Table 1 Selected genes in key functional categories differentially expressed in biofilm compared to planktonic cells (both cultured in 4.5 mM [Ca2+]). Genes were selected based on fold change and their functional relevance
Functional group | RefSeq | Product | Fold change (log2) | FDR (adjusted p value) |
|---|---|---|---|---|
EPS/LPS biosynthesis | ||||
| Â | WP_060381967.1 | 1,4-polygalactosaminidase | 1.72 | 1.1E-19 |
WP_060381836.1 | UDP-N-acetylmuramate--alanine ligase | 1.24 | 4.1E-05 | |
WP_060381978.1 | SAM-dependent methyltransferase | 1.04 | 3.8E-07 | |
WP_060382475.1 | Glycosyltransferase | − 1.99 | 9.3E-03 | |
Amino acid metabolism | ||||
|  | WP_060383852.1 | Branched-chain amino acid aminotransferase | −1.53 | 3.52E-16 |
WP_060382313.1 | Anthranilate synthase | −1.35 | 2.71E-10 | |
WP_060382314.1 | Anthranilate phosphoribosyltransferase | −1.03 | 1.18E-06 | |
WP_060382792.1 | Glycyl aminopeptidase M61 | 1.11 | 2.2E-11 | |
WP_060382658.1 | Von 25illebrand factore type protein | 1.54 | 5.8E-10 | |
T9SS | ||||
|  | WP_060383582.1 | T9SS C-terminal target domain-containing protein | −1.53 | 3.52E-16 |
WP_060383402.1 | T9SS C-terminal target domain-containing protein | −1.13 | 3.07E-05 | |
Nutrient limitation | ||||
| Â | WP_060381920.1 | Abortive phage infection protein | 1.17 | 5.0E-08 |
WP_060383199.1 | Ribosome inactivating protein | 1.30 | 9.27E-10 | |
WP_060381977.1 | Protein-tryosine-phosphatase | 1.04 | 1.39E-09 | |
WP_060382448.1 | DNA starvation protect protein under stressful or poor nutriention conditions | 2.08 | 8.3E-23 | |
Regulatory functions | ||||
| Â | WP_060382614.1 | AraC family transcriptional regulator | 1.71 | 2.9E-11 |
WP_060381931.1 | Transcriptional regulator | 1.31 | 5.4E-08 | |
WP_060381980.1 | ArsR family iron regulation transcriptional regulator | 1.54 | 4.7E-4 | |
Oxidative stress response | ||||
| Â | WP_060381974.1 | Catalase | 2.16 | 8.71E-10 |
WP_060381975.1 | Alkyl hydroperoxide reductase | 1.50 | 8.29E-15 | |
WP_060382235.1 | Cytochrome c peroxidase | 1.41 | 1.31E-10 | |
WP_014164670.1 | Thiol reductase thioredoxin | 1.03 | 2.35E-09 | |
Respiratory metabolism | ||||
| Â | WP_060381919.1 | O-succinylbenzoic acid CoA ligase | 1.11 | 7.3E-03 |
WP_060382480.1 | Cytochrome C oxidase subunit III | −2.12 | 7.45E-06 | |
WP_060382479.1 | Cytochrome c oxidase accessory protein CcoG | −2.03 | 2.9E-06 | |
WP_060382481.1 | Cytochrome C oxidase subunit IV | −1.74 | 2.3E-05 | |
WP_060382478.1 | Cytochrome C oxidase Cbb3 | −1.74 | 1.94E-03 | |
WP_060381577.1 | Cytochrome c oxidase subunit I | − 1.50 | 1.7E-02 | |
WP_060381570.1 | Cytochrome C | −1.39 | 3.7E-04 | |
WP_060381576.1 | Cytochrome C oxidase subunit II | −1.39 | 2.6E-02 | |
WP_060381561.1 | NADH dehydrogenase | −1.27 | 6.5E-03 | |
WP_060381560.1 | NADH oxidoreductase (quinone) subunit F | −1.18 | 6.1E-03 | |
WP_060381566.1 | NADH-quinone oxidoreductase subunit L | −1.07 | 1.7E-03 | |
WP_060381562.1 | NADH:ubiquinone oxidoreductase subunit H | −1.06 | 1.1E-02 | |
WP_014164161.1 | NADH-quinone oxidoreductase subunit I | −1.00 | 9.1E-03 | |