Natural changes in light interact with circadian regulation at promoters to control gene expression in cyanobacteria

Abstract

The circadian clock interacts with other regulatory pathways to tune physiology to predictable daily changes and unexpected environmental fluctuations. However, the complexity of circadian clocks in higher organisms has prevented a clear understanding of how natural environmental conditions affect circadian clocks and their physiological outputs. Here, we dissect the interaction between circadian regulation and responses to fluctuating light in the cyanobacterium Synechococcus elongatus. We demonstrate that natural changes in light intensity substantially affect the expression of hundreds of circadian-clock-controlled genes, many of which are involved in key steps in metabolism. These changes in expression arise from control of RNA polymerase recruitment to promoters by circadian and light-responsive regulation of a network of transcription factors including RpaA and RpaB. Using phenomenological modeling constrained by our data, we reveal simple principles that underlie the small number of stereotyped responses of dusk circadian genes to changes in light.Circadian clocks allow organisms from almost all branches of life to alter physiology in anticipation of diurnal changes in the environment. Circadian clocks keep time using autonomous core oscillators which control output pathways to direct periodic changes in the mRNA levels (expression) of genes, ultimately leading to oscillations in higher order behaviors [1]. Laboratory studies of the outputs of circadian clocks have been primarily performed under constant conditions to isolate circadian regulation from environmental responses. In nature, however, organisms with circadian clocks must also cope with unexpected fluctuations in the environment. Thus a major challenge in chronobiology is to understand circadian clocks and their outputs in dynamic environments.Previous studies suggest that circadian clock output pathways interact with environmental responses to tailor physiological outputs to both the time of day and the current state of the environment. For example, sleep/wake cycles in Drosophila melanogaster and photosynthesis in Arabidopsis thaliana are controlled by both the circadian clock and environmental variables like day length or light [2,3]. Further, circadian clocks can modulate environmental responses based on the time-of-day in a process called circadian gating [4,5]. However, the complexity of higher organisms has prevented a detailed understanding of the interaction between circadian timing information and environmental responses. In contrast, the circadian clock in the cyanobacterium Synechococcus elongatus PCC7942, an obligate photoautotroph, has a simple architecture which controls gene expression oscillations ( Figure 1A) to influence metabolism and growth. S. elongatus must carefully monitor its environment, as the sunlight required for photosynthesis fluctuates on the * These authors contributed equally to this work.† Correspondence: osheae@hhmi.org minute, day, and seasonal timescales (Figure 1B,[6]). While it is well understood how the ...

The circadian clock and darkness control natural competence in cyanobacteria

“…In contrast, a subset of genes required for natural competence, including pilA3, pilW, rntA , and rntB , are circadian with highest expression levels at dusk (Fig. 3a) and are induced by darkness 19,29 (Fig. 3b).…”

“…The RB-TnSeq data for clock histidine kinase genes sasA and cikA had mild negative fitness values, but knockout mutants for either of these genes are still naturally transformable 28 . To delve further, we analyzed available circadian and light/dark transcriptomes for S. elongatus 19,29 (Supplementary Table 1). The data clearly indicate that most of the T4PM is circadian controlled and expressed in the morning.…”

“…Most of the T4PM genes (including pilB, M, N, O, P, Q ) are circadian controlled and expressed in the morning while a subset of genes needed for natural competence such as pilA3, pilW , and rntA and rntB , and the competence genes including comEA, comEC, comF , and dprA , are circadian with highest expression levels at dusk. b , Expression change for genes after a 60-min shade pulse given 8 h after the onset of the day 29 , plotted according to RB-TnSeq fitness values as described for Fig. 1. c , Transmission electron micrographs of cells grown in LD and incubated at different time points (Zeitgeber time, ZT time) for 6 hours after removal of their pili.…”

“…While the induction of dusk genes, including competence genes, is under the control of phosphorylated RpaA (Supplementary Table 1), the mechanism behind increased natural competence in response to darkness is less clear. The expression of hundreds of circadian-regulated genes is affected by changes in light intensity, implicating a network of transcription regulators that is still not well understood 29 . The RB-TnSeq screen revealed the antagonistic importance of two sigma factors in natural competence: sigF2 and rpoD2 (Fig.…”

A model for the regulation of the timing of cell division by the circadian clock in the cyanobacterium Synechococcus elongatus

“…We also enforced X ≥ 0. We determined the values of the free parameters A and φ for each condition (Methods, SM Section 5.2), reflecting the fact that the molecular players that implement y ( θ ) may depend on environmental light conditions [27], which we discuss in detail below. We also assumed that clocks are entrained quickly relative to the duration of the experiments, so that the measured statistics approximate those for cells entrained under imaging conditions, even though the actual protocol entrained the cells under 12:12 LD even for the 16:8 LD imaging condition.…”