Role of short regions of homology in intermolecular illegitimate recombination events.

Abstract

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...

Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair

“…However, there is little support for the existence of such a repair pathway in plant organelles, particularly in plastids (Odom et al, 2008;Kohl and Bock, 2009). Furthermore, whereas MHMRs are detected in the absence or presence of ciprofloxacin, all but one NHEJ-like event are detected in ciprofloxacin-treated plants, thus raising the possibility that these events could be by-products of the ciprofloxacin-mediated DNA gyrase inhibition (Marvo et al, 1983). The fact that mismatches are detected in 91 out of 158 MHMR junctions relative to one or both parental strands (see Supplemental Data Set 1 online) is consistent with the lowspecificity requirements of the MMBIR pairing process.…”

The minimum amount of homology required for homologous recombination in mammalian cells.

“…Other demonstrations of the importance of short homologies include nonhomologous recombinations lacking site specificity. Nonhomologous recombination between phage A DNA and pBR322 DNA in Escherichia coli may involve 10 to 13 base pairs (bp) of homology (18), whereas deletions in E. coli may be formed by recombination between homologous regions of 6 to 17 bp (1).…”

Relationships among the rfb regions of Salmonella serovars A, B, and D

“…The first event was probably an illegitimate recombination event (11) not dependent on homology. The second event presumably did depend on homology, and at position 11.7, although the intergenic region is short, there is some similarity between strains LT2 and Ty2, since, with gaps inserted, the sequences can be represented as CAAIT[ -----------AlCTAICIGGTfIAflGCG (LT2) and ---'l'lG AGGGGGGGGGAflCCCTCIA-TGAhrlC-(Ty2) (homologous bases are underlined).…”