TABLE 3.
Genes downregulated by Rot
| Chip ORF no.a | N315 ORF no.b | N315 geneb | N315 descriptionb | Fold changec | agr or sar effectd | Role categoryd |
|---|---|---|---|---|---|---|
| 4877 | SA1811 | hlb | Truncated beta-hemolysin | 6.9 | ||
| 4218 | SA0143 | adhE | Alcohol-acetaldehyde dehydrogenase | 3.8 | ||
| 1726 | SA0471 | cysK | Cysteine synthase (o-acetylserine sulfhydrylase) homologue | 4.6 | ||
| 1664 | SA2312 | ddh | D-specific d-2-hydroxyacid dehydrogenase | 11.5 | agr, down | Carbohydrate metabolism |
| 904 | SA1267 | ebhA | HP, similar to streptococcal adhesin Emb | 567.4 | ||
| 1885 | SA1268 | ebhB | HP, similar to streptococcal adhesin Emb | Upregulated | agr, up | Virulence factors |
| 1434 | SA1091 | fmhC (eprh) | FmhC protein | Upregulated | ||
| 1527 | SA0309 | geh | Glycerol ester hydrolase | 8.4 | agr, up | Virulence factors |
| 4046 | SA2294 | gntK | Gluconokinase | 3.1 | ||
| 5281 | SA2293 | gntP | Gluconate permease | 4.6 | sar, down | Transport |
| 1928 | SA2209 | hlgB | Gamma-hemolysin component B | 31.9 | agr, up | Virulence factors |
| 1927 | SA2208 | hlgC | Gamma-hemolysin component C | 19.6 | agr, up | Virulence factors |
| 1700 | SA1881 | kdpA | Probable potassium-transporting ATPase A chain | 2.8 | ||
| 4715 | SA1879 | kdpC | Probable potassium-transporting ATPase C chain | 3.7 | ||
| 4583 | SA1090 | lytN | LytN protein | Upregulated | ||
| 5046 | SA0549 | mvaK2 | Phosphomevalonate kinase | Upregulated | ||
| 2268 | SA2334 | mvaS | 3-Hydroxy-3-methylglutaryl CoA synthase | 8.1 | ||
| 3524 | SA2185 | narG | Respiratory nitrate reductase alpha chain | 6.2 | agr, down | Electron transport |
| 431 | SA2435 | pmi | Mannose-6-phosphate isomerase | 3.0 | ||
| 4537 | SA1659 | prsA | Peptidyl-prolyl cis/trans isomerase homolog | 6.5 | ||
| 3551 | SA2326 | ptsG | PTS system, glucose-specific IIABC component | 2.7 | ||
| 1071 | SA1589 | ribD | Riboflavin-specific deaminase | Upregulated | ||
| 5329 | SA1631 | splA | Serine protease SplA (pathogenicity island SaPIn3) | Upregulated | agr, up | Virulence factors |
| 2929 | SA1630 | splB | Serine protease SplB (pathogenicity island SaPIn3) | Upregulated | agr, up | Virulence factors |
| 3742 | SA1629 | splC | Serine protease SplC (pathogenicity island SaPIn3) | 62.5 | ||
| 324 | SA1628 | splD | Serine protease SplD (pathogenicity island SaPIn3) | Upregulated | agr, up | Virulence factors |
| 325 | splE | Serine protease SplE | 133.4 | |||
| 2377 | SA1627 | splF | Serine protease SplF (pathogenicity island SaPIn3) | Upregulated | agr, up | Virulence factors |
| 2174 | SA0900 | sspB | Cysteine protease precursor | 10.4 | agr, up | Virulence factors |
| 2175 | SA0899 | sspC | Cysteine protease | 5.2 | agr, up | Virulence factors |
| 4823 | SA2082 | ureA | Urease gamma subunit | Upregulated | ||
| 4822 | SA2083 | ureB | Urease beta subunit | Upregulated | ||
| 1900 | SA2084 | ureC | Urease alpha subunit | Upregulated | ||
| 4817 | SA2088 | ureD | Urease accessory protein UreD | 2.9 | ||
| 1899 | SA2085 | ureE | Urease accessory protein UreE | 6.7 | ||
| 1898 | SA2086 | ureF | Urease accessory protein UreF | 6.0 | ||
| 1897 | SA2087 | ureG | Urease accessory protein UreG | 23.7 | ||
| 401 | SA0124 | HP, similar to glycosyltransferase TuaA | 5.6 | |||
| 657 | SA2455 | Capsular polysaccharide biosynthesis, CapC | 11.1 | |||
| 849 | SA2414 | HP, similar to glutathione peroxidase | 10.8 | |||
| 1386 | SA0368 | HP, similar to proton/sodium-glutamate symport protein | 6.4 | agr, up | Transport | |
| 1574 | SA2062 | HP | 3.5 | |||
| 1815 | SA2200 | HP, similar to ABC transporter, ATP binding subunit | 3.0 | |||
| 1816 | SA2201 | HP, similar to ABC transporter, permease protein | 3.2 | |||
| 1994 | SA1812 | HP, similar to synergohymenotropic toxin precursor of Staphylococcus intermedius | 3.1 | |||
| 2064 | SA2218 | Reverse complement of HP | 4.4 | |||
| 2067 | SA1437 | Conserved HP | 3.6 | |||
| 2238 | SA2434 | Fructose phosphotransferase system enzyme FruA homolog | 5.4 | |||
| 2543 | SA1725 | Staphopain, cysteine proteinase | 11.9 | |||
| 2612 | SA1093 | DNA topoisomerase I TopA homolog | Upregulated | |||
| 2860 | SA0989 | Conserved HP | 7.2 | |||
| 2926 | SA0663 | HP | 3.0 | |||
| 3017 | SA0127 | HP, similar to capsular polysaccharide synthesis protein 14L | 50.7 | |||
| 3078 | SA0165 | HP, similar to alpha-helical coiled-coil protein SrpF | 2.7 | |||
| 3373 | SA0904 | HP, probable autolysin transcription regulator | Upregulated | |||
| 3768 | SA0850 | HP, similar to oligopeptide ABC transporter oligopeptide- binding protein | Upregulated | |||
| 4061 | SA1007 | Alpha-hemolysin precursor | 24.5 | agr, up | Virulence factors | |
| 4069 | SA0123 | HP, similar to UDP-glucose 4-epimerase (Gale-1) | Upregulated | |||
| 4530 | SA0710 | Conserved HP | Upregulated | |||
| 5131 | SA2297 | HP, similar to GTP-pyrophosphokinase | 2.8 |
a
S. aureus GeneChip ORF number.
b
Based on the published sequence of strain N315 (accession no. NC_002745). For genes not present in N315, the gene name and description are from the COL genome, available from The Institute for Genomic Research Comprehensive Microbial Resource website (http://www.tigr.org). HP, hypothetical protein; CoA, coenzyme A; PTS, phosphotransferase system.
c
Normalized values in the agr rot mutant over values in the agr strain. “Upregulated” denotes genes highly downregulated in the agr strain, such that the transcripts were below detectable levels and the fold change could not be accurately calculated.
d
As described by Dunman et al. (12). up, upregulated; down, downregulated.