Table 5.
List of putative STM 4661 CDS differentially regulated upon metal exposure
| Label* | CDS description and putative function |
Zn / Control |
Cd / Control |
|
||
|---|---|---|---|---|---|---|
| log2 Fold | FDR | log2 Fold | FDR | STM 2683 Homologs § | ||
|
Transport |
|
|
|
|
|
|
|
MESS4v1_360013 |
Heavy metal-translocating P-type ATPase CadA |
5.32 |
1.53E-121 |
3.38 |
1.96E-171 |
MESS2v1_740030 |
| MESS4v1_360015 |
conserved membrane protein of unknown function, putative CDF |
2.2 |
1.10E-29 |
0.88 |
1.12E-02 |
Not found |
|
MESS4v1_520016 |
ABC transporter, periplasmic binding protein, Zn import |
−2.98 |
4.47E-96 |
4.19 |
9.71E-173 |
MESS2v1_300037 |
|
MESS4v1_520017 |
ABC transporter, permease protein, Zn import |
−2.59 |
1.49E-33 |
3.28 |
9.43E-144 |
MESS2v1_300038 |
|
MESS4v1_520018 |
ABC transporter-related protein, Zn import |
−2.61 |
1.01E-23 |
3.4 |
2.99E-59 |
MESS2v1_300039 |
| MESS4v1_670093 |
Transporter protein of unknown function |
−1.75 |
4.35E-06 |
−1.44 |
3.69E-04 |
MESS2v1_580019 |
|
MESS4v1_360039 |
Zinc efflux system ZitB type |
1.11 |
2.35E-02 |
0.55 |
0.91 |
MESS2v1_730268 MESS2v1_730269 fissed MESS2v1_p180001 (fragment) |
|
MESS4v1_610026 |
Zinc, cobalt and lead efflux system ZntA |
1.77 |
1.07E-10 |
−0.11 |
1 |
MESS2v1_980073 |
| MESS4v1_750116 |
Aliphatic sulphonate ABC transporter |
−1.02 |
1.35E-03 |
−0.22 |
1 |
Not found |
| MESS4v1_240016 |
Iron-hydroxamate transporter subunit ; ATP-binding component of ABC superfamily, FhuC |
−0.81 |
0.25 |
−1.3 |
7.08E-05 |
MESS2v1_1320036 |
| MESS4v1_360106 |
ABC transporter, permease protein |
0.13 |
1 |
0.87 |
7.05E-03 |
Not found |
| MESS4v1_360107 |
Transporter protein of unknown function |
−0.28 |
1 |
0.8 |
3.68E-02 |
Not found |
| MESS4v1_670092 |
Hemin transport protein HmuS |
−0.63 |
0.66 |
−0.8 |
6.41E-02 |
MESS2v1_580018 |
|
Metal sequestration |
|
|
|
|
|
|
|
MESS4v1_360040 |
Conserved and cytoplasmic protein of unknown function, contains 2 CPX Zn finger domains |
1.02 |
8.10E-02 |
0.54 |
1 |
MESS2v1_730267, MESS2v1_p180003 |
| MESS4v1_750294 |
Xanthine dehydrogenase, Fe-S binding subunit XdhC, located in the cytoplasm |
0.86 |
5.42E-02 |
0.1 |
1 |
Not found |
| MESS4v1_280090 |
Methyltransferase type 11, located in the cytoplasm |
0.2 |
1 |
1.05 |
1.03E-04 |
MESS2v1_1480043 |
|
MESS4v1_520093 |
Cyclic beta-glucan succinyl transferase OpgC, cytoplasmic membrane |
0.15 |
1 |
0.81 |
4.02E-02 |
MESS2v1_310036 |
|
MESS4v1_360014 |
Cytochrome c biogenesis protein, transmembrane region CcdA, putative, involved in reduction as Zn or Cd Sulfides |
4.07 |
4.31E-48 |
2.22 |
3.75E-31 |
MESS2v1_740029 |
| MESS4v1_360049 |
Thiol:disulfide interchange protein CycY, putative, involved in reduction as Zn or Cd Sulfides, located in the periplasm |
1.12 |
1.07E-04 |
1.93 |
1.30E-24 |
MESS2v1_730262 |
| MESS4v1_360050 |
Reduction as Zn or Cd Sulfides - putative thioredoxin protein |
1.18 |
8.54E-05 |
2.14 |
4.83E-29 |
MESS2v1_730261 |
| MESS4v1_360052 |
Putative oxidoreductase protein involved in reduction as Zn or Cd Sulfides |
0.91 |
1.13E-02 |
1.86 |
9.13E-25 |
MESS2v1_730259 |
| MESS4v1_360053 |
Conserved exported protein of unknown function, putative protein-disulfide isomerase |
0.82 |
4.09E-02 |
1.71 |
3.89E-22 |
MESS2v1_730258 |
|
MESS4v1_360023 |
Signal peptidase II. Aspartic peptidase. MEROPS family A08, located in cytoplasmic membrane |
1.85 |
1.54E-13 |
0.69 |
0.14 |
MESS2v1_740019 |
| MESS4v1_160007 |
Peptide methionine sulfoxide reductase MsrA, putative, involved in reduction as Cd Sulfides |
8.49E-02 |
1 |
1.13 |
3.01E-04 |
MESS2v1_1200004 |
| MESS4v1_360103 |
Glutathione S-transferas, putative, involved in reduction as Cd Sulfides |
−0.26 |
1 |
0.98 |
1.81E-03 |
Not found |
| MESS4v1_310058 |
Fe(3+)-binding periplasmic protein, FbpA |
−0.87 |
9.42E-02 |
−1.01 |
1.37E-03 |
MESS2v1_1490012 |
| MESS4v1_360047 |
Conserved exported protein of unknown function, predicted metal-binding domain |
1.33 |
1.93E-07 |
2.27 |
1.93E-36 |
MESS2v1_730264 |
| MESS4v1_360048 |
Conserved exported protein of unknown function, predicted metal-binding domain |
1.24 |
2.38E-06 |
2.19 |
8.73E-21 |
MESS2v1_730263 |
|
MESS4v1_830506 |
conserved exported protein of unknown function, putative metal-binding protein |
4.76E-02 |
1 |
−0.9 |
5.15E-02 |
MESS2v1_1530017 |
|
Regulation |
|
|
|
|
|
|
| MESS4v1_580068 |
ROK family protein |
−0.84 |
3.37E-02 |
−0.36 |
1 |
MESS2v1_400012 |
|
Oxidoreduction |
|
|
|
|
|
|
| MESS4v1_360054 |
Cytochrome c-type biogenesis protein CdcA (fragment) |
0.92 |
2.06E-02 |
1.59 |
2.89E-18 |
|
| MESS4v1_360046 |
Multicopper oxidase, type 3 |
1.24 |
4.42E-06 |
2.09 |
1.95E-19 |
MESS2v1_730265 |
| MESS4v1_750295 |
Putative Medium FAD-binding subunit of molybdenum enzyme |
1.03 |
1.13E-02 |
0.29 |
1 |
Not found |
| MESS4v1_310027 |
Aldo/keto reductase |
−3.16E-02 |
1 |
0.74 |
7.75E-02 |
MESS2v1_1480132 |
| MESS4v1_340203 |
Exported protein of unknown function, putative hydrolase |
−3.91E-02 |
1 |
0.84 |
4.40E-02 |
Not found |
| MESS4v1_340204 |
Conserved protein of unknown function, putative hydrolase |
−5.32E-02 |
1 |
0.78 |
6.89E-02 |
Not found |
| MESS4v1_360100 |
Putative dioxygenase |
−0.25 |
1 |
0.98 |
4.02E-03 |
Not found |
| MESS4v1_360104 |
3-hydroxybutyryl-coA dehydrogenase |
−0.22 |
1 |
0.8 |
4.28E-02 |
Not found |
| MESS4v1_820066 |
Putative reductase |
−0.1 |
1 |
0.88 |
1.07E-02 |
MESS2v1_790060 |
|
MESS4v1_830086 |
conserved exported protein of unknown function, putative succinate dehydrogenase/fumarate reductase, flavoprotein subunit |
−0.21 |
1 |
2.18 |
2.63E-32 |
MESS2v1_790137 |
|
Others |
|
|
|
|
|
|
|
MESS4v1_830271 |
conserved protein of unknown function - N-acetyltransferase activity |
−1.08 |
3.12E-04 |
−0.47 |
1 |
MESS2v1_1590041 |
| MESS4v1_830272 |
putative ornithine decarboxylase |
−0.98 |
1.42E-02 |
−0.62 |
0.32 |
MESS2v1_1590040 |
| MESS4v1_580067 |
Tagatose-1,6-bisphosphate aldolase, located in the cytoplasm |
−0.94 |
1.87E-02 |
−0.4 |
1 |
MESS2v1_400011 |
| MESS4v1_360102 |
Putative translation initiation inhibitor, yjgF family |
−0.22 |
1 |
0.98 |
1.84E-03 |
Not found |
|
Unclassified |
|
|
|
|
|
|
| MESS4v1_360051 |
protein of unknown function |
0.94 |
1.42E-02 |
1.8 |
3.06E-15 |
Not found |
| MESS4v1_280043 |
conserved protein of unknown function |
0.89 |
3.06E-02 |
0.38 |
1 |
Not found |
| MESS4v1_330155 |
conserved protein of unknown function |
0.83 |
8.89E-02 |
0.59 |
0.51 |
Not found |
| MESS4v1_430174 |
conserved protein of unknown function |
0.88 |
2.49E-02 |
0.17 |
1 |
MESS2v1_130027 |
| MESS4v1_610025 |
protein of unknown function |
1.04 |
2.09E-03 |
−4.88E-02 |
1 |
Not found |
| MESS4v1_690015 |
protein of unknown function |
−1.64 |
1.71E-06 |
0.18 |
1 |
Not found |
| MESS4v1_720075 |
protein of unknown function |
0.84 |
9.38E-02 |
0.43 |
1 |
Not found |
| MESS4v1_830036 |
conserved exported protein of unknown function |
−0.89 |
9.38E-02 |
0.32 |
1 |
MESS2v1_790093 |
| MESS4v1_110143 |
conserved exported protein of unknown function |
2.75E-02 |
1 |
0.76 |
4.41E-02 |
MESS2v1_1080055 |
| MESS4v1_210104 |
protein of unknown function |
0.46 |
1 |
0.76 |
6.06E-02 |
Not found |
| MESS4v1_230034 |
protein of unknown function |
−0.19 |
1 |
0.83 |
2.10E-02 |
Not found |
| MESS4v1_240036 |
conserved exported protein of unknown function |
1.38E-03 |
1 |
0.75 |
6.82E-02 |
Not found |
| MESS4v1_360025 |
protein of unknown function |
0.2 |
1 |
0.83 |
4.41E-02 |
Not found |
| MESS4v1_360101 |
conserved protein of unknown function |
−0.17 |
1 |
0.92 |
6.17E-03 |
Not found |
| MESS4v1_360109 |
protein of unknown function |
−0.12 |
1 |
1.03 |
1.37E-03 |
Not found |
| MESS4v1_490002 |
conserved protein of unknown function |
0.12 |
1 |
0.78 |
6.89E-02 |
MESS2v1_210010 |
| MESS4v1_560009 |
protein of unknown function |
−7.77E-02 |
1 |
0.77 |
4.07E-02 |
Not found |
| MESS4v1_560010 |
conserved exported protein of unknown function |
−0.34 |
1 |
0.88 |
6.33E-03 |
Not found |
| MESS4v1_640142 |
protein of unknown function |
−0.57 |
0.69 |
−0.82 |
3.68E-02 |
Not found |
| MESS4v1_680031 |
protein of unknown function |
−0.69 |
0.25 |
−0.78 |
5.49E-02 |
MESS2v1_590015 |
| MESS4v1_710103 |
conserved membrane protein of unknown function |
−0.33 |
1 |
0.75 |
7.73E-02 |
MESS2v1_650084 |
| MESS4v1_750195 |
conserved protein of unknown function |
0.32 |
1 |
0.81 |
2.31E-02 |
MESS2v1_730184 |
| MESS4v1_830287 |
conserved protein of unknown function |
−8.46E-02 |
1 |
0.76 |
6.14E-02 |
Not found |
| MESS4v1_110128 | conserved membrane protein of unknown function | −0.82 | 3.80E-02 | 0.56 | 0.63 | MESS2v1_1080036 |
* Gene labels (CDS) were obtained from MaGe; CDS significantly regulated (FDR < 0.1) upon metal exposure in both STM 2683 and STM 4661 are in bold. MESS4v1_XXX are genes located on the chromosome and MESS4v1_pXXX are genes located on the plasmid.
§ When detected, STM 2683 homologs are indicated (See Methods for details).