Cyclin A and Cks1 promote kinase consensus switching to non-proline directed CDK1 phosphorylation

Aymen al-Rawi; Svitlana Korolchuk; Jane Endicott; Tony Ly

doi:10.1101/2022.05.24.493195

Cyclin A and Cks1 promote kinase consensus switching to non-proline directed CDK1 phosphorylation

Aymen al-Rawi, Svitlana Korolchuk, Jane Endicott, Tony Ly (Lead / Corresponding author)

Research output: Working paper/Preprint › Preprint

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Abstract

Ordered protein phosphorylation by CDKs is a key mechanism for regulating the cell cycle. How temporal order is enforced in mammalian cells remains unclear. Using a fixed cell kinase assay and phosphoproteomics, we show how CDK1 activity and non-catalytic CDK1 subunits contribute to the choice of substrate and site of phosphorylation. Increases in CDK1 activity alters substrate choice, with intermediate and low sensitivity CDK1 substrates enriched in DNA replication and mitotic functions, respectively. This activity dependence was shared between Cyclin A- and Cyclin B-CDK1. Cks1 has a proteome-wide role as an enhancer of multisite CDK1 phosphorylation. Contrary to the model of CDK1 as an exclusively proline-directed kinase, we show that Cyclin A and Cks1 promote non-proline directed phosphorylation, preferably on sites with a +3 lysine residue. Indeed, 70% of cell cycle regulated phosphorylations, where the kinase carrying out this modification has not been identified, are non-proline directed CDK1 sites.

Original language	English
Place of Publication	Cold Spring Harbour Laboratory
Publisher	BioRxiv
DOIs	https://doi.org/10.1101/2022.05.24.493195
Publication status	Published - 24 May 2022

Keywords

Cell cycle
Cyclin-dependent kinases
Short linear motifs (SLiMs)
Consensus sequence motifs
Mass spectrometry
Proteomics
PTMs

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10.1101/2022.05.24.493195Licence: CC BY-NC-ND

Final Published VersionFinal published version, 16 MBLicence: CC BY-NC-ND

1 Finished

Understanding the Proliferation-Quiescence Switch Using Quantitative Cellular Biochemistry (Sir Henry Dale Fellowship) (Transfer from University of Edinburgh)
Ly, T. (Investigator)
1/12/20 → 12/08/24
Project: Research

1 Article

Cyclin A and Cks1 promote kinase consensus switching to non-proline directed CDK1 phosphorylation
Al-Rawi, A., Kaye, E., Korolchuk, S., Endicott, J. A. & Ly, T. (Lead / Corresponding author), 28 Mar 2023, In: Cell Reports. 42, 3, 21 p., 112139.
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title = "Cyclin A and Cks1 promote kinase consensus switching to non-proline directed CDK1 phosphorylation",

abstract = "Ordered protein phosphorylation by CDKs is a key mechanism for regulating the cell cycle. How temporal order is enforced in mammalian cells remains unclear. Using a fixed cell kinase assay and phosphoproteomics, we show how CDK1 activity and non-catalytic CDK1 subunits contribute to the choice of substrate and site of phosphorylation. Increases in CDK1 activity alters substrate choice, with intermediate and low sensitivity CDK1 substrates enriched in DNA replication and mitotic functions, respectively. This activity dependence was shared between Cyclin A- and Cyclin B-CDK1. Cks1 has a proteome-wide role as an enhancer of multisite CDK1 phosphorylation. Contrary to the model of CDK1 as an exclusively proline-directed kinase, we show that Cyclin A and Cks1 promote non-proline directed phosphorylation, preferably on sites with a +3 lysine residue. Indeed, 70% of cell cycle regulated phosphorylations, where the kinase carrying out this modification has not been identified, are non-proline directed CDK1 sites.",

keywords = "Cell cycle, Cyclin-dependent kinases, Short linear motifs (SLiMs), Consensus sequence motifs, Mass spectrometry, Proteomics, PTMs",

author = "Aymen al-Rawi and Svitlana Korolchuk and Jane Endicott and Tony Ly",

note = "The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. This work is supported by a Wellcome Trust and Royal Society Sir Henry Dale Fellowship to T.L. (206211/Z/17/Z), a Darwin Trust PhD studentship to A. A., a UK Medical Research Council Programme Grant to J.E. (MR/N009738/1), core funding for the Wellcome Centre for Cell Biology (091020), a Wellcome Multi-User Equipment Grant to T.L. (218305/Z/19/Z) and a Wellcome Innovation Award for mass spectrometry equipment (218448/Z/19/Z). ",

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AU - Endicott, Jane

AU - Ly, Tony

N1 - The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. This work is supported by a Wellcome Trust and Royal Society Sir Henry Dale Fellowship to T.L. (206211/Z/17/Z), a Darwin Trust PhD studentship to A. A., a UK Medical Research Council Programme Grant to J.E. (MR/N009738/1), core funding for the Wellcome Centre for Cell Biology (091020), a Wellcome Multi-User Equipment Grant to T.L. (218305/Z/19/Z) and a Wellcome Innovation Award for mass spectrometry equipment (218448/Z/19/Z).

PY - 2022/5/24

Y1 - 2022/5/24

N2 - Ordered protein phosphorylation by CDKs is a key mechanism for regulating the cell cycle. How temporal order is enforced in mammalian cells remains unclear. Using a fixed cell kinase assay and phosphoproteomics, we show how CDK1 activity and non-catalytic CDK1 subunits contribute to the choice of substrate and site of phosphorylation. Increases in CDK1 activity alters substrate choice, with intermediate and low sensitivity CDK1 substrates enriched in DNA replication and mitotic functions, respectively. This activity dependence was shared between Cyclin A- and Cyclin B-CDK1. Cks1 has a proteome-wide role as an enhancer of multisite CDK1 phosphorylation. Contrary to the model of CDK1 as an exclusively proline-directed kinase, we show that Cyclin A and Cks1 promote non-proline directed phosphorylation, preferably on sites with a +3 lysine residue. Indeed, 70% of cell cycle regulated phosphorylations, where the kinase carrying out this modification has not been identified, are non-proline directed CDK1 sites.

AB - Ordered protein phosphorylation by CDKs is a key mechanism for regulating the cell cycle. How temporal order is enforced in mammalian cells remains unclear. Using a fixed cell kinase assay and phosphoproteomics, we show how CDK1 activity and non-catalytic CDK1 subunits contribute to the choice of substrate and site of phosphorylation. Increases in CDK1 activity alters substrate choice, with intermediate and low sensitivity CDK1 substrates enriched in DNA replication and mitotic functions, respectively. This activity dependence was shared between Cyclin A- and Cyclin B-CDK1. Cks1 has a proteome-wide role as an enhancer of multisite CDK1 phosphorylation. Contrary to the model of CDK1 as an exclusively proline-directed kinase, we show that Cyclin A and Cks1 promote non-proline directed phosphorylation, preferably on sites with a +3 lysine residue. Indeed, 70% of cell cycle regulated phosphorylations, where the kinase carrying out this modification has not been identified, are non-proline directed CDK1 sites.

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KW - Cyclin-dependent kinases

KW - Short linear motifs (SLiMs)

KW - Consensus sequence motifs

KW - Mass spectrometry

KW - Proteomics

KW - PTMs

U2 - 10.1101/2022.05.24.493195

DO - 10.1101/2022.05.24.493195

M3 - Preprint

BT - Cyclin A and Cks1 promote kinase consensus switching to non-proline directed CDK1 phosphorylation

PB - BioRxiv

CY - Cold Spring Harbour Laboratory

ER -

Cyclin A and Cks1 promote kinase consensus switching to non-proline directed CDK1 phosphorylation

Abstract

Keywords

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Projects

Understanding the Proliferation-Quiescence Switch Using Quantitative Cellular Biochemistry (Sir Henry Dale Fellowship) (Transfer from University of Edinburgh)

Research output

Cyclin A and Cks1 promote kinase consensus switching to non-proline directed CDK1 phosphorylation

Cite this