Among prokaryotes, cyanobacteria have an exclusive position due to the fact that they perform oxygenic photosynthesis. Cyanobacteria substantially differ from other bacteria in further aspects, e.g. they evolved a plethora of unique regulatory mechanisms to control primary metabolism. This is exemplified by the regulation of glutamine synthetase (GS) via small proteins termed inactivating factors (IFs). Here we reveal another small, 51 amino acid protein, which is encoded by the ssr0692 gene, to regulate flux into the ornithine-ammonia cycle (OAC), the key hub of cyanobacterial nitrogen stockpiling and remobilization. This regulation is achieved by the interaction with the central carbon/nitrogen control protein P_II, which commonly controls the entry into the OAC by activating the key enzyme of arginine synthesis, N-acetyl-L-glutamate kinase (NAGK). We suggest that Ssr0692 competes with NAGK for P_II binding and thereby prevents NAGK activation, which in turn lowers arginine synthesis. Accordingly, we termed it P_II-interacting regulator of arginine synthesis (PirA). Similar to the GS IFs, PirA accumulates in response to ammonium upshift due to relief from repression by the global nitrogen-control transcription factor NtcA. Consistently, deletion of PirA affects the cell to balance metabolite pools of the OAC in response to ammonium shocks. Moreover, its interaction with P_II requires ADP and is prevented by P_II mutations affecting the T-loop conformation, the major protein-interaction surface of this signal processing protein. Thus, we propose that PirA is an integrator determining flux into N storage compounds not only depending on the N availability but also the energy state of the cell.

Importance Cyanobacteria contribute a significant portion to the annual oxygen yield and play important roles in biogeochemical cycles, e.g. as major primary producers. Due to their photosynthetic lifestyle cyanobacteria also arouse interest as hosts for the sustainable production of fuel components and high-value chemicals. However, their broad application as microbial cell factories is hampered by limited knowledge about the regulation of metabolic fluxes in these organisms. Our research identified a novel regulatory protein that controls nitrogen flux, in particular arginine synthesis in the cyanobacterial model strain Synechocystis sp. PCC 6803. Beside its role as proteinogenic amino acid, arginine is a precursor for the cyanobacterial storage compound cyanophycin, which is of potential interest to biotechnology. The obtained results will therefore not only enhance our understanding of flux control in these organisms, it will also help to provide a scientific fundament for targeted metabolic engineering and hence the design of photosynthesis-driven biotechnological applications.