Entry created on 1 July 2019 (Revision 1.0) Annotator: Bálint Mészáros
Basic protein information
Accession Q13148
Common name TDP-43, TDP43
Gene TARDBP
Organism Homo sapiens
Uniprot name TAR DNA-binding protein 43
Basic LLPS information
Organelle cytoplasmic stress granule; cytoplasmic ribonucleoprotein granule
Type of experimental evidence
Protein region(s) mediating LLPS
1
-
102
N-terminal region (ubiquitin-like domain+disordered region)
263
-
414
C-terminal region (prion-like domain, low complexity, G-rich IDR)
Based on the experimental results of the following publication: 29555476
Molecular features viewer
PDB structures
View on PDBe
Extended LLPS information
Functional description
The TAR-DNA-binding protein-43 (TDP-43) was initially identified to be a host-cell protein capable of binding the TAR DNA of HIV and repressing transcription. TDP-43 belongs to a group of human RNA-binding proteins with prion-like domains incorporating low complexity sequences. The RNA-binding ability of TDP-43 is conferred by two RNA recognition motifs, while the C-terminal prion-like glycine-rich region mediates protein-protein interactions. One key feature of TDP-43 is its functional involvement in forming cellular granules containing both RNA-binding proteins (RBPs) and nucleic acids. TDP-43 is recruited to these cytoplasmic RNA granules (stress granules, SGs) following exposure to various environmental stresses (oxidative, osmotic, heat shock, viral infection). SGs follow a linear dynamic featuring an initial nucleation/formation followed by assembly into larger structures, and eventual disassembly as the cell recovers. In transformed cell lines, depletion of TDP-43 has a negative impact on each of these steps, indicating a key role for TDP-43 in the regulation of this essential cell survival mechanism (PMID:29765078, PMID:29555476).
Literature supporting the LLPS: 22579281, 22454397, 27545621, 28112502, 28988034, 29511089, 29438978, 28265061, 30814253, 30728452, 30826182, 30853299, 30100264, 29555476
Functional class of membraneless organelle: activation/nucleation/signal amplification/bioreactor; protective storage/reservoir; sensor
Binding partners (at biological protein concentrations)
N/A
Type of RNA(s) required/used for the LLPS at biological protein concentrations
RNA not required.
Molecular interaction types contributing to LLPS
protein-DNA interaction (PMID:29555476) helix-helix interaction driven oligomerization (PMID:28988034) simple coacervation of hydrophobic residues (PMID:29511089) linear oligomerization (PMID:30826182)
Determinants of phase separation and droplet properties
1) RNA concentration 2) concentration of poly(ADP-ribose) (PAR) 3) DNA concentration
Membrane cluster No
Partner-dependent No
RNA-dependent No
PTM required No
Domain-motif interactions No
Discrete oligomerization No
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
The C-terminal domain (CTD) of TDP-43 was knocked-in and were expressein in bacterial cells, to show in vitro using differential interference contrast microscopy that this protein region is enough to form liquid droplets. The particle size and count of CTD droplets showed that single stranded DNA (ssDNA) enhances the LLPS, leading to the formation of an increased number of larger droplets. The extent of this enhancement follows the change in DNA concentration, and this effect is largely independent of the DNA sequence and length. In addition, ssDNA also induced the LLPS of the similarly expressed N-terminal domain fragment (NTD) of TDP-43 in vitro, also followed by differential interference contrast microscopy. The ability of NTD to undergo LLPS is heavily modulated by changes in the protein concentration and changes in the DNA concertraion (or the ratio of these two concentrations). The transition of NTD to the liquid phase is largely independent of the actual DNA sequence, and instead depends mostly on DNA length and concentration. NMR studies also show that at low protein concentrations, NTD exists as a folded entity, while at increasing ssDNA concentrations, the DNA forms aspecific interactions with NTD and induces LLPS (PMID:29555476). In another study, it has been shown that in vitro TDP-43 interacts with poly(ADP-ribose) (PAR) through its nuclear localization signal (NLS) in the NTD (residues 80-100). In vivo analysis of TDP-43 localization in transgenic drosophila nerve cells using co-immunoprecipitation showed, that PAR and TDP-43 coexist in the same protein complex. The TDP-43:PAR binding was confirmed in vitro, using a PAR-binding dot-blot, where a GST-tagged TDP-43 was spotted onto a membrane, and was incubated with PAR polymer followed by immunoblotting with an antibody directed to PAR. TDP-43 undergoes LLPS, as evidenced by in vitro studies, using a change in salt concentration and the concentration of a crowding agent (dextran), showing that TDP-43 alone pontaneously formed dynamic spherical droplets that fused and increased in size, indicating liquid-like properties, followed using microscopy (PMID:30100264).
Experimental observations supporting the liquid material state of the condensate
morphological traits (PMID:29555476) dynamic movement/reorganization of molecules within the droplet (PMID:30826182) sensitivity to 1,6-hexanediol (PMID:28265061) other: NMR (PMID:29555476)