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

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.

Effects of low temperature on tropical and temperate isolates of marine Synechococcus

“…Cell culture and growth All Synechococcus isolates used in the study were grown in synthetic ocean water-based medium with 13.4 μM Na 2 EDTA.2H 2 O, 87.6 μM K 2 HPO 4 , 96.8 μM Na 2 CO 3 and 9 mM NaNO 3 (Morel et al, 1979;Su et al, 2006). Cultures were grown at 18°C and 22°C under constant illumination of 20 μmol photons m −2 s − 1 and agitation at 100 r.p.m.…”

Ecological Genomics of Marine Picocyanobacteria

“…strain WH7803 is inactivated by insertion of a kanamycin resistance gene (228). Approximately 17 to 54 NtcA targets were identified using bioinformatic approaches in single-genome and cross-genome analyses (276,278). DNA microarray data indicate that 18 to 81 genes were upregulated in Prochlorococcus sp.…”

“…Many of the NtcA targets in Synechococcus and Prochlorococcus are genes or operons that encode the acquisition of alternative N sources (276,278), and global expression of these genes is largely consistent with NtcA action (22,147,149,296). Interestingly, the genes encoding assimilation pathways for the main N sources other than ammonium are confined to an approximately 60-kb conserved region of the Synechococcus genome (Fig.…”

“…strain PCC6803 (305). All urea-utilizing strains of marine picocyanobacteria carry the urt and ure gene complement, and urtA, which encodes the periplasmic substrate-binding component, was identified as a prime target for NtcA control (278,296). However, Synechococcus sp.…”

Molecular biology techniques and applications for ocean sensing

“…Whole genome microarrays have thus far been applied for marine cyanobacteria Synechococcus spp. (Palenik et al, 2003(Palenik et al, , 2006Su et al, 2006) and recently a DMSP degrading Proteobacterium Silicibacter pomeroy from the Roseobacter clade (Burgmann et al, 2007). Genome data and analyses of several marine microbes have been published, including the uncultivated marine Archaeon Cenarchaeum symbiosum , the anoxygenic anaerobic phototrophic Proteobacterium Roseobacter denitrificans (Swingley et al, 2007), the cyanobacterial diazotroph Crocosphaera watsonii , and a marine planctomycete Pirellula sp.…”