Extended Data Fig. 3: The role of RNA in metabolite condensate partitioning.

a, To assess whether changes in generic phage RNA concentration alter condensate metabolomes, we compared nucleocapsid condensate metabolomes after varying the added RNA concentration. Median log₂-fold enrichment of phospholipids (blue, n = 51), lysophospholipids (green, n = 14), fatty acids (black, n = 21) and all other metabolites (orange, n = 257) in the nucleocapsid condensate fraction relative to input sample with 150 nM RNA (x-axis) was plotted against median log₂-fold enrichment with no RNA (y-axis; left) or 600 nM RNA (y-axis; right). Enrichment with 150 nM RNA correlates with enrichment in no RNA (r = 0.78, Pearson’s correlation coefficient) and 600 nM RNA (r = 0.85, Pearson’s correlation coefficient) samples. No metabolites were significantly different between 0 and 150 nM or 150 and 600 nM RNA samples (FDR > 0.1 for all metabolites, two-sided paired t-test with Benjamini-Hochberg adjustment). N = 3 for 150 nM RNA sample, n = 2 for other samples. b, To determine whether RNA concentration alters fatty acyl-dependent phospholipid partitioning, we compared the median log₂-fold condensate enrichment of phospholipids (n = 51), lysophospholipids (containing one fatty acyl moiety, n = 14) and glycerophosphoryl head groups (for example glycerophosphocholine, n = 3) in the condensate fraction of nucleocapsid with different RNA concentrations. Phospholipids and lysophospholipids are enriched relative to head groups in condensates formed with 0 nM (green; p = 0.004105, phospholipids; p = 0.002941, lysophospholipids), 150 nM (purple; p = 0.004105, phospholipids; p = 0.002941, lysophospholipids, also shown in Fig. 3a) or 600 nM (black; p = 0.004105, phospholipids; p = 0.002941, lysophospholipids) RNA. Individual metabolites are represented by dots, lines in violin plots represent quartiles. *p < 0.05 **p < 0.005, two-sided Wilcoxon rank-sum test (n = 3 for 150 nM RNA sample, n = 2 for other samples). c, A heat map was used to further analyze whether RNA concentration impacts phospholipid enrichment in nucleocapsid condensates. Each glycerophosphoryl head group, lysophospholipid and phospholipid’s median log₂-fold enrichment (blue indicates condensate de-enrichment and red indicates enrichment) is plotted for nucleocapsid condensates formed with 0 (left), 150 nM (middle) or 600 nM (right) RNA. Glycerophosphoryl head groups are sorted alphabetically, while lysophospholipids and phospholipids are sorted by the sum of carbons in their fatty acyl moieties after being grouped by head-group as demarked (y-axis).

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