Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure DOI Creative Commons
Daniel Scholl, Tumara Boyd, Andrew P. Latham

et al.

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

Published: Dec. 28, 2024

Abstract Biomolecular condensates play key roles in the spatiotemporal regulation of cellular processes. Yet, relationship between atomic features and condensate function remains poorly understood. We studied this using polar organizing protein Z (PopZ) as a model system, revealing how its material properties depend on ultrastructure. revealed PopZ’s hierarchical assembly into filamentous by integrating cryo-electron tomography, biochemistry, single-molecule techniques, molecular dynamics simulations. The helical domain drives filamentation condensation, while disordered inhibits them. Phase-dependent conformational changes prevent interfilament contacts dilute phase expose client binding sites dense phase. These findings establish multiscale framework that links interactions ultrastructure to macroscopic drive function.

Language: Английский

Disordered regions of condensate-promoting proteins have distinct molecular signatures associated with cellular function DOI
Shubham Vashishtha, Benjamin R. Sabari

Journal of Molecular Biology, Journal Year: 2025, Volume and Issue: unknown, P. 168953 - 168953

Published: Jan. 1, 2025

Language: Английский

Citations

3
Real-time visualization of reconstituted transcription reveals RNA polymerase II activation mechanisms at single promoters DOI Creative Commons
Megan Palacio, Dylan J. Taatjes

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

Published: Jan. 6, 2025

RNA polymerase II (RNAPII) is regulated by sequence-specific transcription factors (TFs) and the pre-initiation complex (PIC): TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, Mediator. TFs Mediator contain intrinsically-disordered regions (IDRs) form phase-separated condensates, but how IDRs control RNAPII function remains poorly understood. Using purified PIC factors, we developed a Real-time In-vitro Fluorescence Transcription assay (RIFT) for second-by-second visualization of at hundreds promoters simultaneously. We show rapid activation IDR-dependent, without condensate formation. For example, MED1-IDR can functionally replace native TF, activating with similar (not identical) kinetics; however, squelches as condensate, activates single-protein. cooperatively activate bursting re-initiation surprisingly, drive TF-promoter recruitment, TF-DNA binding. Collectively, RIFT addressed questions largely intractable cell-based methods, yielding mechanistic insights about IDRs, enhancer-promoter communication, that complement live-cell imaging data.

Language: Английский

Citations

2
Peptide-Mediated Liquid-Liquid Phase Separation and Biomolecular Condensates DOI

Guangle Li,

Chengqian Yuan, Xuehai Yan

et al.

Soft Matter, Journal Year: 2025, Volume and Issue: 21(10), P. 1781 - 1812

Published: Jan. 1, 2025

Peptide-mediated liquid–liquid phase separation (LLPS) underpins the formation of dynamic biomolecular condensates, regulated by diverse molecular interactions, and highlights potential applications in drug delivery synthetic biology.

Language: Английский

Citations

2
Dynamic interactions of retroviral Gag condensates with nascent viral RNA at transcriptional burst sites: implications for genomic RNA packaging DOI Creative Commons
Rebecca J. Kaddis Maldonado, Leslie J. Parent

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

Published: Jan. 12, 2025

Abstract Retroviruses are responsible for significant pathology in humans and animals, including the acquired immunodeficiency syndrome a wide range of malignancies. A crucial yet poorly understood step replication cycle is recognition selection unspliced viral RNA (USvRNA) by retroviral Gag protein, which binds to psi (Ψ) packaging sequence 5’ leader, package it as genomic (gRNA) into nascent virions. It was previously thought that initially bound gRNA cytoplasm. However, previous studies demonstrated Rous sarcoma virus (RSV) protein traffics transiently through nucleus, necessary efficient packaging. These data formed strong premise hypothesis selects at transcription sites location highest concentration USvRNA molecules cell. In support this model, using fixed cells infected with RSV revealed co-localizes large nuclear foci representing transcriptional burst sites. To test idea, we used single molecule labeling imaging techniques visualize fluorescently-tagged, actively transcribing genomes, proteins living cells. condensates were observed co-localized sites, forming co- localized ribonucleoprotein complexes (vRNPs). results novel paradigm assembly interacts dynamic kissing interaction capture incorporation

Language: Английский

Citations

0
The metabolic enzyme GYS1 condenses with NONO/p54nrb in the nucleus to spatiotemporally regulate glycogenesis and myogenic differentiation DOI Open Access
Shujun Peng, Canrong Li, Yifan Wang

et al.

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

Published: Jan. 22, 2025

Abstract Accumulating evidence indicates that metabolic enzymes can directly couple signals to transcriptional adaptation and cell differentiation. Glycogen synthase 1 (GYS1), the key enzyme for glycogenesis, is a nucleocytoplasmic shuttling protein compartmentalized in cytosol nucleus. However, spatiotemporal regulation biological function of nuclear GYS1 (nGYS1) microcompartments remain unclear. Here, we show dynamically reorganizes into condensates under conditions glycogen depletion or transcription inhibition. nGYS1 complexes with factor NONO/p54 nrb undergoes liquid-liquid phase separation form biomolecular condensates, leading its retention inhibition biosynthesis. Compared their wild-type littermates, Nono-deficient mice exhibit exercise intolerance, higher muscle content, smaller myofibers. Additionally, Gys1 Nono deficiency prevents C2C12 differentiation cardiotoxin-induced regeneration mice. Mechanistically, NONO co-condense myogenic MyoD preinitiation complex (PIC) proteins driving gene expression during myoblast These results reveal subcellular glycogenesis myogenesis, providing mechanistic insights glycogenoses muscular dystrophy.

Language: Английский

Citations

0
Emergent 3D genome reorganization from the stepwise assembly of transcriptional condensates DOI Creative Commons
Surabhi Chowdhary, Sarah Paracha, Lisa Dyer

et al.

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

Published: Feb. 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

Language: Английский

Citations

0
An Overview of Liquid-Liquid Phase Separation and Its Mechanisms in Sepsis DOI Creative Commons
Meiling Cao, Xinyi Zhang, Xiaohan Wang

et al.

Journal of Inflammation Research, Journal Year: 2025, Volume and Issue: Volume 18, P. 3969 - 3980

Published: March 1, 2025

Sepsis is a systemic inflammatory response syndrome triggered by the invasion of bacteria or pathogenic microorganisms into human body, which may lead to variety serious complications and pose threat patient's life health. Liquid-liquid phase separation (LLPS) biomolecular process in different biomolecules, such as proteins nucleic acids, form liquid condensates through interactions, these play key roles cellular physiological processes. LLPS affect development sepsis several pathways, modulation factors, immune responses, cell death, altering function activity which, turn, infection inflammation. In this paper, we first discuss mechanism separation, then summarize studies sepsis, finally propose potential application treatment strategies, while pointing out limitations existing directions for future research.

Language: Английский

Citations

0
The metabolic enzyme GYS1 condenses with NONO/p54nrb in the nucleus and spatiotemporally regulates glycogenesis and myogenic differentiation DOI

Shouyong Peng,

Canrong Li, Yifan Wang

et al.

Cell Death and Differentiation, Journal Year: 2025, Volume and Issue: unknown

Published: April 8, 2025

Language: Английский

Citations

0
Deregulated enhancer‐promoter communication in cancer through altered nuclear architecture DOI Creative Commons
Isabelle Seufert, Claire Vargas, Sina Jasmin Wille

et al.

International Journal of Cancer, Journal Year: 2025, Volume and Issue: unknown

Published: April 12, 2025

Enhancers are critical regulators of gene expression. Structural variations in cancer genomes can lead to enhancer hijacking, where oncogenes activated by mistargeted activity. Novel enhancer-promoter interactions may also arise through chromosomal rearrangements that create extrachromosomal DNA elements. Additionally, fusion proteins and other mutation-induced alterations protein properties the aberrant assembly into large complexes on size scale 0.1-1 μm termed onco-condensates. Transcription factors co-activators accumulate with cis-regulatory elements these structures, driving oncogenic programs. Here, we review current evidence how altered genome architecture macromolecular result deregulated communication. We discuss emerging strategies exploit mechanisms for clinical applications.

Language: Английский

Citations

0
RNA polymerase II partitioning is a shared feature of diverse oncofusion condensates DOI
Heankel Lyons, Prashant Pradhan, Gopinath Prakasam

et al.

Cell, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

Citations

0