TABLE 2.

Genes that are reduced at least 3-fold in at least one of the three microarray comparisons: the ΔMWX strain versus the wt, the Δ7ECF strain versus the wt, and the ΔMWX strain versus the Δ7ECF strain

Gene/operona	Fold change			Regulatorb	Functionsc
	ΔMWX/wt	Δ7ECF/wt	Δ7ECF/ΔMWX
σMWX target genes
sigM	0.03	0.02	1.0	M	ECF σ factor M
sigX	0.03	0.04	1.0	X	ECF σ factor X
sigW	0.04	0.01	1.0	W	ECF σ factor W
abh	0.02	0.03	1.3	MWX	Transcriptional regulator
yjbD (spx)	0.2	0.2	1.0	MWX	Redox-sensitive regulator enzyme; anti-alpha, global transcriptional regulator
dltABCDE	0.03	0.03	1.0	MX	dltABCDE operon; d-alanylation of teichoic acids
maf	0.1	0.1	0.7	M	Putative septum formation DNA-binding protein
radC (ysxA)	0.1	0.1	1.0	M	Putative DNA repair protein
rapD	0.2	0.2	0.6	M	Response regulator aspartate phosphatase
yebC	0.2	0.2	0.9	M	Putative integral inner membrane protein
yngC	0.3	0.2	0.8	M	Putative integral inner membrane protein
yceC	0.3	0.2	0.8	M	Putative stress adaptation protein
yfnI	0.4	0.2	1.3	M	Similar to lipoteichoic acid synthase
yeaA	0.01	0.01	1.0	W	Unknown
yqeZ yqfAB	0.03	0.03	1.0	W	Sublancin resistance
ydbST	0.1	0.1	1.0	W	Unknown
yvlABCD	0.1	0.2	1.0	W	Unknown
sppA	0.2	0.1	0.9	W	Signal peptide peptidase
yteJ	0.2	0.1	1.1	W	Putative integral inner membrane protein
yaaN	0.2	0.3	0.8	W	Unknown
lytR	0.4	0.2	0.9	X	Membrane-bound transcriptional regulator
yxiT	0.1	0.1	0.8		Unknown
des	0.2	0.4	1.2	DesKR	Fatty acid desaturase
yhjA	0.6	0.3	0.9		Unknown
σECF target genes
yrhI (bscR)	0.4	0.2	0.03	MX	Transcriptional regulator of cypB
rodA	0.3	0.3	0.2	M	Cell division membrane protein
ywtF	0.6	0.3	0.5	M	Transcriptional regulator; LytR family
ythP	0.1	0.03	0.2	W	Putative ABC transporter
ybfO	0.1	0.1	0.4	W	Putative exported hydrolase
sunA-sunT-bdbA-yolJ-bdbB	0.1	0.06	0.3	Abh	Sublancin 168 production, modification, and transportation
epsABCDEFGHKJKLMNO	0.4	0.2	0.2	SinR/AbrB	Exopolysaccharide biosynthesis.
tasA	0.2	0.1	0.5	SinR	Major protein component of biofilm matrix
pel	0.5	0.1	0.3	TnrA	Pectate lyase
yjhA	0.6	0.3	0.6		Similar to putative lipoprotein
σY YlaC target genes
sigY	0.8	0.008	0.003	Y	ECF σ factor Y
yxlCDEFG	0.8	0.1	0.07	Y	sigY yxlCDEFG operon; negative regulator of σY
ylaC	0.8	0.4	0.5	YlaC	ECF σ factor YlaC
ybgB	1.0	0.5	0.1	Y	Unknown
yddK	0.9	0.0002	0.0004		ICEBs1 gene
yddM	0.9	0.005	0.008		ICEBs1 gene; putative helicase
ydcN (immR)	1.7	0.1	0.01		ICEBs1 gene; transcriptional regulator (Xre family)
ybdN	1.3	0.3	0.03		Homologous to antimicrobial protein YbdN in Bacillus licheniformis
yolA	0.6	0.2	0.3		spβ prophage genes; secreted
yolB	0.8	0.1	0.3		spβ prophage gene
ysbAB	0.6	0.2	0.2		Homologous to lrgAB in Staphylococcus aureus
ykuA (pbpH)	0.7	0.2	0.2		Penicillin binding protein (class B)
yqeB	0.7	0.3	0.2		Putative membrane protein
ytzE	0.6	0.3	0.3		Similar to transcriptional regulator (DeoR family)
ptb-bcd-buk-lpdV-bkdAA-bkdAB-bkdB	1.4	0.3	0.3	CodY/BkdR/σL	Degradation of the branched-chain amino acids leucine, isoleucine, and valine
yppF	0.9	0.4	0.3	Spo0A	Unknown
ecsA	0.9	0.4	0.3		ABC transporter (ATPase)
yjcOPQ	1.2	0.4	0.3	σD	Unknown
yjcM	1.9	0.3	0.2	Spo0A	Similar to alcohol dehydrogenase and to coat-associated protein YhbB
yybNMLK	1.2	0.5	0.2	Rok	Unknown
yweA	1.8	0.3	0.1		Unknown
ykuV	1.2	0.4	0.3		Thiol:disulfide oxidoreductase, membrane protein
gntP	1.2	0.5	0.3		Gluconate permease
yclJ	1.2	0.6	0.2		Putative response regulator of YclJK two-component regulatory system.
yvrPON	2.1	0.5	0.2		Similar to ABC transporter

^aGenes in operons are shown in bold. The fold change for an operon is the average of fold changes of genes in bold in the table.

^bM refers to σ^M, W refers to σ^W, X refers to σ^X, and Y refers to σ^Y.

^cFunction annotations are based mainly on GenoList (http://genodb.pasteur.fr/cgi-bin/WebObjects/GenoList) (6).