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Low red to far-red light environments alter nitrogen assimilation in corn (Zea mays)

ABSTRACT: Low red to far-red light environments alter nitrogen assimilation in corn (Zea mays)

PROVIDER: PRJNA883250 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21676500_1.fastq.gz	Fastqsanger.gz
	SRR21676500_2.fastq.gz	Fastqsanger.gz
	SRR21676501_1.fastq.gz	Fastqsanger.gz
	SRR21676501_2.fastq.gz	Fastqsanger.gz
	SRR21676502_1.fastq.gz	Fastqsanger.gz

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Low red to far-red light environments alter nitrogen assimilation in corn (Zea mays)

Project description:The goal of this work was to investigate the influence of low red to far-red (R:FR) signals generated by a biological weedy and an artificial source of far-red light on the nitrate assimilation pathway in maize. In the absence of direct resource competition, far-red light reflected from neighboring weeds compromises light quality (red to far-red ratio; R/FR) and causes a wide range of morphological and physiological responses at early growth stages of crop plants. This study has investigated the effects of low R/FR light signals on nitrate assimilation in maize seedlings. The transcript levels of genes, metabolites, and activities of enzyme in the nitrate assimilation pathway under a biological and a simulated low R:FR light environment were compared with a high R:FR control environment. Low R:FR signals stimulated nitrate accumulation in maize leaves, which did not appear to result from the upregulation of nitrate transporter genes. A significant reduction in ferredoxin-dependent glutamine:2-oxoglutarate aminotransferase activity appears to play a major role in nitrate accumulation under low R:FR light environments, while activities of other enzymes of the nitrate assimilation pathway remain unchanged.

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Transcription profiling of Arabidopsis Col-0 and pil5 imbibed seeds after far-red or far-red/red light irradiation.

Project description:PIL5 is a key negative regulator of phytochrome mediated seed germination and PIL5 protein is degraded by red light irradiation through phytochrome. The microarray aimed to find various red light-regulated genes and PIL5-regulated genes in the imbibed seeds. Experiment Overall Design: Col-0 and pil5 seeds were irradiated by far-red light or far-red/red light and then, incubated in the dark for 12 hours. Total three biological replicates were used for the microarray.

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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.

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Transcriptional characterization of Arabidopsis thaliana seeds treated with a red- or far red-light pulse

Project description:The goal of this study was to compare the transcriptional profile (RNA-seq) of imbibed Arabidopsis thaliana Columbia-0 ecotype seeds that were treated with a 20 min red or far red pulse. The red-light pulse induces germination.

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Expression data from Arabidopsis thaliana under dark and far-red light

Project description:FAR-RED ELONGATED HYPOCOTYL 3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE 1 (FAR1) are two transposase-derived transcription factors initially identified as the key components in phytochrome A signaling and recently shown to function in the circadian clock. However, whether FHY3 and FAR1 are involved in other processes of plant development remains largely unknown. Here, we explored chromatin immunoprecipitation-based sequencing (ChIP-seq) analysis to identify 1745 and 1171 FHY3 direct binding target genes in darkness and far-red light conditions, respectively in the Arabidopsis thaliana genome. This analysis revealed that FHY3 preferentially binds to the gene promoters through the previously identified typical FHY3/FAR1 binding motif. Interestingly, FHY3 also binds to two novel motifs in the 178-bp repeats of the Arabidopsis centromere regions in vivo. Comparison between the ChIP-seq and microarray data indicates that FHY3 regulates the expression of 196 and 85 genes in dark and far-red respectively by directly binding to their promoters. FHY3 also co-regulates a number of common target genes with PHYTOCHROME INTERACTING FACTOR 3-LIKE 5 (PIL5) and ELONGATED HYPOCOTYL 5 (HY5). Moreover, our genome-wide identification of FHY3 direct target genes ultimately led to the discovery and validation of a new role of FHY3 in controlling chloroplast development, by directly activating the expression of ACCUMULATION AND REPLICATION OF CHLOROPLASTS5 (ARC5), a key gene regulating chloroplast constriction and division. Taken together, our data suggest that FHY3 is involved in regulating multiple facets of plant development, thus providing new insights into the functions of this type of transposase-derived transcription factors.

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ChIP-Seq data from Arabidopsis thaliana under dark and far-red light

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Expression data from Col-0 and pil5 imbibed seeds after far-red or far-red/red light irradiation.

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Genome-wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL 3 Reveals Its Novel Function in Arabidopsis Development

Project description:This SuperSeries is composed of the following subset Series: GSE30711: ChIP-Seq data from Arabidopsis thaliana under dark and far-red light GSE30712: Expression data from Arabidopsis thaliana under dark and far-red light Refer to individual Series

2011-12-31 | E-GEOD-30713 | biostudies-arrayexpress

Transcriptional characterization of Arabidopsis thaliana seeds treated with a red- or far red-light pulse

Project description:Transcriptional characterization of Arabidopsis thaliana seeds treated with a red- or far red-light pulse

| PRJNA553510 | ENA