Conservation of the binding site for the arginine repressor in all bacterial lineages

Table 1 Comparison of three transcriptional regulator families with predominantly single representatives from each bacterial genome

Definition	Regulated pathway	Pattern of species^*	Type of DNA-binding domain and fused domain	DNA-binding domain conservation^†	Recognition site^‡	Sites per genome	Reference^§
LexA (Gram-negative)	SOS repair	ADC-VEBMH----	'Winged helix'^¶ HTH and serine protease (S24 family)	2.20 ± 0.28	SOS box (Gram-negative): CTGTatatatatMCAG	8-20	[3,4]
DinR (Gram-positive)					Cheo box (Gram-positive): cGAACrnryGTTYg
HrcA	Heat shock	A-CS-EBM-XYTP	Predicted 'winged helix' HTH and uncharacterized domain possibly responsible for activation by chaperonin GroE	1.72 ± 0.22	CIRCE box: TTAGCACTCn₉GAGTGCTAA	1-2	[5,6]
ArgR (Gram-negative)	Arginine metabolism	ADC-VEBMH---P	'Winged helix' HTH and arginine-binding domain	1.81 ± 0.22	ARG box: TGMATwwwwATKCA	1-20	[8,9,10,11]
AhrC (Gram-positive)

^*Abbreviations for species: B, Bacillus subtilis; C, Clostridium acetobutylicum; M, Mycobacterium tuberculosis; D, Deinococcus radiodurans; A, Thermotoga maritima; S, Synechocystis sp; H, Haemophilus influenzae; E, Escherichia coli; P, Chlamydia pneumoniae; T, Chlamydia trachomatis; Z, Mycoplasma genitalium; Y, Mycoplasma pneumoniae; V, Vibrio cholerae. ^†The estimate was obtained as the average maximum likelihood distance between the last-step UPGMA clusters (of the corresponding tree reconstructed by the PHYLIP package program NEIGHBOR) counted using distance matrix (calculated by PHYLIP package program PROTDIST) only for DNA-binding domains [39]. ^‡ Letter codes used in consensus sequences are the following: M = A or C; Y = T or C; R/r =A or G; W/w =A or T; K = G or T; N/n = any nucleotide, where upper-case letters denote strongly conserved nucleotides and lower-case letters denote less conserved nucleotides. ^§ References correspond to the two last columns. ^¶The 'winged helix' superfamily is defined in the SCOP database [40]; LexA [41] and ArgR [42,43,44] DNA-binding domains have been resolved by X-ray crystallography. The same type of domain was predicted for HrsA using PSIBLAST program.

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