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

Abstract

SummaryThe 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 did not generally crosshybridize. 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. Energyoptimized modelling predicted that the 3Ј strand of the terminal palindromes can form extensive hairpin structures that are similar to the 3Ј 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.

Chromosomal Circularization inStreptomyces griseusby Nonhomologous Recombination of Deletion Ends

“…24,25) Fischer et al 26) reported that homologous recombination of two sigma factor-like ORFs caused chromosomal arm replacement in S. ambofaciens, which generated unusually long TIRs in the mutants. We also found that in S. griseus mutant MM9, homologous recombination between two similar lipoprotein-like ORFs caused chromosomal arm replacement and generated 450-kb TIRs in place of the original 24-kb TIRs.…”

A linear megaplasmid, p1CP, carrying the genes for chlorocatechol catabolism of Rhodococcus opacus 1CP

“…Two copies of the motif GCTXCGC were found in each terminus and it was already assumed earlier that these structures are essential for replication (Kalkus et al, 1998;Shimizu et al, 2001). Essentially the same central motif with the potential to form a stable single C-residue loop close to the sheared T : C pairing was found in the linear Streptomyces plasmids pSCL1 (Wu & Roy, 1993), pSLA2 (Hirochika et al, 1984) and SLP2 , as well as in the terminal segments of several linear Streptomyces chromosomes (Huang et al, 1998). In pSLA2 these structures were shown to be essential for replication and propagation of linearity (Qin & Cohen, 1998).…”

“…However, in p1CP-J the palindrome of position 12-34 is imperfect because of a mismatch at position 14. Both palindromic structures contain the central motif GCTXCGC, already obtained for other plasmid termini of rhodococci (Kalkus et al, 1998;Shimizu et al, 2001) and streptomycetes (Bey et al, 2000;Huang et al, 1998). Several other regions of striking similarity were identified (alignment positions 1-2, 5-7 and 49-62).…”

“…In pSLA2 these structures were shown to be essential for replication and propagation of linearity (Qin & Cohen, 1998). The specific binding of TPs (Huang et al, 1998) and the patching of the singlestranded gaps at the 39 termini during replication (Chen, 1996) are two possible functions of palindromes. Additionally, a conserved CCXXCGG motif with an unknown, but probably important function, was found at the very end of all termini, including those of p1CP.…”

Giant linear plasmids in Streptomyces: a treasure trove of antibiotic biosynthetic clusters

“…13 These two features proved to be conserved in most of linear plasmids and chromosomes in actinobacteria. Cloning and sequencing of the terminal fragments revealed that the telomere sequence of SCP1 could not form a Y-shaped foldback structure, 14 a feature conserved in most Streptomyces linear replicons, 15 which may function in terminal replication. 16 Figure 2 The gross structures of the linear plasmids, SCP1 and pSLA2-L (a), and possible secondary telomere structures deduced from their sequences (b).…”