The use of synthetic oligonucleotides with universal templates for rapid DNA sequencing: results with staphylococcal replicon pC221

Abstract

A rapid sequencing strategy has been devised and applied to determine the complete nucleotide sequence (4555 bp) of Staphylococcus aureus plasmid pC221. The entire replicon was cloned into phage M13mp8 in both orientations to provide 'universal templates' for primed DNA synthesis from internally-sited oligonucleotide primers. The latter were synthesized by a modification of a recently described paper disc method which employs phosphotriester chemistry. Less than 4 weeks was required for the synthesis of the required primers and for the sequencing experiments. Plasmid pC221 bears a substrate-inducible chloramphenicol acetyltransferase (CAT) gene that shares much homology with its counterparts in pC194 (S. aureus) and the chromosomal cat-86 gene of Bacillus pumilus, both in coding regions and upstream sequences believed to be involved in the induction phenomenon. A second plasmid-specified protein, REP D, has an 81% identity in the REP C polypeptide that has been shown to be essential for the replication of staphylococcal plasmid pT181. The 5' flanking region of rep D shows striking similarities with its counterpart in rep C that determines copy number and incompatibility. The nucleotide sequence reveals two additional and overlapping open reading frames that may specify proteins that play roles in plasmid relaxation and transfer.