biostudies-literatureDumelie JGU.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of HealthNICHD NIH HHSNIEHS NIH HHSNINDS NIH HHSNCI NIH HHSNIAMS NIH HHSU.S. Department of Health & Human Services | National Institutes of HealthNIH HHS302-313https://www.ebi.ac.uk/biostudies/studies/S-EPMC10922641biostudies-literatureUnknown20(3)Proteins and RNA can phase separate from the aqueous cellular environment to form subcellular compartments called condensates. This process results in a protein-RNA mixture that is chemically different from the surrounding aqueous phase. Here, we use mass spectrometry to characterize the metabolomes of condensates. To test this, we prepared mixtures of phase-separated proteins and extracts of cellular metabolites and identified metabolites enriched in the condensate phase. Among the most condensate-enriched metabolites were phospholipids, due primarily to the hydrophobicity of their fatty acyl moieties. We found that phospholipids can alter the number and size of phase-separated condensates and in some cases alter their morphology. Finally, we found that phospholipids partition into a diverse set of endogenous condensates as well as artificial condensates expressed in cells. Overall, these data show that many condensates are protein-RNA-lipid mixtures with chemical microenvironments that are ideally suited to facilitate phospholipid biology and signaling.Nature chemical biologyBiomolecular condensates create phospholipid-enriched microenvironments.PMC10922641R21ES032347R01 CA186702R35 NS111631R01CA186702P01 HD067244R21 NS118233R21 ES032347R01AR076029R35NS111631R21NS118633S10 OD030335R01 AR076029Dumelie JGGross SSChen QAttarwala NMiller DJaffrey SRfalseBiomolecular condensates create phospholipid-enriched microenvironments.Proteins and RNA can phase separate from the aqueous cellular environment to form subcellular compartments called condensates. This process results in a protein-RNA mixture that is chemically different from the surrounding aqueous phase. Here, we use mass spectrometry to characterize the metabolomes of condensates. To test this, we prepared mixtures of phase-separated proteins and extracts of cellular metabolites and identified metabolites enriched in the condensate phase. Among the most condensate-enriched metabolites were phospholipids, due primarily to the hydrophobicity of their fatty acyl moieties. We found that phospholipids can alter the number and size of phase-separated condensates and in some cases alter their morphology. Finally, we found that phospholipids partition into a diverse set of endogenous condensates as well as artificial condensates expressed in cells. Overall, these data show that many condensates are protein-RNA-lipid mixtures with chemical microenvironments that are ideally suited to facilitate phospholipid biology and signaling.2024-01-01T00:00:00Z2024 Mar2026-06-02T19:15:43.037Z2025-04-04T02:47:50.253ZS-EPMC109226413797388910.1038/s41589-023-01474-4