MetR is a global regulator controlling phytochrome-dependent light responses in Aspergillus nidulans
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PROVIDER: PRJNA656574 | ENA |
REPOSITORIES: ENA
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Project description:Phytochrome-dependent light signaling has been studied in several fungi. In Aspergillus nidulans light-stimulated phytochrome activates the HOG signaling pathway and thereby controls the expression of a large number of genes, many of which are related to stress responses. In a genome-wide expression analysis in A. nidulans we found that phytochrome, fphA, is under strict expression control of the central regulator of the sulfur-starvation response, MetR. This transcriptional regulator is required for the expression of genes involved in inorganic sulfur assimilation. In the presence of organic sulfur, MetR is probably ubiquitinated and possibly degraded and the transcription of sulfur-assimilation genes, e.g. sulfate permease, is turned off. The expression analysis described here revealed, however, that MetR additionally controls the expression of hundreds of genes, many of which are required for secondary metabolite production. We also show that metR mutation phenocopies fphA deletion, and five other histidine-hybrid kinases are down-regulated in the metR1 mutant. Furthermore, we show that light and phytochrome regulate the expression of at least three carbon-sulfur hydrolases. This work is a further step towards understanding the interplay between light sensing and metabolic pathways.
2020-12-01 | GSE156068 | GEO
Project description:Light is a major environmental signal regulating many different biological processes. In Aspergillus nidulans light controls asexual and sexual development as well as the production of secondary metabolites. In order to get a global view of genes regulated during asexual development and of genes involved in other light-regulated biological processes, a genome-wide approach was undertaken. Total RNA was isolated from surface-grown, developmentally competent mycelia of the wild-type strain FGSC4 exposed to white light (11 W/m2) for 30 minutes or grown in the dark, labelled, and hybridized to a spotted microarray of A. nidulans.
2011-06-06 | E-MEXP-3218 | biostudies-arrayexpress
Project description:To identify and characterize genes required for tissue-specific phytochrome responses during hypocotyl development in far-red-light grown bvr lines, we performed gene transcriptional profiling using bvr lines with mesophyll-specific phytochrome inactivation (cab3: :pBVR2). We identified several candidate genes whose expression is significantly altered in lines with mesophyll tissue-specific BVR expression (Cab3::pBVR2), compared to constitutive phytochrome inactivation lines, i.e. 35S-driven BVR lines (35S::pBVR3). No-0 is used as wild-type (WT)
2013-03-01 | GSE38989 | GEO
Project description:Phytochromes are evolutionarily conserved photoreceptors in bacteria, fungi, and plants. The prototypical phytochrome comprises an N-terminal photosensory module and a C-terminal histidine kinase signaling-output module. However, the plant phytochrome has been postulated to transduce light signals by interacting with a group of nodal Phytochrome-Interacting transcription Factors (PIFs) and triggering their degradation via the N-terminal photosensory module, while its C-terminal output module, including a Histidine Kinase-Related Domain (HKRD), is thought not to participate directly in signaling. Here, we show that the C-terminal module of Arabidopsis phytochrome B (PHYB) is unexpectedly sufficient to mediate the degradation of PIF3 and to induce a distinct set of PIF-regulated photosynthetic genes. These signaling functions require the HKRD and particularly its dimerization. A D1040V mutation, which disrupts the dimerization of HKRD and the interaction between the C-terminal module and PIF3, abrogates the early light signaling functions of PHYB in nuclear accumulation, photobody biogenesis, and PIF3 degradation. In contrast, disruption of the interaction between PIF3 and PHYB’s N-terminal photosensory module has little effect on PIF3 degradation. Together, this study provides novel insight into the central mechanism of early phytochrome signaling that the C-terminal signaling-output module of PHYB interacts with PIF3 in the nucleus to mediate PIF3 degradation by light.
2017-12-31 | GSE90925 | GEO
Project description:To identify and characterize genes required for tissue-specific phytochrome responses during hypocotyl development in far-red-light grown bvr lines, we performed gene transcriptional profiling using bvr lines with mesophyll-specific phytochrome inactivation (cab3: :pBVR2). We identified several candidate genes whose expression is significantly altered in lines with mesophyll tissue-specific BVR expression (Cab3::pBVR2), compared to constitutive phytochrome inactivation lines, i.e. 35S-driven BVR lines (35S::pBVR3). No-0 is used as wild-type (WT) Seeds of No-0 WT, 35S::pBVR3 and CAB3::pBVR2 on MS plates were exposed to Red (R) light of 75 M-BM-5mol m-2 s-1 for 5 min and imbibing seeds were cold-stratified at 4 M-BM-0C in darkness for 3 d. Seedlings were grown under continuous far-red illumination for 7 d. Seven-day-old vegetative whole seedlings (300 M-bM-^@M-^S 500 mg) were quickly (<1 min) harvested and immediately frozen in liquid nitrogen inside the FR chamber. Seedlings were grown under continuous far-red illumination for 7 d.
2013-03-01 | E-GEOD-38989 | biostudies-arrayexpress
Project description:Light is an ever-changing environmental parameter affecting almost every aspects of plant growth and development. It is perceived by photoreceptors, among them phytochromes (PHY) are responsible for monitoring the red and far-red part of the spectrum. Arabidopsis thaliana possesses five phytochromes genes, named through phyA-phyE. Whereas the function of phyA and phyB – that mediate most of the phytochrome responses – is extensively studied, our knowledge on other phytochromes are still rudimentary. To analyze phyD function we expressed it at high levels in different phytochrome deficient genetic backgrounds. We found that overexpressed phyD governs effective light signaling at low temperatures but only in cooperation with functional phyC. Under these conditions, opposite to phyB, phyD accumulates to high levels and this pool is stable under light illumination. Furthermore, the detectable photoconvertible phyD amount is proportional with the available protein amount indicating that the phyD pool contains fully functional photoreceptors. The thermal reversion of phyD is very fast suggesting that the thermosensing of phyD is based on its protein amount and not on its Pfr conformer stability, which was described for phyB. We also found that phyD and phyB associate to identical genomic locations and mediate similar gene expression changes, however the efficiency of phyD is lower. Taken together our data suggest that under certain conditions synergistic interaction of phyD and phyC substitutes phyB function thus increases the ability of plants to respond more flexible to environmental changes.
2024-01-19 | GSE253236 | GEO
Project description:Light is an ever-changing environmental parameter affecting almost every aspects of plant growth and development. It is perceived by photoreceptors, among them phytochromes (PHY) are responsible for monitoring the red and far-red part of the spectrum. Arabidopsis thaliana possesses five phytochromes genes, named through phyA-phyE. Whereas the function of phyA and phyB – that mediate most of the phytochrome responses – is extensively studied, our knowledge on other phytochromes are still rudimentary. To analyze phyD function we expressed it at high levels in different phytochrome deficient genetic backgrounds. We found that overexpressed phyD governs effective light signaling at low temperatures but only in cooperation with functional phyC. Under these conditions, opposite to phyB, phyD accumulates to high levels and this pool is stable under light illumination. Furthermore, the detectable photoconvertible phyD amount is proportional with the available protein amount indicating that the phyD pool contains fully functional photoreceptors. The thermal reversion of phyD is very fast suggesting that the thermosensing of phyD is based on its protein amount and not on its Pfr conformer stability, which was described for phyB. We also found that phyD and phyB associate to identical genomic locations and mediate similar gene expression changes, however the efficiency of phyD is lower. Taken together our data suggest that under certain conditions synergistic interaction of phyD and phyC substitutes phyB function thus increases the ability of plants to respond more flexible to environmental changes.
2024-01-19 | GSE253043 | GEO
Project description:The red/far-red light photoreceptor phytochrome mediates photomorphological responses in plants. For light sensing and signaling, phytochromes need to associate with open-chain tetrapyrrole molecules as the chromophore. Biosynthesis of tetrapyrrole chromophores requires members of ferredoxin-dependent bilin reductases (FDBRs). There are two FDBRs in Physcomitrella patens, HY2 and PUBS. Knocking out both generates the phytochrome-deficient mutant. Datasets here provides the transcriptome profiling of Physcomitrella protonema grown in the dark and exposed to one hour red light. Wild type and the hy2 pubs double mutant were used to dissect the regulated genes of moss phytochromes. For details, please see PMID: .
2012-05-08 | GSE36274 | GEO
Project description:PIL5 is a key negative regulator of phytochrome mediated seed germination and PIL5 protein is degraded by red light irradiation through phytochrome. The microarray aimed to find various red light-regulated genes and PIL5-regulated genes in the imbibed seeds. Keywords: genetic modification
2010-01-12 | GSE14374 | GEO
Project description:Phytochromes are red/far red photosensors regulating numerous developmental programs in plants. Among them phytochrome A (phyA) is essential to enable seedling de-etiolation in continuous far-red (FR) light a condition mimicking the environment under a dense canopy. The ecological relevance of this response is demonstrated by the high mortality rate of phyA mutants germinating in deep vegetational shade. phyA signaling involves a direct interaction of the photoreceptor with members of the bHLH transcription factor family, PIF1 and PIF3 (Phytochrome Interacting Factor). Here we investigated the involvement of PIF4 and PIF5 in phyA signaling and found that they redundantly control de-etiolation in FR light. The pif4pif5 double mutant is hypersensitive to low fluence rates of FR light. This phenotype is dependent on FR light perception by phyA but does not rely on alterations of the phyA level. Our microarrays analysis shows that PIF4 and PIF5 are part of an inhibitory mechanism repressing the expression of some light-responsive genes in the dark and are also needed for full expression of several growth-related genes in the light. Unlike PIF1 and PIF3, PIF4 and PIF5 are not degraded in response to FR light indicating that they are light-regulated by a different mechanism. Our genetic analysis suggests that this is achieved through the sequestration of these PIFs by the closely related bHLH transcription factor HFR1 (long Hypocotyl in FR light).
2009-08-19 | GSE16333 | GEO