Site-2 Protease Slr1821 Regulates Carbon/Nitrogen Homeostasis during Ammonium Stress Acclimation in Cyanobacterium Synechocystis sp. PCC 6803

Site-2 protease Sll0528 interacts with RbcR to regulate carbon/nitrogen homeostasis in the cyanobacterium Synechocystis sp. PCC 6803

Cyanobacteria play pivotal roles in global biogeochemical cycles through oxygenic photosynthesis. To maintain cellular homeostasis, these organisms utilize sophisticated acclimation mechanisms to adapt to environmental fluctuations, particularly concerning nitrogen availability. While nitrogen deprivation induces dormancy, excess ammonium can have toxic effects on cyanobacteria and other photosynthetic organisms-a phenomenon for which the acclimation mechanisms remain poorly understood. Through the physiological characterization of knockout and overexpression mutants in Synechocystis sp. PCC 6803, we identified the site-2 protease Sll0528 as a critical regulator of ammonium stress acclimation. TurboID-based proximity labeling, coupled with quantitative proteomics, revealed a robust set of putative Sll0528-interacting proteins, some of which were subsequently validated through bacterial two-hybrid assays and transcriptomic profiling. Notably, we confirmed the physical interaction between Sll0528 and RbcR, a low-carbon-responsive transcriptional regulator. Transcriptomic analysis showed that the knockout of sll0528 led to a significant downregulation of the RbcR regulon, including the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) operon rbcLXS. Further analysis suggests that this downregulation might result from improper post-transcriptional regulation of RbcR, which depends on its interaction with Sll0528. Our findings reveal novel regulatory crosstalk between a cyanobacterial S2P protease and the carbon-responsive transcriptional machinery, providing new mechanistic insights into the control of cyanobacterial carbon-nitrogen homeostasis during nitrogen fluctuations. This study offers insights into the functional characterization of other S2P proteases in photosynthetic organisms and may facilitate the cyanobacteria-based bioremediation of ammonium-rich wastewater.

Protein NirP1 regulates nitrite reductase and nitrite excretion in cyanobacteria

When the supply of inorganic carbon is limiting, photosynthetic cyanobacteria excrete nitrite, a toxic intermediate in the ammonia assimilation pathway from nitrate. It has been hypothesized that the excreted nitrite represents excess nitrogen that cannot be further assimilated due to the missing carbon, but the underlying molecular mechanisms are unclear. Here, we identified a protein that interacts with nitrite reductase, regulates nitrogen metabolism and promotes nitrite excretion. The protein, which we named NirP1, is encoded by an unannotated gene that is upregulated under low carbon conditions and controlled by transcription factor NtcA, a central regulator of nitrogen homeostasis. Ectopic overexpression of nirP1 in Synechocystis sp. PCC 6803 resulted in a chlorotic phenotype, delayed growth, severe changes in amino acid pools, and nitrite excretion. Coimmunoprecipitation experiments indicated that NirP1 interacts with nitrite reductase, a central enzyme in the assimilation of ammonia from nitrate/nitrite. Our results reveal that NirP1 is widely conserved in cyanobacteria and plays a crucial role in the coordination of C/N primary metabolism by targeting nitrite reductase.