TABLE 3.
Genes differentially expressed in MSMEGΔzur, zinc dependent (including TPEN, zinc, and ΔsmtBΔzur results)
| RCNa | Annotationc | Orthologous gene (% similarity) |
q valued | Fold changee |
Putative functionf | ||||
|---|---|---|---|---|---|---|---|---|---|
| MTB | MAP | Δzur | TPEN | Zn | ΔΔ | ||||
| —b | *MSMEG_1123 | — | MAP1730c (43.1) | <0.0001 | 8.64 | 7.56 | 7.50 | Cobalamin synthesis protein | |
| — | MSMEG_6045 | Rv2060 (43.7) | MAP3774c (70.1) | <0.0001 | 24.62 | 21.29 | 24.42 | Heavy metal ABC transporter inner membrane protein | |
| — | MSMEG_6046 | — | MAP3775c (61.2) | <0.0001 | 20.65 | 19.04 | 19.90 | ABC transporter ATP-binding protein | |
| — | **MSMEG_6047 | — | MAP3776c (56.4) | <0.0001 | 26.24 | 43.8 | 25.50 | Cation ABC transporter periplasmic cation-binding protein | |
| — | **MSMEG_6048 | — | MAP3772c (72.6) | 1 | 3288.50 | 456.0 | 2,903.00 | Cobalamin synthesis protein/P47K | |
| — | MSMEG_6049 | — | — | <0.0001 | 494.44 | 624.5 | 443.56 | Secreted protein | |
| — | MSMEG_6050 | — | — | <0.0001 | 917.25 | 556.5 | 849.0 | ABC-type Zn uptake system solute-binding lipoprotein | |
| — | MSMEG_6051 | — | — | <0.0001 | 777.0 | 227.0 | 632.0 | Pseudo ABC transporter transmembrane protein | |
| — | *MSMEG_6052 | — | — | <0.0001 | 18.17 | 54.00 | 23.42 | ABC transporter ATP-binding protein | |
| — | **MSMEG_6055 | — | — | 1.00 | 498.00 | 28.00 | 511.00 | Class I SAM-dependent methyltransferase | |
| — | MSMEG_6057 | — | — | <0.0001 | 435.00 | 52.00 | 393.0 | MspD protein | |
| — | MSMEG_6058 | Rv3270 (77.2) | MAP3384 (77.7) | <0.0001 | 9.21 | 17.59 | 9.59 | Cadmium transporting P-type ATPase | |
| — | MSMEG_6059 | Rv3269 (71.6) | MAP3383 (69.1) | <0.0001 | 13.42 | 15.22 | 11.73 | Hypothetical protein | |
| — | MSMEG_6064 | — | — | <0.0001 | 27.42 | 6.52 | 21.76 | Lipoprotein | |
| rpsR | MSMEG_6065 | Rv2055c (63.4) | MAP3767c (63.9) | 1.00 | 5107.67 | 521.00 | 3,080.0 | 30S ribosomal protein S18 | |
| rpsN | MSMEG_6066 | Rv2056c (72.3) | MAP3768c (75.2) | 1.00 | 5778.50 | 279.80 | 3,983.5 | 30S ribosomal protein S14 | |
| rpmG | MSMEG_6067 | Rv2057c (87.0) | MAP3769c (92.6) | 1.00 | 5856.67 | 1043.50 | 5,015.0 | 50S ribosomal protein L33 | |
| rpmB | *MSMEG_6068 | Rv2058c (82.1) | — | 1.00 | 5372.69 | 449.65 | 4,055.32 | 50S ribosomal protein L28 | |
| — | *MSMEG_6069 | Rv0106 (62.1) | MAP3770 (57.8) | 1.00 | 3492.00 | 406.31 | 4,340.00 | CobW/P47K domain-containing protein | |
| rpmE2 | MSMEG_6070 | — | MAP3771 (79.3) | 1.00 | 1460.33 | 1233.00 | 1,603.0 | 50S ribosomal protein L31 | |
| — | MSMEG_6071 | Rv3577 (68.3) | MAP0485c (66.9) | <0.0001 | 27.95 | 5.20 | 33.42 | Metallo-beta-lactamase superfamily protein | |
| — | MSMEG_6237 | — | — | <0.0001 | −6.93 | 7.40 | −11.22 | −4.62 | Class I SAM-dependent methyltransferase |
| — | MSMEG_6240 | — | — | <0.0001 | −24.38 | (−3.01) | −8.48 | Hypothetical protein | |
| — | MSMEG_6241 | Rv2426c (45.9) | MAP2246c (44.9) | <0.0001 | −24.63 | (−3.74) | −8.66 | ATPase AAA | |
| — | MSMEG_6242 | — | — | <0.0001 | −27.59 | −4.64 | −8.35 | Alcohol 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.