Biology subjects

Faktorova, D.

Publications and source records attributed to Faktorova, D..

5 recordsLinked to original sources

bioRxiv2025

Complexome profile of mitochondrial complexes in the myzozoan parasite of oysters, Perkinsus marinus

Mitochondrial complexes, such as the mitochondrial electron transport chain (mETC), the F1Fo-ATP synthase and the mitochondrial ribosome, are centrally important for mitochondrial function. Recently, an unexpected diversity in the composition of these complexes across unicellular eukaryotic lineages, with the apicomplexan parasites featuring prominently, has been revealed. However, whether the observed enlarged and divergent mitochondrial complexes are conserved across the wider Myzozoan lineage has not been investigated. Here, using a complexome profiling proteomic approach, we have characterised the composition of the mitochondrial complexes of the myzozoan parasite of oysters, Perkinsus marinus. We show that it shares with Plasmodium and Toxoplasma huge ATP synthase and mETC complexes. Moreover, the Perkinsus mitoribosome possesses many of the divergent features recently discovered in apicomplexans, such as an expanded subunit repertoire and the inclusion of RAP-domain and ApiAP2-like proteins as ribosomal proteins. Our study reveals the divergent subunit composition of mitochondrial complexes is an ancestral and highly conserved feature of Myzozoa.

microbiology↗

bioRxiv2025

Subcellular proteomics of Paradiplonema papillatum reveals digestive capacity of the cell membrane and the plasticity of peroxisomes across euglenozoans

Diplonemids are among the most diverse and abundant protists in the deep ocean, have extremely complex and ancient cellular systems, and exhibit unique metabolic capacities. Despite this, we know very little about this major group of eukaryotes. To establish a model organism for comprehensive investigation, we performed subcellular proteomics on Paradiplonema papillatum and localized 4,870 proteins to 22 cellular compartments. We additionally confirmed the predicted location of several proteins by epitope tagging and fluorescence microscopy. To probe the metabolic capacities of P. papillatum, we explored the proteins predicted to the cell membrane compartment in our subcellular proteomics dataset. Our data revealed an accumulation of many carbohydrate active enzymes (CAZymes). Our predictions suggest that these CAZymes are exposed to extracellular space, supporting proposals that diplonemids may specialize in breaking down carbohydrates in plant and algal cell walls. Further exploration of carbohydrate metabolism revealed an evolutionary divergence in the function of glycosomes (modified peroxisomes) in diplonemids versus kinetoplastids. Our subcellular proteome provides a resource for future investigations into the unique cell biology of diplonemids.

cell biology↗

bioRxiv2025

Discovery of unique mitotic mechanisms in Paradiplonema papillatum

Diplonemids are highly diverse and abundant marine plankton with significant ecological importance. However, little is known about their biology, even in the model diplonemid Paradiplonema papillatum whose genome sequence is available. Examining the subcellular localization of proteins using fluorescence microscopy is a powerful approach to infer their putative function. Here we report a plasmid-based method that enables YFP-tagging of a gene at the endogenous locus. By examining the localization of proteins whose homologs are involved in chromosome segregation in other eukaryotes, we discovered several interesting features in mitotically dividing P. papillatum cells. Cohesin is enriched on condensed interphase chromatin. During mitosis, chromosomes organize into two rings (termed metaphase rings herein) that surround the elongating nucleolus. Homologs of chromosomal passenger complex components (INCENP, two Aurora kinases, and KIN-A), a CLK1 kinase, spindle checkpoint protein Mad1, and microtubule regulator XMAP215 localize in between the two metaphase rings, suggesting that kinetochores may assemble in between them. We also found that a homolog of the meiotic chromosome axis protein SYCP2L1 is enriched in between metaphase rings during mitosis. These features have some resemblance to the bivalent bridge (also known as the modified synaptonemal complex), which is thought to mediate the linkage between homologous chromosomes using axis components in Bombyx mori female meiotic metaphase I. By representing the first molecular characterization of mitotic mechanisms in P. papillatum and raising a number of questions, this study forms the foundation for dissecting mitotic mechanisms in diplonemids.

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↗

bioRxiv2022

Functional differentiation of Sec13 paralogs in the euglenozoan protists

The {beta}-propeller protein Sec13 plays roles in at least three distinct processes by virtue of being a component of the COPII endoplasmic reticulum export vesicle coat, the nuclear pore complex (NPC) and the Seh1-associated (SEA)/GATOR nutrient-sensing complex, suggesting that regulatory mechanisms coordinating these cellular activities may operate via Sec13. The NPC, COPII and SEA/GATOR are all ancient features of eukaryotic cells. In the vast majority of eukaryotes, a single Sec13 gene is present, but here we report that the Euglenozoa, a lineage encompassing the diplonemid, kinetoplastid and euglenid protists contain two Sec13 paralogs. Furthermore, based on protein interactions and localization studies we show that Sec13 functions in diplonemids are divided between the Sec13a and Sec13b paralogs. Specifically, Sec13a interacts with COPII and the NPC, but Sec13b interacts with Sec16 and components of the SEA/GATOR complex. We infer that euglenozoan Sec13a is responsible for NPC functions and canonical anterograde transport activities while Sec13b acts within nutrient and autophagy-related pathways, indicating a fundamentally distinct organization of coatomer complexes in the euglenozoan flagellates.

evolutionary biology↗