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

Table 3.

SNPs concordantly significantly associated with classification as MBO by Subsequent and Simultaneous statistical tests

SNP p-value score G1P1 G0P0 G1P0 G0P1 Locus Protein Description Essentiality Notes from Mycobrowser
147,873 0 1 4100 2250 9 3 Intergenic, upstream of elongation factor G FusA2 (Rv0120c) n/a
184,727 0 1 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) n/a
268,277 0 1 4100 2250 9 3 Rv0224c Possible methyltransferase (methylase) In vitro essential per multiple studies (Minato 2019; DeJesus 2017; Sassetti 2003; Griffin 2011)
277,862 0 1 4100 2250 9 3 Intergenic, downstream of FadE4 (Rv0231) and upstream of probable transcriptional regulatory protein (probably TetR/AcrR-family) (Rv0232) n/a
1,234,657 0 1 4100 2250 9 3 Rv1108c XseA Probable exodeoxyribonuclease VII (large subunit) XseA (exonuclease VII large subunit) n/a
1,478,312 0 1 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)
1,499,291 0 1 4100 2250 9 4 Rv1330c PncB1 Nicotinic acid phosphoribosyltransferase PncB1 n/a
1,739,294 0 1 4100 2250 9 3 Rv1536 IleS Isoleucyl-tRNA synthetase IleS In vitro essential per multiple studies (Minato 2019; DeJesus 2017; Lamichhane 2003; Griffin 2011)
1,830,295 0 1 4100 2250 9 3 Rv1628c Conserved protein n/a
2,475,888 0 1 4100 2250 9 3 Rv2210c IlvE Branched-chain amino acid transaminase IlvE In vitro essential (DeJesus 2017; Sassetti 2003; Griffin 2011), non-essential in rich media (Minato 2019)
2,528,773 0 1 4100 2250 9 3 Rv2254c Probable integral membrane protein n/a
2,658,676 0 1 4100 2250 9 3 Rv2379c MbtF Peptide synthetase MbtF (peptide synthase) n/a
2,682,593 0 1 4100 2250 9 3 Rv2388c HemN Probable oxygen-independent coproporphyrinogen III oxidase HemN (coproporphyrinogenase) (coprogen oxidase) Essential in murine spleen (Sassetti and Rubin, 2003)
2,912,516 0 1 4100 2250 9 3 Rv2585c Possible conserved lipoprotein n/a
2,927,291 0 1 4080 2250 9 21 Rv2598 Conserved hypothetical protein n/a
3,140,153 0 1 4100 2250 9 4 Rv2833c UgpB Probable Sn-glycerol-3-phosphate-binding lipoprotein UgpB Disruption provides growth advantage (DeJesus 2017)
3,371,365 0 1 4100 2250 9 3 Rv3011c GatA Probable glutamyl-tRNA(GLN) amidotransferase (subunit A) GatA (Glu-ADT subunit A) In vitro essential per multiple studies (Minato 2019; DeJesus 2017; Sassetti 2003; Griffin 2011)
3,534,980 0 1 4100 2250 9 3 Rv3166c Conserved hypothetical protein n/a
3,877,256 0 1 4100 2250 9 3 Rv3456c RplQ 50S ribosomal protein L17 RplQ In vitro essential (Minato 2019; Griffin 2011), or mutant shows growth defect (DeJesus 2017)
3,904,490 0 1 4100 2250 9 3 Rv3484 CpsA Possible conserved protein CpsA Essential in murine spleen (Sassetti and Rubin, 2003)
4,157,578 0 1 4100 2250 9 3 Rv3712 Possible ligase In vitro essential per multiple studies (Minato 2019; DeJesus 2017; Sassetti 2003; Griffin 2011)
4,171,113 0 1 4100 2250 9 3 Rv3725 Possible oxidoreductase Disruption provides growth advantage (DeJesus 2017)

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/]. This list is a subset of only variants called in both Tables 1 and 2