Transcriptomic and metabolomic shifts in rice roots in response to Cr (VI) stress

Abstract

BackgroundWidespread 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.ResultsDetailed 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.ConclusionThese 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.

Comprehensive analysis of regulatory elements of the promoters of rice sulfate transporter gene family and functional characterization ofOsSul1;1promoter under different metal stress

“…29 Such an analysis has been carried out in differentially expressed genes and provided very useful information in terms of heavy metal stress and cis-acting elements. 8,15 Analysis resulted highly significant (<e ¡100 ) putative conserved motifs of 6-8 nucleotide length present in all the promoters. Motif based sequence analysis tool MEME depicted the location, consensus sequence and the level of conservation in promoters.…”

“…3,4,5,6 It has been suggested that identification of stress-responsive components and regulatory mechanisms are important for the understanding of the molecular processes involved in abiotic stress tolerance in plants. 7,8,9,10 Studies suggest that responses of plants to the environmental stresses are governed at various steps of the gene regulation. These steps include transcription, RNA processing, translation and post translational events such as protein stability and modification.…”

Influence of Sulfur on Transcription of Genes Involved in Arsenic Accumulation in Rice Grains

“…OsABCC9 have been reported response to Cr(IV) stress (Dubey et al 2010). Many ABC transporter genes are up-regulated in roots and shoots under As stress in rice seedlings (Yu et al 2012).…”

Respuestas morfogénicas de las raíces de Arabidopsis thaliana (Magnoliophyta: Brassicales) al estrés de Cr(VI)

“…Una de las explicaciones sobre el porqué la raíz se adapta mejor a condiciones graduales de estrés, puede estar relacionada con la inducción de la expresión de genes que codifi can para enzimas que se encargan de reducir los niveles de ROS y genes que codifi can para proteínas que modifi can el metabolismo hormonal, ya que se ha demostrado que diferentes tipos de estrés abiótico inducen la expresión de este tipo de genes (Dubey et al 2010, Suzuki et al 2011, Hernández-Madrigal 2011. Además, se ha reportado que para la señalización y respuesta al estrés nutricional de sacarosa en A. thaliana se requiere la síntesis de proteínas (Zhang et al 2011).…”