Table 1. List of up- and downregulated genes when overexpressing RR07.
Protein activities were attributed based on information retrieved from the KEGG and Uniprot databases as well as literature searches. See Fig 1 for criteria of up- and downregulated genes. anames given for convenience in model illustration (Fig 9). aour experiments suggest that the decrease of competence gene expression is due to an artefact from overexpression of RR07.
| Locus tag | Name | Activity | Log2FC |
|---|---|---|---|
| Host glycan metabolism | |||
| N-Glycan metabolism | |||
| SPD_0063 | StrH | β-N-acetylhexosaminidase [32] | 6.6 |
| SPD_0088 | NgtP1 | ABC transporter permease [26] | 5.3 |
| SPD_0089 | NgtP2 | ABC transporter permease [26] | 6.2 |
| SPD_0090 | NgtS | ABC transporter substrate-binding protein [26] | 6.7 |
| SPD_0444 | EndoD (GH85) | Endo-β-N-acetylglucosaminidase [26][33] | 7.1 |
| SPD_1969 | GH20 | Exo-β-hexosaminidase [34] | 9.3 |
| SPD_1970 | ROK | ROK family protein [26] | 8.6 |
| SPD_1971 | GH38 | Putative exo-α-1.3-mannosidase | 8.8 |
| SPD_1972 | GH125 | Exo-α-1.6-mannosidase [35] | 8.5 |
| SPD_1973 | GH92 | α-1.2-mannosidase [26] | 5.0 |
| SPD_1974 | GH29 | α-1.3/4-fucosidase [36] | 8.0 |
| Carbohydrate metabolism | |||
| Glycosyl hydrolases and transferases | |||
| SPD_0138 | GT1a | Glycosyl transferase family 1 protein | 5.3 |
| SPD_0139 | GT2a | Glycosyl transferase family 2 protein | 5.5 |
| SPD_0140 | ABCa | ABC transporter ATP-binding protein | 5.8 |
| SPD_0247 | BglA3 | Glycosyl hydrolase family protein [23] | 7.6 |
| Mannose and fructose metabolism | |||
| SPD_0641 | ManA | Mannose-6-phosphate isomerase [37] | 5.8 |
| SPD_1531 | ScrK | Fructokinase [38] | 6.1 |
| Starch and sucrose metabolism | |||
| SPD_1663 | TreC | α.α-phosphotrehalase | 3.1 |
| Competencea | |||
| Bacteriocin | |||
| SPD_0046 | BlpU | Bacteriocin | -2.1 |
| SPD_0132 | - | Bacteriocin | -9.3 |
| SPD_0133 | - | Bacteriocin | -9.4 |
| Competence | |||
| SPD_0049 | ComA | Competence factor transporter [39] | -5.3 |
| SPD_0050 | ComB | Competence factor transporter [39] | -5.6 |
| SPD_0844 | ComEC | Competence protein ComEC [40] | -6.6 |
| SPD_1711 | SsbB | Single-strand DNA-binding protein [41] | -7.5 |
| SPD_1740 | CinA | Competence induced protein [42] | -3.0 |
| SPD_1857 | ComGG | Competence protein ComGG [40] | -8.9 |
| SPD_1858 | ComGF | Competence protein ComGF [40] | -9.4 |
| SPD_1859 | ComGE | Competence protein ComGE [40] | -8.7 |
| SPD_1860 | ComGD | Competence protein ComGD [40] | -9.2 |
| SPD_1861 | CglC | Competence protein CglC [43] | -9.0 |
| SPD_1862 | CglB | Competence protein CglB [43] | -10.1 |
| SPD_1863 | CglA | Competence protein CglA [43] | -9.0 |
| SPD_2063 | ComE | Competence response regulator [39] | -5.6 |
| SPD_2064 | ComD | Competence histidine kinase [39] | -5.7 |
| SPD_2065 | ComC1 | Competence-stimulating peptide type 1 [39] | -5.5 |
| Other | |||
| Known | |||
| SPD_0994 | RibF | Riboflavin biosynthesis protein | -2.4 |
| SPD_1086 | MutY | A/G-specific adenine glycosylase [44] | 2.1 |
| Unkown | |||
| SPD_0023 | - | Hypothetical protein | -5.5 |
| SPD_0092 | - | Hypothetical protein | 2.8 |
| SPD_0104 | - | LysM domain-containing protein | -3.0 |
| SPD_0466 | - | Hypothetical protein | -3.3 |
| SPD_0474 | - | Hypothetical protein | -2.2 |
| SPD_0475 | - | Uncharacterized protein | -2.5 |