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PMID: 2848243 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 85 ·No. 23 ·1988-12-00 ·Pages 8850-4

Yang Y, Ames GF

Abstract

A family of repetitive extragenic palindromic (REP) sequences is composed of hundreds of copies distributed throughout the chromosome. Their palindromic nature and conservation suggested that they are specifically recognized by a protein(s). We have identified DNA gyrase [DNA topoisomerase (ATP-hydrolysing), EC 5.99.1.3] as one of the REP-binding proteins. Gyrase has at least a 10-fold higher affinity for DNA containing REP sequences than for DNA not containing REP sequences. Binding effectiveness correlates directly with the number of REP sequences in the DNA. DNase I footprinting shows that gyrase protects 205 base pairs on a REP-containing DNA fragment enclosing the REP sequences. In agreement with the above results, a comparison of the REP consensus sequence with the sequence of previously identified pBR322 "strong" gyrase cleavage sites reveals a high degree of homology. Because REP sequences are numerous and found throughout the genome, we suggest they have physiological functions mediated through their interaction with gyrase, such as being sites of action for the maintenance of DNA supercoiling. In addition, we speculate that these interactions may be of a structural nature, such as involvement in the higher-order structure of the bacterial chromosome.

MeSH Terms
Base Sequence DNA Topoisomerases, Type II/metabolism Escherichia coli/enzymology Kinetics Molecular Sequence Data Repetitive Sequences, Nucleic Acid Substrate Specificity
Chemicals
DNA Topoisomerases, Type II
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Yang Y
Department of Biochemistry, University of California, Berkeley 94720.
Ames G F
References (37)
37 references, click to expand
  1. Purification of subunits of Escherichia coli DNA gyrase and reconstitution of enzymatic activity.
    Proc Natl Acad Sci U S A. 1978 Apr;75(4):1773-7 PMID: 347446
  2. The partition locus of plasmid pSC101 is a specific binding site for DNA gyrase.
    EMBO J. 1988 Jun;7(6):1889-95 PMID: 2844527
  3. Site-specific cleavage of DNA by E. coli DNA gyrase.
    Cell. 1979 May;17(1):175-84 PMID: 378403
  4. DNA gyrase on the bacterial chromosome: DNA cleavage induced by oxolinic acid.
    J Mol Biol. 1979 Jun 25;131(2):287-302 PMID: 226717
  5. Mapping the topography of DNA wrapped around gyrase by nucleolytic and chemical probing of complexes of unique DNA sequences.
    Cell. 1981 Mar;23(3):721-9 PMID: 6261954
  6. Contacts between DNA gyrase and its binding site on DNA: features of symmetry and asymmetry revealed by protection from nucleases.
    Proc Natl Acad Sci U S A. 1981 Mar;78(3):1416-20 PMID: 6262797
  7. A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system.
    Nucleic Acids Res. 1981 Jul 10;9(13):3047-60 PMID: 6269071
  8. Site-specific interaction of DNA gyrase with DNA.
    Proc Natl Acad Sci U S A. 1981 Jul;78(7):4165-9 PMID: 6270661
  9. Structure and properties of the bacterial nucleoid.
    Cell. 1982 Oct;30(3):667-9 PMID: 6291779
  10. Gyrase . DNA complexes visualized as looped structures by electron microscopy.
    J Biol Chem. 1983 Apr 10;258(7):4612-7 PMID: 6300092
  11. Homology is not required for recombination mediated by DNA gyrase of Escherichia coli.
    Mol Gen Genet. 1984;193(2):238-43 PMID: 6319962
  12. DNA binding and antigenic specifications of DNA gyrase.
    Nucleic Acids Res. 1984 Jan 25;12(2):901-14 PMID: 6198633
  13. Bacterial chromosome segregation: evidence for DNA gyrase involvement in decatenation.
    Cell. 1984 Apr;36(4):1081-8 PMID: 6323018
  14. Nucleotide sequence of the sucA gene encoding the 2-oxoglutarate dehydrogenase of Escherichia coli K12.
    Eur J Biochem. 1984 Jun 1;141(2):351-9 PMID: 6376123
  15. Repetitive extragenic palindromic sequences: a major component of the bacterial genome.
    Cell. 1984 Jul;37(3):1015-26 PMID: 6378385
  16. A protein binds to a satellite DNA repeat at three specific sites that would be brought into mutual proximity by DNA folding in the nucleosome.
    Cell. 1984 Jul;37(3):889-901 PMID: 6540146
  17. A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli.
    EMBO J. 1984 Jun;3(6):1417-21 PMID: 6378622
  18. The DNA dependence of the ATPase activity of DNA gyrase.
    J Biol Chem. 1984 Dec 10;259(23):14472-80 PMID: 6094559
  19. Sites of reaction of Escherichia coli DNA gyrase on pBR322 in vivo as revealed by oxolinic acid-induced plasmid linearization.
    J Mol Biol. 1985 Jan 5;181(1):63-74 PMID: 2984430
  20. Localization of topoisomerase II in mitotic chromosomes.
    J Cell Biol. 1985 May;100(5):1716-25 PMID: 2985626
  21. DNA topoisomerases: enzymes that control DNA conformation.
    Curr Top Microbiol Immunol. 1985;114:19-102 PMID: 2986908
  22. In situ localization of DNA topoisomerase II, a major polypeptide component of the Drosophila nuclear matrix fraction.
    Proc Natl Acad Sci U S A. 1985 Jun;82(12):4142-6 PMID: 2987966
  23. Two distinct transcription factors bind to the HSV thymidine kinase promoter in vitro.
    Cell. 1985 Sep;42(2):559-72 PMID: 2992804
  24. A nuclear factor that binds to a conserved sequence motif in transcriptional control elements of immunoglobulin genes.
    Nature. 1986 Jan 9-15;319(6049):154-8 PMID: 3079885
  25. DNA gyrase complex with DNA: determinants for site-specific DNA breakage.
    EMBO J. 1986 Jun;5(6):1411-8 PMID: 3015604
  26. Metaphase chromosome structure. Involvement of topoisomerase II.
    J Mol Biol. 1986 Apr 20;188(4):613-29 PMID: 3016287
  27. Multiple DNA-protein interactions governing high-precision DNA transactions.
    Science. 1986 Sep 5;233(4768):1050-6 PMID: 2943018
  28. Palindromic units from E. coli as binding sites for a chromoid-associated protein.
    FEBS Lett. 1986 Oct 6;206(2):323-8 PMID: 3530812
  29. Mechanistic aspects of DNA topoisomerases.
    Adv Protein Chem. 1986;38:69-107 PMID: 3026152
  30. Stabilization of translationally active mRNA by prokaryotic REP sequences.
    Cell. 1987 Jan 30;48(2):297-310 PMID: 2433046
  31. Structure of the DNA gyrase-DNA complex as revealed by transient electric dichroism.
    J Mol Biol. 1987 Feb 5;193(3):555-69 PMID: 3035196
  32. Species specificity of bacterial palindromic units.
    J Mol Evol. 1987;25(4):371-3 PMID: 3118050
  33. Quinolone-resistant mutations of the gyrA gene of Escherichia coli.
    Mol Gen Genet. 1988 Jan;211(1):1-7 PMID: 2830458
  34. Role of the intercistronic region in post-transcriptional control of gene expression in the histidine transport operon of Salmonella typhimurium: involvement of REP sequences.
    Mol Microbiol. 1988 Jan;2(1):141-52 PMID: 3130541
  35. Scaffold attachment of DNA loops in metaphase chromosomes.
    J Mol Biol. 1988 Mar 5;200(1):101-9 PMID: 3132557
  36. The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins.
    Science. 1988 Jun 24;240(4860):1759-64 PMID: 3289117
  37. DNA-DNA gyrase complex: the wrapping of the DNA duplex outside the enzyme.
    Cell. 1978 Nov;15(3):979-84 PMID: 153201
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.85.23.8850
Published
1988-12-00
Pages
8850-4
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC282604
Subset
IM
Grants
NIDDK NIH HHS · DK12121 · United States
External Links
PubMed source DOI: 10.1073/pnas.85.23.8850 PMC Full Text View journal details
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