Table 3.

Genes with ≥2 times higher expression in wild-type S. aureus Newman than in the ΔyabJ-spoVG mutant SM148

Newman TIGR locus namea	Gene symbolb	Descriptionb	Newman/SM148 fold changec	Newman/MS64 fold changec	Reference(s) with reported σB dependence	σB promoterd	Transcription unit 5′-3′e	Patternf
NWMN_0095*	capA	Capsular polysaccharide biosynthesis protein Cap5A	9.3	2.8	7, 25, 36, 38	No	nwmn_0095-0110	i
NWMN_0096	capB	Capsular polysaccharide biosynthesis protein Cap5B	11.0	2.8	7, 38	No	nwmn_0095-0110
NWMN_0097	capC	Capsular polysaccharide biosynthesis protein Cap5C	9.5	2.5	7, 38	No	nwmn_0095-0110
NWMN_0098	capD	Capsular polysaccharide biosynthesis protein Cap5D	12.1	2.8	7, 38	No	nwmn_0095-0110
NWMN_0099	capE	Capsular polysaccharide biosynthesis protein Cap5E	7.2	2.4	7, 38	No	nwmn_0095-0110
NWMN_0100	capF	Capsular polysaccharide biosynthesis protein Cap5F	7.5		7, 38	No	nwmn_0095-0110
NWMN_0101	capG	Capsular polysaccharide biosynthesis protein Cap5G	6.0		7, 38	No	nwmn_0095-0110
NWMN_0102	capH	Capsular polysaccharide biosynthesis protein Cap5H	4.4	2.1	7, 38	No	nwmn_0095-0110
NWMN_0103	capI	Capsular polysaccharide biosynthesis protein Cap5I	4.9	2.4	7, 38	No	nwmn_0095-0110
NWMN_0104	capJ	Capsular polysaccharide biosynthesis protein Cap5J	3.1	2.1	7, 38	No	nwmn_0095-0110
NWMN_0105	capK	Capsular polysaccharide biosynthesis protein Cap5K	2.7	2.1	7, 38	No	nwmn_0095-0110
NWMN_0106	capL	Capsular polysaccharide biosynthesis protein Cap5L	2.1		7, 38	No	nwmn_0095-0110
NWMN_0107	capM	Capsular polysaccharide biosynthesis protein Cap5M	2.2	2.1	7, 38	No	nwmn_0095-0110
NWMN_0108	capN	Capsular polysaccharide biosynthesis protein Cap5N	2.0		7, 38	No	nwmn_0095-0110
NWMN_0152		Maltose ABC transporter substrate-binding protein, putative	2.8		25	No	nwmn_0151-0156	iii
NWMN_0218*		Staphyloxanthin biosynthesis protein, putative	2.9	0.5	7, 25	No	nwmn_0218	ii
NWMN_0219*	esxA	Virulence factor EsxA	2.7			Yes	nwmn_0219	iii (ii)
NWMN_0220	esaA	Membrane protein EsaA	2.2		7, 25	No	nwmn_0220-0227	iii
NWMN_0451		Conserved hypothetical protein	2.1			No	nwmn_0451-0452	iii
NWMN_0460	yabJ	YabJ protein	254.0	3.6	7, 36, 46	Yes	nwmn_0460-0461	−
NWMN_0461	spoVG	Regulatory protein SpoVG	77.6	4.1	7, 36, 46	No	nwmn_0460-0461	−
NWMN_0525	sdrE	Ser-Asp rich fibrinogen/bone sialoprotein-binding protein SdrE	2.2	0.4		No	nwmn_0525	ii
NWMN_0559		Conserved hypothetical protein	2.3			No	nwmn_0559-0560	iii
NWMN_0753		Lipoprotein, putative	2.1			No	nwmn_0753	iii
NWMN_0760*	nuc	Thermonuclease precursor	3.0		7, 25, 38	No	nwmn_0760	iii (ii)
NWMN_1279	trpE	Anthranilate synthase component I	2.1			No	nwmn_1279-1285	iii
NWMN_1560*	abrB	Ammonia monooxygenase	2.4	3.3		No	nwmn_1560	i
NWMN_1702*	splE	Serine protease SplE	2.1	0.1	7, 54	No	nwmn_1702	ii
NWMN_1708		Conserved hypothetical protein	2.0			No	nwmn_1708	iii
NWMN_1718*	lukD	Leucotoxin LukD	2.9	0.1		No	nwmn_1719-1718	ii
NWMN_1719	lukE	Leucotoxin LukE	2.7	0.1		No	nwmn_1719-1718
NWMN_2061	fmtB	Methicillin resistance determinant FmtB protein	2.5			No	nwmn_2061	iii
NWMN_2365		Conserved hypothetical protein	2.2		38	No	nwmn_2367-2365	iii
NWMN_2553	hsa	LPXTG cell wall surface anchor family protein	2.1		7	Yes	nwmn_2553	iii
NWMN_2569*	lip	Lipase	2.3	0.3	7, 54	No	nwmn_2569	ii

^aLocus number for S. aureus Newman (http://www.tigr.org). *, genes selected for Northern blot analysis.

^bGene symbol and description of the gene based on the TIGR annotation (http://www.tigr.org).

^cFold change of gene transcription comparing S. aureus Newman with either SM148 or MS64.

^dORFs preceded by a promoter sequence that resembles the σ^B consensus sequence of S. aureus described by Homerova et al. (27). Sequences matching the GNNTNN-12-15-NGGTAN consensus, with no more than three mismatches of the degenerated bases from the GTTTAA-12-15-GGGTAT sequence and lying within a range of 500 bp upstream of the ORF were accepted.

^eTranscription units were deduced from Northern blot analyses done in this study or published by Pané-Farré et al. (38) or Meier et al. (36). Where no experimental data were available, the operons are indicated as predicted by Wang et al. (52).

^fAssignment of transcription units into regulatory patterns: i, upregulated by YabJ/SpoVG and σ^B; ii, upregulated by YabJ/SpoVG, downregulated by σ^B; iii, upregulated by YabJ/SpoVG; −, deleted yabJ-spoVG operon, upregulated by σ^B; in parentheses, assignment to class ii according to Northern blot analyses.