Effect of reversed orientation and length of An.Tn DNA binding sequences in the -35 and spacer domains of a consensus-like Escherichia coli promoter on its strength in vivo and gross structure of the open complex in vitro

• Autorzy: Lozinski T. , Wierzchowski K.L.
• Języki publikacji: EN

Abstrakty

EN

In continuation of an earlier study (Łoziński ct at., 1991 Nucleic Acids Res. 19, 2947-2953) a series of consensus-like E. coli promoters with bending An Tn sequences of different length (n = 3-8) and orientation in the -35 and spacer domains was constructed, cloned into the plasmid pDS3 and their strength in vivo measured in relation to an internal transcriptional standard. Gel mobilities of free DNA restriction fragments carrying these promoters and of open transcriptional complexes with cognate RNA polymerase were determined by polyacrylamide gel electrophoresis and the gross structure of the complexes interpreted in terms of the theoretically predicted superstructure of DNA restriction fragments. The results obtained together with those reported earlier show that bending of the DNA helix axis immediately upstream of the -35 domain generally lowers the promoter strength in vivo and brings about shortening of the mean square end-to-end distance between free DNA ends in the open complex in vitro. T4Í-34...-37) and Ts(-34...-38) tracts located in the nontemplate DNA strand had the largest and comparable effect on the promoter strength, while the As T5 (-37...-41) sequence in either orientation (As tract in the template or nontemplate strand) exerted a much smaller effect. Promoters with the spacer bent by about 40° but in different directions, by two An (n = 5 or 6) tracts aligned in phase with the B-DNA repeat and located either in the template or nontemplate strands, had somewhat lower strength in vivo but the gross geometry of the respective open complexes was the same as that of a control promoter with straight spacer. Implications of these findings are discussed in connection with the existing model of E. coli transcriptional open complex.

Słowa kluczowe

EN

DNA curvature; promoter strength; measurement; length; in vivo; DNA binding; gel shift assay; Escherichia coli; RNA polymerase; in vitro

• Wydawca: -
• Czasopismo: Acta Biochimica Polonica
• Rocznik: 1996
• Tom: 43
• Numer: 1
• Opis fizyczny: p.265-279,fig.

Twórcy

autor

Lozinski T.

• Polish Academy of Sciences, A.Pawinskiego 5a, 02-106 Warsaw, Poland

autor

Wierzchowski K.L.

Bibliografia

• 1. von Hippel, P.H., Bear, D.G., Morgan, W.D. & McSwiggen, S.A. (1984) Protein-nucleic acid interaction in transcription: a molecular analysis. Annu. Rev. Biochem. 53, 389-446.
• 2. McClure, W.R. (1985) Mechanism and control of transcription in prokaryotes. Annu. Rev. Biochem. 54,171-204.
• 3. Travers, A.A. (1989) DNA conformation and protein binding. Annu. Rev. Biochem. 58, 427-452.
• 4. Horwitz, M.S.Z. & Loeb, L..A. (1990) Structure- function relationships in Escherichia coli promoter DNA. Progr. Nucleic Acids Molec. Biol. 38,137-164.
• 5. Leirmo, S. & Record M.T., Jr. (1990) Structural, thermodynamic and kinetic studies of the interaction of Ea70 RNA polymerase with promoter DNA; in Nucleic Acids and Molecular Biology (Ekstein. F. & Lilley, D.M.J., eds) vol. 4, Springer-Verlag, Heidelberg.
• 6. Knaus, R. & Bujard, H. (1990) Principles governing the activity of E. coli promoters; in Nucleic Acids and Molecular Biology (Ekstein, F. & Lilley, D.M.J., eds.) vol. 4, pp. 110-122, Springer-Verlag, Heidelberg.
• 7. de Haseth, P.L. & Heimann, J.D. (1995) Open complex formation by Escherichia coli RNA polymerase: the mechanism of polvmerase- induccd strand separation of double helical DNA. Mol. Microbiol. 16, 817-824.
• 8. Darst, S.A., Kubalek, E.W. & Romberg, R.D. (1989) Three-dimensional structure of Escherichia coli RNA polymerase holoenzyme determined by electron crystallography. Nature (London) 340, 730-732.
• 9. Polyakov, A., Seven nova, E. & Darst, S.A. (1995) Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme. Cell 83,365-373.
• 10. Helmann, J.D. & Chamberlin. M.J. 11988) Structure and function of bacterial sigma factors. Annu. Rev. Biochem. 57, 839-872.
• 11. Gardclla, T., Movie, H. & Suskind. M.M. (1989) A mutant Escherichia coli o'° subunit of RNA polymerase with altered promoter specificity. /. Mol Biol. 206, 579-590.
• 12. Siegele. D.A., Hu, J.C., Walter. W.A. Sz Gross C.A. (1989) Altered promoter recognition by mutant forms of the a'0 subunit of Escherichia coli RNA polymerase. /. Mol. Biol. 206. 591-603.
• 13. Dombroski, A.J., Walter, W.A.. Record, M.T., Siegele, D.A. & Gross, C.A. (1992) Polvpeptides containing highly conserved reeions of transcription initiation factor o7 exhibit specificity of binding to promoter DNA. Cell 70, 501-512.
• 14. Gopal, V., Ma, H.-W., Kumaran, M.K. & Chatterji, D. (1994) A point mutation at the junction of domain 2.3/2.4 of transcription factor o/f) abrogates productive transcription and restores its expected mobility on a denaturing gel. /. Mol. Biol. 242, 9-22.
• 15. Auble, D.T., Allen. T.L & de Haseth, P.L. (1986) Promoter recognition by E. coli RNA polymerase. Effect of substitutions in the spacer DNA separating the -10 and -35 regions. J. Biol. Client. 261,11202-11206.
• 16. Auble, D.T. & de Haseth, P.L. (1988) Promoter recognition by E. coli RNA polymerase. Influence of DNA structure in the spacer separating the -10 and -35 regions. /. Mol. Biol. 202. 471-482.
• 17. Avers, D.G., Auble, D.T. & de Haseth, P.L. (1989) Promoter recognition bv E. coli RNA poly­merase. Role of the spacer DNA in functional complex formation. J. Mol. Biol. 207,749-756.
• 18. Warne. S.E. & de Haseth. P.L. (1993) Promoter recognition by Escherichia coli RNA polymerase. Effects of single base pair deletions and insertions in the spacer DNA separating the -10 and -35 regions are dependent on the spacer sequence. Biochemistry 32, 6134-6140.
• 19. Werel, W„ Schickor, P. & Heumann, H. (1991) Flexibility of DNA enhances promoter affinity of Escherichia coli RNA polymerase. EMBO /. 10, 2589-2594.
• 20. Schickor, P., Metzger,W., Warel, W., Lederer, H. & Heumann, H. (1990) Topography of interme­diates in transcription initiation of E. coli. EMBO J. 9,2212-2220.
• 21. NewlandsJ.T., Ross, W.,Gosink,K.K.& Course, R.L. (1991) Factor independent activation of Escherichia coli rRNA transcription. II. Characterization of complexes of rrttB PI promoters containing or lacking the upstream activator region with Escherichia coli RNA polymerase. /. Mol. Biol. 220, 569-583.
• 22. O'Hal lora n, T.V., Frantz, B.,Shin, M.K.. Ralston, D. M. & Wright, J.G. (1989) The Mer heavy metal receptor mediates positive activation in a topologically novel transcription complex. Cell 56,119-129.
• 23. Łoziński, T., Markiewicz, W.T., Wvrzykiewicz. T.K. & Wierzchowski, K.L. (1989) Effect of the sequence-dependent structure of the 17 bp AT spacer on the strength of consensus-like E. coli promoters in vivo. Nucleic Acids Res. 17. 3855-3863.
• 24. Łoziński, T., Adrych-Rozek, K., Markiewicz, W.T. & Wierzchowski, K.L. (1991) Effect of DNA bending in various regions of the consensus-like Escherichia coli promoter on its strength in vivo and structure of the open complex in vitro. Nucleic Acids Res. 19. 2947-2953.
• 25. Zinkel, S.S. & Crothers, D.M. (1987) DNA bend direction by phase sensitive detection. Nature (London)328,178-181.
• 26. Koo, H.-S. & Crothers. D.M. (1988) Calibration of DNA curvature and a unified description of sequence-directed bending. Proc. Natl. Acad. Sci. U.S.A. 85, 1763-1767.
• 27. Koo, H.-S., Drak, J., Rice, J.A. & Crothers, D.M. (1990) Determination of the extent of DNA ben­ding by an adenine-thymine tract. Biochemistry 29, 4227-4234.
• 28. Nelson, H.C.M., Finch,J.T.. Luisi, B.F. & Klug, A. (1987) The structure of an oligo(dA)-oligo(dT) tract and its biological implications. Nature (London) 330,221-226.
• 29. DeSantis, P., Palleschi. A.,Savino, M. & Scipioni. A. (1988) A theoretical model of DNAcurvature. Biophys. Chem. 32.305-317.
• 30. Burgess, R.R. & Jendrisak, J.). (1975) A procedure for rapid, large-scale purification of E. coli DNA-dependent RNA polymerase invol­ving polymin P precipitation and DNA- cellulose chromatography. Biochemistry 14, 4634-4638.
• 31. Deuschle, L'.. Kammerer, W.,Gentz, R. & Bujard, H. (1986) Promoters of E. coli: a hierarchy of in vivo strength indicates alternate structures. LMBO J. 5, 2987-2994
• 32. Mulligan, M.E., Haw ley, D.K., Entriken. R. & McCiure, VV.R. (1984) E. coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acid> Res. 12, 789-800.
• 33. HI linger, T., Behnke. D.( Knaus, R., Bujard, H. & Gralla, J.D. (1994) Context-dependent effects of upstream A-tracts. Stimulation of inhibition of Escherichia coli promoter function. /. Mol. Biol. 239, 466-47=».
• 34. Hirota, Y. & Ohyama, T. (1995) Adjacent up­stream superhelical writhe influences an Escherichia coli promoter as measured by in vivo strength and in vitro open complex formation. /. Mol. Biol. 254, 566-578.
• 35. Lerman, LS. & Frish. H.L (1982) Why does the electrophoretic mobility of DNA in gels vary with the length of the molecule? Biopolwners 21, 995-997.
• 36. Lumpkin, O.J. & Zimm, B.H. (1982) Mobility of DNA in gel electrophoresis. Biopolymcrs 21, 2315-2316.
• 37. Straney, D.C. & Crothers, D M. (1987) A stressed intermediate in the formation of stably initiated RNA chains at the E. coli tacUVS promoter. /. Mol. Biol. 193. 267-278.
• 38. Straney, D.C. & Crothers. D.M. (1987) Comparison of the open complexes formed by RNA polymerase at the £. coli lacUV5 promoter. /. Mol. Biol. 193, 279-292.
• 39. Kuhnke, G., Fritz, H.-J. & Fhring, R. (1987) I.'nusual properties of promoter mutations in the E. coli galactose operon and evidence suggesting RNA polymerase-induced DNA bending. EMBO /. 6, 507-513.
• 40. Heumann, H., Ricchetti, M. & Were!, W. (1988) DNA-dependent RNA polymerase of £. coli induces bending or an increased flexibility of DNA bv specific complex formation. F.MBO J. 7, 4379-4381.
• 41. Starr, D.B., Hoopes, B.C. & Hawley, D.K. (1995) DNA bending is an important component of site-specific recognition by the TATA binding protein. /. Mol. Biol. 250. 434-446.
• 42. Boffelli, D.. De Santis. P., Palleschi, A.. Risuleo. G. & Savino, M. (1992) A theoretical method to predict DNA permutation gel electrophoresis from the sequence. FEB5 Lett. 300.175-178.
• 43. Wu, H.-M. & Crothers, D.M. (1984) The locus of sequence-directed and protein-induced DNA bending. Nature (London) 308, 509-513.
• 44. Mayer-Almes, F.J., Heumann, H. & Porschke, D. (1994) The structure of the RNA polymerase- promoter complex. DNA-bending-angle by quantitative electrooptics. /. Mol. Biol. 236,1-6.
• 45. DeSantis,P.,Palleschi,A.,Savino,M.&Scipioni, A. (1990) Validity of the nearest-neighbor approximation in the evaluation of the electro­phoretic manifestations of DNA curvature. Biochemistry 29,9269-9273.
• 46. Hagerman, P.J. (1992) Straightening out the bends in curved DNA. Biochim. Biophys. Acta 1131,125-132.
• 47. Ross, W., Gosink, K.K., Salomon, J., Igarashi, K., Zou, Ch., Ishihama, A., Severinov, K. & Course, R.L. (1993) A third recognition element in bac­terial promoters: DNA binding by the et subunit of RNA polymerase. Science 262,1407-1413.
• 48. Dubbendorff, J.W., de Haseth, P.L., Rosendahl, M S. & Caruthers, M.H. (1987) DNA functional groups required for formation of open com­plexes between E. coli RNA polymerase and the lambda Pr promoter. Identification via base analog substitution. /. Biol. Chem. 262,892-898.
• 49. Erie, D.A., Yang, G., Schultz, H.C. & Bustamante, C. (1994) DNA bending by Cro protein in specific and nonspecific complexes: implications for protein site recognition and specificity. Science 266,1562-1566.
• 50. Strauss, J.K. & Maher. L.J. Ill (1994) DNA bending by asymmetric phosphate neutra­lization. Science 266,1829-1834.
• 51. Yang, Y., Westcott, T.P., Pedersen, S.C., Tobias, I. & Olson, W.K. (1995) Effects of localized bending on DNA supercoiling. Trends Biochem. Sci. 20, 313-319.
• 52. Laundon, C.H. & Griffith, J.D. (1988) Curved helix segments can uniquely orient topology of supertwisted DNA. Cell 52,545-549.