Biology subjects

Gheber, L.

Publications and source records attributed to Gheber, L..

7 recordsLinked to original sources

bioRxiv2026

Cell Cycle Phases, Spindle Dynamics and Kinesin-5 Motor LocalizationCharacterized by Deep Learning, Dual Segmentation and Decision-Tree Pipeline

Three-dimensional live-cell fluorescence imaging of yeast cells is crucial for studying cell-cycle mechanics and regulation. However, extracting multi-channel phenotypes within dense cell clusters remains an image-processing bottleneck. Standard deep-learning models segment cells but fail to track mother-bud boundaries, mitotic spindle shapes and spindle-localizing proteins. Investigators rely on labour-intensive manual coordinate plotting, introducing observer bias and often exclude clustered cell data due to visual complexity. Here, we present an open-source Fiji pipeline for automated yeast cell image processing and deterministic classification of cell-cycle, spindle and protein dynamics. The workflow utilizes a dual-segmentation architecture via custom Cellpose models to capture the mother-bud cell boundaries. Extracted masks are integrated with multi-channel fluorescence data using a Difference-of-Gaussians framework to resolve SPB coordinates and localized protein kinetics, which a rule-based decision-tree maps to precise mitotic phenotypes. Validation demonstrates a 50-fold acceleration with ~6% deviation from manual analysis. Availability: Zenodo at https://doi.org/10.5281/zenodo.22083016.

cell biology↗

bioRxiv2025

Dimeric Cin8 motors have an inherent plus-end bias and weak inter-head coordination

Kinesin-5 motors are bipolar tetramers that crosslink and slide antiparallel microtubules during mitotic spindle assembly. Fungal kinesin-5 motors, such as Cin8, exhibit bidirectional motility, switching between minus- and plus-end-directed stepping in response to environmental conditions; however, the molecular basis of this directional switching remains unclear. To better understand the origin of this bidirectional behavior, we investigated the motility and ATPase kinetics of two Cin8 dimers, created by fusing the motor domains to a stable coiled-coil domain from kinesin-1. To investigate the role of the proximal neck coiled-coil region in coordinating motor activity, we compared Cin8 dimers that included or lacked the first four heptads of the Cin8 neck-coil domain. By analyzing the stepping kinetics, microtubule residence times, and directional switching dynamics, we found that these Cin8 dimers move processively with a net plus-end directionality along with undirected movements, behaviors that mimic the plus-ended motility state of wild-type Cin8. However, fast minus-ended motility seen in wild-type Cin8 tetramers was not observed in the dimers. The instantaneous velocity distributions and ATPase rates were inconsistent with the undirected movement being solely due to passive diffusion, suggesting that they reflect random bidirectional stepping. Fewer undirected movements were seen on yeast microtubules, their native physiological substrate, compared to on bovine microtubules. Replacing the Cin8 neck-coil domain with a stable coiled-coil led to faster plus-end stepping, fewer undirected movements, a reduction in the microtubule binding duration, and enhanced coupling between ATP hydrolysis and plus-end stepping. Our results suggest that the native Cin8 neck coil confers flexibility between the two motor domains that contributes to bidirectional stepping, and that sustained minus-end movement requires regions outside the motor domain. Statement of SignificanceThe kinesin-5 family of motors, which contain two pairs of heads located on either end of a long stalk domain, power mitotic spindle formation by sliding antiparallel microtubules. The yeast kinesin-5, Cin8 moves to microtubule minus-ends under specific conditions, breaking the dogma that N-terminal kinesins move to microtubule plus-ends. To gain insight into how Cin8 changes its walking direction, we analyzed engineered Cin8 dimers, models of one half of full-length Cin8. The dimers step erratically, consistent with stepping in both directions, but have a plus-end bias. We find evidence that the two heads poorly coordinate, which contrasts with other kinesins, and suggest that the stepping direction may be regulated by altering the degree of inter-head coordination.

biophysics↗

bioRxiv2021

The mechanochemical origins of the microtubule sliding motility within the kinesin-5 domain organization

The conserved kinesin-5 bipolar tetrameric motors slide apart microtubules during mitotic spindle assembly and elongation. Kinesin-5 bipolar organization originates from its conserved tetrameric helical minifilament, which position the C-terminal tail domains of two subunits near the N-terminal motor domains of two anti-parallel subunits (Scholey et al, 2014). This unique tetrameric structure enables kinesin-5 to simultaneously engage two microtubules and transmit forces between them, and for multiple kinesin-5 motors to organize via tail to motor interactions during microtubule sliding (Bodrug et al, 2020). Here, we show how these two structural adaptations, the kinesin-5 tail-motor domain interactions and the length of the tetrameric minifilament, determine critical aspects of kinesin-5 motility and sliding mechanisms. An x-ray structure of the 34-nm kinesin-5 minifilament reveals how the dual dimeric N-terminal coiled-coils emerge from the tetrameric central bundle. Using this structure, we generated active bipolar mini-tetrameric motors from Drosophila and human orthologs, which are half the length of native kinesin-5. Using single-molecule motility assays, we show that kinesin-5 tail domains promote mini-tetramers static pauses that punctuate processive motility. During such pauses, kinesin-5 mini-tetramers form multi-motor clusters mediated via tail to motor domain cross-interactions. These clusters undergo slow and highly processive motility and accumulate at microtubule plus-ends. In contrast to native kinesin-5, mini-tetramers require tail domains to initiate microtubule crosslinking. Although mini-tetramers are highly strained in initially aligning microtubules, they slide microtubules more efficiently than native kinesin-5, due to their decreased minifilament flexibility. Our studies reveal that the conserved kinesin-5 motor-tail mediated clustering and the length of the tetrameric minifilament are key features for sliding motility and are critical in organizing microtubules during mitotic spindle assembly and elongation.

cell biology↗

bioRxiv2020

Flexibility of the neck-linker during docking is pivotal for function of bi directional kinesin

The role of the neck-linker (NL) element in regulating the functions of bi-directional kinesins is unknown. We report that replacing the NL of the bi-directional kinesin-5 Cin8 with sequences from plus-end directed kinesins produces non-functional Cin8 with defective spindle localization and abolished minus-end directionality and microtubule-crosslinking in vitro. Mutation of a single glycine in the NL of Cin8 to asparagine (proposed to serve as an N-latch that stabilizes the docked conformation of the NL in the plus-end directed kinesins) causes defects in the functions of Cin8. Strikingly, in a non-functional Cin8 containing the NL of the plus-end directed kinesin-5 Eg5, a single mutation of the N-latch asparagine back to glycine rescues the in vivo and in vitro defects. Since such replacement eliminates stabilizing interactions between the docked NL and the motor domain, we conclude that flexibility of NL during docking is pivotal for the function of bi-directional kinesin motors.

biophysics↗

bioRxiv2020

Drag-induced directionality switching of kinesin-5 Cin8 revealed by cluster-motility analysis

Directed active motion of motor proteins is a vital process in virtually all eukaryotic cells. Nearly a decade ago, the discovery of directionality switching of mitotic kinesin-5 motors challenged the long-standing paradigm that individual kinesin motors are characterized by an intrinsic directionality. While several kinesin motors have now been shown to exhibit context-dependent directionality that can be altered under diverse experimental conditions, the underlying mechanism remains unknown. Here, we studied clustering-induced directionality switching of the mitotic kinesin-5 Cin8, using a fluorescence-based single-molecule motility assay combined with biophysical theory. Based on the detailed characterization of the motility of single motors and clusters of Cin8, we developed a predictive molecular model, that quantitatively agrees with experimental data. This combined approach allowed us to quantify the response of Cin8 motors to external forces as well as the interactions between Cin8 motors, and thereby develop a detailed understanding of the molecular mechanism underlying directionality switching. The main insight is that directionality switching is caused by a single feature of Cin8: an asymmetric response of active motion to forces that oppose motion, here referred to as drag. This general mechanism explains why bidirectional motor proteins are capable of reversing direction in response to seemingly unrelated experimental factors including clustering, changes in the ionic strength of the buffer, increased motor density and molecular crowding, and in motility assays. Significance StatementKinesin-5 motor proteins perform essential functions in chromosome segregation during mitotic cell division. Surprisingly, several kinesin-5 motors have the ability to reverse directionality under different experimental conditions, which contradicts the long-standing paradigm that individual kinesin motors are characterized by an intrinsic directionality. The mechanism underlying this ability to switch directionality has remained elusive. Here, we combine fluorescence-based motility assays and theoretical modeling to analyze cluster-size-dependent motility of the bidirectional kinesin-5 Cin8. Our results show that bidirectional motors can switch directionality because they exhibit an asymmetric response of active motion to drag. This mechanism explains multiple seemingly unrelated experimental factors that have been shown to cause directionality switching of kinesin motors.

biophysics↗

bioRxiv2019

The Kinesin-5 Tail Domain Directly Modulates the Mechanochemical Cycle of the Motor for Anti-Parallel Microtubule Sliding

Kinesin-5 motors organize mitotic spindles by sliding apart anti-parallel microtubules. They are homotetramers composed of two antiparallel dimers placing orthogonal motor and tail domains at opposite ends of a bipolar minifilament. Here, we describe a regulatory mechanism, involving direct binding of the tail to motor domain and reveal its fundamental role in microtubule sliding motility. Biochemical analyses reveal that the tail down-regulates microtubule-activated ATP hydrolysis by specifically engaging the motor in the nucleotide-free or ADP-bound states. Cryo-EM structures reveal that the tail stabilizes a unique conformation of the motor N-terminal subdomain opening its active site. Full-length kinesin-5 motors undergo slow motility and cluster together along microtubules, while tail-deleted motors exhibit rapid motility without clustering along microtubules. The tail is critical for motors to zipper together two microtubules by generating substantial forces within sliding zones. The tail domain is essential for kinesin-5 mitotic spindle localization in vivo, which becomes severely reduced when the tail is deleted. Our studies suggest a revised microtubule-sliding model, in which tail domains directly engage motor domains at both ends of kinesin-5 homotetramers enhancing stability of the dual microtubule-bound states leading to slow motility yet high force production.

biophysics↗

bioRxiv2018

Synthetic-evolution reveals that phosphoregulation of the mitotic kinesin-5 Cin8 is constrained

Cdk1 has been found to phosphorylate the majority of its substrates in disordered regions. These phosphorylation sites do not appear to require precise positioning for their function. The mitotic kinesin-5 Cin8 was shown to be phosphoregulated at three Cdk1 sites in disordered loops within its catalytic motor domain. Here, we examined the flexibility of Cin8 phosphoregulation by analyzing the phenotypes of synthetic Cdk1-sites that were systematically generated by single amino-acid substitutions, starting from a phosphodeficient variant of Cin8. Out of 29 synthetic Cdk1 sites that we created, eight were non-functional; 19 were neutral, similar to the phosphodeficient variant; and two gave rise to phosphorylation-dependent spindle phenotypes. Of these two, one site resulted in novel phosphoregulation, and only one site, immediately adjacent to a native Cdk1 site, produced phosphoregulation similar to wild-type. This study shows that, while the gain of a single phosphorylation site can confer regulation and modulate the dynamics of the spindle, to achieve optimal regulation of a mitotic kinesin-5 motor protein, phosphoregulation has to be site-specific and precise.

cell biology↗