Controlling the Cyanobacterial Clock by Synthetically Rewiring Metabolism

Abstract

Summary Circadian clocks are oscillatory systems and allow organisms to anticipate rhythmic changes in the environment. Several studies have shown that circadian clocks are connected to metabolism, but it is not generally clear whether metabolic signaling is one voice among many that influence the clock, or whether metabolic cycling is the major clock synchronizer. To address this question in cyanobacteria, we used a synthetic biology approach to make normally autotrophic cells capable of growth on exogenous sugar. This allowed us to manipulate metabolism independently from the light and dark. We found that feeding sugar to cultures blocked the clock-resetting effect of a dark pulse. Further, in the absence of light, the clock efficiently synchronizes to metabolic cycles driven by rhythmic feeding. We conclude that metabolic activity, independent of its source, is the primary clock driver in cyanobacteria.

Circadian Oscillators: Around the Transcription–Translation Feedback Loop and on to Output

“…Unlike fungal and animal clocks where light is perceived by dedicated photoreceptors, light resetting in cyanobacteria works exclusively via photosynthesis and metabolism [91]. Prior work showed that light-driven changes in energy charge or oxidized quinones are sufficient to reset the clock [92, 93] but did not eliminate metabolism-independent Input pathways.…”

“…Prior work showed that light-driven changes in energy charge or oxidized quinones are sufficient to reset the clock [92, 93] but did not eliminate metabolism-independent Input pathways. Pattanayak et al [91] demonstrated that when obligate photoautotrophic strains were engineered to grow in the dark on glucose,, they were rhythmic and blind to light exposure, suggesting that all clock resetting in cyanobacteria works through light-driven metabolism. In the cyanobacterial clock, Output feeds back to Input when the TTFL drives circadian expression of the Kai genes and RpaA, thus supplying non-phosphorylated KaiC in a cyclic manner on a daily basis [94] [95].…”

Period Robustness and Entrainability of the Kai System to Changing Nucleotide Concentrations

“…It is becoming clear that the daily shifts in the metabolic state of organisms, ranging from cyanobacteria to mammals, are an important Zeitgeber for their circadian clocks (26,38,39). Recent experiments show that the daily shifts in the cytoplasmic ATP level of the cyanobacterium Synechococcus elongatus are an important cue for the entrainment of its Kai circadian clock (30). To find out how changes in the ATP level affect the Kai oscillator, we compared two widely-used models of the post-translational oscillator, the hexamer model by Van Zon et.…”

“…The phase response curve of the Rust model is thus asymmetric: an ADP pulse can induce a much stronger phase advance than a phase delay. However, it was experimentally shown that the phase response curve of the in-vitro Kai system is very symmetric (26,30). When the pulse is given at the moment that leads to a maximum phase delay, then, in all three models, the ADP pulse only slows down the increase of the phosphorylation level.…”

Toward Multiscale Models of Cyanobacterial Growth: A Modular Approach

“…While there is increasing evidence how the clock is influenced by, and itself influences, photosynthetic light reactions and metabolism, via sensing metabolic activity (Pattanayak et al, 2015) and redox state (Kim et al, 2012) and controlling transcription regulation, the precise evolutionary role of the clock remains insufficiently understood. Elucidating how the circadian clock interacts with other cellular processes and to integrate models of the cyanobacterial circadian clock into a broader cellular context, with the aim to understand how timing mechanisms affect cellular fitness, is a timely question for further computational research.…”