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Article ; Online: Peroxisomal compartmentalization of amino acid biosynthesis reactions imposes an upper limit on compartment size.

Gu, Ying / Alam, Sara / Oliferenko, Snezhana

2023 Volume 14, Issue 1, Page(s) 5544

Abstract: 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 ... ...

Abstract	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
MeSH term(s)	NAD ; Bandages ; Lysine ; Paclitaxel ; Peroxisomes
Chemical Substances	NAD (0U46U6E8UK) ; Lysine (K3Z4F929H6) ; Paclitaxel (P88XT4IS4D)
Language	English
Publishing date	2023-09-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-41347-x
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Article ; Online: Understanding eukaryotic chromosome segregation from a comparative biology perspective.

Oliferenko, Snezhana

Journal of cell science

2018 Volume 131, Issue 14

Abstract: A long-appreciated variation in fundamental cell biological processes between different species is becoming increasingly tractable due to recent breakthroughs in whole-genome analyses and genome editing techniques. However, the bulk of our mechanistic ... ...

Abstract	A long-appreciated variation in fundamental cell biological processes between different species is becoming increasingly tractable due to recent breakthroughs in whole-genome analyses and genome editing techniques. However, the bulk of our mechanistic understanding in cell biology continues to come from just a few well-established models. In this Review, I use the highly diverse strategies of chromosome segregation in eukaryotes as an instrument for a more general discussion on phenotypic variation, possible rules underlying its emergence and its utility in understanding conserved functional relationships underlying this process. Such a comparative approach, supported by modern molecular biology tools, might provide a wider, holistic view of biology that is difficult to achieve when concentrating on a single experimental system.
MeSH term(s)	Animals ; Biology ; Chromosome Segregation ; Chromosomes/genetics ; Eukaryota/genetics ; Genome ; Humans ; Mitosis
Language	English
Publishing date	2018-07-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.203653
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Article ; Online: Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features.

Etherington, Graham J / Wu, Pei-Shang / Oliferenko, Snezhana / Uhlmann, Frank / Nieduszynski, Conrad A

Yeast (Chichester, England)

2024 Volume 41, Issue 3, Page(s) 73–86

Abstract: 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 ... ...

Abstract	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 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 RNA genes, transfer RNA genes, 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.
MeSH term(s)	Schizosaccharomyces/genetics ; Telomere/genetics ; Centromere/genetics
Language	English
Publishing date	2024-03-07
Publishing country	England
Document type	Journal Article
ZDB-ID	632636-5
ISSN	1097-0061 ; 0749-503X
ISSN (online)	1097-0061
ISSN	0749-503X
DOI	10.1002/yea.3912
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Article ; Online: Diacylglycerol at the inner nuclear membrane fuels nuclear envelope expansion in closed mitosis.

Foo, Sherman / Cazenave-Gassiot, Amaury / Wenk, Markus R / Oliferenko, Snezhana

Journal of cell science

2023 Volume 136, Issue 3

Abstract: 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) ... ...

Abstract	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 the implications are of changes in their flux for mitotic fidelity are 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 catalyzed by the diacylglycerol kinase Dgk1 (also known as Ptp4) and direct glycerophospholipid synthesis from DG by diacylglycerol cholinephosphotransferase/ethanolaminephosphotransferase Ept1 reinforce NE expansion. We conclude that DG consumption through both the de novo pathway and the Kennedy pathway fuels a spike in glycerophospholipid biosynthesis, controlling NE expansion and, ultimately, mitotic fidelity.
MeSH term(s)	Nuclear Envelope/metabolism ; Diglycerides/metabolism ; Mitosis ; Cell Nucleus Division ; Schizosaccharomyces/metabolism ; Glycerophospholipids/metabolism
Chemical Substances	Diglycerides ; Glycerophospholipids
Language	English
Publishing date	2023-02-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.260568
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Article ; Online: Optimization of energy production and central carbon metabolism in a non-respiring eukaryote.

Alam, Sara / Gu, Ying / Reichert, Polina / Bähler, Jürg / Oliferenko, Snezhana

Current biology : CB

2023 Volume 33, Issue 11, Page(s) 2175–2186.e5

Abstract: Most eukaryotes respire oxygen, using it to generate biomass and energy. However, a few organisms have lost the capacity to respire. Understanding how they manage biomass and energy production may illuminate the critical points at which respiration feeds ...

Abstract	Most eukaryotes respire oxygen, using it to generate biomass and energy. However, a few organisms have 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 through the use of 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 pathway, sustaining amino acid production. Finally, we propose that it has optimized glycolysis to maintain high ATP/ADP ratio, in part by using the pentose phosphate pathway as a glycolytic shunt, reducing allosteric inhibition of glycolysis and supporting biomass generation. 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.
MeSH term(s)	Carbon/metabolism ; Eukaryota/metabolism ; NAD/metabolism ; Energy Metabolism ; Glycolysis ; Amino Acids/metabolism ; Adenosine Triphosphate/metabolism ; Oxygen
Chemical Substances	Carbon (7440-44-0) ; NAD (0U46U6E8UK) ; Amino Acids ; Adenosine Triphosphate (8L70Q75FXE) ; Oxygen (S88TT14065)
Language	English
Publishing date	2023-05-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2023.04.046
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Article ; Online: Cell Biology: An Open Solution for Closed Mitosis.

Mori, Risa / Oliferenko, Snezhana

Current biology : CB

2020 Volume 30, Issue 16, Page(s) R942–R944

Abstract: At the end of mitosis, cells must remodel their nuclear envelope to produce two identical daughter nuclei. Two new studies using Schizosaccharomyces pombe provide insight into how compartmentalized nuclear pore complex disassembly allows cells that ... ...

Abstract	At the end of mitosis, cells must remodel their nuclear envelope to produce two identical daughter nuclei. Two new studies using Schizosaccharomyces pombe provide insight into how compartmentalized nuclear pore complex disassembly allows cells that undergo closed mitosis to achieve nuclear division.
MeSH term(s)	Mitosis ; Nuclear Envelope ; Nuclear Pore ; Schizosaccharomyces/genetics ; Schizosaccharomyces pombe Proteins/genetics
Chemical Substances	Schizosaccharomyces pombe Proteins
Language	English
Publishing date	2020-08-18
Publishing country	England
Document type	Journal Article ; Comment
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2020.06.067
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Article ; Online: The principles of cellular geometry scaling.

Gu, Ying / Oliferenko, Snezhana

Current opinion in cell biology

2020 Volume 68, Page(s) 20–27

Abstract: Cellular dimensions profoundly influence cellular physiology. For unicellular organisms, this has direct bearing on their ecology and evolution. The morphology of a cell is governed by scaling rules. As it grows, the ratio of its surface area to volume ... ...

Abstract	Cellular dimensions profoundly influence cellular physiology. For unicellular organisms, this has direct bearing on their ecology and evolution. The morphology of a cell is governed by scaling rules. As it grows, the ratio of its surface area to volume is expected to decrease. Similarly, if environmental conditions force proliferating cells to settle on different size optima, cells of the same type may exhibit size-dependent variation in cellular processes. In fungi, algae and plants where cells are surrounded by a rigid wall, division at smaller size often produces immediate changes in geometry, decreasing cell fitness. Here, we discuss how cells interpret their size, buffer against changes in shape and, if necessary, scale their polarity to maintain optimal shape at different cell volumes.
MeSH term(s)	Animals ; Cell Division ; Cell Shape ; Cell Size ; Evolution, Molecular ; Fungi ; Gene Expression ; Humans ; Plant Cells ; Plants ; Prokaryotic Cells
Language	English
Publishing date	2020-09-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1026381-0
ISSN	1879-0410 ; 0955-0674
ISSN (online)	1879-0410
ISSN	0955-0674
DOI	10.1016/j.ceb.2020.08.013
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Article ; Online: Schizosaccharomyces versatilis represents a distinct evolutionary lineage of fission yeast.

Etherington, Graham J / Gil, Elisa Gomez / Haerty, Wilfried / Oliferenko, Snezhana / Nieduszynski, Conrad A

Yeast (Chichester, England)

2023 Volume 41, Issue 3, Page(s) 95–107

Abstract: 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% identity to ... ...

Abstract	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% 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.
MeSH term(s)	Schizosaccharomyces/genetics ; Phylogeny ; Biological Evolution
Language	English
Publishing date	2023-12-26
Publishing country	England
Document type	Journal Article
ZDB-ID	632636-5
ISSN	1097-0061 ; 0749-503X
ISSN (online)	1097-0061
ISSN	0749-503X
DOI	10.1002/yea.3919
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Article ; Online: JaponicusDB: rapid deployment of a model organism database for an emerging model species.

Rutherford, Kim M / Harris, Midori A / Oliferenko, Snezhana / Wood, Valerie

Genetics

2022 Volume 220, Issue 4

Abstract: 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- ... ...

Abstract	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 realize 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.
MeSH term(s)	Databases, Factual ; Schizosaccharomyces/genetics
Language	English
Publishing date	2022-03-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1093/genetics/iyab223
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Article ; Online: Cellular geometry scaling ensures robust division site positioning.

Gu, Ying / Oliferenko, Snezhana

Nature communications

2019 Volume 10, Issue 1, Page(s) 268

Abstract: Cells of a specific cell type may divide within a certain size range. Yet, functionally optimal cellular organization is typically maintained across different cell sizes, a phenomenon known as scaling. The mechanisms underlying scaling and its ... ...

Abstract	Cells of a specific cell type may divide within a certain size range. Yet, functionally optimal cellular organization is typically maintained across different cell sizes, a phenomenon known as scaling. The mechanisms underlying scaling and its physiological significance remain elusive. Here we approach this problem by interfering with scaling in the rod-shaped fission yeast Schizosaccharomyces japonicus that relies on cellular geometry cues to position the division site. We show that S. japonicus uses the Cdc42 polarity module to adjust its geometry to changes in the cell size. When scaling is prevented resulting in abnormal cellular length-to-width aspect ratio, cells exhibit severe division site placement defects. We further show that despite the generally accepted view, a similar scaling phenomenon can occur in the sister species, Schizosaccharomyces pombe. Our results demonstrate that scaling is required for normal cell function and delineate possible rules for cellular geometry maintenance in populations of proliferating cells.
MeSH term(s)	Cell Division/physiology ; Gene Expression Regulation, Fungal/physiology ; Schizosaccharomyces/cytology ; Schizosaccharomyces/physiology ; Schizosaccharomyces pombe Proteins/genetics ; Schizosaccharomyces pombe Proteins/metabolism
Chemical Substances	Schizosaccharomyces pombe Proteins
Language	English
Publishing date	2019-01-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-018-08218-2
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