Gene expression in the rcb (regulator for chloroplast biogenesis) mutant in red light conditions
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PROVIDER: PRJNA504796 | ENA |
REPOSITORIES: ENA
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Project description:The regulator for chloroplast biogenesis (rcb) mutant was identified as a mutant defective in phytochrome-mediated chloroplast biogenesis. The rcb mutant has long hypocotyl and albino phenotypes. RCB initiates chloroplast biogenesis in the nucleus by promoting the degradation of the master repressors for chloroplast biogenesis, the PIFs (Phytochrome Interacting Factors). To understand how RCB regulates the expression of PIF-regulated genes, we performed genome-wide expression analysis of RCB-dependent genes using a rcb-10 null allele.
2019-06-20 | GSE122351 | GEO
Project description:Light and microRNAs (miRNAs) are key external and internal signals for plant development respectively. However the relationship between light signaling and miRNA biogenesis pathways remains unknown. Here we found that miRNA processer DCL1/HYL1 interacts with a basic helix–loop–helix (bHLH) transcription factor, phytochrome-interacting factor 4 (PIF4), which mediates the destabilization of DCL1 during dark-red light transition. PIF4 acts as a transcription factor for some miRNA genes and is necessary for the proper accumulation of miRNAs. DCL1/HYL1 and mature miRNAs play roles in the regulation of plant hypocotyl growth. These results uncovered a previously unknown crosstalk between miRNA biogenesis and red light signaling through the PIF4-dependent regulation of miRNA transcription and processing to affect red light-directed plant photomorhogenesis.
2018-02-27 | GSE109038 | GEO
Project description:Light initiates the seedling deetiolation transition by promoting major changes in gene expression mainly regulated by phytochrome (phy) photoreceptors. During the initial dark-to-light transition, phy photoactivation induces rapid changes in gene expression that eventually lead to the photomorphogenic development. Recent reports indicate that this process is achieved by phy-induced degradation of Phy-Interacting bHLH transcription Factors (PIFs) PIF1, PIF3 PIF4 and PIF5, which are partly redundant constitutive repressors of photomorphogenesis that accumulate in darkness. In order to test whether light/phy-regulated gene expression occurs through these PIFs, we have performed whole-genome expression analysis in the pif1pif3pif4pif5 quadruple mutant (pifq).
2009-11-01 | GSE17159 | GEO
Project description:This application is the second part of a BBSRC-funded grant to compare and contrast the plastid-signalling pathways disrupted by Norflurazon and far-red light treatment of Arabidopsis seedlings. The first application of this laboratory to GARNet's Affymetrix service (2002-08-25-17.41.49_McCormac) addressed the Norflurazon pathway; this application addresses the far-red pathway. The assembly of photosynthetic complexes in developing chloroplasts is critical to the establishment of the autotrophic plant. This requires light-mediated upregulation of both nuclear- and chloroplast-encoded genes. The expression of such photosynthetically-associated nuclear genes is also often dependant on a retrograde plastid signal which emanates from chloroplasts to modulate nuclear transcription. Extensive studies using the herbicide Norflurazon to knock-out the plastid signal (including this lab's previous Affymetrix application to GARNet) are identifying the affected gene sets. However, genetic studies have indicated the existence of more than one plastid signalling pathway. We have recently investigated a phytochrome A-mediated, far-red (FR) input pathway which blocks subsequent chloroplast development under white light (WL). This has also been found to inhibit the transcription of a small group of known nuclear-encoded plastidic proteins. Here we wish to establish how wide-reaching this FR-effect is on nuclear transcription, and will directly compare the affected gene groups with those identified from our earlier (and other's) studies with a Norflurazon treatment. In this array experiment we will compare RNA from seedlings grown in complete darkness (D) before transfer to WL, with that of seedlings preconditioned under a restricted wavelength FR source before exposure to WL. This comparison of FR- and Norflurazon-affected gene groupings will indicate whether the plastid signalling pathways are likely to be the same, overlapping or highly divergent. As well as wild-type seedlings, the gun1,gun5 mutant line is to be used as both these alleles are well established as alleviating the Norflurazon-inhibited pathway, but their affect on the FR-pathway is less clear. A single replicate of a phyA-null mutant line will also be included in order to differentiate between specific phytochromeA-mediated responses and other FR effects. It is envisaged that, in general, D- and FR-treated samples of the phyA mutant line will respond in the same way as each other and as the wild-type D-treated samples and, thus, the lack of a biological repeat in this case is not a major short-fall. The proposed experiment will consist of: wild-type: D-pretreated (x2 biological replicates) wild-type: FR-preconditioned (x2) gun1,gun5: D-pretreated (x2) gun1,gun5: FR-preconditioned (x2) phyA: D-pretreated (x1) phyA: FR-preconditioned (x1) Keywords: strain_or_line_design
2007-01-22 | GSE6169 | GEO
Project description:Light initiates the seedling deetiolation transition by promoting major changes in gene expression mainly regulated by phytochrome (phy) photoreceptors. During the initial dark-to-light transition, phy photoactivation induces rapid changes in gene expression that eventually lead to the photomorphogenic development. Recent reports indicate that this process is achieved by phy-induced degradation of Phy-Interacting bHLH transcription Factors (PIFs) PIF1, PIF3 PIF4 and PIF5, which are partly redundant constitutive repressors of photomorphogenesis that accumulate in darkness. In order to test whether light/phy-regulated gene expression occurs through these PIFs, we have performed whole-genome expression analysis in the pif1pif3pif4pif5 quadruple mutant (pifq). Wild-type and pifq mutant seeds were plated on GM medium without sucrose at room temperature. During this procedure the seeds were routinely exposed to white light (WL) for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness, induced to germinate with a 5-min red pulse (Rp) (46 μmol/m2/s) and then incubated in the dark for 3h at 21°C before exposure to a terminal 5-min far red pulse (FRp) (58 μmol/m2/s) to suppress pseudo-dark effects. Seeds were then placed in either dark (D) or constant red light (Rc) (6.7 μmol/ m2/s) at 21°C for 45h (2d-old seedlings). Alternatively, 2d-old dark-grown seedlings were treated with 1h of red light (R1) (7.5 μmol/m2/s). Seed samples were harvested after stratification (5d stratified seeds).
2009-10-31 | E-GEOD-17159 | biostudies-arrayexpress
Project description:Chloroplast biogenesis represents a crucial step in seedling development, and is essential for the transition to autotrophic growth in plants. This light-controlled process relies on the transcription of nuclear and plastid genomes that drives the effective assembly and regulation of the photosynthetic machinery. Here we reveal a novel regulation level for this process by showing the involvement of chromatin remodelling in the coordination of nuclear and plastid gene expression for proper chloroplast biogenesis and function. The two Arabidopsis homologs of the yeast EPL1 proteins, core components of the NuA4 histone acetyl-transferase complex, are essential for the correct assembly and performance of chloroplasts. EPL1 proteins are necessary for the coordinated expression of nuclear genes encoding most of the components of chloroplast transcriptional machinery, specifically promoting H4K5Ac deposition in these loci. These data unveil a key participation of epigenetic regulatory mechanisms in the coordinated expression of the nuclear and plastid genomes.
2022-07-26 | GSE180614 | GEO
Project description:This application is the second part of a BBSRC-funded grant to compare and contrast the plastid-signalling pathways disrupted by Norflurazon and far-red light treatment of Arabidopsis seedlings. The first application of this laboratory to GARNet's Affymetrix service (2002-08-25-17.41.49_McCormac) addressed the Norflurazon pathway; this application addresses the far-red pathway. The assembly of photosynthetic complexes in developing chloroplasts is critical to the establishment of the autotrophic plant. This requires light-mediated upregulation of both nuclear- and chloroplast-encoded genes. The expression of such photosynthetically-associated nuclear genes is also often dependant on a retrograde plastid signal which emanates from chloroplasts to modulate nuclear transcription. Extensive studies using the herbicide Norflurazon to knock-out the plastid signal (including this lab's previous Affymetrix application to GARNet) are identifying the affected gene sets. However, genetic studies have indicated the existence of more than one plastid signalling pathway. We have recently investigated a phytochrome A-mediated, far-red (FR) input pathway which blocks subsequent chloroplast development under white light (WL). This has also been found to inhibit the transcription of a small group of known nuclear-encoded plastidic proteins. Here we wish to establish how wide-reaching this FR-effect is on nuclear transcription, and will directly compare the affected gene groups with those identified from our earlier (and other's) studies with a Norflurazon treatment. In this array experiment we will compare RNA from seedlings grown in complete darkness (D) before transfer to WL, with that of seedlings preconditioned under a restricted wavelength FR source before exposure to WL. This comparison of FR- and Norflurazon-affected gene groupings will indicate whether the plastid signalling pathways are likely to be the same, overlapping or highly divergent. As well as wild-type seedlings, the gun1,gun5 mutant line is to be used as both these alleles are well established as alleviating the Norflurazon-inhibited pathway, but their affect on the FR-pathway is less clear. A single replicate of a phyA-null mutant line will also be included in order to differentiate between specific phytochromeA-mediated responses and other FR effects. It is envisaged that, in general, D- and FR-treated samples of the phyA mutant line will respond in the same way as each other and as the wild-type D-treated samples and, thus, the lack of a biological repeat in this case is not a major short-fall. The proposed experiment will consist of: wild-type: D-pretreated (x2 biological replicates) wild-type: FR-preconditioned (x2) gun1,gun5: D-pretreated (x2) gun1,gun5: FR-preconditioned (x2) phyA: D-pretreated (x1) phyA: FR-preconditioned (x1)
2022-11-21 | E-NASC-41 | biostudies-arrayexpress
Project description:Photosynthetic capacity is the result of chloroplast biogenesis, but whether photosynthesis itself is required for chloroplast biogenesis has not been investigated. In this study we use 680nm red light to overexcite Photosystem II to disrupt photosynthesis in two conditional mutants (var2 and abc1k1) and demonstrate that this arrests chloroplast biogenesis. During their biogenesis, chloroplasts import the majority of proteins associated with photosynthesis and some are transported further across the thylakoid membrane by the evolutionarily conserved SEC (Secretory) and TAT (Twin Arginine Translocation) pathways, energized by ATP and the proton gradient, respectively. Most luminal thylakoid proteins are synthesized in the cytoplasm with bi-partite, cleavable targeting sequences (first for the chloroplast envelope, second for the thylakoid membrane). Two-step cleavage of these peptides is essential for chloroplast biogenesis. Linked to the photosynthetic defect in var2 and abc1k1 under red light, six incompletely cleaved essential proteins at the thylakoid lumen side of Photosystems I and II accumulated to high levels in the mutants. In summary, the results show that the processing of a specific module of photosynthesis-associated proteins and concomitantly progression of chloroplast biogenesis depend on photosynthesis at the earliest stages of seedling development.
2024-12-13 | PXD050814 | Pride
Project description:The red-light regulated transcription factors FHY3 and FAR1 form a key point of light input to the plant circadian clock in positively regulating expression of genes within the central clock. However, the fhy3 mutant shows an additional red light-specific disruption of rhythmicity which is inconsistent with this role. Here we demonstrate that only fhy3 and not far1 mutants show this red specific disruption of rhythmicity. We examined the differences in rhythmic transcriptome in red versus white light and reveal differences in patterns of rhythmicity among the central clock proteins suggestive of a change in emphasis withing the central mechanism of the clock, changes which underlie the red specificity of the fhy3 mutant. In particular, changes in enrichment of promoter elements were consistent with a key role for the HY5 transcription factor, a known integrator of the ratio of red to blue light in regulation of the clock. Examination of differences in the rhythmic transcriptome in the fhy3 mutant in red light which identified specific disruption of the CCA1-regulated ELF3 and LUX central clock genes, while the CCA1 target TBS element, TGGGCC, was enriched among genes that became arrhythmic. Coupled with the known interaction of FHY3 but not FAR1 with CCA1 we propose that the red-specific circadian phenotype of fhy3 may involve disruption of the previously-demonstrated moderation of CCA1 activity by FHY3 rather than a disruption of its own transcriptional regulatory activity. Together, this evidence suggests a conditional redundancy between FHY3 and HY5 in the integration of red and blue light input to the clock in order to enable a plasticity in response to light and optimise plant adaptation. Furthermore, our evidence also suggests changes in CCA1 activity between red and white light transcriptomes. This, together with the documented interaction of HY5 with CCA1, leads us to propose a model whereby this integration of red and blue signals may at least partly occur via direct FHY3 and HY5 interaction with CCA1 leading to moderation of CCA1 activity.
2022-05-23 | GSE201929 | GEO
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.
2022-09-27 | GSE213949 | GEO