TABLE 5.
Genes differentially expressed in MSMEGΔsmtB, zinc dependent (including TPEN, zinc, and ΔsmtBΔzur results) or zinc independent
| Gene category | RCNa | Annotationc | Orthologous gene (% similarity) |
q valued | Fold changee
|
Putative functionf | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| MTB | MAP | ΔsmtB | TPEN | Zn | ΔΔ | |||||
| Zinc dependent | —b | MSMEG_0755 | Rv0359 (68.8) | MAP3865c (76.8) | <0.0001 | 80.92 | −34.0 | 14.36 | 64.08 | Cobalt-zinc-cadmium resistance protein |
| — | MSMEG_5117 | Rv1188 (68.3) | MAP2592c (71.6) | <0.0001 | 4.32 | 11.75 | 5.9 | Proline dehydrogenase | ||
| rpmB | *MSMEG_6068 | Rv2058c (82.1) | — | <0.0001 | 7.17 | 449.65 | 4055.32 | 50S ribosomal protein L28 |
||
| — | MSMEG_6237 | — | — | <0.0001 | −5.39 | 7.40 | −11.22 | −4.62 | Class I SAM-dependent methyltransferase |
|
| — | MSMEG_6240 | — | — | <0.0001 | −4.64 | (−3.01) | −8.48 | Hypothetical protein | ||
| — | MSMEG_6241 | Rv2426c (45.9) | MAP2246c (44.9) | <0.0001 | −5.14 | (−3.74) | −8.66 | ATPase AAA | ||
| — | MSMEG_6242 | — | — | <0.0001 | −6.40 | −4.64 | −8.35 | Alcohol dehydrogenase | ||
| Zinc independent | ald | MSMEG_2659 | Rv2780 (80.6) | MAP2888 (76.2) | <0.0001 | 4.33 | Alanine dehydrogenase | |||
| — | MSMEG_3959 | — | — | <0.0001 | 4.40 | 4.70 | FadR-like transcriptional regulator |
|||
| — | MSMEG_3960 | Rv0067c (45.8) | — | <0.0001 | 7.56 | 8.11 | Transcriptional regulator | |||
| zur | MSMEG_4487 | Rv2359 (80.5) | MAP2139 (79.0) | <0.0001 | 14.13 | Zinc uptake regulation protein |
||||
| — | MSMEG_6422 | Rv3841 (71.8) | — | <0.0001 | 5.33 | Ferritin family protein | ||||
RCN, reference common name.
—, no reference common name/orthologous gene.
Italics indicate genes organized in an operon. Asterisks indicate the presence of one or more predicted Zur binding sites.
q value of differentially expressed genes in MSMEGwt versus MSMEGΔsmtB calculated by Rockhopper analysis. A q value of <0.01 is considered significant.
Gene expression values of MSMEGΔsmtB and MSMEGΔsmtBΔzur (ΔΔ) divided by gene expression values of MSMEGwt from RNA-Seq as well as results from transcriptome analysis after TPEN and ZnSO4 treatment.
Putative function based on NCBI blastx analysis or the TB database. Values in brackets () show differential expression <4 of genes, which belong to the same operon.