Crossover hot-spot instigator (Chi) sequences in Escherichia coli occupy distinct recombination/transcription islands

Crossover hot-spot instigator (Chi) sequences (5'-GCTGGTGG-3') are orientat ion-dependent, strand-specific sequences implicated in RecA-mediated DNA re combination. In Escherichia coli and Haemaphilus influenzae Chi and Chi-lik e sequences preferentially locate to approx. 1 kb recombination 'islands' i n the mRNA-synonymous strands of open reading frames (ORFs). Since mRNA-syn onymous strands follow Szybalski's transcription direction rule in being G- rich, and the average ORF is about 1 kb, then, on this basis alone, Chi seq uences are seen to reside in 1 kb G-rich 'islands'. However, RecA preferent ially binds GT-rich sequences, suggesting that genomic context might potent iate Chi action. Consistent with this, we report for E. coli that 1 kb sequ ence windows with Chi near their centres are a distinct subset of total 1 k b windows, the mRNA-synonymous strands being preferentially enriched in bot h G and T. Chi function might be particularly important for bacteria that s urvive high temperature and radiation. These often exist in habitats where recombination with E. coli DNA would be unlikely, so canonical Chi sequence s might not confer a selective disadvantage in this respect. In general, Ch i sequences are not more frequent in thermophilic bacteria and Deinococcus radiodurans, than in E. coli and other mesophilic bacteria. Only two of fiv e thermophilic bacteria examined showed preferential location of Chi sequen ces to mRNA-synonymous strands. In the thermophile Methanococcus jannaschii , windows containing the canonical Chi sequence do not form a distinct subs et. We suggest that in thermophilic bacteria and D. radiodurans the Chi fun ction may be achieved by sequences that differ from the canonical Chi seque nce, or that the number of these sequences is sufficient, or that the Chi f unction is unnecessary. (C) 2000 Elsevier Science B.V. All rights reserved.