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Table 3 Predicted GlnR regulon in Streptococcus pneumoniae (A) and Streptococcus mutans (B)

From: Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli

gene/operon name locus tag* annotation score (rank) rank in exp.
A) Streptococcus pneumoniae
glnR,A SP_0501,0502 GlnR regulator, Glutamine synthetase 0.95 (1) k.o.
glnP HH ,Q SP_1241,1242 Gln/Glu ABC transport system 0.92 (2) 1,2, SP_1243: 3
gdh SP_1306 Glutamate dehydrogenase 0.90 (5) 4
arcA,B a SP_2148,2150 Arginine deiminase, Ornithine carbamoyltransferase 0.91 (3) b -
glnQ,H,M,P a SP_0610-0607 Gln/Glu ABC transport system 0.84 b -
B) Streptococcus mutans (UA159)
glnR,A Smu.363,364 GlnR, Glutamine synthetase 0.95 (1) k.o.
amtB,glnK Smu.1658,1657c Ammonium transport system, GlnK regulator 0.95 (1) 1
glnQ,H,M,P Smu.1519-1522 Gln/Glu ABC transport system 0.95 (2) 2
citB,Z,idh Smu.670,671,672 Aconitate hydratase, Citrate synthase, Isocitrate dehydrogenase 0.95 (1) 3
Smu.807 Smu.807 Putative membrane protein 0.95 (1) 4
glnP HH ,Q Smu.806c,805c Gln/Glu ABC transport system 0.95 (1) 5
gdh Smu.913 Glutamate dehydrogenase 0.95 (1) -
Smu.68, thrC Smu.68,70 Hypothetical, Threonine synthase 0.92 (5) -
  1. The GlnR-binding site identifications were made as described in the methods for all strains with a published genome (data in Additional file 4). The composition of the regulon appeared identical between strains although the similarity scores of particular binding sites varied slightly. The table lists the numbers obtained with strains TIGR4 and UA159, respectively. Column 4: The ranking is based on the scores obtained with the similar motif search procedure, which provides various sites with identical scores and thus identical ranking. The absence of certain high scoring sites (e.g. ranked 4) was caused by the conservative criteria we applied for a site to qualify as a putative binding site. Column 5 gives the observed ranking on basis of the transcriptional response towards a glnR knock out mutation (k.o.) as derived from [25] and the ranking of operons that are downregulated in a S. mutans glnR knock out after exposure to acid stress for 30 minutes [26]. The ranking score was calculated by dividing the fold change in the glnR mutant by the fold change in the wild-type. Column 1 (a): In some strains the arcA and glnQ ORFs have not been called. The published sequence of strain R6 suggests arcA and glnQ are truncated in this strain. Column 4 (b): The composition of the binding site upstream of arcAB and glnQHMP varies between strains.
  2. * Although [25] studied the effects in strain D39, the used microarrays were based on strains TIGR4 and R6. For reasons of comparison we have therefore listed the locus tags in strain TIGR4.