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Expression data from Arabidopsis wild-type, sicy-192, and sicy-192 gun1-101 plants

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE50857 | GEO | 2013/09/14

SECONDARY ACCESSION(S): PRJNA219177

REPOSITORIES: GEO

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Expression data from Arabidopsis wild-type, sicy-192, and sicy-192 gun1-101 plants

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. Wild-type, sicy-192, and sicy-192 gun1-101 plants were grown on MS medium containing 100 mM sucrose in a growth chamber kept at 25Â°C during 16 h of light (100 Âµmol/m2/s) and at 22Â°C during 8 h of darkness for 4 days. At 4 days of age, cotyledons were collected as samples for microarray analysis.

2013-09-14 | E-GEOD-50857 | biostudies-arrayexpress

Effect of knockout of GUN1 or NAC103 on gene expression in roots of the WT or rab8d-2

Project description:We analyzed the root transcriptome profiles in WT, gun1-101, nac103-11, rab8d-2, gun1-101 rab8d-2, and nac103-11 rab8d-2. Our analysis showed that, compared to WT, approximately 108 genes were misregulated in gun1-101, while 78 genes were affected in nac103-11. Only two genes were influenced by both gun1-101 and nac103-11. In contrast, in the rab8d-2 background, blocking the function of GUN1 (gun1-101 rab8d-2) or NAC103 (nac103-11 rab8d-2) significantly altered the expression levels of approximately 948 and 267 genes, respectively. Importantly, over 72% (about 193) of the misregulated genes in nac103-11 rab8d-2 overlapped with those in gun1-101 rab8d-2, indicating a convergence of the GUN1- and NAC103-dependent signaling pathways in rab8d-2.

2023-12-24 | GSE242010 | GEO

Lincomycin treatment of Col-0 and gun1-101

Project description:Retrograde signals emanate from the DNA-containing cell organelles (plastids and mitochondria) and control the expression of a large number of nuclear genes in response to environmental and developmental cues. GENOMES UNCOUPLED1 (GUN1) participating in multiple retrograde signaling pathways that collectively regulate the nuclear transcriptome. We used microarrays to further investigate the regulation of nuclear gene expression by PGE retrograde signals mediated by GUN1.

2019-06-05 | GSE122667 | GEO

GUN1 controls the accumulation of NEP-dependent transcripts in Arabidopsis cotyledons

Project description:GUN1 proteins controls protein homeostasis in chloroplast development in cotyledons of the model plant Arabidopsis thaliana, via coordination of nuclear encoded polymerase (NEP)-dependent chloroplast genes expression with plastid encoded polymerase (PEP)-dependent chloroplast genes expression. Lack of GUN1 leads to development of abnormal plastids and, consequently, accumulation of nuclear-encoded chloroplast-targeted (NECT) proteins which in many cases have been found still in their precursor form. Data dependent acquisition (DDA) mass spectrometry analysis of cotyledons soluble fractions, as well as targeted proteomics analysis of specific FtsH protease forms recognized by FtsH antibodies in western blotting, have been performed to identify peptides from the chloroplast transit peptide (cTP) of NECT in cotyledons extracts of wild type and GUN1 knocked-out mutant plants. The aim was to compare the number of cTPs found in 6 days after sowing (DAS) seedlings grown on plates with or without the inhibitor of plastid translation lincomycin.

2019-11-15 | PXD015078 | Pride

col0,gun1,abi4-102, w/wo lincomycin

Project description:To test the relationship between GUN1 and ABI4 Keywords: does response, mutant

2006-09-09 | GSE5770 | GEO

Functional relationship of GUN1 and FUG1 in plastid proteostasis

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

Quantification of Tic-Toc subunits in gun1

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

gun1_vs_WT

Project description:Series of 8 repetitions of hybridization of treatment (gun1) and control (WT) each. Comparison of Arabidopsis gun1-1 mutant defective in plastid signaling (protein unknown) versus WT. R.E. Susek et al., Cell 74 (1993), pp. 787-799 Keywords: repeat sample

2005-01-01 | GSE1185 | GEO

Functional relationship of GUN1 and FUG1 in plastid proteostasis

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

lincomycin treatment wild type and gun1-101

Project description:Retrograde signals emanate from the DNA-containing cell organelles (plastids and mitochondria) and control the expression of a large number of nuclear genes in response to environmental and developmental cues. Previous studies on retrograde signaling mainly analyzed the regulation of nuclear gene expression at the transcriptional level. To determine the contribution of post-transcriptional regulation to plastid retrograde signaling, we combined label-free proteomics with transcriptomic analysis of Arabidopsis thaliana seedlings and studied the response in whichto interference with the plastid gene expression (PGE) pathway of retrograde signaling.

2019-06-05 | PXD011759 | Pride

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