• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of embojLink to Publisher's site
EMBO J. Dec 16, 1985; 4(13A): 3605–3616.
PMCID: PMC554704

Binding and bending of the lambda replication origin by the phage O protein.

Abstract

We have characterized the binding of lambda phage replication initiation protein O to the phage origin of replication. The minimal DNA segment required for O binding is the single iteron, a 19-bp sequence of hyphenated dyad symmetry that is repeated with variations four times in the origin. The isolated amino terminus of O protein is also sufficient to bind DNA. Electrophoretic studies show that the amino terminus of O protein induces bending of a single iteron. The DNA-protein interaction was characterized by ethylation interference, dimethyl sulfate protection and neocarzinostatin footprinting. Points of DNA-protein contact are largely concentrated in two areas symmetrically disposed with respect to the dyad symmetry of the iteron. This suggests the protein interacts as a dimer with half sites in the DNA. However, a few non-symmetrical contacts are found, indicating that O protein may distort the helix. This may correlate with the bending effects demonstrated electrophoretically. Cylindrical DNA projections were used to model O protein binding to the lambda origin and compare it with the lambda repressor-operator interaction. Whereas bound repressor nearly encircles the DNA in the major groove, O protein leaves the major groove on the opposite side exposed.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (3.5M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Zahn K, Blattner FR. Sequence-induced DNA curvature at the bacteriophage lambda origin of replication. Nature. 1985 Oct 3;317(6036):451–453. [PubMed]
  • Chou PY, Fasman GD. Prediction of protein conformation. Biochemistry. 1974 Jan 15;13(2):222–245. [PubMed]
  • Denniston-Thompson K, Moore DD, Kruger KE, Furth ME, Blattner FR. Physical structure of the replication origin of bacteriophage lambda. Science. 1977 Dec 9;198(4321):1051–1056. [PubMed]
  • Echols H, Dodson M, Better M, Roberts JD, McMacken R. The role of specialized nucleoprotein structures in site-specific recombination and initiation of DNA replication. Cold Spring Harb Symp Quant Biol. 1984;49:727–733. [PubMed]
  • Eisen H, Pereira da Silva L, Jacob F. The regulation and mechanism of DNA synthesis in bacteriophage lambda. Cold Spring Harb Symp Quant Biol. 1968;33:755–764. [PubMed]
  • Fried M, Crothers DM. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 1981 Dec 11;9(23):6505–6525. [PMC free article] [PubMed]
  • Friedman DI, Olson ER, Georgopoulos C, Tilly K, Herskowitz I, Banuett F. Interactions of bacteriophage and host macromolecules in the growth of bacteriophage lambda. Microbiol Rev. 1984 Dec;48(4):299–325. [PMC free article] [PubMed]
  • Furth ME, Blattner FR, McLeester C, Dove WF. Genetic structure of the replication origin of bacteriophage lambda. Science. 1977 Dec 9;198(4321):1046–1051. [PubMed]
  • Furth ME, McLeester C, Dove WF. Specificity determinants for bacteriophage lambda DNA replication. I. A chain of interactions that controls the initiation of replication. J Mol Biol. 1978 Dec 5;126(2):195–225. [PubMed]
  • Gronenborn AM, Nermut MV, Eason P, Clore GM. Visualization of cAMP receptor protein-induced DNA kinking by electron microscopy. J Mol Biol. 1984 Nov 15;179(4):751–757. [PubMed]
  • Grosschedl R, Hobom G. DNA sequences and structural homologies of the replication origins of lambdoid bacteriophages. Nature. 1979 Feb 22;277(5698):621–627. [PubMed]
  • Hobom G, Grosschedl R, Lusky M, Scherer G, Schwarz E, Kössel H. Functional analysis of the replicator structure of lambdoid bacteriophage DNAs. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):165–178. [PubMed]
  • Johnson AD, Meyer BJ, Ptashne M. Interactions between DNA-bound repressors govern regulation by the lambda phage repressor. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5061–5065. [PMC free article] [PubMed]
  • Johnsrud L. Contacts between Escherichia coli RNA polymerase and a lac operon promoter. Proc Natl Acad Sci U S A. 1978 Nov;75(11):5314–5318. [PMC free article] [PubMed]
  • Klein A, Lanka E, Schuster H. Isolation of a complex between the P protein of phage lambda and the dnaB protein of Escherichia coli. Eur J Biochem. 1980 Mar;105(1):1–6. [PubMed]
  • Levene SD, Crothers DM. A computer graphics study of sequence-directed bending in DNA. J Biomol Struct Dyn. 1983 Oct;1(2):429–435. [PubMed]
  • Lewis M, Jeffrey A, Wang J, Ladner R, Ptashne M, Pabo CO. Structure of the operator-binding domain of bacteriophage lambda repressor: implications for DNA recognition and gene regulation. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):435–440. [PubMed]
  • Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. [PMC free article] [PubMed]
  • Moore DD, Denniston-Thompson K, Kruger KE, Furth ME, Williams BG, Daniels DL, Blattner FR. Dissection and comparative anatomy of the origins of replication of lambdoid phages. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):155–163. [PubMed]
  • Moore DD, Denniston KJ, Blattner FR. Sequence organization of the origins of DNA replication in lambdoid coliphages. Gene. 1981 Jun-Jul;14(1-2):91–101. [PubMed]
  • Norrander J, Kempe T, Messing J. Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis. Gene. 1983 Dec;26(1):101–106. [PubMed]
  • Ogawa T, Tomizawa J. Replication of bacteriophage DNA. I. Replication of DNA of lambda phage defective in early functions. J Mol Biol. 1968 Dec 14;38(2):217–225. [PubMed]
  • Pabo CO, Sauer RT. Protein-DNA recognition. Annu Rev Biochem. 1984;53:293–321. [PubMed]
  • Povirk LF, Goldberg IH. Covalent adducts of DNA and the nonprotein chromophore of neocarzinostatin contain a modified deoxyribose. Proc Natl Acad Sci U S A. 1982 Jan;79(2):369–373. [PMC free article] [PubMed]
  • Rambach A. Replicator mutants of bacteriophage lambda: characterization of two subclasses. Virology. 1973 Jul;54(1):270–277. [PubMed]
  • Ross W, Landy A, Kikuchi Y, Nash H. Interaction of int protein with specific sites on lambda att DNA. Cell. 1979 Oct;18(2):297–307. [PMC free article] [PubMed]
  • Scherer G. Nucleotide sequence of the O gene and of the origin of replication in bacteriophage lambda DNA. Nucleic Acids Res. 1978 Sep;5(9):3141–3156. [PMC free article] [PubMed]
  • Schnös M, Inman RB. Position of branch points in replicating lambda DNA. J Mol Biol. 1970 Jul 14;51(1):61–73. [PubMed]
  • Siebenlist U, Gilbert W. Contacts between Escherichia coli RNA polymerase and an early promoter of phage T7. Proc Natl Acad Sci U S A. 1980 Jan;77(1):122–126. [PMC free article] [PubMed]
  • Sutcliffe JG. Complete nucleotide sequence of the Escherichia coli plasmid pBR322. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):77–90. [PubMed]
  • Takeda Y, Ohlendorf DH, Anderson WF, Matthews BW. DNA-binding proteins. Science. 1983 Sep 9;221(4615):1020–1026. [PubMed]
  • Tsurimoto T, Matsubara K. Purification of bacteriophage lambda O protein that specifically binds to the origin of replication. Mol Gen Genet. 1981;181(3):325–331. [PubMed]
  • Tsurimoto T, Matsubara K. Purified bacteriophage lambda O protein binds to four repeating sequences at the lambda replication origin. Nucleic Acids Res. 1981 Apr 24;9(8):1789–1799. [PMC free article] [PubMed]
  • Weber IT, Steitz TA. Model of specific complex between catabolite gene activator protein and B-DNA suggested by electrostatic complementarity. Proc Natl Acad Sci U S A. 1984 Jul;81(13):3973–3977. [PMC free article] [PubMed]
  • Wickner SH. DNA replication proteins of Escherichia coli and phage lambda. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):303–310. [PubMed]
  • Wu HM, Crothers DM. The locus of sequence-directed and protein-induced DNA bending. Nature. 1984 Apr 5;308(5959):509–513. [PubMed]

Articles from The EMBO Journal are provided here courtesy of The European Molecular Biology Organization

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • Compound
    Compound
    PubChem Compound links
  • MedGen
    MedGen
    Related information in MedGen
  • PubMed
    PubMed
    PubMed citations for these articles
  • Substance
    Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...