TABLE 2.
Top genes exhibiting mutualism-abolished fitness defectsa
| Gene | Gene product/general roleb | Monoculture |
Nx coculture |
NxΔAmtB coculture |
||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Fitness score |
|Mean t-score| | Fitness score |
|Mean t-score| | Fitness score |
|Mean t-score| | |||||
| Mean | SD | Mean | SD | Mean | SD | |||||
| purH | Purine biosynthesis | –4.38 | 0.17 | 21.62 | 0.27 | 0.15 | 2.14 | –0.18 | 0.27 | 1.53 |
| sucD | Succinyl-CoA synthetase subunit | –4.14 | 0.76 | 5.69 | –0.93 | 0.26 | 2.45 | –0.44 | 0.13 | 1.24 |
| purF | Purine biosynthesis | –4.02 | 0.78 | 11.85 | –0.71 | 0.19 | 3.35 | –0.20 | 0.11 | 1.18 |
| purD | Purine biosynthesis | –3.91 | 0.28 | 16.73 | –0.02 | 0.13 | 0.06 | 0.08 | 0.13 | 0.55 |
| sucC | Succinyl-CoA synthetase subunit | –3.81 | 0.11 | 10.47 | –0.89 | 0.43 | 4.51 | –0.14 | 0.15 | 0.79 |
| purL | Purine biosynthesis | –3.77 | 0.06 | 18.86 | 0.50 | 0.09 | 3.70 | 0.03 | 0.13 | 0.21 |
| purK | Purine biosynthesis | –3.70 | 0.53 | 13.84 | 1.45 | 0.17 | 9.73 | 0.17 | 0.24 | 1.13 |
| purE | Purine biosynthesis | –3.68 | 0.34 | 6.70 | 1.13 | 0.26 | 5.00 | 0.23 | 0.22 | 0.96 |
| purM | Purine biosynthesis | –3.54 | 0.38 | 9.72 | 0.06 | 0.16 | 0.31 | 0.05 | 0.07 | 0.21 |
| purC | Purine biosynthesis | –3.23 | 0.42 | 4.95 | 1.32 | 0.18 | 4.24 | 0.39 | 0.19 | 1.44 |
| pdxJ | Vitamin B6 biosynthesis | –3.06 | 0.44 | 8.89 | –0.91 | 0.26 | 2.83 | –0.52 | 0.11 | 2.19 |
| pdxA | Vitamin B6 biosynthesis | –2.95 | 0.09 | 15.11 | –0.94 | 0.40 | 5.73 | –0.18 | 0.15 | 1.36 |
| eda | KHG/KDPG aldolase | –2.78 | 0.33 | 4.25 | 1.32 | 0.35 | 3.88 | –0.51 | 0.38 | 1.22 |
| gcvR | Transcriptional regulator | –2.76 | 0.35 | 8.30 | –0.63 | 0.16 | 2.92 | –0.53 | 0.22 | 2.63 |
| ptsG | Glucose transport | –2.55 | 0.26 | 13.72 | 1.00 | 0.23 | 7.38 | 0.11 | 0.08 | 0.78 |
| pdxB | Vitamin B6 biosynthesis | –2.51 | 0.29 | 12.70 | –0.71 | 0.42 | 4.03 | –0.09 | 0.03 | 0.63 |
| argD | Arginine/ornithine biosynthesis | –1.98 | 0.11 | 15.35 | –0.50 | 0.04 | 4.07 | –0.25 | 0.05 | 2.14 |
| ptsN | Phosphotransferase system enzyme | –1.84 | 0.12 | 7.28 | 0.91 | 0.32 | 4.59 | –0.74 | 0.18 | 3.33 |
| pgl | 6-Phosphogluconolactonase | –1.49 | 0.61 | 4.46 | 1.38 | 0.21 | 5.37 | 0.04 | 0.26 | 0.17 |
| spoT | (p)ppGpp synthase/hydrolase | –1.43 | 0.07 | 6.83 | 1.45 | 0.12 | 8.32 | –0.35 | 0.36 | 1.75 |
| nadA | NAD biosynthesis | –1.39 | 0.24 | 6.90 | –0.07 | 0.17 | 0.41 | –0.03 | 0.07 | 0.15 |
a
Genes had negative fitness scores in monoculture but negligible effects or positive fitness scores in one or both cocultures (based on our thresholds of |mean fitness| > 1 and |mean t-score| > 3). The top genes were identified as sorted by mean fitness score in monoculture.
b
More detailed descriptions are provided in Table S3.