Dataset Information

Transcriptome responses to aluminum stress in roots of aspen (Populus tremula).

ABSTRACT:

Background

Ionic aluminum (mainly Al3+) is rhizotoxic and can be present in acid soils at concentrations high enough to inhibit root growth. Many forest tree species grow naturally in acid soils and often tolerate high concentrations of Al. Previously, we have shown that aspen (Populus tremula) releases citrate and oxalate from roots in response to Al exposure. To obtain further insights into the root responses of aspen to Al, we investigated root gene expression at Al conditions that inhibit root growth.

Results

Treatment of the aspen roots with 500 ?M Al induced a strong inhibition of root growth within 6 h of exposure time. The root growth subsequently recovered, reaching growth rates comparable to that of control plants. Changes in gene expression were determined after 6 h, 2 d, and 10 d of Al exposure. Replicated transcriptome analyses using the Affymetrix poplar genome array revealed a total of 175 significantly up-regulated and 69 down-regulated genes, of which 70% could be annotated based on Arabidopsis genome resources. Between 6 h and 2 d, the number of responsive genes strongly decreased from 202 to 26, and then the number of changes remained low. The responses after 6 h were characterized by genes involved in cell wall modification, ion transport, and oxidative stress. Two genes with prolonged induction were closely related to the Arabidopsis Al tolerance genes ALS3 (for Al sensitive 3) and MATE (for multidrug and toxin efflux protein, mediating citrate efflux). Patterns of expression in different plant organs and in response to Al indicated that the two aspen genes are homologs of the Arabidopsis ALS3 and MATE.

Conclusion

Exposure of aspen roots to Al results in a rapid inhibition of root growth and a large change in root gene expression. The subsequent root growth recovery and the concomitant reduction in the number of responsive genes presumably reflect the success of the roots in activating Al tolerance mechanisms. The aspen genes ALS3 and MATE may be important components of these mechanisms.

SUBMITTER: Grisel N

PROVIDER: S-EPMC3017830 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Transcriptome responses to aluminum stress in roots of aspen (Populus tremula).

Grisel Nadine N Zoller Stefan S Künzli-Gontarczyk Marzanna M Lampart Thomas T Münsterkötter Martin M Brunner Ivano I Bovet Lucien L Métraux Jean-Pierre JP Sperisen Christoph C

BMC plant biology 20100823

<h4>Background</h4>Ionic aluminum (mainly Al3+) is rhizotoxic and can be present in acid soils at concentrations high enough to inhibit root growth. Many forest tree species grow naturally in acid soils and often tolerate high concentrations of Al. Previously, we have shown that aspen (Populus tremula) releases citrate and oxalate from roots in response to Al exposure. To obtain further insights into the root responses of aspen to Al, we investigated root gene expression at Al conditions that in ...[more]

PMID: 20727216

Similar Datasets

Project description:Background Ionic aluminum (mainly Al3+) is rhizotoxic and can be present in acid soils at concentrations high enough to inhibit root growth. Many forest tree species grow naturally in acid soils and often tolerate high concentrations of Al. Previously, we have shown that aspen (Populus tremula) releases citrate and oxalate from roots in response to Al exposure. To obtain further insights into the root responses of aspen to Al, we investigated root gene expression at Al conditions that inhibit root growth. Results Treatment of the aspen roots with 500 µM Al induced a strong inhibition of root growth within 6 h of exposure time. The root growth subsequently recovered, reaching growth rates comparable to that of control plants. Changes in gene expression were determined after 6 h, 2 d, and 10 d of Al exposure. Replicated transcriptome analyses using the Affymetrix poplar genome array revealed a total of 175 significantly up-regulated and 69 down-regulated genes, of which 70% could be annotated based on Arabidopsis genome resources. Between 6 h and 2 d, the number of responsive genes strongly decreased from 202 to 26, and then the number of changes remained low. The responses after 6 h were characterized by genes involved in cell wall modification, ion transport, and oxidative stress. Two genes with prolonged induction were closely related to the Arabidopsis Al tolerance genes ALS3 (for Al sensitive 3) and MATE (for multidrug and toxin efflux protein, mediating citrate efflux). Patterns of expression in different plant organs and in response to Al indicated that the two aspen genes are homologs of the Arabidopsis ALS3 and MATE. Conclusion Exposure of aspen roots to Al results in a rapid inhibition of root growth and a large change in root gene expression. The subsequent root growth recovery and the concomitant reduction in the number of responsive genes presumably reflect the success of the roots in activating Al tolerance mechanisms. The aspen genes ALS3 and MATE may be important components of these mechanisms.

Project description:Background: Solubilized aluminum (Al) is rhizotoxic and can be present in acid soils at levels that inhibit root growth. Acid soils are found throughout the world and often support forests. However, unlike in herbaceous plants, little is known about the mechanisms by which forest trees respond to and tolerate Al. To begin to elucidate these mechanisms, we characterized transcriptomic changes in response to Al in roots of aspen (Populus tremula L.). Results: Aspen roots were treated with Al in solution culture for 6 h, 54 h, and 246 h. Transcriptomic changes were assessed by the Affymetrix GeneChip Poplar Genome Array. The analysis revealed 176 induced and 66 suppressed genes. The majority of these genes were regulated at 6 h, presumably reflecting root growth, which was strongly inhibited at 6 h and partially was recovered at 2 d and 10 d. Enrichment analysis identified sets of functionally related genes whose members were statistically over-represented compared to the genes on the microarray. These sets included genes related to cell wall modification, oxidative stress, cell death, and transport processes. Two of the genes involved in transport were related to the Arabidopsis Al tolerance genes AtALS3 (aluminum sensitive 3), possibly mediating redistribution of Al, and AtMATE (multi-drug and toxin extrusion), facilitating exudation of citrate. Expression patterns in response to Al in different plant tissues indicated that the two aspen genes are homologs of AtALS3 and AtMATE, suggesting that aspen and Arabidopsis share common mechanisms to cope with Al. Conclusion: This is the first survey of transcriptomic changes in response to Al in a forest tree. The results of our study provide a valuable set of data, which will help to further our understanding of the mechanisms and their regulation that enable aspen to grow in environments with toxic levels of Al. Aspen roots were treated with Al in solution culture for 6 h, 54 h, 246 h to cover a broad range of exposure times. Transcriptomic changes were assessed by the Affymetrix GeneChip Poplar Genome Array. For each time point, root tips of three independant plants were analyzed.

Project description:Plants have evolved heavy metal tolerance mechanisms to adapt and cope with nickel (Ni) toxicity. Decrypting whole gene expression of Trembling Aspen (Pinus tremuloides) under nickel stress could elucidate the nickel resistance/tolerance mechanisms. The main objectives of the present research were to 1) characterize the P. tremuloides transcriptome, and 2) compare gene expression dynamics between nickel-resistant and nickel-susceptible P. tremuloides genotypes with Whole Transcriptome (WT) sequencing. Illumina Sequencing generated 27-45 million 2X150 paired-end reads of raw data per sample. The alignment performed with StringTie Software added two groups of transcripts to the draft genome annotation. One group contained 32,677 new isoforms that match to 17,254 genes. The second group contained 17,349 novel transcripts that represent 16,157 novel genes. Overall, 52,987 genes were identified from which 36,770 genes were selected as differently expressed. With the high stringency (two-fold change, FDR value ≤ 0.05 and logFC value ≥1 (upregulated) or ≤ -1 (downregulated), after GSEA analysis and filtering for gene set size, 575 gene sets were upregulated and 146 were downregulated in nickel resistant phenotypes compared to susceptible genotypes. For biological process, genes associated with translation were significantly upregulated while signal transduction and cellular protein process genes were downregulated in resistant compared to susceptible genotypes. For molecular function, there was a significant downregulation of genes associated with DNA binding in resistant compared to susceptible lines. Significant upregulation was observed in genes located in ribosome while downregulation of genes in chloroplast and mitochondrion were preponderant in resistant genotypes compared to susceptible. Hence, from a whole transcriptome level, an upregulation in ribosomal and translation activities was identified as the main response to Ni toxicity in the resistant plants. More importantly, this study revealed that a metal transport protein (Potrs038704g29436 -ATOX1-related copper transport) was among the top upregulated genes in resistant genotypes when compared to susceptible plants. Other identified upregulated genes associated with abiotic stress include genes coding for Dirigent Protein 10, GATA transcription factor, Zinc finger protein, Auxin response factor, Bidirectional sugar transporter, and thiamine thiazole synthase.

Dataset Information

Transcriptome responses to aluminum stress in roots of aspen (Populus tremula).

Background

Results

Conclusion

Publications

Transcriptome responses to aluminum stress in roots of aspen (Populus tremula).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets