Fig. 5: Quantitative global proteome analysis of WT, ΔSEP-yp1, and ΔSEP-yp1-compl (compl) reveals that SEP-yp1 deletion reduces the expression of virulence proteins.

a Experimental workflow of label-free quantitative proteomics for screening the altered proteins in the bacteria due to SEP-yp1 deletion. N = 3 in each group. The multiple line plot shows the 189 proteins filtered by the criteria: opposite alteration trends between ΔSEP-yp1/WT and Compl/ΔSEP-yp1, p value (ΔSEP-yp1/WT) < 0.05, p value (Compl/ΔSEP-yp1) < 0.05, and p value (Compl/WT) > 0.05. b PCA analysis of all the quantifiable proteins in the three groups. c Scatter plots show the alteration of four altered virulence factors as well as RovA by quantitative proteomics. The statistical significance was calculated by unpaired t test adjusted by Benjamini–Hochberg procedure with FDR < 0.01. *P value < 0.05 and **p value < 0.01; ns nonsignificant. Error bars represent SEM. d Orthogonal validation of altered proteins by Western blotting. Each experiment has three biological replicates. e Schematic representation of Yersinia type III secretion apparatus. f KEGG analysis of the 189 altered proteins due to SEP-yp1 knockout. g Mapping the altered proteins onto the protein interaction network using the STRING database. One cluster represents the proteins involved in the metabolic pathways from KEGG analysis and another is associated with bacterial virulence. Refer to Supplementary Data 5 for details.