Biology subjects

Obornik, M.

Publications and source records attributed to Obornik, M..

10 recordsLinked to original sources

bioRxiv2026

Transcriptomic and lipidomic profiles reveal higher thermal adaptability in a tropical versus a temperate isolate of Chromera velia

The apicomplexan alga Chromera velia is the closest known phototrophic relative of apicomplexan parasites (Sporozoa). Despite its scientific importance as a model for the evolution of parasitic Apicomplexa, only two strains are available in culture. The first isolate (SH), obtained from stony coral in the cold waters of Sydney Harbour, was used for the original species description. The second isolate (OTI) originates from tropical corals at One Tree Island in the Great Barrier Reef. In this study, we compare their growth, transcriptomic, and lipidomic profiles at 20{degrees}C and 26{degrees}C. Both strains grew faster at 26{degrees}C, yet they responded differently to higher temperature. In SH, warming downregulated nearly 85% of its thermally responsive genes, with motility-, cytoskeleton-, and lipid-associated genes most strongly affected, while at 26{degrees}C, SH retained higher expression of translation and nitrogen, amide, and peptide biosynthesis genes than OTI. OTI, by contrast, mounted a smaller, more balanced response and maintained stable expression of cilium, axoneme, and microtubule genes across both temperatures. The lipidomes of the two strains showed both shared and divergent responses. Both isolates sense and respond to increasing temperature in the same basic way, but OTI stabilizes its membranes, whereas SH redirects lipid synthesis from membrane lipids to storage lipids. OTI membranes were also constitutively less unsaturated than those of SH at both temperatures, consistent with a membrane already suited to warmer water that needs less remodeling. Our data show that two isolates of the same species, originating from different thermal environments, respond to elevated temperature through distinct transcriptomic and lipidomic programs. This suggests that the tropical OTI isolate is adapted to higher temperatures and demonstrates how reef-associated algae respond to rising ocean temperatures.

evolutionary biology↗

bioRxiv2026

Characterization of starch metabolism pathways in dinoflagellates, chromerids and apicomplexans highlights the presence of a starch accumulating symbiont in their common ancestor

Unlike most other heterotrophic protist lineages which synthesize glycogen, alveolates accumulate -glucan storage polysaccharides in the form of starch. Within Alveolata, ciliates do so by using a simple pathway analogous to that used for glycogen metabolism in eukaryotes. However, Myzozoa have evolved five additional enzymatic steps which are common to Dinoflagellata, Chromerids and Apicomplexa. Moreover, dinoflagellates have acquired seven additional enzymes that distinguish them from the Chromerids-Apicompexa lineages, while chromerids possess only a single enzyme not found in dinoflagellates. Such modifications are not found in other eukaryotic lineages save for those resulting directly from primary or secondary plastid endosymbiosis. The many differences affecting the starch pathway of Myzozoa can be explained by a single secondary or tertiary plastid endosymbiosis of a starch-containing alga followed by distinct compartmentalisation outcomes of starch metabolism in Dinoflagellata relative to chromerids and Apicomplexa.

evolutionary biology↗

bioRxiv2026

Crystalline guanine packed within vacuoles serves as nitrogen store in Chromera velia

Nitrogen is an important element for all living organisms. Photoautotrophic organisms need to assimilate nitrogen from the environment, therefore changes in nitrogen availability have a strong influence on their growth and metabolism. Many microalgae have been known to contain crystalline inclusions, and recently, it has been shown that many of these consist of purines like guanine and thus must be linked to the cellular nitrogen metabolisms. The alveolate alga Chromera velia contains such guanine crystals, and during its lifecycle, the alga is thought to be subjected to strong changes in external nitrogen availability. Here, we investigated the formation or decline of crystalline guanine in dependence of the availability of inorganic nitrogen in the growth medium. Cells were examined using polarised light microscopy, Raman micro-spectroscopy, chromatography (HPLC), transmission and scanning electron microscopy. The cellular guanine crystal content decreased during nitrogen starvation and increased upon transfer of the cells back to standard growth medium containing nitrate. Raman micro-spectroscopy showed that the crystals were composed of anhydrous guanine in beta-polytype. They appear in unspecific positions throughout the cell, and staining with the green dye Lysotracker DND-26 suggests that they are within vacuoles. Stacks of crystals could be observed in cells via freeze fracture and freeze etching electron microscopy, which unambiguously showed a membrane around the crystal aggregates, in a similar arrangement as has been shown for guanine storage vacuoles (GSV) in Chlamydomonas reinhardtii. We developed a method to isolate the guanine crystals from whole cells, and were able to obtain crystals which retained their flat, plate-like structure, matching the electron microscopic observations from whole cells. The isolated crystals were shown to consist of nitrogen rich compounds via energy-dispersive X-ray (EDX) analysis, and Raman micro-spectroscopy confirmed that they consist of guanine.

cell biology↗

bioRxiv2024

Dynamic relocalization and divergent expression of a major facilitator carrier subfamily in diatoms

Eukaryotic organisms, including microbial members such as protists and green algae, utilise suites of transporter proteins to move essential metabolites across cell organelle membranes. Amongst these different transporter families, the MCF (Mitochondrial Carrier Family) is one of the most diverse, encompassing essential NAD+ and ADP/ ATP translocators, as well as amino acid, sugar and cofactor transporters. They are typically associated with the mitochondrial inner membrane but some display more dynamic localization. Here, we perform a brief census of MCF domains in the genome of the model diatom alga Phaeodactylum tricornutum, identifying a new family of three proteins (termed here and elsewhere "MCFc") with strong internal sequence conservation but limited similarity to other MCF proteins. Considering both phylogenetic data and experimental localization, we posit that MCFc is widespread across algae with complex red chloroplasts alongside some primary green algae, and contains multiple sub-families targeted to diatom mitochondria, plastids, and endomembranes. Finally, using data from Tara Oceans, we identify putative roles for MCFc in diatom cells, including a probable association of the plastid-targeted Phatr3_J46742 sub-family in cellular nitrate assimilation. Our data provide insights into the evolutionary diversification of the membrane transport mechanisms associated with diatoms and other eukaryotic algae.

cell biology↗

bioRxiv2022

Paradigm shift in eukaryotic biocrystallization

Despite the widespread occurrence of crystalline inclusions in unicellular eukaryotes, scant attention has been paid to their composition, functions, and evolutionary origins, assuming just their inorganic contents. The advent of Raman microscopy, still scarcely used for biological samples, allowed chemical characterization of cellular inclusions in vivo. Using this method, herein we provide a substantial revision of the cellular crystalline inclusions across the broad diversity of eukaryotes examining all major supergroups. Surprisingly, here we show that 80 % of these crystalline inclusions contain purines, mostly anhydrous guanine (62 %), guanine monohydrate (2 %), uric acid (12 %) and xanthine (4 %). Hence, our findings indicate that purine biocrystallization is a very general and an ancestral eukaryotic process operating by an as-yet-unknown mechanism. Purine crystalline inclusions are high-capacity and rapid-turnover reserves of nitrogen of a great metabolic importance, as well as optically active elements, e.g., present in the light sensing eyespots of flagellates, possessing even more hypothetical functions. Thus, we anticipate our work to be a starting point for more in-depth studies of this phenomenon on the detailed level spanning from cell biology to global ecology, with further potential applications in biotechnologies, bio-optics or in human medicine.

microbiology↗

bioRxiv2021

Phylogenetic profiling suggests early origin of the core subunits of Polycomb Repressive Complex 2 (PRC2)

Polycomb Repressive Complex 2 (PRC2) is involved in establishing transcriptionally silent chromatin states through its ability to methylate lysine 27 of histone H3 by the catalytic subunit Enhancer of zeste [E(z)]. Polycomb group (PcG) proteins play a crucial role in the maintenance of cell identity and in developmental regulation. Previously, the diversity of PRC2 subunits within some eukaryotic lineages has been reported and its presence in early eukaryotic evolution has been hypothesized. So far however, systematic survey of the presence of PRC2 subunits in species of all eukaryotic lineages is missing. Here, we report the diversity of PRC2 core subunit proteins in different eukaryotic supergroups with emphasis on the early-diverged lineages and explore the molecular evolution of PRC2 subunits by phylogenetics. In detail, we investigate the SET-domain protein sequences and their evolution across the four domains of life and particularly focus on the structural diversity of the SET-domain subfamily containing E(z), the catalytic subunit of PRC2. We show that PRC2 subunits are already present in early eukaryotic lineages, strengthening the support for PRC2 emergence prior to diversification of eukaryotes. We identify a common presence of E(z) and ESC, suggesting that Su(z)12 may have emerged later and/or may be dispensable from the evolutionarily conserved functional core of PRC2. Furthermore, our results broaden our understanding of the E(z) evolution within the SET-domain protein family, suggesting possibilities of function evolution. Through this, we shed light on a possible emerging point of the PRC2 and the evolution of its function in eukaryotes.

evolutionary biology↗

bioRxiv2019

Phytotransferrin endocytosis mediates a direct cell surface-to-chloroplast iron trafficking axis in marine diatoms

Iron is a biochemically critical metal cofactor in enzymes involved in photosynthesis, cellular respiration, nitrate assimilation, nitrogen fixation, and reactive oxygen species defense. Marine microeukaryotes have evolved a phytotransferrin-based iron uptake system to cope with iron scarcity, a major factor limiting primary productivity in the global ocean. Diatom phytotransferrin is endocytosed, however proteins downstream of this environmentally ubiquitous iron receptor are unknown. We applied engineered ascorbate peroxidase APEX2-based subcellular proteomics to catalog proximal proteins of phytotransferrin in the model marine diatom Phaeodactylum tricornutum. Proteins encoded by poorly characterized iron-sensitive genes were identified including three that are expressed from a chromosomal gene cluster. Two of them showed unambiguous colocalization with phytotransferrin adjacent to the chloroplast. Further phylogenetic, domain, and biochemical analyses suggest their involvement in intracellular iron processing. Proximity proteomics holds enormous potential to glean new insights into iron acquisition pathways and beyond in these evolutionarily, ecologically, and biotechnologically important microalgae.

cell biology↗

bioRxiv2019

An unprecedented combination of metabolic pathways in the cryptic plastid of a non-photosynthetic euglenophyte

Most secondarily non-photosynthetic eukaryotes have retained residual plastids whose physiological role is often still unknown. One such example is Euglena longa, a close non-photosynthetic relative of Euglena gracilis harbouring a plastid organelle of enigmatic function. By mining transcriptome data from E. longa we finally provide an overview of metabolic processes localized to its elusive plastid. The organelle plays no role in biosynthesis of isoprenoid precursors and fatty acids, and has a very limited repertoire of pathways concerning nitrogen-containing metabolites. In contrast, the synthesis of phospholipids and glycolipids has been preserved, curiously with the last step of sulfoquinovosyldiacylglycerol synthesis being catalysed by the SqdX form of the enzyme so far known only from bacteria. Notably, we show that the E. longa plastid synthesizes tocopherols and a phylloquinone derivative, the first such report for non-photosynthetic plastids studied so far. The most striking attribute of the organelle is the presence of a linearized Calvin-Benson (CB) pathway including RuBisCO yet lacking the gluconeogenetic part of the standard cycle, together with ferredoxin-NADP+ reductase (FNR) and the ferredoxin/thioredoxin systems. We hypothesize that FNR passes electrons to the ferredoxin/thioredoxin systems from NADPH to activate the linear CB pathway in response to the redox status of the E. longa cell. In effect, the pathway may function as a redox valve bypassing the glycolytic oxidation of glyceraldehyde-3-phosphate to 3-phosphoglycerate. Altogether, the E. longa plastid defines a new class of relic plastids that is drastically different from the best studied organelle of this category, the apicoplast. ImportanceColourless plastids incapable of photosynthesis evolved in many plant and algal groups, but what functions they perform is still unknown in many cases. Here we study the elusive plastid of Euglena longa, a non-photosynthetic cousin of the familiar green flagellate Euglena gracilis. We document an unprecedented combination of metabolic functions that the E. longa plastid exhibits in comparison with previously characterized non-photosynthetic plastids. For example, and truly surprisingly, it has retained the synthesis of tocopherols (vitamin E) and a phylloquinone (vitamin K) derivative. In addition, we offer a possible solution of the long-standing conundrum of the presence of the CO2-fixing enzyme RuBisCO in E. longa. Our work provides a detailed account on a unique variant of relic plastids, the first among non-photosynthetic plastids that evolved by secondary endosymbiosis from a green algal ancestor, and suggests that it has persisted for reasons not previously considered in relation to non-photosynthetic plastids.

evolutionary biology↗

bioRxiv2019

Subcellular compartments interplay for carbon and nitrogen allocation in Chromera velia and Vitrella brassicaformis

Endosymbioses necessitate functional cooperation of cellular compartments to avoid pathway redundancy and streamline the control of biological processes. To gain insight into the metabolic compartmentation in chromerids, phototrophic relatives to apicomplexan parasites, we prepared a reference set of proteins probably localized to mitochondria, cytosol and the plastid, taking advantage of available genomic and transcriptomic data. Training of prediction algorithms with the reference set now allows a genome-wide analysis of protein localization in C. velia and V. brassicaformis. We confirm that the chromerid plastids house enzymatic pathways needed for their maintenance and photosynthetic activity, but for carbon and nitrogen allocation, metabolite exchange is necessary with the cytosol and mitochondria. This indeed suggests that the regulatory mechanisms operate in the cytosol to control carbon metabolism based on the availability of both light and nutrients. We discuss that this arrangement is largely shared with apicomplexans and dinoflagellates, possibly stemming from a common ancestral metabolic architecture, and supports the mixotrophy of the chromerid algae.

genomics↗

bioRxiv2018

Peculiar features of the plastids of the colourless alga Euglena longa and photosynthetic euglenophytes unveiled by transcriptome analyses

Background: Euglenophytes are an interesting algal group that emerged within the ancestrally plastid-lacking Euglenozoa phylum by acquiring a plastid from a green algal donor. However, the knowledge of euglenophyte plastid biology and evolution is highly incomplete, partly because euglenophytes have so far been little studied on a genome- and transcriptome-wide scale. Transcriptome data from only a single species, Euglena gracilis, have been exploited to functional insights, but aspects of the plastid biology have been largely neglected.\n\nResults: To expand the resources for studying euglenophyte biology and to improve our knowledge of the euglenophyte plastid function and evolution, we sequenced and analysed the transcriptome of the non-photosynthetic species Euglena longa. The transcriptomic data confirmed the absence of genes for the photosynthetic machinery in this species, but provided a number of candidate plastid-localized proteins bearing the same type of N-terminal bipartite topogenic signals (BTSs) as known from the photosynthetic species E. gracilis. Further comparative analyses using transcriptome assemblies available for E. gracilis and two additional photosynthetic euglenophytes of the genus Eutreptiella enabled us to unveil several salient aspects of the basic plastid infrastructure in euglenophytes. First, a number of plastidial proteins seem to reach the organelle as C-terminal translational fusions with other BTS-bearing proteins. Second, the conventional eubacteria-derived plastidial ribosomal protein L24 is missing and seems to have been replaced by very different homologs of the archaeo-eukaryotic origin. Third, no homologs of any key component of the TOC/TIC system (translocon of the outer/inner chloroplast membrane) and the plastid division apparatus are discernible in euglenophytes, and the machinery for intraplastidial protein targeting has been simplified by the loss of the cpSRP/cpFtsY system and the SEC2 translocon. Lastly, euglenophytes proved to encode a plastid-targeted homolog of the termination factor Rho horizontally acquired from a Lambdaproteobacteria-related donor, suggesting an unprecedented modification of the transcription mechanism in their plastid.\n\nConclusions: Our study suggests that the euglenophyte plastid has been substantially remodelled comparted to its green algal progenitor by both loss of original and acquisition of novel molecular components, making it a particularly interesting subject for further studies.

evolutionary biology↗