TABLE 2.

Signal transduction and transcriptional regulator proteins affected by the loss of CtrA

GeneSize of protein (aa)Predicted function (signaling and regulatory domain[s]a)Transcript fold changeb (log phase, stationary phase)
rcc00180109Phosphorelay (HPT)26.3, 25.3
rcc00181409Response regulator (REC, PP2C)17.4, 10.8c
rcc00346514c-di-GMP signaling (GGDEF, EAL)7.6, 4.7c
rcc00537247Response regulator (REC)28.4, 23.7
rcc00620610Response regulator and c-di-GMP signaling (REC, GGDEF, EAL)14.0, 6.3
rcc00621619Sensor kinase (CHASE4, SK)5.7, 5.0
rcc006451,245c-di-GMP signaling (GGDEF, EAL, PAS)7.7, 25.9c
rcc01849253Unknown (PAS)3.3, 1.7
rcc02075416Unknown (PAS)5.8, 3.6
rcc02539627c-di-GMP signaling (GGDEF, EAL)8.1, 4.1
rcc02629353c-di-GMP signaling (GGDEF)8.1, 2.8
rcc02675170Transcriptional regulator (HTH)19.3, 5.9
rcc02856412Unknown (PAS)13.9, 2.7
rcc028571,158c-di-GMP signaling (GGDEF, EAL, PAS)12.5, 5.6
rcc03176411Unknown (PAS)17.1, 10.0c
rcc03177284c-di-GMP signaling (EAL)19.5, 17.6
rcc033011,284c-di-GMP signaling (GGDEF, EAL, PAS)4.5, 3.0
rcc03323115Anti-antisigma factor (STAS)32.3, 8.7
rcc03324163Antisigma regulatory factor (HATPase)22.0, 9.4
rcc03452743Sensor kinase (SK, REC)9.8, 3.0
rcp00117280c-di-GMP signaling (EAL)24.9, 12.1c
rcp00137412Unknown (PAS)9.0, 9.4
  • a Conserved domains were identified by BLAST analyses at the NCBI Conserved Domain Database. HPT, histidine phosphotransfer; REC, response-regulator receiver; PP2C, serine/threonine phosphatase; GGDEF, diguanylate cyclase; EAL, c-di-GMP phosphodiesterase; CHASE4, extracellular sensory domain; SK, sensor kinase; PAS, Per-Arnt-Sim; HTH, helix-turn-helix; STAS, antisigma factor antagonist; HATPase, histidine kinase-like ATPase.

  • b Transcript fold change is shown as level for wild type/level for mutant.

  • c Protein detected in proteome and matching transcript trend; data are available in Table S5 in the supplemental material.