Table 2.

agr-upregulated genes

ORFaGenebPatterncSarA effectdFunctioneFold changefN315 ORFgRole categoryhSar boxi
373pyrAA1 (1)UpCarbamoyl-phosphate synthetase3.3SA1045Nucleic acid metabolism
5911 (1)UpCytidylate kinase2.3SA0515Nucleic acid metabolism
3298cap5J1 (2)UpCapsule gene3.6SA0153Adaptation
831dps2 (2)IndirectGeneral stress protein 20U3.0SA1941Adaptation
4897fmt1 (2)IndirectMethionyl-tRNA formyltransferase2.8SA1059Aminoacyl tRNA synthetases
4084arcA2 (2)IndirectArginine deaminase5.7SA2428Amino acid metabolism
422arcB1 (1)IndirectAspartate/ornithine carbamoyltransferase8.7SA2427Amino acid metabolism
1220arcC2 (3)DownCarbamate kinase7.9SA2425Amino acid metabolism
1321aroC1 (1)UpChorismate synthetase3.1SA1299Amino acid metabolism
5609cpsA1 (1)IndirectAmino acid amidohydrolase2.6SA0507Amino acid metabolism
3360gltB1 (2)IndirectGlutamate synthase2.3SA0431Amino acid metabolism
997hutG1 (1)UpArginase4.5SA2125Amino acid metabolismYes
774hutH2 (3)IndirectHistidine ammonia-lyase4.0SA0008Amino acid metabolism
1001hutI2 (2)IndirectImidazolone-5-propionate hydrolase41.5SA2121Amino acid metabolismUpstream
1000hutU1 (1)IndirectUroconate hydratase23.3SA2122Amino acid metabolismYes
4969ocd1 (1)IndirectOrnithine-cyclodecarboxylase2.5SA0113Amino acid metabolism
2628pepF2 (3)UpPeptidase3.4SA1216Amino acid metabolism
6sdhA1 (3)Indirectl-Serine deaminase6.5SA2318Amino acid metabolism
7sdhB1 (2)Upl-Serine dehydratase beta subunit7.6SA2319Amino acid metabolism
1765epiF1 (2)UpABC-type multidrug transport system2.4Antibiotic production
4746epiP1 (2)UpSerine protease2.5Antibiotic production
36991 (1)UpAntibacterial peptide synthesis5.1SA0173Antibiotic production
11421 (2)Bacteriophage gene2.3SA1786Bacteriophage related
11321 (1)IndirectPutative integrase activator3.6SAS062Bacteriophage related
5455femB1 (4)mecresistance2.2SA1207Cell wall
26181 (1)UTP-glucose-1-phosphate uridylyltransferase2.6Cell wall
4659moaB1 (2)IndirectMolybdenum cofactor2.7SA2070Coenzyme metabolism
3390recQ1 (6)IndirectProbable DNA helicase2.8SA0676DNA replication
3585rocA1 (2)IndirectNAD-dependent aldehyde dehydrogenases2.7SA2341Electron transport
4103pckA1 (2)IndirectPhosphoenolpyruvate carboxykinase3.6SA1609Glycolysis
3898crtN1 (2)UpPutative phytoene dehydrogenase2.1SA2351Lipid metabolism
8821 (2)IndirectAcyl-coenzyme A dehydrogenase2.2SA2080Lipid metabolism
1399chiB1 (1)IndirectPredicted chitinase B2.8SA0914Miscellaneous
13981 (1)IndirectPredicted chitinase B2.7SA0914Miscellaneous
51631 (3)IndirectPutative GTPase2.7SA1086Miscellaneous
10441 (1)IndirectCysteine sulfinate desulfinase2.9SA1450Miscellaneous
2444agrA1 (1)Indirectagrresponse5.8SA1844Signal transductionUpstream
1426agrB1 (1)Indirectagrresponse3.4SA1842Signal transductionYes
2443agrC2 (2)Indirectagrresponse4.8SA1843Signal transductionUpstream
1425agrD1 (1)Indirectagrresponse5.9SAS066Signal transductionUpstream
884odhA6 (6)Indirect2-Oxoglutarate dehydrogenase2.3SA1245TCA cycle
885odhB2 (2)Indirect2-Oxoglutarate dehydrogenase3.1SA1244TCA cycle
1221arcR1 (1)DownTranscriptional regulator, Crp/Fnr family18.9SA2424Transcriptional regulation
4367pyrR1 (2)IndirectTranscriptional attenuator, pyrimidine biosynthesis2.8SA1041Transcriptional regulation
38062 (3)IndirectTranscriptional regulator, RpiR family2.5SA0187Transcriptional regulationUpstream
52591 (3)UpTranscriptional regulator, GntR family5.2SA0434Transcriptional regulation
28521 (1)UpPutative transcriptional regulator, GntR family2.4SA1120Transcriptional regulation
50051 (2)IndirectAcetyltransferases3.0SA2052Translation
421arcD2 (2)IndirectArginine/ornithine antiporter6.4SA2426Transport
4309fhuD1 (2)UpFerrichrome-binding periplasmic proteins3.2SA2079Transport
5224gltP-22 (4)IndirectProton/sodium-glutamate transport4.3SA0368TransportYes
2883lysP1 (1)IndirectLysine-specific permease2.3SA1505Transport
2606opp-1F1 (3)IndirectOligopeptide transporter, ATPase domain2.3SA2251Transport
2601opp-2B1 (3)UpOligopeptide transporter2.4SA1214TransportYes
3147potD1 (2)IndirectSpermidine/putrescine transport protein D2.3SA0953Transport
29781 (1)IndirectABC-type Mn/Zn transporter2.5SA0588Transport
9222 (2)IndirectABC-type Mn/Zn transport system component2.7SA0589Transport
2096veg1 (1)Indirect2.7SA0452Unknown
9871 (1)IndirectConserved hypothetical12.6SA0170Unknown
9921 (3)UpConserved hypothetical14.3SA0174Unknown
27562 (4)IndirectConserved hypothetical7.0SA0184UnknownYes
30902 (2)Indirect2.2SA0185UnknownUpstream
49272 (2)Conserved hypothetical3.0SA0271Unknown
43701 (2)Up3.4SA1037Unknown
24791 (2)Conserved hypothetical7.0SA1275Unknown
27821 (2)UpHypothetical protein2.3SA1319Unknown
20541 (1)IndirectPredicted membrane protein2.4SA1379Unknown
20651 (2)IndirectConserved hypothetical3.0SA1436Unknown
23941 (1)IndirectConserved hypothetical2.2SA1684Unknown
21221 (2)IndirectConserved hypothetical3.4SA2128Unknown
15551 (2)UpAcetyltransferase2.0SA2161Unknown
91 (1)UpHypothetical protein3.6SA2321Unknown
371 (1)UpHypothetical protein17.3SA2343Unknown
39821 (2)UpConserved hypothetical4.7SA2491Unknown
2371 (1)IndirectHypothetical protein2.1SAS013Unknown
6441 (1)UpHypothetical protein5.7SAS016Unknown
2031 (1)DownHypothetical protein3.2Unknown
14941 (1)IndirectHypothetical protein2.3Unknown
22751 (1)UpHypothetical protein2.4Unknown
26171 (2)IndirectHypothetical protein2.1Unknown
28271 (1)IndirectHypothetical protein4.3Unknown
29681 (1)IndirectHypothetical protein2.3Unknown
55001 (3)IndirectHypothetical protein2.3Unknown
3653aur1 (5)IndirectAureolysin2.8SA2430Virulence factorsUpstream
396clfB3 (6)IndirectClumping factor B2.7Virulence factors
583geh2 (2)IndirectLipase (glycerol ester hydrolase)3.5SA0309Virulence factors
4061hla1 (1)UpAlpha-toxin38.8SA1007Virulence factorsYes
1427hld2 (2)IndirectDelta-hemolysin7.9SAS065Virulence factorsYes
1928hlgB1 (1)UpGamma-hemolysin component B48.6SA2209Virulence factorsUpstream
1927hlgC1 (1)UpGamma-hemolysin component C6.3SA2208Virulence factorsYes
667lip2 (2)Lipase3.4SA2463Virulence factorsYes
1175pls1 (2)UpRelated to surface protein LPXTG motif3.3SA2284Virulence factors
2036set81 (3)IndirectExotoxin 22.2SA0384Virulence factors
2928splA2 (2)IndirectSerine protease2.5SA1631Virulence factorsYes
2929splB1 (1)UpSerine protease9.6SA1630Virulence factorsUpstream
324splD2 (2)UpSerine proteaseNDSA1628Virulence factorsUpstream
327splF2 (2)UpSerine protease11.3SA1627Virulence factorsUpstream
2175sspC1 (1)DownProtease2.4SA0899Virulence factors
29271 (10)Similar to streptococcal adhesin Emb3.0SA1268Virulence factors
10291 (2)UpRelated to map protein-surface protein7.7SA2006Virulence factors
43742 (2)UpSurface protein map3.1SA2006Virulence factors
51473 (15)IndirectHomolog of streptococcal hemagglutinin3.1SA2447Virulence factors
45232 (2)UpPhenol-soluble modulin beta 26.2Virulence factors
  • a Designated S. aureusGeneChip ORF number.

  • b Previously described gene name.

  • c Many genes are represented on the S. aureus GeneChip in a redundant manner as full or partial fragments. Values are the number of times a gene transcript was identified as fitting a pattern (number of times the gene was either partially or completely represented on the GeneChip).

  • d Expected SarA contribution toagr-regulated gene transcription.

  • e Previously described gene product function.

  • f Fold change in expression ofagr-regulated genes as cells transition from the early-log to the stationary phase of growth.

  • g Corresponding designated S. aureusstrain N315 gene (20).

  • h Expected metabolic role. TCA, tricarboxylic acid.

  • i Yes, putative Sar box identified within the gene's promoter region. Upstream, the gene is expected to be part of an operon with a potential Sar box located in an upstream promoter region.