Good Prion, Bad Prion: TDP-43 Domain Plays Both Sides

What do prion-like proteins do when not converting neighbors to dangerous conformations? One of them helps stabilize functional protein complexes, according to a paper in the April 3 Nature Communications. The authors report that a prion-like domain is key to TDP-43’s cellular location in the nucleus and its function in RNA splicing. They theorize that the domain either brings together normal TDP-43 molecules or binds up abnormal fragments in pathological aggregates. The outcome hinges on the prion sequence itself. When harboring amyotrophic lateral sclerosis-linked mutations, TDP--43’s carboxyl terminus, including the prionesque domain, is released by proteolysis to form the undesirable inclusions, but in the normal form, the same domain promotes associations needed for the protein’s regular function, the authors conclude. TDP-43 is also involved in some forms of frontotemporal lobar dementia (Neumann et al., 2007; Mackenzie et al., 2010).

The results suggest that in TDP-43-linked diseases, neurons suffer when the prion-like domain fails in its regular duties and compromises the protein’s normal function, wrote study first author I--Fan Wang of the Academia Sinica, the national research center in Taipei, Taiwan, in an email to ARF. Che-Kun James Shen, at the same institute, was senior author.

Sequence gazing, Wang and colleagues observed several years ago that the carboxyl end of TDP-43 contains a prion-like stretch similar to that of the yeast protein SupN (Wang et al., 2008). TDP-43’s propensity to aggregate also points to a prionesque phenotype (see ARF related news story on Fuentealba et al., 2010). However, the segment does not fit all aspects of the prion definition, Wang noted; for example, it does not interact with the amyloid-specific dye Congo red. The Taiwan group is one of a handful of labs investigating TDP-43’s prion-like properties (see ARF related news story on Guo et al., 2011; ARF related news story on Fuentealba et al., 2010; ARF related news story on Sun et al., 2011 and Ju et al., 2011).

The current study supports others that found prion-like sequences were part of the problem, but it also emphasizes their natural, healthy role, said James Shorter of the University of Pennsylvania in Philadelphia. In so doing, Shorter said, the work offers a solution to a nagging question: Why would a protein like TDP-43 evolve a prion-like domain if prions cause pathology? According to these data, “the prion-like portion of TDP-43 is like a double-edged sword,” Shorter said. “You need it to achieve TDP-43 function, but at the same time [it] causes problems in protein folding.” Shorter was not involved with the study.

To investigate the similarities between the TDP-43 and yeast prion domains, the researchers swapped TDP-43’s prion-like section for the SupN version and found that anything TDP-43 could do, their TDPSupN construct could do, too. When expressed in 293T human embryonic kidney cultures, each formed two different kinds of nuclear structures visible on fluorescence microscopy: stable granules sized 50-200 nanometers across, and irregular puncta that rapidly formed and dissolved. TDP-43, an RNA-binding protein, is well known to aid excision of exon 9 of the cystic fibrosis transmembrane conductance regulator (CFTR) gene—although the precise mechanism is unknown (Buratti et al., 2001)—and the chimera also completed this task, the team discovered.

TDP-43 appeared to need a prion-like domain to self-assemble into functional complexes. A deletion mutant without that section remained diffuse in the nucleus and associated poorly with full-length TDP-43 in co-immunoprecipitation assays. The deletion construct also failed to properly splice CFTR. Similarly, a mutation in the prionesque section designed to break up the protein’s structure (proline for glutamine 303) downgraded CFTR splicing efficiency by roughly 24 percent. In some transfected cells, this construct moved into the cytoplasm, as occurs in many TDP-43 mutant systems and in ALS. This mutant also partially broke down, forming 24-kDa carboxyl-terminal fragments previously linked to ALS pathology (see ARF related news story on Zhang et al., 2007; ARF related news story on Pesiridis et al., 2011). “There is suspicion that this fragment causes a lot of the problems,” Shorter said. Other ALS-linked mutations in the prion-analog segment (348-cysteine and 361-serine) also partially reduced the exon-skipping skills of full-length TDP-43. However, these mutants assembled normal nuclear complexes, and did not fragment or move into the cytosol. Perhaps, the authors suggested, the mutations only slightly disrupted the prion fold, but not enough to cause full pathology or eliminate splicing activity.

The team also made a structure-breaking glycine-25-proline substitution in their TDPSupN construct (Chang et al., 2008). This version was less able to splice CFTR than the wild-type construct, and was found in both the nucleus and cytoplasm. A carboxyl-terminal fragment broke off at what could be the same cleavage site that releases the 24 kDa fragments from full-length TDP-43. “Impairing prion-like interactions of TDP-43 caused its degradation into a fragment identified in patients with early-stage TDP-43 proteinopathies,” Wang concluded. That is, without the normal interactions mediated by the prion domain, the protein is likely to fall apart—perhaps due to caspase action. Not only does this cause loss of TDP-43’s normal nuclear function, but it also potentially causes a gain of function in the production of toxic fragments that form pathological aggregates. Conversely, in the normal full-length TDP-43, the authors propose that the prion domain is a good player, helping put together the complexes needed to process RNAs. A similar good-prion, bad-prion pathway may be occurring in other ALS-linked proteins that have prion-like domains, such as FUS, Shorter said (see ARF related news story on Couthouis et al., 2011).

Promoting the good prion interaction while combating the bad one, then, should prevent TDP-43 proteinopathy. “Compounds that stabilize functional aggregates of aggregation-prone domains may be investigated as therapies for protein misfolding,” the authors wrote. “This is particularly true for TDP-43 proteinopathies, because cleavage of TDP-43 proteins occurs before inclusion formation during disease progression.” Last November, for example, the European Commission approved tafamidis, a drug that stabilizes tetramers of transthyretin, to treat familial amyloid angiopathy. This disease occurs when transthyretin tetramers dissociate and form insoluble aggregates. Could a similar strategy work for ALS? In their cell cultures, Wang and colleagues tried out a green tea derivative, epigallocatechin gallate (EGCG), which is thought to stabilize oligomers and disassemble amyloids (Roberts et al., 2009; Bieschke et al., 2010). EGCG treatment blocked the degradation of TDP-43, TDPSupN, and the Q303P mutant. Wang has started a company, Garage Brain Science in Taichung, Taiwan, to screen for treatments, including a compound from traditional Chinese medicine.—Amber Dance

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References

News Citations

  1. Toxic TDP-43 Too Tough to Degrade, Plays Prion?
  2. ALS-Linked TDP-43 Turns Amyloid in the Lab
  3. Yeast Models Say TDP-43 and FUS Are Not Cut From the Same Cloth
  4. Progranulin Controls Cutting of Inclusion Protein
  5. Double Down: TDP-43 Fragments Bust Cells on Second Hit
  6. DC: New ALS Genetics Hog the Limelight at Satellite Conference

Paper Citations

  1. Neumann M, Mackenzie IR, Cairns NJ, Boyer PJ, Markesbery WR, Smith CD, Taylor JP, Kretzschmar HA, Kimonis VE, Forman MS. TDP-43 in the ubiquitin pathology of frontotemporal dementia with VCP gene mutations. J Neuropathol Exp Neurol. 2007 Feb;66(2):152-7. PubMed.
  2. Mackenzie IR, Rademakers R, Neumann M. TDP-43 and FUS in amyotrophic lateral sclerosis and frontotemporal dementia. Lancet Neurol. 2010 Oct;9(10):995-1007. PubMed.
  3. Wang IF, Wu LS, Shen CK. TDP-43: an emerging new player in neurodegenerative diseases. Trends Mol Med. 2008 Nov;14(11):479-85. PubMed.
  4. Fuentealba RA, Udan M, Bell S, Wegorzewska I, Shao J, Diamond MI, Weihl CC, Baloh RH. Interaction with polyglutamine aggregates reveals a Q/N-rich domain in TDP-43. J Biol Chem. 2010 Aug 20;285(34):26304-14. PubMed.
  5. Guo W, Chen Y, Zhou X, Kar A, Ray P, Chen X, Rao EJ, Yang M, Ye H, Zhu L, Liu J, Xu M, Yang Y, Wang C, Zhang D, Bigio EH, Mesulam M, Shen Y, Xu Q, Fushimi K, Wu JY. An ALS-associated mutation affecting TDP-43 enhances protein aggregation, fibril formation and neurotoxicity. Nat Struct Mol Biol. 2011 Jul;18(7):822-30. PubMed.
  6. Sun Z, Diaz Z, Fang X, Hart MP, Chesi A, Shorter J, Gitler AD. Molecular determinants and genetic modifiers of aggregation and toxicity for the ALS disease protein FUS/TLS. PLoS Biol. 2011 Apr;9(4):e1000614. PubMed.
  7. Ju S, Tardiff DF, Han H, Divya K, Zhong Q, Maquat LE, Bosco DA, Hayward LJ, Brown RH, Lindquist S, Ringe D, Petsko GA. A Yeast Model of FUS/TLS-Dependent Cytotoxicity. PLoS Biol. 2011 Apr;9(4):e1001052. PubMed.
  8. Buratti E, Dörk T, Zuccato E, Pagani F, Romano M, Baralle FE. Nuclear factor TDP-43 and SR proteins promote in vitro and in vivo CFTR exon 9 skipping. EMBO J. 2001 Apr 2;20(7):1774-84. PubMed.
  9. Zhang YJ, Xu YF, Dickey CA, Buratti E, Baralle F, Bailey R, Pickering-Brown S, Dickson D, Petrucelli L. Progranulin mediates caspase-dependent cleavage of TAR DNA binding protein-43. J Neurosci. 2007 Sep 26;27(39):10530-4. PubMed.
  10. Pesiridis GS, Tripathy K, Tanik S, Trojanowski JQ, Lee VM. A "two-hit" hypothesis for inclusion formation by carboxyl-terminal fragments of TDP-43 protein linked to RNA depletion and impaired microtubule-dependent transport. J Biol Chem. 2011 May 27;286(21):18845-55. PubMed.
  11. Chang HY, Lin JY, Lee HC, Wang HL, King CY. Strain-specific sequences required for yeast [PSI+] prion propagation. Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13345-50. PubMed.
  12. Couthouis J, Hart MP, Shorter J, Dejesus-Hernandez M, Erion R, Oristano R, Liu AX, Ramos D, Jethava N, Hosangadi D, Epstein J, Chiang A, Diaz Z, Nakaya T, Ibrahim F, Kim HJ, Solski JA, Williams KL, Mojsilovic-Petrovic J, Ingre C, Boylan K, Graff-Radford NR, Dickson DW, Clay-Falcone D, Elman L, McCluskey L, Greene R, Kalb RG, Lee VM, Trojanowski JQ, Ludolph A, Robberecht W, Andersen PM, Nicholson GA, Blair IP, King OD, Bonini NM, Van Deerlin V, Rademakers R, Mourelatos Z, Gitler AD. Feature Article: From the Cover: A yeast functional screen predicts new candidate ALS disease genes. Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):20881-90. PubMed. Correction.
  13. Roberts BE, Duennwald ML, Wang H, Chung C, Lopreiato NP, Sweeny EA, Knight MN, Shorter J. A synergistic small-molecule combination directly eradicates diverse prion strain structures. Nat Chem Biol. 2009 Dec;5(12):936-46. PubMed.
  14. Bieschke J, Russ J, Friedrich RP, Ehrnhoefer DE, Wobst H, Neugebauer K, Wanker EE. EGCG remodels mature alpha-synuclein and amyloid-beta fibrils and reduces cellular toxicity. Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7710-5. PubMed.

Further Reading

Papers

  1. Münch C, O'brien J, Bertolotti A. Prion-like propagation of mutant superoxide dismutase-1 misfolding in neuronal cells. Proc Natl Acad Sci U S A. 2011 Mar 1;108(9):3548-53. PubMed.
  2. Reiniger L, Lukic A, Linehan J, Rudge P, Collinge J, Mead S, Brandner S. Tau, prions and Aβ: the triad of neurodegeneration. Acta Neuropathol. 2011 Jan;121(1):5-20. PubMed.
  3. Wang HY, Wang IF, Bose J, Shen CK. Structural diversity and functional implications of the eukaryotic TDP gene family. Genomics. 2004 Jan;83(1):130-9. PubMed.
  4. Davidson Y, Kelley T, Mackenzie IR, Pickering-Brown S, Du Plessis D, Neary D, Snowden JS, Mann DM. Ubiquitinated pathological lesions in frontotemporal lobar degeneration contain the TAR DNA-binding protein, TDP-43. Acta Neuropathol. 2007 May;113(5):521-33. PubMed.
  5. Cushman M, Johnson BS, King OD, Gitler AD, Shorter J. Prion-like disorders: blurring the divide between transmissibility and infectivity. J Cell Sci. 2010 Apr 15;123(Pt 8):1191-201. PubMed.
  6. Mackenzie IR, Rademakers R. The role of transactive response DNA-binding protein-43 in amyotrophic lateral sclerosis and frontotemporal dementia. Curr Opin Neurol. 2008 Dec;21(6):693-700. PubMed.

Primary Papers

  1. Wang IF, Chang HY, Hou SC, Liou GG, Way TD, James Shen CK. The self-interaction of native TDP-43 C terminus inhibits its degradation and contributes to early proteinopathies. Nat Commun. 2012;3:766. PubMed.

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