Biology subjects

Koivomägi, M.

Publications and source records attributed to Koivomägi, M..

4 recordsLinked to original sources

bioRxiv2026

Phosphorylation-dependent binding of the Adenomatous Polyposis Coli protein to β-TrCP1 regulates β-catenin destruction

Wnt signaling controls cellular development by regulating levels of {beta}-catenin, a dual transcription factor and adhesion protein. The tumor suppressor gene Adenomatous Polyposis coli (APC) is a negative regulator of Wnt signaling that acts by interacting with multiple proteins in the destruction complex to drive {beta}-catenin degradation. Mutations in APC cause deregulation of Wnt/{beta}-catenin signaling contributing to the development of several types of cancer, especially colorectal cancers. Tumors are not null mutant for APC - instead they accumulate truncated proteins. Many APC proteins are truncated between the second and third 20-amino acid repeats, a region known as the {beta}-catenin inhibition domain (CID), which is essential for {beta}-catenin destruction, but its mechanism of action is unclear. Here we find that cyclin dependent kinases and GSK3{beta} phosphorylate the CID region of APC in vitro. This allows the APC CID to bind to the E3 ubiquitin ligase component {beta}-TrCP1 in a phosphorylation dependent manner and this in turn regulates the rate of {beta}-catenin ubiquitylation. {beta} TrCP1 binding to the phosphorylated CID favors the retention and stabilization of the SCF {beta}-TrCP1 E3 ligase in the destruction complex and ensures that SCF {beta}-TrCP1 remains available for {beta}-catenin ubiquitylation. These findings provide a mechanism for the vital role of APCs CID region in {beta}-catenin destruction.

biochemistry↗

bioRxiv2026

Direct Mapping of CDK2 Substrates in Embryonic Stem Cells Uncovers an AP-Site Repair Mechanism via HMCES Phosphorylation

Embryonic stem cells (ESCs) proliferate rapidly while robustly maintaining genomic integrity and exhibiting high cell-cycle kinase activity. How this activity contributes to genome integrity remains unclear. Here, using mouse ESCs engineered to express an analog-sensitive CDK2, we combine thiophosphate labeling with mass spectrometry to define a high-confidence CDK2 substrate landscape. We uncovered 65 CDK2 substrates in total, including both known and previously unrecognized substrates. Among these, HMCES, a sensor of apurinic/apyrimidinic (AP) sites, was identified as a specific cyclin E-CDK2 substrate. We mapped three CDK2-dependent phosphorylation sites in HMCES and showed that phosphorylation of these sites decreased HMCES binding to ssDNA. Mutational analysis further revealed that HMCES docks to cyclin E-CDK2 complexes via the hydrophobic patch on cyclin E. Finally, we demonstrated that HMCES phosphorylation contributes to AP-site repair and promotes ESC proliferation. Together, our findings uncover a CDK2-HMCES signaling axis that links rapid cell-cycle progression to the preservation of genome stability in mouse ESCs.

developmental biology↗

bioRxiv2026

Uncovering cancer dependencies in peptide-interacting protein pockets

Cancer cells often become dependent on specific molecular functions. As many proteins perform multiple functions mediated by different pockets and interfaces, we hypothesized that we could identify distinct cancer dependencies and therapeutic vulnerabilities by disrupting peptide-binding pockets. To test this hypothesis, we screened a proteome-wide library of 7152 genetically encoded peptides across nine cancer cell lines. We identify common and selective dependencies on peptide-binding pockets and find that gene knockout and peptide-mediated inhibition of pockets often drive divergent phenotypes. For the common-essential gene HCF1, we identify a therapeutic window by using inhibitory peptides with varying affinity. Moreover, peptides targeting TLE1-4 reveal a dependency hidden in genetic screens by homolog redundancy. We also uncover that peptides inhibiting cyclin D drive specific suppression of leukemia cell proliferation and demonstrate that these peptides improve the potency of CDK4/6 inhibitors. Overall, our screening platform facilitates data-driven prioritization of molecular pockets for subsequent therapeutic translation.

cancer biology↗

bioRxiv2018

Cyclin D-Cdk4,6 drives cell cycle progression via the retinoblastoma protein’s C-terminal helix

The cyclin-dependent kinases Cdk4 and Cdk6 form complexes with D-type cyclins to drive cell proliferation. A well-known target of cyclin D-Cdk4,6 is the retinoblastoma protein, Rb, which inhibits cell cycle progression until its inactivation by phosphorylation. However, the role of cyclin D-Cdk4,6 phosphorylation of Rb in cell cycle progression is unclear because Rb can be phosphorylated by other cyclin-Cdk complexes and cyclin D-Cdk4,6 complexes have other targets that may drive cell division. Here, we show that cyclin D-Cdk4,6 docks one side of an alpha-helix in the C-terminus of Rb, which is not recognized by cyclins E, A, and B. This helix-based docking mechanism is shared by the p107 and p130 Rb-family members across metazoans. Mutation of the Rb C-terminal helix prevents phosphorylation, promotes G1 arrest, and enhances Rbs tumor suppressive function. Our work conclusively demonstrates that the cyclin D-Rb interaction drives cell division and defines a new class of cyclin-based docking mechanisms.

cell biology↗