TABLE 4

CiaR-regulated genes, distributed over 18 operonsa

GeneProductTPM at 0 minLog2 fold change at:Note
3 min10 min20 min
ccnCcsRNA31554.41.20.0Also ComE regulon
SPV_0098Glycosyltransferase, group 2 family218−0.51.00.3
ccnEcsRNA5320.60.80.2
ccnAcsRNA127−2.0−1.4−1.0
ccnBcsRNA22−0.62.8−1.5
ccnDcsRNA4250.41.90.0
manLMannose-specific PTS IIAB components3,3790.03.3−1.0Also CcpA-binding site
manMMannose-specific PTS IIC component3,2960.13.11.1
manNMannose-specific PTS IID component4,7500.23.31.0
rimPBacterial ribosome SSU maturation protein228−0.21.00.8CiaR-binding motif on opposite strand
nusATranscription termination/antitermination protein2060.11.00.9
SPV_0480Putative transcription termination protein1170.51.21.1
SPV_0481L7Ae family ribosomal protein1030.61.41.4
infBTranslation initiation factor 22770.80.70.9
rbfARibosome-binding factor A1941.00.50.8
ciaRTwo-component system response regulator2250.23.20.3
ciaHTwo-component system sensor histidine kinase1640.33.20.2
SPV_0775Acetyltransferase280.44.81.0
prsAPutative parvulin type peptidyl-prolyl isomerase2671.33.90.6Potentially also ComX regulon
SPV_0913Extracellular protein552.05.91.3
rlmCD23S rRNA [uracil(1939)-C(5)]-methyltransferase38−0.42.00.4Secondary
tarIbRibitol-5-phosphate cytidylyltransferase3080.60.40.2
tarJbRibulose-5-phosphate reductase3620.40.30.1
licAbCholine kinase3190.60.20.1
licBbCholine permease3970.60.0−0.1
licCbCholinephosphate cytidylyltransferase4220.80.00.0
srf-21ncRNA of unknown function3250.73.20.3
axe1Acetyl xylan esterase 1/cephalosporin-C deacetylase580.84.20.2Secondary
SPV_1769Membrane protein4970.01.9−0.4
malQ4-Alpha-glucanotransferase (amylomaltase)690.14.2−0.2
malPMaltodextrin phosphorylase830.24.2−0.4
dltXd-Alanyl-lipoteichoic acid biosynthesis protein277−0.61.90.2CiaR-binding motif on opposite strand
dltAd-Alanine-poly(phosphoribitol) ligase subunit 1392−0.31.60.1
dltBd-Alanyl transfer protein3220.01.60.0
dltCd-Alanine-poly(phosphoribitol) ligase subunit 24290.01.50.1
dltDPoly(glycerophosphate chain) d-alanine transfer protein3260.31.50.0
htrASerine protease491.57.01.5
parBChromosome partitioning protein570.96.51.4Secondary
  • a The 18 operons are indicated by the 9 blocks of data in a gray background and the 9 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]). PTS, phosphotransferase system; SSU, small subunit.

  • b The indicated operon has two different detected TSSs. The TSS at 1159217 (−) is under the control of CiaR.