Figure 3. Ribosomal proteins (RPs) and RNA-binding proteins (RBPs) show distinct patterns of polysome enrichment.

(A) The label-free quantification (LFQ) intensities for each RP identified in all conditions F1–F5 were normalised to Rps3/uS3 on a fraction-by-fraction basis and then to unstressed F1. Boxplots showing the distribution of normalised LFQ intensities in each sample. (B) Polysome association profiles for three example RPs normalised to Rps3/uS3. Shaded areas show mean ± standard deviation (SD). (C) Clustered ‘polysome enrichment profiles’ for proteins identified under all three conditions in F1–F4. The LFQ intensities for each protein were normalised only to its own mean across the unstressed fractions. T – total. The overall ribosome association and PE during stress for each cluster or group of clusters is indicated: Poly – polysome-enriched, Mono – monosome-enriched, Even – equally enriched in all fractions.

Figure 3—figure supplement 1. Metabolic functions are enriched among RNA-binding proteins (RBPs) identified in polysomal fractions.

Overrepresentation analysis of gene ontology (GO) terms associated with proteins in all conditions F1–F4, performed using the R package clusterProfiler. p values were calculated using Fisher’s exact test, with false discovery rate (FDR) correction for multiple testing. The set of all proteins identified in at least one mass spectrometry (MS) sample was used as the background (Supplementary file 1 – sheet 1). To focus on RBPs and other proteins, ribosomal proteins (RPs) and translation factors were also excluded from both the test set and the background set. Only enriched terms with p value ≤0.01 (−log₁₀(adjusted p value) ≥2) are shown. Gene ratio is the proportion of the test set annotated with a given GO term. BP – biological process, MF – molecular function. No cellular component (CC) terms were significantly enriched in this set. See Supplementary file 1 – sheet 4 for the full list of proteins associated with each term.