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Chapter 36 : Initiation and Termination of Chromosome Replication

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Abstract:

In this chapter, emphasis is on the processes of initiation and termination of replication of the chromosome. As an introduction to the discussion of these topics, a brief account is given of the work that has afforded a general picture of the topology of the chromosome through the three phases of the replication cycle. This account will be followed by a description of currently identified DNA replication genes in and a summary of what is known about the enzymology of the elongation phase of DNA replication in this organism. Initiation of bacterial chromosome replication was first defined as the step that requires synthesis of new proteins, while elongation proceeds to completion without concomitant synthesis of proteins. In this review, emphasis is also based on the universal mechanism commonly found in other bacterial species, particularly . The effect of a mutation on the two types of membrane-DNA complexes is described. The cycle of chromosome replication commences with initiation. Termination is defined here as the meeting and fusion of the forks to yield two separate and continuous double-stranded segments of DNA spanning the site of fusion. Termination of chromosome replication in also involves arrest of replication forks, which is effected by protein-DNA interactions analogous to those observed in .

Citation: Yoshikawa H, Wake R. 1993. Initiation and Termination of Chromosome Replication, p 507-528. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch36
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Image of Figure 1
Figure 1

Gene replication order map of as the basis for the circular genetic linkage map. (A) Chromosome depicted as a linear structure with replication starting at position 0 (origin) and proceeding sequentially through the markers (genes) indicated towards 1.0 (terminus) ( ). (B) The same genes, with their order of replication (genes 1 through 10) on the Harford-Dedonder circular linkage map ( ).

Citation: Yoshikawa H, Wake R. 1993. Initiation and Termination of Chromosome Replication, p 507-528. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch36
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Image of Figure 2
Figure 2

Autoradiographic visualization of the replicated portion of a reinitiated chromosome and suggestion of bidirectional replication to explain the result obtained. (A) The autoradiograph shows two smaller (reinitiated) loops contained within a larger loop. (B) Scheme for the formation of the structure seen by autoradiography from a circular chromosome containing a single site (filled circle). Arrows indicate directions of movement of replication forks. The broken line represents the parental strand, and the solid line represents the newly synthesized one (taken from reference ).

Citation: Yoshikawa H, Wake R. 1993. Initiation and Termination of Chromosome Replication, p 507-528. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch36
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Figure 3

Conservation and variations of genes and their organization in the replication origin regions of abacterial chromosomes. Locations of ORFs (deduced from nucleotide sequences) are shown for three species. ORFs conserved between two or more species are indicated by various shadings. Open boxes are unique for one species. Sizes of ORFs are roughly to scale. Dotted lines in ORF boxes show the regions not yet sequenced. ORFs whose functions have not been identified by mutations are named either with ORF followed by the number of amino acids or with the molecular weight of the gene product. DnaA box regions are shown on a magnified scale with filled arrows for consensus boxes and open arrows for boxes different from the consensus by one base. The region contains a region (dotted) of approximately 45 kb. Directions of transcription are indicated by solid arrows. Exceptions from the general rule are shown by dotted arrows.

Citation: Yoshikawa H, Wake R. 1993. Initiation and Termination of Chromosome Replication, p 507-528. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch36
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Figure 4

Evolutionary relationships of replication origins. Hypothetical evolutionary relationships between three bacterial origins are shown schematically. The main filled arrow shaded arrows (other conserved genes flanking and open arrow show the organization and orientations of genes in the replication origin region. The numbers and orientations of DnaA boxes (small filled arrows) are arbitrary, showing that there are multiple repeats of DnaA boxes. The DnaA box region linked to is exceptional because there is only one DnaA box. Reprinted from Yoshikawa and Ogasawara ( ) with permission.

Citation: Yoshikawa H, Wake R. 1993. Initiation and Termination of Chromosome Replication, p 507-528. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch36
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Figure 5

Correlation between the cell's capacity for initiation and the amount of DnaA protein analyzed in a mutant cell. Cells of a A1mutant of were grown in brain heart infusion medium for about six generations at 30°C, and then the culture was shifted to 49°C. At various times during incubation at 49°C, aliquots were shifted to 30°C in the presence of chloramphenicol (CP). At times indicated at both 49 and 30°C, ratios of the chromosomal DNAs were determined. In parallel, the relative amounts of DnaA protein per unit volume of the culture incubated for indicated times at 49°C were determined by Western blotting (immunoblotting) using an anti-DnaA antibody. (A) Normalized ratios are plotted against the time of incubation at 49°C (?) and at 30°C following incubation at 49°C for 15 min (?), 30 min (?), and 45 min (x). Bent arrows indicate times of shift-down to 30°C. (B) Data in panel A were replotted together with data for DnaA content of the cell. The ratios at 150 min after temperature shift-down to 30°C are plotted against the incubation period at 49°C before the shift-down (?). The value for 60 min was taken from the data in a separate experiment. Datum points for DnaA content are averages of two experiments (?). Reprinted from Moriya et al. ( ) with permission.

Citation: Yoshikawa H, Wake R. 1993. Initiation and Termination of Chromosome Replication, p 507-528. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch36
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Figure 6

Functional elements in DnaA box regions of the chromosome. Structural elements that show various functions in initiation of chromosomal replication and its regulation are shown schematically. DnaA box regions are to scale, while the gene is reduced. Within the DnaA box regions, DnaA boxes are shown as filled vertical strips for consensus boxes and shaded vertical strips for boxes different from the consensus by one base. AT-rich 16-mers are indicated by triangles, and an AT-rich stretch is indicated by a shaded square. Promoters and directions of transcription are indicated by bent arrows. Regions responsible for activity and required for activity are indicated.

Citation: Yoshikawa H, Wake R. 1993. Initiation and Termination of Chromosome Replication, p 507-528. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch36
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Figure 7

Model for control of the initiation cycle and for expression and function of DnaA protein. (A) DnaA box regions release DnaA protein temporarily after they are replicated. (B) gene expression is derepressed and actively transcribed to produce DnaA protein (?). (C) DnaA protein preferentially binds to the region of the DnaA box region to repress gene expression. (D) DnaA box regions form the initiation complex (initiosome); DnaB protein and binding to the cell membrane may be involved in this stage. Preformed DnaA protein now binds to all regions within at least two DnaA box regions to form the active conformation. (E) Initiation and consequent replication of take place. The relative sizes of the regions and the gene are as shown in Fig. 3 and 6 .

Citation: Yoshikawa H, Wake R. 1993. Initiation and Termination of Chromosome Replication, p 507-528. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch36
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Figure 8

Sequence features of the region of the chromosome. (A) The region located at 174° on the physical map ( ) and slightly offset in relation to the origin comprises the gene for and the upstream IRR, which is made up of IRI plus IRII. The clockwise-fork arrest site is shown as (see also Fig. 9 ). (B) Arrangement of sequences (ORFs) over a more extended chromosomal segment (-3 kb) spanning the region (IRR + ( ). Strain W23 contains an additional ORF (ORF405) that strain 168 does not contain, which is inserted just left of the IRR. The and genes lie ∼1.5 kb to the right of the chromosomal segment sequenced, and the gene lies ∼90 kb to the left of it.

Citation: Yoshikawa H, Wake R. 1993. Initiation and Termination of Chromosome Replication, p 507-528. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch36
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Figure 9

Putative RTP recognition sequences within the functional IRI of the chromosome. The two 8-bp segments (A and B, shaded) proposed as recognition sequences have been identified from the relative positionings of DNase I-protected regions and comparison of sequences within a total of 8 IRs. The heavy arrow defines IRI as originally described ( ). The −10 region of the promoter is located just to the left of A. The region of arrest of the leading strand of the clockwise replication fork is based on the work of Jannière and coworkers ( ).

Citation: Yoshikawa H, Wake R. 1993. Initiation and Termination of Chromosome Replication, p 507-528. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch36
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Image of Figure 10
Figure 10

Model for clockwise-fork arrest and fork fusion within the region (IRR + of the chromosome. See text for explanation of model. ?, ?, binding sites for RTP; □, RTP; P, promoter.

Citation: Yoshikawa H, Wake R. 1993. Initiation and Termination of Chromosome Replication, p 507-528. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch36
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References

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1. Adams, R. T.,, and R. G. Wake. 1980. Highly specific labeling of the Bacillus subtilis chromosome terminus. J. Bacteriol. 143: 1036 1038.
2. Ahn, K. S.,, M. S. Malo,, M. T. Smith,, and R. G. Wake. Submitted for publication.
3. Ahn, K. S.,, and R. G. Wake. 1991. Variations and coding features of the sequence spanning the replication terminus of Bacillus subtilis 168 and W23 chromosomes. Gene 98: 107 112.
3a.. Allen, G. C.,, and A. Romberg. 1991. Fine balance in the regulation of DnaB helicase by DnaC protein in replication in Escherichia coli. J. Biol. Chem. 266: 22096 22101.
4. Alonso, J. C.,, C. A. Stiege,, R. H. Tailor,, and J.-F. Viret. 1988. Functional analysis of the dna(Ts) mutants of Bacillus subtilis. Plasmid pUB110 replication as a model system. Mol. Gen. Genet. 214: 482 489.
5. Andersen, J.,, and A. T. Ganesan. 1975. Temperature-sensitive deoxyribonucleic acid replication in a dnaC mutant of Bacillus subtilis. J. Bacteriol. 121: 173 183.
5a.. Atlung, T. Personal communication.
6. Atlung, T. 1984. Allele-specific suppression of dnaA(ts) mutations in Escherichia coli. Mol. Gen. Genet. 197: 125 128.
7. Atlung, T.,, A. Lobner-Olesen,, and F. G. Hansen. 1987. Overproduction of DnaA protein stimulates initiation of chromosome and minichromosome replication in Escherichia coli. Mol. Gen. Genet. 206: 51 59.
8. Attolini, C.,, G. Mazza,, A. Fortunate,, G. Ciarrocchl,, G. Mastromei,, S. Riva,, and A. Falaschi. 1976. On the identity of dnaP and dnaF genes of Bacillus subtilis. Mol. Gen. Genet. 148: 9 17.
9. Bakker, A.,, and D. W. Smith. 1989. Methylation of GATC sites is required for precise timing between rounds of DNA replication in Escherichia coli. J. Bacteriol. 171: 5738 5742.
10. Barnes, M. H.,, R. A. Hammond,, K. A. Foster,, J. A. Michener,, and N. C. Brown. 1989. The cloned polC gene of Bacillus subtilis: characterization of the azp12 mutation and controlled in vitro synthesis of active DNA polymerase III. Gene 85: 177 186.
11. Benjamin, P.,, and W. Firshein. 1983. Initiation of DNA replication in vitro by a DNA-membrane complex extracted from Bacillus subtilis. Proc. Natl. Acad. Sci. USA 80: 6214 6218.
12. Benjamin, P.,, P. Strumph,, M. Kenny,, and W. Firshein. 1982. DNA synthesis in purified DNA-membrane complexes extracted from a Bacillus subtilis polA mutant. Nature (London) 298: 769 771.
13. Bernad, A.,, L. Blanco,, J. M. Lazaro,, G. Martin,, and M. Salas. 1989. A conserved 3′ → 5′ exonuclease active site in prokaryotic and eukaryotic DNA polymerases. Cell 59: 219 228.
14. Bourne, H. R.,, D. A. Sanders,, and F. McCormick. 1991. The GTPase superfamily: conserved structure and molecular mechanisms. Nature (London) 349: 117 127.
15. Boye, E.,, and A. Lebner-Olesen. 1990. The role of dam methyltransferase in the control of DNA replication in E. coli. Cell 62: 981 989.
16. Bramhill, D.,, and A. Kornberg. 1988. A model for initiation at origins of DNA replication. Cell 54: 915 918.
17. Bramhill, D.,, and A. Kornberg. 1988. Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell 52: 743 755.
18. Braun, R. E.,, K. O'Day,, and A. Wright. 1985. Autoregulation of the DNA replication gene dnaA in E. coli K-12. Cell 40: 159 169.
19. Brewer, B. J. 1988. When polymerases collide: replication and the transcriptional organization of the Escherichia coli chromosome. Cell 53: 679 686.
19a.. Brewer, B. J.,, and W. L. Fangman. 1987. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51: 463 471.
20. Bruand, C.,, S. D. Ehrlich,, and L. Janniere. 1991. Unidirectional theta replication of the structurally stable Enterococcus faecalis plasmid pAM β1. EMBO J. 10: 2171 2178.
21. Cairns, J. 1963. The bacterial chromosome and its manner of replication as seen by autoradiography. J. Mol. Biol. 6: 208 213.
22. Carrigan, C. M.,, J. A. Haarsma,, M. T. Smith,, and R. G. Wake. 1987. Sequence features of the replication terminus of the Bacillus subtilis chromosome. Nucleic Acids Res. 15: 8501 8509.
23. Carrigan, C. M.,, R. A. Pack,, M. T. Smith,, and R. G. Wake. 1991. The normal terC-region of the Bacillus subtilis chromosome acts in a polar manner to arrest the clockwise replication fork. J. Mol. Biol. 22: 197 207.
24. Cooper, S. 1991. Bacterial Growth and Division. Academic Press, Inc., San Diego, Calif..
25. Donachie, W. D. 1968. Relationship between cell size and time of initiation of DNA replication. Nature (London) 219: 1077 1079.
26. Dunn, G.,, P. Jeffs,, N. H. Mann,, D. M. Torgerson,, and M. Young. 1978. The relationship between DNA replication and the induction of sporulation in Bacillus subtilis. J. Gen. Microbiol. 108: 189 195.
27. Freese, E.,, P. Fortnagel,, R. Schmitt,, W. Klofat,, E. Chappelle,, and G. Picclolo,. 1969. Biochemical genetics of initial sporulation stages, p. 82 101. In L. L. Campbell (ed.), Spores IV. American Society for Microbiology, Bethesda, Md..
28. Fujita, M. Q.,, H. Yoshikawa,, and N. Ogasawara. 1989. Structure of the dnaA region of Pseudomonas putida. Conservation among three bacteria, Bacillus subtilis, Escherichia coli and Pseudomonas putida. Mol. Gen. Genet. 215: 381 387.
29. Fujita, M. Q.,, H. Yoshikawa,, and N. Ogasawara. 1990. Structure of the dnaA region of Micrococcus luteus. Conservation and variation among eubacteria. Gene 93: 73 78.
30. Fujita, M. Q.,, H. Yoshikawa,, and N. Ogasawara. 1992. Structure of the dnaA and DnaA-box region in the Mycoplasma capricolum chromosome: conservation and variation in the course of evolution. Gene 110: 17 23.
31. Fukuoka, T.,, S. Moriya,, H. Yoshikawa,, and N. Ogasawara. 1990. Purification and characterization of an initiation protein for chromosomal replication, DnaA, in Bacillus subtilis. J. Biochem. 107: 732 739.
32. Fuller, R.,, B. E. Funnell,, and A. Komberg. 1984. The dnaA protein complex with the E. coli chromosomal origin (oriC) and other DNA sites. Cell 38: 889 900.
33. Ganesan, A. T.,, and J. Lederberg. 1965. A cell-membrane bound fraction of bacterial DNA. Biochem. Biophys. Res. Commun. 18: 824 835.
34. Gass, K. B.,, and N. R. Cozzarelli. 1973. Further genetic and enzymological characterization of the three Bacillus subtilis deoxyribonucleic acid polymerases. J. Biol. Chem. 248: 7688 7700.
35. Gutierrez, C.,, G. Martin,, J. M. Sogo,, and M. Salas. 1991. Mechanism of stimulation of DNA replication by bacteriophage φ29 single-strand DNA-binding protein p5. J. Biol. Chem. 266: 2104 2111.
36. Gyuraslts, E. B.,, and R. G. Wake. 1973. Bidirectional chromosome replication in Bacillus subtilis. J. Mol. Biol. 73: 55 63.
37. Hammond, R. A.,, H. M. Barnes,, S. L. Mack,, J. A. Mitchener,, and N. C. Brown. 1991. Bacillus subtilis DNA polymerase III: complete sequence, overexpression and characterization of the polC gene. Gene 98: 29 36.
38. Hanley, P. J. B.,, C. M. Carrigan,, D. B. Rowe,, and R. G. Wake. 1987. Breakdown and quantitation of the forked termination of replication intermediate of Bacillus subtilis. J. Mol. Biol. 196: 721 727.
38a.. Hansen, F. Personal communication.
39. Hara, H.,, and H. Yoshikawa. 1973. Asymmetric bidirectional replication of Bacillus subtilis chromosome. Nature New Biol. 244: 200 203.
40. Harmon, J. M.,, and H. W. Taber. 1977. Some properties of a membrane-deoxyribonucleic acid complex isolated from Bacillus subtilis. J. Bacteriol. 129: 789 795.
41. Henckes, G.,, F. Harper,, A. Levine,, F. Vannier,, and S. J. Séror. 1989. Overreplication of the origin region in the dnaB37 mutant of Bacillus subtilis: postinitiation control of chromosomal replication. Proc. Natl. Acad. Set. USA 86: 8660 8664.
42. Henckes, G.,, F. Vannier,, A. Buu,, and L. S. Seror. 1982. Possible involvement of DNA-linked RNA in the initiation of Bacillus subtilis chromosome replication. J. Bacteriol. 149: 79 91.
43. Hidaka, M.,, T. Kobayashi,, and T. Horiuchi. 1991. A newly identified DNA replication terminus site. TerE, on the Escherichia coli chromosome. J. Bacteriol. 173: 391 393.
44. Hill, T. M.,, A. J. PeUetier,, M. L. Tecklenburg,, and P. J. Kuempel. 1988. Identification of the DNA sequence from die E. coli terminus region that halts replication forks. Cell 55: 459 466.
45. Horiuchi, T.,, and M. Hidaka. 1988. Core sequence of two separable terminus sites of the R6K plasmid that exhibit polar inhibition of replication is a 20bp inverted repeat. Cell 54: 515 523.
46. Horowitz, S.,, R. J. Doyle,, F. E. Young,, and U. N. Streips. 1979. Selective association of the chromosome with membrane in a stable L-form of Bacillus subtilis. J. Bacteriol. 138: 915 922.
47. Hoshino, T.,, T. McKenzie,, S. Schmidt,, T. Tanaka,, and N. Sueoka. 1987. Nucleotide sequence of Bacillus subtilis dnaB. A gene essential for DNA replication initiation and membrane attachment. Proc. Natl. Acad. Sci. USA 84: 653 657.
48. Iismaa, T. P.,, M. T. Smith,, and R. G. Wake. 1984. Physical map of the Bacillus subtilis replication terminus region: its confirmation, extension and genetic orientation. Gene 32: 171 180.
49. Iismaa, T. P.,, and R. G. Wake. 1987. The normal replication terminus of the Bacillus subtilis chromosome, terC, is dispensable for vegetative growth and sporulation. J. Mol. Biol. 195: 299 310.
50. Imada, S.,, L. E. Carroll,, and N. Sueoka. 1980. Genetic mapping of a group of temperature-sensitive dna initiation mutants in Bacillus subtilis. Genetics 94: 809 823.
51. Itaya, M.,, and T. Tanaka. 1991. Complete physical map of the Bacillus subtilis 168 chromosome constructed by a gene-directed mutagenesis method. J. Mol. Biol. 220: 631 648.
52. Jacob, F.,, S. Brenner,, and F. Cuzin. 1963. On the regulation of DNA replication in bacteria. Cold Spring Harbor Symp. Quant. Biol. 28: 329 348.
53. Karamata, D.,, and J. D. Gross. 1970. Isolation and genetic analysis of temperature-sensitive mutants of B. subtilis defective in DNA synthesis. Mol. Gen. Genet. 108: 277 287.
53a.. Kato, J.,, Y. Nlshlmura,, R. Imamura,, H. Niki,, S. Hiraga,, and H. Suzuki. 1990. New topoisomerase essential for chromosome segregation in E. coli. Cell 63: 393 404.
54. Kejzlarova-Lepesant, J.,, N. Harford,, J.-A. Lepesant,, and R. Dedonder,. 1975. Revised genetic map for Bacillus subtilis 168, p. 592 595. In P. Gerhardt,, R. N. Costilow,, and H. L. Sadoff (ed.), Spores VI. American Society for Microbiology, Washington, D.C..
55. Khatri, G. S.,, T. MacAllister,, P. R. Sista,, and D. Bastia. 1989. The replication terminator protein of E. coli is a DNA sequence-specific contra-helicase. Cell 59: 667 674.
56. Kuempel, P. L.,, A. J. PeUetier, andT. M. Hill. 1989. Tus and the terminators: the arrest of replication in prokaryotes. Cell 59: 581 583.
57. Laflan, J.,, and W. Firshein. 1988. Origin specific DNA binding membrane-associated protein may be involved in repression of initiation in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 85: 7452 7456.
58. Lai, C.-J.,, and D. Nathans. 1975. Non-specific termination of simian virus 40 DNA replication. J. Mol. Biol. 97: 113 118.
59. Lampe, M. F., and K. F. Bott. 1985. Genetic and physical organization of the cloned gyrA and gyrB genes of Bacillus subtilis. J. Bacteriol. 162: 78 84.
60. Laurent, S. J. 1973. Initiation of deoxyribonucleic acid replication in a temperature-sensitive mutant of B. subtilis. Evidence for a transcriptional step. J. Bacteriol. 116: 141 145.
61. Laurent, S. J.,, and F. S. Vannier. 1973. Temperature-sensitive initiation of chromosome replication in a mutant of Bacillus subtilis. J. Bacteriol. 114: 474 484.
62. Lee, S. H.,, A. Kornberg,, M. Hidaka,, T. Kobayashi,, and T. Horiuchi. 1989. The E. coli replication termination protein impedes the action of helicases. Proc. Natl. Acad. Sci. USA 86: 9104 9108.
63. Lee, S.,, P. Kanda,, R. C. Kennedy,, and J. R. Walker. 1987. Relation of the Escherichia coli dnaX gene to its two products—the τ and �� subunits of DNA polymerase III holoenzyme. Nucleic Acids Res. 15: 7663 7675.
64. Levine, A.,, G. Henckes,, F. Vannier,, and S. J. Seror. 1987. Chromosomal initiation in Bacillus subtilis may involve two closely linked origins. Mol. Gen. Genet. 208: 37 44.
65. Levine, A.,, F. Vannier,, M. Dehbi,, G. Henckes,, and S. J. Seror. 1991. The stringent response blocks DNA replication outside the ori region in Bacillus subtilis and at the origin in Escherichia coli. J. Mol. Biol. 219: 605 613.
66. Lewis, P. J.,, G. B. Ralston,, R. I. Christopherson,, and R. G. Wake. 1990. 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. 214: 73 84.
67. Lewis, P. J.,, M. T. Smith,, and R. G. Wake. 1989. A protein involved in termination of chromosome replication in Bacillus subtilis binds specifically to the terC site. J. Bacteriol. 171: 3564 3567.
68. Lewis, P. J.,, and R. G. Wake. 1989. DNA and protein sequence conservation at the replication terminus in Bacillus subtilis 168 and W23. J. Bacteriol. 171: 1402 1408.
69. Løbner-Olesen, A.,, K. Skarstad,, F. G. Hansen,, K. von Meyenburg,, and E. Boye. 1989. The DnaA protein determines the initiation mass of Escherichia coli K-12. Cell 57: 881 889.
70. Lovett, P. S.,, and F. E. Young. 1969. Identification of Bacillus subtilis NRRL B-3275 as a strain of Bacillus pumilis. J. Bacteriol. 100: 658 661.
71. Low, R. L.,, S. A. Rashbaum,, and N. R. Cozzarelli. 1976. Purification and characterization of DNA polymerase III from Bacillus subtilis. J. Biol. Chem. 251: 1311 1325.
72. Makl, H.,, S. Makl,, and A. Kornberg. 1988. DNA polymerase III holoenzyme of Escherichia coli. IV. The holoenzyme is an asymmetric dimer with twin active sites. J. Biol. Chem. 263: 6570 6578.
73. Marsh, R. C.,, and A. Worcel. 1977. A DNA fragment containing the origin of replication of the Escherichia coli chromosome. Proc. Natl. Acad. Set. USA 74: 2720 2724.
74. Matsushita, T.,, K. White,, and N. Sueoka. 1971. Chromosome replication in toluenized Bacillus subtilis cells. Nature New Biol. 232: 111 114.
75. McGinness, T.,, and R. G. Wake. 1979. Division septation in the absence of chromosome termination in Bacillus subtilis. J. Mol. Biol. 134: 251 264.
76. McMacken, R.,, L. Silver,, and C. Georgopoulos,. 1987. DNA replication, p. 564 612. In F. C. Neidhardt,, J. L. Ingraham,, K. B. Low,, B. Magasanik,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, vol. 1. American Society for Microbiology, Washington, D.C..
77. Mendelson, N. H.,, and J. D. Gross. 1967. Characterization of a temperature-sensitive mutant of Bacillus subtilis defective in deoxyribonucleic acid replication. J. Bacteriol. 94: 1603 1608.
78. Messer, W.,, and M. Noyer-Weidner. 1988. Timing and targeting: the biological functions of Dam methylation in E. coli. Cell 54: 735 737.
79. Moriya, S.,, T. Atlung,, F. G. Hansen,, H. Yoshikawa,, and N. Ogasawara. 1992. Cloning of autonomously replicating sequence (ars) from the Bacillus subtilis chromosome. Mol. Microbiol. 6: 309 315.
80. Moriya, S.,, T. Fukuoka,, N. Ogasawara,, and H. Yoshikawa. 1988. Regulation of initiation of the chromosomal replication by DnaA-boxes in the origin region of the Bacillus subtilis chromosome. EMBO J. 7: 2911 2917.
81. Moriya, S.,, K. Kato,, H. Yoshikawa,, and N. Ogasawara. 1990. Isolation of a dnaA mutant of Bacillus subtilis defective in initiation of replication: amount of DnaA protein determines cells' initiation potential. EMBO J. 9: 2905 2910.
82. Moriya, S.,, N. Ogasawara,, and H. Yoshikawa. 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.
83. Murakami, S.,, N. Inuzuka,, M. Yamaguchi,, K. Yamaguchi,, and H. Yoshikawa. 1976. Initiation of DNA replication in Bacillus subtilis. III. Analysis of molecular events involved in the initiation using a temperature-sensitive dna mutant. J. Mol. Biol. 108: 683 704.
84. Murakami, S.,, and H. Yoshikawa. 1976. Gene that controls initiation of chromosome replication and prophage induction in Bacillus subtilis. Nature (London) 259: 215 218.
85. Mysliwiec, T. H.,, J. Errington,, A. B. Vaidya,, and M. G. Bramucci. 1991. The Bacillus subtilis spo0J gene: evidence for involvement in catabolite repression of sporulation. J. Bacteriol. 173: 1911 1919.
86. Nordstrom, K. 1990. Control of plasmid replicationhow do DNA iterons set the replication frequency? Cell 63: 1121 1124.
86a.. O'DonnelI, M. Personal communication.
87. Ogasawara, N.,, S. Mizumoto,, and H. Yoshikawa. 1984. Replication origin of the Bacillus subtilis chromosome determined by hybridization of the first-replicating DNA with cloned fragments from the replication origin region of the chromosome. Gene 30: 173 182.
88. Ogasawara, N.,, S. Moriya,, P. G. Mazza,, and H. Yoshikawa. 1986. Nucleotide sequence and organization of dnaB gene and neighbouring genes on the Bacillus subtilis chromosome. Nucleic Acids Res. 14: 9989 9999.
89. Ogasawara, N.,, S. Moriya,, K. von Meyenburg,, F. G. Hansen,, and H. Yoshikawa. 1985. Conservation of genes and their organization in the chromosomal replication origin region of Bacillus subtilis and Escherichia coli. EMBO J. 4: 3345 3350.
90. Ogasawara, N.,, and H. Yoshikawa. Genes and their organization in replication origin region of bacterial chromosome. Mol. Microbiol, in press.
91. Oka, A.,, K. Sugimoto,, M. Takanami,, and Y. Hirota. 1980. Replication origin of the Escherichia coli K-12 chromosome. J. Mol. Biol. 176: 443 458.
92. Okazaki, R.,, and A. Kornberg. 1964. Enzymatic synthesis of deoxyribonucleic acid. XV. Purification and properties of a polymerase from Bacillus subtilis. J. Biol. Chem. 239: 259 268.
93. O'Sullivan, A.,, and C. Anagnostopoulos. 1982. Replication terminus of the Bacillus subtilis chromosome. J. Bacteriol. 151: 135 143.
94. O'Sullivan, A.,, and N. Sueoka. 1967. Sequential replication of the Bacillus subtilis chromosome. IV. Genetic mapping by density transfer experiment. J. Mol. Biol. 27: 349 368.
95. O'Sullivan, M. A.,, and N. Sueoka. 1972. Membrane attachment of the replication origins of a multifork (dichotomous) chromosome in Bacillus subtilis. J. Mol. Biol. 69: 237 248.
96. Ott, R. W.,, M. H. Barnes,, N. C. Brown,, and A. T. Ganesan. 1986. Cloning and characterization of the polC region of Bacillus subtilis. J. Bacteriol. 165: 951 957.
97. Perego, M.,, E. Ferrari,, M. T. Bassi,, A. Galizzi,, and P. Mazza. 1987. Molecular cloning of Bacillus subtilis genes involved in DNA metabolism. Mol. Gen. Genet. 209: 8 14.
98. Piggot, P. J., 1990. Genetic map of Bacillus subtilis 168, p. 107 146. In K. Drlica, and M. Riley (ed.), The Bacterial Chromosome. American Society for Microbiology, Washington, D.C..
99. Rasmussen, K. V.,, T. Atlung,, G. Kerszman,, G. E. Hansen,, and F. G. Hansen. 1983. Conditional change of DNA replication control in an RNA polymerase mutant of Escherichia coli. J. Bacteriol. 154: 443 451.
100. Ryter, A.,, Y. Hirota,, and F. Jacob. 1968. DNA-membrane complex and nuclear segregation in bacteria. Cold Spring Harbor Symp. Quant. Biol. 33: 669 676.
101. Sanjanwala, B.,, and A. T. Ganesan. 1989. DNA polymerase III gene of Bacillus subtilis. Proc. Natl. Acad. Sci. USA 86: 4421 4424.
102. Sargent, M. G. 1980. Specific labeling of the Bacillus subtilis chromosome terminus. J. Bacteriol. 143: 1033 1035.
103. Sargent, M. G.,, and M. F. Bennett. 1985. Amplification of a major membrane-bound DNA sequence of Bacillus subtilis. J. Bacteriol. 161: 589 595.
104. Schneider, A.-M.,, M. Gaisne,, and C. Anagnostopoulos. 1982. Genetic structure and internal rearrangements of stable merodiploids from Bacillus subtilis strains carrying the trpE26 mutation. Genetics 101: 189 210.
105. Seiki, M.,, N. Ogasawara,, and H. Yoshikawa. 1979. Structure of the region of the replication origin of the Bacillus subtilis chromosome. Nature (London) 281: 699 701.
106. Seki, T.,, T. Oshima,, and Y. Oshima. 1975. Taxonomic study of Bacillus by deoxyribonucleic acid-deoxyribo-nucleic acid hybridization and interspecific transformation. Int. J. Syst. Bacteriol. 25: 258 270.
107. Sekimizu, K.,, D. Bramhill,, and A. Romberg. 1987. ATP activates dnaA protein in initiating replication of plasmids bearing the origin of the E. coli chromosome. Cell 50: 259 265.
108. Séror, S. J.,, F. Vannier,, A. Levine,, and G. Henckes. 1986. Stringent control of chromosomal replication in Bacillus subtilis. Nature (London) 321: 709 710.
109. Smith, M. T.,, C. Aynsley,, and R. G. Wake. 1985. Cloning and localization of the Bacillus subtilis chromosome replication terminus, terC. Gene 38: 9 17.
110. Smith, M. T.,, and R. G. Wake. 1988. DNA sequence requirements for replication fork arrest at terC in Bacillus subtilis. J. Bacteriol. 170: 4083 4090.
111. Smith, M. T.,, and R. G. Wake. 1989. Expression of the rtp gene of Bacillus subtilis is required for replication fork arrest at the chromosome terminus. Gene 85: 187 192.
112. Smith, M. T.,, and R. G. Wake. 1992. Definition and polarity of action of DNA replication terminators in Bacillus subtilis. J. Mol. Biol. 227: 648 657.
113. Steck, T. R.,, and K. Drlica. 1984. Bacterial chromosome segregation: evidence for DNA gyrase involvement in decatenation. Cell 36: 1081 1088.
114. Struck, J. C. R.,, D. W. Vogel,, N. Ulbrich,, and V. A. Erdmann. 1986. A dnaZX-like open reading frame downstream from the Bacillus subtilis scRNA gene. Nucleic Acids Res. 16: 2720.
115. Sueoka, N.,, and W. G. Quinn. 1968. Membrane attachment of the chromosome replication origin in Bacillus subtilis. Cold Spring Harbor Symp. Quant. Biol. 33: 695 705.
116. Sugino, A.,, and K. F. Bott. 1980. Bacillus subtilis deoxyribonucleic acid gyrase. J. Bacteriol. 141: 1331 1339.
117. Valenzuela, M. S.,, D. Freifelder,, and R. B. Inman. 1976. Lack of a unique termination site for the first round of bacteriophage lambda DNA replication. J. Mol. Biol. 102: 569 589.
118. von Meyenburg, K.,, and F. G. Hansen,. 1987. Regulation of chromosome replication, p. 1555 1577. In F. C. Neidhardt,, J. L. Ingraham,, K. B. Low,, B. Magasanik,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, vol. 2. American Society for Microbiology, Washington D.C..
119. Wahle, E.,, R. S. Lasken,, and A. Kornberg. 1989. The dnaB-dnaC replication protein complex of Escherichia coli. I. Formation and properties. J. Biol. Chem. 264: 2463 2468.
120. Wake, R. G. 1972. Visualization of reinitiated chromosomes in Bacillus subtilis. J. Mol. Biol. 68: 501 509.
121. Wake, R. G. 1973. Circularity of the Bacillus subtilis chromosome and further studies on its bidirectional replication. J. Mol. Biol. 77: 569 575.
122. Wake, R. G.,, P. J. Lewis,, and M. T. Smith,. 1990. The rtp gene and termination of chromosome replication in Bacillus subtilis, p. 99 108. In M. Zukowski,, A. T. Ganesan,, and J. A. Hoch (ed.). Genetics and Biotechnology of Bacilli, vol. 3. Academic Press, Inc., San Diego, Calif..
123. Wang, L.-F.,, C. W. Price,, and R. H. Doi. 1985. Bacillus subtilis dnaE encodes a protein homologous to DNA primase of Escherichia coli. J. Biol. Chem. 260: 3368 3372.
124. Wang, Q.,, and M. Kaguni. 1987. Transcriptional repression of the dnaA gene of Escherichia coli by dnaA protein. Mol. Gen. Genet. 209: 518 525.
125. Weiss, A. S.,, I. R. Hariharan,, and R. G. Wake. 1981. Analysis of the terminus region of the Bacillus subtilis chromosome. Nature (London) 293: 673 675.
126. Weiss, A. S.,, and R. G. Wake. 1983. Restriction map of DNA spanning the replication terminus of the Bacillus subtilis chromosome. J. Mol. Biol. 171: 119 137.
127. Weiss, A. S.,, and R. G. Wake. 1984. A unique DNA intermediate associated with termination of chromosome replication in Bacillus subtilis. Cell 39: 683 689.
128. Weiss, A. S.,, R. G. Wake,, and R. B. Inman. 1986. An immobilized fork as a termination of replication intermediate in Bacillus subtilis. J. Mol. Biol. 188: 199 205.
129. Williams, N. R.,, and R. G. Wake. 1989. Sequence limits of DNA strands in the arrested replication fork at the Bacillus subtilis chromosome terminus. Nucleic Acids Res. 17: 9947 9956.
130. Winston, S.,, and T. Matsushita. 1975. Permanent loss of chromosome initiation in toluene-treated Bacillus subtilis cells. J. Bacteriol. 123: 921 927.
131. Winston, S.,, and N. Sueoka. 1980. DNA-membrane association is necessary for initiation of chromosomal and plasmid replication in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 77: 2834 2838.
132. Winston, S.,, and N. Sueoka,. 1982. DNA replication in Bacillus subtilis, p. 35 69. In D. A. Dubnau (ed.). The Molecular Biology of the Bacilli, vol. 1. Bacillus subtilis. Academic Press, Inc., New York.
133. Yamaguchi, R.,, S. Murakami,, and H. Yoshikawa. 1971. Chromosome-membrane association in Bacillus subtilis. I. DNA release from membrane fraction. Biochem. Biophys. Res. Commun. 44: 1559 1565.
134. Yamaguchi, K.,, and H. Yoshikawa. 1973. Topography of chromosome membrane junction in Bacillus subtilis. Nature New Biol. 244: 204 206.
135. Yamaguchi, K.,, and H. Yoshikawa. 1977. Chromosome-membrane association in Bacillus subtilis. III. Isolation and characterization of a DNA-protein complex carrying replication origin markers. J. Mol. Biol. 110: 219 253.
136. Yee, Y. W.,, and D. W. Smith. 1990. Pseudomonas chromosomal replication origins: a bacterial class distinct from Escherichia coli type origins. Proc. Natl. Acad. Sci. USA 87: 1278 1282.
137. Yoshikawa, H.,, and N. Ogasawara. 1991. Structure and function of DnaA and the DnaA-box in eubacteria: evolutionary relationships of bacterial replication origin. Mol. Microbiol. 5: 2589 2597.
138. Yoshikawa, H.,, A. O'Sullivan,, and N. Sueoka. 1964. Sequential replication of the Bacillus subtilis chromosome. III. Regulation of initiation. Proc. Natl. Acad. Sci. USA 52: 973 980.
139. Yoshikawa, H.,, and N. Sueoka. 1963. Sequential replication of Bacillus subtilis chromosome. I. Comparison of marker frequencies in exponential and stationary growth phases. Proc. Natl. Acad. Sci. USA 49: 555 566.
140. Yoshikawa, H., and Sueoka. 1963. Sequential replication of the Bacillus subtilis chromosome. II. Isotopic transfer experiments. Proc. Natl. Acad. Sci. USA 49: 806 813.
141. Yoshikawa, H.,, K. Yamaguchi,, M. Seiki,, N. Ogasawara,, and H. Toyoda. 1979. Organization of the replication-origin region of the Bacillus subtilis chromosome. Cold Spring Harbor Symp. Quant. Biol. 43: 569 576.
142. Zahler, S. A., 1982. Specialized transduction in Bacillus subtilis, p. 269 305. In D. A. Dubnau (ed.), Molecular Biology of the Bacilli. Academic Press, Inc., New York.
143. Zeigler, D. R., 1989. Genetic map of Bacillus subtilis 168, p. 4.1 4.29. In D. R. Zeigler, and D. H. Dean (ed.), Bacillus Genetic Stock Center Strains and Data, 4th ed. Ohio State University, Columbus.
144. Zeigler, D. R.,, and D. H. Dean. 1990. Orientation of genes in the Bacillus subtilis chromosome. Genetics 125: 703 708.

Tables

Generic image for table
Table 1

DNA replication genes of 168

Citation: Yoshikawa H, Wake R. 1993. Initiation and Termination of Chromosome Replication, p 507-528. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch36
Generic image for table
Table 2

Essential proteins (and genes) for DNA chain growth and replication fork movement (elongation phase) in and equivalent proteins and genes in

Citation: Yoshikawa H, Wake R. 1993. Initiation and Termination of Chromosome Replication, p 507-528. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch36

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