TABLE 5

Competence-induced genes that are part of the VraR, CtsR, and/or HrcA regulonsa

GeneProductTPM at 0 minLog2 fold change at:Regulon(s)Note
3 min10 min20 min
spxA2Transcriptional regulator SpxA27720.01.40.0VraR
SPV_0179Hypothetical protein163−0.21.70.1VraRSecondary
clpLClp protease ATP-binding subunit ClpL24−0.26.63.7CtsR
vraTCell wall-active antibiotic response protein VraT620.12.4−0.1VraR
vraSTwo-component system sensor histidine kinase VraS520.02.20.0VraR
vraRTwo-component transcriptional regulator VraR480.12.2−0.3VraR
alkDbDNA alkylation repair enzyme AlkD430.02.20.0VraR
SPV_0355Hypothetical protein118−0.21.20.5VraRSecondary
cbpGaCholine-binding protein CbpG156−0.21.10.4VraRSecondary
cbpKCholine-binding protein CbpK1510.11.00.3VraRSecondary
hrcAHeat-inducible transcription repressor HrcA650−0.22.70.1VraR, HrcA
grpEHeat shock protein GrpE600−0.32.7−0.1VraR, HrcA
dnaKChaperone protein DnaK1,005−0.62.5−0.2VraR, HrcA
SPV_2171Hypothetical protein679−0.82.3−0.1VraR, HrcA
dnaJChaperone protein DnaJ551−0.62.1−0.1VraR, HrcA
clpEClp protease ATP-binding subunit ClpE1680.21.40.9CtsR
SPV_0803Putative phage shock protein C3160.11.7−0.1VraR, HrcA
groESHeat shock protein 60 family cochaperone GroES1,0990.52.50.6CtsR, HrcA
groELHeat shock protein 60 family chaperone GroEL1,1460.32.20.6CtsR, HrcA
ctsRTranscriptional regulator CtsR162−0.21.31.2CtsR
clpCClp protease ATP-binding subunit ClpC257−0.11.00.9CtsR
SPV_2021Hypothetical protein2200.31.11.0CtsR?
SPV_2020Two-component system response regulator1670.10.91.1CtsR?
SPV_2019Two-component system sensor histidine kinase860.41.11.2CtsR?
  • 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.