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Journal List > Proc Natl Acad Sci U S A > v.93(8); Apr 16, 1996

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Proc Natl Acad Sci U S A. 1996 April 16; 93(8): 3253–3258.
PMCID: PMC39592
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The dimer-dimer interaction surface of the replication terminator protein of Bacillus subtilis and termination of DNA replication.
A C Manna, K S Pai, D E Bussiere, S W White, and D Bastia
Department of Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
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Abstract
The replication terminator protein (RTP) of Bacillus subtilis causes polar fork arrest at replication termini by sequence-specific interaction of two dimeric proteins with the terminus sequence. The crystal structure of the RTP protein has been solved, and the structure has already provide valuable clues regarding the structural basis of its function. However, it provides little information as to the surface of the protein involved in dimer-dimer interaction. Using site-directed mutagenesis, we have identified three sites on the protein that appear to mediate the dimer-dimer interaction. Crystallographic analysis of one of the mutant proteins (Y88F) showed that its structure is unaltered when compared to the wild-type protein. The locations of the three sites suggested a model for the dimer-dimer interaction that involves an association between two beta-ribbon motifs. This model is supported by a fourth mutation that was predicted to disrupt the interaction and was shown to do so. Biochemical analyses of these mutants provide compelling evidence that cooperative protein-protein interaction between two dimers of RTP is essential to impose polar blocks to the elongation of both DNA and RNA chains.
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Selected References
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  • Lovett MA, Sparks RB, Helinski DR. Bidirectional replication of plasmid R6K DNA in Escherichia coli; correspondence between origin of replication and position of single-strand break in relaxed complex. Proc Natl Acad Sci U S A. 1975 Aug;72(8):2905–2909. [PubMed]
  • Crosa JH, Luttropp LK, Falkow S. Mode of replication of the conjugative R-plasmid RSF1040 in Escherichia coli. J Bacteriol. 1976 Apr;126(1):454–466. [PubMed]
  • Bastia D, Germino J, Crosa JH, Ram J. The nucleotide sequence surrounding the replication terminus of R6K. Proc Natl Acad Sci U S A. 1981 Apr;78(4):2095–2099. [PubMed]
  • Louarn J, Patte J, Louarn JM. Evidence for a fixed termination site of chromosome replication in Escherichia coli K12. J Mol Biol. 1977 Sep 25;115(3):295–314. [PubMed]
  • Kuempel PL, Duerr SA, Seeley NR. Terminus region of the chromosome in Escherichia coli inhibits replication forks. Proc Natl Acad Sci U S A. 1977 Sep;74(9):3927–3931. [PubMed]
  • Weiss AS, Wake RG. Restriction map of DNA spanning the replication terminus of the Bacillus subtilis chromosome. J Mol Biol. 1983 Dec 5;171(2):119–137. [PubMed]
  • Lewis PJ, Ralston GB, Christopherson RI, Wake RG. Identification of the replication terminator protein binding sites in the terminus region of the Bacillus subtilis chromosome and stoichiometry of the binding. J Mol Biol. 1990 Jul 5;214(1):73–84. [PubMed]
  • Hill TM, Pelletier AJ, Tecklenburg ML, Kuempel PL. Identification of the DNA sequence from the E. coli terminus region that halts replication forks. Cell. 1988 Nov 4;55(3):459–466. [PubMed]
  • Horiuchi T, Hidaka M. Core sequence of two separable terminus sites of the R6K plasmid that exhibit polar inhibition of replication is a 20 bp inverted repeat. Cell. 1988 Aug 12;54(4):515–523. [PubMed]
  • Sista PR, Mukherjee S, Patel P, Khatri GS, Bastia D. A host-encoded DNA-binding protein promotes termination of plasmid replication at a sequence-specific replication terminus. Proc Natl Acad Sci U S A. 1989 May;86(9):3026–3030. [PubMed]
  • Smith MT, Wake RG. Definition and polarity of action of DNA replication terminators in Bacillus subtilis. J Mol Biol. 1992 Oct 5;227(3):648–657. [PubMed]
  • Kaul S, Mohanty BK, Sahoo T, Patel I, Khan SA, Bastia D. The replication terminator protein of the gram-positive bacterium Bacillus subtilis functions as a polar contrahelicase in gram-negative Escherichia coli. Proc Natl Acad Sci U S A. 1994 Nov 8;91(23):11143–11147. [PubMed]
  • Sahoo T, Mohanty BK, Patel I, Bastia D. Termination of DNA replication in vitro: requirement for stereospecific interaction between two dimers of the replication terminator protein of Bacillus subtilis and with the terminator site to elicit polar contrahelicase and fork impedance. EMBO J. 1995 Feb 1;14(3):619–628. [PubMed]
  • Sahoo T, Mohanty BK, Lobert M, Manna AC, Bastia D. The contrahelicase activities of the replication terminator proteins of Escherichia coli and Bacillus subtilis are helicase-specific and impede both helicase translocation and authentic DNA unwinding. J Biol Chem. 1995 Dec 8;270(49):29138–29144. [PubMed]
  • Khatri GS, MacAllister T, Sista PR, Bastia D. The replication terminator protein of E. coli is a DNA sequence-specific contra-helicase. Cell. 1989 Nov 17;59(4):667–674. [PubMed]
  • Lee EH, Kornberg A, Hidaka M, Kobayashi T, Horiuchi T. Escherichia coli replication termination protein impedes the action of helicases. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9104–9108. [PubMed]
  • Hiasa H, Marians KJ. Differential inhibition of the DNA translocation and DNA unwinding activities of DNA helicases by the Escherichia coli Tus protein. J Biol Chem. 1992 Jun 5;267(16):11379–11385. [PubMed]
  • Bussiere DE, Bastia D, White SW. Crystal structure of the replication terminator protein from B. subtilis at 2.6 A. Cell. 1995 Feb 24;80(4):651–660. [PubMed]
  • Mehta PP, Bussiere DE, Hoffman DW, Bastia D, White SW. Crystallization and preliminary structural analysis of the replication terminator protein of Bacillus subtilis. J Biol Chem. 1992 Sep 15;267(26):18885–18889. [PubMed]
  • Ruiz-Echevarría MJ, Giménez-Gallego G, Sabariegos-Jareño R, Díaz-Orejas R. Kid, a small protein of the parD stability system of plasmid R1, is an inhibitor of DNA replication acting at the initiation of DNA synthesis. J Mol Biol. 1995 Apr 7;247(4):568–577. [PubMed]
  • Jones TA, Zou JY, Cowan SW, Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A. 1991 Mar 1;47(Pt 2):110–119. [PubMed]
  • Elledge SJ, Sugiono P, Guarente L, Davis RW. Genetic selection for genes encoding sequence-specific DNA-binding proteins. Proc Natl Acad Sci U S A. 1989 May;86(10):3689–3693. [PubMed]
  • Wickelgren I. Protein sculptors that help turn on genes. Science. 1995 Dec 8;270(5242):1587–1589. [PubMed]
  • Swindells MB. Identification of a common fold in the replication terminator protein suggests a possible mode for DNA binding. Trends Biochem Sci. 1995 Aug;20(8):300–302. [PubMed]
  • Hill TM, Tecklenburg ML, Pelletier AJ, Kuempel PL. tus, the trans-acting gene required for termination of DNA replication in Escherichia coli, encodes a DNA-binding protein. Proc Natl Acad Sci U S A. 1989 Mar;86(5):1593–1597. [PubMed]
  • Sista PR, Hutchinson CA, 3rd, Bastia D. DNA-protein interaction at the replication termini of plasmid R6K. Genes Dev. 1991 Jan;5(1):74–82. [PubMed]
  • Langley DB, Smith MT, Lewis PJ, Wake RG. Protein-nucleoside contacts in the interaction between the replication terminator protein of Bacillus subtilis and the DNA terminator. Mol Microbiol. 1993 Nov;10(4):771–779. [PubMed]
  • Friedman AM, Fischmann TO, Steitz TA. Crystal structure of lac repressor core tetramer and its implications for DNA looping. Science. 1995 Jun 23;268(5218):1721–1727. [PubMed]
  • Lee W, Harvey TS, Yin Y, Yau P, Litchfield D, Arrowsmith CH. Solution structure of the tetrameric minimum transforming domain of p53. Nat Struct Biol. 1994 Dec;1(12):877–890. [PubMed]
  • Hunt JF, Weaver AJ, Landry SJ, Gierasch L, Deisenhofer J. The crystal structure of the GroES co-chaperonin at 2.8 A resolution. Nature. 1996 Jan 4;379(6560):37–45. [PubMed]
  • Davies C, White SW, Ramakrishnan V. The crystal structure of ribosomal protein L14 reveals an important organizational component of the translational apparatus. Structure. 1996 Jan 15;4(1):55–66. [PubMed]
  • Tanaka I, Appelt K, Dijk J, White SW, Wilson KS. 3-A resolution structure of a protein with histone-like properties in prokaryotes. Nature. 310(5976):376–381. [PubMed]
  • Whipple FW, Kuldell NH, Cheatham LA, Hochschild A. Specificity determinants for the interaction of lambda repressor and P22 repressor dimers. Genes Dev. 1994 May 15;8(10):1212–1223. [PubMed]
  • Lewis PJ, Smith MT, Wake RG. A protein involved in termination of chromosome replication in Bacillus subtilis binds specifically to the terC site. J Bacteriol. 1989 Jun;171(6):3564–3567. [PubMed]
  • Miron A, Mukherjee S, Bastia D. Activation of distant replication origins in vivo by DNA looping as revealed by a novel mutant form of an initiator protein defective in cooperativity at a distance. EMBO J. 1992 Mar;11(3):1205–1216. [PubMed]
  • Miron A, Patel I, Bastia D. Multiple pathways of copy control of gamma replicon of R6K: mechanisms both dependent on and independent of cooperativity of interaction of tau protein with DNA affect the copy number. Proc Natl Acad Sci U S A. 1994 Jul 5;91(14):6438–6442. [PubMed]
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