Table 4.
List of putative STM 2683 CDS differentially regulated upon metal exposure
| Label* | CDS description and putative function |
Zn / Control |
Cd / Control |
|
||
|---|---|---|---|---|---|---|
| log2 Fold | FDR | log2 Fold | FDR | STM 4661 Homologs § | ||
|
Transport |
|
|
|
|
|
|
|
MESS2v1_p180001 |
Cation efflux system protein czcD-type (fragment) |
1.97 |
2.5E-16 |
1.41 |
2E-08 |
MESS4v1_360039 |
|
MESS2v1_300037 |
ABC transporter, periplasmic binding protein, Zn import |
−4.09 |
2E-60 |
2.54 |
1.3E-24 |
MESS4v1_520016 |
|
MESS2v1_300038 |
ABC transporter, permease protein, Zn import |
−4.13 |
3E-116 |
2.49 |
4.5E-43 |
MESS4v1_520017 |
|
MESS2v1_300039 |
ABC transporter-related protein, Zn import |
−4.37 |
2E-127 |
2.32 |
4E-24 |
MESS4v1_520018 |
|
MESS2v1_740030 |
Heavy metal-translocating P-type ATPase CadA |
3.07 |
6.7E-21 |
2.2 |
2.2E-12 |
MESS4v1_360013 |
| MESS2v1_980072 |
Transporter protein of unknown function |
3.36 |
3E-42 |
2.2 |
4.9E-17 |
Not found |
|
MESS2v1_980073 |
Zinc, cobalt and lead efflux system ZntA |
4.65 |
2E-134 |
3.48 |
6E-131 |
MESS4v1_610026 |
| MESS2v1_620035 |
Multidrug efflux system, subunit C, MdtC |
0.93 |
0.0283 |
0.13 |
1 |
MESS4v1_690033 |
| MESS2v1_620036 |
Multidrug efflux system, subunit A, MtdA |
0.95 |
0.0116 |
0.0714 |
1 |
MESS4v1_690034 |
|
MESS2v1_730268 |
Putative cation efflux system protein (Cobalt-zinc-cadmium resistance CzcD-like), CDF family (fragment, part 1) |
1.12 |
0.0182 |
0.67 |
0.69 |
MESS4v1_360039 |
|
MESS2v1_730269 |
Putative cation efflux system protein (Cobalt-zinc-cadmium resistance CzcD-like), CDF family (fragment, part 2) |
1.26 |
0.00012 |
0.64 |
0.48 |
MESS4v1_360039 |
| MESS2v1_320039 |
ABC transporter, permease protein, sugar transporter |
0.44 |
1 |
0.82 |
0.0364 |
MESS4v1_530098 |
| MESS2v1_730254 |
Efflux transporter, RND family, MFP subunit |
−0.32 |
1 |
1.2 |
9.6E-05 |
Not found |
|
Metal sequestration |
|
|
|
|
|
|
|
MESS2v1_p180003 |
conserved and cytoplasmic protein of unknown function, contains 2 CPX Zn finger domain |
2.01 |
4.4E-17 |
1.42 |
5.5E-08 |
MESS4v1_360040 |
|
MESS2v1_730267 |
conserved and cytoplasmic protein of unknown function, contains 2 CPX Zn finger domain |
1.09 |
0.0263 |
0.58 |
1 |
MESS4v1_360040 |
| MESS2v1_1150003 |
conserved and cytoplasmic protein of unknown function, contains 2 CPX Zn finger domain |
−0.78 |
0.0792 |
−0.3 |
1 |
Not found |
|
MESS2v1_310036 |
Cyclic beta-glucan succinyl transferase OpgC, cytoplasmic membrane |
−0.14 |
1 |
0.76 |
0.0813 |
MESS4v1_520093 |
| MESS2v1_1210019 |
Antibiotic biosynthesis monooxygenase, putative, involved in the biosynthesis of extracellular polysaccharides |
−0.0992 |
1 |
0.77 |
0.0654 |
MESS4v1_160035 |
|
MESS2v1_740029 |
Cytochrome c biogenesis protein, transmembrane region CcdA, putative, involved in reduction as Zn or Cd Sulfides |
3.04 |
6.2E-29 |
2.17 |
1.9E-30 |
MESS4v1_360014 |
| MESS2v1_740015 |
Phosphoesterase PA-phosphatase-related (fragment), located in cytoplasmic membrane |
1.19 |
3E-05 |
0.73 |
0.23 |
Not found |
|
MESS2v1_740019 |
Signal peptidase II. Aspartic peptidase. MEROPS family A08, located in cytoplasmic membrane |
1.64 |
1.5E-12 |
0.65 |
0.3 |
MESS4v1_360023 |
| MESS2v1_440031 |
Rhodanese domain protein, putative, involved in reduction as sulfide |
−0.0727 |
1 |
0.88 |
0.0481 |
MESS4v1_590053 |
| MESS2v1_1160006 |
Transcription regulator, putative, involved in reduction as Cd Sulfides |
0.0363 |
1 |
0.93 |
0.00391 |
MESS4v1_120164 |
| MESS2v1_1660011 |
Putative cytochrome c biogenesis protein, involved in reduction as Cd sulfide, located in cytoplasmic membrane |
0.1 |
1 |
1.59 |
2.9E-11 |
Not found |
| MESS2v1_1660012 |
Thioredoxin-related, putative, involved in reduction as Cd sulfide |
−0.0234 |
1 |
1.68 |
9.2E-12 |
Not found |
| MESS2v1_160018 |
Serine endoprotease, periplasmic DegQ, putative, involved in Zn periplasmic binding |
1.7 |
1.7E-10 |
0.24 |
1 |
MESS4v1_440007 |
| MESS2v1_160022 |
Glutamate-ammonia-ligase adenylyltransferase GlnE, putative, involved in Zn periplasmic binding and participating to degQ activity |
0.94 |
0.00988 |
0.33 |
1 |
MESS4v1_440011 |
|
MESS2v1_1530017 |
conserved exported protein of unknown function, putative metal-binding protein |
−0.45 |
1 |
−1.58 |
3.9E-06 |
MESS4v1_830506 |
|
Regulation |
|
|
|
|
|
|
| MESS2v1_160020 |
putative Two-component transcriptional regulator; transcriptional regulator involved in heavy-metal (Cu/Zn) homeostasis |
1.12 |
0.00012 |
0.0744 |
1 |
MESS4v1_440009 |
| MESS2v1_160021 |
Sensor protein |
0.87 |
0.0294 |
0.17 |
1 |
MESS4v1_440010 |
| MESS2v1_300035 |
Transcriptional regulator, AsnC family |
−0.38 |
1 |
1.12 |
0.00047 |
MESS4v1_520012 |
|
Oxidoreduction |
|
|
|
|
|
|
| MESS2v1_110046 |
Alpha/beta hydrolase fold protein |
−0.87 |
0.0228 |
0.18 |
1 |
Not found |
| MESS2v1_620027 |
NAD(P)H:quinone oxidoreductase |
1.1 |
0.00721 |
0.19 |
1 |
Not found |
| MESS2v1_1150002 |
Haloalkane dehalogenase |
−0.83 |
0.0623 |
−0.74 |
0.21 |
Not found |
| MESS2v1_300036 |
conserved protein of unknown function, putative, hydrolase activity |
−0.77 |
0.27 |
1.5 |
4.2E-07 |
MESS4v1_520015 |
|
MESS2v1_790137 |
conserved exported protein of unknown function, putative, succinate dehydrogenase/fumarate reductase, flavoprotein subunit |
−0.26 |
1 |
1.08 |
0.00047 |
MESS4v1_830086 |
|
Others |
|
|
|
|
|
|
|
MESS2v1_1590041 |
conserved protein of unknown function - N-acetyltransferase activity |
−0.94 |
0.00626 |
−0.65 |
0.3 |
MESS4v1_830271 |
| MESS2v1_10049 |
Protein folding- Stress - chaperonin groES |
−0.91 |
0.0796 |
−0.51 |
1 |
MESS4v1_60077, MESS4v1_430231, MESS4v1_510195 |
| MESS2v1_900005 |
transposase |
−0.0531 |
1 |
0.95 |
0.0027 |
|
| MESS2v1_980071 |
protein of unknown function, putative transposase |
0.8 |
0.0689 |
−0.0345 |
1 |
Not found |
| MESS2v1_1530018 |
Nuclear export factor GLE1 (fragment) |
−0.4 |
1 |
−1.54 |
2.6E-09 |
Not found |
| MESS2v1_1660010 |
conserved protein of unknown function, putative, antirestriction protein ArdC |
−0.0576 |
1 |
0.89 |
0.00928 |
Not found |
|
Unclassified |
|
|
|
|
|
|
| MESS2v1_p180002 |
protein of unknown function |
2.02 |
1.8E-14 |
1.29 |
1.1E-06 |
Not found |
| MESS2v1_740028 |
exported protein of unknown function |
2 |
3.1E-28 |
1.41 |
5E-07 |
Not found |
| MESS2v1_740031 |
protein of unknown function |
2.17 |
2.4E-39 |
1.43 |
1.4E-09 |
Not found |
| MESS2v1_1030151 |
protein of unknown function |
−1.5 |
2.7E-12 |
−1.75 |
2.1E-14 |
Not found |
| MESS2v1_1280026 |
protein of unknown function |
1.73 |
6.8E-13 |
1.82 |
3.4E-13 |
Partial MESS4v1_220037 |
| MESS2v1_1520011 |
protein of unknown function |
−0.94 |
0.0626 |
−0.99 |
0.0116 |
Not found |
| MESS2v1_160019 |
protein of unknown function |
1.71 |
1.1E-12 |
0.27 |
1 |
Not found |
| MESS2v1_280030 |
protein of unknown function |
−0.79 |
0.0689 |
−0.66 |
0.29 |
Not found |
| MESS2v1_460011 |
protein of unknown function |
0.79 |
0.0689 |
0.13 |
1 |
Not found |
| MESS2v1_620020 |
conserved exported protein of unknown function |
−0.98 |
0.0834 |
0.12 |
1 |
Not found |
| MESS2v1_740027 |
protein of unknown function |
1.18 |
3.5E-05 |
0.67 |
0.41 |
Not found |
| MESS2v1_980070 |
protein of unknown function |
1.72 |
8.8E-08 |
0.92 |
0.62 |
Not found |
| MESS2v1_p110013 |
protein of unknown function |
−0.72 |
0.73 |
−1.25 |
0.0192 |
Not found |
| MESS2v1_50011 |
protein of unknown function |
−0.57 |
0.93 |
−0.99 |
0.0167 |
Not found |
| MESS2v1_310082 |
protein of unknown function |
0.35 |
1 |
0.75 |
0.0813 |
Not found |
| MESS2v1_360012 |
protein of unknown function |
−0.53 |
1 |
−0.77 |
0.0585 |
Not found |
| MESS2v1_600022 |
protein of unknown function |
0.28 |
1 |
0.89 |
0.0833 |
Not found |
| MESS2v1_600023 |
conserved exported protein of unknown function |
0.33 |
1 |
1.1 |
0.00014 |
MESS4v1_680074 |
| MESS2v1_660006 |
protein of unknown function |
−0.34 |
1 |
−0.75 |
0.0813 |
Not found |
| MESS2v1_730256 |
conserved protein of unknown function |
−0.083 |
1 |
0.93 |
0.0049 |
Not found |
| MESS2v1_760133 |
protein of unknown function |
−0.65 |
0.4 |
−0.75 |
0.0833 |
Not found |
| MESS2v1_1100024 |
conserved exported protein of unknown function |
−0.41 |
1 |
0.94 |
0.0226 |
MESS4v1_120015 |
| MESS2v1_1100025 |
conserved exported protein of unknown function |
−0.12 |
1 |
1.05 |
0.00597 |
MESS4v1_120016 |
| MESS2v1_1100026 |
conserved exported protein of unknown function |
−0.22 |
1 |
1.05 |
0.00426 |
MESS4v1_120016 |
| MESS2v1_1210020 |
conserved protein of unknown function |
−0.71 |
0.44 |
1.36 |
5.1E-07 |
MESS4v1_160036 |
| MESS2v1_1210021 |
conserved protein of unknown function |
0.0842 |
1 |
1.2 |
0.00105 |
MESS4v1_160037 |
| MESS2v1_1270078 |
conserved exported protein of unknown function |
−0.0732 |
1 |
0.84 |
0.0503 |
MESS4v1_220001 |
| MESS2v1_1530016 |
protein of unknown function |
−0.42 |
1 |
−1.52 |
4.5E-05 |
Not found |
| MESS2v1_1660004 |
membrane protein of unknown function |
0.16 |
1 |
1.04 |
0.00032 |
Not found |
| MESS2v1_1660005 | conserved protein of unknown function | 0.38 | 1 | 1.5 | 4.1E-12 | Not found |
* 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. MESS2v1_XXX are genes located on the chromosome and MESS2v1_pXXX are genes located on the plasmid.
§ When detected, STM 4661 homologs are indicated (See Methods for details).