Skip Navigation



DNA Research Advance Access published online on October 10, 2007
DNA Research, doi:10.1093/dnares/dsm017
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
14/4/155    most recent
dsm017v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Request Permissions
Google Scholar
Right arrow Articles by Ishikawa, S.
Right arrow Articles by Ogasawara, N.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ishikawa, S.
Right arrow Articles by Ogasawara, N.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2007. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Distribution of Stable DnaA-Binding Sites on the Bacillus Subtilis Genome Detected using a Modified ChIP-chip Method

Shu Ishikawa, Yoshitoshi Ogura {dagger}, Mika Yoshimura, Hajime Okumura, Eunha Cho, Yoshikazu Kawai {ddagger}, Ken Kurokawa, Taku Oshima and Naotake Ogasawara*

Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan

Received 24 July 2007 ; revised 10 September 2007

We developed a modified ChIP-chip method, designated ChAP-chip (Chromatin Affinity Precipitation coupled with tiling chip). The binding sites of Bacillus subtilis Spo0J determined using this technique were consistent with previous findings. A DNA replication initiator protein, DnaA, formed stable complexes at eight intergenic regions on the B. subtilis genome. Characterization of the binding sequences suggested that two factors—the local density of DnaA boxes and their affinities for DnaA—are critical for stable binding. We further showed that in addition to autoregulation, DnaA directly modulate the expression of sda in a positive, and ywlC and yydA in a negative manner. Examination of possible stable DnaA-binding sequences in other Bacillus species suggested that DnaA-dependent regulation of those genes is maintained in most bacteria examined, supporting their biological significance. In addition, a possible stable DnaA-binding site downstream of gcp is also suggested to be conserved. Furthermore, potential DnaA-binding sequences specific for each bacterium have been identified, generally in close proximity to oriC. These findings suggest that DnaA plays several additional roles, such as control of the level of effective initiator, ATP-DnaA, and/or stabilization of the domain structure of the genome around oriC for the proper initiation of chromosome replication.

Key words: ChIP-chip analysis; Bacillus subtilis; DnaA protein; DnaA box; high-density tiling chip

* To whom correspond should be addressed. Tel. +81 743-72-5430. Fax. +81 743-72-5439. E-mail: nogasawa{at}bs.naist.jp

Edited by Katsumi Isono

{dagger} Current address: Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.

{ddagger} Current address: Faculty of Medical Sciences, Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Framlington Place, NE2 4HH, UK.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Genes Dev.Home page
J.-W. Veening, H. Murray, and J. Errington
A mechanism for cell cycle regulation of sporulation initiation in Bacillus subtilis
Genes & Dev., August 15, 2009; 23(16): 1959 - 1970.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
A. M. Breier and A. D. Grossman
Dynamic Association of the Replication Initiator and Transcription Factor DnaA with the Bacillus subtilis Chromosome during Replication Stress
J. Bacteriol., January 15, 2009; 191(2): 486 - 493.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
N. V. Sernova and M. S. Gelfand
Identification of replication origins in prokaryotic genomes
Brief Bioinform, September 1, 2008; 9(5): 376 - 391.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
T. Morimoto, R. Kadoya, K. Endo, M. Tohata, K. Sawada, S. Liu, T. Ozawa, T. Kodama, H. Kakeshita, Y. Kageyama, et al.
Enhanced Recombinant Protein Productivity by Genome Reduction in Bacillus subtilis
DNA Res, April 1, 2008; 15(2): 73 - 81.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.