Southern blot analysis showing insertional inactivation of clpP and clpX in mutant derivatives of serovar Typhimurium χ3306. The clpP or clpX region was amplified by PCR, using genomic DNA prepared from strains χ3306 (lanes a, c, e, g, and i), CS2007 (clpP:Cm; lanes b and d), CS2016 (clpP:Km; lanes f and h), and CS2018 (clpX:Cm; lane j) as templates and three sets of oligonucleotide primers, S529-A1110 (a and b), S589-A1211 (e and f), and S66-A2828 (c, d, g, h, i, and j). The nucleotide sequences of these primers are shown in Materials and Methods. The PCR products were separated on a 1% agarose gel by electrophoresis and subjected to Southern hybridization using the DNA fragments between nt 529 and 1110, covering the entire clpP open reading frame (a to h), and between nt 1743 and 2391, carrying a part of the clpX gene (i to j), as probes. Sizes are shown in nt.