Short repeated palindromes in enterobacteria


Bacterial Interspersed Mosaic Elements (BIMEs)


The PU motifs


Palindromic Units were the first repeated palindromes identified in Enterobacteria (Higgins et al. 1982, Gilson et al. 1984). They have also been named REP sequences for Repetitive Extragenic Palindromic sequences (Stern et al. 1984). These short non-coding sequences are found in extragenic locations, either between successive genes in an operon, or after the last gene of the operon. The first consensus derived from the alignment of all PU sequences was 40 bp-long, with a central part variable in length and sequence.

Original PU consensus


PUs are imperfect palindromes, with asymmetry elements (bold letters on the figure) allowing them to be given an orientation, from tail (5' end of the consensus on the figure) to head. A typical schematic drawing of a PU is shown, the triangle pointing towards the head.
We defined two types of PUs, called Y and Z, according to two critical positions (7 and 32, in red on the figure) of this original consensus. In the Y PUs, these nucleotides are a G and a C respectively, while in the Z PUs, they are a T and a A. We then subdivided the Z PUs in two motifs, called Z1 and Z2, according to differences in size and sequence. The three PU motifs are aligned below.

Alignement of the three <I>E. coli </I> PU motifs

A fourth class of PUs, called PU* or Y*, is found between convergently transcribed operons. Y* are shorter than the motifs described above, they do not contain the CTACR sequence at the 3' end but are flanked by a stretch of Ts, and are used as rhoindependant transcription terminators (Gilson et al. 1986a).

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