TABLE 1 .

Differential gene expression in D39 relative to that in D39ΔluxS with or without AI-2^a

D39 ORFb	Gene	Description	D39 vs D39ΔluxS	D39ΔluxS vs D39ΔluxS + AI-2	D39 vs D39 + AI-2
SPD_0091		Conserved hypothetical protein		2.7	1.7
SPD_0114		Hypothetical protein	3.9
SPD_0115		Hypothetical protein	3.9
SPD_0116		Hypothetical protein	4.5
SPD_0117		Hypothetical protein	0.4
SPD_0265	adhA	Alcohol dehydrogenase			0.7
SPD_0309	luxS	LuxS S-ribosylhomocysteine lyase	0.0003
SPD_0334	aliA	Oligopeptide-binding protein AliA	2.1
SPD_0404	ilvB	Lactose phosphotransferase system repressor	1.7
SPD_0405	ilvN	Acetolactate synthase	1.7
SPD_0406	ilvC	Ketol-acid reductoisomerase	1.7
SPD_0407		Conserved hypothetical protein	1.8
SPD_0408		Conserved hypothetical protein	1.8
SPD_0420	pflB	Formate acetyltransferase		0.4	0.6
SPD_0451		Type I restriction-modification system	1.7
SPD_0546	brnQ	Branched-chain amino acid transport system II carrier protein	1.5	2.9	2.3
SPD_0558	prtA	Cell wall-associated serine protease PrtA		0.5
SPD_0732		30S ribosomal protein			1.6
SPD_0771	lacR1	Lactose phosphotransferase system repressor	1.9	0.3	0.6
SPD_0772	fruB	1-Phosphofructokinase	1.9	0.3	0.5
SPD_0773	fruA	PTS, fructose-specific IIABC components	1.7	0.4	0.7c
SPD_0900	asd	Aspartate-semialdehyde dehydrogenase	1.6
SPD_0901	dapA	Dihydrodipicolinate synthase	1.6
SDP_1004	gapN	Glyceraldehyde-3-phosphate dehydrogenase			0.6
SPD_1256		Peptidase, U32 family protein			0.6
SPD_1257		Conserved hypothetical protein			0.6
SPD_1258		Peptidase, U32 family protein			0.6
SPD_1360		Conserved hypothetical protein			1.7
SPD_1408		Conserved hypothetical protein	1.8		1.7
SPD_1415		Oxidoreductase, pyridine nucleotide-disulfide			1.5
SPD_1504	nanA	Sialidase A (neuraminidase A)			0.5
SPD_1563	dctA	Serine/threonine transporter SstT	1.6
SPD_1649	piuA	Iron compound ABC transporter	1.6	2.0	1.6
SPD_1650		Iron compound ABC transporter			1.5
SPD_1834	adhE	Bifunctional acetaldehyde-coenzyme A/alcohol dehydrogenase	2.0	0.1	0.1
SPD_1956	ilvD	Dihydroxy-acid dehydratase			0.6
SPD_2012	glpO	Alpha-glycerophosphate oxidase			1.7
SPD_2013	glpK	Glycerol kinase			1.6

^aDifferential gene expression was determined by RNA-seq analysis as described in Materials and Methods. Data shown are fold changes in gene expression for the comparisons indicated. Genes commonly differentially expressed in all three comparisons are shown in bold type. Only genes with statistically significant differential expression (adjusted P < 0.05) are shown, except where indicated otherwise.

^bORF, open reading frame.

^cNo statistically significant differential expression.