Characteristics of Chi distribution on different bacterial genomes

The availability of full genome sequences provides the bases for analyzing global properties of the genetic text. For example, oligonucleotide sequenc es that are over- or underrepresented can be identified by taking into acco unt the overall genome composition and organization. One of the most overre presented oligonucleotides in Escherichia coli is the Chi site, an octanucl eotide that stimulates DNA repair by homologous recombination. Here we anal yze the genomic distribution of Chi in E. coli and in the three other bacte ria where a Chi sequence has been identified; note that Chi is a different sequence in each organism. For each bacterial genome, Chi sequences are fre quent, regularly distributed, and overrepresented. This suggests that selec tion for Chi may have occurred during evolution to favor efficient repair o f a damaged chromosome. Other characteristics of Chi distribution are not c onserved and might reflect specific features of DNA repair in each host. Th e different sequence and characteristics of Chi in each microorganism sugge st that selection for Chi occurred independently in different bacteria. (C) 1999 Editions scientifiques et medicales Elsevier SAS.