Regulation of transcription elongation anticipates alternative gene expression strategies across the cell cycle

PLoS ONE, Год журнала: 2025, Номер 20(5), С. e0317650 - e0317650

Опубликована: Май 7, 2025

A growing body of evidence supports the idea that RNA polymerase II (RNAP II) activity during transcription elongation can be regulated to control rates. Using genomic run-on and RNAP chromatin immunoprecipitation, we measured both active total across bodies genes at three different stages mitotic cell cycle in Saccharomyces cerevisiae : G1, S, G2/M. Comparison levels these revealed distinct patterns throughout cycle. Previously characterized cycling were associated with some patterns. cluster highly divergent immunoprecipitation was notably enriched related ribosome biogenesis structural components ribosome. We confirmed expression mRNAs increases after G1 but decreases following mitosis. Finally, analyzed contribution mRNA stability each found a coordinated regulation decay is necessary fully understand alternative strategies gene

Язык: Английский

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Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression

Molecular Systems Biology, Год журнала: 2025, Номер unknown

Опубликована: Июнь 5, 2025

Abstract Kidney fibrosis, characterized by excessive extracellular matrix deposition, is a progressive disease that, despite affecting 10% of the population, lacks specific treatments and suitable biomarkers. This study presents comprehensive, time-resolved multi-omics analysis kidney fibrosis using an in vitro model system based on human PDGFRβ + mesenchymal cells aimed at unraveling mechanisms. Using transcriptomics, proteomics, phosphoproteomics, secretomics, we quantified over 14,000 biomolecules across seven time points following TGF-β stimulation. revealed distinct temporal patterns expression activity known potential markers modulators. Data integration resulted multi-omic network models which allowed us to propose mechanisms related progression through early transcriptional reprogramming. siRNA knockdowns phenotypic assays, validated predictions regulatory underlying fibrosis. In particular, show that several early-activated transcription factors, including FLI1 E2F1, act as negative regulators collagen deposition molecular work advances our understanding pathogenesis provides resource be further leveraged community.

Язык: Английский

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An Optimized and Versatile Counter-Flow Centrifugal Elutriation Workflow to Obtain Synchronized Eukaryotic Cells

Frontiers in Cell and Developmental Biology, Год журнала: 2021, Номер 9

Опубликована: Апрель 20, 2021

Cell synchronization is a powerful tool to understand cell cycle events and its regulatory mechanisms. Counter-flow centrifugal elutriation (CCE) more generally desirable method synchronize cells because it does not significantly alter behavior and/or progression, however, adjusting specific parameters in type/equipment-dependent manner can be challenging. In this paper, we used the unicellular eukaryotic model organism, Tetrahymena thermophila as testing system for optimizing CCE workflow. Firstly, flow cytometry conditions were identified that reduced nuclei adhesion improved assessment of stage. We then systematically examined how achieve optimal three critical factors affecting outcome CCE, including loading rate, collection rate volume. Using our optimized workflow, obtained large population highly synchronous G1-phase measured by 5-ethynyl-2′-deoxyuridine (EdU) incorporation into nascent DNA strands, bulk content changes cytometry, progression light microscopy. This detailed protocol easily adapted other cells.

Язык: Английский

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Translational control of MPS1 links protein synthesis with the initiation of cell division and spindle pole body duplication in Saccharomyces cerevisiae

Genetics, Год журнала: 2024, Номер 227(3)

Опубликована: Май 7, 2024

Abstract Protein synthesis underpins cell growth and controls when cells commit to a new round of division at point in late G1 the cycle called Start. Passage through Start also coincides with duplication microtubule-organizing centers, yeast spindle pole bodies, which will form 2 poles mitotic that segregates chromosomes mitosis. The conserved Mps1p kinase governs body (SPB) Saccharomyces cerevisiae. Here, we show MPS1 transcript has short upstream open reading frame (uORF) represses Mps1p. Mutating uORF makes smaller, accelerates appearance G1, promotes completion Monitoring SPB using structured illumination microscopy revealed mutating enabled duplicate their earlier smaller size. accelerated mutants depends on cyclin Cln3p transcriptional repressor Whi5p but not Cln1,2p cyclins. These results identify inputs mechanisms control center implicate these processes coupling division.

Язык: Английский

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Patterns of protein synthesis in the budding yeast cell cycle: variable or constant?

Microbial Cell, Год журнала: 2024, Номер 11, С. 321 - 327

Опубликована: Авг. 20, 2024

Abstract Proteins are the principal macromolecular constituent of proliferating cells, and protein synthesis is viewed as a primary metric cell growth. While there celebrated examples proteins whose levels periodic in cycle (e.g., cyclins), concentration most was not thought to change cycle, but some recent results challenge this notion. The ‘bulk’ focus article, specifically rate its synthesis, budding yeast Saccharomyces cerevisiae .

Язык: Английский

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PKA regulatory subunit Bcy1 couples growth, lipid metabolism, and fermentation during anaerobic xylose growth in Saccharomyces cerevisiae

PLoS Genetics, Год журнала: 2023, Номер 19(7), С. e1010593 - e1010593

Опубликована: Июль 6, 2023

Organisms have evolved elaborate physiological pathways that regulate growth, proliferation, metabolism, and stress response. These must be properly coordinated to elicit the appropriate response an ever-changing environment. While individual been well studied in a variety of model systems, there remains much uncover about how are integrated produce systemic changes cell, especially dynamic conditions. We previously showed deletion Protein Kinase A (PKA) regulatory subunit BCY1 can decouple growth metabolism Saccharomyces cerevisiae engineered for anaerobic xylose fermentation, allowing robust fermentation absence division. This provides opportunity understand PKA signaling normally coordinates these processes. Here, we transcriptomic, lipidomic, phospho-proteomic responses upon glucose shift across series strains with different genetic mutations promoting either coupled or decoupled xylose-dependent metabolism. Together, results suggested defects lipid homeostasis limit bcy1Δ strain despite To further this mechanism, performed adaptive laboratory evolutions re-evolve parental strain. The harbored TPK1 regulator OPI1 , among other genes, profiles gene expression. Deletion opi1 partially reverted strain’s phenotype parent, reduced fermentation. suggest several models cells coordinate budding yeast restructuring processes enables utilization.

Язык: Английский

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Optogenetic control of Cdc48 for dynamic metabolic engineering in yeast

Metabolic Engineering, Год журнала: 2023, Номер 79, С. 97 - 107

Опубликована: Июль 7, 2023

Язык: Английский

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Branched‐chain amino acid synthesis is coupled to TOR activation early in the cell cycle in yeast

EMBO Reports, Год журнала: 2023, Номер 24(9)

Опубликована: Июль 27, 2023

Abstract How cells coordinate their metabolism with division determines the rate of cell proliferation. Dynamic patterns metabolite synthesis during cycle are unexplored. We report first isotope tracing analysis in synchronous, growing budding yeast cells. Synthesis leucine, a branched‐chain amino acid (BCAA), increases through G1 phase cycle, peaking later DNA replication. Cells lacking Bat1, mitochondrial aminotransferase that synthesizes BCAAs, grow slower, smaller, and delayed phase, phenocopying which growth‐promoting kinase complex TORC1 is moderately inhibited. Loss Bat1 lowers levels BCAAs reduces activity. Exogenous provision valine and, to lesser extent, leucine promotes division. Valine addition also In wild‐type cells, activity dynamic starting low early but increasing cycle. These results suggest link between BCAA from glucose activation

Язык: Английский

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Metabolic dynamics during the cell cycle

Current Opinion in Systems Biology, Год журнала: 2022, Номер 30, С. 100415 - 100415

Опубликована: Фев. 11, 2022

While we have a solid understanding of the cell biological and biochemical control aspects eukaryotic growth division process, much less is known about metabolic biosynthetic dynamics during cycle. Here, review recent discoveries made at single-cell population level that show budding yeast (Saccharomyces cerevisiae) metabolism oscillates in synchrony with cycle actively dividing cells, as well independently when halted. In fact, emerging evidence suggests cycle-independent oscillations interact elements machinery via several possible mechanisms. Furthermore, reports indicate different processes exhibit temporally changing activity patterns Thus, resources are drawn from primary dynamic manner, potentially giving rise to oscillations. Finally, highlight work mammalian cells indicating similar might also exist higher eukaryotes.

Язык: Английский

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The biosynthesis of phospholipids is linked to the cell cycle in a model eukaryote

Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, Год журнала: 2021, Номер 1866(8), С. 158965 - 158965

Опубликована: Май 14, 2021

The structural challenges faced by eukaryotic cells through the cell cycle are key for understanding viability and proliferation. We tested hypothesis that biosynthesis of lipids is linked to cycle. If true, this would suggest cell's structure important progress perhaps even control Lipidomics (31P NMR MS), proteomics (Western immunoblotting) transcriptomics (RT-qPCR) techniques were used profile lipid fraction characterise aspects its metabolism at seven stages model eukaryote, Desmodesmus quadricauda. found considerable, transient increases in abundance phosphatidylethanolamine during G1 phase (+35%, ethanolamine phosphate cytidylyltransferase increased 2·5×) phosphatidylglycerol (+100%, synthase 22×) over G1/pre-replication boundary. relative phosphatidylcholine fell ~35% G1. N-Methyl transferases conversion into not de novo transcriptome profile, though a choline transferase was found, suggesting Kennedy pathway principal route synthesis PC. fatty acid profiles four most abundant suggested these generally converted between one another. This study shows first time there considerable changes three phospholipid classes normal D. quadricauda, margins large enough elicit physical properties membranes.

Язык: Английский

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