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Nucleic Acids Research 2006 34(3):1050-1065; doi:10.1093/nar/gkj496
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Published online 10 February 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102

Zhengchang Su1,2, Fenglou Mao1, Phuongan Dam1,2, Hongwei Wu1,2, Victor Olman1, Ian T. Paulsen3, Brian Palenik4 and Ying Xu1,2,*

1Department of Biochemistry and Molecular Biology, University of Georgia Athens, GA 30602, USA 2Computational Biology Institute, Oak Ridge National Laboratory Oak Ridge, TN 37831, USA 3The Institute of Genome Research Rockville, MD 20850, USA 4Scripps Institution of Oceanography, University of California at San Diego San Diego, CA 92093, USA

*To whom correspondence should be addressed at Department of Biochemistry and Molecular Biology, A110 Life Sciences Building, 120 Green Street, University of Georgia, Athens, GA, 30602. Tel: +1 706 542 9779; Fax: +1 706 542 9751; Email: xyn{at}bmb.uga.edu

Received October 6, 2005. Revised December 20, 2005. Accepted January 23, 2006.

Deciphering the regulatory networks encoded in the genome of an organism represents one of the most interesting and challenging tasks in the post-genome sequencing era. As an example of this problem, we have predicted a detailed model for the nitrogen assimilation network in cyanobacterium Synechococcus sp. WH 8102 (WH8102) using a computational protocol based on comparative genomics analysis and mining experimental data from related organisms that are relatively well studied. This computational model is in excellent agreement with the microarray gene expression data collected under ammonium-rich versus nitrate-rich growth conditions, suggesting that our computational protocol is capable of predicting biological pathways/networks with high accuracy. We then refined the computational model using the microarray data, and proposed a new model for the nitrogen assimilation network in WH8102. An intriguing discovery from this study is that nitrogen assimilation affects the expression of many genes involved in photosynthesis, suggesting a tight coordination between nitrogen assimilation and photosynthesis processes. Moreover, for some of these genes, this coordination is probably mediated by NtcA through the canonical NtcA promoters in their regulatory regions.


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