Intergenic Repeat Units
(Enterobacterial Repetitive Intergenic Consensus)


Intergenic Repeat Units (IRUs) were initially identified during the analysis of the 3' end region of the E. coli tls gene (Sharples and Lloyd, 1990). 21 IRUs are found on the E. coli K-12 chromosome, but similar sequences also exist in other enterobacteria, as well as in Vibrio cholerae. A second laboratory identified the same repeat and named it ERIC for Enterobacterial Repetitive Intergenic Consensus (Hulton et al. 1991).

IRUs are imperfect palindromic sequences which are 127 nucleotides long ; they may form a stem-loop structure and can be oriented. They have been detected simultaneously in several bacterial species in which their sequence is very homogenous, which allows a consensus to be derived. These sequences are always extragenic, with one exception in V. cholerae: an IRU is contained within the 5' end of gene sulA. The majority of these sequences are transcribed. In contrast to BIMEs, IRUs are sometimes associated with promoter regions (at least 6 occurrences). They are dispersed on the bacterial chromosome and have not been detected in bacteriophages or in plasmids. Their total number in bacterial genomes has been estimated between 30 and 150 (see references above). For example IRUs seem more abundant in S. typhimurium (26 IRUs in annotated sequences) than in E. coli (21 IRUS on the whole genome).

As in the case of a number of BIMEs, some IRUs are located in corresponding intergenic regions of different bacterial species: metE-R and ahpC-F in S. typhimurium and E. coli, rpsU-dnaG in S. typhimurium, L. malonatica, C. freundii and C. amalonaticus (Versalovic et al. 1993).

So far, IRUs have been identified in a number of species, listed below:

Escherichia coli
Salmonella typhimurium, S. typhi, S. paratyphi
Klebsiella pneumoniae, K. oxytoca
Citrobacter freundii
Erwinia carotovora, E. chrysantemi
Proteus mirabilis
Vibrio cholerae
Xenorhabdus luminescens
Photorhabdus luminescens
Yerinia pestis, Y. enterocolitica, Y. pseudotuberculosis

A few examples of IRUs (3 in S. typhimurium, 1 in K. pneumoniae and E. chrysanthemi) are interrupted by a 68 bp intervening sequence (Cromie et al. 1997, Sharp 1997 and SB, unpublished observations), conserved both in sequence and location within the repeat. The insertion does not not destroy the secondary structure of the IRU.

The sequences of IRUs do not vary much from one species to another, at least in comparison with BIMEs; for example, IRUs from E. coli, Klebsiella and even Vibrio have homologous sequences, which can be detected by hybridization or by computer search in sequence libraries. Due to the small number of IRUs known for each bacterial genus, it is not possible to decide whether the variations with respect to the consensus from one species to another reflect a species specificity. It does seem clear however that, if there is a species specificity for IRUs, it is much less apparent than in the case of BIMEs. Their sequences are indeed mostly conserved in distant species, which can be explained in several ways. They may have appeared recently and been dispersed for example via an association with a transposable element, or by some other type of horizontal transfer. On the contrary, it is possible to assume that IRUs are ancient elements the sequence of which has been conserved either because of gene conversion or because these sequences have a function which is selected for. The fact that IRUs are dispersed on the chromosome suggests a transposition step, but since there is no open reading frame, they do not carry information for a protein involved in transposition. There is no known functions for IRUs. All the data can be interpreted by saying that the IRUs are (or were) very mobile sequences, susceptible to local rearrangements (Versalovic et al., 1993).

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