Biology subjects

Barral, Y.

Publications and source records attributed to Barral, Y..

13 recordsLinked to original sources

bioRxiv2026

Low-affinity binding motif in microtubule plus-end condensates specializes microtubule function

The microtubule plus-end tracking proteins (+TIPs) CLIP-170/Bik1 and EB/Bim1 form a condensate, the +TIP body, at the plus-end of most microtubules in vivo. Remarkably, however, these +TIP bodies typically impart different dynamics and interaction profiles to distinct microtubules, according to their cellular function. The molecular mechanisms underlying the functional versatility of the +TIP body are unknown. Here, we show that the +TIP Kar9 utilizes repeats of a lysine-aspartate-lysine (KDK)-centered short linear motif (SLiM) to interact with Bik1 on a restricted subset of cytoplasmic microtubules during yeast mitosis. Furthermore, these multivalent Kar9-Bik1 interactions tune the material behavior of the +TIP body to specify proper microtubule function. Indicating that KDK serves as generic Bik1-interaction motif, similar motifs are also present in Kip2, where they mediate Bik1-dependent recruitment of Kip2 to the +TIP body. Together, our study provides insights into how low-affinity Bik1 interactors diversify microtubule function by locally specializing the content and behavior of +TIP bodies.

Cell Biology↗

bioRxiv2026

Plasticity of genetic regulation during cellular learning

Even under physiological conditions, cells are exposed to multiple, spatially and temporally complex signals and need to regularly adjust their response to survive and function. At least in some cases, identifying the appropriate response relies on the ability cells to learn from experience. For example, budding yeast cells learn to ignore futile mating signals. Using this paradigm, we investigated the genetic requirements supporting learning in single cells. We show that it arises from the dynamics of a large, highly redundant and plastic genetic network, where the contribution of most genes to learning varies across experimental replicates. Furthermore, this network is highly resistant to genetic perturbations and involves a broad panel of cellular functions and sensing pathways, suggesting that it can integrate a large diversity of inputs. Together, our data support the notion that cellular learning is an emerging feature of the information storage capability inherent to large sets of interacting genes, indicating that it should be widely conserved across cell types.

cell biology↗

bioRxiv2026

RNAi-based discrimination of exogenous DNA by mitotic heterochromatin in fission yeast

Various mechanisms protect prokaryotic cells from invasive exogenous (exo)DNA. However, these are rarely conserved in eukaryotes, where the existence of such processes remains elusive. Here, we uncover how fission yeast eliminates exoDNA through unequal partitioning. We show that intrinsic transcriptional features of plasmidial exoDNA produce small interfering (si)RNAs that recruit heterochromatin onto the plasmid. An active, heterochromatin-dependent clustering mechanism then causes its asymmetric partitioning during mitosis. The mitotic kinase Aurora B, which dissociates heterochromatin on segregating chromosomes, is distinctively hypoactive on plasmidial DNA, facilitating its unequal partitioning and, ultimately, elimination from the cell population. Thus, an interplay between RNAi-mediated exoDNA heterochromatinization and chromosomal phosphorylation enables fission yeast to discriminate self-from non-self-DNA, uncovering a hitherto undescribed cell-autonomous immune process in eukaryotic cells.

cell biology↗

bioRxiv2024

Dissociation of the nuclear basket triggers chromosome loss in aging yeast

In many organisms, aging is a clear risk factor for chromosome mis-segregation, the main source of aneuploidy. Here, we report that old yeast cells lose chromosomes by partitioning them asymmetrically to their daughter cells together with the pre-existing (old) spindle pole body (SPB, centrosome equivalent in yeast). Strikingly, remodelling of the nuclear pore complex (NPC) and the displacement of its nuclear basket triggered these asymmetric chromosome segregation events. Simultaneously, nuclear basket displacement caused unspliced pre-mRNAs to leak into the cytoplasm. We show that removing the introns of three genes involved in chromosome segregation was sufficient to fully suppress chromosome loss in old cells. Promoting pre-mRNA leakage in young cells also caused asymmetric chromosome partitioning and loss through the same three introns. Therefore, we propose that basket displacement from NPCs and its consequences for pre-mRNA quality control are key triggers of aging phenotypes such as aneuploidy.

cell biology↗

bioRxiv2024

A fluid droplet harvests the force generated by shrinking microtubules in living cells

The energy-consuming dynamic instability of microtubules generates significant forces which are thought to be harnessed to move large cargos in cells. However, identification of mechanisms which can capture the force released during microtubule depolymerization to move large loads has been elusive. In this work we show that a biomolecular condensate provides an elegant solution to this problem. Using live cell super-resolution microscopy, we directly observe that budding yeast +TIP bodies are nanoscale droplets with classic fluid-like behaviors which accumulate type V myosin (Myo2) at their surfaces. We find that conserved self-oligomerization interfaces in the protein Kar9 tune the biophysical properties of the viscoelastic +TIP body and its ability to e]iciently move the mitotic spindle. Our findings introduce a paradigm for how forces generated by microtubule dynamics are harnessed in cells and open a frontier of research on nanoscale biomolecular condensates in their native environment.

biophysics↗

bioRxiv2024

A protein condensation network contextualises cell fate decisions

For cells to thrive, they must make appropriate fate decisions based on a myriad of internal and external stimuli. But how do they integrate these different forms of information to contextualise their decisions? Old yeast cells showed an ability to dampen their proliferation as they entered senescence. Conversely, they had an enhanced ability to promote proliferation during escape from pheromone stimulation. A network of nucleoprotein condensation states involving processing bodies (P-bodies) and the prion-like RNA-binding protein, Whi3, controlled these opposing fate decisions. In old but not in young cells, condensation of Whi3 was both necessary and sufficient for senescence entry. In old cells, Whi3 localised to age-dependent P-bodies. Preventing their formation stopped Whi3 condensation from driving senescence entry. Challenging old cells with an external stimulus, pheromone, revealed that the condensates had a second function: potentiating the cells ability to trigger escape from the mating pheromone response. These findings identify biomolecular condensation as an integrator of contextual information as cells make decisions, enabling them to navigate overlapping life events.

cell biology↗

bioRxiv2023

Global analysis of aging-related protein structural changes uncovers enzyme polymerization-based control of longevity

Aging is associated with progressive phenotypic changes over time. Virtually all cellular phenotypes are produced by proteins and structural alterations in proteins can lead to age-related diseases. Nonetheless, comprehensive knowledge of proteins undergoing structural-functional changes during cellular aging and their contribution to age-related phenotypes is lacking. Here, we conducted proteome-wide analysis of early age-related protein structural changes in budding yeast using limited proteolysis-mass spectrometry. The results, compiled in online ProtAge-catalog, unravelled age-related functional changes in regulators of translation, protein folding and amino acid metabolism. Mechanistically, we found that folded glutamate synthase Glt1 polymerizes into supramolecular self-assemblies during aging causing breakdown of cellular amino acid homeostasis. Inhibiting Glt1 polymerization by mutating the polymerization interface restored amino acid levels in aged cells, attenuated mitochondrial dysfunction and led to life span extension. Altogether, this comprehensive map of protein structural changes enables identifying novel mechanisms of age-related phenotypes and offers opportunities for their reversal.

cell biology↗

bioRxiv2022

Fission-independent compartmentalization of mitochondria during budding yeast cell division

Lateral diffusion barriers compartmentalize membranes to generate polarity or asymmetrically partition membrane-associated macromolecules. Budding yeasts assemble such barriers in the endoplasmic reticulum (ER) and the outer nuclear envelope at the bud neck to retain aging factors in the mother cell and generate naive and rejuvenated daughter cells. However, little is known about whether other organelles are similarly compartmentalized. Here, we show that the membranes of mitochondria are laterally compartmentalized at the bud neck and near the cell poles. The barriers in the inner mitochondrial membrane are constitutive, whereas those in the outer membrane form in response to stresses. The strength of mitochondrial diffusion barriers is regulated positively by spatial cues from the septin axis, and negatively by retrograde (RTG) signaling. These data indicate that mitochondria are compartmentalized in a fission-independent manner. We propose that these diffusion barriers may promote mitochondrial polarity and contribute to mitochondrial quality control.

cell biology↗

bioRxiv2022

Mitotic chromosome condensation resets chromatin to maintain transcriptional homeostasis

Mitotic entry correlates with the condensation of the chromosomes, remodeling of histone modifications, exclusion of transcription factors from DNA and the broad downregulation of transcription. However, whether mitotic condensation influences transcription in the subsequent interphase is unknown. Here, we show that preventing one chromosome to condense during mitosis causes it to fail resetting transcription. Rather it diverted the transcription machinery and underwent unscheduled initiation of gene expression. This caused the activation of inducible transcriptional programs, such as the GAL genes, even in absence of the relevant stimuli. Strikingly, aberrant gene expression persisted into the next interphase. Thus, our study identifies the maintenance of transcriptional homeostasis as an unexpected and yet unexplored function of mitotic chromosome condensation. One-Sentence SummaryMitotic chromatin condensation resets the transcriptome to protect cells from transcriptional drifting after anaphase.

molecular biology↗

bioRxiv2021

High interaction valency ensures cohesion and persistence of a microtubule +TIP body at the plus-end of a single specialized microtubule in yeast

Microtubule plus-end tracking proteins (+TIPs) control microtubule specialization and are as such essential notably during eukaryotic cell division. Here, we investigated interactions and functions of the budding yeast Kar9 network consisting of the core +TIPs components Kar9 (functional homologue of APC, MACF, and SLAIN), Bim1 (orthologue of EB1), and Bik1 (orthologue of CLIP-170). Our data indicate that a redundant, multivalent web of interactions links the three +TIPs together to form a "Kar9 body" at the tip of a single cytoplasmic microtubule. They further suggest that this body is a liquid-like condensate, allowing it to persist on both growing and shrinking microtubule tips, and functions as a mechanical coupling device between microtubules and actin cables during mitosis. Our study underlines the power of dissecting the web of low-affinity interactions driving liquid-liquid phase separation of proteins in order to demonstrate the importance and establish the functional roles of condensation processes in vivo.

cell biology↗

bioRxiv2021

Role of mitotic diffusion barriers in regulating the asymmetric division of activated CD8 T cells

Upon their activation, naive CD8 T cells divide and differentiate into short-lived effector cells, relevant for exerting immune control, and long-lived memory cells, relevant for long-term immunity. The proportion of memory cells generated depends highly on the context of activation and whether the activated cell divides symmetrically or asymmetrically. However, how T cells control the extent of their asymmetry during their first division in response to contextual signals is not known. Using fluorescence loss in photo-bleaching (FLIP) experiments, we show that the metabolic and plasma membrane asymmetry of mitotic T cells depend on the regulated assembly of a lateral diffusion barrier in their endoplasmic reticulum (ER-) membrane. In asymmetrically dividing T cells, the degrees of asymmetry correlated tightly to barrier strength, whereas symmetrically dividing T cells did not establish such a barrier. Direct positive or negative interference with barrier assembly enhanced or abrogated metabolic and plasma membrane asymmetry, respectively, indicating that barrier strength is a direct and decisive determinant of mitotic asymmetry. Thus, together our data identify diffusion barrier-mediated compartmentalization as a mechanism for how asymmetric T cell regulate their long-term response as a function of the activatory context.

immunology↗

bioRxiv2021

Specialization of chromatin-bound nuclear pore complexes promotes yeast aging

The nuclear pore complex (NPC) mediates nearly all exchanges between nucleus and cytoplasm, and changes composition in many species as the organism ages. However, how these changes arise and whether they contribute themselves to aging is poorly understood. We show that in replicatively aging yeast cells attachment of DNA circles to NPCs drives the displacement of the NPCs nuclear basket and cytoplasmic complexes. Remodeling of the NPC resulted from the regulation of basket components by SAGA, rather than from damages. These changes affected NPC interaction with mRNA export factors, without affecting the residence of import factors or engaging the NPC quality control machinery. Mutations preventing NPC remodeling extended the replicative lifespan of the cells. Thus, our data indicate that DNA circles accumulating in the mother cell drive aging at least in part by triggering NPC specialization. We suggest that antagonistic pleiotropic effects of NPC specialization are key drivers of aging.

cell biology↗

bioRxiv2020

A mechanism to prevent transformation of the Whi3 mnemon into a prion.

In response to deceptive courtship, budding yeast cells escape pheromone induced cell cycle arrest through coalescence of the G1/S inhibitor Whi3 into a dominant inactive super-assembly. Strikingly, Whi3 super-assemblies remain stable over many cell cycles in the mother cells and are not passed on to the daughter cells. Thereby, Whi3 coalescence encodes memory, conferring to it the property of a mnemon (Whi3mnem), a protein which conformational change maintain a trait that is permanent in the mother cell but is not inherited by daughter cells. Mnemons share structural features with prions, which are self-templating protein conformations that are inherited by daughter cells. Yet, how the maintenance and asymmetric inheritance of Whi3mnem are achieved is unknown. Here, we report that Whi3mnem is closely associated with endoplasmic reticulum (ER) membranes and retained in the mother cell by the presence of lateral membrane diffusion barriers at the bud neck. Strikingly, barrier defects made Whi3mnem propagate in a mitotically stable manner, like a prion. Alike Whi3mnem, transformation of Whi3 into a prion required its poly-glutamine prion-like domain. Thus, we propose that Whi3mnem is in a self-templating state, lending temporal stability to the memory that it encodes, while its anchorage into the compartmentalized membranes of the ER ensures its confinement in the mother cell and prevents its infectious propagation. These results suggest that confined self-templating super-assembly is a powerful mechanism for the long-term encoding of information.

cell biology↗