TABLE 2.
Iron- and IdeR-repressed genesa
| Rv no. | Gene | mRNA ratio
|
Gene productb | ||
|---|---|---|---|---|---|
| WT LI/HI | ST22 HI/WT HI | ST52 HI/WT HI | |||
| 0116c | 2.3 ± 0.3 | 2.1 ± 0.3 | 2.7 ± 0.6 | CHMP | |
| 0282 | 3.9 ± 0.5 | 3.2 ± 0.3 | 1.0 | CHP | |
| 0283 | 2.9 ± 0.6 | 2.9 ± 0.5 | 1.0 | CHMP | |
| 0284 | 4.1 ± 0.6 | 3.7 ± 0.5 | 1.0 | CHMP | |
| 0285 | 3.0 ± 0.5 | 2.7 ± 0.1 | 1.0 | PE subfamily | |
| 0286 | 2.6 ± 0.3 | 2.3 ± 0.2 | 1.0 | PPE subfamily | |
| 0287 | 4.0 ± 0.6 | 4.9 ± 0.9 | 1.0 | Probable transcriptional regulator; PE subfamily | |
| 0288 | 3.5 ± 0.4 | 4.2 ± 0.1 | 1.0 | CHP; ESAT-6 family | |
| 0289 | 3.2 ± 0.2 | 2.7 ± 0.3 | 1.0 | CHP | |
| 0290 | 2.0 ± 0.2 | 1.9 ± 0.2 | 1.0 | Unknown | |
| 0291 | 3.0 ± 0.3 | 2.3 ± 0.4 | 1.0 | Probable secreted protease | |
| 0292 | 2.7 ± 0.3 | 1.8 ± 0.2 | 1.0 | Unknown | |
| 0766c | 3.3 ± 0.4 | 2.9 ± 0.3 | 1.0 | Cytochrome P-450 | |
| 0450c | mmpL4 | 2.1 ± 0.3 | 2.5 ± 0.1 | 1.0 | Conserved large membrane protein |
| 0451c | mmpS4 | 3.1 ± 0.4 | 3.6 ± 0.6 | 1.0 | Conserved small membrane protein |
| 0587 | yrbE2A | 2.2 ± 0.2 | 2.1 ± 0.2 | 2.5 ± 0.3 | Part of the mce2 operon |
| 1343c | 2.5 ± 0.5 | 2.1 ± 0.2 | 1.0 | CHP | |
| 1344 | 3.9 ± 0.6 | 3.2 ± 0.4 | 1.0 | Probable acyl carrier protein | |
| 1345 | fadD33 | 3.4 ± 0.4 | 2.7 ± 0.5 | 1.0 | Acyl-CoA synthase |
| 1346 | fadE14 | 4.9 ± 0.9 | 3.3 ± 0.5 | 1.0 | Acyl-CoA dehydrogenase |
| 1347c* | 7.9 ± 1.7 | 6.4 ± 0.5 | 1.0 | IucB-like protein | |
| 1348* | 5.1 ± 0.7 | 5.3 ± 1.0 | 1.0 | YbtP-like protein | |
| 1349* | 4.3 ± 1.2 | 4.6 ± 0.7 | 1.0 | YbtQ-like protein | |
| 1519 | 3.7 ± 0.4 | 2.9 ± .03 | 1.0 | CHP | |
| 2122c* | hisE | 3.1 ± 0.3 | 2.5 ± 0.4 | 1.0 | Phosphoribosyl-AMP cyclohydrolase |
| 2123 | 10.1 ± 2.1 | 10.1 ± 3.9 | 1.0 | PPE subfamily | |
| 2377c | mbtH | 5.4 ± 1.9 | 5.6 ± 1.5 | 1.0 | Mycobactin synthesis |
| 2378c | mbtG | 5.5 ± 1.5 | 4.7 ± 0.8 | 1.0 | Lysine-N-oxygenase mycobactin synthesis |
| 2379c | mbtF | 3.6 ± 0.7 | 2.4 ± 0.4 | 1.0 | Peptide synthase; mycobactin synthesis |
| 2380c | mbtE | 7.1 ± 0.9 | 5.4 ± 1.1 | 1.0 | Peptide synthase; mycobactin synthesis |
| 2381c | mbtD | 9.9 ± 1.8 | 7.5 ± 0.9 | 1.8 ± 0.1 | Polyketide synthase; mycobactin synthesis |
| 2382c | mbtC | 5.3 ± 0.4 | 3.6 ± 0.8 | 1.0 | Polyketide synthase; mycobactin synthesis |
| 2383c | mbtB | 5.4 ± 0.8 | 3.9 ± 0.8 | 1.0 | Peptide synthase; mycobactin synthesis |
| 2384 | mbtA | 1.9 ± 0.3 | 1.8 ± 0.2 | 1.0 | Salicylate-AMP ligase; mycobactin synthesis |
| 2385 | lipK | 3.6 ± 0.6 | 3.2 ± 0.6 | 1.0 | Probable acetyl-hydrolase |
| 2386c | mbtI (trpE2) | 8.6 ± 1.8 | 9.3 ± 1.8 | 1.9 ± 0.2 | Isochorismate synthase |
| Mycobactin synthesis | |||||
| 3402c* | 9.7 ± 2.5 | 5.1 ± 1.0 | 1.0 | EryCIV-like protein | |
| 3403c | 5.6 ± 1.0 | 3.0 ± 0.3 | 1.0 | Unknown | |
| 3839 | 19.3 ± 7.0 | 14.1 ± 3.7 | 1.0 | Unknown | |
| 3840 | 2.6 ± 0.5 | 6.7 ± 0.5 | 1.0 | Probable transcriptional regulator | |
A DNA microarray was used to measure mRNA levels in cultures of M. tuberculosis H37Rv (WT) during exponential growth under iron-deficient (2 μM FeCl3) (LI) or -sufficient (50 μM FeCl3) (HI) conditions and in exponential cultures of strains ST22 and ST52 grown in iron-sufficient medium. Differences in gene-specific RNA levels of twofold or more are listed. Genes contiguous to included genes and with a ratio of >1.6 after the standard deviation was subtracted are also listed. Genes that required IdeR for repression were repressed under high-iron conditions in the wild-type strain (WT LI/HI > 2.0), derepressed in the ideR mutant ST22 under high-iron conditions (ST22 HI/WT HI > 2.0), and repressed in the mutant complemented strain ST52 under high-iron conditions to the same levels observed in the wild type under high iron conditions (ST52 HI/WT HI = 1.0). The genes are annotated as described by the Pasteur Institute on TUBERCULIST (http://genolist.pasteur.fr/Tuberculist), except for those indicated by an asterisk. Those genes are annotated based on individual BLAST searches. Genes that are separated by <50 bp and probably coregulated are grouped.
CHP, conserved hypothetical protein. CHMP, conserved hypothetical membrane protein; CoA, coenzyme A.