TABLE 2.
Significant S. aureus pathways for survival within untreated and/or IL-10-treated HMDMsa
| Untreated | IL-10 | Outgrowth | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| S. aureus— REFLIST (2,889) | Essential genes (396) | Fold enrichment | q-value | Essential genes (439) | Fold enrichment | q-value | Essential genes (364) | Fold enrichment | q-value | |
| Untreated unique essential pathways | ||||||||||
| Purine nucleobase biosynthetic process (GO:0009113) | 5 | 5 | 7.3 | 0.040* | 5 | 6.58 | 0.060 | 4 | 6.35 | 0.105 |
| Nucleotide salvage (GO:0043173) | 7 | 6 | 6.25 | 0.026* | 4 | 3.76 | 0.301 | 2 | 2.27 | 0.758 |
| Pyrimidine nucleobase biosynthetic process (GO:0019856) | 8 | 6 | 5.47 | 0.040* | 5 | 4.11 | 0.164 | 5 | 4.96 | 0.092 |
| Purine nucleoside triphosphate biosynthetic process (GO:0009145) | 10 | 7 | 5.11 | 0.026* | 6 | 3.95 | 0.116 | 6 | 4.76 | 0.057 |
| Cellular metabolic compound salvage (GO:0043094) | 11 | 7 | 4.64 | 0.037* | 5 | 2.99 | 0.308 | 3 | 2.16 | 0.793 |
| DNA duplex unwinding (GO:0032508) | 15 | 8 | 3.89 | 0.041* | 7 | 3.07 | 0.160 | 7 | 3.7 | 0.073 |
| RNA phosphodiester bond hydrolysis (GO:0090501) | 18 | 9 | 3.65 | 0.034* | 9 | 3.29 | 0.061 | 7 | 3.09 | 0.136 |
| Tetrapyrrole metabolic process (GO:0033013) | 19 | 9 | 3.46 | 0.043* | 8 | 2.77 | 0.160 | 8 | 3.34 | 0.071 |
| RNA modification (GO:0009451) | 47 | 17 | 2.64 | 0.016* | 13 | 1.82 | 0.317 | 11 | 1.86 | 0.464 |
| Cellular response to DNA damage stimulus (GO:0006974) | 57 | 19 | 2.43 | 0.021* | 14 | 1.62 | 0.510 | 10 | 1.39 | 0.836 |
| Cellular response to stress (GO:0033554) | 77 | 24 | 2.27 | 0.011* | 19 | 1.62 | 0.361 | 14 | 1.44 | 0.671 |
| DNA metabolic process (GO:0006259) | 121 | 32 | 1.93 | 0.016* | 27 | 1.47 | 0.432 | 20 | 1.31 | 0.772 |
| Cellular response to stimulus (GO:0051716) | 132 | 34 | 1.88 | 0.016* | 28 | 1.4 | 0.544 | 18 | 1.08 | 1.000 |
| Response to stress (GO:0006950) | 117 | 30 | 1.87 | 0.030* | 24 | 1.35 | 0.650 | 18 | 1.22 | 0.949 |
| Response to stimulus (GO:0050896) | 199 | 47 | 1.72 | 0.013* | 41 | 1.36 | 0.409 | 28 | 1.12 | 1.000 |
| IL-10 unique essential pathways | ||||||||||
| mRNA metabolic process (GO:0016071) | 7 | 4 | 4.17 | 0.212 | 6 | 5.64 | 0.044* | 4 | 4.54 | 0.195 |
| rRNA metabolic process (GO:0016072) | 29 | 11 | 2.77 | 0.058 | 13 | 2.95 | 0.029* | 10 | 2.74 | 0.079 |
| Negative regulation of macromolecule metabolic process (GO:0010605) | 36 | 12 | 2.43 | 0.101 | 16 | 2.92 | 0.011* | 10 | 2.2 | 0.228 |
| Negative regulation of macromolecule biosynthetic process (GO:0010558) | 30 | 10 | 2.43 | 0.168 | 13 | 2.85 | 0.033* | 9 | 2.38 | 0.247 |
| Negative regulation of metabolic process (GO:0009892) | 37 | 12 | 2.37 | 0.111 | 16 | 2.85 | 0.020* | 10 | 2.15 | 0.236 |
| Negative regulation of biological process (GO:0048519) | 39 | 12 | 2.24 | 0.131 | 16 | 2.7 | 0.025* | 10 | 2.04 | 0.377 |
| Untreated and IL-10 shared essential pathways | ||||||||||
| Purine nucleobase metabolic process (GO:0006144) | 6 | 6 | 7.3 | 0.017* | 6 | 6.58 | 0.031* | 4 | 5.29 | 0.152 |
| Translational elongation (GO:0006414) | 7 | 6 | 6.25 | 0.027* | 6 | 5.64 | 0.044* | 5 | 5.67 | 0.067 |
| rRNA processing (GO:0006364) | 28 | 11 | 2.87 | 0.050* | 12 | 2.82 | 0.045* | 10 | 2.83 | 0.069 |
| Regulation of biological process (GO:0050789) | 224 | 51 | 1.66 | 0.012* | 57 | 1.67 | 0.009* | 44 | 1.56 | 0.061 |
| Outgrowth unique essential pathways | ||||||||||
| Pyridine-containing compound biosynthetic process (GO:0072525) | 6 | 5 | 6.08 | 0.059 | 5 | 5.48 | 0.089 | 5 | 6.61 | 0.045* |
| Folic acid-containing compound biosynthetic process (GO:0009396) | 6 | 4 | 4.86 | 0.173 | 5 | 5.48 | 0.089 | 5 | 6.61 | 0.045* |
| Regulation of translational fidelity (GO:0006450) | 11 | 6 | 3.98 | 0.101 | 6 | 3.59 | 0.152 | 7 | 5.05 | 0.025* |
| Ribonucleoprotein complex subunit organization (GO:0071826) | 11 | 2 | 1.33 | 1.000 | 5 | 2.99 | 0.309 | 7 | 5.05 | 0.025* |
| Ribosome assembly (GO:0042255) | 13 | 2 | 1.12 | 1.000 | 7 | 3.54 | 0.105 | 8 | 4.88 | 0.015* |
| RNA biosynthetic process (GO:0032774) | 20 | 9 | 3.28 | 0.054 | 8 | 2.63 | 0.186 | 11 | 4.37 | 0.005* |
| Organelle assembly (GO:0070925) | 15 | 2 | 0.97 | 1.000 | 7 | 3.07 | 0.158 | 8 | 4.23 | 0.027* |
| Purine nucleoside diphosphate metabolic process (GO:0009135) | 16 | 7 | 3.19 | 0.126 | 8 | 3.29 | 0.088 | 8 | 3.97 | 0.035* |
| DNA-templated transcription (GO:0006351) | 16 | 6 | 2.74 | 0.243 | 5 | 2.06 | 0.686 | 8 | 3.97 | 0.034* |
| Protein-containing complex organization (GO:0043933) | 23 | 6 | 1.9 | 0.588 | 10 | 2.86 | 0.079 | 11 | 3.8 | 0.010* |
| Protein-containing complex assembly (GO:0065003) | 19 | 4 | 1.54 | 0.756 | 8 | 2.77 | 0.159 | 9 | 3.76 | 0.027* |
| Fatty acid metabolic process (GO:0006631) | 29 | 11 | 2.77 | 0.059 | 10 | 2.27 | 0.220 | 13 | 3.56 | 0.006* |
a
A statistical overrepresentation test using S. aureus essential gene lists from untreated or IL-10-treated HMDMs, shared between untreated and IL-10-treated HMDMs, and outgrowth control was performed in PANTHER using PANTHER GO Biological Process Complete pathways (FDR-adjusted P-value < 0.01; Fisher’s exact test). REFLIST, S. aureus reference gene list.