TABLE 2

ComE-regulated genes, distributed over 15 operonsa

GeneProductTPM at 0 minLog2 fold change at:Note(s)
3 min10 min20 min
comX1Competence-specific sigma factor89.13.83.1
tRNA-Glu-1tRNA-Glu-UUC3872.80.1−0.6Secondary
comWCompetence positive regulator179.14.73.0
purAAdenylosuccinate synthetase6194.41.00.0Secondary
ccnCcsRNA31554.41.20.0Secondary; also CiaR regulon
srf-03ncRNA of unknown function397.12.01.5
comACSP ABC transporter ATP-binding protein219.34.13.4
comBCSP ABC transporter permease249.54.43.3
briCBiofilm-regulating peptide974.91.70.7
ydiLbPutative membrane peptidase675.32.41.0
blpTBlpT protein83.90.71.5BlpR regulon
blpAbPeptide ABC transporter permease/ATP-binding protein25.12.12.5BlpR regulon
blpBbPeptide ABC transporter permease34.52.22.4BlpR regulon
blpCPeptide pheromone34.42.71.9BlpR regulon
pncWPutative bacteriocin134.01.12.0BlpR regulon
blpYBacteriocin immunity protein174.31.42.2BlpR regulon
blpZImmunity protein134.31.51.9BlpR regulon
pncPPutative protease144.21.31.9BlpR regulon
SPV_2249Hypothetical protein501.20.30.8BlpR regulon
SPV_0817CAAX amino terminal protease family protein451.30.20.4BlpR regulon
ribFFMN adenylyltransferase/riboflavin kinase1475.21.20.7
def2Peptide deformylase1773.70.0−0.1
SPV_1380Cell shape-determining protein2763.90.10.0Secondary
SPV_1379Hypothetical protein1833.30.0−0.1Secondary
yaaAUPF0246 protein851.20.0−0.3Secondary
qsrAABC transporter ATP-binding protein-Na+ export2234.50.60.2Secondary
qsrBABC transporter permease-Na+ export2164.50.4−0.2Secondary
srf-22ncRNA of unknown function544.10.2−0.7Secondary
comMImmunity factor98.04.42.8
tsaEtRNA processing protein2803.10.30.2Secondary
SPV_1742Acetyltransferase3192.70.30.2Secondary
lytRLytR-CpsA-Psr family protein3552.80.10.1Secondary
comX2Competence-specific sigma factor89.13.83.1
tRNA-Glu-3tRNA-Glu-UUC3872.80.1−0.6Secondary
ybbKPutative membrane protease subunit7952.10.60.6TSS too far from ComE-binding site
comC1Competence-stimulating peptide precursor368.85.14.6
comDTwo-component system sensor histidine kinase278.44.33.8
comETwo-component system response regulator388.34.03.5
tRNA-Glu-5tRNA-Glu-UUC635.81.91.5Secondary
tRNA-Asn-2tRNA-Asn-GUU1815.10.80.4Secondary
  • 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.