TABLE 3.
Influence of graR* expression on up- and down-regulated genes in VISA strain Mu50 relative to hetero-VISA strain Mu3
| N315 ORFID | Gene name | Producta | Ratio of transcripts between strains of indicated combinationb
|
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Mu50/Mu3 | Mu3(pgraR*)/Mu3(pgraRn) | Mu3(pgraR*)/Mu3(pYT3) | Mu3(pgraRn)/Mu3(pYT3) | Mu3ΔgraSR/Mu3 | Mu50/N315 | N315(pgraR*)/N315(pgraRn) | N315(pgraR*)/N315(pYT3) | N315ΔgraSR/N315 | Relative amt of transcriptsc | |||
| Up-regulated | ||||||||||||
| SA0616 | vraF | ABC transporter ATP-binding protein | 2.92 | 5.43 | 12.6 | 1.59 | 0.89 | 3.4 | 2.53 | 1.35 | 1.16 | Mu50 > Mu3 = N315 |
| SA0617 | vraG | ABC transporter permease | 2.26 | 4.48 | 9.98 | 1.6 | 0.81 | 5.71 | 2.55 | 1.36 | 1.24 | Mu50 > Mu3 > N315 |
| SA2493 | vraE | HP similar to ABC transporter permease | 2.16 | 13.9 | 6.04 | 0.5 | 1.39 | 66.9 | 3.91 | 7.05 | 1.63 | Mu50 > Mu3 ≫ N315 |
| SAS091 | HP | 2.06 | 3.5 | 1.84 | 0.58 | 0.79 | 13.7 | 2.84 | 0.02 | 1.45 | Mu50 > Mu3 ≫ N315 | |
| SA1713 | HP similar to RNA methyltransferase | 1.99 | 1.08 | 0.1 | 1.08 | 1.21 | 0.98 | 1.05 | 0.69 | 1.23 | Mu50 > Mu3 = N315 | |
| SA1193 | mprF | Lysylphospha-tidylglycerol synthetase | 1.88 | 2.79 | 7.48 | 2.38 | 0.49 | 1.8 | 1.79 | 0.83 | 0.67 | Mu50 > Mu3 = N315 |
| SA1710 | HP similar to DNA polymerase III, alpha chain PolC type | 1.87 | 1.09 | 1.29 | 0.74 | 1.49 | 3.89 | 0.99 | 0.61 | 0.91 | Mu50 > Mu3 > N315 | |
| SA1149 | glnR | Glutamine synthetase repressor | 1.85 | 2.6 | 12.9 | 1.16 | 0.82 | 3.23 | 1.33 | 1.05 | 1.4 | Mu50 > Mu3 = N315 |
| SA1030 | CHP | 1.84 | 1.41 | 1.21 | 1.06 | 0.82 | 1.03 | 1.8 | 0.48 | 0.79 | Mu50 = N315 > Mu3 | |
| SA1082 | rimM | Probable 16S rRNA-processing protein | 1.8 | 0.74 | 1 | 0.91 | 1.19 | 0.72 | 0.84 | 0.72 | 1.44 | Mu50 = N315 > Mu3 |
| SA2492 | vraD | HP similar to ABC transporter ATP-binding protein | 1.74 | 21 | 6.66 | 0.77 | 0.18 | 13.5 | 4.04 | 2.23 | 0.57 | Mu50 > Mu3 ≫ N315 |
| SA1690 | CHP | 1.74 | 0.89 | 1.26 | 1.07 | 0.93 | 0.57 | 1.26 | 0.45 | 0.83 | N315 > Mu50 > Mu3 | |
| SA0962 | CHP | 1.73 | 1.02 | 1.92 | 1.13 | 0.55 | 3.28 | 1.37 | 0.52 | 0.87 | Mu50 > Mu3 > N315 | |
| SA1633 | HP similar to beta-lactamase | 1.73 | 1.34 | 0.99 | 0.63 | 1.23 | 2.13 | 0.65 | 0.29 | 1.22 | Mu50 > Mu3 > N315 | |
| Reference genes | ||||||||||||
| SA2431 | isaB | Immunodominant antigen B | 1.21 | 5.25 | 1.9 | 1.76 | 0.78 | 0.79 | 1.69 | 1.1 | 0.56 | Mu50 = Mu3 = N315 |
| SA0615 | graS | HP similar to two-component sensor histidine kinase | 1.16 | 1.98 | 1.63 | 1.68 | 0.002 | 0.66 | 1.36 | 1.14 | 0.002 | Mu50 = Mu3 = N315 |
| SA0614 | graR | HP similar to two-component response regulator | 1.1 | 1.44 | 16.1 | 29.1 | 0.093 | 0.73 | 1.17 | 10.3 | 0.001 | Mu50 = Mu3 = N315 |
| SA1701 | vraS | Two-component sensor histidine kinase | 1.1 | 1.27 | 0.84 | 1.05 | 0.89 | 1.97 | 1.53 | 0.74 | 0.71 | Mu50 = Mu3 > N315 |
| SA1700 | vraR | Two-component response regulator | 1.05 | 1.12 | 1.5 | 0.99 | 0.81 | 2.69 | 1.19 | 0.55 | 0.64 | Mu50 = Mu3 > N315 |
| Down-regulated | ||||||||||||
| SA0055 | CHP | 0.37 | 1.27 | 0.15 | 0.94 | 0.45 | EXd | 0.87 | EX | EX | ||
| SA0058 | ccrA | Cassette chromosome recombinase A | 0.44 | 1.04 | 1.56 | 0.94 | 1.07 | EX | 1.02 | 0.04 | EX | |
| SA0108 | sarH1 (sarS) | Staphylococcal accessory regulator A homologue | 0.45 | 0.74 | 0.6 | 0.83 | 1.01 | 0.26 | 0.88 | 0.41 | 0.54 | N315 > Mu3 > Mu50 |
| SA0107 | spa | Immunoglobulin G binding protein A precursor | 0.47 | 0.75 | 0.45 | 0.77 | 1.03 | 0.29 | 0.65 | 0.57 | 0.59 | N315 > Mu3 > Mu50 |
a
HP, hypothetical protein; CHP, conserved hypothetical protein.
b
Boldface indicates values either significant (<0.5 or >1.7) or referred to in the text.
c
>, greater than 1.7-fold; ≫, greater than 2.89 (1.7 × 1.7)-fold; =, comparable; based on the experiments with Mu50/Mu3 and Mu50/N315.
d
EX, excluded. Both the Cy3 and Cy5 signals were less than 0.1.