Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Aggresomes protect mRNA under stress in Escherichia coli

ABSTRACT: Membraneless droplets formed through liquid-liquid phase separation of ribonucleoprotein particles contribute to mRNA storage in eukaryotic cells. How such aggresomes contribute to mRNA dynamics under stress, and their functional role, is less understood in bacteria. Here we used multiple approaches including imaging, modelling and transcriptomics to show that prolonged stress leading to ATP depletion in Escherichia coli results in increased aggresome formation, their compaction, and enrichment of mRNA within aggresomes compared to the cytosol. Transcript length was longer in aggresomes compared to the cytosol. Mass spectrometry showed exclusion of mRNA ribonucleases from aggresomes, which was due to negative charge repulsion. Experiments with fluorescent reporters and disruption of aggresome formation showed that mRNA storage within aggresomes promoted translation and associated with reduced lag phases during growth after stress removal. Our findings suggest that mRNA storage within aggresomes confers an advantage for bacterial survival and recovery from stress.

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

PROVIDER: GSE293685 | GEO | 2025/06/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Cytoplasmic Location of Translation Controls Protein Output [CLIP-seq]

Project description:The cytoplasm contains membrane-bound organelles and membraneless compartments. The TIS granule network is formed through assembly of the RNA-binding protein TIS11B together with its bound mRNAs and associates with a portion of the rough endoplasmic reticulum (ER) – one of the major sites of protein synthesis. Subcellular mRNA localization is widespread in polarized cells. However, it is largely unknown if mRNA localization is also widespread in non-polarized cells and if the location of protein synthesis has biological consequences. To identify compartment-specific cellular functions, we used fluorescent particle sorting to isolate TIS granules, the ER surface, and the cytosol and determined their mRNA contents.

2022-11-15 | GSE215769 | GEO

Cytoplasmic Location of Translation Controls Protein Output [RNA-seq]

2022-11-15 | GSE215768 | GEO

HP1β dependent phase separation regulates embryonic stem cells exit from naïve pluripotent state

Project description:Liquid-liquid phase separation has drawn great attention as a physical process that mediates the formation of membraneless organelles in cells to coordinate biological reactions in space and time. Previously, it was proposed that the formation of phase-separated droplets is a unique property of HP1α. Here, we show that HP1β, but not HP1α and HP1ɤ, forms nucleosome dependent phase separated droplets. We demonstrate that H3K9me3 is required for HP1β dependent phase separation. Importantly, HP1β dependent phase separation regulates heterochromatin formation, thus controlling embryonic stem cells differentiation. In response to pluripotency exit, HP1β is phosphorylated at serine 89 recruiting KAP1, a pluripotency regulator, and sequestering it in the heterochromatin compartment. This induces changes in the level of pluripotency factors and triggers pluripotency exit. We propose that such a trapping mechanism creates a fast and dynamic mode of remote control of gene expression to regulate cell fate decisions solely based on membraneless organelles.

2022-05-01 | E-MTAB-8329 | biostudies-arrayexpress

Ribosome profiling on heat shocked wild type and Mettl14 -/- mES cells

Project description:Abstract : "A hallmark of the cellular response to environmental stress is the formation of stress granules. Stress granules are RNA-protein assemblies that provide an adaptive response to stress; however, the basis for their formation and how they contribute to the stress response remains incompletely understood. Here we show that the mRNA modification N6-methyladenosine (m6A) is a mark that targets mRNAs to stress granules. We find that m6A mRNAs are highly enriched in stress granules, and this is mediated by m6A-induced liquid-liquid phase separation of the YTHDF family of m6A-binding proteins. These proteins bind poly-methylated m6A mRNAs, causing them to form liquid droplets that partition into stress granules. Moreover, disrupting either m6A or YTHDF proteins prevents stress granule formation." The goal of this experiment is to understand how recruitment of m6A mRNA to stress granules influences the translational response to heat shock. Result: we found that m6A-containing mRNA are preferentially repressed during stress, and that m6A is required for translational recovery after heat shock

2021-01-15 | GSE109253 | GEO

The Parkinson's disease protein alpha-synuclein is a direct modulator of Processing-bodies and mRNA stability

Project description:Hallacli E, Kayatekin C, Nazeen S, Wang XH, Sheinkopf Z, Sathyakumar S, Sarkar S, Jiang X, Dong X, Di Maio R, Wang W, Keeney MT, Felsky D, Sandoe J, Vahdatshoar A, Udeshi ND, Mani DR,Carr SA, de Jager P, Myers CL, Lindquist S, Greenmyre TJ, Bartel DP, Feany MB, Sunyaev S, Chung CY and Khurana V. Alpha-synuclein, Syn, is a conformationally plastic protein that reversibly binds to cellular membranes. It aggregates and is genetically linked to Parkinson's disease (PD). Here, we show that Syn directly modulates Processing-bodies (P-bodies), membraneless organelles that function in mRNA turnover and storage. The N-terminus of alpha Syn, but not other synucleins, dictates mutually exclusive binding either to cellular membranes or to P-bodies in the cytosol. Syn binds directly to multiple decapping proteins in close proximity on the Edc4 scaffold. As Syn pathologically accumulates, aberrant interaction with Edc4 occurs at the expense of physiologic decapping-module interactions. mRNA-decay kinetics within PD-relevant pathways are consequently disrupted in PD patient neurons and brain. Genetic modulation of P-body components alters Syn toxicity, and human genetic analysis lends support to the disease-relevance of these interactions. Beyond revealing an unexpected aspect of Syn function and pathology, our data highlight the versatility of conformationally plastic proteins with high intrinsic disorder.

2022-03-09 | MSV000089026 | MassIVE

Expression data from Ribonuclease Inhibitor (RI/Rnh1) deficient Human K562 cells

Project description:Summary: Ribonuclease Inhibitor (RI also known as Rnh1) is a 50 kDa, ubiquitously expressed leucine-rich repeat (LRR) protein. It is localized in cytosol and binds to pancreatic-type ribonucleases and inhibit their function. However, the entire biological role for Rnh1 is unknown. We generated RNH1 knock out K562 cells by CRISPR/Cas9 method. Here we studied differential gene expression from wild type and RNH1 knock out K562 cells by RNA-Seq analysis. Overall design: Total RNA was isolated from wild type and RNH1 deficient K562 cells.

2017-03-05 | E-MTAB-5162 | biostudies-arrayexpress

Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase-transition

Project description:Polycomb group proteins play a critical role in silencing transcription during development. It is commonly proposed that Polycomb dependent changes in genome folding, which compact chromatin, contribute directly to repression by blocking binding of activating complexes. Recently, it has also been argued that liquid-liquid demixing of Polycomb proteins facilitates this compaction and repression by phase-separating target genes into a membraneless compartment. To test these models, we utilized Optical Reconstruction of Chromatin Architecture (ORCA) to trace the Hoxa gene cluster, a canonical Polycomb target, in thousands of single cells. Across multiple cell types, we find that Polycomb-bound chromatin frequently explores decompact states and partial mixing with neighboring chromatin, while remaining uniformly repressed, challenging the repression-by-compaction or phase-separation models. Using polymer simulations, we show that these observed flexible ensembles can be explained by “spatial feedback”: transient contacts that contribute to propagation of the epigenetic state, (epigenetic memory) without inducing a globular organization.

2024-02-08 | GSE237501 | GEO

Phosphorylation of the NBDY microprotein promotes dissociation of biomolecular condensates

Project description:Proteogenomic identification of translated small open reading frames in human has revealed thousands of microproteins, or polypeptides of fewer than 100 amino acids, that were previously invisible to geneticists. Hundreds of microproteins have been shown to be essential for cell growth and proliferation, and many regulate macromolecular complexes, but the vast majority remain functionally uncharacterized, lack secondary structure, and exhibit limited evolutionary conservation. One such intrinsically disordered microprotein is NBDY, a 68-amino acid component of membraneless organelles known as P-bodies. In this work, we show that NBDY can undergo liquid-liquid phase separation, a biophysical process thought to underlie the formation of membraneless organelles, in the presence of RNA in vitro. Phosphorylation of NBDY drives liquid phase remixing in vitro and macroscopic P-body dissociation in cells undergoing growth factor signaling and cell division. These results suggest that NBDY phosphorylation is a key regulator of P-body dynamics in cells, and more broadly that intrinsically disordered microproteins may contribute to liquid-liquid phase separation and remixing behavior in cells.

2022-10-14 | PXD026098 | Pride

Identify QKI-bound transcripts via RIP-seq

Project description:N7-methylguanosine (m7G) modification, routinely occurring at the 5’ cap of mRNA or within tRNA and rRNA, also exists internally in mRNA. Although essential for mRNA translation as well as stress response, the “reader” protein for mRNA internal m7G modification is still unrevealed. Here, we reported that Quaking protein (QKI), especially QKI7, can selectively recognize the internal mRNA m7G decoration in the cytosol of various cell types. We identified over 1000 confident m7G-modified and QKI binding RNA targets with a conserved motif, “GANGAN (N=A/U/G)”. More strikingly, internal m7G reader QKI7 directly interacts with the SG core protein G3BP1 and can shuttle a subset of m7G-modified transcripts into SG mRNA pool under oxidative stress condition. Additionally, by sequestering mRNA within SGs, QKI7 modulates the translation efficiency of selected transcripts. Moreover, in line with the observation that doxorubicin triggers the assembly of SGs, QKI7 mediates the sensitivity of cancer cells to chemotherapy drug treatment.

2023-05-17 | GSE193036 | GEO

Identify QKI7-bound transcripts via RIP-seq

2023-05-17 | GSE192847 | GEO