TABLE 2.
ComE-regulated genes, distributed over 15 operonsa
| Gene | Product | TPM at 0 min | Log2 fold change at: |
Note(s) | ||
|---|---|---|---|---|---|---|
| 3 min | 10 min | 20 min | ||||
| comX1 | Competence-specific sigma factor | 8 | 9.1 | 3.8 | 3.1 | |
| tRNA-Glu-1 | tRNA-Glu-UUC | 387 | 2.8 | 0.1 | −0.6 | Secondary |
| comW | Competence positive regulator | 17 | 9.1 | 4.7 | 3.0 | |
| purA | Adenylosuccinate synthetase | 619 | 4.4 | 1.0 | 0.0 | Secondary |
| ccnC | csRNA3 | 155 | 4.4 | 1.2 | 0.0 | Secondary; also CiaR regulon |
| srf-03 | ncRNA of unknown function | 39 | 7.1 | 2.0 | 1.5 | |
| comA | CSP ABC transporter ATP-binding protein | 21 | 9.3 | 4.1 | 3.4 | |
| comB | CSP ABC transporter permease | 24 | 9.5 | 4.4 | 3.3 | |
| briC | Biofilm-regulating peptide | 97 | 4.9 | 1.7 | 0.7 | |
| ydiLb | Putative membrane peptidase | 67 | 5.3 | 2.4 | 1.0 | |
| blpT | BlpT protein | 8 | 3.9 | 0.7 | 1.5 | BlpR regulon |
| blpAb | Peptide ABC transporter permease/ATP-binding protein | 2 | 5.1 | 2.1 | 2.5 | BlpR regulon |
| blpBb | Peptide ABC transporter permease | 3 | 4.5 | 2.2 | 2.4 | BlpR regulon |
| blpC | Peptide pheromone | 3 | 4.4 | 2.7 | 1.9 | BlpR regulon |
| pncW | Putative bacteriocin | 13 | 4.0 | 1.1 | 2.0 | BlpR regulon |
| blpY | Bacteriocin immunity protein | 17 | 4.3 | 1.4 | 2.2 | BlpR regulon |
| blpZ | Immunity protein | 13 | 4.3 | 1.5 | 1.9 | BlpR regulon |
| pncP | Putative protease | 14 | 4.2 | 1.3 | 1.9 | BlpR regulon |
| SPV_2249 | Hypothetical protein | 50 | 1.2 | 0.3 | 0.8 | BlpR regulon |
| SPV_0817 | CAAX amino terminal protease family protein | 45 | 1.3 | 0.2 | 0.4 | BlpR regulon |
| ribF | FMN adenylyltransferase/riboflavin kinase | 147 | 5.2 | 1.2 | 0.7 | |
| def2 | Peptide deformylase | 177 | 3.7 | 0.0 | −0.1 | |
| SPV_1380 | Cell shape-determining protein | 276 | 3.9 | 0.1 | 0.0 | Secondary |
| SPV_1379 | Hypothetical protein | 183 | 3.3 | 0.0 | −0.1 | Secondary |
| yaaA | UPF0246 protein | 85 | 1.2 | 0.0 | −0.3 | Secondary |
| qsrA | ABC transporter ATP-binding protein-Na+ export | 223 | 4.5 | 0.6 | 0.2 | Secondary |
| qsrB | ABC transporter permease-Na+ export | 216 | 4.5 | 0.4 | −0.2 | Secondary |
| srf-22 | ncRNA of unknown function | 54 | 4.1 | 0.2 | −0.7 | Secondary |
| comM | Immunity factor | 9 | 8.0 | 4.4 | 2.8 | |
| tsaE | tRNA processing protein | 280 | 3.1 | 0.3 | 0.2 | Secondary |
| SPV_1742 | Acetyltransferase | 319 | 2.7 | 0.3 | 0.2 | Secondary |
| lytR | LytR-CpsA-Psr family protein | 355 | 2.8 | 0.1 | 0.1 | Secondary |
| comX2 | Competence-specific sigma factor | 8 | 9.1 | 3.8 | 3.1 | |
| tRNA-Glu-3 | tRNA-Glu-UUC | 387 | 2.8 | 0.1 | −0.6 | Secondary |
| ybbK | Putative membrane protease subunit | 795 | 2.1 | 0.6 | 0.6 | TSS too far from ComE-binding site |
| comC1 | Competence-stimulating peptide precursor | 36 | 8.8 | 5.1 | 4.6 | |
| comD | Two-component system sensor histidine kinase | 27 | 8.4 | 4.3 | 3.8 | |
| comE | Two-component system response regulator | 38 | 8.3 | 4.0 | 3.5 | |
| tRNA-Glu-5 | tRNA-Glu-UUC | 63 | 5.8 | 1.9 | 1.5 | Secondary |
| tRNA-Asn-2 | tRNA-Asn-GUU | 181 | 5.1 | 0.8 | 0.4 | Secondary |
a
The 15 operons are indicated by the eight blocks of data highlighted in gray and the seven blocks of data highlighted in white. Members of the BlpR regulon are included as indicated in the Note(s) column. “Secondary” indicates either read-through after incomplete termination or the influence of an additional TSS. For complete supplemental information, including TSS positions, see Table S5. Boldface data indicate significance (P < 0.001; log2 FC > 1; DESeq [91]). FMN, flavin mononucleotide; ncRNA, noncoding RNA.
b
Pseudogene.