TABLE 4.

Genes upregulated by Rot

Chip ORF no.aN315 ORF no.bN315 genebN315 descriptionbFold changecagr or sar effectdRole categoryd
3994SA1736aldHAldehyde dehydrogenase2.1
5372clfBClumping factor B2.9
2462SA2336clpLATP-dependent Clp proteinase chain ClpL2.7sar, downAdaptation
3833coaCoagulase4.3
2163SA1253ctpAProbable carboxy-terminal processing proteinase CtpA2.9
5110SA1164dhoMHomoserine dehydrogenase2.3
4873SA0796dltDPoly(glycerophosphate chain) d-alanine transfer protein2.0agr, downTransport
3383epiALantibiotic gallidermin precursor EpiA2.6
84SA0602fhuAFerrichrome transport ATP-binding protein2.1
4551SA2172gltTProton/sodium-glutamate symport protein2.2
4042SA2288gtaBUTP-glucose-1-phosphate uridyltransferase2.4
3984SA0189hsdRProbable type I restriction enzyme restriction chain2.4
2883SA1505lysPLysine-specific permease2.4agr, upTransport
4486SA0250lytSTwo-component sensor histidine kinase2.3
1047SA1194msrAPeptide methionine sulfoxide reductase homolog2.4
854SA2410nrdDAnaerobic ribonucleoside-triphosphate reductase2.1
4205SA0685nrdINrdI protein involved in ribonucleotide reductase function2.9
4390SA0374pbuXXanthine permease2.3
4905SA0923purMPhosphoribosylformylglycinamidine cyclo-ligase PurM2.2sar, downNucleotide and nucleic acid metabolism
2800SA0676recQProbable DNA helicase2.8agr, upDNA replication
1079SA1583rotRepressor of toxins Rot12.0
2343sdrCSdrC protein2.7sar, upVirulence factors
2119SA0107spaImmunoglobulin G binding protein A precursor15.6agr, downVirulence factors
5112SA1166thrBHomoserine kinase homolog3.9
3239SA1165thrCThreonine synthase3.8
5075SA0373xprTXanthine phosphoribosyltransferase3.0
17HP2.0
18SA0220HP, similar to glycerophosphodiester phosphodiesterase2.9
237SAS013Reverse complement of HP (pathogenicity island SaPIn2)2.3agr, upUnknown
392SA0739Conserved HP2.4
442SA0651HP2.2
457SA1613Conserved HP2.5
477SA0428Conserved HP2.5
493SA2378Conserved HP3.2agr, downUnknown
534SA1717Glutamyl-tRNAGln amidotransferase subunit C2.6
600SA0523HP, similar to poly (GP) alpha-glucosyltransferase (TA biosynthesis)2.2sar, upCell wall
616SA2133Conserved HP2.8
678SA0682HP, similar to di-tripeptide ABC transporter2.1
748SA2261HP, similar to efflux pump3.0
873SAS088HP2.2
1027SA2007HP, similar to alpha-acetolactate decarboxylase2.1
1082SA0620Secretory antigen SsaA homologue2.0
1175SA2284HP, similar to accumulation-associated protein2.5agr, upVirulence factors
1353HP2.7
1356SA2170HP, similar to general stress protein 262.1
1357SA2171HP2.0
1398SA0914Reverse complement of HP, similar to chitinase B3.0agr, upMiscellaneous
1563SA0407Conserved HP2.0
1564SA0408HP2.3
1592HP3.0
1597HP2.0
1666SA2303HP, similar to membrane-spanning protein3.2
1765Epidermin immunity protein F4.7agr, upAntibiotic production
1991SA0439HP, similar to lysine decarboxylase2.5
2032SA1059Methionyl-tRNA formyltransferase2.4agr, upAminoacyl tRNA synthetases
20762.4
2077SA0291HP3.1
2078SA0292HP2.5
2103SA0271Conserved HP6.3agr, upUnknown
2132SA2131Conserved HP4.9
2133SA2132HP, similar to ABC transporter (ATP-binding protein)2.4
2232SA2440HP2.0
2255HP2.1
2337SA2001HP, similar to oxidoreductase, aldo/ketoreductase family2.0
2454SA1320HP4.4
2507SA0380Conserved HP (pathogenicity island SaPIn2)3.5
2697SA2442Preprotein translocase SecA homolog2.2
3259SA0675HP, similar to ABC transporter ATP-binding protein3.0
3313SA2436HP, similar to phage infection protein2.1sar, upBacteriophage related
3391Conserved HP2.0
3426SA1924HP, similar to aldehyde dehydrogenase2.5
3599ABC transporter, ATP-binding protein2.6
3698SA0173HP, similar to surfactin synthetase2.9agr, upAntibiotic production
3888SA2339HP, similar to antibiotic transport-associated protein2.1
4153SA0310HP2.1
4253SA0003Conserved HP2.2
4282SA1942Conserved HP2.5
4525SA1016Reverse complement of conserved HP2.4
4550HP2.3
4667SA0973Phosphopantetheine adenyltransferase homolog3.2
4752SA1056HP3.5
5065SA2256Conserved HP15.8
5245SA0827HP, similar to ATP-dependent nuclease subunit B2.3
5437SA0246Hypotheticl protein, similar to d-xylulose reductase2.1
5471SA1131HP, similar to 2-oxoacid ferredoxin oxidoreductase, alpha subunit2.3
5554SA1679HP, similar to d-3-phosphoglycerate dehydrogenase2.0
  • 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 (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; TA, teichoic acid.

  • c Normalized values in the agr strain over values in the agr rot double mutant.

  • d As described by Dunman et al. (12). up, upregulated; down, downregulated.