Skip to main content
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1997 Dec;179(23):7544–7550. doi: 10.1128/jb.179.23.7544-7550.1997

Conserved motifs II to VI of DNA helicase II from Escherichia coli are all required for biological activity.

G Zhang 1, E Deng 1, L R Baugh 1, C M Hamilton 1, V F Maples 1, S R Kushner 1
PMCID: PMC179708  PMID: 9393722

Abstract

There are seven conserved motifs (IA, IB, and II to VI) in DNA helicase II of Escherichia coli that have high homology among a large family of proteins involved in DNA metabolism. To address the functional importance of motifs II to VI, we employed site-directed mutagenesis to replace the charged amino acid residues in each motif with alanines. Cells carrying these mutant alleles exhibited higher UV and methyl methanesulfonate sensitivity, increased rates of spontaneous mutagenesis, and elevated levels of homologous recombination, indicating defects in both the excision repair and mismatch repair pathways. In addition, we also changed the highly conserved tyrosine(600) in motif VI to phenylalanine (uvrD309, Y600F). This mutant displayed a moderate increase in UV sensitivity but a decrease in spontaneous mutation rate, suggesting that DNA helicase II may have different functions in the two DNA repair pathways. Furthermore, a mutation in domain IV (uvrD307, R284A) significantly reduced the viability of some E. coli K-12 strains at 30 degrees C but not at 37 degrees C. The implications of these observations are discussed.

Full Text

The Full Text of this article is available as a PDF (213.4 KB).

Selected References

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

  1. Appleyard R K. Segregation of New Lysogenic Types during Growth of a Doubly Lysogenic Strain Derived from Escherichia Coli K12. Genetics. 1954 Jul;39(4):440–452. doi: 10.1093/genetics/39.4.440. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arthur H. M., Lloyd R. G. Hyper-recombination in uvrD mutants of Escherichia coli K-12. Mol Gen Genet. 1980;180(1):185–191. doi: 10.1007/BF00267368. [DOI] [PubMed] [Google Scholar]
  3. Brosh R. M., Jr, Matson S. W. A partially functional DNA helicase II mutant defective in forming stable binary complexes with ATP and DNA. A role for helicase motif III. J Biol Chem. 1996 Oct 11;271(41):25360–25368. doi: 10.1074/jbc.271.41.25360. [DOI] [PubMed] [Google Scholar]
  4. Brosh R. M., Jr, Matson S. W. A point mutation in Escherichia coli DNA helicase II renders the enzyme nonfunctional in two DNA repair pathways. Evidence for initiation of unwinding from a nick in vivo. J Biol Chem. 1997 Jan 3;272(1):572–579. doi: 10.1074/jbc.272.1.572. [DOI] [PubMed] [Google Scholar]
  5. Brosh R. M., Jr, Matson S. W. Mutations in motif II of Escherichia coli DNA helicase II render the enzyme nonfunctional in both mismatch repair and excision repair with differential effects on the unwinding reaction. J Bacteriol. 1995 Oct;177(19):5612–5621. doi: 10.1128/jb.177.19.5612-5621.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Caron P. R., Kushner S. R., Grossman L. Involvement of helicase II (uvrD gene product) and DNA polymerase I in excision mediated by the uvrABC protein complex. Proc Natl Acad Sci U S A. 1985 Aug;82(15):4925–4929. doi: 10.1073/pnas.82.15.4925. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Casadaban M. J., Cohen S. N. Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J Mol Biol. 1980 Apr;138(2):179–207. doi: 10.1016/0022-2836(80)90283-1. [DOI] [PubMed] [Google Scholar]
  8. Colasanti J., Denhardt D. T. The Escherichia coli rep mutation. X. Consequences of increased and decreased Rep protein levels. Mol Gen Genet. 1987 Sep;209(2):382–390. doi: 10.1007/BF00329669. [DOI] [PubMed] [Google Scholar]
  9. Cunningham B. C., Wells J. A. High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. Science. 1989 Jun 2;244(4908):1081–1085. doi: 10.1126/science.2471267. [DOI] [PubMed] [Google Scholar]
  10. Feinstein S. I., Low K. B. Hyper-recombining recipient strains in bacterial conjugation. Genetics. 1986 May;113(1):13–33. doi: 10.1093/genetics/113.1.13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Fishel R. A., Siegel E. C., Kolodner R. Gene conversion in Escherichia coli. Resolution of heteroallelic mismatched nucleotides by co-repair. J Mol Biol. 1986 Mar 20;188(2):147–157. doi: 10.1016/0022-2836(86)90300-1. [DOI] [PubMed] [Google Scholar]
  12. George J. W., Brosh R. M., Jr, Matson S. W. A dominant negative allele of the Escherichia coli uvrD gene encoding DNA helicase II. A biochemical and genetic characterization. J Mol Biol. 1994 Jan 14;235(2):424–435. doi: 10.1006/jmbi.1994.1003. [DOI] [PubMed] [Google Scholar]
  13. Graves-Woodward K. L., Gottlieb J., Challberg M. D., Weller S. K. Biochemical analyses of mutations in the HSV-1 helicase-primase that alter ATP hydrolysis, DNA unwinding, and coupling between hydrolysis and unwinding. J Biol Chem. 1997 Feb 14;272(7):4623–4630. doi: 10.1074/jbc.272.7.4623. [DOI] [PubMed] [Google Scholar]
  14. Grilley M., Holmes J., Yashar B., Modrich P. Mechanisms of DNA-mismatch correction. Mutat Res. 1990 Sep-Nov;236(2-3):253–267. doi: 10.1016/0921-8777(90)90009-t. [DOI] [PubMed] [Google Scholar]
  15. Guyer M. S., Reed R. R., Steitz J. A., Low K. B. Identification of a sex-factor-affinity site in E. coli as gamma delta. Cold Spring Harb Symp Quant Biol. 1981;45(Pt 1):135–140. doi: 10.1101/sqb.1981.045.01.022. [DOI] [PubMed] [Google Scholar]
  16. Hamilton C. M., Aldea M., Washburn B. K., Babitzke P., Kushner S. R. New method for generating deletions and gene replacements in Escherichia coli. J Bacteriol. 1989 Sep;171(9):4617–4622. doi: 10.1128/jb.171.9.4617-4622.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hill C. W., Harnish B. W. Inversions between ribosomal RNA genes of Escherichia coli. Proc Natl Acad Sci U S A. 1981 Nov;78(11):7069–7072. doi: 10.1073/pnas.78.11.7069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hodgman T. C. A new superfamily of replicative proteins. Nature. 1988 May 5;333(6168):22–23. doi: 10.1038/333022b0. [DOI] [PubMed] [Google Scholar]
  19. Horii Z., Clark A. J. Genetic analysis of the recF pathway to genetic recombination in Escherichia coli K12: isolation and characterization of mutants. J Mol Biol. 1973 Oct 25;80(2):327–344. doi: 10.1016/0022-2836(73)90176-9. [DOI] [PubMed] [Google Scholar]
  20. Husain I., Van Houten B., Thomas D. C., Abdel-Monem M., Sancar A. Effect of DNA polymerase I and DNA helicase II on the turnover rate of UvrABC excision nuclease. Proc Natl Acad Sci U S A. 1985 Oct;82(20):6774–6778. doi: 10.1073/pnas.82.20.6774. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Klinkert M. Q., Klein A., Abdel-Monem M. Studies on the functions of DNA helicase I and DNA helicase II of Escherichia coli. J Biol Chem. 1980 Oct 25;255(20):9746–9752. [PubMed] [Google Scholar]
  22. Kushner S. R. In vivo studies of temperature-sensitive recB and recC mutants. J Bacteriol. 1974 Dec;120(3):1213–1218. doi: 10.1128/jb.120.3.1213-1218.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lahue R. S., Au K. G., Modrich P. DNA mismatch correction in a defined system. Science. 1989 Jul 14;245(4914):160–164. doi: 10.1126/science.2665076. [DOI] [PubMed] [Google Scholar]
  24. Lloyd R. G. lexA dependent recombination in uvrD strains of Escherichia coli. Mol Gen Genet. 1983;189(1):157–161. doi: 10.1007/BF00326069. [DOI] [PubMed] [Google Scholar]
  25. Luria S. E., Delbrück M. Mutations of Bacteria from Virus Sensitivity to Virus Resistance. Genetics. 1943 Nov;28(6):491–511. doi: 10.1093/genetics/28.6.491. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Maples V. F., Kushner S. R. DNA repair in Escherichia coli: identification of the uvrD gene product. Proc Natl Acad Sci U S A. 1982 Sep;79(18):5616–5620. doi: 10.1073/pnas.79.18.5616. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Marinus M. G. Influence of uvrD3, uvrE502, and recL152 mutations on the phenotypes of Escherichia coli K-12 dam mutants. J Bacteriol. 1980 Jan;141(1):223–226. doi: 10.1128/jb.141.1.223-226.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Matson S. W., Bean D. W., George J. W. DNA helicases: enzymes with essential roles in all aspects of DNA metabolism. Bioessays. 1994 Jan;16(1):13–22. doi: 10.1002/bies.950160103. [DOI] [PubMed] [Google Scholar]
  29. Matson S. W. Escherichia coli helicase II (urvD gene product) translocates unidirectionally in a 3' to 5' direction. J Biol Chem. 1986 Aug 5;261(22):10169–10175. [PubMed] [Google Scholar]
  30. Matson S. W., George J. W. DNA helicase II of Escherichia coli. Characterization of the single-stranded DNA-dependent NTPase and helicase activities. J Biol Chem. 1987 Feb 15;262(5):2066–2076. [PubMed] [Google Scholar]
  31. Mendonca V. M., Kaiser-Rogers K., Matson S. W. Double helicase II (uvrD)-helicase IV (helD) deletion mutants are defective in the recombination pathways of Escherichia coli. J Bacteriol. 1993 Aug;175(15):4641–4651. doi: 10.1128/jb.175.15.4641-4651.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Modrich P. Mechanisms and biological effects of mismatch repair. Annu Rev Genet. 1991;25:229–253. doi: 10.1146/annurev.ge.25.120191.001305. [DOI] [PubMed] [Google Scholar]
  33. Morel P., Hejna J. A., Ehrlich S. D., Cassuto E. Antipairing and strand transferase activities of E. coli helicase II (UvrD). Nucleic Acids Res. 1993 Jul 11;21(14):3205–3209. doi: 10.1093/nar/21.14.3205. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Nevers P., Spatz H. C. Escherichia coli mutants uvr D and uvr E deficient in gene conversion of lambda-heteroduplexes. Mol Gen Genet. 1975 Aug 27;139(3):233–243. doi: 10.1007/BF00268974. [DOI] [PubMed] [Google Scholar]
  35. Orren D. K., Selby C. P., Hearst J. E., Sancar A. Post-incision steps of nucleotide excision repair in Escherichia coli. Disassembly of the UvrBC-DNA complex by helicase II and DNA polymerase I. J Biol Chem. 1992 Jan 15;267(2):780–788. [PubMed] [Google Scholar]
  36. Peluso R. W., Rosenberg G. H. Quantitative electrotransfer of proteins from sodium dodecyl sulfate-polyacrylamide gels onto positively charged nylon membranes. Anal Biochem. 1987 May 1;162(2):389–398. doi: 10.1016/0003-2697(87)90409-x. [DOI] [PubMed] [Google Scholar]
  37. Rayssiguier C., Thaler D. S., Radman M. The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature. 1989 Nov 23;342(6248):396–401. doi: 10.1038/342396a0. [DOI] [PubMed] [Google Scholar]
  38. Richet E., Kohiyama M. Purification and characterization of a DNA-dependent ATPase from Escherichia coli. J Biol Chem. 1976 Feb 10;251(3):808–812. [PubMed] [Google Scholar]
  39. Runyon G. T., Bear D. G., Lohman T. M. Escherichia coli helicase II (UvrD) protein initiates DNA unwinding at nicks and blunt ends. Proc Natl Acad Sci U S A. 1990 Aug;87(16):6383–6387. doi: 10.1073/pnas.87.16.6383. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Runyon G. T., Lohman T. M. Escherichia coli helicase II (uvrD) protein can completely unwind fully duplex linear and nicked circular DNA. J Biol Chem. 1989 Oct 15;264(29):17502–17512. [PubMed] [Google Scholar]
  41. Sancar A. Mechanisms of DNA excision repair. Science. 1994 Dec 23;266(5193):1954–1956. doi: 10.1126/science.7801120. [DOI] [PubMed] [Google Scholar]
  42. Siegel E. C., Race H. M. Phenotypes of UV-sensitive uvrD3, recL152, and uvrE15 mutants of Escherichia coli. Mutat Res. 1981 Aug;83(1):49–59. doi: 10.1016/0027-5107(81)90070-1. [DOI] [PubMed] [Google Scholar]
  43. Siegel E. C. Ultraviolet-sensitive mutator strain of Escherichia coli K-12. J Bacteriol. 1973 Jan;113(1):145–160. doi: 10.1128/jb.113.1.145-160.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Tabor S., Richardson C. C. A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes. Proc Natl Acad Sci U S A. 1985 Feb;82(4):1074–1078. doi: 10.1073/pnas.82.4.1074. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Walker J. E., Saraste M., Runswick M. J., Gay N. J. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1982;1(8):945–951. doi: 10.1002/j.1460-2075.1982.tb01276.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Wang R. F., Kushner S. R. Construction of versatile low-copy-number vectors for cloning, sequencing and gene expression in Escherichia coli. Gene. 1991 Apr;100:195–199. [PubMed] [Google Scholar]
  47. Washburn B. K., Kushner S. R. Characterization of DNA helicase II from a uvrD252 mutant of Escherichia coli. J Bacteriol. 1993 Jan;175(2):341–350. doi: 10.1128/jb.175.2.341-350.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Washburn B. K., Kushner S. R. Construction and analysis of deletions in the structural gene (uvrD) for DNA helicase II of Escherichia coli. J Bacteriol. 1991 Apr;173(8):2569–2575. doi: 10.1128/jb.173.8.2569-2575.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Wechsler J. A., Adelberg E. A. Antipolarity in the ilv operon of Escherichia coli K-12. J Bacteriol. 1969 Jun;98(3):1179–1194. doi: 10.1128/jb.98.3.1179-1194.1969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Wertman K. F., Drubin D. G., Botstein D. Systematic mutational analysis of the yeast ACT1 gene. Genetics. 1992 Oct;132(2):337–350. doi: 10.1093/genetics/132.2.337. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Willetts N. S., Clark A. J., Low B. Genetic location of certain mutations conferring recombination deficiency in Escherichia coli. J Bacteriol. 1969 Jan;97(1):244–249. doi: 10.1128/jb.97.1.244-249.1969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Zieg J., Kushner S. R. Analysis of genetic recombination between two partially deleted lactose operons of Escherichia coli K-12. J Bacteriol. 1977 Jul;131(1):123–132. doi: 10.1128/jb.131.1.123-132.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Zieg J., Maples V. F., Kushner S. R. Recombinant levels of Escherichia coli K-12 mutants deficient in various replication, recombination, or repair genes. J Bacteriol. 1978 Jun;134(3):958–966. doi: 10.1128/jb.134.3.958-966.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES