Table 4.
Top 20 upregulated and downregulated M. chelonae genes in the double lysogen (BPs, McProf) relative to WT M. chelonae (McProf)
| MCHa gene ID | Predicted functionb | log2FCc | FDRd | MABe Gene ID | MAB Gene Description | MTBf Gene ID | MTB Gene Description |
|---|---|---|---|---|---|---|---|
| BB28_RS04255 | flotillin protein | 6.6 | 6.4E-124 | NA | NA | NA | NA |
| BB28_RS19005 | hypothetical protein | 6.1 | 9.1E-18 | MAB_3786c | Hypothetical protein | NA | NA |
| BB28_RS23100 | N-acetyltransferase | 5.6 | 4.4E-38 | MAB_4621c | Putative acetyltransferase | NA | NA |
| BB28_RS23095 | hypothetical protein | 5.3 | 2.8E-35 | MAB_4620c | Hypothetical protein | NA | NA |
| BB28_RS17590 | WhiB7 transcriptional regulator | 4.7 | 1.3E-73 | MAB_3508c | Putative transcriptional regulator | Rv3197A | transcriptional regulator WhiB7 |
| BB28_RS05390 | GNAT family N-acetyltransferase (eis1) | 4.1 | 5.8E-12 | MAB_1125c | Hypothetical acetyltransferase, GNAT family | Rv1947 | hypothetical protein |
| BB28_RS04260 | class I SAM-dependent methyltransferase | 3.9 | 1.0E-120 | MAB_0963c | Putative polyketide synthase protein | NA | NA |
| BB28_RS03915 | hypothetical protein | 3.8 | 2.8E-116 | MAB_0857 | Putative monooxygenase | NA | NA |
| BB28_RS20465 | KR domain-containing protein | 3.8 | 3.4E-26 | MAB_4053c | Putative short chain dehydrogenase/reductase | NA | NA |
| BB28_RS16665 | iron ABC transporter permease | 3.8 | 4.5E-31 | MAB_2262c | Hypothetical ABC transporter ATP-binding protein | Rv1348 | iron ABC transporter ATP-binding protein/permease IrtA |
| BB28_RS06460 | NAD(P)-dependent oxidoreductase | 3.4 | 1.2E-21 | MAB_1344c | Putative DTDP-glucose-4,6-dehydratase-related protein | Rv3468c | dTDP-glucose 4,6-dehydratase |
| BB28_RS11540 | ABC transporter ATP-binding protein | 3.3 | 3.5E-64 | MAB_2355c | Putative ABC transporter ATP-binding protein | NA | NA |
| BB28_RS22650 | GNAT family N-acetyltransferase (eis2) | 3.3 | 1.4E-176 | MAB_4532c | hypothetical protein | NA | NA |
| BB28_RS06750 | tap multidrug efflux transporter | 3.3 | 7.3E-35 | MAB_1409c | Putative drug antiporter protein precursor | Rv1258c | multidrug-efflux transporter |
| BB28_RS13560 | TetV Efflux Pump | 3.3 | 9.8E-94 | MAB_2780c | Putative transporter | NA | NA |
| BB28_RS20470 | pyridoxamine 5'-phosphate oxidase family protein | 3.2 | 4.1E-29 | MAB_4054c | hypothetical protein | NA | NA |
| BB28_RS03190 | EamA family transporter | 3.2 | 3.5E-06 | MAB_0677c | Conserved hypothetical protein | NA | NA |
| BB28_RS17050 | hypothetical protein | 3.2 | 5.1E-32 | MAB_3424c | hypothetical protein | NA | NA |
| BB28_RS06235 | acyltransferase | 3.1 | 2.7E-39 | MAB_1297c | hypothetical protein | NA | NA |
| BB28_RS01940 | N-acetyltransferase | 3.0 | 2.9E-11 | MAB_0404c | Putative acetyltransferase | NA | NA |
| BB28_RS13285 | ferrochelatase | -2.1 | 4.5E-40 | MAB_2721c | Ferrochelatase (Protoheme ferro-lyase) | Rv1485 | ferrochelatase |
| BB28_RS19235 | alpha-hydroxy-acid oxidizing enzyme | -2.1 | 2.9E-35 | MAB_3834c | Possible L-lactate dehydrogenase (cytochrome) LldD1 | Rv0694 | mycofactocin system heme/flavin oxidoreductase MftD |
| BB28_RS08645 | epoxide hydrolase | -2.2 | 2.4E-07 | MAB_1628c | hypothetical protein | NA | NA |
| BB28_RS13295 | beta-ketoacyl-ACP reductase | -2.3 | 3.4E-56 | MAB_2723c | 3-oxoacyl- | Rv1483 | 3-oxoacyl-ACP reductase FabG |
| BB28_RS13290 | enoyl-acyl-carrier-protein reductase FabI | -2.4 | 2.0E-60 | MAB_2722c | Enoyl-(acyl-carrier-protein) reductase (NADH) | Rv1484 | NADH-dependent enoyl-ACP reductase |
| BB28_RS08640 | hypothetical protein | -2.4 | 2.6E-04 | NA | NA | NA | NA |
| BB28_RS19655 | universal stress protein | -2.7 | 1.2E-03 | MAB_3904 | hypothetical protein | Rv2028c | universal stress protein |
| BB28_RS16545 | acyl-ACP desaturase | -2.9 | 1.3E-75 | MAB_3354 | Probable acyl- | NA | NA |
| BB28_RS05070 | cytochrome c oxidase subunit I | -3.2 | 2.8E-16 | MAB_1042c | Probable cytochrome c oxidase polypeptide I | NA | NA |
| BB28_RS11065 | iron ABC transporter permease | -4.0 | 3.8E-16 | NA | NA | NA | NA |
| BB28_RS01880 | DUF58 domain-containing protein | -6.2 | 5.8E-06 | MAB_0388c | hypothetical protein | Rv3693 | membrane protein |
| BB28_RS01835 | glycerol uptake glpF | -6.2 | 4.5E-06 | MAB_0381 | Glycerol uptake facilitator protein (GlpF) | NA | NA |
| BB28_RS01885 | MoxR family ATPase | -6.5 | 1.2E-06 | MAB_0389c | Putative regulatory protein | Rv3692 | methanol dehydrogenase transcriptional regulator MoxR |
| BB28_RS01875 | stage II sporulation protein M | -6.6 | 1.2E-06 | MAB_0387 | hypothetical protein | Rv3694c | transmembrane protein |
| BB28_RS24340 | RDD family protein | -7.0 | 2.4E-07 | MAB_0386c | hypothetical protein | Rv3695 | membrane protein |
| BB28_RS01830 | KR domain-containing protein | -7.1 | 1.5E-07 | MAB_0380 | Probable short-chain dehydrogenase/reductase | NA | NA |
| BB28_RS01890 | DUF4350 domain-containing protein | -7.3 | 4.6E-08 | MAB_0390c | hypothetical protein | Rv3691 | hypothetical protein |
| BB28_RS01900 | membrane protein | -7.8 | 2.0E-09 | MAB_0392c | hypothetical protein | Rv3689 | transmembrane protein |
| BB28_RS01845 | PadR family transcriptional regulator | -8.3 | 1.4E-10 | MAB_0383c | Putative transcriptional regulator, PadR-like | NA | NA |
| BB28_RS01840 | glycerol kinase | -9.0 | 1.1E-12 | MAB_0382 | Glycerol kinase (GlpK) | Rv3696c | glycerol kinase |
aMCH = Mycobacterium chlelonae
bGenes that belong to the WhiB7 regulon are in bold
cLog2 Fold Change for the double lysogen (+BPs+McProf) of M. chelonae
dFDR = False Discovery Rate
eMAB = Mycobacterium abscessus
fMTB = Mycobacterium tuberculosis