REP SEQUENCES

REP sequences or REP elements stand for Repetitive Extragenic Palindromic unit sequences that occur mostly in bacteria. These are well- conserved in bacterial genome and occur outside of structural genes as the name suggests already. A complex of REP sequences called BIMES (Bacterial interspersed mosaic elements) is characteristic of bacterial nucleoid structure. These sequences are about 20-70 base pairs in length and are often associated with DNA polymerase and DNA gyrase. However a typical REP sequence is 38 bp in length and with a 5 bp variable loop.

DISCOVERY: REP elements were discovered in 1982 by Higgins et al., in the entero-bacteriacea family of eubacteria. Later many such sequences like ERIC (Enterobacterial repetitive intergenic consensus) sequences were discovered to be ubiquitously distributed among diverse bacterial families. Identification of repetitive DNA is based on their differences in thermodynamic stability and reassociation kinetics. FUNCTIONS: REP elements are palindromes and consensus (well-conserved) sequences. As a palindromic sequence they are same when read in same polarity i.e. in same direction. In a bacterial genome there might be 100-500 such sequences. The functions are though not wellestablished; these sequences are known to modulate mRNA functions. These sequences interact with DNA polymerase, DNA gyrase and IHF (Integration Host Factor) and possibly play an integral part in bacterial DNA physiology. These elements are integral in forming stem loop structures in tRNA and hair-pin loops as well as stable stem loop structures in DNA. Another important aspect of functionality of these sequences is that they are target sequences for transposases and DNA duplication events. SIGNIFICANCE: While interspersed repetitive DNA sequence elements have been extensively studied in Eukaryotes; those in prokaryotes are a relatively newer dimension to be explored. Today technology based on such sequences like REP PCR and ERIC PCR has enabled study of soil bacteria manifold easier. Furthermore they are a tool for species identification just like VNTRs in mammals.

REFERENCES: 1) Raquel Tobes and Eduardo Pareja, Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements BMC Genomics 2006, 7:62 2) James Versalovic, Thearith Koeuth and James R.Lupski Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes Nucleic Acids Research, 1991, Vol. 19, No. 24 3) FRANS J. DE BRUIJN Use of Repetitive (Repetitive Extragenic Palindromic and Enterobacterial Repetitive Intergeneric Consensus) Sequences and the Polymerase Chain Reaction To Fingerprint the Genomes of Rhizobium meliloti Isolates and Other Soil Bacteria APPLIED AND ENVIRONMENTAL MICROBIOLOGY, July 1992, p. 2180-2187 4) YOUNG YANG AND GIOVANNA FERRO-LUZZI AMES DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences Proc. NatI. Acad. Sci. USA Vol' 85, pp. 8850-8854, 1988 5) Venkatakrishna Shyamala, Erwin Schneider and Giovanna Ferro-Luzzi Ames Tandem chromosomal duplications: role of REP sequences in the recombination event at the join-point The EMBO Journal vol.9 no.3 pp.939 - 946, 1990