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

BMC Genomics

Research Article

Rakesh Tuli¹  Smita Kumar²  Sumit K Bag²  Manju Shri²  Sanjay Dwivedi²  Debasis Chakrabarty²  Preeti Tripathi²  Prabodh K Trivedi²  Arti Rai²  Rudra D Tripathi²  Prashant Misra²  Sandipan Chatterjee²  Sonali Dubey²  Mehar H Asif²  Shrikant Mantri³ 

[1] National Agri-Food Biotechnology Institute (Department of Biotechnology, New Delhi), Mohali, Punjab, India;National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, 226 001, Lucknow, India;National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, 226 001, Lucknow, India;National Agri-Food Biotechnology Institute (Department of Biotechnology, New Delhi), Mohali, Punjab, India;

关键词: Proline;    Rice Root;    Heavy Metal Stress;    WRKY Transcription Factor;    Sulfate Transporter;   

DOI  :  10.1186/1471-2164-11-648

 received in 2010-05-25, accepted in 2010-11-20,  发布年份 2010

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Dubey et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.