Circadian Clocks in the Real World: Effects of Dynamic Light Regimes on the Regulation of Circadian Gene Expression in Cyanobacteria

Abstract

Organisms use internal oscillators to control their physiology in conjunction with the predictable environmental changes of the day/night cycle. However, it is not always clear how internal timing information is used by molecular pathways called output pathways to change physiology. Further, these autonomous systems must operate in constantly fluctuating natural environments, and it is not clear how the functions of circadian clocks are affected by these conditions. We use the simple circadian clock in the model cyanobacterium Synechococcus elongatus PC7942 as a model system to explore these questions. We asked how timing information encoded in the circadian clock in cyanobacteria is used to control a simple circadian output in the form of genome-wide changes in transcription (Chapter 2). We find that the gene encoding the transcription factor RpaA is required for genome-wide transcription rhythms. Further, we show that clock-controlled changes in the phosphorylation state of RpaA allow the protein to bind to promoters to activate expression of rhythmic genes. We demonstrate that phosphorylated RpaA drives dynamic expression patterns of hundreds of clock-controlled genes. Thus, the core circadian clock controls gene expression through phosphorylated RpaA, which acts as a master regulator to enact changes in expression of hundreds of genes. Next, we asked how the transcriptional output of the circadian clock is affected by naturally-relevant changes in environmental conditions (Chapter 3). We grew cyanobacteria under dynamic light regimes mimicking natural conditions to demonstrate that the expression of clock-controlled genes is a function of changes in environmental light intensity. Using genomics, we identify that these environmentally-responsive changes in gene expression are enacted by modulating the recruitment of RNA polymerase to promoters. Using a combination of genomics and mathematical modeling, we implicate light-induced changes in the phosphorylation of the transcription factor RpaB as an important mechanism by which environmental changes modulate the expression of clock-controlled genes. Further, we find that RpaA activity itself can be affected by environmental changes. Our work demonstrates the basic principles governing the integration of changes in light with the output of the circadian clock, and suggests several possible mechanisms underlying this behavior. Our work demonstrates that relatively simple circuitry underlies the conversion of timing information from the circadian clock to genome-wide gene expression in cyanobacteria. Further, we demonstrate principles describing how circadian clock output will change in conjunction with environmental changes in nature.