TABLE 3.

Potential CtrA binding sites in the R. capsulatus genome

GeneDescriptionLocation of predicted siteaTranscript fold changeb (log phase, stationary phase)Quantitative proteome datac (log phase, stationary phase)
TTAA-N7-TTAACTTAACCAT
rcc00042PAS/PAC sensor domain protein−4712.6, 14.9ND
rcc00222DNA repair protein RadC−307.6, 21.8ND
rcc00280Hemolysin-type calcium-binding repeat family protein−1001.2, −1.1ND
rcc00393UvrABC system protein C−372−1.3, −1.7ND
rcc00434Hypothetical protein−57−541.4, 3.9ND
rcc00459Glutathione S-transferase domain proteind−49−1.4, −1.30.97, −0.43
rcc00463Protein of unknown function UPF0102−3154.4, 13.7ND
rcc00498Transglycosylase, Slt family−249−1.25, −1.1ND
rcc00516Tyrosine phenol-lyase−570−1.7, −1.4−1.43, −1.47
rcc00645Diguanylate cyclase/phosphodiesterase with PAS/PAC sensor−687.7, 25.9−1.14, 0.74
rcc00844Conserved hypothetical protein−82−9021.3, 28.7ND
rcc00845Hypothetical protein−273−1185.2, 17.8
rcc00872Alcohol dehydrogenase, zinc-binding domain protein−193−1.3, −1.1−0.05, −0.50
rcc01237Glycosyl transferase, family 2−1662.4, 5.1ND
rcc01324Type I restriction-modification system, R subunit−475−1.4. −1.1ND
rcc01384UvrABC system protein B−65−1.4, 0−2.42, 1.25
rcc01462Ribonucleoside-diphosphate reductase NrdJ−491−1.3, 1.6−2.06, 1.23
rcc01749Histidine kinase CckA−961.4, −1.11.33, 1.12
rcc01849Protein of unknown function DUF1457−403.3, 1.7ND
rcc01932Glycosyl transferase, family 4−183−1.7, −1.4ND
rcc01940Hemolysin-type calcium-binding repeat family protein−129−5.0, −2.5ND
rcc03000Conserved hypothetical protein−2412.0. 1.7ND
rcc03209Protein containing DUF484−462.6, 2.11.98, 3.09
rcc03214Protein of unknown function DUF1127−131−1.3, −2.5ND
  • a Position of the last (3′) base of the predicted binding site relative to the first base of the predicted start codon for the gene.

  • b Positive values indicate higher transcript levels in the wild type, and negative values indicate higher levels in the ctrA mutant.

  • c Absolute difference in Z-score data for each protein, with positive values representing larger amounts in the wild type and negative values representing larger amounts in the ctrA mutant. ND, not detected.

  • d Gene rcc00460 is predicted to be cotranscribed with rcc00459 and is affected by loss of CtrA.