Table 1.

Characterized Rex binding sites in S. aureus.

Locusa	Genea	Descriptiona	Posb	Rex binding motifsc	EMSAd	mRNAe	Prote
SACOL0135	(adhE)	Alcohol dehydrogenase, iron-containing	−39		Shift	Up	Up
SACOL0301	(nirC)	Formate/nitrite transporter family protein	−51		Shift
SACOL1478	ald1	Alanine dehydrogenase	−38		Shift	Up
SACOL0660	(adh1)	Alcohol dehydrogenase	−306		Shift	Up	Up
SACOL1535	srrA	DNA-binding response regulator SrrA	−103		Shift	No change	Up
SACOL2535	(ddh)	d-isomer specific 2-hydroxyacid dehydrogenase family protein	−102		Shift
SACOL2534	frp	NAD(P)H-flavin oxidoreductase	−185		[Shift]f
SACOL0204	pflB	Formate acetyltransferase	−96		Shift	Up	Up
SACOL0222	ldh1-1	l-lactate dehydrogenase	−227		Shiftg	Up	Up
SACOL0220	(hmp)h	Flavohemoprotein, putative	−363		[Shift]
SACOL0222	ldh1-2h	l-lactate dehydrogenase	−169		Shifti	Up	up
SACOL2006	(lukM)	Aerolysin/leucocidin family protein	−66		Shift
SACOL2007		Unknown	−386		[Shift]j
SACOL2363	(lctP)	l-lactate permease	−124		Shift	Up
SACOL2364		Conserved hypothetical protein	−210		[Shift]k
SACOL0019	yycF (vicR)	DNA-binding response regulator YycF	−85		Shiftl	No change
SACOL0966	pgi	Glucose-6-phosphate isomerase	−69		No shift
SACOL2399	nirR	Transcriptional regulator NirR	−64		Shift	Up
SACOL2657	arcA	Arginine deiminase	−79		Shift
SA2185	narG	Respiratory nitrate reductase alpha chain	−107		Shift	Up
SArRNA04	5sRNA	5S ribosomal RNA	−85		No shift
SACOL1889	hemE	Uroporphyrinogen decarboxylase	−91		No shift

^aLoci, symbols and descriptions are based on TIGR annotation of S. aureus COL (http://cmr.jcvi.org). Gene symbols in brackets refer to common annotations found for other S. aureus strains.

^bPositions of the Rex binding motifs related to the gene start.

^cMismatches to the Rex consensus sequence are underlined.

^dRex binding sites verified by EMSA are indicated by ‘shift’. Motifs showing no Rex binding affinity are indicated by ‘no shift’.

^eThe influence of Rex on transcript level or protein synthesis. Up = induction in the mutant.

^fddh and frp share the same binding site.

^gEMSA was done with the distal binding site ldh1-2.

^hldh and hmp share the same binding site (ldh1-2).

ⁱEMSA was done with the proximal binding site ldh1-1.

^jlukM and SACOL2007 share the same binding site.

^klctP and SACOL2364 share the same binding site.

^lIn EMSA, a distinct shifted band of the regulatory region of vicR was only observed in the presence of NAD⁺.