Transcriptomic and metabolomic shifts in rice roots in response to Cr (VI) stress.
Transcriptomic and metabolomic shifts in rice roots in response to Cr (VI) stress.
复制标题
DOI：
10.1186/1471-2164-11-648
复制
发表时间：
2010-11-20
期刊：
影响因子：
4.4
通讯作者：
Tuli R
中科院分区：
文献类型：
--
作者：
Dubey S;Misra P;Dwivedi S;Chatterjee S;Bag SK;Mantri S;Asif MH;Rai A;Kumar S;Shri M;Tripathi P;Tripathi RD;Trivedi PK;Chakrabarty D;Tuli R
由于粗心和不当的废水排放管理措施（主要来自冶金、电镀、油漆和颜料生产、制革和木材防腐等行业），铬（Cr）污染田地的广泛使用提高了其在表层土壤中的浓度，并最终进入水稻和谷物。尽管以前对铬胁迫的影响进行了许多研究，但与铬植物毒性影响、植物对铬暴露的防御反应以及水稻中的易位和积累相关的精确分子机制仍然知之甚少。本文报道了在 Cr-植物相互作用后对水稻根部全基因组转录组图谱的详细分析。此类研究对于鉴定负责植物对铬胁迫的耐受性、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，将差异转录组数据与水稻中受 Cr (VI) 胁迫影响的生物过程联系起来。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着过度表达，对这些基序在整个基因组序列中的出现情况进行了分析。在全基因组背景下，这 14 和 13 个基序的提升值在测试数据集中显着较高。虽然没有为任何基序指定功能作用，但所有这些都作为启动子基序存在于直系同源启动子数据库中。这些发现清楚地表明，复杂的调控途径网络可以调节水稻的 Cr 反应。经过适当的归一化和初始计算后，转录组和代谢组数据的整合矩阵为我们提供了成分之间相关性的直观图像。基因子集中不同基序的优势表明基序特异性转录调节蛋白参与了水稻的铬胁迫反应。
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.
登录
查看更多内容
DOI：
10.1073/pnas.011404098
发表时间：
2001-01-02
影响因子：
11.1
作者：
Li, C;Wong, WH
通讯作者：
Wong, WH
影响因子：
6.5
作者：
Bailly, C;Corbineau, F;van Doorn, WG
通讯作者：
van Doorn, WG
影响因子：
8.8
作者：
Bhattacharyya, P;Chakraborty, A;Powell, MA
通讯作者：
Powell, MA
影响因子：
5.3
作者：
Doi K;Hosaka A;Nagata T;Satoh K;Suzuki K;Mauleon R;Mendoza MJ;Bruskiewich R;Kikuchi S
通讯作者：
Kikuchi S
影响因子：
2
作者：
Iqbal, N.;Farooq, S.;Hameed, A.
通讯作者：
Hameed, A.