. 2013 Dec 3;289(4):1892–1904. doi: 10.1074/jbc.M113.517714

TABLE 1.

Bacterial strains and plasmids used in this study

Strain or plasmid	Relevant genotype or phenotype^a	Reference or source
E. coli strains
DH10B	F′, mcrA Δ(mrr hsdRMS-mcrBC) φ80dlacΔM15 ΔlacX74 deoR recA1 araD139 Δ(ara-leu)7697 galU galK rpsL (Sm^r) endA1 nupG	Invitrogen
M15	Strain for regulated high level expression with pQE vectors	Qiagen
MC4100	araD139 Δ(argF-lac)U169 rpsL150 (Sm^r) relA1 flbB5301 deoC1 ptsF25 rbsR	28
AFMCP_N	Km^r Rf^r, MC4100 spontaneous rifampicin-resistant mutant harboring a chromosomal insertion of the P_N::lacZ translational fusion	23
SM10 λpir	Km^r thi-1 thr leu tonA lacY supE recA::RP4–2-Tc::Mu λpir lysogen	29
S17-1λpir	Tp^r Sm^r recA thi hsdRM⁺ RP4::2-Tc::Mu::Km Tn7 λpir lysogen	30
XLI-Bue MRA (P2)	Δ(mcrA)183, Δ(mcrCB-hsdSMR-mrr)173, endA1, gyrA96, supE44, relA1, thi-1, lac, P2 lysogen	Stratagene

Azoarcus sp. CIB strains
CIB	Wild-type strain	20
CIBΔaccR	Azoarcus sp. strain CIB with a deletion of the accR gene	This work

Plasmids
pQE32	Ap^r, oriColE1, T5 promoter lac operator, λ t_o/E. coli rrnB T1 terminators, N-terminal His₆	Qiagen
pQE32-His₆-AccR	Ap^r, pQE32 derivative for expression of His₆-accR; carries a 636-bp BamHI to PstI fragment generated using primers 5′HisaccR and 3′HisaccR (Table 2)	This work
pQE32-His₆-CAccR	Ap^r, pQE32 derivative for expression of His₆-CaccR; carries a 232-bp BamHI to PstI fragment generated using 5′HisCaccR and 3′HisaccR (Table 2)	This work
pQE32-His₆-AccRD60E	Ap^r, pQE32 derivative for expression of His₆-accRD60E; carries a 636-bp BamHI to PstI fragment generated using flanking primers 5′HisaccR and 3′HisaccR and overlapping PCR mutagenesis primers 5′AccRD60E and 3′AccRD60E	This work
pREP4	Km^r, plasmid that expresses the lacI repressor	Qiagen
pECOR7	Ap^r, pUC19 harboring a 7.1-kb EcoRI fragment containing the bzdRNO genes	20
pKNG101	Sm^r, oriR6K, Mob⁺. Suicide vector with a sacB selection marker for gene replacement by double site homologous recombination	31
pKNG101ΔaccR	Sm^r, pKNG101 derivative carrying the ΔaccR allele as a 1.4-kb BamHI to SpeI fragment assembled using the four AccRmut primers listed in Table 2	This work
pIZ1016	Gm^r, oripBBR1, Mob⁺, lacZα, Ptac/lacI^q, broad-host-range cloning and expression vector	32
pIZAccSR	Gm^r, pIZ1016 derivative expressing accR from the Ptac promoter; carries a 3.3-kb SalI to SpeI fragment amplified using primers 5′AccSR and 3′AccSR (Table 2)	This work
pIZAccRD60E	Gm^r, pIZ1016 derivative expressing the His₆-accRD60E from the Ptac promoter; carries a 0.6-kb BamHI to PstI fragment derived from pQE32-His₆-AccRD60E	This work
pBBR1MCS-5	Gm^r, oripBBR1, Mob⁺, lacZα, Plac, broad-host-range cloning and expression vector	33
pBBR5AccR	Gm^r, pBBR1MCS-5 derivative expressing the accR gene from the Plac promoter; carries a 697-bp BamHI to XbaI fragment generated using primers 5′AccRExt and 3′AccRExt (Table 2)	This work
pBBR5P_N	Gm^r, pBBR1MCS-5 derivative harboring a P_N::lacZ translational fusion	23
pBBR5P_NI	Gm^r, pBBR1MCS-5 derivative harboring a 4.2-kb BamHI to XbaI fragment that expresses the P_NI::lacZ translational fusion. The truncated P_NI promoter spans from position −61 to +79 with respect to the transcription start site	This work
pIZP_B1	Gm^r, pIZ1016 derivative harboring a P_B1::lacZ translational fusion	34
pJCD-P_N	Ap^r, pJCD01 derivative harboring a 585-bp EcoRI fragment that includes the P_N promoter	25

^a Ap^r, ampicillin-resistant; Gm^r, gentamicin-resistant; K_m^r, kanamycin-resistant; Rf^r, rifampicin-resistant; Sm^r, streptomycin-resistant.