CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform

Gagnot, Séverine; Tamby, Jean-Philippe; Martin‐Magniette, Marie‐Laure; Bitton, Frédérique; Taconnat, Ludivine; Balzergue, Sandrine; Aubourg, Santiago P.; Renou, Jean-Pierre; Lecharny, Alain; Brunaud, Véronique

doi:10.1093/nar/gkm757

Cited by 154 publications

(183 citation statements)

References 21 publications

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“…In the CATMA analysis pipeline, family-wise error rate proved to be the best solution to balance the estimated number of false positives and false negatives 36 . As described before 37 , when the Bonferroni P-value was lower than 0.05, the gene was declared differentially expressed. Microarray data were deposited in GEO under the accession number GSE39261.…”

Section: Methodsmentioning

confidence: 99%

Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants

et al. 2013

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Nitrate is both an important nutrient and a signalling molecule for plants. Although several components of the nitrate signalling pathway have been identified, their hierarchical organization remains unclear. Here we show that the localization of NLP7, a member of the RWP-RK transcription factor family, is regulated by nitrate via a nuclear retention mechanism. Genome-wide analyses revealed that NLP7 binds and modulates a majority of known nitrate signalling and assimilation genes. Our findings indicate that plants, like fungi and mammals, rely on similar nuclear retention mechanisms to instantaneously respond to the availability of key nutrients.

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Section: Methodsmentioning

confidence: 99%

Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants

et al. 2013

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“…We considered as being differentially expressed the spots with a Bonferroni P value # 0.05. A detailed description of the normalization step and of the variance modeling used in the differential analysis is available in Gagnot et al (2008).…”

Section: Transcriptomic Studiesmentioning

confidence: 99%

Geminiviruses Subvert Ubiquitination by Altering CSN-Mediated Derubylation of SCF E3 Ligase Complexes and Inhibit Jasmonate Signaling inArabidopsis thaliana

et al. 2011

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Viruses must create a suitable cell environment and elude defense mechanisms, which likely involves interactions with host proteins and subsequent interference with or usurpation of cellular machinery. Here, we describe a novel strategy used by plant DNA viruses (Geminiviruses) to redirect ubiquitination by interfering with the activity of the CSN (COP9 signalosome) complex. We show that geminiviral C2 protein interacts with CSN5, and its expression in transgenic plants compromises CSN activity on CUL1. Several responses regulated by the CUL1-based SCF ubiquitin E3 ligases (including responses to jasmonates, auxins, gibberellins, ethylene, and abscisic acid) are altered in these plants. Impairment of SCF function is confirmed by stabilization of yellow fluorescent protein-GAI, a substrate of the SCF SLY1 . Transcriptomic analysis of these transgenic plants highlights the response to jasmonates as the main SCF-dependent process affected by C2. Exogenous jasmonate treatment of Arabidopsis thaliana plants disrupts geminivirus infection, suggesting that the suppression of the jasmonate response might be crucial for infection. Our findings suggest that C2 affects the activity of SCFs, most likely through interference with the CSN. As SCFs are key regulators of many cellular processes, the capability of viruses to selectively interfere with or hijack the activity of these complexes might define a novel and powerful strategy in viral infections.

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“…Microarray data from this article were deposited at Array Express (http:// www.ebi.ac.uk/arrayexpress/) under accession number E-MEXP-508 and at CATdb (Gagnot et al, 2008; http://urgv.evry.inra.fr/CATdb/; Project RS05-08_NO) according to the Minimum Information About a Microarray Experiment standards.…”

Section: Qrt-pcr Analysismentioning

confidence: 99%

Nitric Oxide Contributes to Cadmium Toxicity in Arabidopsis by Promoting Cadmium Accumulation in Roots and by Up-Regulating Genes Related to Iron Uptake

et al. 2009

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Nitric oxide (NO) functions as a cell-signaling molecule in plants. In particular, a role for NO in the regulation of iron homeostasis and in the plant response to toxic metals has been proposed. Here, we investigated the synthesis and the role of NO in plants exposed to cadmium (Cd 2+ ), a nonessential and toxic metal. We demonstrate that Cd 2+ induces NO synthesis in roots and leaves of Arabidopsis (Arabidopsis thaliana) seedlings. This production, which is sensitive to NO synthase inhibitors, does not involve nitrate reductase and AtNOA1 but requires IRT1, encoding a major plasma membrane transporter for iron but also Cd 2+ . By analyzing the incidence of NO scavenging or inhibition of its synthesis during Cd 2+ treatment, we demonstrated that NO contributes to Cd 2+ -triggered inhibition of root growth. To understand the mechanisms underlying this process, a microarray analysis was performed in order to identify NO-modulated root genes up-and down-regulated during Cd 2+ treatment. Forty-three genes were identified encoding proteins related to iron homeostasis, proteolysis, nitrogen assimilation/metabolism, and root growth. These genes include IRT1. Investigation of the metal and ion contents in Cd 2+ -treated roots in which NO synthesis was impaired indicates that IRT1 up-regulation by NO was consistently correlated to NO's ability to promote Cd 2+ accumulation in roots. This analysis also highlights that NO is responsible for Cd 2+ -induced inhibition of root Ca 2+ accumulation. Taken together, our results suggest that NO contributes to Cd 2+ toxicity by favoring Cd 2+ versus Ca 2+ uptake and by initiating a cellular pathway resembling those activated upon iron deprivation.

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CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform

Cited by 154 publications

References 21 publications

Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants

Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants

Geminiviruses Subvert Ubiquitination by Altering CSN-Mediated Derubylation of SCF E3 Ligase Complexes and Inhibit Jasmonate Signaling inArabidopsis thaliana

Nitric Oxide Contributes to Cadmium Toxicity in Arabidopsis by Promoting Cadmium Accumulation in Roots and by Up-Regulating Genes Related to Iron Uptake

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