Fig. 3

Comparative secretome analysis of S. lividans TK24 and RG1.9 strains. (A) Proteins secreted by the parental and by the RG1.9 strains were differentially abundant. Blue: more abundant in the parental strain; red: more abundant in the RG1.9 strain. The secretome amount that was produced by a fixed amount of cell biomass was loaded for both strains for proteomics analysis. (B) The summary of proteins that were differentially abundant in the secretome of the parental and the RG1.9 strains is shown as volcano plots (for detailed description see panel C and Table S1). Each dot represents one protein. Blue: more abundant in the parental strain; Red: more abundant in the RG1.9 strain. Plotted on the x axis is the fold difference (in log₂ scale) of the mean protein abundance in the parental strain over that in RG1.9, and on the y axis the p-value derived from a t-test between the two strains (–log₁₀, adjusted from [64]. (C) Classification of the differentially abundant proteins based on their biological function, as described [52]. The ratio ‘number of differentially abundant proteins that belong to the indicated functional group/ total number of differentially abundant proteins in the same strain’ is plotted. The dataset was filtered in order to retain secreted proteins and eliminate contaminating cytoplasmic proteins. Functional groups are coded with latin numbers as indicated. (D) Clustering of iBAQ values for proteins that showed differential abundance in the secretome of the parental and of the RG1.9 strains. Proteins have been annotated with both S. lividans TK24 (SLIV) and S. coelicolor (SCO) gene IDs. Latin numbers next to gene IDs indicate protein functions as these were grouped in panel C