This Article Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Reprints and Permissions Copyright Information Books from ASM Press MicrobeWorld Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Brikun, I Articles by Berg, D E Search for Related Content PubMed PubMed Citation Articles by Brikun, I Articles by Berg, D E

 Previous Article  |  Next Article 

J Bacteriol. 1994 March; 176(6): 1673-1682

research-article

DNA sequence divergence among derivatives of Escherichia coli K-12 detected by arbitrary primer PCR (random amplified polymorphic DNA) fingerprinting.

Department of Molecular Microbiology, Washington University Medical School, St. Louis, Missouri 63110.

ABSTRACT

Derivatives of Escherichia coli K-12 of known ancestry were characterized by random amplified polymorphic DNA (RAPD) fingerprinting to better understand genome evolution in this family of closely related strains. This sensitive method entails PCR amplification with arbitrary primers at low stringency and yields arrays of anonymous DNA fragments that are strain specific. Among 150 fragments scored, eight were polymorphic in that they were produced from some but not all strains. Seven polymorphic bands were chromosomal, and one was from the F-factor plasmid. Five of the six mapped polymorphic chromosomal bands came from just 7% of the genome, a 340-kb segment that includes the terminus of replication. Two of these were from the cryptic Rac prophage, and the inability to amplify them from strains was attributable to deletion (excision) or to rearrangement of Rac. Two other terminus-region segments that resulted in polymorphic bands appeared to have sustained point mutations that affected the ability to amplify them. Control experiments showed that RAPD bands from the 340-kb terminus-region segment and also from two plasmids (P1 and F) were represented in approximate proportion to their size. Optimization experiments showed that the concentration of thermostable polymerase strongly affected the arrays of RAPD products obtained. Comparison of RAPD polymorphisms and positions of strains exhibiting them in the pedigree suggests that many sequence changes occurred in these historic E. coli strains during their storage. We propose that the clustering of such mutations near the terminus reflects errors during completion of chromosome replication, possibly during slow growth in the stab cultures that were often used to store E. coli strains in the early years of bacterial genetics.

This article has been cited by other articles:

• Finger, S. A., Velapatino, B., Kosek, M., Santivanez, L., Dailidiene, D., Quino, W., Balqui, J., Herrera, P., Berg, D. E., Gilman, R. H. (2006). Effectiveness of Enterobacterial Repetitive Intergenic Consensus PCR and Random Amplified Polymorphic DNA Fingerprinting for Helicobacter pylori Strain Differentiation.. Appl. Environ. Microbiol. 72: 4713-4716 [Abstract] [Full Text]  
• van Leeuwen, W., Verbrugh, H., van der Velden, J., van Leeuwen, N., Heck, M., van Belkum, A. (1999). Validation of Binary Typing for Staphylococcus aureus Strains. J. Clin. Microbiol. 37: 664-674 [Abstract] [Full Text]  
• Berlyn, M. K. B. (1998). Linkage Map of Escherichia coli K-12, Edition 10: The Traditional Map. Microbiol. Mol. Biol. Rev. 62: 814-984 [Abstract] [Full Text]  
• Sakallah, S A, Lanning, R W, Cooper, D L (1995). DNA fingerprinting of crude bacterial lysates using degenerate RAPD primers.. Genome Res 4: 265-268 [Abstract]