Biology subjects

Kops, G. J. P. L.

Publications and source records attributed to Kops, G. J. P. L..

8 recordsLinked to original sources

bioRxiv2025

Unconventional components complement the cryptic kinetochore of the ciliate Tetrahymena thermophila

The accurate segregation of chromosomes is mediated by kinetochores, multi-protein structures that connect centromeric chromatin to the dynamic microtubules of the spindle apparatus. Comparative genomics surveys predict a complex kinetochore in the last eukaryotic common ancestor (LECA) and recurrent loss or replacement of its subcomplexes across the eukaryotic tree of life. Understanding kinetochore composition and organization in diverse lineages can reveal the trajectories of kinetochore evolution in eukaryotes and aid in dissecting the function of each subcomplex. Tetrahymena thermophila is a unicellular eukaryote of the phylum Ciliophora with a largely elusive kinetochore composition. Here, we leverage proximity proteomics coupled to deep homology detection approaches to identify 16 kinetochore proteins in T. thermophila, dubbed KiTTs (Kinetochore of Tetrahymena thermophila 1-16). We find that nine KiTTs (3-9 + 15-16) are cryptic orthologs of conventional kinetochore proteins that previously remained undetected due to extensive sequence divergence. Four KiTTs (10-13) are not orthologous to known subunits and therefore represent unconventional kinetochore proteins. Super-resolution imaging places three of these novel proteins (KiTT10/11/13) at the inner kinetochore, whereas the fourth (KiTT12) localizes near the MIS12 complex at the outer kinetochore. RNAi-mediated depletion of KiTT12 reduces levels of the outer kinetochore protein KiTT1NDC80 and causes chromosome segregation errors, showcasing a bona fide role at the kinetochore. Our work reveals a unique kinetochore composition in a ciliate, providing new insights into the evolution of an essential cellular protein machine.

cell biology↗

bioRxiv2025

Distinct aneuploid karyotypes are universally selected for across cancers

Aneuploid karyotype evolution leads to immense variability in cancer patient prognosis, so characterizing relevant trends has been an important objective (1-9). Recurrent chromosome gains and losses as well as oncogenic mutations have been associated with specific cancers (10-14), but a general trend in aneuploidy evolution has not yet been identified. Here we show a universal selection principle for karyotypes composed entirely of disomies and trisomies that is conserved across many different cancer types and even in yeast. This finding is surprising enough on its own, as cancers do not typically have generalized trends, but we also see that these karyotypes exhibit a 3 times lower mutation rate of the cancer suppressor gene TP53 compared to other aneuploid karyotypes. We find that, in general, karyotypes composed of combinations of any two chromosome copy numbers, termed binary karyotypes, make up over three-quarters of the Mitelman database, which we explain by a 15% increased fitness relative to other aneuploid karyotypes. In conclusion, our results reveal binary karyotypes as a distinct category of aneuploid karyotypes that are tolerated by p53 and universally selected for independent of encoded genes or any other chromosome-specific feature, shifting the current paradigm of aneuploid cell classification.

cancer biology↗

bioRxiv2025

A Universal Scaling Law for Mitotic Spindles Driven by Chromosome Crowding

Cells regulate the size of their internal structures to maintain function in diverse biological settings1. The mitotic spindle, a molecular micro-machine responsible for chromosome segregation2, must scale to accommodate genomes varying in size by over 10,000-fold across eukaryotes3. Yet, how spindle biomechanics adapts to vastly different genome sizes remains unknown. Here, we uncover a universal spindle scaling law, where metaphase plate width scales with genome size following a power law with an exponent of [~]1/3. We hypothesize that chromosome crowding within the metaphase plate generates compressive forces as chromosomes push against each other, thereby determining spindle size and shape. Our experiments with altered chromosome number and mechanical properties in healthy and cancerous human and mouse cells, together with a theoretical model based on inter-chromosome pushing forces and mechanical manipulations of cells, confirm this hypothesis. Extending these insights across eukaryotes, we demonstrate that chromosome crowding predicts the observed power-law scaling. The biophysical constraint of chromosome crowding offers a mechanistic explanation for the evolution of open mitosis and mitotic cell rounding, enabling the division of larger genomes. Spindle adaptability to larger genomes may promote the proliferation of polyploid cells, driving not only tumor progression but also speciation during evolution.

biophysics↗

bioRxiv2022

Increased sampling and intra-complex homologies favor vertical over horizontal inheritance of the Dam1 complex

Kinetochores connect chromosomes to spindle microtubules to ensure their correct segregation during cell division. Kinetochores of human and yeast are largely homologous, their ability to track depolymerizing microtubules however is carried out by the non-homologous complexes Ska1-C and Dam1-C, respectively. We previously reported the unique anti-correlating phylogenetic profiles of Dam1-C and Ska-C found amongst a wide variety of eukaryotes. Based on these profiles and the limited presence of Dam1-C, we speculated that horizontal gene transfer (HGT) could have played a role in the evolutionary history of Dam1-C. Here, we present expanded analyses of Dam1-c evolution, using additional genome as well as transcriptome sequences and recently acquired 3D structure data. This analysis revealed a wider and more complete presence of Dam1-C in Cryptista, Rhizaria, Ichthyosporea, CRuMs, and Colponemidia. The fungal Dam1-C cryo-EM structure supports earlier hypothesized intra-complex homologies, which enables the reconstruction of rooted and unrooted phylogenies. The rooted tree of concatenated Dam1-C subunits is statistically consistent with the species tree of eukaryotes, suggesting that Dam1-C is ancient, and that the present-day phylogenetic distribution is best explained by multiple, independent losses and no HGT was involved. Furthermore, we investigated the ancient origin of Dam1-C via profile-profile searches. Homology among eight out of the ten Dam1-C subunits suggested that the complex largely evolved from a single multimerizing subunit that diversified into an octameric core via stepwise duplication and sub-functionalization of the subunits before the origin of the Last Common Ancestor. SignificanceThe Dam1 complex has a crucial role in cell division yet its distribution across species is very patchy. To resolve the evolutionary origin of this peculiar distribution, we used the recently acquired 3D structure to obtain a rooted phylogeny. This study makes an important step in discovering the evolutionary history of the Dam1 complex, by determining that Dam1-C was part of the Last eukaryotic Common Ancestor and arose via stepwise duplications during the transition from prokaryotes to eukaryotes.

evolutionary biology↗

bioRxiv2022

Condensin reorganizes centromeric chromatin during mitotic entry into a bipartite structure stabilized by cohesin

The Structural Maintenance of Chromosomes (SMC) complexes cohesin and condensin establish the 3D organization of mitotic chromosomes1-3. Cohesin is essential to maintain sister chromatid pairing until anaphase onset4, while condensin is important for mitotic centromere structure and elastic resistance to spindle forces5-8. Both complexes are also important to form productive kinetochore-spindle attachments6, 8, 9. How condensin and cohesin work together to shape the mitotic centromere to ensure faithful chromosome segregation remains unclear. Here we show by super-resolution imaging, Capture-C analysis and polymer modeling that vertebrate centromeres are partitioned into two distinct condensin-dependent subdomains during mitosis. This bipartite sub-structure is found in human, mouse and chicken centromeres and also in human neocentromeres devoid of satellite repeats, and is therefore a fundamental feature of vertebrate centromere identity. Super-resolution imaging reveals that bipartite centromeres assemble bipartite kinetochores with each subdomain capable of binding a distinct microtubule bundle. Cohesin helps to link the centromere subdomains, limiting their separation in response to mitotic spindle forces. In its absence, separated bipartite kinetochores frequently engage in merotelic spindle attachments. Consistently, uncoupling of centromere subdomains is a common feature of lagging chromosomes in cancer cells. The two-domain structure of vertebrate regional centromeres described here incorporates architectural roles for both condensin and cohesin and may have implications for avoiding chromosomal instability in cancer cells.

cell biology↗

bioRxiv2021

A free-living protist that lacks canonical eukaryotic DNA replication and segregation systems

Cells must replicate and segregate their DNA with precision. In eukaryotes, these processes are part of a regulated cell-cycle that begins at S-phase with the replication of DNA and ends after M-phase. Previous studies showed that these processes were present in the last eukaryotic common ancestor and the core parts of their molecular systems are conserved across eukaryotic diversity. However, some unicellular parasites, such as the metamonad Giardia intestinalis, have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a high-quality draft genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. We found that parasitic and free-living metamonads harbor a conspicuously incomplete set of canonical proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and other replisome components, most structural kinetochore subunits including the Ndc80 complex, as well as several canonical cell-cycle checkpoint proteins. Carpediemonas is the first eukaryote known to have lost this large suite of conserved complexes, suggesting that it has a highly unusual cell cycle and that unlike any other known eukaryote, it must rely on novel or alternative set of mechanisms to carry out these fundamental processes.

evolutionary biology↗

bioRxiv2020

Chromosomal instability by mutations in a novel specificity factor of the minor spliceosome

Aneuploidy is the leading cause of miscarriage and congenital birth defects, and a hallmark of cancer. Despite this strong association with human disease, the genetic causes of aneuploidy remain largely unknown. Through exome sequencing of patients with constitutional mosaic aneuploidy, we identified biallelic truncating mutations in CENATAC (CCDC84). We show that CENATAC is a novel component of the minor (U12-dependent) spliceosome that promotes splicing of a specific, rare minor intron subtype. This subtype is characterized by AT-AN splice sites and relatively high basal levels of intron retention. CENATAC depletion or expression of disease mutants resulted in excessive retention of AT-AN minor introns in ~100 genes enriched for nucleocytoplasmic transport and cell cycle regulators, and caused chromosome segregation errors. Our findings reveal selectivity in minor intron splicing with a specific impact on the chromosome segregation process, and show how defects herein can cause constitutional aneuploidy.

molecular biology↗

bioRxiv2018

Spindle checkpoint silencing at kinetochores with submaximal microtubule occupancy

The spindle assembly checkpoint (SAC) ensures proper chromosome segregation by monitoring kinetochore-microtubule interactions. SAC proteins are shed from kinetochores once stable attachments are achieved. Human kinetochores consist of hundreds of SAC protein recruitment modules and bind up to 20 microtubules, raising the question how the SAC responds to intermediate attachment states. We show that the RZZS-MAD1/2 module of the SAC is removed from kinetochores at low microtubule occupancy and remains absent at higher occupancies, while the BUB1/R1 module is retained at substantial levels irrespective of attachment states. Artificially tuning the affinity of kinetochores for microtubules further shows that ~50% occupancy is sufficient to shed MAD2 and silence the SAC. Kinetochores thus responds as a single unit to shut down SAC signaling at submaximal occupancy states, but retains one SAC module. This may ensure continued SAC silencing on kinetochores with fluctuating occupancy states while maintaining the ability for fast SAC re-activation.

cell biology↗