Abstract
Research into how the young and old differ, and which biomarkers reflect the diverse biological processes underlying ageing, is a current and fast-growing field. Biological clocks provide a means to evaluate whether a molecule, cell, tissue or even an entire organism is old or young. Here we summarize established and emerging molecular clocks as timepieces. We emphasize that intrinsically disordered proteins (IDPs) tend to transform into a β-sheet-rich aggregated state and accumulate in non-dividing or slowly dividing cells as they age. We hypothesize that understanding these protein-based molecular ageing mechanisms might provide a conceptual pathway to determining a cell’s health age by probing the aggregation state of IDPs, which we term the IDP clock.
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References
Moqri, M. et al. Biomarkers of aging for the identification and evaluation of longevity interventions. Cell 186, 3758–3775 (2023).
López-Otín, C., Blasco, M. A., Partridge, L., Serrano, M. & Kroemer, G. Hallmarks of aging: an expanding universe. Cell 186, 243–278 (2023).
Gladyshev, V. N. et al. Molecular damage in aging. Nat. Aging 1, 1096–1106 (2021).
Horvath, S. & Raj, K. DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat. Rev. Genet. 19, 371–384 (2018).
Field, A. E. et al. DNA methylation clocks in aging: categories, causes, and consequences. Mol. Cell 71, 882–895 (2018).
Lee, H. Y., Lee, S. D. & Shin, K.-J. Forensic DNA methylation profiling from evidence material for investigative leads. BMB Rep. 49, 359–369 (2016).
Jackson, S. H. D., Weale, M. R. & Weale, R. A. Biological age—what is it and can it be measured? Arch. Gerontol. Geriatr. 36, 103–115 (2003).
Vaiserman, A. & Krasnienkov, D. Telomere length as a marker of biological age: state-of-the-art, open issues, and future perspectives. Front. Genet. 11, 630186 (2020).
Babu, M. M., Kriwacki, R. W. & Pappu, R. V. Structural biology. Versatility from protein disorder. Science 337, 1460–1461 (2012).
Dyson, H. J. & Wright, P. E. Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol. 6, 197–208 (2005).
Dobson, C. M. Protein misfolding, evolution and disease. Trends Biochem. Sci. 24, 329–332 (1999).
Scheres, S. H. W., Ryskeldi-Falcon, B. & Goedert, M. Molecular pathology of neurodegenerative diseases by cryo-EM of amyloids. Nature 621, 701–710 (2023).
Arseni, D. et al. Structure of pathological TDP-43 filaments from ALS with FTLD. Nature 601, 139–143 (2022).
Chatani, E. & Yamamoto, N. Recent progress on understanding the mechanisms of amyloid nucleation. Biophys. Rev. 10, 527–534 (2018).
Ke, P. C. et al. Half a century of amyloids: past, present and future. Chem. Soc. Rev. 49, 5473–5509 (2020).
Dobson, C. M., Knowles, T. P. J. & Vendruscolo, M. The amyloid phenomenon and its significance in biology and medicine. Cold Spring Harb. Perspect. Biol. 12, a033878 (2020).
Chiti, F. & Dobson, C. M. Protein misfolding, amyloid formation, and human disease: a summary of progress over the last decade. Annu. Rev. Biochem. 86, 27–68 (2017).
Iadanza, M. G., Jackson, M. P., Hewitt, E. W., Ranson, N. A. & Radford, S. E. A new era for understanding amyloid structures and disease. Nat. Rev. Mol. Cell Biol. 19, 755–773 (2018).
Alberti, S. & Hyman, A. A. Biomolecular condensates at the nexus of cellular stress, protein aggregation disease and ageing. Nat. Rev. Mol. Cell Biol. 22, 196–213 (2021).
Vendruscolo, M. & Fuxreiter, M. Sequence determinants of the aggregation of proteins within condensates generated by liquid-liquid phase separation. J. Mol. Biol. 434, 167201 (2022).
Alberti, S. & Dormann, D. Liquid-liquid phase separation in disease. Annu Rev. Genet 53, 171–194 (2019).
Serio, T. R. et al. Nucleated conformational conversion and the replication of conformational information by a prion determinant. Science 289, 1317–1321 (2000).
Serio, T. R. & Lindquist, S. L. Protein-only inheritance in yeast: something to get [PSI+]-ched about. Trends Cell Biol. 10, 98–105 (2000).
Šarić, A., Chebaro, Y. C., Knowles, T. P. J. & Frenkel, D. Crucial role of non-specific interactions in amyloid nucleation. Proc. Natl Acad. Sci. USA 111, 17869–17874 (2014).
Ray, S. et al. Mass photometric detection and quantification of nanoscale α-synuclein phase separation. Nat. Chem. 15, 1306–1316 (2023).
Kar, M. et al. Phase separating RNA binding proteins form heterogeneous distributions of clusters in subsaturated solutions. Proc. Natl Acad. Sci. USA 119, e2202222119 (2022).
Shin, Y. & Brangwynne, C. P. Liquid phase condensation in cell physiology and disease. Science 357, eaaf4382 (2017).
Boeynaems, S. et al. Protein phase separation: a new phase in cell biology. Trends Cell Biol. 28, 420–435 (2018).
Patel, A. et al. A liquid-to-solid phase transition of the ALS protein FUS accelerated by disease mutation. Cell 162, 1066–1077 (2015).
Zhang, P. et al. Chronic optogenetic induction of stress granules is cytotoxic and reveals the evolution of ALS-FTD pathology. eLife 8, e39578 (2019).
Shen, Y. et al. The liquid-to-solid transition of FUS is promoted by the condensate surface. Proc. Natl Acad. Sci. USA 120, e2301366120 (2023).
Linsenmeier, M. et al. The interface of condensates of the hnRNPA1 low-complexity domain promotes formation of amyloid fibrils. Nat. Chem. 15, 1340–1349 (2023).
Emmanouilidis, L. et al. A solid beta-sheet structure is formed at the surface of FUS droplets during aging. Nat. Chem. Biol. https://doi.org/10.1038/s41589-024-01573-w (2024).
Lashuel, H. A. Rethinking protein aggregation and drug discovery in neurodegenerative diseases: why we need to embrace complexity? Curr. Opin. Chem. Biol. 64, 67–75 (2021).
Bolognesi, B. et al. The mutational landscape of a prion-like domain. Nat. Commun. 10, 4162 (2019).
Labbadia, J. & Morimoto, R. I. The biology of proteostasis in aging and disease. Annu. Rev. Biochem. 84, 435–464 (2015).
Hipp, M. S., Kasturi, P. & Hartl, F. U. The proteostasis network and its decline in ageing. Nat. Rev. Mol. Cell Biol. 20, 421–435 (2019).
Patel, A. et al. ATP as a biological hydrotrope. Science 356, 753–756 (2017).
Gallotta, I. et al. Extracellular proteostasis prevents aggregation during pathogenic attack. Nature 584, 410–414 (2020).
Rutledge, B. S., Choy, W.-Y. & Duennwald, M. L. Folding or holding?—Hsp70 and Hsp90 chaperoning of misfolded proteins in neurodegenerative disease. J. Biol. Chem. 298, 101905 (2022).
Hofweber, M. et al. Phase separation of FUS is suppressed by its nuclear import receptor and arginine methylation. Cell 173, 706–719.e13 (2018).
Yoshizawa, T. et al. Nuclear import receptor inhibits phase separation of FUS through binding to multiple sites. Cell 173, 693–705.e22 (2018).
Guo, L. et al. Nuclear-import receptors reverse aberrant phase transitions of rna-binding proteins with prion-like domains. Cell 173, 677–692.e20 (2018).
Milles, S. et al. Facilitated aggregation of FG nucleoporins under molecular crowding conditions. EMBO Rep. 14, 178–183 (2013).
Mateju, D. et al. An aberrant phase transition of stress granules triggered by misfolded protein and prevented by chaperone function. EMBO J. 36, 1669–1687 (2017).
Bah, A. & Forman-Kay, J. D. Modulation of intrinsically disordered protein function by post-translational modifications. J. Biol. Chem. 291, 6696–6705 (2016).
Hofweber, M. & Dormann, D. Friend or foe—Post-translational modifications as regulators of phase separation and RNP granule dynamics. J. Biol. Chem. 294, 7137–7150 (2019).
Simandi, Z. et al. Arginine methyltransferase PRMT8 provides cellular stress tolerance in aging motoneurons. J. Neurosci. 38, 7683–7700 (2018).
Das, T. et al. Metastable condensates suppress conversion to amyloid fibrils. Preprint at bioRxiv https://doi.org/10.1101/2024.02.28.582569 (2024).
Mann, J. R. et al. RNA binding antagonizes neurotoxic phase transitions of TDP-43. Neuron 102, 321–338.e8 (2019).
Maharana, S. et al. RNA buffers the phase separation behavior of prion-like RNA binding proteins. Science 360, 918–921 (2018).
Simonsen, A. & Wollert, T. Don’t forget to be picky – selective autophagy of protein aggregates in neurodegenerative diseases. Curr. Opin. Cell Biol. 75, 102064 (2022).
Adriaenssens, E., Ferrari, L. & Martens, S. Orchestration of selective autophagy by cargo receptors. Curr. Biol. 32, R1357–R1371 (2022).
Noda, N. N., Wang, Z. & Zhang, H. Liquid-liquid phase separation in autophagy. J. Cell Biol. 219, e202004062 (2020).
Zhang, Y. et al. SEPA-1 mediates the specific recognition and degradation of P granule components by autophagy in C. elegans. Cell 136, 308–321 (2009).
Yamasaki, A. et al. Liquidity is a critical determinant for selective autophagy of protein condensates. Mol. Cell 77, 1163–1175.e9 (2020).
Wong, Y. C. & Holzbaur, E. L. F. The regulation of autophagosome dynamics by huntingtin and HAP1 is disrupted by expression of mutant huntingtin, leading to defective cargo degradation. J. Neurosci. 34, 1293–1305 (2014).
Si, K. Prions: what are they good for? Annu. Rev. Cell Dev. Biol. 31, 149–169 (2015).
Berchowitz, L. E. et al. Regulated formation of an amyloid-like translational repressor governs gametogenesis. Cell 163, 406–418 (2015).
Fowler, D. M. et al. Functional amyloid formation within mammalian tissue. PLoS Biol. 4, e6 (2006).
Lechler, M. C. et al. Reduced insulin/IGF-1 signaling restores the dynamic properties of key stress granule proteins during aging. Cell Rep. 18, 454–467 (2017).
Harel, I. et al. Identification of protein aggregates in the aging vertebrate brain with prion-like and phase separation properties. Preprint at bioRxiv https://doi.org/10.1101/2022.02.26.482115 (2022).
Chen, Y. R. et al. Tissue-specific landscape of protein aggregation and quality control in an aging vertebrate. Preprint at bioRxiv https://doi.org/10.1101/2022.02.26.482120 (2022).
Vecchi, G. et al. Proteome-wide observation of the phenomenon of life on the edge of solubility. Proc. Natl Acad. Sci. USA 117, 1015–1020 (2020).
Hampel, H. et al. Blood-based biomarkers for Alzheimer’s disease: current state and future use in a transformed global healthcare landscape. Neuron 111, 2781–2799 (2023).
Jucker, M. & Walker, L. C. Propagation and spread of pathogenic protein assemblies in neurodegenerative diseases. Nat. Neurosci. 21, 1341–1349 (2018).
Privé, G. G. Detergents for the stabilization and crystallization of membrane proteins. Methods 41, 388–397 (2007).
Gwosch, K. C. et al. MINFLUX nanoscopy delivers 3D multicolor nanometer resolution in cells. Nat. Methods 17, 217–224 (2020).
Xu, M., Ren, W., Tang, X., Hu, Y. & Zhang, H. Advances in development of fluorescent probes for detecting amyloid-β aggregates. Acta Pharmacol. Sin. 37, 719–730 (2016).
Strømland, Ø., Jakubec, M., Furse, S. & Halskau, Ø. Detection of misfolded protein aggregates from a clinical perspective. J. Clin. Transl. Res 2, 11–26 (2016).
Altay, M. F. et al. Development and validation of an expanded antibody toolset that captures alpha-synuclein pathological diversity in Lewy body diseases. NPJ Parkinsons Dis. 9, 161 (2023).
Fang, Y.-S. et al. Full-length TDP-43 forms toxic amyloid oligomers that are present in frontotemporal lobar dementia-TDP patients. Nat. Commun. 5, 4824 (2014).
Shuken, S. R. et al. Limited proteolysis–mass spectrometry reveals aging-associated changes in cerebrospinal fluid protein abundances and structures. Nat. Aging 2, 379–388 (2022).
Dasari, S. et al. Amyloid typing by mass spectrometry in clinical practice: a comprehensive review of 16,175 samples. Mayo Clin. Proc. 95, 1852–1864 (2020).
Ling, S.-C., Polymenidou, M. & Cleveland, D. W. Converging mechanisms in ALS and FTD: disrupted RNA and protein homeostasis. Neuron 79, 416–438 (2013).
Tziortzouda, P., Van Den Bosch, L. & Hirth, F. Triad of TDP43 control in neurodegeneration: autoregulation, localization and aggregation. Nat. Rev. Neurosci. 22, 197–208 (2021).
Partridge, L., Deelen, J. & Slagboom, P. E. Facing up to the global challenges of ageing. Nature 561, 45–56 (2018).
McMahon, M., Forester, C. & Buffenstein, R. Aging through an epitranscriptomic lens. Nat. Aging 1, 335–346 (2021).
Galkin, F. et al. Human gut microbiome aging clock based on taxonomic profiling and deep learning. iScience 23, 101199 (2020).
Krištić, J. et al. Glycans are a novel biomarker of chronological and biological ages. J. Gerontology: Ser. A 69, 779–789 (2014).
Sayed, N. et al. An inflammatory aging clock (iAge) based on deep learning tracks multimorbidity, immunosenescence, frailty and cardiovascular aging. Nat. Aging 1, 598–615 (2021).
Lehallier, B. et al. Undulating changes in human plasma proteome profiles across the lifespan. Nat. Med. 25, 1843–1850 (2019).
Oh, H. S.-H. et al. Organ aging signatures in the plasma proteome track health and disease. Nature 624, 164–172 (2023).
Acknowledgements
We thank all members of the Dormann and Lemke laboratories for discussions, and P. Baumann and C. Niehrs for discussions on the telomere and methylation clocks. We are grateful to N. Heinss for her creative work on illustrations. D.D. and E.A.L. acknowledge funding from the CRC1551 “Polymer concepts in cellular function” of the Deutsche Forschungsgemeinschaft (project number 464588647).
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Dormann, D., Lemke, E.A. Adding intrinsically disordered proteins to biological ageing clocks. Nat Cell Biol 26, 851–858 (2024). https://doi.org/10.1038/s41556-024-01423-w
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DOI: https://doi.org/10.1038/s41556-024-01423-w