AT-rich region and repeated sequences - the essential elements of replication origins of bacterial replicons

FEMS Microbiology Reviews

Volumn 36, Issue 2, 2012, Pages 408-434

  Rajewska, Magdalena ^a   Wegrzyn, Katarzyna ^a   Konieczny, Igor ^a  

^a UNIVERSITY OF GDA SK   (Poland)

Author keywords

13 mers; DnaA; DUE; Rep; Replication origin

Indexed keywords

ADENINE; BACTERIAL DNA; BACTERIOPHAGE DNA; HELICASE; NUCLEOTIDE; PLASMID DNA; REPLICATION INITIATOR PROTEIN DNAA; THYMINE;

AMINO ACID SEQUENCE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; CHROMOSOME ANALYSIS; CHROMOSOME SIZE; COMPLEX FORMATION; DNA METHYLATION; DNA REPLICATION ORIGIN; DNA SEQUENCE; GENOMIC INSTABILITY; NONHUMAN; PROTEIN DNA BINDING; PROTEIN MOTIF; REPEATED SEQUENCE; REPLICON; REVIEW; SEQUENCE ANALYSIS;

BACTERIA; BASE SEQUENCE; MOLECULAR SEQUENCE DATA; REPETITIVE SEQUENCES, NUCLEIC ACID; REPLICATION ORIGIN; REPLICON;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA;

EID: 84856726126     PISSN: 01686445     EISSN: 15746976     Source Type: Journal    
DOI: 10.1111/j.1574-6976.2011.00300.x     Document Type: Review

References (258)

1. Abdurashidova G, Deganuto M, Klima R, Riva S, Biamonti G, Giacca M & Falaschi A (2000) Start sites of bidirectional DNA synthesis at the human lamin B2 origin. Science 287: 2023-2026.
2. Abeles AL (1986) P1 plasmid replication. Purification and DNA-binding activity of the replication protein RepA. J Biol Chem 261: 3548-3555.
3. Abeles AL, Snyder KM & Chattoraj DK (1984) P1 plasmid replication: replicon structure. J Mol Biol 173: 307-324.
4. Abeles AL, Reaves LD & Austin SJ (1990) A single DnaA box is sufficient for initiation from the P1 plasmid origin. J Bacteriol 172: 4386-4391.
5. Abeles A, Brendler T & Austin S (1993) Evidence of two levels of control of P1 oriR and host oriC replication origins by DNA adenine methylation. J Bacteriol 175: 7801-7807.
6. Abhyankar MM, Zzaman S & Bastia D (2003) Reconstitution of R6K DNA replication in vitro using 22 purified proteins. J Biol Chem 278: 45476-45484.
7. Asai T, Takanami M & Imai M (1990) The AT richness and gid transcription determine the left border of the replication origin of the E. coli chromosome. EMBO J 9: 4065-4072.
8. Bell SP & Dutta A (2002) DNA replication in eukaryotic cells. Annu Rev Biochem 71: 333-374.
9. Bernander R, Dasgupta S & Nordstrom K (1991) The E. coli cell cycle and the plasmid R1 replication cycle in the absence of the DnaA protein. Cell 64: 1145-1153.
10. Bernander R, Krabbe M & Nordstrom K (1992) Mapping of the in vivo start site for leading strand DNA synthesis in plasmid R1. EMBO J 11: 4481-4487.
11. Berquist BR & DasSarma S (2003) An archaeal chromosomal autonomously replicating sequence element from an extreme halophile, Halobacterium sp. strain NRC-1. J Bacteriol 185: 5959-5966.
12. Bielinsky AK & Gerbi SA (1998) Discrete start sites for DNA synthesis in the yeast ARS1 origin. Science 279: 95-98.
13. Bielinsky AK & Gerbi SA (1999) Chromosomal ARS1 has a single leading strand start site. Mol Cell 3: 477-486.
14. Bielinsky AK & Gerbi SA (2001) Where it all starts: eukaryotic origins of DNA replication. J Cell Sci 114: 643-651.
15. Blaesing F, Weigel C, Welzeck M & Messer W (2000) Analysis of the DNA-binding domain of Escherichia coli DnaA protein. Mol Microbiol 36: 557-569.
16. Bowers LM, Kruger R & Filutowicz M (2007) Mechanism of origin activation by monomers of R6K-encoded pi protein. J Mol Biol 368: 928-938.
17. Bramhill D & Kornberg A (1988a) A model for initiation at origins of DNA replication. Cell 54: 915-918.
18. Bramhill D & Kornberg A (1988b) Duplex opening by DnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell 52: 743-755.
19. Breier AM, Chatterji S & Cozzarelli NR (2004) Prediction of Saccharomyces cerevisiae replication origins. Genome Biol 5: R22.
20. Brendler T, Abeles A & Austin S (1991a) Critical sequences in the core of the P1 plasmid replication origin. J Bacteriol 173: 3935-3942.
21. Brendler TG, Abeles AL, Reaves LD & Austin SJ (1991b) Unique sequence requirements for the P1 plasmid replication origin. Res Microbiol 142: 209-216.
22. Brendler T, Abeles A & Austin S (1995) A protein that binds to the P1 origin core and the oriC 13mer region in a methylation-specific fashion is the product of the host seqA gene. EMBO J 14: 4083-4089.
23. Camara JE, Breier AM, Brendler T, Austin S, Cozzarelli NR & Crooke E (2005) Hda inactivation of DnaA is the predominant mechanism preventing hyperinitiation of Escherichia coli DNA replication. EMBO Rep 6: 736-741.
24. Carr KM & Kaguni JM (2001) Stoichiometry of DnaA and DnaB protein in initiation at the Escherichia coli chromosomal origin. J Biol Chem 276: 44919-44925.
25. Caspi R, Pacek M, Consiglieri G, Helinski DR, Toukdarian AE & Konieczny I (2001) A broad host range replicon with different requirements for replication initiation in three bacterial species. EMBO J 20: 3262-3271.
26. Chattoraj DK, Snyder KM & Abeles AL (1985) P1 plasmid replication: multiple functions of RepA protein at the origin. P Natl Acad Sci USA 82: 2588-2592.
27. Chew DS, Leung MY & Choi KP (2007) AT excursion: a new approach to predict replication origins in viral genomes by locating AT-rich regions. BMC Bioinformatics 8: 163.
28. Chiang CS, Xu YC & Bremer H (1991) Role of DnaA protein during replication of plasmid pBR322 in Escherichia coli. Mol Gen Genet 225: 435-442.
29. Churchward G, Linder P & Caro L (1983) The nucleotide sequence of replication and maintenance functions encoded by plasmid pSC101. Nucleic Acids Res 11: 5645-5659.
30. Coker JA, DasSarma P, Capes M et al. (2009) Multiple replication origins of Halobacterium sp. strain NRC-1: properties of the conserved orc7-dependent oriC1. J Bacteriol 191: 5253-5261.
31. Crosa JH, Luttropp LK & Falkow S (1978) Molecular cloning of replication and incompatibility regions from the R-plasmid R6K. J Mol Biol 124: 443-468.
32. Danbara H, Timmis JK, Lurz R & Timmis KN (1980) Plasmid replication functions: two distinct segments of plasmid R1, RepA and RepD, express incompatibility and are capable of autonomous replication. J Bacteriol 144: 1126-1138.
33. Datta HJ, Khatri GS & Bastia D (1999) Mechanism of recruitment of DnaB helicase to the replication origin of the plasmid pSC101. P Natl Acad Sci USA 96: 73-78.
34. Davey MJ, Fang L, McInerney P, Georgescu RE & O'Donnell M (2002) The DnaC helicase loader is a dual ATP/ADP switch protein. EMBO J 17: 3148-3159.
35. del Solar G, Giraldo R, Ruiz-Echevarria MJ, Espinosa M & Diaz-Orejas R (1998) Replication and control of circular bacterial plasmids. Microbiol Mol Biol Rev 62: 434-464.
36. Dellis S & Filutowicz M (1991) Integration host factor of Escherichia coli reverses the inhibition of R6K plasmid replication by pi initiator protein. J Bacteriol 173: 1279-1286.
37. Dellis S, Feng J & Filutowicz M (1996) Replication of plasmid R6K gamma origin in vivo and in vitro: dependence on IHF binding to the ihf1 site. J Mol Biol 257: 550-560.
38. DePamphilis ML (1999) Replication origins in metazoan chromosomes: fact or fiction? Bioessays 21: 5-16.
39. Diaz R & Staudenbauer WL (1982) Origin and direction of mini-R1 plasmid DNA replication in cell extracts of Escherichia coli. J Bacteriol 150: 1077-1084.
40. Diaz-Lopez T, Lages-Gonzalo M, Serrano-Lopez A, Alfonso C, Rivas G, Diaz-Orejas R & Giraldo R (2003) Structural changes in RepA, a plasmid replication initiator, upon binding to origin DNA. J Biol Chem 278: 18606-18616.
41. Dijkwel PA & Hamlin JL (1995) The Chinese hamster dihydrofolate reductase origin consists of multiple potential nascent-strand start sites. Mol Cell Biol 15: 3023-3031.
42. Dodson M, McMacken R & Echols H (1989) Specialized nucleoprotein structures at the origin of replication of bacteriophage lambda. Protein association and disassociation reactions responsible for localized initiation of replication. J Biol Chem 264: 10719-10725.
43. Doran KS, Konieczny I & Helinski DR (1998) Replication origin of the broad host range plasmid RK2. Positioning of various motifs is critical for initiation of replication. J Biol Chem 273: 8447-8453.
44. Doran KS, Helinski DR & Konieczny I (1999a) A critical DnaA box directs the cooperative binding of the Escherichia coli DnaA protein to the plasmid RK2 replication origin. J Biol Chem 274: 17918-17923.
45. Doran KS, Helinski DR & Konieczny I (1999b) Host-dependent requirement for specific DnaA boxes for plasmid RK2 replication. Mol Microbiol 33: 490-498.
46. Duderstadt KE, Mott ML, Crisona NJ, Chuang K, Yang H & Berger JM (2010) Origin remodeling and opening in bacteria rely on distinct assembly states of the DnaA initiator. J Biol Chem 285: 28229-28239.
47. Egan ES & Waldor MK (2003) Distinct replication requirements for the two Vibrio cholerae chromosomes. Cell 114: 521-530.
48. Eichenlaub R, Figurski D & Helinski DR (1977) Bidirection replication from a unique origin in a mini-F plasmid. P Natl Acad Sci USA 74: 1138-1141.
49. Erzberger JP, Pirruccello MM & Berger JM (2002) The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation. EMBO J 21: 4763-4773.
50. Fang L, Davey MJ & O'Donnell M (1999) Replisome assembly at oriC, the replication origin of E. coli, reveals an explanation for initiation sites outside an origin. Mol Cell 4: 541-553.
51. Fekete RA, Venkova-Canova T, Park K & Chattoraj DK (2006) IHF-dependent activation of P1 plasmid origin by dnaA. Mol Microbiol 62: 1739-1751.
52. Filutowicz M & Appelt K (1988) The integration host factor of Escherichia coli binds to multiple sites at plasmid R6K gamma origin and is essential for replication. Nucleic Acids Res 16: 3829-3843.
53. Frank AC & Lobry JR (2000) Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes. Bioinformatics 16: 560-561.
54. Freeman JM, Plasterer TN, Smith TF & Mohr SC (1998) Patterns of genome organization in bacteria. Science 279: 1827.
55. Fukuoka T, Moriya S, Yoshikawa H & Ogasawara N (1990) Purification and characterization of an initiation protein for chromosomal replication, DnaA, in Bacillus subtilis. J Biochem 107: 732-739.
56. Fuller RS, Funnell BE & Kornberg A (1984) The dnaA protein complex with the E. coli chromosomal replication origin (oriC) and other DNA sites. Cell 38: 889-900.
57. Gajiwala KS & Burley SK (2000) Winged helix proteins. Curr Opin Struct Biol 10: 110-116.
58. Gao F & Zhang CT (2007) DoriC: a database of oriC regions in bacterial genomes. Bioinformatics 23: 1866-1867.
59. Gao F & Zhang CT (2008) Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes. BMC Bioinformatics 9: 79.
60. Gaylo PJ, Turjman N & Bastia D (1987) DnaA protein is required for replication of the minimal replicon of the broad-host-range plasmid RK2 in Escherichia coli. J Bacteriol 169: 4703-4709.
61. Geier GE & Modrich P (1979) Recognition sequence of the dam methylase of Escherichia coli K12 and mode of cleavage of Dpn I endonuclease. J Biol Chem 254: 1408-1413.
62. Gerbi SA & Bielinsky AK (1997) Replication initiation point mapping. Methods 13: 271-280.
63. Gille H & Messer W (1991) Localized DNA melting and structural pertubations in the origin of replication, oriC, of Escherichia coli in vitro and in vivo. EMBO J 10: 1579-1584.
64. Gille H, Egan JB, Roth A & Messer W (1991) The FIS protein binds and bends the origin of chromosomal DNA replication, oriC, of Escherichia coli. Nucleic Acids Res 19: 4167-4172.
65. Giraldo R (2003) Common domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya: combined structural, functional and phylogenetic perspectives. FEMS Microbiol Rev 26: 533-554.
66. Giraldo R & Diaz R (1992) Differential binding of wild-type and a mutant RepA protein to oriR sequence suggests a model for the initiation of plasmid R1 replication. J Mol Biol 228: 787-802.
67. Giraldo R & Fernandez-Tresguerres ME (2004) Twenty years of the pPS10 replicon: insights on the molecular mechanism for the activation of DNA replication in iteron-containing bacterial plasmids. Plasmid 52: 69-83.
68. Gomez M & Antequera F (1999) Organization of DNA replication origins in the fission yeast genome. EMBO J 18: 5683-5690.
69. Gonzalez-Soltero R, Botello E & Jimenez-Sanchez A (2006) Initiation of heat-induced replication requires DnaA and the L-13-mer of oriC. J Bacteriol 188: 8294-8298.
70. Graumann P & Marahiel MA (1994) The major cold shock protein of Bacillus subtilis CspB binds with high affinity to the ATTGG- and CCAAT sequences in single stranded oligonucleotides. FEBS Lett 338: 157-160.
71. Graumann P, Wendrich TM, Weber MH, Schroder K & Marahiel MA (1997) A family of cold shock proteins in Bacillus subtilis is essential for cellular growth and for efficient protein synthesis at optimal and low temperatures. Mol Microbiol 25: 741-756.
72. Grigoriev A (1998) Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res 26: 2286-2290.
73. Grimwade JE, Torgue JJ, McGarry KC, Rozgaja T, Enloe ST & Leonard AC (2007) Mutational analysis reveals Escherichia coli oriC interacts with both DnaA-ATP and DnaA-ADP during pre-RC assembly. Mol Microbiol 66: 428-439.
74. Guarne A, Zhao Q, Ghirlando R & Yang W (2002) Insights into negative modulation of E. coli replication initiation from the structure of SeqA-hemimethylated DNA complex. Nat Struct Biol 9: 839-843.
75. Guarne A, Brendler T, Zhao Q, Ghirlando R, Austin S & Yang W (2005) Crystal structure of a SeqA-N filament: implications for DNA replication and chromosome organization. EMBO J 24: 1502-1511.
76. Hamlin JL & Dijkwel PA (1995) On the nature of replication origins in higher eukaryotes. Curr Opin Genet Dev 5: 153-161.
77. Han JS, Kang S, Lee H, Kim HK & Hwang DS (2003) Sequential binding of SeqA to paired hemi-methylated GATC sequences mediates formation of higher order complexes. J Biol Chem 278: 34983-34989.
78. Hansen EB & Yarmolinsky MB (1986) Host participation in plasmid maintenance: dependence upon dnaA of replicons derived from P1 and F. P Natl Acad Sci USA 83: 4423-4427.
79. Hansen FG, Christensen BB, Nielsen CB & Atlung T (2006) Insights into the quality of DnaA boxes and their cooperativity. J Mol Biol 355: 85-95.
80. Herrick J, Kern R, Guha S, Landoulsi A, Fayet O, Malki A & Kohiyama M (1994) Parental strand recognition of the DNA replication origin by the outer membrane in Escherichia coli. EMBO J 13: 4695-4703.
81. Hsu J, Bramhill D & Thompson CM (1994) Open complex formation by DnaA initiator protein at the Escherichia coli chromosomal origin requires the 13-mer precisely spaced relative to the 9-mers. Mol Microbiol 11: 903-911.
82. Hwang DS & Kornberg A (1990) A novel protein binds a key origin sequence to block replication of an E. coli minichromosome. Cell 63: 325-331.
83. Hwang DS & Kornberg A (1992a) Opening of the replication origin of Escherichia coli by DnaA protein with protein HU or IHF. J Biol Chem 267: 23083-23086.
84. Hwang DS & Kornberg A (1992b) Opposed actions of regulatory proteins, DnaA and IciA, in opening the replication origin of Escherichia coli. J Biol Chem 267: 23087-23091.
85. Inselburg J (1974) Replication of colicin E1 plasmid DNA in minicells from a unique replication initiation site. P Natl Acad Sci USA 71: 2256-2259.
86. Ishiai M, Wada C, Kawasaki Y & Yura T (1994) Replication initiator protein RepE of mini-F plasmid: functional differentiation between monomers (initiator) and dimers (autogenous repressor). P Natl Acad Sci USA 91: 3839-3843.
87. Ishida T, Akimitsu N, Kashioka T et al. (2004) DiaA, a novel DnaA-binding protein, ensures the timely initiation of Escherichia coli chromosome replication. J Biol Chem 279: 45546-45555.
88. Jacob F & Brenner S (1963) [On the regulation of DNA synthesis in bacteria: the hypothesis of the replicon]. CR Hebd Seances Acad Sci 256: 298-300.
89. Jakimowicz D, Majka J & Messer W et al. (1998) Structural elements of the Streptomyces oriC region and their interactions with the DnaA protein. Microbiology 144 (Pt 5): 1281-1290.
90. Jezewska MJ, Kim US & Bujalowski W (1996) Binding of Escherichia coli primary replicative helicase DnaB protein to single-stranded DNA. Long-range allosteric conformational changes within the protein hexamer. Biochemistry 35: 2129-2145.
91. Jiang W, Hou Y & Inouye M (1997) CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone. J Biol Chem 272: 196-202.
92. Jiang Y, Pacek M, Helinski DR, Konieczny I & Toukdarian A (2003) A multifunctional plasmid-encoded replication initiation protein both recruits and positions an active helicase at the replication origin. P Natl Acad Sci USA 100: 8692-8697.
93. Kang S, Lee H, Han JS & Hwang DS (1999) Interaction of SeqA and Dam methylase on the hemimethylated origin of Escherichia coli chromosomal DNA replication. J Biol Chem 274: 11463-11468.
94. Kang S, Han JS, Kim KP, Yang HY, Lee KY, Hong CB & Hwang DS (2005) Dimeric configuration of SeqA protein bound to a pair of hemi-methylated GATC sequences. Nucleic Acids Res 33: 1524-1531.
95. Kano Y, Ogawa T, Ogura T, Hiraga S, Okazaki T & Imamoto F (1991) Participation of the histone-like protein HU and of IHF in minichromosomal maintenance in Escherichia coli. Gene 103: 25-30.
96. Katayama T, Kubota T, Kurokawa K, Crooke E & Sekimizu K (1998) The initiator function of DnaA protein is negatively regulated by the sliding clamp of the E. coli chromosomal replicase. Cell 94: 61-71.
97. Katayama T, Ozaki S, Keyamura K & Fujimitsu K (2010) Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC. Nat Rev Microbiol 8: 163-170.
98. Kawasaki Y, Matsunaga F, Kano Y, Yura T & Wada C (1996) The localized melting of mini-F origin by the combined action of the mini-F initiator protein (RepE) and HU and DnaA of Escherichia coli. Mol Gen Genet 253: 42-49.
99. Kelley WL & Bastia D (1992) Activation in vivo of the minimal replication origin beta of plasmid R6K requires a small target sequence essential for DNA looping. New Biol 4: 569-580.
100. Kelley WL, Patel I & Bastia D (1992) Structural and functional analysis of a replication enhancer: separation of the enhancer activity from origin function by mutational dissection of the replication origin gamma of plasmid R6K. P Natl Acad Sci USA 89: 5078-5082.
101. Kelman Z & O'Donnell M (1995) DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine. Annu Rev Biochem 64: 171-200.
102. Kelman Z, Yuzhakov A, Andjelkovic J & O'Donnell M (1998) Devoted to the lagging strand-the subunit of DNA polymerase III holoenzyme contacts SSB to promote processive elongation and sliding clamp assembly. EMBO J 17: 2436-2449.
103. Keyamura K, Abe Y, Higashi M, Ueda T & Katayama T (2009) DiaA dynamics are coupled with changes in initial origin complexes leading to helicase loading. J Biol Chem 284: 25038-25050.
104. Kim MS, Bae SH, Yun SH et al. (2005) Cnu, a novel oriC-binding protein of Escherichia coli. J Bacteriol 187: 6998-7008.
105. Kline BC, Kogoma T, Tam JE & Shields MS (1986) Requirement of the Escherichia coli dnaA gene product for plasmid F maintenance. J Bacteriol 168: 440-443.
106. Koch B, Ma X & Lobner-Olesen A (2010) Replication of Vibrio cholerae chromosome I in Escherichia coli: dependence on dam methylation. J Bacteriol 192: 3903-3914.
107. Kolter R & Helinski DR (1978) Construction of plasmid R6K derivatives in vitro: characterization of the R6K replication region. Plasmid 1: 571-580.
108. Kolter R & Helinski DR (1982) Plasmid R6K DNA replication. II. Direct nucleotide sequence repeats are required for an active gamma-origin. J Mol Biol 161: 45-56.
109. Komori H, Matsunaga F, Higuchi Y, Ishiai M, Wada C & Miki K (1999) Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 A resolution. EMBO J 18: 4597-4607.
110. Konieczny I (2003) Strategies for helicase recruitment and loading in bacteria. EMBO Rep 4: 37-41.
111. Konieczny I & Helinski DR (1997) Helicase delivery and activation by DnaA and TrfA proteins during the initiation of replication of the broad host range plasmid RK2. J Biol Chem 272: 33312-33318.
112. Konieczny I, Doran KS, Helinski DR & Blasina A (1997) Role of TrfA and DnaA proteins in origin opening during initiation of DNA replication of the broad host range plasmid RK2. J Biol Chem 272: 20173-20178.
113. Kornberg A & Baker T (1992) DNA Replication. W.H. Freeman & Co., New York.
114. Kowalczyk L, Rajewska M & Konieczny I (2005) Positioning and the specific sequence of each 13-mer motif are critical for activity of the plasmid RK2 replication origin. Mol Microbiol 57: 1439-1449.
115. Kowalski D & Eddy MJ (1989) The DNA unwinding element: a novel, cis-acting component that facilitates opening of the Escherichia coli replication origin. EMBO J 8: 4335-4344.
116. Krause M, Ruckert B, Lurz R & Messer W (1997) Complexes at the replication origin of Bacillus subtilis with homologous and heterologous DnaA protein. J Mol Biol 274: 365-380.
117. Kruger R & Filutowicz M (2000) Dimers of pi protein bind the A+T-rich region of the R6K gamma origin near the leading-strand synthesis start sites: regulatory implications. J Bacteriol 182: 2461-2467.
118. Kruger R & Filutowicz M (2003) pi protein- and ATP-dependent transitions from 'closed' to 'open' complexes at the gamma ori of plasmid R6K. Nucleic Acids Res 31: 5993-6003.
119. Kruger R, Konieczny I & Filutowicz M (2001) Monomer/dimer ratios of replication protein modulate the DNA strand-opening in a replication origin. J Mol Biol 306: 945-955.
120. Kunnimalaiyaan S, Kruger R, Ross W, Rakowski SA & Filutowicz M (2004) Binding modes of the initiator and inhibitor forms of the replication protein pi to the gamma ori iteron of plasmid R6K. J Biol Chem 279: 41058-41066.
121. Kurz M, Dalrymple B, Wijffels G & Kongsuwan K (2004) Interaction of the sliding clamp beta-subunit and Hda, a DnaA-related protein. J Bacteriol 186: 3508-3515.
122. Kuzminov A, Schabtach E & Stahl FW (1997) Study of plasmid replication in Escherichia coli with a combination of 2D gel electrophoresis and electron microscopy. J Mol Biol 268: 1-7.
123. Lanka E & Schuster H (1983) The dnaC protein of Escherichia coli. Purification, physical properties and interaction with dnaB protein. Nucleic Acids Res 11: 987-997.
124. Learn BA, Um S-J, Li H & McMacken R (1997) Cryptic single-stranded-DNA binding activities of the phage lambda P and Escherichia coli DnaC replication initiation proteins facilitate the transfer of E. coli DnaB helicase onto DNA. P Natl Acad Sci USA 94: 1154-1159.
125. LeBowitz JH & McMacken R (1986) The Escherichia coli dnaB replication protein is a DNA helicase. J Biol Chem 261: 4738-4748.
126. Lee H, Kang S, Bae SH, Choi BS & Hwang DS (2001a) SeqA protein aggregation is necessary for SeqA function. J Biol Chem 276: 34600-34606.
127. Lee YS, Han JS, Jeon Y & Hwang DS (2001b) The arc two-component signal transduction system inhibits in vitro Escherichia coli chromosomal initiation. J Biol Chem 276: 9917-9923.
128. Leonard AC & Grimwade JE (2005) Building a bacterial orisome: emergence of new regulatory features for replication origin unwinding. Mol Microbiol 55: 978-985.
129. Levchenko I & Filutowicz M (1996) Initiator protein pi can bind independently to two domains of the gamma origin core of plasmid R6K: the direct repeats and the A+T-rich segment. Nucleic Acids Res 24: 1936-1942.
130. Lobry JR (1996a) Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 13: 660-665.
131. Lobry JR (1996b) A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria. Biochimie 78: 323-326.
132. Lopez P, Philippe H, Myllykallio H & Forterre P (1999) Identification of putative chromosomal origins of replication in Archaea. Mol Microbiol 32: 883-886.
133. Lopez P, Forterre P, le Guyader H & Philippe H (2000) Origin of replication of Thermotoga maritima. Trends Genet 16: 59-60.
134. Lu M, Campbell JL, Boye E & Kleckner N (1994) SeqA: a negative modulator of replication initiation in E. coli. Cell 77: 413-426.
135. Lu Y, Datta HJ & Bastia D (1998) Mechanistic studies of initiator-initiator interaction and replication initiation. EMBO J 17: 5192-5200.
136. Lundgren M, Andersson A, Chen L, Nilsson P & Bernander R (2004) Three replication origins in Sulfolobus species: synchronous initiation of chromosome replication and asynchronous termination. P Natl Acad Sci USA 101: 7046-7051.
137. MacAllister TW, Kelley WL, Miron A, Stenzel TT & Bastia D (1991) Replication of plasmid R6K origin gamma in vitro. Dependence on dual initiator proteins and inhibition by transcription. J Biol Chem 266: 16056-16062.
138. Mackiewicz P, Gierlik A, Kowalczuk M, Dudek MR & Cebrat S (1999a) How does replication-associated mutational pressure influence amino acid composition of proteins? Genome Res 9: 409-416.
139. Mackiewicz P, Gierlik A, Kowalczuk M, Dudek MR & Cebrat S (1999b) Asymmetry of nucleotide composition of prokaryotic chromosomes. J Appl Genet 40: 1-14.
140. Mackiewicz P, Zakrzewska-Czerwinska J, Zawilak A, Dudek MR & Cebrat S (2004) Where does bacterial replication start? Rules for predicting the oriC region. Nucleic Acids Res 32: 3781-3791.
141. Manen D & Caro L (1991) The replication of plasmid pSC101. Mol Microbiol 5: 233-237.
142. Manen D, Upegui-Gonzalez LC & Caro L (1992) Monomers and dimers of the RepA protein in plasmid pSC101 replication: domains in RepA. P Natl Acad Sci USA 89: 8923-8927.
143. Marczynski GT & Shapiro L (1992) Cell-cycle control of a cloned chromosomal origin of replication from Caulobacter crescentus. J Mol Biol 226: 959-977.
144. Margolin W & Long SR (1993) Isolation and characterization of a DNA replication origin from the 1, 700-kilobase-pair symbiotic megaplasmid pSym-b of Rhizobium meliloti. J Bacteriol 175: 6553-6561.
145. Margulies C & Kaguni JM (1996) Ordered and sequential binding of DnaA protein to oriC, the chromosomal origin of Escherichia coli. J Biol Chem 271: 17035-17040.
146. Marszalek J & Kaguni JM (1994) DnaA protein directs the binding of DnaB protein in initiation of DNA replication in Escherichia coli. J Biol Chem 269: 4883-4890.
147. Masson L & Ray DS (1988) Mechanism of autonomous control of the Escherichia coli F plasmid: purification and characterization of the repE gene product. Nucleic Acids Res 16: 413-424.
148. Matsui M, Oka A, Takanami M, Yasuda S & Hirota Y (1985) Sites of dnaA protein-binding in the replication origin of the Escherichia coli K-12 chromosome. J Mol Biol 184: 529-533.
149. Matsunaga F, Kawasaki Y, Ishiai M, Nishikawa K, Yura T & Wada C (1995) DNA-binding domain of the RepE initiator protein of mini-F plasmid: involvement of the carboxyl-terminal region. J Bacteriol 177: 1994-2001.
150. Matsunaga F, Forterre P, Ishino Y & Myllykallio H (2001) In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance proteins with the replication origin. P Natl Acad Sci USA 98: 11152-11157.
151. Maurizi MR & Li CC (2001) AAA proteins: in search of a common molecular basis. International Meeting on Cellular Functions of AAA Proteins. EMBO Rep 2: 980-985.
152. McEachern MJ, Filutowicz M & Helinski DR (1985) Mutations in direct repeat sequences and in a conserved sequence adjacent to the repeats result in a defective replication origin in plasmid R6K. P Natl Acad Sci USA 82: 1480-1484.
153. McGarry KC, Ryan VT, Grimwade JE & Leonard AC (2004) Two discriminatory binding sites in the Escherichia coli replication origin are required for DNA strand opening by initiator DnaA-ATP. P Natl Acad Sci USA 101: 2811-2816.
154. McLean MJ, Wolfe KH & Devine KM (1998) Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J Mol Evol 47: 691-696.
155. Meijer M, Beck E, Hansen FG, Bergmans HE, Messer W, von Meyenburg K & Schaller H (1979) Nucleotide sequence of the origin of replication of the Escherichia coli K-12 chromosome. P Natl Acad Sci USA 76: 580-584.
156. Mendelson I, Gottesman M & Oppenheim AB (1991) HU and integration host factor function as auxiliary proteins in cleavage of phage lambda cohesive ends by terminase. J Bacteriol 173: 1670-1676.
157. Messer W (2002) The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol Rev 26: 355-374.
158. Messer W, Meijer M, Bergmans HE, Hansen FG, von Meyenburg K, Beck E & Schaller H (1979) Origin of replication, oriC, of the Escherichia coli K12 chromosome: nucleotide sequence. Cold Spring Harb Symp Quant Biol 43 (Pt 1): 139-145.
159. Messer W, Blaesing F, Jakimowicz D et al. (2001) Bacterial replication initiator DnaA. Rules for DnaA binding and roles of DnaA in origin unwinding and helicase loading. Biochimie 83: 5-12.
160. Meyer RR & Laine PS (1990) The single-stranded DNA-binding protein of Escherichia coli. Microbiol Rev 54: 342-380.
161. Miller C, Ingmer H, Thomsen LE, Skarstad K & Cohen SN (2003) DpiA binding to the replication origin of Escherichia coli plasmids and chromosomes destabilizes plasmid inheritance and induces the bacterial SOS response. J Bacteriol 185: 6025-6031.
162. Moriya S, Ogasawara N & Yoshikawa H (1985) Structure and function of the region of the replication origin of the Bacillus subtilis chromosome. III. Nucleotide sequence of some 10, 000 base pairs in the origin region. Nucleic Acids Res 13: 2251-2265.
163. Moriya S, Atlung T, Hansen FG, Yoshikawa H & Ogasawara N (1992) Cloning of an autonomously replicating sequence (ars) from the Bacillus subtilis chromosome. Mol Microbiol 6: 309-315.
164. Moriya S, Firshein W, Yoshikawa H & Ogasawara N (1994) Replication of a Bacillus subtilis oriC plasmid in vitro. Mol Microbiol 12: 469-478.
165. Mott ML & Berger JM (2007) DNA replication initiation: mechanisms and regulation in bacteria. Nat Rev Microbiol 5: 343-354.
166. Mott ML, Erzberger JP, Coons MM & Berger JM (2008) Structural synergy and molecular crosstalk between bacterial helicase loaders and replication initiators. Cell 135: 623-634.
167. Mrazek J & Karlin S (1998) Strand compositional asymmetry in bacterial and large viral genomes. P Natl Acad Sci USA 95: 3720-3725.
168. Mukherjee S, Patel I & Bastia D (1985) Conformational changes in a replication origin induced by an initiator protein. Cell 43: 189-197.
169. Mukherjee S, Erickson H & Bastia D (1988) Enhancer-origin interaction in plasmid R6K involves a DNA loop mediated by initiator protein. Cell 52: 375-383.
170. Mukhopadhyay G, Carr KM, Kaguni JM & Chattoraj DK (1993) Open-complex formation by the host initiator, DnaA, at the origin of P1 plasmid replication. EMBO J 12: 4547-4554.
171. Murakami Y, Ohmori H, Yura T & Nagata T (1987) Requirement of the Escherichia coli dnaA gene function for ori-2-dependent mini-F plasmid replication. J Bacteriol 169: 1724-1730.
172. Murakami A, Sugiura S & Yamaguchi K (1997) DNA bending of pSC101 ori induced by Rep, a replication initiator protein and IHF. J Gen Appl Microbiol 43: 189-197.
173. Murotsu T, Matsubara K, Sugisaki H & Takanami M (1981) Nine unique repeating sequences in a region essential for replication and incompatibility of the mini-F plasmid. Gene 15: 257-271.
174. Mushegian AR & Koonin EV (1996) Gene order is not conserved in bacterial evolution. Trends Genet 12: 289-290.
175. Myllykallio H, Lopez P, Lopez-Garcia P et al. (2000) Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon. Science 288: 2212-2215.
176. Neuwald AF, Aravind L, Spouge JL & Koonin EV (1999) AAA+: a class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res 9: 27-43.
177. Nieto C, Giraldo R, Fernandez-Tresguerres E & Diaz R (1992) Genetic and functional analysis of the basic replicon of pPS10, a plasmid specific for Pseudomonas isolated from Pseudomonas syringae patovar savastanoi. J Mol Biol 223: 415-426.
178. Nievera C, Torgue JJ, Grimwade JE & Leonard AC (2006) SeqA blocking of DnaA-oriC interactions ensures staged assembly of the E. coli pre-RC. Mol Cell 24: 581-592.
179. Norais C, Hawkins M, Hartman AL, Eisen JA, Myllykallio H & Allers T (2007) Genetic and physical mapping of DNA replication origins in Haloferax volcanii. PLoS Genet 3: e77.
180. Ogura T & Wilkinson AJ (2001) AAA+ superfamily ATPases: common structure-diverse function. Genes Cells 6: 575-597.
181. Ogura T, Niki H, Kano Y, Imamoto F & Hiraga S (1990) Maintenance of plasmids in HU and IHF mutants of Escherichia coli. Mol Gen Genet 220: 197-203.
182. Ohkubo S & Yamaguchi K (1995) Two enhancer elements for DNA replication of pSC101, par and a palindromic binding sequence of the Rep protein. J Bacteriol 177: 558-565.
183. Oka A, Sugimoto K, Takanami M & Hirota Y (1980) Replication origin of the Escherichia coli K-12 chromosome: the size and structure of the minimum DNA segment carrying the information for autonomous replication. Mol Gen Genet 178: 9-20.
184. Ortega-Jimenez S, Giraldo-Suarez R, Fernandez-Tresguerres ME, Berzal-Herranz A & Diaz-Orejas R (1992) DnaA dependent replication of plasmid R1 occurs in the presence of point mutations that disrupt the dnaA box of oriR. Nucleic Acids Res 20: 2547-2551.
185. Ozaki S, Fujimitsu K, Kurumizaka H & Katayama T (2006) The DnaA homolog of the hyperthermophilic eubacterium Thermotoga maritima forms an open complex with a minimal 149-bp origin region in an ATP-dependent manner. Genes Cells 11: 425-438.
186. Ozaki S, Kawakami H, Nakamura K et al. (2008) A common mechanism for the ATP-DnaA-dependent formation of open complexes at the replication origin. J Biol Chem 283: 8351-8362.
187. Pacek M, Konopa G & Konieczny I (2001) DnaA box sequences as the site for helicase delivery during plasmid RK2 replication initiation in Escherichia coli. J Biol Chem 276: 23639-23644.
188. Papp PP, Chattoraj DK & Schneider TD (1993) Information analysis of sequences that bind the replication initiator RepA. J Mol Biol 233: 219-230.
189. Papp PP, Mukhopadhyay G & Chattoraj DK (1994) Negative control of plasmid DNA replication by iterons. Correlation with initiator binding affinity. J Biol Chem 269: 23563-23568.
190. Park K & Chattoraj DK (2001) DnaA boxes in the P1 plasmid origin: the effect of their position on the directionality of replication and plasmid copy number. J Mol Biol 310: 69-81.
191. Park K, Mukkopadhyay S & Chattoraj DK (1998) Requirements for and regulation of origin opening of plasmid P1. J Biol Chem 273: 24906-24911.
192. Park K, Han E, Paulsson J & Chattoraj DK (2001) Origin pairing ('handcuffing') as a mode of negative control of P1 plasmid copy number. EMBO J 20: 7323-7332.
193. Pearson CE, Zorbas H, Price GB & Zannis-Hadjopoulos M (1996) Inverted repeats, stem-loops, and cruciforms: significance for initiation of DNA replication. J Cell Biochem 63: 1-22.
194. Pelizon C, Diviacco S, Falaschi A & Giacca M (1996) High-resolution mapping of the origin of DNA replication in the hamster dihydrofolate reductase gene domain by competitive PCR. Mol Cell Biol 16: 5358-5364.
195. Perri S & Helinski DR (1993) DNA sequence requirements for interaction of the RK2 replication initiation protein with plasmid origin repeats. J Biol Chem 268: 3662-3669.
196. Phadtare S & Inouye M (1999) Sequence-selective interactions with RNA by CspB, CspC and CspE, members of the CspA family of Escherichia coli. Mol Microbiol 33: 1004-1014.
197. Picardeau M, Lobry JR & Hinnebusch BJ (1999) Physical mapping of an origin of bidirectional replication at the centre of the Borrelia burgdorferi linear chromosome. Mol Microbiol 32: 437-445.
198. Pierechod M, Nowak A, Saari A, Purta E, Bujnicki JM & Konieczny I (2009) Conformation of a plasmid replication initiator protein affects its proteolysis by ClpXP system. Protein Sci 18: 637-649.
199. Polaczek P, Kwan K & Campbell JL (1998) Unwinding of the Escherichia coli origin of replication (oriC) can occur in the absence of initiation proteins but is stabilized by DnaA and histone-like proteins IHF or HU. Plasmid 39: 77-83.
200. Rajewska M, Kowalczyk L, Konopa G & Konieczny I (2008) Specific mutations within the AT-rich region of a plasmid replication origin affect either origin opening or helicase loading. P Natl Acad Sci USA 105: 11134-11139.
201. Rampakakis E, Gkogkas C, Di Paola D & Zannis-Hadjopoulos M (2010) Replication initiation and DNA topology: the twisted life of the origin. J Cell Biochem 110: 35-43.
202. Riber L, Olsson JA, Jensen RB, Skovgaard O, Dasgupta S, Marinus MG & Lobner-Olesen A (2006) Hda-mediated inactivation of the DnaA protein and dnaA gene autoregulation act in concert to ensure homeostatic maintenance of the Escherichia coli chromosome. Genes Dev 20: 2121-2134.
203. Richter S, Hess WR, Krause M & Messer W (1998) Unique organization of the dnaA region from Prochlorococcus marinus CCMP1375, a marine cyanobacterium. Mol Gen Genet 257: 534-541.
204. Robinson NP, Dionne I, Lundgren M, Marsh VL, Bernander R & Bell SD (2004) Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus. Cell 116: 25-38.
205. Rocha EP, Danchin A & Viari A (1999) Universal replication biases in bacteria. Mol Microbiol 32: 11-16.
206. Romero J & Lee H (2008) One-way PCR-based mapping of a replication initiation point (RIP). Nat Protoc 3: 1729-1735.
207. Roten CA, Gamba P, Barblan JL & Karamata D (2002) Comparative Genometrics (CG): a database dedicated to biometric comparisons of whole genomes. Nucleic Acids Res 30: 142-144.
208. Rowen L & Kornberg A (1978) Primase, the dnaG protein of Escherichia coli. An enzyme which starts DNA chains. J Biol Chem 253: 758-764.
209. Ryan VT, Grimwade JE, Nievera CJ & Leonard AC (2002) IHF and HU stimulate assembly of pre-replication complexes at Escherichia coli oriC by two different mechanisms. Mol Microbiol 46: 113-124.
210. Ryan VT, Grimwade JE, Camara JE, Crooke E & Leonard AC (2004) Escherichia coli prereplication complex assembly is regulated by dynamic interplay among Fis, IHF and DnaA. Mol Microbiol 51: 1347-1359.
211. Saha A, Haralalka S & Bhadra RK (2004) A naturally occurring point mutation in the 13-mer R repeat affects the oriC function of the large chromosome of Vibrio cholerae O1 classical biotype. Arch Microbiol 182: 421-427.
212. Salzberg SL, Salzberg AJ, Kerlavage AR & Tomb JF (1998) Skewed oligomers and origins of replication. Gene 217: 57-67.
213. Schaefer C & Messer W (1991) DnaA protein/DNA interaction. Modulation of the recognition sequence. Mol Gen Genet 226: 34-40.
214. Schaper S & Messer W (1995) Interaction of the initiator protein DnaA of Escherichia coli with its DNA target. J Biol Chem 270: 17622-17626.
215. Schnos M, Zahn K, Inman RB & Blattner FR (1988) Initiation protein induced helix destabilization at the lambda origin: a prepriming step in DNA replication. Cell 52: 385-395.
216. Schvartzman JB, Martinez-Robles ML, Hernandez P & Krimer DB (2010) Plasmid DNA replication and topology as visualized by two-dimensional agarose gel electrophoresis. Plasmid 63: 1-10.
217. Seitz H, Weigel C & Messer W (2000) The interaction domains of the DnaA and DnaB replication proteins of Escherichia coli. Mol Microbiol 37: 1270-1279.
218. Sekimizu K, Bramhill D & Kornberg A (1988) Sequential early stages in the in vitro initiation of replication at the origin of the Escherichia coli chromosome. J Biol Chem 263: 7124-7130.
219. Shaheen SM, Ouimet MC & Marczynski GT (2009) Comparative analysis of Caulobacter chromosome replication origins. Microbiology 155: 1215-1225.
220. Sharma S, Sathyanarayana BK, Bird JG, Hoskins JR, Lee B & Wickner S (2004) Plasmid P1 RepA is homologous to the F plasmid RepE class of initiators. J Biol Chem 279: 6027-6034.
221. Shon M, Germino J & Bastia D (1982) The nucleotide sequence of the replication origin beta of the plasmid R6K. J Biol Chem 257: 13823-13827.
222. Sibley CD, MacLellan SR & Finan T (2006) The Sinorhizobium meliloti chromosomal origin of replication. Microbiology 152: 443-455.
223. Skarstad K, Thony B, Hwang DS & Kornberg A (1993) A novel binding protein of the origin of the Escherichia coli chromosome. J Biol Chem 268: 5365-5370.
224. Slater S, Wold S, Lu M, Boye E, Skarstad K & Kleckner N (1995) E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration. Cell 82: 927-936.
225. Speck C & Messer W (2001) Mechanism of origin unwinding: sequential binding of DnaA to double- and single-stranded DNA. EMBO J 20: 1469-1476.
226. Speck C, Weigel C & Messer W (1999) ATP- and ADP-dnaA protein, a molecular switch in gene regulation. EMBO J 18: 6169-6176.
227. Stalker DM, Kolter R & Helinski DR (1979) Nucleotide sequence of the region of an origin of replication of the antibiotic resistance plasmid R6K. P Natl Acad Sci USA 76: 1150-1154.
228. Stalker DM, Thomas CM & Helinski DR (1981) Nucleotide sequence of the region of the origin of replication of the broad host range plasmid RK2. Mol Gen Genet 181: 8-12.
229. Stalker DM, Kolter R & Helinski DR (1982) Plasmid R6K DNA replication. I. Complete nucleotide sequence of an autonomously replicating segment. J Mol Biol 161: 33-43.
230. Stenzel TT, MacAllister T & Bastia D (1991) Cooperativity at a distance promoted by the combined action of two replication initiator proteins and a DNA bending protein at the replication origin of pSC101. Genes Dev 5: 1453-1463.
231. Stinchcomb DT, Struhl K & Davis RW (1979) Isolation and characterisation of a yeast chromosomal replicator. Nature 282: 39-43.
232. Sugimoto K, Oka A, Sugisaki H, Takanami M, Nishimura A, Yasuda Y & Hirota Y (1979) Nucleotide sequence of Escherichia coli K-12 replication origin. P Natl Acad Sci USA 76: 575-579.
233. Sugiura S, Ohkubo S & Yamaguchi K (1993) Minimal essential origin of plasmid pSC101 replication: requirement of a region downstream of iterons. J Bacteriol 175: 5993-6001.
234. Suhan M, Chen SY, Thompson HA, Hoover TA, Hill A & Williams JC (1994) Cloning and characterization of an autonomous replication sequence from Coxiella burnetii. J Bacteriol 176: 5233-5243.
235. Sutton MD, Carr KM, Vicente M & Kaguni JM (1998) Escherichia coli DnaA protein. The N-terminal domain and loading of DnaB helicase at the E. coli chromosomal origin. J Biol Chem 273: 34255-34262.
236. Taghbalout A, Landoulsi A, Kern R et al. (2000) Competition between the replication initiator DnaA and the sequestration factor SeqA for binding to the hemimethylated chromosomal origin of E. coli in vitro. Genes Cells 5: 873-884.
237. Thony B, Hwang DS, Fradkin L & Kornberg A (1991) iciA, an Escherichia coli gene encoding a specific inhibitor of chromosomal initiation of replication in vitro. P Natl Acad Sci USA 88: 4066-4070.
238. Tillier ER & Collins RA (2000) The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J Mol Evol 50: 249-257.
239. Tomizawa J, Sakakibara Y & Kakefuda T (1974) Replication of colicin E1 plasmid DNA in cell extracts. Origin and direction of replication. P Natl Acad Sci USA 71: 2260-2264.
240. Tomizawa JI, Ohmori H & Bird RE (1977) Origin of replication of colicin E1 plasmid DNA. P Natl Acad Sci USA 74: 1865-1869.
241. Torheim NK & Skarstad K (1999) Escherichia coli SeqA protein affects DNA topology and inhibits open complex formation at oriC. EMBO J 18: 4882-4888.
242. Wei T & Bernander R (1996) Interaction of the IciA protein with AT-rich regions in plasmid replication origins. Nucleic Acids Res 24: 1865-1872.
243. Weigel C & Seitz H (2002) Strand-specific loading of DnaB helicase by DnaA to a substrate mimicking unwound oriC. Mol Microbiol 46: 1149-1156.
244. Weigel C, Schmidt A, Ruckert B, Lurz R & Messer W (1997) DnaA protein binding to individual DnaA boxes in the Escherichia coli replication origin, oriC. EMBO J 16: 6574-6583.
245. Wickner S (1977) DNA or RNA priming of bacteriophage G4 DNA synthesis by Escherichia coli dnaG protein. P Natl Acad Sci USA 74: 2815-2819.
246. Wickner S & Hurwitz J (1975) Interaction of Escherichia coli dnaB and dnaC(D) gene products in vitro. P Natl Acad Sci USA 72: 921-925.
247. Wickner S, Hoskins J, Chattoraj D & McKenney K (1990) Deletion analysis of the mini-P1 plasmid origin of replication and the role of Escherichia coli DnaA protein. J Biol Chem 265: 11622-11627.
248. Woelker B & Messer W (1993) The structure of the initiation complex at the replication origin, oriC, of Escherichia coli. Nucleic Acids Res 21: 5025-5033.
249. Wu F, Goldberg I & Filutowicz M (1992) Roles of a 106-bp origin enhancer and Escherichia coli DnaA protein in replication of plasmid R6K. Nucleic Acids Res 20: 811-817.
250. Wu F, Wu J, Ehley J & Filutowicz M (1996) Preponderance of Fis-binding sites in the R6K gamma origin and the curious effect of the penicillin resistance marker on replication of this origin in the absence of Fis. J Bacteriol 178: 4965-4974.
251. Yamanaka K, Zheng W, Crooke E, Wang YH & Inouye M (2001) CspD, a novel DNA replication inhibitor induced during the stationary phase in Escherichia coli. Mol Microbiol 39: 1572-1584.
252. Yee TW & Smith DW (1990) Pseudomonas chromosomal replication origins: a bacterial class distinct from Escherichia coli-type origins. P Natl Acad Sci USA 87: 1278-1282.
253. Yoshikawa H & Wake RG (1993) 36. Initiation and termination of chromosome replication. Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology, and Molecular Genetics (Sonenshein AL, Hoch JA & Losick R, eds), pp. 507-528. ASM, Washington, DC.
254. You Z, Ishimi Y, Mizuno T, Sugasawa K, Hanaoka F & Masai H (2003) Thymine-rich single-stranded DNA activates Mcm4/6/7 helicase on Y-fork and bubble-like substrates. EMBO J 22: 6148-6160.
255. Zawilak A, Durrant MC, Jakimowicz P, Backert S & Zakrzewska-Czerwinska J (2003) DNA binding specificity of the replication initiator protein, DnaA from Helicobacter pylori. J Mol Biol 334: 933-947.
256. Zhang CT & Zhang R (2002) Evaluation of gene-finding algorithms by a content-balancing accuracy index. J Biomol Struct Dyn 19: 1045-1052.
257. Zhang R & Zhang CT (2005) Identification of replication origins in archaeal genomes based on the Z-curve method. Archaea 1: 335-346.
258. Zzaman S, Abhyankar MM & Bastia D (2004) Reconstitution of F factor DNA replication in vitro with purified proteins. J Biol Chem 279: 17404-17410.