Linear ends of Streptomyces rimosus replicons

Most chromosomal and linear plasmid ends in Streptomyces are similar and share terminal proteins. In S. rochei the different copies of terminal protein genes (tpg) that differ slightly in sequence seem to be used interchangeably and the pSLA2 ends can be replicated in S. lividans 66 and S. coelicolor A3(2) that have slight differences in the terminal proteins from S. rochei. It seems likely that the two ends of an element may interact with each other &#8211 ; ; the circular genetic maps of the chromosome may be due to this. One would expect that the linear plasmid DNA is negatively supercoiled in the cell like other DNA and this would be most easily achieved by the end proteins interacting. This may prevent stable existence of a plasmid with two totally different ends. There are at least three candidates for such elements in S. rimosus: pPZG102 does not have long IRs [1] and elements (pPZG103 and chromosome of MV25) formed by single cross overs between pPZG101 and the chromosome does not have much homology at the ends [2]. The end fragments of pPZG101, pPZG102 and the chromosome were cloned and sequenced. They only differ by a few bp from each other and fit the consensus for the other ends. Thus, there is no reason that they need different Tpgs. It is striking that the changes in the early palindromes are such that pairing would be conserved. This suggests that the secondary structure is important. The AseI patterns of the chromosomes in R6-65 and R6-501 are indistinguishable as are the macrorestriction maps of one half of pPZG101 and one end of pPZG102. Surprisingly, in both cases the terminal fragments showed small differences in size. Sequencing showed that these differences were not in the terminal 200 bp, but they are within 0.9 kb in the plasmid and 4.7 kb in the chromosome. This indicates that there is genetic lability associated with the ends of linear elements. DNA sequencing will show the nature of the changes. Ideas for explaining lability: maybe DNA topology &#8211 ; ; the ends could often be in a non-supercoiled state during replication ; maybe the end protein can sometimes prime DNA synthesis past the single stranded region resulting in strand displacement and ssDNA regions. [1] Gravius, B., Glocker, D., Pigac, J., Pandža, K., Hranueli, D. and Cullum, J. 1994. Microbiol. 140: 2271-2277. [2] Pandza, S., Biuković, G., Paravić, A., Dadbin, A., Cullum, J. and Hranueli, D. 1998. Mol. Microbiol. 28: 1165-1176.