TABLE 1.
Functional categories of genes with 1.7-fold more expression in M. tuberculosis H37Rv than in the sigD mutant strain
| Gene family and name | Fold change | FDR | Product, its function, and additional comments |
|---|---|---|---|
| Regulatory | |||
| Rv3414c | 4.4 | <0.001 | SigD, ECF sigma factor |
| Rv3413c | 2.8 | <0.001 | RsdA, probable anti-sigma factor |
| MT1932 | 8.0 | <0.001 | RpfC, resuscitation promoting factor |
| MT1931.1 | 2.6 | <0.001 | Downstream gene of rpfC, probable part of rpfC operon |
| Rv1883c | 2.7 | <0.001 | Same as MT1931.1, except for a five-amino-acid gap |
| Rv1815 | 3.0 | <0.001 | Probable transcriptional regulation associated with Rv1816 |
| Rv1816 | 1.7 | 0.008 | Transcriptional regulatory protein, similar to tetR family |
| Heat shock response | |||
| Rv0350 | 2.6 | <0.001 | DnaK, heat shock protein Hsp70 |
| Rv0351 | 2.5 | 0.001 | GrpE, Hsp70 cofactor, plays a role in adaptation |
| MT0366 | 2.3 | 0.008 | Same as Rv0351 |
| Rv0440 | 4.7 | <0.001 | GroEL2, chaperonin 2, prevents misfolding and promotes refolding |
| Rv3417c | 2.1 | <0.001 | GroEL1, chaperonin 1, prevents misfolding and promotes refolding |
| Rv3418c | 3.7 | <0.001 | GroES, chaperonin |
| Lipid metabolism | |||
| MT0137 | 2.0 | 0.013 | FbpC, fibronectin binding protein, required for biogenesis of cord factor, maintains cell wall integrity |
| MT0870 | 1.7 | <0.001 | LpqS, probable lipoprotein |
| MT1041 | 1.9 | 0.001 | Putative polyketide synthase |
| Rv1182 | 1.7 | <0.001 | PapA3, probable polyketide synthase-associated protein |
| Rv1270 | 2.0 | 0.005 | LprA, lipoprotein |
| Rv1750 | 1.9 | <0.001 | FadD1, fatty acid-CoA synthase |
| Rv2187 | 1.9 | <0.001 | FadD15, fatty acid CoA synthase, involved in fatty acid degradation |
| Cell wall process | |||
| Rv0341 | 7.2 | 0.001 | IniB, INH-inducible protein |
| Rv0342 | 2.4 | <0.001 | IniA, INH-inducible protein |
| Rv1860 | 1.8 | 0.001 | ModD, fibronectin attachment protein |
| Rv2301 | 1.8 | 0.004 | Probable cutinase, hydrolysis cutin |
| Rv3890c | 1.8 | 0.002 | EsxC, ESAT-6-like protein 11 |
| Rv3891c | 2.4 | 0.004 | EsxD, ESAT-6-like protein |
| Intermediary metabolism and respiration | |||
| MT0455 | 1.8 | <0.001 | Probable dehydrogenase |
| Rv2455c | 1.7 | 0.048 | Possible oxidoreductase |
| Rv3914 | 2.2 | 0.035 | TrxC, thioredoxin, participates in various redox reactions |
| Adaptation | |||
| Rv3846 | 2.5 | 0.002 | SodA, superoxide dismutase A, involved in detoxification and adaptation |
| Unknown function | |||
| MT0196 | 1.9 | <0.001 | Hypothetical protein |
| MT1020 | 1.8 | <0.001 | Hypothetical protein |
| MT1628 | 1.9 | 0.025 | Hypothetical protein |
| MT2422 | 1.8 | 0.004 | PPE family proteins |
| MT2890 | 1.9 | <0.001 | CRISPR-associated protein, TM1811 family |
| MT3258 | 2.2 | <0.001 | Hypothetical protein |
| Rv0257c | 2.0 | 0.041 | Hypothetical protein |
| Rv0276 | 2.0 | <0.001 | Hypothetical protein |
| Rv0309 | 1.7 | 0.004 | Conserved exported protein |
| Rv1687c | 1.9 | <0.001 | Hypothetical protein |
| Rv1779c | 1.7 | 0.050 | Hypothetical integral membrane protein |
| Rv2159c | 1.7 | 0.007 | Hypothetical protein |
| Rv2348c | 1.7 | 0.008 | Hypothetical protein |
| Rv2633c | 2.1 | <0.001 | Hypothetical protein |
| Rv2699c | 1.9 | 0.001 | Hypothetical protein |
| Rv2822c | 1.9 | <0.001 | Hypothetical protein |
| Rv3169 | 1.7 | <0.001 | Hypothetical protein |
| Rv3354 | 2.3 | <0.001 | Hypothetical protein |
| Rv3614c | 2.0 | 0.001 | Hypothetical protein |
| Rv3615c | 2.2 | <0.001 | Hypothetical protein |
| Rv3675 | 1.8 | 0.002 | Membrane protein |