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Genomic Changes Arising in Long-Term Stab Cultures of Escherichia coli

D. Faure,^1, R. Frederick,² D. Woch,^1, P. Portier,^1,¶ M. Blot,^1,|| and J. Adams^1,2*

Plasticité et Expression des Génomes Microbiens, CNRS FRE2383, Université Joseph-Fourier, Grenoble, France,¹ Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan²

Received 2 April 2004/ Accepted 29 June 2004

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 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.

This paper is dedicated to the memory of Michel Blot, whose contributions to the microbial evolution community will long be remembered.

Present address: Institut des Sciences du Végétal, CNRS UPR2355, Centre National de la Recherche Scientifique, 91 198 Gif-sur-Yvette, France.

Present address: Institute of Environmental Sciences, Jagiellonian University, 30-387 Cracow, Poland.

^¶ Present address: Laboratoire d'Ecologie Microbienne, CNRS UMR5557, Université Claude-Bernard Lyon 1, Villeurbanne, France.

^|| Deceased (8 September 2002).

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