Short repeated palindromes in enterobacteria


Bacterial Interspersed Mosaic Elements (BIMEs)


BIMEs in other bacteria

Salmonella typhimurium

Palindromic Units have been originally discovered both in E. coli and S. typhimurium. They exhibit a sequence specificity : there is an additional G (in green on the figure below) in Salmonella's PUs (Gilson E. et al., 1987). In this species, we have identified four PU motifs : Z1, Z2, Y and "D". The consensus derived from the alignments are shown below.

consensus of the four <I>Salmonella'</I>s PU motifs


Salmonella's PUs belong to BIME-like structures, slightly different from the one described in E. coli. From the BIME-containing regions present in annotated DNA databases, we can infer that the extra-PU motifs do not exhibit a high level of nucleotide or size conservation. For example, we have not been able to detect any equivalent of the "L" motif. To the contrary of E. coli, the Z1 PU is the most frequently found motif in Salmonella. The same intergenic regions in both enterobacteria sometimes contain BIMEs, as shown on the table below.

Klebsiella sp.

K. pneumoniae and K. aerogenes

The sequencing of several intergenic regions of K. pneumoniae led us to identify Klebsiella's PUs in BIME-like structures (Bachellier S. et al., 1993). Searches in the annotated databases revealed a few more sequences, listed in this table.
Klebsiella's PUs exhibit the same sequence specificity as Salmonella's, but they are otherwise quite different (the G+C% is much higher). They seem to form mosaic structures with extra-PU motifs : in K. aerogenes pulA region, two PUs are in a BIME-1 like structure, with a L motif very similar to the E. coli motif, and containing an IHF binding site. The small number of PU-containing regions available in annotated databases does not allow to say whether extra-PU motifs are conserved like in E. coli, or variable like in Salmonella.

K. oxytoxa

PUs with different sequences have been found in K. oxytoca. The G+C% of the palindromes is even higher than in K. pneumoniae/K. aerogenes, but they keep features specific of PUs (namely the sequence CTAC at their heads). Three BIME-containing regions are found in GenBank (see the table), two of them contain a similar 22bp-long extra-PU motif.

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Please send questions and comments to Sophie.Bachellier@pasteur.fr.