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

Michael Haffner; Andreas M Enkerlin; Oliver Mantovani; Philipp Spät; Boris Maček; Martin Hagemann; Karl Forchhammer; Khaled A Selim

doi:10.1016/j.isci.2025.113261

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

iScience. 2025 Aug 5;28(9):113261. doi: 10.1016/j.isci.2025.113261. eCollection 2025 Sep 19.

Authors

Michael Haffner¹, Andreas M Enkerlin², Oliver Mantovani³, Philipp Spät^{1

4}, Boris Maček⁴, Martin Hagemann³, Karl Forchhammer¹, Khaled A Selim^{1

2}

Affiliations

¹ Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Tübingen University, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
² Microbial Biochemistry Group, Institute of Phototrophic Microbiology, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
³ Plant Physiology Department, Institute of Biological Sciences, Rostock University, Rostock, Germany.
⁴ Quantitative Proteomics, Interfaculty Institute for Cell Biology (IFIZ), 72076 Tübingen, Germany.

Abstract

The photoautotrophic lifestyle of cyanobacteria has to cope with the successive diurnal changes. We previously highlighted a unique function of the carbon control protein, SbtB, and its effector molecule c-di-AMP, for nighttime survival 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 a better understanding, we compared the metabolomic and proteomic landscapes of ΔsbtB and the c-di-AMP-free (ΔdacA) mutants of Synechocystis sp. PCC 6803. While our results indicated that the cellular role of SbtB is restricted to carbon/glycogen metabolism, the diurnal lethality of ΔdacA seemed to be a sum of the dysregulation of multiple processes, including photosynthesis and redox regulation. Further, we showed an impact of c-di-AMP on central carbon/nitrogen metabolism, which is linked to NtcA transcription regulation and highlighted by an imbalance of glutamine/glutamate ratio as well as the reduction of arginine pathway metabolites. We further identified the HCO₃ ^- uptake systems, BicA and BCT1, as novel SbtB targets, in agreement with its broader role in regulating carbon homeostasis.

Keywords: Biochemistry; Biological sciences; Carbon/Nitrogen metabolism; Cyanobacteria; Cyanophycin; Microbiology; PII-like protein SbtB; Photosynthesis; Reactive oxygen species (ROS); Redox imbalance; c-di-AMP signaling.