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Table 1 Genes directly regulated by CodY in S. salivarius 57.I

From: Impact of growth pH and glucose concentrations on the CodY regulatory network in Streptococcus salivarius

Function category/
Locus_tag
Gene/
Homologa
ΔcodY/57.Ib Position(nt)c Predicated CodY binding sequence Noted
20 mM Glu 100 mM Glu
pH 7 pH 5.5 pH 7 pH 5.5
Peptide uptake and degradation
 Ssal_00190 oppA ns ns 1.5 ns 94 AATATTCAGAAAGTA  
 Ssal_00280 pepP ns 4.3 ns 1.3 39 TAAAGTCTGAAAATT  
 Ssal_01946 pepC 3.3 ns ns ns 42 AATTTTCAGAAATTA  
Amino acid uptake and biosynthesis
 Ssal_00127 thrC 1.6 ns 2.9 1.45 43 AATATTCTGACAATT  
 Ssal_00131 ilvD 3.2 7.7 ns 3.1 66 AATATTCTGAAAATT  
 Ssal_00132 ilvB 3.6 4.0 88.1 5.1 30 AATTTTTAGACAATT Ssal_00132–00134 are predicted to be an operon
 Ssal_00133 ilvH 5.1 6.3 4.4 2.4   
 Ssal_00134 ilvC 5.3 9.7 2.4 1.6   
 Ssal_00456 5.4 ns ns 1.6 336 AATTAACAGAAAATT Ssal_00456–00465 are predicted to be an operon
 Ssal_00457 trpE 1.5 2.5 ns 1.6   
 Ssal_00458 trpG ns 3.5 ns ns   
 Ssal_00459 trpD ns 2.3 ns 1.6   
 Ssal_00461 trpC ns 2.4 ns ns   
 Ssal_00462 trpF ns 2.1 ns ns   
 Ssal_00464 trpB ns 2.7 ns ns   
 Ssal_00465 trpA ns 2.2 ns 1.5   
 Ssal_00537 serC 2.0 2.6 2.5 2.6 38 AATATTCAGAAAATT Ssal_00537–00539 are a predicted to be an operon
 Ssal_00538 1.5 5.0 2.3 1.7   
 Ssal_00539 serA 3.1 6.5 1.7 2.6   
 Ssal_00884 dapA 1.8 ns 1.6 ns 74 CGTTTTCAGAAAATT  
 Ssal_00898 pdxU2 2.6 3.3 2.8 3.8 41 AATCGTCAGAATTTT Ssal_00898–00900 are predicted to be an operon
 Ssal_00899 pdxK 4.6 4.6 2.8 3.3   
 Ssal_00900 pdxU 3.9 2.6 4.3 3.1   
 Ssal_01037 ilvB 3.6 5.3 1.8 ns 154 AAAATTCACAATCTT  
129 GATTGTCTGAAAACT
 Ssal_01272 leuD 1.8 ns ns ns    Ssal_01276–01272 are predicted to be an operon
 Ssal_01273 leuC 2.4 3.1 2.2 ns   
 Ssal_01275 leuB 2.8 2.8 20.5 ns   
 Ssal_01276 leuA 3.1 4.4 1.8 ns 242 AAAAGTCAGTCAATT
 Ssal_01351 mprF 1.8 2.9 3.5 1.6    Ssal_01352–01351 are predicted to be an operon
 Ssal_01352 ns 2.7 23.2 ns 134 AATATTCTGACTCTT
 Ssal_01567 ilvE 5.8 3.6 11.1 4.2 75 AATTGTCAGAATTTT  
 Ssal_01655 pheP 5.1 2.3 2.2 4.0 95 AAAATTCTGAATATT  
 Ssal_01693 thrB 2.5 ns ns 1.7    Ssal_01694–01693 are predicted to be an operon
 Ssal_01694 1.8 1.8 ns ns 98 AATTTTCAGTAAAAA
55 AATATTCTGTCAATT
 Ssal_01811 lysC 5.9 5.2 9.4 5.6 39 AATTGTCAGAATTTT  
 Ssal_01812 asnA 3.3 2.1 ns 1.7 61 AATTGTTGGAAAATT  
41 ATTTTTCTGAAAAAT
 Ssal_01828 livF 1.7 4.3 2.2 1.7    Ssal_01832–01828 are predicted to be an operon
 Ssal_01829 livG 1.5 6.7 4.3 1.8   
 Ssal_01830 livM ns 3.5 36.1 1.3   
 Ssal_01831 livH ns 9.2 3.4 2.6   
 Ssal_01832 livK ns 12.5 5.5 2.0 192 ACTATTCTGATATTG
14 AATTGTCTGATAATT
 Ssal_01840 metB ns ns 5.0 ns 215 ATGTTTCAGGCACTT  
62 TATTTTCAGAAAATA
 Ssal_02023 ilvA 3.1 3.3 ns 1.7 45 TTTTTTCTGAAAATT  
       17 AATAGTTTGAATATT  
Urease operon
 Ssal_01891 ureO 8.0 8.3 2.3 ns    Ssal_01903–01891 are predicted to be an operon
Ssal_01903 and Ssal_01904 are in opposite orientations
 Ssal_01892 ureQ 3.5 5.0 2.4 1.8   
 Ssal_01894 ureM 2.0 3.3 2.2 1.6   
 Ssal_01895 ureD ns 6.3 1.7 ns   
 Ssal_01896 ureG ns 3.5 4.6 ns   
 Ssal_01897 ureF ns 4.3 2.0 ns   
 Ssal_01898 ureE ns 3.8 2.9 1.2   
 Ssal_01900 ureC 4.1 2.5 ns 2.6   
 Ssal_01901 ureB ns ns 1.9 ns   
 Ssal_01902 ureA ns 2.8 1.8 ns   
 Ssal_01903 ureI 2.0 3.5 2.2 1.6 211 TATTGTCAGAAACAG
58 AAATTTCTGAAAATT
 Ssal_01904 6.1 2.0 12.2 4.3 334 AATTTTCAGAAATTT  
       181 CTGTTTCTGACAATA  
Other transporters  
 Ssal_00845 2.5 2.0 57.1 13.8 69 TAATTTCAGAAAATT  
 Ssal_00908 33.9 16.7 55.1 16.6 92 ATTTTTCAGAAAATA  
60 ATTATTCCAACAATT
19 ATTATTCTGAAAATT
 Ssal_01154 ns 2.8 7.8 1.3 144 AATATTCGGAAAATA  
 Ssal_01464 7.1 7.1 7.1 2.4    Ssal_01466–01464 are predicted to be an operon
 Ssal_01465 fhuC 4.9 7.1 2.7 2.5   
 Ssal_01466 hmuU 8.7 7.9 3.9 4.7 116 AATTTTCTGACATTA
Regulation
 Ssal_00404 codY nd nd nd nd 116 AATTTTCAGACAATT  
 Ssal_00555 cidA 2.2 ns 2.1 1.4 175 AAATATTTGACTATT Ssal_00555–00556 are predicted to be an operon
79 AATTTACTGAAAACT
 Ssal_00556 cidB 1.6 ns 3.2 1.7   
 Ssal_00962 21.8 18.6 21.9 19.8 108 AAGTATCTGAAATAG  
39 AATTTTCAGAATATT
 Ssal_01667 glnB 43.2 8.4 3.4 6.0    Ssal_01668–01667 are predicted to be an operon
 Ssal_01668 nrgA 15.2 19.9 61.2 7.5 361 CTATTTCAGAAGTTT
292 GAGCTTCTGAAAATG
78 AATTATCAAAAAATT
 Ssal_01704 2.5 ns 9.1 2.1 10 AATTATCAGAAAAGG  
 Ssal_01769 nadR ns ns 4.9 1.4 288 AATTTTCAGAATCTT  
264 TATTTTCTGCTATTT
Carbon metabolism
 Ssal_01359 2.4 3.1 4.1 3.4    Ssal_01360–01359 are predicted to be an operon
 Ssal_01360 gapN 3.4 6.3 ns 1.5 74 AATTTTCTGAATAAT
 Ssal_01545 4.7 2.7 3.3 3.1    Ssal_01546–01545 are predicted to be an operon
 Ssal_01546 folD 3.8 4.9 3.0 3.2 138 CATAATCAGAAAAAA
72 AAAATTTAGAAAATT
 Ssal_01768 gdhA 12.9 15.7 3.5 6.3 353 GCTTTCCTGATAATT  
61 AAATAGCAGAAAATA
 Ssal_01810 pgmB ns ns 3.6 ns 75 AAAATTCTGACAATT  
Others
 Ssal_00112 3.5 2.3 4.4 1.4 44 AATCGTCTGAATATT  
 Ssal_00214 ns ns ns 2.1 324 CATCTTCTGAAATTT  
 Ssal_00216 3.3 2.1 2.8 ns 229 AAATTTCAGAAGATG  
 Ssal_00672 72.1 247.7 73.6 41.8 178 AATTGTCAGACAACT  
123 AATTGTCAGAATGTT
 Ssal_00714 ns 7.3 2.2 ns 108 ACTTTTCTAAAAATT  
 Ssal_01153 udg 1.9 ns ns 4.1 129 TATTTTCCGAATATT  
 Ssal_01428 lysM ns 3.9 ns 8.7 143 AAATGTCAGATAAAT  
 Ssal_01429 lysS ns 3.2 ns 1.215 69 ATTTATCTGACATTT  
  1. a, −, no assigned gene name
  2. b, The values are the RPKM of the locus in S. salivarius ΔcodY divided by that in wild-type 57.I under the same growth condition. ns, no significant difference. nd, not determined
  3. c, The distance (in nucleotides) of the predicted CodY binding consensus to the translation start site of the locus
  4. d, Operons started with a lower tag number are transcribed from the minus strand