Genomic changes arising in long-term stab cultures of Escherichia coli

Abstract

Genomic scans of clones isolated from long-term stab cultures of Escherichia coli K-12 showed the loss of two large segments of the genome, with each lost segment being approximately 20 kb long. A detailed analysis of one of the deletions, located between 5.4 and 5.9 min, revealed that similar deletions had arisen in several other stab cultures. All deletions of this type exhibited a right terminus ending precisely at an IS5A element and a left terminus that varied over an approximately 5-kb range but was bordered in all but two cases by sequences belonging to the preferred consensus target sequence for IS5, YTAR. The ubiquity of such deletions in independent stab cultures and the increase in their frequency over time argue that they have a selective advantage. It is speculated that the loss of the crl locus is responsible for the selective advantage of the deletions.

FIG. 1.

Comparative genomic hybridization of strain W3110 and strain Y34. Genes are plotted by their coordinates according to the E. coli K-12 genome map (6). Confidence intervals were calculated as described in the text.

FIG. 2.

Increase in average frequency of proline auxotrophs with age of stab culture. Error bars indicate standard errors.

FIG. 3.

The type I deletions can be grouped into the following 12 categories: B52 (D22), H122 (H148), F10, G113 (G92 and G95), Y54 (Y34, Y42, Y50, and Y59), E26 (HB101, W2914, and W2915), Z22 (Z27, Z28, and Z57), Z14 (Z29), Y39 (Y4, Y5, Y15, Y24, Y26, Y35, Y45, Y46, Y49, Y58, and Y60), Y52 (Y51 and Y53), Z20 (Z24), and E41. The deletions are displayed as thick lines. Comparisons of the deletion lengths distinguish variable and common deleted regions. At the opposite end from the IS element, the last open reading frame in the common deleted region is crl. The IS30 element is inserted inside an inactivated single copy of IS911. The distances are given (in kilobases) according to the published E. coli K-12 genome (6).

FIG. 4.

Sequences of the flanking regions of type 1 deletions. The sequences at the left boundary for H122, B52, F10, G113, Y54, E26, HB101, Y39, Y52, Z20, and E41 matched the consensus preferred target sequence, YTAR, for IS5. The sequences for Y14 and Z52 differed from this consensus sequence by one base. The end of IS5A is underlined and shown in lowercase, and the target sequences of the IS5 insertion are shown in bold. The nucleotide positions on the chromosome are given according the E. coli K-12 genomic sequence (6).