A Clock-Phased Sigma Factor Cascade Is Required for Global Circadian Transcriptional Rhythms in Cyanobacteria

Abstract

The circadian clock of the cyanobacterium Synechococcus elongatus PCC 7942 drives oscillations in global mRNA transcript abundances with 24 h periodicity under continuous light conditions. The transcription factor RpaA controls the timing of circadian gene expression, but the mechanisms underlying RpaA’s indirect control of 90-percent of circadian transcripts are not well understood. Here we show that four RpaA-dependent sigma factors – rpoD2, rpoD6, rpoD5, and sigF2 – are sequentially activated downstream of active RpaA and are required for proper expression of circadian genes. We find that the sigma factors RpoD6, RpoD5, and SigF2 exhibit circadian oscillations with different timing relative to each other at the level of their mRNA expression, protein abundance, and binding enrichment at genomic targets in constant light conditions. We measure global gene expression in strains modified to individually lack rpoD2, rpoD6, rpoD5, and sigF2, and identify how expression of circadian genes – including expression of sigma factor genes – is altered in the absence of each sigma factor. Broadly, our findings suggest that a single transcription factor, RpaA, is sufficient to generate complex circadian expression patterns in part by regulating an interdependent sigma factor cascade.