TABLE 3.
RHA1 genes involved in EG catabolism and MFT biosynthesis
| Gene | ORFa | Gene product | Closest characterized homologb | IDc (%) | FCd (EG) | Refe |
|---|---|---|---|---|---|---|
| EG catabolism and regulation | ||||||
| madA | RS29605 | MFT-dependent alcohol dehydrogenase | Mno, M. smegmatis mc2155 (A0R5M3) | 92 | 482 | (27) |
| madB | RS29610 | MoxR family ATPase | None | - | 389 | - |
| madC | RS29615 | VWA domain-containing protein | None | - | 302 | - |
| madD | RS29620 | Iron-dependent alcohol dehydrogenase | ErcA, Pseudomonas aeruginosa PAO1 (Q9I2B8) | 42 | 7 | (46) |
| madS | RS29625 | Sensor histidine kinase | MnoS, M. smegmatis mc2155 (A0R5L9) | 60 | 10 | (29) |
| madR | RS29630 | Response regulator transcription factor | MnoR, M. smegmatis mc2155 (A0R5L8) | 76 | 8 | (29) |
| Glyoxylate catabolism, GCL1 pathway | ||||||
| garK1 | RS12580 | Glycerate kinase | GlxK/GarK, E. coli K-12 (P77364/P23524) | 40 | 69 | (47, 48) |
| gcl1 | RS12585 | Glyoxylate carboligase | Gcl, E. coli K-12 (P0AEP8) | 73 | 78 | (47) |
| glxR1 | RS12590 | Tartronate semialdehyde reductase | GlxR, Streptomyces coelicolor (Q9Z597) | 60 | 161 | (49) |
| hyi1 | RS12595 | Hydroxypyruvate isomerase | Hyi, S. coelicolor (Q9Z596) | 53 | 133 | (49) |
| Glycolate/glyoxylate catabolism, GCL2 pathway | ||||||
| gcl2 | RS15645 | Glyoxylate carboligase | Gcl, E. coli K-12 (P0AEP8) | 72 | 1186 | (47) |
| glxR2 | RS15650 | Tartronate semialdehyde reductase | GlxR, S. coelicolor (Q9Z597) | 61 | 426 | (49) |
| hyi2 | RS15655 | Hydroxypyruvate isomerase | Hyi, S. coelicolor (Q9Z596) | 52 | 459 | (49) |
| glcD | RS15665 | FAD-linked oxidase | GlcD, (P0AEP9, E. coli K-12) | 39 | 165 | (50) |
| garK2 | RS15675 | Glycerate kinase | GlxK/GarK, E. coli K-12 (P77364/P23524) | 39 | 174 | (47, 48) |
| Mycofactocin (MFT) biosynthesis | ||||||
| mftR | RS29670 | MFT system transcriptional regulator | MftR, M. smegmatis mc2155 (A0QSB5) | 52 | 2 | (28) |
| mftA | RS45350 | MFT precursor | MftA, M. smegmatis mc2155 (A0QSB6) | 77 | 6 | (28) |
| mftB | RS29675 | MFT biosynthesis chaperone | MftB, M. smegmatis mc2155 (A0QSB7) | 64 | 4 | (28) |
| mftC | RS29680 | MFT radical SAM maturase | MftC, M. smegmatis mc2155 (A0QSB8) | 77 | 3 | (28) |
| mftD | RS29685 | MFT biosynthesis FMN-dependent deaminase | MftD, M. smegmatis mc2155 (A0QSB9) | 75 | 4 | (28) |
| mftH | RS29690 | MFT system FadH/OYE family oxidoreductase 1 | DgcA, P. aeruginosa PAO1 (Q9HTG6) | 28 | 7 | (51) |
| mftI | RS29695 | MFT-coupled SDR family oxidoreductase | Rv0687, Mtb H37Rv (P9WGS7) | 58 | 6 | (33) |
| mftJ | RS29700 | MFT system FadH/OYE family oxidoreductase 2 | DgcA, P. aeruginosa PAO1 (Q9HTG6) | 33 | 6 | (51) |
| mftE | RS29705 | MFT biosynthesis peptidyl-dipeptidase | MftE, M. smegmatis mc2155 (A0QSC0) | 58 | 1 | (28) |
| mftF | RS29710 | MFT biosynthesis glycosyltransferase | MftF, M. smegmatis mc2155 (A0QSC1) | 55 | 1 | (28) |
| mftG | RS29715 | MFT system GMC family oxidoreductase | None | - | 2 | - |
a
The prefix RHA1 was omitted for simplicity.
b
Closest homolog with an experimentally verified function (species, gene identifier). Rv0687, uncharacterized short-chain dehydrogenase with solved structure.
c
Percent amino acid sequence identity calculated over the entire length of the proteins.
d
Fold-change during growth on EG versus acetate (padj <0.0001). ND, not detected.
e
Reference.