TABLE 3.

Microarray results showing genes that are differentially regulated in the vncR mutant HS0603, the vncS mutant HS0604, and the vex3 mutants HS0601 and HR0601 in the absence of erythromycin^a

Microarray IDb	Annotation	Fold change for:
		HS0603	HS0604	HS0601	HR0601
vex-vncRS locus
SP0598	Hypothetical protein			62.0
SP0599	Transmembrane protein, vex1			114.7
SP0600	ABC transporter, ATP-binding protein, vex2			121.6
SP0601	Transmembrane protein, vex3			−33.0	−10.4
SP0603	DNA-binding response regulator, vncR	−150.6		14.8
SP0604	Sensor histidine kinase, vncS		−45.5	14.5
Transport functions
SP0729	Cation-transporting ATPase, E1-E2 family				−2.5
SP1062	ABC transporter, ATP-binding protein				2.1
SP1215	Transporter, FNT family, putative				−2.7
SP1241	Amino acid ABC transporter, permease protein				2.9
SP1242	Amino acid ABC transporter, ATP-binding protein				2.4
SP1394	Amino acid ABC transporter			−1.7	2.0
SP1527	ABC transporter, oligopeptide-binding protein, aliB			−2.0
SP1572	Nonheme iron-containing ferritin				2.5
SP1848	Xanthine permease, pbuX		−2.0
SP1871	Iron-compound ABC transporter				−3.0
SP2108	Maltodextrin ABC transporter, malX				−1.7
SP2109	Maltodextrin ABC transporter, malC				−2.0
SP2110	Maltodextrin ABC transporter, malD				−1.8
Ribosomal proteins
SP0441	Ribosomal protein L28, rpmB			−2.4
SP1107	Ribosomal protein L27, rpmA				2.3
SP1299	Ribosomal protein L31, rpmE	2.0
Biosynthesis and degradation of polysaccharides
SP0107	LysM domain protein				2.8
SP0268	Alkaline amylopullulanase, putative				−2.4
SP2106	Glycogen phosphorylase family protein				−2.2
SP0240	Phosphoglycerate mutase family protein				2.1
SP0285	Alcohol dehydrogenase, zinc containing				−2.2
SP0447	Ketol acid reductoisomerase, ilvC				2.1
SP0502	Glutamine synthetase, glnA				3.4
SP0730	Pyruvate oxidase, spxB				−2.1
SP0837	DNA topology modulation protein FlaR, putative				2.3
SP0965	Endo-beta-N-acetylglucosaminidase, lytB				2.0
SP1052	Phosphoesterase, putative				2.1
SP1113	DNA-binding protein HU, hup				2.1
SP1470	Thiamine biosynthesis protein ApbE, putative				−2.6
SP1471	Oxidoreductase, putative				−3.1
SP1472	Oxidoreductase, putative				−2.8
SP1963	CBS domain protein				2.2
SP2026	Alcohol dehydrogenase, iron containing				−4.0
SP2056	N-acetylglucosamine-6-P deacetylase, nagA				−2.1
SP2157	Alcohol dehydrogenase, iron containing				−2.6
SP2216	Secreted 45-kDa protein, usp45				2.4
Hypothetical proteins
SP0088	Hypothetical protein				2.0
SP0097	Conserved domain protein				−3.7
SP2107	4-Alpha-glucanotransferase, malQ				−2.0
Regulatory functions
SP0501	Transcriptional regulator, MerR family				3.3
SP0837	DNA topology modulation protein FlaR, putative				2.3
SP1061	Protein kinase, putative				2.7
SP1362	Putative transcriptional regulator, mecA				2.0
SP1809	Transcriptional regulator				2.0
SP1821	Sugar-binding transcriptional regulator, LacI family				2.1
SP2234	Transcriptional regulator, TetR family			−2.2
SP2235	Response regulator, comE				2.9
SP2236	Putative sensor histidine kinase, comD				2.5
Cell surface proteins
SP0462	Cell wall surface anchor family protein	2.7		4.6
SP0463	Cell wall surface anchor family protein	3.1		4.2
SP0464	Cell wall surface anchor family protein	2.6		4.3
SP2190	Choline binding protein A, cbpA			3.3
Various functions
SP0054	Phosphoribosylaminoimidazole carboxylase, purK		−2.5
SP0098	Hypothetical protein				−4.4
SP0099	Hypothetical protein				−4.2
SP0100	Conserved hypothetical protein				−3.2
SP0430	Hypothetical protein				−2.2
SP0448	Hypothetical protein				2.4
SP0728	Hypothetical protein				−2.0
SP0742	Conserved hypothetical protein				2.8
SP0861	Hypothetical protein				2.2
SP0958	Hypothetical protein				−2.2
SP1053	Conserved domain protein				2.1
SP1059	Hypothetical protein				3.3
SP1140	Hypothetical protein				2.0
SP1141	Hypothetical protein				2.1
SP1145	Hypothetical protein				2.0
SP1793	Hypothetical protein				2.0
SP1810	Hypothetical protein				2.0
SP2191	Conserved hypothetical protein			2.3
SP2232	Conserved hypothetical protein, authentic frameshift			−4.3
SP2233	Hypothetical protein			−3.4	−3.7

^aMean changes (n-fold) from three independent biological samples are shown. Genes that are differentially regulated more than twofold are shown. Statistical significance was verified by ANOVA.

^bMicroarray ID, identification number from microarray analysis.