*2.2. Global Proteome Profiles of P. rubra S4059 Grown on Chitin*

The proteomes of *P. rubra* S4059 grown on different carbon sources were analyzed by liquid chromatography–tandem mass spectrometry (LC-MS/MS)-based label-free quantitative proteomics approach. The analyses were done on both cells and culture supernatant (excreted proteins) of S4059 grown in crystalline chitin or mannose containing medium. A total of 2813 proteins were identified in the global proteome of S4059, of which 738 and 142 proteins were up- and downregulated in S4059 culture supernatant when grown on crystalline chitin as compared to growth on mannose (Figure 1A). Simultaneously, 1861 and 141 proteins were up- and downregulated in S4059 cells when grown on crystalline chitin compared to on mannose (Figure 1B). Proteins involved in bacterial chemotaxis, cell division, flagellar assembly, and Type IV pilus assembly were upregulated when S4059 was grown on crystalline chitin (Table S3). Proteins associated with the core metabolism were also upregulated on chitin (Table S3). A protein involved in mannosidase from the GH92 family was upregulated when grown on mannose compared to when grown on crystalline chitin (Table S3).

**Figure 1.** Comparison of identified proteins in the culture supernatant (**A**) and cells (**B**) of *Pseudoalteromonas rubra* S4059

when grown on chitin compared to on mannose. The dotted lines indicated that a threshold value for the cut off was a combination of *p*-value ≤ 0.05 and Log2 fold-change ≥ 1.5. Red dots represent upregulated proteins, and blue dots represent downregulated proteins. Chitinolytic enzymes with significant fold changes are highlighted by enlarged dots with protein names in (**A**,**B**). Heat map comparison of identified chitinolytic enzymes in the supernatant and cells of *Pseudoalteromonas rubra* S4059 is color-coded by increasing abundance (**C**). C–WT–cell: cells of S4059 grown on chitin; M–WT–cell: cells of S4059 grown on mannose; C–WT–sup: culture supernatant of S4059 grown on chitin; M–WT–sup: culture supernatant of S4059 grown on mannose. White denotes proteins not detected under this condition. 'Overlap' indicates these proteins were detected in both chitin and mannose-grown samples, and an asterisk (\*) highlights proteins significantly upregulated when grown on chitin compared to on mannose.
