The phase separation landscape of genome-wide genetic perturbations DOI Creative Commons
Meta Heidenreich, S. Mathur, Tong Shu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 27, 2024

Summary Biomolecular organization is central to cell function. While phase separation a key mechanism orchestrating this organization, we lack comprehensive view of genes that can globally influence process in vivo . To identify such genes, combined functional genomics and synthetic biology. We developed bioorthogonal system changes the intracellular milieu tune separation. measured diagrams across >25 million cells 2,888 yeast knockouts, identified 68 whose deletion alters boundaries system, an unexpected result given system’s design. Genes involved TORC1 signaling metabolism, particularly carbohydrate-, amino acid- nucleotide synthesis were enriched. The mutants changed also showed high pleiotropy, suggesting interrelates with many aspects Highlights - A protein reveals genetic environmental tunability Genetic knockouts affecting are highly pleiotropic Carbohydrate, acid, metabolism contribute modulating potential Protein tunable property environment

Language: Английский

Peptide Coacervates: Formation, Mechanism, and Biological Applications DOI

Jiewei Yuan,

Y. Richard Yang, Kehua Dai

et al.

ACS Applied Materials & Interfaces, Journal Year: 2025, Volume and Issue: unknown

Published: April 30, 2025

Biomolecular coacervates, dynamic compartments formed via liquid-liquid phase separation (LLPS), are essential for orchestrating intracellular processes and have emerged as versatile tools in bioengineering. Peptides, with their modular amino acid sequences, exhibit unique potential coacervate design due to ability undergo LLPS while offering precise control over molecular architecture environmental responsiveness. Their simplicity, synthetic accessibility, tunability make peptide-based coacervates particularly attractive biomedical materials applications. However, the formation stability of these systems depend on a delicate balance intrinsic factors (e.g., sequence charge, hydrophobicity, chain length) extrinsic conditions pH, ionic strength, temperature), necessitating deeper understanding interplay. This review synthesizes recent advances mechanisms driving peptide coacervation, emphasizing how cues govern behavior. We further highlight groundbreaking applications, from drug delivery platforms protocell mimics, discuss strategies translate mechanistic insights into functional materials. By bridging fundamental principles innovative this work aims accelerate development programmable, multifunctional systems, roadmap next-generation biochemical technologies.

Language: Английский

Citations

1
Giant KASH proteins and ribosomes synergistically establish cytoplasmic biophysical properties in vivo DOI Creative Commons
Xin Shun Ding, Hongyan Hao, Daniel Elnatan

et al.

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

Published: Jan. 12, 2025

Understanding how cells control their biophysical properties during development remains a fundamental challenge. While cytoplasmic macromolecular crowding affects multiple cellular processes in single cells, its regulation living animals poorly understood. Using genetically encoded multimeric nanoparticles for vivo rheology, we discovered that C. elegans tissues maintain distinct differ from those observed across diverse systems, including bacteria, yeast species, and cultured mammalian cells. We identified two conserved mechanisms controlling diffusion: ribosome concentration, known regulator of crowding, works concert with previously unknown function the giant KASH protein ANC-1 scaffolding endoplasmic reticulum. These findings reveal by which establish properties, implications understanding organization species. Living unique intracellular under constraints crowding.

Language: Английский

Citations

0
Translation of unspliced retroviral genomic RNA in the host cell is regulated in both space and time DOI Creative Commons
Felipe Leon-Diaz, Célia Chamontin, Sébastien Lainé

et al.

The Journal of Cell Biology, Journal Year: 2025, Volume and Issue: 224(4)

Published: Jan. 27, 2025

Retroviruses carry a genomic intron-containing RNA with long structured 5'-untranslated region, which acts either as genome encapsidated in the viral progeny or an mRNA encoding key structural protein, Gag. We developed single-molecule microscopy approach to simultaneously visualize and nascent Gag protein during translation directly cell. found that minority of molecules serve they are translated fast efficient process. Surprisingly, polysomes were also observed at cell periphery, indicating is regulated both space time. Virus near plasma membrane may benefit from reduced competition for ribosomes most cellular cytoplasmic mRNAs. In addition, local must spare energy produce proteins, where accumulate assemble new particles, potentially allowing virus evade host's antiviral defenses.

Language: Английский

Citations

0
Dynamic structure of the cytoplasm DOI Creative Commons
Hyo-Jun Kim, Morgan Delarue

Current Opinion in Cell Biology, Journal Year: 2025, Volume and Issue: 94, P. 102507 - 102507

Published: April 6, 2025

The cytoplasm is a dense and complex milieu in which plethora of biochemical reactions occur. Its structure not understood so far, albeit being central to cellular functioning. In this review, we highlight novel perspective the physical properties are regulated space time actively contribute function. Furthermore, underscore recent findings that dynamic formation local assemblies within cytoplasm, such as condensates polysomes, serves key regulator mesoscale cytoplasmic dynamics.

Language: Английский

Citations

0
Phase separation of the PRPP amidotransferase into dynamic condensates promotes de novo purine synthesis in yeast DOI Creative Commons
Masak Takaine, Rikuri Morita, Yuto Yoshinari

et al.

PLoS Biology, Journal Year: 2025, Volume and Issue: 23(4), P. e3003111 - e3003111

Published: April 10, 2025

De novo purine synthesis (DPS) is up-regulated under conditions of high demand to ensure the production genetic materials and chemical energy, thereby supporting cell proliferation. However, regulatory mechanisms governing DPS remain unclear. We herein show that PRPP amidotransferase (PPAT), rate-limiting enzyme in DPS, forms dynamic motile condensates Saccharomyces cerevisiae cells a purine-depleted environment. The formation maintenance requires phase separation, which driven by target rapamycin complex 1 (TORC1)-induced ribosome biosynthesis. self-assembly PPAT molecules facilitates condensate formation, with intracellular nucleotides both regulating this self-assembly. Moreover, molecular dynamics simulations suggest clustering-mediated activation occurs through intermolecular substrate channeling. Cells unable form exhibit growth defects, highlighting physiological importance condensation. These results indicate condensation an adaptive mechanism regulates response TORC1 activity cellular demands.

Language: Английский

Citations

0
Molecular and Biophysical Perspectives on Dormancy Breaking: Lessons from Yeast Spore DOI Creative Commons
Keiichiro Sakai, Yohei Kondo, Kazuhiro Aoki

et al.

Biomolecules, Journal Year: 2025, Volume and Issue: 15(5), P. 701 - 701

Published: May 11, 2025

Dormancy is a physiological state that enables cells to survive under adverse conditions by halting their proliferation while retaining the capacity resume growth when become favorable. This remarkable transition between dormant and proliferative states occurs across wide range of species, including bacteria, fungi, plants, tardigrades. Among these organisms, yeast have emerged as powerful model systems for elucidating molecular biophysical principles governing dormancy breaking. In this review, we provide comprehensive summary current knowledge on mechanisms underlying cellular dormancy, with particular focus two major yeasts: Saccharomyces cerevisiae Schizosaccharomyces pombe. Recent advances in multifaceted approaches—such single-cell RNA-seq, proteomic analysis, live-cell imaging—have revealed dynamic changes gene expression, proteome composition, viability. Furthermore, insights into properties cytoplasm offered new understanding cell regulation through cytoplasmic fluidity. These contribute both stability exit upon environmental cues, deepening our fundamental survival strategies diverse species.

Language: Английский

Citations

0
Polysomes and mRNA control the biophysical properties of the eukaryotic cytoplasm DOI Open Access
Vamshidhar R. Gade, Stephanie Heinrich, Matteo Paloni

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 15, 2024

Abstract The organization and biophysical properties of the cytoplasm influence all cellular reactions, including molecular interactions mobility biomolecules. It has become clear that does not behave like a simple fluid but instead is densely crowded highly organized environment. Yet, detailed cytoplasm, mechanisms control them how they biochemistry cells remain poorly understood. Here, we investigate diffusive in silico vivo, employing mRNPs ( m essenger r ibo n ucleo p rotein) GEM g enetically e ncoded ultimeric) particles as rheological probes proliferating cells. We demonstrate cytoplasmic diffusivity increases upon polysome disassembly due to translation inhibition or reduction mRNA levels. Reducing ribosome concentration by up 20-25% without change levels no effect vivo . In addition, show disassembly, condensation into P-bodies affect cytosolic diffusion budding yeast. Altogether, our results mRNAs their polysomes eukaryotic cytoplasm. Highlights Polysomes mRNP enhanced leads Perturbation an increase diffusion.

Language: Английский

Citations

2
Far from the cytoplasmic crowd DOI

Eytan Zlotorynski

Nature Reviews Molecular Cell Biology, Journal Year: 2024, Volume and Issue: 25(10), P. 761 - 761

Published: Aug. 19, 2024

Language: Английский

Citations

0
The phase separation landscape of genome-wide genetic perturbations DOI Creative Commons
Meta Heidenreich, S. Mathur, Tong Shu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 27, 2024

Summary Biomolecular organization is central to cell function. While phase separation a key mechanism orchestrating this organization, we lack comprehensive view of genes that can globally influence process in vivo . To identify such genes, combined functional genomics and synthetic biology. We developed bioorthogonal system changes the intracellular milieu tune separation. measured diagrams across >25 million cells 2,888 yeast knockouts, identified 68 whose deletion alters boundaries system, an unexpected result given system’s design. Genes involved TORC1 signaling metabolism, particularly carbohydrate-, amino acid- nucleotide synthesis were enriched. The mutants changed also showed high pleiotropy, suggesting interrelates with many aspects Highlights - A protein reveals genetic environmental tunability Genetic knockouts affecting are highly pleiotropic Carbohydrate, acid, metabolism contribute modulating potential Protein tunable property environment

Language: Английский

Citations

0