Characteristics of Chi distribution
on different bacterial genomes

Meriem EL KAROUI, Véronique BIAUDET, Sophie SCHBATH
and Alexandra GRUSS

Research in Microbiology 150, 579-587, 1999.


The availability of full genome sequences provides the bases for analyzing global properties of the genetic text. For example, oligonucleotide sequences that are over- or under-represented can be identified by taking into account the overall genome composition and organization. One of the most over-represented oligonucleotides in E. coli is the Chi site, an oligonucleotide that stimulates DNA repair by homologous recombination. Here, we analyze the genomic distribution of Chi in E. coli and in the 3 other bacteria where a Chi sequence has been identified; note that Chi is a different sequence in each organism. For each bacterial genome, Chi sequences are frequent, regularly distributed, and over-represented. This suggests that Chi was selected for during evolution, probably to favor efficient repair of a damaged chromosome. Other characteristics of Chi distribution are not conserved and might reflect specific features of DNA repair in each host. The different sequence and characteristics of Chi in each micro-organism suggest that selection for Chi occurred independently in different bacteria.

Key words and phrases Chi sequences, over-represented oligonucleotides, DNA repair.

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