Biology subjects

Koivomagi, M.

Publications and source records attributed to Koivomagi, M..

5 recordsLinked to original sources

bioRxiv2026

Identification and inhibition of the Cyclin D Rb-docking interface that drives cell division

The animal cell division cycle is initiated by the cyclin-dependent kinases CDK4 and CDK6 in complex with D-type cyclins. Cyclin D-CDK4/6 complex formation is promoted by the assembly factors p21 and p27, which bind both subunits. p27 binds the hydrophobic patch on cyclin D that is similar to the patch used by other cell cycle cyclins to dock their substrates. This raised the question as to how cyclin D could find its substrates if its hydrophobic patch were already occupied? Here, we show that D-type cyclins use their A2 helix to dock the retinoblastoma protein Rb, a key substrate regulating cell cycle progression. The specific interface of cyclin Ds A2 helix is unique among cyclins and its mutation slows proliferation. Taken together, our work identifies a cyclin D-substrate docking mechanism that can be targeted by novel cancer therapeutics.

biochemistry↗

bioRxiv2025

Distinct allosteric networks in CDK4 and CDK6 in the cell cycle and in drug resistance

Cyclin-dependent kinases 4 and 6 (CDK4 and CDK6) are key regulators of the G1-S phase transition in the cell cycle. In cancer cells, CDK6 overexpression often outcompetes CDK4 in driving cell cycle progression, contributing to resistance against CDK4/6 inhibitors (CDK4/6i). This suggests distinct functional and conformational differences between these two kinases, despite their striking structural and sequence similarities. Understanding the mechanisms that differentiate CDK4 and CDK6 is crucial, as resistance to CDK4/6i--frequently linked to CDK6 overexpression--remains a significant therapeutic challenge. Notably, CDK6 is often upregulated in CDK4/6i-resistant cancers and rapidly proliferating hematopoietic stem cells, underscoring its unique regulatory roles. We hypothesize that their distinct conformational dynamics explain their differences in phosphorylation of retinoblastoma protein, Rb, inhibitor efficacy, and cell cycle control. This leads us to question how their dissimilar conformational dynamics encode their distinct actions. To elucidate their differential activities, molecular mechanisms, and inhibitor binding, we combine biochemical assays and molecular dynamics (MD) simulations. We discover that CDK4 and CDK6 have distinct allosteric networks connecting the {beta}3-C loop and the G-loop. CDK6 exhibits stronger coupling and shorter path lengths between these regions, resulting in higher kinase activity upon cyclin binding and impacting inhibitor specificity. We also discover an unrecognized role of the unstructured CDK6 C-terminus, which allosterically connects and stabilizes the R-spine, facilitating slightly higher activity. Our findings bridge the gap between the structural similarity and functional divergence of CDK4 and CDK6, advancing the understanding of kinase regulation in cancer biology. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/640857v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@cbdc16org.highwire.dtl.DTLVardef@1de54deorg.highwire.dtl.DTLVardef@195ed04org.highwire.dtl.DTLVardef@1fbc860_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

Whi5 hypo- and hyper- phosphorylation dynamics control cell cycle entry and progression

Progression through the cell cycle depends on the phosphorylation of key substrates by cyclin-dependent kinases. In budding yeast, these substrates include the transcriptional inhibitor Whi5 that regulates the G1/S transition. In early G1 phase, Whi5 is hypo-phosphorylated and inhibits the SBF complex that promotes transcription of the cyclins CLN1 and CLN2. In late-G1, Whi5 is rapidly hyper-phosphorylated by Cln1,2 in complex with the cyclin-dependent kinase Cdk1. This hyper-phosphorylation inactivates Whi5 and excludes it from the nucleus. Here, we set out to determine the molecular mechanisms responsible for Whi5s multi-site phosphorylation and how they regulate the cell cycle. To do this, we first identified the 19 Whi5 sites that are appreciably phosphorylated and then determined which of these sites are responsible for G1 hypo-phosphorylation. Mutation of 7 sites removed G1 hypo-phosphorylation, increased cell size, and delayed the G1/S transition. Moreover, the rapidity of Whi5 hyper-phosphorylation in late G1 depends on priming sites that dock the Cks1 subunit of Cln1,2-Cdk1 complexes. Hyper-phosphorylation is crucial for Whi5 nuclear export, normal cell size, full expression of SBF target genes, and timely progression through both the G1/S transition and S/G2/M phases. Thus, our work shows how Whi5 phosphorylation regulates the G1/S transition and how it is required for timely progression through S/G2/M phases and not only G1 as previously thought.

cell biology↗

bioRxiv2021

Localized phosphorylation of RNA Polymerase II by G1 cyclin-Cdk promotes cell cycle entry

The cell cycle is thought to be initiated by cyclin-dependent kinases (Cdk) inactivating transcriptional inhibitors of cell cycle gene-expression(1, 2). In budding yeast, the G1 cyclin Cln3-Cdk1 complex is thought to directly phosphorylate Whi5, thereby releasing the transcription factor SBF and committing cells to division(3-7). Here, we report that Cln3-Cdk1 does not phosphorylate Whi5, but instead phosphorylates the RNA Polymerase II subunit Rpb1s C-terminal domain (CTD) on S5 of its heptapeptide repeats. Cln3-Cdk1 binds SBF-regulated promoters(8) and Cln3s function can be performed by the canonical S5 kinase(9) Ccl1-Kin28 when synthetically recruited to SBF. Thus, Cln3-Cdk1 triggers cell division by phosphorylating Rpb1 at SBF-regulated promoters to activate transcription. Our findings blur the distinction between cell cycle and transcriptional Cdks to highlight the ancient relationship between these processes.

cell biology↗

bioRxiv2020

Whi5 is diluted and protein synthesis does not dramatically increase in pre-Start G1

In their manuscript, Litsios et al.1 report a new model for how cell growth and biosynthetic activity control the G1/S transition in budding yeast. In essence, Litsios et al. claim that Start is driven by an increasing concentration of the G1 cyclin Cln3 due to a dramatic acceleration of protein synthesis in pre-Start G1 and not by the dilution of the cell cycle inhibitor Whi5. While we previously reported that Start was in part driven by cell growth during G1 diluting out the Start inhibitor Whi52, Litsios et al. report that Whi5 remains at constant concentration during G1, and changes in Whi5 concentration therefore do not contribute to Start. Since Litsios et al. directly contradict several key points of our own model of how cell growth triggers Start, we decided to investigate their claims and data. More specifically, we decided to investigate Litsios et al.s three major claims: O_LIWhi5 concentration remains constant during G1 C_LIO_LICln3 concentration strongly increases prior to Start C_LIO_LIGlobal protein synthesis rates increase by 2-3 fold prior to Start C_LI We investigated each of these three claims and found that the evidence presented by Litsios et al. does not support their claims due to inadequate analysis methods and flaws in their experiments.

molecular biology↗