Genome-wide in silico identification and experimental confirmation of abscisic acid-regulated genes in Arabidopsis

Huang, Ming Der; Wu, Wen Luan

doi:10.1016/j.plantsci.2006.01.004

Cited by 6 publications

(5 citation statements)

References 38 publications

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“…Proteins of this family are likely to interact and protect various cellular membranes during dehydration (Candat et al 2014 ). In A. thaliana seedlings, the expression of AT3G53040 was shown to respond to ABA, but without inducible expression to stress conditions (Huang and Wu 2006 ; Bies-Ethève et al 2008 ). AT3G53040 and AT2G36640 are very similar to each other in sequence and expression pattern and are considered to form a pair derived from a whole genome duplication (Hundertmark and Hincha 2008 ; Bies-Ethève et al 2008 ).…”

Section: Discussionmentioning

confidence: 99%

A gene co-expression network predicts functional genes controlling the re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds

Costa

Righetti

Nijveen

et al. 2015

Planta

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Main conclusionDuring re-establishment of desiccation tolerance (DT), early events promote initial protection and growth arrest, while late events promote stress adaptation and contribute to survival in the dry state.Mature seeds of Arabidopsis thaliana are desiccation tolerant, but they lose desiccation tolerance (DT) while progressing to germination. Yet, there is a small developmental window during which DT can be rescued by treatment with abscisic acid (ABA). To gain temporal resolution and identify relevant genes in this process, data from a time series of microarrays were used to build a gene co-expression network. The network has two regions, namely early response (ER) and late response (LR). Genes in the ER region are related to biological processes, such as dormancy, acquisition of DT and drought, amplification of signals, growth arrest and induction of protection mechanisms (such as LEA proteins). Genes in the LR region lead to inhibition of photosynthesis and primary metabolism, promote adaptation to stress conditions and contribute to seed longevity. Phenotyping of 12 hubs in relation to re-establishment of DT with T-DNA insertion lines indicated a significant increase in the ability to re-establish DT compared with the wild-type in the lines cbsx4, at3g53040 and at4g25580, suggesting the operation of redundant and compensatory mechanisms. Moreover, we show that re-establishment of DT by polyethylene glycol and ABA occurs through partially overlapping mechanisms. Our data confirm that co-expression network analysis is a valid approach to examine data from time series of transcriptome analysis, as it provides promising insights into biologically relevant relations that help to generate new information about the roles of certain genes for DT.Electronic supplementary materialThe online version of this article (doi:10.1007/s00425-015-2283-7) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

A gene co-expression network predicts functional genes controlling the re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds

Costa

Righetti

Nijveen

et al. 2015

Planta

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“…This possibility is supported by recent work showing that ABREs are over-represented in the promoter regions of genes corresponding to several diVerent stress cDNA collections (Mahalingam et al 2003). However, the presence of multiple ABRE elements in a promoter is not a random event, since only 137 genes out of 26,207 genes in the Arabidopsis genome have multiple ABREs (Huang and Wu 2006). Interactions between ABA and JA signaling during the wound response might be mediated by AtMYC2 (review by Lorenzo and Solano 2005).…”

Section: Discussionmentioning

confidence: 99%

Impact of transcriptional, ABA-dependent, and ABA-independent pathways on wounding regulation of RNS1 expression

et al. 2008

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Injured plants induce a wide range of genes whose products are thought to help to repair the plant or to defend against opportunistic pathogens that might infect the wounded plant. In Arabidopsis thaliana L., oligogalacturonides (OGAs) and jasmonic acid (JA) are the main regulators of the signaling pathways that control the local and systemic wound response, respectively. RNS1, a secreted ribonuclease, is induced by wounding in Arabidopsis independent of these two signals, thus indicating that another wound-response signal exists. Here we show that abscisic acid (ABA), which induces wound-responsive genes in other systems, also induces RNS1. In the absence of ABA signaling, wounding induces only approximately 45% of the endogenous levels of RNS1 mRNA. However, significant levels of RNS1 still accumulate in the absence of ABA signaling. Our results suggest that wound-responsive increases in ABA production may amplify induction of RNS1 by a novel ABA-independent pathway. To elucidate this novel pathway, we show here that the wound induction of RNS1 is due in part to transcriptional regulation by wounding and ABA. We also show evidence of post-transcriptional regulation which may contribute to the high levels of RNS1 transcript accumulation in response to wounding.

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“…In a previous computational screen for ABA-regulated genes, we identified a gene, two or more ABREs-containing gene 2 (TMAC2), which was up-regulated by not only ABA but also salinity stress (Huang and Wu 2006). In the current study, we further characterized the expression pattern and in planta function of TMAC2 in Arabidopsis.…”

Section: Introductionmentioning

confidence: 90%

“…To facilitate the genetic analysis of the ABA response, we have identified novel ABA-regulated genes using an in silico method by searching for genes possessing two more ABREs within the promoter region in Arabidopsis (Huang and Wu 2006). One of these genes, TMAC2, in the locus At3g02140, contains three ABREs within the 600-bp region upstream of the translation start site.…”

Section: Cloning and Characterization Profile Of Tmac2mentioning

confidence: 99%

“…The typical mutation screens based on germination under high concentrations of ABA have isolated mutants altered in ABA responsiveness (Finkelstein et al 2002). Recently, hundreds of ABA-responsive genes were identified and characterized by high-throughput methods, such as microarray and bioinformatics technologies (Seki et al 2002;Huang and Wu 2006). ABA signaling genes encode proteins that play roles in transcription, protein phosphorylation, farnesylation or RNA processing and modulate ABA response in a multiple overlapping pathway (Fedoroff 2002;Finkelstein et al 2002).…”

Section: Introductionmentioning

confidence: 99%

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Overexpression of TMAC2, a novel negative regulator of abscisic acid and salinity responses, has pleiotropic effects in Arabidopsis thaliana

Huang

2006

Plant Mol Biol

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Phytohormone abscisic acid (ABA) regulates many aspects of plant development and growth. To explore the molecular mechanism of ABA, we identified the novel ABA-regulated genes in Arabidopsis thaliana by searching for genes possessing two or more ABREs (ABA-responsive elements). One of these genes, two or more ABREs-containing gene 2 (TMAC2) is highly induced by ABA and NaC1. Database searches revealed that TMAC2 encodes a protein with no domains of known function. Expression of TMAC2-GFP fusion protein in Arabidopsis mesophyll protoplasts indicated that TMAC2 is targeted to the nucleus. Although the gene has a basal level of expression in various Arabidopsis organs/tissues except for adult leaves, a high expression level was detected in roots. Constitutive overexpression of TMAC2 in plants resulted in the insensitivity to ABA and NaCl, suggesting that TMAC2 plays a negative role in ABA and salt stress responses. Furthermore, TMAC2-overexpressing plants exhibited the short roots, late flowering and starch-excess phenotypes. RT-PCR analysis showed that decreased expression of two floral- and one starch degradation-related genes, SOC1/AGL20 and SEP3/AGL9, and SEX1, respectively, may lead to altered phenotypes of TMAC2-overexpressing plants. Taken together, our data reveal that TMAC2 acts in the nucleus and is an important negative regulator of ABA and salt stress responses, and could play a critical role in controlling root elongation, floral initiation and starch degradation.

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Genome-wide in silico identification and experimental confirmation of abscisic acid-regulated genes in Arabidopsis

Cited by 6 publications

References 38 publications

A gene co-expression network predicts functional genes controlling the re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds

A gene co-expression network predicts functional genes controlling the re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds

Impact of transcriptional, ABA-dependent, and ABA-independent pathways on wounding regulation of RNS1 expression

Overexpression of TMAC2, a novel negative regulator of abscisic acid and salinity responses, has pleiotropic effects in Arabidopsis thaliana

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