Arabidopsis thaliana
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PROVIDER: PRJNA182913 | ENA |
REPOSITORIES: ENA
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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:Photosystem I (PSI) is a critical component of the photosynthetic machinery in plants. Under conditions of environmental stress, PSI becomes photoinhibited, leading to redox imbalance in the chloroplast. PSI photoinhibition is caused by an increase in electron pressure within PSI, which damages the iron-sulfur centers. In this study, we investigated the effect of PSI electron acceptors on the susceptibility of PSI to photoinhibition at different CO2 concentrations in the plant environment. We also analyzed the global gene expression in plants exposed to PSI photoinhibition. PSI was photoinhibited using a specific illumination technique that inhibited PSI with minimal effect on PSII. CO2 levels neither increased nor decreased the likelihood of PSI photodamage. PSI photoinhibition, independent of CO2 levels, upregulated the genes involved in the response to iron excess in plants and downregulated the genes involved in iron deficiency. It also induced the genes of photosynthetic proteins that act as electron acceptors for PSI. We propose that PSI photoinhibition causes a release of iron from iron-sulfur centers, which initiates a retrograde signal from the chloroplast to the nucleus to modify gene expression. In addition, deprivation of CO2 from the air initiated a signal that induced flavonoid biosynthesis genes, probably via jasmonate production.
2023-11-29 | GSE242125 | GEO
Project description:Aim: To identify regulatory factors that control: (1) chloroplast protein importand (2) chloroplast-to-nucleus signalling. This project is a joint proposal from the Jarvis lab which is interested in chloroplast protein import [1] and the Moller lab which is interested in plastid-to-nucleus signalling [2]. Background: The majority of chloroplast proteins are encoded in the nucleus and imported post-translationally into chloroplasts. The abundance of chloroplast proteins may therefore be regulated at multiple levels. It is well documented that the nuclear gene expression is responsive to (largely unknown) signals from the chloroplast [23] and evidence is now emerging that protein import is also a regulated process [1]. Protein import into chloroplasts is mediated by protein complexes in the outer and inner envelope membranes called Toc and Tic respectively. Biochemical studies of pea chloroplasts identified several Toc/Tic components. These proteins are mechanistic or structural components of the import apparatus. Arabidopsis homologues of the pea Toc/Tic proteins were identified by the AGI. Pea Toc34 is represented in Arabidopsis by two genes "Toc33 and Toc34" and pea Toc75 is represented by three genes. These different Tocs have different expression patterns and are proposed to have different precursor protein recognition specificities. The factors that regulate Toc expression in concert with the needs of plastids in developmentally different cells are unknown. Proposal: Two Arabidopsis mutants will be analysed. The ppi1 mutant is null for the putative precursor protein receptor Toc33 [1]and the ppi3 mutant is null for a putative component of the protein import channel Toc75-IV (on chromosome IV). ppi1 plants are yellow-green in appearance but remarkably healthy and grow only slightly more slowly than wild type. By contrast ppi3 plants are indistinguishable from wild type by eye although analysis of the mutant's chloroplast proteome is beginning to reveal some differences (K. Lilley personal communication). Gene expression changes in ppi1 are likely to be quite extensive. Retardation of chloroplast development in ppi1 will activate retrograde signalling pathways so that many nuclear photosynthetic genes are down-regulated. Changes in the expression of photosynthetic genes and of the genes responsible for mediating these responses may therefore be observed. Any regulatory and signalling genes identified will be of interest to the Moller lab. The expression of factors that regulate Toc/Tic gene expression may also be altered in ppi1. It should be possible to distinguish these factors from those involved in the general control of chloroplast gene expression by comparing the results from the two mutants. Genes affected in both mutants are more likely to be involved in regulating chloroplast import since it is unlikely that widespread changes in gene expression will be observed in ppi3. Changes in the expression of factors that regulate import post-translationallyand of the Toc/Tic genes themselves (many are on the RNA) may also be observed. References: 1. Jarvis P. et al. (1998) Science 282: 100-103. 2. Moller S.G. et al. (2001) Genes Dev. 15:90-103. 3. Jarvis P. (2001) Curr. Biol. 11: R307-R310.
2022-11-21 | E-NASC-35 | 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:For establishing the photosynthetic apparatus plant cells must orchestrate the expression of genes encoded in both nucleus and chloroplast. Therefore a crosstalk between the two compartments is necessary. We employed a trivalent gene expression profiling approach in order to elucidate the changes in gene expression that occur during the early steps of light-induced chloroplast biogenesis.
2017-12-01 | GSE88988 | GEO
Project description:To analyze the impact of photosynthetic redox signals, light sources with spectral qualities that preferentially excite either Photosystem I (PSI light) or Photosystem II (PSII light) were used. The light sources have been described in (Wagner et al, Planta 2008). Strong reduction signals were induced by light shifts from PSI to PSII light (PSI-II). In order to find primary regulated genes the acclimation responses were monitored at 30 min and 60 min after a light shift. The control was continuous Psi light at the same time. We used stn7 (a thylakoid redox regulated kinase) to specifically block transduction of photosynthetic redox signal in order to compare “real” redox regulated with that of other light acclimation pathways. Keywords: photosynthesis, redox regulation, light acclimation, retrograde signalling, long term response
2015-03-23 | GSE42710 | GEO
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:Canonical retrograde signalling comprises information transmission from organelles to the nucleus and in particular controls gene expression for organellar proteins. The need to re-assess this paradigm was suggested by discrepancies between de novo protein synthesis and transcript abundance in response to excess light. Here we uncover major components of a translation-dependent retrograde signalling pathway that first impacts translation and then transcription. The response realization depends on the kinases Mitogen-activated protein kinase 6 (MPK6) and Sucrose non-fermenting 1-related kinase (SnRK1) subunit, AKIN10. Global ribosome foot-printing revealed differential ribosome association of 951 transcripts within 10 min after transfer from low to high light. Despite predominant translational repression, 15 % of transcripts were increased in translation and enriched for chloroplast-localized photosynthetic proteins. About one third of these transcripts, including Stress associated proteins (SAP) 2 and 3, share regulatory motifs in their 5`-UTR that act as binding sites for glyceraldehyde-3-phosphate dehydrogenase (GAPC) and light responsive RNA binding proteins (RBPs). SAP2 and 3 are both translationally regulated and interact with the calcium sensor Calmodulin-like 49 (CML49), which promotes relocation to the nucleus inducing a translation-dependent nuclear stress response. Thus, translation-dependent retrograde signalling bifurcates to directly regulate a translational circuit of chloroplast proteins and simultaneously initiate a nuclear circuit synchronizing retrograde and anterograde response pathways, serving as a rapid mechanism for functional acclimation of the chloroplast.
2022-08-24 | GSE211494 | GEO
Project description:For establishing the photosynthetic apparatus plant cells must orchestrate the expression of genes encoded in both nucleus and chloroplast. Therefore a crosstalk between the two compartments is necessary. We employed a gene expression profiling approach in order to elucidate the changes in gene expression that occur at different stages of plastid development.
2020-02-07 | GSE144694 | GEO
Project description:Because the minimal chloroplast genome carries very limited genetic information, plants rely on signals sent from the chloroplasts to the nucleus for proper chloroplast development as well as for recovery from photoinhibition and response to photo-oxidative stress. In this study, we report the discovery of several factors involved in the reduced PQ pool-driven chloroplast-to-nucleus signaling process. High-throughput RNA-Seq expression profiling of tanorexia-1 (tnr-1) mutants in comparison to wild-type. From these experiments, we found out that the HSF and HAC1 transcription factors have broad effects on HL-driven nuclear gene expression. The DEAD-box RNA helicase 38, CRY1 and a previously uncharacterized G-patch domain-containing protein are also involved in the signaling.
2013-10-02 | E-MTAB-4255 | biostudies-arrayexpress