TABLE 1.
Gene expression ratios for genes differentially expressed in M. tuberculosis WT compared to opp KO mutant
| Rv or MT numbera | Fold change WT/opp KO OD600 0.3 | Fold change WT/opp KO OD600 1.0 | Fold change WT/opp KO OD600 2.0 | Annotationb or similarityc to protein domains |
|---|---|---|---|---|
| MT0719.1 | 1.3 | 0.6 | 1.3 | HP, 62 aa |
| MT1178 | 0.6 | 0.9 | 1.4 | HP, 51 aa |
| MT1585.1 | 1.0 | 1.8 | 1.4 | HP 55 aa |
| MT1676 | 1.2 | 1.3 | 1.6 | CHP similar to PspA/IM30 |
| MT2466 | 1.0 | 1.6 | 2.0 | HP, 71 aa, PhoP-dependent |
| MT2467 | 1.1 | 2.1 | 2.3 | HP, 54 aa |
| MT3220.2 | 1.0 | 1.9 | 1.5 | HP, 81 aa |
| MT3412 | 1.0 | 1.4 | 1.9 | HP, 56 aa |
| MT3413 | 1.1 | 1.5 | 2.3 | Rv3312A |
| MT3972.1 | 1.1 | 2.2 | 0.9 | HP, 46 aa |
| Rv0046c | 0.8 | 1.7 | 0.9 | Ino1 |
| Rv0059 | 1.1 | 1.6 | 1.0 | HP, 230 aa |
| Rv0060 | 1.0 | 1.6 | 1.0 | CHP, high-affinity ADP-ribose binding module |
| Rv0082 | 1.1 | 1.7 | 1.3 | Probable oxidoreductase |
| Rv0242c | 0.9 | 1.0 | 0.6 | FabG4 |
| Rv0244c | 0.3 | 1.1 | 2.4 | FadE5 |
| Rv0290 | 1.0 | 0.6 | 1.1 | Probable conserved transmembrane protein |
| Rv0341 | 1.1 | 0.8 | 0.6 | IniB |
| Rv0404 | 1.9 | 0.4 | 0.9 | FadD30 |
| Rv0440 | 0.7 | 1.6 | 1.0 | GroEL2 |
| Rv0467 | 0.3 | 0.9 | 1.1 | Icl |
| Rv0475 | 0.6 | 1.1 | 1.0 | HbhA |
| Rv0508 | 1.0 | 0.6 | 0.9 | CHP similar to thiol-disulfide isomerase |
| Rv0509 | 1.3 | 0.5 | 1.1 | HemA |
| Rv0583c | 1.6 | 0.5 | 0.9 | LpqN |
| Rv0593c | 1.1 | 0.5 | 1.0 | LprL |
| Rv0595c | 1.3 | 0.6 | 1.1 | CHP, PIN domain |
| Rv0651 | 1.1 | 1.6 | 0.8 | RplJ |
| Rv0693 | 1.4 | 0.5 | 1.2 | PqqE |
| Rv0700 | 1.1 | 1.6 | 1.1 | NusE |
| Rv0702 | 1.1 | 1.6 | 1.0 | RplD |
| Rv0704 | 1.2 | 1.6 | 1.1 | RplB |
| Rv0706 | 1.2 | 1.9 | 1.3 | RplV |
| Rv0708 | 1.1 | 1.6 | 1.1 | RplP |
| Rv0710 | 1.1 | 1.6 | 1.1 | RpsQ |
| Rv0714 | 1.1 | 1.6 | 1.2 | RplN |
| Rv0716 | 1.1 | 1.6 | 1.1 | RplE |
| Rv0722 | 1.1 | 1.6 | 1.1 | RpmD |
| Rv0859 | 0.4 | 1.2 | 1.8 | FadA |
| Rv0860 | 0.3 | 1.3 | 1.6 | FadB |
| Rv0878c | 2.2 | 1.9 | 1.7 | PPE13 |
| Rv0963c | 0.7 | 0.6 | 0.7 | CHP similar to Streptomyces secreted protein |
| Rv0973c | 0.3 | 1.3 | 1.7 | AccA2 |
| Rv0974c | 0.6 | 1.0 | 1.1 | AccD2 |
| Rv0975c | 0.4 | 1.1 | 1.8 | FadE13 |
| Rv1110 | 1.3 | 0.6 | 1.1 | LytB2 |
| Rv1130 | 0.3 | 0.9 | 1.6 | PrpD |
| Rv1131 | 0.3 | 0.9 | 1.4 | GltA1 |
| Rv1180 | 1.0 | 1.0 | 1.7 | Pks3 |
| Rv1181 | 0.9 | 0.9 | 1.6 | Pks4 |
| Rv1182 | 1.0 | 1.4 | 1.7 | PapA3 |
| Rv1183 | 0.9 | 0.9 | 1.6 | MmpL10 |
| Rv1184c | 1.0 | 1.3 | 2.1 | Similar to PE proteins |
| Rv1195 | 0.4 | 0.9 | 1.4 | PE13 |
| Rv1258c | 0.9 | 0.9 | 0.6 | Probable conserved integral membrane transport protein |
| Rv1361c | 0.5 | 0.9 | 1.0 | PPE19 |
| Rv1448c | 1.1 | 0.4 | 0.8 | Probable transaldolase |
| Rv1535 | 1.1 | 1.9 | 1.2 | HP, 78 aa |
| Rv1594 | 1.4 | 0.6 | 1.0 | NadA |
| Rv1596 | 1.3 | 1.7 | 1.0 | NadC |
| Rv1623c | 0.9 | 0.6 | 0.9 | CydA |
| Rv1642 | 1.0 | 1.6 | 1.4 | RpmI |
| Rv1653 | 1.3 | 1.6 | 0.9 | ArgJ |
| Rv1687c | 1.0 | 0.6 | 1.0 | Probable conserved ATP-binding transporter |
| Rv1806 | 1.0 | 2.0 | 1.5 | PE20 |
| Rv1807 | 1.2 | 1.9 | 1.2 | PPE31 |
| Rv1808 | 1.0 | 1.7 | 1.2 | PPE32 |
| Rv1809 | 1.0 | 1.7 | 1.4 | PPE33 |
| Rv1810 | 0.9 | 1.4 | 1.7 | CHP similar to LprJ |
| Rv1843c | 1.1 | 0.5 | 1.0 | GuaB1 |
| Rv1855c | 0.5 | 1.4 | 2.2 | Possible tetrahydromethanopterin reductase |
| Rv1856c | 0.3 | 2.1 | 4.3 | Possible short-chain dehydrogenase |
| Rv1857 | 0.4 | 1.5 | 2.2 | ModA |
| Rv2023c | 1.0 | 0.6 | 1.0 | HP, 119 aa |
| Rv2055c | 0.9 | 1.4 | 1.6 | RpsR2 |
| Rv2056c | 0.9 | 1.4 | 1.7 | RpsN2 |
| Rv2057c | 0.9 | 1.5 | 1.8 | RpmG1 |
| Rv2147c | 1.2 | 1.7 | 1.1 | CHP similar to L. plantarum putative cell division protein |
| Rv2160c | 1.1 | 0.5 | 1.1 | CHP, similar to G. violaceous TetR-family transcriptional regulatory protein |
| Rv2243 | 1.9 | 1.5 | 1.2 | FabD |
| Rv2244 | 2.0 | 1.5 | 1.2 | AcpM |
| Rv2245 | 1.6 | 1.0 | 1.0 | KasA |
| Rv2246 | 1.7 | 1.2 | 1.3 | KasB |
| Rv2253 | 1.2 | 1.7 | 1.1 | Possible secreted unknown protein |
| Rv2280 | 1.1 | 0.6 | 0.9 | Probable dehydrogenase |
| Rv2369c | 1.4 | 1.3 | 1.6 | HP, 100 aa |
| Rv2430c | 1.0 | 1.6 | 1.4 | PPE41 |
| Rv2524c | 2.7 | 1.2 | 0.5 | Fas |
| Rv2542 | 1.2 | 0.6 | 1.1 | CHP, α/β hydrolase fold |
| Rv2557 | 1.2 | 0.4 | 1.4 | CHP, thought to be involved in the persistence in the host |
| Rv2616 | 1.1 | 0.6 | 1.0 | CHP similar to C. glutamicum GTPase |
| Rv2724c | 0.5 | 1.3 | 1.4 | FadE20 |
| Rv2784c | 1.1 | 1.6 | 1.2 | LppU |
| Rv2821c | 1.1 | 0.6 | 0.9 | CHP, CRISPR-associated protein |
| Rv2840c | 1.1 | 1.6 | 1.5 | CHP, COG2740 implicated in transcription antitermination |
| Rv2846c | 1.6 | 1.5 | 1.9 | EfpA |
| Rv2931 | 1.2 | 1.7 | 1.7 | PpsA |
| Rv2932 | 1.3 | 1.8 | 1.8 | PpsB |
| Rv2933 | 1.1 | 1.6 | 1.7 | PpsC |
| Rv2987c | 1.0 | 1.6 | 0.5 | LeuD |
| Rv2989 | 1.1 | 1.6 | 0.6 | Probable IclR-family transcriptional regulator. |
| Rv2990c | 0.9 | 0.6 | 1.3 | HP, SAM-dependent methyltransferase family protein |
| Rv3135 | 0.8 | 2.2 | 1.4 | PPE50 |
| Rv3136 | 1.0 | 1.9 | 1.5 | PPE51 |
| Rv3229c | 0.1 | 0.2 | 1.4 | DesA3 |
| Rv3230c | 0.2 | 0.3 | 0.8 | Hypothetical oxidoreductase |
| Rv3285 | 1.5 | 0.6 | 1.1 | AccA3 |
| Rv3307 | 1.5 | 0.5 | 1.0 | DeoD |
| Rv3414c | 1.5 | 1.7 | 1.3 | SigD |
| Rv3418c | 0.9 | 1.8 | 1.4 | GroES |
| Rv3460c | 1.1 | 1.7 | 1.3 | RpsM |
| Rv3462c | 1.2 | 1.6 | 1.3 | InfA |
| Rv3487c | 1.0 | 1.7 | 2.2 | LipF |
| Rv3763 | 1.2 | 0.6 | 1.1 | LpqH |
| Rv3788 | 1.2 | 1.6 | 1.1 | HP, GreA/GreB domain |
| Rv3822 | 1.1 | 1.4 | 1.8 | CHP, COG3008, paraquat-inducible protein |
| Rv3824c | 1.0 | 1.4 | 1.6 | PapA1 |
| Rv3862c | 1.3 | 1.5 | 1.5 | WhiB6 |
| Rv3872 | 1.1 | 1.7 | 1.6 | PE35 |
| Rv3873 | 1.1 | 1.4 | 1.6 | PPE68 |
| Rv3874 | 1.2 | 1.5 | 1.8 | EsxB, CFP-10 |
| Rv3875 | 1.1 | 1.6 | 1.6 | EsxA, ESAT-6 |
Gene induction ratios were calculated from the comparison with RNA of each strain isolated at the same growth phase, as stated in the Materials and Methods section.
a
According to Cole et al. (15) and database (http://genolist.pasteur.fr/TubercuList/ or http://cmr.tigr.org/tigr-scripts/CMR/GenomePage.cgi?database=gmt).
b
nnotation corresponding to Cole et al. (15) and database (http://genolist.pasteur.fr/TubercuList/).
c
Similarity as predicted by tools (http://blast.ncbi.nlm.nih.gov/Blast.cgi and http://smart.embl-heidelberg.de/smart/set_mode. cgi?NORMAL=1).