TARDBP

TAR DNA binding protein
2nd RRM motif of TDP-43. PDB rendering based on 1wf0.
Available structures PDB Ortholog search: PDBe, RCSB List of PDB id codes 1WF0​, 2CQG​, 4BS2​, 4IUF​, 2N4P​
Identifiers
Symbols	TARDBP ; ALS10; TDP-43
External IDs	OMIM: 605078 MGI: 2387629 HomoloGene: 7221 GeneCards: TARDBP Gene
Gene ontology Molecular function • nucleotide binding • transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding • double-stranded DNA binding • transcription factor activity, sequence-specific DNA binding • RNA binding • mRNA 3'-UTR binding • protein binding • identical protein binding • poly(A) RNA binding Cellular component • nucleus • nucleoplasm • perichromatin fibrils • cytoplasm • nuclear speck • interchromatin granule Biological process • negative regulation of protein phosphorylation • transcription from RNA polymerase II promoter • mRNA processing • RNA splicing • negative regulation of gene expression • nuclear fragmentation involved in apoptotic nuclear change • positive regulation of insulin secretion • response to endoplasmic reticulum stress • negative regulation by host of viral transcription • positive regulation of transcription from RNA polymerase II promoter • regulation of cell cycle • 3'-UTR-mediated mRNA stabilization • nuclear inner membrane organization Sources: Amigo / QuickGO
RNA expression pattern
More reference expression data
Orthologs
Species	Human	Mouse
Entrez	23435	230908
Ensembl	ENSG00000120948	ENSMUSG00000041459
UniProt	Q13148	Q921F2
RefSeq (mRNA)	NM_007375	NM_001003898
RefSeq (protein)	NP_031401	NP_001003898
Location (UCSC)	Chr 1: 11.01 – 11.03 Mb	Chr 4: 148.61 – 148.63 Mb
PubMed search

TAR DNA-binding protein 43 (TDP-43, transactive response DNA binding protein 43 kDa), is a protein that in humans is encoded by the TARDBP gene.^[1]

Function

TDP-43 is a transcriptional repressor that binds to chromosomally integrated TAR DNA and represses HIV-1 transcription. In addition, this protein regulates alternate splicing of the CFTR gene. In particular, TDP-43 is a splicing factor binding to the intron8/exon9 junction of the CFTR gene and to the intron2/exon3 region of the apoA-II gene.^[2] A similar pseudogene is present on chromosome 20.^[3]

TDP-43 has been shown to bind both DNA and RNA and have multiple functions in transcriptional repression, pre-mRNA splicing and translational regulation. Recent work has characterized the transcriptome-wide binding sites revealing that thousands of RNAs are bound by TDP-43 in neurons.^[4]

TDP-43 was originally identified as a transcriptional repressor that binds to chromosomally integrated trans-activation response element (TAR) DNA and represses HIV-1 transcription.^[1] It was also reported to regulate alternate splicing of the CFTR gene and the apoA-II gene.

In spinal motor neurons TDP-43 has also been shown in humans to be a low molecular weight microfilament (hNFL) mRNA-binding protein.^[5] It has also shown to be a neuronal activity response factor in the dendrites of hippocampal neurons suggesting possible roles in regulating mRNA stability, transport and local translation in neurons.^[6]

Clinical significance

Hyper-phosphorylated, ubiquitinated and cleaved form of TDP-43, known as pathologic TDP43, is the major disease protein in ubiquitin-positive, tau-, and alpha-synuclein-negative frontotemporal dementia (FTLD-TDP, previously referred to as FTLD-U^[7]) and in Amyotrophic lateral sclerosis (ALS).^[8] Elevated levels of the TDP-43 protein have also been identified in individuals diagnosed with chronic traumatic encephalopathy, a condition that often mimics ALS and that has been associated with athletes who have experienced multiple concussions and other types of head injury.^[9] Abnormalities of TDP-43 also occur in an important subset of Alzheimer's disease patients, correlating with clinical and neuropathologic features indexes.^[10]

HIV-1, the causative agent of acquired immunodeficiency syndrome (AIDS), contains an RNA genome that produces a chromosomally integrated DNA during the replicative cycle. Activation of HIV-1 gene expression by the transactivator "Tat" is dependent on an RNA regulatory element (TAR) located "downstream" (i.e. to-be transcribed at a later point in time) of the transcription initiation site.

Mutations in the TARDBP gene are associated with neurodegenerative disorders including frontotemporal lobar degeneration and amyotrophic lateral sclerosis (ALS).^[11] In particular, the TDP-43 mutants M337V and Q331K are being studied for their roles in ALS.^[12][13] Cytoplasmic TDP-43 pathology is the dominant histopathological feature of multisystem proteinopathy.^[14] The N-terminal domain, which contributes importantely to the aggregation of the C-terminal region, has a novel structure with two negatively charged loops.^[15]

References

1. Ou SH, Wu F, Harrich D, García-Martínez LF, Gaynor RB (1995). "Cloning and characterization of a novel cellular protein, TDP-43, that binds to human immunodeficiency virus type 1 TAR DNA sequence motifs". Journal of Virology 69 (6): 3584–96. PMC 189073. PMID 7745706.
2. Kuo PH, Doudeva LG, Wang YT, Shen CK, Yuan HS (2009). "Structural insights into TDP-43 in nucleic-acid binding and domain interactions". Nucleic Acids Research 37 (6): 1799–808. doi:10.1093/nar/gkp013. PMC 2665213. PMID 19174564.
3. Gene Result
4. Sephton CF, Cenik C, Kucukural A, Dammer EB, Cenik B, Han Y, Dewey CM, Roth FP, Herz J, Peng J, Moore MJ, Yu G (2011). "Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes.". J Biol Chem. 286 (2): 1204–15. doi:10.1074/jbc.M110.190884. PMID 21051541.
5. Strong MJ, Volkening K, Hammond R, Yang W, Strong W, Leystra-Lantz C, Shoesmith C (2007). "TDP43 is a human low molecular weight neurofilament (hNFL) mRNA-binding protein". Molecular and Cellular Neuroscience 35 (2): 320–7. doi:10.1016/j.mcn.2007.03.007. PMID 17481916.
6. Wang IF, Wu LS, Chang HY, Shen CK (2008). "TDP-43, the signature protein of FTLD-U, is a neuronal activity-responsive factor". Journal of Neurochemistry 105 (3): 797–806. doi:10.1111/j.1471-4159.2007.05190.x. PMID 18088371.
7. Mackenzie IR, Neumann M, Baborie A, Sampathu DM, Du Plessis D, Jaros E, Perry RH, Trojanowski JQ, Mann DM, Lee VM (July 2011). "A harmonized classification system for FTLD-TDP pathology". Acta Neuropathol. 122 (1): 111–3. doi:10.1007/s00401-011-0845-8. PMC 3285143. PMID 21644037.
8. Neumann M, Sampathu DM, Kwong LK, Truax AC, Micsenyi MC, Chou TT, Bruce J, Schuck T, Grossman M, Clark CM, McCluskey LF, Miller BL, Masliah E, Mackenzie IR, Feldman H, Feiden W, Kretzschmar HA, Trojanowski JQ, Lee VM (2006). "Ubiquitinated TDP-43 in Frontotemporal Lobar Degeneration and Amyotrophic Lateral Sclerosis". Science 314 (5796): 130–3. doi:10.1126/science.1134108. PMID 17023659.
9. Schwarz, Alan. "Study Says Brain Trauma Can Mimic A.L.S.", The New York Times, August 18, 2010. Accessed August 18, 2010.
10. Tremblay C, St-Amour I, Schneider J, Bennett DA, Calon F. (2011). "Accumulation of transactive response DNA binding protein 43 in mild cognitive impairment and Alzheimer disease.". J Neuropathol Exp Neurol. 70 (9): 788–98. doi:10.1097/nen.0b013e31822c62cf. PMC 3197017. PMID 21865887.
11. Kwong LK, Neumann M, Sampathu DM, Lee VM, Trojanowski JQ (2007). "TDP-43 proteinopathy: The neuropathology underlying major forms of sporadic and familial frontotemporal lobar degeneration and motor neuron disease". Acta Neuropathologica 114 (1): 63–70. doi:10.1007/s00401-007-0226-5. PMID 17492294.
12. Sreedharan J, Blair IP, Tripathi VB, Hu X, Vance C, Rogelj B, Ackerley S, Durnall JC, Williams KL, Buratti E, Baralle F, de Belleroche J, Mitchell JD, Leigh PN, Al-Chalabi A, Miller CC, Nicholson G, Shaw CE (2008). "TDP-43 Mutations in Familial and Sporadic Amyotrophic Lateral Sclerosis". Science 319 (5870): 1668–72. doi:10.1126/science.1154584. PMID 18309045.
13. Gendron TF, Rademakers R, Petrucelli L (2013). "TARDBP mutation analysis in TDP-43 proteinopathies and deciphering the toxicity of mutant TDP-43". Journal of Alzheimer's Disease 33 (suppl 1): S35–S45. doi:10.3233/JAD-2012-129036. PMC 3532959. PMID 22751173.
14. Kim HJ, Kim NC, Wang YD, Scarborough EA, Moore J, Diaz Z, MacLea KS, Freibaum B, Li S, Molliex A, Kanagaraj AP, Carter R, Boylan KB, Wojtas AM, Rademakers R, Pinkus JL, Greenberg SA, Trojanowski JQ, Traynor BJ, Smith BN, Topp S, Gkazi AS, Miller J, Shaw CE, Kottlors M, Kirschner J, Pestronk A, Li YR, Ford AF, Gitler AD, Benatar M, King OD, Kimonis VE, Ross ED, Weihl CC, Shorter J, Taylor JP (March 2013). "Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS". Nature 495 (7442): 467–73. doi:10.1038/nature11922. PMC 3756911. PMID 23455423.
15. .Mompean, Miguel; Romano, Valentina; Pantoja-Uceda, David; Stuani, Cristiana; Baralle, Francisco E.; Buratti, Emanuele; Laurents, Douglas V. (2016-01-01). "The TDP-43 N-Terminal Domain Structure at High Resolution". FEBS Journal: n/a–n/a. doi:10.1111/febs.13651. ISSN 1742-4658.

Further reading

• Kwong LK, Neumann M, Sampathu DM, Lee VM, Trojanowski JQ (2007). "TDP-43 proteinopathy: The neuropathology underlying major forms of sporadic and familial frontotemporal lobar degeneration and motor neuron disease". Acta Neuropathologica 114 (1): 63–70. doi:10.1007/s00401-007-0226-5. PMID 17492294.
• Maruyama K, Sugano S (1994). "Oligo-capping: A simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides". Gene 138 (1–2): 171–4. doi:10.1016/0378-1119(94)90802-8. PMID 8125298.
• Tokai N, Fujimoto-Nishiyama A, Toyoshima Y, Yonemura S, Tsukita S, Inoue J, Yamamota T (1996). "Kid, a novel kinesin-like DNA binding protein, is localized to chromosomes and the mitotic spindle". The EMBO Journal 15 (3): 457–67. PMC 449964. PMID 8599929.
• Bonaldo MF, Lennon G, Soares MB (1996). "Normalization and subtraction: Two approaches to facilitate gene discovery". Genome Research 6 (9): 791–806. doi:10.1101/gr.6.9.791. PMID 8889548.
• Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, Suyama A, Sugano S (1997). "Construction and characterization of a full length-enriched and a 5′-end-enriched cDNA library". Gene 200 (1–2): 149–56. doi:10.1016/S0378-1119(97)00411-3. PMID 9373149.
• Hartley JL, Temple GF, Brasch MA (2000). "DNA Cloning Using in Vitro Site-Specific Recombination". Genome Research 10 (11): 1788–95. doi:10.1101/gr.143000. PMC 310948. PMID 11076863.
• Wiemann S, Weil B, Wellenreuther R, Gassenhuber J, Glassl S, Ansorge W, Böcher M, Blöcker H, Bauersachs S, Blum H, Lauber J, Düsterhöft A, Beyer A, Köhrer K, Strack N, Mewes HW, Ottenwälder B, Obermaier B, Tampe J, Heubner D, Wambutt R, Korn B, Klein M, Poustka A (2001). "Toward a Catalog of Human Genes and Proteins: Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs". Genome Research 11 (3): 422–35. doi:10.1101/gr.GR1547R. PMC 311072. PMID 11230166.
• Buratti E, Dörk T, Zuccato E, Pagani F, Romano M, Baralle FE (2001). "Nuclear factor TDP-43 and SR proteins promote in vitro and in vivo CFTR exon 9 skipping". The EMBO Journal 20 (7): 1774–84. doi:10.1093/emboj/20.7.1774. PMC 145463. PMID 11285240.
• Buratti E, Baralle FE (2001). "Characterization and Functional Implications of the RNA Binding Properties of Nuclear Factor TDP-43, a Novel Splicing Regulator of CFTR Exon 9". Journal of Biological Chemistry 276 (39): 36337–43. doi:10.1074/jbc.M104236200. PMID 11470789.
• Wang IF, Reddy NM, Shen CK (2002). "Higher order arrangement of the eukaryotic nuclear bodies". Proceedings of the National Academy of Sciences 99 (21): 13583–8. doi:10.1073/pnas.212483099. PMC 129717. PMID 12361981.
• Lehner B, Sanderson CM (2004). "A Protein Interaction Framework for Human mRNA Degradation". Genome Research 14 (7): 1315–23. doi:10.1101/gr.2122004. PMC 442147. PMID 15231747.
• Wiemann S, Arlt D, Huber W, Wellenreuther R, Schleeger S, Mehrle A, Bechtel S, Sauermann M, Korf U, Pepperkok R, Sültmann H, Poustka A (2004). "From ORFeome to Biology: A Functional Genomics Pipeline". Genome Research 14 (10b): 2136–44. doi:10.1101/gr.2576704. PMC 528930. PMID 15489336.
• Buratti E, Brindisi A, Giombi M, Tisminetzky S, Ayala YM, Baralle FE (2005). "TDP-43 Binds Heterogeneous Nuclear Ribonucleoprotein A/B through Its C-terminal Tail: AN IMPORTANT REGION FOR THE INHIBITION OF CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR EXON 9 SPLICING". Journal of Biological Chemistry 280 (45): 37572–84. doi:10.1074/jbc.M505557200. PMID 16157593.
• Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, Toksöz E, Droege A, Krobitsch S, Korn B, Birchmeier W, Lehrach H, Wanker EE (2005). "A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome". Cell 122 (6): 957–68. doi:10.1016/j.cell.2005.08.029. PMID 16169070.
• Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M (2005). "Towards a proteome-scale map of the human protein–protein interaction network". Nature 437 (7062): 1173–8. doi:10.1038/nature04209. PMID 16189514.
• Mehrle A, Rosenfelder H, Schupp I, del Val C, Arlt D, Hahne F, Bechtel S, Simpson J, Hofmann O, Hide W, Glatting KH, Huber W, Pepperkok R, Poustka A, Wiemann S (2006). "The LIFEdb database in 2006". Nucleic Acids Research 34 (90001): D415. doi:10.1093/nar/gkj139. PMC 1347501. PMID 16381901.

External links

• GeneReviews/NCBI/NIH/UW entry on TARDBP-Related Amyotrophic Lateral Sclerosis