TABLE 2.
Comparison of gene expression in F. novicida ΔpmrA and wild-type F. novicida, determined by microarray analysis and qRT-PCR
| F. tularensis Schu S4 open reading frame | Gene or gene product identity or function | Fold change (mean ± SD) by:
|
|
|---|---|---|---|
| Microarray analysis | qRT-PCR | ||
| Genes downregulated in ΔpmrA mutant | |||
| 03c | Conserved hypothetical membrane protein | 1.86 | NAa |
| 05 | Succinate-semialdehyde dehydrogenase | 1.53 | NA |
| 029c | Hypothetical protein | 2.58 | 4.89 ± 0.45 |
| 070c | Major facilitator superfamily transport protein | 2.07 | NA |
| 097 | Hypothetical protein | 1.62 | NA |
| 174 | YggT family protein | 1.62 | NA |
| 177c | Acetyltransferase | 2.34 | NA |
| 224c | Pseudogene | 1.71 | NA |
| 254c | Hypothetical protein | 2.13 | NA |
| 267 | Hypothetical protein | 2.05 | NA |
| 383 | Hypothetical protein | 2.38 | NA |
| 403 | Peptide deformylase | 2.19 | NA |
| 421 | Pseudogene | 1.74 | NA |
| 514 | Pseudogene | 1.62 | NA |
| 573 | Alanine racemase | 1.62 | NA |
| 611c | Beta-lactamase | 3.59 | NA |
| 613c | Hypothetical protein | 2.34 | NA |
| 726c | Glycerophosphoryl diester phosphodiesterase family protein | 2.41 | NA |
| 866c | Pseudogene | 1.86 | NA |
| 988 | Hypothetical protein | 2.52 | NA |
| 1000c | Cobalamin synthesis protein P47K family protein | 2.34 | NA |
| 1012 | Pseudogene | 2.05 | NA |
| 1032 | Pseudogene | 4.53 | NA |
| 1033 | Pseudogene | 1.97 | NA |
| 1083c | Hypothetical protein | 2.05 | NA |
| 1087c | ATP-dependent DNA helicase | 1.62 | NA |
| 1119 | LysR transcriptional regulator family protein | 1.62 | NA |
| 1127 | Rhodanese-like family protein | 1.92 | NA |
| 1231 | PP-loop family protein | 1.64 | NA |
| 1345_s | pdpB | 2.48 | |
| 1346_s | Hypothetical protein | 3.87 | 6 ± 0.825 |
| 1347_s | Hypothetical protein | 2.29 | 4.3 ± 0.65 |
| 1349_s | Hypothetical protein | 2.22 | NA |
| 1351_s | Hypothetical protein | 3.58 | NA |
| 1352_s | Hypothetical protein | 2.56 | NA |
| 1353_s | Hypothetical protein | 3.18 | NA |
| 1354_s | Hypothetical protein | 2.34 | 3.2 ± 0.375 |
| 1356c_s | Intracellular growth locus, subunit D | 2.22 | 7.5 ± 1.1 |
| 1357c | Intracellular growth locus, subunit C | 1.92 | 1.8 ± 0.25 |
| 1360c | pdpD | 2.29 | 950 ± 8.5 |
| 1441 | Hypothetical protein | 2.41 | NA |
| 1541c | Hypothetical protein | 2.79 | NA |
| 1553c | RNase R | 1.69 | NA |
| 1554c | tRNA pseudouridine synthetase B | 7.09 | NA |
| 1555c | RNase III | 7.59 | 8.2 ± 1.5 |
| 1556c | Signal peptidase I | 6.31 | 68 ± 3.45 |
| 1558c | Pseudogene | 1.69 | NA |
| 1589c | Hypothetical protein | 1.86 | NA |
| 1650c | Chorismate mutase | 3.57 | NA |
| 1682 | Pseudogene | 2.34 | NA |
| 1766 | O-Methyltransferase | 1.62 | NA |
| 1793c | Aminopeptidase N | 1.62 | NA |
| Genes upregulated in ΔpmrA mutant | |||
| 172 | Hypothetical membrane protein, fragment | 4.78 | NA |
| 272 | Hypothetical membrane protein | 5.25 | NA |
| 293 | Hypothetical membrane protein | 1.54 | NA |
| 317 | Undecaprenyl pyrophosphate synthetase | 1.52 | NA |
| 401 | Hypothetical protein | 1.95 | NA |
| 465 | Hypothetical protein | 3.6 | NA |
| 879 | Superoxide dismuate (Cu-Zn) precursor | 1.52 | NA |
| 949c | Pseudogene | 1.73 | NA |
| 1242 | Hypothetical protein (FNU466)/FNU467 | 16.35 | 95.5 ± 5.5/2.57 ± 0.45 |
| 1437c | Pseudogene | 1.55 | NA |
| 1565c | Pseudogene | 3.18 | NA |
| 1761 | Hypothetical protein | 1.55 | NA |
| 1801c | Pseudogene | 1.55 | NA |
a
NA, not applicable.