PMC

Hierarchical clustering of E. coli Big-Six group strains outer membrane proteins: The relative protein expression of outer membrane proteins was shown in a heat map. The fold-change value with K12 is log₂-transformed.

Result summary of E. coli Big-Six group strains secretome: (A) Venn diagram depicting the strains of secreted proteins from technical replicates. (B) The detailed summary of protein identifications from combined technical replicate analysis.

Hierarchical clustering of E. coli Big-Six group strains extracellular proteins: The relative protein expression of extracellular proteins was shown in a heat map. Two unique clusters were shown in clusters A and B in O103:H11 and O121:H19 strains, respectively.

Identification of strain-specific proteins in E. coli Big-Six group strains. (A) The strain-specific proteins in E. coli Big-Six group strains are shown. The genome of each strain was translated and mapped to each of the identified peptide. The presence of each strain-specific protein is shown as red. (B) Representative MS/MS spectrum of an identified peptide, DEAWVILEGHIVK of membrane protein (yhha) in E. coli O121:H19.

Hierarchical clustering of E. coli Big-Six group strains T3SS. The relative protein expression of T3SS system was shown in a heat map. Each row value for a given strain is a log₂ value of fold change with K12. Higher expression of T3SS-secreted proteins was observed in O45:H2 and O121:H19 strains.

MS-based quantitative profiling of E. coli Big-Six group strains secretome. A schematic illustration of E. coli Big-Six group strains. Bacteria were harvested and filtered using 0.22 µm filters and concentrated using 3 kDa cutoff filters. Equal amount of proteins from each bacteria were trypsin-digested, cleaned using Sep-Pak C18 cartridges, and TMTs labeling was carried out. Labeled peptides were pooled and fractionated using bRPLC fractions and analyzed on Orbitrap Elite mass spectrometer.