TABLE 1.
Down-regulated genes in the ΔstkP mutant strain
| Functional category | Gene no. | Gene product (gene) | Mean of log2 ratios | P value | Expression ratioa |
|---|---|---|---|---|---|
| Cell wall | spr0096 | Hypothetical protein, LysM domain protein | −3.46 | 6.57E-07 | −11.01 |
| spr0867 | Endo-beta-N-acetylglucosaminidase (lytB) | −2.26 | 3.25E-11 | −4.78 | |
| spr2021 | General stress protein PcsB (pcsB) | −3.24 | 5.37E-09 | −9.47 | |
| Glycerol metabolism | spr1344 | Glycerol uptake facilitator protein paralog (glpF) | −1.05 | 2.02E-06 | −2.08 |
| spr1990 | Glycerol-3-phosphate dehydrogenase, truncation (glpD) | −1.01 | 6.00E-04 | −2.01 | |
| spr1991 | Glycerol kinase (glpK) | −1.37 | 4.82E-05 | −2.58 | |
| Pyrimidine metabolism | spr0613 | Orotidine-5′-decarboxylase (pyrF) | −1.54 | 8.75E-09 | −2.90 |
| spr0614 | Orotate phosphoribosyltransferase (pyrE) | −1.55 | 1.92E-10 | −2.92 | |
| spr0865 | Dihydroorotate dehydrogenase electron transfer subunit (pyrDII) | −2.07 | 2.84E-08 | −4.19 | |
| spr0866 | Dihydroorotate dehydrogenase (pyrD) | −2.38 | 2.49E-11 | −5.21 | |
| spr1053 | Dihydroorotase (pyrC) | −1.50 | 7.59E-07 | −2.83 | |
| spr1153 | Carbamoylphosphate synthase (ammonia), heavy subunit (carB) | −1.43 | 1.21E-08 | −2.69 | |
| spr1154 | Carbamoylphosphate synthase (glutamine-hydrolyzing) light subunit (carA) | −1.27 | 4.64E-09 | −2.41 | |
| spr1155 | Aspartate carbamoyltransferase (pyrB) | −1.30 | 6.19E-10 | −2.47 | |
| spr1156 | Transcriptional attenuation of the pyrimidine operon/uracil phosphoribosyltransferase activity (pyrR) | −1.49 | 5.80E-08 | −2.80 | |
| spr1165 | Uracil permease (pyrP) | −1.94 | 3.65E-09 | −3.83 | |
| DNA repair | spr1054 | 8-oxo-dGTP nucleoside triphosphatase (mutX) | −1.95 | 4.63E-10 | −3.88 |
| spr1055 | DNA-uracil glycosylase (ung) | −2.03 | 1.48E-09 | −4.08 | |
| spr1317 | O6-methylguanine-DNA methyltransferase (ogt) | −1.02 | 8.51E-11 | −2.02 | |
| spr1660 | Exodeoxyribonuclease (exoA) | −1.20 | 5.16E-05 | −2.30 | |
| Iron uptake | spr0934 | ABC transporter substrate binding protein-iron transport | −1.16 | 1.30E-05 | −2.23 |
| spr1684 | ABC transporter membrane-spanning permease-ferric iron transport (fatD) | −1.04 | 1.86E-02 | −2.10 | |
| spr1685 | ABC transporter membrane-spanning permease-ferric iron transport (fatC) | −1.51 | 1.15E-04 | −2.85 | |
| spr1686 | ABC transporter ATP binding protein-ferric iron transport (fecE) | −1.67 | 1.93E-03 | −3.17 | |
| spr1687 | ABC transporter substrate binding protein-ferric iron transport (fatB) | −2.23 | 1.43E-04 | −4.70 | |
| Oxidative stress | spr1321 | Conserved hypothetical protein, similar to amidotransferase, SNO family | −1.25 | 2.08E-03 | −2.38 |
| spr1322 | Pyridoxine biosynthesis protein (pdx1) | −1.10 | 1.22E-03 | −2.14 | |
| spr1495 | Thioredoxin-linked thiol peroxidase (psaD) | −1.15 | 2.88E-03 | −2.21 | |
| Other | spr0551 | Branched-chain amino acid transport system carrier protein (brnQ) | −1.21 | 3.18E-05 | −2.31 |
| spr1047 | Lipoate protein ligase A (lplA) | −1.01 | 4.08E-05 | −2.02 | |
| spr1048 | Dihydrolipoamide dehydrogenase (acoL) | −1.10 | 3.91E-04 | −2.14 | |
| spr1577 | Eukaryotic-type serine/threonine kinase (stkP) | −4.46 | 3.66E-04 | −22.04 | |
| spr1657 | ABC transporter ATP binding/membrane spanning protein | −1.01 | 3.37E-06 | −2.01 | |
| Hypothetical genes | spr0084 | Conserved hypothetical protein, rhodanese-like protein | −1.70 | 5.31E-06 | −3.24 |
| spr0552 | Conserved hypothetical protein, M42 glutamyl aminopeptidase homologue | −1.23 | 9.50E-04 | −2.34 | |
| spr0652 | Conserved hypothetical protein, degV family | −2.20 | 4.94E-10 | −4.61 | |
| spr0709 | Hypothetical protein | −1.14 | 6.85E-05 | −2.20 | |
| spr0755 | Conserved hypothetical protein, putative lipoprotein precursor | −1.04 | 1.22E-04 | −2.06 | |
| spr1052 | Conserved hypothetical protein, MATE efflux protein family | −1.08 | 6.76E-07 | −2.12 | |
| spr1056 | Hypothetical protein | −3.14 | 3.76E-04 | −8.81 | |
| spr1057 | Conserved hypothetical protein, hydrolase HAD-like family | −5.87 | 3.33E-10 | −58.52 | |
| spr1316 | Conserved hypothetical protein, similar to arsenate reductase | −1.08 | 1.16E-10 | −2.12 | |
| spr1318 | Hypothetical protein, putative acetyltransferase | −1.13 | 1.72E-08 | −2.19 | |
| spr1319 | Hypothetical protein | −2.69 | 1.76E-06 | −6.47 | |
| spr1320 | Conserved hypothetical protein, similar to hemolysin III | −3.34 | 1.66E-05 | −10.16 | |
| spr1436 | Conserved hypothetical protein, methyltransferase-like protein | −1.57 | 3.01E-05 | −2.98 | |
| spr1498 | Conserved hypothetical protein, putative large secreted protein | −1.03 | 2.33E-04 | −2.05 | |
| spr1790 | Conserved hypothetical protein, related to sporulation protein, SpoIIIJ | −1.17 | 5.43E-08 | −2.26 |
a
The ratio of the gene expression level in the ΔstkP mutant strain compared to that of the wild-type strain.