Diurnal rhythm causes metabolic crises in the cyanobacterial mutants of c-di-AMP signalling cascade

Abstract

In nature, the photoautotrophic lifestyle of cyanobacteria has to cope with the successive diurnal changes in light supply. Light supply throughout the day enables photosynthesis and glycogen biosynthesis, while night phases require the switch to a heterotrophic-like lifestyle relying on glycogen catabolism. We previously highlighted a unique function of the carbon control protein, SbtB, and its effector molecule c-di-AMP, for the nighttime survival of cyanobacteria through the regulation of glycogen anabolism. However, the extent to which c-di-AMP and SbtB impact the cellular metabolism for day-night survivability remained elusive. To gain better understanding of cellular processes regulated by SbtB or c-di-AMP, we compared the metabolomic and proteomic landscapes of ΔsbtBand the c-di-AMP-free (ΔdacA) mutants of the model strainSynechocystissp. PCC 6803. While our results indicate that the cellular role of SbtB is restricted to carbon/glycogen metabolism, the diurnal lethality of ΔdacAseems to be a sum of dysregulation of multiple metabolic processes. These processes include photosynthesis and redox regulation, which lead to elevated levels of intracellular ROS and glutathione. Further, we show an impact of c-di-AMP on central carbon as well as on nitrogen metabolism. Effects on nitrogen metabolism are linked to reduced levels of the global nitrogen transcription regulator NtcA and highlighted by an imbalance of the glutamine to glutamate ratio as well as reduced metabolite levels of the arginine pathway. We further identified the HCO3-uptake systems, BicA and BCT1 as novel SbtB targets, in agreement with its broader role in regulating carbon homeostasis.

The second messenger c-di-AMP controls natural competence via ComFB signaling protein

“…The full proteomics analysis of the Synechocystis sp. PCC 6803 wildtype, Δ sbtB and Δ dacA cells, growing under day-night cycles, was done as described previously in (Haffner et al 2023b). The full proteomics data sets are described in (Haffner et al 2023b).…”

“…PCC 6803 wildtype, Δ sbtB and Δ dacA cells, growing under day-night cycles, was done as described previously in (Haffner et al 2023b). The full proteomics data sets are described in (Haffner et al 2023b). The pulldown experiments to identify the potential c-di-AMP target proteins was done as described previously (Selim et al 2021a) using Synechocystis sp.…”

“…In cyanobacteria, c-di-AMP seems to control additional processes, including the diurnal metabolism via its binding to the carbon control protein SbtB to regulate glycogen metabolism (Rubin et al 2018; Selim et al 2021a). Although important roles for c-di-AMP have been acknowledged since its discovery, recent studies suggest broader regulatory impacts of c-di-AMP signaling with further functions yet to be elucidated (Mantovani et al 2022; Haffner et al 2023b). For instance, a role for c-di-AMP in controlling natural competence has been speculated in Streptococcus pneumoniae , although the molecular mechanism remained elusive (Zarrella et al 2020).…”

“…To gain insights into the molecular basis of c-di-AMP-dependent control of natural competence, we checked how the lack of this second messenger affects pilus biogenesis. Proteome analysis of the Δ dacA mutant compared to WT cells under day-night cycle, a condition triggering pili biogenesis and natural competence (Taton et al 2020), revealed a strong downregulation of specific proteins involved in pilus biogenesis and DNA uptake in the Δ dacA mutant (Haffner et al 2023b). These changes were marked by a reduced abundance of PilT1 (Slr0161), PilM (Slr1274), PilN (Slr1275), PilO (Slr1276), and Sll0180 proteins (Table S1).…”

“…The lack of nonretractable pili explains the inability of the Δ dacA strain to take up DNA. Interestingly, the downregulation of the above-mentioned proteins was not detected in the Δ sbtB mutant, which lacks the only known cyanobacterial c-di-AMP receptor (Table S3) (Selim et al 2021a; Haffner et al 2023b). Additionally, Δ sbtB behaved like the WT in our natural competence assays (Figs.…”