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Temporal oscillation of phospholipids promotes metabolic efficiency

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.

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Fig. 1: Phospholipids exhibit robust oscillations in abundance as a function of the YMC.
Fig. 2: The periodic pattern of phospholipid abundance varies depending on the head group and acyl composition.
Fig. 3: TAG abundance fluctuates in a burst-and-taper mode during the YMC.
Fig. 4: TAG fuels temporal oscillations in PE and PC production.
Fig. 5: Oscillatory transcriptional control of the PS–PE–PC metabolic axis sustains the YMC.
Fig. 6: Disruption of the Henry regulatory circuit shifts temporal oscillations in phospholipids, compromising competitive growth during the YMC.

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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.

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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.).

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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.

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Correspondence to Cunqi Ye.

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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.

Source data

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).

Source data

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.

Source data

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.

Source data

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.

Source data

Supplementary information

Reporting Summary

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

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Source Data Extended Data Fig. 1

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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

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