Chih-Hung Huang, Yi-Shing Lin1, Ya-Ling Yang2, Shu-wen Huang, Carton W. Chen*

The telomeres of Streptomyces chromosomes contain conserved palindromic sequences
with potential to form complex secondary structures

ABSTRACT

The chromosomes of the gram positive soil bacteria Streptomyces are linear DNA molecules usually of about 8 Mb, containing a centrally-located origin of replication and covalently bound terminal proteins (which are presumably involved in the completion of replication of the telomeres). The ends of the chromosomes contain inverted repeats of variable lengths. The terminal segments of five Streptomyces chromosomes and plasmids were cloned and sequenced. The sequences showed a high degree of conservation in the first 166-168 bp. Beyond the terminal homology, the sequences diverged and generally did not cross-hybridize. The homologous regions contained seven palindromes with a few nucleotide differences. Many of these differences occur in complementary pairs such that the palindromicity is preserved. Energy optimized modeling predicted that the 3' strand of the terminal palindromes can form extensive hairpin structures that are similar to the 3' ends of autonomous parvovirus genomes. Most of the putative hairpins have a GCGCAGC sequence at the loop with the potential to form a stable single-C residue loop closed by a sheared G:A pairing. The similarity between the terminal structures of the Streptomyces replicons and the autonomous parvoviral genomes suggests that they may share some structural and/or replication features.