The genomes uncoupled dependent signaling pathway coordinates plastid biogenesis with the synthesis of anthocyanins
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE104868 | GEO | 2019/10/18
REPOSITORIES: GEO
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Project description:Investigation of the function of GUN1 in the chloroplast (post)-transcriptome We performed gene expression profiling analysis using data obtained from lncRNA-seq of gun1 seedlings with white, marble or green cotyledons
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Project description:Analysis of transcriptome response of norflurazon treated or untreated 5-day old whole seedlings with genotypes: Col6-3 (wild type), gun1-9 and MORF2 overexpression lines. GUN1 and MORF2 are involved in chloroplast-to-nucleus retrograde signaling. Results provide insight into the nuclear genes expression profile under control of GUN1 retrograde pathways and the regulation similarity between gun1-9 and MORF2 overexpression lines.
2019-05-02 | GSE110125 | 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:GUN1 integrates retrograde signals in the chloroplast but the underlying mechanism is elusive. FUG1, a chloroplast translation initiation factor, and GUN1 are co-expressed at the transcript level, and FUG1 co-immunoprecipitates with GUN1. We used mutants of GUN1 (gun1-103) and FUG1 (fug1-3) to analyse their functional relationship at the physiological and systems-wide level, the latter including transcriptome and proteome analyses. Absence of GUN1 aggravates the effects of decreased FUG1 levels on chloroplast protein translation, resulting in transient additive phenotypes with respect to photosynthesis, leaf coloration, growth and cold acclimation. Variegation of the var2 mutant is enhanced by gun1-103 in terms of increasing the fraction of white sectors, in contrast to fug1-3 that acts as suppressor. The transcriptomes of fug1-3 and gun1-103 are very similar, but absence of GUN1 alone has almost no effects on protein levels, whereas chloroplast protein accumulation is markedly decreased in fug1-3. In gun1 fug1 double mutants, effects on transcriptomes and particularly proteomes are enhanced. Our results show that GUN1 function becomes critical when chloroplast proteostasis is perturbed by decreased translation (fug1) or degradation (var2) of chloroplast proteins. The functions of FUG1 and GUN1 appear to be related, corroborating the view that GUN1 operates in chloroplast proteostasis.
2019-04-23 | GSE123583 | 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: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) Experiment Overall Design: Number of plants pooled:300 seedlings
2008-06-14 | E-GEOD-6169 | biostudies-arrayexpress
Project description:Quantification of Tic-Toc subunits in the wild type and gun1-101 mutants in the control conditions and treated with lincomycin or norflurazon to determine if there are differences between genotypes.
2019-04-23 | PXD013005 | Pride
Project description:In recent years, it has become evident that plants perceive, integrate and communicate abiotic stress signals through chloroplasts. During the process of acclimation plastid-derived, retrograde signals control nuclear gene expression in response to developmental and environmental cues leading to complex genetic and metabolic reprogramming to preserve cellular homeostasis under challenging environmental conditions. Upon stress-induced dysfunction of chloroplasts, GENOMES UNCOUPLED (GUN) proteins participate in the repression of PHOTOSYNTHESIS-ASSOCIATED NUCLEAR GENES (PHANGs). Here, we show that the retrograde signal emitted by, or communicated through, GUN-proteins is also essential to induce the accumulation of photoprotective anthocyanin pigments when chloroplast development is attenuated. Comparative whole transcriptome sequencing and genetic analysis reveal GUN1 and GUN5-dependent signals as a source for the regulation of genes involved in anthocyanin biosynthesis. The signal transduction cascade includes well-known transcription factors for the control of anthocyanin biosynthesis, which are deregulated in gun mutants. We propose that regulation of PHANGs and genes contributing to anthocyanin biosynthesis are two, albeit oppositely, co-regulated processes during plastid biogenesis. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.
| S-EPMC7209955 | biostudies-literature
Project description:Plastid gene expression (PGE) acts as a signal that regulates the expression of photosynthesis-associated nuclear genes (PhANGs) via GENOMES UNCOUPLED1 (GUN1)-dependent retrograde signaling. We recently isolated Arabidopsis sugar-inducible cotyledon yellow-192 (sicy-192), a gain-of-function mutant of plastidic invertase (INV-E), and showed that following the treatment of this mutant with sucrose, the expression of PhANGs decreased while that of nitrate reductase 1 (NIA1) increased. Plastid-encoded RNA polymerase (PEP)-dependent PGE was markedly suppressed in the sicy-192 mutant by the sucrose treatment. A double mutant of sicy-192 and gun1-101, a null mutant of GUN1, revealed that metabolic perturbation in the sucrose-treated sicy-192 mutant was, at least in part, dependent on GUN1. To confirm whether there is a relationship between plastid sugar metabolism and nuclear gene expression, we performed a microarray analysis using Suc-treated 3 genotypes consisting of wild-type, sicy-192, and sicy-192 gun1-101 plants.
2013-09-14 | GSE50857 | GEO
Project description:We have previously identified the chloroplast translation initiation factor IF-2, or FUG1, as a GUN1 interactor based on co-immunoprecipitation and co-expression analysis (Tadini et al., 2016). To further investigate the functional relationship between these two proteins, the double mutant gun1-103 fug1-3 was generated by crossing the single gun1-103 knock-out mutant and the fug1-3 knock-down mutant. We performed comparative proteomics on gun1-103 and fug1-3, as well as on the double mutant gun1-103 fug1-3.
2019-06-26 | PXD012067 | Pride