Transcriptional profiling in cadmium-treated rice seedling roots using suppressive subtractive hybridization

Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
Plant Physiology and Biochemistry (Impact Factor: 2.76). 08/2011; 50(1):79-86. DOI: 10.1016/j.plaphy.2011.07.015
Source: PubMed


Cadmium (Cd), a non-essential metal, is a kind of toxic heavy metal to life, which can accumulate in rice tissues including seeds, thus posing a risk to human health through food chain. To investigate the molecular mechanisms of rice response to Cd exposure, suppression subtractive hybridization and mirror orientation selection were used to compare gene expression profiles in seedling roots of Cd-exposed and control (unexposed) rice plants (Oryza sativa L., Nipponbare). Approximately 1700 positive clones, with insertions ranging from 250 to 1300 bp, were identified through reverse cDNA microarray analysis. Gene expression was further confirmed by real time RT-PCR. A number of differentially expressed genes were found in Cd-exposed rice roots, including 28 up-regulated genes and 19 down-regulated genes. They were found to be involved in diverse biological processes, such as metabolism, stress response, ion transport and binding, protein structure and synthesis, as well as signal transduction. Notably a number of known functional genes were identified encoding membrane proteins and stress-related proteins such as heat shock proteins, monosaccharide transporters, CBL-interacting serine/threonine-protein kinases and metal tolerance proteins. The cDNAs isolated in this study contribute to our understanding of genes and the biochemical pathways that may play a key role in the response of plants to metal exposure in the environment.

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Available from: Xuncheng Liu, Mar 24, 2015
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    • "Recently, expanding transcriptome data sets have uncovered a global picture of Cd stress-responsive genes in some commonly researched plant species, such as Arabidopsis (Herbette et al., 2006; Weber et al., 2006), rice (Zhang et al., 2012), pea (Romero-Puertas et al., 2007), tobacco (Martin et al., 2012), and barley (Tamas et al., 2008). A large number of genes involved in Cd tolerance regulation have been identified and characterized in previous studies (Zhu et al., 1999; Fusco et al., 2005; Courbot et al., 2007; DalCorso et al., 2010; Farinati et al., 2010; Han et al., 2014). "
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    ABSTRACT: Cadmium (Cd) contamination in agricultural soils has become a major environmental problem in China. Ramie, a fiber crop, has frequently been proposed for use as a phytoremediation crop for the restoration of Cd-contaminated farmlands. However, high levels of Cd can greatly inhibit stem growth in ramie, which reduces its economic value as a crop. To understand the potential mechanisms behind this phenomenon, the ramie genes involved in the Cd stress response were identified using Illumina pair-end sequencing on two Cd-stressed plants (CdS1 and CdS2) and two control plants (CO1 and CO2). Approximately 48.7, 51.6, 41.2, and 47.1 million clean sequence reads were generated from the libraries of CO1, CO2, CdS1, and CdS2, respectively, and de novo assembled to yield 56,932 non-redundant unigenes. A total of 26,686 (46.9%) genes were annotated for their function. Comparison of gene expression levels in CO and CdS ramie revealed 155 differentially expressed genes (DEGs) between treatment and control conditions. Sixteen DEGs were further analyzed for expression differences by using real-time quantitative PCR (qRT-PCR). Among these 16 DEGs, 2 genes encoding GA2-oxidase (a major enzyme for deactivating bioactive gibberellins [GAs]) showed markedly up-regulated expression in Cd stressed ramie. This might be responsible for the growth inhibition of Cd-stressed ramie. Pathway enrichment analysis revealed that the cutin, suberine and wax biosynthesis pathway was markedly enriched by DEGs. The discovery of these Cd stress-responsive genes and pathways will be helpful in further understanding the mechanism of Cd-stress response and improving Cd stress tolerance in ramie. Copyright © 2014. Published by Elsevier B.V.
    Full-text · Article · Dec 2014 · Gene
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    • "In particular, Cd is absorbed by the roots from the soil and transported to the shoot, negatively affecting nutrient uptake and homeostasis in plants, even at low concentrations. It is also known to adversely impact various biochemical and physiological processes including changes in the transcriptome and proteome of plants, resulting in inhibited root and shoot growth and, ultimately, reduced yield [1], [2], [3]. Cd pollution in arable soil has dramatically increased worldwide over the last several decades through the use of phosphate fertilizers, sludge, and irrigation water containing Cd. Furthermore, accumulation of Cd in the edible parts of plants such as seed grains places humans at a risk when ingesting them because of its highly toxic effects on human health. "
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    ABSTRACT: Plant growth is severely affected by toxic concentrations of the non-essential heavy metal cadmium (Cd). Comprehensive transcriptome analysis by RNA-Seq following cadmium exposure is required to further understand plant responses to Cd and facilitate future systems-based analyses of the underlying regulatory networks. In this study, rice plants were hydroponically treated with 50 µM Cd for 24 hours and ∼60,000 expressed transcripts, including transcripts that could not be characterized by microarray-based approaches, were evaluated. Upregulation of various ROS-scavenging enzymes, chelators and metal transporters demonstrated the appropriate expression profiles to Cd exposure. Gene Ontology enrichment analysis of the responsive transcripts indicated the upregulation of many drought stress-related genes under Cd exposure. Further investigation into the expression of drought stress marker genes such as DREB suggested that expression of genes in several drought stress signal pathways was activated under Cd exposure. Furthermore, qRT-PCR analyses of randomly selected Cd-responsive metal transporter transcripts under various metal ion stresses suggested that the expression of Cd-responsive transcripts might be easily affected by other ions. Our transcriptome analysis demonstrated a new transcriptional network linking Cd and drought stresses in rice. Considering our data and that Cd is a non-essential metal, the network underlying Cd stress responses and tolerance, which plants have developed to adapt to other stresses, could help to acclimate to Cd exposure. Our examination of this transcriptional network provides useful information for further studies of the molecular mechanisms of plant adaptation to Cd exposure and the improvement of tolerance in crop species.
    Full-text · Article · May 2014 · PLoS ONE
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    • "Suppression subtractive hybridization (SSH) is a powerful technique for the isolation of differentially expressed genes from two distinct mRNA populations (Diatchenko et al., 1996). In addition, this method has been successfully used to explore the differentially expressed genes of flower buds (Zhang et al., 2009; Ma et al., 2010), and also the genes involved in the abiotic stress responses of plants (Nguyen et al., 2009; Zhang et al., 2012). In this study, SSH was adopted, together with macroarray and RT-PCR analyses , to reveal the molecular mechanisms of abortive petunia flower buds induced under short light periods. "
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    ABSTRACT: The long-day plant Petunia x hybrida 'Fantasy Red' was found to produce a considerable number of premature abortive flower buds when placed under short light period stress. Suppression subtractive hybridization (SSH) was performed to compare the gene expression profiles between normal and abortive petunia flower buds as induced by short light periods. Using reverse northern blotting, a total of 912 positive clones were successfully identified and sequenced, and 289 non-redundant, differentially expressed transcripts were obtained. According to the Blast2GO and KEGG pathway analyses, the significant distinct cellular component was identified as mitochondrion, and the notable different metabolic pathways were ascribed to carbohydrate metabolism and lipid metabolism. The quality of the SSH libraries was verified through quantitative real-time reverse transcription-PCR (qRT-PCR) analysis of 14 genes. In addition, six of these genes were demonstrated to be of temporal and/or spatial specificity using qRT-PCR, implying that they might be responsible for the premature flower abortion. Furthermore, Phms2 (KC465381), a sequence sharing a high degree of similarity with male sterility 2 gene was characterized, and its inconsistent expression pattern predicted a novel role for Phms2 in flower bud abortion. The data presented here provide insight into the molecular mechanisms of premature flower abortion under short light periods and, hence, may be of value for assessing candidate genes with potential for creating novel germplasms with enhanced photoperiod stress tolerance. Crown Copyright
    Full-text · Article · Dec 2013 · Scientia Horticulturae
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