Table 5. Genes differentially regulated in the PittII Msf-KO strain compared to the WT strain that are associated with virulence or anaerobiosis.
| SGH-Array Cluster ID | WT-avg | KO-avg | FOLD | Bon pVal | ANNOTATION |
|---|---|---|---|---|---|
| cluster2470b | 13281 | 318 | -41.71 | <1E-16 | Tripeptide aminopeptidase (EC 3.4.11.4) |
| cluster2051k | 1247 | 49 | -25.47 | 2.08E-12 | SlrVA protein (macrophage survival factor, msfA), Sel1-like repeat |
| cluster2554 | 3054 | 160 | -19.11 | 5.08E-09 | Antiholin-like protein LrgA |
| cluster2197 | 15370 | 1139 | -13.49 | 2.08E-13 | lrgA-associated membrane protein LrgB |
| cluster3031 | 23039 | 1161 | -19.84 | <1E-16 | Putative oxidoreductase component of anaerobic de-hydrogenases; Chaperone protein TorD |
| cluster231a | 35163 | 2771 | -12.69 | <1E-16 | DmsC, Anaerobic dimethyl sulfoxide reductase chain C(EC 1.8.99.-) |
| cluster9 | 5634 | 453 | -12.44 | 2.08E-12 | Ferredoxin-type protein NapF (periplasmic nitrate reductase) |
| cluster2028 | 39430 | 3932 | -10.03 | <1E-16 | DmsB, Anaerobic dimethyl sulfoxide reductase chain B(EC 1.8.99.-) |
| cluster2113 | 34130 | 4302 | -7.93 | <1E-16 | DmsA, anaerobic dimethyl sulfoxide reductase chain A |
| cluster2142 | 21050 | 2728 | -7.72 | 5.27E-11 | Cytochrome c-type protein NrfB |
| cluster947 | 22732 | 3112 | -7.30 | 6.36E-10 | NrfC protein |
| cluster1427 | 23876 | 4006 | -5.96 | 1.32E-09 | NrfD formate-dependent nitrite reductase membrane component |
| cluster2328 | 42169 | 9033 | -4.67 | 2.84E-11 | Cytochrome c552 precursor (EC 1.7.2.2) NrfA |
| cluster599 | 3329 | 518 | -6.43 | 1.73E-03 | Molybdenum cofactor biosynthesis protein A, MoaA |
| cluster320 | 4404 | 1282 | -3.44 | 1.80E-06 | Molybdenum cofactor biosynthesis protein D; Molybdopterin converting factor subunit 1, MoaD |
| cluster47 | 7095 | 2493 | -2.85 | 8.78E-06 | Molybdenum cofactor biosynthesis protein C, MoaC |
| cluster581 | 11177 | 2113 | -5.29 | 2.54E-09 | ABC transporter involved in cytochrome c biogenesis ATPase component CcmA |
| cluster6 | 8347 | 1664 | -5.02 | 6.83E-09 | ABC transporter involved in cytochrome c biogenesis CcmB |
| cluster230 | 10899 | 2220 | -4.91 | 9.50E-07 | Cytochrome c-type biogenesis protein CcmD interacts with CcmCE |
| cluster544 | 7343 | 1624 | -4.52 | 1.98E-07 | Cytochrome c-type biogenesis protein CcmC putative heme lyase for CcmE |
| cluster1241 | 9123 | 2686 | -3.40 | 3.41E-07 | Cytochrome c heme lyase subunit CcmF |
| cluster1025 | 2451 | 863 | -2.84 | 3.82E-03 | Cytochrome c-type biogenesis protein CcmG/DsbE thiol:disulfide oxidoreductase |
| cluster419 | 22511 | 8061 | -2.79 | 1.88E-05 | Cytochrome c-type biogenesis protein CcmE heme chaperone |
| cluster735 | 6383 | 2438 | -2.62 | 6.88E-05 | Cytochrome c heme lyase subunit CcmL |
| cluster2103 | 6210 | 1306 | -4.75 | 1.64E-06 | Nitric oxide-dependent regulator DnrN or NorA |
| cluster2947b | 37123 | 9336 | -3.98 | 1.91E-10 | TorY, Cytochrome c-type protein |
| cluster3059 | 41761 | 15459 | -2.70 | 6.45E-08 | TorZ, Trimethylamine-N-oxide reductase (TMAO) (EC 1.6.6.9) |
| cluster3019 | 49753 | 20427 | -2.44 | 2.59E-07 | C4-dicarboxylate like transporter |
| cluster1162 | 25682 | 12292 | -2.09 | 2.30E-03 | Aerobic respiration control protein ArcA |
| cluster478 | 1553 | 26795 | 17.25 | 1.95E-11 | Candidate type III effector Hop protein |
| cluster2202 | 7564 | 34197 | 4.52 | 1.60E-05 | ATP-dependent hsl protease ATP-binding subunit HslU |
| cluster1261 | 2285 | 8453 | 3.70 | 5.63E-05 | Manganese superoxide dismutase (EC 1.15.1.1) SodA |
WT-avg and KO-avg: Average expression values for PittII WT and Msf-KO strains. FOLD defined as KO expression level relative to WT. Bon pVal: Bonferroni-corrected p-value. Genes in likely operons or found in tandem on the chromosome are grouped together and ordered roughly by the magnitude of fold changes.