Biology subjects

Oliferenko, S.

Publications and source records attributed to Oliferenko, S..

12 recordsLinked to original sources

bioRxiv2026

Dynamics of phosphofructokinase condensation are regulated by metabolic and redox cues

Condensation of phosphofructokinase, the rate-limiting enzyme of glycolysis, into granules has been observed across species and in various stress conditions. However, it remains unclear what mechanisms govern this process. Here, we show that the two subunits of yeast phosphofructokinase, Pfk1 and Pfk2, assemble into granules even in the absence of exogenous stress, challenging the notion that PFK condensation in yeast is restricted to quiescent or stressed cells. While phosphofructokinase granules are predominant in replicatively aged cells, they are independent of cell division and can form before or after cells cease dividing. We further demonstrate that both subunits can co-localise to the same granules and that Pfk2 requires the disordered N-terminus of Pfk1 for assembly. Strikingly, phosphofructokinase granules are largely absent in cells engaged in respiration or lacking respiratory capacity, but their formation is strongly induced during the metabolic transition from fermentation to respiration. This suggests that phosphofructokinase condensation is tightly linked to the metabolic strategy of the cell. Moreover, we find that reactive oxygen species signaling, mediated by superoxide dismutase 1 (Sod1), modulates phosphofructokinase granule formation, as cells deficient in Sod1 exhibit impaired granule assembly. Overall, our results indicate that phosphofructokinase condensation is a dynamic process regulated by metabolic and redox cues.

cell biology↗

bioRxiv2025

Adaptation of eukaryotic membrane homeostasis to species-specific cellular lipid landscapes

The physicochemical properties of biological membranes must be maintained within a range compatible with cellular physiology. In the face of external perturbations, membrane lipid homeostasis mechanisms sense and control membrane features. How such mechanisms evolve to function in organisms with different cellular lipid make-up is unknown. Here, we address this fundamental question by exploiting the natural divergence in membrane lipid composition between the related fission yeasts S. pombe and S. japonicus. Using lipidomics and transcriptomics, we show that the activity of the membrane-bound transcriptional activator Mga2, which regulates the {Delta}-9 desaturase Ole1 expression, is set to sense distinct levels of membrane unsaturation in the two species. Through retro-engineering and physiological experiments, we identify an evolutionary divergent but functionally constrained element within the juxtamembrane region of Mga2, which fine-tunes its performance to species-specific lipid composition. Our experiments indicate that high baseline expression of ole1, set by cis-regulatory elements in its upstream non-coding region, has redefined the dynamic range of Mga2 activation in S. pombe, supporting high lipidome unsaturation. Our work explores an "experiment of nature" to highlight the broad principles underlying the organisation and evolution of membrane homeostasis, which should be applicable to other genetic networks supporting cellular homeostatic processes.

cell biology↗

bioRxiv2024

Horizontal gene transfer-initiated reorganization of lipid metabolism drives lifestyle innovation in a eukaryote

Horizontal gene transfer is a source of metabolic innovation and adaptation to new environments. Yet, how horizontally transferred metabolic functionalities are integrated into host cell biology remains an open question. Here, we use the fission yeast Schizosaccharomyces japonicus to probe how eukaryotic lipid metabolism is rewired in response to the acquisition of a horizontally transferred squalene-hopene cyclase Shc1. We show that Shc1-dependent production of hopanoids, the structural mimics of eukaryotic sterols, allows S. japonicus to thrive in anoxia, where sterol biosynthesis is not possible. We further demonstrate that glycerophospholipid fatty acyl asymmetry, prevalent in S. japonicus, is crucial for accommodating both sterols and hopanoids in membranes, and explain how Shc1 functions alongside the native sterol biosynthetic pathway to support membrane properties. Through engineering experiments in the sister species S. pombe, which naturally lacks Shc1, we show that the acquisition of Shc1 may entail new physiological traits; however, to maximize Shc1 performance, sterol biosynthesis must be dampened. Our work sheds new light on the mechanisms underlying cellular integration of horizontally transferred genes in eukaryotes and provides broader insights into the evolution of membrane organization and function.

cell biology↗

bioRxiv2023

Schizosaccharomyces versatilis represents a distinct evolutionary lineage.

The fission yeast species Schizosaccharomyces japonicus is currently divided into two varieties - S. japonicus var. japonicus and S. japonicus var. versatilis. Here we examine the var. versatilis isolate CBS5679. The CBS5679 genome shows 88% coding sequence identity to the reference genome of S. japonicus var. japonicus at the coding sequence level, with phylogenetic analyses suggesting that it has split from the S. japonicus lineage 25 million years ago. The CBS5679 genome contains a reciprocal translocation between chromosomes 1 and 2, together with several large inversions. The products of genes linked to the major translocation are associated with "metabolism" and "cellular assembly" ontology terms. We further show that CBS5679 does not generate viable progeny with the reference strain of S. japonicus. Although CBS5679 shares closer similarity to the "type" strain of var. versatilis as compared to S. japonicus, it is not identical to the type strain, suggesting population structure within var. versatilis. We recommend that the taxonomic status of S. japonicus var. versatilis is raised, with it being treated as a separate species, Schizosaccharomyces versatilis. Take-awayO_LIThe taxonomic status of Schizosaccharomyces versatilis is addressed. C_LIO_LIS. versatilis diverged from S. japonicus around 25 million years ago. C_LIO_LIS. versatilis does not produce viable progeny in crosses with S. japonicus. C_LIO_LIS. versatilis has a reciprocal translocation between chromosomes 1 and 2. C_LIO_LIThe Gene Ontology terms for genes in the translocations are enriched for terms connected to "metabolism" and "cellular assembly". C_LI

evolutionary biology↗

bioRxiv2023

Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features

Schizosaccharomyces japonicus belongs to the single-genus class Schizosaccharomycetes, otherwise known as fission yeasts. As part of a composite model system with its widely studied S. pombe sister species, S. japonicus has provided critical insights into the workings and the evolution of cell biological mechanisms. Furthermore, its divergent biology makes S. japonicus a valuable model organism in its own right. However, the currently available short-read genome assembly contains gaps and has been unable to resolve centromeres and other repeat-rich chromosomal regions. Here we present a telomere-to-telomere long-read genome assembly of the S japonicus genome. This includes the three megabase-length chromosomes, with centromeres hundreds of kilobases long, rich in 5S ribosomal RNAs, transfer RNAs, long terminal repeats, and short repeats. We identify a gene-sparse region on chromosome 2 that resembles a 331 kb centromeric duplication. We revise the genome size of S. japonicus to at least 16.6 Mb and possibly up to 18.12 Mb, at least 30% larger than previous estimates. Our whole genome assembly will support the growing S. japonicus research community and facilitate research in new directions, including centromere and DNA repeat evolution, and yeast comparative genomics. Take-awayO_LIA telomere-to-telomere genome assembly of the fission yeast S. japonicus C_LIO_LIChromosome 2 harbours a previously unknown second centromere-like region C_LIO_LIThe estimated genome size of S. japonicus may be up to 18.12 Mb C_LI

genomics↗

bioRxiv2023

Peroxisomal compartmentalization of amino acid biosynthesis reactions imposes an upper limit on compartment size

Cellular metabolism relies on just a few redox cofactors. Selective compartmentalization may prevent competition between metabolic reactions requiring the same cofactor. Is such compartmentalization necessary for optimal cell function? Is there an optimal compartment size? Here we probe these fundamental questions using peroxisomal compartmentalization of the last steps of lysine and histidine biosynthesis in the fission yeast Schizosaccharomyces japonicus. We show that compartmentalization of these NAD+ dependent reactions together with a dedicated NADH/NAD+ recycling enzyme supports optimal growth when an increased demand for anabolic reactions taxes cellular redox balance. In turn, compartmentalization constrains the size of individual organelles, with larger peroxisomes accumulating all the required enzymes but unable to support both biosynthetic reactions at the same time. We propose that compartmentalized biosynthetic reactions are sensitive to the size of the compartment, likely due to scaling-dependent changes within the system, such as enzyme packing density.

cell biology↗

bioRxiv2022

Optimization of energy production and central carbon metabolism in a non-respiring eukaryote

Most eukaryotes respire oxygen, using it to generate biomass and energy. Yet, a few organisms lost the capacity to respire. Understanding how they manage biomass and energy production may illuminate the critical points at which respiration feeds into central carbon metabolism and explain possible routes to its optimization. Here we use two related fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces japonicus, as a comparative model system. We show that although S. japonicus does not respire oxygen, unlike S. pombe, it is capable of efficient NADH oxidation, amino acid synthesis and ATP generation. We probe possible optimization strategies using stable isotope tracing metabolomics, mass isotopologue distribution analysis, genetics, and physiological experiments. S. japonicus appears to have optimized cytosolic NADH oxidation via glycerol-3-phosphate synthesis. It runs a fully bifurcated TCA cycle, supporting higher amino acid production. Finally, it uses the pentose phosphate pathway both to support faster biomass generation and as a shunt to optimize glycolytic flux, thus producing more ATP than the respiro-fermenting S. pombe. By comparing two related organisms with vastly different metabolic strategies, our work highlights the versatility and plasticity of central carbon metabolism in eukaryotes, illuminating critical adaptations supporting the preferential use of glycolysis over oxidative phosphorylation.

cell biology↗

bioRxiv2022

Diacylglycerol consumption at the inner nuclear membrane fuels nuclear envelope expansion required for closed mitosis

Nuclear envelope (NE) expansion must be controlled to maintain nuclear shape and function. The nuclear membrane expands massively during closed mitosis, enabling chromosome segregation within an intact NE. Phosphatidic acid (PA) and diacylglycerol (DG) can both serve as biosynthetic precursors for membrane lipid synthesis. How they are regulated in time and space and what are the implications of changes in their flux for mitotic fidelity is largely unknown. Using genetically encoded PA and DG probes, we show that DG is depleted from the inner nuclear membrane during mitosis in the fission yeast Schizosaccharomyces pombe, but PA does not accumulate, indicating that it is rerouted to membrane synthesis. We demonstrate that DG-to-PA conversion catalysed by the diacylglycerol kinase Dgk1 and direct glycerophospholipid synthesis from DG by diacylglycerol cholinephosphotransferase / ethanolaminephosphotransferase Ept1 reinforce NE expansion. We conclude that DG consumption through both de novo and the Kennedy pathways fuels a spike in glycerophospholipid biosynthesis, controlling NE expansion, and ultimately, mitotic fidelity.

cell biology↗

bioRxiv2022

mNeonGreen-tagged fusion proteins and nanobodies reveal localization of tropomyosin to patches, cables, and contractile actomyosin rings in live yeast cells

Tropomyosins are structurally conserved -helical coiled-coil dimeric proteins that bind along the length of filamentous actin (F-actin) in fungi and animals. Tropomyosins play essential roles in the stability of actin filaments in non-muscle cells and are essential for calcium regulation of myosin II contractility in the muscle. Despite the crucial role of tropomyosin in actin cytoskeletal regulation, in vivo investigations of tropomyosin are limited, mainly due to the suboptimal live cell imaging tools currently available in many organisms. Here, we report mNeon-Green (mNG) tagged tropomyosin, with native promoter and linker length configuration, that clearly reports tropomyosin localization and dynamics in Schizosaccharomyces pombe (Cdc8), Schizosaccharomyces japonicus (Cdc8), and Saccharomyces cerevisiae (Tpm1 and Tpm2), in vivo and in isolated S. pombe cell division apparatuses. We extended this approach to also visualize the mammalian TPM2 isoform. Finally, we generated a camelid-nanobody against S. pombe Cdc8, which mimics the localization of mNG-Cdc8 in vivo without significantly influencing cell growth and dynamics of actin cytoskeleton. Using these tools, we report the presence of tropomyosin in previously unappreciated patch-like structures in fission and budding yeasts, show flow of tropomyosin (F-actin) cables to the cytokinetic actomyosin ring, and identify rearrangements of the actin cytoskeleton during mating. These powerful tools and strategies will aid better analyses of tropomyosin and actin cables in vivo.

cell biology↗

bioRxiv2021

JaponicusDB: Rapid deployment of a model organism database for an emerging model species

The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realise the full potential of studying a newly emerging model species, and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge.

bioinformatics↗

bioRxiv2019

Delineating the rules for structural adaptation of membrane-associated proteins to evolutionary changes in membrane lipidome

Membrane function is fundamental to life. Each species explores membrane lipid diversity within a genetically predefined range of possibilities. How membrane lipid composition in turn defines the functional space available for evolution of membrane-centered processes remains largely unknown. We address this fundamental question using related fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus. We show that unlike S. pombe that generates membranes where both glycerophospholipid acyl tails are predominantly 16-18 carbons long, S. japonicus synthesizes unusual asymmetrical glycerophospholipids where the tails differ in length by 6-8 carbons. This results in stiffer bilayers with distinct lipid packing properties. Retroengineered S. pombe synthesizing the S. japonicus-type phospholipids exhibits unfolded protein response and downregulates secretion. Importantly, our protein sequence comparisons and domain swap experiments indicate that transmembrane helices co-evolve with membranes, suggesting that, on the evolutionary scale, changes in membrane lipid composition may necessitate extensive adaptation of the membrane-associated proteome.

cell biology↗

bioRxiv2019

ESCRT-III/Vps4 controls heterochromatin-nuclear envelope attachments

In eukaryotes chromosomes are compartmentalized within the nucleus delimited by the double membrane of the nuclear envelope (NE). Defects in the function and structure of the NE are linked to disease1,2. During interphase, the NE organizes the genome and regulates its expression3. As cells enter mitosis, chromosomes are released from the NE, which is then remodelled to form the daughter nuclei at mitotic exit4. Interactions between the NE and chromatin underpinning both interphase and post-mitotic NE functions are executed by inner nuclear membrane (INM) proteins such as members of the evolutionarily conserved chromatin-binding LEM-domain family5-8. How chromatin tethering by these transmembrane proteins is controlled in interphase and if such a regulation contributes to subsequent NE dynamics in mitosis remains unclear. Here we probe these fundamental questions using an emerging model organism, the fission yeast Schizosaccharomyces japonicus, which breaks and reforms the NE during mitosis9,10. We show that attachments between heterochromatin and the transmembrane Lem2-Nur1 complex are continuously remodelled in interphase by the ESCRT-III/AAA-ATPase Vps4 machinery. ESCRT-III/Vps4 mediates the release of Lem2-Nur1 from heterochromatin as a prerequisite for the timely progression through mitosis. Failure in this process leads to persistent association of chromosomes with the INM, which prevents Lem2-Nur1 from re-localizing to the sites of NE sealing around the mitotic spindle and severely delays re-establishment of nucleocytoplasmic compartmentalization. Our work establishes the INM transmembrane Lem2-Nur1 complex as a substrate for ESCRT-III/Vps4 to couple dynamic tethering of chromosomes to the INM with the establishment of nuclear compartmentalization.

cell biology↗