KaiC-dependent circadian positioning of RNA polymerase and ribosome in cyanobacteria

Circadian rhythms in Synechococcus elongatus PCC 7942 ( S. elongatus ) orchestrate global gene expression by regulating chromosomal DNA dynamics, transitioning between diffuse, and compacted states. While DNA dynamics have been extensively characterized, how the clock influences the spatial organization of transcriptional and translational machinery remains unclear. Using live-cell fluorescence imaging, we examined the circadian dynamics of RNA polymerase (RNAP) and ribosome localization in S. elongatus . We found that RNAPs colocalize with DNA during both diffuse and compacted states, whereas ribosomes colocalize with diffuse DNA but redistribute toward thylakoid membrane regions during DNA compaction. These rhythmic localization patterns persist under continuous light and dark conditions, remain stable within the tested time window following transcriptional or translational inhibition, and require a functional KaiC protein. Together, our findings support a model in which the cyanobacterial circadian clock coordinates RNAP, ribosome, and nucleoid spatial dynamics, revealing spatiotemporal organization as a layer of prokaryotic circadian regulation.