TABLE 5.
Competence-induced genes that are part of the VraR, CtsR, and/or HrcA regulonsa
| Gene | Product | TPM at 0 min | Log2 fold change at: |
Regulon(s) | Note | ||
|---|---|---|---|---|---|---|---|
| 3 min | 10 min | 20 min | |||||
| spxA2 | Transcriptional regulator SpxA2 | 772 | 0.0 | 1.4 | 0.0 | VraR | |
| SPV_0179 | Hypothetical protein | 163 | −0.2 | 1.7 | 0.1 | VraR | Secondary |
| clpL | Clp protease ATP-binding subunit ClpL | 24 | −0.2 | 6.6 | 3.7 | CtsR | |
| vraT | Cell wall-active antibiotic response protein VraT | 62 | 0.1 | 2.4 | −0.1 | VraR | |
| vraS | Two-component system sensor histidine kinase VraS | 52 | 0.0 | 2.2 | 0.0 | VraR | |
| vraR | Two-component transcriptional regulator VraR | 48 | 0.1 | 2.2 | −0.3 | VraR | |
| alkDb | DNA alkylation repair enzyme AlkD | 43 | 0.0 | 2.2 | 0.0 | VraR | |
| SPV_0355 | Hypothetical protein | 118 | −0.2 | 1.2 | 0.5 | VraR | Secondary |
| cbpGa | Choline-binding protein CbpG | 156 | −0.2 | 1.1 | 0.4 | VraR | Secondary |
| cbpK | Choline-binding protein CbpK | 151 | 0.1 | 1.0 | 0.3 | VraR | Secondary |
| hrcA | Heat-inducible transcription repressor HrcA | 650 | −0.2 | 2.7 | 0.1 | VraR, HrcA | |
| grpE | Heat shock protein GrpE | 600 | −0.3 | 2.7 | −0.1 | VraR, HrcA | |
| dnaK | Chaperone protein DnaK | 1,005 | −0.6 | 2.5 | −0.2 | VraR, HrcA | |
| SPV_2171 | Hypothetical protein | 679 | −0.8 | 2.3 | −0.1 | VraR, HrcA | |
| dnaJ | Chaperone protein DnaJ | 551 | −0.6 | 2.1 | −0.1 | VraR, HrcA | |
| clpE | Clp protease ATP-binding subunit ClpE | 168 | 0.2 | 1.4 | 0.9 | CtsR | |
| SPV_0803 | Putative phage shock protein C | 316 | 0.1 | 1.7 | −0.1 | VraR, HrcA | |
| groES | Heat shock protein 60 family cochaperone GroES | 1,099 | 0.5 | 2.5 | 0.6 | CtsR, HrcA | |
| groEL | Heat shock protein 60 family chaperone GroEL | 1,146 | 0.3 | 2.2 | 0.6 | CtsR, HrcA | |
| ctsR | Transcriptional regulator CtsR | 162 | −0.2 | 1.3 | 1.2 | CtsR | |
| clpC | Clp protease ATP-binding subunit ClpC | 257 | −0.1 | 1.0 | 0.9 | CtsR | |
| SPV_2021 | Hypothetical protein | 220 | 0.3 | 1.1 | 1.0 | CtsR? | |
| SPV_2020 | Two-component system response regulator | 167 | 0.1 | 0.9 | 1.1 | CtsR? | |
| SPV_2019 | Two-component system sensor histidine kinase | 86 | 0.4 | 1.1 | 1.2 | CtsR? | |
a
The different operons are indicated by blocks of data in a gray background and blocks of data in a white background. “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]).
b
Pseudogene.