Short repeated palindromes in enterobacteria

Bacterial Interspersed Mosaic Elements (BIMEs)

The mosaic organisation of BIMEs

Only 84 out of the 584 PUs of the E. coliK-12 chromosome are single occurrences. All the others appear in clusters, containing up to twelve PUs. The distribution of PU number in BIMEs is shown below.

PU number in BIMEs

In these clusters, successive PUs alternate both in type and in orientation, and they are separated by short sequence motifs, located either between two heads (Head Internal Sequences or HIS) or two tails (Tail Internal Sequences or TIS). Two external motifs, A and B, flanking the tails of the last PUs, are found in some BIMEs. The figure below presents a typical organisation of PUs and "extra-PU" motifs in BIMEs.

BIME schematic structure

Two different motifs can be found between to PU heads (HIS) : S is defined as a 12-14 bp-long sequence, with no strong sequence conservation, while L is 32-34 bp-long, with a very conserved nucleotide sequence, leading to the definition of a consensus. In the middle of this motif is found an IHF-binding site (in red).
There are three TIS : l is 8-9 bp-long, s is 1 bp-long, and r has a variable size (ranging from 18 to 31 bp).
There are two Tail External Motifs (TES), called A and B. They both were originally defined as 20 bp-long sequences, but a recent analysis of E. coli sequences lead us to lengthen the B motif, which is 27 bp-long. The extra-PU motifs data are summarized in the table below.

Extra-PU motifs Motifs' names and sizes Consensus
Head Internal Sequences  L : 32-34 bp
 S : 12-14 bp
Tail Internal Sequences  l : 8-9 bp
 s : 1 bp
 r : 18-31 bp
Tail External Sequences  A : 20 nt
 B : 27 nt

The mosaic structure of BIMEs theoretically allows a lot of different combinations to occur. Remarkably, the diversity in BIME motif schemes can be accounted for by a simple rule : within a BIME, all the occurrences of internal sequences (HIS or TIS) consist of the same motif. In other words, all the HIS are either S or L, and all the TIS are either r or s or l. The same rule applies to the Z PUs : a BIME contains either Z1 or Z2. Thus, BIMEs with more than two PUs can be described as direct repetitions of a basal motif association.
We defined two major BIME families according to preferential motif associations. Members of the BIME-1 family are composed of only two PUs, one Y and one Z1, separated by the L motif, and frequently associated to external motifs (A on the Z1 side, B on the Y side). 61 intergenic regions of E. coli K-12 contain BIME-1, and in 21 the BIME-1 sequences are bracketed by direct repeats, 18 bp to 40 bp long (list these regions). Members of the BIME-2 family contains from two to twelve Y and Z2 PUs, separated by S and either r, s or l. Every other motif association (for example Z1 and S or Z2 with L) will be referred to as "atypical BIME". You can display a table listing all the E. coli intergenic regions containing BIMEs.

Schematic structure of <I>E. coli</I> major BIME families

BIMEs are scattered over the E. coli chromosome. The region of termination of replication exhibits a lower BIMEs' density than the rest of the chromosome. This region is totally deprived of BIME-2 (from ycdB-phoH to yebE-yebF), which represents a segment of 844 kb. Only two Z2 are present in the centre of this region, delineating two Z2-free fragments of 297 kb and 519 kb. The terminus region is also deprived of BIMEs containing IHF-binding sites.

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