Principles of signal transduction and gene circuit design governing nitrogen assimilation in Escherichia coli

The nitrogen regulatory (Ntr) system of Escherichia coli regulates the assimilation of nitrogen from a variety of nitrogen-containing compounds. This system processes multiple environmental signals, including carbon and nitrogen availability, and regulates the activity and synthesis of several proteins in response. This study of the signal transduction pathways and genetic circuitry within this system has identified a number of basic regulatory principles conserved in many biological systems.; Genetic mutations that mimic a severely nitrogen starved state revealed that the Ntr system coordinates cell growth with nitrogen availability through Nac. Nitrogen-regulated expression of Nac controlled expression of serA, which is required for purine biosynthesis, protein translation, and other aspects of central metabolism. Monitoring expression of Nac and other Ntr genes during changes in nitrogen availability identified new and distinct roles for the paralogous GlnK and PII proteins. Specifically, nitrogen-regulated expression of GlnK ensures that Ntr genes are only expressed for a few hours after the onset of nitrogen starvation. This adaptive mechanism is critical for cell viability during nitrogen starvation. The constitutively expressed PII regulates Ntr gene expression under nitrogen-rich conditions. Gene fusions that alter the transcriptional properties of GlnK and PII showed that the timing and level of accumulation of these proteins is the key determinant of their functions. GlnK is encoded within the glnKamtB operon, and the phenotypes of non-polar glnK mutations revealed another level of control in that AmtB antagonizes PII and GlnK signaling, presumably by titrating them away from other receptors. In cells lacking GlnK (but containing AmtB), Ntr induction was no longer reversible and was constitutively activated after a single episode of nitrogen starvation. Thus, GlnK also confers reversibility to the Ntr system by regulating AmtB antagonism of PII. Regulatory mechanisms very similar to those identified in the Ntr system have also been identified in Drosophila and C. elegans development. This suggests that complex regulatory systems may be comprised of a number of smaller regulatory “modules”, the combination of which produces specific regulatory features.