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Table 1 Main classes of Sigma-54 related activators and the connected functional data.

From: Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior

  annotation nr % of total phyla/
class
members associated processes
Ia) AtoC-like 408 8.2 16 AtoC, FrgC, HydG, Rrp2, ZraR AtoC: catabolism of short chain fatty acids induced by acetoacetate; biosynthesis of polyhydroxybutyrate; related to motility and expression of flagella r genes [124]; FrgC: developmental association in Myxococcus xanthus [180]; Rrp2: synthesis of lipoproteins in Borrelia [181]; ZraR: responds to cyclic-di-GMP [182]
  NtrC-like 302 6.1 5 NtrC, NRI nitrogen assimilation in Gamma-proteobacteria (see [25]); choline catabolism in Pseudomonas aeruginosa [43]; biosynthesis of EPS and LPS in V. vulnificus [183]and P. aeruginosa [184];
  DctD-like 209 4.2 3 DctD (C4) dicarboxylate transport, associated with symbiosis in Rhizobia [137]
  QseF-like 117 2.4 3 QseF, YfhJ production OM protein in response to host pheromone or sulphate and phosphate stress [185]
  FleR-like 86 1.7 4 FleR, FlrC motility and adhesion to mucin in Pseudomonas aeruginosa [186]
Ib) AcoR-like 216 4.3 6 AcoR acetoin metabolism in B. subtilis [187]
  NorR-like 146 2.9 3 NorR nitric oxide detoxification in E. coli [188]
  PrpR-like 129 2.6 3 PrpR control of propionate metabolism in Salmonella [189]
  FhlA-like 91 1.8 4 FhlA, HyfR FhlA: controls expression of formate hydrogen lyase and is induced by formate [190]
  GabR-like 90 1.8 4 GabR GabR: control of the gamma amino-butyric acid shunt in Bacillus thuringiensis [40]
  FleQ-like 81 1.6 1 FleQ, AdnA, FlrA synthesis of flagella in Legionella pneumophila [115]
  VnfA 51 1.0 11 VnfA control of nitrogenase expression (see [191])
Ic)* PspF 139 2.8 3 PspF* control of membrane stress response (see [80])
II LevR-like 123 2.5 3 CelR, LevR LevR: controls lev operon in B. subtilis. Operon includes PTS transport of polyols and other sugar derivatives [130]; CelR: controls cel operon in Geobacillus stearothermophilus. Operon includes PTS with strong activity towards plant cell wall carbohydrates [131]; EsuR: controls esu operon, which is related to acetyl-sugar uptake and hydrolysis [132]
lmo1721: cel operon in Listeria monocytogenes; control of virulence genes [133]
  1. Column one lists the type of EBP54 and column two a general group annotation. The annotation was based on BLAST scores against a list of 60 experimentally characterized activators (given in additional file 3) and represents around 60% of the identified activators. Columns 3 and 4 provide the (relative) number of activators that are in the group and column 5 gives the number of phyla/classes that are represented (maximum 17). Column 6 lists the characterized activators that are member the group. The final column provides a function description for the specified group member as retrieved from literature, where the main metabolite or process is in bold type.*The EBPs of type Ic, include PspF [80], HrpR (0.3%) [44, 176] and LafK (0.3%) [177] which lack a separate signal recognition domain, Chlamydia CtcC [178] and Helicobacter FlgR [179] which lack a DNA-binding domain. and R. sphaeroides FleT [117] which lacks both domains.