Skip to main content
NCBI home page
Genetics logoLink to Genetics
. 1989 Apr;121(4):651–658. doi: 10.1093/genetics/121.4.651

Palindromy and the Location of Deletion Endpoints in Escherichia Coli

K Weston-Hafer 1, D E Berg 1
PMCID: PMC1203650  PMID: 2656400

Abstract

The contributions of direct and inverted repeats to deletion formation were studied by characterizing Amp(r) revertants of plasmids with a series of insertion mutations at a specific site in the pBR322 ampicillin resistance (amp) gene. The inserts at this site are palindromic, variable in length, and bracketed by 9- or 10-bp direct repeats of amp sequence. There is an additional direct repeat composed of 4 bp within the insert and 4 bp of adjoining amp sequence. DNA sequencing and colony hybridization of Amp(r) revertants showed that they contained either the parental amp sequence, implying deletion endpoints in the flanking 9- or 10-bp repeats, or a specific 1-bp substitution, implying endpoints in the 4-bp repeats. Although generally direct repeats seem to be used as deletion endpoints with a frequency proportional to their lengths, we found that with uninterrupted palindromes longer than 32 bp, the majority of deletions ended in the 4 bp, not the 9- or 10-bp repeats. This preferential use of the shorter direct repeats associated with palindromes is interpreted according to a DNA synthesis-error model in which hairpin structures formed by intrastrand pairing foster the slippage of nascent strands during DNA synthesis.

Full Text

The Full Text of this article is available as a PDF (2.6 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Albertini A. M., Hofer M., Calos M. P., Miller J. H. On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions. Cell. 1982 Jun;29(2):319–328. doi: 10.1016/0092-8674(82)90148-9. [DOI] [PubMed] [Google Scholar]
  2. Arraj J. A., Marinus M. G. Phenotypic reversal in dam mutants of Escherichia coli K-12 by a recombinant plasmid containing the dam+ gene. J Bacteriol. 1983 Jan;153(1):562–565. doi: 10.1128/jb.153.1.562-565.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Backman K., Betlach M., Boyer H. W., Yanofsky S. Genetic and physical studies on the replication of ColE1-type plasmids. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):69–76. doi: 10.1101/sqb.1979.043.01.012. [DOI] [PubMed] [Google Scholar]
  4. Brunier D., Michel B., Ehrlich S. D. Copy choice illegitimate DNA recombination. Cell. 1988 Mar 25;52(6):883–892. doi: 10.1016/0092-8674(88)90430-8. [DOI] [PubMed] [Google Scholar]
  5. Casadaban M. J., Cohen S. N. Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J Mol Biol. 1980 Apr;138(2):179–207. doi: 10.1016/0022-2836(80)90283-1. [DOI] [PubMed] [Google Scholar]
  6. Chang S., Cohen S. N. In vivo site-specific genetic recombination promoted by the EcoRI restriction endonuclease. Proc Natl Acad Sci U S A. 1977 Nov;74(11):4811–4815. doi: 10.1073/pnas.74.11.4811. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Collins J., Volckaert G., Nevers P. Precise and nearly-precise excision of the symmetrical inverted repeats of Tn5; common features of recA-independent deletion events in Escherichia coli. Gene. 1982 Jul-Aug;19(1):139–146. doi: 10.1016/0378-1119(82)90198-6. [DOI] [PubMed] [Google Scholar]
  8. Conley E. C., Saunders V. A., Saunders J. R. Deletion and rearrangement of plasmid DNA during transformation of Escherichia coli with linear plasmid molecules. Nucleic Acids Res. 1986 Nov 25;14(22):8905–8917. doi: 10.1093/nar/14.22.8905. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. DasGupta U., Weston-Hafer K., Berg D. E. Local DNA sequence control of deletion formation in Escherichia coli plasmid pBR322. Genetics. 1987 Jan;115(1):41–49. doi: 10.1093/genetics/115.1.41. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Efstratiadis A., Posakony J. W., Maniatis T., Lawn R. M., O'Connell C., Spritz R. A., DeRiel J. K., Forget B. G., Weissman S. M., Slightom J. L. The structure and evolution of the human beta-globin gene family. Cell. 1980 Oct;21(3):653–668. doi: 10.1016/0092-8674(80)90429-8. [DOI] [PubMed] [Google Scholar]
  11. Falkner F. G., Mocikat R., Zachau H. G. Sequences closely related to an immunoglobulin gene promoter/enhancer element occur also upstream of other eukaryotic and of prokaryotic genes. Nucleic Acids Res. 1986 Nov 25;14(22):8819–8827. doi: 10.1093/nar/14.22.8819. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Ghosal D., Saedler H. IS2-61 and IS2-611 arise by illegitimate recombination from IS2-6. Mol Gen Genet. 1979 Oct 3;176(2):233–238. doi: 10.1007/BF00273217. [DOI] [PubMed] [Google Scholar]
  13. Ikeda H., Moriya K., Matsumoto T. In vitro study of illegitimate recombination: involvement of DNA gyrase. Cold Spring Harb Symp Quant Biol. 1981;45(Pt 1):399–408. doi: 10.1101/sqb.1981.045.01.054. [DOI] [PubMed] [Google Scholar]
  14. Mandecki W. Oligonucleotide-directed double-strand break repair in plasmids of Escherichia coli: a method for site-specific mutagenesis. Proc Natl Acad Sci U S A. 1986 Oct;83(19):7177–7181. doi: 10.1073/pnas.83.19.7177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  16. Michel B., Ehrlich S. D. Illegitimate recombination at the replication origin of bacteriophage M13. Proc Natl Acad Sci U S A. 1986 May;83(10):3386–3390. doi: 10.1073/pnas.83.10.3386. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Michel B., Ehrlich S. D. Illegitimate recombination occurs between the replication origin of the plasmid pC194 and a progressing replication fork. EMBO J. 1986 Dec 20;5(13):3691–3696. doi: 10.1002/j.1460-2075.1986.tb04701.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Miller J. K., Barnes W. M. Colony probing as an alternative to standard sequencing as a means of direct analysis of chromosomal DNA to determine the spectrum of single-base changes in regions of known sequence. Proc Natl Acad Sci U S A. 1986 Feb;83(4):1026–1030. doi: 10.1073/pnas.83.4.1026. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Nag D. K., DasGupta U., Adelt G., Berg D. E. IS50-mediated inverse transposition: specificity and precision. Gene. 1985;34(1):17–26. doi: 10.1016/0378-1119(85)90290-2. [DOI] [PubMed] [Google Scholar]
  20. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Schaaper R. M., Danforth B. N., Glickman B. W. Mechanisms of spontaneous mutagenesis: an analysis of the spectrum of spontaneous mutation in the Escherichia coli lacI gene. J Mol Biol. 1986 May 20;189(2):273–284. doi: 10.1016/0022-2836(86)90509-7. [DOI] [PubMed] [Google Scholar]
  22. Streisinger G., Okada Y., Emrich J., Newton J., Tsugita A., Terzaghi E., Inouye M. Frameshift mutations and the genetic code. This paper is dedicated to Professor Theodosius Dobzhansky on the occasion of his 66th birthday. Cold Spring Harb Symp Quant Biol. 1966;31:77–84. doi: 10.1101/sqb.1966.031.01.014. [DOI] [PubMed] [Google Scholar]
  23. Weaver D. T., DePamphilis M. L. The role of palindromic and non-palindromic sequences in arresting DNA synthesis in vitro and in vivo. J Mol Biol. 1984 Dec 25;180(4):961–986. doi: 10.1016/0022-2836(84)90266-3. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES