Table 6 Genes identified by GWAS associated with fatty acid and cholesterol metabolism
SNP | p-value | score | G1P1 | G0P0 | G1P0 | G0P1 | Locus | Protein | Change | Description | Notes |
|---|---|---|---|---|---|---|---|---|---|---|---|
181,672 | 0 | 0.951 | 4100 | 2100 | 161 | 1 | Rv0153c | PtbB | Asp105Gly | Phosphotyrosine protein phosphatase PTPB (protein-tyrosine-phosphatase) (PTPase) | Required for growth on cholesterol (Griffin 2011) |
294,198 | 0 | 0.997 | 4100 | 2250 | 9 | 8 | Rv0244c | FadE5 | Glu479Ala | Probable acyl-CoA dehydrogenase FadE5 | Required for growth on cholesterol (Griffin 2011) |
1,684,979 | 0 | 0.948 | 4100 | 2080 | 172 | 1 | Rv1493 | MutB | Synonymous | Probable methylmalonyl-CoA mutase large subunit MutB (MCM) | Downstream in cholesterol to propionyl-CoA metabolic pathways (Wilburn 2018) |
1,754,572 | 0 | 0.951 | 4100 | 2100 | 161 | 1 | Rv1550 | FadD11 | Leu286Ser | Probable fatty-acid-CoA ligase FadD11 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase) | Â |
2,997,325 | 0 | 0.951 | 4100 | 2100 | 161 | 1 | Rv2681 | Â | Ala196Val | Conserved hypothetical alanine rich protein | Required for growth on cholesterol (Griffin 2011) |
3,223,303 | 0 | 0.997 | 4100 | 2250 | 9 | 8 | Rv2914c | PknI | Synonymous | 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) |
3,912,636 | 0 | 0.951 | 4100 | 2100 | 162 | 1 | Rv3494c | Mce4F | Asp245Gly | Mce-family protein Mce4F | Required for growth on cholesterol (Griffin 2011) |
3,924,350 | 0 | 0.951 | 4100 | 2100 | 161 | 1 | Rv3505 | FadE27 | Ala218Val | Probable acyl-CoA dehydrogenase FadE27 | Â |
3,987,645 | 0 | 0.997 | 4100 | 2250 | 9 | 8 | Rv3548c | Â | Met218Val | Probable short-chain type dehydrogenase/reductase | Required for growth on cholesterol (Griffin 2011) |
4,004,604 | 0 | 0.997 | 4100 | 2250 | 9 | 8 | Rv3563 | FadE32 | Gln105Arg | Probable acyl-CoA dehydrogenase FadE32 | Required for growth on cholesterol (Griffin 2011), essential in murine spleen (Sassetti and Rubin, 2003) |
3,254,695 | 0 | 0.951 | 4100 | 2100 | 161 | 1 | Rv2932 | PpsB | Synonymous | Phenolpthiocerol synthesis type-I polyketide synthase PpsB | In vitro essential in CDC1551 (Lamichhane 2003), not in H37Rv (Griffin 2011; DeJesus 2017; Minato 2019) |
3,262,628 | 0 | 0.951 | 4100 | 2100 | 161 | 1 | Rv2934 | PpsD | Met127Ile | Phenolpthiocerol synthesis type-I polyketide synthase PpsD | Â |
3,267,715 | 0 | 0.951 | 4100 | 2100 | 161 | 1 | Rv2934 | PpsD | Glu1823Ala | Phenolpthiocerol synthesis type-I polyketide synthase PpsD | Â |
3,320,554 | 0 | 0.951 | 4100 | 2100 | 161 | 1 | Rv2947c | Pks15 | Synonymous | Probable polyketide synthase Pks15, involved in the biosynthesis of phenolphthiocerol glycolipids | Â |