The plasma membrane Na＋/H＋-antiporter salt overly sensitive1 （SOS1） from the halophytic Arabidopsis-relative Thellungiella halophila （ThSOS1） shows conserved sequence and domain structure with the orthologous ge...The plasma membrane Na＋/H＋-antiporter salt overly sensitive1 （SOS1） from the halophytic Arabidopsis-relative Thellungiella halophila （ThSOS1） shows conserved sequence and domain structure with the orthologous genes from Arabidopsis thaliana and other plants. When expression of ThSOSt was reduced by RNA interference （RNAi）, pronounced characteristics of salt-sensitivity were observed. We were interested in monitoring altered transcriptional responses between Thellungiella wild type and thsost-4, a representative RNAi line with particular emphasis on root responses to salt stress at 350 mmol/L NaCI, a concentration that is only moderately stressful for mature wild type plants. Transcript profiling revealed several functional categories of genes that were differently affected in wild-type and RNAi plants. Down-regulation of SOS1 resulted in different gene expression even in the absence of stress. The pattern of gene induction in the RNAi plant under salt stress was similar to that of glycophytic Arabidopsis rather than that of wild type Thellungiella. The RNAi plants failed to down-regulate functions that are normally reduced in wild type Thellungiella upon stress and did not up-regulate functions that characterize the Thellungiella salt stress response. Metabolite changes observed in wild type Thellungiella after salt stress were less pronounced or absent in RNAi plants. Transcript and metabolite behavior suggested SOS1 functions including but also extending its established function as a sodium transporter. The down-regulation of ThSOS1 converted the halophyte Thellungiella into a salt-sensitive plant.展开更多
Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the Array Express database, we constructed an Arabidopsis gene co-expression network, termed At GGM2014, ba...Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the Array Express database, we constructed an Arabidopsis gene co-expression network, termed At GGM2014, based on the graphical Gaussian model, which contains 102,644 co-expression gene pairs among 18,068 genes. The network was grouped into 622 gene co-expression modules. These modules function in diverse house-keeping, cell cycle, development, hormone response, metabolism, and stress response pathways. We developed a tool to facilitate easy visualization of the expression patterns of these modules either in a tissue context or their regulation under different treatment conditions. The results indicate that at least six modules with tissue-specific expression pattern failed to record modular regulation under various stress conditions. This discrepancy could be best explained by the fact that experiments to study plant stress responses focused mainly on leaves and less on roots, and thus failed to recover specific regulation pattern in other tissues. Overall, the modular structures revealed by our network provide extensive information to generate testable hypotheses about diverse plant signaling pathways. At GGM2014 offers a constructive tool for plant systems biology studies.展开更多
文摘The plasma membrane Na＋/H＋-antiporter salt overly sensitive1 （SOS1） from the halophytic Arabidopsis-relative Thellungiella halophila （ThSOS1） shows conserved sequence and domain structure with the orthologous genes from Arabidopsis thaliana and other plants. When expression of ThSOSt was reduced by RNA interference （RNAi）, pronounced characteristics of salt-sensitivity were observed. We were interested in monitoring altered transcriptional responses between Thellungiella wild type and thsost-4, a representative RNAi line with particular emphasis on root responses to salt stress at 350 mmol/L NaCI, a concentration that is only moderately stressful for mature wild type plants. Transcript profiling revealed several functional categories of genes that were differently affected in wild-type and RNAi plants. Down-regulation of SOS1 resulted in different gene expression even in the absence of stress. The pattern of gene induction in the RNAi plant under salt stress was similar to that of glycophytic Arabidopsis rather than that of wild type Thellungiella. The RNAi plants failed to down-regulate functions that are normally reduced in wild type Thellungiella upon stress and did not up-regulate functions that characterize the Thellungiella salt stress response. Metabolite changes observed in wild type Thellungiella after salt stress were less pronounced or absent in RNAi plants. Transcript and metabolite behavior suggested SOS1 functions including but also extending its established function as a sodium transporter. The down-regulation of ThSOS1 converted the halophyte Thellungiella into a salt-sensitive plant.
基金supported by US National Science Foundation grants DBI-0723722 and DBI-1042344 to SPDKUC Davis funds to SPDK
文摘Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the Array Express database, we constructed an Arabidopsis gene co-expression network, termed At GGM2014, based on the graphical Gaussian model, which contains 102,644 co-expression gene pairs among 18,068 genes. The network was grouped into 622 gene co-expression modules. These modules function in diverse house-keeping, cell cycle, development, hormone response, metabolism, and stress response pathways. We developed a tool to facilitate easy visualization of the expression patterns of these modules either in a tissue context or their regulation under different treatment conditions. The results indicate that at least six modules with tissue-specific expression pattern failed to record modular regulation under various stress conditions. This discrepancy could be best explained by the fact that experiments to study plant stress responses focused mainly on leaves and less on roots, and thus failed to recover specific regulation pattern in other tissues. Overall, the modular structures revealed by our network provide extensive information to generate testable hypotheses about diverse plant signaling pathways. At GGM2014 offers a constructive tool for plant systems biology studies.
