The structures of three recombinants between bacteriophage A DNA and plasmid pBR322 that were generated in a recA derivative of Escherichia coli are described. Each resulted from two illegitimate recombination events that resulted in the substitution of part of the A genome by part of the plasmid genome. The nucleotide sequences at the six A-plasmid junctions were determined and compared with the sequences of the A and plasmid genomes before recombination. Each recombination occurred at a short region of homology in the two genomes, and other short regions of homology were found near some of the junctions. The structures of these junctions are similar to those resulting from illegitimate recombination in animal cells. A model to explain how these multiple illegitimate recombination events could result from a cascade of DNA gyrase-catalyzed recombinations is discussed.The mechanisms responsible for generating gross DNA rearrangements such as deletions, substitutions, inversions, amplifications, and translocations are not understood. Recently, two specific models have been proposed that could account for these illegitimate recombination events.Miller and co-workers (1, 2) have found that most deletions in Escherichia coli occur between directly repeated sequences of 5 or more base pairs (bp). Therefore, they suggested that these deletions resulted from a slippage error in replication (2). Efstratiadis et al. (3) have suggested a similar model for the generation of deletions in eukaryotic cells.Another possible explanation for some illegitimate recombination events is that they are generated by DNA gyrase (4-6). Ikeda et aL (4, 5) discovered that illegitimate recombinations between A DNA and plasmid pBR322 occur in extracts of E. coli and that the frequency of recombination is increased by the addition of oxolinic acid (4, 5), which is an inhibitor of DNA gyrase (7,8). Therefore, they suggested that the recombinations result from an exchange of DNA gyrase subunits bound to different sites. The nucleotide sequences at the A-plasmid junctions of one of these recombinants were determined and the results were consistent with this model (5).We have isolated several A-pBR322 recombinants that were generated in recA+ and recA-derivatives of E. coli (6,9). The sequences at the A-pBR322 junctions of four of these recombinants were determined (6). Each resulted from reciprocal recombination between 10-13 bp of homology in A DNA and pBR322, including one (ATA1R) that was isolated in a recAstrain. One of the recombinants, AKA7, had an unusual structure in that it resulted from two of these rare events. DNA gyrase appears to be capable of catalyzing multiple recombinations (4). Therefore, we have suggested that AKA7 may have been generated by a cascade of DNA gyrase-catalyzed recombinations (6).The structures of three additional A-pBR322 recombinants isolated in a recA-strain of E. coli are described here. Each resulted from two recombinations at sites of 1-5 bp of homology in the A and plasmid genomes. Their structur...

Recombination between the IS50 sequences that flank Tn5 has been found to occur readily after the transformation of E. coli recA strains with a plasmid that contains direct repeats of these sequences. Analysis of mutants of IS50 indicates that the polypeptide encoded by IS50 that is required for transposition is also required for the recombination. Surprisingly, the mechanism of recombination appears to be similar to general homologous recombination rather than site-specific recombination. This IS50 recombination system may be responsible for resolving transient cointegrate structures containing direct repeats of IS50 or Tn5 during the transposition of IS50 and Tn5.

The nucleotide sequences involved in the illegitimate recombination of four recombinants between bacteriophage lambda DNA and pBR322 in E. coli (lambda TA6, lambda KA3, lambda TA1R, and lambda KA7) were determined. Each resulted from recombination between regions of homology of 10 to 13 base pairs. The presence of a recA+ allele was found to stimulate recombination between lambda DNA and pBR322 approximately 10-fold. Lambda TA6, lambda KA3, and lambda KA7 were isolated in the presence of a recA+ allele and therefore, may have been generated by the recA recombination system. However, lambda TA1R was isolated in a recA mutant, and was presumably generated by a different recombination system. The possibility that it was generated by DNA gyrase is discussed. Two recombination events were required to form lambda KA7, which may indicate that it also was generated by DNA gyrase.