TABLE 2.

Genes upregulated by σB

N315 ORF no.aN315 geneaN315 descriptionaFold changeb in strain:σB consensusc,dReference(s) with reported σB dependencee for:
COLNewmanGP268S. aureusB. subtilisf
N315-SA1984asp23Alkaline shock protein 23UpUpUpYes24, 26, 44, 55
CAB75732.1bbpBone sialoprotein-binding protein Bbp3.24.54.8?
N315-SA2008budBα-acetolactate synthaseUpUpUpYesd
N315-SA0144cap5ACapsular polysaccharide synthesis enzyme Cap5AUpUp12.8?
N315-SA0145cap5BCapsular polysaccharide synthesis enzyme Cap5BUpUp10.8?
N315-SA0146cap5CCapsular polysaccharide synthesis enzyme Cap8CUpUp8.6?
N315-SA0147cap5DCapsular polysaccharide synthesis enzyme Cap5DUpUp7.3?
N315-SA0148cap5ECapsular polysaccharide synthesis enzyme Cap8EUpUp7.5?
N315-SA0149cap5FCapsular polysaccharide synthesis enzyme Cap5FUpUp7.5?
N315-SA0150cap5GCapsular polysaccharide synthesis enzyme Cap5GUpUp6.8?
N315-SA0151cap5HCapsular polysaccharide synthesis enzyme Cap5HUpUp5.1?
N315-SA0152cap5ICapsular polysaccharide synthesis enzyme Cap5IUpUp5.7?
N315-SA0153cap5JCapsular polysaccharide synthesis enzyme Cap5JUpUp3.5?
N315-SA0155cap5LCapsular polysaccharide synthesis enzyme Cap5LUpUp5.1?
N315-SA0156cap5MCapsular polysaccharide synthesis enzyme Cap5MUpUp4.5?
N315-SA0157cap5NCapsular polysaccharide synthesis enzyme Cap5N2.7Up5.2?
N315-SA0158cap5OCapsular polysaccharide synthesis enzyme Cap8O2.6Up4.2?
CAA79304clfAClumping factor A35.7Up7.8Yes33, 60
N315-SA2336clpLATP-dependent Clp proteinase chain ClpL17.313.2UpYes25, 33
N315-SA2349crtMSqualene desaturaseUpUpUpYesd2666 (yisP)
N315-SA2348crtNSqualene synthaseUpUpUpYesd26
N315-SA1452csbDHP, σB-controlled gene product CsbD (Csb8)37.0UpUpYes25, 3330, 66 (ywmG)
COL-SA1872epiEEpidermin immunity protein EpiEUpUpUpYesd
COL-SA1873epiFEpidermin immunity protein EpiFUpUpUpYes
N315-SA1634epiGEpidermin immunity protein EpiGUpUpUpYesd
N315-SA2260fabGHP, similar to glucose l-dehydrogenaseUpUpUpYes30 (yxbG)
N315-SA1901fabZ(3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase2.25.12.0Yesd
N315-SA2125hutGHP, similar to formiminoglutamase3.714.62.9Yes
N315-SA1505lysPLysine-specific permease2.47.92.0?
N315-SA1962mtlAPTS system, mannitol-specific IIA component8.517.2UpYesd
N315-SA1963mtlDMannitol-l-phosphate 5-dehydrogenase8.2UpUpYesd
N315-SA1902murAUDP-N-acetylglucosamine l-carboxyvinyl transferase 12.25.12.0Yesd
N315-SA0547mvaK1Mevalonate kinase2.44.51.3Yes
N315-SA0548mvaDMevalonate diphosphate decarboxylase3.37.31.8Yesd
N315-SA0549mvaK2Phosphomevalonate kinase3.710.62.2Yesd
N315-SA1987opuDGlycine betaine transporter opuD homologueUpUpUpYes26, 33
N315-SA1871rsbVAnti-σB factor antagonistUpUpUpYes26, 43, 8230, 66
N315-SA1870rsbWAnti-σB factorUpUpUpYesd26, 43, 8230, 66
N315-SA0573sarAStaphylococcal accessory regulator A (Csb35)2.93.82.0Yes4, 15, 25, 55
N315-SA0108sarSStaphylococcal accessory regulator A homologue S2.61.12.1Yes77
N315-SA0099sbtAHP, similar to transmembrane efflux pump proteinUpUpUp?66 (yusP)
N315-SA1869sigBAlternative transcription factor σBUpUpUpYesd26, 43, 8230, 66
N315-SA0456spoVGStage V sporulation protein G homologue4.39.83.0Yesd
N315-SA1114truBtRNA pseudouridine 5S synthase2.1Up2.3Yes
N315-SA2119ydaDHP, similar to dehydrogenase (Csb28)4.833.116.9Yes2530 (yhxD)
N315-SA0084HP, similar to Homo sapiens CG1-44 proteinUpUp3.0Yes
N315-SA0098HP, similar to aminoacylaseUpUpUp?
N315-SA010267 kDa myosin-crossreactive streptococcal antigen homologueUpUpUpYes
N315-SA0105HPUpUpUp?
N315-SA0163HP, similar to cation efflux system membrane protein CzcDUpUpUp?
N315-SA0164HPUpUpUpYes
N315-SA0261HP, similar to rbs operon repressor RbsR2.5UpUpYes
N315-SA0296Conserved HP7.620.53.9Yes
N315-SA0297HP, similar to ABC transporter ATP-binding protein6.313.12.8Yesd
N315-SA0317HP, similar to dihydroflavonol-4-reductase11.620.73.9Yes
N315-SA0326Conserved HP2.52.12.0Yes
N315-SA0327Conserved HP2.22.12.0Yesd
N315-SA0359Conserved HPUpUpUpYes33
N315-SA0360Conserved HPUpUp77.7Yes30, 66 (ydaS)
N315-SA0372HP (Csb12)1.63.32.0Yes25
N315-SA0455Translation initiation inhibitor homologue3.26.22.3Yes33
N315-SA0509Conserved HP2.012.12.0?
N315-SA0528HP, similar to hexulose-6-phosphate synthase (Csb4)1.86.82.0Yes25
N315-SA0529Conserved HP (Csb4-1)1.98.72.0Yesd25
N315-SA0541HP, similar to cationic amino acid transporter11.314.47.7Yes30 (yhdG)
N315-SA0572HP, similar to esterase/lipaseUpUpUpYes
N315-SA0577HP, similar to FimE recombinaseUpUpUp?
N315-SA0578HP, similar to NADH dehydrogenaseUpUpUpYes
N315-SA0579HP, similar to Na+ H+ antiporterUpUp4.0Yesd
N315-SA0580HP, similar to Na+ H+ antiporterUpUpUpYesd
N315-SA0581MnhD homologue, similar to Na+ H+ antiporter subunitUpUp6.0Yesd
N315-SA0582HP, similar to Na+ H+ antiporterUpUp4.0Yesd
N315-SA0583HP, similar to Na+ H+ antiporterUpUp4.7Yesd
N315-SA0584Conserved HPUpUp5.3Yesd
N315-SA0633HP2.08.72.9Yesd33
N315-SA0634Conserved HP1.96.62.3Yesd
N315-SA0635Conserved HP5.114.82.8Yesd
N315-SA0636Conserved HP5.522.92.2Yesd
N315-SA0637Conserved HP5.324.33.5Yes
N315-SA0658HP, similar to plant metabolite dehydrogenases3.010.52.5Yes
N315-SA0659HP, similar to CsbB stress response protein3.310.42.5Yesd30, 66 (csbB)
N315-SA0665Coenzyme PQQ synthesis homologue2.14.51.8?
N315-SA06666-Pyruvoyl tetrahydrobiopterin synthase homologue2.35.72.1?
N315-SA0681HP, similar to multidrug resistance protein (Csb29)2.4UpUpYes2530, 66 (bmrU)
N315-SA0721Conserved HP4.210.32.4Yes
N315-SA0722Conserved HP3.49.41.5Yesd
N315-SA0724HP, similar to cell division inhibitor2.53.82.5Yes30, 66 (yfhF)
N315-SA0725Conserved HPUpUpUp?
N315-SA0740HPUpUpUpYes
N315-SA0741Conserved HPUpUpUpYesd
N315-SA0748HP3.0Up4.8Yesd
N315-SA0749HP2.5Up6.6Yes
N315-SA0751HP4.35.74.1?
N315-SA0752HPUpUpUpYes33
N315-SA0755HP, similar to general stress protein 170UpUpUpYes30, 66 (ykzA)
N315-SA0768Conserved HP2.05.64.5?
N315-SA0772Conserved HPUpUpUpYes3330, 66 (csbD)
N315-SA0774HP, similar to ABC transporter ATP-binding protein homologue (Csb10)2.12.01.4Yes25
N315-SA0780HP, similar to hemolysin3.3Up2.2Yes30, 66 (yqhB)
N315-SA0781HP, similar to 2-nitropropane dioxygenase2.2Up2.0Yesd
N315-SA0933HP13.126.97.1Yes
N315-SA1014Conserved HPUpUpUpYes
N315-SA1057Conserved HP2.43.93.1Yes
N315-SA1559HP, similar to smooth muscle caldesmon3.612.12.1Yesd
N315-SA1560HP, similar to general stress protein homolog2.88.22.2Yes30, 66 (ytxG)
N315-SA1573HP5.921.03.0Yes
N315-SA1590HP2.04.32.1Yes
N315-SA1657Conserved HP2.04.52.4Yes
N315-SA1671HP (Csb33)3.09.42.1Yes25
N315-SA1692Conserved HP (Csb3)1.85.64.0?25
N315-SA1697HP, similar to protein-tyrosine phosphatase2.35.03.7Yes30 (yfkJ)
N315-SA1698HP1.32.92.0Yesd
N315-SA1699HP, similar to transporter5.023.16.1Yesd30, 66 (yfkH)
N315-SA1814HP, similar to succinyl-diaminopimelate desuccinylaseUpUpUp?
N315-SA1903Conserved HP3.710.93.7Yesd
N315-SA1924HP, similar to aldehyde dehydrogenase (Csb24)3.726.13.2Yes25
N315-SA1942Conserved HP2.37.93.6?
N315-SA1946Conserved HP (Csb9)UpUpUpYes25, 33
N315-SA1961HP, similar to transcription AT BglG family9.78.2UpYesd
N315-SA1980Conserved HP3.44.71.1Yesd
N315-SA1981Conserved HP5.77.71.6Yes
N315-SA1985HPUpUpUpYesd26
N315-SA1986HPUpUpUpYes26
N315-SA2006HP, similar to MHC class II analogUpUpUp?
N315-SA2101Conserved HP2.23.31.5Yesd66 (yrhD)
N315-SA2102Conserved HP2.23.31.7Yes
N315-SA2104HP, similar to suppressor protein SuhB2.12.21.8Yes
N315-SA2158HP, similar to TpgX protein2.23.52.5Yes
N315-SA2203HP, similar to multidrug resistance protein2.13.92.2Yes
N315-SA2219Conserved HPUpUp3.0Yes33
N315-SA2240HP, similar to para-nitrobenzyl esterase chain A1.92.02.0?
N315-SA2242Conserved HPUpUpUp?
N315-SA2243HP, similar to ABC transporter (ATP-binding protein)UpUpUp?
N315-SA2262Conserved HP (Csb7)UpUpUpYes25
N315-SA2267HP3.0Up3.9Yes
N315-SA2298Conserved HP3.430.96.1?3330, 66 (ydhT)
N315-SA2309Conserved HP2.02.52.9
N315-SA2327HP, similar to pyruvate oxidase51.1Up17.9?30, 66 (ydhP)
N315-SA2328Conserved HPUpUpUp?66 (yxaC)
N315-SA2350Conserved HPUpUpUpYesd
N315-SA2351HP, similar to phytoene dehydrogenaseUpUpUpYesd
N315-SA2352HPUpUpUpYes
N315-SA2366Conserved HP7.3Up4.5Yes
N315-SA2367Conserved HP10.4Up8.9Yes
N315-SA2374Conserved HPUpUpUp?
N315-SA2398HPUpUpUpYes
N315-SA2403Conserved HP10.3Up8.7Yes
N315-SA2440HP2.35.91.7?
N315-SA2441HP, similar to lipopolysaccharide biosynthesis protein2.56.62.0?
N315-SA2442Preprotein translocase SecA homologue3.58.52.0?
N315-SA2451HPUpUpUpYes33
N315-SA2452Conserved HPUpUp3.5?
N315-SA2479Conserved HPUp4.34.6Yes
N315-SA2485HPUpUpUpYes
N315-SA2488HPUpUpUpYes
N315-SA2489HP, similar to high-affinity nickel-transport proteinUpUpUpYesd
N315-SA2491Conserved HPUpUpUpYes
N315-SAS023HP, similar to thioredoxin2.14.63.2?
N315-SAS049HPUpUpUpYesd
N315-SAS053HP4.012.82.1Yesd
N315-SAS056HP2.05.71.9Yes
N315-SAS068HP5.25.73.3Yes
N315-SAS082HPUpUpUp?
N315-SAS083HPUpUpUp?
N315-SAS089HP2.65.72.3?
COL-SA0866HPUpUpUp?
COL-SA1046HP6.612.09.0Yes
COL-SA2012HP, acetyltransferase (GNAT) family5.82.92.0?
COL-SA2013HPUpUpUp?
COL-SA2379Conserved HP2.217.13.0?
COL-SA2433HP2.63.62.1Yesd
COL-SA2481HPUpUpUpYesd
COL-SA2595HP2.34.12.1?
COL-SA2631Conserved HPUpUp3.8Yes
AAB05395HP, ORF 3 of the sarA locus11.846.66.8Yes4, 15, 52, 55
CAB60754HP32.1Up13.9Yes
  • a Based on the published sequence of strain N315 (accession no. NC_002745). For genes not present in N315, the gene name and description given are from the COL genome, available from The Institute for Genomic Research Comprehensive Microbial Resource website (http://www.tigr.org), or the respective accession number. ABC, ATP binding cassette; GNAT, GCN5-related N-acetyltransferases; HP, hypothetical protein; MHC, major histocompatibility complex; PTS, phosphotransferase system.

  • b Normalized values in the rsbU+V+W+ sigB+ strain over values in the ΔrsbUVW-sigB mutant. “Up” denotes genes highly downregulated in the ΔrsbUVWsigB mutant, such that the transcripts were below detectable levels and the change could not be accurately calculated.

  • c ORFs preceded by a consensus sequence that resembles the σB consensus sequence for B. subtilis as described by Petersohn et al. (64). Only sequences deviating not more than three nucleotides from the consensus GttTww12-15 gGgwAw (w = a, t) sequence and lying within 500 bp upstream of predicted ORFs were considered σB-dependent promoters. ?, genes or operons are not preceded by a σB consensus promoter that matches the criteria given above.

  • d ORFs likely to form an operon.

  • e References reporting an influence of σB on the respective gene or its gene product in S. aureus or the homologues gene in B. subtilis.

  • f B. subtilis gene names are given in parentheses, if different from those of S. aureus. The absence of a homologous ORF in the B. subtilis genome is indicated by a dash.