resistance

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review

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