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PMID: 8013470 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Copy-choice illegitimate DNA recombination revisited.

The EMBO journal ·Vol. 13 ·No. 11 ·1994-06-01 ·Pages 2725-34

d'Alençon E, Petranovic M, Michel B, Noirot P, Aucouturier A, Uzest M, Ehrlich SD

Abstract

Nearly precise excision of a transposon related to Tn10 from an Escherichia coli plasmid was used as a model to study illegitimate DNA recombination between short direct repeats. The excision was stimulated 100-1000 times by induction of plasmid single-stranded DNA synthesis and did not involve transfer of DNA from the parental to the progeny molecule. We conclude that it occurred by copy-choice DNA recombination, and propose that other events of recombination between short direct repeats might be a result of the same process.

MeSH Terms
Base Sequence DNA Replication/genetics DNA Transposable Elements/genetics DNA, Recombinant/metabolism DNA, Single-Stranded/biosynthesis Escherichia coli/genetics,growth & development Inoviridae/physiology Models, Genetic Molecular Sequence Data Multigene Family/genetics Nucleic Acid Conformation Plasmids/genetics,metabolism Recombination, Genetic/genetics Repetitive Sequences, Nucleic Acid Viral Proteins/genetics,metabolism
Chemicals
DNA Transposable Elements DNA, Recombinant DNA, Single-Stranded Viral Proteins
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
d'Alençon E
Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas, France.
Petranovic M
Michel B
Noirot P
Aucouturier A
Uzest M
Ehrlich S D
References (71)
71 references, click to expand
  1. DNA transcription and repressor binding affect deletion formation in Escherichia coli plasmids.
    EMBO J. 1992 Oct;11(10):3629-34 PMID: 1396563
  2. Regulation of bacteriophage f1 DNA replication. I. New functions for genes II and X.
    J Mol Biol. 1988 Sep 5;203(1):49-62 PMID: 3054123
  3. Deletions in plasmid pBR322: replication slippage involving leading and lagging strands.
    Genetics. 1991 Apr;127(4):649-55 PMID: 2029966
  4. Recombination of DNAs in Xenopus oocytes based on short homologous overlaps.
    Nucleic Acids Res. 1987 Feb 11;15(3):971-85 PMID: 3029712
  5. The structure and evolution of the human beta-globin gene family.
    Cell. 1980 Oct;21(3):653-68 PMID: 6985477
  6. Genetic studies of the lac repressor. VII. On the molecular nature of spontaneous hotspots in the lacI gene of Escherichia coli.
    J Mol Biol. 1978 Dec 25;126(4):847-57 PMID: 370408
  7. Cloning and expression of steroid sulfatase cDNA and the frequent occurrence of deletions in STS deficiency: implications for X-Y interchange.
    Cell. 1987 May 22;49(4):443-54 PMID: 3032454
  8. Recombination mechanisms in bacteria.
    J Cell Physiol Suppl. 1955 May;45(Suppl. 2):75-107 PMID: 13242626
  9. Mechanisms of deletion formation in Escherichia coli plasmids. II. Deletions mediated by short direct repeats.
    Mol Gen Genet. 1991 Aug;228(1-2):209-14 PMID: 1679526
  10. Intramolecular recombination during plasmid transformation of Bacillus subtilis competent cells.
    EMBO J. 1982;1(12):1565-71 PMID: 6327279
  11. Structural plasmid instability in Bacillus subtilis: effect of direct and inverted repeats.
    Mol Gen Genet. 1988 Jun;212(3):450-8 PMID: 3138528
  12. The Escherichia coli terB sequence affects maintenance of a plasmid with the M13 phage replication origin.
    J Bacteriol. 1991 Dec;173(23):7695-7 PMID: 1938965
  13. Single-stranded plasmid DNA in Bacillus subtilis and Staphylococcus aureus.
    Proc Natl Acad Sci U S A. 1986 Apr;83(8):2541-5 PMID: 3085097
  14. Effects of palindrome size and sequence on genetic stability in the bacteriophage phi X174 genome.
    J Mol Biol. 1987 Aug 20;196(4):743-55 PMID: 2824789
  15. Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria.
    Nucleic Acids Res. 1992 Jul 11;20(13):3279-85 PMID: 1630899
  16. Replication of a bacterial plasmid and an episome in Escherichia coli.
    Biochemistry. 1970 Jan 20;9(2):399-406 PMID: 4904868
  17. Identification of plasmid and Bacillus subtilis chromosomal recombination sites used for pE194 integration.
    J Bacteriol. 1989 May;171(5):2856-65 PMID: 2496116
  18. Diagnosis of genetic disease using recombinant DNA. Second edition.
    Hum Genet. 1989 Nov;83(4):307-34 PMID: 2572533
  19. Chromosome brekage accompanying genetic recombination in bacteriophage.
    Proc Natl Acad Sci U S A. 1961 Jun 15;47:857-68 PMID: 13769766
  20. Palindromy and the location of deletion endpoints in Escherichia coli.
    Genetics. 1989 Apr;121(4):651-8 PMID: 2656400
  21. Local DNA sequence control of deletion formation in Escherichia coli plasmid pBR322.
    Genetics. 1987 Jan;115(1):41-9 PMID: 3030883
  22. Plasmid replication stimulates DNA recombination in Bacillus subtilis.
    J Mol Biol. 1987 Jul 5;196(1):39-48 PMID: 3116269
  23. Prolonged incubation in calcium chloride improves the competence of Escherichia coli cells.
    Gene. 1979 May;6(1):23-8 PMID: 383576
  24. On the deletion of inverted repeated DNA in Escherichia coli: effects of length, thermal stability, and cruciform formation in vivo.
    Genetics. 1991 Dec;129(4):991-1005 PMID: 1783300
  25. Formation of large deletions by illegitimate recombination in the HPRT gene of primary human fibroblasts.
    Proc Natl Acad Sci U S A. 1993 Feb 15;90(4):1392-6 PMID: 8433997
  26. High-efficiency transformation of bacterial cells by electroporation.
    J Bacteriol. 1988 Jun;170(6):2796-801 PMID: 3286620
  27. The replication termination signal terB of the Escherichia coli chromosome is a deletion hot spot.
    EMBO J. 1991 Sep;10(9):2699-705 PMID: 1868840
  28. Mechanism of F factor-enhanced excision of transposon Tn5.
    Gene. 1983 Apr;22(1):1-7 PMID: 6305767
  29. Are single-stranded circles intermediates in plasmid DNA replication?
    EMBO J. 1986 Mar;5(3):631-7 PMID: 3011418
  30. Generation of deletions in pneumococcal mal genes cloned in Bacillus subtilis.
    Proc Natl Acad Sci U S A. 1984 Aug;81(16):5189-93 PMID: 6089185
  31. The three operators of the lac operon cooperate in repression.
    EMBO J. 1990 Apr;9(4):973-9 PMID: 2182324
  32. Tandem chromosomal duplications: role of REP sequences in the recombination event at the join-point.
    EMBO J. 1990 Mar;9(3):939-46 PMID: 2178927
  33. Processing of plasmid DNA during bacterial conjugation.
    Microbiol Rev. 1984 Mar;48(1):24-41 PMID: 6201705
  34. Structurally stable Bacillus subtilis cloning vectors.
    Gene. 1990 Mar 1;87(1):53-61 PMID: 2110098
  35. Preferential DNA secondary structure mutagenesis in the lagging strand of replication in E. coli.
    Nature. 1991 Aug 8;352(6335):544-7 PMID: 1865910
  36. The chromosomal basis of human neoplasia.
    Science. 1983 Jul 15;221(4607):227-36 PMID: 6336310
  37. Three Tn10-associated excision events: relationship to transposition and role of direct and inverted repeats.
    Cell. 1981 Jan;23(1):215-27 PMID: 6260376
  38. Mechanism of intramolecular recyclization and deletion formation following transformation of Escherichia coli with linearized plasmid DNA.
    Nucleic Acids Res. 1986 Nov 25;14(22):8919-32 PMID: 3537964
  39. Tandem genetic duplications in phage and bacteria.
    Annu Rev Microbiol. 1977;31:473-505 PMID: 334045
  40. Anecdotal, historical and critical commentaries on genetics twenty years of illegitimate recombination.
    Genetics. 1987 Apr;115(4):581-3 PMID: 17246374
  41. Transformation of Saccharomyces cerevisiae with nonhomologous DNA: illegitimate integration of transforming DNA into yeast chromosomes and in vivo ligation of transforming DNA to mitochondrial DNA sequences.
    Mol Cell Biol. 1993 May;13(5):2697-705 PMID: 8386316
  42. Bacteriophage f1 DNA replication genes. II. The roles of gene V protein and gene II protein in complementary strand synthesis.
    J Mol Biol. 1988 Sep 5;203(1):39-48 PMID: 3054122
  43. Recombination between short DNA homologies causes tandem duplication.
    Nature. 1981 Jul 16;292(5820):269-71 PMID: 7019717
  44. A genetical study of thymineless mutants of E. coli K12.
    Genet Res. 1966 Aug;8(1):83-100 PMID: 5329976
  45. Excision sequences in the mitochondrial genome of yeast.
    Gene. 1983 Mar;21(3):193-202 PMID: 6343188
  46. Deletion hot spots in chimeric Escherichia coli plasmids.
    J Bacteriol. 1989 Apr;171(4):1846-53 PMID: 2649476
  47. A rapid alkaline extraction procedure for screening recombinant plasmid DNA.
    Nucleic Acids Res. 1979 Nov 24;7(6):1513-23 PMID: 388356
  48. Diseases of the mitochondrial DNA.
    Annu Rev Biochem. 1992;61:1175-212 PMID: 1497308
  49. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid.
    J Bacteriol. 1978 Jun;134(3):1141-56 PMID: 149110
  50. Illegitimate recombination in Bacillus subtilis: nucleotide sequences at recombinant DNA junctions.
    Mol Gen Genet. 1987 Dec;210(3):578-80 PMID: 3123895
  51. Copy choice illegitimate DNA recombination.
    Cell. 1988 Mar 25;52(6):883-92 PMID: 2832066
  52. Nearly precise excision: a new type of DNA alteration associated with the translocatable element Tn10.
    Cell. 1979 Apr;16(4):733-8 PMID: 455447
  53. Nucleotide sequence and genome organisation of filamentous bacteriophages fl and fd.
    Gene. 1981 Dec;16(1-3):35-58 PMID: 6282703
  54. Deletion mutagenesis independent of recombination in bacteriophage T7.
    J Bacteriol. 1991 Jan;173(2):869-78 PMID: 1846152
  55. Replication of a plasmid containing two origins of bacteriophage.
    J Mol Biol. 1981 Nov 25;153(1):169-76 PMID: 7040678
  56. 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 PMID: 5237214
  57. The effect of the length of direct repeats and the presence of palindromes on deletion between directly repeated DNA sequences in bacteriophage T7.
    Nucleic Acids Res. 1991 Jul 25;19(14):3901-5 PMID: 1861982
  58. On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions.
    Cell. 1982 Jun;29(2):319-28 PMID: 6288254
  59. Spontaneous deletion formation at the aprt locus of hamster cells: the presence of short sequence homologies and dyad symmetries at deletion termini.
    EMBO J. 1986 Jun;5(6):1199-204 PMID: 3015589
  60. Nucleotide sequence of the filamentous bacteriophage M13 DNA genome: comparison with phage fd.
    Gene. 1980 Oct;11(1-2):129-48 PMID: 6254849
  61. Imprecise excision of plasmid pE194 from the chromosomes of Bacillus subtilis pE194 insertion strains.
    J Bacteriol. 1992 Nov;174(21):6997-7002 PMID: 1400250
  62. Retraction: copy choice illegitimate DNA recombination.
    Cell. 1990 Aug 10;62(3):409 PMID: 2199061
  63. Deletion formation in bacteriophage T4.
    J Mol Biol. 1988 Jul 20;202(2):233-43 PMID: 3172217
  64. New Tn10 derivatives for transposon mutagenesis and for construction of lacZ operon fusions by transposition.
    Gene. 1984 Dec;32(3):369-79 PMID: 6099322
  65. EQUILIBRIUM SEDIMENTATION OF MACROMOLECULES IN DENSITY GRADIENTS.
    Proc Natl Acad Sci U S A. 1957 Jul 15;43(7):581-8 PMID: 16590059
  66. Transposon Tn5 excision in yeast: influence of DNA polymerases alpha, delta, and epsilon and repair genes.
    Proc Natl Acad Sci U S A. 1992 May 1;89(9):3785-9 PMID: 1315039
  67. Identification of two Escherichia coli factor Y effector sites near the origins of replication of the plasmids (ColE1 and pBR322.
    Proc Natl Acad Sci U S A. 1980 Nov;77(11):6521-5 PMID: 6109282
  68. The family of highly interrelated single-stranded deoxyribonucleic acid plasmids.
    Microbiol Rev. 1989 Jun;53(2):231-41 PMID: 2666843
  69. Genetic rearrangements and gene amplification in Escherichia coli: DNA sequences at the junctures of amplified gene fusions.
    Genes Dev. 1987 May;1(3):227-37 PMID: 3315849
  70. Site-specific pausing of deoxyribonucleic acid synthesis catalyzed by four forms of Escherichia coli DNA polymerase III.
    Biochemistry. 1983 Oct 25;22(22):5177-88 PMID: 6360204
  71. Excision of transposon Tn5 is dependent on the inverted repeats but not on the transposase function of Tn5.
    Proc Natl Acad Sci U S A. 1981 Jan;78(1):459-63 PMID: 6264444
Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
0261-4189
Published
1994-06-01
Pages
2725-34
Language
English
Region
England
NLM ID
8208664
PMCID
PMC395147
Subset
IM
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