PXD058854-1

PXD058854 is an original dataset announced via ProteomeXchange.

Title	Probing condensate microenvironments and functions with a micropeptide “killswitch”
Description	Biomolecular condensates are implicated in many cellular processes, and are thought to create subcellular microenvironments that regulate specific biochemical activities. For example, in vitro experiments suggest that condensates enable non-stoichiometric enrichment of small molecules within condensates. However, probing the microenvironments of condensates in cells is a major challenge, because tools to selectively manipulate specific condensates in living cells are limited. Here we developed a non-natural micropeptide (i.e., 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 an ability to self-associate, and no homology to human proteins. When recruited to endogenous and disease-specific condensates in human cells, the killswitch arrested the dynamics of the condensate-forming proteins, which led to predicted and unexpected effects. Targeting the killswitch to the nucleolar protein NPM1 altered nucleolar composition, and inhibited the dynamics of a ribosomal protein within nucleoli. Targeting the killswitch to fusion oncoprotein condensates inhibited the dynamics of effector proteins in the condensates, altered condensate composition, and inhibited proliferation of condensate-driven leukemia cells. In adenoviral nuclear condensates, the killswitch inhibited partitioning of capsid protein 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 the dynamics 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 in living systems.
HostingRepository	PRIDE
AnnounceDate	2025-04-15
AnnouncementXML	Submission_2025-04-15_07:11:15.265.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	David Meierhofer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	timsTOF SCP

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-13 07:30:37	ID requested
⏵ 1	2025-04-15 07:11:15	announced

Dataset with its publication pending

submitter keyword: condensates

Denes Hnisz
contact affiliation	Denes Hnisz, PhD Dept. of Genome Regulation Max Planck Institute for Molecular Genetics Ihnestraße 63-73 14195 Berlin, Germany
contact email	hnisz@molgen.mpg.de
lab head
David Meierhofer
contact affiliation	Mass Spectrometry Facility MPIMG
contact email	meierhof@molgen.mpg.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/04/PXD058854

PRIDE project URI

• PRIDE
  1. PXD058854
     1. Label: PRIDE project
     2. Name: Probing condensate microenvironments and functions with a micropeptide “killswitch”