Short repeated palindromes in enterobacteria

Bacterial Interspersed Mosaic Elements (BIMEs)

BIMEs undergo intraspecific variations

We have studied the polymorphism of six BIME-containing intergenic regions in 51 natural isolates of E. coli. In E. coli K-12, araA-araD, malE-malF and lamB-malM regions have BIME-2, while entD-fepA, mtlA-mtlD and yggB-fbahave BIME-1, the last two bracketed by direct repeats (Bachellier S. et al., 1997).
The BIME-2 exhibit length polymorphism : the number of PUs in the araA-araD BIME was 2, 4 or 6. In some cases, another repeated sequence, called boxC, was found next to the BIME. The lamB-malM BIME had either 1, 3, 5 or 7 PUs. The malE-malF BIME exhibited length polymorphism (1 PU instead of 3) in only one strain. From the literature, we know that the BIMEs located in the aceA-aceK, phnA-phnB and glpK-glpX regions also exhibited length polymorphism (see below).
In the three regions we studied, we also observed the presence of an Insertion Sequence (IS1397), absent from E. coli K-12 chromosome, which seems to specifically integrate in PUs.

variations of the araA-D intergenic region

variations of the lamB-malM intergenic region

variations of the malE-malF intergenic region

BIME-1 did not display that kind of length polymorphism. The BIME found between entD and fepA did not vary in the 51 strains we used. The two other BIME-1 studied were absent from several strains, probably due to unequal homologous recombination between the flanking direct repeats. It is interesting to note that the fdnI-f120 region in E. coli K-12 has a duplication of the BIME-1 and flanking repeats, which is the reciprocal recombination product (S. Bachellier, unpublished). A PCR analysis of this region in several natural isolates showed that the number of BIME-1 can be 0, 1, 2, 3 or 4.
In the case of the mtlA-mtlD intergenic region, a rearrangement occurred in several strains, leading to the formation of an "atypical BIME", with a BIME-1 part and a BIME-2 part. Interestingly, the BIME-2 part exhibits length polymorphism in a number of bacteria, and the IS1397 was found in this region as well.
The various structures observed are drawn below.

variations of the mtlA-mtlD intergenic region

From the literature, we know that other BIMEs do vary in E. coli.
1- The phnA - phnB intergenic region contains a BIME-2 with 12 PUs in K-12, but only 10 PUs in E. coli B (Wanner B.L. and Boline J.A. 1990, J. Bacteriol. 172, 1186-1196.)
2- The polymorphism of the aceA - aceK intergenic region has been studied in several strains from the E. coli ECOR collection, showing length variations (from 48 to 280 bp, as compared to 182 bp in K-12). These variations are due to BIME-2 polymorphism (Nelson K., Wang F.S., Boyd E.F. and Selander R.K., 1997, Genetics 147, 1509-1520). The nucleotide sequence of these variants is not available.
3- The glpK - glpX intergenic region contains a single PU in E. coli K-12, and a BIME-2 with 2 PUs in Shigella flexneri (Truniger V., Boos W. and Sweet G. 1992 J. Bacteriol. 174, 6981-6991).

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