A Cyclin-dependent Kinase-mediated Phosphorylation Switch of Disordered Protein Condensation

Overview

Journal Nat Commun

Specialty Biology

Date 2023 Oct 9

PMID 37813838

Authors

Juan Manuel Valverde

Geronimo Dubra

Michael Phillips

Austin Haider

Carlos Elena-Real

Aurelie Fournet

Emile Alghoul

Dhanvantri Chahar

Nuria Andres-Sanchez

Matteo Paloni

Pau Bernado

Guido van Mierlo

Michiel Vermeulen

Henk van den Toorn

Albert J R Heck

Angelos Constantinou

Alessandro Barducci

Kingshuk Ghosh

Nathalie Sibille

Puck Knipscheer

Liliana Krasinska

Daniel Fisher

Maarten Altelaar

Affiliations

Soon will be listed here.

Abstract

Cell cycle transitions result from global changes in protein phosphorylation states triggered by cyclin-dependent kinases (CDKs). To understand how this complexity produces an ordered and rapid cellular reorganisation, we generated a high-resolution map of changing phosphosites throughout unperturbed early cell cycles in single Xenopus embryos, derived the emergent principles through systems biology analysis, and tested them by biophysical modelling and biochemical experiments. We found that most dynamic phosphosites share two key characteristics: they occur on highly disordered proteins that localise to membraneless organelles, and are CDK targets. Furthermore, CDK-mediated multisite phosphorylation can switch homotypic interactions of such proteins between favourable and inhibitory modes for biomolecular condensate formation. These results provide insight into the molecular mechanisms and kinetics of mitotic cellular reorganisation.

Citing Articles

The role of MKI67 in the regulation of 60S pre-ribosome nucleolar export, transcripts, energy supply, and apoptosis.

Iuchi S, Paulo J bioRxiv. 2025; .

PMID: 39990431 PMC: 11844515. DOI: 10.1101/2025.02.13.638155.

Post-Translational Modifications of Proteins Orchestrate All Hallmarks of Cancer.

Bruno P, Arshad A, Gogu M, Waterman N, Flack R, Dunn K Life (Basel). 2025; 15(1).

PMID: 39860065 PMC: 11766951. DOI: 10.3390/life15010126.

Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification.

Muneer G, Chen C, Chen Y Proteomics. 2024; 25(1-2):e202400087.

PMID: 39696887 PMC: 11735659. DOI: 10.1002/pmic.202400087.

Phospho-regulation of ASCL1-mediated chromatin opening during cellular reprogramming.

Azzarelli R, Gillen S, Connor F, Lundie-Brown J, Puletti F, Drummond R Development. 2024; 151(24).

PMID: 39575884 PMC: 11664170. DOI: 10.1242/dev.204329.

Phosphorylation of disordered proteins tunes local and global intramolecular interactions.

Usher E, Fossat M, Holehouse A Biophys J. 2024; 123(23):4082-4096.

PMID: 39539017 PMC: 11628823. DOI: 10.1016/j.bpj.2024.10.021.

References

Hyman A . Whither systems biology. Philos Trans R Soc Lond B Biol Sci. 2011; 366(1584):3635-7. PMC: 3203457. DOI: 10.1098/rstb.2011.0074. View

Ubersax J, Woodbury E, Quang P, Paraz M, Blethrow J, Shah K . Targets of the cyclin-dependent kinase Cdk1. Nature. 2003; 425(6960):859-64. DOI: 10.1038/nature02062. View

Chi Y, Welcker M, Hizli A, Posakony J, Aebersold R, Clurman B . Identification of CDK2 substrates in human cell lysates. Genome Biol. 2008; 9(10):R149. PMC: 2760876. DOI: 10.1186/gb-2008-9-10-r149. View

Blethrow J, Glavy J, Morgan D, Shokat K . Covalent capture of kinase-specific phosphopeptides reveals Cdk1-cyclin B substrates. Proc Natl Acad Sci U S A. 2008; 105(5):1442-7. PMC: 2234163. DOI: 10.1073/pnas.0708966105. View

Holt L, Tuch B, Villen J, Johnson A, Gygi S, Morgan D . Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science. 2009; 325(5948):1682-6. PMC: 2813701. DOI: 10.1126/science.1172867. View

Michowski W, Chick J, Chu C, Kolodziejczyk A, Wang Y, Suski J . Cdk1 Controls Global Epigenetic Landscape in Embryonic Stem Cells. Mol Cell. 2020; 78(3):459-476.e13. PMC: 7214218. DOI: 10.1016/j.molcel.2020.03.010. View

Mahdessian D, Cesnik A, Gnann C, Danielsson F, Stenstrom L, Arif M . Spatiotemporal dissection of the cell cycle with single-cell proteogenomics. Nature. 2021; 590(7847):649-654. DOI: 10.1038/s41586-021-03232-9. View

Olsen J, Vermeulen M, Santamaria A, Kumar C, Miller M, Jensen L . Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal. 2010; 3(104):ra3. DOI: 10.1126/scisignal.2000475. View

Zegerman P, Diffley J . Phosphorylation of Sld2 and Sld3 by cyclin-dependent kinases promotes DNA replication in budding yeast. Nature. 2006; 445(7125):281-5. DOI: 10.1038/nature05432. View

10.

Tanaka S, Umemori T, Hirai K, Muramatsu S, Kamimura Y, Araki H . CDK-dependent phosphorylation of Sld2 and Sld3 initiates DNA replication in budding yeast. Nature. 2006; 445(7125):328-32. DOI: 10.1038/nature05465. View

11.

Orlicky S, Tang X, Willems A, Tyers M, Sicheri F . Structural basis for phosphodependent substrate selection and orientation by the SCFCdc4 ubiquitin ligase. Cell. 2003; 112(2):243-56. DOI: 10.1016/s0092-8674(03)00034-5. View

12.

Nash P, Tang X, Orlicky S, Chen Q, Gertler F, Mendenhall M . Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication. Nature. 2001; 414(6863):514-21. DOI: 10.1038/35107009. View

13.

Ord M, Moll K, Agerova A, Kivi R, Faustova I, Venta R . Multisite phosphorylation code of CDK. Nat Struct Mol Biol. 2019; 26(7):649-658. PMC: 6614033. DOI: 10.1038/s41594-019-0256-4. View

14.

Coudreuse D, Nurse P . Driving the cell cycle with a minimal CDK control network. Nature. 2010; 468(7327):1074-9. DOI: 10.1038/nature09543. View

15.

Krasinska L, Domingo-Sananes M, Kapuy O, Parisis N, Harker B, Moorhead G . Protein phosphatase 2A controls the order and dynamics of cell-cycle transitions. Mol Cell. 2011; 44(3):437-50. DOI: 10.1016/j.molcel.2011.10.007. View

16.

Gavet O, Pines J . Progressive activation of CyclinB1-Cdk1 coordinates entry to mitosis. Dev Cell. 2010; 18(4):533-43. PMC: 3325599. DOI: 10.1016/j.devcel.2010.02.013. View

17.

Purvis J, Lahav G . Encoding and decoding cellular information through signaling dynamics. Cell. 2013; 152(5):945-56. PMC: 3707615. DOI: 10.1016/j.cell.2013.02.005. View

18.

Budnik B, Levy E, Harmange G, Slavov N . SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation. Genome Biol. 2018; 19(1):161. PMC: 6196420. DOI: 10.1186/s13059-018-1547-5. View

19.

Lombard-Banek C, Moody S, Manzini M, Nemes P . Microsampling Capillary Electrophoresis Mass Spectrometry Enables Single-Cell Proteomics in Complex Tissues: Developing Cell Clones in Live Xenopus laevis and Zebrafish Embryos. Anal Chem. 2019; 91(7):4797-4805. PMC: 6688183. DOI: 10.1021/acs.analchem.9b00345. View

20.

Cooper S . The synchronization manifesto: a critique of whole-culture synchronization. FEBS J. 2019; 286(23):4650-4656. DOI: 10.1111/febs.15050. View