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. 1995 Nov 7;92(23):10511–10515. doi: 10.1073/pnas.92.23.10511

A single-stranded DNA binding protein binds the origin of replication of the duplex kinetoplast DNA.

D Avrahami 1, Y Tzfati 1, J Shlomai 1
PMCID: PMC40641  PMID: 7479830

Abstract

Replication of the kinetoplast DNA (kDNA) minicircle of trypanosomatids initiates at a conserved 12-nt sequence, 5'-GGGGTTGGTGTA-3', termed the universal minicircle sequence (UMS). A sequence-specific single-stranded DNA-binding protein from Crithidia fasciculata binds the heavy strand of the 12-mer UMS. Whereas this UMS-binding protein (UMSBP) does not bind a duplex UMS dodecamer, it binds the double-stranded kDNA minicircle as well as a duplex minicircle fragment containing the origin-associated UMS. Binding of the minicircle origin region by the single-stranded DNA binding protein suggested the local unwinding of the DNA double helix at this site. Modification of thymine residues at this site by KMnO4 revealed that the UMS resides within an unwound or otherwise sharply distorted DNA at the minicircle origin region. Computer analysis predicts the sequence-directed curving of the minicircle origin region. Electrophoresis of a minicircle fragment containing the origin region in polyacrylamide gels revealed a significantly lower electrophoretic mobility than expected from its length. The fragment anomalous electrophoretic mobility is displayed only in its native conformation and is dependent on temperature and gel porosity, indicating the local curving of the DNA double helix. We suggest that binding of UMSBP at the minicircle origin of replication is possible through local unwinding of the DNA double helix at the UMS site. It is hypothesized here that this local melting is initiated through the untwisting of unstacked dinucleotide sequences at the bent origin site.

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Selected References

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

  1. Abeliovich H., Tzfati Y., Shlomai J. A trypanosomal CCHC-type zinc finger protein which binds the conserved universal sequence of kinetoplast DNA minicircles: isolation and analysis of the complete cDNA from Crithidia fasciculata. Mol Cell Biol. 1993 Dec;13(12):7766–7773. doi: 10.1128/mcb.13.12.7766. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Birkenmeyer L., Ray D. S. Replication of kinetoplast DNA in isolated kinetoplasts from Crithidia fasciculata. Identification of minicircle DNA replication intermediates. J Biol Chem. 1986 Feb 15;261(5):2362–2368. [PubMed] [Google Scholar]
  3. Bolshoy A., McNamara P., Harrington R. E., Trifonov E. N. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2312–2316. doi: 10.1073/pnas.88.6.2312. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Breslauer K. J., Frank R., Blöcker H., Marky L. A. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3746–3750. doi: 10.1073/pnas.83.11.3746. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Challberg M. D., Englund P. T. The effect of template secondary structure on vaccinia DNA polymerase. J Biol Chem. 1979 Aug 25;254(16):7820–7826. [PubMed] [Google Scholar]
  6. Diekmann S., McLaughlin L. W. DNA curvature in native and modified EcoRI recognition sites and possible influence upon the endonuclease cleavage reaction. J Mol Biol. 1988 Aug 20;202(4):823–834. doi: 10.1016/0022-2836(88)90561-x. [DOI] [PubMed] [Google Scholar]
  7. Diekmann S. The migration anomaly of DNA fragments in polyacrylamide gels allows the detection of small sequence-specific DNA structure variations. Electrophoresis. 1989 May-Jun;10(5-6):354–359. doi: 10.1002/elps.1150100513. [DOI] [PubMed] [Google Scholar]
  8. Englund P. T. Free minicircles of kinetoplast DNA in Crithidia fasciculata. J Biol Chem. 1979 Jun 10;254(11):4895–4900. [PubMed] [Google Scholar]
  9. Englund P. T., Hajduk S. L., Marini J. C. The molecular biology of trypanosomes. Annu Rev Biochem. 1982;51:695–726. doi: 10.1146/annurev.bi.51.070182.003403. [DOI] [PubMed] [Google Scholar]
  10. Englund P. T. The replication of kinetoplast DNA networks in Crithidia fasciculata. Cell. 1978 May;14(1):157–168. doi: 10.1016/0092-8674(78)90310-0. [DOI] [PubMed] [Google Scholar]
  11. Ferguson M., Torri A. F., Ward D. C., Englund P. T. In situ hybridization to the Crithidia fasciculata kinetoplast reveals two antipodal sites involved in kinetoplast DNA replication. Cell. 1992 Aug 21;70(4):621–629. doi: 10.1016/0092-8674(92)90431-b. [DOI] [PubMed] [Google Scholar]
  12. Fujimura F. K. Point mutation in the polyomavirus enhancer alters local DNA conformation. Nucleic Acids Res. 1988 Mar 25;16(5):1987–1997. doi: 10.1093/nar/16.5.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hagerman P. J. Sequence dependence of the curvature of DNA: a test of the phasing hypothesis. Biochemistry. 1985 Dec 3;24(25):7033–7037. doi: 10.1021/bi00346a001. [DOI] [PubMed] [Google Scholar]
  14. Kitchin P. A., Klein V. A., Fein B. I., Englund P. T. Gapped Minicircles. A novel replication intermediate of kinetoplast DNA. J Biol Chem. 1984 Dec 25;259(24):15532–15539. [PubMed] [Google Scholar]
  15. Kitchin P. A., Klein V. A., Ryan K. A., Gann K. L., Rauch C. A., Kang D. S., Wells R. D., Englund P. T. A highly bent fragment of Crithidia fasciculata kinetoplast DNA. J Biol Chem. 1986 Aug 25;261(24):11302–11309. [PubMed] [Google Scholar]
  16. Koo H. S., Wu H. M., Crothers D. M. DNA bending at adenine . thymine tracts. Nature. 1986 Apr 10;320(6062):501–506. doi: 10.1038/320501a0. [DOI] [PubMed] [Google Scholar]
  17. Lee C. C., Cantor C. R., Wittmann-Liebold B. The number of copies of ribosome-bound proteins L7 and L12 required for protein synthesis activity. J Biol Chem. 1981 Jan 10;256(1):41–48. [PubMed] [Google Scholar]
  18. Linial M., Shlomai J. The sequence-directed bent structure in kinetoplast DNA is recognized by an enzyme from Crithidia fasciculata. J Biol Chem. 1987 Nov 5;262(31):15194–15201. [PubMed] [Google Scholar]
  19. Marini J. C., Levene S. D., Crothers D. M., Englund P. T. Bent helical structure in kinetoplast DNA. Proc Natl Acad Sci U S A. 1982 Dec;79(24):7664–7668. doi: 10.1073/pnas.79.24.7664. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. McNamara P. T., Bolshoy A., Trifonov E. N., Harrington R. E. Sequence-dependent kinks induced in curved DNA. J Biomol Struct Dyn. 1990 Dec;8(3):529–538. doi: 10.1080/07391102.1990.10507827. [DOI] [PubMed] [Google Scholar]
  21. McNamara P. T., Harrington R. E. Characterization of inherent curvature in DNA lacking polyadenine runs. J Biol Chem. 1991 Jul 5;266(19):12548–12554. [PubMed] [Google Scholar]
  22. Milton D. L., Casper M. L., Wills N. M., Gesteland R. F. Guanine tracts enhance sequence directed DNA bends. Nucleic Acids Res. 1990 Feb 25;18(4):817–820. doi: 10.1093/nar/18.4.817. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Milton D. L., Gesteland R. F. Bends in SV40 DNA: use of mutagenesis to identify the critical bases involved. Nucleic Acids Res. 1988 May 11;16(9):3931–3949. doi: 10.1093/nar/16.9.3931. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Myler P. J., Glick D., Feagin J. E., Morales T. H., Stuart K. D. Structural organization of the maxicircle variable region of Trypanosoma brucei: identification of potential replication origins and topoisomerase II binding sites. Nucleic Acids Res. 1993 Feb 11;21(3):687–694. doi: 10.1093/nar/21.3.687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Ntambi J. M., Englund P. T. A gap at a unique location in newly replicated kinetoplast DNA minicircles from Trypanosoma equiperdum. J Biol Chem. 1985 May 10;260(9):5574–5579. [PubMed] [Google Scholar]
  26. Ntambi J. M., Shapiro T. A., Ryan K. A., Englund P. T. Ribonucleotides associated with a gap in newly replicated kinetoplast DNA minicircles from Trypanosoma equiperdum. J Biol Chem. 1986 Sep 5;261(25):11890–11895. [PubMed] [Google Scholar]
  27. Ornstein R. L., Fresco J. R. Correlation of Tm and sequence of DNA duplexes with delta H computed by an improved empirical potential method. Biopolymers. 1983 Aug;22(8):1979–2000. doi: 10.1002/bip.360220811. [DOI] [PubMed] [Google Scholar]
  28. Pérez-Morga D. L., Englund P. T. The attachment of minicircles to kinetoplast DNA networks during replication. Cell. 1993 Aug 27;74(4):703–711. doi: 10.1016/0092-8674(93)90517-t. [DOI] [PubMed] [Google Scholar]
  29. Pérez-Morga D., Englund P. T. The structure of replicating kinetoplast DNA networks. J Cell Biol. 1993 Dec;123(5):1069–1079. doi: 10.1083/jcb.123.5.1069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Rajavashisth T. B., Taylor A. K., Andalibi A., Svenson K. L., Lusis A. J. Identification of a zinc finger protein that binds to the sterol regulatory element. Science. 1989 Aug 11;245(4918):640–643. doi: 10.1126/science.2562787. [DOI] [PubMed] [Google Scholar]
  31. Rauch C. A., Perez-Morga D., Cozzarelli N. R., Englund P. T. The absence of supercoiling in kinetoplast DNA minicircles. EMBO J. 1993 Feb;12(2):403–411. doi: 10.1002/j.1460-2075.1993.tb05672.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Ray D. S. Kinetoplast DNA minicircles: high-copy-number mitochondrial plasmids. Plasmid. 1987 May;17(3):177–190. doi: 10.1016/0147-619x(87)90026-6. [DOI] [PubMed] [Google Scholar]
  33. Ryan K. A., Englund P. T. Replication of kinetoplast DNA in Trypanosoma equiperdum. Minicircle H strand fragments which map at specific locations. J Biol Chem. 1989 Jan 15;264(2):823–830. [PubMed] [Google Scholar]
  34. Ryan K. A., Shapiro T. A., Rauch C. A., Englund P. T. Replication of kinetoplast DNA in trypanosomes. Annu Rev Microbiol. 1988;42:339–358. doi: 10.1146/annurev.mi.42.100188.002011. [DOI] [PubMed] [Google Scholar]
  35. Ryan K. A., Shapiro T. A., Rauch C. A., Griffith J. D., Englund P. T. A knotted free minicircle in kinetoplast DNA. Proc Natl Acad Sci U S A. 1988 Aug;85(16):5844–5848. doi: 10.1073/pnas.85.16.5844. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Sasse-Dwight S., Gralla J. D. Footprinting protein-DNA complexes in vivo. Methods Enzymol. 1991;208:146–168. doi: 10.1016/0076-6879(91)08012-7. [DOI] [PubMed] [Google Scholar]
  37. Saucier J. M., Benard J., da Silva J., Riou G. Occurrence of a kinetoplast DNA-protein complex in Trypanosoma cruzi. Biochem Biophys Res Commun. 1981 Aug 14;101(3):988–994. doi: 10.1016/0006-291x(81)91846-5. [DOI] [PubMed] [Google Scholar]
  38. Sheline C., Melendy T., Ray D. S. Replication of DNA minicircles in kinetoplasts isolated from Crithidia fasciculata: structure of nascent minicircles. Mol Cell Biol. 1989 Jan;9(1):169–176. doi: 10.1128/mcb.9.1.169. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Sheline C., Ray D. S. Specific discontinuities in Leishmania tarentolae minicircles map within universally conserved sequence blocks. Mol Biochem Parasitol. 1989 Dec;37(2):151–157. doi: 10.1016/0166-6851(89)90147-3. [DOI] [PubMed] [Google Scholar]
  40. Sherman L. A., Gefter M. L. Studies on the mechanism of enzymatic DNA elongation by Escherichia coli DNA polymerase II. J Mol Biol. 1976 May 5;103(1):61–76. doi: 10.1016/0022-2836(76)90052-8. [DOI] [PubMed] [Google Scholar]
  41. Shliakhtenko L. S., Liubchenko Iu L., Chernov B. K., Zhurkin V. B. Vliianie temperatury i ionnoi sily na élektroforeticheskuiu podvizhnost' sinteticheskikh fragmentov DNK. Mol Biol (Mosk) 1990 Jan-Feb;24(1):79–95. [PubMed] [Google Scholar]
  42. Shlomai J. The assembly of kinetoplast DNA. Parasitol Today. 1994 Sep;10(9):341–346. doi: 10.1016/0169-4758(94)90244-5. [DOI] [PubMed] [Google Scholar]
  43. Shlomai J., Zadok A. Reversible decatenation of kinetoplast DNA by a DNA topoisomerase from trypanosomatids. Nucleic Acids Res. 1983 Jun 25;11(12):4019–4034. doi: 10.1093/nar/11.12.4019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Shpigelman E. S., Trifonov E. N., Bolshoy A. CURVATURE: software for the analysis of curved DNA. Comput Appl Biosci. 1993 Aug;9(4):435–440. doi: 10.1093/bioinformatics/9.4.435. [DOI] [PubMed] [Google Scholar]
  45. Simpson L. The mitochondrial genome of kinetoplastid protozoa: genomic organization, transcription, replication, and evolution. Annu Rev Microbiol. 1987;41:363–382. doi: 10.1146/annurev.mi.41.100187.002051. [DOI] [PubMed] [Google Scholar]
  46. Sloof P., de Haan A., Eier W., van Iersel M., Boel E., van Steeg H., Benne R. The nucleotide sequence of the variable region in Trypanosoma brucei completes the sequence analysis of the maxicircle component of mitochondrial kinetoplast DNA. Mol Biochem Parasitol. 1992 Dec;56(2):289–299. doi: 10.1016/0166-6851(92)90178-m. [DOI] [PubMed] [Google Scholar]
  47. Stuart K., Feagin J. E. Mitochondrial DNA of kinetoplastids. Int Rev Cytol. 1992;141:65–88. doi: 10.1016/s0074-7696(08)62063-x. [DOI] [PubMed] [Google Scholar]
  48. Sugisaki H., Ray D. S. DNA sequence of Crithidia fasciculata kinetoplast minicircles. Mol Biochem Parasitol. 1987 Apr;23(3):253–263. doi: 10.1016/0166-6851(87)90032-6. [DOI] [PubMed] [Google Scholar]
  49. Tal M., Shimron F., Yagil G. Unwound regions in yeast centromere IV DNA. J Mol Biol. 1994 Oct 21;243(2):179–189. doi: 10.1006/jmbi.1994.1645. [DOI] [PubMed] [Google Scholar]
  50. Taylor F. M., Martindale D. W. Retroviral-type zinc fingers and glycine-rich repeats in a protein encoded by cnjB, a Tetrahymena gene active during meiosis. Nucleic Acids Res. 1993 Sep 25;21(19):4610–4614. doi: 10.1093/nar/21.19.4610. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Trifonov E. N. Curved DNA. CRC Crit Rev Biochem. 1985;19(2):89–106. doi: 10.3109/10409238509082540. [DOI] [PubMed] [Google Scholar]
  52. Tzfati Y., Abeliovich H., Avrahami D., Shlomai J. Universal minicircle sequence binding protein, a CCHC-type zinc finger protein that binds the universal minicircle sequence of trypanosomatids. Purification and characterization. J Biol Chem. 1995 Sep 8;270(36):21339–21345. doi: 10.1074/jbc.270.36.21339. [DOI] [PubMed] [Google Scholar]
  53. Tzfati Y., Abeliovich H., Kapeller I., Shlomai J. A single-stranded DNA-binding protein from Crithidia fasciculata recognizes the nucleotide sequence at the origin of replication of kinetoplast DNA minicircles. Proc Natl Acad Sci U S A. 1992 Aug 1;89(15):6891–6895. doi: 10.1073/pnas.89.15.6891. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Webb J. R., McMaster W. R. Molecular cloning and expression of a Leishmania major gene encoding a single-stranded DNA-binding protein containing nine "CCHC" zinc finger motifs. J Biol Chem. 1993 Jul 5;268(19):13994–14002. [PubMed] [Google Scholar]
  55. Xu H. P., Rajavashisth T., Grewal N., Jung V., Riggs M., Rodgers L., Wigler M. A gene encoding a protein with seven zinc finger domains acts on the sexual differentiation pathways of Schizosaccharomyces pombe. Mol Biol Cell. 1992 Jul;3(7):721–734. doi: 10.1091/mbc.3.7.721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Zhurkin V. B., Lysov Y. P., Ivanov V. I. Anisotropic flexibility of DNA and the nucleosomal structure. Nucleic Acids Res. 1979 Mar;6(3):1081–1096. doi: 10.1093/nar/6.3.1081. [DOI] [PMC free article] [PubMed] [Google Scholar]

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