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Table 4 Top 20 upregulated and downregulated M. chelonae genes in the double lysogen (BPs, McProf) relative to WT M. chelonae (McProf)

From: Increased whiB7 expression and antibiotic resistance in Mycobacterium chelonae carrying two prophages

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
  1. aMCH = Mycobacterium chlelonae
  2. bGenes that belong to the WhiB7 regulon are in bold
  3. cLog2 Fold Change for the double lysogen (+BPs+McProf) of M. chelonae
  4. dFDR = False Discovery Rate
  5. eMAB = Mycobacterium abscessus
  6. fMTB = Mycobacterium tuberculosis