The replication origin of the Methylomonas clara plasmid pBE-2

The Methylomonas clara narrow host range plasmids pBE-2 and pBE-3 belong to the class of plasmids encoding a trans acting replication initiation factor. Characteristically for such plasmids, the sequence of the origin of pBE-2 and pBE-3 contains a number of large direct repeats (8 and a half iterons of 19 bp), which by analogy are putative binding sites of the trans acting replication factor. Several additional features typical for the majority of E. coli plasmids were found in the M. clara origin: These include sequences homologous to the E. coli DnaA-box, sequences resembling E. coli IHF binding-sites, an AT-rich region with short repeats (similar to those repeats of E. coli origins responsible for an initial DNA duplex opening), and an AT-rich bent DNA region containing inverted repeats which have homology to small repeated sequences found in several plasmid origins. In addition, in the M. clara plasmid origin, large potential hairpin structures are present and the sequence of one of these participates in site specific recombination.