Plants have developed an internal timing mechanism, the circadian system, that serves to synchronise physiological and metabolic functions with daily, predictable cues such as dawn and dusk. This endogenous oscillator is comprised of biochemical and transcriptional rhythms that are entrained by environmental signals, particularly light and temperature, through the action of input pathways. The circadian system provides plants with an adaptive advantage, and techniques that allow in vivo monitoring of circadian rhythms give valuable insights into the components and mechanisms employed by plants to optimally respond to abiotic signals. This study shows that chlorophyll a fluorescence imaging can be used to describe circadian rhythms of PSII operating efficiency (Fq’/Fm’) in the chloroplasts of Arabidopsis thaliana. These circadian rhythms in Fq’/Fm’ are influenced by the well-defined rhythmic transcriptional feedback loops that comprise the central oscillator in the nucleus, and are maintained under constant blue light by the action of phototropin photoreceptors. Using chlorophyll a fluorescence imaging, the chloroplast-localised enzyme SAL1 was identified as impacting circadian oscillations both in chloroplasts and in the nucleus. SAL1 is a redox-sensitive component of the SAL1-PAP-XRN retrograde signalling pathway, and influences nuclear gene expression in response to stress by modulating the levels of its substrate, 3’-phosphoadenosine 5’-phosphate (PAP). PAP accumulates in chloroplasts under abiotic stress and inhibits the activity of 5’→3’ exoribonucleases (XRNs). This study shows that genetically inducing the SAL1-PAP-XRN pathway in plants lacking SAL1 function induces a long circadian period in a blue light-dependent manner. Application of exogenous PAP or osmotic stress lengthens circadian period, and period lengthening correlates with increases in endogenous PAP levels. Furthermore, plants lacking functional XRNs exhibit a similar long circadian period phenotype. The SAL1-PAP-XRN pathway is therefore proposed to regulate nuclear circadian rhythms in response to changes in chloroplast redox poise, and serves as a possible link between molecular timekeeping and abiotic stress response mechanisms
