TABLE 3

ComX-regulated genes, distributed over 19 operonsa

GeneProductTPM at 0 minLog2 fold change at:Note
3 min10 min20 min
dutDeoxyuridine 5ʹ-triphosphate nucleotidohydrolase782.71.5−0.2
SPV_0028Hypothetical protein942.61.6−0.2
radADNA repair protein962.52.4−0.1
SPV_0030Carbonic anhydrase3880.81.10.1Secondary
srf-01ncRNA of unknown function713.73.30.9Putative pseudogene
SPV_2082bHypothetical protein226.66.32.6
SPV_0034bIS1167 transposase33.63.71.1
cibATwo-peptide bacteriocin peptide812.012.97.4
cibBTwo-peptide bacteriocin peptide1110.211.05.5
cibCCibAB immunity factor1010.612.36.5
SPV_2121Hypothetical protein1244.64.40.6
SPV_0186Competence-damage induced protein2832.42.30.1Secondary
SPV_0683Hypothetical protein1364.24.90.8
comEALate-competence DNA receptor49.89.23.7
comECLate-competence DNA transporter39.59.85.0
SPV_2256Hypothetical protein1564.04.81.4Secondary
SPV_2257bABC transporter ATP-binding protein913.75.01.3Secondary
SPV_0846Hypothetical protein683.95.41.5Secondary
coiACompetence protein18.27.41.2
pepF1Oligoendopeptidase F2521.31.20.0Secondary
SPV_0867O-Methyltransferase family protein1361.41.50.3Secondary
radCDNA repair protein39.89.82.6
dprADNA protecting protein610.18.84.6
SPV_2340bHypothetical protein2222.52.60.2Secondary
pgdAPeptidoglycan N-acetylglucosamine deacetylase3971.41.70.1Secondary
SPV_1308Oxidoreductase of aldo/keto reductase family, subgroup 11820.91.40.3Secondary
cclAType IV prepilin peptidase29.39.03.7
ssbBSingle-stranded DNA-binding protein910.711.96.8
cinAADP-ribose pyrophosphatase/nicotinamide-nucleotide amidase785.86.52.5
recADNA recombination/repair protein3913.03.80.7Secondary
dinFMATE efflux family protein2882.23.80.4Secondary
lytAAutolysin/N-acetylmuramoyl-l-alanine amidase7031.43.20.4Secondary
tygcNA<16.76.84.2
rmuCDNA recombination protein3142.11.8−0.3
yhaM3ʹ→5ʹ exoribonuclease3121.71.7−0.4
SPV_1828Hypothetical protein1426.56.01.4
nadCQuinolinate phosphoribosyltransferase721.73.20.3Secondary
SPV_1825bIS630-Spn1 transposase1620.51.70.0Secondary
SPV_1824ABC transporter, permease340.92.70.2Secondary
comGALate-competence protein149.410.45.1
comGBLate-competence protein89.410.85.4
comGCLate-competence protein69.311.25.3
comGDLate-competence protein410.112.16.3
comGELate-competence protein310.312.36.5
comGFLate-competence protein29.912.26.5
comGGLate-competence protein88.711.05.5
SPV_2427bS-Adenosylmethionine-dependent methyltransferase210.313.07.2
srf-29ncRNA of unknown function39.38.83.0
cbpDCholine-binding protein D69.910.03.8
SPV_2027Cytoplasmic thiamin-binding component of thiamin ABC transporter891.01.2−0.7Secondary
thiXThiamin ABC transporter transmembrane component880.81.2−1.1Secondary
thiYThiamin ABC transporter substrate-binding component1340.80.9−1.1Secondary
thiZThiamin ABC transporter ATPase component1280.61.0−1.2Secondary
comFADNA transporter ATPase39.08.12.9
comFCPhosphoribosyltransferase domain protein38.68.52.7
hpfRibosome hibernation promotion factor6240.91.4−0.3Secondary
  • a The 19 operons are indicated by the 9 blocks of data in a gray background and the 10 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]). NA, data not available.

  • b Pseudogene.

  • c The tyg TSS was previously found to be ComX regulated (32). An artificial 250-nucleotide transcript starting at this TSS was added to the annotation file to allow differential expression analysis.