National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India.
BMC Genomics. 2010 Nov 20;11:648. doi: 10.1186/1471-2164-11-648.
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.
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.
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.
由于对废水排放的疏忽和不当管理，铬（Cr）污染的土地已广泛应用，主要来自与冶金、电镀、油漆和颜料生产、鞣制和木材保护有关的工业。这导致其在地表土壤中的浓度升高，最终进入水稻植株和谷物。尽管已经有许多关于铬胁迫影响的研究，但对于与铬植物毒性、植物对铬暴露的防御反应以及在水稻中的迁移和积累相关的精确分子机制仍知之甚少。
本文报道了在 Cr-植物相互作用后，对水稻根进行全基因组转录组谱分析。这些研究对于鉴定对 Cr 胁迫具有耐受性、积累和防御反应的基因非常重要。还进行了水稻根代谢组分析，以将差异转录组数据与 Cr（VI）胁迫下水稻受影响的生物过程相关联。为了检查 Cr 特异性基序是否确实在 Cr 响应基因的启动子区域中显著过表达，对整个基因组序列中的这些基序进行了检测。在全基因组背景下，这些 14 个和 13 个基序在测试数据集的提升值显著较高。虽然尚未为任何基序分配功能作用，但所有这些基序都存在于同源启动子数据库中作为启动子基序。
这些发现清楚地表明，调控途径的复杂网络调节了水稻的 Cr 反应。经过适当归一化和初步计算的转录组和代谢组数据的综合矩阵为我们提供了组件之间相关性的直观图片。不同基序在基因子集中的优势表明，在水稻的 Cr 应激反应中，涉及基序特异性转录调节蛋白。
