Biology subjects

Raas, M. W. D.

Publications and source records attributed to Raas, M. W. D..

7 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↗

bioRxiv2024

On the possibility of yet a third kinetochore system in the protist phylum Euglenozoa

Transmission of genetic material from one generation to the next is a fundamental feature of all living cells. In eukaryotes, a macromolecular complex called the kinetochore plays crucial roles during chromosome segregation by linking chromosomes to spindle microtubules. Little is known about this process in evolutionarily diverse protists. Within the supergroup Discoba, Euglenozoa forms a speciose group of unicellular flagellates - kinetoplastids, euglenids, and diplonemids. Kinetoplastids have an unconventional kinetochore system, while euglenids have subunits that are conserved amongst most eukaryotes. For diplonemids, a group of extremely diverse and abundant marine flagellates, it remains unclear what kind of kinetochores are present. Here, we employed deep homology detection protocols using profile-versus-profile Hidden Markov Model searches and AlphaFold-based structural comparisons to detect homologies that might have been previously missed. Interestingly, we still could not detect orthologs for most of the kinetoplastid nor canonical kinetochore subunits with few exceptions including a putative centromere-specific histone H3 variant (cenH3/CENP-A), the spindle checkpoint protein Mad2, the chromosomal passenger complex members Aurora and INCENP, and broadly conserved proteins like CLK kinase and the meiotic synaptonemal complex proteins SYCP2/3 that also function at kinetoplastid kinetochores. We examined the localization of five candidate kinetochore-associated proteins in the model diplonemid, Paradiplonema papillatum. PpCENP-A shows discrete dots in the nucleus, implying that it is likely a kinetochore component. PpMad2, PpCLKKKT10/19, PpSYCP2L1KKT17/18 and INCENP reside in the nucleus, but no clear kinetochore localization was observed. Altogether, these results point to the possibility that diplonemids evolved a hitherto unknown type of kinetochore system. IMPORTANCEA macromolecular assembly called the kinetochore is essential for the segregation of genetic material during eukaryotic cell division. Therefore, characterization of kinetochores across species is essential for understanding the mechanisms involved in this key process across the eukaryotic tree of life. In particular, little is known about kinetochores in divergent protists such as Euglenozoa, a group of unicellular flagellates that includes kinetoplastids, euglenids, and diplonemids, the latter being a highly diverse and abundant component of marine plankton. While kinetoplastids have an unconventional kinetochore system and euglenids have a canonical one similar to traditional model eukaryotes, preliminary searches detected neither unconventional nor canonical kinetochore components in diplonemids. Here, we employed state-of-the-art deep homology detection protocols but still could not detect orthologs for the bulk of kinetoplastid-specific nor canonical kinetochore proteins in diplonemids except for a putative centromere-specific histone H3 variant. Our results strongly suggest that diplonemids evolved kinetochores that do not resemble previously known ones.

cell biology↗

bioRxiv2024

Shaping up genomes: Prokaryotic roots and eukaryotic diversification of SMC complexes

Chromosome organization ensures accurate DNA replication, segregation, gene regulation and DNA damage repair. Across the tree of life, protein assemblages termed Structural Maintenance of Chromosomes (SMC) complexes determine chromosome organization. Eukaryotes usually have four SMC complex types (condensin I, condensin II, cohesin, and SMC5/6), whereas prokaryotes mostly have one. The expanded set is probably needed to accommodate the considerably larger eukaryotic genomes. Despite their essential functions, SMC complexes exhibit notable variation among model organisms, suggesting underexplored diversity across eukaryotes. Here, we provide a thorough reconstruction of the evolution of SMC complex subunits and accessory proteins across eukaryotes. We show that the last eukaryotic common ancestor (LECA) had all four complete SMC complexes, supporting the notion that LECA was already a sophisticated cell. At later timepoints, condensin II was lost at least thirty times, rendering it one of the most frequently lost eukaryotic cellular machineries. We identify multiple components (e.g., Sororin, Securin, Nse5, and Nse6) as much more ancient and widespread than previously appreciated. Finally, we traced the prokaryotic origins of these complexes and propose an ancient SMC complex was already duplicated in the ancestor of TACK and Asgard archaea, suggesting a sophisticated chromosome organization in the archaeal ancestor of eukaryotes. The eukaryotic SMC complex inventory was further expanded through gene duplications, highlighting the importance of these events in the emergence of eukaryotic complexity. Altogether, our results address questions and raise new ones about how SMC complex evolution affected the genome organizations of ancestral and contemporary organisms.

cell biology↗

bioRxiv2023

A farnesyl-dependent structural role for CENP-E in expansion of the fibrous corona

Correct chromosome segregation during cell division depends on proper connections between spindle microtubules and kinetochores. During prometaphase, kinetochores are temporarily covered with a dense protein meshwork known as the fibrous corona. Formed by oligomerization of ROD/ZW10/ZWILCH-SPINDLY (RZZ-S) complexes, the fibrous corona promotes spindle assembly, chromosome orientation and spindle checkpoint signaling. The molecular requirements for formation of the fibrous corona are not fully understood. Here we show that the fibrous corona depends on the mitotic kinesin CENP-E, and that poorly expanded fibrous coronas after CENP-E depletion are functionally compromised. This previously unrecognized role for CENP-E does not require its motor activity but instead is driven by farnesyl modification of its C-terminal kinetochore-and microtubule-binding domain. We show that in cells CENP-E interacts with RZZ-S complexes in a farnesyl-dependent manner. CENP-E is recruited to kinetochores following RZZ-S, and - while not required for RZZ-S oligomerization per se - promotes subsequent fibrous corona expansion. Our comparative genomics analyses suggest that the farnesylation motif in CENP-E orthologs emerged alongside the full RZZ-S module in an ancestral lineage close to the fungi-animal split (Obazoa), revealing potential conservation of the mechanisms for fibrous corona formation. Our results show that proper spindle assembly has a potentially conserved non-motor contribution from the kinesin CENP-E through stabilization of the fibrous corona meshwork during its formation.

cell biology↗

bioRxiv2023

Uncoupled evolution of the Polycomb system and deep origin of non-canonical PRC1

Polycomb group (PcG) proteins modulate chromatin states to silence gene transcription in plants and animals. Most PcG proteins function as part of distinct multi-subunit Polycomb repressive complexes (PRCs). Gene repression by the Polycomb system involves chromatin compaction by canonical PRC1 (cPRC1), mono-ubiquitylation of histone H2A (H2Aub1) by non-canonical PRC1 (ncPRC1) and tri-methylation of histone H3K27 (H3K27me3) by PRC2. Prevalent models for Polycomb repression emphasize a tight functional coupling between PRC1 and PRC2. However, whether this paradigm indeed reflects the evolution and functioning of the Polycomb system remains unclear. Here, we examined the relationship between cPRC1, ncPRC1 and PRC2 through a comprehensive analysis of their presence and evolution across the entire eukaryotic tree of life. We show that both PRC1 and PRC2 were present in the Last Eukaryotic Common Ancestor (LECA), but that their subsequent evolution is uncoupled. The identification of orthologs for ncPRC1-defining subunits in unicellular relatives of animals and of fungi suggests that the origin of ncPRC1 predates that of cPRC1, and we develop a scenario for the evolution of cPRC1 from ncPRC1. Our results demonstrate the independent evolution and function of PRC1 and PRC2 and show that crosstalk between these complexes is a secondary development in evolution.

evolutionary biology↗

bioRxiv2022

The rate of adaptive molecular evolution in wild and domesticated Saccharomyces cerevisiae populations

Through its fermentative capacities, Saccharomyces cerevisiae was central in the development of civilization during the Neolithic period, and the yeast remains of importance in industry and biotechnology giving rise to bona fide domesticated populations. Here, we conduct a population genomic study of domesticated and wild populations of S. cerevisiae. Using coalescent analyses, we report that the effective population size of yeast populations decreased since the divergence with S. paradoxus. We fitted models of distribution of fitness effects to infer the rate of adaptive ({omega}a) and non-adaptive ({omega}na) non-synonymous substitutions in protein-coding genes. We report an overall limited contribution of positive selection to S. cerevisiae protein evolution, albeit with higher rates of adaptive evolution in wild compared to domesticated populations. Our analyses revealed the signature of background selection and possibly Hill-Robertson interference, as recombination was found to be negatively correlated with{omega} na and positively correlated with{omega} a. However, the effect of recombination on{omega} a was found to be labile, as it is only apparent after removing the impact of codon usage bias on the synonymous site frequency spectrum and disappears if we control for the correlation with{omega} na, suggesting it could be an artefact of the decreasing population size. Furthermore, the rate of adaptive non-synonymous substitutions is significantly correlated with the residue solvent exposure, a relation that cannot be explained by the populations demography. Together, our results provide a detailed characterization of adaptive mutations in protein-coding genes across S. cerevisiae populations.

evolutionary biology↗

bioRxiv2020

Whole slide imaging to understand Candida biofilm growth and response to antifungals

New strategies that enable fast and accurate visualization of Candida biofilms are necessary to better study their structure and response to antifungals agents. Here, we applied whole slide imaging (WSI) to study biofilm formation of Candida species. Three relevant biofilm-forming Candida species (C. albicans ATCC 10231, C. glabrata ATCC 2001, and C. tropicalis ATCC 750) were cultivated on glass coverslips both in presence and absence of widely used antifungals. Accumulated biofilms were stained with fluorescent markers and scanned in both bright-field and fluorescence modes using a WSI digital scanner. WSI enabled clear assessment of both size and structural features of Candida biofilms. Quantitative analyses readily detected reductions in biofilm-covered surface area upon antifungal exposure. Furthermore, we show that the overall biofilm growth can be adequately assessed across both bright-field and fluorescence modes. At the single-cell level, WSI proved adequate, as morphometric parameters evaluated with WSI did not differ significantly from those obtained with scanning electron microscopy, considered as golden standard at single-cell resolution. Thus, WSI allows for reliable visualization of Candida biofilms enabling both large-scale growth assessment and morphometric characterization of single-cell features, making it an important addition to the available microscopic toolset to image and analyze fungal biofilm growth.

microbiology↗