Skip to main content
NCBI home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1995 Apr 11;92(8):3444–3448. doi: 10.1073/pnas.92.8.3444

Heterogeneity in molecular recognition by restriction endonucleases: osmotic and hydrostatic pressure effects on BamHI, Pvu II, and EcoRV specificity.

C R Robinson 1, S G Sligar 1
PMCID: PMC42183  PMID: 7724581

Abstract

The cleavage specificity of the Pvu II and BamHI restriction endonucleases is found to be dramatically reduced at elevated osmotic pressure. Relaxation in specificity of these otherwise highly accurate and specific enzymes, previously termed "star activity," is uniquely correlated with osmotic pressure between 0 and 100 atmospheres. No other colligative solvent property exhibits a uniform correlation with star activity for all of the compounds tested. Application of hydrostatic pressure counteracts the effects of osmotic pressure and restores the natural selectivity of the enzymes for their canonical recognition sequences. These results indicate that water solvation plays an important role in the site-specific recognition of DNA by many restriction enzymes. Osmotic pressure did not induce an analogous effect on the specificity of the EcoRV endonuclease, implying that selective hydration effects do not participate in DNA recognition in this system. Hydrostatic pressure was found to have little effect on the star activity induced by changes in ionic strength, pH, or divalent cation, suggesting that distinct mechanisms may exist for these observed alterations in specificity. Recent evidence has indicated that BamHI and EcoRI share similar structural motifs, while Pvu II and EcoRV belong to a different structural family. Evidently, the use of hydration water to assist in site-specific recognition is a motif neither limited to nor defined by structural families.

Full text

PDF
3444

Selected References

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

  1. Athanasiadis A., Vlassi M., Kotsifaki D., Tucker P. A., Wilson K. S., Kokkinidis M. Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV. Nat Struct Biol. 1994 Jul;1(7):469–475. doi: 10.1038/nsb0794-469. [DOI] [PubMed] [Google Scholar]
  2. Beece D., Eisenstein L., Frauenfelder H., Good D., Marden M. C., Reinisch L., Reynolds A. H., Sorensen L. B., Yue K. T. Solvent viscosity and protein dynamics. Biochemistry. 1980 Nov 11;19(23):5147–5157. doi: 10.1021/bi00564a001. [DOI] [PubMed] [Google Scholar]
  3. Bennett S. P., Halford S. E. Recognition of DNA by type II restriction enzymes. Curr Top Cell Regul. 1989;30:57–104. doi: 10.1016/b978-0-12-152830-0.50005-0. [DOI] [PubMed] [Google Scholar]
  4. Cheng X., Balendiran K., Schildkraut I., Anderson J. E. Structure of PvuII endonuclease with cognate DNA. EMBO J. 1994 Sep 1;13(17):3927–3935. doi: 10.1002/j.1460-2075.1994.tb06708.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Colombo M. F., Rau D. C., Parsegian V. A. Protein solvation in allosteric regulation: a water effect on hemoglobin. Science. 1992 May 1;256(5057):655–659. doi: 10.1126/science.1585178. [DOI] [PubMed] [Google Scholar]
  6. Di Primo C., Sligar S. G., Hoa G. H., Douzou P. A critical role of protein-bound water in the catalytic cycle of cytochrome P-450 camphor. FEBS Lett. 1992 Nov 9;312(2-3):252–254. doi: 10.1016/0014-5793(92)80946-e. [DOI] [PubMed] [Google Scholar]
  7. Douzou P. Osmotic regulation of gene action. Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1657–1661. doi: 10.1073/pnas.91.5.1657. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dzingeleski G. D., Wolfenden R. Hypersensitivity of an enzyme reaction to solvent water. Biochemistry. 1993 Sep 7;32(35):9143–9147. doi: 10.1021/bi00086a020. [DOI] [PubMed] [Google Scholar]
  9. Feng J. A., Johnson R. C., Dickerson R. E. Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions. Science. 1994 Jan 21;263(5145):348–355. doi: 10.1126/science.8278807. [DOI] [PubMed] [Google Scholar]
  10. George J., Blakesley R. W., Chirikjian J. G. Sequence-specific endonuclease Bam HI. Effect of hydrophobic reagents on sequence recognition and catalysis. J Biol Chem. 1980 Jul 25;255(14):6521–6524. [PubMed] [Google Scholar]
  11. George J., Chirikjian J. G. Sequence-specific endonuclease BamHI: relaxation of sequence recognition. Proc Natl Acad Sci U S A. 1982 Apr;79(8):2432–2436. doi: 10.1073/pnas.79.8.2432. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Gingeras T. R., Greenough L., Schildkraut I., Roberts R. J. Two new restriction endonucleases from Proteus vulgaris. Nucleic Acids Res. 1981 Sep 25;9(18):4525–4536. doi: 10.1093/nar/9.18.4525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Ha J. H., Capp M. W., Hohenwalter M. D., Baskerville M., Record M. T., Jr Thermodynamic stoichiometries of participation of water, cations and anions in specific and non-specific binding of lac repressor to DNA. Possible thermodynamic origins of the "glutamate effect" on protein-DNA interactions. J Mol Biol. 1992 Nov 5;228(1):252–264. doi: 10.1016/0022-2836(92)90504-d. [DOI] [PubMed] [Google Scholar]
  14. Kim Y. C., Grable J. C., Love R., Greene P. J., Rosenberg J. M. Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing. Science. 1990 Sep 14;249(4974):1307–1309. doi: 10.1126/science.2399465. [DOI] [PubMed] [Google Scholar]
  15. Kimura T., Asai T., Imai M., Takanami M. Methylation strongly enhances DNA bending in the replication origin region of the Escherichia coli chromosome. Mol Gen Genet. 1989 Oct;219(1-2):69–74. doi: 10.1007/BF00261159. [DOI] [PubMed] [Google Scholar]
  16. King L., Weber G. Conformational drift of dissociated lactate dehydrogenases. Biochemistry. 1986 Jun 17;25(12):3632–3637. doi: 10.1021/bi00360a023. [DOI] [PubMed] [Google Scholar]
  17. Kolesnikov V. A., Zinoviev V. V., Yashina L. N., Karginov V. A., Baclanov M. M., Malygin E. G. Relaxed specificity of endonuclease BamH1 as determined by identification or recognition sites in SV 40 and pBR 322 DNAs. FEBS Lett. 1981 Sep 14;132(1):101–104. doi: 10.1016/0014-5793(81)80437-1. [DOI] [PubMed] [Google Scholar]
  18. Kornblatt J. A., Kornblatt M. J., Hoa G. H., Mauk A. G. Responses of two protein-protein complexes to solvent stress: does water play a role at the interface? Biophys J. 1993 Sep;65(3):1059–1065. doi: 10.1016/S0006-3495(93)81168-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Lawson C. L., Carey J. Tandem binding in crystals of a trp repressor/operator half-site complex. Nature. 1993 Nov 11;366(6451):178–182. doi: 10.1038/366178a0. [DOI] [PubMed] [Google Scholar]
  20. Liepinsh E., Otting G., Wüthrich K. NMR observation of individual molecules of hydration water bound to DNA duplexes: direct evidence for a spine of hydration water present in aqueous solution. Nucleic Acids Res. 1992 Dec 25;20(24):6549–6553. doi: 10.1093/nar/20.24.6549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Malyguine E., Vannier P., Yot P. Alteration of the specificity of restriction endonucleases in the presence of organic solvents. Gene. 1980 Jan;8(2):163–177. doi: 10.1016/0378-1119(80)90035-9. [DOI] [PubMed] [Google Scholar]
  22. Nasri M., Thomas D. Alteration of the specificity of PvuII restriction endonuclease. Nucleic Acids Res. 1987 Oct 12;15(19):7677–7687. doi: 10.1093/nar/15.19.7677. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Nasri M., Thomas D. The reactions of SacI, PvuII and EcoRI endonucleases. Biomed Biochim Acta. 1986;45(8):997–1005. [PubMed] [Google Scholar]
  24. Newman M., Strzelecka T., Dorner L. F., Schildkraut I., Aggarwal A. K. Structure of restriction endonuclease BamHI and its relationship to EcoRI. Nature. 1994 Apr 14;368(6472):660–664. doi: 10.1038/368660a0. [DOI] [PubMed] [Google Scholar]
  25. Newman M., Strzelecka T., Dorner L. F., Schildkraut I., Aggarwal A. K. Structure of restriction endonuclease bamhi phased at 1.95 A resolution by MAD analysis. Structure. 1994 May 15;2(5):439–452. doi: 10.1016/s0969-2126(00)00045-9. [DOI] [PubMed] [Google Scholar]
  26. Otwinowski Z., Schevitz R. W., Zhang R. G., Lawson C. L., Joachimiak A., Marmorstein R. Q., Luisi B. F., Sigler P. B. Crystal structure of trp repressor/operator complex at atomic resolution. Nature. 1988 Sep 22;335(6188):321–329. doi: 10.1038/335321a0. [DOI] [PubMed] [Google Scholar]
  27. Parsegian V. A., Rand R. P., Fuller N. L., Rau D. C. Osmotic stress for the direct measurement of intermolecular forces. Methods Enzymol. 1986;127:400–416. doi: 10.1016/0076-6879(86)27032-9. [DOI] [PubMed] [Google Scholar]
  28. Peng X., Jonas J., Silva J. L. Molten-globule conformation of Arc repressor monomers determined by high-pressure 1H NMR spectroscopy. Proc Natl Acad Sci U S A. 1993 Mar 1;90(5):1776–1780. doi: 10.1073/pnas.90.5.1776. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Polisky B., Greene P., Garfin D. E., McCarthy B. J., Goodman H. M., Boyer H. W. Specificity of substrate recognition by the EcoRI restriction endonuclease. Proc Natl Acad Sci U S A. 1975 Sep;72(9):3310–3314. doi: 10.1073/pnas.72.9.3310. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Rand R. P., Fuller N. L., Butko P., Francis G., Nicholls P. Measured change in protein solvation with substrate binding and turnover. Biochemistry. 1993 Jun 15;32(23):5925–5929. doi: 10.1021/bi00074a001. [DOI] [PubMed] [Google Scholar]
  31. Rand R. P. Raising water to new heights. Science. 1992 May 1;256(5057):618–618. doi: 10.1126/science.256.5057.618. [DOI] [PubMed] [Google Scholar]
  32. Riddihough G. No limits on restriction. Nature. 1994 Jul 7;370(6484):78–78. doi: 10.1038/370078a0. [DOI] [PubMed] [Google Scholar]
  33. Roberts R. J., Wilson G. A., Young F. E. Recognition sequence of specific endonuclease BamH.I from Bacillus amyloliquefaciens H. Nature. 1977 Jan 6;265(5589):82–84. doi: 10.1038/265082a0. [DOI] [PubMed] [Google Scholar]
  34. Robinson C. R., Sligar S. G. Hydrostatic pressure reverses osmotic pressure effects on the specificity of EcoRI-DNA interactions. Biochemistry. 1994 Apr 5;33(13):3787–3793. doi: 10.1021/bi00179a001. [DOI] [PubMed] [Google Scholar]
  35. Robinson C. R., Sligar S. G. Molecular recognition mediated by bound water. A mechanism for star activity of the restriction endonuclease EcoRI. J Mol Biol. 1993 Nov 20;234(2):302–306. doi: 10.1006/jmbi.1993.1586. [DOI] [PubMed] [Google Scholar]
  36. Ruan K., Weber G. Physical heterogeneity of muscle glycogen phosphorylase revealed by hydrostatic pressure dissociation. Biochemistry. 1993 Jun 22;32(24):6295–6301. doi: 10.1021/bi00075a025. [DOI] [PubMed] [Google Scholar]
  37. Santoro M. M., Liu Y., Khan S. M., Hou L. X., Bolen D. W. Increased thermal stability of proteins in the presence of naturally occurring osmolytes. Biochemistry. 1992 Jun 16;31(23):5278–5283. doi: 10.1021/bi00138a006. [DOI] [PubMed] [Google Scholar]
  38. Silva J. L., Silveira C. F. Energy coupling between DNA binding and subunit association is responsible for the specificity of DNA-Arc interaction. Protein Sci. 1993 Jun;2(6):945–950. doi: 10.1002/pro.5560020608. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Silva J. L., Weber G. Pressure stability of proteins. Annu Rev Phys Chem. 1993;44:89–113. doi: 10.1146/annurev.pc.44.100193.000513. [DOI] [PubMed] [Google Scholar]
  40. Spolar R. S., Record M. T., Jr Coupling of local folding to site-specific binding of proteins to DNA. Science. 1994 Feb 11;263(5148):777–784. doi: 10.1126/science.8303294. [DOI] [PubMed] [Google Scholar]
  41. Taylor J. D., Halford S. E. Discrimination between DNA sequences by the EcoRV restriction endonuclease. Biochemistry. 1989 Jul 25;28(15):6198–6207. doi: 10.1021/bi00441a011. [DOI] [PubMed] [Google Scholar]
  42. Terry B. J., Jack W. E., Rubin R. A., Modrich P. Thermodynamic parameters governing interaction of EcoRI endonuclease with specific and nonspecific DNA sequences. J Biol Chem. 1983 Aug 25;258(16):9820–9825. [PubMed] [Google Scholar]
  43. Vermote C. L., Halford S. E. EcoRV restriction endonuclease: communication between catalytic metal ions and DNA recognition. Biochemistry. 1992 Jul 7;31(26):6082–6089. doi: 10.1021/bi00141a018. [DOI] [PubMed] [Google Scholar]
  44. Vipond I. B., Halford S. E. Structure-function correlation for the EcoRV restriction enzyme: from non-specific binding to specific DNA cleavage. Mol Microbiol. 1993 Jul;9(2):225–231. doi: 10.1111/j.1365-2958.1993.tb01685.x. [DOI] [PubMed] [Google Scholar]
  45. Weber G., Drickamer H. G. The effect of high pressure upon proteins and other biomolecules. Q Rev Biophys. 1983 Feb;16(1):89–112. doi: 10.1017/s0033583500004935. [DOI] [PubMed] [Google Scholar]
  46. Winkler F. K., Banner D. W., Oefner C., Tsernoglou D., Brown R. S., Heathman S. P., Bryan R. K., Martin P. D., Petratos K., Wilson K. S. The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 1993 May;12(5):1781–1795. doi: 10.2210/pdb4rve/pdb. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Zimmerberg J., Parsegian V. A. Polymer inaccessible volume changes during opening and closing of a voltage-dependent ionic channel. Nature. 1986 Sep 4;323(6083):36–39. doi: 10.1038/323036a0. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES