Digested alginate increases expression of genes involved in alginate degradation, uptake and catabolism, as well as flagellar assembly and chemotaxis.
Genome-wide differential expression analysis where the log2 fold changes of gene expression on digested alginate compared to alginate is shown for (A) alginate lyases (PL6, PL7, PL15, PL17, scissors symbol), transporters (porin kdgM, symporter toaB, symporter toaC), and metabolic enzymes shunting into the Entner-Doudoroff pathway (DEHU reductase DehR, kdgK, eda), (B) genes of the flagellar locus associated with flagellar assembly and (C) adjacent chemotaxis genes. Genes displayed in (B) and (C) are part of the KEGG pathways “Bacterial motility proteins” and “Bacterial chemotaxis”. Differential expression analysis was performed to compute the Benjamini-Hochberg-adjusted Wald test p-value (”BH-adj. p-value”, text color and box outline color) and log2 fold change (box fill color) for each gene (box). For better visibility, genes that exhibited a log2 fold gene expression change greater than 1 (i.e., doubling of expression) or less than -1 (i.e., halving of expression) are designated maximum intensity of red or blue, respectively. Genes with BH-adj. p-value smaller than 0.01 were considered significantly differentially expressed. In (A), the location of the gene products was based on Figure 1 of Wargacki et al.31 with the exception of the alginate lyases (PL6, PL7, PL15, PL17) which were placed based on their signal peptides (S: extracellular, LS: membrane-embedded, none: cytosolic). In (B) and (C) the gene location and depiction were based on the KEGG pathway “Flagellar assembly” (map02040), “Bacterial chemotaxis” (map02030), and Figure 3 of Rajagopala et al.40. Genes without known cellular location were omitted here but displayed in the genomic architecture in Fig. S5. Arrow: activation; dashed arrow: modification; “flat” arrow: inhibition; OM: outer membrane; PM: periplasm; IM: inner membrane; PL: polysaccharide lyase family; kdgM: oligogalacturonate-specific outer membrane porin; toaABC: oligoalginate symporter; DEH: 4-deoxy-L-erythro-5-hexoseulose uronic acid; dehR: DEH reductase; KDG: 2-keto-3-deoxy-gluconate; kdgK: KDG kinase; KDPG: 2-keto-3-deoxy-6-phosphogluconate; eda: KDG-6-phosphate aldolase; GAP: glyceraldehyde 3-phosphate; ED: Entner-Doudoroff; ns: not significant, i.e. BH-adj. p-value > 0.01.