Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Microarray-based Analysis of Gene Expression in Lycopersicon esculentum Roots in Response to Cadmium, Chromium, Mercury and Lead

ABSTRACT: We hypothesize that microarray-based analysis of Lycopersicon esculentum is a sensitive tool for the early detection of potential toxicity of heavy metals, as well as an effective tool for identifying the heavy metal-specific genes. To test the hypothesis, the Agilent whole-genome cDNA microarrays were used to assess the effects of heavy metal on L. esculentum at relatively low concentrations (1/10 LC50 of heavy metals). Results showed that the characteristic gene expression profiles induced by Cd, Cr, Hg and Pb were not only distinct from the control but also distinct from one another, demonstrating the feasibility of discriminating between the effects of these four heavy metals present at relatively low concentrations. Moreover, heavy metal-specific genes were identified by microarray analysis. These findings support the above hypothesis. A total of fifteen microarrays (4*44K tomato gene expression microarray; G2519F-022270) were used to hybridize with RNA extracted from Cd-, Cr-, Hg-, Pb-treated and the untreated roots (control) of Lycopersicon esculentum. Each treatment was carried out for three replicates. A total of thirty seedlings were used for each treatment. Root samples from ten seedlings randomly selected from each Petri dish were pooled together to obtain three biological replicates.

ORGANISM(S): Solanum lycopersicum

SUBMITTER: Jing Hou

PROVIDER: E-GEOD-63024 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background: The high number of heavy metal resistance genes in the soil bacterium Cupriavidus metallidurans CH34 makes it an interesting model organism to study microbial responses to heavy metals. Results: In this study the transcriptional response of this bacterium was measured after challenging it to a wide range of sub-lethal concentrations of various essential or toxic metals. Considering the global transcriptional responses for each challenge as well as by identifying the overlap in upregulated genes between different metal responses, the sixteen metals could be clustered in three different groups. Additionally, next to the assessment of the transcriptional response of already known metal resistance genes, new metal response gene clusters were identified. The majority of the metal response loci showed similar expression profiles when cells were exposed to different metals, suggesting complex cross-talk at transcriptional level between the different metal responses. The highly redundant nature of these metal resistant regions – illustrated by the large number of paralogous genes – combined with the phylogenetic distribution of these metal response regions within evolutionary related and other metal resistant bacteria, provides important insights on the recent evolution of this naturally soil dwelling bacterium towards a highly metal-resistant strain found in harsh and anthropogenic environments. Conclusions: The metal-resistant soil bacterium Cupriavidus metallidurans CH34 displays myriads of gene expression patterns when exposed to a wide range of heavy metals at non-lethal concentrations. The interplay between the different gene expression clusters points towards a complex cross-regulated regulatory network governing heavy metal resistance in C. metallidurans CH34. Keywords: Cupriavidus metallidurans CH34, transcriptional regulation, heavy metal resistance Two-condition experiments. Comparing samples after induction with heavy metals versus non-induced samples. Biological duplicate or triplicate. Each array contains 3 or 4 technical replicates.

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Microarray-based Analysis of Gene Expression in Lycopersicon esculentum Roots in Response to Cadmium, Chromium, Mercury and Lead

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