Biology subjects

Liakopoulos, D.

Publications and source records attributed to Liakopoulos, D..

4 recordsLinked to original sources

bioRxiv2026

Questioning the G2 phase in the budding yeast cell cycle with a qualitative and possibilistic model

The budding yeast S. cerevisiae, a foundational model for cell cycle studies, exhibits a complex phase organisation (G1, S, G2/M) governed by checkpoints ensuring faithful cellular inheritance. However, the existence of a distinct G2 phase in yeast remains debated, with some advocating for a prometaphase instead. To address this issue, we developed a discrete-event, qualitative, and possibilistic model, the first one to our knowledge, to integrate organelle-level components (replication forks, sister chromatids, mitotic spindle, bud) while remaining parsimonious. Unlike molecular-centred or overly complex whole-cell models, this approach bridges broad systemic and finer mechanistic scales. Our results demonstrate that the model faithfully recapitulates cell cycle progression and supports the dispensable G2 phase. This possibilistic model inspired from recent applications in ecology advocates in favor of the necessity of prometaphase. This study thus provides a unifying and flexible framework to resolve long-standing ambiguities in yeast cell dynamics, while avoiding the pitfalls of excessive complexity or reductionism.

systems biology↗

bioRxiv2025

Control of mitotic spindle disassembly through SUMO-targeted ubiquitylation of yeast kinesin-5

Faithful cell division requires precise control of spindle assembly and disassembly. In budding yeast, spindle breakdown at mitotic exit depends on Cdk1 inactivation and ubiquitin-mediated degradation of spindle stabilizing factors, including the kinesin-5 Cin8 and the crosslinker Ase1/PRC1. Timely degradation of Cin8 by APCCdh1 prevents spindle over-elongation and deformation. We have identified SUMOylation and the SUMO-targeted ubiquitin ligase Slx5 as regulators of spindle disassembly. Cin8 is SUMOylated and interacts with Slx5, suggesting that it is a substrate of Slx5. Deletion of the SLX5 gene or expression of a SUMOylation-defective Cin8 mutant cause spindle disassembly defects that resemble those of degradation-resistant Cin8 mutants. Reduction of Cin8 SUMOylation partly stabilizes spindles in ase1{Delta} cells. In addition, SUMOylation of Cin8 and Slx5 are required for timely actomyosin-ring contraction and Cin8 clearance from the mitotic spindle. We propose that SUMOylation regulates Cin8 activity and that SUMO-targeted ubiquitylation facilitates removal Cin8 from the spindle, promoting spindle disassembly at the end of mitosis.

cell biology↗

bioRxiv2024

The kinesin Kip2 promotes microtubule growth using a bipartite polymerase module to deliver tubulin to microtubule plus-ends

Kinesin molecular motors are essential for fundamental cellular processes such as chromosome segregation or vesicular transport. To fulfil their function, some kinesins promote microtubule growth, but the molecular mechanism underlying this activity remains unclear. One of the motors with the strongest microtubule growth-promoting activity is Kip2, a kinesin that is required for astral microtubule integrity and spindle positioning in yeast. Here we show that the ability of Kip2 to polymerize microtubules is coupled to binding and transport of free tubulin. We report that the Kip2 N-terminus is required to promote microtubule elongation in vitro and in vivo. Kip2 binds free tubulin through this unstructured, basic domain and delivers it to microtubule plus-ends. In addition to the N-terminus, we find that ATP hydrolysis and motor activity is also required for microtubule polymerisation. Finally, transfer of the Kip2 N-terminus to kinesin-1, a kinesin that lacks polymerase activity, transforms kinesin-1 into a tubulin-transporting microtubule polymerase. We propose that motor-driven tubulin delivery to microtubule plus-ends is an efficient mechanism used by kinesins to promote microtubule polymerization.

cell biology↗

bioRxiv2018

An E2-ubiquitin thioester-driven approach to identify substrates modified with ubiquitin and ubiquitin-like molecules

Covalent modifications of proteins with ubiquitin and ubiquitin-like molecules are instrumental to many biological processes. However, identifying the E3 ligase responsible for these modifications remains a major bottleneck in ubiquitin research. Here, we present an E2-thioester-driven identification (E2~dID) method for the targeted identification of substrates of specific E2 and E3 enzyme pairs. E2~dID exploits the central position of E2-conjugating enzymes in the ubiquitination cascade and provides in vitro generated biotinylated E2~ubiquitin thioester conjugates as the sole source for ubiquitination in extracto. This enables purification and mass spectrometry-based identification of modified proteins under stringent conditions independently of the biological source of the extract. We demonstrate the sensitivity and specificity of E2-dID by identifying and validating substrates of APC/C in human cells. Finally, we perform E2~dID with SUMO in S. cerevisiae, showing that this approach can be easily adapted to other ubiquitin-like modifiers and experimental models.

biochemistry↗