. 2003 Jan;185(2):610–619. doi: 10.1128/JB.185.2.610-619.2003

TABLE 4.

Genes upregulated by Rot

Chip ORF no.^a	N315 ORF no.^b	N315 gene^b	N315 description^b	Fold change^c	agr or sar effect^d	Role category^d
3994	SA1736	aldH	Aldehyde dehydrogenase	2.1
5372		clfB	Clumping factor B	2.9
2462	SA2336	clpL	ATP-dependent Clp proteinase chain ClpL	2.7	sar, down	Adaptation
3833		coa	Coagulase	4.3
2163	SA1253	ctpA	Probable carboxy-terminal processing proteinase CtpA	2.9
5110	SA1164	dhoM	Homoserine dehydrogenase	2.3
4873	SA0796	dltD	Poly(glycerophosphate chain) d-alanine transfer protein	2.0	agr, down	Transport
3383		epiA	Lantibiotic gallidermin precursor EpiA	2.6
84	SA0602	fhuA	Ferrichrome transport ATP-binding protein	2.1
4551	SA2172	gltT	Proton/sodium-glutamate symport protein	2.2
4042	SA2288	gtaB	UTP-glucose-1-phosphate uridyltransferase	2.4
3984	SA0189	hsdR	Probable type I restriction enzyme restriction chain	2.4
2883	SA1505	lysP	Lysine-specific permease	2.4	agr, up	Transport
4486	SA0250	lytS	Two-component sensor histidine kinase	2.3
1047	SA1194	msrA	Peptide methionine sulfoxide reductase homolog	2.4
854	SA2410	nrdD	Anaerobic ribonucleoside-triphosphate reductase	2.1
4205	SA0685	nrdI	NrdI protein involved in ribonucleotide reductase function	2.9
4390	SA0374	pbuX	Xanthine permease	2.3
4905	SA0923	purM	Phosphoribosylformylglycinamidine cyclo-ligase PurM	2.2	sar, down	Nucleotide and nucleic acid metabolism
2800	SA0676	recQ	Probable DNA helicase	2.8	agr, up	DNA replication
1079	SA1583	rot	Repressor of toxins Rot	12.0
2343		sdrC	SdrC protein	2.7	sar, up	Virulence factors
2119	SA0107	spa	Immunoglobulin G binding protein A precursor	15.6	agr, down	Virulence factors
5112	SA1166	thrB	Homoserine kinase homolog	3.9
3239	SA1165	thrC	Threonine synthase	3.8
5075	SA0373	xprT	Xanthine phosphoribosyltransferase	3.0
17			HP	2.0
18	SA0220		HP, similar to glycerophosphodiester phosphodiesterase	2.9
237	SAS013		Reverse complement of HP (pathogenicity island SaPIn2)	2.3	agr, up	Unknown
392	SA0739		Conserved HP	2.4
442	SA0651		HP	2.2
457	SA1613		Conserved HP	2.5
477	SA0428		Conserved HP	2.5
493	SA2378		Conserved HP	3.2	agr, down	Unknown
534	SA1717		Glutamyl-tRNA^Gln amidotransferase subunit C	2.6
600	SA0523		HP, similar to poly (GP) alpha-glucosyltransferase (TA biosynthesis)	2.2	sar, up	Cell wall
616	SA2133		Conserved HP	2.8
678	SA0682		HP, similar to di-tripeptide ABC transporter	2.1
748	SA2261		HP, similar to efflux pump	3.0
873	SAS088		HP	2.2
1027	SA2007		HP, similar to alpha-acetolactate decarboxylase	2.1
1082	SA0620		Secretory antigen SsaA homologue	2.0
1175	SA2284		HP, similar to accumulation-associated protein	2.5	agr, up	Virulence factors
1353			HP	2.7
1356	SA2170		HP, similar to general stress protein 26	2.1
1357	SA2171		HP	2.0
1398	SA0914		Reverse complement of HP, similar to chitinase B	3.0	agr, up	Miscellaneous
1563	SA0407		Conserved HP	2.0
1564	SA0408		HP	2.3
1592			HP	3.0
1597			HP	2.0
1666	SA2303		HP, similar to membrane-spanning protein	3.2
1765			Epidermin immunity protein F	4.7	agr, up	Antibiotic production
1991	SA0439		HP, similar to lysine decarboxylase	2.5
2032	SA1059		Methionyl-tRNA formyltransferase	2.4	agr, up	Aminoacyl tRNA synthetases
2076				2.4
2077	SA0291		HP	3.1
2078	SA0292		HP	2.5
2103	SA0271		Conserved HP	6.3	agr, up	Unknown
2132	SA2131		Conserved HP	4.9
2133	SA2132		HP, similar to ABC transporter (ATP-binding protein)	2.4
2232	SA2440		HP	2.0
2255			HP	2.1
2337	SA2001		HP, similar to oxidoreductase, aldo/ketoreductase family	2.0
2454	SA1320		HP	4.4
2507	SA0380		Conserved HP (pathogenicity island SaPIn2)	3.5
2697	SA2442		Preprotein translocase SecA homolog	2.2
3259	SA0675		HP, similar to ABC transporter ATP-binding protein	3.0
3313	SA2436		HP, similar to phage infection protein	2.1	sar, up	Bacteriophage related
3391			Conserved HP	2.0
3426	SA1924		HP, similar to aldehyde dehydrogenase	2.5
3599			ABC transporter, ATP-binding protein	2.6
3698	SA0173		HP, similar to surfactin synthetase	2.9	agr, up	Antibiotic production
3888	SA2339		HP, similar to antibiotic transport-associated protein	2.1
4153	SA0310		HP	2.1
4253	SA0003		Conserved HP	2.2
4282	SA1942		Conserved HP	2.5
4525	SA1016		Reverse complement of conserved HP	2.4
4550			HP	2.3
4667	SA0973		Phosphopantetheine adenyltransferase homolog	3.2
4752	SA1056		HP	3.5
5065	SA2256		Conserved HP	15.8
5245	SA0827		HP, similar to ATP-dependent nuclease subunit B	2.3
5437	SA0246		Hypotheticl protein, similar to d-xylulose reductase	2.1
5471	SA1131		HP, similar to 2-oxoacid ferredoxin oxidoreductase, alpha subunit	2.3
5554	SA1679		HP, similar to d-3-phosphoglycerate dehydrogenase	2.0

S. aureus GeneChip ORF number.

Based on the published sequence of strain N315 (accession no. NC_002745). For genes not present in N315, the gene name and description are from the COL genome, available from The Institute for Genomic Research Comprehensive Microbial Resource website (NC_002745). For genes not present in N315, the gene name and description are from the COL genome, available from The Institute for Genomic Research Comprehensive Microbial Resource website (http://www.tigr.org). HP, hypothetical protein; TA, teichoic acid.

Normalized values in the agr strain over values in the agr rot double mutant.

As described by Dunman et al. (12). up, upregulated; down, downregulated.