Modified ppk Expression Alters Temporal Transcriptional and Phosphorus–Nitrogen Responses to Phosphate Fluctuation in Synechococcus sp. PCC 7002

Phosphate availability fluctuates widely in aquatic environments, yet how engineering the regulatory context of polyphosphate kinase affects cyanobacterial responses to such fluctuations remains unclear. Here, the wild-type strain of Synechococcus sp. PCC 7002 and Dppk, a modified ppk-expression strain derived from the WT background, were subjected to phosphate starvation followed by phosphate resupply. Dense RT-qPCR sampling was used to resolve rapid ppk-expression dynamics, and time-resolved RNA sequencing was performed at seven stages with four biological replicates per condition. WT displayed rapid, stage-dependent changes in ppk expression, including a pronounced late induction after phosphate resupply, whereas Dppk showed a more moderate temporal pattern. Transcriptome-wide analyses further revealed distinct basal states and response trajectories between the strains. Functional analyses linked these differences to photosynthesis-related processes, phosphate transport, and polyphosphate metabolism. These findings indicate that refactoring ppk expression alters both target-gene kinetics and the temporal organization of the broader phosphate-responsive transcriptional network.