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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Cryptochromes interact directly with PIFs to control plant growth in limiting blue light

ABSTRACT: Sun-loving plants have the ability to detect and avoid shading through sensing of both blue and red light wavelengths. Higher plant cryptochromes (CRYs) control how plants modulate growth in response to changes in blue light. For growth under a canopy, where blue light is diminished, CRY1 and CRY2 perceive this change and respond by directly contacting two bHLH transcription factors, PIF4 and PIF5. These factors are also known to be controlled by phytochromes, the red/far-red photoreceptors; however, transcriptome analyses indicate that the gene regulatory programs induced by the different light wavelengths are distinct. Our results indicate that CRYs signal by modulating PIF activity genome-wide, and that these factors integrate binding of different plant photoreceptors to facilitate growth changes under different light conditions. We performed whole-genome chromatin immunoprecipitation with sequencing (ChIP-Seq) analysis on 5 day old Flash-CRY2, PIF4-Flash and PIF5-Flash treated in low blue-light for 16h.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Joseph Ecker

PROVIDER: E-GEOD-68193 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Cryptochromes interact directly with PIFs to control plant growth in limiting blue light

Project description:Sun-loving plants have the ability to detect and avoid shading through sensing of both blue and red light wavelengths. Higher plant cryptochromes (CRYs) control how plants modulate growth in response to changes in blue light. For growth under a canopy, where blue light is diminished, CRY1 and CRY2 perceive this change and respond by directly contacting two bHLH transcription factors, PIF4 and PIF5. These factors are also known to be controlled by phytochromes, the red/far-red photoreceptors; however, transcriptome analyses indicate that the gene regulatory programs induced by the different light wavelengths are distinct. Our results indicate that CRYs signal by modulating PIF activity genome-wide, and that these factors integrate binding of different plant photoreceptors to facilitate growth changes under different light conditions. We performed whole-genome transcriptome (mRNA-seq) analysis on 5-day-old Arabidopsis thaliana Columbia wild-type (WT) and pif4pif5 seedlings exposed to low blue-light (LBL) or mock-treated for 1, 6 and 24 hours. In addition we performed mRNA-seq on WT, 35S::PIF4-9xMyc-6x-His-3xFlag(Flash) and 35S::PIF5-9xMyc-6x-His-3xFlag (Flash) seedlings treated with LBL or mock-treated for 16 hours.

2015-12-31 | E-GEOD-59699 | biostudies-arrayexpress

Cryptochromes interact directly with PIFs to control plant growth in limiting blue light

2015-12-31 | GSE59699 | GEO

Cryptochromes interact directly with PIFs to control plant growth in limiting blue light

2015-12-31 | GSE68193 | GEO

Transcription profiling of Arabidopsis thaliana phytochrome interacting factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light.

Project description:Phytochromes are red/far red photosensors regulating numerous developmental programs in plants. Among them phytochrome A (phyA) is essential to enable seedling de-etiolation in continuous far-red (FR) light a condition mimicking the environment under a dense canopy. The ecological relevance of this response is demonstrated by the high mortality rate of phyA mutants germinating in deep vegetational shade. phyA signaling involves a direct interaction of the photoreceptor with members of the bHLH transcription factor family, PIF1 and PIF3 (Phytochrome Interacting Factor). Here we investigated the involvement of PIF4 and PIF5 in phyA signaling and found that they redundantly control de-etiolation in FR light. The pif4pif5 double mutant is hypersensitive to low fluence rates of FR light. This phenotype is dependent on FR light perception by phyA but does not rely on alterations of the phyA level. Our microarrays analysis shows that PIF4 and PIF5 are part of an inhibitory mechanism repressing the expression of some light-responsive genes in the dark and are also needed for full expression of several growth-related genes in the light. Unlike PIF1 and PIF3, PIF4 and PIF5 are not degraded in response to FR light indicating that they are light-regulated by a different mechanism. Our genetic analysis suggests that this is achieved through the sequestration of these PIFs by the closely related bHLH transcription factor HFR1 (long Hypocotyl in FR light). Experiment Overall Design: he pif4pif5 double mutant were compared to wild-type plants when kept in the dark or subjected to 1 or 24 hours of 0.5 or 5 Âµmol/m2/s far-red light respectively.

2009-09-17 | E-GEOD-16333 | biostudies-arrayexpress

Transcriptomic measurements of Nannochloropsis oceanica CCMP1779 after pulses of blue or red light

Project description:We investigated light dependent gene expression changes in the marine ochrophyte Nannochloropsis oceanica CCMP1779. These algae have several putative blue light photoreceptors but appear to lack red light photoreceptors. To study early light signaling in N. oceanica and avoid as much as possible secondary downstream events, we quantified gene expression changes in dark-adapted cells after a short blue or red light pulse. More genes were differentially expressed under blue than under red light. In addition, fold change in expression was smaller for the red light-treated samples. For example, the median fold change of induced genes was 3 for blue light and 2.5 for red light. Moreover, hierarchical cluster analysis showed that gene expression after red light treatment was more similar to the dark control than after blue light treatment.

2022-01-05 | GSE164714 | GEO

COP1 SUPPRESSOR 6 promotes photomorphogenesis by repressing the transcription and activity of PIF4 and PIF5

Project description:Light signaling precisely controls the photomorphogenic development in plants. In this study, we report COP1 SUPPRESSOR 6 (CSU6) function as positive regulator of light signaling. Loss of CSU6 function largely rescued the cop1-6 constitutively photomorphogenic phenotype. The hypocotyl length of csu6 mutant seedlings was shorter in the dark, but longer than that of wide-type in the light. CSU6 not only associated with the promoter regions of PIF4 and PIF5 to inhibit their expression during the day, but also directly interacts with both PIF4 and PIF5 to repress their transcriptional activity. CSU6 negatively controls a large group of PIF4- and PIF5-mediated genes' expression. Mutations in PIF4 and/or PIF5 are epistatic to the loss of CSU6, suggesting that CSU6 acts upstream of PIF4 and PIF5. Taken together, CSU6 promotes photomorphogenesis by negatively regulating PIF4 and PIF5 transcription and biochemical activity.

2024-04-23 | GSE201389 | GEO

Phytochrome Interacting Factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light.

2009-08-19 | GSE16333 | GEO

Transcriptome analysis of Arabidopsis thaliana photoreceptor mutants impaired in UV and blue light signaling

Project description:Plants use sunlight as a source of energy for photosynthesis but also as an important environmental cue to regulate growth, development and light acclimation. Wavelengths in the UV-B (280-315 nm) and UV-A/blue (315-500 nm) regions of the spectrum are perceived by UV RESISTANCE LOCUS 8 (UVR8) and cryptochromes (CRY1 and CRY2), respectively. Despite recent advances in our understanding of how these photoreceptors promote photomorphogenesis, very little is known about the molecular mechanisms regulated by UVR8 and CRYs in sunlight exposed plants. Here, a factorial experiment was designed to assess the roles of UVR8 and CRYs in regulating transcriptome wide changes, hormone accumulation, and growth competence of Arabidopsis thaliana plants exposed to solar UV-B, UV-A, and blue radiation.

2019-05-29 | GSE117199 | GEO

Diatom phytochromes reveal the existence of far-red light based sensing in the ocean

Project description:The absorption of visible light in aquatic environments has led to the common assumption that aquatic organisms sense and adapt to penetrative blue/green light wavelengths, but show little or no response to the more attenuated red/far-red wavelengths. Here we show that two marine diatom species, Phaeodactylum tricornutum and Thalassiosira pseudonana, possess a bona fide red/far-red light sensing phytochrome (DPH) that uses biliverdin as a chromophore and displays accentuated red-shifted absorbance peaks compared to other characterized plant and algal phytochromes. Exposure to both red and far-red light causes changes in gene expression in P. tricornutum and the responses to far-red light disappear in DPH knockout cells, demonstrating that P. tricornutum DPH mediates far-red light signaling. The identification of DPH genes in diverse diatom species widely distributed along the water column further emphasizes the ecological significance of far-red light sensing, raising questions about the sources of far-red light. Our analyses indicate that, although far-red wavelengths from sunlight are only detectable at the ocean surface, chlorophyll fluorescence and Raman scattering can generate red/far-red photons in deeper layers. This study opens up novel perspectives on phytochrome-mediated far-red light signaling in the ocean and on the light sensing and adaptive capabilities of marine phototrophs.

2016-05-09 | GSE73915 | GEO

RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways

Project description:The phytochromes (PHYs) are a family of photoreceptors which absorb light of red and far-red wavelengths to modulate developmental responses in photosynthetic organisms. We developed knockout mutants of PHYB and PHYC in wheat and performed replicated RNA-seq studies to analyze and compare the regulons of each phytochrome under long day photoperiods.

2016-06-29 | GSE79049 | GEO

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