The PII-NAGK-PipX-NtcA Regulatory Axis of Cyanobacteria: A Tale of Changing Partners, Allosteric Effectors and Non-covalent Interactions

Abstract

PII, a homotrimeric very ancient and highly widespread (bacteria, archaea, plants) key sensor-transducer protein, conveys signals of abundance or poorness of carbon, energy and usable nitrogen, converting these signals into changes in the activities of channels, enzymes, or of gene expression. PII sensing is mediated by the PII allosteric effectors ATP, ADP (and, in some organisms, AMP), 2-oxoglutarate (2OG; it reflects carbon abundance and nitrogen scarcity) and, in many plants, L-glutamine. Cyanobacteria have been crucial for clarification of the structural bases of PII function and regulation. They are the subject of this review because the information gathered on them provides an overall structure-based view of a PII regulatory network. Studies on these organisms yielded a first structure of a PII complex with an enzyme, (N-acetyl-Lglutamate kinase, NAGK), deciphering how PII can cause enzyme activation, and how it promotes nitrogen stockpiling as arginine in cyanobacteria and plants. They have also revealed the first clear-cut mechanism by which PII can control gene expression. A small adaptor protein, PipX, is sequestered by PII when nitrogen is abundant and is released when is scarce, swapping partner by binding to the 2OG-activated transcriptional regulator NtcA, co-activating it. The structures of PII-NAGK, PII-PipX, PipX alone, of NtcA in inactive and 2OG-activated forms and as NtcA-2OG-PipX complex, explain structurally PII regulatory functions and reveal the changing shapes and interactions of the T-loops of PII depending on the partner and on the allosteric effectors bound to PII. Cyanobacterial studies have also revealed that in the PII-PipX complex PipX binds an additional transcriptional factor, PlmA, thus possibly expanding PipX roles beyond NtcA-dependency. Further exploration of these roles has revealed a functional interaction of PipX with PipY, a pyridoxal-phosphate (PLP) protein involved in PLP homeostasis whose mutations in the human ortholog cause epilepsy. Knowledge of cellular levels of the different components of this PII-PipX regulatory network and of KD values for some of the complexes provides the basic background for gross modeling of the system at high and low nitrogen abundance. The cyanobacterial network can guide searches for analogous components in other organisms, particularly of PipX functional analogs.

Interaction of N‐acetyl‐l‐glutamate kinase with the PII signal transducer in the non‐photosynthetic alga Polytomella parva: Co‐evolution towards a hetero‐oligomeric enzyme

“…A few amino acid substitutions in PII may be sufficient to change the transient PII‐NAGK complex into a stable hetero‐oligomeric enzyme complex. In this respect, one residue at the tip of the T‐loop may be of particular importance: This residue, which corresponds to R47 in bacterial PII proteins, has been shown to be of key function for PII‐AmtB interaction . Moreover, mutation of the R47 residue in a cyanobacterial PII protein to Ala strongly reduced the affinity of Synechococcus PII to NAGK .…”

Nitrogen storage regulation by PII protein: lessons learned from taxonomic outliers

“…Selim et al . find that the PII‐NAGK system of P. parva importantly diverts from the mainstream. Unlike in other photosynthetic organisms, neither ATP + 2OG, ATP, nor ADP showed any influence on P. parva PII‐NAGK association or dissociation or on the arginine sensitivity of the NAGK in that complex.…”

“…This modification (a uridylylation) strongly influences PII effects on its target, ATase, the bifunctional enzyme responsible for adenylylating/deadenylylating GS , showing that changes in the T‐loop are crucial for transducing PII signals to its targets. PII targets are proteins, either enzymes, channels for metabolites like ammonium, or direct or indirect gene expression regulators . From the few known structures of PII complexes with its targets, it appears that the flexible T‐loop adapts its conformation to the target proteins, resulting in interaction and in the induction of functional changes on the target .…”

“…PII targets are proteins, either enzymes, channels for metabolites like ammonium, or direct or indirect gene expression regulators . From the few known structures of PII complexes with its targets, it appears that the flexible T‐loop adapts its conformation to the target proteins, resulting in interaction and in the induction of functional changes on the target . While post‐translational modifications of the T‐loop (uridylylation, adenylylation, and phosphorylation) occur in few organisms, allosteric control of PII by small molecules is general.…”

“…While post‐translational modifications of the T‐loop (uridylylation, adenylylation, and phosphorylation) occur in few organisms, allosteric control of PII by small molecules is general. PII effectors act by influencing in a given way the conformation of the T‐loop, favoring or disfavoring the interaction of PII with specific targets . ADP, ATP, and 2‐oxoglutarate (2OG) are classical allosteric effectors of prokaryotic PII proteins.…”