Table 2.
Grouping of overexpressed ORFs that mediate resistance to metal toxicity
| Same observation reported | Similar observation reported | No similar observation reported | |
|---|---|---|---|
| Cadmium | napA (O) | cbpM (S) | |
| napF (T) | hdfR(B) | ||
| fliN(B) | |||
| Cobalt | cysE (O) | yhhI (S) | fliZ (B) |
| zitB (E) | |||
| yqiA (S) | |||
| acpP (B) | |||
| yfgG (U) | |||
| Copper | acrB (E) | Pnp (T) | fliZ (B) |
| nusA (S) | yfdN (U) | ||
| iraD (S) | gabT (S) | ||
| lysR (S) | nudJ (U) | ||
| yciF (O) | nudL (U) | ||
| Nickel | cysE (O) | acpT (B) | acpH (B) |
| yfeH (E) | ybjC (U) | ||
| yhbS (O) | yedN (U) | ||
| y S (B) | |||
| Silver | rbfA (S) | ydcQ (U) | |
| lysM (B) | yaaY (U) | ||
| yaiI (U) | |||
| ynaE (U) | |||
| Zinc | zitB (E) | hlyD (E) | yhiL (E) |
| cysE (O) | iraD (B) | rfaJ (B) | |
| ydcQ (U) | |||
| ynaE (S) | |||
| perC (B) | |||
| yfdN (U) |
ORFs were placed into three categories based on previous literature reports: If the same observation had been made in E. coli, the gene was placed in the ‘Same observation’ category. If an orthologous or homologous protein was observed to protect from metal toxicity, or if the same ORF was characterized as rescuing from the toxicity of another metal, it was grouped as ‘Similar observation.’ If there was no reported evidence for the ORF’s involved in metal resistance or homeostasis, it was grouped under ‘No similar observation reported.’ Notably, many of the hits were on the same operon (e.g., fli, acp, nap). Also many had overlapping rescue functions (e.g., iraD, cysE, zitB). ORFs were also grouped into the 6 functional categories summarized in Fig. 2: Oxidative stress management (O), Efflux (E), Bio-film/OM related (B), General stress (S), sequestration/ transport (T), and unknown (U). Letter to right of ORF indicates presumed functional grouping. Genotypes, proposed rescue mechanisms, and literature references are provided in Supplementary Material