TABLE 2.

Oligonucleotide PCR primers used in this study

Gene, mutant, protein, or method	Primer or probe	Primer sequence (5′-3′)a
VraR wild-type protein	VraR-Kpn-Nde	GGGGTACCAAGGAGGAACACATATGACGATTAAAGTATTG
	VraR-Pst	CAAACTGCAGCTATTGAATTAAATTATGTTGGAATGC
VraR-D55A protein	VraR D55A-A	GATTTAATTTTAATGGCTTTACTTATGGAAG
	VraR D55A-B	CTTCCATAAGTAAAGCCATTAAAATTAAATC
VraScyt wild-type protein	VraScyt-KpnNde PCR	GGGGTACCAAGGAGGAACACATATGGGTTCGGTACTCGCATACAAAATC
	VraScyt-Pst PCR	CAAACTGCAGTTAATCGTCATACGAATCCTC
VraS-H156A protein	VraS H156A-A	GCTCGAGAACTTGCCGATTCTGTTAGTC
	VraS H156A-B	GACTAACAGAATCGGCAAGTTCTCGAGC
VraS-H238A protein	VraS H238A-A	ATGAAAGTTGTGGCTGAAATACAAGATTTTAAAG
	VraS H238A-B	CTTTAAAATCTTGTATTTCAGCCACAACTTTCAT
VraSΔ[2-160]::ermB	SA1703 Kpn-Bam	GGGGTACCGGATCCATGAACTATGTTGAACGTTATATTGAACAG
	Primer 2 Bam	CGGGATCCGTTCATCGATAAATCACCTCTACG
	Primer 3 Bam	CGGGATCCCAGCAACTTTTTGCGGCAAGTATGA
	SA1699 staEco-Pst	CGGAATTCCTGCAGATGTCGAAAAATCACTCTTCTTCAAAATACC
VraS-H156A chromosomal	SA1703KpnBamHI	GGGGTACCGGATCCATGAACTATGTTGAACGTTATATTGAACAG
mutant	SA1699EcoPstI	CGGAATTCCTGCAGATGTCGAAAAAGGATCACTCTTCTTCAAAATACC
Kan marked vraR-SA1699	3BKpnBamHI	GGGGTACCGGATCCCAGCAACTTTTTGCGGCAAGTATGATGC
intergenic	12ABgl2	GAAGATCTCGTAAGTAACTTTTCTTAATTCGATACG
	12BBgl2	GAAGATCTCCAATCACAATATAACATCAAATAGACAC
	SA1699EcoPstI	CGGAATTCCTGCAGATGTCGAAAAAGGATCACTCTTCTTCAAAATACC
Upstream vraR operon	EYKpn	GGGGGTACCACTTTGATCCAAAAGACAAAACA
promoter	Tet marker upF	CGGGATCCGCTTCACAGAAATTCTAGAAC
	Tet marker downR	ACGCGTCGACTTTTATTACCTACAACTTCTTTA
	Kan marker upF	CGGGATCCGATAAACCCAGCGAACCATTTG
	Kan marker downR	CGGGATCCATCGATACAAATTCCTCGTAGG
qRT-PCR	VraR-450 forward	TGCTTACAGAACGAGAAATGGAAA
	VraR-535 reverse	CCGTTTTAATAGTAATATGCGATGCA
	VraR-473T (TAMRA-FAM)	TGATTGCGAAAGGTTACTCAAATCAAGAAAT

^aUnderlined regions represent restriction enzyme sequences.