title: Transcriptomic and metabolomic shifts in rice roots in response to Cr (VI) stress.
abstract: BACKGROUND
  Widespread use of chromium (Cr) contaminated fields due to careless and inappropriate management practices of effluent discharge, mostly from industries related to metallurgy, electroplating, production of paints and pigments, tanning, and wood preservation elevates its concentration in surface soil and eventually into rice plants and grains. In spite of many previous studies having been conducted on the effects of chromium stress, the precise molecular mechanisms related to both the effects of chromium phytotoxicity, the defense reactions of plants against chromium exposure as well as translocation and accumulation in rice remain poorly understood.
  
  
  RESULTS
  Detailed analysis of genome-wide transcriptome profiling in rice root is reported here, following Cr-plant interaction. Such studies are important for the identification of genes responsible for tolerance, accumulation and defense response in plants with respect to Cr stress. Rice root metabolome analysis was also carried out to relate differential transcriptome data to biological processes affected by Cr (VI) stress in rice. To check whether the Cr-specific motifs were indeed significantly over represented in the promoter regions of Cr-responsive genes, occurrence of these motifs in whole genome sequence was carried out. In the background of whole genome, the lift value for these 14 and 13 motifs was significantly high in the test dataset. Though no functional role has been assigned to any of the motifs, but all of these are present as promoter motifs in the Database of orthologus promoters.
  
  
  CONCLUSIONS
  These findings clearly suggest that a complex network of regulatory pathways modulates Cr-response of rice. The integrated matrix of both transcriptome and metabolome data after suitable normalization and initial calculations provided us a visual picture of the correlations between components. Predominance of different motifs in the subsets of genes suggests the involvement of motif-specific transcription modulating proteins in Cr stress response of rice.
authors.affiliation: National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India.
authors.forename: Sonali
authors.initials: S
authors.lastname: Dubey
authors.forename: Prashant
authors.initials: P
authors.lastname: Misra
authors.forename: Sanjay
authors.initials: S
authors.lastname: Dwivedi
authors.forename: Sandipan
authors.initials: S
authors.lastname: Chatterjee
authors.forename: Sumit K
authors.initials: SK
authors.lastname: Bag
authors.forename: Shrikant
authors.initials: S
authors.lastname: Mantri
authors.forename: Mehar H
authors.initials: MH
authors.lastname: Asif
authors.forename: Arti
authors.initials: A
authors.lastname: Rai
authors.forename: Smita
authors.initials: S
authors.lastname: Kumar
authors.forename: Manju
authors.initials: M
authors.lastname: Shri
authors.forename: Preeti
authors.initials: P
authors.lastname: Tripathi
authors.forename: Rudra D
authors.initials: RD
authors.lastname: Tripathi
authors.forename: Prabodh K
authors.initials: PK
authors.lastname: Trivedi
authors.forename: Debasis
authors.initials: D
authors.lastname: Chakrabarty
authors.forename: Rakesh
authors.initials: R
authors.lastname: Tuli
mesh_terms: D018533:Biomass; D002857:Chromium / Q000633:toxicity*; D016000:Cluster Analysis; D015536:Down-Regulation / Q000187:drug effects / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant / Q000235:genetics; D008315:Malondialdehyde / Q000378:metabolism; D053858:Metabolic Networks and Pathways / Q000187:drug effects; D055432:Metabolomics; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000033:anatomy & histology / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D018520:Plant Shoots / Q000033:anatomy & histology / Q000187:drug effects; D011392:Proline / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics; D036226:Seedlings / Q000187:drug effects / Q000502:physiology; D013312:Stress, Physiological / Q000187:drug effects* / Q000235:genetics; D013438:Sulfhydryl Compounds / Q000378:metabolism; D015854:Up-Regulation / Q000187:drug effects / Q000235:genetics
chemical_list: D010940:Plant Proteins; D013438:Sulfhydryl Compounds; D002857:Chromium; D008315:Malondialdehyde; D011392:Proline