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. 2023 Oct 24;16:260. doi: 10.1186/s12920-023-01695-5

Table 2.

SNPs significantly associated with classification as MBO by Subsequent statistical test

SNP p-value score G1P1 G0P0 G1P0 G0P1 Locus Protein Description Essentiality Notes from Mycobrowser SnpEff Effects
22,264 0 0.948 4100 2080 172 1 Rv0018c PstP Involved in regulation (using dephosphorylation of a specific phosphorylated substrate) Required for survival in murine macrophages (Rengarajan 2005) Synonymous
23,714 0 0.951 4100 2100 161 1 Rv0019c FhaB Conserved protein with FHA domain, FhaB Required for survival in murine macrophages (Rengarajan 2005) Synonymous
147,873 0 0.998 4100 2250 9 3 Intergenic, upstream of elongation factor G FusA2 (Rv0120c) Intergenic
181,672 0 0.951 4100 2100 161 1 Rv0153c PtbB Phosphotyrosine protein phosphatase PTPB (protein-tyrosine-phosphatase) (PTPase) Required for growth on cholesterol (Griffin 2011) Asp105Gly
184,727 0 0.998 4100 2250 9 3 Rv0156 PntAb Probable NAD(P) transhydrogenase (subunit alpha) PntAb [second part; integral membrane protein] (pyridine nucleotide transhydrogenase subunit alpha) (nicotinamide nucleotide transhydrogenase subunit alpha) Tyr2Cys
212,254 0 0.951 4100 2100 161 1 Intergenic, upstream of transmembrane protein (Rv0180) Intergenic
217,863 0 0.951 4100 2100 160 1 Rv0186 BglS Possibly involved in degradation [catalytic activity: hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose] Pro532Arg
262,160 0 0.997 4100 2250 9 8 Rv0218 Probable conserved transmembrane protein Essential in murine spleen (Sassetti and Rubin, 2003) Asp413Asn
268,277 0 0.998 4100 2250 9 3 Rv0224c Possible methyltransferase (methylase) In vitro essential per multiple studies (Minato 2019; DeJesus 2017; Sassetti 2003; Griffin 2011) Phe117Leu
277,862 0 0.998 4100 2250 9 3 Intergenic, downstream of FadE4 (Rv0231) and upstream of probable transcriptional regulatory protein (probably TetR/AcrR-family) (Rv0232) Intergenic
294,198 0 0.997 4100 2250 9 8 Rv0244c FadE5 Probable acyl-CoA dehydrogenase FadE5 Required for growth on cholesterol (Griffin 2011) Glu479Ala
386,060 0 0.997 4100 2250 9 8 Intergenic, upstream of glpQ2 (Rv0317c) Intergenic
397,386 0 0.951 4100 2100 160 1 Intergenic, downstream of putative dehydrogenase/reductase (Rv0331) and upstream of hypothetical protein (Rv0332) Intergenic
398,034 0 0.997 4100 2250 9 8 Rv0332 Conserved protein Glu198Gly
411,100 0 0.948 4100 2090 171 2 Rv0342 IniA Isoniazid inductible gene protein IniA Asn88Ser
1,027,445 0 0.997 4100 2250 9 8 Rv0921 Possible resolvase for IS1535 Synonymous
1,029,936 0 0.951 4100 2100 161 1 Rv0923c Conserved hypothetical protein Synonymous
1,125,316 0 0.951 4100 2100 161 1 Rv1006 Unknown protein Disruption provides growth advantage (DeJesus 2017) Pro535Ser
1,129,160 0 0.997 4100 2250 9 9 Rv1010 KsgA Probable dimethyladenosine transferase KsgA (S-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltransferase) (16S rRNA dimethylase) (high level kasugamycin resistance protein KsgA) (kasugamycin dimethyltransferase) Synonymous
1,129,160 0 0.997 4100 2250 9 9 Rv1009 RpfB Probable resuscitation-promoting factor RpfB Ala357Val
1,234,657 0 0.998 4100 2250 9 3 Rv1108c XseA Probable exodeoxyribonuclease VII (large subunit) XseA (exonuclease VII large subunit) Synonymous
1,260,537 0 0.951 4100 2100 161 1 Rv1133c MetE Probable 5-methyltetrahydropteroyltriglutamate–homocysteine methyltransferase MetE (methionine synthase, vitamin-B12 independent isozyme) In vitro essential (DeJesus 2017; Sassetti 2003; Griffin 2011), non-essential in rich media (Minato 2019) Synonymous
1,307,958 0 0.951 4100 2100 161 1 Rv1175c FadH Probable NADPH dependent 2,4-dienoyl-CoA reductase FadH (2,4-dienoyl coenzyme A reductase) (4-enoyl-CoA reductase) Thr90Asn
1,377,140 0 0.948 4100 2080 172 1 Rv1234 Probable transmembrane protein Glu55Glu
1,393,003 0 0.951 4100 2100 161 1 Rv1248c Multifunctional alpha-ketoglutarate metabolic enzyme In vitro essential per multiple studies (Minato 2019; Sassetti 2003; Griffin 2011; Carvalho 2010) Glu17Ala
1,425,641 0 0.951 4100 2100 161 1 Rv1276c Conserved hypothetical protein Thr92Ser
1,458,076 0 0.951 4100 2100 161 1 Rv1301 Conserved protein In vitro essential (Sassetti 2003; Griffin 2011), non-essential in rich media (Minato 2019) Synonymous
1,478,312 0 0.998 4100 2250 9 3 Rv1317c AlkA Probable bifunctional regulatory protein and DNA repair enzyme AlkA (regulatory protein of adaptative response) (methylphosphotriester-DNA–protein-cysteine S-methyltransferase) Synonymous
1,496,289 0 0.997 4100 2250 9 8 Rv1328 GlgP Probable glycogen phosphorylase GlgP Val576Phe
1,499,291 0 0.998 4100 2250 9 4 Rv1330c PncB1 Nicotinic acid phosphoribosyltransferase PncB1 Gly423Gly
1,562,049 0 0.997 4100 2250 9 8 Rv1387 PPE20 PPE family protein PPE20 Val94Ala
1,609,445 0 0.948 4100 2080 172 1 Rv1431 Conserved membrane protein Lys455Gln
1,671,658 0 0.997 4100 2250 9 8 Rv1481 Probable membrane protein In vitro essential per multiple studies (Minato 2019; DeJesus 2017; Griffin 2011) Synonymous
1,681,928 0 0.951 4100 2100 161 1 Rv1491c Conserved membrane protein Synonymous
1,684,979 0 0.948 4100 2080 172 1 Rv1493 MutB Probable methylmalonyl-CoA mutase large subunit MutB (MCM) Synonymous
1,739,294 0 0.998 4100 2250 9 3 Rv1536 IleS Isoleucyl-tRNA synthetase IleS In vitro essential per multiple studies (Minato 2019; DeJesus 2017; Griffin 2011; Lamichhane 2003) Pro926Ala
1,754,572 0 0.951 4100 2100 161 1 Rv1550 FadD11 Probable fatty-acid-CoA ligase FadD11 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase) Leu286Ser
1,766,620 0 0.951 4100 2100 161 1 Rv1562c TreZ Maltooligosyltrehalose trehalohydrolase TreZ Ala175Thr
1,794,234 0 0.948 4100 2080 172 1 Rv1593c Conserved protein Synonymous
1,804,248 0 0.951 4100 2100 161 1 Rv1604 ImpA Probable inositol-monophosphatase ImpA (imp) Synonymous
1,804,315 0 0.997 4100 2250 9 8 Rv1604 ImpA Probable inositol-monophosphatase ImpA (imp) Tyr93His
1,830,295 0 0.998 4100 2250 9 3 Rv1628c Conserved protein Synonymous
1,834,859 0 0.951 4100 2100 161 1 Rv1630 RpsA 30S ribosomal protein S1 RpsA In vitro essential per multiple studies (Minato 2019; DeJesus 2017; Griffin 2011; Sassetti 2003) Ala440Thr
1,971,029 0 0.997 4100 2250 9 8 Rv1744c Probable membrane protein Arg121Gln
2,013,589 0 0.951 4100 2100 160 1 Rv1779c Possible integral membrane protein Synonymous
2,082,865 0 0.997 4100 2250 10 8 Rv1836c Conserved protein Arg591His
2,092,688 0 0.948 4100 2080 172 1 Rv1843c GuaB1 Probable inosine-5'-monophosphate dehydrogenase GuaB1(imp dehydrogenase) (IMPDH) (IMPD) Disruption provides growth advantage (DeJesus 2017) Synonymous
2,104,270 0 0.997 4100 2250 9 8 Rv1856c Possible oxidoreductase Disruption provides growth advantage (DeJesus 2017) Arg185His
2,280,081 0 0.951 4100 2100 161 1 Rv2032 Acg Conserved protein Acg Pro318Leu
2,475,116 0 0.997 4100 2250 9 8 Rv2210c IlvE Branched-chain amino acid transaminase IlvE In vitro essential (Sassetti 2003; Griffin 2011; DeJesus 2017), non-essential in rich media (Minato 2019) Synonymous
2,475,888 0 0.998 4100 2250 9 3 Rv2210c IlvE Branched-chain amino acid transaminase IlvE In vitro essential (Sassetti 2003; Griffin 2011; DeJesus 2017), non-essential in rich media (Minato 2019) Glu28Ala
2,502,757 0 0.951 4100 2100 161 1 Rv2229c Conserved protein Arg239Gln
2,528,773 0 0.998 4100 2250 9 3 Rv2254c Probable integral membrane protein Ala68Val
2,529,798 0 0.951 4100 2100 161 1 Rv2256c Conserved hypothetical protein Ala26Gly
2,606,813 0 0.951 4100 2100 161 1 Rv2333c Stp Integral membrane drug efflux protein Stp His503Gln
2,646,542 0 0.951 4100 2100 161 1 Rv2364c Era Probable GTP-binding protein Era In vitro essential (Sassetti 2003; Griffin 2011), non-essential in rich media (Minato 2019) Synonymous
2,658,676 0 0.998 4100 2250 9 3 Rv2379c MbtF Peptide synthetase MbtF (peptide synthase) Ala1137Val
2,659,542 0 0.951 4100 2100 161 1 Rv2379c MbtF Peptide synthetase MbtF (peptide synthase) Synonymous
2,682,593 0 0.998 4100 2250 9 3 Rv2388c HemN Probable oxygen-independent coproporphyrinogen III oxidase HemN (coproporphyrinogenase) (coprogen oxidase) Essential in murine spleen (Sassetti and Rubin, 2003) Ala184Thr
2,692,875 0 0.997 4100 2250 9 8 Rv2396 AprC Acid and phagosome regulated protein C, PE-PGRS family protein PE_PGRS41 Ser26Asn
2,760,147 0 0.951 4100 2100 161 1 Rv2458 MmuM Probable homocysteine S-methyltransferase MmuM (S-methylmethionine:homocysteine methyltransferase) (cysteine methyltransferase) Disruption provides growth advantage (DeJesus 2017) Synonymous
2,809,318 0 0.951 4100 2100 161 1 Rv2495c BkdC Probable branched-chain keto acid dehydrogenase E2 component BkdC Arg208Trp
2,812,742 0 0.951 4100 2100 161 1 Rv2498c CitE Probable citrate (pro-3S)-lyase (beta subunit) CitE (citrase) (citratase) (citritase) (citridesmolase) (citrase aldolase) Synonymous
2,817,446 0 0.997 4100 2250 9 8 Rv2502c AccD1 Probable acetyl-/propionyl-CoA carboxylase (beta subunit) AccD1 Essential in murine spleen (Sassetti and Rubin, 2003) Phe343Leu
2,912,516 0 0.998 4100 2250 9 3 Rv2585c Possible conserved lipoprotein Synonymous
2,927,291 0 0.993 4080 2250 9 21 Rv2598 Conserved hypothetical protein Disruption provides growth advantage (DeJesus 2017) Synonymous
2,932,890 0 0.951 4100 2100 161 1 Rv2605c TesB2 Probable acyl-CoA thioesterase II TesB2 (TEII) Phe85Leu
2,997,325 0 0.951 4100 2100 161 1 Rv2681 Conserved hypothetical alanine rich protein Required for growth on cholesterol (Griffin 2011) Ala196Val
3,032,137 0 0.951 4100 2100 161 1 Rv2720 LexA Repressor LexA Val117Ala
3,041,679 0 0.951 4100 2100 161 1 Rv2729c Probable conserved integral membrane alanine valine and leucine rich protein Ala266Val
3,042,353 0 0.997 4100 2250 9 8 Rv2729c Probable conserved integral membrane alanine valine and leucine rich protein Phe41Leu
3,055,922 0 0.997 4100 2250 9 8 Rv2742c Conserved hypothetical arginine rich protein Synonymous
3,140,153 0 0.998 4100 2250 9 4 Rv2833c UgpB Probable Sn-glycerol-3-phosphate-binding lipoprotein UgpB Ser111Ile
3,142,580 0 0.951 4100 2100 161 1 Rv2836c DinF Possible DNA-damage-inducible protein F DinF Pro350Leu
3,152,421 0 0.995 4090 2250 9 13 Rv2845c ProS Probable prolyl-tRNA synthetase ProS (proline–tRNA ligase) (PRORS) (global RNA synthesis factor) (proline translase) Essential in vitro (Minato 2019; DeJesus 2017; Griffin 2011; Sassetti 2003) and in murine spleen (Sassetti and Rubin 2003) His177Arg
3,157,785 0 0.951 4100 2100 161 1 Rv2849c CobO Probable cob(I)alamin adenosyltransferase CobO (corrinoid adenosyltransferase) (corrinoid adotransferase activity) Trp120Cys
3,158,719 0 0.997 4100 2250 9 8 Rv2850c Possible magnesium chelatase Gly446Ser
3,159,237 0 0.951 4100 2100 161 1 Rv2850c Possible magnesium chelatase Arg273Gln
3,174,591 0 0.951 4100 2100 161 1 Rv2862c Conserved hypothetical protein Arg18Pro
3,189,664 0 0.951 4100 2100 161 1 Rv2879c Conserved hypothetical protein Synonymous
3,198,332 0 0.951 4100 2100 161 1 Rv2889c Tsf Probable elongation factor Tsf (EF-ts) In vitro essential (Sassetti 2003; Griffin 2011; DeJesus 2017; Minato 2019) Thr259Met
3,213,089 0 0.951 4100 2100 161 1 Rv2903c LepB Probable signal peptidase I LepB (SPASE I) (leader peptidase I) In vitro essential (Sassetti 2003; Griffin 2011; DeJesus 2017; Minato 2019) Asp256Asn
3,223,303 0 0.997 4100 2250 9 8 Rv2914c PknI Probable transmembrane serine/threonine-protein kinase I PknI (protein kinase I) (STPK I) (phosphorylase B kinase kinase) (hydroxyalkyl-protein kinase) Required for growth on cholesterol (Griffin 2011), mutant shows increased growth in THP-1 cells, SCID mice show faster mortality with mutant (Gopalaswamy 2009) Synonymous
3,235,715 0 0.997 4100 2250 9 8 Rv2922c Smc Probable chromosome partition protein Smc Arg698Gly
3,254,695 0 0.951 4100 2100 161 1 Rv2932 PpsB Phenolpthiocerol synthesis type-I polyketide synthase PpsB In vitro essential in CDC1551 (Lamichhane 2003), not in H37Rv (Griffin 2011; DeJesus 2017; Minato 2019) Synonymous
3,262,628 0 0.951 4100 2100 161 1 Rv2934 PpsD Phenolpthiocerol synthesis type-I polyketide synthase PpsD Met127Ile
3,267,715 0 0.951 4100 2100 161 1 Rv2934 PpsD Phenolpthiocerol synthesis type-I polyketide synthase PpsD Glu1823Ala
3,282,079 0 0.951 4100 2100 161 1 Rv2940c Mas Probable multifunctional mycocerosic acid synthase membrane-associated Mas Ser213Cys
3,320,554 0 0.951 4100 2100 161 1 Rv2947c Pks15 Probable polyketide synthase Pks15, involved in the biosynthesis of phenolphthiocerol glycolipids Synonymous
3,355,417 0 0.997 4100 2250 9 9 Rv2997 Possible alanine rich dehydrogenase Cys107Ser
3,371,365 0 0.998 4100 2250 9 3 Rv3011c GatA Probable glutamyl-tRNA(GLN) amidotransferase (subunit A) GatA (Glu-ADT subunit A) In vitro essential (Sassetti 2003; Griffin 2011; DeJesus 2017; Minato 2019) Ala24Thr
3,388,682 0 0.951 4100 2100 161 1 Rv3029c FixA Probable electron transfer flavoprotein (beta-subunit) FixA (beta-ETF) (electron transfer flavoprotein small subunit) (ETFSS) In vitro essential (Sassetti 2003; Griffin 2011), non-essential in rich media (Minato 2019) Synonymous
3,517,567 0 0.997 4100 2250 9 8 Rv3151 NuoG Probable NADH dehydrogenase I (chain G) NuoG (NADH-ubiquinone oxidoreductase chain G) Synonymous
3,534,980 0 0.998 4100 2250 9 3 Rv3166c Conserved hypothetical protein Synonymous
3,540,144 0 0.951 4100 2100 161 1 Rv3171c Hpx Possible non-heme haloperoxidase Hpx Thr201Met
3,565,449 0 0.951 4100 2100 161 1 Rv3195 Conserved hypothetical protein Synonymous
3,594,851 0 0.997 4100 2250 9 8 Rv3218 Conserved protein Synonymous
3,595,427 0 0.951 4100 2100 161 1 Rv3218 Conserved protein Synonymous
3,624,710 0 0.951 4100 2100 161 1 Rv3244c LpqB Probable conserved lipoprotein LpqB In vitro essential (Sassetti 2003; Griffin 2011; DeJesus 2017; Minato 2019) Synonymous
3,664,615 0 0.951 4100 2100 161 1 Rv3282 Conserved hypothetical protein Ala133Ser
3,678,929 0 0.997 4100 2250 9 8 Rv3296 Lhr Probable ATP-dependent helicase Lhr (large helicase-related protein) Val719Met
3,690,854 0 0.951 4100 2100 161 1 Rv3303c LpdA NAD(P)H quinone reductase LpdA Thr29Ala
3,770,588 0 0.951 4100 2100 161 1 Rv3356c FolD Probable bifunctional protein FolD: methylenetetrahydrofolate dehydrogenase + methenyltetrahydrofolate cyclohydrolase In vitro essential (Sassetti 2003; Griffin 2011; DeJesus 2017; Minato 2019) Gln21Pro
3,857,161 0 0.951 4100 2100 161 1 Rv3437 Possible conserved transmembrane protein Disruption provides growth advantage (DeJesus 2017) Leu84Pro
3,877,256 0 0.998 4100 2250 9 3 Rv3456c RplQ 50S ribosomal protein L17 RplQ In vitro essential (Minato 2019; Griffin 2011) Synonymous
3,904,490 0 0.998 4100 2250 9 3 Rv3484 CpsA Possible conserved protein CpsA Essential in murine spleen (Sassetti and Rubin, 2003) Synonymous
3,907,958 0 0.997 4100 2250 9 8 Rv3488 Conserved hypothetical protein Gly98Arg
3,912,636 0 0.951 4100 2100 162 1 Rv3494c Mce4F Mce-family protein Mce4F Required for growth on cholesterol (Griffin 2011) Asp245Gly
3,924,350 0 0.951 4100 2100 161 1 Rv3505 FadE27 Probable acyl-CoA dehydrogenase FadE27 Ala218Val
3,977,910 0 0.997 4100 2250 9 8 Rv3538 Probable dehydrogenase. Possible 2-enoyl acyl-CoA hydratase Synonymous
3,987,645 0 0.997 4100 2250 9 8 Rv3548c Probable short-chain type dehydrogenase/reductase Required for growth on cholesterol (Griffin 2011) Met218Val
4,004,604 0 0.997 4100 2250 9 8 Rv3563 FadE32 Probable acyl-CoA dehydrogenase FadE32 Required for growth on cholesterol (Griffin 2011), essential in murine spleen (Sassetti and Rubin, 2003) Gln105Arg
4,034,908 0 0.951 4100 2100 161 1 Rv3593 LpqF Probable conserved lipoprotein LpqF In vitro essential (Sassetti 2003; Griffin 2011; Minato 2019) Asn186Ser
4,047,039 0 0.948 4100 2080 172 1 Rv3604c Probable conserved transmembrane protein rich in alanine and arginine and proline In vitro essential (Sassetti 2003; Griffin 2011; Minato 2019) Val153Gly
4,083,511 0 0.951 4100 2100 161 1 Rv3645 Probable conserved transmembrane protein In vitro essential (DeJesus 2017; Griffin 2011) Synonymous
4,090,661 0 0.997 4100 2250 9 8 Rv3649 Probable helicase Essential in murine spleen (Sassetti and Rubin, 2003) Synonymous
4,157,578 0 0.998 4100 2250 9 3 Rv3712 Possible ligase In vitro essential (Sassetti 2003; Griffin 2011; DeJesus 2017; Minato 2019) Gly200Ser
4,171,113 0 0.998 4100 2250 9 3 Rv3725 Possible oxidoreductase Disruption provides growth advantage (DeJesus 2017) Synonymous
4,242,970 0 0.951 4100 2100 161 1 Rv3793 EmbC Integral membrane indolylacetylinositol arabinosyltransferase EmbC (arabinosylindolylacetylinositol synthase) In vitro essential (Sassetti 2003; Goude 2008; Griffin 2011; DeJesus 2017; Minato 2019) Synonymous
4,278,968 0 0.951 4100 2100 161 1 Rv3813c Conserved protein n/a Met83Thr

GWAS results by treeWAS showing single nucleotide polymorphisms (coordinate relative to MTB H37Rv in SNP column) associated with classification of MTBC isolates as M. tuberculosis variant bovis (MBO). For SNPs within genes or ORFs, the classification and putative function is listed, as well as select information about essentiality by transposon mutagenesis studies from Mycobrowser [https://mycobrowser.epfl.ch/]