TABLE 8.

Expression ratios for selected genes as evaluated by DNA arrays and real-time PCR in the early and late exponential phases of growth for the indicated strains compared to prototype strain Newbould^e

ORF (COL)	ORF (N315)	Gene	Description	SigB regulationa	Kinetic typeb	Method	Phasec	Fold changed					Interpretation
								hemB	CF03	CF06	CF07	CF10
Agr markers
2022	SAS065	hld	δ-Hemolysin, RNA III	Not influenced		Array	Early	−5.3	−10.8	−5.6	−6.7	−15.2	Agr not activated in any of the SCVs
						Real-timef	Early	−6,562.2	−225.9	−19.4	−167.7	−116.9	Agr not activated in any of the SCVs
						Real-time	Late	−57,052.0	−8.5	−288.0	−59.3	−661.7	Agr not activated in any of the SCVs
1173	1007	hla	α-Hemolysin	Down-late		Array	Early	1.8	−1.6	−2.4	−1.9	−4.3	hla not up-regulated in any of the SCVs
						Real-time	Early	1.2	−2.7	−7.8	−6.1	−11.2	hla not up-regulated in any of the SCVs
						Real-time	Late	−7.5	−3.8	−119.4	−82.7	−14.2	hla not up-regulated in any of the SCVs
Known SigB markers
2173	1984	asp23	Alkaline shock protein 23	Up-late	2	Array	Early	−4.4	4.6	5.1	4.6	4.7	SigB activity detected early in CF strains but not in hemB
						Real-time	Early	−2.6	23.0	29.2	5.1	32.9	SigB activity detected early in CF strains but not in hemB
						Real-time	Late	−34.1	−4.2	−1.3	−2.3	−2.4	SigB activity detected later in Newbould
787	681		Conserved protein, Csb29	Up-late	2	Array	Early	−1.7	4.4	4.0	5.2	7.8	SigB activity detected early in CF strains but not in hemB
						Real-time	Early	2.9	54.7	110.6	54.6	92.4	SigB activity detected early in CF strains but not in hemB
						Real-time	Late	−5.6	1.3	5.3	5.0	2.2	SigB activity detected later in Newbould
CF up-regulated proteins
2580	2352		Hypothetical protein	Up-late	2	Array	Early	−1.4	1.5	2.3	1.8	4.4	Detected early in CF strains but not in hemB, follows SigB markers
						Real-time	Early	−3.6	4.8	2.3	4.7	9.5	Detected early in CF strains but not in hemB, follows SigB markers
						Real-time	Late	−33.2	−25.8	−6.7	−7.1	−11.5	Detected later in Newbould, follows SigB markers
723	620		Antigenic surface protein, SsaA like	Up-early	1	Array	Early	1.0	3.7	2.5	5.3	3.4	Up-regulation of a surface protein gene in CF strains
						Real-time	Early	2.7	5.2	4.3	6.9	5.3	Up-regulation of a surface protein gene in all SCVs
						Real-time	Late	4.3	4.8	11.8	11.7	9.6	Up-regulation of a surface protein gene in all SCVs
2088e	1898		Exotoxin, SceD like	Up-early	1	Array	Early	1.4	27.8	12.0	14.1	79.4	Up-regulation of an exotoxin gene in CF strains
						Real-time	Early	1.5	42.2	62.0	38.3	85.6	Up-regulation of an exotoxin gene in CF strains
						Real-time	Late	6.5	152.7	1,807.8	377.4	1,458.2	Up-regulation of an exotoxin gene in all SCVs
Other regulator
672	573	sarA	Staphylococcal accessory regulator A	Up-late	2	Array	Early	−1.1	1.9	2.7	2.1	3.9	Detected early in CF strains but not in hemB, follows SigB markers
						Real-time	Early	1.3	7.2	3.2	9.4	15.8	Detected early in CF strains but not in hemB, follows SigB markers
						Real-time	Late	−3.2	−3.0	−1.3	−2.1	−1.1	Detected later in Newbould, follows SigB markers

^aGenes that were shown to be up- or down-regulated by SigB in prototype strains by Bischoff et al. (9). Up-late refers to those genes typically up-regulated in the postexponential phase of growth, and Up-early refers to a smaller set of genes transiently up-regulated in the early phase of growth, i.e., 1 to 3 hours postinoculation.

^bThe kinetic of gene expression over time refers to that exemplified in Fig. 2.

^cSamples were obtained in the early or late exponential phase of growth as described in the legend of Fig. 1.

^dExpression ratios (SCV test strain/Newbould). A decrease is indicated by a minus sign.

^eThe expression ratios evaluated by real-time PCR for the gene SACOL 2088 were calculated for the test SCV versus prototype strain ATCC 29213 instead of Newbould.

^fReal-time, real-time PCR.