Inversions over the terminus region in Salmonella and Escherichia coli: IS200s as the sites of homologous recombination inverting the chromosome of Salmonella enterica serovar typhi

Abstract

Genomic rearrangements (duplications and inversions) in enteric bacteria such as Salmonella enterica serovar Typhimurium LT2 and Escherichia coli K12 are frequent (10(-3) to 10(-5)) in culture, but in wild-type strains these genomic rearrangements seldom survive. However, inversions commonly survive in the terminus of replication (TER) region, where bidirectional DNA replication terminates; nucleotide sequences from S. enterica serovar Typhimurium LT2, S. enterica serovar Typhi CT18, E. coli K12, and E. coli O157:H7 revealed genomic inversions spanning the TER region. Assuming that S. enterica serovar Typhimurium LT2 represents the ancestral genome structure, we found an inversion of 556 kb in serovar Typhi CT18 between two of the 25 IS200 elements and an inversion of about 700 kb in E. coli K12 and E. coli O157:H7. In addition, there is another inversion of 500 kb in E. coli O157:H7 compared with E. coli K12. PCR analysis confirmed that all S. enterica serovar Typhi strains tested, but not strains of other Salmonella serovars, have an inversion at the exact site of the IS200 insertions. We conclude that inversions of the TER region survive because they do not significantly change replication balance or because they are part of the compensating mechanisms to regain chromosome balance after it is disrupted by insertions, deletions, or other inversions.

FIG. 1.

Part of the chromosome of S. enterica serovar Typhimurium LT2 is inverted in Salmonella enterica serovar Typhi CT18 between IS200-11 and -17. The horizontal lines indicate the chromosome of each strain, as determined from their nucleotide sequences, from oriC at the left proceeding clockwise around the chromosome through the TER region and ending with the oriC on the right. The rectangles indicate the tnpA gene within each IS200 element. The horizontal arrows indicate the inverted segments. The numbers immediately below the line indicate the positions in kilobases, based on published sequences (30, 33). The numbers below position numbers indicate the coding sequences for either serovar Typhimurium or serovar Typhi CT18, which are numbered from the gene thrA. The numbers above the boxes have been assigned in order to each IS200 element. + and − indicate the orientation of the tnpA genes and thus of the IS200. (A) Salmonella serovar Typhimurium strain LT2 (STM), showing six IS200 elements. (B) Derivative of serovar Typhimurium, postulated to become the ancestor of Salmonella serovar Typhi (STY). The order of orthologous genes on the chromosome is the same as that in serovar Typhimurium LT2. The number of IS200 elements has increased to 25, presumably due to transposition. IS200 -11 and -17, shown as filled rectangles, are postulated to recombine (see below). (C) Postulated crossover between IS200 -11 and -17. (D) Salmonella serovar Typhi strain CT18 (STY, CT18). The segment between IS200 -11 and -17 is inverted.

FIG.2.

Segments of the chromosome covering the TER region in strains of E coli and Salmonella, showing inverted regions (not drawn to scale). The named genes are indicated above the lines, and the number for each gene (not the kilobase number but the serial number of the gene, based on sequence numbering from thrA) is indicated below the line. Numbered genes above the line on a “Y” formation indicate an island present in one strain but not in others. The order of genes from left to right in S. enterica serovar Typhimurium is considered to be the ancestral order (see text). Orthologous genes in other species are shown, for convenience, in the same order as in serovar Typhimurium, but the actual order on their chromosomes is revealed by the order of their gene numbers. Inverted segments are shown as dotted lines above the maps with arrows from right to left, with the size of the inversion indicated in kilobases. Panels A to E are based on nucleotide sequence data, and panel F is based on PFGE data. (A) E. coli O157:H7 EDL933 (ECH EDL933). The filled squares indicate the ends of the large inverted segment; the squares containing diagonal lines indicate the ends of the inverted segment within it. (B) E. coli O157:H7 Sakai-VT2 (ECH VT2). The filled squares indicate the ends of the large inverted segment. (C) E. coli K12 (ECO K12). The filled squares indicate the ends of the large inverted segment. (D) S. enterica serovar Typhimurium LT2 (STM LT2). The short arrows above and below the map show PCR primers F1, R1, F2, and R2. (E) S. enterica serovar Typhi CT18 (STY CT18). The two filled rectangles indicate the positions of IS200 -11 and -17 elements (containing the tnpA genes); the 556-kb segment between them is inverted in serovar Typhi CT18 compared with serovar Typhimurium LT2. (F) Salmonella enterica serovar Enteritidis (SEN) and Salmonella enterica serovar Pullorum (SPU). The open rectangles indicate sites of inversion, as determined from PFGE data.

FIG. 3.

PCR analysis of inversions in Salmonella. PCR was carried out using template DNA from different strains of Salmonella and using the primer pairs indicated (primers F1, F2, R1, and R2; see Fig. 2C for locations); the PCR products were electrophoresed in 1% agarose. Lanes 1 and 14, size markers; lanes 2 to 5, Salmonella enterica serovar Typhimurium LT2 template DNA (STM); lanes 6 to 9, S. enterica serovar Typhi CT18 template DNA (STY); lanes 10 and 11, S. enterica serovar Arizonae strain SARC5 (SAZ); lanes 12 and 13, S. bongori strain SARC11 (SBG).