Inversions over the Terminus Region in Salmonella and Escherichia coli : IS 200 s 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.The order of orthologous genes on the chromosomes of enteric bacteria such as Escherichia coli K12 and Salmonella enterica serovar Typhimurium LT2 was shown by classical genetic exchange methods to be strongly conserved (24, 37), and this has now been confirmed by nucleotide sequence data (6, 30). This conservation was retained even after the genera diverged over 100 million years ago (32) and in spite of base pair divergence of orthologues, which averages about 15%. In addition, lateral genetic transfer has inserted nonorthologous genes that comprise about 30% of the total genetic structure, resulting in mosaic chromosomes. This conservation is surprising, because during growth in culture, chromosome rearrangements such as duplications occur at high frequencies (10 Ϫ3 to 10 Ϫ5 ) (3, 19) and some inversions and translocations, especially those with end points in the rrn operons, are common (36). These rearrangement types must have been selected against in evolution, because they are rarely detected in wildtype strains from nature. In contrast to this conservation within the enteric bacteria, gene order in most bacteria is not conserved during evolution (10, 21, 31), though species of Chlamydia also show striking conservation (35).However, even in the enteric bacteria, two types of genomic rearrangements are often observed. Firstly, inversions and translocations due to homologous recombination between the seven rrn operons are common in species such as Salmonella enterica serovar Typhi; among 127 wild-type strains there were 21 different genome types, based on differences in order of the fragments between the rrn operons (28). Rearrangements were also found in some ot...

Optical maps distinguish individual strains of Escherichia coli O157 : H7

“…The optical maps revealed the sizes and locations of each inversion, and in each case the inversion was flanked by prophages. The positions of the ends of the inversions suggested that prophages served as targets for recombination, as has been found for inversions between artificially constructed chromosomal repeats (Miesel et al, 1994) or inversions found between copies of rRNA operons (Liu & Sanderson, 1995) and insertion elements in Salmonella (Alokam et al, 2002). The large number of cryptic prophages found in EDL933 and Sakai supply extensive 10-90 kb regions for homologous recombination.…”

DNA Amplification and Rearrangements in Archival Salmonella enterica Serovar Typhimurium LT2 Cultures

“…In fact, insertion sequences have been shown to be a hot spot for genomic rearrangements in Salmonella. Alokam et al recently reported an inversion at IS200 sites in serovar Typhi strain CT18 (1).…”

The Genome of Salmonella enterica Serovar Gallinarum: Distinct Insertions/Deletions and Rare Rearrangements

“…Based on this and other evidence, it was hypothesized that recombination may help the bacteria to rebalance the genome following major genomic insertions or deletions, which may have disrupted the genomic balance (19,30,31), although this hypothesis needs to be tested further as exceptions awaiting explanation also exist. Genomic rebalancing involves homologous recombination, and rrn genes provide ideal sites for this because of their large sizes and multiple copies (12,14,15,21), although homologous recombination occurs also in other multiple-copy sequences, such as IS200 (1).…”