Table 4. Oligonucleotides used in this study.

Oligonucleotides a	Sequence (5’-3’)
bcaP Ups F bcaP Ups R	GGGGACAAGTTTGTACAAAAAAGCAGGCTCAGTCTTCGTATTCACCTGC CTTCCCATAAACTTTCCTCC For generating upstream arm for bcaP deletion
bcaP Dwn F bcaP Dwn R	5’ /Phos/ ACGTAGCTGAATACCACCC GGGGACCACTTTGTACAAGAAAGCTGGGTTGTACCTGCTGACGAAGTAG For generating downstream arm for bcaP deletion
ilvDC F ilvDC R	GATCCCCGGGACCTGCTCCTAAATCTCCG GATCGTCGACACTTCTTGCTGGTGCTTGG For cloning ilvD 5’UTR into pGYlux
ilvDP F ilvDPR	GATCCCCGGGGTACGTCTTACACCAAG GATCGTCGACAGTTGTCGGTTGATGTTC For cloning partial ilvD 5’UTR into pGYlux
ilvDValS-1 F ilvDValS-1 R	CAA ATA TTA TTA TTT TAT aAT ACT CTT TAG GAC TCG CGA GTC CTA AAG AGT ATt ATA AAA TAA TAA TAT TTG For site directed mutagenesis of pGYlux::ilvD
ilvDValS-7 F ilvDValS-7 R	CTA AAC GCT TTA AGT CaT ATT TCT GTT TGA ATG CAT TCA AAC AGA AAT AtG ACT TAA AGC GTT TAG For site directed mutagenesis of pGYlux::ilvD
ilvDValS-9 F ilvDValS-9 R	CTA AAC GCT TTA AGc CCT ATT TCT GTT TG CAA ACA GAA ATA GGg CTT AAA GCG TTT AG For site directed mutagenesis of pGYlux::ilvD
codY F codY R	GATCGGTACCCCGAATGCAGTTGTAGATATTACC GATCGAGGCTCTTATGTCCCAGACTCATCGAC For cloning codY into pRMC2
codY Seq F codY Seq R	GCAATTACTCGCTTAGCTGAG GTGTGTATTGGCTTTATAGCCG For target directed sequencing of codY
ilvD qPCR F ilvD qPCR R	GCTATCTTTTGCTCTGGTGG AGGGCAGGCATTTTGTTCC For qPCR of ilvD
ilvC qPCR F ilvC qPCR R	CAAGATGTAAAAACGGACGC GTCAAAAGAACGACCTGGG For qPCR of ilvC
oAK031	6-FAM/ATCCATTGTTCAATCGTATC
oNW025	GAAGTTGTCGGTTGATGTTC generate ilvD266p for EMSA

^a All primer sequences, except oAK031 and oNW025 (based on UAMS-1), are based on the USA300 FPR3757 genome; restriction sites are underlined; nucleotide mutated in site directed mutagenesis is indicate in lower case.