TABLE 2.

Genes found to be strongly (>3-fold) regulated by coaggregation in a microarray screen

ORF	Gene	Predicted function	Relative fold expression in coaggregates vs monoculturesa
			Microarray	Q-RT-PCRb
Up-regulated
SGO_0292	spxB	Pyruvate oxidase	3.1 ± 0.7	4.7 ± 0.4
SGO_1582	bfbF	6-Phospho-β-glucosidase	4.3 ± 2.0	15.5 ± 3.9
SGO_1581	bfbG	Conserved hypothetical protein	3.1 ± 0.4
SGO_1580	bfbB	PTS, component EIIB	4.2 ± 2.6c
SGO_1579	bfbR	Antiterminator, BglG family	5.3 ± 2.2
SGO_1578	bfbA	PTS, component EIIA	4.3 ± 1.6
SGO_1577	bfbD	Conserved hypothetical protein	9.0 ± 2.4
SGO_1576	bfbC	PTS, component EIIC	7.8 ± 1.8	17.9 ± 1.9
SGO_1308		Conserved hypothetical protein	3.2 ± 0.6
Down-regulated
SGO_0178	rnpA	RNase P	−4.4 ± 0.2
SGO_0177		Hypothetical protein	−5.0 ± 0.4
SGO_0176	argH	Arginosuccinate lyase	−13.9 ± 0.2
SGO_0175	argG	Arginosuccinate synthase	−10.9 ± 0.3	−20.9 ± 0.6
SGO_1716		Hpp family oligopeptide binding lipoprotein	−3.1 ± 0.1
SGO_1590	arcD	Arginine-ornithine antiporter	−4.2 ± 0.3	−2.1 ± 0.4
SGO_1569	argC	N-Acetyl-γ-glutamyl-phosphate reductase	−15.5 ± 0.3	−20.2 ± 0.8
SGO_1568	argJ	Bifunctional arginine biosynthesis protein	−11.8 ± 0.3
SGO_1567	argB	N-Acetylglutamate kinase	−12.3 ± 0.2
SGO_1566	argD	Acetylornithine aminotransferase	−7.7 ± 0.2	−20.8 ± 0.6
SGO_1109	pyrB	Aspartate carbamoyltransferase	−3.5 ± 0.1
SGO_1108	pyrP	Uracil permease	−4.5 ± 0.2
SGO_1104	pyrAb	Carbamoyl phosphate synthase, large subunit	−4.6 ± 0.4	−2.5 ± 0.1
SGO_1103	pyrAa	Carbamoyl phosphate synthase, small subunit	−4.3 ± 0.4

^aGene expression values represent geometric means ± standard deviations for three independent experiments.

^bThe expression of representative genes was further analyzed by Q-RT-PCR. The absence of data indicates that expression levels were not determined.

^cNot considered significant by significance analysis of microarrays.