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

Abstract

The effects of heavy metals in agricultural soils have received special attention due to their potential for accumulation in crops, which can affect species at all trophic levels. Therefore, there is a critical need for reliable bioassays for assessing risk levels due to heavy metals in agricultural soil. In the present study, we used microarrays to investigate changes in gene expression of Lycopersicon esculentum in response to Cd-, Cr-, Hg-, or Pb-spiked soil. Exposure to (1)/10 median lethal concentrations (LC50) of Cd, Cr, Hg, or Pb for 7 days resulted in expression changes in 29 Cd-specific, 58 Cr-specific, 192 Hg-specific and 864 Pb-specific genes as determined by microarray analysis, whereas conventional morphological and physiological bioassays did not reveal any toxicant stresses. Hierarchical clustering analysis showed that the characteristic gene expression profiles induced by Cd, Cr, Hg, and Pb were distinct from not only the control but also one another. Furthermore, a total of three genes related to "ion transport" for Cd, 14 genes related to "external encapsulating structure organization", "reproductive developmental process", "lipid metabolic process" and "response to stimulus" for Cr, 11 genes related to "cellular metabolic process" and "cellular response to stimulus" for Hg, 78 genes related to 20 biological processes (e.g., DNA metabolic process, monosaccharide catabolic process, cell division) for Pb were identified and selected as their potential biomarkers. These findings demonstrated that microarray-based analysis of Lycopersicon esculentum was a sensitive tool for the early detection of potential toxicity of heavy metals in agricultural soil, as well as an effective tool for identifying the heavy metal-specific genes, which should be useful for assessing risk levels due to heavy metals in agricultural soil.

Oxidative stress-induced toxicity of CuO nanoparticles and related toxicogenomic responses in Arabidopsis thaliana

“…This finding is in agreement with the study of Kaveh et al (2013), in which the same category was identified when Arabidopsis was exposed to both Ag NPs and Ag þ . In another study, three genes (AT4G18450, PBP1 and ERF1) related to "response to stimulus" were also differentially expressed in the roots of tomato plant after exposure to heavy metal Cr (Hou et al, 2015). "Response to organic substance" (13%), and "biopolymer modification" (12%) were the other two most representative categories of biological processes.…”

“…Changes in gene expression associated with toxicants could be observed earlier than physiological or morphological responses (Hou et al, 2015). Therefore, microarray was employed to early detect the gene expression of Arabidopsis after CuO NPs exposure.…”

“…Recent studies have highlighted that changes in gene expression upon exposure to environmental contaminants (e.g., heavy metals) can be detected earlier than any changes in physiology and/or morphology of plants (Hou et al, 2015). The obtained gene expression data may yield a better understanding of the molecular mechanism of toxicants.…”

“…The obtained gene expression data may yield a better understanding of the molecular mechanism of toxicants. Microarray analysis is recognized as a sensitive approach for the early detection of potential toxicity of contaminants, and an effective tool for identifying the oxidative stress-related genes (Hou et al, 2015;Van Aerle et al, 2013). For nanotoxicological investigation, the microarray technology has been applied to detect changes in gene expression in human cells (Li et al, 2014), zebrafish embryos (Van Aerle et al, 2013), and bacteria (Escherichia coli) (Cui et al, 2012).…”

Which Genes in a Typical Intertidal Seagrass (Zostera japonica) Indicate Copper-, Lead-, and Cadmium Pollution?

“…The molecular technologies developed over the past 20 years have undoubtedly provided insights into seagrass genetics and their adaptability to environmental stress, especially the analysis of gene expression, which is a powerful approach that can determine how organisms respond to particular abiotic conditions (Hou et al, 2015 ; Hossain et al, 2016 ). Recently developed RNA deep-sequencing technology provides a platform to measure differences in gene expression, which is more sensitive than traditional microarray hybridization techniques (Wilhelm and Landry, 2009 ; Saminathan et al, 2015a ).…”