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. 1996 Aug;178(15):4620–4627. doi: 10.1128/jb.178.15.4620-4627.1996

Defect in general priming conferred by linker region mutants of Escherichia coli dnaB.

L Stordal 1, R Maurer 1
PMCID: PMC178232  PMID: 8755893

Abstract

The dnaB gene of Escherichia coli encodes a bifunctional primase accessory protein/helicase necessary for chromosomal replication. Monomers of DnaB comprise two trypsin-resistant domains connected by a 45-amino-acid linker. To investigate the role of the linker in the structure and function of DnaB, we have purified and characterized three DnaB mutant proteins having single amino acid substitutions in the linker. We find that the mutant proteins retain the two-domain structure and assemble into hexamers that may be less stable than hexamers formed by wild-type DnaB. These mutant hexamers have hydrodynamic properties slightly different from those of the wild type, suggestive of a more open structure. The mutant proteins had reduced or absent ability to stimulate primase and also exhibited slight alterations in ATPase activity compared with the wild type. We conclude that the linker region promotes primase-DnaB interaction, but this effect may be indirect. We propose a model involving repositioning of N-terminal domains to explain the properties of the mutant proteins.

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Selected References

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  1. Arai K., Kornberg A. A general priming system employing only dnaB protein and primase for DNA replication. Proc Natl Acad Sci U S A. 1979 Sep;76(9):4308–4312. doi: 10.1073/pnas.76.9.4308. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arai K., Kornberg A. Mechanism of dnaB protein action. II. ATP hydrolysis by dnaB protein dependent on single- or double-stranded DNA. J Biol Chem. 1981 May 25;256(10):5253–5259. [PubMed] [Google Scholar]
  3. Arai K., Kornberg A. Mechanism of dnaB protein action. III. Allosteric role of ATP in the alteration of DNA structure by dnaB protein in priming replication. J Biol Chem. 1981 May 25;256(10):5260–5266. [PubMed] [Google Scholar]
  4. Arai K., Kornberg A. Mechanism of dnaB protein action. IV. General priming of DNA replication by dnaB protein and primase compared with RNA polymerase. J Biol Chem. 1981 May 25;256(10):5267–5272. [PubMed] [Google Scholar]
  5. Arai K., Yasuda S., Kornberg A. Mechanism of dnaB protein action. I. Crystallization and properties of dnaB protein, an essential replication protein in Escherichia coli. J Biol Chem. 1981 May 25;256(10):5247–5252. [PubMed] [Google Scholar]
  6. Baker T. A., Funnell B. E., Kornberg A. Helicase action of dnaB protein during replication from the Escherichia coli chromosomal origin in vitro. J Biol Chem. 1987 May 15;262(14):6877–6885. [PubMed] [Google Scholar]
  7. Biswas S. B., Chen P. H., Biswas E. E. Structure and function of Escherichia coli DnaB protein: role of the N-terminal domain in helicase activity. Biochemistry. 1994 Sep 20;33(37):11307–11314. doi: 10.1021/bi00203a028. [DOI] [PubMed] [Google Scholar]
  8. Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1006/abio.1976.9999. [DOI] [PubMed] [Google Scholar]
  9. Bujalowski W., Klonowska M. M., Jezewska M. J. Oligomeric structure of Escherichia coli primary replicative helicase DnaB protein. J Biol Chem. 1994 Dec 16;269(50):31350–31358. [PubMed] [Google Scholar]
  10. Godson G. N. An over-expression plasmid for Escherichia coli primase. Gene. 1991 Apr;100:59–64. doi: 10.1016/0378-1119(91)90350-k. [DOI] [PubMed] [Google Scholar]
  11. Kunkel T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. doi: 10.1073/pnas.82.2.488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  13. Lanka E., Geschke B., Schuster H. Escherichia coli dnaB mutant defective in DNA initiation: isolation and properties of the dnaB protein. Proc Natl Acad Sci U S A. 1978 Feb;75(2):799–803. doi: 10.1073/pnas.75.2.799. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. LeBowitz J. H., McMacken R. The Escherichia coli dnaB replication protein is a DNA helicase. J Biol Chem. 1986 Apr 5;261(10):4738–4748. [PubMed] [Google Scholar]
  15. Marszalek J., Kaguni J. M. Defective replication activity of a dominant-lethal dnaB gene product from Escherichia coli. J Biol Chem. 1992 Sep 25;267(27):19334–19340. [PubMed] [Google Scholar]
  16. Matsudaira P. Sequence from picomole quantities of proteins electroblotted onto polyvinylidene difluoride membranes. J Biol Chem. 1987 Jul 25;262(21):10035–10038. [PubMed] [Google Scholar]
  17. Maurer R., Wong A. Dominant lethal mutations in the dnaB helicase gene of Salmonella typhimurium. J Bacteriol. 1988 Aug;170(8):3682–3688. doi: 10.1128/jb.170.8.3682-3688.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Nakayama N., Arai N., Bond M. W., Kaziro Y., Arai K. Nucleotide sequence of dnaB and the primary structure of the dnaB protein from Escherichia coli. J Biol Chem. 1984 Jan 10;259(1):97–101. [PubMed] [Google Scholar]
  19. Nakayama N., Arai N., Kaziro Y., Arai K. Structural and functional studies of the dnaB protein using limited proteolysis. Characterization of domains for DNA-dependent ATP hydrolysis and for protein association in the primosome. J Biol Chem. 1984 Jan 10;259(1):88–96. [PubMed] [Google Scholar]
  20. Reha-Krantz L. J., Hurwitz J. The dnaB gene product of Escherichia coli. I. Purification, homogeneity, and physical properties. J Biol Chem. 1978 Jun 10;253(11):4043–4050. [PubMed] [Google Scholar]
  21. Reha-Krantz L. J., Hurwitz J. The dnaB gene product of Escherichia coli. II. Single stranded DNA-dependent ribonucleoside triphosphatase activity. J Biol Chem. 1978 Jun 10;253(11):4051–4057. [PubMed] [Google Scholar]
  22. Rowen L., Kornberg A. Primase, the dnaG protein of Escherichia coli. An enzyme which starts DNA chains. J Biol Chem. 1978 Feb 10;253(3):758–764. [PubMed] [Google Scholar]
  23. Saluja D., Godson G. N. Biochemical characterization of Escherichia coli temperature-sensitive dnaB mutants dnaB8, dnaB252, dnaB70, dnaB43, and dnaB454. J Bacteriol. 1995 Feb;177(4):1104–1111. doi: 10.1128/jb.177.4.1104-1111.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. San Martin M. C., Stamford N. P., Dammerova N., Dixon N. E., Carazo J. M. A structural model for the Escherichia coli DnaB helicase based on electron microscopy data. J Struct Biol. 1995 May-Jun;114(3):167–176. doi: 10.1006/jsbi.1995.1016. [DOI] [PubMed] [Google Scholar]
  25. Shrimankar P., Stordal L., Maurer R. Purification and characterization of a mutant DnaB protein specifically defective in ATP hydrolysis. J Bacteriol. 1992 Dec;174(23):7689–7696. doi: 10.1128/jb.174.23.7689-7696.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Siegel L. M., Monty K. J. Determination of molecular weights and frictional ratios of proteins in impure systems by use of gel filtration and density gradient centrifugation. Application to crude preparations of sulfite and hydroxylamine reductases. Biochim Biophys Acta. 1966 Feb 7;112(2):346–362. doi: 10.1016/0926-6585(66)90333-5. [DOI] [PubMed] [Google Scholar]
  27. Stamford N. P., Lilley P. E., Dixon N. E. Enriched sources of Escherichia coli replication proteins. The dnaG primase is a zinc metalloprotein. Biochim Biophys Acta. 1992 Aug 17;1132(1):17–25. doi: 10.1016/0167-4781(92)90047-4. [DOI] [PubMed] [Google Scholar]
  28. Studier F. W., Rosenberg A. H., Dunn J. J., Dubendorff J. W. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 1990;185:60–89. doi: 10.1016/0076-6879(90)85008-c. [DOI] [PubMed] [Google Scholar]
  29. Sun W., Tormo J., Steitz T. A., Godson G. N. Domains of Escherichia coli primase: functional activity of a 47-kDa N-terminal proteolytic fragment. Proc Natl Acad Sci U S A. 1994 Nov 22;91(24):11462–11466. doi: 10.1073/pnas.91.24.11462. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Swart J. R., Griep M. A. Primase from Escherichia coli primes single-stranded templates in the absence of single-stranded DNA-binding protein or other auxiliary proteins. Template sequence requirements based on the bacteriophage G4 complementary strand origin and Okazaki fragment initiation sites. J Biol Chem. 1993 Jun 15;268(17):12970–12976. [PubMed] [Google Scholar]
  31. Tougu K., Peng H., Marians K. J. Identification of a domain of Escherichia coli primase required for functional interaction with the DnaB helicase at the replication fork. J Biol Chem. 1994 Feb 11;269(6):4675–4682. [PubMed] [Google Scholar]
  32. Ueda K., McMacken R., Kornberg A. dnaB protein of Escherichia coli. Purification and role in the replication of phiX174 DNA. J Biol Chem. 1978 Jan 10;253(1):261–269. [PubMed] [Google Scholar]
  33. Wu C. A., Zechner E. L., Marians K. J. Coordinated leading- and lagging-strand synthesis at the Escherichia coli DNA replication fork. I. Multiple effectors act to modulate Okazaki fragment size. J Biol Chem. 1992 Feb 25;267(6):4030–4044. [PubMed] [Google Scholar]
  34. Yu X., Jezewska M. J., Bujalowski W., Egelman E. H. The hexameric E. coli DnaB helicase can exist in different Quaternary states. J Mol Biol. 1996 May 31;259(1):7–14. doi: 10.1006/jmbi.1996.0297. [DOI] [PubMed] [Google Scholar]
  35. Zagursky R. J., Berman M. L. Cloning vectors that yield high levels of single-stranded DNA for rapid DNA sequencing. Gene. 1984 Feb;27(2):183–191. doi: 10.1016/0378-1119(84)90139-2. [DOI] [PubMed] [Google Scholar]

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