Non-competent Gram-negative bacteria are frequently mutated by a plasmid-based method, in which plasmid DNA is introduced into the cell by bacterial conjugation [4], and allelic marker exchange is then carried out by homologous recombination between the chromosomal DNA and the introduced allele on a gene replacement plasmid [5–7]. Since single crossover mutants are dominantly obtained in the plasmid-based method, counter-selection markers such as sacB[8], rpsL[9], and mutated pheS[10], which confer sensitivity to sucrose, streptomycin,

and p-chloro-phenylalanine, respectively, are used frequently to further screen JNK-IN-8 purchase double crossover mutants, especially for an unmarked mutation. However, this method is empirically ineffective for deleting large

genes from the chromosome. Thus, it is difficult to characterize the function of a large gene in non-competent bacteria by using an unmarked mutation. Nevertheless, bacteria have large genes that are interesting and important for physiology and potential applications, such as cell surface proteins that have repetitive structures and are involved in cell adhesion and biofilm formation [11–15]. The repeats of a gene also disturb recombination at the targeted site on the chromosome and complicate the introduction of an unmarked mutation. Since there is no effective method for introducing an unmarked mutation eFT508 that targets such large genes in non-competent bacteria, marked mutants have been used to characterize their functions. The site-specific ALK inhibitor recombinase FLP, which is a yeast protein, works efficiently in a variety of prokaryotic and eukaryotic hosts [1, 2, 5, 16, 17]. When FLP recognition target (FRT) sites are aligned on the chromosome of a host cell in the same direction, FLP recombinase

binds to them and specifically excises the region sandwiched Cytidine deaminase between the two FRT sites. In both the PCR-based and the plasmid-based unmarked methods, the FLP/FRT recombination system has been employed to eliminate selectable markers inserted into the chromosome [1, 2, 5, 18]. Acinetobacter sp. Tol 5 is an interesting Gram-negative bacterium that can metabolize various kinds of chemicals, including aromatic hydrocarbons, ethanol, triacylglycerol, and lactate [19, 20], has a hydrophobic cell surface that can adsorb to oil surfaces [21, 22], autoagglutinates [21, 23, 24], and exhibits high adhesiveness to various abiotic surfaces ranging from hydrophobic plastics to hydrophilic glass and stainless steel by bacterionanofibers [20, 24–26]. AtaA is a huge protein (3,630 aa) with a multi-repetitive structure, belongs to the trimeric autotransporter adhesin family [27], and forms an essential nanofiber for the adhesive phenotype of Tol 5 [28]. Previously, we constructed a marked mutant of ataA by exchanging it with a transposon cassette-inserted allele. Since the competency of Tol 5 was quite low, allelic marker exchange was performed by the plasmid-based method using the sacB marker.