Disease‐linked TDP‐43 hyperphosphorylation suppresses TDP‐43 condensation and aggregation

Abstract

Post-translational modifications (PTMs) have emerged as key modulators of protein phase separation and have been linked to protein aggregation in neurodegenerative disorders. The major aggregating protein in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), the RNA-binding protein TDP-43, is hyperphosphorylated in disease on several C-terminal serine residues, which is generally believed to promote TDP-43 aggregation. Here, we show that hyperphosphorylation by Casein kinase 1δ or C-terminal phosphomimetic mutations surprisingly reduce TDP-43 phase separation and aggregation and render TDP-43 condensates more liquid-like and dynamic. Multi-scale simulations reveal reduced homotypic interactions of TDP-43 low complexity domains through enhanced solvation of phosphomimetic residues. Cellular experiments show that phosphomimetic substitutions do not affect nuclear import or RNA regulatory functions of TDP-43, but suppress accumulation of TDP-43 in membrane-less organelles and promote its solubility in neurons. We propose that TDP-43 hyperphosphorylation may be a protective cellular response to counteract TDP-43 aggregation.

References 86

1. 1.

   Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B, Lindahl E (2015 ) GROMACS: high performance molecular simulations through multi‐level parallelism from laptops to supercomputers. SoftwareX 1–2: 19–25

   Not in our library

2. 2.
   Functional and dynamic polymerization of the ALS-linked protein TDP-43 antagonizes its pathologic aggregation · 2017

   No notice
3. 3.

   Alberti S (2017 ) Phase separation in biology. Curr Biol 27: R1097–R1102

   Not in our library10.1016/j.cub.2017.08.069

4. 4.

   Alberti S, Dormann D (2019 ) Liquid‐liquid phase separation in disease. Annu Rev Genet 53: 171–194

   Not in our library10.1146/annurev-genet-112618-043527

5. 5.

   Alberti S, Hyman AA (2021 ) Biomolecular condensates at the nexus of cellular stress, protein aggregation disease and ageing. Nat Rev Mol Cell Biol 22: 196–213

   Not in our library10.1038/s41580-020-00326-6

6. 6.
   Tau Post-translational Modifications: Dynamic Transformers of Tau Function, Degradation, and Aggregation · 2021

   No notice
7. 7.

   Avendano‐Vazquez SE, Dhir A, Bembich S, Buratti E, Proudfoot N, Baralle FE (2012 ) Autoregulation of TDP‐43 mRNA levels involves interplay between transcription, splicing, and alternative polyA site selection. Genes Dev 26: 1679–1684

   Not in our library10.1101/gad.194829.112

8. 8.

   Ayala YM, De Conti L, Avendaño‐Vázquez SE, Dhir A, Romano M, D'Ambrogio A, Tollervey J, Ule J, Baralle M, Buratti E et al (2011 ) TDP‐43 regulates its mRNA levels through a negative feedback loop. EMBO J 30: 277–288

   Not in our library10.1038/emboj.2010.310

9. 9.

   Babinchak WM, Haider R, Dumm BK, Sarkar P, Surewicz K, Choi JK, Surewicz WK (2019 ) The role of liquid‐liquid phase separation in aggregation of the TDP‐43 low‐complexity domain. J Biol Chem 294: 6306–6317

   Not in our library10.1074/jbc.ra118.007222

10. 10.

    Bah A, Forman‐Kay JD (2016 ) Modulation of intrinsically disordered protein function by post‐translational modifications. J Biol Chem 291: 6696–6705

    Not in our library10.1074/jbc.r115.695056

11. 11.

    Benayad Z, von Bulow S, Stelzl LS, Hummer G (2021 ) Simulation of FUS protein condensates with an adapted coarse‐grained model. J Chem Theory Comput 17: 525–537

    Not in our library10.1021/acs.jctc.0c01064

12. 12.
    The mutational landscape of a prion-like domain · 2019

    No notice
13. 13.

    Brady OA, Meng P, Zheng Y, Mao Y, Hu F (2011 ) Regulation of TDP‐43 aggregation by phosphorylation and p62/SQSTM1. J Neurochem 116: 248–259

    Not in our library10.1111/j.1471-4159.2010.07098.x

14. 14.

    Bremer A, Farag M, Borcherds WM, Peran I, Martin EW, Pappu RV, Mittag T (2021 ) Deciphering how naturally occurring sequence features impact the phase behaviors of disordered prion‐like domains. bioRxiv [PREPRINT]

    Not in our library10.1101/2021.01.01.425046

15. 15.

    Buratti E (2015 ) Functional significance of TDP‐43 mutations in disease. Adv Genet 91: 1–53

    Not in our library10.1016/bs.adgen.2015.07.001

16. 16.

    Buratti E (2018 ) TDP‐43 post‐translational modifications in health and disease. Expert Opin Ther Targets 22: 279–293

    Not in our library10.1080/14728222.2018.1439923

17. 17.

    Bussi G, Donadio D, Parrinello M (2007 ) Canonical sampling through velocity rescaling. J Chem Phys 126: 014101

    Not in our library10.1063/1.2408420

18. 18.

    Ceballos AV, McDonald CJ, Elbaum‐Garfinkle S (2018 ) Methods and strategies to quantify phase separation of disordered proteins. Methods Enzymol 611: 31–50

    Not in our library10.1016/bs.mie.2018.09.037

19. 19.

    Choksi DK, Roy B, Chatterjee S, Yusuff T, Bakhoum MF, Sengupta U, Ambegaokar S, Kayed R, Jackson GR (2014 ) TDP‐43 Phosphorylation by casein kinase Iepsilon promotes oligomerization and enhances toxicity in vivo. Hum Mol Genet 23: 1025–1035

    Not in our library10.1093/hmg/ddt498

20. 20.

    Conicella AE, Zerze GH, Mittal J, Fawzi NL (2016 ) ALS mutations disrupt phase separation mediated by alpha‐helical structure in the TDP‐43 low‐complexity C‐terminal domain. Structure 24: 1537–1549

    Not in our library10.1016/j.str.2016.07.007

21. 21.

    Conicella AE, Dignon GL, Zerze GH, Schmidt HB, D'Ordine AM, Kim YC, Rohatgi R, Ayala YM, Mittal J, Fawzi NL (2020 ) TDP‐43 alpha‐helical structure tunes liquid‐liquid phase separation and function. Proc Natl Acad Sci USA 117: 5883–5894

    Not in our library10.1073/pnas.1912055117

22. 22.

    Crabtree MD, Holland J, Kompella P, Babl L, Turner N, Baldwin AJ (2020 ) Repulsive electrostatic interactions modulate dense and dilute phase properties of biomolecular condensates. bioRxiv [PREPRINT]

    Not in our library10.1101/2020.10.29.357863

23. 23.
    Sequence determinants of protein phase behavior from a coarse-grained model · 2018

    No notice
24. 24.

    Dormann D, Capell A, Carlson AM, Shankaran SS, Rodde R, Neumann M, Kremmer E, Matsuwaki T, Yamanouchi K, Nishihara M et al (2009 ) Proteolytic processing of TAR DNA binding protein‐43 by caspases produces C‐terminal fragments with disease defining properties independent of progranulin. J Neurochem 110: 1082–1094

    Not in our library10.1111/j.1471-4159.2009.06211.x

25. 25.

    Durocher D, Henckel J, Fersht AR, Jackson SP (1999 ) The FHA domain is a modular phosphopeptide recognition motif. Mol Cell 4: 387–394

    Not in our library10.1016/s1097-2765(00)80340-8

26. 26.
    Nuclear egress of TDP-43 and FUS occurs independently of Exportin-1/CRM1 · 2018

    No notice
27. 27.

    Fiesel FC, Weber SS, Supper J, Zell A, Kahle PJ (2012 ) TDP‐43 regulates global translational yield by splicing of exon junction complex component SKAR. Nucleic Acids Res 40: 2668–2682

    Not in our library10.1093/nar/gkr1082

28. 28.

    French RL, Grese ZR, Aligireddy H, Dhavale DD, Reeb AN, Kedia N, Kotzbauer PT, Bieschke J, Ayala YM (2019 ) Detection of TAR DNA‐binding protein 43 (TDP‐43) oligomers as initial intermediate species during aggregate formation. J Biol Chem 294: 6696–6709

    Not in our library10.1074/jbc.ra118.005889

29. 29.

    Gasset‐Rosa F, Lu S, Yu H, Chen C, Melamed Z, Guo L, Shorter J, Da Cruz S, Cleveland DW (2019 ) Cytoplasmic TDP‐43 de‐mixing independent of stress granules drives inhibition of nuclear import, loss of nuclear TDP‐43, and cell death. Neuron 102: 339–357.e7

    Not in our library10.1016/j.neuron.2019.02.038

30. 30.

    Gowers RJ, Linke M, Barnoud J, Reddy TJE, Melo MN, Seyler SL, Domański J, Dotson DL, Buchoux S, Kenney IM et al (2016 ) MDAnalysis: a python package for the rapid analysis of molecular dynamics simulations. In Proceedings of the 15th Python in Science Conference, pp 98–105. Austin, TX: SciPy 2016

    Not in our library

31. 31.

    Guo Q, Lehmer C, Martínez‐Sánchez A, Rudack T, Beck F, Hartmann H, Pérez‐Berlanga M, Frottin F, Hipp MS, Hartl FU et al (2018 ) In situ structure of neuronal C9orf72 Poly‐GA aggregates reveals proteasome recruitment. Cell 172: 696–705.e12

    Not in our library10.1016/j.cell.2017.12.030

32. 32.

    Haj‐Yahya M, Gopinath P, Rajasekhar K, Mirbaha H, Diamond MI, Lashuel HA (2020 ) Site‐specific hyperphosphorylation inhibits, rather than promotes, tau fibrillization, seeding capacity, and its microtubule binding. Angew Chem Int Ed Engl 59: 4059–4067

    Not in our library10.1002/anie.201913001

33. 33.

    Halfmann R, Lindquist S (2008 ) Screening for amyloid aggregation by semi‐denaturing detergent‐agarose gel electrophoresis. J Vis Exp

    Not in our library10.3791/838

34. 34.

    Hasegawa M, Arai T, Nonaka T, Kametani F, Yoshida M, Hashizume Y, Beach TG, Buratti E, Baralle F, Morita M et al (2008 ) Phosphorylated TDP‐43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Ann Neurol 64: 60–70

    Not in our library10.1002/ana.21425

35. 35.

    Hofweber M, Dormann D (2019 ) Friend or foe‐Post‐translational modifications as regulators of phase separation and RNP granule dynamics. J Biol Chem 294: 7137–7150

    Not in our library10.1074/jbc.tm118.001189

36. 36.

    Hutten S, Dormann D (2020 ) A quantitative assay to measure stress granule association of proteins and peptides in semi‐permeabilized human cells. Bio‐protocol 10: e3846

    Not in our library10.21769/bioprotoc.3846

37. 37.

    Hutten S, Usluer S, Bourgeois B, Simonetti F, Odeh HM, Fare CM, Czuppa M, Hruska‐Plochan M, Hofweber M, Polymenidou M et al (2020 ) Nuclear import receptors directly bind to arginine‐rich dipeptide repeat proteins and suppress their pathological interactions. Cell Rep 33: 108538

    Not in our library10.1016/j.celrep.2020.108538

38. 38.

    Inukai Y, Nonaka T, Arai T, Yoshida M, Hashizume Y, Beach TG, Buratti E, Baralle FE, Akiyama H, Hisanaga S‐I et al (2008 ) Abnormal phosphorylation of Ser409/410 of TDP‐43 in FTLD‐U and ALS. FEBS Lett 582: 2899–2904

    Not in our library10.1016/j.febslet.2008.07.027

39. 39.

    Josephs KA, Whitwell JL, Weigand SD, Murray ME, Tosakulwong N, Liesinger AM, Petrucelli L, Senjem ML, Knopman DS, Boeve BF et al (2014 ) TDP‐43 is a key player in the clinical features associated with Alzheimer's disease. Acta Neuropathol 127: 811–824

    Not in our library10.1007/s00401-014-1269-z

40. 40.

    Kametani F, Nonaka T, Suzuki T, Arai T, Dohmae N, Akiyama H, Hasegawa M (2009 ) Identification of casein kinase‐1 phosphorylation sites on TDP‐43. Biochem Biophys Res Commun 382: 405–409

    Not in our library10.1016/j.bbrc.2009.03.038

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