Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

Abstract

SUMMARY We present a comprehensive overview of the hierarchical network of intracellular processes revolving around central nitrogen metabolism in Escherichia coli . The hierarchy intertwines transport, metabolism, signaling leading to posttranslational modification, and transcription. The protein components of the network include an ammonium transporter (AmtB), a glutamine transporter (GlnHPQ), two ammonium assimilation pathways (glutamine synthetase [GS]-glutamate synthase [glutamine 2-oxoglutarate amidotransferase {GOGAT}] and glutamate dehydrogenase [GDH]), the two bifunctional enzymes adenylyl transferase/adenylyl-removing enzyme (ATase) and uridylyl transferase/uridylyl-removing enzyme (UTase), the two trimeric signal transduction proteins (GlnB and GlnK), the two-component regulatory system composed of the histidine protein kinase nitrogen regulator II (NRII) and the response nitrogen regulator I (NRI), three global transcriptional regulators called nitrogen assimilation control (Nac) protein, leucine-responsive regulatory protein (Lrp), and cyclic AMP (cAMP) receptor protein (Crp), the glutaminases, and the nitrogen-phosphotransferase system. First, the structural and molecular knowledge on these proteins is reviewed. Thereafter, the activities of the components as they engage together in transport, metabolism, signal transduction, and transcription and their regulation are discussed. Next, old and new molecular data and physiological data are put into a common perspective on integral cellular functioning, especially with the aim of resolving counterintuitive or paradoxical processes featured in nitrogen assimilation. Finally, we articulate what still remains to be discovered and what general lessons can be learned from the vast amounts of data that are available now.

Interplay between tolerance mechanisms to copper and acid stress inEscherichia coli

“…Decreasing the amount of ammonia in the culture medium further exacerbated Cu stress in ΔcopA cells at both pH 7 and pH 5 (SI Appendix, Fig. S11), consistent with GDH becoming more inefficient and increased reliance on GOGAT for making Glu (18) (Fig. 4B).…”

“…Notably, RpoS and CpxR also contribute to the cellular adaptation to excess Cu (41,42). Finally, our results link Cu stress to central nitrogen metabolism and thus additional control by the nitrogen response regulators, such as NtrB and NtrC, may be involved (18). These regulators sense intracellular Gln/Glu/α-KG ratios, which may shift during conditions of Cu stress (Fig.…”

“…Together, GDH, GS, and GOGAT constitute the central pathway for nitrogen assimilation in E. coli. The GDH route is thought to be most efficient when ammonia is abundant, whereas GOGAT is important during ammonia limitation (18).…”

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

“…In pathways like glycolysis, nitrogen assimilation, the citric acid cycle and inorganic ion uptake, gene-expression regulation is important for long-term adaptation to the availability of nitrogen and carbon sources. Shorter term adaptation of these same pathways also seems important as it has given rise to the evolutionary emergence of sophisticated fast cascade control mechanisms [45]. In some amino acid biosynthesis pathways, such as those for glutamate, tyrosine, tryptophan, phenylalanine, arginine and proline, both gene expression and metabolic regulation have been identified.…”

“…Such 'metabolic regulation' provides a fast response to acute extracellular and intracellular perturbations and helps the cell to control the metabolic and Gibbs energy balance. The distribution of different types of regulation of the metabolism of organisms such as Escherichia coli [44,45] and yeast [46] over metabolic, signalling and gene expression has been studied intensively. A comprehensive review [47] outlined the regulation of important metabolic tasks at different levels, including nutrient uptake, energy and amino acid metabolism, and protein synthesis, and highlighted a set of metabolites that carry out specific regulatory functions.…”