TABLE 4.
Genes differentially expressed in MSMEGΔzur, zinc independent
| RCNa | Annotationc | Orthologous gene (% similarity) |
q valued | Fold changee |
Putative functionf | ||||
|---|---|---|---|---|---|---|---|---|---|
| MTB | MAP | Δzur | TPEN | Zn | ΔΔ | ||||
| —b | MSMEG_0584 | — | — | <0.0001 | −5.30 | CoA transferase | |||
| groEL | MSMEG_0880 | Rv0440 (93.4) | MAP3936 (95.0) | <0.0001 | 7.94 | 6.62 | Molecular chaperone GroEL | ||
| — | *MSMEG_1122 | — | — | <0.0001 | 4.69 | 6.14 | Cobalamin synthesis protein P47K | ||
| groES | MSMEG_1582 | Rv3418c (99.0) | MAP4264 (96.0) | <0.0001 | 5.23 | 4.66 | Cochaperonin GroES | ||
| groEL | MSMEG_1583 | Rv3417c (81.1) | MAP4265 (82.5) | <0.0001 | 6.02 | 4.18 | Molecular chaperone GroEL | ||
| — | MSMEG_3787 | — | — | <0.0001 | −4.00 | d-Aminoacylase | |||
| eda | MSMEG_3788 | — | — | <0.0001 | −4.00 | 2-Dehydro-3-deoxyphosphogluconate aldolase | |||
| — | MSMEG_3789 | — | — | <0.0001 | −5.63 | Inner membrane permease YgbN | |||
| thpD | MSMEG_3898 | — | — | <0.0001 | −4.94 | −4.44 | Ectoine hydroxylase | ||
| ectC | MSMEG_3899 | — | — | <0.0001 | −6.47 | −4.55 | l-Ectoine synthase | ||
| ectB | MSMEG_3900 | — | — | <0.0001 | −5.74 | (−3.86) | Diaminobutyrate-2-oxoglutarate aminotransferase | ||
| ectA | MSMEG_3901 | — | — | <0.0001 | −4.05 | (−2.82) | l-2,4-diaminobutyric acid acetyltransferase | ||
| — | MSMEG_4509 | Rv2378c (75.4) | MAP2170c (74.4) | <0.0001 | 4.22 | MbtG protein | |||
| smtB | *MSMEG_4486 | Rv2358 (80.4) | MAP2138 (74.4) | <0.0001 | 94.76 | ArsR family transcriptional regulator | |||
| — | MSMEG_4596 | — | — | <0.0001 | −116.50 | Histidine kinase/Lpps protein | |||
| — | MSMEG_5021 | — | — | <0.0001 | −10.57 | −6.08 | Alcohol dehydrogenase | ||
| — | MSMEG_5022 | — | — | <0.0001 | −21.67 | −5.91 | Flavin-containing monooxygenase FMO | ||
| — | MSMEG_5180 | — | MAP2636 (91.9) | <0.0001 | −5.88 | Hypothetical protein | |||
| — | MSMEG_6062 | Rv1473 (42.5) | — | <0.0001 | 5.97 | 5.04 | Fe uptake system permease | ||
| — | MSMEG_6063 | — | — | <0.0001 | 8.73 | 8.69 | Fe uptake system integral membrane protein | ||
| — | MSMEG_6239 | — | — | <0.0001 | −4.71 | 1,3-Propanediol dehydrogenase | |||
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 MSMEGΔzur calculated by Rockhopper analysis. A q value of <0.01 is considered significant.
Gene expression values of MSMEGΔzur (Δzur) 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. Values in parentheses indicate the differential expression of <4 genes which belong to the same operon.
Putative function based on NCBI blastx analysis or the TB database.