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Table 1 Distribution and GlnR-mediated regulation of genes related to central nitrogen metabolism within the order Bacillales

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

NCBI PROJECT NAME \ GENES codY tnrA glnR glnA gdh bdh glutamin- ase (HA) glutamin- ase (LA) gltAB gltA BC gltS amtB glnK glnQHMP glnP H Q glnT, alsT, yrbD, yflA gltP, dctA, gltT, yhcL, nqt
A) order Bacillales                  
Anoxybacillus flavithermus WK1 1 1 1 2(2) 2 1    1 1   1 d    1 2(1) 1
Geobacillus kaustophilus HTA426 1 1 1 2(1) 2 2 1   1    1 d   1 1 1 2
G. thermodenitrificans NG80-2 1 1 1 2(2) 2 2 1   1    1 d    1 1 5(1)
G. sp. Y412MC61 1 1 1 2(1) 2 2 1   1    2 d 1 1 1 1 2
G. sp. C56-T3 1 1 1 2(1) 2 1 1   1    1 d   1 1 1 2
G. sp. WCH70 1 1 1 1 2 1 1   1 1     1   1 3
Bacillus cereus ATCC 14579 1   1 1 b 1 1 1 1,0   1 1 1   1,2   6(1) 5(1)
B. anthracis str. Ames 1   1 1 1 1 1 1   1 1 0,1   1   6(1) 5(1)
B. thuringiensis str. Al Hakam 1   1 1 1 1 1 1   1 1 1   1   7(1) 6(1)
B. weihenstephanensis KBAB4 1   1 1 2 1 1    1 1 1   1   6(1) 5(1)
B. atrophaeus 1942 1 1 1 1 3 1 1 1 1   1 1 1 1   3(1) 4
B. amyloliquefaciens DSM7 1 1 1 1 2 1 1 1c 1   1 1 1 1   2(1) 3
B. pumilus SAFR-032 1 1 1 1 2 1 1 1 1   1 1 1 1   3 5(1)
B. subtilis str. 168 1 1 1 1 2 1 1 1 1   1 1 1 1,0   4(1) 4
B. licheniformis ATCC 14580 1 1 1 1 2(1) 1 1 1 1    2(1) 2(1)    6(1) 4
B. megaterium DSM319 1 1 1 1 3 1   1 1   1 2(2) 2(2) 1   3(1) 11(1)
B. pseudofirmus OF4 1 1 2(1)e 2(2) 4 1 1 1 1    1    1 3(1) 3
B. clausii KSM-K16 1 1   2 2 1 1   1    1    1 3 3
B. halodurans C-125 1 1   2 5 2 1 1 1    1     5 1
B. selenitireducens MLS10 1 1   1 4 1   1 1b 1   1    1 2  
Lysinibacillus sphaericus C3-41 1   1 2(2) c 2 1       1 1   1 3 5
Oceanobacillus iheyensis HTE831 1 1a 1 1 1 2   1 1   1 1 1   1 3 3
Exiguobacterium sp. AT1b 1 1 1 2(1) 1 1 1   1   1 1     6(1) 1
Paenibacillus polymyxa E681   1 1 2(1) 1   1   1    1 d   2(1) 1 2 2
Pb. sp. JDR-2 1 1 1 2(1) 2 1 1   1   1 3(1d) 1 1    1
Brevibacillus brevis NBRC 100599 1   1 2(2) 2 1 1 1 1b   1 1 d   1 1 1 3
Ab. acidocaldarius DSM 446 1   1 3(1) 2 1     1   2(1) 1     
Listeria innocua Clip11262 1   1 1 1     1    1 1   1   
L. monocytogenes EGD-e 1   1 1 1     1    1 1   1   
L. seeligeri 1/2b str. SLCC3954 1   1 1 1     1    1 1   1   
Staphylococcus aureus Mu50 1   1 1 1     1   1 1    1 2 2
S. carnosus TM300 1   1 2(1) 1     1   1      2 3
S. epidermidis ATCC 12228 1   1 1 1     1   1 1     1 2
S. haemolyticus JCSC1435 1   1 1 1     1   1 1     1 2
S. lugdunensis HKU09-01 1   1 1 1     1   1 1     1 2
S. saprophyticus ATCC 15305 1   1 1 2     1   1 1     2(1) 4
Mc. caseolyticus JCSC5402 1   1 1 1 1           2 3
  1. The table summarizes the data retrieved for all species and strains which can be found in Additional file 1. The number of orthologs/homologs in every genome is indicated. For instance Anoxybacillus flavithermus WK1 contains 2 genes encoding glutamine synthetase. Every species is represented by one strain only. Species abbreviations: Ab., Alicyclobacillus; B., Bacillus; G., Geobacillus; L., Listeria; Mc., Macrococcus; Pb., Paenibacillus; S., Staphylococcus.
  2. Gene content. The included genes encode the established regulators CodY, TnrA and GlnR [4]; the central enzymes Gln synthetase (glnA; [30]), Glu dehydrogenase (gdh; [31, 32]), 3-hydroxybutyrate dehydrogenase (bdh[33, 34]), high affinity (HA) and low affinity (LA) glutaminase, glutamate synthase (NADPH-dependent , large and small subunit gltB and gltA[21, 22]; B. cereus type gltA; ferredoxin dependent gltS[35]), aspartate-ammonia ligase/asparagine synthetase (asnA[36] or asnB[37]), asparaginase (ansA or ansZ[38, 39]); and the transport systems for ammonium (amtB with related regulator glnK; [40]), gln/glu using ATP (ABC-family, glnPHQ and glnQHMP) and glutamine-like proton symport (AGCS-family, glnT alsT yrbD yflA) and glutamate-like proton symport (DAACS-family, gltP gltT yhcl nqt). In the latter two cases a variation in numbers was observed for different strains. In the other cases the numbers were far less variable (the ones that were variable are indicated as comma separated numbers).
  3. GlnR-mediated regulation. Genes/operons that have a clear upstream GlnR binding site are marked by dark grey boxes (similarity score >87%), whereas genes/operons that are preceded by a less clear site are marked light grey (similarity score 80–87%). In case more genes are present encoding the same function then the number of genes with a clear binding site is indicated between brackets and if in addition the other gene(s) are preceded by a less clear site then the cell is marked light grey.
  4. a) A GlnR-binding site is present but downstream of tnrA because the gene has opposite direction when compared to all other species.
  5. b) For one sequence no ORF was called. However the gene could be identified using tBLASTN.
  6. c) One of the sequences in two fragments.
  7. d) Seems part of an operon that includes a gene with DUF294 domain and the gene dnaQ.
  8. e) The glnR and glnA duplicates in B. pseudofirmus OF4 are not part of a single operon and located at different positions on the genome.