In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

Chemical Reviews, Journal Year: 2022, Volume and Issue: 122(10), P. 9497 - 9570

Published: March 31, 2022

In-cell structural biology aims at extracting information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts outlooks of interest both fundamental applied levels. NMR spectroscopy has important contributions on this stage: It brings a broad variety nuclei the atomic scale, which ensures its versatility uniqueness. Here, we detail methods, knowledge, applications biomedical engineering related to in-cell by NMR. We finally propose brief overview main other techniques (EPR, smFRET, cryo-ET, etc.) draw some advisable developments for In era large-scale screenings deep learning, accurate qualitative experimental evidence are as essential ever understand interior life cells. can generate such it does so scale. review meant deliver comprehensive but accessible information, with advanced technical details reflections nature results, future field.

Language: Английский

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Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle

Cell, Journal Year: 2024, Volume and Issue: 187(6), P. 1490 - 1507.e21

Published: March 1, 2024

Cell cycle progression relies on coordinated changes in the composition and subcellular localization of proteome. By applying two distinct convolutional neural networks images millions live yeast cells, we resolved proteome-level dynamics both concentration during cell cycle, with resolution ∼20 classes. We show that a quarter proteome displays periodicity, proteins tending to be controlled either at level or concentration, but not both. Distinct levels protein regulation are preferentially utilized for different aspects being mostly involved control biophysical implementation program. present resource exploring global which will aid understanding fundamental biological process systems level.

Language: Английский

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AUP1 regulates lipid metabolism and induces lipid accumulation to accelerate the progression of renal clear cell carcinoma

Cancer Science, Journal Year: 2022, Volume and Issue: 113(8), P. 2600 - 2615

Published: May 28, 2022

Lipid metabolic reprogramming is a prominent feature of clear cell renal carcinoma (ccRCC). accumulation affects cellular energy homeostasis, biofilm synthesis, lipid signal transduction, and phenotypic transformation in ccRCC. Herein, prognostic-related model was constructed, the prognostic utility AUP1, droplet-regulating very low-density lipoprotein assembly factor, ccRCC determined through multiparameter analysis. AUP1 expression significantly higher clinical samples than normal tissues closely associated with stage. The inhibition impaired proliferation, migration, invasion ACHN A498 cells vitro vivo. RNA-seq analysis revealed that can reduce contents intracellular triglyceride cholesterol regulate growth by cycle arrest, promoting apoptosis reversing epithelial-mesenchymal transition. regulated synthesis esters fatty acids (FAs) targeting sterol O-acyltransferase 1 partially promoted progression also induced de novo FAs (inhibiting protein kinase AMP-activated catalytic subunit alpha 2), inhibiting rate-limiting enzyme FA β oxidation (carnitine palmitoyltransferase 1A), regulating key lipolysis (monoglyceride lipase, MGLL), transporter StAR-related transfer domain containing 5 (STARD5). However, it did not affect pathway. differential significance MGLL STARD5 should be further studied. may serve as new effective potential target marker for

Language: Английский

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Temporal segregation of biosynthetic processes is responsible for metabolic oscillations during the budding yeast cell cycle

Nature Metabolism, Journal Year: 2023, Volume and Issue: 5(2), P. 294 - 313

Published: Feb. 27, 2023

Many cell biological and biochemical mechanisms controlling the fundamental process of eukaryotic division have been identified; however, temporal dynamics biosynthetic processes during cycle are still elusive. Here, we show that key temporally segregated along cycle. Using budding yeast as a model single-cell methods to dynamically measure metabolic activity, observe two peaks in protein synthesis, G1 S/G2/M phase, whereas lipid polysaccharide synthesis only once, phase. Integrating inferred rates into thermodynamic-stoichiometric model, find this segregation causes flux changes primary metabolism, with an acceleration glucose-uptake phase-shifted oscillations oxygen carbon dioxide exchanges. Through experimental validation predictions, demonstrate metabolism oscillates cell-cycle periodicity satisfy changing demands exhibiting unexpected

Language: Английский

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Building blocks are synthesized on demand during the yeast cell cycle

Proceedings of the National Academy of Sciences, Journal Year: 2020, Volume and Issue: 117(14), P. 7575 - 7583

Published: March 25, 2020

For cells to replicate, a sufficient supply of biosynthetic precursors is needed, necessitating the concerted action metabolism and protein synthesis during progressive phases cell division. A global understanding which processes are involved how they temporally regulated replication is, however, currently lacking. Here, quantitative multiomics analysis used generate holistic view eukaryal cycle, using budding yeast Saccharomyces cerevisiae Protein central carbon pathways such as glycolysis amino acid shown synchronize their respective abundance profiles with division, pathway-specific changes in metabolite also being reflected by relative increase mitochondrial volume, fluorescence microscopy. These results show precursor production be meet phase-specific demands

Language: Английский

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Eukaryotic cell size regulation and its implications for cellular function and dysfunction

Physiological Reviews, Journal Year: 2024, Volume and Issue: 104(4), P. 1679 - 1717

Published: June 20, 2024

Depending on cell type, environmental inputs, and disease, the cells in human body can have widely different sizes. In recent years, it has become clear that size is a major regulator of function. However, we are only beginning to understand how optimization function determines given cell’s optimal size. Here, review currently known control strategies eukaryotic intricate link intracellular biomolecular scaling, organelle homeostasis, cycle progression. We detail size-dependent regulation early development impact differentiation. Given importance for normal cellular physiology, must account changing conditions. describe sense stimuli, such as nutrient availability, accordingly adapt their by regulating growth Moreover, discuss correlation pathological states with misregulation long time this was considered downstream consequence dysfunction. newer studies reveal reversed causality, misregulated leading pathophysiological phenotypes senescence aging. summary, highlight important roles dysfunction, which could implications both diagnostics treatment clinic.

Language: Английский

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Translational control of one-carbon metabolism underpins ribosomal protein phenotypes in cell division and longevity

eLife, Journal Year: 2020, Volume and Issue: 9

Published: May 20, 2020

A long-standing problem is how cells that lack one of the highly similar ribosomal proteins (RPs) often display distinct phenotypes. Yeast and other organisms live longer when they specific proteins, especially large 60S subunit ribosome. However, longevity neither associated with generation time RP deletion mutants nor bulk inhibition protein synthesis. Here, we queried actively dividing through cell cycle. Our data link transcriptional, translational, metabolic changes to phenotypes loss paralogous RPs. We uncovered translational control transcripts encoding enzymes methionine serine metabolism, which are part one-carbon (1C) pathways. Cells lacking Rpl22Ap, long-lived, have lower levels metabolites 1C metabolism. Loss increased wild type cells. pathways exist in all targeting relevant could represent interventions.

Language: Английский

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Temporal oscillation of phospholipids promotes metabolic efficiency

Nature Chemical Biology, Journal Year: 2025, Volume and Issue: unknown

Published: April 14, 2025

Language: Английский

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The asymmetric distribution of RNA polymerase II and nucleosomes on replicated daughter genomes is caused by differences in replication timing between the lagging and the leading strand

Genome Research, Journal Year: 2022, Volume and Issue: 32(2), P. 337 - 356

Published: Jan. 18, 2022

Chromatin features are thought to have a role in the epigenetic transmission of transcription states from one cell generation next. It is unclear how chromatin structure survives disruptions caused by genomic replication or whether instructive state underlying gene. We developed method monitor budding yeast replication, transcription, and maturation dynamics on each daughter genome parallel, with which we identified clusters secondary origins surrounding known origins. found difference timing lagging leading strand order minutes at most genes. propose model majority old histones RNA polymerase II (RNAPII) bind gene copy that replicated first, while newly synthesized nucleosomes assembled second. RNAPII enrichment then shifts sister The largely determined genic orientation: If codirectional, replicates first; if they counterdirectional, first. A mutation Mcm2 subunit replicative helicase Mcm2-7 impairs interactions histone H3 slows down forks but does not qualitatively change asymmetry nucleosome distribution observed WT. active inherited simultaneously independently their through recycling machinery histones, respectively. Transcription thus actively contributes reestablishment state.

Language: Английский

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

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 5, 2025

ABSTRACT Increasing evidence supports that the activity of RNA polymerase II (RNA pol II) during transcription elongation can be regulated to control rates. Using genomic run-on (GRO) and chromatin immunoprecipitation (RPCC), we have respectively measured active total present in body genes at 3 different stages mitotic cell cycle Saccharomyces cerevisiae : G1, S G2/M. Comparison values these three points defined patterns across cycle. Previously characterized cycling were found associated some patterns. A cluster with very divergent GRO RPCC was significantly enriched functionally related ribosome biogenesis (RiBi) structural components ribosome. We confirmed RiBi mRNA expression upregulates after START but decreases mitosis. Finally, analysed contribution stability each concerted decay is needed fully understand alternative strategies gene

Language: Английский

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