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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.
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BMC Genomics

ISSN: 1471-2164

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