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Table 2 Genes indirectly 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 Notec
20 mM Glu 100 mM Glu
pH 7 pH 5.5 pH 7 pH 5.5
Genes/operons with a CovR binding consensus
 Ssal_00236 0.01 0.005 0.01 0.01  
 Ssal_00563 0.05 0.04 0.07 0.11  
 Ssal_00678 0.00 0.39 0.21 0.07  
 Ssal_00697 0.04 0.28 0.31 0.18  
 Ssal_00723 0.03 0.01 0.12 0.05  
 Ssal_00725 0.03 0.08 0.21 ns  
 Ssal_00726 ns 0.15 0.30 ns  
 Ssal_00728 0.01 0.03 0.22 0.25  
 Ssal_00729 0.003 0.04 0.13 0.21  
 Ssal_00732 0.08 0.41 0.03 0.32 Ssal_00733–00732 are predicted to be an operon
 Ssal_00733 0.01 0.47 0.02 0.12
 Ssal_00734 0.005 0.03 0.07 0.11 Ssal_00737–00734 are predicted to be an operon
 Ssal_00735 0.001 0.03 0.11 0.15
 Ssal_00736 0.001 0.02 0.05 0.16
 Ssal_00737 0.000 0.03 0.03 0.12
 Ssal_00755 0.004 0.02 0.03 0.30  
 Ssal_00854 0.03 0.35 0.20 0.02  
 Ssal_00871 sacC 0.01 0.01 0.01 0.13  
 Ssal_01340 0.06 0.30 0.05 0.18  
 Ssal_01662 0.06 0.10 0.12 0.12  
 Ssal_01837 sacB 0.01 0.01 0.05 0.08  
 Ssal_01861 manH 0.18 0.25 0.31 0.23  
 Ssal_00446 9.2 2.7 10.7 1.9  
 Ssal_00630 gntR 1.9 2.2 1.7 3.5  
 Ssal_00969 8.9 14.7 2.4 5.4  
 Ssal_01025 3.1 16.7 8.3 1.8  
 Ssal_01086 mnmE 2.6 3.9 3.4 1.9  
 Ssal_01401 endA 3.7 7.4 5.0 7.1  
 Ssal_01479 5.2 2.9 19.1 5.3  
 Ssal_01624 nagB 2.2 1.9 3.8 1.3  
 Ssal_01876 covR 8.8 6.5 3.6 5.7  
 Ssal_02041 tig 1.6 7.3 2.6 1.6  
 Ssal_02096 3.7 2.8 6.0 3.1  
Others
 Ssal_00088 rpsS 0.04 0.48 0.16 0.22  
 Ssal_00221 rpe 0.28 0.44 0.17 0.27  
 Ssal_00318 0.13 0.24 0.36 0.18  
 Ssal_00689 0.11 0.48 0.32 0.23  
 Ssal_00700 0.06 0.35 0.14 0.10  
 Ssal_00703 0.06 0.34 0.24 0.19  
 Ssal_00750 ece1 0.34 0.47 0.21 0.32  
 Ssal_00859 0.18 0.40 0.36 0.25  
 Ssal_01403 0.00 0.02 0.29 0.02  
 Ssal_01497 0.33 0.25 0.36 0.06  
 Ssal_01636 macB 0.12 0.37 0.20 0.06  
 Ssal_01796 accA 0.23 ns 0.14 0.16 Ssal_01807–01796 are predicted to be an operon
 Ssal_01797 accD 0.13 0.40 0.09 0.16
 Ssal_01798 accC 0.12 ns ns1 0.20
 Ssal_01799 0.11 ns 0.05 0.07
 Ssal_01800 fabZ 0.27 ns 0.05 0.21
 Ssal_01801 accB ns ns 0.22 ns
 Ssal_01802 fabF 0.16 0.39 0.05 0.15
 Ssal_01803 fabG 0.10 ns 0.12 0.14
 Ssal_01804 fabD 0.09 0.38 0.12 0.16
 Ssal_01805 fabK 0.06 ns 0.04 0.16
 Ssal_01806 acpP 0.31 0.36 0.16 ns
 Ssal_01807 fabH 0.25 0.50 0.17 0.20
 Ssal_01838 0.21 0.07 0.15 0.19  
 Ssal_02030 cpdB 0.01 0.07 0.12 0.10  
 Ssal_02089 cysE 0.26 0.43 0.10 0.16  
 Ssal_00154 8.3 4.5 ns 2.7  
 Ssal_00402 1.5 2.0 3.6 1.6  
 Ssal_00485 yuaJ 4.6 5.3 6.5 2.7  
 Ssal_00506 2.2 2.3 2.4 1.5  
 Ssal_00665 3.5 2.2 2.4 2.9  
 Ssal_00717 mucB 6 27.3 4.9 3.2  
 Ssal_00738 50.1 193.2 28.3 4.0  
 Ssal_00740 30.7 75.6 6.7 17.9  
 Ssal_00742 3.6 13.2 1.8 1.2  
 Ssal_00975 9.9 5.4 9.4 1.5  
 Ssal_00982 1.9 1.9 1.7 1.2  
  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
  3. c, Operons started with a lower tag number are transcribed from the minus strand