CATMA: a complete Arabidopsis GST database

Crowe, Mark L.; Serizet, Carine; Thareau, Vincent; Aubourg, Santiago P.; Rouzé, Pierre; Hilson, Pierre; Beynon, Jim; Weisbeek, Peter; Hummelen, Paul Van; Reymond, Philippe; Paz‐Ares, Javier; Nietfeld, Wilfried; Trick, Martin

doi:10.1093/nar/gkg071

Cited by 135 publications

(157 citation statements)

References 8 publications

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“…Microarray analysis was carried out at the Research Unit in Plant Genomics in Evry, France, using the CATMA array (V5) containing 24,576 gene-specific tags corresponding to 22,089 genes from Arabidopsis 34 . The analysis was performed as in Lurin et al 35 In short, cRNAs were produced from 2 mg of total RNA (Message Amp aRNA kit, Ambion).…”

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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“…To investigate the mechanisms underlying the effects of NO in roots of Cd 2+ -treated plants, a genomescale expression profiling of Arabidopsis roots was performed using CATMA arrays covering 22,089 nuclear genes (Crowe et al, 2003;Hilson et al, 2004) in order to identify root genes regulated through a NOdependent process. For this purpose, plants were grown hydroponically and then were treated for 24 h with 30 mM Cd 2+ and/or L-NAME.…”

Section: Identification Of No-regulated Root Genes During CD 2+ Treatmentioning

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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“…Therefore, these microarray measurements needed verification by quantitative polymerase chain reaction (Q-PCR). CATMA probes (Crowe et al 2003) for all tested genes were converted to Arabidopsis Genome Initiative (AGI) identifiers (TIGR 6.0; The Institute for Genome Research) for convenience. CATMA probes do not always correspond in a one-to-one relation to AGI identifiers, which can result in a different number of genes with unique AGI codes.…”

Section: Is and Cs Gene Expressionmentioning

confidence: 99%

“…The GST (which are between 150 and 500 bp in length and show no more than 70% identity with any other sequence in the genome) were spotted on GAPSII glass slides (Corning Incorporated, Acton, MA, U.S.A.) using a BioRobotics Microgrid II TAS spotter (Genomic Solutions, Ann Arbor, MI, U.S.A.) and cross-linked for 4 h at 80°C. Detailed information about CATMA and database access can be found at online (Crowe et al 2003).…”

Section: Catma Arraysmentioning

confidence: 99%

Disease-Specific Expression of Host Genes During Downy Mildew Infection of Arabidopsis

Huibers¹,

Jong²,

Dekter³

et al. 2009

MPMI

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Here, we report on the identification of Arabidopsis genes that are induced during compatible but not during incompatible interactions with the downy mildew pathogen Hyaloperonospora arabidopsidis. This set of so-called compatible specific (CS) genes contrasts with the large group of defense-associated genes that is differentially expressed during both compatible and incompatible interactions. From the 17 identified CS genes, 6 belong to the ethylene response factor (ERF) family of transcription factor genes, suggesting that these ERF have a role during compatibility. The majority of CS genes are differentially regulated in response to various forms of abiotic stress. In silico analysis of the CS genes revealed an over-representation of dehydration-responsive element/C-repeat binding factor (DREB1A/ CBF3) binding sites and EveningElement motifs in their promoter regions. The CS-ERF are closely related to the CBF transcription factors and could potentially bind the DREB1A/CBF3 promoter elements in the CS genes. Transcript levels of CS genes peak at 2 to 3 days postinoculation, when pathogen growth is highest, and decline at later stages of infection. The induction of several CS genes was found to be isolate specific. This suggests that the identified CS genes could be the direct or indirect targets of downy mildew effector proteins that promote disease susceptibility.

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CATMA: a complete Arabidopsis GST database

Cited by 135 publications

References 8 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

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

Disease-Specific Expression of Host Genes During Downy Mildew Infection of Arabidopsis

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