Analyses of translation factors Dbp1 and Ded1 reveal the cellular response to heat stress to be separable from stress granule formation DOI Creative Commons

Naohiro Kuwayama,

Emily Nicole Powers, Matej Siketanc

и другие.

Cell Reports, Год журнала: 2024, Номер 43(12), С. 115059 - 115059

Опубликована: Дек. 1, 2024

Ded1 and Dbp1 are paralogous conserved DEAD-box ATPases involved in translation initiation yeast. In long-term starvation states, expression increases decreases, whereas cycling mitotic cells, is absent. Inserting DBP1 place of DED1 cannot replace function supporting translation, partly due to inefficient the coding region. Global measurements, activity mRNA-tethered proteins, growth assays show that-even at matched protein levels-Ded1 better than activating especially for mRNAs with structured 5' leaders. Heat-stressed cells normally downregulate housekeeping transcripts halt growth, but neither occurs Dbp1-expressing cells. This failure response heat not based on deficient stress granule formation or reduce bulk translation. Rather, it depends heat-triggered loss mediated by an 11-amino-acid interval within its intrinsically disordered C terminus.

Язык: Английский

Polysome collapse and RNA condensation fluidize the cytoplasm DOI
Ying Xie, Tong Shu,

Tiewei Liu

и другие.

Molecular Cell, Год журнала: 2024, Номер 84(14), С. 2698 - 2716.e9

Опубликована: Июль 1, 2024

Язык: Английский

Процитировано

7
Emergent 3D genome reorganization from the stepwise assembly of transcriptional condensates DOI Creative Commons
Surabhi Chowdhary, Sarah Paracha, Lisa Dyer

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 27, 2025

Transcriptional condensates are clusters of transcription factors, coactivators, and RNA Pol II associated with high-level gene expression, yet how they assemble function within the cell remains unclear. Here we show that transcriptional form in a stepwise manner to enable both graded three-dimensional (3D) control yeast heat shock response. Molecular dissection revealed condensate cascade. First, factor Hsf1 upon partial dissociation from chaperone Hsp70. Next, coactivator Mediator partitions following further Hsp70 phosphorylation. Finally, condenses, driving emergent coalescence HSR genes. analysis series mutants graded, rather than switch-like, activity. Separation-of-function showed formation can be decoupled activation. Instead, fully assembled promote adaptive 3D genome reconfiguration, suggesting role beyond

Язык: Английский

Процитировано

0
Genome-wide mapping of mesoscale neuronal RNA organization and condensation DOI Creative Commons
Lindsay A. Becker, Sofia A. Quinodoz, Troy J. Comi

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Апрель 20, 2025

SUMMARY Subcellular RNA organization can affect critical cellular functions. However, our understanding of microenvironments, particularly biomolecular condensates, remains limited, largely due to a lack technologies comprehensively interrogate mesoscale organization. Here, we adapt Split-Pool Recognition Interactions by Tag Extension map micron-scale RNA-RNA spatial proximity genome-wide across cell regions (RNA-SPRITE). Deploying RNA-SPRITE, find extensive, conserved mature mRNAs, with increased colocalization between mRNAs that share RNA-binding protein (RBP) motifs or encode functionally related proteins. Both effects are especially strong in dendrites and axons, suggesting prevalent mRNA co-regulation. Moreover, less compact folding, lower translation efficiency, specific RBP more likely be RNA-rich condensates. perturbations broadly dissolve enhance condensation reveal motif encoded protein-mediated colocalizations remain intact, independent condensation. These results demonstrate the power RNA-SPRITE revealing aspects RNA’s functional In Brief Unbiased, maps uncover extensive subcellular its governing principles. Highlights reveals specificity is driven shared function distinct protein-binding condensates Neurites have high degree sequence function-dependent

Язык: Английский

Процитировано

0
Unfolding emergency calls stress granules to the ER DOI
David Pincus, Scott A. Oakes

Nature Cell Biology, Год журнала: 2024, Номер 26(6), С. 845 - 846

Опубликована: Май 31, 2024

Язык: Английский

Процитировано

2
Decoding RNA Metabolism by RNA-linked CRISPR Screening in Human Cells DOI Creative Commons
Patrick Nugent,

Heungwon Park,

Cynthia L. Wladyka

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 26, 2024

Abstract RNAs undergo a complex choreography of metabolic processes in human cells that are regulated by thousands RNA-associated proteins. While the effects individual proteins on RNA metabolism have been extensively characterized, full complement regulators for most events remain unknown. Here we present massively parallel RNA-linked CRISPR (ReLiC) screening approach to measure responses diverse knockout 2,092 genes encoding all known ReLiC screens highlight modular interactions between gene networks regulating splicing, translation, and decay mRNAs. When combined with biochemical fractionation polysomes, reveals striking pathway-specific coupling growth fitness mRNA translation. Perturbing different components translation proteostasis machineries distinct ribosome occupancy, while perturbing transcription leaves occupancy largely intact. Isoform-selective capture differential regulation intron retention exon skipping SF3b subunits. Chemogenomic using decipher translational upstream uncover role collision sensor GCN1 during treatment anti-leukemic drug homoharringtonine. Our work demonstrates as versatile platform discovering dissecting regulatory principles metabolism.

Язык: Английский

Процитировано

1
The G3BP Stress-Granule Proteins Reinforce the Translation Program of the Integrated Stress Response DOI Creative Commons
Jarrett Smith, David P. Bartel

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 5, 2024

ABSTRACT When mammalian cells are exposed to extracellular stress, they coordinate the condensation of stress granules (SGs) through action key nucleating proteins G3BP1 and G3BP2 (G3BPs) and, simultaneously, undergo a massive reduction in translation. 1–5 Although SGs G3BPs have been linked this translation response, their overall impact has unclear. Here, we investigate longstanding question how, indeed whether, shape response. We find that enriched for mRNAs resistant stress-induced shutdown. accurate recruitment these stress-resistant does require context combination optogenetic tools spike-normalized ribosome profiling demonstrates necessary sufficient both help prioritize suppress cytosolic Together results support model which reinforce program by prioritizing resident mRNAs.

Язык: Английский

Процитировано

1
Polysomes and mRNA control the biophysical properties of the eukaryotic cytoplasm DOI Open Access
Vamshidhar R. Gade, Stephanie Heinrich, Matteo Paloni

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Ноя. 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.

Язык: Английский

Процитировано

1
Extrachromosomal circular DNA is required for yeast stress granule assembly DOI Creative Commons
N. Demeshkina, Adrian R. Ferré-D’Amaré

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Окт. 13, 2023

SUMMARY Stress granules are a conserved response of eukaryotic cells to environmental insults. These cytoplasmic ribonucleoprotein condensates have hitherto been primarily studied by microscopy, which showed previously that they comprise dense ≈200 nm cores embedded in diffuse shell. We developed new purifications budding yeast and mammalian (HEK293T cell) stress granule do not rely on immunoprecipitation candidate protein constituents. unbiased preparations reveal discrete particles with variable size (mean, 135 225 nm, human, respectively) shape. Proteomics transcriptomics demonstrate complex composition. The results hybrid chain reaction FISH analyses HEK293T consistent having heterogeneous composition, i.e ., each core particle contains only limited number mRNA species. Biochemical purification now opens the way mechanistic analysis heterogeneity complexity granules.

Язык: Английский

Процитировано

2
Viral condensates formed by Pea enation mosaic virus 2 sequester ribosomal components and suppress translation DOI

Shelby L. Brown,

Jared P. May

Virology, Год журнала: 2024, Номер 601, С. 110301 - 110301

Опубликована: Ноя. 13, 2024

Язык: Английский

Процитировано

0
Pin4 Links Post-transcriptional and Transcriptional Responses to Glucose Starvation in Yeast DOI Creative Commons
Michaela Ristová, Katherine Bexley, Vadim Shchepachev

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Ноя. 15, 2024

ABSTRACT Adaptation to environmental change is essential in all organisms, with RNA-binding proteins (RBPs) playing critical roles rapid cellular responses. We analyzed the largely uncharacterized yeast RBP Pin4, and its involvement adaptation glucose depletion. A UV crosslinking technique identify protein-RNA interactions (reCRAC) revealed that conditions Pin4 selectively binds a specific motif 3’ UTRs of mRNAs involved glycolysis, amino acid, mitochondrial metabolism. Following withdrawal, Pin4-RNA binding was greatly reduced, residual favoring transcripts associated protein translation. Cells lacking were impaired recovery from nutrient starvation hypersensitive oxidative stress, consistent mRNA targets. RNAseq reporter assays indicated loss caused increased target abundance. In wildtype yeast, depletion induces “diauxic shift”, massive changes transcription patterns. Very unexpectedly, this response almost entirely abolished cells or carrying point mutation RNA-recognition motif. conclude contributes energy homeostasis by regulating post-transcriptional transcriptional responses, postulate key stress pathway riboregulated.

Язык: Английский

Процитировано

0