TABLE 3.

DNA microarray results

Gene	Ratioc	Bayesian P value	Function (putative)d
Upregulated genesa
ykoJ	6.87	2.25E−14	Unknown
yvtA	2.66	1.47E−10	htrB, serine protease, secretion stress
htrA	2.39	6.06E−10	Serine protease, secretion stress
spollR	2.33	0.000902	Sporulation
ykzD	2.28	5.95E−05	Unknown, directly downstream of ykoJ
yvqH	2.09	3.12E−06	lial, part of liaRS regulon
cggR	1.97	0.000437	Transcriptional repressor of gapA
yvql	1.95	2.15E−05	liaH, part of liaRS regulon
ldh	1.92	0.000111	l-Lactate dehydrogenase
mtlD	1.92	6.48E−06	PTS, mannitol-specific enzyme
mtlA	1.88	2.57E−06	PTS, mannitol-specific enzyme
cssR	1.76	0.000847	Two-component regulator, secretion stress
Downregulated genesb
purN	−2.61	6.84E−11	Purine biosynthesis
purM	−2.55	1.06E−05	Purine biosynthesis
purH	−2.47	1.49E−08	Purine biosynthesis
rocR	−2.12	1.89E−08	Regulator, binding box upstream of ykoJ
yomM	−1.94	0.00081	Unknown
yddE	−1.9	3.65E−05	Unknown, operon on transposon region
yddB	−1.86	3.72E−05	Unknown, operon on transposon region
yecA	−1.85	0.000455	Transport/binding proteins and lipoproteins
ydcP	−1.8	0.000163	Unknown, operon on transposon region
yosP	−1.79	0.000742	Unknown, operon on transposon region
yddF	−1.77	0.0003	Unknown, operon on transposon region

^aUpregulated genes, higher expression when β-toxoid expression is compared to β-toxin expression.

^bDownregulated genes, lower expression when β-toxoid expression is compared to β-toxin expression.

^cRatio, expression ratio comparing expression level for strain NZ8900 overproducing β-toxoid (target strain) to that for NZ8900 overexpressing β-toxin (control).

^dPTS, phosphotransferase system.