Sequence of the R1 plasmid and comparison to F and R100

- R1 contains a conjugative plasmid backbone, a Tn21-like transposon, and a novel region resembling some Klebsiella sequences.
- The conjugative plasmid backbone is highly similar to F and R100, but varies in which it most closely resembles.
- The Tn21-like transposon of R1 is identical to Tn21 of R100 apart from two IS insertions and deletions.
- The novel region contains a kanamycin resistance gene and putative phage genes.

The R1 antibiotic resistance plasmid, originally discovered in a clinical Salmonella isolate in London, 1963, has served for decades as a key model for understanding conjugative plasmids. Despite its scientific importance, a complete sequence of this plasmid has never been reported. We present the complete genome sequence of R1 along with a brief review of the current knowledge concerning its various genetic systems and a comparison to the F and R100 plasmids. R1 is 97,566 nucleotides long and contains 120 genes. The plasmid consists of a backbone largely similar to that of F and R100, a Tn21-like transposon that is nearly identical to that of R100, and a unique 9-kb sequence that bears some resemblance to sequences found in certain Klebsiella oxytoca strains. These three regions of R1 are separated by copies of the insertion sequence IS1. Overall, the structure of R1 and comparison to F and R100 suggest a fairly stable shared conjugative plasmid backbone into which a variety of mobile elements have inserted to form an “accessory” genome, containing multiple antibiotic resistance genes, transposons, remnants of phage genes, and genes whose functions remain unknown.