Entry created on 1 July 2019 (Revision 1.0) Annotator: Bálint Mészáros
Basic protein information
Accession Q12888
Common name 53BP1
Gene TP53BP1
Organism Homo sapiens
Uniprot name TP53-binding protein 1
Basic LLPS information
Organelle nuclear body
Type of experimental evidence
Protein region(s) mediating LLPS
1203
-
1972
C-terminal half
Based on the experimental results of the following publication: 31267591
Molecular features viewer
PDB structures
Extended LLPS information
Functional description
The DNA damage response (DDR) generates transient repair compartments to concentrate repair proteins and activate signaling factors. Silent heterochromatin domains were shown to phase separate within the nucleus. Moreover, phase separation occurs at gene promoters and super-enhancers. To which extent other chromatin domains rely on phase separation for their spatio-temporal confinement and for their biological functions is a matter of intense investigation. 53BP1-marked repair compartments are dynamic, show droplet-like behavior, and undergo frequent fusion and fission events. The tumor suppressor protein p53 is enriched within 53BP1 droplets, and conditions that disrupt 53BP1 phase separation impair 53BP1-dependent induction of p53 and diminish p53 target gene expression. Thus, 53BP1 phase separation integrates localized DNA damage recognition and repair factor assembly with global p53-dependent gene activation and cell fate decisions.
Literature supporting the LLPS: 31267591
Functional class of membraneless organelle: activation/nucleation/signal amplification/bioreactor
Binding partners (at biological protein concentrations)
1) DNA with double strand breaks (not strictly required) 2) p53 (not strictly required)
Type of RNA(s) required/used for the LLPS at biological protein concentrations
RNA not required.
Molecular interaction types contributing to LLPS
discrete oligomerization (PMID:31267591) cation-π (cation-pi) interactions (PMID:31267591)
Determinants of phase separation and droplet properties
1) osmotic stress/salt concentration 2) temperature 3) 1,6-hexanediol concentration 4) pH
Membrane cluster No
Partner-dependent No
RNA-dependent No
PTM required No
Domain-motif interactions No
Discrete oligomerization Yes
Regulation and disease
Post-translational modifications affecting LLPS
Position Residue PTM Effect Reference Modifying enzyme Notes
Isoforms known to affect LLPS
Isoform Effect Reference
All known isoforms containing sequence changes in the LLPS region(s)
Position type Isoform names from UniProt
Disease mutations affecting LLPS
Mutation dbSNP Disease OMIM Effect Reference Notes
Experimental information
Experimental techniques applied to prove/investigate LLPS
In vivo in time‐lapse microscopy experiments, DNA damage‐induced 53BP1 compartments showed droplet‐like behavior and underwent frequent fusion and occasional fission events (morphology, paricle size and count). Moreover, addition of the aliphatic alcohol 1,6‐hexanediol, resulted in disassembly of 53BP1 foci. After employing CRISPR/Cas9 to engineer the endogenous 53BP1 locus and integrate an in‐frame sequence encoding for the small monomeric red fluorescent protein mScarlet, the resulting fusion protein could be visualized by fluorescence microscopy. The fusion protein did not affect the cell cycle, localized to γH2AX‐positive sites of DNA damage (protein localization), showed the typical cell cycle‐regulated pattern of 53BP1 accumulation, and was sensitive to siRNA treatment targeted against 53BP1, confirming the role of 53BP1 in the formation of the observed compartments. Consistent with prior results, a short hyperosmotic challenge led to disassembly of 53BP1‐mScarlet compartments without affecting γH2AX accumulation. More importantly, however, live cell experiments with endogenously tagged 53BP1 expressed from its native promoter confirmed the dynamic, droplet‐like morphology of 53BP1 assemblies, their spherical shape, and their frequent fusions and fissions. 53BP1 nuclear bodies, occurring spontaneously and at enhanced frequency upon mild replication stress by low‐dose aphidicolin (APH) and ATR inhibitor (ATRi) treatment, showed droplet‐like behavior as well, and underwent frequent fusion events. In order to directly test whether 53BP1 possesses the capacity to phase separate, a system based on mCherry‐labeled Arabidopsis photoreceptor cryptochrome 2 (Cry2) fusion proteins was used to measure target protein optoDroplet formation in living cells. A Cry2‐53BP1 fusion resulted in rapid, light‐induced optoDroplet formation. Introducing a single amino acid mutation (W1495A) within the 53BP1 tandem tudor domain (TTD) to abrogate potentially confounding effects from TTD chromatin and protein interactions, and to assess the intrinsic capacity of 53BP1 to phase separate, further enhanced light‐induced optoDroplet formation. A series of deletion mutants used to identify the sequence elements driving 53BP1 phase separation revealed that the C‐terminus, comprising amino acids 1140–1972, was sufficient for optoDroplet formation, while the largely unstructured N‐terminus of 53BP1 was not, and that the oligomerization domain (OD) was critically involved. The 53BP1 C‐terminus is highly enriched for Arg and Tyr residues, implying that preferential optoDroplet formation of this region relies on cation-pi interactions (PMID:31267591). In vitro, the purified 53BP1 C‐terminus showed condensation into μm‐sized droplets in presence of Ficoll (morphology, particle size and count), and 53BP1 condensates co‐assembled double strand break‐mimicking fluorescently labeled DNA (PMID:31267591).
Experimental observations supporting the liquid material state of the condensate
morphological traits (PMID:31267591) temperature-dependence (PMID:31267591) reversibility of formation and dissolution (PMID:31267591)