. 2007 Nov 16;190(2):590–601. doi: 10.1128/JB.00917-07

TABLE 3.

Genes differentially expressed in D39ΔcodY

Gene name	ID		Annotation^a	MA ratio^b	2D ratio^c	EMSA^d	K_d (nM)^e
Gene name	TIGR4	D39	Annotation^a	MA ratio^b	2D ratio^c	EMSA^d	CodY	CodY (10 nM ILV)
mutR	sp0141	spd0144	Positive transcriptional regulator of MutA	2.51		+	1,115	439
	sp0142	spd0145	Hypothetical protein (bacteriocin)	2.24		+	>2,000	1,938
	sp0143	spd0146	Hypothetical protein	2.48
	sp0144	spd0147	Hypothetical protein	2.84
	sp0145	spd0148	Hypothetical protein	2.43
	sp0159	spd0161	Hypothetical protein	2.46		+	834	73
cps2K		spd0326	UDP-glucose 6-dehydrogenase		1.47
aliA	sp0366	spd0334	Oligopeptide-binding protein	2.18	2.98
pbpA	sp0369	spd0336	Penicillin-binding protein 1A	−0.09	1.92
ilvB	sp0445	spd0404	Acetolactate synthase large subunit	3.02		+	>2,000	284
ilvN	sp0446	spd0405	Acetolactate synthase small subunit	3.24
ilvC	sp0447	spd0406	Ketol-acid reductoisomerase	3.03	2.28
	sp0448	spd0407	Hypothetical protein	2.98
	sp0449	spd0408	Hypothetical protein	3.70
ilvA	sp0450	spd0409	Threonine dehydratase	2.95	1.70
grpE	sp0516	spd0459	Heat shock protein GrpE	0.22	1.26
livJ	sp0749	spd0652	ABC transporter substrate-binding protein, BCAA transport	1.88		+	597	52
livH	sp0750	spd0653	ABC transporter membrane-spanning permease, BCAA transport	1.58
livM	sp0751	spd0654	ABC transporter membrane-spanning permease, BCAA transport	1.90
livG	sp0752	spd0655	ABC transporter ATP-binding protein, BCAA transport	2.25
livF	sp0753	spd0656	ABC transporter ATP-binding protein, BCAA transport	2.30
acuB	sp0754	spd0657	Acetoin utilization protein	1.08		+	>2,000	773
pnp	sp0831	spd0726	Purine-nucleoside phosphorylase	0.35	1.44
ilvE	sp0856	spd0749	BCAA aminotransferase	2.08	—^f	+	482	68
	sp0857	spd0750	ABC-SBP-internal deletion, AliB like (blastN)	2.09
	sp0858	spd0751	Hypothetical protein	2.15
	sp0859	spd0752	Membrane protein	2.07
pcp	sp0860	spd0753	Pyrrolidone-carboxylate peptidase	1.39	1.75
	sp0882	spr0778	Putative esterase, S. suis (blastN)	1.64
	sp0884	spd0780	Putative esterase S. suis (blastN)	1.78		−
	sp0885	spd0781	Putative carbamoylphosphate synthase large subunit (blastN)	1.94
asd	sp1013	spd0900	Aspartate-semialdehyde dehydrogenase	2.06	1.40	+	>2,000	120
dapA	sp1014	spd0901	Dihydrodipicolinate synthase	1.69
gapN	sp1119	spd1004	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase	1.05		+	752	211
glxK	sp1126	spd1011	Glycerate kinase	1.33
gdhA	sp1306	spd1158	Glutamate dehydrogenase (NADP⁺)	1.71	2.80	+	726	156
rplL	sp1354	spd1187	50S ribosomal protein L7/L12	−0.17	2.20
rplJ	sp1355	spd1188	50S ribosomal protein L10	−0.10	1.43
nagB	sp1415	spd1246	N-Acetylglucosamine-6-phosphate isomerase	−0.19	1.37
	sp1578	spd1408	Methyltransferase, putative	1.16		+	>2,000	368
dctA	sp1753	spd1563	Dicarboxylate/amino acid:cation (Na⁺ or H⁺) symporter	2.81
	sp1754	spd1564	Hypothetical protein (integral membrane protein)	2.84
fatD	sp1869	spd1649	Iron compound ABC transporter, permease protein	2.80		+	>2,000	>2,000
fatC	sp1870	spd1650	Iron compound ABC transporter, permease protein	2.44
fecE	sp1871	spd1651	Iron compound ABC transporter, ATP-binding protein	1.37
fatB	sp1872	spd1652	Iron compound ABC transporter, iron-compound-binding protein	1.07
amiD	sp1889	spd1669	Oligopeptide ABC transporter, permease protein	1.20
amiC	sp1890	spd1670	Oligopeptide ABC transporter, permease protein	1.72
amiA	sp1891	spd1671	Oligopeptide ABC transporter, oligopeptide-binding protein	1.21	1.41	+	677	433
	sp2125	spd1954	Hypothetical protein	2.18		+	754	630
rpoA	sp0236	spd0218	DNA-directed RNA polymerase subunit α	−0.12	−1.86
ABC-NBD	sp0483	spd0434	ABC transporter ATP-binding protein, cobalt transport	−0.34	−1.96
fba	sp0605	spd0526	Fructose-bisphosphate aldolase	−0.20	−1.64
pepV	sp0623	spd0542	Dipeptidase	−0.21	−2.42
	sp1429	spd1258	Putative peptidase, U32 family	−1.29	−1.81
pgm	sp1498	spd1326	Phosphoglucomutase	0.11	−1.57
atpB	sp1513	spd1340	Proton-translocating ATPase, F0 sector, subunit a	−0.15	−1.58
dpr	sp1572	spd1402	DNA binding protein starved-cell-like peroxide resistance protein	−2.69	−1.55
codY	sp1584	spd1412	Transcriptional pleiotropic repressor CodY	−1.68		+	>2,000	382
gapA	sp2012	spd1823	Glyceraldehyde-3-phosphate dehydrogenase	−0.20	−1.93
pcpA	sp2136	spd1965	Choline-binding protein PcpA	−1.36		+	>2,000	903
pgsA	sp2222	spd2049	CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase	0.14	−1.67

Annotation is according to the Kyoto Encyclopedia of Genes and Genomes database (www.kegg.com).

Microarray (MA) ratios are given as follows: expression of ΔcodY/expression of wild type (log₂ transformed).

2D DIGE (2D) ratios are given as follows: expression of ΔcodY/expression of wild type (log₂ transformed).

In the EMSA column, a plus sign indicates a shift, while a minus sign indicates no shift.

The K_ds of the promoter region (concentration of CodY at which 50% of the probe is shifted) without addition of BCAAs and in the presence 10 mM BCAAs are shown.

—, only expressed in the codY mutant.