Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Circadian Rhythms in Cyanobacterial Protein Condensation

ABSTRACT: Circadian rhythms are endogenously generated daily cycles in physiology that are closely tied to metabolism and can be found in all kingdoms of life. In cyanobacteria, energy storage through glycogen metabolism is highly rhythmic, but the underlying mechanisms remain unclear. Here we find that the glycogen synthase enzyme, GlgA, is rhythmically condensed during growth in constant light. The appearance of condensed foci of GlgA corresponds to inhibition of glycogen synthesis during the morning hours allowing storage to be coordinated with the demand for energy at dusk. Through mutational analysis, we show that the condensation status of GlgA is dictated by the state of the circadian clock rather than the amount of glycogen in the cell. These results reveal a model of circadian control of glycogen metabolism achieved through rhythmic spatial reorganization of a key enzyme.

INSTRUMENT(S):

ORGANISM(S): Synechococcus Elongatus (strain Pcc 7942) (anacystis Nidulans R2) Bacteria

SUBMITTER: Michael Rust

LAB HEAD: Michael J Rust

PROVIDER: PXD074299 | Pride | 2026-05-25

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Dawn_Pellet_MRCB_8.mzML	Mzml
	Dawn_Pellet_MRCB_8.raw	Raw
	Dawn_Soluble_MRCB_7.mzML	Mzml
	Dawn_Soluble_MRCB_7.raw	Raw
	Dusk_Pellet_MRCB_3.mzML	Mzml

Items per page:

1 - 5 of 12

Publications

Rhythmic protein condensation in the circadian regulation of glycogen metabolism.

Burton Lily A LA Pattanayak Gopal K GK Rust Michael J MJ

iScience 20260403 5

Circadian rhythms are endogenously generated daily cycles in physiology that are closely tied to metabolism and can be found in all kingdoms of life. Because of their genetic simplicity, cyanobacteria provide a unique opportunity to uncover rhythmic mechanisms. In cyanobacteria, glycogen storage is highly rhythmic. Using a combination of mass spectrometry and live cell imaging, we find that the glycogen synthase enzyme (GlgA), is rhythmically condensed. The appearance of condensed foci of GlgA c ...[more]

PMID: 42063545

Similar Datasets

Diurnal glycogen metabolism drives rhythmic liver protein secretion

Project description:The liver secretes most circulating proteins, which are critical for inter-organ communication and systemic energy homeostasis. However, the regulatory mechanisms governing hepatic protein secretion are largely unknown. Using proteomics approaches in humans and mice, we here demonstrate that hepatic protein secretion follows a 24-hour rhythm which is modulated by the timing of food intake. Rhythmic variations in the expression of secretory pathway proteins, involved in protein glycosylation and folding in the endoplasmic reticulum and Golgi apparatus, mediate this process. We find that feeding rhythms and the circadian clock protein BMAL1 regulate diurnal hepatic protein secretion by driving glycogen breakdown which generates glycosylation substrates. Rhythmic secretion was attenuated in a mouse model of obesity and affected by genetic variants associated with glycogen storage disease and congenital disorders of glycosylation. Our study reveals a mechanistic link between glycogen-derived metabolites and protein secretion, thereby connecting nutrient intake with fundamental liver functions.

2026-01-06 | PXD058564 | Pride

Defining the Independence of the Liver Circadian Clock

Project description:Mammals rely on a network of circadian clocks to control daily systemic metabolism and physiology. The central pacemaker in the suprachiasmatic nucleus (SCN) is considered hierarchically dominant over peripheral clocks, whose degree of independence, or tissue-level autonomy, has never been ascertained in vivo. Using arrhythmic Bmal1-null mice, we generated animals with reconstituted circadian expression of BMAL1 exclusively in the liver (Liver-RE). High-throughput transcriptomics and metabolomics show that the liver has independent circadian functions specific for metabolic processes such as the NAD+ salvage pathway and glycogen turnover. However, although BMAL1 occupies chromatin at most genomic targets in Liver-RE mice, circadian expression is restricted to ∼10% of normally rhythmic transcripts. Finally, rhythmic clock gene expression is lost in Liver-RE mice under constant darkness. Hence, full circadian function in the liver depends on signals emanating from other clocks, and light contributes to tissue-autonomous clock function.

2019-06-13 | GSE132659 | GEO

Differential effects of environmental and endogenous 24h rhythms within a deep-coverage spatiotemporal proteome

Project description:The cellular landscape of most eukaryotic cells changes dramatically over the course of a 24h day. Whilst the proteome responds directly to daily environmental cycles, it is also regulated by a cellular circadian clock that anticipates the differing demands of day and night. To quantify the relative contribution of diurnal versus circadian regulation, we mapped spatiotemporal proteome dynamics under 12h:12h light:dark cycles compared with constant light. Using Ostreococcus tauri, a prototypical eukaryotic cell, we achieved 85% coverage of the theoretical proteome and provided an unprecedented insight into the identity of proteins that drive and facilitate rhythmic cellular functions. Surprisingly, the overlap between diurnally- and circadian-regulated proteins was quite modest (11%). These proteins exhibited different phases of oscillation between the two conditions, consistent with an interaction between intrinsic and extrinsic regulatory factors. The relative amplitude of rhythmic protein abundance was much lower than would be expected from daily variations in transcript abundance. Transcript rhythmicity was poorly predictive of daily variation in abundance of the encoded protein. We observed coordination between the rhythmic regulation of organelle-encoded proteins with the nuclear-encoded proteins that are targeted to organelles. Rhythmic transmembrane proteins showed a remarkably different phase distribution compared with rhythmic soluble proteins, indicating the existence of a novel circadian regulatory process specific to the biogenesis and/or degradation of membrane proteins. Taken together, our observations argue that the daily spatiotemporal regulation of cellular proteome composition is not dictated solely by clock-regulated gene expression. Instead, it also involves extensive rhythmic post-transcriptional, translational, and post-translational regulation that is further modulated by environmental timing cues.

2021-10-28 | PXD025009 | Pride

Non-canonical circadian oscillations in Drosophila S2 cells

Project description:Circadian rhythms are cell-autonomous biological oscillations with a period of about 24 hours. Current models propose that transcriptional feedback loops are the principal mechanism for the generation of circadian oscillations. In these models, Drosophila S2 cells are generally regarded as ‘non-rhythmic’ cells, as they do not express several canonical circadian components. Using an unbiased multi-omics approach, we made the surprising discovery that Drosophila S2 cells do in fact display widespread daily rhythms. Transcriptomics and proteomics analyses revealed that hundreds of genes and their products are rhythmically expressed in a 24-hour cycle. Metabolomics analyses extended these findings and illustrated that central carbon metabolism and amino acid metabolism are the main pathways regulated in a rhythmic fashion. We thus demonstrate that daily genome-wide oscillations, coupled to metabolic cycles, take place in eukaryotic cells without the contribution of known circadian regulators.

2018-07-31 | PXD007669 | Pride

Diurnal glycogen metabolism drives rhythmic liver protein secretion [in vivo]

Project description:The liver secretes most circulating proteins, which are critical for inter-organ communication and systemic energy homeostasis. However, the regulatory mechanisms governing hepatic protein secretion are largely unknown. Using proteomics approaches in humans and mice, we here demonstrate that hepatic protein secretion follows a 24-hour rhythm which is modulated by the timing of food intake. Rhythmic variations in the expression of secretory pathway proteins, involved in protein glycosylation and folding in the endoplasmic reticulum and Golgi apparatus, mediate this process. We find that feeding rhythms and the circadian clock protein BMAL1 regulate diurnal hepatic protein secretion by driving glycogen breakdown which generates glycosylation substrates. Rhythmic secretion was attenuated in a mouse model of obesity and affected by genetic variants associated with glycogen storage disease and congenital disorders of glycosylation. Our study reveals a mechanistic link between glycogen-derived metabolites and the protein secretion pathway, thereby connecting nutrient intake with fundamental liver functions.

2025-12-02 | GSE283707 | GEO

Diurnal glycogen metabolism drives rhythmic liver protein secretion [in vitro]

Project description:The liver secretes most circulating proteins, which are critical for inter-organ communication and systemic energy homeostasis. However, the regulatory mechanisms governing hepatic protein secretion are largely unknown. Using proteomics approaches in humans and mice, we here demonstrate that hepatic protein secretion follows a 24-hour rhythm which is modulated by the timing of food intake. Rhythmic variations in the expression of secretory pathway proteins, involved in protein glycosylation and folding in the endoplasmic reticulum and Golgi apparatus, mediate this process. We find that feeding rhythms and the circadian clock protein BMAL1 regulate diurnal hepatic protein secretion by driving glycogen breakdown which generates glycosylation substrates. Rhythmic secretion was attenuated in a mouse model of obesity and affected by genetic variants associated with glycogen storage disease and congenital disorders of glycosylation. Our study reveals a mechanistic link between glycogen-derived metabolites and the protein secretion pathway, thereby connecting nutrient intake with fundamental liver functions.

2025-12-02 | GSE283579 | GEO

Checkpoint kinases regulate the circadian clock after DNA damage by influencing chromatin dynamics [RNA-Seq]

Project description:Circadian rhythms allow organisms to adjust to daily environmental fluctuations. The interplay between the circadian clock, the cell cycle, and DNA repair has been extensively documented, yet the epigenetic control of the circadian clock by the DNA damage response pathway remains relatively unexplored. Here, we showed that checkpoint kinases CHK1 and CHK2 regulate chromatin structure under DNA damage stress in Neurospora crassa to maintain robust circadian rhythms. Under DNA damage stress, deletion of chk1 and chk2 disrupted the rhythmic transcription of the clock gene frq by suppressing the rhythmic binding of the transcription activator WCC at the frq promoter, as the chromatin structure remained condensed. Mechanistically, CHK1 and CHK2 interacted and bound at the frq promoter to phosphorylate H3T11, promoting H3 acetylation, especially H3K56 acetylation, to counteract the histone variant H2A.Z deposition, establishing a suitable chromatin state to maintain the robust circadian rhythm despite DNA damage. Additionally, a genome-wide correlation was discovered between H3T11 phosphorylation and H3K56 acetylation, showing a specific function at the frq promoter that is dependent on CHK1 and CHK2. Furthermore, transcriptome analysis revealed that CHK1 and CHK2 are responsible for robust rhythmic transcription of metabolic and DNA repair genes under DNA damage stress. These findings highlight the essential role of checkpoint kinases in maintaining robust circadian rhythms under DNA damage stress.

2025-02-16 | GSE273617 | GEO

Checkpoint kinases regulate the circadian clock after DNA damage by influencing chromatin dynamics [ChIP-Seq]

2025-02-16 | GSE273616 | GEO

NR5A2 controls gene expression and chromatin contacts of essential circadian metabolic genes in the liver

Project description:Circadian regulation of gene expression relies on the coordinated action of core clock components, tissue-specific transcription factors, and epigenetic mechanisms, including dynamic enhancer–promoter interactions. Although rhythmic chromatin looping has been described in the liver, the transcription factors that mediate these temporal interactions remain poorly defined. Here, we identify the nuclear receptor NR5A2 as a key regulator of circadian enhancer–promoter communication in the mouse liver. We show that NR5A2 protein levels fluctuate over the 24-hour cycle, peaking around Zeitgeber time 0 (ZT0). Genome-wide analysis reveals that NR5A2 preferentially binds H3K27ac-enriched enhancer regions, many of which engage in chromatin looping with promoters of metabolic genes. High-resolution 4C-seq analyses demonstrate that promoters of Elovl5 and Ppp1r3c dynamically interact with NR5A2- and H3K27ac-enriched enhancers in a time-dependent manner, with maximal interactions at ZT0 and reduced contacts at ZT12. Pharmacological inhibition of NR5A2 in vivo leads to alterations in hepatic glycogen and cholesterol accumulation, attenuates the rhythmic expression of circadian metabolic genes, including Ppp1r3c, Cyp8b1, and Elovl5, and disrupts enhancer–promoter contact frequencies at the Elovl5 locus. Together, our findings provide in vivo evidence that NR5A2 integrates circadian and metabolic regulation by modulating enhancer–promoter chromatin interactions, thereby shaping rhythmic liver gene expression.

2026-05-27 | GSE303650 | GEO

Thermal proteome profilng of BMAL1 ligand CCM in U2OS cell lysate

Project description:The master transcription factor BMAL1-CLOCK is crucial for orchestrating rhythmic gene expression and governing circadian rhythms. Pharmacological manipulation of this central circadian regulator requires accessible protein cavities and selective compounds. By targeting BMAL1 through a resident cavity in its PAS-B domain, we demonstrate that the small-molecule Core Circadian Modulator (CCM) penetrates and substantially expands this pocket. Biochemical and cellular analyses validate CCM's target engagement selectivity, enabling direct access to BMAL1's transcriptional activities. Thermal proteome profiling of CCM in U2OS cell lysate was performed at two concentrations (50 µM and 200 µM) and compared to DMSO. The proteome integral stability assay (PISA) setup was used.

2025-02-03 | PXD049298 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data