Palindromic units are part of a new bacterial interspersed mosaic element (BIME)

Abstract

Palindromic Units (PU or REP) were defined as DNA sequences of 40 nucleotides highly repeated on the genome of Escherichia coli and other Enterobacteriaceae. PU are found in clusters of up to six occurrences always localized in extragenic regions. By sorting the DNA sequences of the known PU containing regions into different classes, we show here for the first time that, besides the PU themselves, each PU clusters contains a number of other conserved sequence motifs. Seven such motifs were identified with the present list of PU regions. Remarkably, each PU cluster is exclusively composed of a mosaic combination of PU and of these other sequence motifs. We demonstrate directly by hybridization experiments that one of these motifs (called L) is indeed present at a large number of copies on the Escherichia coli chromosome and that its distribution follows the same species specificity as PU sequences themselves. We propose that the mosaic pattern of motif combination in PU clusters reveals a new type of bacterial genetic element which we propose to call BIME for Bacterial Interspersed Mosaic Element. The Escherichia coli genome contains about 500 BIME.

Bacterial Genome Instability

“…They can be found as single occurrences but are more often organized in pairs or in clusters. A BIME is a pair of REP sequences in an inverse orientation separated by a short linker sequence containing other conserved sequence motifs (56,57). The E. coli chromosome contains Ͼ250 BIMEs, mostly in GC-rich genomic regions.…”

“…BIMEs of one category are bound by the integration host factor (IHF); these structures have been called RIBs (reiterative ihf BIMEs) (61) or RIPs (repetitive IHF-binding palindromic elements) (62). Additionally, DNA gyrase binds and cleaves some BIMEs (56,(63)(64)(65). DNA polymerase I (Pol I) also binds certain BIMEs (56,66).…”

Short, interspersed repetitive DNA sequences in prokaryotic genomes

“…Subsequent studies showed these clusters could contain as many as 10 elements (34). Recently it has been reported that the clusters could also contain other repeated elements in specific arrangements (17,18). These latter complex repeats were termed bacterial interspersed mosaic elements (BIMEs).…”

“…These latter complex repeats were termed bacterial interspersed mosaic elements (BIMEs). The E. coli chromosome was estimated to have about 500 BIME structures, always found in extragenic locations, or about one BIME for every six genes (17,18).…”

An efficient algorithm for identifying matches with errors in multiple long molecular sequences

“…All of these sequences are non-coding. The long common words have considerable parts matching the consensus repetitive extragenic palindromic (REP) sequences first noted by Higgins et al (1982) and reviewed recently by Gilson et al (1991). The functions of these REP elements is currently unknown, although it has been observed that many of them strongly bind DNA gyrase (Yang & Ames 1988).…”