Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Circadian regulation of macromolecular complex turnover and proteome renewal

ABSTRACT: Although energetically costly, maintaining protein homeostasis is indispensable for normal cellular function and long-term health. In mammalian cells and tissues, daily variation in global protein synthesis has been observed, but the changes in total protein levels are comparatively minimal. Here, we used several different pulse-labelling strategies to investigate the proteome-wide relationship between protein synthesis and abundance. We show that protein degradation varies in-phase with protein synthesis, facilitating rhythms in turnover rather than abundance. This results in rhythmic daily proteome renewal whilst minimising changes in proteome composition. Coupled rhythms in synthesis and turnover are especially salient to macromolecular protein complexes, in particular the ribosome, which we observed to nascently assemble with a 24-hour oscillation and no overall changes in ribosome abundance. Finally, circadian turnover and proteasomal degradation rhythms render cells and mice more sensitive to proteotoxic stress at specific times, potentially contributing to daily rhythms in the efficacy of proteasomal inhibitors against cancer. Our findings suggest that circadian rhythms function to minimise the bioenergetic cost of protein homeostasis through temporal consolidation of protein turnover.

SUBMITTER: Ms. Estere Seinkmane

PROVIDER: S-SCDT-10_1038-S44318-024-00121-5 | biostudies-other |

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Circadian regulation of macromolecular complex turnover and proteome renewal

Project description:Although costly to maintain, protein homeostasis is indispensable for normal cellular function and long-term health. In mammalian cells and tissues, daily variation in global protein synthesis has been observed, but its utility and consequences for proteome integrity are not fully understood. Using several different pulse-labelling strategies, here we gain direct insight into the relationship between protein synthesis and abundance proteome- wide. We show that protein degradation varies in-phase with protein synthesis, facilitating rhythms in turnover rather than abundance. This results in daily consolidation of proteome renewal whilst minimising changes in composition. Coupled rhythms in synthesis and turnover are especially salient to the assembly of macromolecular protein complexes, particularly the ribosome, the most abundant species of complex in the cell. Daily turnover and proteasomal degradation rhythms render cells and mice more sensitive to proteotoxic stress at specific times of day, potentially contributing to daily rhythms in the efficacy of proteasomal inhibitors against cancer. Our findings suggest that circadian rhythms function to minimise the bioenergetic cost of protein homeostasis through temporal consolidation of protein turnover.

2024-05-16 | PXD049176 | Pride

Circadian rhythms. Decoupling circadian clock protein turnover from circadian period determination.

Project description:The mechanistic basis of eukaryotic circadian oscillators in model systems as diverse as Neurospora, Drosophila, and mammalian cells is thought to be a transcription-and-translation-based negative feedback loop, wherein progressive and controlled phosphorylation of one or more negative elements ultimately elicits their own proteasome-mediated degradation, thereby releasing negative feedback and determining circadian period length. The Neurospora crassa circadian negative element FREQUENCY (FRQ) exemplifies such proteins; it is progressively phosphorylated at more than 100 sites, and strains bearing alleles of frq with anomalous phosphorylation display abnormal stability of FRQ that is well correlated with altered periods or apparent arrhythmicity. Unexpectedly, we unveiled normal circadian oscillations that reflect the allelic state of frq but that persist in the absence of typical degradation of FRQ. This manifest uncoupling of negative element turnover from circadian period length determination is not consistent with the consensus eukaryotic circadian model.

| S-EPMC4432837 | biostudies-literature

Macromolecular Assemblies of the Mammalian Circadian Clock.

Project description:The mammalian circadian clock is built on a feedback loop in which PER and CRY proteins repress their own transcription. We found that in mouse liver nuclei all three PERs, both CRYs, and Casein Kinase-1? (CK1?) are present together in an ?1.9-MDa repressor assembly that quantitatively incorporates its CLOCK-BMAL1 transcription factor target. Prior to incorporation, CLOCK-BMAL1 exists in an ?750-kDa complex. Single-particle electron microscopy (EM) revealed nuclear PER complexes purified from mouse liver to be quasi-spherical ?40-nm structures. In the cytoplasm, PERs, CRYs, and CK1? were distributed into several complexes of ?0.9-1.1 MDa that appear to constitute an assembly pathway regulated by GAPVD1, a cytoplasmic trafficking factor. Single-particle EM of two purified cytoplasmic PER complexes revealed ?20-nm and ?25-nm structures, respectively, characterized by flexibly tethered globular domains. Our results define the macromolecular assemblies comprising the circadian feedback loop and provide an initial structural view of endogenous eukaryotic clock machinery.

| S-EPMC5679067 | biostudies-literature

Differential regulation of adhesion complex turnover by ROCK1 and ROCK2.

Project description:BackgroundROCK1 and ROCK2 are serine/threonine kinases that function downstream of the small GTP-binding protein RhoA. Rho signalling via ROCK regulates a number of cellular functions including organisation of the actin cytoskeleton, cell adhesion and cell migration.Methodology/principal findingsIn this study we use RNAi to specifically knockdown ROCK1 and ROCK2 and analyse their role in assembly of adhesion complexes in human epidermal keratinocytes. We observe that loss of ROCK1 inhibits signalling via focal adhesion kinase resulting in a failure of immature adhesion complexes to form mature stable focal adhesions. In contrast, loss of ROCK2 expression results in a significant reduction in adhesion complex turnover leading to formation of large, stable focal adhesions. Interestingly, loss of either ROCK1 or ROCK2 expression significantly impairs cell migration indicating both ROCK isoforms are required for normal keratinocyte migration.ConclusionsROCK1 and ROCK2 have distinct and separate roles in adhesion complex assembly and turnover in human epidermal keratinocytes.

| S-EPMC3278444 | biostudies-literature

Orchestration of Circadian Timing by Macromolecular Protein Assemblies.

Project description:Genetically encoded biological clocks are found broadly throughout eukaryotes and in cyanobacteria, where they generate circadian (about a day) rhythms that allow organisms to anticipate regular environmental changes and align their physiology and behavior with Earth's daily light/dark cycle. In recent years, many have sought to expand our biochemical and structural understanding of the clock proteins that constitute the molecular "cogs" of these biological clocks. These new studies are beginning to reveal how macromolecular assemblies of dedicated clock proteins form and evolve to contribute to the generation of clocks that function over the timescale of a day. This review will highlight structural and biochemical studies that provide important insight into the molecular mechanisms of cyanobacterial and vertebrate animal clocks. Collectively, these studies demonstrate emerging biochemical properties that appear to be shared by these different clocks, suggesting that there may be some conservation in the regulation and assembly of circadian macromolecular assemblies.

| S-EPMC8694095 | biostudies-literature

Circadian regulation of genes contributed by rapid RNA turnover in tomato

Project description:Large number of genes whose expression cycles are controlled by circadian rhythm. Circadian period and phase changes were positively selected during domestication in tomato. However, the effect of RNA metabolism on circadian gene oscillations remains largely unclear. In this study, we performed transcriptome and degradome termed genome-wide mapping of uncapped and cleavage transcripts (GMUCT) in tomato leaves at 6 time points in one circadian period. Time-series profiling of RNA-seq data revealed 9342 circadian genes, whose functions enriched in multiple types of metabolic process including RNA metabolism. Proportion Uncapped (PU) metric calculated with normalized GMUCT/RNAseq ratio was used to measure general level of RNA degradation. Using this metric, we found 3885 genes whose PU was rhythmically changed, suggesting they were regulated by circadian RNA degradation. These genes with rhythmic PU were significantly enriched in the gene category with high coordination between mRNA abundance oscillation and PU dynamics. Additionally, we identified 2140 genes undergoing co-translational RNA decay (CTRD) with enriched translational termination stalling of 5’ Phosphate end reads. Remarkably, circadian mRNAs with large amplitude tent to be co-translationally decayed. Finally, we found several genes like miR172-targeted AP2, miR398-targeted CSD2 and miR159-targeted MYB125 whose miRNA cleavage efficiency also oscillated in circadian manner. Taken together, these results uncovered the vital roles of RNA metabolism including general RNA degradation, CTRD and miRNA cleavage efficiency in modulating circadian oscillations of RNA abundance.

2024-02-09 | GSE225098 | GEO

Posttranslational regulation of self-renewal capacity: insights from proteome and phosphoproteome analyses of stem cell leukemia.

Project description:We recently generated 2 phenotypically similar Hoxa9+Meis1 overexpressing acute myeloid leukemias that differ by their in vivo biologic behavior. The first leukemia, named FLA2, shows a high frequency of leukemia stem cells (LSCs; 1 in 1.4 cells), whereas the second, FLB1, is more typical with a frequency of LSCs in the range of 1 per several hundred cells. To gain insights into possible mechanisms that determine LSC self-renewal, we profiled and compared the abundance of nuclear and cytoplasmic proteins and phosphoproteins from these leukemias using quantitative proteomics. These analyses revealed differences in proteins associated with stem cell fate, including a hyperactive p38 MAP kinase in FLB1 and a differentially localized Polycomb group protein Ezh2, which is mostly nuclear in FLA2 and predominantly cytoplasmic in FLB1. Together, these newly documented proteomes and phosphoproteomes represent a unique resource with more than 440 differentially expressed proteins and 11 543 unique phosphopeptides, of which 80% are novel and 7% preferentially phosphorylated in the stem cell-enriched leukemia.

| S-EPMC5289887 | biostudies-literature

Parallel analysis of Arabidopsis circadian clock mutants reveals different scales of transcriptome and proteome regulation.

Project description:The circadian clock regulates physiological processes central to growth and survival. To date, most plant circadian clock studies have relied on diurnal transcriptome changes to elucidate molecular connections between the circadian clock and observable phenotypes in wild-type plants. Here, we have integrated RNA-sequencing and protein mass spectrometry data to comparatively analyse the lhycca1, prr7prr9, gi and toc1 circadian clock mutant rosette at the end of day and end of night. Each mutant affects specific sets of genes and proteins, suggesting that the circadian clock regulation is modular. Furthermore, each circadian clock mutant maintains its own dynamically fluctuating transcriptome and proteome profile specific to subcellular compartments. Most of the measured protein levels do not correlate with changes in their corresponding transcripts. Transcripts and proteins that have coordinated changes in abundance are enriched for carbohydrate- and cold-responsive genes. Transcriptome changes in all four circadian clock mutants also affect genes encoding starch degradation enzymes, transcription factors and protein kinases. The comprehensive transcriptome and proteome datasets demonstrate that future system-driven research of the circadian clock requires multi-level experimental approaches. Our work also shows that further work is needed to elucidate the roles of post-translational modifications and protein degradation in the regulation of clock-related processes.

| S-EPMC5376707 | biostudies-literature

Cross-species Comparison of Proteome Turnover Kinetics.

Project description:The constitutive process of protein turnover plays a key role in maintaining cellular homeostasis. Recent technological advances in mass spectrometry have enabled the measurement of protein turnover kinetics across the proteome. However, it is not known if turnover kinetics of individual proteins are highly conserved or if they have evolved to meet the physiological demands of individual species. Here, we conducted systematic analyses of proteome turnover kinetics in primary dermal fibroblasts isolated from eight different rodent species. Our results highlighted two trends in the variability of proteome turnover kinetics across species. First, we observed a decrease in cross-species correlation of protein degradation rates as a function of evolutionary distance. Second, we observed a negative correlation between global protein turnover rates and maximum lifespan of the species. We propose that by reducing the energetic demands of continuous protein turnover, long-lived species may have evolved to lessen the generation of reactive oxygen species and the corresponding oxidative damage over their extended lifespans.

| S-EPMC5880112 | biostudies-literature

Circadian Analysis of the Mouse Cerebellum Proteome.

Project description:The cerebellum contains a circadian clock, generating internal temporal signals. The daily oscillations of cerebellar proteins were investigated in mice using a large-scale two-dimensional difference in gel electrophoresis (2D-DIGE). Analysis of 2D-DIGE gels highlighted the rhythmic variation in the intensity of 27/588 protein spots (5%) over 24 h based on cosinor regression. Notably, the rhythmic expression of most abundant cerebellar proteins was clustered in two main phases (i.e., midday and midnight), leading to bimodal distribution. Only six proteins identified here to be rhythmic in the cerebellum are also known to oscillate in the suprachiasmatic nuclei, including two proteins involved in the synapse activity (Synapsin 2 [SYN2] and vesicle-fusing ATPase [NSF]), two others participating in carbohydrate metabolism (triosephosphate isomerase (TPI1] and alpha-enolase [ENO1]), Glutamine synthetase (GLUL), as well as Tubulin alpha (TUBA4A). Most oscillating cerebellar proteins were not previously identified in circadian proteomic analyses of any tissue. Strikingly, the daily accumulation of mitochondrial proteins was clustered to the mid-resting phase, as previously observed for distinct mitochondrial proteins in the liver. Moreover, a number of rhythmic proteins, such as SYN2, NSF and TPI1, were associated with non-rhythmic mRNAs, indicating widespread post-transcriptional control in cerebellar oscillations. Thus, this study highlights extensive rhythmic aspects of the cerebellar proteome.

| S-EPMC6515515 | biostudies-literature

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