TABLE 3.
Relative expression of D. alaskensis G20 operons involved in specific cellular functions that were highly expressed during syntrophya
| Operon range | Operon annotation | Expression fold change vs axenic G20 |
Avg normalized expression |
|||
|---|---|---|---|---|---|---|
| Coculture with S. aciditrophicus | Coculture with S. wolfei | On H2-SO42− | S. aciditrophicus coculture | Lactate SO42− | ||
| Flagellum-related genes | ||||||
| Dde_0350-56 | Fli flagellar components | 18.74 | 5.76 | 1.19 | 31.7 | 1.69 |
| Dde_0378-86 | Flh flagellar biosynthesis proteins | 2.32 | 1.35 | 0.82 | 8.65 | 3.72 |
| Dde_1119-20 | Fli flagellar components | 5.33 | 2.05 | 1.09 | 9.98 | 1.87 |
| Dde_1501 | Flagellin | 4.53 | 1.63 | 0.69 | 7.03 | 1.55 |
| Dde_1502 | Flagellin | 3.08 | 1.9 | 1.27 | 57.5 | 18.6 |
| Dde_1570 | Flagellin | 21.7 | 8.6 | 4.24 | 28.8 | 1.32 |
| Dde_1709 | Flagellin | 10.14 | 3.91 | 1.06 | 62.8 | 6.2 |
| Dde_2705-08 | Fli flagellar protein | 3.7 | 1.06 | 0.9 | 5.85 | 1.58 |
| Dde_3149-59 | Flg flagellar components operon | 11.0 | 3.54 | 1.09 | 22.2 | 2.02 |
| Dde_3582-90 | Fli flagellar biosynthesis proteins | 6.35 | 3.06 | 1.04 | 8.21 | 1.29 |
| Chemotaxis-related genes | ||||||
| Dde_0281 | Chemotaxis protein | 2.29 | 0.68 | 0.70 | 7.63 | 3.33 |
| Dde_0369 | Methyl-accepting chemotaxis protein | 2.37 | 0.23 | 0.89* | 1.40 | 0.59 |
| Dde_1322 | Methyl-accepting chemotaxis protein | 1.69 | 1.27* | 1* | 1.05 | 0.62 |
| Dde_1665 | Methyl-accepting chemotaxis protein | 2.07 | 1.57 | 1.68 | 3.25 | 1.57 |
| Dde_2411 | Chemoreceptor protein A | 1.82 | 1.87 | 1.23 | 1.89 | 1.04 |
| Dde_2814 | Methyl-accepting chemotaxis protein | 1.56 | 1.63 | 1.22 | 1.32 | 0.85 |
| Dde_2857 | Chemoreceptor protein A | 2.19 | 2.06 | 1.32 | 27.1 | 12.3 |
| Dde_2968 | Methyl-accepting chemotaxis protein | 2.03 | 2.22 | 0.93* | 1.34 | 0.66 |
| Biofilm-, pilus-, and cell surface-related genes | ||||||
| Dde_0215-17 | Glycosyltransferase | 2.22 | 1.09 | 0.84 | 3.11 | 1.40 |
| Dde_0337 | Glycosyltransferase, group 1 family | 2.01 | 0.53 | 0.68* | 2.04 | 1.01 |
| Dde_0425–28 | Glycosyltransferase operon with a GDP-fucose synthetase | 3.97 | 1.45 | 0.72 | 4.65 | 1.17 |
| Dde_0438-39 | Glycosyl or glycerophosphate transferase | 13.97 | 6.03 | 1.14 | 24.3 | 1.74 |
| Dde_0590 | Cardiolipin synthase | 1.32* | 1.08* | 1.05* | 0.98 | 0.75 |
| Dde_3224-26 | Phage shock protein | 25.7 | 33.4 | 1.03 | 23.1 | 0.90 |
| Dde_2358-70 | Tad pilus operon | 2.6* | 1.7* | 0.95* | 0.30 | 0.12 |
| Alcohol dehydrogenase- heterodisulfide reductase | ||||||
| Dde_3523 | Alcohol dehydrogenase, iron-containing | 260.3 | 60.81 | 11.60 | 118.7 | 0.46 |
| Dde_3524-30 | Heterodisulfide reductase | 79.8 | 12.2 | 4.5 | 7.61 | 0.095 |
| Hydrogenases | ||||||
| Dde_0656-57 | Fe-S cluster binding proteins | 10.78 | 4.24 | 1.87 | ||
| Dde_0081-82 | Hydrogenase (Fe-only) | 0.87 | 0.93 | 10.5 | 0.25 | 0.29 |
| Dde_2134-35 | Hydrogenase (Ni-Fe-Se) | 0.78 | 1.23 | 3.79 | 7.59 | 9.69 |
| Dde_2137-38 | Hydrogenase (Ni-Fe) | 43.56 | 47.13 | 5.17 | 12.5 | 0.29 |
| Dde_3754-56 | Hydrogenase (Ni-Fe) | 5.92 | 3.30 | 1.10 | 0.76 | 0.13 |
| Formate dehydrogenases | ||||||
| Dde_0678-83 | Rhodanese/formate dehydrogenase/oxidoreductase operon | 22.39 | 11.58 | 3.43 | 2.68 | 0.12 |
| Dde_0706-09 | Formate dehydrogenase formation protein | 8.90 | 6.81 | 2.66 | 4.74 | 0.53 |
| Dde_0715-18 | Formate dehydrogenase operon | 46.07 | 31.33 | 6.05 | 17.8 | 0.39 |
a
The relative expression for multiple gene operons was determined as the average change for all of the genes in the operon when grown with S. wolfei, with S. aciditrophicus, or in pure culture on H2-sulfate relative to growth in pure culture on lactate-sulfate. *, a ratio calculated where both samples being compared have low expression (<1 normalized read) values.