Colonies with an insert size greater than 500 bp were selected and grown in 5 mL of LB broth. They were purified using a Plasmid Mini Kit (Qiagen) and submitted to sequencing by Macrogen Inc. (Korea). The DNA MLN8237 research buy sequence data were analyzed with softberry server software (http://linux1.softberry.com/berry.phtml) using

the FgenesB and Bprom algorithms. FgenesB is a suite of bacterial operon and gene prediction programs and is based on Markov chain models of coding regions and translation and termination sites (Tyson et al., 2004). Bprom is an algorithm that recognizes possible promoters in bacterial DNA sequences. The clc main workbench 5 is a versatile software for analyzing DNA, RNA and proteins with a graphical user interface (http://clcbio.com/); the software was used to complement the sequence analysis, specifically for alignments and to locate the different elements [ORF, promoters, inverted repeat sequences (IRs)]. The ORFs predicted by FgenesB were used in blastp, with the search limited to bacterial sequences (http://blast.ncbi.nlm.nih.gov), to determine their possible identities. A comparison with the most similar ISs from the IS6 family found in the ISFinder database (http://www-is.biotoul.fr/) was performed.

In order to determine the prevalence of the IS sequence in natural isolates, oligonucleotide primers were designed to amplify the putative IS already predicted by the sequence analysis. All PCR primers were designed as shown in Table 3, using the Oligo Selleckchem GS 1101 Calc tool (http://www.basic.northwestern.edu/bio-tools/oligocalc.html). The PCR reaction for the three fish isolates was performed

using the following primer set: (1) IR1-F and Tnp-PsaR2 yielded a PCR product of 427 bp and (2) Tnp-PsaF and IR2-R yielded a PCR product of 704 bp. The PCR conditions used were: 94 °C for 5 min, 35 cycles of 94 °C for 30 s, 58 °C for 30 s and 72 °C for 45 s, and a final extension of 72 °C for 5 min. The PCR products were visualized on a 1% agarose gel stained with GelRed™. Piscirickettsia salmonis DNA was partially digested with Sau3AI endonuclease. Because this enzyme has a 4-bp recognition site, excision occurs, on average, every 250 bp, thus generating DNA fragments smaller than 2000 bp (Fig. 1). Fragmented DNA was cloned into the vector pBluescript Selleckchem DAPT KS (+) and electroporated into E. coli, resulting in 4750 recombinant clones. PCR analysis of the cloned P. salmonis inserts yielded 200 clones with inserts larger than 500 bp, which were subsequently sequenced (data not shown). Sequence analysis of the 992-bp insert resulted in a unique 726-bp ORF with a putative in-frame protein of 242 amino acids, an upstream putative promoter containing the expected −10 and −35 regions, and two identical 16-bp IRs flanking the 726-bp ORF (Fig. 1). According to Blastp analysis, the new ORF encodes a putative transposase (Tnp-Psa) with high similarity to Bacillus thuringiensis IS240 protein.