Dynamic association of the replication initiator and transcription factor DnaA with the bacillus subtilis chromosome during replication stress

Journal of Bacteriology

Volumn 191, Issue 2, 2009, Pages 486-493

  Breier, Adam M ^a   Grossman, Alan D ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

REPLICATION INITIATOR PROTEIN DNAA;

ARTICLE; BACILLUS SUBTILIS; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIAL GROWTH; BINDING SITE; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME REPLICATION; CONTROLLED STUDY; CROSS LINKING; DNA BINDING; DNA DETERMINATION; GENE CLUSTER; GENE CONTROL; GENE FUNCTION; GENE INTERACTION; GENE LOCUS; GENE TARGETING; GENOME ANALYSIS; GENOMICS; IN VIVO STUDY; MOLECULAR DYNAMICS; NONHUMAN; ORIC GENE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

BACILLUS SUBTILIS; BACTERIAL PROTEINS; BINDING SITES; CHROMOSOMES, BACTERIAL; DNA REPLICATION; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; REPLICATION ORIGIN;

BACILLUS SUBTILIS;

EID: 58649122688     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.01294-08     Document Type: Article

References (40)

1. Atlung, T., E. S. Clausen, and F. G. Hansen. 1985. Autoregulation of the dnaA gene of Escherichia coli K12. Mol. Gen. Genet. 200:442-450.
2. Berkmen, M. B., and A. D. Grossman. 2007. Subcellular positioning of the origin region of the Bacillus subtilis chromosome is independent of sequences within oriC, the site of replication initiation, and the replication initiator DnaA. Mol. Microbiol. 63:150-165.
3. 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.
4. Breier, A. M., and A. D. Grossman. 2007. Whole-genome analysis of the chromosome partitioning and sporulation protein Spo0J (ParB) reveals spreading and origin-distal sites on the Bacillus subtilis chromosome. Mol. Microbiol. 64:703-718.
5. Britton, R. A., P. Eichenberger, J. E. Gonzalez-Pastor, P. Fawcett, R. Monson, R. Losick, and A. D. Grossman. 2002. Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis. J. Bacteriol. 184:4881-4890.
6. Brown, N. C. 1970. 6-(p-Hydroxyphenylazo)-uracil: a selective inhibitor of host DNA replication in phage-infected Bacillus subtilis. Proc. Natl. Acad. Sci. USA 67:1454-1461.
7. Bruand, C., A. Sorokin, P. Serror, and S. D. Ehrlich. 1995. Nucleotide sequence of the Bacillus subtilis dnaD gene. Microbiology 141:321-322.
8. Bruand, C., M. Velten, S. McGovern, S. Marsin, C. Serena, S. D. Ehrlich, and P. Polard. 2005. Functional interplay between the Bacillus subtilis DnaD and DnaB proteins essential for initiation and re-initiation of DNA replication. Mol. Microbiol. 55:1138-1150.
9. Burkholder, W. F., I. Kurtser, and A. D. Grossman. 2001. Replication initiation proteins regulate a developmental checkpoint in Bacillus subtilis. Cell 104:269-279.
10. Callister, H., S. Le Mesurier, and R. G. Wake. 1977. Initiation of deoxyribonucleic acid replication in germinating spores of Bacillus subtilis 168 carrying the dnaB(Ts)134 mutation. J. Bacteriol. 130:1030-1037.
11. Comella, N., and A. D. Grossman. 2005. Conservation of genes and processes controlled by the quorum response in bacteria: characterization of genes controlled by the quorum-sensing transcription factor ComA in Bacillus subtilis. Mol. Microbiol. 57:1159-1174.
12. Erzberger, J. P., M. L. Mott, and J. M. Berger. 2006. Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling. Nat. Struct. Mol. Biol. 13:676-683.
13. Friedberg, E., G. Walker, W. Siede, R. Wood, R. Schultz, and T. Ellenberger. 2005. DNA repair and mutagenesis, 2nd ed. American Society for Microbiology, Washington, DC.
14. Gon, S., J. E. Camara, H. K. Klungsoyr, E. Crooke, K. Skarstad, and J. Beckwith. 2006. A novel regulatory mechanism couples deoxyribonucleotide synthesis and DNA replication in Escherichia coli. EMBO J. 25:1137-1147.
15. Goranov, A. I., L. Katz, A. M. Breier, C. B. Burge, and A. D. Grossman. 2005. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Proc. Natl. Acad. Sci. USA 102:12932-12937.
16. Goranov, A. I., E. Kuester-Schoeck, J. D. Wang, and A. D. Grossman. 2006. Characterization of the global transcriptional responses to different types of DNA damage and disruption of replication in Bacillus subtilis. J. Bacteriol. 188:5595-5605.
17. Hamoen, L. W., W. K. Smits, A. de Jong, S. Holsappel, and O. P. Kuipers. 2002. Improving the predictive value of the competence transcription factor (ComK) binding site in Bacillus subtilis using a genomic approach. Nucleic Acids Res. 30:5517-5528.
18. Harwood, C. R., and S. M. Cutting. 1990. Molecular biological methods for Bacillus. John Wiley & Sons, Chichester, England.
19. Hassan, A. K., S. Moriya, M. Ogura, T. Tanaka, F. Kawamura, and N. Ogasawara. 1997. Suppression of initiation defects of chromosome replication in Bacillus subtilis dnaA and oriC-deleted mutants by integration of a plasmid replicon into the chromosomes. J. Bacteriol. 179:2494-2502.
20. Ishikawa, S., Y. Ogura, M. Yoshimura, H. Okumura, E. Cho, Y. Kawai, K. Kurokawa, T. Oshima, and N. Ogasawara. 2007. Distribution of stable DnaA-binding sites on the Bacillus subtilis genome detected using a modified ChlP-chip method. DNA Res. 14:155-168.
21. Jaacks, K. J., J. Healy, R. Losick, and A. D. Grossman. 1989. Identification and characterization of genes controlled by the sporulation-regulatory gene spo0H in Bacillus subtilis. J. Bacteriol. 171:4121-4129.
22. Kadoya, R., A. K. Hassan, Y. Kasahara, N. Ogasawara, and S. Moriya. 2002. Two separate DNA sequences within oriC participate in accurate chromosome segregation in Bacillus subtilis. Mol. Microbiol. 45:73-87.
23. Kaguni, J. M. 2006. DnaA: controlling the initiation of bacterial DNA replication and more. Annu. Rev. Microbiol. 60:351-375.
24. Karamata, D., and J. D. Gross. 1970. Isolation and genetic analysis of temperature-sensitive mutants of B. subtilis defective in DNAsynthesis. Mol. Gen. Genet. 108:277-287.
25. Katayama, T. 2008. Roles for the AAA+ motifs of DnaA in the initiation of DNA replication. Biochem. Soc. Trans. 36:78-82.
26. Kucherer, C., H. Lother, R. Kolling, M. A. Schauzu, and W. Messer. 1986. Regulation of transcription of the chromosomal dnaA gene of Escherichia coli. Mol. Gen. Genet. 205:115-121.
27. Kurokawa, K., S. Nishida, A. Emoto, K. Sekimizu, and T. Katayama. 1999. Replication cycle-coordinated change of the adenine nucleotide-bound forms of DnaA protein in Escherichia coli. EMBO J. 18:6642-6652.
28. Lazazzera, B., T. Palmer, J. Quisel, and A. D. Grossman. 1999. Cell density control of gene expression and development in Bacillus subtilis, p. 27-46. In G. M. Dunny and S. C. Winans (ed.), Cell-cell signaling in bacteria. ASM Press, Washington, DC.
29. Lemon, K. P., I. Kurtser, J. Wu, and A. D. Grossman. 2000. Control of initiation of sporulation by replication initiation genes in Bacillus subtilis.J. Bacteriol. 182:2989-2991.
30. 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.
31. Messer, W. 2002. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol. Rev. 26:355-374.
32. Moriya, S., A. K. Hassan, R. Kadoya, and N. Ogasawara. 1997. Mechanism of anucleate cell production in the oriC-deleted mutants of Bacillus subtilis. DNA Res. 4:115-126.
33. Mott, M. L., and J. M. Berger. 2007. DNA replication initiation: mechanisms and regulation in bacteria. Nat. Rev. Microbiol. 5:343-354.
34. Ogura, Y., Y. Imai, N. Ogasawara, and S. Moriya. 2001. Autoregulation of the dnaA-dnaN operon and effects of DnaA protein levels on replication initiation in Bacillus subtilis. J. Bacteriol. 183:3833-3841.
35. Schaper, S., and W. Messer. 1995. Interaction of the initiator protein DnaA of Escherichia coli with its DNA target. J. Biol. Chem. 270:17622-17626.
36. Sekimizu, K., D. Bramhill, and A. Kornberg. 1987. ATP activates dnaA protein in initiating replication of plasmids bearing the origin of the E. coli chromosome. Cell 50:259-265.
37. Speck, C., C. Weigel, and W. Messer. 1999. ATP- and ADP-dnaAprotein, a molecular switch in gene regulation. EMBO J. 18:6169-6176.
38. Wang, J. D., G. M. Sanders, and A. D. Grossman. 2007. Nutritional control of elongation of DNA replication by (p)ppGpp. Cell 128:865-875.
39. Wang, Q. P., and J. M. Kaguni. 1987. Transcriptional repression of the dnaA gene of Escherichia coli by dnaA protein. Mol. Gen. Genet. 209:518-525.
40. Zakrzewska-Czerwinska, J., D. Jakimowicz, A. Zawilak-Pawlik, and W. Messer. 2007. Regulation of the initiation of chromosomal replication in bacteria. FEMS Microbiol. Rev. 31:378-387.