TABLE 3.

Genes downregulated by Rot

Chip ORF no.aN315 ORF no.bN315 genebN315 descriptionbFold changecagr or sar effectdRole categoryd
4877SA1811hlbTruncated beta-hemolysin6.9
4218SA0143adhEAlcohol-acetaldehyde dehydrogenase3.8
1726SA0471cysKCysteine synthase (o-acetylserine sulfhydrylase) homologue4.6
1664SA2312ddhD-specific d-2-hydroxyacid dehydrogenase11.5agr, downCarbohydrate metabolism
904SA1267ebhAHP, similar to streptococcal adhesin Emb567.4
1885SA1268ebhBHP, similar to streptococcal adhesin EmbUpregulatedagr, upVirulence factors
1434SA1091fmhC (eprh)FmhC proteinUpregulated
1527SA0309gehGlycerol ester hydrolase8.4agr, upVirulence factors
4046SA2294gntKGluconokinase3.1
5281SA2293gntPGluconate permease4.6sar, downTransport
1928SA2209hlgBGamma-hemolysin component B31.9agr, upVirulence factors
1927SA2208hlgCGamma-hemolysin component C19.6agr, upVirulence factors
1700SA1881kdpAProbable potassium-transporting ATPase A chain2.8
4715SA1879kdpCProbable potassium-transporting ATPase C chain3.7
4583SA1090lytNLytN proteinUpregulated
5046SA0549mvaK2Phosphomevalonate kinaseUpregulated
2268SA2334mvaS3-Hydroxy-3-methylglutaryl CoA synthase8.1
3524SA2185narGRespiratory nitrate reductase alpha chain6.2agr, downElectron transport
431SA2435pmiMannose-6-phosphate isomerase3.0
4537SA1659prsAPeptidyl-prolyl cis/trans isomerase homolog6.5
3551SA2326ptsGPTS system, glucose-specific IIABC component2.7
1071SA1589ribDRiboflavin-specific deaminaseUpregulated
5329SA1631splASerine protease SplA (pathogenicity island SaPIn3)Upregulatedagr, upVirulence factors
2929SA1630splBSerine protease SplB (pathogenicity island SaPIn3)Upregulatedagr, upVirulence factors
3742SA1629splCSerine protease SplC (pathogenicity island SaPIn3)62.5
324SA1628splDSerine protease SplD (pathogenicity island SaPIn3)Upregulatedagr, upVirulence factors
325splESerine protease SplE133.4
2377SA1627splFSerine protease SplF (pathogenicity island SaPIn3)Upregulatedagr, upVirulence factors
2174SA0900sspBCysteine protease precursor10.4agr, upVirulence factors
2175SA0899sspCCysteine protease5.2agr, upVirulence factors
4823SA2082ureAUrease gamma subunitUpregulated
4822SA2083ureBUrease beta subunitUpregulated
1900SA2084ureCUrease alpha subunitUpregulated
4817SA2088ureDUrease accessory protein UreD2.9
1899SA2085ureEUrease accessory protein UreE6.7
1898SA2086ureFUrease accessory protein UreF6.0
1897SA2087ureGUrease accessory protein UreG23.7
401SA0124HP, similar to glycosyltransferase TuaA5.6
657SA2455Capsular polysaccharide biosynthesis, CapC11.1
849SA2414HP, similar to glutathione peroxidase10.8
1386SA0368HP, similar to proton/sodium-glutamate symport protein6.4agr, upTransport
1574SA2062HP3.5
1815SA2200HP, similar to ABC transporter, ATP binding subunit3.0
1816SA2201HP, similar to ABC transporter, permease protein3.2
1994SA1812HP, similar to synergohymenotropic toxin precursor of Staphylococcus intermedius3.1
2064SA2218Reverse complement of HP4.4
2067SA1437Conserved HP3.6
2238SA2434Fructose phosphotransferase system enzyme FruA homolog5.4
2543SA1725Staphopain, cysteine proteinase11.9
2612SA1093DNA topoisomerase I TopA homologUpregulated
2860SA0989Conserved HP7.2
2926SA0663HP3.0
3017SA0127HP, similar to capsular polysaccharide synthesis protein 14L50.7
3078SA0165HP, similar to alpha-helical coiled-coil protein SrpF2.7
3373SA0904HP, probable autolysin transcription regulatorUpregulated
3768SA0850HP, similar to oligopeptide ABC transporter oligopeptide- binding proteinUpregulated
4061SA1007Alpha-hemolysin precursor24.5agr, upVirulence factors
4069SA0123HP, similar to UDP-glucose 4-epimerase (Gale-1)Upregulated
4530SA0710Conserved HPUpregulated
5131SA2297HP, similar to GTP-pyrophosphokinase2.8
  • 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.