Convergence of Light and ABA Signaling on the ABI5 Promoter

Xu, Dongqing; Li, Jigang; Gangappa, Sreeramaiah N.; Hettiarachchi, Chamari; Lin, Fang; Andersson, Mats X.; Jiang, Yan; Holm, Magnus

doi:10.1371/journal.pgen.1004197

Cited by 175 publications

(220 citation statements)

References 55 publications

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“…In fact, our qRT-PCR data suggest that the tolerance of the hy5 mutant to ER stress conditions was due to the elevated expression of UPR marker genes in these plants. In conclusion, these results are consistent with those of recent studies suggesting that HY5 is a critical component in the integration of light signaling with different defense responses against stress conditions, an important event for plant survival under adverse conditions (10,31,32).…”

Section: Discussionsupporting

confidence: 93%

HY5, a positive regulator of light signaling, negatively controls the unfolded protein response in Arabidopsis

Nawkar

Kang

Maibam

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

103

102

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Light influences essentially all aspects of plant growth and development. Integration of light signaling with different stress response results in improvement of plant survival rates in ever changing environmental conditions. Diverse environmental stresses affect the protein-folding capacity of the endoplasmic reticulum (ER), thus evoking ER stress in plants. Consequently, the unfolded protein response (UPR), in which a set of molecular chaperones is expressed, is initiated in the ER to alleviate this stress. Although its underlying molecular mechanism remains unknown, light is believed to be required for the ER stress response. In this study, we demonstrate that increasing light intensity elevates the ER stress sensitivity of plants. Moreover, mutation of the ELONGATED HYPOCOTYL 5 (HY5), a key component of light signaling, leads to tolerance to ER stress. This enhanced tolerance of hy5 plants can be attributed to higher expression of UPR genes. HY5 negatively regulates the UPR by competing with basic leucine zipper 28 (bZIP28) to bind to the G-box-like element present in the ER stress response element (ERSE). Furthermore, we found that HY5 undergoes 26S proteasome-mediated degradation under ER stress conditions. Conclusively, we propose a molecular mechanism of crosstalk between the UPR and light signaling, mediated by HY5, which positively mediates light signaling, but negatively regulates UPR gene expression.endoplasmic reticulum stress | light signaling | protein-folding capacity | crosstalk | unfolded protein response

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Section: Discussionsupporting

confidence: 93%

HY5, a positive regulator of light signaling, negatively controls the unfolded protein response in Arabidopsis

Nawkar

Kang

Maibam

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

103

102

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“…The current model, which is in general agreement with other defense pathway models, suggests that there are limited sets of TFs that can linearly account for most of the transcriptional regulation in the GLS pathway and that environmental signal integration occurs upstream of these TFs ( Fig. 1B; Dombrecht et al, 2007;Beekwilder et al, 2008;Navarro et al, 2008;Hou et al, 2010;Lackman et al, 2011;Wild et al, 2012;Nakata et al, 2013;Xu et al, 2014). Although there are data supporting this model, specifically that removing two MYB (MYB28 and MYB29) and three MYC (MYC2, MYC3, and MYC4) TFs abolishes all aliphatic GLS accumulation, a closer investigation of published transcriptomic data suggests that this MYB/MYC model does not fully explain the biological observations (Beekwilder et al, 2008;Sønderby et al, 2010b;Schweizer et al, 2013).…”

supporting

confidence: 88%

Promoter-Based Integration in Plant Defense Regulation

Li¹,

Gaudinier

Tang

et al. 2014

Plant Physiology

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A key unanswered question in plant biology is how a plant regulates metabolism to maximize performance across an array of biotic and abiotic environmental stresses. In this study, we addressed the potential breadth of transcriptional regulation that can alter accumulation of the defensive glucosinolate metabolites in Arabidopsis (Arabidopsis thaliana). A systematic yeast one-hybrid study was used to identify hundreds of unique potential regulatory interactions with a nearly complete complement of 21 promoters for the aliphatic glucosinolate pathway. Conducting high-throughput phenotypic validation, we showed that .75% of tested transcription factor (TF) mutants significantly altered the accumulation of the defensive glucosinolates. These glucosinolate phenotypes were conditional upon the environment and tissue type, suggesting that these TFs may allow the plant to tune its defenses to the local environment. Furthermore, the pattern of TF/promoter interactions could partially explain mutant phenotypes. This work shows that defense chemistry within Arabidopsis has a highly intricate transcriptional regulatory system that may allow for the optimization of defense metabolite accumulation across a broad array of environments.An organism's growth and fitness within its environment are largely determined by its ability to efficiently obtain and utilize energy and elements to create biomass to survive. Central to this process is primary metabolism, which determines the use of energy and chemicals from the environment to produce all of the necessary building blocks for cells and the resulting biomass. To optimize fitness, metabolism must be precisely tuned and coordinated to make the most efficient use of available resources. This basic supposition is central to a wide range of biological fields from the study of organismal growth to the study of interactions with the environment, and has led to strong interest in understanding how metabolism is regulated (Karban and Baldwin, 1997;Smith and Stitt, 2007).The last decade has seen an upsurge in studies investigating the transcriptional control over metabolism. This has largely been driven by three key areas of focus: regulation of sugar metabolism, amino acid metabolism, and secondary metabolism (Desvergne et al., 2006). In most organisms, Glc levels cause transcriptional reprograming of sugar metabolism and organismal development often by a mitogen-activated protein kinase cascade (Moore et al., 2003;Rolland et al., 2006). Transcriptional control over amino acid metabolism frequently involves General Control Nonderepressible4, whereas other transcriptional activators play a role in coordinating amino acid metabolism (Hope and Struhl, 1986;Neuwald and Landsman, 1997;Li et al., 2013). Within plants, there are also amino acid pathway-specific transcription factors (TFs) known for a couple of plant amino acid biosynthetic pathways (Celenza et al., 2005;Maruyama-Nakashita et al., 2006). In plants, the transcriptional regulation of secondary metabolites has also received signifi...

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“…By mapping the reads to a reference genome, enriched loci (peaks) can be used to identify TFBS and motifs. For example, inspection of DAP-seq peaks for the bZIP TF ABI5 revealed enrichment at a known regulatory site that contains two adjacent G-box motifs (CACGTG) (Xu et al, 2014), where a ChIP-seq peak was also found ( Figure 1D). The DAP-seq-derived motif matched the motifs derived from both ChIP-seq and PBM , although the DAP-and ChIP-seq motifs shared more sequence similarity at the edges ( Figure 1E).…”

Section: Dap-seqmentioning

confidence: 99%

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

O’Malley¹,

Huang²,

Song³

et al. 2016

Cell

362

482

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SUMMARYThe cistrome is the complete set of transcription factor (TF) binding sites (cis-elements) in an organism, while an epicistrome incorporates tissue-specific DNA chemical modifications and TFspecific chemical sensitivities into these binding profiles. Robust methods to construct comprehensive cistrome and epicistrome maps are critical for elucidating complex transcriptional networks that underlie growth, behavior, and disease. Here, we describe DNA affinity purification sequencing (DAP-seq), a high-throughput TF binding site discovery method that interrogates genomic DNA with in-vitro-expressed TFs. Using DAP-seq, we defined the Arabidopsis cistrome by resolving motifs and peaks for 529 TFs. Because genomic DNA used in DAP-seq retains 5-methylcytosines, we determined that >75% (248/327) of Arabidopsis TFs surveyed were methylation sensitive, a property that strongly impacts the epicistrome landscape. DAP-seq datasets also yielded insight into the biology and binding site architecture of numerous TFs, demonstrating the value of DAP-seq for cost-effective cistromic and epicistromic annotation in any organism.

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Convergence of Light and ABA Signaling on the ABI5 Promoter

Cited by 175 publications

References 55 publications

HY5, a positive regulator of light signaling, negatively controls the unfolded protein response in Arabidopsis

HY5, a positive regulator of light signaling, negatively controls the unfolded protein response in Arabidopsis

Promoter-Based Integration in Plant Defense Regulation

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

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