Biology subjects

Musacchio, A.

Publications and source records attributed to Musacchio, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Set mediates chromosome alignment and Cohesin cleavage independently of direct PP2A-B56-binding in oocyte meiosis

Set promotes cohesion removal in mitosis by evicting phosphorylated Histone H1 and counteracting Sgo1. In addition, Set promotes chromosome alignment by counteracting Aurora B activation. The underlying molecular mechanisms through which Set performs these activities remain insufficiently characterized, but roles of Set as a Histone chaperone and PP2A inhibitor have been proposed. Building on our previous observations that Set promotes pericentromeric Cohesin removal in oocyte meiosis II, we generated an oocyte-specific conditional knock-out of Set to address its functions in meiosis. Similar to mitosis, Set depletion caused chromosome alignment and cohesion defects. We found that Set is required for accurate error correction by localizing Aurora B/C, and for efficient cleavage of the meiosis-specific Cohesin subunit Rec8 by Separase. Paired chromosomes and sister chromatids were often incompletely separated, likely a primary cause of missegregation. Set performed both its roles in a Sgo2-dependent manner, but, unexpectedly, independently of interaction with PP2A-B56. In line with a role of Set as a Histone chaperone, accumulation of phosphorylated Histone H1 in Set knock-out oocytes occurs concomitantly with reduction of oocyte-specific H1foo on chromosome arms, indicating that Set is required to create the optimal chromatin environment for efficient Rec8 cleavage by Separase in meiosis.

cell biology↗

bioRxiv2026

Molecular basis of cooperative assembly of the Ndc80-Ska kinetochore complex on microtubules

Successful chromosome segregation depends on robust kinetochore-microtubule attachments. The outer kinetochore load-bearers Ndc80 and Ska complexes functionally cooperate, but the molecular basis of their interaction remains elusive. Here, we combine cryo-EM and functional investigations of Ndc80:Ska on microtubules. Ndc80 forms longitudinal arrays along single protofilaments using two modules. The HEC1 N-terminal tail stabilizes interactions between microtubule-binding heads regulated by Aurora B. The HEC1 loop, away from microtubules, organizes Ndc80 coiled-coils into stacks matching the periodicity of tubulin subunits. SkaC binds to a previously unknown interface of Ndc80 as well as to microtubules, simultaneously stapling tubulin dimers longitudinally and neighboring protofilaments laterally. Our work demonstrates how several weak interactions of a small number of individual complexes are harnessed to generate a robust and regulated kinetochore coupler.

molecular biology↗

bioRxiv2026

CENP-B binds hairpin motifs in chromosome arms influencing gene expression

CENP-B, a centromeric protein known for its role in binding the B box sequence of centromeric DNA, has long been recognized as important, though not essential, for kinetochore attachment and chromosome segregation. Here, we identify an unexpected, non-centromeric role for CENP-B. We demonstrate that CENP-B binds to specific non-centromeric sites along chromosome arms, predominantly at promoters, and depletion of CENP-B leads to dysregulated gene expression. Binding is enriched in G2 phase cells and, importantly, occurs independently of the canonical B box motif. Instead, CENP-B binding in chromosome arms is defined by regions of negatively supercoiled DNA containing repetitive sequences, such as multiple CCAAT boxes, that are prone to forming secondary structures. Consistently, we find that CENP-B binds to hairpin DNA in vitro via its DNA binding domain. The chromosome arm binding pattern is conserved across cell types and is particularly prominent in the promoters of transcriptionally active replication-dependent histone genes. These findings reveal a previously unrecognized centromere-independent binding activity of CENP-B.

cell biology↗

bioRxiv2025

Molecular requirements for PLK1 activation by T-loop phosphorylation

Activation of PLK1, a master mitotic kinase, requires phosphorylation of its activation segment on Thr210, within a basic consensus sequence for Aurora kinases. Aurora B-dependent phosphorylation of Thr210 has been reported, but other evidence identified a strict requirement for the Aurora A partner Bora for Thr210 phosphorylation. Here, we investigate the elusive mechanistic basis for this requirement. We show that Aurora A:Bora phosphorylates Thr210 of PLK1 in vitro, while Aurora A, other Aurora A:activator complexes, and Aurora B:INCENP fail to target T210 even at high kinase/substrate ratios. A transient interaction of Bora and PLK1, identified by structural modelling and probed mutationally, is uniquely required for Thr210 phosphorylation. Dependency on Bora for Thr210 phosphorylation is eliminated after mutating Lys208, in the Aurora consensus, into arginine. This conservative mutation turns PLK1 into an excellent substrate of nearly all tested active Aurora kinases, especially Aurora B. Collectively, these results shine a new light on the specificity of the PLK1 activation mechanism.

biochemistry↗

bioRxiv2025

M18BP1 valency and a distributed interaction footprint determine epigenetic centromere specification in humans

Deposition of CENP-A, the histone H3 variant considered an epigenetic landmark of centromeres, reflects cell-cycle-regulated assembly of M18BP1, HJURP, and PLK1 on a divalent MIS18/{beta} scaffold. The localization determinants of this machinery remain poorly characterized. Here we report that artificial M18BP1 dimerization bypasses MIS18/{beta}, allowing the identification of at least four determinants of M18BP1 centromere localization. These include the SANTA domain, of which we report the first structure, as well as linear motifs in disordered neighboring regions, of which we characterize the interaction footprint on the CENP-A associated 16-subunit constitutive centromere-associated network (CCAN). Our observations imply that M18BP1, after dimerization, is necessary and sufficient for centromere localization. Its cell-cycle-dependent dimerization on MIS18/{beta} promotes initial recognition of a multivalent centromeric assembly of old CENP-A and associated proteins, followed by cooption of PLK1 and HJURP and new CENP-A deposition. Our results shed new light on the determinants of centromere epigenetic inheritance in humans.

cell biology↗

bioRxiv2025

The BUB1 and BUBR1 paralogs scaffold the kinetochore fibrous corona

The kinetochore corona, a polymeric fibrous structure, facilitates chromosome biorientation and mitotic checkpoint signaling during mitosis. How its main building block, the RZZ complex, assembles on the outer kinetochore remains poorly understood. Harnessing corona biochemical reconstitutions and cell biology, we reveal the paralogous checkpoint proteins BUB1 and BUBR1 promote non-redundant branches of corona assembly. MPS1-kinase-dependent kinetochore docking of BUB1 and subsequent recruitment of BUBR1 initiates assembly. Disrupting the first branch by depleting CENP-E, a kinesin that links BUBR1 to RZZ, uncovered a second assembly pathway mediated by a direct interaction between BUB1 and ROD. Discovery of a direct interaction with the RZZ explains how the SAC protein MAD1 fits this corona assembly scheme. Our findings solve the long-standing puzzle of corona assembly and demonstrate the intimate interweaving of chromosome biorientation and checkpoint signaling.

cell biology↗

bioRxiv2025

Ancient co-option of LTR retrotransposons as yeast centromeres

The evolutionary origins of the genetic point centromere in the brewers yeast Saccharomyces cerevisiae, a member of the order Saccharomycetales, are still unknown. Competing hypotheses suggest that the point centromere tripartite genetic centromere DNA elements (CDEs) either evolved from ancestral epigenetic centromeres by descent with modification or were gained through horizontal transfer from selfish DNA plasmids.1,2 Here, we identified centromeres in the sister order Saccharomycodales and termed them "proto-point centromeres" due to sequence features that bridge the evolutionary gap between point centromeres and ancestral centromeres types. Comparative genomic analyses across multiple yeast orders showed an unexpected evolutionary link between point and proto-point centromeres to the long terminal repeats (LTRs) of Ty5 retrotransposons. Strikingly, one Saccharomycodales species, Saccharomycodes ludwigii, harbors compact Ty5-based centromeres, where its CDEII elements are divergent AT-rich Ty5 LTRs. These living fossil centromeres show how retrotransposon cis-regulation was likely co-opted for genetic centromere specification. These insights show that point centromeres are direct descendants of retrotransposons and have evolved by descent with modification. Ultimately, the many diverse centromere types across the yeast subphylum may share a common ancestry rooted in retrotransposon activity.

evolutionary biology↗

bioRxiv2025

Molecular anatomy of PLK1 master docking motifs

The Polo-box domain (PBD) localizes Polo-like kinase 1 (PLK1) near mitotic substrates required for chromosome biorientation. Recent work on mitotic kinetochores showed PLK1 docking begins hierarchically at master docking motifs on BUB1 and CENP-U. Whether master docking motifs have common molecular features remains poorly understood. Presence on CENP-U of two neighbouring motifs generated by initial CDK1 priming and subsequent PLK1 phosphorylation led us to hypothesize PBD dimerization might be involved. Using biochemical, biophysical, and modelling approaches, we gathered strong evidence that CENP-U contains a single master docking motif. The motif is very high affinity and sufficient to form extensive interactions with the PBD, engaging multiple pockets on its surface without obvious added benefits from dimerization. Comparisons with motifs in BUB1, BUBR1, and PRC1 suggests apparent commonalities of master PLK1 docking motifs. We discuss the implications of our observations for the mechanism of PLK1 activation.

biochemistry↗

bioRxiv2024

POLO kinase inhibits Protein Phosphatase 1 to promote the Spindle Assembly Checkpoint and prevent aneuploidy

Protein phosphatase 1 (PP1) is essential for spindle assembly checkpoint (SAC) silencing and mitotic exit, but its regulation during mitosis remains ill-defined. Here, we demonstrate in vitro and in Drosophila cells that the mitotic kinase POLO phosphorylates PP187B at a conserved residue (T286) within a pocket implicated in the recognition of RVxF-containing target proteins. Phosphorylation of T286 inhibits PP187B binding to the RVxF motif of the SAC kinase MPS1, dampening the dephosphorylation of MPS1 T-loop. Phosphorylation of T286 is dynamically regulated during mitosis. It occurs at unattached/tensionless kinetochores and decreases as chromosomes congress. Expression of phosphomimetic PP187BT286D prevents MPS1 inactivation in metaphase and causes a SAC-dependent delay of anaphase onset. Conversely, an unphosphorylatable PP187BT286A mutant impairs MPS1 activation at unattached kinetochores and weakens the SAC. In vivo, larval neuroblasts expressing PP187BT286 phosphomutants exhibit frequent chromosome mis-segregation and aneuploidy. Thus, our findings identify POLO-mediated phosphorylation of PP187B as a critical regulatory strategy that fine-tunes phosphatase activity to ensure a robust and timely SAC and prevent genome instability.

cell biology↗

bioRxiv2024

Interactions with multiple inner kinetochore proteins determine mitotic localization of FACT

The FAcilitates Chromatin Transcription (FACT) complex is a dimeric histone chaperone that operates on chromatin during transcription and replication. FACT also interacts with a specialized centromeric nucleosome containing the histone H3 variant CENP-A and with CENP-TW, two subunits of CCAN, a 16-protein complex associated with CENP-A. The significance of these interactions remains elusive. Here, we show that FACT has multiple additional binding sites on CCAN. The interaction with CCAN is strongly stimulated by casein kinase II (CK2) phosphorylation of FACT. Mitotic localization of FACT to kinetochores is strictly dependent on specific CCAN subcomplexes. Unexpectedly, we also find that DNA readily displaces FACT from CCAN, suggesting that FACT becomes recruited through a pool of CCAN that is not stably integrated into chromatin. Collectively, our results point to a potential role of FACT in chaperoning CCAN during transcription or in the stabilization of CCAN at the centromere during the cell cycle. TeaserDNA-sensitive, direct interactions with multiple inner kinetochore subunits deliver FACT to the kinetochore.

biochemistry↗

bioRxiv2024

Interplay of kinetochores and catalysts drives rapid assembly of the mitotic checkpoint complex

The spindle assembly checkpoint (SAC) makes mitotic exit contingent on completion of sister chromatid biorientation, but how this coordination is achieved in practice remains poorly understood. Kinetochores, megadalton chromosome attachment sites to spindle microtubules, contribute to SAC signaling. However, it is unclear whether kinetochores are mere docking sites for SAC proteins, or further contribute to co-orientation of SAC catalysts, including MAD1:MAD2 and BUB1:BUB3, to facilitate SAC signaling. Here, we combined biochemical reconstitutions of kinetochores and the SAC to address this question in vitro. We engineered recombinant kinetochore particles that recruit most SAC components and activate SAC signaling after induction with Rapamycin, and challenged them with a battery of impairing mutants. At approximately physiological concentrations of SAC catalysts, kinetochores were crucially required for rapid assembly of the mitotic checkpoint complex (MCC), the SAC effector. Our observations depict kinetochores as a cradle that catalyzes rapid MCC assembly by concentrating and co-orienting distinct SAC catalysts.

biochemistry↗

bioRxiv2024

Condensin II activation by M18BP1

Condensin complexes promote the drastic spatial rearrangement of the genome upon mitotic entry. Condensin II initiates chromosome condensation in early mitosis. To prevent chromosome condensation during interphase, condensin II is inhibited by MCPH1, but the mechanism is unknown. Through genetic and proteomic approaches, we identify M18BP1, a protein previously associated with centromere identity, as a factor required for condensin II localization to chromatin. M18BP1 directly binds condensin IIs CAP-G2 subunit and competes with MCPH1 for binding. Upon mitotic entry, CDK1 mediated phosphorylation may promote a switch from MCPH1 to M18BP1 binding to activate condensin II. Our results identify a fundamental and evolutionarily conserved mechanism of condensin II activation.

cell biology↗

bioRxiv2024

Role of PLK1 in the epigenetic maintenance of centromeres

The centromere, a chromosome locus defined by the histone H3-like protein CENP-A, seeds the kinetochore to bind microtubules during cell division. Centromere maintenance requires CENP-A to be actively replenished by dedicated protein machinery in the early G1 cell-cycle phase, compensating for its two-fold dilution following DNA replication. Cyclin-dependent kinases (CDKs) limit CENP-A deposition to once per cell cycle and function as negative regulators outside early G1. Antithetically, Polo-like kinase 1 (PLK1) promotes CENP-A deposition in early G1, but the molecular details are still unknown. We reveal a phosphorylation network that recruits PLK1 to the deposition machinery to control a conformational switch required for licensing the CENP-A deposition reaction. Our findings solve the long-standing question of how PLK1 contributes to the epigenetic maintenance of centromeres. One-Sentence SummaryPLK1 licenses epigenetic maintenance of centromeres by regulating a conformational switch on the MIS18 protein.

cell biology↗

bioRxiv2023

Ipl1-controlled attachment maturation regulates Mps1 association with its kinetochore receptor

Faithful chromosome segregation requires that sister chromatids establish bi-oriented kinetochore-microtubule attachments. The spindle assembly checkpoint (SAC) prevents premature anaphase onset with incomplete attachments. However, how microtubule attachment and checkpoint signaling are coordinated remains unclear. The conserved kinase Mps1 initiates SAC signaling by localizing transiently to kinetochores in prometaphase and is released upon bi-orientation. Using biochemistry, structure predictions, and cellular assays, we shed light on this dynamic behaviour in Saccharomyces cerevisiae. A conserved N-terminal segment of Mps1 binds the neck region of Ndc80:Nuf2, the main microtubule receptor of kinetochores. Mutational disruption of this interface, located at the backside of the paired CH-domains and opposite the microtubule-binding site, prevents Mps1 localization, eliminates SAC signalling, and impairs growth. The same interface of Ndc80:Nuf2 binds the microtubule-associated Dam1 complex. We demonstrate that the error correction kinase Ipl1/Aurora B controls the competition between Dam1 and Mps1 for the same binding site. Thus, binding of the Dam1 complex to Ndc80:Nuf2 may release Mps1 from the kinetochore to allow anaphase onset.

cell biology↗

bioRxiv2023

Insights into human outer kinetochore assembly and force transmission from a structure-function analysis of the KMN network

The biorientation of chromosomes during cell division is necessary for precise dispatching of a mother cells chromosomes into its two daughters. Kinetochores, large layered structures built on specialized chromosome loci named centromeres, promote biorientation by binding and sensing spindle microtubules. The kinetochore outer layer consists of a 10-subunit apparatus comprising Knl1C, Mis12C, and Ndc80C subcomplexes (KMN network). The KMN network is highly elongated and docks on kinetochores and microtubules using interfaces at its opposite extremes. Here, we combine cryo-EM reconstructions and AlphaFold2 predictions to generate a model of the KMN network that reveals all intra-KMN interfaces. We identify and functionally validate two interaction interfaces that link Mis12C to Ndc80C and Knl1C. Through targeted interference experiments and molecular dynamics simulations we demonstrate this mutual organization stabilizes the KMN network. Our work reports the first comprehensive structural and functional analysis of the microtubule binding machinery of kinetochores and elucidates a path of microtubule-generated force transmission

molecular biology↗

bioRxiv2023

A mechanism that integrates microtubule motors of opposite polarity at the kinetochore corona

Chromosome biorientation on the mitotic spindle is prerequisite to errorless genome inheritance. CENP-E (kinesin 7) and Dynein-Dynactin (DD), microtubule motors with opposite polarity, promote biorientation from the kinetochore corona, a polymeric structure whose assembly requires MPS1 kinase. The coronas building block consists of ROD, Zwilch, ZW10, and the DD adaptor Spindly (RZZS). How CENP-E and DD are scaffolded and mutually coordinated in the corona remains unclear. Here, we report near-complete depletion of RZZS and DD from kinetochores after depletion of CENP-E and the outer kinetochore protein KNL1. With inhibited MPS1, CENP-E, which we show binds directly to RZZS, is required to retain kinetochore RZZS. An RZZS phosphomimetic mutant bypasses this requirement. With active MPS1, CENP-E is dispensable for corona expansion, but strictly required for physiological kinetochore accumulation of DD. Thus, we identify the corona as an integrated scaffold where CENP-E kinesin controls DD kinetochore loading for coordinated bidirectional transport of chromosome cargo.

cell biology↗

bioRxiv2022

Stable kinetochore-microtubule attachment requires loop-dependent Ndc80-Ndc80 binding

During cell division, kinetochores link chromosomes to spindle microtubules. The Ndc80 complex, a crucial microtubule binder, populates each kinetochore with dozens of copies. Whether adjacent Ndc80 complexes cooperate to promote microtubule binding remains unclear. Here we demonstrate that the Ndc80 loop, a short sequence identified across eukaryotes and predicted to interrupt the Ndc80 coiled-coil, promotes direct interactions between full-length Ndc80 complexes. Both in dividing cells and in a fully reconstituted system, these interactions are essential for the formation of force-resistant kinetochore-microtubule attachments, explaining why deletion of the loop ablates chromosome congression. The loop may fold into a more rigid structure than previously assumed and we identify point mutations that impair Ndc80-Ndc80 interactions and recapitulate the effects of loop depletion. The loop also promotes spindle checkpoint signaling, suggesting that the organisation of adjacent Ndc80 complexes is crucial to couple kinetochore-microtubule binding to cell cycle control.

biochemistry↗

bioRxiv2022

The Structural Flexibility of MAD1 Facilitates the Assembly of the Mitotic Checkpoint Complex

The spindle assembly checkpoint (SAC) safeguards the genome during cell division by generating an effector molecule known as the Mitotic Checkpoint Complex (MCC). The MCC comprises two subcomplexes, and during its assembly, formation of the CDC20:MAD2 subcomplex is the rate-limiting step. Recent studies show that the rate of CDC20:MAD2 formation is significantly accelerated by the cooperative binding of CDC20 to SAC proteins MAD1 and BUB1. However, the molecular basis for this acceleration is not fully understood. Here, we demonstrate that the structural flexibility of MAD1 at a conserved hinge near the C-terminus is essential for catalytic MCC assembly. This MAD1 hinge enables the MAD1:MAD2 complex to assume a folded conformation in vivo. Importantly, truncating the hinge reduces the rate of MCC assembly in vitro and SAC signaling in vivo. Conversely, mutations that preserve hinge flexibility retain SAC signaling, indicating that the structural flexibility of the hinge, rather than a specific amino acid sequence, is important for SAC signaling. We summarize these observations in a "knitting" model that explains how the folded conformation of MAD1:MAD2 promotes CDC20:MAD2 assembly.

cell biology↗