Howell2020- Compartmental Logical model of mitotic exit
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ABSTRACT:
SUBMITTER: 
Rowan Howell
PROVIDER: MODEL2007200001 | BioModels | 2020-11-26
REPOSITORIES: BioModels
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Project description:Mitotic exit requires extensive dephosphorylation of Ser/Thr residues by the PP1 and PP2A-B55 protein phosphatases in human cells. Several aspects of this are poorly understood including specific substrates and determinants of phosphatase specificity. Here we develop a novel in vitro assay, MRBLE-dephos, that allows multiplexing of dephosphorylation reactions to determine phosphatase specificity. Using MRBLE-dephos, we establish amino acid preferences of the residues surrounding the phosphorylation site for PP1 and PP2A-B55, which reveals common and unique preferences for the two phosphatases. We use specific inhibition of PP1 and PP2A-B55 in mitotic exit lysates coupled with quantitative phosphoproteomics to identify more than 2000 regulated phosphorylation sites and integrate this with mitotic interactomes to obtain a comprehensive map of mitotic dephosphorylation events. Importantly, the sites dephosphorylated during mitotic exit reveal key signatures that are consistent with the MRBLE-dephos results. We use these insights to specifically alter INCENP dephosphorylation kinetics at mitotic exit resulting in defective cytokinesis underscoring the biological relevance of our determined specificity principles. Finally, we provide a comprehensive characterization of PP1 binding motifs and show how these can shape dephosphorylation and how PP1 primes its own association with these motifs at mitotic exit. Collectively we provide a framework for understanding mitotic exit regulation by dephosphorylation and novel approaches to dissect protein phosphatase specificity.
2023-05-12 | MSV000091928 | MassIVE
Project description:Mathematical model of mitotic exit in budding yeast.
2020-05-18 | BIOMD0000000953 | BioModels
Project description:The genome is thought to be transcriptionally silent during mitosis. Technical limitations have prevented the sensitive mapping of mitotic transcription and transcription reactivation during mitotic exit, and thus the networks by which transcriptome dynamics govern the generation of daughter cells have been unclear. We used 5-ethynyluridine to pulse-label intact transcripts during mitosis and mitotic exit and find that the first round of transcription activates genes that are involved in macromolecular synthesis, rather than cell identity. Many interphase genes exhibit residual transcription in mitosis, as confirmed by different methods of assessment, and a subset of genes are more highly transcribed in mitosis than in interphase. We suggest that mitotic transcription may serve an epigenetic function in restoring proper transcription patterns during mitotic exit.
2017-09-20 | GSE87476 | GEO
Project description:The cell division cycle culminates in mitosis when two daughter cells are born. As cyclin-dependent kinase (Cdk) activity reaches its peak, the Anaphase Promoting Complex (APC) is activated to trigger sister chromatid separation and mitotic spindle elongation, followed by spindle disassembly and cytokinesis. Degradation of mitotic cyclins and activation of Cdk-counteracting phosphatases are thought to cause protein dephosphorylation to control these sequential events. Here, we use budding yeast to analyze phosphorylation dynamics of 3456 phosphosites on 1101 proteins with high temporal resolution as cells progress synchronously through mitosis. This illustrates sequential protein dephosphorylation and reveals that the order arises from successive inactivation of S and M phase Cdks and of the mitotic kinase Polo. Unexpectedly, we detect as many new phosphorylation events as there are dephosphorylation events. These correlate with late mitotic kinase activation and identify numerous candidate targets of these kinases. Our findings revise our view of mitotic exit and portray it as a dynamic process in which a range of mitotic kinases instruct the order of both protein dephosphorylation as well as phosphorylation.
2018-10-15 | PXD008327 | Pride
Project description:In budding yeast, the Mitotic Exit Network (MEN), a GTPase signaling cascade integrates spatial and temporal signals to promote exit from mitosis. This signal integration requires transmission of a signal created on the cytoplasmic face of the spindle pole bodies (SPBs, functional equivalent of the centrosome in yeast) to the nucleolus, where the MEN effector protein Cdc14 resides. In this study, we show that the MEN activating signal at SPBs is relayed to Cdc14 in the nucleolus through the dynamic localization of its terminal kinase complex Dbf2-Mob1. Cdc15, the protein kinase that activates Dbf2-Mob1 at SPBs, also regulates its nuclear access. Once in the nucleus, priming phosphorylation by the Polo kinase Cdc5 targets Dbf2-Mob1 to the nucleolus. Cdc5 phosphorylates the Cdc14 nucleolar anchor Cfi1/Net1 creating a phospho-binding site for Dbf2-Mob1 which allows Dbf2-Mob1 to phosphorylate Cfi1/Net1 and Cdc14, which activates Cdc14. The mechanisms governing intracellular signal transmission that we uncovered in the MEN – regulated nuclear access and effector activation through priming kinases - may well serve as paradigms for intracellular signal transmission in general. As for phosphoproteomics, our analyses suggest a simple model where Cdc5 and Dbf2-Mob1 phosphorylate Cfi1/Net1 to bring about the release of Cdc14 from its inhibitor. Previous studies have shown that Cfi1/Net1 is a highly phosphorylated protein. To map sites in Cfi1/Net1 that are phosphorylated in a CDC5 or MEN-dependent manner, we performed phosphoproteomics analyses on wild-type anaphase cells and cells in which Cdc5 or Cdc15 were inhibited. We synchronized wild-type, cdc5-as1 and cdc15-as1 cells in G1 with α-factor pheromone and released them into the cell cycle with the corresponding inhibitors. Cultures enriched in anaphase cells as judged by anaphase spindle formation (~70% for wild-type cells and ~95% for cdc5-as1 and cdc15-as1 cells) were collected and processed for a reproducible data-independent acquisition mass spectrometry (DIA-MS) analysis with 7 technical replicates for each sample. Also, 10 out of 12 CDC5-only sites identified in anaphase cells are already phosphorylated in cells arrested in metaphase using the microtubule depolymerizing drug nocodazole with 6 of them were also determined to be CDC5-dependent in metaphase, which is consistent with the finding that Cdc5 is already active in metaphase.
2021-01-14 | PXD020369 | Pride
Project description:Temporal control over protein phosphorylation and dephosphorylation is crucial for accurate chromosome segregation and for completion of the cell division cycle during exit from mitosis. In budding yeast, the Cdc14 phosphatase is thought to be a major regulator at this time, while in higher eukaryotes PP2A phosphatases take a dominant role. Here, we use time-resolved phosphoproteome analysis in budding yeast to evaluate the respective contributions of Cdc14 and the two main PP2A isoforms, PP2A(Cdc55) and PP2A(Rts1). This reveals an overlapping requirement for all three phosphatases during mitotic progression. Cdc14 instructs the sequential pattern of phosphorylation changes, in part through its preferential recognition of serine-based cyclin-dependent kinase (Cdk) substrates. PP2A(Cdc55) and PP2A(Rts1) in turn exhibit a broad substrate spectrum with some selectivity for phospho-threonines and a role for PP2A(Rts1) in sustaining Aurora kinase activity. Our results illustrate synergy and coordination between phosphatases as they orchestrate phosphoproteome dynamics during mitotic progression.
2019-11-12 | PXD012860 | Pride
Project description:Once generated, neurons are thought to permanently exit the cell cycle and become irreversibly differentiated. However, neither the precise point at which this post-mitotic state is attained nor the extent of its irreversibility is clearly defined. Here we report that newly born neurons from the upper layers of the mouse cortex, despite initiating axon and dendrite elongation, continue to drive gene expression from the neurogenic intermediate neural progenitor tubulin ?1 promoter (T?1p). These observations suggest an ambiguous post-mitotic neuronal state. Whole transcriptome analysis of sorted upper cortical neurons further revealed that neurons continue to express genes related to cell cycle progression long after mitotic exit until at least post-natal day 3 (P3). These genes are however down regulated thereafter and are associated with a concomitant up regulation of tumor suppressors at P5. Interestingly, newly born neurons located in the cortical plate (CP) at embryonic day 18-19 (E18-E19) and P3 challenged with calcium influx are found in S/G2/M phases of the cell cycle, and still able to undergo division at E18-E19 but not at P3. At P5 however, calcium influx becomes neurotoxic and leads instead to neuronal loss. Our data delineate for the first time the temporal window during which developing neurons acquire a post-mitotic state.
2014-09-29 | GSE61845 | GEO
Project description:This model is from the article:
Downregulation of PP2A(Cdc55) phosphatase by separase initiates mitotic exit in budding yeast.
Queralt E, Lehane C, Novak B, Uhlmann F. Cell.
2006 May 19;125(4):719-32. 16713564
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Abstract:
After anaphase, the high mitotic cyclin-dependent kinase (Cdk) activity is downregulated to promote exit from mitosis. To this end, in the budding yeast S. cerevisiae, the Cdk counteracting phosphatase Cdc14 is activated. In metaphase, Cdc14 is kept inactive in the nucleolus by its inhibitor Net1. During anaphase, Cdk- and Polo-dependent phosphorylation of Net1 is thought to release active Cdc14. How Net1 is phosphorylated specifically in anaphase, when mitotic kinase activity starts to decline, has remained unexplained. Here, we show that PP2A(Cdc55) phosphatase keeps Net1 underphosphorylated in metaphase. The sister chromatid-separating protease separase, activated at anaphase onset, interacts with and downregulates PP2A(Cdc55), thereby facilitating Cdk-dependent Net1 phosphorylation. PP2A(Cdc55) downregulation also promotes phosphorylation of Bfa1, contributing to activation of the "mitotic exit network" that sustains Cdc14 as Cdk activity declines. These findings allow us to present a new quantitative model for mitotic exit in budding yeast.
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2012 The BioModels.net Team.
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To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2009-08-20 | BIOMD0000000409 | BioModels
Project description:To maintain cellular identities during development, gene expression profiles must be faithfully propagated through cell generations. The reestablishment of gene expression patterns upon mitotic exit is thought to be mediated, in part, by mitotic bookmarking by transcription factors (TF). However, the mechanisms and functions of TF mitotic bookmarking during early embryogenesis remain poorly understood. In this study, taking advantage of the naturally synchronized mitoses of Drosophila early embryos, we provide evidence that the pioneer-like transcription factor GAF acts as stable mitotic bookmarker during zygotic genome activation. We report that GAF remains associated to a large fraction of its interphase targets (37%). Mitotically-bound loci include cis-regulatory sequences of key developmental genes, with both active and repressive chromatin signatures. GAF mitotic targets are globally accessible during mitosis and a subset is also mitotically bookmarked via histone acetylation (H4K8ac). By monitoring the kinetics of transcriptional activation in living embryos, we provide evidence that GAF binding establishes competence for rapid activation upon mitotic exit.
2022-02-25 | GSE180812 | GEO
Project description:Candida albicans demonstrates three main growth morphologies yeast, pseudohyphal and true hyphal forms. Cell separation is distinct in these morphological forms and the process of separation is closely linked to the completion of mitosis and cytokinesis. In Saccharomyces cerevisiae the small GTPase Tem1 is known to initiate the mitotic exit network, a signalling pathway involved in signalling the end of mitosis and initiating cytokinesis and cell separation. We have characterised the role of Tem1 in C. albicans, and demonstrate that it is essential for mitotic exit and cytokinesis, and that this essential function is signalled through the kinase Cdc15. Consistent with its role in activating the mitotic exit network Tem1 localised to spindle pole bodies in a cell cycle dependent manner. Cells depleted of Tem1 displayed highly polarised growth but ultimately fail to complete cytokinesis and re-enter the cell cycle following nuclear division. At the transcriptional level genes downregulated following the depletion of Tem1 where significantly enriched for genes whose expression peaks early in the cell cycle and for those associated with glycolysis. For expression analysis triplicate RNA samples were generated from exponentially growing C. albicans yeast cells and from cells following 8 h inhibition of TEM1 expression. Gene expression was determined using RNA-seq on the Illumina HiSeq 2000 platform.
2014-01-01 | E-GEOD-48650 | biostudies-arrayexpress