TABLE 1.
Microarray analysis of M. tuberculosis genes found to be upregulated after sigB KI expression
| Code and gene (or locus tag) | Rv no. | Avg | SD | Q value | Description |
|---|---|---|---|---|---|
| Virulence, detoxification, and adaptation | |||||
| groEL2 | Rv0440 | 4.4 | 0.7 | 0.02 | 60-kDa chaperonin 2 |
| groES | Rv3418c | 4.2 | 3.5 | 0.03 | 10-kDa chaperonin |
| Lipid metabolism | |||||
| pgsA | Rv2612c | 21.8 | 0.6 | 0.00 | Phosphatidylinositol synthase |
| fadD31 | Rv1925 | 18.3 | 5.6 | 0.00 | Acyl-coenzyme A ligase |
| kasA | Rv2245 | 6.4 | 1.5 | 0.01 | 3-Oxoacyl-[acyl-carrier protein] synthase 1 |
| pgsA2 | Rv1822 | 4.1 | 0.9 | 0.01 | Phosphatidyltransferase |
| ppsD | Rv2934 | 4.1 | 0.3 | 0.01 | Phenolphthiocerol synthesis type-I polyketide synthase |
| Information pathways | |||||
| sigB | Rv2710 | 56.2 | 7.2 | 0.00 | RNA polymerase sigma factor |
| dinP | Rv3056 | 6.3 | 0.9 | 0.01 | DNA-damage-inducible protein P |
| dinF | Rv2836c | 5.6 | 0.9 | 0.01 | DNA-damage-inducible protein |
| rpmC | Rv0709 | 5.5 | 1.4 | 0.01 | 50S ribosomal protein l29 |
| tuf | Rv0685 | 5.5 | 0.7 | 0.01 | Iron-regulated elongation factor |
| nrdH | Rv3053c | 5.4 | 0.1 | 0.00 | Glutaredoxin electron transport component of nrdef |
| rplC | Rv0701 | 4.8 | 0.7 | 0.01 | 50S ribosomal protein l3 |
| rplA | Rv0641 | 4.8 | 1.6 | 0.00 | 50S ribosomal protein |
| rplS | Rv2904c | 4.8 | 1.5 | 0.01 | 50S ribosomal protein l19 |
| greA | Rv1080c | 4.2 | 0.9 | 0.02 | Transcription elongation factor |
| Cell wall and cell processes | |||||
| esxB | Rv1398c | 27.4 | 2.2 | 0.01 | 10-kDa culture filtrate antigen |
| Rv2625c | Rv2625c | 7.2 | 2.5 | 0.00 | Conserved transmembrane alanine and leucine-rich protein |
| Rv0463 | Rv0463 | 7.2 | 0.7 | 0.00 | Conserved membrane protein |
| Rv1792 | Rv1792 | 7.1 | 3.7 | 0.01 | ESAT-6 like protein |
| wag31 | Rv2145c | 4.7 | 0.7 | 0.01 | Conserved hypothetical protein |
| Rv2115 | Rv2115 | 4.7 | 0.2 | 0.01 | ATPase |
| secE | Rv0638 | 4.7 | 0.5 | 0.01 | Preprotein translocase |
| mmpS3 | Rv2198c | 4.6 | 0.8 | 0.01 | Conserved membrane protein |
| Rv1410c | Rv1410c | 4.3 | 1.4 | 0.02 | Aminoglycosides |
| yjcE | Rv2287 | 4.3 | 0.2 | 0.00 | Conserved integral membrane transport protein |
| Rv0559c | Rv0559c | 4.2 | 0.4 | 0.01 | Conserved secreted protein |
| Rv1845c | Rv1845c | 4.1 | 0.4 | 0.01 | Conserved hypothetical transmembrane protein |
| Rv2446c | Rv2446c | 4.1 | 0.4 | 0.00 | Conserved integral membrane protein |
| Rv2206 | Rv2206 | 4.1 | 0.8 | 0.00 | Conserved transmembrane protein |
| Rv2136c | Rv2136c | 4.0 | 0.8 | 0.00 | Conserved transmembrane protein |
| Rv0383c | Rv0383c | 4.0 | 0.7 | 0.01 | Conserved secreted protein |
| secF | Rv2586c | 4.0 | 1.1 | 0.00 | Protein-export membrane protein |
| Insertion sequences and phages | |||||
| Rv2978c | Rv2978c | 4.2 | 0.3 | 0.00 | Transposase |
| PE/PPE | |||||
| PE_PGRS | Rv3514 | 49.4 | 4.6 | 0.00 | PE PGRS family protein |
| PE_PGRS | Rv3508 | 11.9 | 1.5 | 0.01 | PE PGRS family protein |
| PE_PGRS | Rv2591 | 9.6 | 0.8 | 0.00 | PE PGRS family protein |
| PPE | Rv0442c | 5.5 | 0.1 | 0.01 | PPE family protein |
| PE_PGRS | Rv0872c | 4.9 | 2.2 | 0.02 | PE PGRS family protein |
| PPE | Rv3136 | 4.8 | 1.7 | 0.01 | PPE family protein |
| PE_PGRS | Rv2490c | 4.7 | 0.3 | 0.00 | PE PGRS family protein |
| PE_PGRS | Rv1818c | 4.2 | 1.1 | 0.01 | PE PGRS family protein |
| PPE | Rv3022c | 4.1 | 0.2 | 0.00 | PPE family protein |
| PE_PGRS | Rv2162c | 4.1 | 0.8 | 0.00 | PE PGRS family protein |
| Intermediary metabolism and respiration | |||||
| lipI | Rv1400c | 10.1 | 1.5 | 0.01 | Lipase |
| cbhK | Rv2202c | 6.8 | 2.9 | 0.00 | Carbohydrate kinase |
| nadB | Rv1595 | 6.1 | 0.4 | 0.00 | l-Aspartate oxidase |
| trpC | Rv1611 | 5.8 | 0.4 | 0.00 | Indole-3-glycerol phosphate synthase |
| ctaC | Rv2200c | 5.3 | 1.3 | 0.01 | Transmembrane cytochrome c oxidase |
| nadC | Rv1596 | 5.0 | 1.2 | 0.01 | Nicotinate-nucleotide pyrophosphatase |
| cysS2 | Rv2130c | 4.8 | 1.0 | 0.01 | Glucopyranoside ligase |
| lldD2 | Rv1872c | 4.6 | 1.1 | 0.02 | l-Lactate dehydrogenase |
| lipN | Rv2970c | 4.5 | 0.9 | 0.01 | Lipase/esterase |
| Rv2850c | Rv2850c | 4.2 | 0.1 | 0.01 | Magnesium chelatase |
| aroG | Rv2178c | 4.1 | 1.0 | 0.00 | 3-Deoxy-d-arabino-heptulosonate 7-phosphate synthase |
| ribC | Rv1412 | 4.1 | 0.8 | 0.01 | Riboflavin synthase alpha chain |
| prcB | Rv2110c | 4.0 | 1.7 | 0.02 | Proteasome (β-subunit) |
| Unknown | |||||
| Rv1046c | Rv1046c | 4.1 | 2.7 | 0.01 | Hypothetical protein |
| Regulatory proteins | |||||
| whiB2 | Rv3260c | 4.0 | 2.1 | 0.01 | Transcriptional regulatory protein |
| Conserved hypotheticals | |||||
| Rv2204c | Rv2204c | 18.2 | 5.0 | 0.00 | Conserved hypothetical protein |
| Rv2137c | Rv2137c | 15.6 | 7.2 | 0.01 | Conserved hypothetical protein |
| Rv2111c | Rv2111c | 10.2 | 2.8 | 0.01 | Conserved hypothetical protein |
| Rv1827 | Rv1827 | 7.0 | 1.1 | 0.00 | Conserved hypothetical protein |
| Rv2182c | Rv2182c | 6.9 | 1.2 | 0.00 | 1-Acylglycerol-3-phosphate O-acyltransferase |
| Rv2974c | Rv2974c | 4.3 | 0.3 | 0.01 | Conserved hypothetical alanine rich protein |
| Rv2132 | Rv2132 | 4.2 | 0.5 | 0.01 | Conserved hypothetical protein |
| Rv1211 | Rv1211 | 4.2 | 1.4 | 0.01 | Conserved hypothetical protein |
| Rv0863 | Rv0863 | 4.1 | 1.8 | 0.02 | Conserved hypothetical protein |
| Rv1429 | Rv1429 | 4.0 | 0.2 | 0.01 | Conserved hypothetical protein |
| Rv0637 | Rv0637 | 4.0 | 0.7 | 0.02 | Conserved hypothetical protein |
| Rv0750 | Rv0750 | 4.0 | 0.8 | 0.01 | Conserved hypothetical protein |
aThe sigB gene was overexpressed using acetamide-inducing promoter at an optical density at 600 nm of ∼0.5, and cells were harvested after 12 h. Code (i.e., the functional categories) and gene annotation data were obtained from the TubercuList database (http://genolist.pasteur.fr/TubercuList/). The Q value was calculated by using SAM software (http://www-stat.stanford.edu/∼tibs/SAM/) with 1% FDR. We performed the real-time RT-PCR on the subset of genes to confirm microarray results (Fig. 2B).