Toxin Effectors of CDI and Rhs Systems Figure 1. E. coli EC93 contains an orphan cdiA-CT/cdiI module. The CDI region of E. coli EC93 is depicted, with cdiB, cdiA and cdiI genes shown in yellow, green and purple, respectively. The cdiA coding region upstream of the encoded VENN motif is shown in light green, and the cdiA-CT sequence is shown in dark green. The orphan cdiA-CT fragment (cdiA-CTo1) and orphan cdiI (cdiIo1) are dark green and purple, respectively. The nucleotide sequence of the cdiI - cdiA-CTo1 junction and the predicted reading frames are shown in detail. Sequences similar to transposable element genes are shown in red. doi:10.1371/journal.pgen.1002217.g001 CT encoded by the adjacent cdiAPB1(II) gene (39% identity over 179 residues), and also to CdiA-CTs from Klebsiella pneumoniae 342 (B5Y0C2; 61% identity over 263 residues) and Dickeya dadantii Ech586 (D2BZ75; 59% identity over 263 residues). Although some CDI systems, such as those in Y. pseudotuberculosis PB1/+ and Neisseria meningitidis FAM18, have well-ordered arrays of orphan cdiA-CT gene fragments downstream of cdiBAI, other species have more complex genomic arrangements. Klebsiella Figure 2. Many bacteria contain orphan cdiA-CT/cdiI modules. The cdi loci from selected bacterial species are presented using the color- coding scheme in Figure 1. Arrowheads indicate the positions of VENN encoding regions. Probable orphan cdiA-CT/cdiI modules are indicated with an ‘‘o’’ and numeral. Note the change in scale for the locus from E. coli EC869. The UniProt accession numbers for the encoded CdiA proteins are: Escherichia coli 254 ser. O113:H21 (A1XT91); Edwardsiella ictaluri 93–146 (C5BAK2); Erwinia pyrifoliae DSM 12163 (D2T668); Edwardsiella tarda EIB202 (D0ZDG0); Klebsiella variicola At-22 (D3RCW8); Neisseria menigitidis FAM18 (A1KSB8); Photorhabdus asymbiotica ATCC 43949 (B6VKN5); Pectobacterium wasabiae WPP163 (D0KFH4); Yersinia pseudotuberculosis PB1/+ (B2K3A8); and Escherichia coli EC869 (B3BM48). The E. coli 254 genomic sequence does not include the 59-end of the cdiA gene. doi:10.1371/journal.pgen.1002217.g002 PLoS Genetics | www.plosgenetics.org 3 August 2011 | Volume 7 | Issue 8 | e1002217