Abstract
Biological timing is a fundamental aspect of life, facilitating efficient resource use and adaptation to environmental changes. In this study, we unveil robust temporal oscillations in phospholipid abundance as a function of the yeast metabolic cycle (YMC). These fluctuations, occurring throughout the cell division cycle, demonstrate a systematic segregation of various phospholipid species over time. Such segregation corresponds logically with their physical properties, generating entropic forces for membrane dynamics and biogenesis. Within the YMC, the temporal oscillations in phosphatidylethanolamine and phosphatidylcholine levels require biosynthesis from triacylglycerol as a crucial lipid reservoir, with phosphatidylinositol and phosphatidylserine synthesized primarily de novo. The orchestrated regulation of gene expression in biosynthesis pathways ensures precise temporal control of phospholipid dynamics, ultimately promoting metabolic efficiency.

This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$32.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout






Similar content being viewed by others
Data availability
All data supporting the findings of this study presented in this article are available within the article, Supplementary Information and source data. Source data are provided with this paper.
References
Van Meer, G., Voelker, D. R. & Feigenson, G. W. Membrane lipids: where they are and how they behave. Nat. Rev. Mol. Cell Biol. 9, 112–124 (2008).
Balla, T. Phosphoinositides: tiny lipids with giant impact on cell regulation. Physiol. Rev. 93, 1019–1137 (2013).
Harayama, T. & Riezman, H. Understanding the diversity of membrane lipid composition. Nat. Rev. Mol. Cell Biol. 19, 281–296 (2018).
Carman, G. M. & Han, G. S. Regulation of phospholipid synthesis in the yeast Saccharomyces cerevisiae. Annu. Rev. Biochem. 80, 859–883 (2011).
Henry, S. A., Kohlwein, S. D. & Carman, G. M. Metabolism and regulation of glycerolipids in the yeast Saccharomyces cerevisiae. Genetics 190, 317–349 (2012).
Zhang, Y. M. & Rock, C. O. Membrane lipid homeostasis in bacteria. Nat. Rev. Microbiol. 6, 222–233 (2008).
Janmey, P. A. & Kinnunen, P. K. Biophysical properties of lipids and dynamic membranes. Trends Cell Biol. 16, 538–546 (2006).
Di Paolo, G. & De Camilli, P. Phosphoinositides in cell regulation and membrane dynamics. Nature 443, 651–657 (2006).
Kutateladze, T. G. Translation of the phosphoinositide code by PI effectors. Nat. Chem. Biol. 6, 507–513 (2010).
Vítová, M. et al. The biosynthesis of phospholipids is linked to the cell cycle in a model eukaryote. Biochim. Biophys. Acta Mol. Cell. Biol. Lipids 1866, 158965 (2021).
Atilla-Gokcumen, G. E. et al. Dividing cells regulate their lipid composition and localization. Cell 156, 428–439 (2014).
Takhaveev, V. et al. Temporal segregation of biosynthetic processes is responsible for metabolic oscillations during the budding yeast cell cycle. Nat. Metab. 5, 294–313 (2023).
Blank, H. M. et al. Abundances of transcripts, proteins, and metabolites in the cell cycle of budding yeast reveal coordinate control of lipid metabolism. Mol. Biol. Cell 31, 1069–1084 (2020).
Ye, C., Sutter, B. M., Wang, Y., Kuang, Z. & Tu, B. P. A metabolic function for phospholipid and histone methylation. Mol. Cell 66, 180–193.e188 (2017).
Zhu, Y. et al. Phospholipid biosynthesis modulates nucleotide metabolism and reductive capacity. Nat. Chem. Biol. 21, 35–46 (2025).
Villasmil, M. L., Gallo-Ebert, C., Liu, H. Y., Francisco, J. & Nickels, J. T. Jr. A link between very long chain fatty acid elongation and mating-specific yeast cell cycle arrest. Cell Cycle 16, 2192–2203 (2017).
Köberlin, M. S. et al. A fast-acting lipid checkpoint in G1 prevents mitotic defects. Nat. Commun. 15, 2441 (2024).
Blank, H. M., Griffith, W. P. & Polymenis, M. Targeting APEX2 to the mRNA encoding fatty acid synthase β in yeast identifies interacting proteins that control its abundance in the cell cycle. Mol. Biol. Cell 34, br20 (2023).
Blank, H. M. et al. Translational control of lipogenic enzymes in the cell cycle of synchronous, growing yeast cells. EMBO J. 36, 487–502 (2017).
Maitra, N., Hammer, S., Kjerfve, C., Bankaitis, V. A. & Polymenis, M. Translational control of lipogenesis links protein synthesis and phosphoinositide signaling with nuclear division in Saccharomyces cerevisiae. Genetics 220, iyab171 (2022).
Tu, B. P., Kudlicki, A., Rowicka, M. & McKnight, S. L. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 310, 1152–1158 (2005).
Cai, L., Sutter, B. M., Li, B. & Tu, B. P. Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes. Mol. Cell 42, 426–437 (2011).
Papagiannakis, A., Niebel, B., Wit, E. C. & Heinemann, M. Autonomous metabolic oscillations robustly gate the early and late cell cycle. Mol. Cell 65, 285–295 (2017).
Cheng, A. et al. A mitotic NADPH upsurge promotes chromosome segregation and tumour progression in aneuploid cancer cells. Nat. Metab. 5, 1141–1158 (2023).
Slavov, N. & Botstein, D. Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast. Mol. Biol. Cell 22, 1997–2009 (2011).
Tu, B. P. & McKnight, S. L. Metabolic cycles as an underlying basis of biological oscillations. Nat. Rev. Mol. Cell Biol. 7, 696–701 (2006).
Von Meyenburg, H. K. Energetics of the budding cycle of Saccharomyces cerevisiae during glucose limited aerobic growth. Arch. Mikrobiol. 66, 289–303 (1969).
Murray, D. B., Beckmann, M. & Kitano, H. Regulation of yeast oscillatory dynamics. Proc. Natl Acad. Sci. USA 104, 2241–2246 (2007).
Murray, D. B., Roller, S., Kuriyama, H. & Lloyd, D. Clock control of ultradian respiratory oscillation found during yeast continuous culture. J. Bacteriol. 183, 7253–7259 (2001).
Klevecz, R. R., Bolen, J., Forrest, G. & Murray, D. B. A genomewide oscillation in transcription gates DNA replication and cell cycle. Proc. Natl Acad. Sci. USA 101, 1200–1205 (2004).
Kuang, Z. et al. High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast. Nat. Struct. Mol. Biol. 21, 854–863 (2014).
Mellor, J. The molecular basis of metabolic cycles and their relationship to circadian rhythms. Nat. Struct. Mol. Biol. 23, 1035–1044 (2016).
Wang, G. Z. et al. Cycling transcriptional networks optimize energy utilization on a genome scale. Cell Rep. 13, 1868–1880 (2015).
Murray, D. B., Klevecz, R. R. & Lloyd, D. Generation and maintenance of synchrony in Saccharomyces cerevisiae continuous culture. Exp. Cell. Res. 287, 10–15 (2003).
Tu, B. P. et al. Cyclic changes in metabolic state during the life of a yeast cell. Proc. Natl Acad. Sci. USA 104, 16886–16891 (2007).
Yang, S., Xue, J. & Ye, C. Protocol for rapid and accurate quantification of phospholipids in yeast and mammalian systems using LC–MS. STAR Protoc. 3, 101769 (2022).
Bier, M., Bakker, B. M. & Westerhoff, H. V. How yeast cells synchronize their glycolytic oscillations: a perturbation analytic treatment. Biophys. J. 78, 1087–1093 (2000).
Tilcock, C. P., Cullis, P. R., Hope, M. J. & Gruner, S. M. Polymorphic phase behavior of unsaturated lysophosphatidylethanolamines: a 31P NMR and X-ray diffraction study. Biochemistry 25, 816–822 (1986).
Hsieh, W. C. et al. Glucose starvation induces a switch in the histone acetylome for activation of gluconeogenic and fat metabolism genes. Mol. Cell 82, 60–74 (2022).
McMaster, C. R. & Bell, R. M. Phosphatidylcholine biosynthesis in Saccharomyces cerevisiae. Regulatory insights from studies employing null and chimeric sn-1,2-diacylglycerol choline- and ethanolaminephosphotransferases. J. Biol. Chem. 269, 28010–28016 (1994).
Loewen, C. J. et al. Phospholipid metabolism regulated by a transcription factor sensing phosphatidic acid. Science 304, 1644–1647 (2004).
Hofbauer, H. F. et al. The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1. J. Cell Biol. 217, 3109–3126 (2018).
Ortega-Arzola, E., Higgins, P. M. & Cockell, C. S. The minimum energy required to build a cell. Sci. Rep. 14, 5267 (2024).
Casanovas, A. et al. Quantitative analysis of proteome and lipidome dynamics reveals functional regulation of global lipid metabolism. Chem. Biol. 22, 412–425 (2015).
Ernst, R., Ballweg, S. & Levental, I. Cellular mechanisms of physicochemical membrane homeostasis. Curr. Opin. Cell Biol. 53, 44–51 (2018).
Bloom, M., Evans, E. & Mouritsen, O. G. Physical properties of the fluid lipid-bilayer component of cell membranes: a perspective. Q. Rev. Biophys. 24, 293–397 (1991).
Bagatolli, L. A., Ipsen, J. H., Simonsen, A. C. & Mouritsen, O. G. An outlook on organization of lipids in membranes: searching for a realistic connection with the organization of biological membranes. Prog. Lipid Res. 49, 378–389 (2010).
Renne, M. F. & de Kroon, A. The role of phospholipid molecular species in determining the physical properties of yeast membranes. FEBS Lett. 592, 1330–1345 (2018).
Baumgart, T., Capraro, B. R., Zhu, C. & Das, S. L. Thermodynamics and mechanics of membrane curvature generation and sensing by proteins and lipids. Annu. Rev. Phys. Chem. 62, 483–506 (2011).
Boumann, H. A., Chin, P. T., Heck, A. J., De Kruijff, B. & De Kroon, A. I. The yeast phospholipid N-methyltransferases catalyzing the synthesis of phosphatidylcholine preferentially convert di-C16:1 substrates both in vivo and in vitro. J. Biol. Chem. 279, 40314–40319 (2004).
Boumann, H. A. et al. The two biosynthetic routes leading to phosphatidylcholine in yeast produce different sets of molecular species. Evidence for lipid remodeling. Biochemistry 42, 3054–3059 (2003).
Schink, K. O., Tan, K. W. & Stenmark, H. Phosphoinositides in Control of Membrane Dynamics. Annu. Rev. Cell Dev. Biol. 32, 143–171 (2016).
Posor, Y., Jang, W. & Haucke, V. Phosphoinositides as membrane organizers. Nat. Rev. Mol. Cell Biol. 23, 797–816 (2022).
Renne, M. F. et al. Molecular species selectivity of lipid transport creates a mitochondrial sink for di-unsaturated phospholipids. EMBO J. 41, e106837 (2022).
Bürgermeister, M., Birner-Grünberger, R., Heyn, M. & Daum, G. Contribution of different biosynthetic pathways to species selectivity of aminoglycerophospholipids assembled into mitochondrial membranes of the yeast Saccharomyces cerevisiae. Biochim. Biophys. Acta 1686, 148–160 (2004).
Carman, G. M. & Henry, S. A. Phospholipid biosynthesis in the yeast Saccharomyces cerevisiae and interrelationship with other metabolic processes. Prog. Lipid Res. 38, 361–399 (1999).
Van Dijken, J. P. et al. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzym. Microb. Technol. 26, 706–714 (2000).
Haider, A. et al. PCYT1A regulates phosphatidylcholine homeostasis from the inner nuclear membrane in response to membrane stored curvature elastic stress. Dev. Cell 45, 481–495 (2018).
Acknowledgements
We thank the technical support from the Core Facility of Life Sciences Institute, Zhejiang University. This work was supported by grants from the National Key Research and Development Program of China (2023YFA1801100 and 2024YFA1803000), the National Natural Science Foundation of China (32270816 and 92057102), Double Thousand Plan of Jiangxi Province (jxsq2023102239), the Fundamental Research Funds for the Central Universities (226-2024-00088), a research fund from Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, the startup fund from the Life Sciences Institute of Zhejiang University and the 1000 Talents Program for Young Scholars (to C.Y.) and the National Natural Science Foundation of China (32321002 to P.X.).
Author information
Authors and Affiliations
Contributions
C.Y. conceptualized the project, acquired funding and administered the project. S.Y. and C.Y. guided methodology development. S.Y., Y.W., S.H. and T.Z. conducted the investigation. S.Y. and Y.W. visualized the project. C.Y. and C.J. supervised the project. P.X. and C.Y. wrote the manuscript. All authors read, edited and approved the manuscript.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Peer review
Peer review information
Nature Chemical Biology thanks Rutilio Fratti, Mike Renne and the other, anonymous reviewer(s) for their contribution to the peer review of this work.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Extended data
Extended Data Fig. 1 Yeast budding rates during the YMC and fluctuating levels of PE, PC and PI throughout the cell budding cycle.
a, Percentage of budding cells throughout the YMC determined by microscopic counting of buds at indicated phases. b, The sine function used for curve-fitting the abundance dynamics in phospholipids throughout two consecutive cycles of the YMC. Ttrough is converted to fractional times in a budding cycle. c, Dynamic changes in PE, PC and PI levels throughout two YMCs, depicted with data points and fitting curves. d, Changes in PE/PC ratio over two YMCs. Shaded areas are used to highlight a budding cycle.
Extended Data Fig. 2 Significant fitting exhibits a bias towards abundant phospholipids.
Analysis of the correlation between species abundance and curve fitting significance. Data are represented as mean ± s.d. (n = 22 biologically independent samples).
Extended Data Fig. 3 RIL to quantify the turnover and synthesis of phospholipids.
a, Schematic of the TAG biosynthesis pathway with genes at respective steps highlighted in red. b, Heatmap depicting the oscillatory expression of genes involved in TAG biosynthesis across the YMC. The heatmap is generated using RNA-seq data previously published31. c, Relative abundance of indicated phospholipid classes with acyl chains, polar head groups and the glycerol backbone individually or combinatorially labeled with 13C and 12C after two rounds of doubling in the RIL experiment. Relative abundance was calculated by normalizing to the total amount of corresponding lipid classes with full 13C labeling before the RIL switch. d, Sine waves fitting of PE, PC, PI and PS abundance in the dga1Δlro1Δ mutant of the YMC, characterized by their acyl composition. Solid lines indicate fitting of statistical significance (P < 0.05), while dashed lines represent nonsignificant fitting. Statistical analyses were performed using a two-sided t-test in d. Shaded areas are used to highlight a budding cycle.
Extended Data Fig. 4 Oscillation in PI abundance and transcripts of genes involved in PI biosynthesis.
a, Temporal oscillations in the abundance of PI and the transcript levels of PI biosynthetic genes within a budding cycle. b, Oxygen consumption curves of WT and ino1Δ mutants with 1 mM myo-inositol.
Extended Data Fig. 5 Disruption of the Henry regulatory circuit shifts temporal oscillations in phospholipids.
a, Representative Opi1–GFP fluorescence images at different YMC phases. Data shown are representative of two independent experiments with similar results. b, Relative mRNA levels of phospholipid biosynthesis genes in WT and opi1Δ cells during the YMC. Data are presented as mean ± s.d. (n = 27 biologically independent samples). c, PE, PC, PI and PS abundance (% PL) in WT (n = 22 biologically independent samples) and opi1Δ cells (n = 26 biologically independent samples) across the YMC. Data are presented as mean ± s.d. d, Hierarchical clustering of phospholipids in opi1Δ cells across the YMC. Data normalized to total ion counts, log-transformed and clustered (Spearman rank). Sankey diagram shows phospholipid class distribution. e, Top, sine waves representing major phospholipid classes in the opi1Δ mutant. Solid lines indicate fitting of statistical significance (P < 0.05), while dashed lines represent nonsignificant fitting. Bottom, summary table of fitting parameters. Shaded areas are used to highlight a budding cycle. f,g, Comparison of PI (f) and PS (g) oscillations between WT and the opi1Δ mutant, showing differences in Ttrough and amplitude across their molecular species. Statistical analyses were performed using an unpaired t test in b and c. Statistical analyses were performed using a two-sided t test in e. Shaded areas are used to highlight a budding cycle.
Supplementary information
Supplementary Data 1–6
Supplementary Data 1: Source data for the curve fitting of WT, opi1Δ, opi1(Y127D) and dga1Δlro1Δ cells. Supplementary Data 2: Relative abundances of phospholipids in WT cells collected from two consecutive YMCs. Supplementary Data 3: Relative abundances of phospholipids in dga1Δlro1Δ cells collected from two consecutive YMCs. Supplementary Data 4: Relative abundances of phospholipids in opi1Δ cells collected from two consecutive YMCs. Supplementary Data 5: The information of strains, primers, and plasmids. Supplementary Data 6: Phospholipid-specific MRM settings.
Source data
Source Data Fig. 1
Statistical source data.
Source Data Fig. 2
Statistical source data.
Source Data Fig. 3
Statistical source data.
Source Data Fig. 4
Statistical source data.
Source Data Fig. 5
Statistical source data.
Source Data Fig. 6
Statistical source data.
Source Data Extended Data Fig. 1
Statistical source data.
Source Data Extended Data Fig. 2
Statistical source data.
Source Data Extended Data Fig. 3
Statistical source data.
Source Data Extended Data Fig. 4
Statistical source data.
Source Data Extended Data Fig. 5
Statistical source data.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Yang, S., Wang, Y., Huang, S. et al. Temporal oscillation of phospholipids promotes metabolic efficiency. Nat Chem Biol 21, 1599–1610 (2025). https://doi.org/10.1038/s41589-025-01885-5
Received:
Accepted:
Published:
Issue date:
DOI: https://doi.org/10.1038/s41589-025-01885-5