TABLE 1.

Oligonucleotide primers used in this study^a

Primer	Nucleotide sequence (5′ to 3′) (enzyme)	Location	Application	Amplification target (bp)
SSP-917B	AAC TGT ACC ACT AAT AAC TCA CAA T	Tn917-lac	PCR	Tn917-lac 5′ flanking region
PBSSK3	PBSSK3: GTA AAA CGA CGG CCA GT	pBluescript	PCR
Kan1 MluI	CGA CGC GTC GCC GTC GAT ACT ATG TTA T (MluI)	pSF151	Mutagenesis	kan (1,073)
Kan2 SalI	CGG TCG ACC GAT CAG AGT ATG GAC AGT T (SalI)	pSF151	Mutagenesis
NosX1	CGG GTA CCC GGG TCT TCC AAG TTC TTA G (KpnI)	nox	Mutagenesis of nosX	nosX 5′ flanking region (972)
NosX2	CGA CGC GTC GGA ATG GAT CTA GAA GTG A (MluI)	nosX	Mutagenesis of nosX
NosX3	CGG TCG ACC GCG TTA TTA CAG AAG ATA ATC (SalI)	nosX	Mutagenesis of nosX	nosX 3′ flanking region (998)
NosX4	CGC TCG AGC GAG CCA TTC AAG TAC AGA T (XhoI)	qor1	Mutagenesis of qor1
O1P1	CGG GTA CCC GGT GAT AAA AGT GGA TCT C (KpnI)	nosX	Mutagenesis of qor1	qor1 5′ flanking region (1,062)
O1P2	CGA CGC GTC GAA AGT GTT TTT GCA TGT A (MluI)	qor1	Mutagenesis of qor1
O1P3	CGG TCG ACC GGT ATC TTC GTG AAG ATT A (SalI)	qor1	Mutagenesis of qor1	qor1 3′ flanking region (858)
O1P4	CGC TCG AGC GCA TAT CGA TTT GGT TAA C (XhoI)	qor2	Mutagenesis of qor1
O2P1	CGG GTA CCC GAT TAC TGT CCA TCC AAG A (KpnI)	qor1	Mutagenesis of qor2	qor2 5′ flanking region (1,018)
O2P2	CGA CGC GTC GAT GAT TGA TCG TAG TTT G (MluI)	qor2	Mutagenesis of qor2
O2P3	CGG TCG ACC GTG GAG GTC ATG GAG AC (SalI)	qor2	Mutagenesis of qor2	qor2 3′ flanking region (698)
O2P4	CGC TCG AGC GAG CTG CAG TGT TTT TAA C (XhoI)	ahpC	Mutagenesis of qor2
O2P1	See above	nosX	RT-PCR	nosX-qor2 (1,018)
O2P2	See above	qor2	RT-PCR
O1P3	See above	qor1	RT-PCR	qor1-qor2 (858)
O1P4	See above	qor2	RT-PCR
NosX RT5′	ATT GGC TTT AAA GAT GCC AGA GT	nosX	Real-time RT-PCR	nosX (101)
NosX RT3′	GAA CGG GCA GTC GGA TCT AAT	nosX	Real-time RT-PCR
O1RT5′	TTG CCA TTG TTG GAA CGA ACT	qor1	Real-time RT-PCR	qor1 (108)
O1RT3′	CCT TGA TTT CAA CAA GTT CAA TTT C	qor1	Real-time RT-PCR
O2RT5′	TTG CTA AAC GTG TAC CAC CTC AA	qor2	Real-time RT-PCR	qor2 (111)
O2RT3′	CGT TGC GAA GTG TTC CGA TA	qor2	Real-time RT-PCR
Nox RT5′	AAC CAA GGA AAG AGA TGT TTG A	nox	Real-time RT-PCR	nox (109)
Nox RT3′	GGT GCT AAC CAC GCA GGT A	nox	Real-time RT-PCR
AhpC RT5′	TTT CTT ACA TGG CCC ACA CCA	ahpC	Real-time RT-PCR
AhpC RT3′	TGA AGT CTA TGG ACG GAA AAA CTG T	ahpC	Real-time RT-PCR	ahpC (98)
23S rRNA RT5′	ACTGCAATGTGGACTCAGAATTTAT	23S rRNA	Real-time RT-PCR	23S rRNA gene (90)
23S rRNA RT3′	TACAGAATCTATTTAAAATACGAGGCTCT	23S rRNA	Real-time RT-PCR

^aEngineered restriction sites not present in the template sequence are in boldface type. The corresponding restriction enzyme is shown in parentheses to the right of the primer sequence.