The alternative sigma factor RpoD4 pulses at division and links the circadian clock and the cell cycle in Synechococcus elongatus

Abstract

The cyanobacterial circadian clock is an extensive regulator of gene expression, generating a 24-hour rhythm in the majority of genes in Synechococcus elongatus PCC 7942. This raises the question of how the cyanobacterial clock regulates, and receives input from, the diverse cellular processes it controls. Alternative sigma factors, which bind to the core RNA polymerase enzyme and direct the synthesis of specific sets of transcripts, are one mechanism for the clock to set the time of its outputs. In this work, we use single-cell time-lapse microscopy to reveal the transcriptional dynamics of RpoD4, an alternative sigma factor that was previously reported as either arrhythmic or circadian. We find instead that RpoD4 pulses at cell division, dynamics missed by previous bulk averaging. The circadian clock modulates the amplitude of RpoD4 expression pulses, as well as the timing of pulses through its control of division timing. In turn, a rpoD4 mutation causes a reduction in clock period. Further, a rpoD4 mutant results in smaller cell size, and increasing expression of RpoD4 results in larger cell sizes in a dose-response manner, allowing tunable control of cell size. Thus, our single-cell analysis has revealed pulsing gene expression dynamics in cyanobacteria, linking the clock, RpoD4 and the cell cycle.