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. 1991 Dec 11;19(23):6391–6398. doi: 10.1093/nar/19.23.6391

Chemical and enzymatic analysis of covalent bonds between peptides and chromosomal DNA.

B Juodka 1, M Pfütz 1, D Werner 1
PMCID: PMC329183  PMID: 1661408

Abstract

DNA from Ehrlich ascites tumor (EAT) cells and from human placenta was examined for covalent bonds between hydroxy amino acid residues in peptides and nucleotide phosphate groups. The residual proteinaceous material in highly purified DNA was radiolabelled with 125Iodine and the linking-groups between peptides and nucleotides released by combined protease and nuclease treatment were investigated with respect to their chemical and enzymatic stabilities. The residual nucleotide(s)-peptide(s) fraction from DNA isolated after prolonged alkaline cell lysis and phenol extraction contains mainly alkali and acid-stable but phosphodiesterase-sensitive peptide-nucleotide complexes which indicates phosphodiesters between tyrosyl residues in peptides and nucleotide phosphates. In contrast, the linking-group fraction from DNA isolated under native conditions contains additional peptide components. (a) Phospho-peptides that co-purify with DNA but that are not covalently bound to nucleotides. (b) A fraction of peptides that is released from nucleotides by alkali in a time and concentration-dependent reaction. Evidence is presented indicating that the latter fraction involves phospho-triesters between hydroxy amino acid residues in peptides and internucleotide phosphates. The phosphodiesters between hydroxy amino acids and nucleotide phosphates representing the predominant class of peptide-nucleotide complexes in alkali-denatured DNA are most likely side products of peptide-nucleotide phospho-triester hydrolysis.

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Selected References

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

  1. Adler S. P., Purich D., Stadtman E. R. Cascade control of Escherichia coli glutamine synthetase. Properties of the PII regulatory protein and the uridylyltransferase-uridylyl-removing enzyme. J Biol Chem. 1975 Aug 25;250(16):6264–6272. [PubMed] [Google Scholar]
  2. Ambros V., Baltimore D. Protein is linked to the 5' end of poliovirus RNA by a phosphodiester linkage to tyrosine. J Biol Chem. 1978 Aug 10;253(15):5263–5266. [PubMed] [Google Scholar]
  3. Avramova Z., Tsanev R. Stable DNA-protein complexes in eukaryotic chromatin. J Mol Biol. 1987 Jul 20;196(2):437–440. doi: 10.1016/0022-2836(87)90704-2. [DOI] [PubMed] [Google Scholar]
  4. Blin N., Stafford D. W. A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Res. 1976 Sep;3(9):2303–2308. doi: 10.1093/nar/3.9.2303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Gianfranceschi G. L., Barra D., Bossa F., Coderoni S., Paparelli M., Venanzi F., Cicconi F., Amici D. Small peptides controlling transcription in vitro are bound to chromatin DNA. Biochim Biophys Acta. 1982 Nov 30;699(2):138–148. doi: 10.1016/0167-4781(82)90147-6. [DOI] [PubMed] [Google Scholar]
  6. Gross-Bellard M., Oudet P., Chambon P. Isolation of high-molecular-weight DNA from mammalian cells. Eur J Biochem. 1973 Jul 2;36(1):32–38. doi: 10.1111/j.1432-1033.1973.tb02881.x. [DOI] [PubMed] [Google Scholar]
  7. Hershey H. V., Werner D. Evidence for non-deoxynucleotide linkers in Ehrlich ascites tumour cell DNA. Nature. 1976 Jul 8;262(5564):148–150. doi: 10.1038/262148a0. [DOI] [PubMed] [Google Scholar]
  8. Krauth W., Werner D. Analysis of the most tightly bound proteins in eukaryotic DNA. Biochim Biophys Acta. 1979 Oct 25;564(3):390–401. doi: 10.1016/0005-2787(79)90030-3. [DOI] [PubMed] [Google Scholar]
  9. Krystal G., Winn P., Millward S., Sakuma S. Evidence for phosphoproteins in reovirus. Virology. 1975 Apr;64(2):505–512. doi: 10.1016/0042-6822(75)90127-0. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. McDaniel C. S., Harper L. L., Wild J. R. Cloning and sequencing of a plasmid-borne gene (opd) encoding a phosphotriesterase. J Bacteriol. 1988 May;170(5):2306–2311. doi: 10.1128/jb.170.5.2306-2311.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Neuer-Nitsche B., Lu X. N., Werner D. Functional role of a highly repetitive DNA sequence in anchorage of the mouse genome. Nucleic Acids Res. 1988 Sep 12;16(17):8351–8360. doi: 10.1093/nar/16.17.8351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Neuer-Nitsche B., Werner D. Sub-set characteristics of DNA sequences involved in tight DNA/polypeptide complexes and their homology to nuclear matrix DNA. Biochem Biophys Res Commun. 1987 Aug 31;147(1):335–339. doi: 10.1016/s0006-291x(87)80126-2. [DOI] [PubMed] [Google Scholar]
  14. Neuer B., Plagens U., Werner D. Phosphodiester bonds between polypeptides and chromosomal DNA. J Mol Biol. 1983 Feb 25;164(2):213–235. doi: 10.1016/0022-2836(83)90076-1. [DOI] [PubMed] [Google Scholar]
  15. Neuer B., Werner D. Screening of isolated DNA for sequences released from anchorage sites in nuclear matrix. J Mol Biol. 1985 Jan 5;181(1):15–25. doi: 10.1016/0022-2836(85)90321-3. [DOI] [PubMed] [Google Scholar]
  16. Pogell B. M., Rowland S. S., Steinmann K. E., Speedie M. K., Hoskin F. C. Genetic and biochemical evidence for the lack of significant hydrolysis of soman by a Flavobacterium parathion hydrolase. Appl Environ Microbiol. 1991 Feb;57(2):610–611. doi: 10.1128/aem.57.2.610-611.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Rothberg P. G., Harris T. J., Nomoto A., Wimmer E. O4-(5'-uridylyl)tyrosine is the bond between the genome-linked protein and the RNA of poliovirus. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4868–4872. doi: 10.1073/pnas.75.10.4868. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Rowland S. S., Speedie M. K., Pogell B. M. Purification and characterization of a secreted recombinant phosphotriesterase (parathion hydrolase) from Streptomyces lividans. Appl Environ Microbiol. 1991 Feb;57(2):440–444. doi: 10.1128/aem.57.2.440-444.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Shapiro B. M., Stadtman E. R. 5'-adenylyl-O-tyrosine. The novel phosphodiester residue of adenylylated glutamine synthetase from Escherichia coli. J Biol Chem. 1968 Jul 10;243(13):3769–3771. [PubMed] [Google Scholar]
  20. Tse Y. C., Kirkegaard K., Wang J. C. Covalent bonds between protein and DNA. Formation of phosphotyrosine linkage between certain DNA topoisomerases and DNA. J Biol Chem. 1980 Jun 25;255(12):5560–5565. [PubMed] [Google Scholar]
  21. Werner D., Krauth W., Hershey H. V. Internucleotide protein linkers in Ehrlich ascites cell DNA. Biochim Biophys Acta. 1980 Jul 29;608(2):243–258. doi: 10.1016/0005-2787(80)90170-7. [DOI] [PubMed] [Google Scholar]
  22. Werner D., Neuer-Nitsche B. Site-specific location of covalent DNA-polypeptide complexes in the chicken genome. Nucleic Acids Res. 1989 Aug 11;17(15):6005–6015. doi: 10.1093/nar/17.15.6005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Werner D., Rest R. Radiolabelling of DNA/polypeptide complexes in isolated bulk DNA and in residual nuclear matrix DNA by nick-translation. Biochem Biophys Res Commun. 1987 Aug 31;147(1):340–345. doi: 10.1016/s0006-291x(87)80127-4. [DOI] [PubMed] [Google Scholar]
  24. Werner D., Zimmermann H. P., Rauterberg E., Spalinger J. Antibodies to the most tightly bound proteins in eukaryotic DNA. Exp Cell Res. 1981 May;133(1):149–157. doi: 10.1016/0014-4827(81)90365-7. [DOI] [PubMed] [Google Scholar]

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