Escherichia coli K-12 F' plasmids carrying insertion sequences IS1 and IS5

Evidence for past integration of IncP-1 plasmids into bacterial chromosomes

Plasmids of the IncP-1 incompatibility group are self-transmissible between and stably maintained in a very broad range of Gram-negative bacteria. A characteristic feature of IncP-1 genomes is the existence of multiple binding sites (OB) for the KorB protein which plays a dual role in active partitioning of plasmid and coordinate regulation of expression of genes for replication, maintenance and transfer. A search of the available bacterial genome sequences revealed a significant number (70 out of 322) with one or more putative KorB binding sites. Binding of KorB to such a site was demonstrated by chromatin immunoprecipitation (ChIP) for Pseudomonas putida KT2440. While such a site may arise by chance, this is unlikely for Pseudomonas aeruginosa UCBPP-PA14 whose genome sequence contains four clustered OB sites and several regions have more than 80% nucleotide identity to traJ, trbJ and trbL of IncP-1 plasmids. A number of other bacterial genomes also contain integrated partial IncP-1 genomes or their remnants. These data provide evidence for multiple past integration events of IncP-1 plasmids into bacterial chromosomes and provide new evidence for IncP-1 plasmids being important elements in gene mobility.

Mapping of insertion element IS5 in the Escherichia coli K-12 chromosome. Chromosomal rearrangements mediated by IS5

We identified phage clones containing insertion element IS5 in a set of 476 lambda phage clones carrying chromosomal segments that cover almost the entire chromosome of Escherichia coli K-12 W3110. Precise locations and orientations of IS5 were then determined by cleavage analysis of phage DNAs containing them. We mapped 23 copies of IS5 (named is5A to is5W) on the W3110 chromosome. Among them, ten were identified as the common elements present at the same locations in both chromosomes of W3110 and another E. coli K-12 strain, JE5519. While most of the mapped IS5 elements were scattered over the W3110 chromosome, four copies of IS5 (designated is5L, is5M, is5N and is5O) were in a region representing tandem duplication of a DNA segment flanked by two copies of IS5. Interestingly, one unit of this DNA segment as well as a portion of it was seen also in a tandem array in a different region where two copies of IS5 (designated is5P and is5Q) were present. In particular two pairs of the mapped IS5 elements may have been involved in inversion of the chromosomal segments in two of the E. coli K-12 derivatives.

Mapping of insertion elements IS1, IS2 and IS3 on the Escherichia coli K-12 chromosome. Role of the insertion elements in formation of Hfrs and F' factors and in rearrangement of bacterial chromosomes

The chromosome of an Escherichia coli K-12 strain W3110 contains seven copies of insertion element IS1, 12 copies of IS2 and six copies of IS3. We determined the approximate locations of six copies of IS1 (named is1A to is1F), ten copies of IS2 (named is2A to is2J), and five copies of IS3 (named is3A to is3E) on the W3110 chromosome by plaque hybridization using the "mini-set" of the lambda phage library that includes 476 clones carrying chromosomal segments that cover the W3110 chromosome almost entirely. Cleavage maps of the W3110 chromosome and cleavage analysis of phage DNAs carrying insertion elements allowed us to assign more precise locations to most of the insertion elements and to determine their orientations. Insertion elements were distributed randomly along the W3110 chromosome in one or other orientation. Several of these were located at the same positions on the chromosome of another E. coli K-12 strain, JE5519, and they were assumed to be the original complement of insertion elements in E. coli K-12 wild-type. Locations and orientations of such insertion elements were correlated well with Hfr points of origin and with crossover points for excision of some F' factors derived from several Hfrs. Insertion elements may be involved also in rearrangement of bacterial chromosomes.

Characterization of a mutation conferring radiation sensitivity, ior, located close to the gene coding for deoxycytidine deaminase in Escherichia coli

The isolation and characterization of a new mutation conferring radiation sensitivity in Escherichia coli is described. This mutation is located close to the gene coding for deoxycytidine deaminase, in the chromosomal region of the gat operon. It is very sensitive to gamma rays and exhibits a decrease in recombination ability. The expression of radiation sensitivity seems to result from the additive effect of the dcd mutation and another mutation of unknown function.

Distribution of DNA insertion element IS5 in natural isolates of Escherichia coli

DNA from Escherichia coli strains in a reference collection of 72 recent natural isolates (ECOR strains) and 25 natural isolates from the "pre-antibiotic" period 1930-1940 (Murray strains) were studied to determine the genomic abundance of insertion element IS5 and the size of genomic restriction fragments carrying sequences homologous to IS5. Among the ECOR strains, nearly two-thirds lack DNA sequences that hybridize with IS5, and one-half of the remainder have only one copy. Among strains in which IS5 is present, extensive variation in the size of IS5-bearing restriction fragments occurs, in many cases allowing distinction among strains that are judged to be nearly identical in genotype because of the identical electrophoretic mobility of the enzyme coded by each of 11 chromosomal loci. Among the Murray strains in which IS5 is present, the average number of elements per strain is larger, but not markedly so, than among recent isolates. Comparison between duplicate strains in the Murray collection suggests that the rate of accumulation of IS5 elements in prolonged storage in stab tubes corresponds to an apparent probability of transposition of approximately 0.008 +/- 0.002 per IS5 element per year. Because of the extensive genetic variation among strains, insertion elements such as IS5 would seem to be convenient genetic markers with which to detect recent common ancestry among strains.