Dataset Information

Zebrafish embryo peptidomics characterization on Orbitrap Astral, Rawls Lab

ABSTRACT: LC-MS/MS characterization of peptidome of zebrafish embryo in adult or larval states.

INSTRUMENT(S):

ORGANISM(S): Danio Rerio (zebrafish) (brachydanio Rerio)

SUBMITTER: Erik Soderblom

LAB HEAD: John Rawls

PROVIDER: PXD058654 | Pride | 2025-01-21

REPOSITORIES: Pride

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			Action	DRS
	ID113914_01_SPD30_OA10034_10472_062924.raw	Raw
	ID113915_01_SPD30_OA10034_10472_062924.raw	Raw
	ID113916_01_SPD30_OA10034_10472_062924.raw	Raw
	ID113917_01_SPD30_OA10034_10472_062924.raw	Raw
	ID113918_01_SPD30_OA10034_10472_062924.raw	Raw

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Project 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.

Dataset Information

Zebrafish embryo peptidomics characterization on Orbitrap Astral, Rawls Lab

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