Multilevel modulation of light signaling by GIGANTEA regulates both the output and pace of the circadian clock
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA533072 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8907160.fastq.gz | Fastqsanger.gz | |||
| SRR8907161.fastq.gz | Fastqsanger.gz | |||
| SRR8907162.fastq.gz | Fastqsanger.gz | |||
| SRR8907163.fastq.gz | Fastqsanger.gz | |||
| SRR8907164.fastq.gz | Fastqsanger.gz |
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Project description:Integration of environmental signals with endogenous biological processes is essential
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Project description:Interaction proteomics time course over 24h every 4h, looking for novel interactors of the circadian clock and flowering time protein GIGANTEA. Plants expressing 35S:GIGANTEA:3xFlag6His were used, as well as WT plants for a background control.
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Project description:Integration of environmental signals with endogenous biological processes is essential for organisms to thrive in their natural environment. Being entrained by periodic environmental changes, the circadian clock incorporates external information to coordinate physiological processes, phasing them to the optimal time of the day and year. Here, we present a pivotal role for the clock component GIGANTEA (GI) as a genome-wide regulator of transcriptional networks mediating growth and adaptive processes in plants. We provide mechanistic details on how GI integrates endogenous timing with light signaling pathways through the global modulation of PHYTOCHROME-INTERACTING FACTORs (PIFs). Gating of the activity of these transcriptional regulators by GI directly affects a wide array of output rhythms, including photoperiodic growth. Furthermore, we uncover a role for PIFs in mediating light input to the circadian oscillator and show how their regulation by GI is required to set the pace of the clock in response to light-dark cycles.
| S-EPMC6597437 | biostudies-literature
Project description:Plants use their endogenous clock to regulate many physiological processes related to their survival and adaptability. GIGANTEA (GI), one of the clock proteins, contributes to the maintenance of circadian period length and amplitude and also regulates flowering time and hypocotyl growth in response to day length. In addition to GI, EARLY FLOWERING 4 (ELF4), another clock regulator, also contributes to these processes. However, little is known about the overall interactions between GI and ELF4 in Arabidopsis. In this study, we investigated the genetic interactions between GI and ELF4 in circadian output regulation. The results show that GI is dominant to ELF4 in flowering time determination, but ELF4 is dominant to GI in hypocotyl growth regulation. Moreover, GI and ELF4 have a synergistic effect on endogenous clock regulation. Further, gene expression profiling of gi-2, elf4, and gi-2 elf4 mutants confirmed that GI and ELF4 had differential dominant effects on circadian physiological outputs at dawn and dusk, respectively. This differential dominance of GI and ELF4 provides a potential means to achieve the diversity in the regulation of circadian physiological outputs including flowering time and hypocotyl growth.
2012-07-01 | GSE32938 | GEO
Project description:Plants use their endogenous clock to regulate many physiological processes related to their survival and adaptability. GIGANTEA (GI), one of the clock proteins, contributes to the maintenance of circadian period length and amplitude and also regulates flowering time and hypocotyl growth in response to day length. In addition to GI, EARLY FLOWERING 4 (ELF4), another clock regulator, also contributes to these processes. However, little is known about the overall interactions between GI and ELF4 in Arabidopsis. In this study, we investigated the genetic interactions between GI and ELF4 in circadian output regulation. The results show that GI is dominant to ELF4 in flowering time determination, but ELF4 is dominant to GI in hypocotyl growth regulation. Moreover, GI and ELF4 have a synergistic effect on endogenous clock regulation. Further, gene expression profiling of gi-2, elf4, and gi-2 elf4 mutants confirmed that GI and ELF4 had differential dominant effects on circadian physiological outputs at dawn and dusk, respectively. This differential dominance of GI and ELF4 provides a potential means to achieve the diversity in the regulation of circadian physiological outputs including flowering time and hypocotyl growth. The genetic interactions between GI and ELF4 could be time-dependent functional dominance along a day, called temporal dominance hereafter. To test this hypothesis, we performed gene expression profiling of WT, gi-2, elf4 and gi elf4 plants at dawn (ZT1) and dusk (ZT16).
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2020-12-01 | GSE162379 | GEO
Project description:Multiomics reveals multilevel control of renal and systemic metabolism by the renal tubular circadian clock
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Project description:ZEILUPE (ZTL), a blue light photoreceptor with E3 ubiquitin ligase activity, communicates end-of-day light conditions to the circadian clock. To function properly, ZTL protein must accumulate but not destablilize target clock transcription factors before dusk, while in the dark ZTL mediates degradation of target proteins. It is not clear how ZTL can accumulate to high levels in the ligh while its targets remain stable. Two deubiquitylating enzymes, UBIQUITIN-SPECIFIC PROTEASE 12 and UBIQUITIN-SPECIFIC PROTEASE 13 (UBP12 and UBP13), which regulate colock period and protein ubiquitylation in a manner opposite to ZTL, were shown to associate with the ZTL protein complex. Here we demonstrate that the ZTL light-dependent interacting partner GIGANTEA (GI), recruites UBP12 and UBP13 to the ZTL photoreceptor complex.
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Project description:Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high pitch content, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of pitch were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea’s pitch metabolism. These results contribute to our fundamental understanding of conifer colonization and carbon cycling processes.
2014-10-01 | GSE53112 | GEO
Project description:Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high pitch content, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of pitch were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea’s pitch metabolism. These results contribute to our fundamental understanding of conifer colonization and carbon cycling processes. Phlebiopsis gigantea was cultivated in media containing one of three carbon sources: freshly harvested loblolly pine (3 replicates), acetone extracted lobollly pine (3 replicates), or glucose (2 replicates). RNA was extracted and processed for Illumina sequencing as described below.
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