Novel alleles of the Escherichia coli dnaA gene

Journal of Molecular Biology

Volumn 271, Issue 5, 1997, Pages 693-703

  Sutton, Mark D ^a   Kaguni, Jon M ^a  

^a Michigan State University   (United States)

Author keywords

DNA replication; DnaA protein; Genetic selection; Novel alleles; pSC101

Indexed keywords

BACTERIAL PROTEIN; DNA A;

ALLELE; ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; CARBOXY TERMINAL SEQUENCE; CHROMOSOME REPLICATION; CONTROLLED STUDY; DELETION MUTANT; DNA BINDING; DNA REPLICATION ORIGIN; ESCHERICHIA COLI; GENE CLUSTER; GENE MUTATION; MISSENSE MUTATION; NONHUMAN; NONSENSE MUTATION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; REPRESSOR GENE; TEMPERATURE SENSITIVE MUTANT;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0031554911     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1209     Document Type: Article

References (76)

1. Bachmann, B. J. (1990). Linkage map of Escherichia coli K-12, edition 8. Microbiol. Rev. 54, 130-197.
2. Beyersmann, D., Messer, W. & Schlicht, M. (1974). Mutants of Escherichia coli B/r defective in deoxyribonucleic acid initiation: dnaI, a new gene for replication. J. Bacteriol. 118, 783-789.
3. Bramhill, D. & Kornberg, A. (1988a). Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell, 52, 743-755.
4. Bramhill, D. & Kornberg, A. (1988b). A model for initiation at origins of DNA replication. Cell, 54, 915-918.
5. Braun, R. E., O'Day, K. & Wright, A. (1987). Cloning and characterization of dnaA(Cs), a mutation which leads to overinitiation of DNA replication in Escherichia coli K-12. J. Bacteriol. 169, 3898-3903.
6. Brenner, S., Cesareni, G. & Karn, J. (1982). Phasmids: hybrids between CoIE1 plasmids and E. coli bacteriophage lambda. Gene, 17, 27-44.
7. Calcutt, M. J. & Schmidt, F. J. (1992). Conserved gene arrangement in the origin region of the Streptomyces coelicolor chromosome. J. Bacteriol. 174, 3220-3226.
8. Carr, K. M. & Kaguni, J. M. (1996). The A184V missense mutation of the dnaA5 and dnaA46 alleles confers a defect in ATP binding and thermolability in initiation of Escherichia coli DNA replication. Mol. Microbiol, 20, 1307-1318.
9. Chandler, M., Silver, L. & Caro, L. (1977). Suppression of an Escherichia coli dnaA mutation by the integrated R factor R100.1: origin of chromosome replication during exponential growth. J. Bacteriol. 131, 421-430.
10. Chang, A. C. Y. & Cohen, S. N. (1978). Construction and characterization of amplifyable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J. Bacteriol. 134, 1141-1156.
11. Chesney, R. H. & Scott, J. R. (1978). Suppression of a thermosensitive dnaA mutation of Escherichia coli by bacteriophage P1 and P7. Plasmid, 1, 145-163.
12. Chesney, R. H., Scott, J. R. & Vapnek, D. (1979). Integration of the plasmid prophages P1 and P7 into the chromosome of Escherichia coli. J. Mol. Biol. 130, 161-173.
13. Cohen, S. N. & Change, A. C. (1977). Revised interpretation of the origin of the pSC101 plasmid. J. Bacteriol. 132, 734-737.
14. Darimont, B. & Sterner, R. (1994). Sequence, assembly and evolution of a primordial ferredoxin from Thermotoga maritima. EMBO J, 13, 1772-1781.
15. Davis, R. W., Botstein, D. & Roth, J. R. (1980). A Manual for Genetic Engineering: Advanced Bacterial Genetics, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
16. Dubendorff, J. W. & Studier, F. W. (1991). Controlling basal expression in an inducible T7 expression system by blocking the target T7 promoter with lac repressor. J. Mol. Biol. 219, 45-59.
17. Eberle, H., Van de Merwe, W., Madden, K., Kampo, G., Wright, L. & Donlon, K. (1989). The nature of an intragenic suppressor of the Escherichia coli dnaA508 temperature-sensitive mutation. Gene, 84, 237-245.
18. Felton, J. & Wright, A. (1979). Plasmid pSC101 replication in integratively suppressed cells requires dnaA function. Mol. Gen. Genet. 175, 231-233.
19. Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A., Kirkness, E. F., Kerlavage, E. F., Bult, C. J., Tomb, J. F., Dougherty, B. A., Merrick, J. M., McKenney, K., Sutton, G., FitzHugh, W., Fields, C., Gocayne, J. D., Scott, J., Shirley, R., Liu, L.-I., Glodek, A., Kelley, J. M., Weidman, J. F., Phillips, C. A., Spriggs, T., Hedblom, E., Cotton, M. D., Utterback, T. R., Hanna, M. C., Nguyen, D. T., Saudek, D.M., Brandon, R. C., Fine, L. D., Fritchman, J. L., Fuhrmann, J. L., Geoghagen, N. S. M., Gnehm, C. L., McDonald, L. A., Small, K. V., Fraser, C. M., Smith, H. O. & Venter, J. C. (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269, 496-512.
20. Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A., Fleischmann, R. D., Bult, C. J., Kerlavage, A. R., Sutton, G., Kelley, J. M., Fritchman, J. L., Weidman, J. F., Small, K. V., Sandusky, M., Fuhrmann, J., Nguyen, D., Utterback, T. R., Saudek, D.M., Phillips, C. A., Merrick, J. M., Tomb, J.-F., Dougherty, B. A., Bott, K. F., Hu, P.-C, Lucier, T. S., Peterson, S. N., Smith, H. O., Hutchison III, C. A. & Venter, J. C. (1995). The minimal gene complement of Mycoplasma genitalium. Science, 270, 397-403.
21. Frey, J., Chandler, M. & Caro, L. (1979). The effects of an Escherichia coli dnaAts mutation on the replication of the plasmids co1E1 pSC101, R100.1 and RTF-TC. Mol. Gen. Genet. 174, 117-126.
22. Frey, J., Chandler, M. & Caro, L. (1984). Overinitiation of chromosome and plasmid replication in a dnaA-cos mutant of Escherichia coli K12. Evidence for dnaA-dnaB interactions. J. Mol. Biol. 179, 171-183.
23. Fujita, M. Q., Yoshikawa, H. & Ogasawara, N. (1989). Structure of the dnaA region of Pseudomonas putida: conservation among three bacteria, Bacillus subtilis, Escherichia coli and P. putida. Mol. Gen. Genet. 215, 381-387.
24. Fujita, M. Q., Yoshikawa, H. & Ogasawara, N. (1990). Structure of the dnaA region of Micrococcus luteus: conservation and variations among eubacteria. Gene, 93, 73-78.
25. Fujita, M. Q., Yoshikawa, H. & Ogasawara, N. (1992). Structure of the dnaA and DnaA-box region in the Mycoplasma capricolum chromosome: conservation and variations in the course of evolution. Gene, 110, 17-23.
26. Fuller, R. S. & Kornberg, A. (1983). Purified dnaA protein in initiation of replication at the Escherichia coli chromosomal origin of replication. Proc. Natl Acad. Sci. U S A, 80, 5817-5821.
27. Fuller, R. S., Funnell, B. E. & Kornberg, A. (1984). The dnaA protein complex with the E. coli chromosomal replication origin (oriC) and other DNA sites. Cell, 38, 889-900.
28. Garner, J. & Crooke, E. (1996). Membrane regulation of the chromosomal replication activity of E. coli DnaA requires a discrete site on the protein. EMBO J, 15, 2313-2321.
29. Gines-Candelaria, E., Blinkova, A. & Walker, J. R. (1995). Mutations in Escherichia coli dnaA which suppress a dnaX(Ts) polymerization mutation and are dominant when located in the chromosomal allele and recessive on plasmids. J. Bacteriol. 177, 705-715.
30. Hansen, E. B. & Yarmolinsky, M. B. (1986). Host participation in plasmid maintainance: dependence upon dnaA of replicons derived from P1 and F. Proc. Natl Acad. Sci. USA, 83, 4423-4427.
31. Hansen, E. B., Hansen, F. G. & von Meyenburg, K. (1982). The nucleotide sequence of the dnaA gene and the first part of the dnaN gene of Escherichia coli K-12. Nucl. Acids Res. 10, 7373-7385.
32. Hansen, E. B., Atlung, T., Hansen, F. G., Skovgaard, O. & von Meyenburg, K. (1984). Fine structure genetic map and complementation analysis of mutations in the dnaA gene of Escherichia coli. Mol. Gen. Genet. 196, 387-396.
33. Hansen, F. G., Koefoed, S. & Atlung, T. (1992). Cloning and nucleotide sequence determination of twelve mutant dnaA genes of Escherichia coli. Mol. Gen. Genet. 234, 14-21.
34. Hasunuma, K. & Sekiguchi, M. (1977). Replication of plasmid pSC101 in Escherichia coli K12: requirement for dnaA function. Mol. Gen. Genet. 154, 225-230.
35. Hubert, H., Himmelreich, R., Plagens, H. & Herrmann, R. (1996). Sequence analysis of 56 kb from the genome of the bacterium Mycoplasma pneumoniae comprising the dnaA region, the atp operon and a cluster of ribosomal protein genes. Nucl. Acids Res. 24, 628-639.
36. Hirota, Y., Ryter, A. & Jacob, F. (1968). Thermosensitive mutants of E. coli affected in the processes of DNA synthesis and cellular division. Cold Spring Harbor Symp. Quant. Biol. 33, 677-693.
37. Huynh, T. V., Young, R. A. & Davis, R. W. (1985). DNA Cloning: A Practical Approach. (Glover, D, ed.), pp. 49-78, IRL Press, Oxford.
38. Jurnak, F. (1985). Structure of the GDP domain of EF-Tu and location of the amino acids homologous to ras oncogene proteins. Science, 230, 32-36.
39. Katayama, T. & Kornberg, A. (1994). Hyperactive initiation of chromosomal replication in vivo and in vitro by a mutant initiator protein, DnaAcos, of Escherichia coli. J. Biol. Chem. 269, 12698-12703.
40. Kellenberger-Gujer, G., Podhajska, A. J. & Caro, L. (1978). A cold sensitive dnaA mutant of E. coli which overinitiates chromosome replication at low temperature. Mol. Gen. Genet. 162, 9-16.
41. Kline, B. C., Kogoma, T., Tam, J. E. & Shields, M. S. (1986). Requirement of the Escherichia coli dnaA gene product for plasmid F maintenance. J. Bacteriol. 168, 440-443.
42. Kohiyama, M., Cousin, D., Ryter, A. & Jacob, F. (1966). Thermosensitive mutants of Escherichia coli K 12. I. Isolation and rapid characterization. Ann. Inst. Pasteur (Paris), 110, 465-486.
43. Konola, J. T., Logan, K. M. & Knight, K. L. (1994). Functional characterization of residues in the P-loop motif of the RecA protein ATP binding site. J. Mol. Biol. 237, 20-34.
44. Lai, C. Y. & Baumann, P. (1992). Genetic analysis of an aphid endosymbiont DNA fragment homologous to the rnpA-rpmH-dnaA-dnaN-gyrB region of eubacteria. Gene, 113, 175-181.
45. Lichens-Park, A., Smith, C. L. & Syvanen, M. (1990). Integration of bacteriophage λ, into the cryptic lambdoid prophages of Escherichia coli. J. Bacteriol. 171, 1574-1584.
46. Lieb, M. (1979). Heat-sensitive lambda repressors retain partial activity during bacteriophage induction. J. Virol. 32, 162-166.
47. Marszalek, J. & Kaguni, J. M. (1994). DnaA protein directs the binding of DnaB protein in initiation of DNA replication in Escherichia coli. J. Biol. Chem. 269, 4883-4890.
48. Marszalek, J., Zhang, W., Hupp, T. R., Margulies, C., Carr, K.M., Cherry, S. & Kaguni, J. M. (1996). Domains of DnaA protein Involved in interaction with DnaB protein, and in unwinding the Escherichia coli chromosomal origin. J. Biol. Chem. 271, 18535-18542.
49. Masai, H. & Arai, K. (1987). RepA and DnaA proteins are required for initiation of R1 plasmid replication in vitro and interact with the oriR sequence. Proc. Natl Acad Sci. USA, 84, 4781-4785.
50. Merlin, S. & Polisky, B. (1993). Analysis of establishment phase replication of the plasmid Co1E1. J. Mol. Biol. 230, 137-150.
51. Messer, W. & Weigel, C. (1996). Initiation of chromosome replication. In Escherichia coli and Salmonella typhimurium. Cellular and Molecular Biology (Neidhardt, F. C., Curtiss III, R., Ingraham, J. L., Lin, E. C. C., Low, B., Magasanik, B., Reznikoff, W. S., Rile, M., Schaechter, M. & Umbarger, H. E., eds), pp. 1579-1601, ASM Press, Washington, D. C..
52. Miller, J. H. (1992). A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria, Cold Spring Harbor Press, Cold Spring Harbor, NY.
53. Molin, S. & Nordstrom, K. (1980). Control of plasmid R1 replication: functions involved in replication, copy number control, incompatibility, and switchoff of replication. J. Bacteriol. 141, 111-120.
54. Myers, R. M., Lerman, L. S. & Maniatis, T. (1985). A general method for saturation mutagenesis of cloned DNA fragments. Science, 229, 242-247.
55. Ogasawara, N., Nakai, S. & Yoshikawa, H. (1994). Systematic sequencing of the 180 kilobase region of the Bacillus subtilis chromosome containing the replication origin. DNA Research, 1, 1-14.
56. Ohmori, H., Kimura, M., Nagata, T. & Sakakibara, Y. (1984). Structural analysis of the dnaA and dnaN genes of Escherichia coli. Gene, 28, 159-170.
57. Old, I. G., Margarita, D. & Saint-Girons, I. (1993). Unique genetic arrangement in the dnaA region of the Borrelia burgdorferi linear chromosome: nucleotide sequence of the dnaA gene. FEMS Microbiol. Letters, 111, 109-114.
58. Ortega, S., Lanka, E. & Diaz, R. (1986). The involvement of host replication proteins and of specific origin sequences in the in vitro replication of miniplasmid R1 DNA. Nucl. Acids Res. 14, 4865-4879.
59. Pai, E. F., Krengel, U., Petsko, G. A., Goody, R. S., Kabsch, W. & Wittinghofer, A. (1990). Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis. EMBO J. 9, 2351-2359.
60. Ptashne, M., Backman, K., Humayun, M. Z., Jeffrey, A., Maurer, R., Meyer, B. & Sauer, R. T. (1976). Autoregulation and function of a repressor in bacteriophage lambda. Science, 194, 156-161.
61. Rajagopalan, M., Qin, M. H., Steingrube, V. A., Nash, D. R., Wallace, R. J. J. & Madiraju, M. V. (1995). Amplification and cloning of the Mycobacterium tuberculosis dnaA gene. Gene, 163, 75-79.
62. Richter, S. & Messer, W. (1995). Genetic structure of the dnaA region of the cyanobacterium Synechocystis sp. strain PCC6803. J. Bacteriol. 177, 4245-4251.
63. Roth, A. & Messer, W. (1995). The DNA binding domain of the initiator protein DnaA. EMBO J. 14, 2106-2111.
64. Salazar, L., Fsihi, H., de Rossi, E., Riccardi, G., Rios, C., Cole, S. T. & Takiff, H. E. (1996). Organization of the origins of replication of the chromosomes of Mycobacterium smegmatis, Mycobacterium leprae and Mycobacterium tuberculosis and isolation of a functional origin for M. smegmatis. Mol. Microbiol. 20, 283-293.
65. Sanger, F., Nicklen, S. & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA, 74, 5463-5467.
66. Sekimizu, K., Bramhill, D. & Kornberg, A. (1987). ATP activates dnaA protein in initiating replication of plasmids bearing the origin of the E. coli chromosome. Cell, 50, 259-265.
67. Skovgaard, O. (1990). Nucleotide sequence of a Proteus mirabilis DNA fragment homologous to the 60K-rnpA-rpmH-dnaA-dnaN-recF-gyrB region of Escherichia coli. Gene, 93, 27-34.
68. Skovgaard, O. & Hansen, F. G. (1987). Comparison of dnaA nucleotide sequences of Escherichia coli, Salmonella typhimurium, and Serratia marcescens. J. Bacteriol. 169, 3976-3981.
69. Sutton, M. D. & Kaguni, J. M. (1995). Novel alleles of the Escherichia coli dnaA gene are defective in replication of pSC101 but not of oriC. J. Bacteriol. 177, 6657-6665.
70. Sutton, M. D. & Kaguni, J. M. Threonine 435 of E. coli DnaA protein confers sequence-specific DNA binding activity. J. Biol. Chem. (In press).
71. Tresguerres, E. F., Nandadasa, H. G. & Pritchard, R. H. (1975). Suppression of initiation-negative strains of Escherichia coli by integration of the sex factor F. J. Bacteriol. 121, 554-561.
72. Tucker, W. T., Miller, C. A. & Cohen, S. N. (1984). Structural and functional analysis of the par region of the pSC101 plasmid. Cell, 38, 191-201.
73. Wegrzyn, G., Wegrzyn, A., Konieczny, I., Bielawski, K., Konopa, G., Obuchowski, M., Helinski, D. & Taylor, K. (1995). Involvement of the host initiator function dnaA in the replication of coliphage λ. Genetics, 139, 1464-1481.
74. Ye, F., Renaudin, J., Bove, J. M. & Laigret, F. (1994). Cloning and sequencing of the replication origin (oriC) of the Spiroplasma citri chromosome and construction of autonomously replicating artificial plasmids. Curr. Microbiol. 29, 23-29.
75. Yoshikawa, M. (1974). Identification and mapping of the replication genes of an R factor, R100-1, integrated into the chromosome of Escherichia coli K-12. J. Bacteriol. 118, 1123-1131.
76. Zweiger, G. & Shapiro, L. (1994). Expression of Caulobacter dnaA as a function of the cell cycle. J. Bacteriol. 176, 401-408.