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

Zhengchang Su, Fenglou Mao, Phuongan Dam, Hongwei Wu, Victor Olman, Ian T. Paulsen, Brian Palenik, Ying Xu*

*Corresponding author for this work

Research output: Contribution to journalArticle

51 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)1050-1065
Number of pages16
JournalNucleic Acids Research
Volume34
Issue number3
DOIs
Publication statusPublished - 2006
Externally publishedYes

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