TABLE 2.
Functions and changes in expression of the genes regulated by CodYSt in S. thermophilus ST2017
| Locus (gene) | Assignment | ST2017/ST2017ΔcodY log2 (normalized fold change) | Presence of CodYSt box |
|---|---|---|---|
| leuA | 2-Isopropylmalate synthase | −2.44 | |
| leuB | 3-Isopropylmalate dehydrogenase | −2.32 | |
| leuC | 3-Isopropylmalate dehydratase, large subunit | −3.08 | |
| leuD | 3-Isopropylmalate dehydratase, small subunit | −3.14 | |
| ilvA | Threonine dehydratase biosynthetic | −1.58 | + |
| ilvB | Acetolactate synthase, catalytic subunit | −2.26 | + |
| ilvH | Acetolactate synthase, small subunit | −2.65 | |
| ilvC | Ketol-acid reductoisomerase | −2.61 | |
| livJ | Branched-chain amino acid ABC transporter substrate binding protein | −3.34 | + |
| livH | Branched-chain amino acid ABC transporter permease protein | −3.87 | |
| livM | ABC-type transport system, permease component | −3.23 | |
| livG | ABC-type branched-chain amino acid transport, ATPase component | −2.54 | |
| livF | ABC-type branched-chain amino acid transport, ATPase component | −2.51 | |
| bcaT | Branched-chain amino acid aminotransferase | −2.06 | + |
| trpA | Tryptophan synthase, alpha chain | −2.79 | |
| trpB | Tryptophan synthase, beta chain | −1.13 | |
| trpF | Anthranilate isomerase | −1.81 | |
| trpC | Indole-3-glycerol phosphate synthase | −1.62 | |
| trpD | Anthranilate phosphoribosyltransferase | −2.53 | |
| trpG | Anthranilate synthase glutamine amidotransferase, component II | −1.38 | |
| trpE | Anthranilate synthase, component I | −1.25 | + |
| argH | Argininosuccinate lyase | −1.93 | |
| argG | Argininosuccinate synthase | −1.58 | |
| cysM2 | Cysteine synthase | −2.80 | |
| metB2 | Cystathionine gamma lyase | −2.66 | |
| cysE2 | Serine acetyltransferase, putative | −3.36 | |
| lysC | Aspartokinase | −2.92 | + |
| thrB | Homoserine kinase | −1.55 | + |
| thrC | Threonine synthase | −1.75 | + |
| hutU | Urocanate hydratase | 2.77 | |
| gdhA | Glutamate dehydrogenase GdhA | −1.74 | + |
| Ortholog of STND_0811 | Chorismate mutase | −2.88 | + |
| purC | Phosphoribosylaminoimidazole-succinocarboxamide synthase | 1.91 | |
| purL | Phosphoribosylformylglycinamidine synthase | 2.00 | |
| purF | Amidophosphoribosyltransferase | 1.71 | |
| purM | Phosphoribosylformylglycinamidine cyclo-ligase | 1.57 | |
| purN | Phosphoribosylglycinamide (GAR) formyltransferase | 2.2 | |
| purH | Phosphoribosylaminoimidazolecarboxamide formyltransferase | 1.61 | |
| purD | Phosphoribosylamine-glycine ligase | 1.25 | |
| purE | Phosphoribosylaminoimidazole carboxylase carboxyltransferase | 1.74 | |
| purK | Phosphoribosylaminoimidazole carboxylase II | 1.65 | |
| pyrK | Dihydroorotate dehydrogenase, electron transfer subunit | −2.66 | |
| pyrDb | Dihydroorotate dehydrogenase B | −1.53 | |
| pyrF | Orotidine 5′-phosphate decarboxylase | −2.77 | |
| pyrE | Orotate phosphoribosyltransferase PyrE | −1.22 | |
| Ortholog of STND_0202 | ABC transporter permease protein | −1.94 | |
| Ortholog of STND_0203 | ABC-type transport system, ATPase component | −2.17 | |
| Ortholog of STND_0733 | Mn2+ and Fe2+ transporter of the NRAMP family | −1.07 | + |
| Ortholog of STND_1235 | Predicted membrane protein | −2.33 | + |
| Ortholog of STND_1233 | Predicted membrane protein | −2.16 | |
| Ortholog of STND_1232 | ATPase component of ABC transporter | −1.24 | |
| hrcA | Heat-inducible transcription repressor HrcA | −1.54 | |
| grpE | Putative Hsp70 cofactor GrpE protein | −1.06 | |
| dnaK | Hsp70-like protein | −1.13 | |
| Ortholog of STND_0135 | Mechanosensitive ion channel (MscS) | 1.53 | |
| groES | 10-kDa chaperonin | −1.10 | |
| Ortholog of STND_0307 | Sensor protein | −1.73 | |
| Ortholog of STND_0658 | CRISPR-associated endonuclease, Csn1 family | −3.49 | |
| Ortholog of STND_0862 | Transcription regulator, GntR family | 1.40 | |
| Ortholog of STND_1346 | Glutamate–cysteine ligase | 1.54 | |
| Ortholog of STND_1572 | Universal stress protein UspA | 2.22 | |
| Ortholog of STND_1784 | Transcriptional regulator | 2.30 | |
| Ortholog of STND_1785 | Permease | 1.20 | |
| Ortholog of STND_0113 | Enzyme of poly-gamma-glutamate biosynthesis | 2.15 | |
| Ortholog of STND_0114 | Cytochrome c oxidase, monoheme subunit | 2.65 | |
| Ortholog of STND_0115 | Glycerol-3-phosphate dehydrogenase NAD(P)+ | 1.94 | |
| Ortholog of STND_0182 | Putative uncharacterized protein | −3.01 | |
| Ortholog of STND_0394 | Hypothetical protein | 1.50 | |
| Ortholog of STND_0393 | Hypothetical protein | 2.31 | |
| Ortholog of STND_0392 | Hypothetical protein | 1.12 | |
| Ortholog of STND_0611 | Methenyltetrahydrofolate cyclohydrolase | −1.47 | + |
| Ortholog of STND_0612 | Predicted sugar kinase | −1.80 | |
| Ortholog of STND_0663 | Hypothetical protein | 1.16 | |
| Ortholog of STND_0664 | Hypothetical protein | 1.96 | |
| Ortholog of STND_0782 | Formate–tetrahydrofolate ligase 2 | 2.24 | |
| Ortholog of STND_1004 | Phosphoglycerate mutase family protein | −1.65 | |
| Ortholog of STND_1003 | Phosphoglycerate mutase family protein | −1.76 | |
| Ortholog of STND_1007 | Phosphatase YbjI | −3.22 | |
| Ortholog of STND_1008 | Hypothetical protein | −4.52 | |
| Ortholog of STND_1212 | NADP-dependent glyceraldehyde-3-phosphate dehydrogenase GapN | −1.50 | + |
| Ortholog of STND_1301 | Hypothetical protein | −1.57 | |
| Ortholog of STND_1308 | Conserved protein | −2.06 | + |
| Ortholog of STND_1569 | Amidase nicotinamidase-like protein | −4.11 | |
| Ortholog of STND_1636 | Peptide chain release factor 2 | 1.90 | |
| Ortholog of STND_1658 | Hydrolase, haloacid dehalogenase-like family | 1.44 | |
| Ortholog of STND_1689 | Hypothetical protein | −2.42 |