Arabidopsis thaliana
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR221561_1.fastq.gz | Fastqsanger.gz | |||
| DRR221561_2.fastq.gz | Fastqsanger.gz | |||
| DRR221562_1.fastq.gz | Fastqsanger.gz | |||
| DRR221562_2.fastq.gz | Fastqsanger.gz | |||
| DRR221563_1.fastq.gz | Fastqsanger.gz |
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Project description:Studies of the GUN plastid-to-nucleus signaling in plants, RNA-seq
| PRJDB9660 | ENA
Project description:Retrograde signaling from the chloroplast to the nucleus is necessary to regulate the chloroplast proteome during development and fluctuating environmental conditions. Although the specific chloroplast process(es) that must occur and the nature of the signal(s) that exits the chloroplast are not well understood, previous studies using drug inhibitors of chloroplast biogenesis have revealed that normal chloroplast development is required to express Photosynthesis Associated Nuclear Genes (PhANGs). In an attempt to determine which specific steps in chloroplast development are involved in retrograde signaling, we analyzed Arabidopsis mutants defective in the six genes encoding sigma factor (Sig) proteins that are utilized by the plastid-encoded RNA polymerase to transcribe specific sets of plastid genes. Here, we demonstrate that both Sig2 and Sig6 have partially redundant roles in not only plastid transcription, but also tetrapyrrole synthesis and retrograde signaling to control PhANG expression. Normal PhANG expression can be partly restored in the sig2 mutant by increasing heme synthesis. Furthermore, there is a genetic interaction between Sig and GUN (genomes uncoupled) genes to generate chloroplast-retrograde signals. These results demonstrate that defective plastid transcription is the source of at least two retrograde signals to the nucleus; one involving tetrapyrrole synthesis and the other involving the accumulation of an unknown plastid transcript. We also propose that the study of sig mutants (with defects in the expression of specific plastid genes) provides a new genetic system, which avoids the use of harsh inhibitors and their potential side effects, to monitor developmental retrograde signaling and to elucidate its mechanisms.
2012-09-18 | E-MTAB-4338 | biostudies-arrayexpress
Project description:Shortly after the release of singlet oxygen (1O2), drastic changes in nuclear gene expression occur in the conditional flu mutant of Arabidopsis that reveal a rapid transfer of signals from the plastid to the nucleus. In contrast to retrograde control of nuclear gene expression by plastid signals described earlier, the primary effect of 1O2 generation in the flu mutant is not the control of chloroplast biogenesis but the activation of a broad range of signaling pathways known to be involved in biotic and abiotic stress responses. This activity of a plastid-derived signal suggests a new function of the chloroplast, namely that of a sensor of environmental changes that activates a broad range of stress responses. Inactivation of the plastid protein EXECUTER1 attenuates the extent of 1O2-induced up-regulation of nuclear gene expression, but it does not fully eliminate these changes. A second related nuclear-encoded protein, dubbed EXECUTER2, has been identified that is also implicated with the signaling of 1O2-dependent nuclear gene expression changes. Like EXECUTER1, EXECUTER2 is confined to the plastid. Inactivation of both EXECUTER proteins in the ex1/ex2/flu triple mutant is sufficient to suppress the up-regulation of almost all 1O2-responsive genes. Retrograde control of 1O2-responsive genes requires the concerted action of both EXECUTER proteins within the plastid compartment. Keywords: biotic and abiotic stress response, nuclear gene expression, plastid-derived signal, Col-0 ecotype, continuous light and then dark-incubated plants
2008-02-14 | GSE10509 | GEO
Project description:Transcriptional profiling of Arabidopsis thaliana 12-days old seedlings comparing Col-0 wild type with transgenic plants with altered expression of dual-targetting plastid/mitochondrial organellar RNA-polymerase RPOTmp. Transgenic plants used for experiment were: overexpressor plants obtained by transformation of Col-0 WT plants with genetic constructs created in [Tarasenko et al., 2016] contained catalytic part of RPOTmp enzyme with transit peptides of RPOTm (mitochondrial) and RPOTp (plastid) by agrobacterial transformation; plants with complementation of RPOTmp functions in mitochondria or chloroplasts obtained from transformation of GABI_286E07 rpotmp knockout-mutant plants with genetic constructs created in [Tarasenko et al., 2016]. Goal was to determine the effects of RPOTmp knockout/overexpression on global Arabidopsis thaliana gene expression.
2023-12-25 | GSE251661 | GEO
Project description:We use Arabidopsis thaliana embryogenesis as a model system for studying intercellular transport via plasmodesmata (PD). A forward genetic screen for altered PD transport identified ise1 and ise2 mutants with increased intercellular transport of fluorescent 10-kDa tracers. Both ise1 and ise2 exhibit increased formation of twinned and branched PD. ISE1 encodes a mitochondrial DEAD-box RNA helicase, while ISE2 encodes a DEVH-type RNA helicase. Here we show that ISE2 foci are localized to the chloroplast stroma. Surprisingly, plastid development is defective in both ise1 and ise2 mutant embryos. In an effort to understand how RNA helicases that localize to different organelles have similar impacts on plastid and PD development/function we performed whole genome expression analyses. The most significantly affected class of transcripts in both mutants encodes products that target to and enable plastid function. These results reinforce the importance of plastid-mitochondria-nucleus crosstalk, add PD as a critical player in the plant cell communication network, and thereby illuminate a new signaling pathway, dubbed organelle-nucleus-plasmodesmata signaling (ONPS). Several genes with roles in cell wall synthesis and modification are also differentially expressed in both mutants, providing new targets for investigating PD development and function.
2011-11-09 | GSE33558 | GEO
Project description:We use Arabidopsis thaliana embryogenesis as a model system for studying intercellular transport via plasmodesmata (PD). A forward genetic screen for altered PD transport identified ise1 and ise2 mutants with increased intercellular transport of fluorescent 10-kDa tracers. Both ise1 and ise2 exhibit increased formation of twinned and branched PD. ISE1 encodes a mitochondrial DEAD-box RNA helicase, while ISE2 encodes a DEVH-type RNA helicase. Here we show that ISE2 foci are localized to the chloroplast stroma. Surprisingly, plastid development is defective in both ise1 and ise2 mutant embryos. In an effort to understand how RNA helicases that localize to different organelles have similar impacts on plastid and PD development/function we performed whole genome expression analyses. The most significantly affected class of transcripts in both mutants encodes products that target to and enable plastid function. These results reinforce the importance of plastid-mitochondria-nucleus crosstalk, add PD as a critical player in the plant cell communication network, and thereby illuminate a new signaling pathway, dubbed organelle-nucleus-plasmodesmata signaling (ONPS). Several genes with roles in cell wall synthesis and modification are also differentially expressed in both mutants, providing new targets for investigating PD development and function. Three biological replicates each of either ise1 or ise2 mutant seeds vs. sister wild-type controls
2011-11-09 | E-GEOD-33558 | biostudies-arrayexpress
Project description:The CHLD and CHLM genes encode proteins involved in tetrapyrrole biosynthesis pathway. It was proposed that intermediates like magnesium protoporphyrin might play a role in retrograde plastid-to-nucleus signaling. In the present work we provide evidence that altered enzymes activity of the tetrapyrrole biosynthesis pathway are causing changes in gene expression of over 200 nuclear genes.
2013-04-01 | GSE41884 | GEO
Project description:Herbicide-resistant plants produced by precision adenine base editing in plastid DNA
| PRJNA1067738 | ENA
Project description:Differential response of gun mutants to norflurazon
| PRJNA110879 | ENA
Project description:The CHLD and CHLM genes encode proteins involved in tetrapyrrole biosynthesis pathway. It was proposed that intermediates like magnesium protoporphyrin might play a role in retrograde plastid-to-nucleus signaling. In the present work we provide evidence that altered enzymes activity of the tetrapyrrole biosynthesis pathway are causing changes in gene expression of over 200 nuclear genes. The expression of the CHLD gene was diminished after inducing the RNAi system by spraying dexamethasone. The expression of the CHLM gene was increased after inducing the overexpressor system by spraying ß-estradiol.
2013-04-01 | E-GEOD-41884 | biostudies-arrayexpress