Skip Navigation

Nucleic Acids Research 2005 33(16):5156-5171; doi:10.1093/nar/gki817
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (3610K) Freely available
Right arrow Screen PDF (1250K) Freely available
Right arrow Supplementary Material
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 ISI Web of Science
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 Search for citing articles in:
ISI Web of Science (13)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Su, Z.
Right arrow Articles by Xu, Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Su, Z.
Right arrow Articles by Xu, Y.
Related Collections
Right arrow Computational methods
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 12 September 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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{at}oxfordjournals.org

Genomics

Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis

Zhengchang Su, Victor Olman, Fenglou Mao and Ying Xu*

Bioinformatics Institute and Department of Biochemistry and Molecular Biology, University of Georgia Athens, GA 30602, USA

*To whom correspondence should be addressed. Tel: 706 542 9779; Fax: 706 542 9751; Email: xyn{at}bmb.uga.edu

Received March 30, 2005. Revised July 8, 2005. Accepted August 19, 2005.

We have developed a new method for prediction of cis-regulatory binding sites and applied it to predicting NtcA regulated genes in cyanobacteria. The algorithm rigorously utilizes concurrence information of multiple binding sites in the upstream region of a gene and that in the upstream regions of its orthologues in related genomes. A probabilistic model was developed for the evaluation of prediction reliability so that the prediction false positive rate could be well controlled. Using this method, we have predicted multiple new members of the NtcA regulons in nine sequenced cyanobacterial genomes, and showed that the false positive rates of the predictions have been reduced on an average of 40-fold compared to the conventional methods. A detailed analysis of the predictions in each genome showed that a significant portion of our predictions are consistent with previously published results about individual genes. Intriguingly, NtcA promoters are found for many genes involved in various stages of photosynthesis. Although photosynthesis is known to be tightly coordinated with nitrogen assimilation, very little is known about the underlying mechanism. We postulate for the fist time that these genes serve as the regulatory points to orchestrate these two important processes in a cyanobacterial cell.


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
 Microbiol. Mol. Biol. Rev.Home page
D. J. Scanlan, M. Ostrowski, S. Mazard, A. Dufresne, L. Garczarek, W. R. Hess, A. F. Post, M. Hagemann, I. Paulsen, and F. Partensky
Ecological Genomics of Marine Picocyanobacteria
Microbiol. Mol. Biol. Rev., June 1, 2009; 73(2): 249 - 299.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
Y. Cheng, J.-H. Li, L. Shi, L. Wang, A. Latifi, and C.-C. Zhang
A Pair of Iron-Responsive Genes Encoding Protein Kinases with a Ser/Thr Kinase Domain and a His Kinase Domain Are Regulated by NtcA in the Cyanobacterium Anabaena sp. Strain PCC 7120
J. Bacteriol., July 1, 2006; 188(13): 4822 - 4829.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Z. Su, F. Mao, P. Dam, H. Wu, V. Olman, I. T. Paulsen, B. Palenik, and Y. Xu
Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102
Nucleic Acids Res., February 10, 2006; 34(3): 1050 - 1065.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Che, G. Li, F. Mao, H. Wu, and Y. Xu
Detecting uber-operons in prokaryotic genomes.
Nucleic Acids Res., January 1, 2006; 34(8): 2418 - 2427.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
T. Osanai, S. Imamura, M. Asayama, M. Shirai, I. Suzuki, N. Murata, and K. Tanaka
Nitrogen Induction of Sugar Catabolic Gene Expression in Synechocystis sp. PCC 6803
DNA Res, January 1, 2006; 13(5): 185 - 195.
[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.