Cells were then plated on LB agar containing kanamycin for selection of mutants whose wild-type genes were replaced by allelic exchange via double crossover recombination. Gene replacement in candidate clones was verified by PCR with upFW and dwRV primers (Figure Angiogenesis inhibitor 6). Allelic replacement in candidate clones was further confirmed by sequencing the CH5424802 cost mutant region in the resulting mutants. Figure 6 Gene replacement. (a) Schematic representation of the strategy used to construct mutants by gene replacement. Small, red and shaded arrows represent the primers, the target

gene, and the kanamycin (Km) resistance cassette, respectively. The three PCR products obtained (PCR1, PCR2, and PCR3) were mixed at equimolar concentrations and subjected to a

nested overlap-extension PCR to generate the desired linear DNA (see Materials and Methods for details). (b) Diagram showing the integration of the linear DNA via two recombination events. (c) Representation of the original genetic material replaced by the recombinant DNA on the A. baumannii chromosome. Knockout construction by gene disruption Plasmid insertion in the omp33 gene (Table 1) was carried out as previously described [10], with slight modifications. Briefly, kanamycin- and zeocin-resistant plasmid pCR-BluntII-TOPO, unable to replicate in A. baumannii, was used as a suicide vector. An internal fragment (387 bp) of the omp33 gene was amplified by PCR with 33intUP and 33intDW primers (Table 2) and genomic DNA buy LY3039478 from A. baumannii ATCC 17978 as a template. The PCR product was cloned into the pCR-BluntII-TOPO vector and electroporated in E. coli to yield the pTOPO33int plasmid (Table 3). Recombinant plasmid (0.1 μg) was then introduced in the kanamycin- and zeocin-susceptible A. baumannii ATCC 17978 strain by electroporation. Mutants were selected on kanamycin-containing plates. Inactivation of the omp33 gene by insertion of the plasmid via single crossover recombination was confirmed by sequencing the amplified PCR products with

the SP6 + 33extUP and T7 + 33extDW primer pairs (Table 2). Construction of pET-RA plasmid for gene expression in A. baumannii In order to complement mutant phenotypes, the pET-RA plasmid [Genbank: HM219006] was constructed, and carried a rifampicin resistance Immune system cassette, a gene coding for a green fluorescent protein (GFP), and the A. baumannii replication origin, which is a plasmid origin of replication (Figure 7). The pET-RA vector was used to express promoterless genes under control of the CTX-M14 β-lactamase gene promoter, previously cloned upstream of the GFP gene (Figure 7). For pET-RA construction, the pMW82 vector [Genbank: EF363313] was amplified by PCR, excluding the coding region of the ampicillin resistance cassette. The rifampicin resistance cassette was then amplified from the pAT-RA vector [Genbank: HM219005] and introduced into the pMW82 vector.