Table 1.
Differentially expressed genes with significant changes found between BCGΔBCG1419c and BCG in planktonic cultures.
| Upregulated in BCGΔBCG1419c vs BCG WT fold-change ≥ 0.585 plus p < 0.05 | ||||||
|---|---|---|---|---|---|---|
| GENE_NAME | GENE_ID | Mtb ortholog | Product | LOG2FOLD | AVG_PVALUE | Regulon |
| rrs | rrs | 16S rRNA | 3.4982 | 0.000104738 | ||
| EBG00001157317 | EBG00001157317 | SSU_rRNA_archaea | 2.9089 | 0.000387952 | ||
| EBG00001157343 | EBG00001157343 | PK-G12rRNA | 2.2264 | 0.034778283 | ||
| secE2 | BCG_0417 | Rv0379 | Possible protein transport protein secE2 with Calcium dodecin domain | 1.6343 | 0.012587538 | |
| EBG00001157360 | EBG00001157360 | 5_8S_rRNA | 1.5695 | 0.005169291 | ||
| BCG_3831c | BCG_3831c | Probable remnant of a transposase | 1.4757 | 0.049151559 | ||
| BCG_3079c | BCG_3079c | Rv3054c | Conserved hypothetical protein with NAD(P)H-dependent FMN reductase domain | 1.3741 | 0.000116064 | |
| EBG00001157348 | EBG00001157348 | LSU_rRNA_bacteria | 1.2775 | 0.005406273 | ||
| rpsN1 | BCG_0767 | Rv0717 | Probable 30S ribosomal protein S14 rpsN1 | 1.2582 | 0.015651912 | |
| BCG_2010c | BCG_2010c | Rv1993c | Conserved hypothetical protein | 1.1703 | 0.013705724 | |
| rrl | rrl | 23S rRNA | 1.1078 | 0.016674466 | ||
| groES | BCG_3488c | Rv3418c | 10 kDa chaperonin groES | 1.098 | 0.020911838 | |
| EBG00001157315 | EBG00001157315 | 5S_rRNA | 1.05 | 0.031607557 | ||
| BCG_2922c | BCG_2922c | Rv2901c | Conserved hypothetical protein | 1.0287 | 0.037531455 | |
| mbtH | BCG_2391c | Rv2377c | Putative conserved protein mbtH | 1.004 | 0.011346227 | |
| BCG_0026c | BCG_0026c | Rv3920c | Hypothetical protein similar to jag protein | 0.9649 | 0.02941768 | |
| phoY1_1 | BCG_3330c | Rv3301c | Probable phosphate-transport system transcriptional regulatory protein phoU homolog 1 phoY1 | 0.9622 | 0.007044978 | |
| PE_PGRS43b | BCG_2509c | Rv2490c | PE-PGRS family protein [second part] | 0.9184 | 0.047561816 | |
| rpmC | BCG_0759 | Rv0709 | Probable 50S ribosomal protein L29 rpmC | 0.9129 | 0.041923764 | |
| glyU | glyU | tRNA-Gly | 0.9079 | 0.000861898 | ||
| phoY1_2 | BCG_3366c | Rv3301c | Probable phosphate-transport system transcriptional regulatory protein phoU homolog 1 phoY1 | 0.8864 | 0.010088291 | |
| BCG_2220c | BCG_2220c | Rv2204c | Conserved hypothetical protein with iron-sulfur cluster assembly accessory protein domain | 0.8801 | 0.04788665 | |
| BCG_0840 | BCG_0840 | Rv0787A | Conserved hypothetical protein with phosphoribosylformylglycinamidine (FGAM) synthase domain | 0.8727 | 0.029136225 | |
| BCG_1418c | BCG_1418c | Rv1356c | Hypothetical protein | 0.8671 | 0.000299023 | |
| serT | serT | tRNA-Ser | 0.8631 | 0.000637902 | ||
| BCG_2827 | BCG_2827 | Rv2809 | Hypothetical protein | 0.8464 | 0.041819341 | |
| PE_PGRS22 | BCG_1151 | Rv1091 | PE-PGRS family protein | 0.8331 | 0.028777497 | |
| PE_PGRS45b | BCG_2641c | Rv2615c | PE-PGRS family protein | 0.7918 | 0.012061469 | |
| TB7.3_1 | BCG_3248c | Rv3221c | Biotinylated protein TB7.3 contains acetyl-CoA carboxylase biotin carboxyl carrier protein subunit domain | 0.791 | 0.013039128 | |
| TB7.3_2 | BCG_3341c | Rv3221c | Biotinylated protein TB7.3 contains acetyl-CoA carboxylase biotin carboxyl carrier protein subunit domain | 0.7188 | 0.019029613 | |
| BCG_2053 | BCG_2053 | Rv2034 | Probable ArsR-type repressor protein | 0.6551 | 0.018687862 | |
| BCG_1420 | BCG_1420 | Rv1358 | Probable transcriptional regulatory protein | 0.6283 | 0.000717219 | |
| BCG_3348c | BCG_3348c | Rv3225c | Possible transferase, GCN5-related N-acetyltransferase, phosphorylase domain | 0.6262 | 0.003293885 | |
| BCG_3227c | BCG_3227c | Rv3202c | Possible ATP-dependent DNA helicase | 0.5937 | 0.000595553 | |
| BCG_3249c | BCG_3249c | Rv3221A | Possible anti-sigma factor RshA regulates the activity of the mycobacterial stress response sigma factor SigH | 0.5886 | 0.042051519 | |
| gid_1 | BCG_3977c | Probable glucose-inhibited division protein B gid | 0.5873 | 0.421759769 | ||
| Downregulated BCGΔBCG1419c vs BCG WT fold-change ≤ − 0.585 plus p < 0.05 | ||||||
|---|---|---|---|---|---|---|
| GENE_NAME | GENE_ID | Mtb ortholog | Product | LOG2FOLD | AVG_PVALUE | Regulon |
| BCG_3715c | BCG_3715c | Rv3657c | Possible conserved alanine rich membrane protein | − 1.1444 | 0.023526035 | |
| BCG_3154 | BCG_3154 | Rv3131 | Conserved hypothetical protein. Putative nitroreductase, member of the DosR-regulon | − 1.0879 | 0.000785114 | |
| cobLa | BCG_2092c | Probable precorrin-6y methyltransferase CobLa [first part] | − 1.0652 | 0.047535781 | ||
| BCG_0295 | BCG_0295 | Rv0257 | Conserved hypothetical protein | − 0.9771 | 0.027386067 | |
| BCG_0788 | BCG_0788 | Rv0738 | Conserved hypothetical protein with DNA damage-inducible protein DinB domain | − 0.9704 | 0.009118011 | |
| BCG_1419c | BCG_1419c | Rv1357c | Conserved hypothetical protein with cyclic diguanylate phosphodiesterase domain | − 0.9519 | 0.009820681 | |
| pirG | BCG_3872 | Rv3810 | Exported repetitive protein precursor pirG/erp | − 0.9464 | 0.000708503 | MtrA regulon |
| lipF | BCG_3551c | Rv3487c | Probable esterase/lipase lipF | − 0.9198 | 0.000144981 | |
| BCG_1496c | BCG_1496c | Rv1435c | Probable conserved Proline, Glycine, Valine-rich secreted protein | − 0.9068 | 0.006275716 | MtrA regulon |
| BCG_1462 | BCG_1462 | Rv1401 | Possible membrane protein | − 0.8878 | 0.002947653 | |
| BCG_3695 | BCG_3695 | Putative transposase | − 0.8857 | 0.041641661 | ||
| murG | BCG_2170c | Rv2153c | UPD-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol-N-acetylglucosamine transferase MurG | − 0.8737 | 0.009443607 | |
| BCG_2763 | BCG_2763 | Rv2747 | Possible transferase, Probable L-glutamate alpha-N-acetyltranferase ArgA (alpha-N-acetylglutamate synthase) | − 0.8719 | 0.005494031 | |
| BCG_0711c | BCG_0711c | Rv0662c | Conserved hypothetical protein Possible antitoxin VapB7 | − 0.865 | 0.031849363 | |
| lpqZ | BCG_1304 | Rv1244 | Putative lipoprotein lpqZ | − 0.8632 | 0.004945189 | |
| serA2 | BCG_0778c | Rv0728c | Possible D-3-phosphoglycerate dehydrogenase serA2 | − 0.8559 | 0.011718358 | |
| BCG_3153c | BCG_3153c | Rv3130c | Conserved hypothetical protein Triacylglycerol synthase (diacylglycerol acyltransferase) Tgs1 | − 0.8421 | 0.034329997 | |
| nirD | BCG_0291 | Rv0253 | Probable nitrite reductase [NAD(P)H] small subunit nirD | − 0.8362 | 0.018275726 | |
| BCG_0518 | BCG_0518 | Rv0477 | Possible conserved secreted protein | − 0.8313 | 0.005587559 | |
| lipR | BCG_3109 | Rv3084 | Probable acetyl-hydrolase/esterase lipR | − 0.828 | 0.010400861 | |
| argB | BCG_1693 | Rv1654 | Probable Acetylglutamate kinase argB | − 0.8205 | 0.003955123 | ArgR regulon |
| BCG_0699 | BCG_0699 | Rv0650 | Possible sugar kinase with ROK family protein domain | − 0.8087 | 0.027255813 | |
| BCG_1762 | BCG_1762 | Rv1723 | Probable hydrolase with CubicO group peptidase, beta-lactamase class C family domain | − 0.8087 | 0.009155488 | |
| BCG_3465 | BCG_3465 | Rv3395A | Probable membrane protein | − 0.7883 | 0.035013964 | |
| BCG_0008c | BCG_0008c | Rv0008c | Possible membrane protein with cell wall synthesis protein CwsA domain | − 0.7879 | 0.037588749 | |
| BCG_1219c | BCG_1219c | Rv1158c | Conserved hypothetical ala-, pro-rich protein | − 0.7862 | 0.005061423 | MtrA regulon |
| BCG_0702c | BCG_0702c | Rv0653c | Possible transcriptional regulatory protein (probably tetR-family) | − 0.7705 | 0.024929043 | |
| BCG_0501 | BCG_0501 | Rv0461 | Probable transmembrane protein | − 0.7693 | 0.005563857 | |
| BCG_2782 | BCG_2782 | Rv2765 | Probable alanine rich hydrolase with dienelactone hydrolase family protein domain | − 0.7689 | 0.026772117 | |
| speE | BCG_2625 | Rv2601 | Putative spermidine synthase speE | − 0.7643 | 0.008314323 | |
| BCG_0673 | BCG_0673 | Rv0627 | Conserved hypothetical protein Possible toxin VapC5 | − 0.7584 | 0.010403475 | |
| BCG_3664c | BCG_3664c | Rv3600c | Conserved hypothetical protein with type III pantothenate kinase domain | − 0.7558 | 0.009655975 | |
| yrbE1A | BCG_0204 | Rv0167 | Conserved hypothetical integral membrane protein yrbE1A | − 0.7506 | 0.004801835 | |
| adhE1 | BCG_0198c | Rv0162c | Putative zinc-type alcohol dehydrogenase (e subunit) adhE | − 0.7478 | 0.024960044 | |
| BCG_1844 | BCG_1844 | Rv1810 | Conserved hypothetical protein | − 0.7437 | 0.011342536 | |
| purT | BCG_0426 | Rv0389 | Probable phosphoribosylglycinamide formyltransferase 2 purT | − 0.7374 | 0.002402391 | |
| argF | BCG_1695 | Rv1656 | Probable Ornithine carbamoyltransferase, anabolic ArgF | − 0.7363 | 0.010148525 | ArgR regulon |
| BCG_2741c | BCG_2741c | Rv2728c | Conserved hypothetical alanine rich protein with class III extradiol ring-cleavage dioxygenase family protein domain | − 0.7323 | 0.016000596 | |
| BCG_0284 | BCG_0284 | Rv0246 | Probable conserved integral membrane protein | − 0.72 | 0.027263273 | |
| cobD | BCG_2253c | Rv2236c | Probable conserved membrane protein CobD | − 0.7136 | 0.033002992 | |
| deoD | BCG_3372 | Rv3307 | Probable purine nucleoside phosphorylase deoD | − 0.7087 | 0.006876059 | |
| pks16 | BCG_1070 | Rv1013 | Putative polyketide synthase pks16 | − 0.7077 | 0.003716129 | |
| BCG_1059c | BCG_1059c | Rv1002c | Conserved membrane protein with dolichyl-phosphate-mannose–protein mannosyltransferase domain | − 0.707 | 0.005819792 | |
| xerC | BCG_2915c | Rv2894c | Probable integrase/recombinase xerC | − 0.7054 | 0.009092191 | MtrA regulon |
| BCG_0891 | BCG_0891 | Rv0839 | Conserved hypothetical protein with class I SAM-dependent methyltransferase domain | − 0.7016 | 0.001141476 | |
| BCG_1349c | BCG_1349c | Rv1290c | Conserved hypothetical protein | − 0.7016 | 0.005788882 | |
| celA1 | BCG_0093 | Rv0062 | Possible cellulase celA1 (ENDOGLUCANASE) | − 0.7013 | 0.011925226 | |
| BCG_1518c | BCG_1518c | Rv1457c | Probable unidentified antibiotic-transport integral membrane ABC transporter | − 0.7011 | 0.017966363 | |
| BCG_0352 | BCG_0352 | Rv0312 | Conserved hypothetical proline and threonine rich protein with Hsp70 family protein domain | − 0.7007 | 0.006180045 | MtrA regulon |
| BCG_0517 | BCG_0517 | Rv0476 | Possible conserved transmembrane protein | − 0.7003 | 0.008443131 | |
| argJ | BCG_1692 | Rv1653 | Probable Glutamate n-acetyltransferase argJ | − 0.6962 | 0.011937422 | ArgR regulon |
| BCG_1061c | BCG_1061c | Rv1004c | Probable membrane protein | − 0.6961 | 0.028415351 | |
| prrA | BCG_0955c | Rv0903c | Two component response transcriptional regulatory protein prrA | − 0.6901 | 0.002751943 | |
| BCG_0934 | BCG_0934 | Rv0882 | Probable transmembrane protein | − 0.6794 | 0.038109383 | |
| BCG_2713 | BCG_2713 | Rv2700 | Possible secreted alanine rich protein with LytR cell envelope-related transcriptional attenuator domain | − 0.6777 | 0.015900774 | |
| BCG_1310 | BCG_1310 | Rv1250 | Probable drug-transport integral membrane protein | − 0.6758 | 0.013796646 | |
| BCG_3054 | BCG_3054 | Rv3031 | Conserved hypothetical protein with glycoside hydrolase family 57 protein domain | − 0.6735 | 0.012038058 | |
| add | BCG_3379c | Rv3313c | Probable adenosine deaminase add | − 0.6725 | 0.022782705 | |
| panC | BCG_3666c | Rv3602c | Probable pantoate–beta-alanine ligase panC | − 0.6717 | 0.008371359 | |
| BCG_1539 | BCG_1539 | Rv1477 | Hypothetical invasion protein (ripA) | − 0.6698 | 0.00493817 | MtrA regulon |
| ephC | BCG_1185 | Rv1124 | Probable epoxide hydrolase ephC | − 0.6668 | 0.024392971 | |
| BCG_0265 | BCG_0265 | Rv0228 | Probable integral membrane acyltransferase | − 0.6665 | 0.031158919 | |
| BCG_1619c | BCG_1619c | Rv1566c | Possible inv protein | − 0.6661 | 0.007192759 | |
| BCG_1001c | BCG_1001c | Probable mycolyl transferase | − 0.6654 | 0.045990406 | ||
| ugpBa | BCG_2853c | Rv2833c | Probable Sn-glycerol-3-phosphate-binding lipoprotein ugpB [first part] | − 0.6645 | 0.035959294 | |
| BCG_1624 | BCG_1624 | Rv1571 | Conserved hypothetical protein with 2′-5′RNA ligase family protein domain | − 0.663 | 0.035162251 | |
| sugI | BCG_3401 | Rv3331 | Probable sugar-transport integral membrane protein sugI | − 0.6629 | 0.018548577 | |
| BCG_3854 | BCG_3854 | Rv3792 | Probable conserved transmembrane protein Arabinofuranosyltransferase AftA | − 0.6629 | 0.007871683 | |
| BCG_3676c | BCG_3676c | Rv3612c | Conserved hypothetical protein | − 0.6601 | 0.003454172 | |
| dedA | BCG_2664 | Rv2637 | Possible transmembrane protein dedA | − 0.6587 | 0.039418929 | |
| BCG_3491c | BCG_3491c | Rv3421c | Conserved hypothetical protein with tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex dimerization subunit type 1 TsaB domain | − 0.6525 | 0.031652896 | |
| BCG_1863 | BCG_1863 | Rv1828 | Conserved hypothetical protein with MerR family transcriptional regulator domain | − 0.6512 | 0.007243893 | |
| BCG_0842c | BCG_0842c | Rv0789c | Hypothetical protein | − 0.65 | 0.042091095 | |
| PPE9 | BCG_0425c | PPE family protein | − 0.6477 | 0.024967853 | ||
| cut4 | BCG_3518 | Rv3452 | Probable cutinase precursor cut4 | − 0.6474 | 0.02589246 | |
| BCG_1218c | BCG_1218c | Rv1157c | Conserved hypothetical ala-, pro-rich protein | − 0.6467 | 0.006357262 | MtrA regulon |
| BCG_3691 | BCG_3691 | Rv3633 | Conserved hypothetical protein with Ectoine hydroxylase-related dioxygenase, phytanoyl-CoA dioxygenase domain | − 0.6456 | 0.004480936 | |
| cobS | BCG_2224 | Rv2208 | Probable cobalamin 5'-phosphate synthase CobS | − 0.6448 | 0.020180231 | |
| BCG_3851 | BCG_3851 | Rv3789 | Conserved hypothetical protein with GtrA domain-containing protein | − 0.6412 | 0.02717627 | |
| echA16 | BCG_2851 | Rv2831 | Probable enoyl-CoA hydratase echa16 | − 0.6407 | 0.040951984 | |
| BCG_3745c | BCG_3745c | Rv3686c | Conserved hypothetical protein | − 0.6383 | 0.023684945 | |
| BCG_0241c | BCG_0241c | Rv0204c | Probable conserved transmembrane protein | − 0.6362 | 0.010034117 | |
| BCG_3015 | BCG_3015 | Rv2994 | Probable conserved integral membrane protein with MFS transporter domain | − 0.6361 | 0.016319392 | |
| leuB | BCG_3016c | Rv2995c | 3-isopropylmalate dehydrogenase leuB | − 0.636 | 0.02535765 | |
| BCG_1657 | BCG_1657 | Rv1619 | Conserved membrane protein | − 0.6359 | 0.029269187 | |
| argD | BCG_1694 | Rv1655 | Probable Acetylornithine aminotransferase argD | − 0.635 | 0.010948399 | ArgR regulon |
| fadD33 | BCG_1407 | Rv1345 | Possible polyketide synthase fadD33 | − 0.6338 | 0.007716787 | |
| BCG_1724c | BCG_1724c | Rv1686c | Probable conserved integral membrane protein ABC transporter | − 0.6334 | 0.03708873 | |
| BCG_2589 | BCG_2589 | Rv2566 | Long conserved hypothetical protein [second part] | − 0.6334 | 0.033570675 | |
| BCG_0388 | BCG_0388 | Rv0349 | Hypothetical protein | − 0.6315 | 0.025410477 | |
| BCG_1540 | BCG_1540 | Rv1478 | Hypothetical invasion protein (ripB) | − 0.6313 | 0.004572077 | MtrA regulon |
| BCG_0330 | BCG_0330 | Rv0290 | Probable conserved transmembrane protein 3 ESX conserved component EccD3. ESX-3 type VII secretion system protein | − 0.6302 | 0.015606343 | |
| BCG_1711c | BCG_1711c | Rv1673c | Conserved hypothetical protein with Transglutaminase-like enzyme, putative cysteine protease domain | − 0.6289 | 0.043524332 | |
| yrbE1B | BCG_0205 | Rv0168 | Conserved hypothetical integral membrane protein yrbE1B | − 0.6288 | 0.016757565 | |
| narL | BCG_0896c | Rv0844c | Possible nitrate/nitrite response transcriptional regulatory protein narL | − 0.627 | 0.010270002 | |
| BCG_0055 | BCG_0055 | Putative secreted protein P60-related protein [second part] | − 0.6268 | 0.026680451 | ||
| BCG_2812c | BCG_2812c | Rv2794c | Conserved hypothetical protein phosphopantetheinyl transferase PptT | − 0.6226 | 0.015274191 | |
| cydD | BCG_1659c | Rv1621c | Probable 'component linked with the assembly of cytochrome' transport transmembrane ATP-binding protein ABC transporter cydD | − 0.6197 | 0.026880206 | |
| BCG_3754 | BCG_3754 | Rv3695 | Possible conserved membrane protein RDD family protein | − 0.6188 | 0.020087176 | |
| BCG_2071c | BCG_2071c | Rv2052c | Conserved hypothetical protein | − 0.6154 | 0.018909791 | |
| BCG_2196 | BCG_2196 | Rv2181 | Probable conserved integral membrane protein Alpha(1→2)mannosyltransferase/manT | − 0.6154 | 0.007679435 | |
| BCG_2692 | BCG_2692 | Rv2679 | Probable enoyl-CoA hydratase echA15 | − 0.6145 | 0.025973179 | |
| pra | BCG_1136 | Rv1078 | Probable Proline-rich antigen homolog pra | − 0.6119 | 0.014551011 | |
| mmsB | BCG_0802c | Rv0751c | Probable 3-hydroxyisobutyrate dehydrogenase mmsB | − 0.6115 | 0.008050415 | |
| mtc28 | BCG_0071c | Rv0040c | Secreted proline rich protein MTC28 (PROLINE RICH 28 KDA ANTIGEN) | − 0.6097 | 0.005413412 | MtrA regulon |
| BCG_3443 | BCG_3443 | Rv3371 | Conserved hypothetical protein possible triacylglycerol synthase (diacylglycerol acyltransferase) | − 0.6089 | 0.006884392 | |
| arsB2 | BCG_3643 | Rv3578 | Possible arsenical pump integral membrane protein arsB2 | − 0.6069 | 0.029200206 | |
| mutA | BCG_1555 | Rv1492 | Probable methylmalonyl-CoA mutase small subunit mutA | − 0.6052 | 0.012106302 | |
| menE | BCG_0586c | Rv0542c | Possible o-succinylbenzoic acid–CoA ligase menE | − 0.6049 | 0.01997206 | |
| BCG_3879 | BCG_3879 | Rv3817 | Putative phosphotransferase | − 0.6039 | 0.027736949 | |
| BCG_1587 | BCG_1587 | Rv1535 | Hypothetical protein | − 0.6026 | 0.024513436 | |
| BCG_1802c | BCG_1802c | Rv1761c | Hypothetical exported protein | − 0.5977 | 0.028422702 | |
| BCG_2479 | BCG_2479 | Rv2459 | Probable conserved integral membrane transport protein MFS transporter | − 0.5973 | 0.007794219 | |
| BCG_3777 | BCG_3777 | Rv3717 | Conserved hypothetical protein with N-acetylmuramoyl-L-alanine amidase domain | − 0.5972 | 0.016730339 | MtrA regulon |
| BCG_1618c | BCG_1618c | Rv1565c | Conserved hypothetical membrane protein with acyltransferase and SGNH domains | − 0.5945 | 0.013232892 | MtrA regulon |
| BCG_0263c | BCG_0263c | Rv0226c | Probable conserved transmembrane protein | − 0.5931 | 0.009766941 | |
| plcD | BCG_1794c | Rv2351c | Probable phospholipase C 4 plcD | − 0.5912 | 0.038388997 | MtrA regulon |
| rfe | BCG_1362 | Rv1302 | Putative undecapaprenyl-phosphate alpha-n-acetylglucosaminyltransferase rfe/wecA | − 0.5904 | 0.032022205 | |
| BCG_0697 | BCG_0697 | Rv0648 | Alpha-mannosidase | − 0.588 | 0.007643403 | |
| BCG_1575 | BCG_1575 | Rv1523 | Probable methyltransferase | − 0.5879 | 0.027733217 | |
| BCG_3514 | BCG_3514 | Rv3448 | Probable conserved integral membrane protein | − 0.5864 | 0.044909115 | |
| BCG_3772 | BCG_3772 | Rv3712 | Possible ligase | − 0.5864 | 0.019375521 | |
| sapM | BCG_3375 | Rv3310 | Possible acid phosphatase | − 0.5853 | 0.010551491 | MtrA regulon |
Genes highlighted in bold correspond to those matching potential pseudogenes/interrupted genes.