2. Academic Validation
  3. Probing condensate microenvironments with a micropeptide killswitch

Probing condensate microenvironments with a micropeptide killswitch

  • Nature. 2025 Jul;643(8073):1107-1116. doi: 10.1038/s41586-025-09141-5.
Yaotian Zhang 1 2,  Ida Stöppelkamp # 1 2,  Pablo Fernandez-Pernas # 3,  Melanie Allram # 3,  Matthew Charman # 4 5 6,  Alexandre P Magalhaes 1,  Melanie Piedavent-Salomon 1,  Gregor Sommer 1,  Yu-Chieh Sung 1,  Katrina Meyer 1,  Nicholas Grams 5,  Edwin Halko 4 6,  Shivali Dongre 7,  David Meierhofer 1,  Michal Malszycki 1,  Ibrahim A Ilik 1,  Tugce Aktas 1,  Matthew L Kraushar 1,  Nadine Vastenhouw 7,  Matthew D Weitzman 4 5 6 8,  Florian Grebien 3 9 10,  Henri Niskanen 11,  Denes Hnisz 12
Affiliations

Affiliations

  • 1 Max Planck Institute for Molecular Genetics, Berlin, Germany.
  • 2 Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany.
  • 3 Centre of Biological Sciences, University of Veterinary Medicine, Vienna, Austria.
  • 4 Division of Protective Immunity, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
  • 5 Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
  • 6 Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
  • 7 Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
  • 8 Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
  • 9 St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
  • 10 CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
  • 11 Max Planck Institute for Molecular Genetics, Berlin, Germany. niskanen@molgen.mpg.de.
  • 12 Max Planck Institute for Molecular Genetics, Berlin, Germany. hnisz@molgen.mpg.de.
  • # Contributed equally.
PMID: 40468084 DOI: 10.1038/s41586-025-09141-5
Abstract

Biomolecular condensates are thought to create subcellular microenvironments that have different physicochemical properties compared with their surrounding nucleoplasm or cytoplasm1-5. However, probing the microenvironments of condensates and their relationship to biological function is a major challenge because tools to selectively manipulate specific condensates in living cells are limited6-9. Here, we develop a non-natural micropeptide (that is, the killswitch) and a nanobody-based recruitment system as a universal approach to probe endogenous condensates, and demonstrate direct links between condensate microenvironments and function in cells. The killswitch is a hydrophobic, aromatic-rich sequence with the ability to self-associate, and has no homology to human proteins. When recruited to endogenous and disease-specific condensates in human cells, the killswitch immobilized condensate-forming proteins, leading to both predicted and unexpected effects. Targeting the killswitch to the nucleolar protein NPM1 altered nucleolar composition and reduced the mobility of a ribosomal protein in nucleoli. Targeting the killswitch to fusion oncoprotein condensates altered condensate compositions and inhibited the proliferation of condensate-driven leukaemia cells. In adenoviral nuclear condensates, the killswitch inhibited partitioning of capsid proteins into condensates and suppressed viral particle assembly. The results suggest that the microenvironment within cellular condensates has an essential contribution to non-stoichiometric enrichment and mobility of effector proteins. The killswitch is a widely applicable tool to alter the material properties of endogenous condensates and, as a consequence, to probe functions of condensates linked to diverse physiological and pathological processes.

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