Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Formation of biomolecular condensates in bacteria by tuning protein electrostatics

ABSTRACT: While eukaryotic cells have a myriad of membrane-bound organelles enabling the isolation of different chemical environments, prokaryotic cells lack these defined reaction vessels. Biomolecular condensates—organelles that lack a membrane—provide a strategy for cellular organization without a physical barrier while allowing for the dynamic, responsive organization of the cell. It is well established that intrinsically disordered protein domains drive condensate formation via liquid–liquid phase separation; however, the role of globular protein domains on intracellular phase separation remains poorly understood. We hypothesized that the overall charge of globular proteins would dictate the formation and concentration of condensates and systematically probed this hypothesis with supercharged proteins and nucleic acids in E. coli. Within this study, we demonstrated that condensates form via electrostatic interactions between engineered proteins and RNA and that these condensates are dynamic and only enrich specific nucleic acid and protein components. Herein, we propose a simple model for the phase separation based on protein charge that can be used to predict intracellular condensate formation. With these guidelines, we have paved the way to designer functional synthetic membraneless organelles with tunable control over globular protein function.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Escherichia Coli (ncbitaxon:562)

SUBMITTER: Allie C. Obermaye Lewis M. Brown

PROVIDER: MSV000085333 | MassIVE | Fri Apr 24 14:39:00 BST 2020

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

An archaeal chromatin protein condenses DNA through bridging-induced phase separation

Project description:Phase separation serves an important role in the three-dimensional chromosome organization and remodeling in eukaryotes. Whether this process is involved in archaeal chromosome organization is unknown. Here we demonstrate that archaeal DNA condensing protein1 (aDCP1) from the hyperthermophilic crenarchaeon Sulfolobus islandicus is able to bridge DNA efficiently and form large protein-DNA condensates with a droplet- or gel-like morphology in vitro. Within the condensates, aDCP1 exhibits a fast dynamic while the DNA appears in a solid-like state. At the single-molecule level, aDCP1 efficiently compacts DNA through a three-step mechanism, which presumably entails the clustering of aDCP1 on the DNA and the subsequent fusion of the clusters. Deletion of the aDCP1 gene results in noticeable changes in chromosome conformation in S. islandicus, which are characterized by enhanced interactions between the A and B compartments and reduced interactions within the self-interacting domains as well as between domains in the same compartment. Taken together, our results indicate that aDCP1 is capable of inducing DNA bridging-induced phase separation and serves a role in chromosome organization in the organism.

2024-11-01 | GSE248862 | GEO

Filamentation and Biofilm Formation are Regulated by the Phase-Separation Capacity of Network Transcription Factors in Candida albicans

Project description:The ability of the fungus Candida albicans to filament and form biofilms contributes to its burden as a leading cause of hospital-acquired infections. Biofilm development involves an interconnected transcriptional regulatory network (TRN) consisting of nine transcription factors (TFs) that bind both to their own regulatory regions and to those of the other network TFs. Here, we show that seven of the nine TFs in the C. albicans biofilm network contain prion-like domains (PrLDs) that have been linked to the ability to form phase-separated condensates. Construction of PrLD mutants in four biofilm TFs reveals that these domains are essential for filamentation and biofilm formation in C. albicans. Moreover, biofilm PrLDs promote the formation of phase-separated condensates in the nuclei of live cells, and PrLD mutations that abolish phase separation (such as the removal of aromatic residues) also prevent biofilm formation. Biofilm TF condensates can selectively recruit other TFs through PrLD-PrLD interactions and can co-recruit RNA polymerase II, implicating condensate formation in the assembly of active transcriptional complexes. Finally, we show that PrLD mutations that block the phase separation of biofilm TFs also prevent filamentation in an in vivo model of gastrointestinal colonization. Together, these studies associate transcriptional condensates with the regulation of filamentation and biofilm formation in C. albicans, and highlight how targeting of PrLD-PrLD interactions could prevent pathogenesis by this species.

2023-11-20 | GSE245897 | GEO

A Phase-Separated Nuclear GBPL Circuit Controls Immunity in Plants

Project description:Liquid-liquid phase separation (LLPS) has emerged as a central paradigm for understanding how membrane-less organelles compartmentalize diverse cellular activities in eukaryotes. Here, we identified a new superfamily of plant Guanylate Binding Protein-Like GTPases (GBPLs) that assemble LLPS-driven condensates within the nucleus to protect against infection and autoimmunity. In Arabidopsis thaliana, two family members - GBPL1 and GBPL3 - undergo phase transition behavior to control transcriptional responses as part of an allosteric switch triggered by exposure to biotic stress. GBPL1, a pseudoGTPase, sequesters catalytically-active GBPL3 under basal conditions but is displaced by LLPS when GBPL3 enters the nucleus following immune cues to drive formation of unique membrane-less organelles termed GDACs (GBPL Defense-Activated Condensates) that we visualized by in situ cryo-electron tomography. Within these mesoscale GDAC structures, native GBPL3 directly bound defense gene promoters and recruited specific transcriptional coactivators of the Mediator complex plus RNA Pol II machinery to massively reprogram host gene expression for disease resistance. Together, our study identifies a new GBPL circuit that reinforces the biological importance of phase-separated condensates, in this case, as indispensable players in plant defense.

2021-03-24 | GSE134651 | GEO

Intrinsic mesoscale properties of a Polycomb protein underpin heterochromatin fidelity

Project description:Little is understood about how the two major types of heterochromatin domains (HP1 and Polycomb) are kept separate. In the yeast Cryptococcus neoformans, the Polycomb-like protein Ccc1 prevents deposition of H3K27me3 at HP1 domains. Here we show that phase separation propensity underpins Ccc1 function. Mutations of the two basic clusters in the intrinsically disordered region or deletion of the coiled-coil dimerization domain alter phase separation behavior of Ccc1 in vitro and have commensurate impacts on formation of Ccc1 condensates in vivo, which are enriched for PRC2. Importantly, mutations that alter phase separation trigger ectopic H3K27me3 at HP1 domains. Supporting a direct condensate-driven mechanism for fidelity, Ccc1 droplets efficiently concentrate recombinant C. neoformans PRC2 in vitro while HP1 droplets do so only weakly. These studies establish a biochemical basis for chromatin regulation in which mesoscale biophysical properties play a key functional role.

2023-04-03 | GSE195824 | GEO

Transcription factors activate genes through the phase separation capacity of their activation domains [RNA-seq]

Project description:Gene expression is controlled by transcription factors (TFs) that consist of DNA-binding domains (DBDs) and activation domains (ADs). The DBDs have been well- characterized, but little is known about the mechanisms by which ADs effect gene activation. Here we report that diverse ADs form phase-separated condensates with the Mediator coactivator. For the OCT4 and GCN4 TFs, we show that the ability to form phase-separated droplets with Mediator in vitro and the ability to activate genes in vivo are dependent on the same amino acid residues. For the estrogen receptor (ER), a ligand-dependent activator, we show that estrogen enhances phase separation with Mediator, again linking phase separation with gene activation. These results suggest that diverse TFs can interact with Mediator through the phase-separating capacity of their ADs and that formation of condensates with Mediator is involved in gene activation.

2018-10-26 | GSE120474 | GEO

Transcription factors activate genes through the phase separation capacity of their activation domains [ChIP-seq]

2018-10-26 | GSE120459 | GEO

Phase separation of YAP fusion proteins drives supratentorial ependymoma (methyl-seq)

Project description:HIPPO-YAP/TAZ signaling has been implicated in supratentorial ependymoma formation from neural progenitor cells (NPC) in the brain, however, the underlying mechanisms to trigger the neural progenitor cell transformation remains elusive. Here, we uncover that patient-derived tumorigenic YAP-fusion proteins (YAP-MAMLD1 and C11ORF95-YAP) promote ependymoma tumorigenesis through forming liquid-liquid phase-separated condensates. Intrinsically disordered regions (IDR) in the fusion proteins promote oligomerization of YAP-transcriptional co-activators and self-assembly of nuclear puncta-like membrane-less organelles. Phase separation of YAP-fusion proteins further facilitates the compartmentalization of transcriptional coactivators, BRD4 and MED1, resulting in pervasive enhancer landscape changes and exclusion of transcriptional repressors such as PRC2 complexes. YAP-fusion proteins-induced nuclear puncta recruit RNA polymerase II to promote transcriptional bursting of multiple oncogenic pathways. Moreover, we show that IDR-mediated phase separation is necessary for YAP-fusion protein-induced tumor formation. Distinct YAP fusion-proteins identified in other human tumors also encompass IDR features. Together, our data suggest that IDR-mediated phase separation is an integral component of YAP-fusion protein-induced tumorigenesis and might serve as a therapeutic target in supratentorial ependymoma.

2022-10-27 | GSE206926 | GEO

Phase separation of YAP fusion proteins drives supratentorial ependymoma I

2022-10-27 | GSE181867 | GEO

Circadian clock regulation by compartmentalized protein translation

Project description:Cells exquisitely compartmentalize many biochemical reactions through phase-separated membrane-less organelles. Besides spatial organization, many biological processes are temporally regulated. While both transcription and translation oscillate in a rhythmic manner, the regulatory mechanism of the latter is understudied. Here we report that the translational regulation during circadian cycles is associated with oscillating phase separation controlled by Ataxin-2 and Ataxin-2L. Ataxin-2/2L forms rhythmic condensates through phase separation in the mammalian central clock suprachiasmatic nucleus to selectively concentrate the transcripts of the core clock genes and recruit the mRNA translation machinery. The rhythmic translational activation is abolished in cells and mouse circadian behavior is altered in the absence of Ataxin-2/2L. During aging or neurodegeneration, Ataxin-2/2L form large, irreversible puncta that no longer regulate translation. Overall, our results unveil Ataxin-2/2L’s role as the master regulators of rhythmic translation via a oscillating phase-separation, and explained the reason for their dysfunction in disease states.

2023-06-24 | GSE222433 | 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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data